2023 |
Vogiatzi, Angeliki; Keklikoglou, Kleoniki; Makris, Konstantinos; Argyrou, Dionysia Stamatia; Zacharopoulos, Athanasios; Sotiropoulou, Varvara; Parthenios, Nikolaos; Gkikas, Angelos; Kokkori, Maria; Richardson, Melodie S W; Fenwick, Aimée L; Archontidi, Sofia; Arvanitidis, Christos; Robertson, Jeremy; Parthenios, John; Zacharakis, Giannis; Twigg, Stephen R F; Wilkie, Andrew O M; Mavrothalassitis, George Development of Erf-Mediated Craniosynostosis and Pharmacological Amelioration Journal Article International Journal of Molecular Sciences, 24 (9), pp. 7961, 2023, ISSN: 1422-0067. @article{vogiatzi_development_2023, title = {Development of Erf-Mediated Craniosynostosis and Pharmacological Amelioration}, author = {Angeliki Vogiatzi and Kleoniki Keklikoglou and Konstantinos Makris and Dionysia Stamatia Argyrou and Athanasios Zacharopoulos and Varvara Sotiropoulou and Nikolaos Parthenios and Angelos Gkikas and Maria Kokkori and Melodie S W Richardson and Aimée L Fenwick and Sofia Archontidi and Christos Arvanitidis and Jeremy Robertson and John Parthenios and Giannis Zacharakis and Stephen R F Twigg and Andrew O M Wilkie and George Mavrothalassitis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Vogiatzi-2023-IJMSci-17.pdf https://www.mdpi.com/1422-0067/24/9/7961}, doi = {10.3390/ijms24097961}, issn = {1422-0067}, year = {2023}, date = {2023-05-02}, urldate = {2023-05-02}, journal = {International Journal of Molecular Sciences}, volume = {24}, number = {9}, pages = {7961}, abstract = {ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway. |
2022 |
Digenis, Markos; Arvanitidis, Christos; Dailianis, Thanos; Gerovasileiou, Vasilis Comparative Study of Marine Cave Communities in a Protected Area of the South-Eastern Aegean Sea, Greece Journal Article Journal of Marine Science and Engineering, 10 (5), pp. 660, 2022, ISSN: 2077-1312. @article{digenis_comparative_2022, title = {Comparative Study of Marine Cave Communities in a Protected Area of the South-Eastern Aegean Sea, Greece}, author = {Markos Digenis and Christos Arvanitidis and Thanos Dailianis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Digenis-jmse-40.pdf https://www.mdpi.com/2077-1312/10/5/660}, doi = {10.3390/jmse10050660}, issn = {2077-1312}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Journal of Marine Science and Engineering}, volume = {10}, number = {5}, pages = {660}, abstract = {Although more than 600 marine caves have been recorded so far along the Greek coasts of the Aegean Sea (Eastern Mediterranean), only a few have been systematically studied for their biodiversity. In this study, the benthic communities of six marine caves within a Protected Area of South-Eastern Aegean were studied for the first time, both qualitatively and quantitatively. The association of different geomorphological and topographical factors of the caves with the benthic community structure was investigated. A total of 120 photographic quadrats covering the entrance and semi-dark cave zones were analysed, with regard to coverage and taxon abundance, while motile taxa were qualitatively recorded by visual census. The ecological quality status of the caves was also assessed under an ecosystem-based approach. In total, 81 sessile and 45 motile taxa were recorded, including 12 protected and 10 non-indigenous species. Multivariate community analysis demonstrated that the geomorphological and topographical variables of the caves are significantly associated with the observed biotic patterns. The ecological quality of the caves was assessed as poor or moderate according to the CavEBQI index, highlighting the necessity for systematic monitoring. This study paves the way for similar studies in marine cave habitats aiming at the development of management and conservation actions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although more than 600 marine caves have been recorded so far along the Greek coasts of the Aegean Sea (Eastern Mediterranean), only a few have been systematically studied for their biodiversity. In this study, the benthic communities of six marine caves within a Protected Area of South-Eastern Aegean were studied for the first time, both qualitatively and quantitatively. The association of different geomorphological and topographical factors of the caves with the benthic community structure was investigated. A total of 120 photographic quadrats covering the entrance and semi-dark cave zones were analysed, with regard to coverage and taxon abundance, while motile taxa were qualitatively recorded by visual census. The ecological quality status of the caves was also assessed under an ecosystem-based approach. In total, 81 sessile and 45 motile taxa were recorded, including 12 protected and 10 non-indigenous species. Multivariate community analysis demonstrated that the geomorphological and topographical variables of the caves are significantly associated with the observed biotic patterns. The ecological quality of the caves was assessed as poor or moderate according to the CavEBQI index, highlighting the necessity for systematic monitoring. This study paves the way for similar studies in marine cave habitats aiming at the development of management and conservation actions. |
Paragkamian, Savvas; Sarafidou, Georgia; Mavraki, Dimitra; Pavloudi, Christina; Beja, Joana; Eliezer, Menashè; Lipizer, Marina; Boicenco, Laura; Vandepitte, Leen; Perez-Perez, Ruben; Zafeiropoulos, Haris; Arvanitidis, Christos; Pafilis, Evangelos; Gerovasileiou, Vasilis Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow Journal Article Frontiers in Marine Science, 9 , pp. 940844, 2022, ISSN: 2296-7745. @article{paragkamian_automating_2022, title = {Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow}, author = {Savvas Paragkamian and Georgia Sarafidou and Dimitra Mavraki and Christina Pavloudi and Joana Beja and Menashè Eliezer and Marina Lipizer and Laura Boicenco and Leen Vandepitte and Ruben Perez-Perez and Haris Zafeiropoulos and Christos Arvanitidis and Evangelos Pafilis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Paragkaminan-fmars-53.pdf }, doi = {10.3389/fmars.2022.940844}, issn = {2296-7745}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {940844}, abstract = {Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research. |
2021 |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Grigoriou, Panagiotis; Arvanitidis, Christos Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells Journal Article Biodiversity Data Journal, 9 , pp. e75358, 2021, ISSN: 1314-2828, 1314-2836, (BIODIV). @article{chatzinikolaou_micro-ct_2021c, title = {Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou and Panagiotis Grigoriou and Christos Arvanitidis}, url = {https://bdj.pensoft.net/article/75358/}, doi = {10.3897/BDJ.9.e75358}, issn = {1314-2828, 1314-2836}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-17}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e75358}, abstract = {Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets. The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus , which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets. The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus , which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data. |
Bompoti, Andreana; Papazoglou, Andreas S; Moysidis, Dimitrios V; Otountzidis, Nikolaos; Karagiannidis, Efstratios; Stalikas, Nikolaos; Panteris, Eleftherios; Ganesh, Vijayakumar; Sanctuary, Thomas; Arvanitidis, Christos; Sianos, Georgios; Michaelson, James S; Herrmann, Markus D Volumetric Imaging of Lung Tissue at Micrometer Resolution: Clinical Applications of Micro-CT for the Diagnosis of Pulmonary Diseases Journal Article Diagnostics, 11 (11), pp. 2075, 2021, ISSN: 2075-4418, (BIODIV). @article{bompoti_volumetric_2021, title = {Volumetric Imaging of Lung Tissue at Micrometer Resolution: Clinical Applications of Micro-CT for the Diagnosis of Pulmonary Diseases}, author = {Andreana Bompoti and Andreas S Papazoglou and Dimitrios V Moysidis and Nikolaos Otountzidis and Efstratios Karagiannidis and Nikolaos Stalikas and Eleftherios Panteris and Vijayakumar Ganesh and Thomas Sanctuary and Christos Arvanitidis and Georgios Sianos and James S Michaelson and Markus D Herrmann}, url = {https://www.mdpi.com/2075-4418/11/11/2075}, doi = {10.3390/diagnostics11112075}, issn = {2075-4418}, year = {2021}, date = {2021-11-01}, urldate = {2022-01-17}, journal = {Diagnostics}, volume = {11}, number = {11}, pages = {2075}, abstract = {Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This scoping review was conducted in accordance with the PRISMA Extension for Scoping Reviews, aiming to include every clinical study reporting on micro-CT imaging of human lung tissues. A literature search yielded 570 candidate articles, out of which 37 were finally included in the review. Of the selected studies, 9 studies explored via micro-CT imaging the morphology and anatomy of normal human lung tissue; 21 studies investigated microanatomic pulmonary alterations due to obstructive or restrictive lung diseases, such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and cystic fibrosis; and 7 studies examined the utility of micro-CT imaging in assessing lung cancer lesions (n = 4) or in transplantation-related pulmonary alterations (n = 3). The selected studies reported that micro-CT could successfully detect several lung diseases providing three-dimensional images of greater detail and resolution than routine optical slide microscopy, and could additionally provide valuable volumetric insight in both restrictive and obstructive lung diseases. In conclusion, micro-CT-based volumetric measurements and qualitative evaluations of pulmonary tissue structures can be utilized for the clinical management of a variety of lung diseases. With micro-CT devices becoming more accessible, the technology has the potential to establish itself as a core diagnostic imaging modality in pathology and to enable integrated histopathologic and radiologic assessment of lung cancer and other lung diseases.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This scoping review was conducted in accordance with the PRISMA Extension for Scoping Reviews, aiming to include every clinical study reporting on micro-CT imaging of human lung tissues. A literature search yielded 570 candidate articles, out of which 37 were finally included in the review. Of the selected studies, 9 studies explored via micro-CT imaging the morphology and anatomy of normal human lung tissue; 21 studies investigated microanatomic pulmonary alterations due to obstructive or restrictive lung diseases, such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and cystic fibrosis; and 7 studies examined the utility of micro-CT imaging in assessing lung cancer lesions (n = 4) or in transplantation-related pulmonary alterations (n = 3). The selected studies reported that micro-CT could successfully detect several lung diseases providing three-dimensional images of greater detail and resolution than routine optical slide microscopy, and could additionally provide valuable volumetric insight in both restrictive and obstructive lung diseases. In conclusion, micro-CT-based volumetric measurements and qualitative evaluations of pulmonary tissue structures can be utilized for the clinical management of a variety of lung diseases. With micro-CT devices becoming more accessible, the technology has the potential to establish itself as a core diagnostic imaging modality in pathology and to enable integrated histopathologic and radiologic assessment of lung cancer and other lung diseases. |
Keklikoglou, Kleoniki; Arvanitidis, Christos; Chatzigeorgiou, Georgios; Chatzinikolaou, Eva; Karagiannidis, Efstratios; Koletsa, Triantafyllia; Magoulas, Antonios; Makris, Konstantinos; Mavrothalassitis, George; Papanagnou, Eleni-Dimitra; Papazoglou, Andreas S; Pavloudi, Christina; Trougakos, Ioannis P; Vasileiadou, Katerina; Vogiatzi, Angeliki Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques Journal Article 7 (9), pp. 172, 2021, ISSN: 2313-433X. @article{keklikoglou_micro-ct_2021, title = {Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques}, author = {Kleoniki Keklikoglou and Christos Arvanitidis and Georgios Chatzigeorgiou and Eva Chatzinikolaou and Efstratios Karagiannidis and Triantafyllia Koletsa and Antonios Magoulas and Konstantinos Makris and George Mavrothalassitis and Eleni-Dimitra Papanagnou and Andreas S Papazoglou and Christina Pavloudi and Ioannis P Trougakos and Katerina Vasileiadou and Angeliki Vogiatzi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Keklikoglou-jimaging-66-1.pdf https://www.mdpi.com/2313-433X/7/9/172}, doi = {10.3390/jimaging7090172}, issn = {2313-433X}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {7}, number = {9}, pages = {172}, abstract = {Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised. |
Chatzinikolaou, Eva; Damianidis, Panagiotis; Pavloudi, Christina; Vasileiadou, Aikaterini; Faulwetter, Sarah; Keklikoglou, Kleoniki; Plaitis, Wanda; Mavraki, Dimitra; Nikolopoulou, Stamatina; Arvanitidis, Christos Benthic communities in three Mediterranean touristic ports: MAPMED project Journal Article Biodiversity Data Journal, 9 , pp. e66420, 2021, ISSN: 1314-2828. @article{chatzinikolaou_benthic_2021, title = {Benthic communities in three Mediterranean touristic ports: MAPMED project}, author = {Eva Chatzinikolaou and Panagiotis Damianidis and Christina Pavloudi and Aikaterini Vasileiadou and Sarah Faulwetter and Kleoniki Keklikoglou and Wanda Plaitis and Dimitra Mavraki and Stamatina Nikolopoulou and Christos Arvanitidis}, url = {https://bdj.pensoft.net/article/66420/ https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatzinikolaou-DioDiv-Data-J-32.pdf}, doi = {10.3897/BDJ.9.e66420}, issn = {1314-2828}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e66420}, abstract = {Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%). |
Maidanou, Maria; Koulouri, Panayota; Karachle, Paraskevi K; Arvanitidis, Christos; Koutsoubas, Drosos; Dounas, Costas Trophic Diversity of a Fish Community Associated with a Caulerpa prolifera (Forsskål) Meadow in a Shallow Semi-Enclosed Embayment Journal Article JMSE, 9 (2), pp. 165, 2021, ISSN: 2077-1312. @article{maidanou_trophic_2021, title = {Trophic Diversity of a Fish Community Associated with a Caulerpa prolifera (Forsskål) Meadow in a Shallow Semi-Enclosed Embayment}, author = {Maria Maidanou and Panayota Koulouri and Paraskevi K Karachle and Christos Arvanitidis and Drosos Koutsoubas and Costas Dounas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Maidanou-JMSE-12.pdf https://www.mdpi.com/2077-1312/9/2/165}, doi = {10.3390/jmse9020165}, issn = {2077-1312}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-24}, journal = {JMSE}, volume = {9}, number = {2}, pages = {165}, abstract = {This study investigates the trophic diversity of fishes living in a meadow of Caulerpa prolifera on a bimonthly basis between May 2006 and April 2007 in a semi-enclosed coastal marine ecosystem of the Mediterranean Sea (Elounda Bay, Crete Island). The study area is shallow and protected from waves, and it is covered by a C. prolifera bed, characterized by high organic input and a highly diverse macrobenthic community. Feeding patterns of the fish, investigated on the basis of stomach content analyses, were described in terms of numerical abundance and frequency of occurrence of prey taxa. A total of 1642 fish individuals, belonging to 17 species, were examined. In total, 45,674 prey individuals were identified belonging to 110 prey taxa, most of which were Malacostraca including their larvae and Copepoda (41,175 individuals identified to 71 taxa). Four different trophic groups were identified: herbivorous, pelagic, benthic (hyperbenthic) and piscivorous. Trophic diversity patterns of the fish species studied were also compared to the relative availability of macrobenthic and zooplanktonic taxa during the same period in the study area. The coexistence of many different, mostly benthic but also pelagic, fishes and their juveniles implies their high trophic flexibility, which is probably important for their survival in this particular habitat. Results of the present study provide basic knowledge on trophic diversity and interactions in the marine ecosystem and, therefore, some evidence as to the protection value of this particular habitat, which is essential for the implementation of a multispecies approach to decision-makers and managers of fisheries sources of the region.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study investigates the trophic diversity of fishes living in a meadow of Caulerpa prolifera on a bimonthly basis between May 2006 and April 2007 in a semi-enclosed coastal marine ecosystem of the Mediterranean Sea (Elounda Bay, Crete Island). The study area is shallow and protected from waves, and it is covered by a C. prolifera bed, characterized by high organic input and a highly diverse macrobenthic community. Feeding patterns of the fish, investigated on the basis of stomach content analyses, were described in terms of numerical abundance and frequency of occurrence of prey taxa. A total of 1642 fish individuals, belonging to 17 species, were examined. In total, 45,674 prey individuals were identified belonging to 110 prey taxa, most of which were Malacostraca including their larvae and Copepoda (41,175 individuals identified to 71 taxa). Four different trophic groups were identified: herbivorous, pelagic, benthic (hyperbenthic) and piscivorous. Trophic diversity patterns of the fish species studied were also compared to the relative availability of macrobenthic and zooplanktonic taxa during the same period in the study area. The coexistence of many different, mostly benthic but also pelagic, fishes and their juveniles implies their high trophic flexibility, which is probably important for their survival in this particular habitat. Results of the present study provide basic knowledge on trophic diversity and interactions in the marine ecosystem and, therefore, some evidence as to the protection value of this particular habitat, which is essential for the implementation of a multispecies approach to decision-makers and managers of fisheries sources of the region. |
Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos 0s and 1s in marine molecular research: a regional HPC perspective Journal Article GigaScience, 10 (8), pp. giab053, 2021, ISSN: 2047-217X. @article{zafeiropoulos_0s_2021, title = {0s and 1s in marine molecular research: a regional HPC perspective}, author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916}, doi = {10.1093/gigascience/giab053}, issn = {2047-217X}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {GigaScience}, volume = {10}, number = {8}, pages = {giab053}, abstract = {Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned. |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Grigoriou, Panagiotis; Arvanitidis, Christos Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells Journal Article Biodiversity Data Journal, 9 , pp. e75358, 2021, ISSN: 1314-2828. @article{chatzinikolaou_micro-ct_2021b, title = {Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou and Panagiotis Grigoriou and Christos Arvanitidis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Chatzinikolaou-BDJ-81.pdf https://bdj.pensoft.net/article/75358/}, doi = {10.3897/BDJ.9.e75358}, issn = {1314-2828}, year = {2021}, date = {2021-01-01}, urldate = {2022-01-12}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e75358}, abstract = {Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets.The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus, which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets.The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus, which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data. |
Papazoglou, Andreas S; Karagiannidis, Efstratios; Moysidis, Dimitrios V; Sofidis, Georgios; Bompoti, Andreana; Stalikas, Nikolaos; Panteris, Eleftherios; Arvanitidis, Christos; Herrmann, Markus D; Michaelson, James S; Sianos, Georgios Current clinical applications and potential perspective of micro-computed tomography in cardiovascular imaging: A systematic scoping review Journal Article Hellenic Journal of Cardiology, 62 (6), pp. 399–407, 2021, ISSN: 11099666, (BIODIV). @article{papazoglou_current_2021, title = {Current clinical applications and potential perspective of micro-computed tomography in cardiovascular imaging: A systematic scoping review}, author = {Andreas S Papazoglou and Efstratios Karagiannidis and Dimitrios V Moysidis and Georgios Sofidis and Andreana Bompoti and Nikolaos Stalikas and Eleftherios Panteris and Christos Arvanitidis and Markus D Herrmann and James S Michaelson and Georgios Sianos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1109966621001068}, doi = {10.1016/j.hjc.2021.04.006}, issn = {11099666}, year = {2021}, date = {2021-01-01}, urldate = {2022-01-17}, journal = {Hellenic Journal of Cardiology}, volume = {62}, number = {6}, pages = {399--407}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Printzi, Alice; Fragkoulis, Stefanos; Dimitriadi, Anastasia; Keklikoglou, Kleoniki; Arvanitidis, Christos; Witten, Eckhard P; Koumoundouros, George Exercise-induced lordosis in zebrafish Danio rerio (Hamilton, 1822) Journal Article Journal of Fish Biology, 98 (4), pp. 987–994, 2021, ISSN: 0022-1112, 1095-8649, (BIODIV). @article{printzi_exercise-induced_2021, title = {Exercise-induced lordosis in zebrafish Danio rerio (Hamilton, 1822)}, author = {Alice Printzi and Stefanos Fragkoulis and Anastasia Dimitriadi and Kleoniki Keklikoglou and Christos Arvanitidis and Eckhard P Witten and George Koumoundouros}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jfb.14240}, doi = {10.1111/jfb.14240}, issn = {0022-1112, 1095-8649}, year = {2021}, date = {2021-01-01}, urldate = {2022-01-17}, journal = {Journal of Fish Biology}, volume = {98}, number = {4}, pages = {987--994}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2020 |
Obst, Matthias; Exter, Katrina; Allcock, Louise A; Arvanitidis, Christos; Axberg, Alizz; Bustamante, Maria; Cancio, Ibon; Carreira-Flores, Diego; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Chrismas, Nathan; Clark, Melody S; Comtet, Thierry; Dailianis, Thanos; Davies, Neil; Deneudt, Klaas; de Cerio, Oihane Diaz; Fortič, Ana; Gerovasileiou, Vasilis; Hablützel, Pascal I; Keklikoglou, Kleoniki; Kotoulas, Georgios; Lasota, Rafal; Leite, Barbara R; Loisel, Stéphane; Lévêque, Laurent; Levy, Liraz; Malachowicz, Magdalena; Mavrič, Borut; Meyer, Christopher; Mortelmans, Jonas; Norkko, Joanna; Pade, Nicolas; Power, Anne Marie; Ramšak, Andreja; Reiss, Henning; Solbakken, Jostein; Staehr, Peter A; Sundberg, Per; Thyrring, Jakob; Troncoso, Jesus S; Viard, Frédérique; Wenne, Roman; Yperifanou, Eleni Ioanna; Zbawicka, Malgorzata; Pavloudi, Christina A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON) Journal Article Frontiers in Marine Science, 7 , pp. 572680, 2020, ISSN: 2296-7745. @article{obst_marine_2020, title = {A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)}, author = {Matthias Obst and Katrina Exter and Louise A Allcock and Christos Arvanitidis and Alizz Axberg and Maria Bustamante and Ibon Cancio and Diego Carreira-Flores and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Nathan Chrismas and Melody S Clark and Thierry Comtet and Thanos Dailianis and Neil Davies and Klaas Deneudt and Oihane Diaz de Cerio and Ana Fortič and Vasilis Gerovasileiou and Pascal I Hablützel and Kleoniki Keklikoglou and Georgios Kotoulas and Rafal Lasota and Barbara R Leite and Stéphane Loisel and Laurent Lévêque and Liraz Levy and Magdalena Malachowicz and Borut Mavrič and Christopher Meyer and Jonas Mortelmans and Joanna Norkko and Nicolas Pade and Anne Marie Power and Andreja Ramšak and Henning Reiss and Jostein Solbakken and Peter A Staehr and Per Sundberg and Jakob Thyrring and Jesus S Troncoso and Frédérique Viard and Roman Wenne and Eleni Ioanna Yperifanou and Malgorzata Zbawicka and Christina Pavloudi}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.572680/full}, doi = {10.3389/fmars.2020.572680}, issn = {2296-7745}, year = {2020}, date = {2020-11-01}, urldate = {2020-12-08}, journal = {Frontiers in Marine Science}, volume = {7}, pages = {572680}, abstract = {Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre ( www.embrc.eu ).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre ( www.embrc.eu ). |
Çinar, Melih Ertan; Féral, Jean‐Pierre; Arvanitidis, Christos; David, Romain; Taşkin, Ergün; Sini, Maria; Dailianis, Thanos; Doğan, Alper; Gerovasileiou, Vasilis; Evcen, Alper; Chenuil, Anne; Dağli, Ertan; Aysel, Veysel; Issaris, Yannis; Bakir, Kerem; Nalmpantı, Melina; Sartoretto, Stephane; Salomidi, Maria; Sapouna, Anastasia; Açik, Sermin; Dimitriadis, Charalampos; Koutsoubas, Drosos; Katağan, Tuncer; Öztürk, Bilal; Koçak, Ferah; Erdogan‐Dereli, Deniz; Önen, Senem; Özgen, Özge; Türkçü, Neslihan; Kirkim, Fevzi; Önen, Mesut Coralligenous assemblages along their geographical distribution: Testing of concepts and implications for management Journal Article Aquatic Conservation: Marine and Freshwater Ecosystems, 30 , pp. 1578–1594, 2020, ISSN: 1052-7613, 1099-0755. @article{cinar_coralligenous_2020, title = {Coralligenous assemblages along their geographical distribution: Testing of concepts and implications for management}, author = {Melih Ertan Çinar and Jean‐Pierre Féral and Christos Arvanitidis and Romain David and Ergün Taşkin and Maria Sini and Thanos Dailianis and Alper Doğan and Vasilis Gerovasileiou and Alper Evcen and Anne Chenuil and Ertan Dağli and Veysel Aysel and Yannis Issaris and Kerem Bakir and Melina Nalmpantı and Stephane Sartoretto and Maria Salomidi and Anastasia Sapouna and Sermin Açik and Charalampos Dimitriadis and Drosos Koutsoubas and Tuncer Katağan and Bilal Öztürk and Ferah Koçak and Deniz Erdogan‐Dereli and Senem Önen and Özge Özgen and Neslihan Türkçü and Fevzi Kirkim and Mesut Önen}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3365}, doi = {10.1002/aqc.3365}, issn = {1052-7613, 1099-0755}, year = {2020}, date = {2020-06-01}, urldate = {2020-08-06}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, volume = {30}, pages = {1578--1594}, abstract = {1. The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non‐destructive photo‐sampling protocol, developed in the framework of the CIGESMED project. 2. The results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Mediterranean ecoregions studied (biotic gradients hypothesis); and (b) the assemblage pattern does not change significantly when the information is aggregated to higher taxonomic levels (taxonomic sufficiency hypothesis). 3. Surrogate taxonomic categories higher than species, such as genus and family, can be used to reveal the multivariate pattern of the coralligenous assemblages. 4. Although preliminary at the pan‐Mediterranean scale, these outcomes set the scene for future comparisons as more data sets become available but also for comparisons between taxonomic and functional patterns.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 1. The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non‐destructive photo‐sampling protocol, developed in the framework of the CIGESMED project. 2. The results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Mediterranean ecoregions studied (biotic gradients hypothesis); and (b) the assemblage pattern does not change significantly when the information is aggregated to higher taxonomic levels (taxonomic sufficiency hypothesis). 3. Surrogate taxonomic categories higher than species, such as genus and family, can be used to reveal the multivariate pattern of the coralligenous assemblages. 4. Although preliminary at the pan‐Mediterranean scale, these outcomes set the scene for future comparisons as more data sets become available but also for comparisons between taxonomic and functional patterns. |
Dimitriou, Panagiotis D; Chatzinikolaou, Eva; Arvanitidis, Christos Ecological status assessment based on benthic macrofauna of three Mediterranean ports: Comparisons across seasons, activities and regions Journal Article Marine Pollution Bulletin, 153 , pp. 110997, 2020, ISSN: 0025-326X. @article{dimitriou_ecological_2020, title = {Ecological status assessment based on benthic macrofauna of three Mediterranean ports: Comparisons across seasons, activities and regions}, author = {Panagiotis D Dimitriou and Eva Chatzinikolaou and Christos Arvanitidis}, url = {http://www.sciencedirect.com/science/article/pii/S0025326X20301156}, doi = {https://doi.org/10.1016/j.marpolbul.2020.110997}, issn = {0025-326X}, year = {2020}, date = {2020-01-01}, journal = {Marine Pollution Bulletin}, volume = {153}, pages = {110997}, abstract = {The present study aimed to compare anthropogenic impacts in three Mediterranean ports (Cagliari-Italy, Heraklion-Greece, El-Kantatoui-Tunisia) employing benthic macrofaunal indices, used in the context of the European Water Framework Directive. Sampling stations were selected within ports according to sector usage categorization and sampled over three seasons. Benthic indices calculated include M-AMBI, BENTIX, BQI and BQI_Family. Comparisons were made between the indices values and ecological status (ES) of each station within and between ports. Overall, few statistically significant differences were observed across different seasons or different stations with the same usage within or across ports. The ES of sampling stations in the leisure/fishing and passenger/cargo ships sectors was mostly “good” or “moderate”, while the shipyard sector had “poor” ES. The results suggest that the indices used were suitable for assessing the ES of Mediterranean ports, led to comparable results even across different countries and contribute to the adaptation of specific port monitoring guidelines.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study aimed to compare anthropogenic impacts in three Mediterranean ports (Cagliari-Italy, Heraklion-Greece, El-Kantatoui-Tunisia) employing benthic macrofaunal indices, used in the context of the European Water Framework Directive. Sampling stations were selected within ports according to sector usage categorization and sampled over three seasons. Benthic indices calculated include M-AMBI, BENTIX, BQI and BQI_Family. Comparisons were made between the indices values and ecological status (ES) of each station within and between ports. Overall, few statistically significant differences were observed across different seasons or different stations with the same usage within or across ports. The ES of sampling stations in the leisure/fishing and passenger/cargo ships sectors was mostly “good” or “moderate”, while the shipyard sector had “poor” ES. The results suggest that the indices used were suitable for assessing the ES of Mediterranean ports, led to comparable results even across different countries and contribute to the adaptation of specific port monitoring guidelines. |
Valdor, Paloma F; Gómez, Aina G; Steinberg, Peter; Tanner, Edwina; Knights, Antony M; Seitz, Rochelle D; Airoldi, Laura; Firth, Louise B; Arvanitidis, Christos; Ponti, Massimo; Chatzinikolaou, Eva; Brooks, Paul R; Crowe, Tasman P; Smith, Alison; Méndez, Gonzalo; Ovejero, Aida; Soares-Gomes, Abilio; Burt, John A; MacLeod, Catriona; Juanes, José A A global approach to mapping the environmental risk of harbours on aquatic systems Journal Article Marine Policy, 119 , pp. 104051, 2020, ISSN: 0308-597X. @article{valdor_global_2020, title = {A global approach to mapping the environmental risk of harbours on aquatic systems}, author = {Paloma F Valdor and Aina G Gómez and Peter Steinberg and Edwina Tanner and Antony M Knights and Rochelle D Seitz and Laura Airoldi and Louise B Firth and Christos Arvanitidis and Massimo Ponti and Eva Chatzinikolaou and Paul R Brooks and Tasman P Crowe and Alison Smith and Gonzalo Méndez and Aida Ovejero and Abilio Soares-Gomes and John A Burt and Catriona MacLeod and José A Juanes}, url = {http://www.sciencedirect.com/science/article/pii/S0308597X19302684}, doi = {https://doi.org/10.1016/j.marpol.2020.104051}, issn = {0308-597X}, year = {2020}, date = {2020-01-01}, journal = {Marine Policy}, volume = {119}, pages = {104051}, abstract = {The goal of this paper is to propose a screening method for assessing the environmental risk to aquatic systems in harbours worldwide. A semi-quantitative method is based on environmental pressures, environmental conditions and societal response. The method is flexible enough to be applied to 15 harbours globally distributed through a multinational test using standardised and homogenised open data that can be obtained for any port worldwide. The method emerges as a useful approach towards the foundation of a global environmental risk atlas of harbours that should guide the harbour sector to develop a more globally informed strategy of sustainable development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The goal of this paper is to propose a screening method for assessing the environmental risk to aquatic systems in harbours worldwide. A semi-quantitative method is based on environmental pressures, environmental conditions and societal response. The method is flexible enough to be applied to 15 harbours globally distributed through a multinational test using standardised and homogenised open data that can be obtained for any port worldwide. The method emerges as a useful approach towards the foundation of a global environmental risk atlas of harbours that should guide the harbour sector to develop a more globally informed strategy of sustainable development. |
Zafeiropoulos, Haris; Viet, Ha Quoc; Vasileiadou, Katerina; Potirakis, Antonis; Arvanitidis, Christos; Topalis, Pantelis; Pavloudi, Christina; Pafilis, Evangelos PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes Journal Article GigaScience, 9 (3), 2020, ISSN: 2047-217X, (_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf). @article{zafeiropoulos_pema_2020, title = {PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes}, author = {Haris Zafeiropoulos and Ha Quoc Viet and Katerina Vasileiadou and Antonis Potirakis and Christos Arvanitidis and Pantelis Topalis and Christina Pavloudi and Evangelos Pafilis}, url = {https://doi.org/10.1093/gigascience/giaa022}, doi = {10.1093/gigascience/giaa022}, issn = {2047-217X}, year = {2020}, date = {2020-01-01}, journal = {GigaScience}, volume = {9}, number = {3}, abstract = {Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers’ needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.}, note = {_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf}, keywords = {}, pubstate = {published}, tppubtype = {article} } Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers’ needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies. |
Koutsouveli, Vasiliki; Manousaki, Tereza; Riesgo, Ana; Lagnel, Jacques; Kollias, Spyros; Tsigenopoulos, Costas S; Arvanitidis, Christos; Dounas, Costas; Magoulas, Antonios; Dailianis, Thanos Frontiers in Marine Science, 6 , pp. 786, 2020, ISSN: 2296-7745. @article{koutsouveli_gearing_2020, title = {Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience}, author = {Vasiliki Koutsouveli and Tereza Manousaki and Ana Riesgo and Jacques Lagnel and Spyros Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Costas Dounas and Antonios Magoulas and Thanos Dailianis}, url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00786/full}, doi = {10.3389/fmars.2019.00786}, issn = {2296-7745}, year = {2020}, date = {2020-01-01}, urldate = {2020-08-06}, journal = {Frontiers in Marine Science}, volume = {6}, pages = {786}, abstract = {The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates. |
2019 |
Manousaki, Tereza; Koutsouveli, Vasiliki; Lagnel, Jacques; Kollias, Spyridon; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Dounas, Costas; Dailianis, Thanos A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts Journal Article BMC Research Notes, 12 (1), pp. 813, 2019, ISSN: 1756-0500. @article{manousaki_novo_2019, title = {A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts}, author = {Tereza Manousaki and Vasiliki Koutsouveli and Jacques Lagnel and Spyridon Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Costas Dounas and Thanos Dailianis}, url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4843-6}, doi = {10.1186/s13104-019-4843-6}, issn = {1756-0500}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-06}, journal = {BMC Research Notes}, volume = {12}, number = {1}, pages = {813}, abstract = {Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host. |
Valdor, Paloma F; Gómez, Aina G; Juanes, José A; Kerléguer, Camille; Steinberg, Peter; Tanner, Edwina; MacLeod, Catriona; Knights, Antony M; Seitz, Rochelle D; Airoldi, Laura; Firth, Louise B; Crowe, Tasman; Chatzinikolaou, Eva; Smith, Alison; Arvanitidis, Christos; Burt, John A; Brooks, Paul R; Ponti, Massimo; Soares-Gomes, Abilio; Ovejero, Aida; Méndez, Gonzalo A global atlas of the environmental risk of marinas on water quality Journal Article Marine Pollution Bulletin, 149 , pp. 110661, 2019, ISSN: 0025-326X. @article{valdor_global_2019, title = {A global atlas of the environmental risk of marinas on water quality}, author = {Paloma F Valdor and Aina G Gómez and José A Juanes and Camille Kerléguer and Peter Steinberg and Edwina Tanner and Catriona MacLeod and Antony M Knights and Rochelle D Seitz and Laura Airoldi and Louise B Firth and Tasman Crowe and Eva Chatzinikolaou and Alison Smith and Christos Arvanitidis and John A Burt and Paul R Brooks and Massimo Ponti and Abilio Soares-Gomes and Aida Ovejero and Gonzalo Méndez}, url = {http://www.sciencedirect.com/science/article/pii/S0025326X19308094}, doi = {https://doi.org/10.1016/j.marpolbul.2019.110661}, issn = {0025-326X}, year = {2019}, date = {2019-12-01}, journal = {Marine Pollution Bulletin}, volume = {149}, pages = {110661}, abstract = {Abstract: Estimating the potential environmental risks of worldwide coastal recreational navigation on water quality is an important step towards designing a sustainable global market. This study proposes the creation of a global atlas of the environmental risk of marinas on water quality by applying the Marina Environmental Risk Assessment (MERA) procedure. Calculations integrate three main risk factors: Pressure, State and Response. Applying the MERA approach to 105 globally distributed marinas has confirmed the utility, versatility and adaptability of this procedure as a novel tool to compare the environmental risks within and among regions (i.e. for area-based management), to identify the world's best practices (i.e. to optimize existing management) and to understand and adjust global risks in future development (i.e. improved planning).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract: Estimating the potential environmental risks of worldwide coastal recreational navigation on water quality is an important step towards designing a sustainable global market. This study proposes the creation of a global atlas of the environmental risk of marinas on water quality by applying the Marina Environmental Risk Assessment (MERA) procedure. Calculations integrate three main risk factors: Pressure, State and Response. Applying the MERA approach to 105 globally distributed marinas has confirmed the utility, versatility and adaptability of this procedure as a novel tool to compare the environmental risks within and among regions (i.e. for area-based management), to identify the world's best practices (i.e. to optimize existing management) and to understand and adjust global risks in future development (i.e. improved planning). |
Arvanitidis, Christos; Gerovasileiou, Vasilis; Karachle, Paraskevi K; Zenetos, Argyro New horizons for the Panhellenic Symposium of Oceanography & Fisheries Journal Article Mediterranean Marine Science, 20 (4), 2019, ISSN: 1791-6763, 1108-393X. @article{arvanitidis_new_2019, title = {New horizons for the Panhellenic Symposium of Oceanography & Fisheries}, author = {Christos Arvanitidis and Vasilis Gerovasileiou and Paraskevi K Karachle and Argyro Zenetos}, url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/22047}, doi = {10.12681/mms.22047}, issn = {1791-6763, 1108-393X}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-21}, journal = {Mediterranean Marine Science}, volume = {20}, number = {4}, abstract = {The Panhellenic Symposium of Oceanography andFisheries was firstly launched in Athens, 35 years agosparked by the enthusiasm of the Greek aquatic scientists,massively supported by the voluntary contributionof the Hellenic Centre for Marine Research (HCMR)employees. Over the last three decades, the Symposiumestablished and flourished as the forum for a wide rangeof marine and freshwater disciplines in the country. It becamea tradition to a large audience since it has attractedresearchers, academicians, students, entrepreneurs andthe industry both from Greece and adjacent countries.The initial enthusiasm and support is growing with theinclusion of Universities and other educational/researchinstitutes in the organization scheme.The “12th Panhellenic Symposium of Oceanographyand Fisheries” 1 did not only deliver big changes in itsoperational mode but also opened new horizons to thescientific communities of Greece and adjacent areas. Ithas been a tipping point in this type of events in manyaspects.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Panhellenic Symposium of Oceanography andFisheries was firstly launched in Athens, 35 years agosparked by the enthusiasm of the Greek aquatic scientists,massively supported by the voluntary contributionof the Hellenic Centre for Marine Research (HCMR)employees. Over the last three decades, the Symposiumestablished and flourished as the forum for a wide rangeof marine and freshwater disciplines in the country. It becamea tradition to a large audience since it has attractedresearchers, academicians, students, entrepreneurs andthe industry both from Greece and adjacent countries.The initial enthusiasm and support is growing with theinclusion of Universities and other educational/researchinstitutes in the organization scheme.The “12th Panhellenic Symposium of Oceanographyand Fisheries” 1 did not only deliver big changes in itsoperational mode but also opened new horizons to thescientific communities of Greece and adjacent areas. Ithas been a tipping point in this type of events in manyaspects. |
Ulman, Aylin; Ferrario, Jasmine; Forcada, Aitor; Seebens, Hanno; Arvanitidis, Christos; Occhipinti‐Ambrogi, Anna; Marchini, Agnese Alien species spreading via biofouling on recreational vessels in the Mediterranean Sea Journal Article Journal of Applied Ecology, 56 (12), pp. 2620–2629, 2019, ISSN: 0021-8901, 1365-2664, (BIODIV). @article{ulman_alien_2019, title = {Alien species spreading via biofouling on recreational vessels in the Mediterranean Sea}, author = {Aylin Ulman and Jasmine Ferrario and Aitor Forcada and Hanno Seebens and Christos Arvanitidis and Anna Occhipinti‐Ambrogi and Agnese Marchini}, editor = {Nessa O'Connor}, url = {https://onlinelibrary.wiley.com/doi/10.1111/1365-2664.13502}, doi = {10.1111/1365-2664.13502}, issn = {0021-8901, 1365-2664}, year = {2019}, date = {2019-12-01}, urldate = {2022-01-17}, journal = {Journal of Applied Ecology}, volume = {56}, number = {12}, pages = {2620--2629}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Massi, Luca; Maselli, Fabio; Rossano, Claudia; Gambineri, Simone; Chatzinikolaou, Evangelia; Dailianis, Thanos; Arvanitidis, Christos; Nuccio, Caterina; Scapini, Felicita; Lazzara, Luigi Reflectance spectra classification for the rapid assessment of water ecological quality in Mediterranean ports Journal Article Oceanologia, 61 (4), pp. 445–459, 2019, ISSN: 00783234. @article{massi_reflectance_2019, title = {Reflectance spectra classification for the rapid assessment of water ecological quality in Mediterranean ports}, author = {Luca Massi and Fabio Maselli and Claudia Rossano and Simone Gambineri and Evangelia Chatzinikolaou and Thanos Dailianis and Christos Arvanitidis and Caterina Nuccio and Felicita Scapini and Luigi Lazzara}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0078323419300284}, doi = {10.1016/j.oceano.2019.04.001}, issn = {00783234}, year = {2019}, date = {2019-10-01}, urldate = {2020-08-06}, journal = {Oceanologia}, volume = {61}, number = {4}, pages = {445--459}, abstract = {Ports are open systems with direct connection to the sea, therefore any potential impact on port waters may have implications for the health of adjacent marine ecosystems. European WFD addressed ports in the category of Heavily Modified Water Bodies (HMWBs) and promoted implementation of protocols to monitor and improve their ecological status. TRIX index, which incorporates the main variables involved in the trophism of marine ecosystems (Nitrogen, Phosphorus, Chlorophyll a, Dissolved Oxygen), is widely utilized in European coastal areas to evaluate trophic status. The relationships between the variables involved in TRIX computation, particularly Chlorophyll a concentration, and water spectral reflectance provides an alternative method to evaluate the quality and ecological status of the port water. Hyperspectral (380–710 nm) water reflectance data were recorded by a portable radiometric system in five ports from the Western and Eastern Mediterranean Basin. The spectral distance between samples was measured by two metrics using both the original and reduced spectra and was implemented within a hierarchical clustering algorithm. The four spectral classes that emerged from this operation were statistically analysed versus standard water quality descriptors and phytoplankton community features to evaluate the ecological significance of the information obtained. The results indicated a substantial coherence of different indicators with more than 60% of the total TRIX variability is accounted for by the proposed classification of reflectance spectra. This classification is therefore proposed as a promising Rapid Assessment Technique of ports water ecological quality, which can serve as an effective monitoring tool for sustainable management of ports.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ports are open systems with direct connection to the sea, therefore any potential impact on port waters may have implications for the health of adjacent marine ecosystems. European WFD addressed ports in the category of Heavily Modified Water Bodies (HMWBs) and promoted implementation of protocols to monitor and improve their ecological status. TRIX index, which incorporates the main variables involved in the trophism of marine ecosystems (Nitrogen, Phosphorus, Chlorophyll a, Dissolved Oxygen), is widely utilized in European coastal areas to evaluate trophic status. The relationships between the variables involved in TRIX computation, particularly Chlorophyll a concentration, and water spectral reflectance provides an alternative method to evaluate the quality and ecological status of the port water. Hyperspectral (380–710 nm) water reflectance data were recorded by a portable radiometric system in five ports from the Western and Eastern Mediterranean Basin. The spectral distance between samples was measured by two metrics using both the original and reduced spectra and was implemented within a hierarchical clustering algorithm. The four spectral classes that emerged from this operation were statistically analysed versus standard water quality descriptors and phytoplankton community features to evaluate the ecological significance of the information obtained. The results indicated a substantial coherence of different indicators with more than 60% of the total TRIX variability is accounted for by the proposed classification of reflectance spectra. This classification is therefore proposed as a promising Rapid Assessment Technique of ports water ecological quality, which can serve as an effective monitoring tool for sustainable management of ports. |
Vitali, Francesco; Mandalakis, Manolis; Chatzinikolaou, Eva; Dailianis, Thanos; Senatore, Giuliana; Casalone, Enrico; Mastromei, Giorgio; Sergi, Simona; Lussu, Raffaela; Arvanitidis, Christos; Tamburini, Elena Frontiers in Marine Science, 6 , pp. 590, 2019, ISSN: 2296-7745. @article{vitali_benthic_2019, title = {Benthic Prokaryotic Community Response to Polycyclic Aromatic Hydrocarbon Chronic Exposure: Importance of Emission Sources in Mediterranean Ports}, author = {Francesco Vitali and Manolis Mandalakis and Eva Chatzinikolaou and Thanos Dailianis and Giuliana Senatore and Enrico Casalone and Giorgio Mastromei and Simona Sergi and Raffaela Lussu and Christos Arvanitidis and Elena Tamburini}, url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00590/full}, doi = {10.3389/fmars.2019.00590}, issn = {2296-7745}, year = {2019}, date = {2019-09-01}, urldate = {2020-08-06}, journal = {Frontiers in Marine Science}, volume = {6}, pages = {590}, abstract = {The present study aimed to evaluate the impact of polycyclic aromatic hydrocarbons (PAHs) produced by multiple emission sources on prokaryotic communities in sediments chronically affected by anthropogenic pressures. In this context, surface sediments were investigated in three Mediterranean touristic ports over three sampling periods and in different port sectors. The levels of 16 priority PAHs varied over three orders of magnitude (25–49,000 ng g–1) covering the range of concentrations previously reported for Mediterranean harbors. Pyrogenic processes were found to be the dominant emission source of PAHs, with considerable differences among ports. The prokaryotic communities were identified by using the terminal restriction fragment length polymorphism, targeting the 16S rRNA gene for Bacteria and Archaea as well as the dsrAB gene for sulphate-reducing bacteria (SRB). The structure of the three benthic prokaryotic communities varied consistently among the ports. The structure of Bacteria and Archaea exhibited strong spatiotemporal variations that did not allow us to specifically link the observed differences in community structures with PAH sources. On the contrary, our study provided, for the first time, evidence that the PAH emission sources play a role in structuring benthic communities of SRB. Our findings indicate that the SRB community can be used as a valuable candidate biotic descriptor for bioremediation monitoring in heavily impacted port sediments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study aimed to evaluate the impact of polycyclic aromatic hydrocarbons (PAHs) produced by multiple emission sources on prokaryotic communities in sediments chronically affected by anthropogenic pressures. In this context, surface sediments were investigated in three Mediterranean touristic ports over three sampling periods and in different port sectors. The levels of 16 priority PAHs varied over three orders of magnitude (25–49,000 ng g–1) covering the range of concentrations previously reported for Mediterranean harbors. Pyrogenic processes were found to be the dominant emission source of PAHs, with considerable differences among ports. The prokaryotic communities were identified by using the terminal restriction fragment length polymorphism, targeting the 16S rRNA gene for Bacteria and Archaea as well as the dsrAB gene for sulphate-reducing bacteria (SRB). The structure of the three benthic prokaryotic communities varied consistently among the ports. The structure of Bacteria and Archaea exhibited strong spatiotemporal variations that did not allow us to specifically link the observed differences in community structures with PAH sources. On the contrary, our study provided, for the first time, evidence that the PAH emission sources play a role in structuring benthic communities of SRB. Our findings indicate that the SRB community can be used as a valuable candidate biotic descriptor for bioremediation monitoring in heavily impacted port sediments. |
Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva; Wils, Patricia; Brecko, Jonathan; Kvaček, Jiří; Metscher, Brian; Arvanitidis, Christos Micro-computed tomography for natural history specimens: a handbook of best practice protocols Journal Article European Journal of Taxonomy, 0 (522), 2019, ISSN: 2118-9773. @article{keklikoglou_micro-computed_2019, title = {Micro-computed tomography for natural history specimens: a handbook of best practice protocols}, author = {Kleoniki Keklikoglou and Sarah Faulwetter and Eva Chatzinikolaou and Patricia Wils and Jonathan Brecko and Jiří Kvaček and Brian Metscher and Christos Arvanitidis}, url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/693}, doi = {10.5852/ejt.2019.522}, issn = {2118-9773}, year = {2019}, date = {2019-04-01}, journal = {European Journal of Taxonomy}, volume = {0}, number = {522}, abstract = {Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included. |
Poursanidis, D; Chatzigeorgiou, G; Dimitriadis, C; Koutsoubas, D; Arvanitidis, C Hydrobiologia, 826 (1), pp. 159–172, 2019, ISSN: 00188158, (Publisher: Springer International Publishing). @article{poursanidis_testing_2019, title = {Testing the robustness of a coastal biodiversity data protocol in the Mediterranean: insights from the molluskan assemblages from the sublittoral macroalgae communities}, author = {D Poursanidis and G Chatzigeorgiou and C Dimitriadis and D Koutsoubas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85052115016&doi=10.1007%2fs10750-018-3725-6&partnerID=40&md5=2fcefb9721d7fe670a2e61f3cc465208}, doi = {10.1007/s10750-018-3725-6}, issn = {00188158}, year = {2019}, date = {2019-01-01}, journal = {Hydrobiologia}, volume = {826}, number = {1}, pages = {159--172}, abstract = {The NaGISA project (Natural Geography Ιn Shore Areas) is a global initiative within the framework of the Census of Marine Life. The Mediterranean Sea has joined with 4 stations, 2 in Italy and 2 on the island of Crete, Greece. Two different sites were sampled during two consecutive years (2007 and 2008) by means of SCUBA diving. On the basis of the evidence offered by the collected material from the hard substrates of Crete, and the literature mined datasets concerning the molluscan assemblages, two main issues are investigated: (a) is the molluscan fauna sampled in the two NaGISA sites representative of the regional Mediterranean one? and (b), is the molluscan fauna sampled from the two sites randomly assembled from the regional species pool across different spatial scales? Although a strong tendency of the local molluskan composition to be randomly sampled from the regional pools at all scales, it is not possible to demonstrate with a degree of certainty whether their observed local diversity is independent of local and regional processes or if it is determined by a combination of the two acting either in concert or antagonistically. © 2018, Springer Nature Switzerland AG.}, note = {Publisher: Springer International Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } The NaGISA project (Natural Geography Ιn Shore Areas) is a global initiative within the framework of the Census of Marine Life. The Mediterranean Sea has joined with 4 stations, 2 in Italy and 2 on the island of Crete, Greece. Two different sites were sampled during two consecutive years (2007 and 2008) by means of SCUBA diving. On the basis of the evidence offered by the collected material from the hard substrates of Crete, and the literature mined datasets concerning the molluscan assemblages, two main issues are investigated: (a) is the molluscan fauna sampled in the two NaGISA sites representative of the regional Mediterranean one? and (b), is the molluscan fauna sampled from the two sites randomly assembled from the regional species pool across different spatial scales? Although a strong tendency of the local molluskan composition to be randomly sampled from the regional pools at all scales, it is not possible to demonstrate with a degree of certainty whether their observed local diversity is independent of local and regional processes or if it is determined by a combination of the two acting either in concert or antagonistically. © 2018, Springer Nature Switzerland AG. |
Ulman, Aylin; Ferrario, Jasmine; Forcada, Aitor; Arvanitidis, Christos; Occhipinti-Ambrogi, Anna; Marchini, Agnese A Hitchhiker's guide to Mediterranean marina travel for alien species Journal Article Journal of Environmental Management, 241 , pp. 328–339, 2019, ISSN: 03014797, (BIODIV). @article{ulman_hitchhikers_2019, title = {A Hitchhiker's guide to Mediterranean marina travel for alien species}, author = {Aylin Ulman and Jasmine Ferrario and Aitor Forcada and Christos Arvanitidis and Anna Occhipinti-Ambrogi and Agnese Marchini}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0301479719304682}, doi = {10.1016/j.jenvman.2019.04.011}, issn = {03014797}, year = {2019}, date = {2019-01-01}, urldate = {2022-01-17}, journal = {Journal of Environmental Management}, volume = {241}, pages = {328--339}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2018 |
Guy‐Haim, Tamar; Lyons, Devin A; Kotta, Jonne; Ojaveer, Henn; Queirós, Ana M; Chatzinikolaou, Eva; Arvanitidis, Christos; Como, Serena; Magni, Paolo; Blight, Andrew J; Orav‐Kotta, Helen; Somerfield, Paul J; Crowe, Tasman P; Rilov, Gil Diverse effects of invasive ecosystem engineers on marine biodiversity and ecosystem functions: A global review and meta‐analysis Journal Article Global Change Biology, 24 (3), pp. 906–924, 2018, ISSN: 1354-1013, 1365-2486. @article{guyhaim_diverse_2018, title = {Diverse effects of invasive ecosystem engineers on marine biodiversity and ecosystem functions: A global review and meta‐analysis}, author = {Tamar Guy‐Haim and Devin A Lyons and Jonne Kotta and Henn Ojaveer and Ana M Queirós and Eva Chatzinikolaou and Christos Arvanitidis and Serena Como and Paolo Magni and Andrew J Blight and Helen Orav‐Kotta and Paul J Somerfield and Tasman P Crowe and Gil Rilov}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14007}, doi = {10.1111/gcb.14007}, issn = {1354-1013, 1365-2486}, year = {2018}, date = {2018-03-01}, urldate = {2020-08-08}, journal = {Global Change Biology}, volume = {24}, number = {3}, pages = {906--924}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Keklikoglou, K; Chatzigeorgiou, G; Faulwetter, S; Kalogeropoulou, V; Plaiti, W; Maidanou, M; Dounas, C; Lampadariou, N; Arvanitidis, C 'Simple' can be good, too: Testing three hard bottom sampling methods on macrobenthic and meiobenthic assemblages Journal Article Journal of the Marine Biological Association of the United Kingdom, 2018, ISSN: 00253154, (Publisher: Cambridge University Press). @article{keklikoglou_simple_2018, title = {'Simple' can be good, too: Testing three hard bottom sampling methods on macrobenthic and meiobenthic assemblages}, author = {K Keklikoglou and G Chatzigeorgiou and S Faulwetter and V Kalogeropoulou and W Plaiti and M Maidanou and C Dounas and N Lampadariou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85055515853&doi=10.1017%2fS0025315418000863&partnerID=40&md5=3cb71874d9e2fbcb00720d2b0f17d0a1}, doi = {10.1017/S0025315418000863}, issn = {00253154}, year = {2018}, date = {2018-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, abstract = {Subtidal hard bottoms are of particular scientific and economic value as they are highly productive systems. They are less well studied compared with soft bottoms, as they often require manual sample collection via scuba diving. Although a multitude of sampling devices is available for soft bottoms, only a few are suitable for hard substrates, and their performance is largely unstudied. In the present study, three hard bottom sampling methods were compared, regarding their sampling efficiency and the damage they may cause to macrobenthic and meiobenthic organisms. Two of the sampling methods examined are typically employed for the study of hard bottom substrates (manual collection, airlift device), while the third involves a newly constructed sampler (MANOSS - Manual Operated Suction Sampler). All three sampling methods were tested at 12 m depth on a hard bottom substrate with algal coverage dominated by Cystoseira spp. No overall significant differences were observed between the sampling efficiency and the damage caused by the three sampling methods regarding the macrofaunal assemblages, with the exception of the MANOSS method which collected more species than the manual method. In addition, significant differences were observed in the collecting performance for the meiobenthic assemblages, presenting significantly higher densities of meiofauna sampled by the MANOSS compared with the manual collection method, while the airlift device presented an intermediate efficiency. However, taking into account other factors such as cost, ease of use and the scope of each study, none of the methods clearly outperforms the others. Copyright © Marine Biological Association of the United Kingdom 2018.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Subtidal hard bottoms are of particular scientific and economic value as they are highly productive systems. They are less well studied compared with soft bottoms, as they often require manual sample collection via scuba diving. Although a multitude of sampling devices is available for soft bottoms, only a few are suitable for hard substrates, and their performance is largely unstudied. In the present study, three hard bottom sampling methods were compared, regarding their sampling efficiency and the damage they may cause to macrobenthic and meiobenthic organisms. Two of the sampling methods examined are typically employed for the study of hard bottom substrates (manual collection, airlift device), while the third involves a newly constructed sampler (MANOSS - Manual Operated Suction Sampler). All three sampling methods were tested at 12 m depth on a hard bottom substrate with algal coverage dominated by Cystoseira spp. No overall significant differences were observed between the sampling efficiency and the damage caused by the three sampling methods regarding the macrofaunal assemblages, with the exception of the MANOSS method which collected more species than the manual method. In addition, significant differences were observed in the collecting performance for the meiobenthic assemblages, presenting significantly higher densities of meiofauna sampled by the MANOSS compared with the manual collection method, while the airlift device presented an intermediate efficiency. However, taking into account other factors such as cost, ease of use and the scope of each study, none of the methods clearly outperforms the others. Copyright © Marine Biological Association of the United Kingdom 2018. |
Vasileiadou, K; Pavloudi, C; Camisa, F; Tsikopoulou, I; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem Journal Article Journal of the Marine Biological Association of the United Kingdom, 98 (4), pp. 777–789, 2018, ISSN: 00253154, (Publisher: Cambridge University Press). @article{vasileiadou_genetic_2018, title = {Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem}, author = {K Vasileiadou and C Pavloudi and F Camisa and I Tsikopoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009786126&doi=10.1017%2fS0025315416001910&partnerID=40&md5=8e7cb2651bd57afe644615018866185a}, doi = {10.1017/S0025315416001910}, issn = {00253154}, year = {2018}, date = {2018-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {98}, number = {4}, pages = {777--789}, abstract = {Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017. |
Bulleri, F; Eriksson, B K; Queirós, A; Airoldi, L; Arenas, F; Arvanitidis, C; Bouma, T J; Crowe, T P; Davoult, D; Guizien, K; Iveša, L; Jenkins, S R; Michalet, R; Olabarria, C; Procaccini, G; Serrão, E A; Wahl, M; Benedetti-Cecchi, L Harnessing positive species interactions as a tool against climate-driven loss of coastal biodiversity Journal Article PLoS Biology, 16 (9), 2018, ISSN: 15449173, (Publisher: Public Library of Science). @article{bulleri_harnessing_2018, title = {Harnessing positive species interactions as a tool against climate-driven loss of coastal biodiversity}, author = {F Bulleri and B K Eriksson and A Queirós and L Airoldi and F Arenas and C Arvanitidis and T J Bouma and T P Crowe and D Davoult and K Guizien and L Iveša and S R Jenkins and R Michalet and C Olabarria and G Procaccini and E A Serrão and M Wahl and L Benedetti-Cecchi}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054862991&doi=10.1371%2fjournal.pbio.2006852&partnerID=40&md5=4428032b5d4a7303fc2c6dd4a3196dea}, doi = {10.1371/journal.pbio.2006852}, issn = {15449173}, year = {2018}, date = {2018-01-01}, journal = {PLoS Biology}, volume = {16}, number = {9}, abstract = {Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions. © 2018 Bulleri et al. http://creativecommons.org/licenses/by/4.0/.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions. © 2018 Bulleri et al. http://creativecommons.org/licenses/by/4.0/. |
Dimitriadi, A; Beis, D; Arvanitidis, C; Adriaens, D; Koumoundouros, G Developmental temperature has persistent, sexually dimorphic effects on zebrafish cardiac anatomy Journal Article Scientific Reports, 8 (1), 2018, ISSN: 20452322, (Publisher: Nature Publishing Group). @article{dimitriadi_developmental_2018, title = {Developmental temperature has persistent, sexually dimorphic effects on zebrafish cardiac anatomy}, author = {A Dimitriadi and D Beis and C Arvanitidis and D Adriaens and G Koumoundouros}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047803313&doi=10.1038%2fs41598-018-25991-8&partnerID=40&md5=a85c0533f8951254ae69f978e3121dee}, doi = {10.1038/s41598-018-25991-8}, issn = {20452322}, year = {2018}, date = {2018-01-01}, journal = {Scientific Reports}, volume = {8}, number = {1}, abstract = {Over the next century, climate change of anthropogenic origin is a major threat to global biodiversity. We show here that developmental temperature can have significant effects on zebrafish cardiac anatomy and swimming performance. Zebrafish embryos were subjected to three developmental temperature treatments (TD = 24, 28 or 32 °C) up to metamorphosis and then all maintained under common conditions (28 °C) to adulthood. We found that developmental temperature affected cardiac anatomy of juveniles and adults even eight months after the different thermal treatments had been applied. The elevation of TD induced a significant increase of the ventricle roundness in juvenile (10% increase) and male (22% increase), but not in female zebrafish. The aerobic exercise performance of adult zebrafish was significantly decreased as TD elevated from 24 to 32 °C. Gene expression analysis that was performed at the end of the temperature treatments revealed significant up-regulation of nppa, myh7 and mybpc3 genes at the colder temperature. Our work provides the first evidence for a direct link between developmental temperature and cardiac form at later life-stages. Our results also add to the emerging rationale for understanding the potential effects of global warming on how fish will perform in their natural environment. © 2018 The Author(s).}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Over the next century, climate change of anthropogenic origin is a major threat to global biodiversity. We show here that developmental temperature can have significant effects on zebrafish cardiac anatomy and swimming performance. Zebrafish embryos were subjected to three developmental temperature treatments (TD = 24, 28 or 32 °C) up to metamorphosis and then all maintained under common conditions (28 °C) to adulthood. We found that developmental temperature affected cardiac anatomy of juveniles and adults even eight months after the different thermal treatments had been applied. The elevation of TD induced a significant increase of the ventricle roundness in juvenile (10% increase) and male (22% increase), but not in female zebrafish. The aerobic exercise performance of adult zebrafish was significantly decreased as TD elevated from 24 to 32 °C. Gene expression analysis that was performed at the end of the temperature treatments revealed significant up-regulation of nppa, myh7 and mybpc3 genes at the colder temperature. Our work provides the first evidence for a direct link between developmental temperature and cardiac form at later life-stages. Our results also add to the emerging rationale for understanding the potential effects of global warming on how fish will perform in their natural environment. © 2018 The Author(s). |
Kissling, W D; Ahumada, J A; Bowser, A; Fernandez, M; Fernández, N; García, E A; Guralnick, R P; Isaac, N J B; Kelling, S; Los, W; McRae, L; Mihoub, J -B; Obst, M; Santamaria, M; Skidmore, A K; Williams, K J; Agosti, D; Amariles, D; Arvanitidis, C; Bastin, L; Leo, De F; Egloff, W; Elith, J; Hobern, D; Martin, D; Pereira, H M; Pesole, G; Peterseil, J; Saarenmaa, H; Schigel, D; Schmeller, D S; Segata, N; Turak, E; Uhlir, P F; Wee, B; Hardisty, A R Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale Journal Article Biological Reviews, 93 (1), pp. 600–625, 2018, ISSN: 14647931, (Publisher: Blackwell Publishing Ltd). @article{kissling_building_2018, title = {Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale}, author = {W D Kissling and J A Ahumada and A Bowser and M Fernandez and N Fernández and E A García and R P Guralnick and N J B Isaac and S Kelling and W Los and L McRae and J -B Mihoub and M Obst and M Santamaria and A K Skidmore and K J Williams and D Agosti and D Amariles and C Arvanitidis and L Bastin and F De Leo and W Egloff and J Elith and D Hobern and D Martin and H M Pereira and G Pesole and J Peterseil and H Saarenmaa and D Schigel and D S Schmeller and N Segata and E Turak and P F Uhlir and B Wee and A R Hardisty}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85026661824&doi=10.1111%2fbrv.12359&partnerID=40&md5=7d9a147f2609cd10e9beb0125cf96c9e}, doi = {10.1111/brv.12359}, issn = {14647931}, year = {2018}, date = {2018-01-01}, journal = {Biological Reviews}, volume = {93}, number = {1}, pages = {600--625}, abstract = {Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society. |
Peck, M A; Arvanitidis, C; Butenschön, M; Canu, D M; Chatzinikolaou, E; Cucco, A; Domenici, P; Fernandes, J A; Gasche, L; Huebert, K B; Hufnagl, M; Jones, M C; Kempf, A; Keyl, F; Maar, M; Mahévas, S; Marchal, P; Nicolas, D; Pinnegar, J K; Rivot, E; Rochette, S; Sell, A F; Sinerchia, M; Solidoro, C; Somerfield, P J; Teal, L R; Travers-Trolet, M; van de Wolfshaar, K E Estuarine, Coastal and Shelf Science, 201 , pp. 40–55, 2018, ISSN: 02727714, (Publisher: Academic Press). @article{peck_projecting_2018, title = {Projecting changes in the distribution and productivity of living marine resources: A critical review of the suite of modelling approaches used in the large European project VECTORS}, author = {M A Peck and C Arvanitidis and M Butenschön and D M Canu and E Chatzinikolaou and A Cucco and P Domenici and J A Fernandes and L Gasche and K B Huebert and M Hufnagl and M C Jones and A Kempf and F Keyl and M Maar and S Mahévas and P Marchal and D Nicolas and J K Pinnegar and E Rivot and S Rochette and A F Sell and M Sinerchia and C Solidoro and P J Somerfield and L R Teal and M Travers-Trolet and K E van de Wolfshaar}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975129749&doi=10.1016%2fj.ecss.2016.05.019&partnerID=40&md5=f10cfc8269e116b0ea77a1f85e03c05e}, doi = {10.1016/j.ecss.2016.05.019}, issn = {02727714}, year = {2018}, date = {2018-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {201}, pages = {40--55}, abstract = {We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of species, 3) food web models, and 4) end-to-end models. Single pressures are rare and, in the future, models must be able to examine multiple factors affecting living marine resources such as interactions between: i) climate-driven changes in temperature regimes and acidification, ii) reductions in water quality due to eutrophication, iii) the introduction of alien invasive species, and/or iv) (over-)exploitation by fisheries. Statistical (correlative) approaches can be used to detect historical patterns which may not be relevant in the future. Advancing predictive capacity of changes in distribution and productivity of living marine resources requires explicit modelling of biological and physical mechanisms. New formulations are needed which (depending on the question) will need to strive for more realism in ecophysiology and behaviour of individuals, life history strategies of species, as well as trophodynamic interactions occurring at different spatial scales. Coupling existing models (e.g. physical, biological, economic) is one avenue that has proven successful. However, fundamental advancements are needed to address key issues such as the adaptive capacity of species/groups and ecosystems. The continued development of end-to-end models (e.g., physics to fish to human sectors) will be critical if we hope to assess how multiple pressures may interact to cause changes in living marine resources including the ecological and economic costs and trade-offs of different spatial management strategies. Given the strengths and weaknesses of the various types of models reviewed here, confidence in projections of changes in the distribution and productivity of living marine resources will be increased by assessing model structural uncertainty through biological ensemble modelling. © 2016 Elsevier Ltd}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of species, 3) food web models, and 4) end-to-end models. Single pressures are rare and, in the future, models must be able to examine multiple factors affecting living marine resources such as interactions between: i) climate-driven changes in temperature regimes and acidification, ii) reductions in water quality due to eutrophication, iii) the introduction of alien invasive species, and/or iv) (over-)exploitation by fisheries. Statistical (correlative) approaches can be used to detect historical patterns which may not be relevant in the future. Advancing predictive capacity of changes in distribution and productivity of living marine resources requires explicit modelling of biological and physical mechanisms. New formulations are needed which (depending on the question) will need to strive for more realism in ecophysiology and behaviour of individuals, life history strategies of species, as well as trophodynamic interactions occurring at different spatial scales. Coupling existing models (e.g. physical, biological, economic) is one avenue that has proven successful. However, fundamental advancements are needed to address key issues such as the adaptive capacity of species/groups and ecosystems. The continued development of end-to-end models (e.g., physics to fish to human sectors) will be critical if we hope to assess how multiple pressures may interact to cause changes in living marine resources including the ecological and economic costs and trade-offs of different spatial management strategies. Given the strengths and weaknesses of the various types of models reviewed here, confidence in projections of changes in the distribution and productivity of living marine resources will be increased by assessing model structural uncertainty through biological ensemble modelling. © 2016 Elsevier Ltd |
Chatzinikolaou, E; Mandalakis, M; Damianidis, P; Dailianis, T; Gambineri, S; Rossano, C; Scapini, F; Carucci, A; Arvanitidis, C Spatio-temporal benthic biodiversity patterns and pollution pressure in three Mediterranean touristic ports Journal Article Science of the Total Environment, 624 , pp. 648–660, 2018, ISSN: 00489697, (Publisher: Elsevier B.V.). @article{chatzinikolaou_spatio-temporal_2018, title = {Spatio-temporal benthic biodiversity patterns and pollution pressure in three Mediterranean touristic ports}, author = {E Chatzinikolaou and M Mandalakis and P Damianidis and T Dailianis and S Gambineri and C Rossano and F Scapini and A Carucci and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038809023&doi=10.1016%2fj.scitotenv.2017.12.111&partnerID=40&md5=e7ce64fb16c0df8f7d6cc0aea715e447}, doi = {10.1016/j.scitotenv.2017.12.111}, issn = {00489697}, year = {2018}, date = {2018-01-01}, journal = {Science of the Total Environment}, volume = {624}, pages = {648--660}, abstract = {The Mediterranean Sea is one of the busiest areas worldwide in terms of maritime activity, facing considerable anthropogenic disturbance, such as pollution by hydrocarbons and heavy metals. The present study has evaluated the environmental and benthic biodiversity characteristics of three touristic ports, Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia), based on the combined assessment of physical parameters, chemical variables (i.e. nutrients, pigments), sediment pollution and macrobenthic biodiversity. Different port sectors (leisure, fishing, passenger, cargo, shipyard) and different seasons (winter, before touristic period, after touristic period) were compared. Salinity and sediment concentration of copper and antimony were the three environmental parameters most highly correlated with benthic species composition and diversity. Both the environmental variables and the benthic biodiversity patterns were significantly different between the three ports (i.e. different geographical locations). Heraklion port was heavily polluted by AHs in surface and anoxic sediments and had the highest percentage of opportunistic species, while Cagliari had the highest levels of PAHs and UCM and low species richness. El Kantaoui port was less polluted and characterised by a richer biodiversity. The shipyard sector in Heraklion port was significantly different from all other sectors in terms of abiotic and biotic parameters. Physico-chemical and pollution variables recorded during the period after tourism (late summer) were significantly different from the ones recorded in winter. Seasonal differences were not significant between benthic species diversity patterns, but were revealed when the patterns derived from the aggregation of higher taxonomic levels were compared. The present study indicates that a regular-basis monitoring plan including evaluation of environmental health based on benthic biodiversity, can provide a basis for perceiving changes and reveal the degree of anthropogenic disturbance in port environments. © 2017 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean Sea is one of the busiest areas worldwide in terms of maritime activity, facing considerable anthropogenic disturbance, such as pollution by hydrocarbons and heavy metals. The present study has evaluated the environmental and benthic biodiversity characteristics of three touristic ports, Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia), based on the combined assessment of physical parameters, chemical variables (i.e. nutrients, pigments), sediment pollution and macrobenthic biodiversity. Different port sectors (leisure, fishing, passenger, cargo, shipyard) and different seasons (winter, before touristic period, after touristic period) were compared. Salinity and sediment concentration of copper and antimony were the three environmental parameters most highly correlated with benthic species composition and diversity. Both the environmental variables and the benthic biodiversity patterns were significantly different between the three ports (i.e. different geographical locations). Heraklion port was heavily polluted by AHs in surface and anoxic sediments and had the highest percentage of opportunistic species, while Cagliari had the highest levels of PAHs and UCM and low species richness. El Kantaoui port was less polluted and characterised by a richer biodiversity. The shipyard sector in Heraklion port was significantly different from all other sectors in terms of abiotic and biotic parameters. Physico-chemical and pollution variables recorded during the period after tourism (late summer) were significantly different from the ones recorded in winter. Seasonal differences were not significant between benthic species diversity patterns, but were revealed when the patterns derived from the aggregation of higher taxonomic levels were compared. The present study indicates that a regular-basis monitoring plan including evaluation of environmental health based on benthic biodiversity, can provide a basis for perceiving changes and reveal the degree of anthropogenic disturbance in port environments. © 2017 Elsevier B.V. |
2017 |
Pavloudi, C; Kristoffersen, J B; Oulas, A; Troch, De M; Arvanitidis, C Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane's 'species minimum' concept Journal Article PeerJ, 2017 (10), 2017, ISSN: 21678359, (Publisher: PeerJ Inc.). @article{pavloudi_sediment_2017, title = {Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane's 'species minimum' concept}, author = {C Pavloudi and J B Kristoffersen and A Oulas and M De Troch and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031101355&doi=10.7717%2fpeerj.3687&partnerID=40&md5=6860a76d415733f23eeb5d4df199a4d5}, doi = {10.7717/peerj.3687}, issn = {21678359}, year = {2017}, date = {2017-01-01}, journal = {PeerJ}, volume = {2017}, number = {10}, abstract = {Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane's concept. © 2017 Pavloudi et al.}, note = {Publisher: PeerJ Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane's concept. © 2017 Pavloudi et al. |
Pavloudi, C; Oulas, A; Vasileiadou, K; Kotoulas, G; Troch, De M; Friedrich, M W; Arvanitidis, C Aquatic Microbial Ecology, 79 (3), pp. 209–219, 2017, ISSN: 09483055, (Publisher: Inter-Research). @article{pavloudi_diversity_2017, title = {Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene}, author = {C Pavloudi and A Oulas and K Vasileiadou and G Kotoulas and M De Troch and M W Friedrich and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021092263&doi=10.3354%2fame01829&partnerID=40&md5=8be345d2d8f932cc9b640cf2072c2bb0}, doi = {10.3354/ame01829}, issn = {09483055}, year = {2017}, date = {2017-01-01}, journal = {Aquatic Microbial Ecology}, volume = {79}, number = {3}, pages = {209--219}, abstract = {Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017. |
Schmeller, D S; Arvanitidis, C; Böhm, M; Brummitt, N; Chatzinikolaou, E; Costello, M J; Ding, H; Gill, M J; Haase, P; Julliard, R; García-Moreno, J; Pettorelli, N; Peng, C; Riginos, C; Schmiedel, U; Simaika, J P; Waterman, C; Wu, J; Xu, H; Belnap, J Case Studies of Capacity Building for Biodiversity Monitoring Incollection The GEO Handbook on Biodiversity Observation Networks, Springer International Publishing, 2017, ISBN: 978-3-319-27288-7 978-3-319-27286-3, (Publication Title: The GEO Handbook on Biodiversity Observation Networks). @incollection{schmeller_case_2017, title = {Case Studies of Capacity Building for Biodiversity Monitoring}, author = {D S Schmeller and C Arvanitidis and M Böhm and N Brummitt and E Chatzinikolaou and M J Costello and H Ding and M J Gill and P Haase and R Julliard and J García-Moreno and N Pettorelli and C Peng and C Riginos and U Schmiedel and J P Simaika and C Waterman and J Wu and H Xu and J Belnap}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028882628&doi=10.1007%2f978-3-319-27288-7_13&partnerID=40&md5=bfb4a4008ff090d95b2c5d49284822e3}, doi = {10.1007/978-3-319-27288-7_13}, isbn = {978-3-319-27288-7 978-3-319-27286-3}, year = {2017}, date = {2017-01-01}, booktitle = {The GEO Handbook on Biodiversity Observation Networks}, publisher = {Springer International Publishing}, abstract = {Monitoring the status and trends of species is critical to their conservation and management. However, the current state of biodiversity monitoring is insufficient to detect such for most species and habitats, other than in a few localised areas. One of the biggest obstacles to adequate monitoring is the lack of local capacity to carry out such programs. Thus, building the capacity to do such monitoring is imperative. We here highlight different biodiversity monitoring efforts to illustrate how capacity building efforts are being conducted at different geographic scales and under a range of resource, literacy, and training constraints. Accordingly, we include examples of monitoring efforts from within countries (Kenya, France, and China), within regions (Central America and the Arctic) and larger capacity building programs including EDGE (Evolutionarily Distinct and Globally Endangered) of Existence and the National Red List Alliance. © The Author(s) 2017. All rights reserved.}, note = {Publication Title: The GEO Handbook on Biodiversity Observation Networks}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } Monitoring the status and trends of species is critical to their conservation and management. However, the current state of biodiversity monitoring is insufficient to detect such for most species and habitats, other than in a few localised areas. One of the biggest obstacles to adequate monitoring is the lack of local capacity to carry out such programs. Thus, building the capacity to do such monitoring is imperative. We here highlight different biodiversity monitoring efforts to illustrate how capacity building efforts are being conducted at different geographic scales and under a range of resource, literacy, and training constraints. Accordingly, we include examples of monitoring efforts from within countries (Kenya, France, and China), within regions (Central America and the Arctic) and larger capacity building programs including EDGE (Evolutionarily Distinct and Globally Endangered) of Existence and the National Red List Alliance. © The Author(s) 2017. All rights reserved. |
Faulwetter, S; Simboura, N; Katsiaras, N; Chatzigeorgiou, G; Arvanitidis, C Polychaetes of Greece: An updated and annotated checklist Journal Article Biodiversity Data Journal, 5 , 2017, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{faulwetter_polychaetes_2017, title = {Polychaetes of Greece: An updated and annotated checklist}, author = {S Faulwetter and N Simboura and N Katsiaras and G Chatzigeorgiou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85041492895&doi=10.3897%2fBDJ.5.e20997&partnerID=40&md5=ee1c85d4bb69c5fc4187d70e3acc2d7f}, doi = {10.3897/BDJ.5.e20997}, issn = {13142828}, year = {2017}, date = {2017-01-01}, journal = {Biodiversity Data Journal}, volume = {5}, abstract = {Background The last annotated checklist of marine polychaetes in Greece was published in 2001. Since then, global taxonomic progress, combined with many new species records for Greece, required a thorough review of the taxonomic, nomenclatural and biogeographic status of the national species list. This checklist revises the status of all extant polychaete species reported from the Greek Exclusive Economic Zone since 1832. The work was undertaken as part of the efforts on compiling a national species inventory (Greek Taxon Information System initiative) in the framework of the LifeWatchGreece Research Infrastructure. New information This checklist comprises an updated and annotated inventory of polychaete species in Greek waters, compiled from literature reports, online databases, museum collections and unpublished datasets. The list provides information on 836 species-level taxa from Greece, of which 142 are considered questionable. An additional 84 species reported in the past are currently considered absent from Greece; reasons for the exclusion of each species are given. Fourteen species are reported here for the first time from Greek waters. At least 52 species in the present list constitute in fact a complex of cryptic or pseudo-cryptic species. Forty-seven species are considered non-native to the area. In addition to the species-level taxa reported in this checklist, eleven genera have been recorded from Greece with no representatives identified to species level. One replacement name is introduced. For each species, a comprehensive bibliographic list of occurrence records in Greece and the synonyms used in these publications are provided as supplementary material. Where necessary, the taxonomic, nomenclatural or biogeographic status is discussed. Finally, the findings are discussed in the wider context of Mediterranean polychaete biogeography, taxonomic practice and worldwide research progress. © Faulwetter S et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background The last annotated checklist of marine polychaetes in Greece was published in 2001. Since then, global taxonomic progress, combined with many new species records for Greece, required a thorough review of the taxonomic, nomenclatural and biogeographic status of the national species list. This checklist revises the status of all extant polychaete species reported from the Greek Exclusive Economic Zone since 1832. The work was undertaken as part of the efforts on compiling a national species inventory (Greek Taxon Information System initiative) in the framework of the LifeWatchGreece Research Infrastructure. New information This checklist comprises an updated and annotated inventory of polychaete species in Greek waters, compiled from literature reports, online databases, museum collections and unpublished datasets. The list provides information on 836 species-level taxa from Greece, of which 142 are considered questionable. An additional 84 species reported in the past are currently considered absent from Greece; reasons for the exclusion of each species are given. Fourteen species are reported here for the first time from Greek waters. At least 52 species in the present list constitute in fact a complex of cryptic or pseudo-cryptic species. Forty-seven species are considered non-native to the area. In addition to the species-level taxa reported in this checklist, eleven genera have been recorded from Greece with no representatives identified to species level. One replacement name is introduced. For each species, a comprehensive bibliographic list of occurrence records in Greece and the synonyms used in these publications are provided as supplementary material. Where necessary, the taxonomic, nomenclatural or biogeographic status is discussed. Finally, the findings are discussed in the wider context of Mediterranean polychaete biogeography, taxonomic practice and worldwide research progress. © Faulwetter S et al. |
Chatzigeorgiou, G; Keklikoglou, K; Faulwetter, S; Badalamenti, F; Kitsos, M -S; Arvanitidis, C Marine Ecology, 38 (1), 2017, ISSN: 01739565, (Publisher: Blackwell Publishing Ltd). @article{chatzigeorgiou_midlittoral_2017, title = {Midlittoral polychaete communities in the Eastern Mediterranean Sea: new information from the implementation of the Natural Geography in Shore Areas (NaGISA) protocol and comparisons at local and regional scales}, author = {G Chatzigeorgiou and K Keklikoglou and S Faulwetter and F Badalamenti and M -S Kitsos and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85012193815&doi=10.1111%2fmaec.12339&partnerID=40&md5=3478bb4cfa991f54c0693917b733dc30}, doi = {10.1111/maec.12339}, issn = {01739565}, year = {2017}, date = {2017-01-01}, journal = {Marine Ecology}, volume = {38}, number = {1}, abstract = {The aim of this study was to attempt to fill current knowledge gaps on midlittoral Mediterranean biodiversity at local and regional scales, by using benthic polychaetes as a model taxon. Two different data sets were analysed: (i) a quantitative data set from the two Natural Geography in Shore Areas (NaGISA) study sites in Crete and (ii) a qualitative data set from multiple sites across the Mediterranean. At the local scale, the results provide evidence that (i) discrete species communities are formed in midlittoral Mediterranean habitats, which vary by geographical location and year, depending on the scale of observation; (ii) macrophyte coverage and Chl-a are the only environmental variables associated, albeit weakly, with the above pattern; (iii) although naturally disturbed, the Cretan NaGISA sites do not seem to experience any anthropogenic stress; (iv) environmental heterogeneity and history seem to be much less important in shaping the polychaete communities than inter-specific interactions; however, it is not possible to specify at this stage whether local or regional processes or even their interactions may shape the polychaete communities. At the regional scale, the results indicate that (i) the only factor that seems to be involved in the regional pattern is the identity of the study providing the data sets, which implies variability and bias in how research projects are carried out, from the sampling design through to data collection and analysis; (ii) the Cretan NaGISA sites may be considered as representative of the habitat in the Mediterranean, under certain conditions. © 2017 Blackwell Verlag GmbH}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this study was to attempt to fill current knowledge gaps on midlittoral Mediterranean biodiversity at local and regional scales, by using benthic polychaetes as a model taxon. Two different data sets were analysed: (i) a quantitative data set from the two Natural Geography in Shore Areas (NaGISA) study sites in Crete and (ii) a qualitative data set from multiple sites across the Mediterranean. At the local scale, the results provide evidence that (i) discrete species communities are formed in midlittoral Mediterranean habitats, which vary by geographical location and year, depending on the scale of observation; (ii) macrophyte coverage and Chl-a are the only environmental variables associated, albeit weakly, with the above pattern; (iii) although naturally disturbed, the Cretan NaGISA sites do not seem to experience any anthropogenic stress; (iv) environmental heterogeneity and history seem to be much less important in shaping the polychaete communities than inter-specific interactions; however, it is not possible to specify at this stage whether local or regional processes or even their interactions may shape the polychaete communities. At the regional scale, the results indicate that (i) the only factor that seems to be involved in the regional pattern is the identity of the study providing the data sets, which implies variability and bias in how research projects are carried out, from the sampling design through to data collection and analysis; (ii) the Cretan NaGISA sites may be considered as representative of the habitat in the Mediterranean, under certain conditions. © 2017 Blackwell Verlag GmbH |
Maidanou, M; Koulouri, P; Arvanitidis, C; Koutsoubas, D; Dounas, C Macrobenthic assemblage structure associated with a Caulerpa prolifera meadow in the eastern Mediterranean Sea (Elounda Bay, Crete Island) Journal Article Regional Studies in Marine Science, 14 , pp. 1–14, 2017, ISSN: 23524855, (Publisher: Elsevier B.V.). @article{maidanou_macrobenthic_2017, title = {Macrobenthic assemblage structure associated with a Caulerpa prolifera meadow in the eastern Mediterranean Sea (Elounda Bay, Crete Island)}, author = {M Maidanou and P Koulouri and C Arvanitidis and D Koutsoubas and C Dounas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018339510&doi=10.1016%2fj.rsma.2017.04.004&partnerID=40&md5=5537690cc92ad9e5af4b198854bb8110}, doi = {10.1016/j.rsma.2017.04.004}, issn = {23524855}, year = {2017}, date = {2017-01-01}, journal = {Regional Studies in Marine Science}, volume = {14}, pages = {1--14}, abstract = {The present study investigates the structure and intra-annual variation of the benthic macrofaunal community associated with a monospecific C. prolifera meadow in a shallow semi-enclosed coastal marine ecosystem of the eastern Mediterranean Sea (Elounda Bay, Crete Island). The samples were collected on five occasions (May, September and November 2006, February and April 2007) by using an epibenthic sledge (0.5 mm mesh size). The analysis of the macrofauna revealed 319 taxa with densities ranging from 71 to 410 individuals m−2. The most diversified animal groups were polychaetes, gastropods and amphipods. Crustaceans were by far the most abundant group with densities exceeding 50% of the total macrofauna during the study period. The dominant species were the amphipods Caprella acanthifera acanthifera, C. rapax and Microdeutopus stationis, the gastropod Pusillina lineolata, the tanaid Leptochelia sp. and the bivalve Abra alba. The results of the present study revealed a relatively high diversified and abundant benthic macrofauna, which is supported by the presence of the dense and continuous canopy of C. prolifera in this shallow wave-sheltered area characterized by high organic matter input. © 2017 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study investigates the structure and intra-annual variation of the benthic macrofaunal community associated with a monospecific C. prolifera meadow in a shallow semi-enclosed coastal marine ecosystem of the eastern Mediterranean Sea (Elounda Bay, Crete Island). The samples were collected on five occasions (May, September and November 2006, February and April 2007) by using an epibenthic sledge (0.5 mm mesh size). The analysis of the macrofauna revealed 319 taxa with densities ranging from 71 to 410 individuals m−2. The most diversified animal groups were polychaetes, gastropods and amphipods. Crustaceans were by far the most abundant group with densities exceeding 50% of the total macrofauna during the study period. The dominant species were the amphipods Caprella acanthifera acanthifera, C. rapax and Microdeutopus stationis, the gastropod Pusillina lineolata, the tanaid Leptochelia sp. and the bivalve Abra alba. The results of the present study revealed a relatively high diversified and abundant benthic macrofauna, which is supported by the presence of the dense and continuous canopy of C. prolifera in this shallow wave-sheltered area characterized by high organic matter input. © 2017 Elsevier B.V. |
Cascarano, M C; Keklikoglou, K; Arvanitidis, C; Katharios, P Zootaxa, 4337 (1), pp. 91–108, 2017, ISSN: 11755326, (Publisher: Magnolia Press). @article{cascarano_contribution_2017, title = {Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae)by using combined histology, micro-CT and SEM}, author = {M C Cascarano and K Keklikoglou and C Arvanitidis and P Katharios}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031712662&doi=10.11646%2fzootaxa.4337.1.4&partnerID=40&md5=2af1dcba738b14946bfe874ad9b1eb88}, doi = {10.11646/zootaxa.4337.1.4}, issn = {11755326}, year = {2017}, date = {2017-01-01}, journal = {Zootaxa}, volume = {4337}, number = {1}, pages = {91--108}, abstract = {The ozobranchid leech, Ozobranchus margoi (Apáthy, 1890), parasite of the loggerhead turtle, Caretta caretta (Linnaeus), was described through a multilevel approach including three different techniques: scanning electronic microscopy, histology and micro-CT. New insights are provided concerning the structure of the sensilla on the body, the eyes with emphasis on the structure of photoreceptors, the digestive system and the reproductive organs. Copyright © 2017 Magnolia Press.}, note = {Publisher: Magnolia Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The ozobranchid leech, Ozobranchus margoi (Apáthy, 1890), parasite of the loggerhead turtle, Caretta caretta (Linnaeus), was described through a multilevel approach including three different techniques: scanning electronic microscopy, histology and micro-CT. New insights are provided concerning the structure of the sensilla on the body, the eyes with emphasis on the structure of photoreceptors, the digestive system and the reproductive organs. Copyright © 2017 Magnolia Press. |
Schmeller, D S; Böhm, M; Arvanitidis, C; Barber-Meyer, S; Brummitt, N; Chandler, M; Chatzinikolaou, E; Costello, M J; Ding, H; García-Moreno, J; Gill, M; Haase, P; Jones, M; Juillard, R; Magnusson, W E; Martin, C S; McGeoch, M; Mihoub, J -B; Pettorelli, N; Proença, V; Peng, C; Regan, E; Schmiedel, U; Simaika, J P; Weatherdon, L; Waterman, C; Xu, H; Belnap, J Building capacity in biodiversity monitoring at the global scale Journal Article Biodiversity and Conservation, 26 (12), pp. 2765–2790, 2017, ISSN: 09603115, (Publisher: Springer Netherlands). @article{schmeller_building_2017, title = {Building capacity in biodiversity monitoring at the global scale}, author = {D S Schmeller and M Böhm and C Arvanitidis and S Barber-Meyer and N Brummitt and M Chandler and E Chatzinikolaou and M J Costello and H Ding and J García-Moreno and M Gill and P Haase and M Jones and R Juillard and W E Magnusson and C S Martin and M McGeoch and J -B Mihoub and N Pettorelli and V Proença and C Peng and E Regan and U Schmiedel and J P Simaika and L Weatherdon and C Waterman and H Xu and J Belnap}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021143065&doi=10.1007%2fs10531-017-1388-7&partnerID=40&md5=66fbb334d842082ef75a2030a81627e7}, doi = {10.1007/s10531-017-1388-7}, issn = {09603115}, year = {2017}, date = {2017-01-01}, journal = {Biodiversity and Conservation}, volume = {26}, number = {12}, pages = {2765--2790}, abstract = {Human-driven global change is causing ongoing declines in biodiversity worldwide. In order to address these declines, decision-makers need accurate assessments of the status of and pressures on biodiversity. However, these are heavily constrained by incomplete and uneven spatial, temporal and taxonomic coverage. For instance, data from regions such as Europe and North America are currently used overwhelmingly for large-scale biodiversity assessments due to lesser availability of suitable data from other, more biodiversity-rich, regions. These data-poor regions are often those experiencing the strongest threats to biodiversity, however. There is therefore an urgent need to fill the existing gaps in global biodiversity monitoring. Here, we review current knowledge on best practice in capacity building for biodiversity monitoring and provide an overview of existing means to improve biodiversity data collection considering the different types of biodiversity monitoring data. Our review comprises insights from work in Africa, South America, Polar Regions and Europe; in government-funded, volunteer and citizen-based monitoring in terrestrial, freshwater and marine ecosystems. The key steps to effectively building capacity in biodiversity monitoring are: identifying monitoring questions and aims; identifying the key components, functions, and processes to monitor; identifying the most suitable monitoring methods for these elements, carrying out monitoring activities; managing the resultant data; and interpreting monitoring data. Additionally, biodiversity monitoring should use multiple approaches including extensive and intensive monitoring through volunteers and professional scientists but also harnessing new technologies. Finally, we call on the scientific community to share biodiversity monitoring data, knowledge and tools to ensure the accessibility, interoperability, and reporting of biodiversity data at a global scale. © 2017, Springer Science+Business Media B.V.}, note = {Publisher: Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human-driven global change is causing ongoing declines in biodiversity worldwide. In order to address these declines, decision-makers need accurate assessments of the status of and pressures on biodiversity. However, these are heavily constrained by incomplete and uneven spatial, temporal and taxonomic coverage. For instance, data from regions such as Europe and North America are currently used overwhelmingly for large-scale biodiversity assessments due to lesser availability of suitable data from other, more biodiversity-rich, regions. These data-poor regions are often those experiencing the strongest threats to biodiversity, however. There is therefore an urgent need to fill the existing gaps in global biodiversity monitoring. Here, we review current knowledge on best practice in capacity building for biodiversity monitoring and provide an overview of existing means to improve biodiversity data collection considering the different types of biodiversity monitoring data. Our review comprises insights from work in Africa, South America, Polar Regions and Europe; in government-funded, volunteer and citizen-based monitoring in terrestrial, freshwater and marine ecosystems. The key steps to effectively building capacity in biodiversity monitoring are: identifying monitoring questions and aims; identifying the key components, functions, and processes to monitor; identifying the most suitable monitoring methods for these elements, carrying out monitoring activities; managing the resultant data; and interpreting monitoring data. Additionally, biodiversity monitoring should use multiple approaches including extensive and intensive monitoring through volunteers and professional scientists but also harnessing new technologies. Finally, we call on the scientific community to share biodiversity monitoring data, knowledge and tools to ensure the accessibility, interoperability, and reporting of biodiversity data at a global scale. © 2017, Springer Science+Business Media B.V. |
