2025 |
Kapelonis, Zacharias; Chatzigeorgiou, Georgios; Ntoumas, Manolis; Grigoriou, Panos; Pettas, Manos; Michelinakis, Spyros; Correia, Ricardo; Lemos, Catarina Rasquilha; Pinheiro, Luis Menezes; Lomba, Caio; Fortuna, João; Loureiro, Rui; Santos, André; Chatzinikolaou, Eva Flying Robots Teach Floating Robots—A Machine Learning Approach for Marine Habitat Mapping Based on Combined Datasets Journal Article Journal of Marine Science and Engineering, 13 (3), pp. 611, 2025, ISSN: 2077-1312. @article{kapelonis_flying_2025, title = {Flying Robots Teach Floating Robots—A Machine Learning Approach for Marine Habitat Mapping Based on Combined Datasets}, author = {Zacharias Kapelonis and Georgios Chatzigeorgiou and Manolis Ntoumas and Panos Grigoriou and Manos Pettas and Spyros Michelinakis and Ricardo Correia and Catarina Rasquilha Lemos and Luis Menezes Pinheiro and Caio Lomba and João Fortuna and Rui Loureiro and André Santos and Eva Chatzinikolaou}, url = {https://www.mdpi.com/2077-1312/13/3/611 /wp-content/uploads/2025/04/2025-Kapelonis-Mar-Sci-Eng-19.pdf}, doi = {10.3390/jmse13030611}, issn = {2077-1312}, year = {2025}, date = {2025-04-11}, urldate = {2025-04-11}, journal = {Journal of Marine Science and Engineering}, volume = {13}, number = {3}, pages = {611}, abstract = {Unmanned aerial and autonomous surface vehicles (UAVs and ASVs, respectively) are two emerging technologies for the mapping of coastal and marine environments. Using UAV photogrammetry, the sea-bottom composition can be resolved with very high fidelity in shallow waters. At greater depths, acoustic methodologies have far better propagation properties compared to optics; therefore, ASVs equipped with multibeam echosounders (MBES) are better-suited for mapping applications in deeper waters. In this work, a sea-bottom classification methodology is presented for mapping the protected habitat of Mediterranean seagrass Posidonia oceanica (habitat code 1120) in a coastal subregion of Heraklion (Crete, Greece). The methodology implements a machine learning scheme, where knowledge obtained from UAV imagery is embedded (through training) into a classifier that utilizes acoustic backscatter intensity and features derived from the MBES data provided by an ASV. Accuracy and precision scores of greater than 85% compared with visual census ground-truth data for both optical and acoustic classifiers indicate that this hybrid mapping approach is promising to mitigate the depth-induced bias in UAV-only models. The latter is especially interesting in cases where the studied habitat boundaries extend beyond depths that can be studied via aerial devices’ optics, as is the case with P. oceanica meadows.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Unmanned aerial and autonomous surface vehicles (UAVs and ASVs, respectively) are two emerging technologies for the mapping of coastal and marine environments. Using UAV photogrammetry, the sea-bottom composition can be resolved with very high fidelity in shallow waters. At greater depths, acoustic methodologies have far better propagation properties compared to optics; therefore, ASVs equipped with multibeam echosounders (MBES) are better-suited for mapping applications in deeper waters. In this work, a sea-bottom classification methodology is presented for mapping the protected habitat of Mediterranean seagrass Posidonia oceanica (habitat code 1120) in a coastal subregion of Heraklion (Crete, Greece). The methodology implements a machine learning scheme, where knowledge obtained from UAV imagery is embedded (through training) into a classifier that utilizes acoustic backscatter intensity and features derived from the MBES data provided by an ASV. Accuracy and precision scores of greater than 85% compared with visual census ground-truth data for both optical and acoustic classifiers indicate that this hybrid mapping approach is promising to mitigate the depth-induced bias in UAV-only models. The latter is especially interesting in cases where the studied habitat boundaries extend beyond depths that can be studied via aerial devices’ optics, as is the case with P. oceanica meadows. |
Brecko, Jonathan; Mathys, Aurore; Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Blettery, Jonathan; Green, Laura; Musson, Alicia; Paton, Alan; Phillips, Sarah; Bastir, Markus; Wiltschke, Karin; Rainer, Heimo; Kroh, Andreas; Haston, Elspeth; Semal, Patrick DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections Journal Article European Journal of Taxonomy, 976 , 2025, ISSN: 2118-9773. @article{brecko_digit-key_2025, title = {DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections}, author = {Jonathan Brecko and Aurore Mathys and Eva Chatzinikolaou and Kleoniki Keklikoglou and Jonathan Blettery and Laura Green and Alicia Musson and Alan Paton and Sarah Phillips and Markus Bastir and Karin Wiltschke and Heimo Rainer and Andreas Kroh and Elspeth Haston and Patrick Semal}, url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2797 /wp-content/uploads/2025/03/2025-Brecko-EuJTax-9.pdf}, doi = {10.5852/ejt.2025.976.2797}, issn = {2118-9773}, year = {2025}, date = {2025-03-04}, urldate = {2025-03-04}, journal = {European Journal of Taxonomy}, volume = {976}, abstract = {Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access. |
Daraghmeh, Nauras; Exter, Katrina; Pagnier, Justine; Balazy, Piotr; Cancio, Ibon; Chatzigeorgiou, Giorgos; Chatzinikolaou, Eva; Chelchowski, Maciej; Chrismas, Nathan Alexis Mitchell; Comtet, Thierry; Dailianis, Thanos; Deneudt, Klaas; Cerio, Oihane Diaz De; Digenis, Markos; Gerovasileiou, Vasilis; González, José; Kauppi, Laura; Kristoffersen, Jon Bent; Kukliński, Piotr; Lasota, Rafał; Levy, Liraz; Małachowicz, Magdalena; Mavrič, Borut; Mortelmans, Jonas; Paredes, Estefania; Poćwierz‐Kotus, Anita; Reiss, Henning; Santi, Ioulia; Sarafidou, Georgia; Skouradakis, Grigorios; Solbakken, Jostein; Staehr, Peter A U; Tajadura, Javier; Thyrring, Jakob; Troncoso, Jesus S; Vernadou, Emmanouela; Viard, Frederique; Zafeiropoulos, Haris; Zbawicka, Małgorzata; Pavloudi, Christina; Obst, Matthias A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020 Journal Article Molecular Ecology Resources, pp. e14073, 2025, ISSN: 1755-098X, 1755-0998. @article{daraghmeh_longterm_2025, title = {A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020}, author = {Nauras Daraghmeh and Katrina Exter and Justine Pagnier and Piotr Balazy and Ibon Cancio and Giorgos Chatzigeorgiou and Eva Chatzinikolaou and Maciej Chelchowski and Nathan Alexis Mitchell Chrismas and Thierry Comtet and Thanos Dailianis and Klaas Deneudt and Oihane Diaz De Cerio and Markos Digenis and Vasilis Gerovasileiou and José González and Laura Kauppi and Jon Bent Kristoffersen and Piotr Kukliński and Rafał Lasota and Liraz Levy and Magdalena Małachowicz and Borut Mavrič and Jonas Mortelmans and Estefania Paredes and Anita Poćwierz‐Kotus and Henning Reiss and Ioulia Santi and Georgia Sarafidou and Grigorios Skouradakis and Jostein Solbakken and Peter A U Staehr and Javier Tajadura and Jakob Thyrring and Jesus S Troncoso and Emmanouela Vernadou and Frederique Viard and Haris Zafeiropoulos and Małgorzata Zbawicka and Christina Pavloudi and Matthias Obst}, url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.14073 /wp-content/uploads/2025/02/2025-Daraghmeh-MolEcoRes-6.pdf}, doi = {10.1111/1755-0998.14073}, issn = {1755-098X, 1755-0998}, year = {2025}, date = {2025-02-05}, urldate = {2025-02-05}, journal = {Molecular Ecology Resources}, pages = {e14073}, abstract = {ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols. |
2024 |
Los, Wouter; Năpăruş-Aljančič, Magdalena; Bileva, Tatyana; Chatzinikolaou, Eva; Graber-Soudry, Ohad; Moncuit, Lucas De; Neto, Marta; Pesole, Graziano; Abascal, Maria Vallejo; Grozdanova, Dafinka The lifeblood of LifeWatch ERIC: national in-kind contributions Journal Article Research Ideas and Outcomes, 10 , pp. e121887, 2024, ISSN: 2367-7163. @article{los_lifeblood_2024, title = {The lifeblood of LifeWatch ERIC: national in-kind contributions}, author = {Wouter Los and Magdalena Năpăruş-Aljančič and Tatyana Bileva and Eva Chatzinikolaou and Ohad Graber-Soudry and Lucas De Moncuit and Marta Neto and Graziano Pesole and Maria Vallejo Abascal and Dafinka Grozdanova}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/04/2024-Wouter-RIOA-19.pdf https://riojournal.com/article/121887/}, doi = {10.3897/rio.10.e121887}, issn = {2367-7163}, year = {2024}, date = {2024-04-08}, urldate = {2024-04-08}, journal = {Research Ideas and Outcomes}, volume = {10}, pages = {e121887}, abstract = {A distributed research infrastructure such as LifeWatch ERIC necessitates close cooperation among the various components that constitute the research infrastructure and contribute to the overall services, facilities and resources it offers to the user community. In-kind contributions are non-monetary contributions, consisting of labour, services, facilities and access to resources, typically provided by the distributed components of the research infrastructure. The financing for in-kind contributions is usually provided by the national funding agency on behalf of the LifeWatch member country or by the member directly, with a value being accredited towards the member's funding obligations to LifeWatch ERIC. The management and validation of in-kind contributions towards shared objectives are integral to the legal framework supporting LifeWatch ERIC. This involves a rigorous assessment process to verify each in-kind contribution. This short article outlines that process and explores the function of the In-Kind Contributions Committee (IKCC) at LifeWatch ERIC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A distributed research infrastructure such as LifeWatch ERIC necessitates close cooperation among the various components that constitute the research infrastructure and contribute to the overall services, facilities and resources it offers to the user community. In-kind contributions are non-monetary contributions, consisting of labour, services, facilities and access to resources, typically provided by the distributed components of the research infrastructure. The financing for in-kind contributions is usually provided by the national funding agency on behalf of the LifeWatch member country or by the member directly, with a value being accredited towards the member's funding obligations to LifeWatch ERIC. The management and validation of in-kind contributions towards shared objectives are integral to the legal framework supporting LifeWatch ERIC. This involves a rigorous assessment process to verify each in-kind contribution. This short article outlines that process and explores the function of the In-Kind Contributions Committee (IKCC) at LifeWatch ERIC. |
Vasileiadou, Katerina; Chatzinikolaou, Eva; Klayn, Stefania; Pavloudi, Christina; Reizopoulou, Sofia Editorial: Marine biodiversity hotspots – challenges and resilience Journal Article Frontiers in Marine Science, 11 , pp. 1338242, 2024, ISSN: 2296-7745. @article{vasileiadou_editorial_2024, title = {Editorial: Marine biodiversity hotspots – challenges and resilience}, author = {Katerina Vasileiadou and Eva Chatzinikolaou and Stefania Klayn and Christina Pavloudi and Sofia Reizopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/01/2024-Vasileiadou-fmars-3.pdf https://www.frontiersin.org/articles/10.3389/fmars.2024.1338242/full}, doi = {10.3389/fmars.2024.1338242}, issn = {2296-7745}, year = {2024}, date = {2024-01-17}, urldate = {2024-01-22}, journal = {Frontiers in Marine Science}, volume = {11}, pages = {1338242}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2023 |
Sarafidou, Georgia; Tsaparis, Dimitris; Issaris, Yiannis; Chatzigeorgiou, Giorgos; Grigoriou, Panos; Chatzinikolaou, Eva; Pavloudi, Christina Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea Journal Article PeerJ, 11 , pp. e16491, 2023, ISSN: 2167-8359. @article{sarafidou_insights_2023, title = {Insights on \textit{Pinna nobilis} population genetic structure in the Aegean and Ionian Sea}, author = {Georgia Sarafidou and Dimitris Tsaparis and Yiannis Issaris and Giorgos Chatzigeorgiou and Panos Grigoriou and Eva Chatzinikolaou and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/12/2023-Sarafidou-peerj-61.pdf https://peerj.com/articles/16491}, doi = {10.7717/peerj.16491}, issn = {2167-8359}, year = {2023}, date = {2023-12-01}, urldate = {2023-12-01}, journal = {PeerJ}, volume = {11}, pages = {e16491}, abstract = {The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e. , by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e. , by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management. |
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. |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki Micro-CT protocols for scanning and 3D analysis of Hexaplex trunculus during its different life stages Journal Article 9 , pp. e71542, 2021, ISSN: 1314-2828. @article{chatzinikolaou_micro-ct_2021, title = {Micro-CT protocols for scanning and 3D analysis of Hexaplex trunculus during its different life stages}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Chatzinikolaou-and-Keklikoglou-BDJournal-70.pdf https://bdj.pensoft.net/article/71542/}, doi = {10.3897/BDJ.9.e71542}, issn = {1314-2828}, year = {2021}, date = {2021-09-15}, urldate = {2021-09-22}, volume = {9}, pages = {e71542}, abstract = {Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biological studies focusing on taxonomy and functional morphology. The creation of virtual representations of specimens can increase availability of otherwise underexploited and inaccessible samples. The 3D model dataset can be also further processed through volume rendering and morphometric analysis. The success of micro-CT as a visualisation technique depends on several methodological manipulations, including the use of contrast enhancing staining agents, filters, scanning mediums, containers, exposure time and frame averaging. The aim of this study was to standardise a series of micro-CT scanning and 3D analysis protocols for a marine gastropod species, Hexaplex trunculus. The analytical protocols have followed all the developmental stages of this gastropod, from egg capsules and embryos to juveniles and adults.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biological studies focusing on taxonomy and functional morphology. The creation of virtual representations of specimens can increase availability of otherwise underexploited and inaccessible samples. The 3D model dataset can be also further processed through volume rendering and morphometric analysis. The success of micro-CT as a visualisation technique depends on several methodological manipulations, including the use of contrast enhancing staining agents, filters, scanning mediums, containers, exposure time and frame averaging. The aim of this study was to standardise a series of micro-CT scanning and 3D analysis protocols for a marine gastropod species, Hexaplex trunculus. The analytical protocols have followed all the developmental stages of this gastropod, from egg capsules and embryos to juveniles and adults. |
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. |
Nikolopoulou, Stamatina; Berov, Dimitar; Klayn, Stefania; Dimitrov, Lyubomir; Velkovsky, Kiril; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Karamfilov, Ventzislav; Pavloudi, Christina Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea) Journal Article 9 , pp. e71972, 2021, ISSN: 1314-2828, 1314-2836. @article{nikolopoulou_benthic_2021, title = {Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea)}, author = {Stamatina Nikolopoulou and Dimitar Berov and Stefania Klayn and Lyubomir Dimitrov and Kiril Velkovsky and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Ventzislav Karamfilov and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Nikolopoulou-BDJ-64.pdf https://bdj.pensoft.net/article/71972/}, doi = {10.3897/BDJ.9.e71972}, issn = {1314-2828, 1314-2836}, year = {2021}, date = {2021-08-23}, urldate = {2021-09-16}, volume = {9}, pages = {e71972}, abstract = {Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined a priori classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined a priori classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System. |
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%). |
Karagiannidis, Efstratios; Papazoglou, Andreas S; Stalikas, Nikolaos; Deda, Olga; Panteris, Eleftherios; Begou, Olga; Sofidis, Georgios; Moysidis, Dimitrios V; Kartas, Anastasios; Chatzinikolaou, Evangelia; Keklikoglou, Kleoniki; Bompoti, Andreana; Gika, Helen; Theodoridis, Georgios; Sianos, Georgios Serum Ceramides as Prognostic Biomarkers of Large Thrombus Burden in Patients with STEMI: A Micro-Computed Tomography Study Journal Article Journal of Personalized Medicine, 11 (2), pp. 89, 2021. @article{karagiannidis_serum_2021, title = {Serum Ceramides as Prognostic Biomarkers of Large Thrombus Burden in Patients with STEMI: A Micro-Computed Tomography Study}, author = {Efstratios Karagiannidis and Andreas S Papazoglou and Nikolaos Stalikas and Olga Deda and Eleftherios Panteris and Olga Begou and Georgios Sofidis and Dimitrios V Moysidis and Anastasios Kartas and Evangelia Chatzinikolaou and Kleoniki Keklikoglou and Andreana Bompoti and Helen Gika and Georgios Theodoridis and Georgios Sianos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Karagiannidis-Chatzinikolaou-Keklikoglou-JPMed-9.pdf https://www.mdpi.com/2075-4426/11/2/89}, doi = {10.3390/jpm11020089}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-05}, journal = {Journal of Personalized Medicine}, volume = {11}, number = {2}, pages = {89}, abstract = {ST-elevation myocardial infarction (STEMI) remains one of the leading causes of mortality worldwide. The identification of novel metabolic and imaging biomarkers could unveil key pathophysiological mechanisms at the molecular level and promote personalized care in patients with acute coronary syndromes. We studied 38 patients with STEMI who underwent primary percutaneous coronary intervention and thrombus aspiration. We sought to correlate serum ceramide levels with micro-CT quantified aspirated thrombus volume and relevant angiographic outcomes, including modified TIMI thrombus grade and pre- or post-procedural TIMI flow. Higher ceramide C16:0 levels were significantly but weakly correlated with larger aspirated thrombus volume (Spearman r = 0.326}, keywords = {}, pubstate = {published}, tppubtype = {article} } ST-elevation myocardial infarction (STEMI) remains one of the leading causes of mortality worldwide. The identification of novel metabolic and imaging biomarkers could unveil key pathophysiological mechanisms at the molecular level and promote personalized care in patients with acute coronary syndromes. We studied 38 patients with STEMI who underwent primary percutaneous coronary intervention and thrombus aspiration. We sought to correlate serum ceramide levels with micro-CT quantified aspirated thrombus volume and relevant angiographic outcomes, including modified TIMI thrombus grade and pre- or post-procedural TIMI flow. Higher ceramide C16:0 levels were significantly but weakly correlated with larger aspirated thrombus volume (Spearman r = 0.326 |
Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Grigoriou, Panos Morphological Properties of Gastropod Shells in a Warmer and More Acidic Future Ocean Using 3D Micro-Computed Tomography Journal Article Frontiers in Marine Science, 8 , 2021, ISSN: 2296-7745. @article{chatzinikolaou_morphological_2021, title = {Morphological Properties of Gastropod Shells in a Warmer and More Acidic Future Ocean Using 3D Micro-Computed Tomography}, author = {Eva Chatzinikolaou and Kleoniki Keklikoglou and Panos Grigoriou}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.645660/full https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatzinikolaou-Frontiers-34.pdf}, doi = {10.3389/fmars.2021.645660}, issn = {2296-7745}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {Frontiers in Marine Science}, volume = {8}, abstract = {The increased absorption of atmospheric CO2 by the ocean reduces pH and affects the carbonate chemistry of seawater, thus interfering with the shell formation processes of marine calcifiers. The present study aims to examine the effects of ocean acidification and warming on the shell morphological properties of two intertidal gastropod species, Nassarius nitidus and Columbella rustica. The experimental treatments lasted for 3 months and combined a temperature increase of 3 °C and a pH reduction of 0.3 units. The selected treatments reflected the high emissions (RCP 8.5) “business as usual” scenario of the Intergovernmental Panel on Climate Change models for eastern Mediterranean. The morphological and architectural properties of the shell, such as density, thickness and porosity were examined using 3D micro-computed tomography, which is a technique giving the advantage of calculating values for the total shell (not only at specific points) and at the same time leaving the shells intact. Nassarius nitidus had a lower shell density and thickness and a higher porosity when the pH was reduced at ambient temperature, but the combination of reduced pH and increased temperature did not have a noticeable effect in comparison to the control. The shell of Columbella rustica was less dense, thinner and more porous under acidic and warm conditions, but when the temperature was increased under ambient pH the shells were thicker and denser than the control. Under low pH and ambient temperature, shells showed no differences compared to the control. The vulnerability of calcareous shells to ocean acidification and warming appears to be variable among species. Plasticity of shell building organisms as an acclimation action towards a continuously changing marine environment needs to be further investigated focusing on species or shell region specific adaptation mechanisms.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The increased absorption of atmospheric CO2 by the ocean reduces pH and affects the carbonate chemistry of seawater, thus interfering with the shell formation processes of marine calcifiers. The present study aims to examine the effects of ocean acidification and warming on the shell morphological properties of two intertidal gastropod species, Nassarius nitidus and Columbella rustica. The experimental treatments lasted for 3 months and combined a temperature increase of 3 °C and a pH reduction of 0.3 units. The selected treatments reflected the high emissions (RCP 8.5) “business as usual” scenario of the Intergovernmental Panel on Climate Change models for eastern Mediterranean. The morphological and architectural properties of the shell, such as density, thickness and porosity were examined using 3D micro-computed tomography, which is a technique giving the advantage of calculating values for the total shell (not only at specific points) and at the same time leaving the shells intact. Nassarius nitidus had a lower shell density and thickness and a higher porosity when the pH was reduced at ambient temperature, but the combination of reduced pH and increased temperature did not have a noticeable effect in comparison to the control. The shell of Columbella rustica was less dense, thinner and more porous under acidic and warm conditions, but when the temperature was increased under ambient pH the shells were thicker and denser than the control. Under low pH and ambient temperature, shells showed no differences compared to the control. The vulnerability of calcareous shells to ocean acidification and warming appears to be variable among species. Plasticity of shell building organisms as an acclimation action towards a continuously changing marine environment needs to be further investigated focusing on species or shell region specific adaptation mechanisms. |