Schmeller, D S; Mihoub, J -B; Bowser, A; Arvanitidis, C; Costello, M J; Fernandez, M; Geller, G N; Hobern, D; Kissling, W D; Regan, E; Saarenmaa, H; Turak, E; Isaac, N J B An operational definition of essential biodiversity variables Journal Article Biodiversity and Conservation, 26 (12), pp. 2967–2972, 2017, ISSN: 09603115, (Publisher: Springer Netherlands). @article{schmeller_operational_2017, title = {An operational definition of essential biodiversity variables}, author = {D S Schmeller and J -B Mihoub and A Bowser and C Arvanitidis and M J Costello and M Fernandez and G N Geller and D Hobern and W D Kissling and E Regan and H Saarenmaa and E Turak and N J B Isaac}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020693404&doi=10.1007%2fs10531-017-1386-9&partnerID=40&md5=6b97d8105c78d687e3e2dd6a6e67456a}, doi = {10.1007/s10531-017-1386-9}, issn = {09603115}, year = {2017}, date = {2017-01-01}, journal = {Biodiversity and Conservation}, volume = {26}, number = {12}, pages = {2967--2972}, abstract = {The concept of essential biodiversity variables (EBVs) was proposed in 2013 to improve harmonization of biodiversity data into meaningful metrics. EBVs were conceived as a small set of variables which collectively capture biodiversity change at multiple spatial scales and within time intervals that are of scientific and management interest. Despite the apparent simplicity of the concept, a plethora of variables that describes not only biodiversity but also any environmental features have been proposed as potential EBV (i.e. candidate EBV). The proliferation of candidates reflects a lack of clarity on what may constitute a variable that is essential to track biodiversity change, which hampers the operationalization of EBVs and therefore needs to be urgently addressed. Here, we propose that an EBV should be defined as a biological state variable in three key dimensions (time, space, and biological organization) that is critical to accurately document biodiversity change. © 2017, Springer Science+Business Media B.V.}, note = {Publisher: Springer Netherlands}, keywords = {}, pubstate = {published}, tppubtype = {article} } The concept of essential biodiversity variables (EBVs) was proposed in 2013 to improve harmonization of biodiversity data into meaningful metrics. EBVs were conceived as a small set of variables which collectively capture biodiversity change at multiple spatial scales and within time intervals that are of scientific and management interest. Despite the apparent simplicity of the concept, a plethora of variables that describes not only biodiversity but also any environmental features have been proposed as potential EBV (i.e. candidate EBV). The proliferation of candidates reflects a lack of clarity on what may constitute a variable that is essential to track biodiversity change, which hampers the operationalization of EBVs and therefore needs to be urgently addressed. Here, we propose that an EBV should be defined as a biological state variable in three key dimensions (time, space, and biological organization) that is critical to accurately document biodiversity change. © 2017, Springer Science+Business Media B.V. |
Hummel, H; Avesaath, Van P; Wijnhoven, S; Kleine-Schaars, L; Degraer, S; Kerckhof, F; Bojanic, N; Skejic, S; Vidjak, O; Rousou, M; Orav-Kotta, H; Kotta, J; Jourde, J; Pedrotti, M L; Leclerc, J -C; Simon, N; Rigaut-Jalabert, F; Bachelet, G; Lavesque, N; Arvanitidis, C; Pavloudi, C; Faulwetter, S; Crowe, T; Coughlan, J; Benedetti-Cecchi, L; Bello, Dal M; Magni, P; Como, S; Coppa, S; Ikauniece, A; Ruginis, T; Jankowska, E; Weslawski, J M; Warzocha, J; Gromisz, S; Witalis, B; Silva, T; Ribeiro, P; Matos, Fernandes De V K; Sousa-Pinto, I; Veiga, P; Troncoso, J; Guinda, X; Pena, Juanes De La J A; Puente, A; Espinosa, F; Pérez-Ruzafa, A; Frost, M; McNeill, C L; Peleg, O; Rilov, G Geographic patterns of biodiversity in European coastal marine benthos Journal Article Journal of the Marine Biological Association of the United Kingdom, 97 (3), pp. 507–523, 2017, ISSN: 00253154, (Publisher: Cambridge University Press). @article{hummel_geographic_2017, title = {Geographic patterns of biodiversity in European coastal marine benthos}, author = {H Hummel and P Van Avesaath and S Wijnhoven and L Kleine-Schaars and S Degraer and F Kerckhof and N Bojanic and S Skejic and O Vidjak and M Rousou and H Orav-Kotta and J Kotta and J Jourde and M L Pedrotti and J -C Leclerc and N Simon and F Rigaut-Jalabert and G Bachelet and N Lavesque and C Arvanitidis and C Pavloudi and S Faulwetter and T Crowe and J Coughlan and L Benedetti-Cecchi and M Dal Bello and P Magni and S Como and S Coppa and A Ikauniece and T Ruginis and E Jankowska and J M Weslawski and J Warzocha and S Gromisz and B Witalis and T Silva and P Ribeiro and V K Fernandes De Matos and I Sousa-Pinto and P Veiga and J Troncoso and X Guinda and J A Juanes De La Pena and A Puente and F Espinosa and A Pérez-Ruzafa and M Frost and C L McNeill and O Peleg and G Rilov}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84987600709&doi=10.1017%2fS0025315416001119&partnerID=40&md5=8af26b11dedcb6c3ee86e02f6517eb15}, doi = {10.1017/S0025315416001119}, issn = {00253154}, year = {2017}, date = {2017-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {97}, number = {3}, pages = {507--523}, abstract = {Within the COST action EMBOS (European Marine Biodiversity Observatory System) the degree and variation of the diversity and densities of soft-bottom communities from the lower intertidal or the shallow subtidal was measured at 28 marine sites along the European coastline (Baltic, Atlantic, Mediterranean) using jointly agreed and harmonized protocols, tools and indicators. The hypothesis tested was that the diversity for all taxonomic groups would decrease with increasing latitude. The EMBOS system delivered accurate and comparable data on the diversity and densities of the soft sediment macrozoobenthic community over a large-scale gradient along the European coastline. In contrast to general biogeographic theory, species diversity showed no linear relationship with latitude, yet a bell-shaped relation was found. The diversity and densities of benthos were mostly positively correlated with environmental factors such as temperature, salinity, mud and organic matter content in sediment, or wave height, and related with location characteristics such as system type (lagoons, estuaries, open coast) or stratum (intertidal, subtidal). For some relationships, a maximum (e.g. Temperature from 15-20°C; mud content of sediment around 40%) or bimodal curve (e.g. salinity) was found. In lagoons the densities were twice higher than in other locations, and at open coasts the diversity was much lower than in other locations. We conclude that latitudinal trends and regional differences in diversity and densities are strongly influenced by, i.e. merely the result of, particular sets and ranges of environmental factors and location characteristics specific to certain areas, such as the Baltic, with typical salinity clines (favouring insects) and the Mediterranean, with higher temperatures (favouring crustaceans). Therefore, eventual trends with latitude are primarily indirect and so can be overcome by local variation of environmental factors. Copyright © Marine Biological Association of the United Kingdom 2016.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Within the COST action EMBOS (European Marine Biodiversity Observatory System) the degree and variation of the diversity and densities of soft-bottom communities from the lower intertidal or the shallow subtidal was measured at 28 marine sites along the European coastline (Baltic, Atlantic, Mediterranean) using jointly agreed and harmonized protocols, tools and indicators. The hypothesis tested was that the diversity for all taxonomic groups would decrease with increasing latitude. The EMBOS system delivered accurate and comparable data on the diversity and densities of the soft sediment macrozoobenthic community over a large-scale gradient along the European coastline. In contrast to general biogeographic theory, species diversity showed no linear relationship with latitude, yet a bell-shaped relation was found. The diversity and densities of benthos were mostly positively correlated with environmental factors such as temperature, salinity, mud and organic matter content in sediment, or wave height, and related with location characteristics such as system type (lagoons, estuaries, open coast) or stratum (intertidal, subtidal). For some relationships, a maximum (e.g. Temperature from 15-20°C; mud content of sediment around 40%) or bimodal curve (e.g. salinity) was found. In lagoons the densities were twice higher than in other locations, and at open coasts the diversity was much lower than in other locations. We conclude that latitudinal trends and regional differences in diversity and densities are strongly influenced by, i.e. merely the result of, particular sets and ranges of environmental factors and location characteristics specific to certain areas, such as the Baltic, with typical salinity clines (favouring insects) and the Mediterranean, with higher temperatures (favouring crustaceans). Therefore, eventual trends with latitude are primarily indirect and so can be overcome by local variation of environmental factors. Copyright © Marine Biological Association of the United Kingdom 2016. |
Bello, Dal M; Leclerc, J -C; Benedetti-Cecchi, L; Lucia, Andrea De G; Arvanitidis, C; Avesaath, Van P; Bachelet, G; Bojanic, N; Como, S; Coppa, S; Coughlan, J; Crowe, T; Degraer, S; Espinosa, F; Faulwetter, S; Frost, M; Guinda, X; Jankowska, E; Jourde, J; Pena, Juanes De La J A; Kerckhof, F; Kotta, J; Lavesque, N; Magni, P; Matos, De V; Orav-Kotta, H; Pavloudi, C; Pedrotti, M L; Peleg, O; Pérez-Ruzafa, A; Puente, A; Ribeiro, P; Rigaut-Jalabert, F; Rilov, G; Rousou, M; Rubal, M; Ruginis, T; Silva, T; Simon, N; Sousa-Pinto, I; Troncoso, J; Warzocha, J; Weslawski, J M; Hummel, H Consistent patterns of spatial variability between NE Atlantic and Mediterranean rocky shores Journal Article Journal of the Marine Biological Association of the United Kingdom, 97 (3), pp. 539–547, 2017, ISSN: 00253154, (Publisher: Cambridge University Press). @article{dal_bello_consistent_2017, title = {Consistent patterns of spatial variability between NE Atlantic and Mediterranean rocky shores}, author = {M Dal Bello and J -C Leclerc and L Benedetti-Cecchi and G Andrea De Lucia and C Arvanitidis and P Van Avesaath and G Bachelet and N Bojanic and S Como and S Coppa and J Coughlan and T Crowe and S Degraer and F Espinosa and S Faulwetter and M Frost and X Guinda and E Jankowska and J Jourde and J A Juanes De La Pena and F Kerckhof and J Kotta and N Lavesque and P Magni and V De Matos and H Orav-Kotta and C Pavloudi and M L Pedrotti and O Peleg and A Pérez-Ruzafa and A Puente and P Ribeiro and F Rigaut-Jalabert and G Rilov and M Rousou and M Rubal and T Ruginis and T Silva and N Simon and I Sousa-Pinto and J Troncoso and J Warzocha and J M Weslawski and H Hummel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84995532117&doi=10.1017%2fS0025315416001491&partnerID=40&md5=2960e83afbd9938d643b92f5bb8d29af}, doi = {10.1017/S0025315416001491}, issn = {00253154}, year = {2017}, date = {2017-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {97}, number = {3}, pages = {539--547}, abstract = {Examining how variability in population abundance and distribution is allotted among different spatial scales can inform of processes that are likely to generate that variability. Results of studies dealing with scale issues in marine benthic communities suggest that variability is concentrated at small spatial scales (from tens of centimetres to few metres) and that spatial patterns of variation are consistent across ecosystems characterized by contrasting physical and biotic conditions, but this has not been formally tested. Here we quantified the variability in the distribution of intertidal rocky shore communities at a range of spatial scales, from tens of centimetres to thousands of kilometres, both in the NE Atlantic and the Mediterranean, and tested whether the observed patterns differed between the two basins. We focused on canopy-forming macroalgae and associated understorey assemblages in the low intertidal, and on the distribution of Patella limpets at mid intertidal levels. Our results highlight that patterns of spatial variation, at each scale investigated, were consistent between the Atlantic and the Mediterranean, suggesting that similar ecological processes operate in these regions. In contrast with former studies, variability in canopy cover, species richness and limpet abundance was equally distributed among spatial scales, possibly reflecting the fingerprint of multiple processes. Variability in community structure of low intertidal assemblages, instead, peaked at the largest scale, suggesting that oceanographic processes and climatic gradients may be important. We conclude that formal comparisons of variability across scales nested in contrasting systems are needed, before any generalization on patterns and processes can be made. Copyright © Marine Biological Association of the United Kingdom 2016.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Examining how variability in population abundance and distribution is allotted among different spatial scales can inform of processes that are likely to generate that variability. Results of studies dealing with scale issues in marine benthic communities suggest that variability is concentrated at small spatial scales (from tens of centimetres to few metres) and that spatial patterns of variation are consistent across ecosystems characterized by contrasting physical and biotic conditions, but this has not been formally tested. Here we quantified the variability in the distribution of intertidal rocky shore communities at a range of spatial scales, from tens of centimetres to thousands of kilometres, both in the NE Atlantic and the Mediterranean, and tested whether the observed patterns differed between the two basins. We focused on canopy-forming macroalgae and associated understorey assemblages in the low intertidal, and on the distribution of Patella limpets at mid intertidal levels. Our results highlight that patterns of spatial variation, at each scale investigated, were consistent between the Atlantic and the Mediterranean, suggesting that similar ecological processes operate in these regions. In contrast with former studies, variability in canopy cover, species richness and limpet abundance was equally distributed among spatial scales, possibly reflecting the fingerprint of multiple processes. Variability in community structure of low intertidal assemblages, instead, peaked at the largest scale, suggesting that oceanographic processes and climatic gradients may be important. We conclude that formal comparisons of variability across scales nested in contrasting systems are needed, before any generalization on patterns and processes can be made. Copyright © Marine Biological Association of the United Kingdom 2016. |
Kotta, J; Orav-Kotta, H; Jänes, H; Hummel, H; Arvanitidis, C; Avesaath, Van P; Bachelet, G; Benedetti-Cecchi, L; Bojanić, N; Como, S; Coppa, S; Coughlan, J; Crowe, T; Bello, Dal M; Degraer, S; Pena, De La J A J; Matos, Fernandes De V K; Espinosa, F; Faulwetter, S; Frost, M; Guinda, X; Jankowska, E; Jourde, J; Kerckhof, F; Lavesque, N; Leclerc, J -C; Magni, P; Pavloudi, C; Pedrotti, M L; Peleg, O; Pérez-Ruzafa, A; Puente, A; Ribeiro, P; Rilov, G; Rousou, M; Ruginis, T; Silva, T; Simon, N; Sousa-Pinto, I; Troncoso, J; Warzocha, J; Weslawski, J M Essence of the patterns of cover and richness of intertidal hard bottom communities: A pan-European study Journal Article Journal of the Marine Biological Association of the United Kingdom, 97 (3), pp. 525–538, 2017, ISSN: 00253154, (Publisher: Cambridge University Press). @article{kotta_essence_2017, title = {Essence of the patterns of cover and richness of intertidal hard bottom communities: A pan-European study}, author = {J Kotta and H Orav-Kotta and H Jänes and H Hummel and C Arvanitidis and P Van Avesaath and G Bachelet and L Benedetti-Cecchi and N Bojanić and S Como and S Coppa and J Coughlan and T Crowe and M Dal Bello and S Degraer and J A J De La Pena and V K Fernandes De Matos and F Espinosa and S Faulwetter and M Frost and X Guinda and E Jankowska and J Jourde and F Kerckhof and N Lavesque and J -C Leclerc and P Magni and C Pavloudi and M L Pedrotti and O Peleg and A Pérez-Ruzafa and A Puente and P Ribeiro and G Rilov and M Rousou and T Ruginis and T Silva and N Simon and I Sousa-Pinto and J Troncoso and J Warzocha and J M Weslawski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84990183671&doi=10.1017%2fS0025315416001351&partnerID=40&md5=99f1c2fafcfd35575a76d4e7b1a7befb}, doi = {10.1017/S0025315416001351}, issn = {00253154}, year = {2017}, date = {2017-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {97}, number = {3}, pages = {525--538}, abstract = {Coastal ecosystems are highly complex and driven by multiple environmental factors. To date we lack scientific evidence for the relative contribution of natural and anthropogenic drivers for the majority of marine habitats in order to adequately assess the role of different stressors across the European seas. Such relationship can be investigated by analysing the correlation between environmental variables and biotic patterns in multivariate space and taking into account non-linearities. Within the framework of the EMBOS (European Marine Biodiversity Observatory System) programme, hard bottom intertidal communities were sampled in a standardized way across European seas. Links between key natural and anthropogenic drivers and hard bottom communities were analysed using Boosted Regression Trees modelling. The study identified strong interregional variability and showed that patterns of hard bottom macroalgal and invertebrate communities were primarily a function of tidal regime, nutrient loading and water temperature (anomalies). The strength and shape of functional form relationships varied widely however among types of organisms (understorey algae composing mostly filamentous species, canopy-forming algae or sessile invertebrates) and aggregated community variables (cover or richness). Tidal regime significantly modulated the effect of nutrient load on the cover and richness of understorey algae and sessile invertebrates. In contrast, hydroclimate was more important for canopy algae and temperature anomalies and hydroclimate separately or interactively contributed to the observed patterns. The analyses also suggested that climate-induced shifts in weather patterns may result in the loss of algal richness and thereby in the loss of functional diversity in European hard bottom intertidal areas. Copyright © Marine Biological Association of the United Kingdom 2016.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coastal ecosystems are highly complex and driven by multiple environmental factors. To date we lack scientific evidence for the relative contribution of natural and anthropogenic drivers for the majority of marine habitats in order to adequately assess the role of different stressors across the European seas. Such relationship can be investigated by analysing the correlation between environmental variables and biotic patterns in multivariate space and taking into account non-linearities. Within the framework of the EMBOS (European Marine Biodiversity Observatory System) programme, hard bottom intertidal communities were sampled in a standardized way across European seas. Links between key natural and anthropogenic drivers and hard bottom communities were analysed using Boosted Regression Trees modelling. The study identified strong interregional variability and showed that patterns of hard bottom macroalgal and invertebrate communities were primarily a function of tidal regime, nutrient loading and water temperature (anomalies). The strength and shape of functional form relationships varied widely however among types of organisms (understorey algae composing mostly filamentous species, canopy-forming algae or sessile invertebrates) and aggregated community variables (cover or richness). Tidal regime significantly modulated the effect of nutrient load on the cover and richness of understorey algae and sessile invertebrates. In contrast, hydroclimate was more important for canopy algae and temperature anomalies and hydroclimate separately or interactively contributed to the observed patterns. The analyses also suggested that climate-induced shifts in weather patterns may result in the loss of algal richness and thereby in the loss of functional diversity in European hard bottom intertidal areas. Copyright © Marine Biological Association of the United Kingdom 2016. |
Puente, A; Guinda, X; Juanes, J A; Ramos, E; Echavarri-Erasun, B; Hoz, De La C F; Degraer, S; Kerckhof, F; Bojanić, N; Rousou, M; Orav-Kotta, H; Kotta, J; Jourde, J; Pedrotti, M L; Leclerc, J -C; Simon, N; Bachelet, G; Lavesque, N; Arvanitidis, C; Pavloudi, C; Faulwetter, S; Crowe, T P; Coughlan, J; Cecchi, L B; Bello, Dal M; Magni, P; Como, S; Coppa, S; Lucia, De G A; Rugins, T; Jankowska, E; Weslawski, J M; Warzocha, J; Silva, T; Ribeiro, P; Matos, De V; Sousa-Pinto, I; Troncoso, J; Peleg, O; Rilov, G; Espinosa, F; Ruzafa, A P; Frost, M; Hummel, H; Avesaath, Van P The role of physical variables in biodiversity patterns of intertidal macroalgae along European coasts Journal Article Journal of the Marine Biological Association of the United Kingdom, 97 (3), pp. 549–560, 2017, ISSN: 00253154, (Publisher: Cambridge University Press). @article{puente_role_2017, title = {The role of physical variables in biodiversity patterns of intertidal macroalgae along European coasts}, author = {A Puente and X Guinda and J A Juanes and E Ramos and B Echavarri-Erasun and C F De La Hoz and S Degraer and F Kerckhof and N Bojanić and M Rousou and H Orav-Kotta and J Kotta and J Jourde and M L Pedrotti and J -C Leclerc and N Simon and G Bachelet and N Lavesque and C Arvanitidis and C Pavloudi and S Faulwetter and T P Crowe and J Coughlan and L B Cecchi and M Dal Bello and P Magni and S Como and S Coppa and G A De Lucia and T Rugins and E Jankowska and J M Weslawski and J Warzocha and T Silva and P Ribeiro and V De Matos and I Sousa-Pinto and J Troncoso and O Peleg and G Rilov and F Espinosa and A P Ruzafa and M Frost and H Hummel and P Van Avesaath}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85006276987&doi=10.1017%2fS0025315416001673&partnerID=40&md5=db3f3559d7c51f85e9d9f64a427a569e}, doi = {10.1017/S0025315416001673}, issn = {00253154}, year = {2017}, date = {2017-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {97}, number = {3}, pages = {549--560}, abstract = {In the frame of the COST ACTION 'EMBOS' (Development and implementation of a pan-European Marine Biodiversity Observatory System), coverage of intertidal macroalgae was estimated at a range of marine stations along the European coastline (Subarctic, Baltic, Atlantic, Mediterranean). Based on these data, we tested whether patterns in macroalgal diversity and distribution along European intertidal rocky shores could be explained by a set of meteo-oceanographic variables. The variables considered were salinity, sea surface temperature, photosynthetically active radiation, significant wave height and tidal range and were compiled from three different sources: remote sensing, reanalysis technique and in situ measurement. These variables were parameterized to represent average conditions (mean values), variability (standard deviation) and extreme events (minimum and maximum values). The results obtained in this study contribute to reinforce the EMBOS network approach and highlight the necessity of considering meteo-oceanographic variables in long-term assessments. The broad spatial distribution of pilot sites has allowed identification of latitudinal and longitudinal gradients manifested through species composition, diversity and dominance structure of intertidal macroalgae. These patterns follow a latitudinal gradient mainly explained by sea surface temperature, but also by photosynthetically active radiation, salinity and tidal range. Additionally, a longitudinal gradient was also detected and could be linked to wave height. Copyright © Marine Biological Association of the United Kingdom 2016.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } In the frame of the COST ACTION 'EMBOS' (Development and implementation of a pan-European Marine Biodiversity Observatory System), coverage of intertidal macroalgae was estimated at a range of marine stations along the European coastline (Subarctic, Baltic, Atlantic, Mediterranean). Based on these data, we tested whether patterns in macroalgal diversity and distribution along European intertidal rocky shores could be explained by a set of meteo-oceanographic variables. The variables considered were salinity, sea surface temperature, photosynthetically active radiation, significant wave height and tidal range and were compiled from three different sources: remote sensing, reanalysis technique and in situ measurement. These variables were parameterized to represent average conditions (mean values), variability (standard deviation) and extreme events (minimum and maximum values). The results obtained in this study contribute to reinforce the EMBOS network approach and highlight the necessity of considering meteo-oceanographic variables in long-term assessments. The broad spatial distribution of pilot sites has allowed identification of latitudinal and longitudinal gradients manifested through species composition, diversity and dominance structure of intertidal macroalgae. These patterns follow a latitudinal gradient mainly explained by sea surface temperature, but also by photosynthetically active radiation, salinity and tidal range. Additionally, a longitudinal gradient was also detected and could be linked to wave height. Copyright © Marine Biological Association of the United Kingdom 2016. |
Gerovasileiou, V; Dimitriadis, C; Arvanitidis, C; Voultsiadou, E Taxonomic and functional surrogates of sessile benthic diversity in Mediterranean marine caves Journal Article PLoS ONE, 12 (9), 2017, ISSN: 19326203, (Publisher: Public Library of Science). @article{gerovasileiou_taxonomic_2017, title = {Taxonomic and functional surrogates of sessile benthic diversity in Mediterranean marine caves}, author = {V Gerovasileiou and C Dimitriadis and C Arvanitidis and E Voultsiadou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028966068&doi=10.1371%2fjournal.pone.0183707&partnerID=40&md5=7e7304a8993fd3d5cba9f088e165a47d}, doi = {10.1371/journal.pone.0183707}, issn = {19326203}, year = {2017}, date = {2017-01-01}, journal = {PLoS ONE}, volume = {12}, number = {9}, abstract = {Hard substrates host globally a rich biodiversity, orders of magnitude higher in species number than that in surrounding soft substrates. Among them, marine caves support unique biodiversity and fragile communities but suffer lack of quantitative data on their structure and function, hindering their conservation status assessment. A first approach to the nondestructive ecological monitoring of marine caves by testing surrogates of structural and functional composition of sessile benthos was attempted in two species-rich Mediterranean marine caves. Photographic sampling was performed in different positions on the cave walls, across the horizontal axis, from the entrance inwards. Eighty-four taxa were identified and assigned to 6 biological traits and 32 modalities related to morphology, behavior and ecological affinities, with sponges being the dominant taxon in species richness and coverage. In quest of possible biological surrogates, we examined the spatial variability of the total community structure and function and separately the sponge community structure and function. The observed patterns of the above metrics were significantly correlated with the distance from the entrance, the small-scale variability and their interaction. A positive correlation was found between all examined pairs of those metrics, supporting that: (i) the developed functional approach could be used for the study of marine cave sessile communities, and (ii) sponges could be used as a surrogate taxon for the structural and functional study of these communities. The suggested method could be tested in other types of hard substrate habitats and in multiple locations of the Mediterranean waters, facilitating monitoring schemes and conservation actions. © 2017 Gerovasileiou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hard substrates host globally a rich biodiversity, orders of magnitude higher in species number than that in surrounding soft substrates. Among them, marine caves support unique biodiversity and fragile communities but suffer lack of quantitative data on their structure and function, hindering their conservation status assessment. A first approach to the nondestructive ecological monitoring of marine caves by testing surrogates of structural and functional composition of sessile benthos was attempted in two species-rich Mediterranean marine caves. Photographic sampling was performed in different positions on the cave walls, across the horizontal axis, from the entrance inwards. Eighty-four taxa were identified and assigned to 6 biological traits and 32 modalities related to morphology, behavior and ecological affinities, with sponges being the dominant taxon in species richness and coverage. In quest of possible biological surrogates, we examined the spatial variability of the total community structure and function and separately the sponge community structure and function. The observed patterns of the above metrics were significantly correlated with the distance from the entrance, the small-scale variability and their interaction. A positive correlation was found between all examined pairs of those metrics, supporting that: (i) the developed functional approach could be used for the study of marine cave sessile communities, and (ii) sponges could be used as a surrogate taxon for the structural and functional study of these communities. The suggested method could be tested in other types of hard substrate habitats and in multiple locations of the Mediterranean waters, facilitating monitoring schemes and conservation actions. © 2017 Gerovasileiou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
Ulman, A; Ferrario, J; Occhpinti-Ambrogi, A; Arvanitidis, C; Bandi, A; Bertolino, M; Bogi, C; Chatzigeorgiou, G; Çiçek, B A; Deidun, A; Ramos-Esplá, A; Koçak, C; Lorenti, M; Martinez-Laiz, G; Merlo, G; Princisgh, E; Scribano, G; Marchini, A A massive update of non-indigenous species records in Mediterranean marinas Journal Article PeerJ, 2017 (10), 2017, ISSN: 21678359, (Publisher: PeerJ Inc.). @article{ulman_massive_2017, title = {A massive update of non-indigenous species records in Mediterranean marinas}, author = {A Ulman and J Ferrario and A Occhpinti-Ambrogi and C Arvanitidis and A Bandi and M Bertolino and C Bogi and G Chatzigeorgiou and B A Çiçek and A Deidun and A Ramos-Esplá and C Koçak and M Lorenti and G Martinez-Laiz and G Merlo and E Princisgh and G Scribano and A Marchini}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032227826&doi=10.7717%2fpeerj.3954&partnerID=40&md5=d24f063896a3c2b1bc44f97388b7ad3b}, doi = {10.7717/peerj.3954}, issn = {21678359}, year = {2017}, date = {2017-01-01}, journal = {PeerJ}, volume = {2017}, number = {10}, abstract = {The Mediterranean Sea is home to over 2/3 of the world's charter boat traffic and hosts an estimated 1.5 million recreational boats. Studies elsewhere have demonstrated marinas as important hubs for the stepping-stone transfer of non-indigenous species (NIS), but these unique anthropogenic, and typically artificial habitats have largely gone overlooked in the Mediterranean as sources of NIS hot-spots. From April 2015 to November 2016, 34 marinas were sampled across the following Mediterranean countries: Spain, France, Italy, Malta, Greece, Turkey and Cyprus to investigate the NIS presence and richness in the specialized hard substrate material of these marina habitats. All macroinvertebrate taxa were collected and identified. Additionally, fouling samples were collected from approximately 600 boat-hulls from 25 of these marinas to determine if boats host diverse NIS not present in the marina. Here, we present data revealing that Mediterranean marinas indeed act as major hubs for the transfer of marine NIS, and we also provide evidence that recreational boats act as effective vectors of spread. From this wide-ranging geographical study, we report here numerous new NIS records at the basin, subregional, country and locality level. At the basin level, we report three NIS new to the Mediterranean Sea (Achelia sawayai sensu lato, Aorides longimerus, Cymodoce aff. fuscina), and the re-appearance of two NIS previously known but currently considered extinct in the Mediterranean (Bemlos leptocheirus, Saccostrea glomerata).We also compellingly update the distributions of many NIS in theMediterranean Sea showing some recent spreading; we provide details for 11 new subregional records for NIS (Watersipora arcuata, Hydroides brachyacantha sensu lato and Saccostrea glomerata now present in theWesternMediterranean; Symplegma brakenhielmi, Stenothoe georgiana, Spirobranchus tertaceros sensu lato, Dendostrea folium sensu lato and Parasmittina egyptiaca now present in the Central Mediterranean, and W. arcuata, Bemlos leptocheirus and Dyspanopeus sayi in the Eastern Mediterranean). We also report 51 new NIS country records from recreational marinas: 12 for Malta, 10 for Cyprus, nine for Greece, six for Spain and France, five for Turkey and three for Italy, representing 32 species. Finally, we report 20 new NIS records (representing 17 species) found on recreational boat-hulls (mobile habitats), not yet found in the same marina, or in most cases, even the country. For each new NIS record, their native origin and global and Mediterranean distributions are provided, along with details of the new record. Additionally, taxonomic characters used for identification and photos of the specimens are also provided. These new NIS records should now be added to the relevant NIS databases compiled by several entities. Records of uncertain identity are also discussed, to assess the probability of valid non-indigenous status. © 2017 Ulman et al.}, note = {Publisher: PeerJ Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean Sea is home to over 2/3 of the world's charter boat traffic and hosts an estimated 1.5 million recreational boats. Studies elsewhere have demonstrated marinas as important hubs for the stepping-stone transfer of non-indigenous species (NIS), but these unique anthropogenic, and typically artificial habitats have largely gone overlooked in the Mediterranean as sources of NIS hot-spots. From April 2015 to November 2016, 34 marinas were sampled across the following Mediterranean countries: Spain, France, Italy, Malta, Greece, Turkey and Cyprus to investigate the NIS presence and richness in the specialized hard substrate material of these marina habitats. All macroinvertebrate taxa were collected and identified. Additionally, fouling samples were collected from approximately 600 boat-hulls from 25 of these marinas to determine if boats host diverse NIS not present in the marina. Here, we present data revealing that Mediterranean marinas indeed act as major hubs for the transfer of marine NIS, and we also provide evidence that recreational boats act as effective vectors of spread. From this wide-ranging geographical study, we report here numerous new NIS records at the basin, subregional, country and locality level. At the basin level, we report three NIS new to the Mediterranean Sea (Achelia sawayai sensu lato, Aorides longimerus, Cymodoce aff. fuscina), and the re-appearance of two NIS previously known but currently considered extinct in the Mediterranean (Bemlos leptocheirus, Saccostrea glomerata).We also compellingly update the distributions of many NIS in theMediterranean Sea showing some recent spreading; we provide details for 11 new subregional records for NIS (Watersipora arcuata, Hydroides brachyacantha sensu lato and Saccostrea glomerata now present in theWesternMediterranean; Symplegma brakenhielmi, Stenothoe georgiana, Spirobranchus tertaceros sensu lato, Dendostrea folium sensu lato and Parasmittina egyptiaca now present in the Central Mediterranean, and W. arcuata, Bemlos leptocheirus and Dyspanopeus sayi in the Eastern Mediterranean). We also report 51 new NIS country records from recreational marinas: 12 for Malta, 10 for Cyprus, nine for Greece, six for Spain and France, five for Turkey and three for Italy, representing 32 species. Finally, we report 20 new NIS records (representing 17 species) found on recreational boat-hulls (mobile habitats), not yet found in the same marina, or in most cases, even the country. For each new NIS record, their native origin and global and Mediterranean distributions are provided, along with details of the new record. Additionally, taxonomic characters used for identification and photos of the specimens are also provided. These new NIS records should now be added to the relevant NIS databases compiled by several entities. Records of uncertain identity are also discussed, to assess the probability of valid non-indigenous status. © 2017 Ulman et al. |
Voultsiadou, E; Gerovasileiou, V; Vandepitte, L; Ganias, K; Arvanitidis, C Aristotle's scientific contributions to the classification, nomenclature and distribution of marine organisms Journal Article Mediterranean Marine Science, 18 (3), pp. 468–478, 2017, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research). @article{voultsiadou_aristotles_2017, title = {Aristotle's scientific contributions to the classification, nomenclature and distribution of marine organisms}, author = {E Voultsiadou and V Gerovasileiou and L Vandepitte and K Ganias and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85041532062&doi=10.12681%2fmms.13874&partnerID=40&md5=0942c77f9cb51a440a40262d2c62cd58}, doi = {10.12681/mms.13874}, issn = {1108393X}, year = {2017}, date = {2017-01-01}, journal = {Mediterranean Marine Science}, volume = {18}, number = {3}, pages = {468--478}, abstract = {The biological works of the Greek philosopher Aristotle include a significant amount of information on marine animals. This study is an overview of Aristotle's scientific contribution to the knowledge of marine biodiversity and specifically to taxonomic classification, nomenclature and distribution of marine species. Our results show that Aristotle's approach looks remarkably familiar to present day marine biologists since: (i) although not directly aiming at it, he gave a taxonomic classification of marine animals, which includes physical groups ranked on three levels at least; (ii) most of Aristotle's marine "major groups" correspond to taxa of the order rank in Linnaeus's classification and to taxa of the class rank in the current classification; (iii) a positive correlation was found between the number of taxa per group identified in Aristotle's writings and those described by Linnaeus; (iv) Aristotle's classification system exhibits similarities with the current one regarding the way taxa are distributed to higher categories; (v) a considerable number of Aristotle's marine animal names have been used for the creation of the scientific names currently in use; (vi) he was the first to give an account of Mediterranean marine fauna, focusing on the Aegean Sea and adjacent areas. In view of the above, we suggest that the foundations of marine taxonomy as laid down by Aristotle are still echoing today. © 2017, Hellenic Centre for Marine Research.}, note = {Publisher: Hellenic Centre for Marine Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The biological works of the Greek philosopher Aristotle include a significant amount of information on marine animals. This study is an overview of Aristotle's scientific contribution to the knowledge of marine biodiversity and specifically to taxonomic classification, nomenclature and distribution of marine species. Our results show that Aristotle's approach looks remarkably familiar to present day marine biologists since: (i) although not directly aiming at it, he gave a taxonomic classification of marine animals, which includes physical groups ranked on three levels at least; (ii) most of Aristotle's marine "major groups" correspond to taxa of the order rank in Linnaeus's classification and to taxa of the class rank in the current classification; (iii) a positive correlation was found between the number of taxa per group identified in Aristotle's writings and those described by Linnaeus; (iv) Aristotle's classification system exhibits similarities with the current one regarding the way taxa are distributed to higher categories; (v) a considerable number of Aristotle's marine animal names have been used for the creation of the scientific names currently in use; (vi) he was the first to give an account of Mediterranean marine fauna, focusing on the Aegean Sea and adjacent areas. In view of the above, we suggest that the foundations of marine taxonomy as laid down by Aristotle are still echoing today. © 2017, Hellenic Centre for Marine Research. |
2016 |
Faulwetter, Sarah; Pafilis, Evangelos; Fanini, Lucia; Bailly, Nicolas; Agosti, Donat; Arvanitidis, Christos; Boicenco, Laura; Capatano, Terry; Claus, Simon; Dekeyzer, Stefanie; Georgiev, Teodor; Legaki, Aglaia; Mavraki, Dimitra; Oulas, Anastasis; Papastefanou, Gabriella; Penev, Lyubomir; Sautter, Guido; Schigel, Dmitry; Senderov, Viktor; Teaca, Adrian; Tsompanou, Marilena EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Journal Article Research Ideas and Outcomes, 2 , pp. e9774, 2016, ISSN: 2367-7163. @article{faulwetter_emodnet_2016, title = {EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases}, author = {Sarah Faulwetter and Evangelos Pafilis and Lucia Fanini and Nicolas Bailly and Donat Agosti and Christos Arvanitidis and Laura Boicenco and Terry Capatano and Simon Claus and Stefanie Dekeyzer and Teodor Georgiev and Aglaia Legaki and Dimitra Mavraki and Anastasis Oulas and Gabriella Papastefanou and Lyubomir Penev and Guido Sautter and Dmitry Schigel and Viktor Senderov and Adrian Teaca and Marilena Tsompanou}, url = {http://rio.pensoft.net/articles.php?id=9774}, doi = {10.3897/rio.2.e9774}, issn = {2367-7163}, year = {2016}, date = {2016-07-01}, urldate = {2020-09-21}, journal = {Research Ideas and Outcomes}, volume = {2}, pages = {e9774}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vasileiadou, K; Pavloudi, C; Kalantzi, I; Apostolaki, E T; Chatzigeorgiou, G; Chatzinikolaou, E; Pafilis, E; Papageorgiou, N; Fanini, L; Konstas, S; Fragopoulou, N; Arvanitidis, C Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece) Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{vasileiadou_environmental_2016, title = {Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece)}, author = {K Vasileiadou and C Pavloudi and I Kalantzi and E T Apostolaki and G Chatzigeorgiou and E Chatzinikolaou and E Pafilis and N Papageorgiou and L Fanini and S Konstas and N Fragopoulou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018621471&doi=10.3897%2fBDJ.4.e8233&partnerID=40&md5=91104fbd24f94063ee946df8c2486376}, doi = {10.3897/BDJ.4.e8233}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons. © Vasileiadou K et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons. © Vasileiadou K et al. |
Pavloudi, C; Oulas, A; Vasileiadou, K; Sarropoulou, E; Kotoulas, G; Arvanitidis, C Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) Journal Article Marine Genomics, 28 , pp. 71–81, 2016, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{pavloudi_salinity_2016, title = {Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)}, author = {C Pavloudi and A Oulas and K Vasileiadou and E Sarropoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955611416&doi=10.1016%2fj.margen.2016.01.005&partnerID=40&md5=a226c6872c0a3044831db4a1b5f65ca3}, doi = {10.1016/j.margen.2016.01.005}, issn = {18747787}, year = {2016}, date = {2016-01-01}, journal = {Marine Genomics}, volume = {28}, pages = {71--81}, abstract = {Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V. |
Keklikoglou, K; Faulwetter, S; Chatzinikolaou, E; Michalakis, N; Filiopoulou, I; Minadakis, N; Panteri, E; Perantinos, G; Gougousis, A; Arvanitidis, C Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT) Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{keklikoglou_micro-ctvlab_2016, title = {Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT)}, author = {K Keklikoglou and S Faulwetter and E Chatzinikolaou and N Michalakis and I Filiopoulou and N Minadakis and E Panteri and G Perantinos and A Gougousis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018643360&doi=10.3897%2fBDJ.4.e8740&partnerID=40&md5=450c2ceab515e072b612c9c046e0c7bc}, doi = {10.3897/BDJ.4.e8740}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create submicron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab ) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro- CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices. © Keklikoglou K et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create submicron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab ) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro- CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices. © Keklikoglou K et al. |
Pafilis, E; Buttigieg, P L; Ferrell, B; Pereira, E; Schnetzer, J; Arvanitidis, C; Jensen, L J EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation Journal Article Database, 2016 , 2016, ISSN: 17580463, (Publisher: Oxford University Press). @article{pafilis_extract_2016, title = {EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation}, author = {E Pafilis and P L Buttigieg and B Ferrell and E Pereira and J Schnetzer and C Arvanitidis and L J Jensen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85052188662&doi=10.1093%2fdatabase%2fbaw005&partnerID=40&md5=9d2901b712db55c2768dcd9c3d5cfbc3}, doi = {10.1093/database/baw005}, issn = {17580463}, year = {2016}, date = {2016-01-01}, journal = {Database}, volume = {2016}, abstract = {The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. © The Author(s) 2016.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. © The Author(s) 2016. |
Vasileiadou, K; Pavloudi, C; Sarropoulou, E; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea Journal Article Aquatic Biology, 25 , pp. 7–15, 2016, ISSN: 18647782, (Publisher: Inter-Research). @article{vasileiadou_unique_2016, title = {Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea}, author = {K Vasileiadou and C Pavloudi and E Sarropoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971596901&doi=10.3354%2fab00654&partnerID=40&md5=4039a8b37d89de3fef4adb17862554df}, doi = {10.3354/ab00654}, issn = {18647782}, year = {2016}, date = {2016-01-01}, journal = {Aquatic Biology}, volume = {25}, pages = {7--15}, abstract = {The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016. |