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. |
2020 |
Karagiannidis, Efstratios; Konstantinidis, Nikolaos V; Sofidis, Georgios; Chatzinikolaou, Evangelia; Sianos, Georgios BMC Cardiovascular Disorders, 20 (1), pp. 125, 2020, ISSN: 1471-2261. @article{karagiannidis_rationale_2020, title = {Rationale and design of a prospective, observational study for the QUantitative EStimation of Thrombus burden in patients with ST-Elevation Myocardial Infarction using micro-computed tomography: the QUEST-STEMI trial}, author = {Efstratios Karagiannidis and Nikolaos V Konstantinidis and Georgios Sofidis and Evangelia Chatzinikolaou and Georgios Sianos}, url = {https://bmccardiovascdisord.biomedcentral.com/articles/10.1186/s12872-020-01393-5}, doi = {10.1186/s12872-020-01393-5}, issn = {1471-2261}, year = {2020}, date = {2020-12-01}, journal = {BMC Cardiovascular Disorders}, volume = {20}, number = {1}, pages = {125}, abstract = {Although the presence of thrombus in patients with ST-elevation myocardial infarction (STEMI) has been linked to adverse outcomes, routine thrombus aspiration has not been proven effective. A potential explanation is that these patients should be risk-stratified. Traditional clinical, laboratory and angiographic parameters used in clinical trials have been proven inadequate to classify patients. Aspirated thrombotic material characteristics might be an additional important parameter that has not yet been addressed. In this report, we aim to describe a methodological analysis of thrombus aspirated from coronary arteries during primary PCI using micro-Computed $textbackslashTau$omography (micro-CT). These data will be combined with traditional factors to develop a risk-stratification system with high discriminative power for these patients.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although the presence of thrombus in patients with ST-elevation myocardial infarction (STEMI) has been linked to adverse outcomes, routine thrombus aspiration has not been proven effective. A potential explanation is that these patients should be risk-stratified. Traditional clinical, laboratory and angiographic parameters used in clinical trials have been proven inadequate to classify patients. Aspirated thrombotic material characteristics might be an additional important parameter that has not yet been addressed. In this report, we aim to describe a methodological analysis of thrombus aspirated from coronary arteries during primary PCI using micro-Computed $textbackslashTau$omography (micro-CT). These data will be combined with traditional factors to develop a risk-stratification system with high discriminative power for these patients. |
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 ). |
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. |
Karagiannidis, E; Konstantinidis, N V; Sofidis, G; Chatzinikolaou, E; Sianos, G European Heart Journal - Cardiovascular Imaging, 21 (Supplement_1), pp. jez319.298, 2020, ISSN: 2047-2404, (_eprint: https://academic.oup.com/ehjcimaging/article-pdf/21/Supplement_1/jez319.298/31864446/jez319.298.pdf). @article{karagiannidis_imaging_2020, title = {Imaging and quantitative estimation of thrombus burden in patients with ST elevation acute myocardial infarction (STEMI) with the use of micro-computed tomography-A methodological approach}, author = {E Karagiannidis and N V Konstantinidis and G Sofidis and E Chatzinikolaou and G Sianos}, url = {https://doi.org/10.1093/ehjci/jez319.298}, doi = {10.1093/ehjci/jez319.298}, issn = {2047-2404}, year = {2020}, date = {2020-01-01}, journal = {European Heart Journal - Cardiovascular Imaging}, volume = {21}, number = {Supplement_1}, pages = {jez319.298}, abstract = {Operational Program "Human Resources Development, Education and Lifelong Learning" - co-financed by the European Social Fund and Greek national fundsAcute myocardial infarction with ST elevation (STEMI) remains one of the leading causes of mortality. High thrombus burden has been proven to be an independent risk factor for stent thrombosis and for Major Adverse Clinical outcomes. However randomized controlled trials concerning thrombus aspiration showed controversial results, providing no evidence of benefits for thrombus aspiration. A possible explanation is that aspiration was performed as a routine strategy, whereas these patients should be considered as a heterogeneous group and they should be risk-stratified. Thus, it is important to classify patients according to the volume of thrombus burden. The currently existing classifications of thrombus burden are based on visual assessment of angiographic characteristics and they are not reflecting the volume of the thrombi in actual numbers. To the best of our knowledge, never before has the exact volume of thrombus burden been quantified.The study aims to assess for the first time, through the application of innovative technologies (micro-Computed Tomography, micro-CT), important characteristics of aspirated thrombi (volume and density), which might be linked to certain clinical outcomes, in patients with STEMI.After being aspirated, thrombi are preserved in formalin. As they consist of soft tissue with low X-ray absorption, thrombi have to be stained using contrast enhancing chemicals prior to scanning; in particular a solution containing 0.3% phosphotungstic acid is used (Metscher protocol). The scanning procedure results into a series of projection images arranged in the form of image stacks which, in turn, are reformed in sections with the use of special software, which applies a modified algorithm of backward projection Feldkamp. The resulting sections are combined to create the 3D models which are further analyzed to extract useful measurements for the characteristics of the thrombi, such as volume and density.From January 2018 to May 2019, 66 patients were enrolled in the study. Mean age was 60.36 (±11.71) years and the majority of them (78.7%) were men. Revascularization was achieved in mean 358 ± 255 minutes from symptom onset. Distal embolization was observed in 27.5% of the patients and no-reflow phenomenon was seen in 11.6%. Angiographically evident residual thrombus burden was observed in 6 patients (8.7%). Micro-CT managed to effectively quantify the volume and the density of aspirated thrombi. Mean volume was 12.98 ± 10.84 mm3, mean density was 2992 ± 872 HU and mean surface was 0.206 ± 0.19.Micro-CT can be used as a tool to effectively assess important characteristics of aspirated thrombi, which might be linked to certain clinical outcomes. This method could become the gold standard for the exact measurement of thrombus burden and could be used in larger, clinically-oriented trials to help stratify patients with thrombus burden according to their risk for adverse outcomes.Abstract 568 Figure. Coronary thrombi as depicted on micro-CT}, note = {_eprint: https://academic.oup.com/ehjcimaging/article-pdf/21/Supplement_1/jez319.298/31864446/jez319.298.pdf}, keywords = {}, pubstate = {published}, tppubtype = {article} } Operational Program "Human Resources Development, Education and Lifelong Learning" - co-financed by the European Social Fund and Greek national fundsAcute myocardial infarction with ST elevation (STEMI) remains one of the leading causes of mortality. High thrombus burden has been proven to be an independent risk factor for stent thrombosis and for Major Adverse Clinical outcomes. However randomized controlled trials concerning thrombus aspiration showed controversial results, providing no evidence of benefits for thrombus aspiration. A possible explanation is that aspiration was performed as a routine strategy, whereas these patients should be considered as a heterogeneous group and they should be risk-stratified. Thus, it is important to classify patients according to the volume of thrombus burden. The currently existing classifications of thrombus burden are based on visual assessment of angiographic characteristics and they are not reflecting the volume of the thrombi in actual numbers. To the best of our knowledge, never before has the exact volume of thrombus burden been quantified.The study aims to assess for the first time, through the application of innovative technologies (micro-Computed Tomography, micro-CT), important characteristics of aspirated thrombi (volume and density), which might be linked to certain clinical outcomes, in patients with STEMI.After being aspirated, thrombi are preserved in formalin. As they consist of soft tissue with low X-ray absorption, thrombi have to be stained using contrast enhancing chemicals prior to scanning; in particular a solution containing 0.3% phosphotungstic acid is used (Metscher protocol). The scanning procedure results into a series of projection images arranged in the form of image stacks which, in turn, are reformed in sections with the use of special software, which applies a modified algorithm of backward projection Feldkamp. The resulting sections are combined to create the 3D models which are further analyzed to extract useful measurements for the characteristics of the thrombi, such as volume and density.From January 2018 to May 2019, 66 patients were enrolled in the study. Mean age was 60.36 (±11.71) years and the majority of them (78.7%) were men. Revascularization was achieved in mean 358 ± 255 minutes from symptom onset. Distal embolization was observed in 27.5% of the patients and no-reflow phenomenon was seen in 11.6%. Angiographically evident residual thrombus burden was observed in 6 patients (8.7%). Micro-CT managed to effectively quantify the volume and the density of aspirated thrombi. Mean volume was 12.98 ± 10.84 mm3, mean density was 2992 ± 872 HU and mean surface was 0.206 ± 0.19.Micro-CT can be used as a tool to effectively assess important characteristics of aspirated thrombi, which might be linked to certain clinical outcomes. This method could become the gold standard for the exact measurement of thrombus burden and could be used in larger, clinically-oriented trials to help stratify patients with thrombus burden according to their risk for adverse outcomes.Abstract 568 Figure. Coronary thrombi as depicted on micro-CT |
2019 |
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). |
Chatzinikolaou, Eva; Grigoriou, Panos; Martini, Evangelia; Sterioti, Aspasia Impact of ocean acidification and warming on the feeding behaviour of two gastropod species Journal Article Mediterranean Marine Science, 20 (4), pp. 669, 2019, ISSN: 1791-6763, 1108-393X. @article{chatzinikolaou_impact_2019, title = {Impact of ocean acidification and warming on the feeding behaviour of two gastropod species}, author = {Eva Chatzinikolaou and Panos Grigoriou and Evangelia Martini and Aspasia Sterioti}, url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/19187}, doi = {10.12681/mms.19187}, issn = {1791-6763, 1108-393X}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-20}, journal = {Mediterranean Marine Science}, volume = {20}, number = {4}, pages = {669}, abstract = {Increased atmospheric CO2 produced by anthropogenic activities will be absorbed by the oceans over the next century causing ocean acidification and changes in the seawater carbonate chemistry. Elevated CO2 causes sublethal physiological and behavioural responses on the locomotion and foraging behaviour of marine organisms. This study aims to investigate the independent and synergistic effects of long term exposure to low pH and increased temperature on the feeding behaviour of two gastropod species, Hexaplex trunculus and Nassarius nitidus, both in adults and juveniles. Gastropods were maintained under controlled conditions of temperature (ambient = 20°C}, keywords = {}, pubstate = {published}, tppubtype = {article} } Increased atmospheric CO2 produced by anthropogenic activities will be absorbed by the oceans over the next century causing ocean acidification and changes in the seawater carbonate chemistry. Elevated CO2 causes sublethal physiological and behavioural responses on the locomotion and foraging behaviour of marine organisms. This study aims to investigate the independent and synergistic effects of long term exposure to low pH and increased temperature on the feeding behaviour of two gastropod species, Hexaplex trunculus and Nassarius nitidus, both in adults and juveniles. Gastropods were maintained under controlled conditions of temperature (ambient = 20°C |
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. |
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} } |
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 |
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. |
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. |
Chatzinikolaou, E; Grigoriou, P; Keklikoglou, K; Faulwetter, S; Papageorgiou, N The combined effects of reduced pH and elevated temperature on the shell density of two gastropod species measured using micro-CT imaging Journal Article ICES Journal of Marine Science, 74 (4), pp. 1135–1149, 2017, ISSN: 10543139, (Publisher: Oxford University Press). @article{chatzinikolaou_combined_2017, title = {The combined effects of reduced pH and elevated temperature on the shell density of two gastropod species measured using micro-CT imaging}, author = {E Chatzinikolaou and P Grigoriou and K Keklikoglou and S Faulwetter and N Papageorgiou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028694685&doi=10.1093%2ficesjms%2ffsw219&partnerID=40&md5=cf6590e0597069849206bf3da507e986}, doi = {10.1093/icesjms/fsw219}, issn = {10543139}, year = {2017}, date = {2017-01-01}, journal = {ICES Journal of Marine Science}, volume = {74}, number = {4}, pages = {1135--1149}, abstract = {The increased absorption of atmospheric CO2 by the ocean affects carbonate chemistry and calcification rates of marine organisms. The impacts of low pH and seawater warming were investigated for the intertidal gastropods Nassarius nitidus and Columbella rustica. The combined effect of reduced pH (7.6) and increased temperature (25 °C) was studied at intermediate time intervals for a total period of 3 months in order to investigate variability and fluctuations of the shell structure and density over time. The pH and temperature conditions used for the experiment were selected according to the predictions of the Intergovernmental Panel on Climate Change. Deterioration of the external surface structure and reduction of shell density of the gastropods were confirmed using an innovative imaging and analysis method based on microcomputed tomography. The effect of low pH at ambient temperature was detrimental for N. nitidus with a 38.1% reduction of density in the shell lip and a 47.7% decrease in the apex, which is the oldest shell region. C. rustica was also affected, although to a much lesser degree (the maximum reduction observed was 8% at the apex). The negative effects of reduced pH were further reinforced for C. rustica when the temperature was increased, while N. nitidus was not affected significantly by the combination of the two factors. Increased temperature at ambient pH had an inhibitory effect on the shell density of N. nitidus causing a reduction of about 40%, whereas the shell density of the widest and lip regions of the C. rustica were increased under the same conditions. Different species are characterised by different vulnerability and tolerance responses regarding ocean acidification and warming, and this variability may affect ecological interactions and marine biodiversity. © International Council for the Exploration of the Sea 2016.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The increased absorption of atmospheric CO2 by the ocean affects carbonate chemistry and calcification rates of marine organisms. The impacts of low pH and seawater warming were investigated for the intertidal gastropods Nassarius nitidus and Columbella rustica. The combined effect of reduced pH (7.6) and increased temperature (25 °C) was studied at intermediate time intervals for a total period of 3 months in order to investigate variability and fluctuations of the shell structure and density over time. The pH and temperature conditions used for the experiment were selected according to the predictions of the Intergovernmental Panel on Climate Change. Deterioration of the external surface structure and reduction of shell density of the gastropods were confirmed using an innovative imaging and analysis method based on microcomputed tomography. The effect of low pH at ambient temperature was detrimental for N. nitidus with a 38.1% reduction of density in the shell lip and a 47.7% decrease in the apex, which is the oldest shell region. C. rustica was also affected, although to a much lesser degree (the maximum reduction observed was 8% at the apex). The negative effects of reduced pH were further reinforced for C. rustica when the temperature was increased, while N. nitidus was not affected significantly by the combination of the two factors. Increased temperature at ambient pH had an inhibitory effect on the shell density of N. nitidus causing a reduction of about 40%, whereas the shell density of the widest and lip regions of the C. rustica were increased under the same conditions. Different species are characterised by different vulnerability and tolerance responses regarding ocean acidification and warming, and this variability may affect ecological interactions and marine biodiversity. © International Council for the Exploration of the Sea 2016. |
2016 |
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. |
Mavraki, D; Fanini, L; Tsompanou, M; Gerovasileiou, V; Nikolopoulou, S; Chatzinikolaou, E; Plaitis, W; Faulwetter, S Rescuing biogeographic legacy data: The "Thor" Expedition, a historical oceanographic expedition to the Mediterranean Sea Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{mavraki_rescuing_2016, title = {Rescuing biogeographic legacy data: The "Thor" Expedition, a historical oceanographic expedition to the Mediterranean Sea}, author = {D Mavraki and L Fanini and M Tsompanou and V Gerovasileiou and S Nikolopoulou and E Chatzinikolaou and W Plaitis and S Faulwetter}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018653928&doi=10.3897%2fBDJ.4.e11054&partnerID=40&md5=d548ea13a533ece32aee66df08954a37}, doi = {10.3897/BDJ.4.e11054}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background This article describes the digitization of a series of historical datasets based ?n the reports of the 1908-1910 Danish Oceanographical Expeditions to the Mediterranean and adjacent seas. All station and sampling metadata as well as biodiversity data regarding calcareous rhodophytes, pelagic polychaetes, and fish (families Engraulidae and Clupeidae) obtained during these expeditions were digitized within the activities of the LifeWatchGreece Research ?nfrastructure project and presented in the present paper. The aim was to safeguard public data availability by using an open access infrastructure, and to prevent potential loss of valuable historical data on the Mediterranean marine biodiversity. New information The datasets digitized here cover 2,043 samples taken at 567 stations during a time period from 1904 to 1930 in the Mediterranean and adjacent seas. The samples resulted in 1,588 occurrence records of pelagic polychaetes, fish (Clupeiformes) and calcareous algae (Rhodophyta). In addition, basic environmental data (e.g. sea surface temperature, salinity) as well as meterological conditions are included for most sampling events. In addition to the description of the digitized datasets, a detailed description of the problems encountered during the digitization of this historical dataset and a discussion on the value of such data are provided. © Mavraki D et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background This article describes the digitization of a series of historical datasets based ?n the reports of the 1908-1910 Danish Oceanographical Expeditions to the Mediterranean and adjacent seas. All station and sampling metadata as well as biodiversity data regarding calcareous rhodophytes, pelagic polychaetes, and fish (families Engraulidae and Clupeidae) obtained during these expeditions were digitized within the activities of the LifeWatchGreece Research ?nfrastructure project and presented in the present paper. The aim was to safeguard public data availability by using an open access infrastructure, and to prevent potential loss of valuable historical data on the Mediterranean marine biodiversity. New information The datasets digitized here cover 2,043 samples taken at 567 stations during a time period from 1904 to 1930 in the Mediterranean and adjacent seas. The samples resulted in 1,588 occurrence records of pelagic polychaetes, fish (Clupeiformes) and calcareous algae (Rhodophyta). In addition, basic environmental data (e.g. sea surface temperature, salinity) as well as meterological conditions are included for most sampling events. In addition to the description of the digitized datasets, a detailed description of the problems encountered during the digitization of this historical dataset and a discussion on the value of such data are provided. © Mavraki D et al. |
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. |
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} } |
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. |
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/. |
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 |
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. |
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} } |