Lyons, D A; Arvanitidis, C; Blight, A J; Chatzinikolaou, E; Guy-Haim, T; Kotta, J; Queirós, A M; Rilov, G; Somerfield, P J; Crowe, T P There are no whole truths in meta-analyses: All their truths are half-truths Journal Article Global Change Biology, 22 (3), pp. 968–971, 2016, ISSN: 13541013, (Publisher: Blackwell Publishing Ltd). @article{lyons_there_2016, title = {There are no whole truths in meta-analyses: All their truths are half-truths}, author = {D A Lyons and C Arvanitidis and A J Blight and E Chatzinikolaou and T Guy-Haim and J Kotta and A M Queirós and G Rilov and P J Somerfield and T P Crowe}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959290290&doi=10.1111%2fgcb.12989&partnerID=40&md5=f644005cfc44649d71f73588106cf0ca}, doi = {10.1111/gcb.12989}, issn = {13541013}, year = {2016}, date = {2016-01-01}, journal = {Global Change Biology}, volume = {22}, number = {3}, pages = {968--971}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Poursanidis, D; Koutsoubas, D; Arvanitidis, C; Chatzigeorgiou, G ReefMedMol: Mollusca from the infralittoral rocky shores - The biocoenosis of photophilic algae - In the Mediterranean Sea Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{poursanidis_reefmedmol_2016, title = {ReefMedMol: Mollusca from the infralittoral rocky shores - The biocoenosis of photophilic algae - In the Mediterranean Sea}, author = {D Poursanidis and D Koutsoubas and C Arvanitidis and G Chatzigeorgiou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018645652&doi=10.3897%2fBDJ.4.e7516&partnerID=40&md5=431c03e4dabf230bab653468841338ef}, doi = {10.3897/BDJ.4.e7516}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background This paper describes two datasets on the molluscan fauna from the Mediterranean infralittoral reef ecosystem - the biocoenosis of photophilic algae. The first dataset is taken from the East Mediterranean node of the NAGISA project. The second one is a compilation based on the available published material in peer - reviewed journals as well as from the accessible grey literature. These datasets cover a time period of 43 years from 1969 to 2012 from several locations spanning the Mediterranean Sea. New information This dataset is the only one available from this important Mediterranean Habitat, coded as 1170 in the Habitats Directive (92/43/EEC) and can provide valuable information on the needs of ecosystems functions and services assessment, habitat and species conservation as well as marine spatial planning. © Poursanidis D et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background This paper describes two datasets on the molluscan fauna from the Mediterranean infralittoral reef ecosystem - the biocoenosis of photophilic algae. The first dataset is taken from the East Mediterranean node of the NAGISA project. The second one is a compilation based on the available published material in peer - reviewed journals as well as from the accessible grey literature. These datasets cover a time period of 43 years from 1969 to 2012 from several locations spanning the Mediterranean Sea. New information This dataset is the only one available from this important Mediterranean Habitat, coded as 1170 in the Habitats Directive (92/43/EEC) and can provide valuable information on the needs of ecosystems functions and services assessment, habitat and species conservation as well as marine spatial planning. © Poursanidis D et al. |
Gerovasileiou, V; Dailianis, T; Panteri, E; Michalakis, N; Gatti, G; Sini, M; Dimitriadis, C; Issaris, Y; Salomidi, M; Filiopoulou, I; Doğan, A; d'Avray, L T V; David, R; Çinar, M E; Koutsoubas, D; Féral, J -P; Arvanitidis, C Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{gerovasileiou_cigesmed_2016, title = {CIGESMED for divers: Establishing a citizen science initiative for the mapping and monitoring of coralligenous assemblages in the Mediterranean Sea}, author = {V Gerovasileiou and T Dailianis and E Panteri and N Michalakis and G Gatti and M Sini and C Dimitriadis and Y Issaris and M Salomidi and I Filiopoulou and A Doğan and L T V d'Avray and R David and M E Çinar and D Koutsoubas and J -P Féral and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018641504&doi=10.3897%2fBDJ.4.e8692&partnerID=40&md5=44c645ca189b05f7ffb7e1d895a0db95}, doi = {10.3897/BDJ.4.e8692}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Over the last decade, inventorying and monitoring of marine biodiversity has significantly benefited from the active engagement of volunteers. Although several Citizen Science projects concern tropical reef ecosystems worldwide, none of the existing initiatives has yet specifically focused on their Mediterranean equivalents. Mediterranean coralline reefs, known as "coralligenous", are bioherms primarily built by calcifying rhodophytes on hard substrates under dim-light conditions; they are considered hotspots of biodiversity and are extremely popular among divers due to their complex structure, conspicuous biological wealth and high aesthetic value. Nevertheless, data on their distribution, structure and conservation status is lacking for several Mediterranean areas while they are vulnerable to an increasing number of threats. New information In the framework of CIGESMED SeasEra (ERAnet) project a specialized Citizen Science project was launched, aiming to engage enthusiast divers in the study and monitoring of Mediterranean coralligenous assemblages through the gathering of basic information regarding their spatial occurrence, assemblage structure and associated pressures or threats. For its active implementation, a data collection protocol and a multilingual website were developed, comprising an educational module and a data submission platform. Georeferenced data reporting focuses on: (a) basic topographic and abiotic features for the preliminary description of each site, and the creation of data series for sites receiving multiple visits; (b) presence and relative abundance of typical conspicuous species, as well as (c) existence of pressures and imminent threats, for the characterization and assessment of coralligenous assemblages. A variety of tools is provided to facilitate end users, while divers have the choice to report additional information and are encouraged to upload their photographs. The long-term goal is the development of an active community of amateur observers providing widespread and ecologically significant data on coralligenous assemblages. © Gerovasileiou V et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Over the last decade, inventorying and monitoring of marine biodiversity has significantly benefited from the active engagement of volunteers. Although several Citizen Science projects concern tropical reef ecosystems worldwide, none of the existing initiatives has yet specifically focused on their Mediterranean equivalents. Mediterranean coralline reefs, known as "coralligenous", are bioherms primarily built by calcifying rhodophytes on hard substrates under dim-light conditions; they are considered hotspots of biodiversity and are extremely popular among divers due to their complex structure, conspicuous biological wealth and high aesthetic value. Nevertheless, data on their distribution, structure and conservation status is lacking for several Mediterranean areas while they are vulnerable to an increasing number of threats. New information In the framework of CIGESMED SeasEra (ERAnet) project a specialized Citizen Science project was launched, aiming to engage enthusiast divers in the study and monitoring of Mediterranean coralligenous assemblages through the gathering of basic information regarding their spatial occurrence, assemblage structure and associated pressures or threats. For its active implementation, a data collection protocol and a multilingual website were developed, comprising an educational module and a data submission platform. Georeferenced data reporting focuses on: (a) basic topographic and abiotic features for the preliminary description of each site, and the creation of data series for sites receiving multiple visits; (b) presence and relative abundance of typical conspicuous species, as well as (c) existence of pressures and imminent threats, for the characterization and assessment of coralligenous assemblages. A variety of tools is provided to facilitate end users, while divers have the choice to report additional information and are encouraged to upload their photographs. The long-term goal is the development of an active community of amateur observers providing widespread and ecologically significant data on coralligenous assemblages. © Gerovasileiou V et al. |
Dimitriadis, C; Koutsoubas, D; Arvanitidis, C On the use of predator traits and distribution in environmental impact assessment: the trophic/dispersal sufficiency concept Journal Article Marine Biodiversity, 46 (3), pp. 603–613, 2016, ISSN: 18671616, (Publisher: Springer Verlag). @article{dimitriadis_use_2016, title = {On the use of predator traits and distribution in environmental impact assessment: the trophic/dispersal sufficiency concept}, author = {C Dimitriadis and D Koutsoubas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84944699274&doi=10.1007%2fs12526-015-0407-8&partnerID=40&md5=24cfedd7a7c5649f5ed2fa035bc03e6b}, doi = {10.1007/s12526-015-0407-8}, issn = {18671616}, year = {2016}, date = {2016-01-01}, journal = {Marine Biodiversity}, volume = {46}, number = {3}, pages = {603--613}, abstract = {Environmental change can alter both species distribution range patterns at a regional scale and their feeding habits at a local scale. While several studies have highlighted the mechanisms driving such changes separately, little is known on their combined effect on the local communities. In this manuscript, we used both feeding and distributional traits of macro-benthic species and examined their combined response across an environmental gradient induced by an aquaculture unit. Our results mainly suggest that specialized predators with narrow geographic distributions and niches were more sensitive to environmental change than the less specialized groups. Moreover, under harsh environmental conditions, predatory species with a wide dispersion capacity can sustain viable populations through niche generalization. In contrast, in areas of low environmental disturbance, predatory species with a more restricted dispersal capability (i.e. some endemic species) can coexist via niche differentiation. In this context, our findings contribute towards a better understanding of benthic communities’ functional response to environmental change and may be of use in environmental impact assessment. © 2015, Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg.}, note = {Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } Environmental change can alter both species distribution range patterns at a regional scale and their feeding habits at a local scale. While several studies have highlighted the mechanisms driving such changes separately, little is known on their combined effect on the local communities. In this manuscript, we used both feeding and distributional traits of macro-benthic species and examined their combined response across an environmental gradient induced by an aquaculture unit. Our results mainly suggest that specialized predators with narrow geographic distributions and niches were more sensitive to environmental change than the less specialized groups. Moreover, under harsh environmental conditions, predatory species with a wide dispersion capacity can sustain viable populations through niche generalization. In contrast, in areas of low environmental disturbance, predatory species with a more restricted dispersal capability (i.e. some endemic species) can coexist via niche differentiation. In this context, our findings contribute towards a better understanding of benthic communities’ functional response to environmental change and may be of use in environmental impact assessment. © 2015, Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg. |
Arvanitidis, C; Chatzinikolaou, E; Gerovasileiou, V; Panteri, E; Bailly, N; Minadakis, N; Hardisty, A; Los, W LifeWatchGreece: Construction and operation of the National Research Infrastructure (ESFRI) Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{arvanitidis_lifewatchgreece_2016, title = {LifeWatchGreece: Construction and operation of the National Research Infrastructure (ESFRI)}, author = {C Arvanitidis and E Chatzinikolaou and V Gerovasileiou and E Panteri and N Bailly and N Minadakis and A Hardisty and W Los}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018632519&doi=10.3897%2fBDJ.4.e10791&partnerID=40&md5=f22c1a62b4935d0cf013e712070da1b5}, doi = {10.3897/BDJ.4.e10791}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Chatzinikolaou, E; Faulwetter, S; Mavraki, D; Bourtzis, T; Arvanitidis, C Data policy and data sharing agreement in the LifeWatchGreece Research Infrastructure Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{chatzinikolaou_data_2016, title = {Data policy and data sharing agreement in the LifeWatchGreece Research Infrastructure}, author = {E Chatzinikolaou and S Faulwetter and D Mavraki and T Bourtzis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018657276&doi=10.3897%2fBDJ.4.e10849&partnerID=40&md5=ba19fabe3629875c6bf9bab0e6adf07d}, doi = {10.3897/BDJ.4.e10849}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {The LifeWatchGreece Research Infrastructure (LWG RI) stores biodiversity data and information from all biology-related disciplines derived from the Greek territory (or the Mediterranean Sea for the marine data). The aim of LWG RI is to facilitate data sharing and dissemination under harmonised standards in order to maximize the socio-economic benefits of research and knowledge transfer to the public. This publication describes the rationale behind the data policy of LWG RI, outlines the current legal situation for sharing research data and presents the Data Sharing Agreement which is signed between the data owner/provider and the LWG RI for each dataset, describing in detail the rights and duties of each party, as well as the license type and the embargo period under which the data are released. © Chatzinikolaou E et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The LifeWatchGreece Research Infrastructure (LWG RI) stores biodiversity data and information from all biology-related disciplines derived from the Greek territory (or the Mediterranean Sea for the marine data). The aim of LWG RI is to facilitate data sharing and dissemination under harmonised standards in order to maximize the socio-economic benefits of research and knowledge transfer to the public. This publication describes the rationale behind the data policy of LWG RI, outlines the current legal situation for sharing research data and presents the Data Sharing Agreement which is signed between the data owner/provider and the LWG RI for each dataset, describing in detail the rights and duties of each party, as well as the license type and the embargo period under which the data are released. © Chatzinikolaou E et al. |
Bailly, N; Gerovasileiou, V; Arvanitidis, C; Legakis, A Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{bailly_introduction_2016, title = {Introduction to the Greek Taxon Information System (GTIS) in LifeWatchGreece: The construction of the Preliminary Checklists of Species of Greece}, author = {N Bailly and V Gerovasileiou and C Arvanitidis and A Legakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018650313&doi=10.3897%2fBDJ.4.e7959&partnerID=40&md5=1f6351c142359acb9fee6b2e29b73393}, doi = {10.3897/BDJ.4.e7959}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {The Greek Taxon Information System is an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that is resuming efforts to compile a complete checklist of all species reported from the Greek territory. Such an effort is necessary as a requirement for all signatories of the Convention on Biological Diversity (Greece is a signatory since 1994). Over an estimation published in 2004 according to which 50,000 species are present in Greece, belonging to most kingdoms except bacteria and viruses, a list of 35,000 valid species (and subspecies) has been assembled from previous national and European initiatives and specialized databases on various groups. A new database will be progressively set up in the LifeWatchGreece Infrastructure within the near future. Before the dissemination of this dataset, it is important that the checklists will be validated by specialists for each taxonomic group. The first step already accomplished was to build and publish Preliminary Checklists for some taxonomic groups of marine fauna, which have been validated by specialists on the basis of their expertise and secondary literature. The publication of these Preliminary Checklists is expected to increase the visibility and usability of the database in the future not only to the scientific community but also to the broader domain of biodiversity management, especially in cases where no such checklists have been published yet. The guidelines used to test the first taxonomic groups are presented in this paper. © Bailly N et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Greek Taxon Information System is an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that is resuming efforts to compile a complete checklist of all species reported from the Greek territory. Such an effort is necessary as a requirement for all signatories of the Convention on Biological Diversity (Greece is a signatory since 1994). Over an estimation published in 2004 according to which 50,000 species are present in Greece, belonging to most kingdoms except bacteria and viruses, a list of 35,000 valid species (and subspecies) has been assembled from previous national and European initiatives and specialized databases on various groups. A new database will be progressively set up in the LifeWatchGreece Infrastructure within the near future. Before the dissemination of this dataset, it is important that the checklists will be validated by specialists for each taxonomic group. The first step already accomplished was to build and publish Preliminary Checklists for some taxonomic groups of marine fauna, which have been validated by specialists on the basis of their expertise and secondary literature. The publication of these Preliminary Checklists is expected to increase the visibility and usability of the database in the future not only to the scientific community but also to the broader domain of biodiversity management, especially in cases where no such checklists have been published yet. The guidelines used to test the first taxonomic groups are presented in this paper. © Bailly N et al. |
Anastasiou, T I; Chatzinikolaou, E; Mandalakis, M; Arvanitidis, C Imposex and organotin compounds in ports of the Mediterranean and the Atlantic: Is the story over? Journal Article Science of the Total Environment, 569-570 , pp. 1315–1329, 2016, ISSN: 00489697, (Publisher: Elsevier B.V.). @article{anastasiou_imposex_2016, title = {Imposex and organotin compounds in ports of the Mediterranean and the Atlantic: Is the story over?}, author = {T I Anastasiou and E Chatzinikolaou and M Mandalakis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978807299&doi=10.1016%2fj.scitotenv.2016.06.209&partnerID=40&md5=f0a46f0f9141ca86261409181b4d0d9b}, doi = {10.1016/j.scitotenv.2016.06.209}, issn = {00489697}, year = {2016}, date = {2016-01-01}, journal = {Science of the Total Environment}, volume = {569-570}, pages = {1315--1329}, abstract = {Organotin compounds are toxic substances released into the marine environment from antifouling paints. Sixty-two years following their first application and 9 years after the complete ban on their use as biocides in 2003 (EC No. 782/2003), their negative impact on mollusks was still evident, as illustrated by imposex (i.e. the masculinization of female gastropods). This phenomenon is widely used to investigate tributyltin (TBT) pollution, with Hexaplex trunculus and Nassarius nitidus being considered as sensitive bioindicators. H. trunculus specimens and sediment samples collected from the ports of Cagliari (Sardinia), El Kantaoui (Tunisia) and Olhão (Portugal), along with N. nitidus individuals from the port of Faro (Portugal), were used for the assessment of imposex intensity and organotin pollution in these areas. High imposex frequency and organotin concentrations (TBT, triphenyltin (TPhT) and their degradation products) were observed, especially in Sardinia, implying that these chemicals remain a significant pollution issue in the specific Mediterranean ports. Moreover, the highly significant relationship established between penis length of imposex-affected females H. trunculus and TBT/TPhT concentrations offers a rapid and nonsacrificial proxy model for assessing the impact of organotins in coastal environments. Finally, the complementary use of more than one TBT bioindicator is advised in order to obtain more accurate results in detailed monitoring studies of TBT pollution. © 2016 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Organotin compounds are toxic substances released into the marine environment from antifouling paints. Sixty-two years following their first application and 9 years after the complete ban on their use as biocides in 2003 (EC No. 782/2003), their negative impact on mollusks was still evident, as illustrated by imposex (i.e. the masculinization of female gastropods). This phenomenon is widely used to investigate tributyltin (TBT) pollution, with Hexaplex trunculus and Nassarius nitidus being considered as sensitive bioindicators. H. trunculus specimens and sediment samples collected from the ports of Cagliari (Sardinia), El Kantaoui (Tunisia) and Olhão (Portugal), along with N. nitidus individuals from the port of Faro (Portugal), were used for the assessment of imposex intensity and organotin pollution in these areas. High imposex frequency and organotin concentrations (TBT, triphenyltin (TPhT) and their degradation products) were observed, especially in Sardinia, implying that these chemicals remain a significant pollution issue in the specific Mediterranean ports. Moreover, the highly significant relationship established between penis length of imposex-affected females H. trunculus and TBT/TPhT concentrations offers a rapid and nonsacrificial proxy model for assessing the impact of organotins in coastal environments. Finally, the complementary use of more than one TBT bioindicator is advised in order to obtain more accurate results in detailed monitoring studies of TBT pollution. © 2016 Elsevier B.V. |
Varsos, C; Patkos, T; Oulas, A; Pavloudi, C; Gougousis, A; Ijaz, U Z; Filiopoulou, I; Pattakos, N; Berghe, E V; Fernández-Guerra, A; Faulwetter, S; Chatzinikolaou, E; Pafilis, E; Bekiari, C; Doerr, M; Arvanitidis, C Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab) Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{varsos_optimized_2016, title = {Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)}, author = {C Varsos and T Patkos and A Oulas and C Pavloudi and A Gougousis and U Z Ijaz and I Filiopoulou and N Pattakos and E V Berghe and A Fernández-Guerra and S Faulwetter and E Chatzinikolaou and E Pafilis and C Bekiari and M Doerr and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018640003&doi=10.3897%2fBDJ.4.e8357&partnerID=40&md5=6003e9caf6582fdde7f4bffec91e154f}, doi = {10.3897/BDJ.4.e8357}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/ microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data - Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pclinux- gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https:// portal.lifewatchgreece.eu/.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Parallel data manipulation using R has previously been addressed by members of the R community, however most of these studies produce ad hoc solutions that are not readily available to the average R user. Our targeted users, ranging from the expert ecologist/ microbiologists to computational biologists, often experience difficulties in finding optimal ways to exploit the full capacity of their computational resources. In addition, improving performance of commonly used R scripts becomes increasingly difficult especially with large datasets. Furthermore, the implementations described here can be of significant interest to expert bioinformaticians or R developers. Therefore, our goals can be summarized as: (i) description of a complete methodology for the analysis of large datasets by combining capabilities of diverse R packages, (ii) presentation of their application through a virtual R laboratory (RvLab) that makes execution of complex functions and visualization of results easy and readily available to the end-user. New information In this paper, the novelty stems from implementations of parallel methodologies which rely on the processing of data on different levels of abstraction and the availability of these processes through an integrated portal. Parallel implementation R packages, such as the pbdMPI (Programming with Big Data - Interface to MPI) package, are used to implement Single Program Multiple Data (SPMD) parallelization on primitive mathematical operations, allowing for interplay with functions of the vegan package. The dplyr and RPostgreSQL R packages are further integrated offering connections to dataframe like objects (databases) as secondary storage solutions whenever memory demands exceed available RAM resources. The RvLab is running on a PC cluster, using version 3.1.2 (2014-10-31) on a x86_64-pclinux- gnu (64-bit) platform, and offers an intuitive virtual environmet interface enabling users to perform analysis of ecological and microbial communities based on optimized vegan functions. A beta version of the RvLab is available after registration at: https:// portal.lifewatchgreece.eu/. |
Minadakis, N; Marketakis, Y; Doerr, M; Bekiari, C; Papadakos, P; Gougousis, A; Bailly, N; Arvanitidis, C LifeWatch Greece data-services: Discovering biodiversity data using semantic web technologies Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{minadakis_lifewatch_2016, title = {LifeWatch Greece data-services: Discovering biodiversity data using semantic web technologies}, author = {N Minadakis and Y Marketakis and M Doerr and C Bekiari and P Papadakos and A Gougousis and N Bailly and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018630619&doi=10.3897%2fBDJ.4.e8443&partnerID=40&md5=e7d3559ed33e73168bed99db15f46b3d}, doi = {10.3897/BDJ.4.e8443}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Biodiversity data is characterized by its cross-disciplinary character, the extremely broad range of data types and structures, and the variety of semantic concepts that it encompasses. Furthermore there is a plethora of different data sources providing resources for the same piece of information in a heterogeneous way. Even if we restrict our attention to Greek biodiversity domain, it is easy to see that biodiversity data remains unconnected and widely distributed among different sources. New information To cope with these issues, in the context of the LifeWatch Greece project, i) we supported cataloguing and publishing of all the relevant metadata information of the Greek biodiversity domain, ii) we integrated data from heterogeneous sources by supporting the definitions of appropriate models, iii) we provided means for efficiently discovering biodiversity data of interest and iv) we enabled the answering of complex queries that could not be answered from the individual sources. This work has been exploited, evaluated and scientificaly confirmed by the biodiversity community through the services provided by the LifeWatch Greece portal. © Minadakis N et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Biodiversity data is characterized by its cross-disciplinary character, the extremely broad range of data types and structures, and the variety of semantic concepts that it encompasses. Furthermore there is a plethora of different data sources providing resources for the same piece of information in a heterogeneous way. Even if we restrict our attention to Greek biodiversity domain, it is easy to see that biodiversity data remains unconnected and widely distributed among different sources. New information To cope with these issues, in the context of the LifeWatch Greece project, i) we supported cataloguing and publishing of all the relevant metadata information of the Greek biodiversity domain, ii) we integrated data from heterogeneous sources by supporting the definitions of appropriate models, iii) we provided means for efficiently discovering biodiversity data of interest and iv) we enabled the answering of complex queries that could not be answered from the individual sources. This work has been exploited, evaluated and scientificaly confirmed by the biodiversity community through the services provided by the LifeWatch Greece portal. © Minadakis N et al. |
Chatzigeorgiou, G; Faulwetter, S; Dailianis, T; Smith, V S; Koulouri, P; Dounas, C; Arvanitidis, C Testing the robustness of Citizen Science projects: Evaluating the results of pilot project COMBER Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{chatzigeorgiou_testing_2016, title = {Testing the robustness of Citizen Science projects: Evaluating the results of pilot project COMBER}, author = {G Chatzigeorgiou and S Faulwetter and T Dailianis and V S Smith and P Koulouri and C Dounas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018623784&doi=10.3897%2fBDJ.4.e10859&partnerID=40&md5=5e1065f8df7260a055f72bdac84bccf2}, doi = {10.3897/BDJ.4.e10859}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Citizen Science (CS) as a term implies a great deal of approaches and scopes involving many different fields of science. The number of the relevant projects globally has been increased significantly in the recent years. Large scale ecological questions can be answered only through extended observation networks and CS projects can support this effort. Although the need of such projects is apparent, an important part of scientific community cast doubt on the reliability of CS data sets. New information The pilot CS project COMBER has been created in order to provide evidence to answer the aforementioned question in the coastal marine biodiversity monitoring. The results of the current analysis show that a carefully designed CS project with clear hypotheses, wide participation and data sets validation, can be a valuable tool for the large scale and long term changes in marine biodiversity pattern change and therefore for relevant management and conservation issues. © Chatzigeorgiou G et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Citizen Science (CS) as a term implies a great deal of approaches and scopes involving many different fields of science. The number of the relevant projects globally has been increased significantly in the recent years. Large scale ecological questions can be answered only through extended observation networks and CS projects can support this effort. Although the need of such projects is apparent, an important part of scientific community cast doubt on the reliability of CS data sets. New information The pilot CS project COMBER has been created in order to provide evidence to answer the aforementioned question in the coastal marine biodiversity monitoring. The results of the current analysis show that a carefully designed CS project with clear hypotheses, wide participation and data sets validation, can be a valuable tool for the large scale and long term changes in marine biodiversity pattern change and therefore for relevant management and conservation issues. © Chatzigeorgiou G et al. |
Pearson, S; Windupranata, W; Pranowo, S W; Putri, A; Ma, Y; Vila-Concejo, A; Fernández, E; Méndez, G; Banks, J; Knights, A M; Firth, L B; Breen, B B; Jarvis, R; Aguirre, J D; Chen, S; Smith, A N H; Steinberg, P; Chatzinikolaou, E; Arvanitidis, C Conflicts in some of the World harbours: what needs to happen next? Journal Article Maritime Studies, 15 (1), 2016, ISSN: 18727859, (Publisher: Springer Verlag). @article{pearson_conflicts_2016, title = {Conflicts in some of the World harbours: what needs to happen next?}, author = {S Pearson and W Windupranata and S W Pranowo and A Putri and Y Ma and A Vila-Concejo and E Fernández and G Méndez and J Banks and A M Knights and L B Firth and B B Breen and R Jarvis and J D Aguirre and S Chen and A N H Smith and P Steinberg and E Chatzinikolaou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983239161&doi=10.1186%2fs40152-016-0049-x&partnerID=40&md5=39cb6bb169026a893bc8dac361e65934}, doi = {10.1186/s40152-016-0049-x}, issn = {18727859}, year = {2016}, date = {2016-01-01}, journal = {Maritime Studies}, volume = {15}, number = {1}, abstract = {Harbours are a focus of intensive and diverse activities and thus have a high potential to become centres of conflict between users. Reviewing the multiple uses associated with harbours provides important insights into maritime communities and the management of conflict. In this paper, seven international, multi-disciplinary groups provide their expert synthesis of individual harbours. After a detailed discussion experts from Sydney, Qingdao, Vigo, Auckland, Jakarta, Crete and Plymouth synthesised and shared their harbour’s characteristics, user conflicts and how such conflicts have been researched and managed. The paper addresses an omission of “conflict” in most of the research literature about harbours, and ports and scopes a research agenda that includes integration, risk appreciation and other approaches to these increasingly contentious maritime environments. This process provided an opportunity for global researchers to share the ways harbour conflicts are mitigated and the kinds of adaptations that are possible. © 2016, Pearson et al.}, note = {Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } Harbours are a focus of intensive and diverse activities and thus have a high potential to become centres of conflict between users. Reviewing the multiple uses associated with harbours provides important insights into maritime communities and the management of conflict. In this paper, seven international, multi-disciplinary groups provide their expert synthesis of individual harbours. After a detailed discussion experts from Sydney, Qingdao, Vigo, Auckland, Jakarta, Crete and Plymouth synthesised and shared their harbour’s characteristics, user conflicts and how such conflicts have been researched and managed. The paper addresses an omission of “conflict” in most of the research literature about harbours, and ports and scopes a research agenda that includes integration, risk appreciation and other approaches to these increasingly contentious maritime environments. This process provided an opportunity for global researchers to share the ways harbour conflicts are mitigated and the kinds of adaptations that are possible. © 2016, Pearson et al. |
Chatzinikolaou, E; Arvanitidis, C Status, values and present threats in Heraklion harbour (Crete, Greece) Journal Article Regional Studies in Marine Science, 8 , pp. 252–258, 2016, ISSN: 23524855, (Publisher: Elsevier B.V.). @article{chatzinikolaou_status_2016, title = {Status, values and present threats in Heraklion harbour (Crete, Greece)}, author = {E Chatzinikolaou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971353979&doi=10.1016%2fj.rsma.2016.01.010&partnerID=40&md5=ad5f3b5d5e0110497b5917341e1194a9}, doi = {10.1016/j.rsma.2016.01.010}, issn = {23524855}, year = {2016}, date = {2016-01-01}, journal = {Regional Studies in Marine Science}, volume = {8}, pages = {252--258}, abstract = {Heraklion harbour is located on the northern coast of Crete and it is one of the most important and active national ports in the Eastern Mediterranean basin. This review aims to provide an insight on the history of the Heraklion harbour, as well as on its current biological, social and economic values and threats. An overview of the present management strategy of the port describing the involved stakeholders, as well as their role in the operation, development, control and conflict solving processes, is provided. © 2016 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Heraklion harbour is located on the northern coast of Crete and it is one of the most important and active national ports in the Eastern Mediterranean basin. This review aims to provide an insight on the history of the Heraklion harbour, as well as on its current biological, social and economic values and threats. An overview of the present management strategy of the port describing the involved stakeholders, as well as their role in the operation, development, control and conflict solving processes, is provided. © 2016 Elsevier B.V. |
2015 |
Pafilis, E; Frankild, S P; Schnetzer, J; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, K; Leary, P; Hammock, J; Schulz, K; Parr, C S; Arvanitidis, C; Jensen, L J ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life Journal Article Bioinformatics, 31 (11), pp. 1872–1874, 2015, ISSN: 13674803, (Publisher: Oxford University Press). @article{pafilis_environments_2015, title = {ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life}, author = {E Pafilis and S P Frankild and J Schnetzer and L Fanini and S Faulwetter and C Pavloudi and K Vasileiadou and P Leary and J Hammock and K Schulz and C S Parr and C Arvanitidis and L J Jensen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941662911&doi=10.1093%2fbioinformatics%2fbtv045&partnerID=40&md5=521c1035d81d477752f37d09c638a7c0}, doi = {10.1093/bioinformatics/btv045}, issn = {13674803}, year = {2015}, date = {2015-01-01}, journal = {Bioinformatics}, volume = {31}, number = {11}, pages = {1872--1874}, abstract = {Summary: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary- based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press. All rights reserved.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Summary: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary- based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press. All rights reserved. |
Faulwetter, S; Papageorgiou, N; Koulouri, P; Fanini, L; Chatzinikolaou, E; Markantonatou, V; Pavloudi, C; Chatzigeorgiou, G; Keklikoglou, K; Vasileiadou, K; Basset, A; Pinna, M; Rosati, I; Reizopoulou, S; Nicolaidou, A; Arvanitidis, C Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons Journal Article Journal of Sea Research, 98 , pp. 73–82, 2015, ISSN: 13851101, (Publisher: Elsevier). @article{faulwetter_resistance_2015, title = {Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons}, author = {S Faulwetter and N Papageorgiou and P Koulouri and L Fanini and E Chatzinikolaou and V Markantonatou and C Pavloudi and G Chatzigeorgiou and K Keklikoglou and K Vasileiadou and A Basset and M Pinna and I Rosati and S Reizopoulou and A Nicolaidou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930278022&doi=10.1016%2fj.seares.2014.09.003&partnerID=40&md5=4f1ebcb9d504ea078f66a78cf0199509}, doi = {10.1016/j.seares.2014.09.003}, issn = {13851101}, year = {2015}, date = {2015-01-01}, journal = {Journal of Sea Research}, volume = {98}, pages = {73--82}, abstract = {The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V.}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V. |
Oulas, A; Pavloudi, C; Polymenakou, P; Pavlopoulos, G A; Papanikolaou, N; Kotoulas, G; Arvanitidis, C; Iliopoulos, I Metagenomics: Tools and insights for analyzing next-generation sequencing data derived from biodiversity studies Journal Article Bioinformatics and Biology Insights, 9 , pp. 75–88, 2015, ISSN: 11779322, (Publisher: Libertas Academica Ltd.). @article{oulas_metagenomics_2015, title = {Metagenomics: Tools and insights for analyzing next-generation sequencing data derived from biodiversity studies}, author = {A Oulas and C Pavloudi and P Polymenakou and G A Pavlopoulos and N Papanikolaou and G Kotoulas and C Arvanitidis and I Iliopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84981483022&doi=10.4137%2fBBI.S12462&partnerID=40&md5=c1dbc4e466d691d4a86eecd6ba7d7a08}, doi = {10.4137/BBI.S12462}, issn = {11779322}, year = {2015}, date = {2015-01-01}, journal = {Bioinformatics and Biology Insights}, volume = {9}, pages = {75--88}, abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards. © the authors.}, note = {Publisher: Libertas Academica Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards. © the authors. |
Queirós, A M; Fernandes, J A; Faulwetter, S; Nunes, J; Rastrick, S P S; Mieszkowska, N; Artioli, Y; Yool, A; Calosi, P; Arvanitidis, C; Findlay, H S; Barange, M; Cheung, W W L; Widdicombe, S Scaling up experimental ocean acidification and warming research: From individuals to the ecosystem Journal Article Global Change Biology, 21 (1), pp. 130–143, 2015, ISSN: 13541013, (Publisher: Blackwell Publishing Ltd). @article{queiros_scaling_2015, title = {Scaling up experimental ocean acidification and warming research: From individuals to the ecosystem}, author = {A M Queirós and J A Fernandes and S Faulwetter and J Nunes and S P S Rastrick and N Mieszkowska and Y Artioli and A Yool and P Calosi and C Arvanitidis and H S Findlay and M Barange and W W L Cheung and S Widdicombe}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84917740783&doi=10.1111%2fgcb.12675&partnerID=40&md5=488e13bba54cb58e2df99bfe384c369b}, doi = {10.1111/gcb.12675}, issn = {13541013}, year = {2015}, date = {2015-01-01}, journal = {Global Change Biology}, volume = {21}, number = {1}, pages = {130--143}, abstract = {Understanding long-term, ecosystem-level impacts of climate change is challenging because experimental research frequently focuses on short-term, individual-level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14-month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual-level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual-level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large-scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local-environmental conditions and resource availability. Such changes in macro-scale distributions cannot be predicted by investigating individual-level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long-term, multiscale responses to multiple stressors, in an ecosystem context. © 2014 John Wiley & Sons Ltd.}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding long-term, ecosystem-level impacts of climate change is challenging because experimental research frequently focuses on short-term, individual-level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14-month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual-level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual-level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large-scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local-environmental conditions and resource availability. Such changes in macro-scale distributions cannot be predicted by investigating individual-level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long-term, multiscale responses to multiple stressors, in an ecosystem context. © 2014 John Wiley & Sons Ltd. |
Herman, P; Warwick, R; Aller, R; Arvanitidis, C; Hewitt, J; Stal, L; Vincx, M Protecting marine biodiversity to preserve ecosystem functioning: A tribute to Carlo Heip Journal Article Journal of Sea Research, 98 , pp. 1–3, 2015, ISSN: 13851101, (Publisher: Elsevier). @article{herman_protecting_2015, title = {Protecting marine biodiversity to preserve ecosystem functioning: A tribute to Carlo Heip}, author = {P Herman and R Warwick and R Aller and C Arvanitidis and J Hewitt and L Stal and M Vincx}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930667750&doi=10.1016%2fj.seares.2015.03.003&partnerID=40&md5=88757845c6fdc22ab499be8ff2b0dab2}, doi = {10.1016/j.seares.2015.03.003}, issn = {13851101}, year = {2015}, date = {2015-01-01}, journal = {Journal of Sea Research}, volume = {98}, pages = {1--3}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
de Jong, Y; Kouwenberg, J; Boumans, L; Hussey, C; Hyam, R; Nicolson, N; Kirk, P; Paton, A; Michel, E; Guiry, M D; Boegh, P S; Pedersen, H; Enghoff, H; von Raab-Straube, E; Güntsch, A; Geoffroy, M; Müller, A; Kohlbecker, A; Berendsohn, W; Appeltans, W; Arvanitidis, C; Vanhoorne, B; Declerck, J; Vandepitte, L; Hernandez, F; Nash, R; Costello, M J; Ouvrard, D; Bezard-Falgas, P; Bourgoin, T; Wetzel, F T; Glöckler, F; Korb, G; Ring, C; Hagedorn, G; Häuser, C; Aktaç, N; Asan, A; Ardelean, A; Borges, P A V; Dhora, D; Khachatryan, H; Malicky, M; Ibrahimov, S; Tuzikov, A; Wever, De A; Moncheva, S; Spassov, N; Chobot, K; Popov, A; Boršic, I; Sfenthourakis, S; Kõljalg, U; Uotila, P; Olivier, G; Dauvin, J -C; Tarkhnishvili, D; Chaladze, G; Tuerkay, M; Legakis, A; Peregovits, L; Gudmundsson, G; ólafsson, E; Lysaght, L; Galil, B S; Raimondo, F M; Domina, G; Stoch, F; Minelli, A; Spungis, V; Budrys, E; Olenin, S; Turpel, A; Walisch, T; Krpach, V; Gambin, M T; Ungureanu, L; Karaman, G; Kleukers, R M J C; Stur, E; Aagaard, K; Valland, N; Moen, T L; Bogdanowicz, W; Tykarski, P; Weslawski, J M; Kedra, M; Martins, A M F; Abreu, A D; Silva, R; Medvedev, S; Ryss, A; Šimic, S; Marhold, K; Stloukal, E; Tome, D; Ramos, M A; Valdés, B; Pina, F; Kullander, S; Telenius, A; Gonseth, Y; Tschudin, P; Sergeyeva, O; Vladymyrov, V; Rizun, V B; Raper, C; Lear, D; Stoev, P; Penev, L; Rubio, A C; Backeljau, T; Saarenmaa, H; Ulenberg, S PESI - A taxonomic backbone for Europe Journal Article Biodiversity Data Journal, 3 (1), 2015, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{de_jong_pesi_2015, title = {PESI - A taxonomic backbone for Europe}, author = {Y de Jong and J Kouwenberg and L Boumans and C Hussey and R Hyam and N Nicolson and P Kirk and A Paton and E Michel and M D Guiry and P S Boegh and H Pedersen and H Enghoff and E von Raab-Straube and A Güntsch and M Geoffroy and A Müller and A Kohlbecker and W Berendsohn and W Appeltans and C Arvanitidis and B Vanhoorne and J Declerck and L Vandepitte and F Hernandez and R Nash and M J Costello and D Ouvrard and P Bezard-Falgas and T Bourgoin and F T Wetzel and F Glöckler and G Korb and C Ring and G Hagedorn and C Häuser and N Aktaç and A Asan and A Ardelean and P A V Borges and D Dhora and H Khachatryan and M Malicky and S Ibrahimov and A Tuzikov and A De Wever and S Moncheva and N Spassov and K Chobot and A Popov and I Boršic and S Sfenthourakis and U Kõljalg and P Uotila and G Olivier and J -C Dauvin and D Tarkhnishvili and G Chaladze and M Tuerkay and A Legakis and L Peregovits and G Gudmundsson and E ólafsson and L Lysaght and B S Galil and F M Raimondo and G Domina and F Stoch and A Minelli and V Spungis and E Budrys and S Olenin and A Turpel and T Walisch and V Krpach and M T Gambin and L Ungureanu and G Karaman and R M J C Kleukers and E Stur and K Aagaard and N Valland and T L Moen and W Bogdanowicz and P Tykarski and J M Weslawski and M Kedra and A M F Martins and A D Abreu and R Silva and S Medvedev and A Ryss and S Šimic and K Marhold and E Stloukal and D Tome and M A Ramos and B Valdés and F Pina and S Kullander and A Telenius and Y Gonseth and P Tschudin and O Sergeyeva and V Vladymyrov and V B Rizun and C Raper and D Lear and P Stoev and L Penev and A C Rubio and T Backeljau and H Saarenmaa and S Ulenberg}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018594265&doi=10.3897%2fBDJ.3.e5848&partnerID=40&md5=db841557b86b31bcf91ce86cac1464d4}, doi = {10.3897/BDJ.3.e5848}, issn = {13142828}, year = {2015}, date = {2015-01-01}, journal = {Biodiversity Data Journal}, volume = {3}, number = {1}, abstract = {Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as highquality and complete taxonomic data sets, but these are generally lacking for nonspecialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. © de Jong Y et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as highquality and complete taxonomic data sets, but these are generally lacking for nonspecialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. © de Jong Y et al. |
Dimitriou, P D; Papageorgiou, N; Arvanitidis, C; Assimakopoulou, G; Pagou, K; Papadopoulou, K N; Pavlidou, A; Pitta, P; Reizopoulou, S; Simboura, N; Karakassis, I One step forward: Benthic pelagic coupling and indicators for environmental status Journal Article PLoS ONE, 10 (10), 2015, ISSN: 19326203, (Publisher: Public Library of Science). @article{dimitriou_one_2015, title = {One step forward: Benthic pelagic coupling and indicators for environmental status}, author = {P D Dimitriou and N Papageorgiou and C Arvanitidis and G Assimakopoulou and K Pagou and K N Papadopoulou and A Pavlidou and P Pitta and S Reizopoulou and N Simboura and I Karakassis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84949921046&doi=10.1371%2fjournal.pone.0141071&partnerID=40&md5=f238a9bc0346925c70e4043d7a101a10}, doi = {10.1371/journal.pone.0141071}, issn = {19326203}, year = {2015}, date = {2015-01-01}, journal = {PLoS ONE}, volume = {10}, number = {10}, abstract = {A large data set from the Eastern Mediterranean was analyzed to explore the relationship between seawater column variables and benthic community status. Our results showed a strong quantitative link between the seawater column variables (Chlorophyll a and Eutrophication Index) and various indicators describing benthic diversity and community composition. The percentage of benthic opportunistic species increased significantly in the stations with high trophic status of the seawater column and so did the strength of the coupling between values of seawater column and benthic indicators. The Eutrophication Index threshold level of 0.85, separating the "Bad and Poor" from "Moderate to High" conditions could serve as an acceptable critical value above which there is a readily observable change in benthic community composition. © 2015 Dimitriou et al.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } A large data set from the Eastern Mediterranean was analyzed to explore the relationship between seawater column variables and benthic community status. Our results showed a strong quantitative link between the seawater column variables (Chlorophyll a and Eutrophication Index) and various indicators describing benthic diversity and community composition. The percentage of benthic opportunistic species increased significantly in the stations with high trophic status of the seawater column and so did the strength of the coupling between values of seawater column and benthic indicators. The Eutrophication Index threshold level of 0.85, separating the "Bad and Poor" from "Moderate to High" conditions could serve as an acceptable critical value above which there is a readily observable change in benthic community composition. © 2015 Dimitriou et al. |