Bulleri, F; Benedetti-Cecchi, L; Chatzinikolaou, E; Crowe, T; Kotta, J; Lyons, D; Mant, R; Rilov, G; Rindi, L; Maggi, E Collaboration for Environmental Evidence, pp. CEE review 12–002, 2015. @article{bulleri_what_2015, title = {What is the effect of non-native seaweeds on resident benthic assemblages? Variability between trophic levels and influence of background environmental and biological conditions}, author = {F Bulleri and L Benedetti-Cecchi and E Chatzinikolaou and T Crowe and J Kotta and D Lyons and R Mant and G Rilov and L Rindi and E Maggi}, url = {www.environmentalevidence.org}, year = {2015}, date = {2015-01-01}, journal = {Collaboration for Environmental Evidence}, pages = {CEE review 12--002}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Maggi, E; Benedetti-Cecchi, L; Castelli, A; Chatzinikolaou, E; Crowe, T P; Ghedini, G; Kotta, J; Lyons, D A; Ravaglioli, C; Rilov, G; Rindi, L; Bulleri, F Ecological impacts of invading seaweeds: A meta-analysis of their effects at different trophic levels Journal Article Diversity and Distributions, 21 (1), pp. 1–12, 2015, ISSN: 13669516, (Publisher: Blackwell Publishing Ltd). @article{maggi_ecological_2015, title = {Ecological impacts of invading seaweeds: A meta-analysis of their effects at different trophic levels}, author = {E Maggi and L Benedetti-Cecchi and A Castelli and E Chatzinikolaou and T P Crowe and G Ghedini and J Kotta and D A Lyons and C Ravaglioli and G Rilov and L Rindi and F Bulleri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84919337078&doi=10.1111%2fddi.12264&partnerID=40&md5=f5f14a78e5d37af6e23418ea6b5a4258}, doi = {10.1111/ddi.12264}, issn = {13669516}, year = {2015}, date = {2015-01-01}, journal = {Diversity and Distributions}, volume = {21}, number = {1}, pages = {1--12}, abstract = {Aim: Biological invasions are among the main threats to biodiversity. To promote a mechanistic understanding of the ecological impacts of non-native seaweeds, we assessed how effects on resident organisms vary according to their trophic level. Location: Global. Methods: We performed meta-analytical comparisons of the effects of non-native seaweeds on both individual species and communities. We compared the results of analyses performed on the whole dataset with those obtained from experimental data only and, when possible, between rocky and soft bottoms. Results: Meta-analyses of data from 100 papers revealed consistent negative effects of non-native seaweeds across variables describing resident primary producer communities. In contrast, negative effects of seaweeds on consumers emerged only on their biomass and, limited to rocky bottoms, diversity. At the species level, negative effects were consistent across primary producers' response variables, while only the survival of consumers other than herbivores or predators (e.g. deposit/suspension feeders or detritivores) decreased due to invasion. Excluding mensurative data, negative effects of seaweeds persisted only on resident macroalgal communities and consumer species survival, while switched to positive on the diversity of rocky-bottom consumers. However, negative effects emerged for biomass and, in rocky habitats, density of consumers other than herbivores or predators. Main conclusions: Our results support the hypothesis that seaweeds' effects on resident biodiversity are generally more negative within the same trophic level than on higher trophic guilds. Finer trophic grouping of resident organisms revealed more complex impacts than previously detected. High heterogeneity in the responses of some consumer guilds suggests that impacts of non-native seaweeds at higher trophic levels may be more invader- and species-specific than competitive effects at the same trophic level. Features of invaded habitats may further increase variability in seaweeds' impacts. More experimental data on consumers' response to invasion are needed to disentangle the effects of non-native seaweeds from those of other environmental stressors. © 2014 John Wiley & Sons Ltd.}, note = {Publisher: Blackwell Publishing Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aim: Biological invasions are among the main threats to biodiversity. To promote a mechanistic understanding of the ecological impacts of non-native seaweeds, we assessed how effects on resident organisms vary according to their trophic level. Location: Global. Methods: We performed meta-analytical comparisons of the effects of non-native seaweeds on both individual species and communities. We compared the results of analyses performed on the whole dataset with those obtained from experimental data only and, when possible, between rocky and soft bottoms. Results: Meta-analyses of data from 100 papers revealed consistent negative effects of non-native seaweeds across variables describing resident primary producer communities. In contrast, negative effects of seaweeds on consumers emerged only on their biomass and, limited to rocky bottoms, diversity. At the species level, negative effects were consistent across primary producers' response variables, while only the survival of consumers other than herbivores or predators (e.g. deposit/suspension feeders or detritivores) decreased due to invasion. Excluding mensurative data, negative effects of seaweeds persisted only on resident macroalgal communities and consumer species survival, while switched to positive on the diversity of rocky-bottom consumers. However, negative effects emerged for biomass and, in rocky habitats, density of consumers other than herbivores or predators. Main conclusions: Our results support the hypothesis that seaweeds' effects on resident biodiversity are generally more negative within the same trophic level than on higher trophic guilds. Finer trophic grouping of resident organisms revealed more complex impacts than previously detected. High heterogeneity in the responses of some consumer guilds suggests that impacts of non-native seaweeds at higher trophic levels may be more invader- and species-specific than competitive effects at the same trophic level. Features of invaded habitats may further increase variability in seaweeds' impacts. More experimental data on consumers' response to invasion are needed to disentangle the effects of non-native seaweeds from those of other environmental stressors. © 2014 John Wiley & Sons Ltd. |
Keklikoglou, K; Chatzinikolaou, E; Faulwetter, S; Grigoriou, P; Papageorgiou, N; Queirós, A; Rühl, S; Schmidbaur, H Revealing effects of ocean acidification on the calcified structures of marine invertebrates through micro-computed tomography (micro-CT) Inproceedings Bruker microCT 2015 user meeting, Belgium, pp. 21–31, 2015. @inproceedings{keklikoglou_revealing_2015, title = {Revealing effects of ocean acidification on the calcified structures of marine invertebrates through micro-computed tomography (micro-CT)}, author = {K Keklikoglou and E Chatzinikolaou and S Faulwetter and P Grigoriou and N Papageorgiou and A Queirós and S Rühl and H Schmidbaur}, year = {2015}, date = {2015-01-01}, booktitle = {Bruker microCT 2015 user meeting, Belgium}, pages = {21--31}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2014 |
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. |
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. |
2013 |
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} } |
Bulleri, F; Mant, R; Benedetti-Cecchi, L; Chatzinikolaou, Eva; Crowe, T; Kotta, J; Lyons, D; Rilov, G; Maggi, E The ecological impacts of exotic seaweeds: variation between trophic levels and across environmental conditions Inproceedings Vancouver, Canada, 2013, (Publication Title: 8th International Conference on Marine Bioinvasions (ICMB)). @inproceedings{bulleri_ecological_2013, title = {The ecological impacts of exotic seaweeds: variation between trophic levels and across environmental conditions}, author = {F Bulleri and R Mant and L Benedetti-Cecchi and Eva Chatzinikolaou and T Crowe and J Kotta and D Lyons and G Rilov and E Maggi}, year = {2013}, date = {2013-01-01}, address = {Vancouver, Canada}, note = {Publication Title: 8th International Conference on Marine Bioinvasions (ICMB)}, 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} } |
2012 |
Chatzinikolaou, E Use and limitations of ecological models Journal Article Transitional Waters Bulletin, 6 (2), pp. 34–41, 2012, ISSN: 1825229X, (Publisher: University of Salento). @article{chatzinikolaou_use_2012, title = {Use and limitations of ecological models}, author = {E Chatzinikolaou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028768383&doi=10.1285%2fi1825229Xv6n2p34&partnerID=40&md5=45f5f3df6dd4e229ef8ec0a316df61d3}, doi = {10.1285/i1825229Xv6n2p34}, issn = {1825229X}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, number = {2}, pages = {34--41}, abstract = {1 - Modelling of ecological processes is not a recent area of scientific research but it is currently evolving fast due to the technological advances in computing power. 2 - Mathematical models can be readily used as tools for the efficient assessment of environmental quality, for studying the ecosystem functioning properties and for monitoring biodiversity. 3 - Conclusions based on ecological models are often used to reinforce policy design and environmental planning and management. A variety of different ecological models exists at the moment, each one with its advantages and disadvantages. 4 - The question that needs to be answered and the type of data available in each case, define the most suitable type of model. The limitations and malpractices occasionally observed during the use of ecological models are described. © 2012 University of Salento - SIBA.}, note = {Publisher: University of Salento}, keywords = {}, pubstate = {published}, tppubtype = {article} } 1 - Modelling of ecological processes is not a recent area of scientific research but it is currently evolving fast due to the technological advances in computing power. 2 - Mathematical models can be readily used as tools for the efficient assessment of environmental quality, for studying the ecosystem functioning properties and for monitoring biodiversity. 3 - Conclusions based on ecological models are often used to reinforce policy design and environmental planning and management. A variety of different ecological models exists at the moment, each one with its advantages and disadvantages. 4 - The question that needs to be answered and the type of data available in each case, define the most suitable type of model. The limitations and malpractices occasionally observed during the use of ecological models are described. © 2012 University of Salento - SIBA. |
Rilov, Gil; Mant, Rebecca; Lyons, Devin; Bulleri, Fabio; Benedetti-Cecchi, Lisandro; Kotta, Jonne; Queirós, Ana M; Chatzinikolaou, Eva; Crowe, Tasman; Guy-Haim, Tamar Environmental Evidence, 1 (1), pp. 10, 2012, ISSN: 2047-2382. @article{rilov_how_2012, title = {How strong is the effect of invasive ecosystem engineers on the distribution patterns of local species, the local and regional biodiversity and ecosystem functions?}, author = {Gil Rilov and Rebecca Mant and Devin Lyons and Fabio Bulleri and Lisandro Benedetti-Cecchi and Jonne Kotta and Ana M Queirós and Eva Chatzinikolaou and Tasman Crowe and Tamar Guy-Haim}, url = {http://environmentalevidencejournal.biomedcentral.com/articles/10.1186/2047-2382-1-10}, doi = {10.1186/2047-2382-1-10}, issn = {2047-2382}, year = {2012}, date = {2012-01-01}, urldate = {2020-08-26}, journal = {Environmental Evidence}, volume = {1}, number = {1}, pages = {10}, abstract = {Background: One of the most influential forms of biological invasions is that of invasive ecosystem engineers, species that affect other biota via alterations to the abiotic environment. Such species can have wide-reaching consequences because they alter ecosystems and essentially "change the rules of existence" for a broad suite of resident biota. They thus affect resources or stressors that affect other organisms.The objective of this systematic review will be to quantify the positive and negative impacts of invasive ecosystem engineers on ecosystem structure and functioning, and to identify factors that cause their effects to vary. Methods: We will search a number of online databases to gather empirical evidence from the literature on the impacts of invasive ecosystem engineers on: (1) species richness and other univariate and multivariate measures of biodiversity; (2) productivity and abundance of algae, and animals; and (3) biogeochemical cycling and other flows of energy and materials, including trophic interactions. Data from relevant studies will be extracted and used in a random effects meta-analysis in order to estimate the average effect size of invasive ecosystem engineers on each response of interest. © 2012 Rilov et al.; licensee BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: One of the most influential forms of biological invasions is that of invasive ecosystem engineers, species that affect other biota via alterations to the abiotic environment. Such species can have wide-reaching consequences because they alter ecosystems and essentially "change the rules of existence" for a broad suite of resident biota. They thus affect resources or stressors that affect other organisms.The objective of this systematic review will be to quantify the positive and negative impacts of invasive ecosystem engineers on ecosystem structure and functioning, and to identify factors that cause their effects to vary. Methods: We will search a number of online databases to gather empirical evidence from the literature on the impacts of invasive ecosystem engineers on: (1) species richness and other univariate and multivariate measures of biodiversity; (2) productivity and abundance of algae, and animals; and (3) biogeochemical cycling and other flows of energy and materials, including trophic interactions. Data from relevant studies will be extracted and used in a random effects meta-analysis in order to estimate the average effect size of invasive ecosystem engineers on each response of interest. © 2012 Rilov et al.; licensee BioMed Central Ltd. |
Bulleri, Fabio; Mant, Rebecca; Benedetti-Cecchi, Lisandro; Chatzinikolaou, Eva; Crowe, Tasman; Kotta, Jonne; Lyons, Devin; Rilov, Gil; Maggi, Elena Environmental Evidence, 1 (1), pp. 8, 2012, ISSN: 2047-2382. @article{bulleri_effects_2012, title = {The effects of exotic seaweeds on native benthic assemblages: variability between trophic levels and influence of background environmental and biological conditions}, author = {Fabio Bulleri and Rebecca Mant and Lisandro Benedetti-Cecchi and Eva Chatzinikolaou and Tasman Crowe and Jonne Kotta and Devin Lyons and Gil Rilov and Elena Maggi}, url = {http://environmentalevidencejournal.biomedcentral.com/articles/10.1186/2047-2382-1-8}, doi = {10.1186/2047-2382-1-8}, issn = {2047-2382}, year = {2012}, date = {2012-01-01}, urldate = {2020-08-26}, journal = {Environmental Evidence}, volume = {1}, number = {1}, pages = {8}, abstract = {Background: Biological invasions are among the most severe threats to marine biodiversity. The impacts of introduced seaweeds on native macroalgal assemblages have been thoroughly reviewed. In contrast, no attempt has been made to synthesize the available information on the effects of exotic seaweeds on other trophic levels. In addition, it has not been clarified whether the effects of introduced seaweeds on native assemblages vary according to background physical and biological conditions. Methods: This protocol provides details of our proposed method to carry out a systematic review aiming to identify and synthesize existing knowledge to answer the following primary questions: a) how does the impact of the presence of exotic seaweeds on native primary consumers (across trophic levels) compare in magnitude and extent to that observed on native primary producers (same trophic level)?; b) does the intensity of the effects of the presence of exotic seaweeds on native benthic ecosystems vary along a gradient of human disturbance (i.e. from urban/industrial areas to extra-urban areas to pristine areas) © 2012 Bulleri et al.; licensee BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Biological invasions are among the most severe threats to marine biodiversity. The impacts of introduced seaweeds on native macroalgal assemblages have been thoroughly reviewed. In contrast, no attempt has been made to synthesize the available information on the effects of exotic seaweeds on other trophic levels. In addition, it has not been clarified whether the effects of introduced seaweeds on native assemblages vary according to background physical and biological conditions. Methods: This protocol provides details of our proposed method to carry out a systematic review aiming to identify and synthesize existing knowledge to answer the following primary questions: a) how does the impact of the presence of exotic seaweeds on native primary consumers (across trophic levels) compare in magnitude and extent to that observed on native primary producers (same trophic level)?; b) does the intensity of the effects of the presence of exotic seaweeds on native benthic ecosystems vary along a gradient of human disturbance (i.e. from urban/industrial areas to extra-urban areas to pristine areas) © 2012 Bulleri et al.; licensee BioMed Central Ltd. |
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. |
Chatzinikolaou, E Diversity in the growth patterns of marine gastropods Incollection Gastropods: Diversity, Habitat and Genetics, Nova Science Publishers, Inc., 2011, ISBN: 978-1-61324-695-5, (Publication Title: Gastropods: Diversity, Habitat and Genetics). @incollection{chatzinikolaou_diversity_2011, title = {Diversity in the growth patterns of marine gastropods}, author = {E Chatzinikolaou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84895341204&partnerID=40&md5=448fb27fa87432e78e2b386d7e45edb8}, isbn = {978-1-61324-695-5}, year = {2011}, date = {2011-01-01}, booktitle = {Gastropods: Diversity, Habitat and Genetics}, publisher = {Nova Science Publishers, Inc.}, abstract = {Diversity in growth patterns of marine gastropod populations may be attributed to varying parameters. Factors such as maturity status, gender and population density may determine the actual growth rate of individuals. The geographic variability of growth rate in conspecific populations may be the result of different environmental pressures. Seawater temperature, type and availability of food, wave exposure and predation have been proved to affect shell size and shell thickness. Also differences in population dynamics and growth patterns have been recorded between populations of gastropods inhabiting different localities. Individuals inhabiting exposed shores have a faster growth rate but may reach a smaller maximum asymptotic length in comparison to whelks living in sheltered environments. Gastropods living in coastal environments hosting a great number of predatory crabs develop thicker shells that offer higher protection against predation stress. Increased seawater temperature and high food availability result in faster growth rates. Seawater temperature may also affect the duration and seasonality of the growth period. © 2012 by Nova Science Publishers, Inc. All rights reserved.}, note = {Publication Title: Gastropods: Diversity, Habitat and Genetics}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } Diversity in growth patterns of marine gastropod populations may be attributed to varying parameters. Factors such as maturity status, gender and population density may determine the actual growth rate of individuals. The geographic variability of growth rate in conspecific populations may be the result of different environmental pressures. Seawater temperature, type and availability of food, wave exposure and predation have been proved to affect shell size and shell thickness. Also differences in population dynamics and growth patterns have been recorded between populations of gastropods inhabiting different localities. Individuals inhabiting exposed shores have a faster growth rate but may reach a smaller maximum asymptotic length in comparison to whelks living in sheltered environments. Gastropods living in coastal environments hosting a great number of predatory crabs develop thicker shells that offer higher protection against predation stress. Increased seawater temperature and high food availability result in faster growth rates. Seawater temperature may also affect the duration and seasonality of the growth period. © 2012 by Nova Science Publishers, Inc. All rights reserved. |
2010 |
Chatzinikolaou, E; Richardson, C A Parental size and environmental conditions affect egg capsule production by Nassarius reticulatus (Linnaeus 1758) (Gastropoda: Nassariidae) Journal Article Journal of Experimental Marine Biology and Ecology, 390 (1), pp. 14–21, 2010, ISSN: 00220981, (Publisher: Elsevier B.V.). @article{chatzinikolaou_parental_2010, title = {Parental size and environmental conditions affect egg capsule production by Nassarius reticulatus (Linnaeus 1758) (Gastropoda: Nassariidae)}, author = {E Chatzinikolaou and C A Richardson}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78349303900&doi=10.1016%2fj.jembe.2010.04.029&partnerID=40&md5=3e8d7d213badcc7ee0c55640d4db1717}, doi = {10.1016/j.jembe.2010.04.029}, issn = {00220981}, year = {2010}, date = {2010-01-01}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {390}, number = {1}, pages = {14--21}, abstract = {In shallow coastal habitats scavenging netted whelks Nassarius reticulatus attached egg capsules to the stipes of red algae Chondrus crispus and occasionally on Furcellaria lumbricalis and Plumaria plumose. In the laboratory egg capsules were laid on aquaria sides and lids by individuals ≥21 mm shell length. Larger size classes produced more egg capsules and spawned over a longer period and in doing so partitioned less energy into shell growth. Large netted whelks (25-28.9 mm) produced larger capsules which contained significantly more and larger eggs than those produced by smaller individuals (21-24.9 mm). Egg capsule production continued throughout the year by regularly fed N. reticulatus held at ambient seawater temperatures. Egg production increased in the spring and summer with peak production during June (15 °C), decreased between August and October and resumed again during the winter (November to February at 7 °C). During the summer (15-16 °C) egg capsules were smaller and contained smaller eggs than those deposited during the winter (7-10 °C), although the number of eggs·capsule-1 was similar. Enforced food limitation reduced the number and size of the egg capsules, the number and size of eggs produced·female-1 and the duration of the breeding period. Hatching success of N. reticulatus egg capsules was high (95%) even at winter seawater temperatures (11-8.5 °C) and the duration of embryonic development was fastest between 15 and 17.5 °C. © 2010 Elsevier B.V. All rights reserved.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In shallow coastal habitats scavenging netted whelks Nassarius reticulatus attached egg capsules to the stipes of red algae Chondrus crispus and occasionally on Furcellaria lumbricalis and Plumaria plumose. In the laboratory egg capsules were laid on aquaria sides and lids by individuals ≥21 mm shell length. Larger size classes produced more egg capsules and spawned over a longer period and in doing so partitioned less energy into shell growth. Large netted whelks (25-28.9 mm) produced larger capsules which contained significantly more and larger eggs than those produced by smaller individuals (21-24.9 mm). Egg capsule production continued throughout the year by regularly fed N. reticulatus held at ambient seawater temperatures. Egg production increased in the spring and summer with peak production during June (15 °C), decreased between August and October and resumed again during the winter (November to February at 7 °C). During the summer (15-16 °C) egg capsules were smaller and contained smaller eggs than those deposited during the winter (7-10 °C), although the number of eggs·capsule-1 was similar. Enforced food limitation reduced the number and size of the egg capsules, the number and size of eggs produced·female-1 and the duration of the breeding period. Hatching success of N. reticulatus egg capsules was high (95%) even at winter seawater temperatures (11-8.5 °C) and the duration of embryonic development was fastest between 15 and 17.5 °C. © 2010 Elsevier B.V. All rights reserved. |