Ruggeri, C; Mandalakis, M; Sergi, S; Bullita, E; Frigau, N; Tamburini, E; Chatzinikolaou, E; Dailianis, T; Arvanitidis, C Characterisation of pollution status and hydrocarbon degraders in seawater of Mediterranean tourist ports Inproceedings 6th European Bioremediation Conference, pp. 596–600, Chania, Crete, Greece, 2015. @inproceedings{ruggeri_characterisation_2015, title = {Characterisation of pollution status and hydrocarbon degraders in seawater of Mediterranean tourist ports}, author = {C Ruggeri and M Mandalakis and S Sergi and E Bullita and N Frigau and E Tamburini and E Chatzinikolaou and T Dailianis and C Arvanitidis}, year = {2015}, date = {2015-01-01}, booktitle = {6th European Bioremediation Conference}, pages = {596--600}, address = {Chania, Crete, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Anastasiou, T; Chatzinikolaou, E; Mandalakis, M; Arvanitidis, C Imposex status and organotin concentrations in Hexaplex trunculus (Linnaeus, 1758) from the port of Cagliari (Sardinia) Inproceedings 11th Panhellenic Symposium on Oceanography and Fisheries, Mytilene, Greece, 2015. @inproceedings{anastasiou_imposex_2015, title = {Imposex status and organotin concentrations in Hexaplex trunculus (Linnaeus, 1758) from the port of Cagliari (Sardinia)}, author = {T Anastasiou and E Chatzinikolaou and M Mandalakis and C Arvanitidis}, year = {2015}, date = {2015-01-01}, booktitle = {11th Panhellenic Symposium on Oceanography and Fisheries}, address = {Mytilene, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Faulwetter, Sarah; Minadakis, N; Keklikoglou, Kleoniki; Doerr, M; Arvanitidis, Christos First steps towards the development of an integrated metadata management system for biodiversity-related micro-CT Inproceedings pp. 149–159, Brugge, Belgium, 2015, (Publication Title: Bruker MicroCT user meeting 2015 Type: Conference Paper). @inproceedings{faulwetter_first_2015, title = {First steps towards the development of an integrated metadata management system for biodiversity-related micro-CT}, author = {Sarah Faulwetter and N Minadakis and Kleoniki Keklikoglou and M Doerr and Christos Arvanitidis}, year = {2015}, date = {2015-01-01}, pages = {149--159}, address = {Brugge, Belgium}, note = {Publication Title: Bruker MicroCT user meeting 2015 Type: Conference Paper}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Koulouri, P; Dounas, C; Arvanitidis, C; Koutsoubas, D; Tselepides, A; Eleftheriou, A A field experiment on trophic relations within the benthic boundary layer (BBL) over an oligotrophic continental shelf Journal Article Estuarine, Coastal and Shelf Science, 164 , pp. 392–407, 2015, ISSN: 02727714, (Publisher: Academic Press). @article{koulouri_field_2015, title = {A field experiment on trophic relations within the benthic boundary layer (BBL) over an oligotrophic continental shelf}, author = {P Koulouri and C Dounas and C Arvanitidis and D Koutsoubas and A Tselepides and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939607766&doi=10.1016%2fj.ecss.2015.07.029&partnerID=40&md5=bd870466fe027569f055b2da46d553de}, doi = {10.1016/j.ecss.2015.07.029}, issn = {02727714}, year = {2015}, date = {2015-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {164}, pages = {392--407}, abstract = {The benthic boundary layer (BBL) macrofauna consists of epibenthic, hyperbenthic and zooplanktonic organisms with different degrees of mobility and bottom dependence. The top-level predators within this habitat include demersal fish species. The BBL species are considered to be the most readily available prey for these fish making them an attractive source of food and therefore key taxa in marine food webs. The present study is a field experiment in the oligotrophic continental shelf of Heraklion Bay (Cretan Sea, eastern Mediterranean) investigating the ways in which demersal fish utilize BBL sources as food. Species diversity patterns derived from samples collected by using a modified hyperbenthic sledge as well as different benthic, hyperbenthic and pelagic samplers are described. These patterns are compared with those derived from stomach content analysis of demersal fish species inhabiting the same area. Results reveal that BBL macrofaunal communities which comprise most of the available prey communities are largely exploited by demersal fish species. Furthermore, the application of different samplers provides complementary information on prey selectivity of macrofaunal organisms by demersal fish species, highlighting further the trophic interactions within the BBL habitat. © 2015 Elsevier Ltd.}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The benthic boundary layer (BBL) macrofauna consists of epibenthic, hyperbenthic and zooplanktonic organisms with different degrees of mobility and bottom dependence. The top-level predators within this habitat include demersal fish species. The BBL species are considered to be the most readily available prey for these fish making them an attractive source of food and therefore key taxa in marine food webs. The present study is a field experiment in the oligotrophic continental shelf of Heraklion Bay (Cretan Sea, eastern Mediterranean) investigating the ways in which demersal fish utilize BBL sources as food. Species diversity patterns derived from samples collected by using a modified hyperbenthic sledge as well as different benthic, hyperbenthic and pelagic samplers are described. These patterns are compared with those derived from stomach content analysis of demersal fish species inhabiting the same area. Results reveal that BBL macrofaunal communities which comprise most of the available prey communities are largely exploited by demersal fish species. Furthermore, the application of different samplers provides complementary information on prey selectivity of macrofaunal organisms by demersal fish species, highlighting further the trophic interactions within the BBL habitat. © 2015 Elsevier Ltd. |
2014 |
Faulwetter, Sarah; Dailianis, Thanos; Vasileiadou, Katerina; Kouratoras, Michail; Arvanitidis, Christos Can micro-CT become an essential tool for the 21st century taxonomist? – an evaluation using marine polychaetes Journal Article Microscopy and Analysis, 28 , pp. 10–13, 2014. @article{faulwetter_can_2014, title = {Can micro-CT become an essential tool for the 21st century taxonomist? – an evaluation using marine polychaetes}, author = {Sarah Faulwetter and Thanos Dailianis and Katerina Vasileiadou and Michail Kouratoras and Christos Arvanitidis}, year = {2014}, date = {2014-02-01}, journal = {Microscopy and Analysis}, volume = {28}, pages = {10--13}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lyons, D; Blight, A; Queirós, A; Somerfield, P; Arvanitidis, Christos; Chatzinikolaou, Eva; Green, D; Guy-Haim, T; Kotta, J; Marchini, A; Paterson, D; Rilov, G; Crowe, T Biological Traits Analysis as an indicator of ecosystem functioning based on biodiversity data Inproceedings Qingdao, China, 2014, (Publication Title: WCMB 2014 - World conference on Marine Biodiversity). @inproceedings{lyons_biological_2014, title = {Biological Traits Analysis as an indicator of ecosystem functioning based on biodiversity data}, author = {D Lyons and A Blight and A Queirós and P Somerfield and Christos Arvanitidis and Eva Chatzinikolaou and D Green and T Guy-Haim and J Kotta and A Marchini and D Paterson and G Rilov and T Crowe}, year = {2014}, date = {2014-01-01}, address = {Qingdao, China}, note = {Publication Title: WCMB 2014 - World conference on Marine Biodiversity}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Lyons, D A; Arvanitidis, C; Blight, A J; Chatzinikolaou, E; Guy-Haim, T; Kotta, J; Orav-Kotta, H; Queirós, A M; Rilov, G; Somerfield, P J; Crowe, T P Macroalgal blooms alter community structure and primary productivity in marine ecosystems Journal Article Global Change Biology, 20 (9), pp. 2712–2724, 2014, ISSN: 13541013, (Publisher: Blackwell Publishing Ltd). @article{lyons_macroalgal_2014, title = {Macroalgal blooms alter community structure and primary productivity in marine ecosystems}, author = {D A Lyons and C Arvanitidis and A J Blight and E Chatzinikolaou and T Guy-Haim and J Kotta and H Orav-Kotta and A M Queirós and G Rilov and P J Somerfield and T P Crowe}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905560282&doi=10.1111%2fgcb.12644&partnerID=40&md5=9934ddec1dece2e4d656f97865ab8fd7}, doi = {10.1111/gcb.12644}, issn = {13541013}, year = {2014}, date = {2014-01-01}, journal = {Global Change Biology}, volume = {20}, number = {9}, pages = {2712--2724}, abstract = {Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programmes. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulphide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta-analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services. © 2014 John Wiley & Sons Ltd.}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programmes. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulphide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta-analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services. © 2014 John Wiley & Sons Ltd. |
Chatzigeorgiou, G; Sarropoulou, E; Vasileiadou, K; Brown, C; Faulwetter, S; Kotoulas, G; Arvanitidis, C D Community structure and population genetics of Eastern Mediterranean polychaetes Journal Article Frontiers in Marine Science, 1 (OCT), 2014, ISSN: 22967745, (Publisher: Frontiers Media S. A). @article{chatzigeorgiou_community_2014, title = {Community structure and population genetics of Eastern Mediterranean polychaetes}, author = {G Chatzigeorgiou and E Sarropoulou and K Vasileiadou and C Brown and S Faulwetter and G Kotoulas and C D Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85008950428&doi=10.3389%2ffmars.2014.00047&partnerID=40&md5=594f48af64289b71d3a629d8968248df}, doi = {10.3389/fmars.2014.00047}, issn = {22967745}, year = {2014}, date = {2014-01-01}, journal = {Frontiers in Marine Science}, volume = {1}, number = {OCT}, abstract = {Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis.}, note = {Publisher: Frontiers Media S. A}, keywords = {}, pubstate = {published}, tppubtype = {article} } Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis. |
Paterson, G L J; Sykes, D; Faulwetter, S; Merk, R; Ahmed, F; Hawkins, L E; Dinley, J; Ball, A D; Arvanitidis, C The pros and cons of using micro-computed tomography in gross and microanatomical assessments of polychaetous annelids Journal Article Memoirs of Museum Victoria, 71 , pp. 237–246, 2014, ISSN: 14472546, (Publisher: Museum Victoria). @article{paterson_pros_2014, title = {The pros and cons of using micro-computed tomography in gross and microanatomical assessments of polychaetous annelids}, author = {G L J Paterson and D Sykes and S Faulwetter and R Merk and F Ahmed and L E Hawkins and J Dinley and A D Ball and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84918829508&doi=10.24199%2fj.mmv.2014.71.18&partnerID=40&md5=43b79d817aad9f02fd9cda20378a02a4}, doi = {10.24199/j.mmv.2014.71.18}, issn = {14472546}, year = {2014}, date = {2014-01-01}, journal = {Memoirs of Museum Victoria}, volume = {71}, pages = {237--246}, abstract = {The use of micro-CT scanners in the study of anatomy and functional morphology of marine invertebrates is becoming more common. The advantages and disadvantages of this methodology for the study of the internal anatomy of polychaetes are discussed. Soft-bodied invertebrates such as polychaetes pose some specific problems. It can be difficult to gain sufficient contrast between different types of tissues to be able to image them with X-rays. A range of stains can help enhance the contrast between tissues. In this study we investigate a number of stains, concentrating on those considered reversible. The advantages of such stains in the study of museum specimens and the resulting possibilities for large-scale comparative morphology studies are outlined. © 2014, Museum Victoria. All rights reserved.}, note = {Publisher: Museum Victoria}, keywords = {}, pubstate = {published}, tppubtype = {article} } The use of micro-CT scanners in the study of anatomy and functional morphology of marine invertebrates is becoming more common. The advantages and disadvantages of this methodology for the study of the internal anatomy of polychaetes are discussed. Soft-bodied invertebrates such as polychaetes pose some specific problems. It can be difficult to gain sufficient contrast between different types of tissues to be able to image them with X-rays. A range of stains can help enhance the contrast between tissues. In this study we investigate a number of stains, concentrating on those considered reversible. The advantages of such stains in the study of museum specimens and the resulting possibilities for large-scale comparative morphology studies are outlined. © 2014, Museum Victoria. All rights reserved. |
David, Romain; Dubois, Sophie; Erga, Zinovia; Guillemain, Dorian; de Ville, Laure Thierry; Arvanitidis, Christos; Çinar, Melih; Sartoretto, Stéphane; Zuberer, Frédéric; Chenuil, Anne; Féral, Jean-Pierre; contributors, With Other; Çinar, Açik S CIGESMED's Protocol And Network (Coralligenous Based Indicators To Evaluate And Monitor The "Good Environmental Status" Of Mediterranean Coastal Waters) Inproceedings Proceedings of the 5th Symposium “Monitoring of Mediterranean coastal areas: problems and measurement techniques”, pp. 1–13, Livorno, 2014. @inproceedings{david_cigesmeds_2014, title = {CIGESMED's Protocol And Network (Coralligenous Based Indicators To Evaluate And Monitor The "Good Environmental Status" Of Mediterranean Coastal Waters)}, author = {Romain David and Sophie Dubois and Zinovia Erga and Dorian Guillemain and Laure Thierry de Ville and Christos Arvanitidis and Melih Çinar and Stéphane Sartoretto and Frédéric Zuberer and Anne Chenuil and Jean-Pierre Féral and With Other contributors and Açik S Çinar}, year = {2014}, date = {2014-01-01}, booktitle = {Proceedings of the 5th Symposium “Monitoring of Mediterranean coastal areas: problems and measurement techniques”}, pages = {1--13}, address = {Livorno}, abstract = {M., Bricout R., Celik C., Chatzigeorgiou G., Chatzinikolaou E., Chenesseau S., Dağli E., Dailianis T., Dimitriadis C., Doğan A., Dounas C., Egea E., Emery E., Evcen A., Faulwetter S., Gatti G., Gerovasileiou V., Güçver S.M., Issaris Y., Katağan T., Keklikoglou K., Kirkim F., Koçak F., Koutsoubas D., Marschal C., Önen M., Önen S., Öztürk B., Panayiotidis P., Pavloudi C., Pergent G., Pergent-Martini C., Poursanidis D., Ravel C., Reizopoulou S., Rocher C., Ruiton S., Salomidi M., Sarropoulou E., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M. Abstract-Coralligenous habitats are part of the most important Mediterranean marine ecosystems in terms of complexity and biodiversity. They provide protection, feeding and reproduction areas for more than 1600 species. This biodiversity is essential for economic activities such as fishing and scuba diving. The European program CIGESMED (ERA-NET funding), involving France, Greece and Turkey, investigates the "Good Environmental Status" of these habitats in the framework of the MFSD (Marine Strategy Framework Directive). One major objective of CIGESMED is to propose an operational, long-term, large-scale protocol to monitor coralligenous habitats in the Mediterranean Sea. This protocol is currently tested in French sites: the effects of (sampling) methods, materials and operators are studied in order to evaluate the influence of protocol implementation, and to find the easiest and most reliable procedure that could be implemented by and for a large public, also consisting of non-scientists, and would provide workable data for long-term monitoring. This protocol is based on photo-quadrats observations. The analyses are done on occurrences, relative abundances, species associations and species' favourite environmental profile. In parallel, complementary protocols are implemented: one concerns the cartography of coralligenous habitats, and two are about population genetics of significant habitat-forming species Myriapora truncata (Pallas, 1766) and Lithophyllum cabiochiae ((Areschoug) Hauck, 1877)). All the data and results are organized as a non-centralized information system, with configurable plugins that can be installed free by all new partners.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } M., Bricout R., Celik C., Chatzigeorgiou G., Chatzinikolaou E., Chenesseau S., Dağli E., Dailianis T., Dimitriadis C., Doğan A., Dounas C., Egea E., Emery E., Evcen A., Faulwetter S., Gatti G., Gerovasileiou V., Güçver S.M., Issaris Y., Katağan T., Keklikoglou K., Kirkim F., Koçak F., Koutsoubas D., Marschal C., Önen M., Önen S., Öztürk B., Panayiotidis P., Pavloudi C., Pergent G., Pergent-Martini C., Poursanidis D., Ravel C., Reizopoulou S., Rocher C., Ruiton S., Salomidi M., Sarropoulou E., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M. Abstract-Coralligenous habitats are part of the most important Mediterranean marine ecosystems in terms of complexity and biodiversity. They provide protection, feeding and reproduction areas for more than 1600 species. This biodiversity is essential for economic activities such as fishing and scuba diving. The European program CIGESMED (ERA-NET funding), involving France, Greece and Turkey, investigates the "Good Environmental Status" of these habitats in the framework of the MFSD (Marine Strategy Framework Directive). One major objective of CIGESMED is to propose an operational, long-term, large-scale protocol to monitor coralligenous habitats in the Mediterranean Sea. This protocol is currently tested in French sites: the effects of (sampling) methods, materials and operators are studied in order to evaluate the influence of protocol implementation, and to find the easiest and most reliable procedure that could be implemented by and for a large public, also consisting of non-scientists, and would provide workable data for long-term monitoring. This protocol is based on photo-quadrats observations. The analyses are done on occurrences, relative abundances, species associations and species' favourite environmental profile. In parallel, complementary protocols are implemented: one concerns the cartography of coralligenous habitats, and two are about population genetics of significant habitat-forming species Myriapora truncata (Pallas, 1766) and Lithophyllum cabiochiae ((Areschoug) Hauck, 1877)). All the data and results are organized as a non-centralized information system, with configurable plugins that can be installed free by all new partners. |
Faulwetter, S; Markantonatou, V; Pavloudi, C; Papageorgiou, N; Keklikoglou, K; Chatzinikolaou, E; Pafilis, E; Chatzigeorgiou, G; Vasileiadou, K; Dailianis, T; Fanini, L; Koulouri, P; Arvanitidis, C Polytraits: A database on biological traits of marine polychaetes Journal Article Biodiversity Data Journal, 2 (1), 2014, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{faulwetter_polytraits_2014, title = {Polytraits: A database on biological traits of marine polychaetes}, author = {S Faulwetter and V Markantonatou and C Pavloudi and N Papageorgiou and K Keklikoglou and E Chatzinikolaou and E Pafilis and G Chatzigeorgiou and K Vasileiadou and T Dailianis and L Fanini and P Koulouri and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018193846&doi=10.3897%2fBDJ.2.e1024&partnerID=40&md5=621b076567d09921bf9b5146a7f8844e}, doi = {10.3897/BDJ.2.e1024}, issn = {13142828}, year = {2014}, date = {2014-01-01}, journal = {Biodiversity Data Journal}, volume = {2}, number = {1}, abstract = {The study of ecosystem functioning - the role which organisms play in an ecosystem - is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The study of ecosystem functioning - the role which organisms play in an ecosystem - is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al. |
Prentiss, N K; Vasileiadou, K; Faulwetter, S; Arvanitidis, C; Hove, Ten H A A new genus and species of Serpulidae (Annelida, Polychaeta, Sabellida) from the Caribbean Sea Journal Article Zootaxa, 3900 (2), pp. 204–222, 2014, ISSN: 11755326, (Publisher: Magnolia Press). @article{prentiss_new_2014, title = {A new genus and species of Serpulidae (Annelida, Polychaeta, Sabellida) from the Caribbean Sea}, author = {N K Prentiss and K Vasileiadou and S Faulwetter and C Arvanitidis and H A Ten Hove}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84919628735&doi=10.11646%2fzootaxa.3900.2.2&partnerID=40&md5=c759f115417f237ae2f185ed2fd4198c}, doi = {10.11646/zootaxa.3900.2.2}, issn = {11755326}, year = {2014}, date = {2014-01-01}, journal = {Zootaxa}, volume = {3900}, number = {2}, pages = {204--222}, abstract = {A new genus and species of Serpulidae (Annelida, Polychaeta) from the Caribbean Sea. Turbocavus secretus (gen. nov. and sp. nov.) is described from shallow hard substrates (0.5-3 m) in wind-sheltered bays of St. John, U.S. Virgin Islands and Curaçao, as well as from diving depths (46-49 m) around Bonaire (Leeward Antilles), Caribbean Sea. The new taxon, which has from 7 to 19 thoracic chaetigers and up to 335 abdominal chaetigers, bears a unique type of thoracic chaeta which is multifolded at the base and continues with a groove tapering to the capillary tip. The new serpulid has unique 18S rRNA sequences and genetic analysis of the 18S rRNA gene situates the new genus at the basis of the serpulid cladogram, well separated from other genera, and close to Filograna/Salmacina and Protula. Copyright © 2014 Magnolia Press.}, note = {Publisher: Magnolia Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new genus and species of Serpulidae (Annelida, Polychaeta) from the Caribbean Sea. Turbocavus secretus (gen. nov. and sp. nov.) is described from shallow hard substrates (0.5-3 m) in wind-sheltered bays of St. John, U.S. Virgin Islands and Curaçao, as well as from diving depths (46-49 m) around Bonaire (Leeward Antilles), Caribbean Sea. The new taxon, which has from 7 to 19 thoracic chaetigers and up to 335 abdominal chaetigers, bears a unique type of thoracic chaeta which is multifolded at the base and continues with a groove tapering to the capillary tip. The new serpulid has unique 18S rRNA sequences and genetic analysis of the 18S rRNA gene situates the new genus at the basis of the serpulid cladogram, well separated from other genera, and close to Filograna/Salmacina and Protula. Copyright © 2014 Magnolia Press. |
2013 |
Hardisty, A; R, David; Alonso, E; Arvanitidis, C; Badia, R M; Basset, A; Blonda, P; Castelli, D; Culham, A; Glockner, F O; Hagedorn, G; de Jong, Y; Konijn, J; Los, W; Manouselis, N; Obst, M; Sierra, S; Wever, De A; Wremp, A -M A call to forge biodiversity links Journal Article Nature, 502 , pp. 171, 2013, (Type: Correspondence/Comment). @article{hardisty_call_2013, title = {A call to forge biodiversity links}, author = {A Hardisty and David R and E Alonso and C Arvanitidis and R M Badia and A Basset and P Blonda and D Castelli and A Culham and F O Glockner and G Hagedorn and Y de Jong and J Konijn and W Los and N Manouselis and M Obst and S Sierra and A De Wever and A -M Wremp}, url = {https://doi.org/10.1038/502171d}, year = {2013}, date = {2013-10-01}, journal = {Nature}, volume = {502}, pages = {171}, note = {Type: Correspondence/Comment}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pafilis, E; Frankild, S; I, Umer; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Schnetzer, J; Vasileiadou, A; Arvanitidis, C; Quince, C; Jensen, L J Identification of Environment Ontology terms in Text and Annotation of Biodiversity (ENVIRONMENTS-EOL) and Genomics (SEQenv) Information Inproceedings Pafilis, E (Ed.): Biodiversity Information Standards TDWG Conference, Florence, Italy, 2013. @inproceedings{pafilis_identification_2013, title = {Identification of Environment Ontology terms in Text and Annotation of Biodiversity (ENVIRONMENTS-EOL) and Genomics (SEQenv) Information}, author = {E Pafilis and S Frankild and Umer I and Lucia Fanini and Sarah Faulwetter and C Pavloudi and J Schnetzer and A Vasileiadou and C Arvanitidis and C Quince and L J Jensen}, editor = {E Pafilis}, year = {2013}, date = {2013-10-01}, booktitle = {Biodiversity Information Standards TDWG Conference, Florence, Italy}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Faulwetter, Sarah; Dailianis, Thanos; Vasileiadou, Aikaterini; Arvanitidis, Christos Contrast enhancing techniques for the application of micro-CT in marine biodiversity studies Journal Article Microscopy and Analysis, 27 (2), pp. S4–S7, 2013. @article{faulwetter_contrast_2013, title = {Contrast enhancing techniques for the application of micro-CT in marine biodiversity studies}, author = {Sarah Faulwetter and Thanos Dailianis and Aikaterini Vasileiadou and Christos Arvanitidis}, url = {http://www.microscopy-analysis.com/sites/default/files/2013_March_Faulwetter.pdf}, year = {2013}, date = {2013-02-01}, journal = {Microscopy and Analysis}, volume = {27}, number = {2}, pages = {S4--S7}, abstract = {X-ray micro-computed tomography holds large potential for zoology and taxonomy in particular. The scanning of soft-bodied invertebrates requires however some form of contrast enhancement to produce useful results. Here, we apply three different methods (tissue staining with iodine and with phosphotungstic acid and drying with hexamethyldisilazane) to three different invertebrates and compare their effects. The effects of each method on different organisms and their advantages and disadvantages are discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } X-ray micro-computed tomography holds large potential for zoology and taxonomy in particular. The scanning of soft-bodied invertebrates requires however some form of contrast enhancement to produce useful results. Here, we apply three different methods (tissue staining with iodine and with phosphotungstic acid and drying with hexamethyldisilazane) to three different invertebrates and compare their effects. The effects of each method on different organisms and their advantages and disadvantages are discussed. |
Faulwetter, S; Vasileiadou, A; Kouratoras, M; Dailianis, T; Arvanitidis, C Micro-computed tomography: Introducing new dimensions to taxonomy Journal Article ZooKeys, 263 , pp. 1–45, 2013, ISSN: 13132989. @article{faulwetter_micro-computed_2013, title = {Micro-computed tomography: Introducing new dimensions to taxonomy}, author = {S Faulwetter and A Vasileiadou and M Kouratoras and T Dailianis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873465745&doi=10.3897%2fzookeys.263.4261&partnerID=40&md5=79eb83ef960d142fc3d30b24f193ab45}, doi = {10.3897/zookeys.263.4261}, issn = {13132989}, year = {2013}, date = {2013-01-01}, journal = {ZooKeys}, volume = {263}, pages = {1--45}, abstract = {Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. © 2013 Sarah Faulwetter.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. © 2013 Sarah Faulwetter. |
Pafilis, E; Frankild, S P; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text Journal Article PLoS ONE, 8 (6), 2013, ISSN: 19326203. @article{pafilis_species_2013, title = {The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text}, author = {E Pafilis and S P Frankild and L Fanini and S Faulwetter and C Pavloudi and A Vasileiadou and C Arvanitidis and L J Jensen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879162734&doi=10.1371%2fjournal.pone.0065390&partnerID=40&md5=fee446181731231a273637d3d09c5002}, doi = {10.1371/journal.pone.0065390}, issn = {19326203}, year = {2013}, date = {2013-01-01}, journal = {PLoS ONE}, volume = {8}, number = {6}, abstract = {The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al. |
Keklikoglou, K; Faulwetter, S; Chatzigeorgiou, G; Badalamenti, F; Spyridon, M; Arvanitidis, C MidMedPol: Polychaetes from midlittoral rocky shores in Greece and Italy (Mediterranean Sea) Journal Article Biodiversity Data Journal, 1 (1), 2013, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{keklikoglou_midmedpol_2013, title = {MidMedPol: Polychaetes from midlittoral rocky shores in Greece and Italy (Mediterranean Sea)}, author = {K Keklikoglou and S Faulwetter and G Chatzigeorgiou and F Badalamenti and M Spyridon and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018193598&doi=10.3897%2fBDJ.1.e961&partnerID=40&md5=92b1136dee2d3ca04e5b69cf49c763c3}, doi = {10.3897/BDJ.1.e961}, issn = {13142828}, year = {2013}, date = {2013-01-01}, journal = {Biodiversity Data Journal}, volume = {1}, number = {1}, abstract = {This paper describes a dataset of polychaetes (Annelida) from 14 midlittoral rocky shore sampling sites in Greece and Italy (Mediterranean Sea). The dataset combines the outcome of four different projects studying the hard substrate midlittoral zone in the Mediterranean between 1984 and 2009. Samples were collected by scraping and collecting the organisms from a framed area. The maximal sampling depth was 1.5 m. In total, 123 polychaete species were recorded, five of which are new records for the respective biogeographic sectors of the Mediterranean. The dataset contains 788 occurrence records, fully annotated with all required metadata. These data contribute to the knowledge of a previously very understudied regional habitat, since at present, comprehensive lists of the midlittoral communities in the Mediterranean are provided through only a few, paper-based, studies. This dataset is one of the first electronic data compilations of the Mediterranean midlittoral zone communities and certainly the most comprehensive of its kind, contributing to the ongoing efforts of the Ocean Biogeographic Information System (OBIS) which aims at filling the gaps in our current knowledge of the world's oceans. It is accessible at http://ipt.vliz.be/resource.do? r=mediterraneanpolychaetaintertidal. © Keklikoglou K et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper describes a dataset of polychaetes (Annelida) from 14 midlittoral rocky shore sampling sites in Greece and Italy (Mediterranean Sea). The dataset combines the outcome of four different projects studying the hard substrate midlittoral zone in the Mediterranean between 1984 and 2009. Samples were collected by scraping and collecting the organisms from a framed area. The maximal sampling depth was 1.5 m. In total, 123 polychaete species were recorded, five of which are new records for the respective biogeographic sectors of the Mediterranean. The dataset contains 788 occurrence records, fully annotated with all required metadata. These data contribute to the knowledge of a previously very understudied regional habitat, since at present, comprehensive lists of the midlittoral communities in the Mediterranean are provided through only a few, paper-based, studies. This dataset is one of the first electronic data compilations of the Mediterranean midlittoral zone communities and certainly the most comprehensive of its kind, contributing to the ongoing efforts of the Ocean Biogeographic Information System (OBIS) which aims at filling the gaps in our current knowledge of the world's oceans. It is accessible at http://ipt.vliz.be/resource.do? r=mediterraneanpolychaetaintertidal. © Keklikoglou K et al. |
Pafilis, E; Pavlopoulos, G A; Satagopam, V P; Papanikolaou, N; Horn, H; Arvanitidis, C; Jensen, L J; Schneider, R; Iliopoulos, I OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction Inproceedings 13th IEEE International Conference on BioInformatics and BioEngineering, IEEE BIBE 2013, 2013, ISBN: 978-1-4799-3163-7. @inproceedings{pafilis_onthefly_2013, title = {OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction}, author = {E Pafilis and G A Pavlopoulos and V P Satagopam and N Papanikolaou and H Horn and C Arvanitidis and L J Jensen and R Schneider and I Iliopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84894224481&doi=10.1109%2fBIBE.2013.6701679&partnerID=40&md5=dd43a25d9b79b4eafa0c9125bc8a1925}, doi = {10.1109/BIBE.2013.6701679}, isbn = {978-1-4799-3163-7}, year = {2013}, date = {2013-01-01}, booktitle = {13th IEEE International Conference on BioInformatics and BioEngineering, IEEE BIBE 2013}, abstract = {Retrieving all of the necessary information from databases about bioentities mentioned in an article is not a trivial or an easy task. Following the daily literature about a specific biological topic and collecting all the necessary information about the bioentities mentioned in the literature manually is tedious and time consuming. OnTheFly 2.0 is a web application mainly designed for non-computer experts which aims to automate data collection and knowledge extraction from biological literature in a user friendly and efficient way. OnTheFly 2.0 is able to extract bioentities from individual articles such as text, Microsoft Word, Excel and PDF files. With a simple drag-and-drop motion, the text of a document is extensively parsed for bioentities such as protein/gene names and chemical compound names. Utilizing high quality data integration platforms, OnTheFly allows the generation of informative summaries, interaction networks and at-a-glance popup windows containing knowledge related to the bioentities found in documents. OnTheFly 2.0 provides a concise application to automate the extraction of bioentities hidden in various documents and is offered as a web based application. It can be found at: http://onthefly.embl.de, http://onthefly.med.uoc.gr or http://onthefly.hcmr.gr. © 2013 IEEE.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Retrieving all of the necessary information from databases about bioentities mentioned in an article is not a trivial or an easy task. Following the daily literature about a specific biological topic and collecting all the necessary information about the bioentities mentioned in the literature manually is tedious and time consuming. OnTheFly 2.0 is a web application mainly designed for non-computer experts which aims to automate data collection and knowledge extraction from biological literature in a user friendly and efficient way. OnTheFly 2.0 is able to extract bioentities from individual articles such as text, Microsoft Word, Excel and PDF files. With a simple drag-and-drop motion, the text of a document is extensively parsed for bioentities such as protein/gene names and chemical compound names. Utilizing high quality data integration platforms, OnTheFly allows the generation of informative summaries, interaction networks and at-a-glance popup windows containing knowledge related to the bioentities found in documents. OnTheFly 2.0 provides a concise application to automate the extraction of bioentities hidden in various documents and is offered as a web based application. It can be found at: http://onthefly.embl.de, http://onthefly.med.uoc.gr or http://onthefly.hcmr.gr. © 2013 IEEE. |
Rossano, C; Gambineri, S; Massi, L; Chatzinikolaou, E; Dafnomili, E; Zivanovic, S; Arvanitidis, C; Scapini, F; Lazzara, L Characterisation of port waters through optical measurements within the MAPMED project Journal Article Biologia Marina Mediterranea, 20 , pp. 220–221, 2013. @article{rossano_characterisation_2013, title = {Characterisation of port waters through optical measurements within the MAPMED project}, author = {C Rossano and S Gambineri and L Massi and E Chatzinikolaou and E Dafnomili and S Zivanovic and C Arvanitidis and F Scapini and L Lazzara}, year = {2013}, date = {2013-01-01}, journal = {Biologia Marina Mediterranea}, volume = {20}, pages = {220--221}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hardisty, A; Roberts, D; Addink, W; Aelterman, B; Agosti, D; Amaral-Zettler, L; Ariño, AH; Arvanitidis, C; Backeljau, T; Bailly, N; Belbin, L; Berendsohn, W; Bertrand, N; Caithness, N; Campbell, D; Cochrane, G; Conruyt, N; Culham, A; Damgaard, C; Davies, N; Fady, B; Faulwetter, Sarah; Feest, A; Field, D; Garnier, E; Geser, G; Gilbert, J; Grosche, B; Grosser, D; Herbinet, B; Hobern, D; Jones, A; de Jong, Y; King, D; Knapp, S; Koivula, H; Los, W; Meyer, C; Morris, RA; Morrison, N; Morse, D; Obst, M; Pafilis, E; Page, LM; Page, R; Pape, T; Parr, C; Paton, A; Patterson, D; Paymal, E; Penev, L; Pollet, M; Pyle, R; von Raab-Straube, E; Robert, V; Robertson, T; Rovellotti, O; Saarenmaa, H; Schalk, P; Schaminee, J; Schofield, P; Sier, A; Sierra, S; Smith, V; van Spronsen, E; Thornthon-Wood, S; van Tienderen, P; van Tol, J; Tuama, É Ó; Uetz, P; Vaas, L; Lebbe, Vignes R; Vision, T; Vu, D; Wever, De A; White, R; Willis, K; Young, F A decadal view of biodiversity informatics: challenges and priorities Journal Article BMC Ecology, 13 , pp. 16, 2013. @article{hardisty_decadal_2013, title = {A decadal view of biodiversity informatics: challenges and priorities}, author = {A Hardisty and D Roberts and W Addink and B Aelterman and D Agosti and L Amaral-Zettler and AH Ariño and C Arvanitidis and T Backeljau and N Bailly and L Belbin and W Berendsohn and N Bertrand and N Caithness and D Campbell and G Cochrane and N Conruyt and A Culham and C Damgaard and N Davies and B Fady and Sarah Faulwetter and A Feest and D Field and E Garnier and G Geser and J Gilbert and B Grosche and D Grosser and B Herbinet and D Hobern and A Jones and Y de Jong and D King and S Knapp and H Koivula and W Los and C Meyer and RA Morris and N Morrison and D Morse and M Obst and E Pafilis and LM Page and R Page and T Pape and C Parr and A Paton and D Patterson and E Paymal and L Penev and M Pollet and R Pyle and E von Raab-Straube and V Robert and T Robertson and O Rovellotti and H Saarenmaa and P Schalk and J Schaminee and P Schofield and A Sier and S Sierra and V Smith and E van Spronsen and S Thornthon-Wood and P van Tienderen and J van Tol and É Ó Tuama and P Uetz and L Vaas and R Vignes Lebbe and T Vision and D Vu and A De Wever and R White and K Willis and F Young}, url = {http://www.biomedcentral.com/1472-6785/13/16}, doi = {10.1186/1472-6785-13-16}, year = {2013}, date = {2013-01-01}, journal = {BMC Ecology}, volume = {13}, pages = {16}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Prentiss, N; Vasileiadou, A; Faulwetter, Sarah; Arvanitidis, C A new serpulid genus, (Polychaeta; Serpulidae) from the Caribbean Inproceedings Sydney, 2013, (Publication Title: 11th International Polychaete Conference Type: Abstract/Poster). @inproceedings{prentiss_new_2013, title = {A new serpulid genus, (Polychaeta; Serpulidae) from the Caribbean}, author = {N Prentiss and A Vasileiadou and Sarah Faulwetter and C Arvanitidis}, url = {https://custom.cvent.com/33FC1B6811EC461DA18796A3281D21F3/files/3f76df8999754bb1a17b584a686c1d0a.pdf}, year = {2013}, date = {2013-01-01}, address = {Sydney}, note = {Publication Title: 11th International Polychaete Conference Type: Abstract/Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Vasileiadou, A; Pavloudi, C; Chatzinikolaou, E; Gonzalez-Wanguemert, M; Tsikopoulou, I; Kotoulas, G; Arvanitidis, C Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems Inproceedings Lisbon (Portugal), 2013, (Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster). @inproceedings{vasileiadou_genetic_2013, title = {Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems}, author = {A Vasileiadou and C Pavloudi and E Chatzinikolaou and M Gonzalez-Wanguemert and I Tsikopoulou and G Kotoulas and C Arvanitidis}, year = {2013}, date = {2013-01-01}, address = {Lisbon (Portugal)}, note = {Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Sykes, D; Hawkins, L; Ahmed, F; Faulwetter, Sarah; Arvanitidis, C; Paterson, G 3D Virtual Histology of Polychaetes Using Micro-CT Journal Article Microscopy and Microanalysis, 19 , pp. 644–645, 2013. @article{sykes_3d_2013, title = {3D Virtual Histology of Polychaetes Using Micro-CT}, author = {D Sykes and L Hawkins and F Ahmed and Sarah Faulwetter and C Arvanitidis and G Paterson}, url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9032095}, doi = {http://dx.doi.org/10.1017/S1431927613005217}, year = {2013}, date = {2013-01-01}, journal = {Microscopy and Microanalysis}, volume = {19}, pages = {644--645}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Paterson, G; Ahmed, F; Faulwetter, Sarah; Ball, A; Dinley, J; Hawkins, L; Sykes, D; Arvanitidis, C Searching for apomorphies: using microCT to investigate pharyngeal anatomy in the Articulata Inproceedings Sydney, Australia, 2013, (Publication Title: 11th International Polychaete Conference Type: Abstract). @inproceedings{paterson_searching_2013, title = {Searching for apomorphies: using microCT to investigate pharyngeal anatomy in the Articulata}, author = {G Paterson and F Ahmed and Sarah Faulwetter and A Ball and J Dinley and L Hawkins and D Sykes and C Arvanitidis}, url = {https://custom.cvent.com/33FC1B6811EC461DA18796A3281D21F3/files/3f76df8999754bb1a17b584a686c1d0a.pdf}, year = {2013}, date = {2013-01-01}, address = {Sydney, Australia}, note = {Publication Title: 11th International Polychaete Conference Type: Abstract}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2012 |
Boyen, C; Heip, C; Cury, P; Baisnée, P-F; Brownlee, C; Tessmar-Raible, K; Allen, I; Arvanitidis, C; Austen, M; Bolhuis, H; Bouget, F-Y; Clark, M; Coll-Montón, M; Crise, A; Dupont, S; Garcon, V; Grigorov, I; Hummel, H; Ianora, A; Kooistra, W; Mariani, P; Möllmann, C; Sköld, Nilsson H; Not, F; Olsen, J; Pinto, Souza I; Queguiner, B; Reygondeau, G; d’Alcala, Ribera M; Santos, Serrão R; Sluijs, A; Soetaert, K; Solidoro, C; Thorndyke, M; Tsigenopoulos, C S; Viard, F; Volckaert, F; textbackslash, J M Węs EuroMarine Research Strategy Report Technical Report 2012, (Publisher: EUROMARINE Project Type: Report). @techreport{boyen_euromarine_2012, title = {EuroMarine Research Strategy Report}, author = {C Boyen and C Heip and P Cury and P-F Baisnée and C Brownlee and K Tessmar-Raible and I Allen and C Arvanitidis and M Austen and H Bolhuis and F-Y Bouget and M Clark and M Coll-Montón and A Crise and S Dupont and V Garcon and I Grigorov and H Hummel and A Ianora and W Kooistra and P Mariani and C Möllmann and H Nilsson Sköld and F Not and J Olsen and I Souza Pinto and B Queguiner and G Reygondeau and M Ribera d’Alcala and R Serrão Santos and A Sluijs and K Soetaert and C Solidoro and M Thorndyke and C S Tsigenopoulos and F Viard and F Volckaert and J M Węs{textbackslash}lawski}, url = {www.euromarineconsortium.eu}, year = {2012}, date = {2012-11-01}, pages = {1--36}, abstract = {EuroMarine is a Coordination and Support Action funded by the European Commission for two years (FP7, 2011-2013). Its aim is the integration of three major European marine FP6 Networks of Excellence (NoE) (Eur-oCEanS, MarBEF and Marine genomics Europe) into one durable organization EuroMarine+, bringing together leading European marine scientists and organizations to create a major internationally competitive network that will facilitate collaboration and promote interdisciplinary approaches in the marine sciences. EuroMarine’s main responsibilities therefore lie, firstly, in the definition of the vision, the specific role and the organizational and operational modes of EuroMarine+, and secondly, in a timely launch of EuroMarine+. One key objective of EuroMarine is, founded on the achievements, conclusions and prospective from each of the three NoEs, to develop a common vision on research priorities and a common research strategy based on a shared vision for the oceans, regional seas and coasts of tomorrow, in order to create a strong marine R&D leadership for Europe based on scientific excellence.}, note = {Publisher: EUROMARINE Project Type: Report}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } EuroMarine is a Coordination and Support Action funded by the European Commission for two years (FP7, 2011-2013). Its aim is the integration of three major European marine FP6 Networks of Excellence (NoE) (Eur-oCEanS, MarBEF and Marine genomics Europe) into one durable organization EuroMarine+, bringing together leading European marine scientists and organizations to create a major internationally competitive network that will facilitate collaboration and promote interdisciplinary approaches in the marine sciences. EuroMarine’s main responsibilities therefore lie, firstly, in the definition of the vision, the specific role and the organizational and operational modes of EuroMarine+, and secondly, in a timely launch of EuroMarine+. One key objective of EuroMarine is, founded on the achievements, conclusions and prospective from each of the three NoEs, to develop a common vision on research priorities and a common research strategy based on a shared vision for the oceans, regional seas and coasts of tomorrow, in order to create a strong marine R&D leadership for Europe based on scientific excellence. |
Pafilis, E; Frankild, S; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J SPECIES: Organism Name Identification in the Scientific Literature Inproceedings Pafilis, E (Ed.): 7th conference of the Hellenic Society for Computational Biology and Bioinformatics, Heraklion, Greece, 2012. @inproceedings{pafilis_species_2012, title = {SPECIES: Organism Name Identification in the Scientific Literature}, author = {E Pafilis and S Frankild and Lucia Fanini and Sarah Faulwetter and C Pavloudi and A Vasileiadou and C Arvanitidis and L J Jensen}, editor = {E Pafilis}, year = {2012}, date = {2012-10-01}, booktitle = {7th conference of the Hellenic Society for Computational Biology and Bioinformatics, Heraklion, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Rice, J; Arvanitidis, C; Borja, A; Frid, C; Hiddink, J G; Krause, J; Lorance, P; Ragnarsson, S A; Sköld, M; Trabucco, B; Enserink, L; Norkko, A Indicators for sea-floor integrity under the european marine strategy framework directive Journal Article Ecological Indicators, 12 (1), pp. 174–184, 2012, ISSN: 1470160X. @article{rice_indicators_2012, title = {Indicators for sea-floor integrity under the european marine strategy framework directive}, author = {J Rice and C Arvanitidis and A Borja and C Frid and J G Hiddink and J Krause and P Lorance and S A Ragnarsson and M Sköld and B Trabucco and L Enserink and A Norkko}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052577426&doi=10.1016%2fj.ecolind.2011.03.021&partnerID=40&md5=7ffb06cbfb690d06f4087a048d235e93}, doi = {10.1016/j.ecolind.2011.03.021}, issn = {1470160X}, year = {2012}, date = {2012-01-01}, journal = {Ecological Indicators}, volume = {12}, number = {1}, pages = {174--184}, abstract = {The European Marine Strategy Framework Directive (MSFD) requires European states to maintain their marine waters in 'Good Environmental Status'. The MSFD includes 11 descriptors of "Good Environmental Status" (GES), including "Sea-floor Integrity". This descriptor is defined as: "Sea-floor integrity is at a level that ensures that the structure and functions of the ecosystems are safeguarded and benthic ecosystems, in particular, are not adversely affected." This contribution briefly summarizes the main conclusions of an international expert group established to review the scientific basis for making this concept operational. The experts concluded that consideration of 8 attributes of the seabed system would provide adequate information to meet requirements of the MSFD: (i) substratum, (ii) bioengineers, (iii) oxygen concentration, (iv) contaminants and hazardous substances, (v) species composition, (vi) size distribution, (vii) trophodynamics and (viii) energy flow and life history traits. The experts further concluded that "Good Environmental Status" cannot be defined exclusively as "pristine Environmental Status", but rather status when impacts of all uses were sustainable. Uses are sustainable if two conditions are met:the pressures associated with those uses do not hinder the ecosystem components to retain their natural diversity, productivity and dynamic ecological processesrecovery from perturbations such that the attributes lie within their range of historical natural variation must be rapid and secure. No single specific suite of indicators is proposed, both because no single set of indicators will meet the needs of all EU countries in all regional seas, and because according to the MSFD indicator selection is the prerogative of individual states. However, the need for conceptual consistency in assessing GES throughout European seas should be served if the selection of indicators and the integration of their information content in assessing GES follow the guidance in the report of the TG on Seafloor Integrity. This guidance is presented here in summary form. Informed by this report European Commission selected as indicators for the Sea-floor Integrity: (i) type, abundance, biomass and areal extent of relevant biogenic substrate; (ii) extent of the seabed significantly affected by human activities for the different substrate types; (iii) presence of particularly sensitive and/or tolerant species; (iv) multi-metric indices assessing benthic community condition and functionality, such as species diversity and richness, proportion of opportunistic to sensitive species; (v) proportion of biomass or number of individuals in the macrobenthos above some specified length/size; and (vi) parameters describing the characteristics (shape, slope and intercept) of the size spectrum of the benthic community.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European Marine Strategy Framework Directive (MSFD) requires European states to maintain their marine waters in 'Good Environmental Status'. The MSFD includes 11 descriptors of "Good Environmental Status" (GES), including "Sea-floor Integrity". This descriptor is defined as: "Sea-floor integrity is at a level that ensures that the structure and functions of the ecosystems are safeguarded and benthic ecosystems, in particular, are not adversely affected." This contribution briefly summarizes the main conclusions of an international expert group established to review the scientific basis for making this concept operational. The experts concluded that consideration of 8 attributes of the seabed system would provide adequate information to meet requirements of the MSFD: (i) substratum, (ii) bioengineers, (iii) oxygen concentration, (iv) contaminants and hazardous substances, (v) species composition, (vi) size distribution, (vii) trophodynamics and (viii) energy flow and life history traits. The experts further concluded that "Good Environmental Status" cannot be defined exclusively as "pristine Environmental Status", but rather status when impacts of all uses were sustainable. Uses are sustainable if two conditions are met:the pressures associated with those uses do not hinder the ecosystem components to retain their natural diversity, productivity and dynamic ecological processesrecovery from perturbations such that the attributes lie within their range of historical natural variation must be rapid and secure. No single specific suite of indicators is proposed, both because no single set of indicators will meet the needs of all EU countries in all regional seas, and because according to the MSFD indicator selection is the prerogative of individual states. However, the need for conceptual consistency in assessing GES throughout European seas should be served if the selection of indicators and the integration of their information content in assessing GES follow the guidance in the report of the TG on Seafloor Integrity. This guidance is presented here in summary form. Informed by this report European Commission selected as indicators for the Sea-floor Integrity: (i) type, abundance, biomass and areal extent of relevant biogenic substrate; (ii) extent of the seabed significantly affected by human activities for the different substrate types; (iii) presence of particularly sensitive and/or tolerant species; (iv) multi-metric indices assessing benthic community condition and functionality, such as species diversity and richness, proportion of opportunistic to sensitive species; (v) proportion of biomass or number of individuals in the macrobenthos above some specified length/size; and (vi) parameters describing the characteristics (shape, slope and intercept) of the size spectrum of the benthic community. |
Chatzigeorgiou, G; Faulwetter, S; López, E; Sardá, R; Arvanitidis, C Hydrobiologia, 691 (1), pp. 147–156, 2012, ISSN: 00188158, (Publisher: Kluwer Academic Publishers). @article{chatzigeorgiou_can_2012, title = {Can coastal biodiversity measured in four Mediterranean sites be representative of the region? A test for the robustness of the NaGISA protocol by using the hard substrate syllid (Annelida, Polychaeta) taxo-communities as a surrogate}, author = {G Chatzigeorgiou and S Faulwetter and E López and R Sardá and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861613722&doi=10.1007%2fs10750-012-1065-5&partnerID=40&md5=43e6bf8958272b946a03e47479809f71}, doi = {10.1007/s10750-012-1065-5}, issn = {00188158}, year = {2012}, date = {2012-01-01}, journal = {Hydrobiologia}, volume = {691}, number = {1}, pages = {147--156}, abstract = {The global NaGISA (Natural Geography in Shore Areas) initiative focusing on long-term monitoring of coastal biodiversity has recently been expanded to the Mediterranean. On the basis of datasets from four Mediterranean hard substrate sites and by using the most abundant polychaete family (Syllidae), two questions are addressed in this study: (a) Is the biodiversity sampled in the two NaGISA sites, based on the family Syllidae, representative of the regional one of the Mediterranean Sea? (b) Are local syllid taxo-communities assembled at random from the regional species pool? Randomisation tests determining to what extent local species lists and their phylogenetic relationships are assembled at random from a regional one showed that at small observational scales (e. g. replicate units, depths) the phylogenetic diversity is assembled at random from the one known to exist locally. It is assumed, therefore, that local processes here have a stronger influence on community assembly than historical-evolutionary processes. The latter is in accordance with previous results derived from using polychaetes to test the same hypotheses at a pan-European level. Local syllid biodiversity in the western Mediterranean is a random subset of the Mediterranean one, whereas that of the NaGISA sites in the eastern Mediterranean is only under certain conditions. Therefore, the currently observed biodiversity of the Mediterranean sites can be considered as representative of that of the entire regional sea only under certain assumptions, as far as the syllid taxo-communities are concerned, demonstrating the potential of the taxon as a surrogate of the polychaete biodiversity. © 2012 Springer Science+Business Media B.V.}, note = {Publisher: Kluwer Academic Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The global NaGISA (Natural Geography in Shore Areas) initiative focusing on long-term monitoring of coastal biodiversity has recently been expanded to the Mediterranean. On the basis of datasets from four Mediterranean hard substrate sites and by using the most abundant polychaete family (Syllidae), two questions are addressed in this study: (a) Is the biodiversity sampled in the two NaGISA sites, based on the family Syllidae, representative of the regional one of the Mediterranean Sea? (b) Are local syllid taxo-communities assembled at random from the regional species pool? Randomisation tests determining to what extent local species lists and their phylogenetic relationships are assembled at random from a regional one showed that at small observational scales (e. g. replicate units, depths) the phylogenetic diversity is assembled at random from the one known to exist locally. It is assumed, therefore, that local processes here have a stronger influence on community assembly than historical-evolutionary processes. The latter is in accordance with previous results derived from using polychaetes to test the same hypotheses at a pan-European level. Local syllid biodiversity in the western Mediterranean is a random subset of the Mediterranean one, whereas that of the NaGISA sites in the eastern Mediterranean is only under certain conditions. Therefore, the currently observed biodiversity of the Mediterranean sites can be considered as representative of that of the entire regional sea only under certain assumptions, as far as the syllid taxo-communities are concerned, demonstrating the potential of the taxon as a surrogate of the polychaete biodiversity. © 2012 Springer Science+Business Media B.V. |
Dimitriou, P D; Apostolaki, E T; Papageorgiou, N; Reizopoulou, S; Simboura, N; Arvanitidis, C; Karakassis, I Meta-analysis of a large data set with Water Framework Directive indicators and calibration of a Benthic Quality Index at the family level Journal Article Ecological Indicators, 20 , pp. 101–107, 2012, ISSN: 1470160X. @article{dimitriou_meta-analysis_2012, title = {Meta-analysis of a large data set with Water Framework Directive indicators and calibration of a Benthic Quality Index at the family level}, author = {P D Dimitriou and E T Apostolaki and N Papageorgiou and S Reizopoulou and N Simboura and C Arvanitidis and I Karakassis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857984350&doi=10.1016%2fj.ecolind.2012.02.008&partnerID=40&md5=e3f8d83cd52772a7dc1b4ab9f5117f2f}, doi = {10.1016/j.ecolind.2012.02.008}, issn = {1470160X}, year = {2012}, date = {2012-01-01}, journal = {Ecological Indicators}, volume = {20}, pages = {101--107}, abstract = {A large data set of marine benthic samples from the Eastern Mediterranean was used to develop Benthic Quality Index (BQI)-family, a new indicator based on the BQI index, which was calibrated by maximizing the consensus with other existing indicators namely BQI, Shannon diversity H', AZTI Marine Biotic Index (AMBI) and BENTIX. The values calculated for the BQI-family indicator are significantly and highly correlated (p textless 0.0001) to those calculated for all the aforementioned indicators and it provides judgment on ecological status close to their average. Furthermore, it combines the strong points of all these methods with the increased reliability, speed and low cost of the identification at higher taxonomic levels. © 2012 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A large data set of marine benthic samples from the Eastern Mediterranean was used to develop Benthic Quality Index (BQI)-family, a new indicator based on the BQI index, which was calibrated by maximizing the consensus with other existing indicators namely BQI, Shannon diversity H', AZTI Marine Biotic Index (AMBI) and BENTIX. The values calculated for the BQI-family indicator are significantly and highly correlated (p textless 0.0001) to those calculated for all the aforementioned indicators and it provides judgment on ecological status close to their average. Furthermore, it combines the strong points of all these methods with the increased reliability, speed and low cost of the identification at higher taxonomic levels. © 2012 Elsevier Ltd. |
Malea, P; Kevrekidis, T; Papageorgiou, N; Mogias, A; Arvanitidis, C Do interrelationships among benthic components mirror disturbance levels? Journal Article Journal of the Marine Biological Association of the United Kingdom, 92 (2), pp. 235–243, 2012, ISSN: 00253154. @article{malea_interrelationships_2012, title = {Do interrelationships among benthic components mirror disturbance levels?}, author = {P Malea and T Kevrekidis and N Papageorgiou and A Mogias and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856701695&doi=10.1017%2fS0025315411001251&partnerID=40&md5=46ca8d2b01371119b3c8bf34660ee12b}, doi = {10.1017/S0025315411001251}, issn = {00253154}, year = {2012}, date = {2012-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {92}, number = {2}, pages = {235--243}, abstract = {The hypothesis tested in this study is that changes in benthic ecosystem components interrelationships may mirror the degree of environmental stress in the Mediterranean coastal lagoons. Multivariate matrices deriving from four benthic components (macrophytes, zoobenthos, epibenthic decapods and demersal fish) from four lagoonal stations along a well-defined disturbance gradient were compared by means of second-stage non-metric multidimensional scaling (MDS). The resulting inter-matrix distances were used as a proxy for the identification of the degree of disturbance. The approach followed is novel in that it uses information from higher levels of the biological organization by taking into account more than a single benthic component, thus representing broad categories of functional groups. The second-stage MDS plots depict differences between inter-component distances in the sampling stations according to the degree of disturbance they experience and the BIOENV analysis demonstrates that certain components are correlated with the environmental variables at a higher degree in the most disturbed stations. © 2011 Marine Biological Association of the United Kingdom.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hypothesis tested in this study is that changes in benthic ecosystem components interrelationships may mirror the degree of environmental stress in the Mediterranean coastal lagoons. Multivariate matrices deriving from four benthic components (macrophytes, zoobenthos, epibenthic decapods and demersal fish) from four lagoonal stations along a well-defined disturbance gradient were compared by means of second-stage non-metric multidimensional scaling (MDS). The resulting inter-matrix distances were used as a proxy for the identification of the degree of disturbance. The approach followed is novel in that it uses information from higher levels of the biological organization by taking into account more than a single benthic component, thus representing broad categories of functional groups. The second-stage MDS plots depict differences between inter-component distances in the sampling stations according to the degree of disturbance they experience and the BIOENV analysis demonstrates that certain components are correlated with the environmental variables at a higher degree in the most disturbed stations. © 2011 Marine Biological Association of the United Kingdom. |
Arvanitidis, C; Basset, A; Herman, H Extending biodiversity theory in the context of Theme 1 of the MarBEF Network of Excellence: final considerations Journal Article Transitional Waters Bulletin, 6 , pp. 50–52, 2012. @article{arvanitidis_extending_2012, title = {Extending biodiversity theory in the context of Theme 1 of the MarBEF Network of Excellence: final considerations}, author = {C Arvanitidis and A Basset and H Herman}, url = {http://siba-ese.unisalento.it/index.php/twb/article/view/12800}, doi = {10.1285/i1825229Xv6n2p50}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, pages = {50--52}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, C S; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, N; Kotoulas, G; Arvanitidis, C Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem Journal Article Transitional Waters Bulletin, 6 , pp. 20–33, 2012. @article{vasileiadou_genetic_2012, title = {Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem}, author = {A Vasileiadou and E Sarropoulou and C S Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and N Simboura and G Kotoulas and C Arvanitidis}, url = {http://siba-ese.unisalento.it/index.php/twb/article/view/12797/11396}, doi = {10.1285/i1825229Xv6n2p20}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, pages = {20--33}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2011 |
Arvanitidis, C; Faulwetter, S; Chatzigeorgiou, G; Penev, L; Bánki, O; Dailianis, T; Pafilis, E; Kouratoras, M; Chatzinikolaou, E; Fanini, L; Vasileiadou, A; Pavloudi, C; Vavilis, P; Koulouri, P; Dounas, C Engaging the broader community in biodiversity research: The concept of the COMBER pilot project for divers in vibrant Journal Article ZooKeys, 150 , pp. 211–229, 2011, ISSN: 13132989. @article{arvanitidis_engaging_2011, title = {Engaging the broader community in biodiversity research: The concept of the COMBER pilot project for divers in vibrant}, author = {C Arvanitidis and S Faulwetter and G Chatzigeorgiou and L Penev and O Bánki and T Dailianis and E Pafilis and M Kouratoras and E Chatzinikolaou and L Fanini and A Vasileiadou and C Pavloudi and P Vavilis and P Koulouri and C Dounas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856457337&doi=10.3897%2fzookeys.150.2149&partnerID=40&md5=48d27ff65c2def3588c3e0f3a8b72a92}, doi = {10.3897/zookeys.150.2149}, issn = {13132989}, year = {2011}, date = {2011-01-01}, journal = {ZooKeys}, volume = {150}, pages = {211--229}, abstract = {This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far. |
Chatzigeorgiou, G; Reizopoulou, S; Maidanou, M; Naletaki, M; Orneraki, E; Apostolaki, E; Arvanitidis, C Estuarine, Coastal and Shelf Science, 94 (1), pp. 111–121, 2011, ISSN: 02727714. @article{chatzigeorgiou_macrobenthic_2011, title = {Macrobenthic community changes due to dystrophic events and freshwater inflow: Changes in space and time in a Mediterranean lagoon (Gialova lagoon, SW Greece)}, author = {G Chatzigeorgiou and S Reizopoulou and M Maidanou and M Naletaki and E Orneraki and E Apostolaki and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960576402&doi=10.1016%2fj.ecss.2011.06.001&partnerID=40&md5=ddb48bc65096f3c8b2c5ea1b7e19081a}, doi = {10.1016/j.ecss.2011.06.001}, issn = {02727714}, year = {2011}, date = {2011-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {94}, number = {1}, pages = {111--121}, abstract = {This paper considers the hypothesis that changes in community structure through the control of the larvae maintenance and of the biological traits of the species mostly contribute to the spatio-temporal community pattern. This is supported by the results of the study, the changes to the macrobenthic community pattern deriving from two sampling periods in Gialova lagoon (SW Greece), carried out on a seasonal basis for two yearly periods: 1994-95 and 1998-99. Cognetti's hypothesis that populations of the tolerant species occupying coastal marine habitats may belong to different species is another alternative hypothesis still to be tested. The importance of alternative management plans aiming at the amelioration of the hydrodynamic conditions of the lagoons and supported by continuous scientific monitoring is highlighted. Two canals bringing fresh water were opened at the beginning of the second sampling period, an intervention among others, suggested by the management plan proposed after the end of the first sampling period. The results show considerable variations in the values of the key environmental variables, for instance long periods with negative Redox potential values, decreased salinity and increased concentrations of the particulate organic matter and of the nutrients. The variables were correlated with the spatio-temporal community pattern, characterized during the second sampling period by: (i) greater dissimilarities among stations/seasons; (ii) disruption of the periodic trend observed on the seasonal scale; (iii) larger relative dissimilarities among the patterns stemming from the macrobenthos and the most abundant groups (polychaetes, molluscs, crustaceans); (iv) significant decrease in abundance or even the disappearance of several marine origin species, along with increased abundance in a few brackish-water species. All of the above changes in the community pattern are considered as early warning signals leading towards degradation, which has not yet been registered in the phylogenetic/taxonomic structure of the macrobenthic community. © 2011 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper considers the hypothesis that changes in community structure through the control of the larvae maintenance and of the biological traits of the species mostly contribute to the spatio-temporal community pattern. This is supported by the results of the study, the changes to the macrobenthic community pattern deriving from two sampling periods in Gialova lagoon (SW Greece), carried out on a seasonal basis for two yearly periods: 1994-95 and 1998-99. Cognetti's hypothesis that populations of the tolerant species occupying coastal marine habitats may belong to different species is another alternative hypothesis still to be tested. The importance of alternative management plans aiming at the amelioration of the hydrodynamic conditions of the lagoons and supported by continuous scientific monitoring is highlighted. Two canals bringing fresh water were opened at the beginning of the second sampling period, an intervention among others, suggested by the management plan proposed after the end of the first sampling period. The results show considerable variations in the values of the key environmental variables, for instance long periods with negative Redox potential values, decreased salinity and increased concentrations of the particulate organic matter and of the nutrients. The variables were correlated with the spatio-temporal community pattern, characterized during the second sampling period by: (i) greater dissimilarities among stations/seasons; (ii) disruption of the periodic trend observed on the seasonal scale; (iii) larger relative dissimilarities among the patterns stemming from the macrobenthos and the most abundant groups (polychaetes, molluscs, crustaceans); (iv) significant decrease in abundance or even the disappearance of several marine origin species, along with increased abundance in a few brackish-water species. All of the above changes in the community pattern are considered as early warning signals leading towards degradation, which has not yet been registered in the phylogenetic/taxonomic structure of the macrobenthic community. © 2011 Elsevier Ltd. |
Faulwetter, S; Chatzigeorgiou, G; Galil, B S; Nicolaidou, A; Arvanitidis, C ZooKeys, 150 , pp. 327–345, 2011, ISSN: 13132989, (Publisher: Pensoft Publishers). @article{faulwetter_sphaerosyllis_2011, title = {Sphaerosyllis levantina sp. n. (annelida) from the Eastern Mediterranean, with notes on character variation in sphaerosyllis hystrix claparède, 1863}, author = {S Faulwetter and G Chatzigeorgiou and B S Galil and A Nicolaidou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856445135&doi=10.3897%2fzookeys.150.1877&partnerID=40&md5=a1014fd41924b680f9bb768edb65107f}, doi = {10.3897/zookeys.150.1877}, issn = {13132989}, year = {2011}, date = {2011-01-01}, journal = {ZooKeys}, volume = {150}, pages = {327--345}, abstract = {Examination of polychaete specimens from Haifa Bay (Israel, eastern Mediterranean Sea) revealed several individuals exhibiting morphological characteristics similar to Sphaerosyllis hystrix Claparede, 1863. A detailed morphometrical analysis of the Israeli specimens in comparison to specimens of S. hystrix and S. boeroi Musco, Cinar & Giangrande, 2005 supported the description of the former as a new species, S. levantina sp. n. Individuals of S. hystrix formed a very heterogeneous group with strong character variations in the analysis and the presumed cosmopolitan distribution of the species is discussed based on literature records. © Sarah Faulwetter et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Examination of polychaete specimens from Haifa Bay (Israel, eastern Mediterranean Sea) revealed several individuals exhibiting morphological characteristics similar to Sphaerosyllis hystrix Claparede, 1863. A detailed morphometrical analysis of the Israeli specimens in comparison to specimens of S. hystrix and S. boeroi Musco, Cinar & Giangrande, 2005 supported the description of the former as a new species, S. levantina sp. n. Individuals of S. hystrix formed a very heterogeneous group with strong character variations in the analysis and the presumed cosmopolitan distribution of the species is discussed based on literature records. © Sarah Faulwetter et al. |
Faulwetter, S; Chatzigeorgiou, G; Galil, B S; Arvanitidis, C ZooKeys, 150 , pp. 281–326, 2011, ISSN: 13132989, (Publisher: Pensoft Publishers). @article{faulwetter_account_2011, title = {An account of the taxonomy and distribution of syllidae (annelida, polychaetes) in the Eastern Mediterranean, with notes on the genus prosphaerosyllis san martín, 1984 in the Mediterranean}, author = {S Faulwetter and G Chatzigeorgiou and B S Galil and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856498145&doi=10.3897%2fzookeys.150.2146&partnerID=40&md5=cd3c298ee3e154f81c6973b083e663bb}, doi = {10.3897/zookeys.150.2146}, issn = {13132989}, year = {2011}, date = {2011-01-01}, journal = {ZooKeys}, volume = {150}, pages = {281--326}, abstract = {The syllid fauna of three locations in Crete and Israel (eastern Mediterranean Sea) was studied, yielding 82 syllid species, many of which were found for the first time in the respective areas: Seventeen species were recorded for the first time on the Israeli coasts and 20 in Greek waters. Perkinsyllis augeneri (Hartmann-Schröder, 1979) and Prosphaerosyllis chauseyensis Olivier et al., 2011 are new records for the Mediterranean Sea. Detailed information is given on the morphology, ecology and distribution of the species recorded for the first time in the studied areas. In addition, an update on the distribution of the genus Prosphaerosyllis San Marti ́n, 1984 in the Mediterranean is given and an identification key to the Mediterranean species is provided. © Sarah Faulwetter et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The syllid fauna of three locations in Crete and Israel (eastern Mediterranean Sea) was studied, yielding 82 syllid species, many of which were found for the first time in the respective areas: Seventeen species were recorded for the first time on the Israeli coasts and 20 in Greek waters. Perkinsyllis augeneri (Hartmann-Schröder, 1979) and Prosphaerosyllis chauseyensis Olivier et al., 2011 are new records for the Mediterranean Sea. Detailed information is given on the morphology, ecology and distribution of the species recorded for the first time in the studied areas. In addition, an update on the distribution of the genus Prosphaerosyllis San Marti ́n, 1984 in the Mediterranean is given and an identification key to the Mediterranean species is provided. © Sarah Faulwetter et al. |
2010 |
Markantonatou, V; Faulwetter, Sarah; Chatzigeorgiou, G; Arvanitidis, C Comparison of taxonomic and functional patterns in Mediterranean transitional waters. An approach with Polychaetes Inproceedings Lecce, Italy, 2010, (Publication Title: 10th International Polychaete Conference Type: Abstract). @inproceedings{markantonatou_comparison_2010, title = {Comparison of taxonomic and functional patterns in Mediterranean transitional waters. An approach with Polychaetes}, author = {V Markantonatou and Sarah Faulwetter and G Chatzigeorgiou and C Arvanitidis}, year = {2010}, date = {2010-01-01}, address = {Lecce, Italy}, note = {Publication Title: 10th International Polychaete Conference Type: Abstract}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Surugiu, V; Revkov, N; Todorova, V; Papageorgiou, N; Valavanis, V; Arvanitidis, C Spatial patterns of biodiversity in the Black Sea: An assessment using benthic polychaetes Journal Article Estuarine, Coastal and Shelf Science, 88 (2), pp. 165–174, 2010, ISSN: 02727714. @article{surugiu_spatial_2010, title = {Spatial patterns of biodiversity in the Black Sea: An assessment using benthic polychaetes}, author = {V Surugiu and N Revkov and V Todorova and N Papageorgiou and V Valavanis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953134052&doi=10.1016%2fj.ecss.2010.03.012&partnerID=40&md5=2a8045e772ea34e57f03e6632f2dd4ad}, doi = {10.1016/j.ecss.2010.03.012}, issn = {02727714}, year = {2010}, date = {2010-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {88}, number = {2}, pages = {165--174}, abstract = {The current study broadens the biodiversity information available for the Black Sea and neighbouring regions and improves our knowledge about the polychaete biogeographic patterns to be discerned in them. There appears to be a well-defined zoogeocline from the Marmara Sea and Bosphorus Strait to the inner parts of the region (Azov Sea), depicted both as a multivariate pattern and in terms of species (or taxa) numbers. The emergent multivariate pattern complies, to a certain extent, with Jakubova's (1935) views: three main sectors can be defined in the basin: (a) Prebosphoric, (b) the Black Sea and, (c) the Azov Sea, whereas the Bosphorus Strait and Marmara Sea show less faunal affinities with the afore-mentioned sectors. Patterns derived both from the cosmopolitan and Atlanto-Mediterranean species closely follow the one coming from the polychaete species and genera inventories. As a general trend, species numbers decrease along with the decrease in salinity towards the inner parts of the region. The trend is homologous to that seen in the benthic invertebrate inventories of all the major European semi-enclosed regional seas. Salinity and food availability appear to be the dominant abiotic factors correlated, though weakly, with the various patterns deriving from the taxonomic/zoogeographic categories. With the exception of the Anatolia, polychaete inventories from all sectors appear to be random samples of the total inventory of the region, in terms of taxonomic distinctness values. Therefore, these sectoral inventories can be used for future biodiversity/environmental impact assessment studies. A massive invasion of Mediterranean species after the opening of the Black Sea, in the lower Quaternary period, appears to be the likely biogeographic mechanism through which the old Sarmatic fauna was almost completely replaced by species of marine origin. © 2010 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The current study broadens the biodiversity information available for the Black Sea and neighbouring regions and improves our knowledge about the polychaete biogeographic patterns to be discerned in them. There appears to be a well-defined zoogeocline from the Marmara Sea and Bosphorus Strait to the inner parts of the region (Azov Sea), depicted both as a multivariate pattern and in terms of species (or taxa) numbers. The emergent multivariate pattern complies, to a certain extent, with Jakubova's (1935) views: three main sectors can be defined in the basin: (a) Prebosphoric, (b) the Black Sea and, (c) the Azov Sea, whereas the Bosphorus Strait and Marmara Sea show less faunal affinities with the afore-mentioned sectors. Patterns derived both from the cosmopolitan and Atlanto-Mediterranean species closely follow the one coming from the polychaete species and genera inventories. As a general trend, species numbers decrease along with the decrease in salinity towards the inner parts of the region. The trend is homologous to that seen in the benthic invertebrate inventories of all the major European semi-enclosed regional seas. Salinity and food availability appear to be the dominant abiotic factors correlated, though weakly, with the various patterns deriving from the taxonomic/zoogeographic categories. With the exception of the Anatolia, polychaete inventories from all sectors appear to be random samples of the total inventory of the region, in terms of taxonomic distinctness values. Therefore, these sectoral inventories can be used for future biodiversity/environmental impact assessment studies. A massive invasion of Mediterranean species after the opening of the Black Sea, in the lower Quaternary period, appears to be the likely biogeographic mechanism through which the old Sarmatic fauna was almost completely replaced by species of marine origin. © 2010 Elsevier Ltd. All rights reserved. |
J, Rice; C, Arvanitidis; A, Borja; C, Frid; J, Hiddink; J, Krause; P, Lorance; SÁ, Ragnarsson; M, Sköld; B, Trabucco Marine Strategy Framework Directive: Task Group 6 Report Technical Report 2010, (ISBN: 978-92-79-15647-2 DOI 10.2788/85484). @techreport{rice_j_marine_2010, title = {Marine Strategy Framework Directive: Task Group 6 Report}, author = {Rice J and Arvanitidis C and Borja A and Frid C and Hiddink J and Krause J and Lorance P and Ragnarsson SÁ and Sköld M and Trabucco B}, url = {http://bookshop.europa.eu/is-bin/INTERSHOP.enfinity/WFS/EU-Bookshop-Site/en_GB/-/EUR/ViewPublication-Start?PublicationKey=LBNA24334}, year = {2010}, date = {2010-01-01}, pages = {73}, note = {ISBN: 978-92-79-15647-2 DOI 10.2788/85484}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } |
2009 |
Arvanitidis, C; Somerfield, P J; Chatzigeorgiou, G; Reizopoulou, S; Kevrekidis, T; Eleftheriou, A Do multivariate analyses incorporating changes in pattern across taxonomic levels reveal anthropogenic stress in Mediterranean lagoons? Journal Article Journal of Experimental Marine Biology and Ecology, 369 (2), pp. 100–109, 2009, ISSN: 00220981. @article{arvanitidis_multivariate_2009, title = {Do multivariate analyses incorporating changes in pattern across taxonomic levels reveal anthropogenic stress in Mediterranean lagoons?}, author = {C Arvanitidis and P J Somerfield and G Chatzigeorgiou and S Reizopoulou and T Kevrekidis and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-59049104828&doi=10.1016%2fj.jembe.2008.10.032&partnerID=40&md5=7f4883979c84fdc6947d5b2b5772aa5c}, doi = {10.1016/j.jembe.2008.10.032}, issn = {00220981}, year = {2009}, date = {2009-01-01}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {369}, number = {2}, pages = {100--109}, abstract = {It is accepted that observed patterns in community structure change as analyses are carried out at higher taxonomic levels. Univariate analyses which incorporate higher taxonomic structure within assemblages have been shown to be informative. In this paper we suggest ways in which changes in multivariate relationships at higher taxonomic levels and associated with higher taxonomic/phylogenetic structure of the community may be incorporated into multivariate analyses, an aspect never occurred before in this type of analysis. Four approaches, namely: biodiversity MDS (bdMDS), number of taxa MDS (ntMDS), delta MDS (δMDS) and lambda MDS (λMDS), are proposed, and applied to theoretical data as well as to data collected from the literature on the Mediterranean lagoonal environment. Results show that these approaches have the capacity to distinguish severely impacted lagoons from naturally disturbed ones, although in practice the simplest method (ntMDS) was the most successful. Analyses based on the most abundant groups (polychaetes, molluscs, crustaceans) did not always match analyses based on the entire macrofauna, mirroring the performance of taxonomic distinctness indices in the Mediterranean lagoons. The important characteristics of the approaches introduced, as well as potential criticisms are provided. Application of these techniques on smaller scales and to other habitats, is suggested prior to their wider use in the region. © 2008 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It is accepted that observed patterns in community structure change as analyses are carried out at higher taxonomic levels. Univariate analyses which incorporate higher taxonomic structure within assemblages have been shown to be informative. In this paper we suggest ways in which changes in multivariate relationships at higher taxonomic levels and associated with higher taxonomic/phylogenetic structure of the community may be incorporated into multivariate analyses, an aspect never occurred before in this type of analysis. Four approaches, namely: biodiversity MDS (bdMDS), number of taxa MDS (ntMDS), delta MDS (δMDS) and lambda MDS (λMDS), are proposed, and applied to theoretical data as well as to data collected from the literature on the Mediterranean lagoonal environment. Results show that these approaches have the capacity to distinguish severely impacted lagoons from naturally disturbed ones, although in practice the simplest method (ntMDS) was the most successful. Analyses based on the most abundant groups (polychaetes, molluscs, crustaceans) did not always match analyses based on the entire macrofauna, mirroring the performance of taxonomic distinctness indices in the Mediterranean lagoons. The important characteristics of the approaches introduced, as well as potential criticisms are provided. Application of these techniques on smaller scales and to other habitats, is suggested prior to their wider use in the region. © 2008 Elsevier B.V. All rights reserved. |
Arvanitidis, C; Somerfield, P J; Rumohr, H; Faulwetter, S; Valavanis, V; Vasileiadou, A; Chatzigeorgiou, G; Berghe, Vanden E; Vanaverbeke, J; Labrune, C; Grémare, A; Zettler, M L; Kȩdra, M; Włodarska-Kowalczuk, M; Aleffi, I F; Amouroux, J M; Anisimova, N; Bachelet, G; Büntzow, M; Cochrane, S J; Costello, M J; Craeymeersch, J; Dahle, S; Degraer, S; Denisenko, S; Dounas, C; Duineveld, G; Emblow, C; Escavarage, V; Fabri, M C; Fleischer, D; Gray, J S; Heip, C H R; Herrmann, M; Hummel, H; Janas, U; Karakassis, I; Kendall, M A; Kingston, P; Kotwicki, L; Laudien, J; Mackie, A S Y; Nevrova, E L; Occhipinti-Ambrogi, A; Oliver, P G; Olsgard, F; Palerud, R; Petrov, A; Rachor, E; Revkov, N K; Rose, A; Sardá, R; Sistermans, W C H; Speybroeck, J; Hoey, Van G; Vincx, M; Whomersley, P; Willems, W; Zenetos, A Biological geography of the European seas: Results from the MacroBen database Journal Article Marine Ecology Progress Series, 382 , pp. 265–278, 2009, ISSN: 01718630. @article{arvanitidis_biological_2009, title = {Biological geography of the European seas: Results from the MacroBen database}, author = {C Arvanitidis and P J Somerfield and H Rumohr and S Faulwetter and V Valavanis and A Vasileiadou and G Chatzigeorgiou and E Vanden Berghe and J Vanaverbeke and C Labrune and A Grémare and M L Zettler and M Kȩdra and M Włodarska-Kowalczuk and I F Aleffi and J M Amouroux and N Anisimova and G Bachelet and M Büntzow and S J Cochrane and M J Costello and J Craeymeersch and S Dahle and S Degraer and S Denisenko and C Dounas and G Duineveld and C Emblow and V Escavarage and M C Fabri and D Fleischer and J S Gray and C H R Heip and M Herrmann and H Hummel and U Janas and I Karakassis and M A Kendall and P Kingston and L Kotwicki and J Laudien and A S Y Mackie and E L Nevrova and A Occhipinti-Ambrogi and P G Oliver and F Olsgard and R Palerud and A Petrov and E Rachor and N K Revkov and A Rose and R Sardá and W C H Sistermans and J Speybroeck and G Van Hoey and M Vincx and P Whomersley and W Willems and A Zenetos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649133743&doi=10.3354%2fmeps07955&partnerID=40&md5=b494b7aad3e4476e31b82b871b6c26e6}, doi = {10.3354/meps07955}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {265--278}, abstract = {This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipun-culans and the last 5 groups combined. In order to test the discriminating power of these groups, 3 criteria were used: (1) proximity, which refers to the expected closer faunal resemblance of adjacent areas relative to more distant ones; (2) randomness, which in the present context is a measure of the degree to which the inventories of the various sectors, provinces or regions may in each case be considered as a random sample of the inventory of the next largest province or region in a hierarchy of geographic scales; and (3) differentiation, which provides a measure of the uniqueness of the pattern. Results show that only polychaetes fulfill all 3 criteria and that the only marine biogeographic system supported by the analyses is the one proposed by Longhurst (1998). Energy fluxes and other interactions between the planktonic and benthic domains, acting over evolutionary time scales, can be associated with the multivariate pattern derived from the macrobenthos datasets. Third-stage multidimensional scaling ordination reveals that polychaetes produce a unique pattern when all systems are under consideration. Average island distance from the nearest coast, number of islands and the island surface area were the geographic variables best correlated with the community patterns produced by polychaetes. Biogeographic patterns suggest a vicariance model dominating over the founder-dispersal model except for the semi-closed regional seas, where a model substantially modified from the second option could be supported. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipun-culans and the last 5 groups combined. In order to test the discriminating power of these groups, 3 criteria were used: (1) proximity, which refers to the expected closer faunal resemblance of adjacent areas relative to more distant ones; (2) randomness, which in the present context is a measure of the degree to which the inventories of the various sectors, provinces or regions may in each case be considered as a random sample of the inventory of the next largest province or region in a hierarchy of geographic scales; and (3) differentiation, which provides a measure of the uniqueness of the pattern. Results show that only polychaetes fulfill all 3 criteria and that the only marine biogeographic system supported by the analyses is the one proposed by Longhurst (1998). Energy fluxes and other interactions between the planktonic and benthic domains, acting over evolutionary time scales, can be associated with the multivariate pattern derived from the macrobenthos datasets. Third-stage multidimensional scaling ordination reveals that polychaetes produce a unique pattern when all systems are under consideration. Average island distance from the nearest coast, number of islands and the island surface area were the geographic variables best correlated with the community patterns produced by polychaetes. Biogeographic patterns suggest a vicariance model dominating over the founder-dispersal model except for the semi-closed regional seas, where a model substantially modified from the second option could be supported. © Inter-Research 2009. |
Berghe, Vanden E; Claus, S; Appeltans, W; Faulwetter, S; Arvanitidis, C; Somerfield, P J; Aleffi, I F; Amouroux, J M; Anisimova, N; Bachelet, G; Cochrane, S J; Costello, M J; Craeymeersch, J; Dahle, S; Degraer, S; Denisenko, S; Dounas, C; Duineveld, G; Emblow, C; Escaravage, V; Fabri, M C; Fleischer, D; Grémare, A; Herrmann, M; Hummel, H; Karakassis, I; Kȩdra, M; Kendall, M A; Kingston, P; Kotwicki, L; Labrune, C; Laudien, J; Nevrova, E L; Occhipinti-Ambrogi, A; Olsgard, F; Palerud, R; Petrov, A; Rachor, E; Revkov, N; Rumohr, H; Sardá, R; Sistermans, W C H; Speybroeck, J; Janas, U; Hoey, Van G; Vincx, M; Whomersley, P; Willems, W; Włodarska-Kowalczuk, M; Zenetos, A; Zettler, M L; Heip, C H R MacroBen integrated database on benthic invertebrates of European continental shelves: A tool for large-scale analysis across Europe Journal Article Marine Ecology Progress Series, 382 , pp. 225–238, 2009, ISSN: 01718630. @article{vanden_berghe_macroben_2009, title = {MacroBen integrated database on benthic invertebrates of European continental shelves: A tool for large-scale analysis across Europe}, author = {E Vanden Berghe and S Claus and W Appeltans and S Faulwetter and C Arvanitidis and P J Somerfield and I F Aleffi and J M Amouroux and N Anisimova and G Bachelet and S J Cochrane and M J Costello and J Craeymeersch and S Dahle and S Degraer and S Denisenko and C Dounas and G Duineveld and C Emblow and V Escaravage and M C Fabri and D Fleischer and A Grémare and M Herrmann and H Hummel and I Karakassis and M Kȩdra and M A Kendall and P Kingston and L Kotwicki and C Labrune and J Laudien and E L Nevrova and A Occhipinti-Ambrogi and F Olsgard and R Palerud and A Petrov and E Rachor and N Revkov and H Rumohr and R Sardá and W C H Sistermans and J Speybroeck and U Janas and G Van Hoey and M Vincx and P Whomersley and W Willems and M Włodarska-Kowalczuk and A Zenetos and M L Zettler and C H R Heip}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649129962&doi=10.3354%2fmeps07826&partnerID=40&md5=f1bf83439047ae44d644ea4aafa672e9}, doi = {10.3354/meps07826}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {225--238}, abstract = {We describe an integrated database on European macrobenthic fauna, developed within the framework of the European Network of Excellence MarBEF, and the data and data integration exercise that provided its content. A total of 44 datasets including 465 354 distribution records from soft-bottom macrobenthic species were uploaded into the relational MacroBen database, corresponding to 22 897 sampled stations from all European seas, and 7203 valid taxa. All taxonomic names were linked to the European Register of Marine Species, which was used as the taxonomic reference to standardise spelling and harmonise synonymy. An interface was created, allowing the user to explore, subselect, export and analyse the data by calculating different indices. Although the sampling techniques and intended use of the datasets varied tremendously, the integrated database proved to be robust, and an important tool for studying and understanding large-scale long-term distributions and abundances of marine benthic life. Crucial in the process was the willingness and the positive data-sharing attitude of the different data contributors. Development of a data policy that is highly aware of sensitivities and ownership issues of data providers was essential in the creation of this goodwill. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We describe an integrated database on European macrobenthic fauna, developed within the framework of the European Network of Excellence MarBEF, and the data and data integration exercise that provided its content. A total of 44 datasets including 465 354 distribution records from soft-bottom macrobenthic species were uploaded into the relational MacroBen database, corresponding to 22 897 sampled stations from all European seas, and 7203 valid taxa. All taxonomic names were linked to the European Register of Marine Species, which was used as the taxonomic reference to standardise spelling and harmonise synonymy. An interface was created, allowing the user to explore, subselect, export and analyse the data by calculating different indices. Although the sampling techniques and intended use of the datasets varied tremendously, the integrated database proved to be robust, and an important tool for studying and understanding large-scale long-term distributions and abundances of marine benthic life. Crucial in the process was the willingness and the positive data-sharing attitude of the different data contributors. Development of a data policy that is highly aware of sensitivities and ownership issues of data providers was essential in the creation of this goodwill. © Inter-Research 2009. |
Somerfield, P J; Arvanitidis, C; Berghe, Vanden E; Avesaath, Van P; Hummel, H; Heip, C H R MarBEF, databases, and the legacy of John Gray Journal Article Marine Ecology Progress Series, 382 , pp. 221–224, 2009, ISSN: 01718630. @article{somerfield_marbef_2009, title = {MarBEF, databases, and the legacy of John Gray}, author = {P J Somerfield and C Arvanitidis and E Vanden Berghe and P Van Avesaath and H Hummel and C H R Heip}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649112253&doi=10.3354%2fmeps08045&partnerID=40&md5=b69d7fd473e83cb1dc103300cdd33b3e}, doi = {10.3354/meps08045}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {221--224}, abstract = {Within the European Network of Excellence (NoE) on Marine Biodiversity and Ecosystem Functioning (MarBEF), marine biodiversity scientists from across Europe have been brought together to focus on 3 broad themes. Theme 1 describes large-scale (and long-term) distribution patterns of marine biodiversity, Theme 2 examines the consequences of changes in marine biodiversity for the functioning of marine ecosystems, and Theme 3 explores and disseminates the socio-economic consequences of changes in marine biodiversity and biodiversity-mediated processes. Within MarBEF Theme 1, a large collaborative effort has produced an integrated database of species occurrence information (MacroBen), which contains data of quantitative samples of soft-sediment benthic infauna collected in European continental waters, from the Arctic to the Black Sea. Papers in this Theme Section describe initial studies based on the database. The late Prof. John S. Gray led activities within MarBEF Theme 1 for the first 2.5 yr, during which time the majority of the work described in this Theme Section was set in motion, and he continued to be involved in the work until his untimely death. We dedicate this body of work to his memory. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Within the European Network of Excellence (NoE) on Marine Biodiversity and Ecosystem Functioning (MarBEF), marine biodiversity scientists from across Europe have been brought together to focus on 3 broad themes. Theme 1 describes large-scale (and long-term) distribution patterns of marine biodiversity, Theme 2 examines the consequences of changes in marine biodiversity for the functioning of marine ecosystems, and Theme 3 explores and disseminates the socio-economic consequences of changes in marine biodiversity and biodiversity-mediated processes. Within MarBEF Theme 1, a large collaborative effort has produced an integrated database of species occurrence information (MacroBen), which contains data of quantitative samples of soft-sediment benthic infauna collected in European continental waters, from the Arctic to the Black Sea. Papers in this Theme Section describe initial studies based on the database. The late Prof. John S. Gray led activities within MarBEF Theme 1 for the first 2.5 yr, during which time the majority of the work described in this Theme Section was set in motion, and he continued to be involved in the work until his untimely death. We dedicate this body of work to his memory. © Inter-Research 2009. |
C, Heip; H, Hummel; van P, Avesaath; W, Appeltans; C, Arvanitidis; R, Aspden; M, Austen; F, Boero; TJ, Bouma; G, Boxshall; F, Buchholz; T, Crowe; A, Delaney; T, Deprez; C, Emblow; JP, Feral; JM, Gasol; A, Gooday; J, Harder; A, Ianora; A, Kraberg; B, Mackenzie; H, Ojaveer; D, Paterson; H, Rumohr; D, Schiedek; A, Sokolowski; P, Somerfield; I, Sousa Pinto; M, Vincx; textbackslash, Węs; R, Nash Marine Biodiversity and Ecosystem Functioning Technical Report 2009, (ISBN: 2009-2539). @techreport{heip_c_marine_2009, title = {Marine Biodiversity and Ecosystem Functioning}, author = {Heip C and Hummel H and Avesaath van P and Appeltans W and Arvanitidis C and Aspden R and Austen M and Boero F and Bouma TJ and Boxshall G and Buchholz F and Crowe T and Delaney A and Deprez T and Emblow C and Feral JP and Gasol JM and Gooday A and Harder J and Ianora A and Kraberg A and Mackenzie B and Ojaveer H and Paterson D and Rumohr H and Schiedek D and Sokolowski A and Somerfield P and Sousa Pinto I and Vincx M and Węs textbackslash and Nash R}, year = {2009}, date = {2009-01-01}, pages = {100 pp}, note = {ISBN: 2009-2539}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } |
Somerfield, P J; Arvanitidis, C; Faulwetter, S; Chatzigeorgiou, G; Vasileiadou, A; Amouroux, J M; Anisimova, N; Cochrane, S J; Craeymeersch, J; Dahle, S; Denisenko, S; Dounas, K; Duineveld, G; Grémare, A; Heip, C H R; Herrmann, M; Karakassis, I; Kȩdra, M; Kendall, M A; Kingston, P; Kotwicki, L; Labrune, C; Laudien, J; Nevrova, H; Nicolaidou, A; Occhipinti-Ambrogi, A; Palerud, R; Petrov, A; Rachor, E; Revkov, N; Rumohr, H; Sardá, R; Janas, U; Berghe, Vanden E; Włodarska-Kowalczuk, M Assessing evidence for random assembly of marine benthic communities from regional species pools Journal Article Marine Ecology Progress Series, 382 , pp. 279–286, 2009, ISSN: 01718630. @article{somerfield_assessing_2009, title = {Assessing evidence for random assembly of marine benthic communities from regional species pools}, author = {P J Somerfield and C Arvanitidis and S Faulwetter and G Chatzigeorgiou and A Vasileiadou and J M Amouroux and N Anisimova and S J Cochrane and J Craeymeersch and S Dahle and S Denisenko and K Dounas and G Duineveld and A Grémare and C H R Heip and M Herrmann and I Karakassis and M Kȩdra and M A Kendall and P Kingston and L Kotwicki and C Labrune and J Laudien and H Nevrova and A Nicolaidou and A Occhipinti-Ambrogi and R Palerud and A Petrov and E Rachor and N Revkov and H Rumohr and R Sardá and U Janas and E Vanden Berghe and M Włodarska-Kowalczuk}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649136488&doi=10.3354%2fmeps07934&partnerID=40&md5=dcce15cc6eb45417bba0ef6f162fb1df}, doi = {10.3354/meps07934}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {279--286}, abstract = {Local species diversity may be determined by processes operating locally, such as disturbance, predation and competition, or by regional processes, such as environmental structuring or history. Classical theory focusing on competition predicts that the species combining to form communities will be less similar to each other than they would be if they were assembled at random from a regional species pool. Theory focusing on environmental structuring predicts that species will be more similar to each other than expected by chance. A randomisation test that determines the extent to which local species lists represent random selections from a regional list, based on the average relatedness between species, was applied to data held in the MacroBen database. Little or no evidence was found for species lists of whole faunas at any scale being random subsets of species lists at larger scales. Species tend to be more closely related to each other than would be expected if they were assembled at random. Thus marine soft-sediment macrofauna are not locally assembled at random from regional species pools and it is likely that regional processes determine the assembly of communities. Focusing on the most abundant class within the macrofauna, a different pattern emerges, in that there is a much stronger tendency for local polychaete composition to be a random subset from regional pools at all scales. Thus it is not possible to determine whether local polychaete diversity is independent of both local and regional processes, or determined by a combination of both acting antagonistically. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Local species diversity may be determined by processes operating locally, such as disturbance, predation and competition, or by regional processes, such as environmental structuring or history. Classical theory focusing on competition predicts that the species combining to form communities will be less similar to each other than they would be if they were assembled at random from a regional species pool. Theory focusing on environmental structuring predicts that species will be more similar to each other than expected by chance. A randomisation test that determines the extent to which local species lists represent random selections from a regional list, based on the average relatedness between species, was applied to data held in the MacroBen database. Little or no evidence was found for species lists of whole faunas at any scale being random subsets of species lists at larger scales. Species tend to be more closely related to each other than would be expected if they were assembled at random. Thus marine soft-sediment macrofauna are not locally assembled at random from regional species pools and it is likely that regional processes determine the assembly of communities. Focusing on the most abundant class within the macrofauna, a different pattern emerges, in that there is a much stronger tendency for local polychaete composition to be a random subset from regional pools at all scales. Thus it is not possible to determine whether local polychaete diversity is independent of both local and regional processes, or determined by a combination of both acting antagonistically. © Inter-Research 2009. |
2008 |
Faulwetter, S; Vasileiadou, A; Papageorgiou, N; Arvanitidis, C Zootaxa, (1847), pp. 1–18, 2008, ISSN: 11755326. @article{faulwetter_description_2008, title = {Description of a new species of Streptosyllis (Polychaeta: Syllidae) from the Mediterranean and Canary Islands with a re-description of Streptosyllis arenae and comments on the taxonomy of Streptosyllis and some morphologically similar genera}, author = {S Faulwetter and A Vasileiadou and N Papageorgiou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-49949102313&partnerID=40&md5=b42a78644d6b92d3f2632c2d783a2b69}, issn = {11755326}, year = {2008}, date = {2008-01-01}, journal = {Zootaxa}, number = {1847}, pages = {1--18}, abstract = {A new Streptosyllis species, S. nunezi n. sp., is described from shallow sandy substrates in the Mediterranean and the Canary Islands. The new species is distinguished by a unique combination of characters: teeth of the shafts of the compound chaetae covered by hyaline hood; 1-2 lateral tips formed by the hyaline hood covering the blades of the compound chaetae; strongly serrated dorsal simple chaetae which appear as 2-4 robust teeth when viewed laterally. The re-description of its closest congener, the type species S. arenae Webster and Benedict, 1884, is also provided based on the type material, as well as a key to the currently valid species and table of characters for the genus. Finally, some comments are made for the characters distinguishing the genera Streptosyllis, Syllides, Anoplosyllis, Astreptosyllis and Streptospinigera, which are listed in a table and a potential key for their identification is proposed. Copyright © 2008 Magnolia Press.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new Streptosyllis species, S. nunezi n. sp., is described from shallow sandy substrates in the Mediterranean and the Canary Islands. The new species is distinguished by a unique combination of characters: teeth of the shafts of the compound chaetae covered by hyaline hood; 1-2 lateral tips formed by the hyaline hood covering the blades of the compound chaetae; strongly serrated dorsal simple chaetae which appear as 2-4 robust teeth when viewed laterally. The re-description of its closest congener, the type species S. arenae Webster and Benedict, 1884, is also provided based on the type material, as well as a key to the currently valid species and table of characters for the genus. Finally, some comments are made for the characters distinguishing the genera Streptosyllis, Syllides, Anoplosyllis, Astreptosyllis and Streptospinigera, which are listed in a table and a potential key for their identification is proposed. Copyright © 2008 Magnolia Press. |
Faulwetter, S; Gotsis, P; Reizopoulou, S; Orfanidis, S; Kevrekidis, T; Nicolaidou, A; Simboura, N; Malea, P; Dounas, C; Mogias, A; Valavanis, V; Arvanitidis, C Aquatic Conservation: Marine and Freshwater Ecosystems, 18 (SUPPL. 1), pp. S135–S142, 2008, ISSN: 10527613. @article{faulwetter_elnet_2008, title = {ElNet: The Greek biodiversity transitional waters information system. An exemplar for the development of distributed information networks in Europe}, author = {S Faulwetter and P Gotsis and S Reizopoulou and S Orfanidis and T Kevrekidis and A Nicolaidou and N Simboura and P Malea and C Dounas and A Mogias and V Valavanis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-51649091896&doi=10.1002%2faqc.950&partnerID=40&md5=915c8d6c7967b0b89bcc42cd20a019b7}, doi = {10.1002/aqc.950}, issn = {10527613}, year = {2008}, date = {2008-01-01}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, volume = {18}, number = {SUPPL. 1}, pages = {S135--S142}, abstract = {1. Transitional waters are ecosystems of special importance for a number of reasons and require effective management. In Greece, biodiversity and environmental data that help to manage these ecosystems do exist, although they are scattered and not easily accessible. An overarching, publicly accessible system combining all kinds of information has not been available until now. 2. The ElNet system was developed to serve these requirements. The system is a functional application consisting of a comprehensive database and an online interface with an interactive map, and search capabilities for biological and environmental data on Greek transitional waters. Nine datasets have already been integrated and are available online. Data and their metadata are documented and checked for quality to allow comparisons and reduce bias in resulting analyses. 3. The data assembled cover a broad geographical and temporal range, allowing large-scale analyses of transitional waters. These in turn produce new scientific knowledge and provide a sound basis of information for scientists, environmental managers and policy-makers. 4. Examination of the data revealed an overall insufficient quality control practice during data acquisition and digitization. A good data management and archive system can significantly improve the quality of data. To encourage scientists to submit their data to a data management centre, a clear data policy document regulating rights and duties could form an incentive for data sharing. 5. Results from a case study carried out on the macrobenthic inventories of the lagoonal systems included in the system demonstrate the potential use of this simple type of information by environmental managers and scientists. 6. The system, still in its initial phase, will be improved by integrating new datasets and developing tools for data retrieval and analyses. The database will be linked to other biodiversity databases to participate in a distributed information network and disseminate the information through other global biodiversity portals. Copyright © 2008 John Wiley & Sons, Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 1. Transitional waters are ecosystems of special importance for a number of reasons and require effective management. In Greece, biodiversity and environmental data that help to manage these ecosystems do exist, although they are scattered and not easily accessible. An overarching, publicly accessible system combining all kinds of information has not been available until now. 2. The ElNet system was developed to serve these requirements. The system is a functional application consisting of a comprehensive database and an online interface with an interactive map, and search capabilities for biological and environmental data on Greek transitional waters. Nine datasets have already been integrated and are available online. Data and their metadata are documented and checked for quality to allow comparisons and reduce bias in resulting analyses. 3. The data assembled cover a broad geographical and temporal range, allowing large-scale analyses of transitional waters. These in turn produce new scientific knowledge and provide a sound basis of information for scientists, environmental managers and policy-makers. 4. Examination of the data revealed an overall insufficient quality control practice during data acquisition and digitization. A good data management and archive system can significantly improve the quality of data. To encourage scientists to submit their data to a data management centre, a clear data policy document regulating rights and duties could form an incentive for data sharing. 5. Results from a case study carried out on the macrobenthic inventories of the lagoonal systems included in the system demonstrate the potential use of this simple type of information by environmental managers and scientists. 6. The system, still in its initial phase, will be improved by integrating new datasets and developing tools for data retrieval and analyses. The database will be linked to other biodiversity databases to participate in a distributed information network and disseminate the information through other global biodiversity portals. Copyright © 2008 John Wiley & Sons, Ltd. |
Basset, A; Sabetta, L; Sangiorgio, F; Pinna, M; Migoni, D; Fanizzi, F; Barbone, E; Galuppo, N; Umani, Fonda S; Reizopoulou, S; Nicolaidou, A; Arvanitidis, C; Moncheva, S; Trajanova, A; Georgescu, L; Beqiraj, S Biodiversity conservation in Mediterranean and Black Sea lagoons: A trait-oriented approach to benthic invertebrate guilds Journal Article Aquatic Conservation: Marine and Freshwater Ecosystems, 18 (SUPPL. 1), pp. S4–S15, 2008, ISSN: 10527613. @article{basset_biodiversity_2008, title = {Biodiversity conservation in Mediterranean and Black Sea lagoons: A trait-oriented approach to benthic invertebrate guilds}, author = {A Basset and L Sabetta and F Sangiorgio and M Pinna and D Migoni and F Fanizzi and E Barbone and N Galuppo and S Fonda Umani and S Reizopoulou and A Nicolaidou and C Arvanitidis and S Moncheva and A Trajanova and L Georgescu and S Beqiraj}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-51649124928&doi=10.1002%2faqc.979&partnerID=40&md5=2fdb30a6a2525e34186a0924768ceec1}, doi = {10.1002/aqc.979}, issn = {10527613}, year = {2008}, date = {2008-01-01}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, volume = {18}, number = {SUPPL. 1}, pages = {S4--S15}, abstract = {1. The extent to which conservation of biodiversity enforces the protection of ecosystem functioning, goods and services is a key issue in conservation ecology. 2. In order to address this conservation issue, this work focused on community organization, linking community structure, as described both in taxonomic and functional terms, to community functioning and ecosystem processes. 3. Body size is an individual functional trait that is deterministically related to components of ecosystem functioning such as population dynamics and energy flow, and which determines components of community structure. Since body size is an individual trait that reflects numerous factors, it is also exposed to trait selection and the niche filtering underlying the community. 4. An analysis of the relevance of body size to community organization in transitional water ecosystems in the eastern Mediterranean and Black Sea regions is presented, based on field research conducted on a sample of 15 transitional water ecosystems. 5. 250 taxa were identified, clumped in five orders of magnitude of body size. All body size patterns showed triangular distributions with an optimal size range of 0.13 mg to 1.0 mg individual body mass. 6. Deterministic components of size structure were emphasized and a hierarchical organization with dominance of large sizes was demonstrated by the slopes of the body size-abundance distributions, consistently larger than the EER threshold (b = -0.75), and by the direct relationship of energy use to body size for most of the body size range. 7. Consistent variations of body size-related descriptors were observed on three main gradients of environmental stress: eutrophication, confinement and metal pollution. 8. The results support the relevance of constraints imposed by individual body size on community organization in transitional water ecosystems and the adequacy of size patterns as an indicator for ecological conservation of these fragile ecosystems. Copyright © 2008 John Wiley & Sons, Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 1. The extent to which conservation of biodiversity enforces the protection of ecosystem functioning, goods and services is a key issue in conservation ecology. 2. In order to address this conservation issue, this work focused on community organization, linking community structure, as described both in taxonomic and functional terms, to community functioning and ecosystem processes. 3. Body size is an individual functional trait that is deterministically related to components of ecosystem functioning such as population dynamics and energy flow, and which determines components of community structure. Since body size is an individual trait that reflects numerous factors, it is also exposed to trait selection and the niche filtering underlying the community. 4. An analysis of the relevance of body size to community organization in transitional water ecosystems in the eastern Mediterranean and Black Sea regions is presented, based on field research conducted on a sample of 15 transitional water ecosystems. 5. 250 taxa were identified, clumped in five orders of magnitude of body size. All body size patterns showed triangular distributions with an optimal size range of 0.13 mg to 1.0 mg individual body mass. 6. Deterministic components of size structure were emphasized and a hierarchical organization with dominance of large sizes was demonstrated by the slopes of the body size-abundance distributions, consistently larger than the EER threshold (b = -0.75), and by the direct relationship of energy use to body size for most of the body size range. 7. Consistent variations of body size-related descriptors were observed on three main gradients of environmental stress: eutrophication, confinement and metal pollution. 8. The results support the relevance of constraints imposed by individual body size on community organization in transitional water ecosystems and the adequacy of size patterns as an indicator for ecological conservation of these fragile ecosystems. Copyright © 2008 John Wiley & Sons, Ltd. |
2007 |
Berghe, Vanden E; Arvanitidis, C; Faulwetter, Sarah Biodiversity on-line: MarBEF Data Management. What about integration? Inproceedings Arvanitidis, C; as representative of, MarBEF Consortium (Ed.): 38th CIESM Congress, Istanbul, Turkey, 2007, (Place: Istanbul, Turkey Type: Abstract). @inproceedings{vanden_berghe_biodiversity_2007, title = {Biodiversity on-line: MarBEF Data Management. What about integration?}, author = {E Vanden Berghe and C Arvanitidis and Sarah Faulwetter}, editor = {C Arvanitidis and MarBEF Consortium as representative of}, year = {2007}, date = {2007-04-01}, booktitle = {38th CIESM Congress}, address = {Istanbul, Turkey}, note = {Place: Istanbul, Turkey Type: Abstract}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Dounas, C; Davies, I; Triantafyllou, G; Koulouri, P; Petihakis, G; Arvanitidis, C; Sourlatzis, G; Eleftheriou, A Large-scale impacts of bottom trawling on shelf primary productivity Journal Article Continental Shelf Research, 27 (17), pp. 2198–2210, 2007, ISSN: 02784343. @article{dounas_large-scale_2007, title = {Large-scale impacts of bottom trawling on shelf primary productivity}, author = {C Dounas and I Davies and G Triantafyllou and P Koulouri and G Petihakis and C Arvanitidis and G Sourlatzis and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34648836863&doi=10.1016%2fj.csr.2007.05.006&partnerID=40&md5=a703ee6ad51b8813b094665c60804525}, doi = {10.1016/j.csr.2007.05.006}, issn = {02784343}, year = {2007}, date = {2007-01-01}, journal = {Continental Shelf Research}, volume = {27}, number = {17}, pages = {2198--2210}, abstract = {Disturbance of the seabed resulting from bottom trawling affects ecosystem processes, such as the rate and magnitude of nutrient regeneration. The potential responses of the plankton community arising from such effects can be modelled, provided that reliable data on the effects on nutrient fluxes are available. In a north Cretan outer continental shelf and upper slope fishing ground (Heraklion Bay, Crete, Eastern Mediterranean) we applied a new field instrument which can simulate the passage of trawl groundropes across the sea floor and made direct seasonal measurements of the rate of dissolved and particulate nutrient releases resulting from seabed disturbance. These observational data were then integrated in a 3D ecosystem model. Results revealed that bottom trawling may trigger off considerable productivity pulses, in addition to pulses from the natural seasonal cycle. © 2007 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Disturbance of the seabed resulting from bottom trawling affects ecosystem processes, such as the rate and magnitude of nutrient regeneration. The potential responses of the plankton community arising from such effects can be modelled, provided that reliable data on the effects on nutrient fluxes are available. In a north Cretan outer continental shelf and upper slope fishing ground (Heraklion Bay, Crete, Eastern Mediterranean) we applied a new field instrument which can simulate the passage of trawl groundropes across the sea floor and made direct seasonal measurements of the rate of dissolved and particulate nutrient releases resulting from seabed disturbance. These observational data were then integrated in a 3D ecosystem model. Results revealed that bottom trawling may trigger off considerable productivity pulses, in addition to pulses from the natural seasonal cycle. © 2007 Elsevier Ltd. All rights reserved. |
Papageorgiou, N; Moreno, M; Marin, V; Baiardo, S; Arvanitidis, C; Fabiano, M; Eleftheriou, A Interrelationships of bacteria, meiofauna and macrofauna in a Mediterranean sedimentary beach (Maremma Park, NW Italy) Journal Article Helgoland Marine Research, 61 (1), pp. 31–42, 2007, ISSN: 1438387X. @article{papageorgiou_interrelationships_2007, title = {Interrelationships of bacteria, meiofauna and macrofauna in a Mediterranean sedimentary beach (Maremma Park, NW Italy)}, author = {N Papageorgiou and M Moreno and V Marin and S Baiardo and C Arvanitidis and M Fabiano and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33847182409&doi=10.1007%2fs10152-006-0051-6&partnerID=40&md5=bca215e4bb5cf140a6bbdb64990435cb}, doi = {10.1007/s10152-006-0051-6}, issn = {1438387X}, year = {2007}, date = {2007-01-01}, journal = {Helgoland Marine Research}, volume = {61}, number = {1}, pages = {31--42}, abstract = {Collelungo beach (Maremma Park, NW Italy), was sampled quantitatively for macrofauna, meiofauna and bacteria in May 2003; several physicochemical variables and variables associated with food availability and sediment structure were also measured. Replicated samples were collected from three sites representing natural conditions, an erosion regime, and the influence of the Ombrone River, respectively, as well as from four stations each located in the surf and sublittoral zones. Both uni- and multivariate techniques were used to assess the benthic community structure and the associated environmental variables. Different diversity indices revealed no pattern; in contrast, multivariate techniques applied on the macrobenthic fauna and the polychaete taxocommunity distinguished between the sites located in natural and eroding conditions from the one located nearby the discharges of the Ombrone river. The community patterns deriving from meio- and macrofauna are clearly divergent. The overall benthic faunal community appears to be influenced by both groups of organisms. The patterns of the meio- and macrofaunal communities seem to be affected synergistically by a number of environmental variables, in accordance with the multicausal environmental severity hypothesis. Meiofaunal patterns are more often correlated with bacteria and the protein concentration than are macrofaunal patterns, indicating a potential utilization of bacteria as a food source by the meiofaunal organisms. Total bacterial numbers are associated with the macrofaunal pattern under the erosion regime, probably as a consequence of competition for food between macrofauna and meiofauna. © Springer-Verlag and AWI 2006.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Collelungo beach (Maremma Park, NW Italy), was sampled quantitatively for macrofauna, meiofauna and bacteria in May 2003; several physicochemical variables and variables associated with food availability and sediment structure were also measured. Replicated samples were collected from three sites representing natural conditions, an erosion regime, and the influence of the Ombrone River, respectively, as well as from four stations each located in the surf and sublittoral zones. Both uni- and multivariate techniques were used to assess the benthic community structure and the associated environmental variables. Different diversity indices revealed no pattern; in contrast, multivariate techniques applied on the macrobenthic fauna and the polychaete taxocommunity distinguished between the sites located in natural and eroding conditions from the one located nearby the discharges of the Ombrone river. The community patterns deriving from meio- and macrofauna are clearly divergent. The overall benthic faunal community appears to be influenced by both groups of organisms. The patterns of the meio- and macrofaunal communities seem to be affected synergistically by a number of environmental variables, in accordance with the multicausal environmental severity hypothesis. Meiofaunal patterns are more often correlated with bacteria and the protein concentration than are macrofaunal patterns, indicating a potential utilization of bacteria as a food source by the meiofaunal organisms. Total bacterial numbers are associated with the macrofaunal pattern under the erosion regime, probably as a consequence of competition for food between macrofauna and meiofauna. © Springer-Verlag and AWI 2006. |
Simboura, N; Reizopoulou, S; Arvanitidis, C; Basset, A Transitional Waters Bulletin, 1 (4), pp. 53–58, 2007, ISSN: 1825229X. @article{simboura_new_2007, title = {New Information On The Biogeographical And Ecological Distribution Of Pionosyllis anophthalma Capaccioni and San Martín, 1989 (Polychaeta, Syllidae)}, author = {N Simboura and S Reizopoulou and C Arvanitidis and A Basset}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79955952606&doi=10.1285%2fi1825229Xv1n4p53&partnerID=40&md5=5a5325105834973686b2b3ccd2810a70}, doi = {10.1285/i1825229Xv1n4p53}, issn = {1825229X}, year = {2007}, date = {2007-01-01}, journal = {Transitional Waters Bulletin}, volume = {1}, number = {4}, pages = {53--58}, abstract = {Two individuals of the Mediterranean endemic species Pionosyllis anophthalma Capaccioni & San Martín, 1989 were found in a brackish water coastal lagoon in Northern Greece (Agiasma, Nestos river). The species is reported for the first time in Greece and in a non-tidal brackish water coastal lagoon. The record adds some new information concerning the geographical and habitat distributional ranges of the species. Pionosyllis anophthalma is associated with vegetated bottoms and shows a wide tolerance to salinity variations. An intraspecific morphological variation was observed in the material examined compared to the species' holotype. © 2007 University of Salento.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Two individuals of the Mediterranean endemic species Pionosyllis anophthalma Capaccioni & San Martín, 1989 were found in a brackish water coastal lagoon in Northern Greece (Agiasma, Nestos river). The species is reported for the first time in Greece and in a non-tidal brackish water coastal lagoon. The record adds some new information concerning the geographical and habitat distributional ranges of the species. Pionosyllis anophthalma is associated with vegetated bottoms and shows a wide tolerance to salinity variations. An intraspecific morphological variation was observed in the material examined compared to the species' holotype. © 2007 University of Salento. |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, K; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, M; Kotoulas, G; Arvanitidis, C Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results Journal Article MarBEF Newsletter, 6 , pp. 26–27, 2007. @article{vasileiadou_polychaete_2007, title = {Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results}, author = {A Vasileiadou and E Sarropoulou and K Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and M Simboura and G Kotoulas and C Arvanitidis}, url = {http://www.marbef.org/outreach/newsletter.php}, year = {2007}, date = {2007-01-01}, journal = {MarBEF Newsletter}, volume = {6}, pages = {26--27}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2006 |
Arvanitidis, C; Valavanis, V D; Eleftheriou, A; Costello, M J; Faulwetter, S; Gotsis, P; Kitsos, M S; Kirmtzoglou, I; Zenetos, A; Petrov, A; Galil, B; Papageorgiou, N MedOBIS: Biogeographic information system for the eastern Mediterranean and Black Sea Journal Article Marine Ecology Progress Series, 316 , pp. 225–230, 2006, ISSN: 01718630. @article{arvanitidis_medobis_2006, title = {MedOBIS: Biogeographic information system for the eastern Mediterranean and Black Sea}, author = {C Arvanitidis and V D Valavanis and A Eleftheriou and M J Costello and S Faulwetter and P Gotsis and M S Kitsos and I Kirmtzoglou and A Zenetos and A Petrov and B Galil and N Papageorgiou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33746589895&doi=10.3354%2fmeps316225&partnerID=40&md5=e72c488455d8d116da5aae7d7faf91b4}, doi = {10.3354/meps316225}, issn = {01718630}, year = {2006}, date = {2006-01-01}, journal = {Marine Ecology Progress Series}, volume = {316}, pages = {225--230}, abstract = {Recent online initiatives in sharing marine biological data, such as the European Register of Marine Species (ERMS) and the Ocean Biogeographic Information System (OBIS), identified gaps in data from the eastern Mediterranean and Black Sea. Such data are now being collected, formatted and disseminated by MedOBIS (the Mediterranean Ocean Biogeographic Information System) initiative involving Greece, the Ukraine and Israel (test version available at: www.medobis.org). The aim is to develop a taxon-based biogeography database and online data server with links to survey and satellite environmental data. MedOBIS is currently undergoing 4 stages of development, namely, data assembly, formatting, analysis and dissemination. The primary features of the MedOBIS application are its offline GIS (Geographic Information Systems) data formatting capabilities and its online Java- and JavaScript-enabling data server with taxon-based search, mapping and data down-loading capabilities. It is an independent source of biological and environmental data, as well as an online GIS tool designed to facilitate access to historical and current data by marine researchers. As more data become available and are inserted into the system, MedOBIS will function as the eastern Mediterranean and Black Sea node of EurOBIS (the European node of the international OBIS initiative, part of the 'Census of Marine Life'). © Inter-Research 2006.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent online initiatives in sharing marine biological data, such as the European Register of Marine Species (ERMS) and the Ocean Biogeographic Information System (OBIS), identified gaps in data from the eastern Mediterranean and Black Sea. Such data are now being collected, formatted and disseminated by MedOBIS (the Mediterranean Ocean Biogeographic Information System) initiative involving Greece, the Ukraine and Israel (test version available at: www.medobis.org). The aim is to develop a taxon-based biogeography database and online data server with links to survey and satellite environmental data. MedOBIS is currently undergoing 4 stages of development, namely, data assembly, formatting, analysis and dissemination. The primary features of the MedOBIS application are its offline GIS (Geographic Information Systems) data formatting capabilities and its online Java- and JavaScript-enabling data server with taxon-based search, mapping and data down-loading capabilities. It is an independent source of biological and environmental data, as well as an online GIS tool designed to facilitate access to historical and current data by marine researchers. As more data become available and are inserted into the system, MedOBIS will function as the eastern Mediterranean and Black Sea node of EurOBIS (the European node of the international OBIS initiative, part of the 'Census of Marine Life'). © Inter-Research 2006. |
Koulouri, P; Dounas, C; Arvanitidis, C; Koutsoubas, D; Eleftheriou, A Molluscan diversity along a Mediterranean soft bottom sublittoral ecotone Journal Article Scientia Marina, 70 (4), pp. 573–583, 2006, ISSN: 02148358, (Publisher: CSIC Consejo Superior de Investigaciones Cientificas 2). @article{koulouri_molluscan_2006, title = {Molluscan diversity along a Mediterranean soft bottom sublittoral ecotone}, author = {P Koulouri and C Dounas and C Arvanitidis and D Koutsoubas and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846020553&doi=10.3989%2fscimar.2006.70n4573&partnerID=40&md5=7281e64db760bd5bee1e6b6611feef33}, doi = {10.3989/scimar.2006.70n4573}, issn = {02148358}, year = {2006}, date = {2006-01-01}, journal = {Scientia Marina}, volume = {70}, number = {4}, pages = {573--583}, abstract = {Molluscan diversity associated with sublittoral soft-bottoms was studied in Heraklion Bay as part of a long-term multidisciplinary research programme in the coastal environment of northern Crete (eastern Mediterranean). Quantitative benthic samples were collected in a pilot survey from a grid of 28 stations, followed by a seasonal sampling carried out over a seven- station transect located from 10 to 40 m depth. Univariate and multivariate analyses indicated the presence of a clear zonation along the depth gradient for the molluscan fauna and three main associations were identified in bathymetric zones parallel to the coastline. The structure of the local molluscan communities revealed the existence of an extended transition zone (ecotone) between a shallow sandy association and a deeper muddy one and a functional pattern, based on the feeding guilds, was evident along the environmental gradient. Application of graphical techniques, by using molluscan taxocoenosis, indicated a rather naturally disturbed habitat. Beta-diversity measures indicated different seasonal community adaptations to the prevailing environmental conditions. Results derived from this study revealed that beta-diversity may be a good descriptor for the assessment of the strength and breadth of sublittoral transition zones along environmental gradients.}, note = {Publisher: CSIC Consejo Superior de Investigaciones Cientificas 2}, keywords = {}, pubstate = {published}, tppubtype = {article} } Molluscan diversity associated with sublittoral soft-bottoms was studied in Heraklion Bay as part of a long-term multidisciplinary research programme in the coastal environment of northern Crete (eastern Mediterranean). Quantitative benthic samples were collected in a pilot survey from a grid of 28 stations, followed by a seasonal sampling carried out over a seven- station transect located from 10 to 40 m depth. Univariate and multivariate analyses indicated the presence of a clear zonation along the depth gradient for the molluscan fauna and three main associations were identified in bathymetric zones parallel to the coastline. The structure of the local molluscan communities revealed the existence of an extended transition zone (ecotone) between a shallow sandy association and a deeper muddy one and a functional pattern, based on the feeding guilds, was evident along the environmental gradient. Application of graphical techniques, by using molluscan taxocoenosis, indicated a rather naturally disturbed habitat. Beta-diversity measures indicated different seasonal community adaptations to the prevailing environmental conditions. Results derived from this study revealed that beta-diversity may be a good descriptor for the assessment of the strength and breadth of sublittoral transition zones along environmental gradients. |
Papageorgiou, N; Arvanitidis, C; Eleftheriou, A Multicausal environmental severity: A flexible framework for microtidal sandy beaches and the role of polychaetes as an indicator taxon Journal Article Estuarine, Coastal and Shelf Science, 70 (4), pp. 643–653, 2006, ISSN: 02727714. @article{papageorgiou_multicausal_2006, title = {Multicausal environmental severity: A flexible framework for microtidal sandy beaches and the role of polychaetes as an indicator taxon}, author = {N Papageorgiou and C Arvanitidis and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33751414872&doi=10.1016%2fj.ecss.2005.11.033&partnerID=40&md5=4604b4489092bbe973f264257fe4cf43}, doi = {10.1016/j.ecss.2005.11.033}, issn = {02727714}, year = {2006}, date = {2006-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {70}, number = {4}, pages = {643--653}, abstract = {The aim of this paper is to study the macrofaunal community dynamics and the biological-environmental interactions in the mid- and sublittoral ecosystems of the microtidal Mediterranean sandy shores. Four sandy beaches, three on the island of Crete and one on the northwest coast of Italy were selected to investigate the spatial and temporal changes in the community structure and the associated environmental variables. The littoral zone, which has not been adequately studied in the Eastern Mediterranean, presents special interest not only from the scientific point of view but also for practical reasons of ecological management. The multivariate techniques revealed that the community pattern of the sandy beach macrofauna is mainly spatial rather than temporal. There are pronounced differences in species composition and abundance of the macrofaunal assemblages of the mid- and sublittoral zone. The multicausal environmental severity hypothesis appears to be valid for the sandy beach macrofaunal communities of the Mediterranean. The abundance and composition of the macrofaunal assemblages are highly variable and are affected by the synergistic effects of many environmental variables. The polychaete taxonomic assemblage structure closely follows the macrofaunal community pattern. Differences between the two patterns may arise from the different responses that polychaetes may show to the environmental stress. © 2006 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this paper is to study the macrofaunal community dynamics and the biological-environmental interactions in the mid- and sublittoral ecosystems of the microtidal Mediterranean sandy shores. Four sandy beaches, three on the island of Crete and one on the northwest coast of Italy were selected to investigate the spatial and temporal changes in the community structure and the associated environmental variables. The littoral zone, which has not been adequately studied in the Eastern Mediterranean, presents special interest not only from the scientific point of view but also for practical reasons of ecological management. The multivariate techniques revealed that the community pattern of the sandy beach macrofauna is mainly spatial rather than temporal. There are pronounced differences in species composition and abundance of the macrofaunal assemblages of the mid- and sublittoral zone. The multicausal environmental severity hypothesis appears to be valid for the sandy beach macrofaunal communities of the Mediterranean. The abundance and composition of the macrofaunal assemblages are highly variable and are affected by the synergistic effects of many environmental variables. The polychaete taxonomic assemblage structure closely follows the macrofaunal community pattern. Differences between the two patterns may arise from the different responses that polychaetes may show to the environmental stress. © 2006 Elsevier Ltd. All rights reserved. |
Claus, S; Arvanitidis, C; Fleddum, A; Berghe, Vanden E MarBEF theme 1: global patterns of marine biodiversity across ecosystems. Progress with theme I data analysis activities Journal Article MarBEF Newsletter, 4 , pp. 3–4, 2006. @article{claus_marbef_2006, title = {MarBEF theme 1: global patterns of marine biodiversity across ecosystems. Progress with theme I data analysis activities}, author = {S Claus and C Arvanitidis and A Fleddum and E Vanden Berghe}, url = {http://www.marinespecies.org/imis.php?module=ref&refid=98966}, year = {2006}, date = {2006-01-01}, journal = {MarBEF Newsletter}, volume = {4}, pages = {3--4}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Papageorgiou, Nafsika; Arvanitidis, C; Eleftheriou, A Macrofaunal Biodiversity of the Mediterranean Sandy Beach Environment Inproceedings The Mediterranean Coastal Areas from Watershed to the Sea : Interctions and Changes : Proceedings of the Medcore International Conference, pp. 263–274, Firenze, ITALY, 2006, (Publication Title: The Mediterranean Coastal Areas from Watershed to the Sea : Interctions and Changes : Proceedings of the Medcore International Conference Type: Conference Paper). @inproceedings{papageorgiou_macrofaunal_2006, title = {Macrofaunal Biodiversity of the Mediterranean Sandy Beach Environment}, author = {Nafsika Papageorgiou and C Arvanitidis and A Eleftheriou}, year = {2006}, date = {2006-01-01}, booktitle = {The Mediterranean Coastal Areas from Watershed to the Sea : Interctions and Changes : Proceedings of the Medcore International Conference}, pages = {263--274}, address = {Firenze, ITALY}, abstract = {Information collected both from sampling activities in the Eastern and Western Mediterranean sandy beaches as well as from the literature has reveled: (i) Severe fluctuations in the values of the abiotic data, consistent with the “multicausal environmental severity hypothesis”; (ii) A tentatively defined zoogeocline from the Eastern to the Western Mediterranean; (iii) Many of the sandy beaches show higher than expected Taxonomic Distinctness values, a fact which is indicative of the less scientific effort spent, and which results in many oligo- or monotypic taxa; (iv) The most plausible results were derived from the taxon of polychaetes, which have also proved to be a successful indicator taxon in other transitional Mediterranean ecosystems.}, note = {Publication Title: The Mediterranean Coastal Areas from Watershed to the Sea : Interctions and Changes : Proceedings of the Medcore International Conference Type: Conference Paper}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Information collected both from sampling activities in the Eastern and Western Mediterranean sandy beaches as well as from the literature has reveled: (i) Severe fluctuations in the values of the abiotic data, consistent with the “multicausal environmental severity hypothesis”; (ii) A tentatively defined zoogeocline from the Eastern to the Western Mediterranean; (iii) Many of the sandy beaches show higher than expected Taxonomic Distinctness values, a fact which is indicative of the less scientific effort spent, and which results in many oligo- or monotypic taxa; (iv) The most plausible results were derived from the taxon of polychaetes, which have also proved to be a successful indicator taxon in other transitional Mediterranean ecosystems. |
2005 |
Kitsos, M -S; Christodoulou, M; Arvanitidis, C; Mavidis, M; Kirmitzoglou, I; Koukouras, A Composition of the organismic assemblage associated with Caretta caretta Journal Article Journal of the Marine Biological Association of the United Kingdom, 85 (2), pp. 257–261, 2005, ISSN: 00253154. @article{kitsos_composition_2005, title = {Composition of the organismic assemblage associated with Caretta caretta}, author = {M -S Kitsos and M Christodoulou and C Arvanitidis and M Mavidis and I Kirmitzoglou and A Koukouras}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-18244363640&doi=10.1017%2fS0025315405011136h&partnerID=40&md5=557179d4cedaf466179b5740074433b9}, doi = {10.1017/S0025315405011136h}, issn = {00253154}, year = {2005}, date = {2005-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {85}, number = {2}, pages = {257--261}, abstract = {The organismic assemblage associated with Caretta caretta was studied in 37 loggerhead turtles, washed ashore dead at various localities in the northern Aegean Sea. A total number of 63 macrobenthic species and 17 species of macroalgae were identified. From these species, 41 and 13 respectively are reported for the first time as epibionts of this turtle. Analysis of the epibiont species distribution on six loggerhead turtles gave some evidence regarding the settlement preferences of certain epibiont species. From a biogeographical point of view, 61.3% of the epibiont species were cosmopolitan, 30.7% had an Atlanta-Mediterranean distribution, while 8% were Mediterranean endemics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The organismic assemblage associated with Caretta caretta was studied in 37 loggerhead turtles, washed ashore dead at various localities in the northern Aegean Sea. A total number of 63 macrobenthic species and 17 species of macroalgae were identified. From these species, 41 and 13 respectively are reported for the first time as epibionts of this turtle. Analysis of the epibiont species distribution on six loggerhead turtles gave some evidence regarding the settlement preferences of certain epibiont species. From a biogeographical point of view, 61.3% of the epibiont species were cosmopolitan, 30.7% had an Atlanta-Mediterranean distribution, while 8% were Mediterranean endemics. |
Arvanitidis, C; Chatzigeorgiou, G; Koutsoubas, D; Kevrekidis, T; Dounas, C; Eleftheriou, A; Koulouri, P; Mogias, A Estimating lagoonal biodiversity in Greece: Comparison of rapid assessment techniques Journal Article Helgoland Marine Research, 59 (3), pp. 177–186, 2005, ISSN: 1438387X. @article{arvanitidis_estimating_2005, title = {Estimating lagoonal biodiversity in Greece: Comparison of rapid assessment techniques}, author = {C Arvanitidis and G Chatzigeorgiou and D Koutsoubas and T Kevrekidis and C Dounas and A Eleftheriou and P Koulouri and A Mogias}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-24944557295&doi=10.1007%2fs10152-005-0216-8&partnerID=40&md5=b9d9a7372762c2833f2e6ea1c70d270e}, doi = {10.1007/s10152-005-0216-8}, issn = {1438387X}, year = {2005}, date = {2005-01-01}, journal = {Helgoland Marine Research}, volume = {59}, number = {3}, pages = {177--186}, abstract = {An attempt is made to compare the results of different rapid biodiversity assessment techniques at the pan-Mediterranean, sectorial and local levels. A uniform multivariate pattern exists at the pan-Mediterranean and national (sectorial) levels: lagoons can be different when they host only a few species, but as species numbers increase, lagoons become homogenous in composition. Multivariate techniques cannot distinguish anthropogenically-impacted lagoons from those, which are naturally disturbed. In the pan-Mediterranean context it is the higher taxonomic levels, but in the national and local context it is the most abundant macrobenthic groups (polychaetes, molluscs and crustaceans) and meiobenthos which provide patterns closest to that derived from the species level. Taxonomic distinctness indices applied to polychaete and mollusc inventories provide meaningful results at most levels and scales of observation. These indices seem to be robust enough to discriminate anthropogenically impacted from naturally disturbed lagoons. © Springer-Verlag and AWI 2005.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An attempt is made to compare the results of different rapid biodiversity assessment techniques at the pan-Mediterranean, sectorial and local levels. A uniform multivariate pattern exists at the pan-Mediterranean and national (sectorial) levels: lagoons can be different when they host only a few species, but as species numbers increase, lagoons become homogenous in composition. Multivariate techniques cannot distinguish anthropogenically-impacted lagoons from those, which are naturally disturbed. In the pan-Mediterranean context it is the higher taxonomic levels, but in the national and local context it is the most abundant macrobenthic groups (polychaetes, molluscs and crustaceans) and meiobenthos which provide patterns closest to that derived from the species level. Taxonomic distinctness indices applied to polychaete and mollusc inventories provide meaningful results at most levels and scales of observation. These indices seem to be robust enough to discriminate anthropogenically impacted from naturally disturbed lagoons. © Springer-Verlag and AWI 2005. |
Arvanitidis, C; Atzigeorgiou, G; Koutsoubas, D; Dounas, C; Eleftheriou, A; Koulouri, P Mediterranean lagoons revisited: Weakness and efficiency of the rapid biodiversity assessment techniques in a severely fluctuating environment Journal Article Biodiversity and Conservation, 14 (10), pp. 2347–2359, 2005, ISSN: 09603115. @article{arvanitidis_mediterranean_2005, title = {Mediterranean lagoons revisited: Weakness and efficiency of the rapid biodiversity assessment techniques in a severely fluctuating environment}, author = {C Arvanitidis and G Atzigeorgiou and D Koutsoubas and C Dounas and A Eleftheriou and P Koulouri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-24944484401&doi=10.1007%2fs10531-004-1668-x&partnerID=40&md5=164959659412afbcf4b012e66162f526}, doi = {10.1007/s10531-004-1668-x}, issn = {09603115}, year = {2005}, date = {2005-01-01}, journal = {Biodiversity and Conservation}, volume = {14}, number = {10}, pages = {2347--2359}, abstract = {The purpose of this paper is to test the performance of rapid biodiversity assessment techniques in the lagoonal environment at the pan-Mediterranean scale. The multivariate techniques can produce patterns of lagoonal biodiversity along the Mediterranean. Additionally, it is shown that the polychaete inventory can preferably be used rather than the aggregation of information at the family level for the purposes of rapid biodiversity assessment. These techniques, however, appear to be weak for the environmental assessment because they cannot detect differences between the naturally disturbed and the anthropogenically impacted lagoons. Both taxonomic distinctness indices are found to be robust in providing meaningful results for rapid biodiversity/environmental assessment when the crustacean inventory and the polychaete and molluscan ones are used for the estimation of the average taxonomic distinctness and of the variation in taxonomic distinctness values, correspondingly. Conversely, information on the distribution of the macrofaunal species to the Mediterranean lagoons appears to be inadequate for the needs of such rapid biodiversity assessment at a regional scale. It is suggested that information on ecological convergence of the macrofaunal species would probably provide biodiversity indices with additional power, at least in the lagoonal environment. © Springer 2005.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The purpose of this paper is to test the performance of rapid biodiversity assessment techniques in the lagoonal environment at the pan-Mediterranean scale. The multivariate techniques can produce patterns of lagoonal biodiversity along the Mediterranean. Additionally, it is shown that the polychaete inventory can preferably be used rather than the aggregation of information at the family level for the purposes of rapid biodiversity assessment. These techniques, however, appear to be weak for the environmental assessment because they cannot detect differences between the naturally disturbed and the anthropogenically impacted lagoons. Both taxonomic distinctness indices are found to be robust in providing meaningful results for rapid biodiversity/environmental assessment when the crustacean inventory and the polychaete and molluscan ones are used for the estimation of the average taxonomic distinctness and of the variation in taxonomic distinctness values, correspondingly. Conversely, information on the distribution of the macrofaunal species to the Mediterranean lagoons appears to be inadequate for the needs of such rapid biodiversity assessment at a regional scale. It is suggested that information on ecological convergence of the macrofaunal species would probably provide biodiversity indices with additional power, at least in the lagoonal environment. © Springer 2005. |
Dounas, C; Davies, I; Hayes, P; Arvanitidis, C; Koulouri, P The effect of different types of otter trawl groundrope on benthic nutrient fluxes and sediment biogeochemistry Journal Article American Fisheries Society Symposium, 41 , pp. 539–544, 2005. @article{dounas_effect_2005, title = {The effect of different types of otter trawl groundrope on benthic nutrient fluxes and sediment biogeochemistry}, author = {C Dounas and I Davies and P Hayes and C Arvanitidis and P Koulouri}, url = {http://fisheries.org/shop/x54041xm}, year = {2005}, date = {2005-01-01}, journal = {American Fisheries Society Symposium}, volume = {41}, pages = {539--544}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2003 |
Arvanitidis, C; Bellan, G; Drakopoulos, P; Valavanis, V; Dounas, C; Koukouras, A; Eleftheriou, A Testing hypotheses on the biodiversity patterns occurring in the Mediterranean and Black Seas: the example of the benthic polychaetes Inproceedings Chersonisos, Crete, Greece, 2003, (Publication Title: Seventh Symposium on Oceanography and Fisheries). @inproceedings{arvanitidis_testing_2003, title = {Testing hypotheses on the biodiversity patterns occurring in the Mediterranean and Black Seas: the example of the benthic polychaetes}, author = {C Arvanitidis and G Bellan and P Drakopoulos and V Valavanis and C Dounas and A Koukouras and A Eleftheriou}, year = {2003}, date = {2003-01-01}, address = {Chersonisos, Crete, Greece}, note = {Publication Title: Seventh Symposium on Oceanography and Fisheries}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Heip, C; Costello, M; Hummel, H; Avesaath, Van P; Arvanitidis, C; Eleftheriou, A The status of Marine Biodiversity in Europe Inproceedings Arvanitidis, C; as representative of, MARBENA Consortium (Ed.): ΙΑSON: International Conference on the Sustainable Development of the Mediterranean and Black Sea Environment, Thessaloniki, Greece, 2003. @inproceedings{heip_status_2003, title = {The status of Marine Biodiversity in Europe}, author = {C Heip and M Costello and H Hummel and P Van Avesaath and C Arvanitidis and A Eleftheriou}, editor = {C Arvanitidis and MARBENA Consortium as representative of}, year = {2003}, date = {2003-01-01}, booktitle = {ΙΑSON: International Conference on the Sustainable Development of the Mediterranean and Black Sea Environment}, address = {Thessaloniki, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Naletaki, M; Koutsoubas, D; Dounas, C; Arvanitidis, C Structure and dynamics of the macrobenthic crustaceans in the Gialova lagoon (SW Peloponnese) Inproceedings Chersonisos, Crete, Greece, 2003, (Publication Title: Seventh Symposium on Oceanography and Fisheries). @inproceedings{naletaki_structure_2003, title = {Structure and dynamics of the macrobenthic crustaceans in the Gialova lagoon (SW Peloponnese)}, author = {M Naletaki and D Koutsoubas and C Dounas and C Arvanitidis}, year = {2003}, date = {2003-01-01}, address = {Chersonisos, Crete, Greece}, note = {Publication Title: Seventh Symposium on Oceanography and Fisheries}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2002 |
Moreno, A; Pereira, J; Arvanitidis, C; Robin, J -P; Koutsoubas, D; Perales-Raya, C; Cunha, M M; Balguerias, E; Denis, V Biological variation of Loligo vulgaris (Cephalopoda: Loliginidae) in the eastern Atlantic and Mediterranean Journal Article Bulletin of Marine Science, 71 (1), pp. 515–534, 2002, ISSN: 00074977. @article{moreno_biological_2002, title = {Biological variation of Loligo vulgaris (Cephalopoda: Loliginidae) in the eastern Atlantic and Mediterranean}, author = {A Moreno and J Pereira and C Arvanitidis and J -P Robin and D Koutsoubas and C Perales-Raya and M M Cunha and E Balguerias and V Denis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038414518&partnerID=40&md5=697c23d401ca449162a83e6eebe8c623}, issn = {00074977}, year = {2002}, date = {2002-01-01}, journal = {Bulletin of Marine Science}, volume = {71}, number = {1}, pages = {515--534}, abstract = {The biological characteristics of the squid Loligo vulgaris from north France, northwest Portugal, the Saharan Bank, and the Greek Seas were analyzed to describe large-scale biological patterns and to evaluate geographical variation in the Atlantic and the Mediterranean. In northwest Portugal and on the Saharan Bank population length structures are more complex due to extended spawning and recruitment periods. Squid spawn only between November and April in north France and the Greek Seas. Gonadosomatic indices decreased with decreasing latitude in the Atlantic, while the highest indices were found in the Mediterranean. Full maturity occurred at smaller size in northwest Portugal than in other areas of the Atlantic, and at similar size to Mediterranean squid. Length-weight relationship slopes increased from the north to the south in the Atlantic and in the Mediterranean. Multivariate analysis of seasonal biological indices demonstrated significant biological differences between squid of different areas, mainly in terms of size at maturity, male GSI and average body size and weight. Biological variability between areas was considered related to plasticity of responses to large-scale geographic environmental conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The biological characteristics of the squid Loligo vulgaris from north France, northwest Portugal, the Saharan Bank, and the Greek Seas were analyzed to describe large-scale biological patterns and to evaluate geographical variation in the Atlantic and the Mediterranean. In northwest Portugal and on the Saharan Bank population length structures are more complex due to extended spawning and recruitment periods. Squid spawn only between November and April in north France and the Greek Seas. Gonadosomatic indices decreased with decreasing latitude in the Atlantic, while the highest indices were found in the Mediterranean. Full maturity occurred at smaller size in northwest Portugal than in other areas of the Atlantic, and at similar size to Mediterranean squid. Length-weight relationship slopes increased from the north to the south in the Atlantic and in the Mediterranean. Multivariate analysis of seasonal biological indices demonstrated significant biological differences between squid of different areas, mainly in terms of size at maturity, male GSI and average body size and weight. Biological variability between areas was considered related to plasticity of responses to large-scale geographic environmental conditions. |
Valavanis, V D; Georgakarakos, S; Koutsoubas, D; Arvanitidis, C; Haralabous, J Development of a marine information system for cephalopod fisheries in Eastern Mediterranean Journal Article Bulletin of Marine Science, 71 (2), pp. 867–882, 2002, ISSN: 00074977. @article{valavanis_development_2002, title = {Development of a marine information system for cephalopod fisheries in Eastern Mediterranean}, author = {V D Valavanis and S Georgakarakos and D Koutsoubas and C Arvanitidis and J Haralabous}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037847554&partnerID=40&md5=58a9f1fdcd43728aa0d3c54aa022065c}, issn = {00074977}, year = {2002}, date = {2002-01-01}, journal = {Bulletin of Marine Science}, volume = {71}, number = {2}, pages = {867--882}, abstract = {An interfaced marine information system is developed for integrated analysis of fisheries of five commercially important cephalopod species in Greek waters of the Eastern Mediterranean. The system combines data on the spatial and temporal patterns of cephalopod population dynamics focusing on geo-distribution of abundance, environmental variation, fisheries, spawning areas and migration habits. The system is developed as a customisation of a workstation ARC/INFO environment and features a series of innovative GIS map-overlay and integration routines for analysis and modelling of surveyed, statistical, and remote-sensed data. Geo-referenced datasets include cephalopod catch and landings, coastline-bathymetry, bottom substrate types, and a set of environmental variables provided by satellite sensors (AVHRR/sea surface temperature and SeaWiFS/chlorophyll-a concentration) and climatologic datasets (sea surface salinity). The innovative aspect of this marine system is the integration of species life history data to GIS analysis. Species preferences on certain spawning conditions, migration habits, and depth ranges are used as constraints in GIS analysis and integration. The application of GIS and Remote Sensing technologies has proved useful for the mapping of seasonal spatial components of cephalopod population dynamics. Results from this application may be used for information-based species management proposals, which is the goal of further development of this marine information system.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An interfaced marine information system is developed for integrated analysis of fisheries of five commercially important cephalopod species in Greek waters of the Eastern Mediterranean. The system combines data on the spatial and temporal patterns of cephalopod population dynamics focusing on geo-distribution of abundance, environmental variation, fisheries, spawning areas and migration habits. The system is developed as a customisation of a workstation ARC/INFO environment and features a series of innovative GIS map-overlay and integration routines for analysis and modelling of surveyed, statistical, and remote-sensed data. Geo-referenced datasets include cephalopod catch and landings, coastline-bathymetry, bottom substrate types, and a set of environmental variables provided by satellite sensors (AVHRR/sea surface temperature and SeaWiFS/chlorophyll-a concentration) and climatologic datasets (sea surface salinity). The innovative aspect of this marine system is the integration of species life history data to GIS analysis. Species preferences on certain spawning conditions, migration habits, and depth ranges are used as constraints in GIS analysis and integration. The application of GIS and Remote Sensing technologies has proved useful for the mapping of seasonal spatial components of cephalopod population dynamics. Results from this application may be used for information-based species management proposals, which is the goal of further development of this marine information system. |
Georgakarakos, S; Haralabous, J; Valavanis, V; Arvanitidis, C; Koutsoubas, D; Kapantagakis, A Loliginid and ommastrephid stock prediction in greek waters using time series analysis techniques Journal Article Bulletin of Marine Science, 71 (1), pp. 269–287, 2002, ISSN: 00074977. @article{georgakarakos_loliginid_2002, title = {Loliginid and ommastrephid stock prediction in greek waters using time series analysis techniques}, author = {S Georgakarakos and J Haralabous and V Valavanis and C Arvanitidis and D Koutsoubas and A Kapantagakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0012558157&partnerID=40&md5=ba8fe464323fefdcf7bb74558465a3f4}, issn = {00074977}, year = {2002}, date = {2002-01-01}, journal = {Bulletin of Marine Science}, volume = {71}, number = {1}, pages = {269--287}, abstract = {Time series of loliginid and ommastrephid landings were analysed taking into account spatio-temporal descriptors of sea surface temperature (SST). The data are based on fisheries statistics recorded from the three most important fishing ports in the Northern Aegean Sea (1984-1999) and NOAA satellite images processed using GIS and image analysis tools. Autocorrelation (AC) and partial autocorrelation (PAC) functions were estimated leading to the identification and construction of seasonal ARIMA models, suitable for explaining the time series and forecasting future abundance values. The performance of the models was tested by comparing the predicted against the observed data of the last year (1999) and by examining the distribution and the AC of the residuals. The analysis provided results characterizing the different fishing patterns in each geographic area, as well as new series containing seasonally adjusted values, trend, cycle and error components of the model. Time series of several statistical parameters describing spatio-temporal variations of the S ST were estimated and analysed aiming at the detection of anomalies and possible stock-environment relationships. Cross-correlation analysis between SST parameters and stock biomass indexes showed significant correlation coefficients, before and after compensation of the seasonal fluctuations by seasonal differencing. The results suggest that SST can be a leading indicator for stock prediction of the target species in the survey area.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Time series of loliginid and ommastrephid landings were analysed taking into account spatio-temporal descriptors of sea surface temperature (SST). The data are based on fisheries statistics recorded from the three most important fishing ports in the Northern Aegean Sea (1984-1999) and NOAA satellite images processed using GIS and image analysis tools. Autocorrelation (AC) and partial autocorrelation (PAC) functions were estimated leading to the identification and construction of seasonal ARIMA models, suitable for explaining the time series and forecasting future abundance values. The performance of the models was tested by comparing the predicted against the observed data of the last year (1999) and by examining the distribution and the AC of the residuals. The analysis provided results characterizing the different fishing patterns in each geographic area, as well as new series containing seasonally adjusted values, trend, cycle and error components of the model. Time series of several statistical parameters describing spatio-temporal variations of the S ST were estimated and analysed aiming at the detection of anomalies and possible stock-environment relationships. Cross-correlation analysis between SST parameters and stock biomass indexes showed significant correlation coefficients, before and after compensation of the seasonal fluctuations by seasonal differencing. The results suggest that SST can be a leading indicator for stock prediction of the target species in the survey area. |
Arvanitidis, C; Bellan, G; Drakopoulos, P; Valavanis, V; Dounas, C; Koukouras, A; Eleftheriou, A Seascape biodiversity patterns along the Mediterranean and the Black Sea: Lessons from the biogeography of benthic polychaetes Journal Article Marine Ecology Progress Series, 244 , pp. 139–152, 2002, ISSN: 01718630, (Publisher: Inter-Research). @article{arvanitidis_seascape_2002, title = {Seascape biodiversity patterns along the Mediterranean and the Black Sea: Lessons from the biogeography of benthic polychaetes}, author = {C Arvanitidis and G Bellan and P Drakopoulos and V Valavanis and C Dounas and A Koukouras and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037196059&doi=10.3354%2fmeps244139&partnerID=40&md5=24de7c68fd8f96fef3454bcff8471663}, doi = {10.3354/meps244139}, issn = {01718630}, year = {2002}, date = {2002-01-01}, journal = {Marine Ecology Progress Series}, volume = {244}, pages = {139--152}, abstract = {The purpose of this paper is to investigate seascape biodiversity patterns along the Mediterranean and the Black Sea through the study of the benthic polychaete biogeography of the region. A set of non-parametric multivariate analyses and recently developed diversity indices were performed on the benthic polychaete inventories of the areas of the Mediterranean and the Black Sea. Both the numbers of species and the multivariate analyses demonstrate a west-east zoogeocline, shown by the decreasing number of species and by the multivariate similarity pattern of the areas. The performance of the 'second-stage' multi-dimensional scaling (MDS) shows, when species information is aggregated to genera, results belonging practically to the same similarity pattern, independent of the similarity coefficients utilized. The same similarity pattern is derived when species information is aggregated to the zoogeographical categories of amphi-Atlantic, Atlanto-Mediterranean, cosmopolitan and endemic species. BIO-ENV analysis reveals a large number of geographic, climatic and trophic variables to be highly correlated with the similarity pattern derived from the various taxonomic/zoogeographical categories. The synergy, however, of the environmental variables is best reflected in the case of the endemic Mediterranean species. The latter category is considered as the critical zoogeographic category with respect to providing information on the evolutionary history of the taxon in the region. The application of the average taxonomic distinctness and the variation of taxonomic distinctness indices resulted in a diversity ranking of the areas, which appears to be independent of the number of species hosted in each area. However, this is not the case for the phylogenetic diversity (PD) index. Additionally, the former 2 indices indicate that the benthic polychaete species-pool, hosted in the Mediterranean and the Black Sea areas, may well serve as a useful basis for future comparisons in environmental assessment studies. Finally, results from the application of the area-diversity formula show that the equilibrium model can be applicable for the endemic benthic polychaetes of the region: the number of endemic species can be considered as a function of the degree of isolation of the area from the source region against the degree of within-area isolated habitats.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The purpose of this paper is to investigate seascape biodiversity patterns along the Mediterranean and the Black Sea through the study of the benthic polychaete biogeography of the region. A set of non-parametric multivariate analyses and recently developed diversity indices were performed on the benthic polychaete inventories of the areas of the Mediterranean and the Black Sea. Both the numbers of species and the multivariate analyses demonstrate a west-east zoogeocline, shown by the decreasing number of species and by the multivariate similarity pattern of the areas. The performance of the 'second-stage' multi-dimensional scaling (MDS) shows, when species information is aggregated to genera, results belonging practically to the same similarity pattern, independent of the similarity coefficients utilized. The same similarity pattern is derived when species information is aggregated to the zoogeographical categories of amphi-Atlantic, Atlanto-Mediterranean, cosmopolitan and endemic species. BIO-ENV analysis reveals a large number of geographic, climatic and trophic variables to be highly correlated with the similarity pattern derived from the various taxonomic/zoogeographical categories. The synergy, however, of the environmental variables is best reflected in the case of the endemic Mediterranean species. The latter category is considered as the critical zoogeographic category with respect to providing information on the evolutionary history of the taxon in the region. The application of the average taxonomic distinctness and the variation of taxonomic distinctness indices resulted in a diversity ranking of the areas, which appears to be independent of the number of species hosted in each area. However, this is not the case for the phylogenetic diversity (PD) index. Additionally, the former 2 indices indicate that the benthic polychaete species-pool, hosted in the Mediterranean and the Black Sea areas, may well serve as a useful basis for future comparisons in environmental assessment studies. Finally, results from the application of the area-diversity formula show that the equilibrium model can be applicable for the endemic benthic polychaetes of the region: the number of endemic species can be considered as a function of the degree of isolation of the area from the source region against the degree of within-area isolated habitats. |
Arvanitidis, C; Koutsoubas, D; Robin, J -P; Pereira, J; Moreno, A; Cunha, Da M M; Valavanis, V; Eleftheriou, A Bulletin of Marine Science, 71 (1), pp. 129–146, 2002, ISSN: 00074977. @article{arvanitidis_comparison_2002, title = {A comparison of the fishery biology of three Illex coindetii Vérany, 1839 (Cephalopoda: Ommastrephidae) populations from the European Atlantic and Mediterranean waters}, author = {C Arvanitidis and D Koutsoubas and J -P Robin and J Pereira and A Moreno and M M Da Cunha and V Valavanis and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038066629&partnerID=40&md5=28717355f1e10d2ec68ace387c5860bc}, issn = {00074977}, year = {2002}, date = {2002-01-01}, journal = {Bulletin of Marine Science}, volume = {71}, number = {1}, pages = {129--146}, abstract = {Three populations of the short-finned squid Illex coindetii were simultaneously sampled and studied from the Southern Celtic Sea and Bay of Biscay, Portuguese waters and Greek Seas, during a EU funded project (FAIR CT 1520). Dorsal mantle length (DML) ranged from 24 mm to 360 mm and body weight (BW) from 2.4 g to 1630 g. Modal progression analysis (MPA) indicated a female life span of 13-18 mo and in male life span of 11 mo. Length-weight relationship was found to be positively allometric for males and negatively allometric for females in all three populations. Sex ratio did not differ significantly from 1:1 over the entire sampling period. Differences among the three populations were observed for the following life-cycle parameters: (1) males from the Portuguese waters had significantly different length-weight slopes from those from the remainder areas; (2) size at full recruitment was determined at 110 mm in females from the Portuguese waters whereas in females from the Southern Celtic Sea and Bay of Biscay and from the Greek Seas was 170 mm; (3) female recruitment peaks were recorded only during autumn in samples from the Southern Celtic Sea and Bay of Biscay while in those from the Portuguese waters and the Greek Seas the recruitment peaks were recorded at various seasons; (4) maturing and mature males were found abundantly over the entire sampling period in the samples from the Southern Celtic Sea and Bay of Biscay and the Greek Seas whereas in those from the Portuguese waters maturing and mature males were at higher percentages than immature ones only during spring and summer; peaks of the Gonadosomatic index, calculated for mature females from the Southern Celtic Sea and Bay of Biscay, were scored from February to April of 1998 and 1999 and during September of 1998 while in the samples from the Greek waters during April and August 1998 and during January and May 1999; (5) L50 (mantle length at which 50% of the individuals are mature) values estimated for both females and males from the three studied areas were gradually decreased from the North Atlantic to the Mediterranean; (6) length data suggest that females from the Greek Seas potentially mature at two modal sizes while those from the remainder areas show only one modal size at maturity. Environmental variables (sea surface temperature and chlorophyll-a concentration) were correlated with some of the biological indices of the I. coindetii populations. Finally, results on biological indices of the I. coindetii are compared with those calculated for its congeneric species I. illecebrosus, I. argentinus as well as with another European ommastrephid species Todaropsis eblanae.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Three populations of the short-finned squid Illex coindetii were simultaneously sampled and studied from the Southern Celtic Sea and Bay of Biscay, Portuguese waters and Greek Seas, during a EU funded project (FAIR CT 1520). Dorsal mantle length (DML) ranged from 24 mm to 360 mm and body weight (BW) from 2.4 g to 1630 g. Modal progression analysis (MPA) indicated a female life span of 13-18 mo and in male life span of 11 mo. Length-weight relationship was found to be positively allometric for males and negatively allometric for females in all three populations. Sex ratio did not differ significantly from 1:1 over the entire sampling period. Differences among the three populations were observed for the following life-cycle parameters: (1) males from the Portuguese waters had significantly different length-weight slopes from those from the remainder areas; (2) size at full recruitment was determined at 110 mm in females from the Portuguese waters whereas in females from the Southern Celtic Sea and Bay of Biscay and from the Greek Seas was 170 mm; (3) female recruitment peaks were recorded only during autumn in samples from the Southern Celtic Sea and Bay of Biscay while in those from the Portuguese waters and the Greek Seas the recruitment peaks were recorded at various seasons; (4) maturing and mature males were found abundantly over the entire sampling period in the samples from the Southern Celtic Sea and Bay of Biscay and the Greek Seas whereas in those from the Portuguese waters maturing and mature males were at higher percentages than immature ones only during spring and summer; peaks of the Gonadosomatic index, calculated for mature females from the Southern Celtic Sea and Bay of Biscay, were scored from February to April of 1998 and 1999 and during September of 1998 while in the samples from the Greek waters during April and August 1998 and during January and May 1999; (5) L50 (mantle length at which 50% of the individuals are mature) values estimated for both females and males from the three studied areas were gradually decreased from the North Atlantic to the Mediterranean; (6) length data suggest that females from the Greek Seas potentially mature at two modal sizes while those from the remainder areas show only one modal size at maturity. Environmental variables (sea surface temperature and chlorophyll-a concentration) were correlated with some of the biological indices of the I. coindetii populations. Finally, results on biological indices of the I. coindetii are compared with those calculated for its congeneric species I. illecebrosus, I. argentinus as well as with another European ommastrephid species Todaropsis eblanae. |
2000 |
Arvanitidis, C Polychaete fauna of the Aegean Sea: Inventory and new information Journal Article Bulletin of Marine Science, 66 (1), pp. 73–96, 2000, ISSN: 00074977, (Publisher: Rosenstiel School of Marine and Atmospheric Science). @article{arvanitidis_polychaete_2000, title = {Polychaete fauna of the Aegean Sea: Inventory and new information}, author = {C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034580549&partnerID=40&md5=2f5e5caaa482887d362e82dfe1ece550}, issn = {00074977}, year = {2000}, date = {2000-01-01}, journal = {Bulletin of Marine Science}, volume = {66}, number = {1}, pages = {73--96}, abstract = {Examination of collections from the Aegean Sea and a review of the literature revealed that 592 polychaete species have been recorded from this area. Five of the species identified are reported for the first time from the Mediterranean and the Black Sea, 38 species are new records for the Eastern Mediterranean and 55 are new elements for the Aegean polychaete fauna. Information on the habitat and the geographic distribution of the species newly reported from the Eastern Mediterranean is given. The checklist of the Aegean Polychaeta is presented. Although being located in the vicinity of the Eastern Mediterranean province and the Black Sea which are characterized as faunistically impoverished areas, the Aegean hosts a rich polychaete fauna, second in order in species diversity after the Western Mediterranean. The latter demonstrates the importance of this area in the understanding the patterns of polychaete distribution along the Mediterranean and the Black Sea.}, note = {Publisher: Rosenstiel School of Marine and Atmospheric Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } Examination of collections from the Aegean Sea and a review of the literature revealed that 592 polychaete species have been recorded from this area. Five of the species identified are reported for the first time from the Mediterranean and the Black Sea, 38 species are new records for the Eastern Mediterranean and 55 are new elements for the Aegean polychaete fauna. Information on the habitat and the geographic distribution of the species newly reported from the Eastern Mediterranean is given. The checklist of the Aegean Polychaeta is presented. Although being located in the vicinity of the Eastern Mediterranean province and the Black Sea which are characterized as faunistically impoverished areas, the Aegean hosts a rich polychaete fauna, second in order in species diversity after the Western Mediterranean. The latter demonstrates the importance of this area in the understanding the patterns of polychaete distribution along the Mediterranean and the Black Sea. |
Koutsoubas, D; Arvanitidis, C; Dounas, C; Drummond, L Community structure and dynamics of the Molluscan Fauna in a Mediterranean lagoon (Gialova lagoon, SW Greece) Journal Article Belgian Journal of Zoology, 130 (SUPPL. 1), pp. 131–138, 2000, ISSN: 07776276. @article{koutsoubas_community_2000, title = {Community structure and dynamics of the Molluscan Fauna in a Mediterranean lagoon (Gialova lagoon, SW Greece)}, author = {D Koutsoubas and C Arvanitidis and C Dounas and L Drummond}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649411533&partnerID=40&md5=0db45fbd7fa9f9b765b6564d3c978855}, issn = {07776276}, year = {2000}, date = {2000-01-01}, journal = {Belgian Journal of Zoology}, volume = {130}, number = {SUPPL. 1}, pages = {131--138}, abstract = {The molluscan community of a shallow Mediterranean lagoon (Gialova lagoon, SW Greece, Ionian Sea) was studied on a seasonal basis during 1995-1996. A total of 23 species were recorded from the lagoon. Two of them namely: Placida viridis and Polycerella emertoni are reported for the first time from the Greek seas and the Eastern Mediterranean respectively. The dominant species were the gastropods Bittium reticulatum, Cerithium vulgatum, Pirenella conica, Hydrobia acuta, Cyclope neritea and the bivalves Cerastoderma glaucum, Abra ovata. Uni- and multivariate methods were employed to study the community structure and dynamics. On the basis of the multivariate pattern of the molluscan community a coenocline is observed which is strongly related with the degree of isolation. Two main zones with different faunal composition can be distinguished: one narrow zone close to the channel of communication with the sea and another in the innermost part of the lagoon. Following the confinement scale suggested for lagoonal ecosystems by GUELORGET & PERTHUISOT (1992) the first zone can be assigned to the "zone III" and the second to "zones IVV". The distribution pattern of the molluscan community is governed by a different set of environmental variables in each season, discussed in detail. Although no disturbance due to anthropogenic impact was revealed, this narrow lagoonal habitat was proved to suffer severe "dystrophic episodes", during late summer and the beginning of autumn, but successfully recovered, demonstrating a seasonal community pattern.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The molluscan community of a shallow Mediterranean lagoon (Gialova lagoon, SW Greece, Ionian Sea) was studied on a seasonal basis during 1995-1996. A total of 23 species were recorded from the lagoon. Two of them namely: Placida viridis and Polycerella emertoni are reported for the first time from the Greek seas and the Eastern Mediterranean respectively. The dominant species were the gastropods Bittium reticulatum, Cerithium vulgatum, Pirenella conica, Hydrobia acuta, Cyclope neritea and the bivalves Cerastoderma glaucum, Abra ovata. Uni- and multivariate methods were employed to study the community structure and dynamics. On the basis of the multivariate pattern of the molluscan community a coenocline is observed which is strongly related with the degree of isolation. Two main zones with different faunal composition can be distinguished: one narrow zone close to the channel of communication with the sea and another in the innermost part of the lagoon. Following the confinement scale suggested for lagoonal ecosystems by GUELORGET & PERTHUISOT (1992) the first zone can be assigned to the "zone III" and the second to "zones IVV". The distribution pattern of the molluscan community is governed by a different set of environmental variables in each season, discussed in detail. Although no disturbance due to anthropogenic impact was revealed, this narrow lagoonal habitat was proved to suffer severe "dystrophic episodes", during late summer and the beginning of autumn, but successfully recovered, demonstrating a seasonal community pattern. |
Koutsoubas, D; Dounas, C; Arvanitidis, C; Kornilios, S; Petihakis, G; Triantafyllou, G; Eleftheriou, A Macrobenthic community structure and disturbance assessment in Gialova Lagoon, Ionian Sea Journal Article ICES Journal of Marine Science, 57 (5), pp. 1472–1480, 2000, ISSN: 10543139, (Publisher: Academic Press). @article{koutsoubas_macrobenthic_2000, title = {Macrobenthic community structure and disturbance assessment in Gialova Lagoon, Ionian Sea}, author = {D Koutsoubas and C Dounas and C Arvanitidis and S Kornilios and G Petihakis and G Triantafyllou and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034493473&doi=10.1006%2fjmsc.2000.0905&partnerID=40&md5=ab96a84ab0a1dbac9ddf62aba60edc11}, doi = {10.1006/jmsc.2000.0905}, issn = {10543139}, year = {2000}, date = {2000-01-01}, journal = {ICES Journal of Marine Science}, volume = {57}, number = {5}, pages = {1472--1480}, abstract = {Gialova Lagoon, a coastal marine ecosystem in the Ionian Sea, suffered the impact of an oil spill incident in October 1993, leading to the extensive fish deaths when the oil tanker "Iliad" hit bottom in the entrance of the neighbouring Navarino Bay. A multidisciplinary study investigating the structure and functioning of Gialova Lagoon for the development of an integrated economic, social, and environmental management policy consistent with its conservation was carried out on a seasonal basis during 1995/1996. One of the research priorities was to investigate the structure and dynamics of the macrozoobenthic communities and assess whether these communities had recovered from the impact of the oil spill. The various methods applied (abundance/biomass comparison, distribution of species in geometric abundance and geometric size classes) revealed no detectable disturbance of the macrobenthic communities due to anthropogenic impact. However, it was proved that the lagoonal macrofauna suffered extreme natural disturbance due to a dystrophic crisis that occurred during autumn although they successfully recovered in subsequent seasons. Different sets of environmental factors were found to be highly correlated with the temporal and spatial distribution pattern of the macrobenthic communities and are discussed in detail. The coenocline observed in Gialova Lagoon appears to be strongly correlated with the degree of water exchange with adjacent marine and continental environments. © 2000 International Council for the Exploration of the Sea.}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gialova Lagoon, a coastal marine ecosystem in the Ionian Sea, suffered the impact of an oil spill incident in October 1993, leading to the extensive fish deaths when the oil tanker "Iliad" hit bottom in the entrance of the neighbouring Navarino Bay. A multidisciplinary study investigating the structure and functioning of Gialova Lagoon for the development of an integrated economic, social, and environmental management policy consistent with its conservation was carried out on a seasonal basis during 1995/1996. One of the research priorities was to investigate the structure and dynamics of the macrozoobenthic communities and assess whether these communities had recovered from the impact of the oil spill. The various methods applied (abundance/biomass comparison, distribution of species in geometric abundance and geometric size classes) revealed no detectable disturbance of the macrobenthic communities due to anthropogenic impact. However, it was proved that the lagoonal macrofauna suffered extreme natural disturbance due to a dystrophic crisis that occurred during autumn although they successfully recovered in subsequent seasons. Different sets of environmental factors were found to be highly correlated with the temporal and spatial distribution pattern of the macrobenthic communities and are discussed in detail. The coenocline observed in Gialova Lagoon appears to be strongly correlated with the degree of water exchange with adjacent marine and continental environments. © 2000 International Council for the Exploration of the Sea. |
Triantafyllou, G; Petihakis, G; Dounas, C; Koutsoubas, D; Arvanitidis, C; Eleftheriou, A Temporal variations in benthic communities and their response to physicochemical forcing: A numerical approach Journal Article ICES Journal of Marine Science, 57 (5), pp. 1507–1516, 2000, ISSN: 10543139, (Publisher: Academic Press). @article{triantafyllou_temporal_2000, title = {Temporal variations in benthic communities and their response to physicochemical forcing: A numerical approach}, author = {G Triantafyllou and G Petihakis and C Dounas and D Koutsoubas and C Arvanitidis and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034492083&doi=10.1006%2fjmsc.2000.0923&partnerID=40&md5=37dbe9cbf95e8c4e2e62b7f6e7c163d2}, doi = {10.1006/jmsc.2000.0923}, issn = {10543139}, year = {2000}, date = {2000-01-01}, journal = {ICES Journal of Marine Science}, volume = {57}, number = {5}, pages = {1507--1516}, abstract = {A generic complex ecological model, the European Regional Seas Ecosystem Model (ERSEM), was applied to a shallow lagoon system in the Eastern Mediterranean. Model results depicting the seasonal variation of nutrients and Chl-α in the water column, as well as three benthic functional groups (suspended feeders, deposit feeders, and benthic carnivores), are validated with in situ data. The likely effect of a technical intervention (river input) increasing the freshwater nutrient inputs on ecosystem functioning is also investigated. Detailed annual carbon fluxes and benthic fauna biomasses are calculated, before and after the river input. The importance of external physical/chemical forcing on the pelagic system and its subsequent effect on the benthic system are demonstrated. Model experiments indicate the shift of the ecosystem from nitrate limitation to predator control with external inputs. Model experiments also show a significant increase in the amount of carbon entering the benthic system through the activity of filter feeders when river inputs are implemented. © 2000 International Council for the Exploration of the Sea.}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } A generic complex ecological model, the European Regional Seas Ecosystem Model (ERSEM), was applied to a shallow lagoon system in the Eastern Mediterranean. Model results depicting the seasonal variation of nutrients and Chl-α in the water column, as well as three benthic functional groups (suspended feeders, deposit feeders, and benthic carnivores), are validated with in situ data. The likely effect of a technical intervention (river input) increasing the freshwater nutrient inputs on ecosystem functioning is also investigated. Detailed annual carbon fluxes and benthic fauna biomasses are calculated, before and after the river input. The importance of external physical/chemical forcing on the pelagic system and its subsequent effect on the benthic system are demonstrated. Model experiments indicate the shift of the ecosystem from nitrate limitation to predator control with external inputs. Model experiments also show a significant increase in the amount of carbon entering the benthic system through the activity of filter feeders when river inputs are implemented. © 2000 International Council for the Exploration of the Sea. |
Dounas, C; Arvanitidis, C; Koulouri, P Artificial reefs as a management tool for the delineation, protection and enhancement of coastal ecosystems Journal Article Fishing News, 228 , pp. 94–96 (In Greek), 2000. @article{dounas_artificial_2000, title = {Artificial reefs as a management tool for the delineation, protection and enhancement of coastal ecosystems}, author = {C Dounas and C Arvanitidis and P Koulouri}, year = {2000}, date = {2000-01-01}, journal = {Fishing News}, volume = {228}, pages = {94--96 (In Greek)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1999 |
Arvanitidis, C; Koutsoubas, D; Dounas, C; Eleftheriou, A Annelid fauna of a Mediterranean lagoon (Gialova Lagoon, south-west Greece): Community structure in a severely fluctuating environment Journal Article Journal of the Marine Biological Association of the United Kingdom, 79 (5), pp. 849–856, 1999, ISSN: 00253154. @article{arvanitidis_annelid_1999, title = {Annelid fauna of a Mediterranean lagoon (Gialova Lagoon, south-west Greece): Community structure in a severely fluctuating environment}, author = {C Arvanitidis and D Koutsoubas and C Dounas and A Eleftheriou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032745818&doi=10.1017%2fS0025315499001010&partnerID=40&md5=b5ac264673a03e1f15a7a88f2be04fd2}, doi = {10.1017/S0025315499001010}, issn = {00253154}, year = {1999}, date = {1999-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {79}, number = {5}, pages = {849--856}, abstract = {The annelid community of a shallow Mediterranean lagoon (Gialova Lagoon, Ionian Sea) was studied on a seasonal basis. Out of the 39 species identified eight are reported for the first time from the central Mediterranean. The dominant species were the polychaetes Capitella capitata, Neodexiospira pseudocorrugata, Malacoceros fuliginosus, Perinereis cultrifera, Hediste diversicolor, Heteromastus filiformis and the oligochaete Limnodriloides maslinicensis. Uni- and multivariate methods were employed to study the community structure. The coenocline observed is strongly related to the degree of isolation; its main features (i.e. number of species, density, geometric abundance and size-classes) in space and time are presented and discussed in detail. The distribution pattern of the annelid community has been found to be governed by a different set of environmental factors in each season. Although this narrow lagoonal habitat suffers severe dystrophic episodes it manages to recover, demonstrating a seasonal community pattern.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The annelid community of a shallow Mediterranean lagoon (Gialova Lagoon, Ionian Sea) was studied on a seasonal basis. Out of the 39 species identified eight are reported for the first time from the central Mediterranean. The dominant species were the polychaetes Capitella capitata, Neodexiospira pseudocorrugata, Malacoceros fuliginosus, Perinereis cultrifera, Hediste diversicolor, Heteromastus filiformis and the oligochaete Limnodriloides maslinicensis. Uni- and multivariate methods were employed to study the community structure. The coenocline observed is strongly related to the degree of isolation; its main features (i.e. number of species, density, geometric abundance and size-classes) in space and time are presented and discussed in detail. The distribution pattern of the annelid community has been found to be governed by a different set of environmental factors in each season. Although this narrow lagoonal habitat suffers severe dystrophic episodes it manages to recover, demonstrating a seasonal community pattern. |
1998 |
Dounas, C; Koutsoubas, D; Arvanitidis, C; Petihakis, G; Drummond, L; A, Eleftheriou Biodiversity and the impact of anthropogenic activities in Mediterranean lagoons: The case of Gialova lagoon, SW Greece Journal Article Oebalia, 24 , pp. 77–91, 1998. @article{dounas_biodiversity_1998, title = {Biodiversity and the impact of anthropogenic activities in Mediterranean lagoons: The case of Gialova lagoon, SW Greece}, author = {C Dounas and D Koutsoubas and C Arvanitidis and G Petihakis and L Drummond and Eleftheriou A}, year = {1998}, date = {1998-01-01}, journal = {Oebalia}, volume = {24}, pages = {77--91}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
1997 |
Arvanitidis, C; Koukouras, A The genus Paradiopatra (Polychaeta, Onuphidae) in the Mediterranean with the description of Paradiopatra calliopae sp. nov. Journal Article Ophelia, 46 (1), pp. 51–63, 1997, ISSN: 00785326. @article{arvanitidis_genus_1997, title = {The genus Paradiopatra (Polychaeta, Onuphidae) in the Mediterranean with the description of Paradiopatra calliopae sp. nov.}, author = {C Arvanitidis and A Koukouras}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030893558&doi=10.1080%2f00785326.1997.10432477&partnerID=40&md5=493ee746ab970481fdc7617b2e1a3eba}, doi = {10.1080/00785326.1997.10432477}, issn = {00785326}, year = {1997}, date = {1997-01-01}, journal = {Ophelia}, volume = {46}, number = {1}, pages = {51--63}, abstract = {Sampling in circalittoral and bathyal zones of the North Aegean Sea, yielded a considerable number of specimens belonging to two species of the genus Paradiopatra Ehlers, 1887: P. quadricuspis (M. Sars, 1872) and P. calliopae sp. nov. P. quadricuspis from the North Aegean show slight differences from the type material. In addition, some features of the species, not reported by previous authors, are given. Also, the holotype of the Atlantic species P. bihanica (Intes & Le Loeuff, 1975) was re-examined and useful conclusions about the status of this species and its distinction from the new species are drawn. Re-examination of a specimen from the Ionian Sea, reported as Onuphis lepta, shows that it possibly belongs to the new species. The new species is compared with its closest congeners (P. quadricuspis, P. bihanica, and P. fauchaldi (Kirkegaard, 1988)) and the characters distinguishing them are given. The status of the genus in the Mediterranean is discussed. © 1997 Taylor & Francis Group, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sampling in circalittoral and bathyal zones of the North Aegean Sea, yielded a considerable number of specimens belonging to two species of the genus Paradiopatra Ehlers, 1887: P. quadricuspis (M. Sars, 1872) and P. calliopae sp. nov. P. quadricuspis from the North Aegean show slight differences from the type material. In addition, some features of the species, not reported by previous authors, are given. Also, the holotype of the Atlantic species P. bihanica (Intes & Le Loeuff, 1975) was re-examined and useful conclusions about the status of this species and its distinction from the new species are drawn. Re-examination of a specimen from the Ionian Sea, reported as Onuphis lepta, shows that it possibly belongs to the new species. The new species is compared with its closest congeners (P. quadricuspis, P. bihanica, and P. fauchaldi (Kirkegaard, 1988)) and the characters distinguishing them are given. The status of the genus in the Mediterranean is discussed. © 1997 Taylor & Francis Group, LLC. |
Koutsoubas, D; Dounas, C; Petihakis, G; Arvanitidis, C; Triantafyllou, G; Dafnomili, E; Zivanovic, S Dynamics of the physicochemical parameters in water column and in the sediments of the Gialova lagoon (NW Peloponnese, Ionian Sea) Inproceedings pp. 351–353, Kavala, Greece, 1997, (Publication Title: Seventh Symposium on Oceanography and Fisheries, Κavala). @inproceedings{koutsoubas_dynamics_1997, title = {Dynamics of the physicochemical parameters in water column and in the sediments of the Gialova lagoon (NW Peloponnese, Ionian Sea)}, author = {D Koutsoubas and C Dounas and G Petihakis and C Arvanitidis and G Triantafyllou and E Dafnomili and S Zivanovic}, year = {1997}, date = {1997-01-01}, volume = {II}, pages = {351--353}, address = {Kavala, Greece}, note = {Publication Title: Seventh Symposium on Oceanography and Fisheries, Κavala}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Koutsoubas, D; Arvanitidis, C; Petihakis, G; Drummond, L; Dounas, C Structure and dynamics of the macrobenthic populations in Gialova lagoon (Ionian Sea) Inproceedings 1997, (Publication Title: Seventh Symposium on Oceanography and Fisheries, Κavala). @inproceedings{koutsoubas_structure_1997, title = {Structure and dynamics of the macrobenthic populations in Gialova lagoon (Ionian Sea)}, author = {D Koutsoubas and C Arvanitidis and G Petihakis and L Drummond and C Dounas}, year = {1997}, date = {1997-01-01}, volume = {II}, note = {Publication Title: Seventh Symposium on Oceanography and Fisheries, Κavala}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
1996 |
Koukouras, A; Russo, A; Voultsiadou-Koukoura, E; Arvanitidis, C; Stefanidou, D Macrofauna associated with sponge species of different morphology Journal Article Marine Ecology, 17 (4), pp. 569–582, 1996, ISSN: 01739565, (Publisher: Blackwell Verlag GmbH Berlin). @article{koukouras_macrofauna_1996, title = {Macrofauna associated with sponge species of different morphology}, author = {A Koukouras and A Russo and E Voultsiadou-Koukoura and C Arvanitidis and D Stefanidou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030427632&doi=10.1111%2fj.1439-0485.1996.tb00418.x&partnerID=40&md5=ab85ea94afe5115359c48dad5fa7b5fb}, doi = {10.1111/j.1439-0485.1996.tb00418.x}, issn = {01739565}, year = {1996}, date = {1996-01-01}, journal = {Marine Ecology}, volume = {17}, number = {4}, pages = {569--582}, abstract = {The macrofaunas associated with the three morphologically different North Aegean Sea sponge species Agelas oroides, Aplysina aerophoba, and Axinella cannabina were compared. The faunal abundance was not related to sponge surface area for any of the three species. Each sponge species supported a significantly different number of individuals per unit canal volume; A. aerophoba supported the most, A. oroides the least. A. aerophoba supported the highest species richness, A. cannabina the lowest. Canal volume was a good predictor of associated faunal abundance and species richness for two of the three sponge species. Faunal abundance was also directly related to sponge mean canal diameter. The species composition of associated fauna was similar on A. aerophoba and A, oroides and significantly different on A. cannabina.}, note = {Publisher: Blackwell Verlag GmbH Berlin}, keywords = {}, pubstate = {published}, tppubtype = {article} } The macrofaunas associated with the three morphologically different North Aegean Sea sponge species Agelas oroides, Aplysina aerophoba, and Axinella cannabina were compared. The faunal abundance was not related to sponge surface area for any of the three species. Each sponge species supported a significantly different number of individuals per unit canal volume; A. aerophoba supported the most, A. oroides the least. A. aerophoba supported the highest species richness, A. cannabina the lowest. Canal volume was a good predictor of associated faunal abundance and species richness for two of the three sponge species. Faunal abundance was also directly related to sponge mean canal diameter. The species composition of associated fauna was similar on A. aerophoba and A, oroides and significantly different on A. cannabina. |
Dounas, C; Koutsoubas, Drosos; Arvanitidis, Christos; Petihakis, George; Drummond, A; Eleftheriou, A Βiodiversity in the Μediterranean lagoons: Τhe case of Gialova lagoon, SW Greece Inproceedings Frankfurt a.M., Germany, 1996, (Publication Title: Second Ιnternational Βiodiversity Conference, Frankfurt a.M., Germany). @inproceedings{dounas_iodiversity_1996, title = {Βiodiversity in the Μediterranean lagoons: Τhe case of Gialova lagoon, SW Greece}, author = {C Dounas and Drosos Koutsoubas and Christos Arvanitidis and George Petihakis and A Drummond and A Eleftheriou}, year = {1996}, date = {1996-01-01}, address = {Frankfurt a.M., Germany}, note = {Publication Title: Second Ιnternational Βiodiversity Conference, Frankfurt a.M., Germany}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
1995 |
Arvanitidis, C; Koukouras, A Ophelia, 40 (3), pp. 219–227, 1995, ISSN: 00785326. @article{arvanitidis_amphitritides_1995, title = {Amphitritides kuehlmanni sp. nov. (Polychaeta, terebellidae, amphitritinae) From the aegean sea, with comments on the genus amphitritides augener}, author = {C Arvanitidis and A Koukouras}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0008052656&doi=10.1080%2f00785326.1995.10430587&partnerID=40&md5=1d9f4ac3229430ce5afd424dee8fc704}, doi = {10.1080/00785326.1995.10430587}, issn = {00785326}, year = {1995}, date = {1995-01-01}, journal = {Ophelia}, volume = {40}, number = {3}, pages = {219--227}, abstract = {A new species of Terebellidae Polychaeta, Amphitritides kuehlmanni, is described from shallow waters in the North Aegean. The new species is compared to the other known species of the genus. The status of the genus Amphitritides Augener is discussed. © 1995, Taylor & Francis Group. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new species of Terebellidae Polychaeta, Amphitritides kuehlmanni, is described from shallow waters in the North Aegean. The new species is compared to the other known species of the genus. The status of the genus Amphitritides Augener is discussed. © 1995, Taylor & Francis Group. All rights reserved. |
1994 |
Arvanitidis, C; Koukouras, A Ρolychaete fauna associated with the coral Cladocora caespitosa (L.) in the Εastern Μediterranean Journal Article Μémoires du Μuséum Nationale d’Ηistoire Naturelle, 162 , pp. 347–353, 1994. @article{arvanitidis_olychaete_1994, title = {Ρolychaete fauna associated with the coral Cladocora caespitosa (L.) in the Εastern Μediterranean}, author = {C Arvanitidis and A Koukouras}, year = {1994}, date = {1994-01-01}, journal = {Μémoires du Μuséum Nationale d’Ηistoire Naturelle}, volume = {162}, pages = {347--353}, abstract = {Analysis of the polychaetefauna in 14 colonies of Cladocora caespitosa at two localities of Chalkidiki peninsula. N. Aegean Se, revealed 87 species, 58 of which are recorded for the first time as associated with this scleractinian coral. Larger colonies (up to 7 kg) contained more species, more individuals and a greater biomass. In one location, depth 3-5 m, Serpulidae were dominant (Vermiliopsis infundibulum, Hydroides pseudouncinata pseudouncinata, Veriiliopsis striaticeps, Spirobranchus polytrema and Serpula vermicularis) but at 16-19 m these were replaced in abundance by errant species, especially Ceratonereis costae.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Analysis of the polychaetefauna in 14 colonies of Cladocora caespitosa at two localities of Chalkidiki peninsula. N. Aegean Se, revealed 87 species, 58 of which are recorded for the first time as associated with this scleractinian coral. Larger colonies (up to 7 kg) contained more species, more individuals and a greater biomass. In one location, depth 3-5 m, Serpulidae were dominant (Vermiliopsis infundibulum, Hydroides pseudouncinata pseudouncinata, Veriiliopsis striaticeps, Spirobranchus polytrema and Serpula vermicularis) but at 16-19 m these were replaced in abundance by errant species, especially Ceratonereis costae. |