2009 |
Chatzinikolaou, Eva E-lessons for student education on sustainable development Miscellaneous 2009, (Place: Athens Publisher: The Education Research Centre of Greece). @misc{chatzinikolaou_e-lessons_2009, title = {E-lessons for student education on sustainable development}, author = {Eva Chatzinikolaou}, url = {www.kee.gr/perivallontiki/greeting.html}, year = {2009}, date = {2009-01-01}, address = {Athens, Greece}, note = {Place: Athens Publisher: The Education Research Centre of Greece}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
2008 |
Chatzinikolaou, E; Richardson, C A Population dynamics and growth of Nassarius reticulatus (Gastropoda: Nassariidae) in Rhosneigr (Anglesey, UK) Journal Article Marine Biology, 153 (4), pp. 605–619, 2008, ISSN: 00253162. @article{chatzinikolaou_population_2008, title = {Population dynamics and growth of Nassarius reticulatus (Gastropoda: Nassariidae) in Rhosneigr (Anglesey, UK)}, author = {E Chatzinikolaou and C A Richardson}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-38349171182&doi=10.1007%2fs00227-007-0835-5&partnerID=40&md5=2e0b388abcb21022878c02ba4874f096}, doi = {10.1007/s00227-007-0835-5}, issn = {00253162}, year = {2008}, date = {2008-01-01}, journal = {Marine Biology}, volume = {153}, number = {4}, pages = {605--619}, abstract = {Seasonal changes in catch rate, growth and mortality of Nassarius reticulatus from an intertidal lagoon and a wave-exposed beach at Rhosneigr (Anglesey, North Wales, UK) are described. The number of N. reticulatus caught in baited traps from the lagoon was significantly higher (>125 individuals trap-1) during the summer (>18°C), than at <12°C (<65 individuals trap-1), and the numbers caught in the lagoon were an order of magnitude greater than on the beach, >13 individuals trap-1 in July (>16°C), and <5 individuals trap -1 between December and April (<9.5°C). Predictions of shell growth attained by N. reticulatus annually in the lagoon using graphical modal progression analysis (MPA) of length frequency data, were similar to the growth of marked and recaptured lagoon N. reticulatus. Predictions of shell growth using computerised length frequency distribution analysis (LFDA), however, did not reflect the growth as accurately as MPA. Modal progression analysis demonstrated that N. reticulatus from the lagoon achieved a higher asymptotic maximum shell length (L ∞) and a lower growth constant (K) than animals from the beach. Shell growth was seasonal with growth of the lagoon individuals slowing down towards the end of September and resuming in early April, about a month later than the beach individuals. Mortality of N. reticulatus was greater during the summer, and survival was lower in the lagoon than on the beach. Recruitment patterns were similar in the lagoon and on the beach, and MPA and LFDA predicted that larval N. reticulatus settled between late summer and early autumn, with juveniles (7-8.9 mm) appearing in the population the following year, between February and April. Growth of male and female N. reticulatus in the laboratory was similar and was temperature and size dependent. The different growth patterns between N. reticulatus from the two habitats, predicted using MPA, were maintained when individuals were reared under laboratory conditions for ∼6 months; N. reticulatus <21 mm from the beach grew faster than individuals from the lagoon, although N. reticulatus >21 mm from the lagoon grew faster and attained a larger length (26 mm) than individuals from the beach (24 mm). Low food availability did not affect N. reticulatus survival in the laboratory but significantly suppressed shell growth. © 2007 Springer-Verlag.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Seasonal changes in catch rate, growth and mortality of Nassarius reticulatus from an intertidal lagoon and a wave-exposed beach at Rhosneigr (Anglesey, North Wales, UK) are described. The number of N. reticulatus caught in baited traps from the lagoon was significantly higher (>125 individuals trap-1) during the summer (>18°C), than at <12°C (<65 individuals trap-1), and the numbers caught in the lagoon were an order of magnitude greater than on the beach, >13 individuals trap-1 in July (>16°C), and <5 individuals trap -1 between December and April (<9.5°C). Predictions of shell growth attained by N. reticulatus annually in the lagoon using graphical modal progression analysis (MPA) of length frequency data, were similar to the growth of marked and recaptured lagoon N. reticulatus. Predictions of shell growth using computerised length frequency distribution analysis (LFDA), however, did not reflect the growth as accurately as MPA. Modal progression analysis demonstrated that N. reticulatus from the lagoon achieved a higher asymptotic maximum shell length (L ∞) and a lower growth constant (K) than animals from the beach. Shell growth was seasonal with growth of the lagoon individuals slowing down towards the end of September and resuming in early April, about a month later than the beach individuals. Mortality of N. reticulatus was greater during the summer, and survival was lower in the lagoon than on the beach. Recruitment patterns were similar in the lagoon and on the beach, and MPA and LFDA predicted that larval N. reticulatus settled between late summer and early autumn, with juveniles (7-8.9 mm) appearing in the population the following year, between February and April. Growth of male and female N. reticulatus in the laboratory was similar and was temperature and size dependent. The different growth patterns between N. reticulatus from the two habitats, predicted using MPA, were maintained when individuals were reared under laboratory conditions for ∼6 months; N. reticulatus <21 mm from the beach grew faster than individuals from the lagoon, although N. reticulatus >21 mm from the lagoon grew faster and attained a larger length (26 mm) than individuals from the beach (24 mm). Low food availability did not affect N. reticulatus survival in the laboratory but significantly suppressed shell growth. © 2007 Springer-Verlag. |
2007 |
Chatzinikolaou, E; Richardson, C A Evaluating growth and age of netted whelk Nassarius reticulatus (Gastropoda: Nassariidae) using statolith growth rings Journal Article Marine Ecology Progress Series, 342 , pp. 163–176, 2007, ISSN: 01718630. @article{chatzinikolaou_evaluating_2007, title = {Evaluating growth and age of netted whelk Nassarius reticulatus (Gastropoda: Nassariidae) using statolith growth rings}, author = {E Chatzinikolaou and C A Richardson}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34548143428&doi=10.3354%2fmeps342163&partnerID=40&md5=e991e92111cbc1b4ce5e470e7807ee1f}, doi = {10.3354/meps342163}, issn = {01718630}, year = {2007}, date = {2007-01-01}, journal = {Marine Ecology Progress Series}, volume = {342}, pages = {163--176}, abstract = {The periodicity of growth rings in the statoliths of Nassarius reticulatus (Linnaeus, 1758) was validated using laboratory-reared larvae and juveniles of known age. Formation of the first ring occurred at larval settlement and subsequent rings were deposited annually. Wider light increments formed between March and June when seawater temperatures increased from 10.9 to 19.4°C, whereas darker narrow rings formed between the late summer and winter. Counts of the annual statolith rings were used to determine the age of N. reticulatus collected from six locations around the Anglesey coast, North Wales. The oldest whelks, 7 and 6 yr respectively, occurred in a sheltered lagoon at Rhosneigr and from a sheltered area between Cemlyn Bay and Carmel Head. Lack of geographical variations in settlement ring size suggests that the larvae spend a similar period of time in the plankton before settlement. Significant differences in the diameters of the annual rings indicate that wave exposure and food availability may affect growth at different locations. The relationship between statolith diameter (SDi) and shell length (ShL) for larvae, juvenile and adult N. reticulatus (0.3 to 31 mm) was SDi (μm) = 36.31 x ShL (mm)0.464. No statistically significant differences in this relationship were found amongst the 6 Anglesey locations or between whelks of different gender. Using the equation, ShL at formation of each annual ring was estimated, and von Bertalanffy growth (VBG) curves fitted to the length-age data. Whelks from the sheltered Rhosneigr lagoon had the highest asymptotic maximum ShL (L ∞) and the lowest growth constant (K), suggesting a slow growth over a period of time. Growth rates of males, females and imposex-affected females were similar. © Inter-Research 2007.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The periodicity of growth rings in the statoliths of Nassarius reticulatus (Linnaeus, 1758) was validated using laboratory-reared larvae and juveniles of known age. Formation of the first ring occurred at larval settlement and subsequent rings were deposited annually. Wider light increments formed between March and June when seawater temperatures increased from 10.9 to 19.4°C, whereas darker narrow rings formed between the late summer and winter. Counts of the annual statolith rings were used to determine the age of N. reticulatus collected from six locations around the Anglesey coast, North Wales. The oldest whelks, 7 and 6 yr respectively, occurred in a sheltered lagoon at Rhosneigr and from a sheltered area between Cemlyn Bay and Carmel Head. Lack of geographical variations in settlement ring size suggests that the larvae spend a similar period of time in the plankton before settlement. Significant differences in the diameters of the annual rings indicate that wave exposure and food availability may affect growth at different locations. The relationship between statolith diameter (SDi) and shell length (ShL) for larvae, juvenile and adult N. reticulatus (0.3 to 31 mm) was SDi (μm) = 36.31 x ShL (mm)0.464. No statistically significant differences in this relationship were found amongst the 6 Anglesey locations or between whelks of different gender. Using the equation, ShL at formation of each annual ring was estimated, and von Bertalanffy growth (VBG) curves fitted to the length-age data. Whelks from the sheltered Rhosneigr lagoon had the highest asymptotic maximum ShL (L ∞) and the lowest growth constant (K), suggesting a slow growth over a period of time. Growth rates of males, females and imposex-affected females were similar. © Inter-Research 2007. |
Richardson, C A; Chatzinikolaou, Eva; Saurel, C Gastropod Statoliths: a tool for reconstructing the growth of gastropods Inproceedings St. Petersburg, Florida, USA, 2007, (Publication Title: First International Sclerochronology Conference). @inproceedings{richardson_gastropod_2007, title = {Gastropod Statoliths: a tool for reconstructing the growth of gastropods}, author = {C A Richardson and Eva Chatzinikolaou and C Saurel}, year = {2007}, date = {2007-01-01}, address = {St. Petersburg, Florida, USA}, note = {Publication Title: First International Sclerochronology Conference}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2005 |
Richardson, C A; Kingsley-Smith, P R; Seed, R; Chatzinikolaou, E Marine Biology, 148 (2), pp. 319–326, 2005, ISSN: 00253162. @article{richardson_age_2005, title = {Age and growth of the naticid gastropod Polinices pulchellus (Gastropoda: Naticidae) based on length frequency analysis and statolith growth rings}, author = {C A Richardson and P R Kingsley-Smith and R Seed and E Chatzinikolaou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-28444483588&doi=10.1007%2fs00227-005-0072-8&partnerID=40&md5=037cebd2b1e1ca9d1ed2d2bbb9e5bc45}, doi = {10.1007/s00227-005-0072-8}, issn = {00253162}, year = {2005}, date = {2005-01-01}, journal = {Marine Biology}, volume = {148}, number = {2}, pages = {319--326}, abstract = {In Red Wharf Bay, UK the naticid gastropod, Polinices pulchellus, was more abundant and more highly aggregated during the summer months (June-August 2001) than during the winter (December 2000). Whilst small numbers of juvenile P. pulchellus (4-6 mm shell length) were present throughout the year the population consisted mainly of individuals of 12-14 mm shell length. Juvenile snails grew rapidly in size during the winter and early spring; growth then virtually ceased between May and June, following which there was a further period of rapid growth between August and February. Densities ranged between 57 and 4,073 ha-1 and the largest individual collected during this investigation measured 16.2 mm in shell length. Statoliths from adult P. pulchellus revealed the presence of a settlement ring and two prominent growth rings (rings 1 and 2). A curvilinear relationship exists between statolith diameter and shell length in snails up to 16 mm in length. Settlement rings ranged in diameter from 19.7 to 45.2 μm (mean 29.8 μm; SE=0.41) giving an estimated shell length of the settled juvenile of 1.1 mm. The diameter of ring 1 and ring 2 were significantly correlated indicating that rapid growth during the first year is maintained during year 2. Shell lengths estimated from the diameters of the prominent statolith rings and those obtained from length frequency data analysis (LFDA), were broadly congruent strongly suggesting an annual periodicity to the statolith rings. The largest snails (>15 mm) present within this population were estimated to be between 2 and 3 years old. Von Bertallanfy seasonal growth curves obtained from the LFDA predicted values of L∞, K and t 0 of 14.32 mm, 1.54 and -0.14 years, respectively, suggesting that P. pulchellus rapidly attains its maximum asymptotic size. © Springer-Verlag 2005.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In Red Wharf Bay, UK the naticid gastropod, Polinices pulchellus, was more abundant and more highly aggregated during the summer months (June-August 2001) than during the winter (December 2000). Whilst small numbers of juvenile P. pulchellus (4-6 mm shell length) were present throughout the year the population consisted mainly of individuals of 12-14 mm shell length. Juvenile snails grew rapidly in size during the winter and early spring; growth then virtually ceased between May and June, following which there was a further period of rapid growth between August and February. Densities ranged between 57 and 4,073 ha-1 and the largest individual collected during this investigation measured 16.2 mm in shell length. Statoliths from adult P. pulchellus revealed the presence of a settlement ring and two prominent growth rings (rings 1 and 2). A curvilinear relationship exists between statolith diameter and shell length in snails up to 16 mm in length. Settlement rings ranged in diameter from 19.7 to 45.2 μm (mean 29.8 μm; SE=0.41) giving an estimated shell length of the settled juvenile of 1.1 mm. The diameter of ring 1 and ring 2 were significantly correlated indicating that rapid growth during the first year is maintained during year 2. Shell lengths estimated from the diameters of the prominent statolith rings and those obtained from length frequency data analysis (LFDA), were broadly congruent strongly suggesting an annual periodicity to the statolith rings. The largest snails (>15 mm) present within this population were estimated to be between 2 and 3 years old. Von Bertallanfy seasonal growth curves obtained from the LFDA predicted values of L∞, K and t 0 of 14.32 mm, 1.54 and -0.14 years, respectively, suggesting that P. pulchellus rapidly attains its maximum asymptotic size. © Springer-Verlag 2005. |
2004 |
Tzovenis, I; Triantaphyllidis, G; Naihong, X; Chatzinikolaou, E; Papadopoulou, K; Xouri, G; Tafas, T Cryopreservation of marine microalgae and potential toxicity of cryoprotectants to the primary steps of the aquacultural food chain Journal Article Aquaculture, 230 (1-4), pp. 457–473, 2004, ISSN: 00448486, (Publisher: Elsevier). @article{tzovenis_cryopreservation_2004, title = {Cryopreservation of marine microalgae and potential toxicity of cryoprotectants to the primary steps of the aquacultural food chain}, author = {I Tzovenis and G Triantaphyllidis and X Naihong and E Chatzinikolaou and K Papadopoulou and G Xouri and T Tafas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0842310593&doi=10.1016%2fS0044-8486%2803%2900444-7&partnerID=40&md5=2ebddbf8a832f68bfc915dcafcbffe6e}, doi = {10.1016/S0044-8486(03)00444-7}, issn = {00448486}, year = {2004}, date = {2004-01-01}, journal = {Aquaculture}, volume = {230}, number = {1-4}, pages = {457--473}, abstract = {Cryopreservation, a technique of high potential for culture collections, might offer a solution for reliable supply of microalgae in aquaculture units. Marine microalgae used in aquaculture were cryopreserved under 4, -20 and -80°C using common cryoprotectants (methanol, dimethylsulfoxide (DMSO), propylene glycol and polyvinylpyrrolidone (PVP)) with promising results for Chlorella minutissima, Chlorella stigmatophora, Isochrysis galbana and Dunaliella tertiolecta. As cryoprotectants usually are toxic above certain concentrations and exposure time, and assuming that low amounts of cryoprotectants will remain in regenerated cultures, an experimental scheme was employed to explore the lower limits of safety for these algae and their primary consumers in hatchery food chains. Results showed that methanol was well tolerated by C. stigmatophora and D. tertiolecta up to a concentration of 1.6% (v/v) while I. galbana could not survive in culture at any concentration and C. minutissima exhibited some 30% of the control's yield at 0.2%. DMSO was highly tolerated up to 1.0% by all strains with the Chlorella strains surviving well up to 2%. Propylene glycol was not only tolerated up to 8% by Dunaliella but induced mixotrophic growth as well, while for Isochrysis it was lethal at any concentration. Among zooplanktonic consumers, brine shrimp Artemia nauplii could tolerate very high concentrations of the tested cryoprotectants, the rotifer Brachionus plicatilis was found sensitive to low amounts of PVP, while the nauplii of the shrimp Penaeus japonicus and the crab Eriocheir sinensis were in general very sensitive to all cryoprotectants and in several cases to much lower amounts than 1%. However, as long as the residues of cryoprotectants are kept below 1% in the regenerated cultures, there will be no problem with the animal consumers. © 2004 Elsevier B.V. All rights reserved.}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cryopreservation, a technique of high potential for culture collections, might offer a solution for reliable supply of microalgae in aquaculture units. Marine microalgae used in aquaculture were cryopreserved under 4, -20 and -80°C using common cryoprotectants (methanol, dimethylsulfoxide (DMSO), propylene glycol and polyvinylpyrrolidone (PVP)) with promising results for Chlorella minutissima, Chlorella stigmatophora, Isochrysis galbana and Dunaliella tertiolecta. As cryoprotectants usually are toxic above certain concentrations and exposure time, and assuming that low amounts of cryoprotectants will remain in regenerated cultures, an experimental scheme was employed to explore the lower limits of safety for these algae and their primary consumers in hatchery food chains. Results showed that methanol was well tolerated by C. stigmatophora and D. tertiolecta up to a concentration of 1.6% (v/v) while I. galbana could not survive in culture at any concentration and C. minutissima exhibited some 30% of the control's yield at 0.2%. DMSO was highly tolerated up to 1.0% by all strains with the Chlorella strains surviving well up to 2%. Propylene glycol was not only tolerated up to 8% by Dunaliella but induced mixotrophic growth as well, while for Isochrysis it was lethal at any concentration. Among zooplanktonic consumers, brine shrimp Artemia nauplii could tolerate very high concentrations of the tested cryoprotectants, the rotifer Brachionus plicatilis was found sensitive to low amounts of PVP, while the nauplii of the shrimp Penaeus japonicus and the crab Eriocheir sinensis were in general very sensitive to all cryoprotectants and in several cases to much lower amounts than 1%. However, as long as the residues of cryoprotectants are kept below 1% in the regenerated cultures, there will be no problem with the animal consumers. © 2004 Elsevier B.V. All rights reserved. |
1999 |
Triantafyllidis, G; Pantazis, G; Xouri, G; Papadopoulou, K -N; Chatzinikolaou, Eva; Economou, A N; Tafas, T Cryopreservation of microalgae and toxicity of cryoprotectants for aquaculture Inproceedings Proceedings 21st Panhellenic Meeting of Hellenic Society of Biological Sciences, Syros, Greece, 1999, (Publication Title: Proceedings 21st Panhellenic Meeting of Hellenic Society of Biological Sciences). @inproceedings{triantafyllidis_cryopreservation_1999, title = {Cryopreservation of microalgae and toxicity of cryoprotectants for aquaculture}, author = {G Triantafyllidis and G Pantazis and G Xouri and K -N Papadopoulou and Eva Chatzinikolaou and A N Economou and T Tafas}, year = {1999}, date = {1999-01-01}, booktitle = {Proceedings 21st Panhellenic Meeting of Hellenic Society of Biological Sciences}, address = {Syros, Greece}, note = {Publication Title: Proceedings 21st Panhellenic Meeting of Hellenic Society of Biological Sciences}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |