2021 |
Karamanlidis, Alexandros A; Skrbinšek, Tomaž; Amato, George; Dendrinos, Panagiotis; Gaughran, Stephen; Kasapidis, Panagiotis; Kopatz, Alexander; Stronen, Astrid Vik Sci Rep, 11 (1), pp. 373, 2021, ISSN: 2045-2322. @article{karamanlidis_genetic_2021, title = {Genetic and demographic history define a conservation strategy for earth’s most endangered pinniped, the Mediterranean monk seal Monachus monachus}, author = {Alexandros A Karamanlidis and Tomaž Skrbinšek and George Amato and Panagiotis Dendrinos and Stephen Gaughran and Panagiotis Kasapidis and Alexander Kopatz and Astrid Vik Stronen}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Karamanlidis-SciRep-3.pdf http://www.nature.com/articles/s41598-020-79712-1}, doi = {10.1038/s41598-020-79712-1}, issn = {2045-2322}, year = {2021}, date = {2021-12-01}, urldate = {2021-02-02}, journal = {Sci Rep}, volume = {11}, number = {1}, pages = {373}, abstract = {Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival. |
Reitmeier, Sandra; Hitch, Thomas C A; Treichel, Nicole; Fikas, Nikolaos; Hausmann, Bela; Ramer-Tait, Amanda E; Neuhaus, Klaus; Berry, David; Haller, Dirk; Lagkouvardos, Ilias; Clavel, Thomas Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling Journal Article ISME Communications, 1 (1), pp. 31, 2021, ISSN: 2730-6151. @article{reitmeier_handling_2021, title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling}, author = {Sandra Reitmeier and Thomas C A Hitch and Nicole Treichel and Nikolaos Fikas and Bela Hausmann and Amanda E Ramer-Tait and Klaus Neuhaus and David Berry and Dirk Haller and Ilias Lagkouvardos and Thomas Clavel}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Reitmer-ISME-52-1.pdf http://www.nature.com/articles/s43705-021-00033-z}, doi = {10.1038/s43705-021-00033-z}, issn = {2730-6151}, year = {2021}, date = {2021-12-01}, urldate = {2021-07-26}, journal = {ISME Communications}, volume = {1}, number = {1}, pages = {31}, abstract = {Abstract 16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta -diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha -diversity across studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract 16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta -diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha -diversity across studies. |
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. |
Oikonomou, Stavroula; Tsakogiannis, Alexandros; Kriaridou, Christina; Danis, Theodoros; Manousaki, Tereza; Chatziplis, Dimitris; Papandroulakis, Nikos; Mylonas, Constantinos C; Triantafyllidis, Alexandros; Tsigenopoulos, Costas S 21 , pp. 100855, 2021, ISSN: 23525134. @article{oikonomou_first_2021, title = {First linkage maps and a pilot QTL analysis for early growth performance in common dentex (Dentex dentex) and sharpsnout seabream (Diplodus puntazzo)}, author = {Stavroula Oikonomou and Alexandros Tsakogiannis and Christina Kriaridou and Theodoros Danis and Tereza Manousaki and Dimitris Chatziplis and Nikos Papandroulakis and Constantinos C Mylonas and Alexandros Triantafyllidis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Oikonomou-AquaReports-68.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513421002714}, doi = {10.1016/j.aqrep.2021.100855}, issn = {23525134}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {21}, pages = {100855}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cascarano, Maria Chiara; Stavrakidis-Zachou, Orestis; Mladineo, Ivona; Thompson, Kim D; Papandroulakis, Nikos; Katharios, Pantelis Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species Journal Article 10 (9), pp. 1205, 2021. @article{cascarano_mediterranean_2021, title = {Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species}, author = {Maria Chiara Cascarano and Orestis Stavrakidis-Zachou and Ivona Mladineo and Kim D Thompson and Nikos Papandroulakis and Pantelis Katharios}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Cascarano-pathogens-71.pdf https://www.mdpi.com/2076-0817/10/9/1205}, doi = {10.3390/pathogens10091205}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {10}, number = {9}, pages = {1205}, abstract = {Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea. |
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. |
Stavrakidis-Zachou, Orestis; Lika, Konstadia; Michail, Pavlidis; Tsalafouta, Aleka; Mohamed, Asaad H; Nikos, Papandroulakis Thermal tolerance, metabolic scope and performance of meagre, Argyrosomus regius, reared under high water temperatures Journal Article 100 , pp. 103063, 2021, ISSN: 03064565. @article{stavrakidis-zachou_thermal_2021, title = {Thermal tolerance, metabolic scope and performance of meagre, Argyrosomus regius, reared under high water temperatures}, author = {Orestis Stavrakidis-Zachou and Konstadia Lika and Pavlidis Michail and Aleka Tsalafouta and Asaad H Mohamed and Papandroulakis Nikos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Stavrakidis-JoTB-65-pre-print.pdf https://linkinghub.elsevier.com/retrieve/pii/S030645652100231X}, doi = {10.1016/j.jtherbio.2021.103063}, issn = {03064565}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-16}, volume = {100}, pages = {103063}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
Gasco, L; Józefiak, A; Henry, M Beyond the protein concept: health aspects of using edible insects on animals Journal Article 7 (5), pp. 715–741, 2021, ISSN: 2352-4588. @article{gasco_beyond_2021, title = {Beyond the protein concept: health aspects of using edible insects on animals}, author = {L Gasco and A Józefiak and M Henry}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Gasco-Henry-JIFF-67.pdf https://www.wageningenacademic.com/doi/10.3920/JIFF2020.0077}, doi = {10.3920/JIFF2020.0077}, issn = {2352-4588}, year = {2021}, date = {2021-08-13}, urldate = {2021-09-22}, volume = {7}, number = {5}, pages = {715--741}, abstract = {There is an increasing interest in the use of insects in animal feed since they contain high proteins levels, lipids, vitamins and minerals. In particular, insect-derived proteins are seen as one of the potential solution to face the increasing protein shortage and are able to fully substitute soybean meal or fishmeal in aquaculture or livestock feeds. However, beside their interesting nutritional composition, insects are also rich in bioactive compounds such as chitin, antimicrobial peptides or specific fatty acids with immunostimulating, antimicrobial and/or anti-inflammatory properties able to sustain animal health, increase their resistance to diseases. Further studies will also have to investigate whether insects share similarities with bacterial or parasitical pathogens and may act as immunostimulants. These recent findings may launch insects beyond the protein concept into healthy animal feeds. This review presents the effects of insects and their bioactive compounds on fish and crustaceans, poultry, pigs and rabbits immune system, gut health, microbiota and resistance to diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is an increasing interest in the use of insects in animal feed since they contain high proteins levels, lipids, vitamins and minerals. In particular, insect-derived proteins are seen as one of the potential solution to face the increasing protein shortage and are able to fully substitute soybean meal or fishmeal in aquaculture or livestock feeds. However, beside their interesting nutritional composition, insects are also rich in bioactive compounds such as chitin, antimicrobial peptides or specific fatty acids with immunostimulating, antimicrobial and/or anti-inflammatory properties able to sustain animal health, increase their resistance to diseases. Further studies will also have to investigate whether insects share similarities with bacterial or parasitical pathogens and may act as immunostimulants. These recent findings may launch insects beyond the protein concept into healthy animal feeds. This review presents the effects of insects and their bioactive compounds on fish and crustaceans, poultry, pigs and rabbits immune system, gut health, microbiota and resistance to diseases. |
Medvecky, Matej; Mandalakis, Manolis PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems Journal Article Frontiers in Chemistry, 9 , pp. 722087, 2021, ISSN: 2296-2646. @article{medvecky_pepmandis_2021, title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems}, author = {Matej Medvecky and Manolis Mandalakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Mandalakis-FiChem-62.pdf https://www.frontiersin.org/articles/10.3389/fchem.2021.722087/full}, doi = {10.3389/fchem.2021.722087}, issn = {2296-2646}, year = {2021}, date = {2021-08-01}, urldate = {2021-08-23}, journal = {Frontiers in Chemistry}, volume = {9}, pages = {722087}, abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest. |
Fanini, Lucia; Costa, Leonardo Lopes; Zalmon, Ilana Rosental; Riechers, Maraja Social and Ecological Elements for a Perspective Approach to Citizen Science on the Beach Journal Article Frontiers in Ecology and Evolution, 9 , pp. 694487, 2021, ISSN: 2296-701X. @article{fanini_social_2021, title = {Social and Ecological Elements for a Perspective Approach to Citizen Science on the Beach}, author = {Lucia Fanini and Leonardo Lopes Costa and Ilana Rosental Zalmon and Maraja Riechers}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Fanini-fevo-61.pdf https://www.frontiersin.org/articles/10.3389/fevo.2021.694487/full}, doi = {10.3389/fevo.2021.694487}, issn = {2296-701X}, year = {2021}, date = {2021-08-01}, urldate = {2021-08-23}, journal = {Frontiers in Ecology and Evolution}, volume = {9}, pages = {694487}, abstract = {Sandy beaches are ecotonal environments connecting land and sea, hosting exclusive resident organisms and key life stages of (often charismatic) fauna. Humans also visit sandy beaches where tourism, in particular, moves billions of people every year. However, instead of representing a connection to nature, the attitude toward visiting the beach is biased concerning its recreational use. Such “sun, sea, and sand” target and its display seem to be deeply rooted in social systems. How could scientists engage the newest generations and facilitate an exit from this loop, fostering care (including participative beach science), and ultimately sustainable sandy beach use? To tackle this question, we applied the concept of social–ecological systems to the Littoral Active Zone (LAZ). The LAZ is a unit sustaining beach functionalities, though it includes relevant features making a beach attractive to the public. Out of the analysis of the system LAZ in its social and ecological templates, we extracted elements suitable to the planning of citizen science programs. The perspective of leverage points was integrated to the needs identified in the analysis, through reconnecting–restructuring–rethinking the components of the system. Two cross-cutting approaches were marked as important to social and ecological designs and break through the dominant perception of beaches as mere piles of sand: the physical dimension (LAZ) of the beach as a unit, and the use of communication through social media, suitable to both monitoring and scientific data collection, and to data communication and hedonistic display of a day on the beach.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sandy beaches are ecotonal environments connecting land and sea, hosting exclusive resident organisms and key life stages of (often charismatic) fauna. Humans also visit sandy beaches where tourism, in particular, moves billions of people every year. However, instead of representing a connection to nature, the attitude toward visiting the beach is biased concerning its recreational use. Such “sun, sea, and sand” target and its display seem to be deeply rooted in social systems. How could scientists engage the newest generations and facilitate an exit from this loop, fostering care (including participative beach science), and ultimately sustainable sandy beach use? To tackle this question, we applied the concept of social–ecological systems to the Littoral Active Zone (LAZ). The LAZ is a unit sustaining beach functionalities, though it includes relevant features making a beach attractive to the public. Out of the analysis of the system LAZ in its social and ecological templates, we extracted elements suitable to the planning of citizen science programs. The perspective of leverage points was integrated to the needs identified in the analysis, through reconnecting–restructuring–rethinking the components of the system. Two cross-cutting approaches were marked as important to social and ecological designs and break through the dominant perception of beaches as mere piles of sand: the physical dimension (LAZ) of the beach as a unit, and the use of communication through social media, suitable to both monitoring and scientific data collection, and to data communication and hedonistic display of a day on the beach. |
Peñaloza, C; Manousaki, T; Franch, R; Tsakogiannis, A; Sonesson, A K; Aslam, M L; Allal, F; Bargelloni, L; Houston, R D; Tsigenopoulos, C S Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) Journal Article Genomics, 113 (4), pp. 2096–2107, 2021, ISSN: 08887543. @article{penaloza_development_2021, title = {Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)}, author = {C Peñaloza and T Manousaki and R Franch and A Tsakogiannis and A K Sonesson and M L Aslam and F Allal and L Bargelloni and R D Houston and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Penaloza-Genomics-39.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321001713}, doi = {10.1016/j.ygeno.2021.04.038}, issn = {08887543}, year = {2021}, date = {2021-07-01}, urldate = {2021-06-24}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2096--2107}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nikolaivits, Efstratios; Siaperas, Romanos; Agrafiotis, Andreas; Ouazzani, Jamal; Magoulas, Antonios; Gioti, Αnastasia; Topakas, Evangelos Science of The Total Environment, 775 , pp. 145818, 2021, ISSN: 00489697. @article{nikolaivits_functional_2021, title = {Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus}, author = {Efstratios Nikolaivits and Romanos Siaperas and Andreas Agrafiotis and Jamal Ouazzani and Antonios Magoulas and Αnastasia Gioti and Evangelos Topakas}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721008858}, doi = {10.1016/j.scitotenv.2021.145818}, issn = {00489697}, year = {2021}, date = {2021-06-01}, urldate = {2021-03-17}, journal = {Science of The Total Environment}, volume = {775}, pages = {145818}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kumar, Neeraj; Hitch, Thomas C A; Haller, Dirk; Lagkouvardos, Ilias; Clavel, Thomas MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes Journal Article Microbial Biotechnology, pp. 1751–7915.13845, 2021, ISSN: 1751-7915, 1751-7915. @article{kumar_mimic_2021, title = {MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes}, author = {Neeraj Kumar and Thomas C A Hitch and Dirk Haller and Ilias Lagkouvardos and Thomas Clavel}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Kumar-MicBio-50.pdf https://onlinelibrary.wiley.com/doi/10.1111/1751-7915.13845}, doi = {10.1111/1751-7915.13845}, issn = {1751-7915, 1751-7915}, year = {2021}, date = {2021-06-01}, urldate = {2021-07-26}, journal = {Microbial Biotechnology}, pages = {1751--7915.13845}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kogiannou, Dimitra; Nikoloudaki, Chrysanthi; Katharios, Pantelis; Triga, Adriana; Rigos, George Evaluation of absorption and depletion of florfenicol in European seabass textitDicentrarchus labrax Journal Article Veterinary Medicine and Science, 7 (3), pp. 987–997, 2021, ISSN: 2053-1095, 2053-1095. @article{kogiannou_evaluation_2021, title = {Evaluation of absorption and depletion of florfenicol in European seabass textitDicentrarchus labrax}, author = {Dimitra Kogiannou and Chrysanthi Nikoloudaki and Pantelis Katharios and Adriana Triga and George Rigos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Kogiannou-VetMed-Sci-40.pdf https://onlinelibrary.wiley.com/doi/10.1002/vms3.415}, doi = {10.1002/vms3.415}, issn = {2053-1095, 2053-1095}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Veterinary Medicine and Science}, volume = {7}, number = {3}, pages = {987--997}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rigos, George; Kogiannou, Dimitra; Vasilaki, Antigoni; Kotsiri, Mado Evaluation of Praziquantel Efficacy against Zeuxapta seriolae Infections in Greater Amberjack, Seriola dumerili Journal Article Applied Sciences, 11 (10), pp. 4656, 2021, ISSN: 2076-3417. @article{rigos_evaluation_2021, title = {Evaluation of Praziquantel Efficacy against Zeuxapta seriolae Infections in Greater Amberjack, Seriola dumerili}, author = {George Rigos and Dimitra Kogiannou and Antigoni Vasilaki and Mado Kotsiri}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Rigos-ApllSciences-41l.pdf https://www.mdpi.com/2076-3417/11/10/4656}, doi = {10.3390/app11104656}, issn = {2076-3417}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Applied Sciences}, volume = {11}, number = {10}, pages = {4656}, abstract = {The aim of this study was to evaluate the efficacy of dietary praziquantel (PZQ), a promising fish anthelminthic, against Zeuxapta seriolae, a lethal ectoparasite of greater amberjack (Seriola dumerili Risso) farmed in the Mediterranean and elsewhere. The trial was carried out in small cages (3 m3) in situ, harbouring fish (125 ± 14 g) naturally infected with Z. seriolae, at 25 ± 1 °C water temperature. Praziquantel-medicated diet (150 mg PZQ/kg fish) was delivered for three days against a control group. Measurement of both adults and oncomiracidia of Z. seriolae in sampled gill arches revealed significant differences between the tested groups (PZQ: 19.3 ± 9.8 vs. Control: 3.8 ± 6.3). Considering an estimated efficacy of 80.4% in the medicated fish, the present study indicates that oral PZQ treatments can confront Z. seriolae infections considerably in farmed greater amberjack and, perhaps, replace the commonly used hydrogen peroxidase baths.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this study was to evaluate the efficacy of dietary praziquantel (PZQ), a promising fish anthelminthic, against Zeuxapta seriolae, a lethal ectoparasite of greater amberjack (Seriola dumerili Risso) farmed in the Mediterranean and elsewhere. The trial was carried out in small cages (3 m3) in situ, harbouring fish (125 ± 14 g) naturally infected with Z. seriolae, at 25 ± 1 °C water temperature. Praziquantel-medicated diet (150 mg PZQ/kg fish) was delivered for three days against a control group. Measurement of both adults and oncomiracidia of Z. seriolae in sampled gill arches revealed significant differences between the tested groups (PZQ: 19.3 ± 9.8 vs. Control: 3.8 ± 6.3). Considering an estimated efficacy of 80.4% in the medicated fish, the present study indicates that oral PZQ treatments can confront Z. seriolae infections considerably in farmed greater amberjack and, perhaps, replace the commonly used hydrogen peroxidase baths. |
Ragkousis, Michail; Digenis, Markos; Kovačić, Marcelo; Katsanevakis, Stelios; Gerovasileiou, Vasilis Rarely Reported Cryptobenthic Fish in Marine Caves of the Eastern Mediterranean Sea Journal Article Journal of Marine Science and Engineering, 9 (6), pp. 557, 2021, ISSN: 2077-1312. @article{ragkousis_rarely_2021, title = {Rarely Reported Cryptobenthic Fish in Marine Caves of the Eastern Mediterranean Sea}, author = {Michail Ragkousis and Markos Digenis and Marcelo Kovačić and Stelios Katsanevakis and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Ragkousis-jmse-09-00557-43.pdf https://www.mdpi.com/2077-1312/9/6/557}, doi = {10.3390/jmse9060557}, issn = {2077-1312}, year = {2021}, date = {2021-05-01}, urldate = {2021-06-24}, journal = {Journal of Marine Science and Engineering}, volume = {9}, number = {6}, pages = {557}, abstract = {Data on the distribution and ecology of cryptobenthic fish of marine caves in the Mediterranean Sea are extremely scarce but necessary for scientists and marine managers alike in order to understand these fish’s ecological role and assess their conservation status. Broadscale surveys by implementing underwater visual census and photographic sampling in marine caves of the northeastern Mediterranean Sea, within different expeditions during the last 5 years, brought to light new records of eight rarely reported cryptobenthic fish species. To a smaller extent, complementary citizen science data from diving professionals of Crete were used to fill distribution gaps. A total of 36 new records (66 individuals) from 18 marine caves and caverns of the Aegean and northeastern Levantine Seas were assembled, belonging to the gobies Corcyrogobius liechtensteini, Didogobius splechtnai, Gammogobius steinitzi, and Thorogobius ephippiatus, the blenny Microlipophrys nigriceps, the tripterygiid Tripterygion melanurum, the speleophilic bythitid Grammonus ater, and the gobiesocid Lepadogaster cf. lepadogaster. The above species have been rarely reported from the Eastern Mediterranean Sea, with D. splechtnai and G. steinitzi being recorded for the first and second time from Greek waters, respectively, while L. cf. lepadogaster constitutes the second record of a clingfish species in a marine cave of the Aegean Sea. Interesting behavioral and ecological habits were also noted for some species, based on in situ observations and photographic evidence. Our study contributes to filling gaps in the knowledge of cave fish diversity and demonstrates that cryptobenthic mobile species in understudied cryptic habitats are more common than previously thought in the Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Data on the distribution and ecology of cryptobenthic fish of marine caves in the Mediterranean Sea are extremely scarce but necessary for scientists and marine managers alike in order to understand these fish’s ecological role and assess their conservation status. Broadscale surveys by implementing underwater visual census and photographic sampling in marine caves of the northeastern Mediterranean Sea, within different expeditions during the last 5 years, brought to light new records of eight rarely reported cryptobenthic fish species. To a smaller extent, complementary citizen science data from diving professionals of Crete were used to fill distribution gaps. A total of 36 new records (66 individuals) from 18 marine caves and caverns of the Aegean and northeastern Levantine Seas were assembled, belonging to the gobies Corcyrogobius liechtensteini, Didogobius splechtnai, Gammogobius steinitzi, and Thorogobius ephippiatus, the blenny Microlipophrys nigriceps, the tripterygiid Tripterygion melanurum, the speleophilic bythitid Grammonus ater, and the gobiesocid Lepadogaster cf. lepadogaster. The above species have been rarely reported from the Eastern Mediterranean Sea, with D. splechtnai and G. steinitzi being recorded for the first and second time from Greek waters, respectively, while L. cf. lepadogaster constitutes the second record of a clingfish species in a marine cave of the Aegean Sea. Interesting behavioral and ecological habits were also noted for some species, based on in situ observations and photographic evidence. Our study contributes to filling gaps in the knowledge of cave fish diversity and demonstrates that cryptobenthic mobile species in understudied cryptic habitats are more common than previously thought in the Mediterranean Sea. |
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%). |
Kourkouta, Chara; Printzi, Alice; Geladakis, George; Mitrizakis, Nikos; Papandroulakis, Nikos; Koumoundouros, George Scientific Reports, 11 (1), pp. 8787, 2021, ISSN: 2045-2322. @article{kourkouta_long_2021, title = {Long lasting effects of early temperature exposure on the swimming performance and skeleton development of metamorphosing Gilthead seabream ( Sparus aurata L.) larvae}, author = {Chara Kourkouta and Alice Printzi and George Geladakis and Nikos Mitrizakis and Nikos Papandroulakis and George Koumoundouros}, url = {https://www.nature.com/articles/s41598-021-88306-4 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Kourkouta-SciReports-31-1.pdf }, doi = {10.1038/s41598-021-88306-4}, issn = {2045-2322}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Scientific Reports}, volume = {11}, number = {1}, pages = {8787}, abstract = {Temperatures experienced during early ontogeny significantly influence fish phenotypes, with clear consequences for the wild and reared stocks. We examined the effect of temperature (17, 20, or 23 °C) during the short embryonic and yolk-sac larval period, on the swimming performance and skeleton of metamorphosing Gilthead seabream larvae. In the following ontogenetic period, all fish were subjected to common temperature (20 °C). The critical swimming speed of metamorphosing larvae was significantly decreased from 9.7 ± 0.6 TL/s (total length per second) at 17 °C developmental temperature (DT) to 8.7 ± 0.6 and 8.8 ± 0.7 TL/s at 20 and 23 °C DT respectively (p textless 0.05). Swimming performance was significantly correlated with fish body shape (p textless 0.05). Compared with the rest groups, fish of 17 °C DT presented a slender body shape, longer caudal peduncle, terminal mouth and ventrally transposed pectoral fins. Moreover, DT significantly affected the relative depth of heart ventricle (VD/TL, p textless 0.05), which was comparatively increased at 17 °C DT. Finally, the incidence of caudal-fin abnormalities significantly decreased (p textless 0.05) with the increase of DT. To our knowledge, this is the first evidence for the significant effect of DT during the short embryonic and yolk-sac larval period on the swimming performance of the later stages.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Temperatures experienced during early ontogeny significantly influence fish phenotypes, with clear consequences for the wild and reared stocks. We examined the effect of temperature (17, 20, or 23 °C) during the short embryonic and yolk-sac larval period, on the swimming performance and skeleton of metamorphosing Gilthead seabream larvae. In the following ontogenetic period, all fish were subjected to common temperature (20 °C). The critical swimming speed of metamorphosing larvae was significantly decreased from 9.7 ± 0.6 TL/s (total length per second) at 17 °C developmental temperature (DT) to 8.7 ± 0.6 and 8.8 ± 0.7 TL/s at 20 and 23 °C DT respectively (p textless 0.05). Swimming performance was significantly correlated with fish body shape (p textless 0.05). Compared with the rest groups, fish of 17 °C DT presented a slender body shape, longer caudal peduncle, terminal mouth and ventrally transposed pectoral fins. Moreover, DT significantly affected the relative depth of heart ventricle (VD/TL, p textless 0.05), which was comparatively increased at 17 °C DT. Finally, the incidence of caudal-fin abnormalities significantly decreased (p textless 0.05) with the increase of DT. To our knowledge, this is the first evidence for the significant effect of DT during the short embryonic and yolk-sac larval period on the swimming performance of the later stages. |
Skliros, Dimitrios; Kalatzis, Panos G; Kalloniati, Chrysanthi; Komaitis, Fotios; Papathanasiou, Sokratis; Kouri, Evangelia D; Udvardi, Michael K; Kokkari, Constantina; Katharios, Pantelis; Flemetakis, Emmanouil The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy Journal Article Viruses, 13 (4), pp. 656, 2021. @article{skliros_development_2021, title = {The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy}, author = {Dimitrios Skliros and Panos G Kalatzis and Chrysanthi Kalloniati and Fotios Komaitis and Sokratis Papathanasiou and Evangelia D Kouri and Michael K Udvardi and Constantina Kokkari and Pantelis Katharios and Emmanouil Flemetakis}, url = {https://www.mdpi.com/1999-4915/13/4/656 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Sκliros-viruses-29-1.pdf}, doi = {10.3390/v13040656}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Viruses}, volume = {13}, number = {4}, pages = {656}, abstract = {Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology. |
Tsaparis, Dimitris; Konstantinidis, Ioannis; Palandacic, Anja; Kalogianni, Eleni; Stoumboudi, Maria Th.; Barbieri, Roberta; Vardakas, Leonidas; Koutsikos, Nicholas; Tsigenopoulos, Costas S Hydrobiologia, 848 (5), pp. 1163–1176, 2021, ISSN: 0018-8158, 1573-5117. @article{tsaparis_dna_2021, title = {DNA barcoding provides new insights on the distribution, systematics and conservation of the freshwater genus Pelasgus (Cypriniformes: Cyprinidae) in Greece}, author = {Dimitris Tsaparis and Ioannis Konstantinidis and Anja Palandacic and Eleni Kalogianni and Maria Th. Stoumboudi and Roberta Barbieri and Leonidas Vardakas and Nicholas Koutsikos and Costas S Tsigenopoulos}, url = {http://link.springer.com/10.1007/s10750-021-04526-9}, doi = {10.1007/s10750-021-04526-9}, issn = {0018-8158, 1573-5117}, year = {2021}, date = {2021-03-01}, urldate = {2021-02-24}, journal = {Hydrobiologia}, volume = {848}, number = {5}, pages = {1163--1176}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rotter, Ana; Barbier, Michéle; Bertoni, Francesco; Bones, Atle M; Cancela, Leonor M; Carlsson, Jens; Carvalho, Maria F; Cegłowska, Marta; Chirivella-Martorell, Jerónimo; Dalay, Meltem Conk; Cueto, Mercedes; Dailianis, Thanos; Deniz, Irem; Díaz-Marrero, Ana R; Drakulovic, Dragana; Dubnika, Arita; Edwards, Christine; Einarsson, Hjörleifur; Erdoǧan, Ayşegül; Eroldoǧan, Orhan Tufan; Ezra, David; Fazi, Stefano; FitzGerald, Richard J; Gargan, Laura M; Gaudêncio, Susana P; Udovič, Marija Gligora; DeNardis, Nadica Ivošević; Jónsdóttir, Rósa; Kataržytė, Marija; Klun, Katja; Kotta, Jonne; Ktari, Leila; Ljubešić, Zrinka; Bilela, Lada Lukić; Mandalakis, Manolis; Massa-Gallucci, Alexia; Matijošytė, Inga; Mazur-Marzec, Hanna; Mehiri, Mohamed; Nielsen, Søren Laurentius; Novoveská, Lucie; Overlingė, Donata; Perale, Giuseppe; Ramasamy, Praveen; Rebours, Céline; Reinsch, Thorsten; Reyes, Fernando; Rinkevich, Baruch; Robbens, Johan; Röttinger, Eric; Rudovica, Vita; Sabotič, Jerica; Safarik, Ivo; Talve, Siret; Tasdemir, Deniz; Schneider, Xenia Theodotou; Thomas, Olivier P; Toruńska-Sitarz, Anna; Varese, Giovanna Cristina; Vasquez, Marlen I The Essentials of Marine Biotechnology Journal Article Front. Mar. Sci., 8 , pp. 629629, 2021, ISSN: 2296-7745. @article{rotter_essentials_2021, title = {The Essentials of Marine Biotechnology}, author = {Ana Rotter and Michéle Barbier and Francesco Bertoni and Atle M Bones and Leonor M Cancela and Jens Carlsson and Maria F Carvalho and Marta Cegłowska and Jerónimo Chirivella-Martorell and Meltem Conk Dalay and Mercedes Cueto and Thanos Dailianis and Irem Deniz and Ana R Díaz-Marrero and Dragana Drakulovic and Arita Dubnika and Christine Edwards and Hjörleifur Einarsson and Ayşegül Erdoǧan and Orhan Tufan Eroldoǧan and David Ezra and Stefano Fazi and Richard J FitzGerald and Laura M Gargan and Susana P Gaudêncio and Marija Gligora Udovič and Nadica Ivošević DeNardis and Rósa Jónsdóttir and Marija Kataržytė and Katja Klun and Jonne Kotta and Leila Ktari and Zrinka Ljubešić and Lada Lukić Bilela and Manolis Mandalakis and Alexia Massa-Gallucci and Inga Matijošytė and Hanna Mazur-Marzec and Mohamed Mehiri and Søren Laurentius Nielsen and Lucie Novoveská and Donata Overlingė and Giuseppe Perale and Praveen Ramasamy and Céline Rebours and Thorsten Reinsch and Fernando Reyes and Baruch Rinkevich and Johan Robbens and Eric Röttinger and Vita Rudovica and Jerica Sabotič and Ivo Safarik and Siret Talve and Deniz Tasdemir and Xenia Theodotou Schneider and Olivier P Thomas and Anna Toruńska-Sitarz and Giovanna Cristina Varese and Marlen I Vasquez}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.629629/full https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Rotter-Frontiers-MS-26.pdf }, doi = {10.3389/fmars.2021.629629}, issn = {2296-7745}, year = {2021}, date = {2021-03-01}, urldate = {2021-03-17}, journal = {Front. Mar. Sci.}, volume = {8}, pages = {629629}, abstract = {Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs. |
Fanini, Lucia; Piscart, Christophe; Pranzini, Enzo; Kerbiriou, Christian; Viol, Isabelle Le; Pétillon, Julien Estuarine, Coastal and Shelf Science, 250 , pp. 107148, 2021, ISSN: 02727714. @article{fanini_extended_2021, title = {The extended concept of littoral active zone considering soft sediment shores as social-ecological systems, and an application to Brittany (North-Western France)}, author = {Lucia Fanini and Christophe Piscart and Enzo Pranzini and Christian Kerbiriou and Isabelle Le Viol and Julien Pétillon}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/Riechers-et-al.-2021-2.pdf https://linkinghub.elsevier.com/retrieve/pii/S0272771420308799 }, doi = {10.1016/j.ecss.2020.107148}, issn = {02727714}, year = {2021}, date = {2021-03-01}, urldate = {2021-02-02}, journal = {Estuarine, Coastal and Shelf Science}, volume = {250}, pages = {107148}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L; Berrios, Daniel C; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V; Damerow, Joan; Duncan, William D; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M; Gibbons, Sean M; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L; Jaiswal, Pankaj; Joachimiak, Marcin P; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pafilis, Evangelos; Reddy, T B K; Richardson, Lorna; Roux, Simon; Shaffer, Justin P; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R; Timme, Ruth E; Zheng, Jie; Wood-Charlson, Elisha M; Eloe-Fadrosh, Emiley A Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities Journal Article 6 , 2021. @article{2021Vangay,PafilismSystems, title = {Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities}, author = {Pajau Vangay and Josephine Burgin and Anjanette Johnston and Kristen L Beck and Daniel C Berrios and Kai Blumberg and Shane Canon and Patrick Chain and John-Marc Chandonia and Danielle Christianson and Sylvain V Costes and Joan Damerow and William D Duncan and Jose Pablo Dundore-Arias and Kjiersten Fagnan and Jonathan M Galazka and Sean M Gibbons and David Hays and Judson Hervey and Bin Hu and Bonnie L Hurwitz and Pankaj Jaiswal and Marcin P Joachimiak and Linda Kinkel and Joshua Ladau and Stanton L Martin and Lee Ann McCue and Kayd Miller and Nigel Mouncey and Chris Mungall and Evangelos Pafilis and T B K Reddy and Lorna Richardson and Simon Roux and Justin P Shaffer and Jagadish Chandrabose Sundaramurthi and Luke R Thompson and Ruth E Timme and Jie Zheng and Elisha M Wood-Charlson and Emiley A Eloe-Fadrosh}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Vangay-Pafilis-mSystems-19-1.pdf}, doi = {https://doi.org/10.1128/mSystems.01194-20}, year = {2021}, date = {2021-02-23}, volume = {6}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rosso, Antonietta; Sanfilippo, Rossana; Guido, Adriano; Gerovasileiou, Vasilis; Ruggiero, Emma Taddei; Belmonte, Genuario Colonisers of the dark: biostalactite‐associated metazoans from “lu Lampiùne” submarine cave (Apulia, Mediterranean Sea) Journal Article Mar Ecol, 42 (1), 2021, ISSN: 0173-9565, 1439-0485. @article{rosso_colonisers_2021, title = {Colonisers of the dark: biostalactite‐associated metazoans from “lu Lampiùne” submarine cave (Apulia, Mediterranean Sea)}, author = {Antonietta Rosso and Rossana Sanfilippo and Adriano Guido and Vasilis Gerovasileiou and Emma Taddei Ruggiero and Genuario Belmonte}, url = {https://onlinelibrary.wiley.com/doi/10.1111/maec.12634}, doi = {10.1111/maec.12634}, issn = {0173-9565, 1439-0485}, year = {2021}, date = {2021-02-01}, urldate = {2021-03-17}, journal = {Mar Ecol}, volume = {42}, number = {1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kousteni, Vasiliki; Mazzoleni, Sofia; Vasileiadou, Katerina; Rovatsos, Michail Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs Journal Article Genes, 12 (3), pp. 324, 2021, ISSN: 2073-4425. @article{kousteni_complete_2021, title = {Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs}, author = {Vasiliki Kousteni and Sofia Mazzoleni and Katerina Vasileiadou and Michail Rovatsos}, url = {https://www.mdpi.com/2073-4425/12/3/324 https://imbbc.hcmr.gr/wp-content/uploads/2021/03/Kousteni-2021-GENES-20.pdf}, doi = {10.3390/genes12030324}, issn = {2073-4425}, year = {2021}, date = {2021-02-01}, urldate = {2021-03-17}, journal = {Genes}, volume = {12}, number = {3}, pages = {324}, abstract = {Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes. |
Pham, Thuy Thi Thanh; Friðriksdóttir, Ragnhildur; Weber, Charlotte T; Viðarsson, Jónas R; Papandroulakis, Nikos; Baudron, Alan R; Olsen, Petter; Hansen, Juliana A; Laksá, Unn; Fernandes, Paul G; Bahri, Tarub; Ragnarsson, Sigurður Ö; Aschan, Michaela Guidelines for co-creating climate adaptation plans for fisheries and aquaculture Journal Article Climatic Change, 164 (3-4), pp. 62, 2021, ISSN: 0165-0009, 1573-1480. @article{pham_guidelines_2021, title = {Guidelines for co-creating climate adaptation plans for fisheries and aquaculture}, author = {Thuy Thi Thanh Pham and Ragnhildur Friðriksdóttir and Charlotte T Weber and Jónas R Viðarsson and Nikos Papandroulakis and Alan R Baudron and Petter Olsen and Juliana A Hansen and Unn Laksá and Paul G Fernandes and Tarub Bahri and Sigurður Ö Ragnarsson and Michaela Aschan}, url = {http://link.springer.com/10.1007/s10584-021-03041-z https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Pham-Climatic-change-23.pdf}, doi = {10.1007/s10584-021-03041-z}, issn = {0165-0009, 1573-1480}, year = {2021}, date = {2021-02-01}, urldate = {2021-03-17}, journal = {Climatic Change}, volume = {164}, number = {3-4}, pages = {62}, abstract = {Abstract Climate change is having a significant impact on the biology and ecology of fish stocks and aquaculture species and will affect the productivity within seafood supply chains in the future. The challenges are further amplified when actors within the fisheries and aquaculture sectors have very different ideas and assumptions about climate change and what risks and opportunities they entail. In order to address the challenges of climate change, several countries have developed national adaptation plans. However, fisheries and aquaculture are rarely included in these plans, resulting in a general lack of documented adaptation strategies within these sectors in most countries. This paper introduces guidelines for the development of climate adaptation plans (CAPs) within fisheries and aquaculture, applying a co-creation approach that requires the participation of scientists, industry representatives, policymakers, and other relevant stakeholders. The objective is to provide a stepwise approach to facilitate and enable stakeholders to plan strategies toward climate adaptation. The guidelines are based on practical experience and include a three-step process: (1) assessment of risks and opportunities; (2) identification of adaptation measures, and (3) operationalization of CAPs. The three-step process is also part of a larger cycle, including implementation, monitoring, and evaluation, again generating iterative feedback loops over time. Lessons learned are discussed, and we highlight the advantages and challenges of developing CAPs. While the guidelines are designed for and tested within fisheries and aquaculture systems, the CAP approach is also employable for other natural resource-based systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Climate change is having a significant impact on the biology and ecology of fish stocks and aquaculture species and will affect the productivity within seafood supply chains in the future. The challenges are further amplified when actors within the fisheries and aquaculture sectors have very different ideas and assumptions about climate change and what risks and opportunities they entail. In order to address the challenges of climate change, several countries have developed national adaptation plans. However, fisheries and aquaculture are rarely included in these plans, resulting in a general lack of documented adaptation strategies within these sectors in most countries. This paper introduces guidelines for the development of climate adaptation plans (CAPs) within fisheries and aquaculture, applying a co-creation approach that requires the participation of scientists, industry representatives, policymakers, and other relevant stakeholders. The objective is to provide a stepwise approach to facilitate and enable stakeholders to plan strategies toward climate adaptation. The guidelines are based on practical experience and include a three-step process: (1) assessment of risks and opportunities; (2) identification of adaptation measures, and (3) operationalization of CAPs. The three-step process is also part of a larger cycle, including implementation, monitoring, and evaluation, again generating iterative feedback loops over time. Lessons learned are discussed, and we highlight the advantages and challenges of developing CAPs. While the guidelines are designed for and tested within fisheries and aquaculture systems, the CAP approach is also employable for other natural resource-based systems. |
Corriero, Aldo; Wylie, Matthew J; Nyuji, Mitsuo; Zupa, Rosa; Mylonas, Constantinos C Reproduction of greater amberjack (Seriola dumerili) and other members of the family Carangidae Journal Article Rev Aquacult, pp. raq.12544, 2021, ISSN: 1753-5123, 1753-5131. @article{corriero_reproduction_2021, title = {Reproduction of greater amberjack (Seriola dumerili) and other members of the family Carangidae}, author = {Aldo Corriero and Matthew J Wylie and Mitsuo Nyuji and Rosa Zupa and Constantinos C Mylonas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Corriero-RAQ-pre-print.pdf https://onlinelibrary.wiley.com/doi/10.1111/raq.12544}, doi = {10.1111/raq.12544}, issn = {1753-5123, 1753-5131}, year = {2021}, date = {2021-02-01}, urldate = {2021-02-24}, journal = {Rev Aquacult}, pages = {raq.12544}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Katsika, Lydia; Flores, Mario Huesca; Kotzamanis, Yannis; Estevez, Alicia; Chatzifotis, Stavros Animals, 11 (2), pp. 392, 2021. @article{katsika_understanding_2021, title = {Understanding the Interaction Effects between Dietary Lipid Content and Rearing Temperature on Growth Performance, Feed Utilization, and Fat Deposition of Sea Bass (Dicentrarchus labrax)}, author = {Lydia Katsika and Mario Huesca Flores and Yannis Kotzamanis and Alicia Estevez and Stavros Chatzifotis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Katsika-animals-10.pdf https://www.mdpi.com/2076-2615/11/2/392}, doi = {10.3390/ani11020392}, year = {2021}, date = {2021-02-01}, urldate = {2021-02-05}, journal = {Animals}, volume = {11}, number = {2}, pages = {392}, abstract = {This study was conducted to elucidate the interaction effects of temperature and dietary lipid levels (2 × 2 factorial experiment) on the growth performance, muscle, and liver composition in adult farmed European sea bass (Dicentrarchus labrax). Two groups of fish (190 g; 60 fish per group) were distributed in 12 tanks in triplicates and kept at two different temperature regimes; one starting at 23 °C and then changed to 17 °C for 61 days, and the other starting at 17 °C and then changed to 23 °C for 39 days. Two commercial diets containing both textasciitilde44% crude protein but incorporating different dietary lipid levels, 16.5% (D16) and 20.0% (D20) (dry matter (DM)), were fed to the fish to apparent satiation; the type of diet fed to each fish group remained constant throughout the experiment. Final body weight, weight gain, and specific growth rate were significantly higher for the fish group held at 23 °C compared to the fish group at 17 °C (before the temperature changes), while the dietary fat content did not have any profound effect in both groups. Furthermore, the different temperature regimes did not affect muscle or liver composition, but, on the contrary, dietary lipids affected hepatosomatic, perivisceral fat, and visceral indexes. Feed conversion ratio and specific growth rate were not affected by the dietary lipid level. An interaction of temperature and dietary lipid content was observed in daily feed consumption (DFC) and final body weight (FBW).}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study was conducted to elucidate the interaction effects of temperature and dietary lipid levels (2 × 2 factorial experiment) on the growth performance, muscle, and liver composition in adult farmed European sea bass (Dicentrarchus labrax). Two groups of fish (190 g; 60 fish per group) were distributed in 12 tanks in triplicates and kept at two different temperature regimes; one starting at 23 °C and then changed to 17 °C for 61 days, and the other starting at 17 °C and then changed to 23 °C for 39 days. Two commercial diets containing both textasciitilde44% crude protein but incorporating different dietary lipid levels, 16.5% (D16) and 20.0% (D20) (dry matter (DM)), were fed to the fish to apparent satiation; the type of diet fed to each fish group remained constant throughout the experiment. Final body weight, weight gain, and specific growth rate were significantly higher for the fish group held at 23 °C compared to the fish group at 17 °C (before the temperature changes), while the dietary fat content did not have any profound effect in both groups. Furthermore, the different temperature regimes did not affect muscle or liver composition, but, on the contrary, dietary lipids affected hepatosomatic, perivisceral fat, and visceral indexes. Feed conversion ratio and specific growth rate were not affected by the dietary lipid level. An interaction of temperature and dietary lipid content was observed in daily feed consumption (DFC) and final body weight (FBW). |
Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos 0s and 1s in marine molecular research: a regional HPC perspective Journal Article GigaScience, 10 (8), pp. giab053, 2021, ISSN: 2047-217X. @article{zafeiropoulos_0s_2021, title = {0s and 1s in marine molecular research: a regional HPC perspective}, author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916}, doi = {10.1093/gigascience/giab053}, issn = {2047-217X}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {GigaScience}, volume = {10}, number = {8}, pages = {giab053}, abstract = {Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned. |
Santi, Ioulia; Kasapidis, Panagiotis; Karakassis, Ioannis; Pitta, Paraskevi A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes Journal Article Diversity, 13 (5), pp. 180, 2021. @article{santi_comparison_2021, title = {A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes}, author = {Ioulia Santi and Panagiotis Kasapidis and Ioannis Karakassis and Paraskevi Pitta}, url = {https://www.mdpi.com/1424-2818/13/5/180 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Santi-DIVERSITY-33.pdf}, doi = {10.3390/d13050180}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {Diversity}, volume = {13}, number = {5}, pages = {180}, abstract = {The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes. |
Kogiannou, Dimitra; Nikoloudaki, Chrysanthi; Rigos, George Absorption and depletion of dietary administered praziquantel in greater amberjack, Seriola dumerili Journal Article Aquaculture, 535 , pp. 736354, 2021, ISSN: 00448486. @article{kogiannou_absorption_2021, title = {Absorption and depletion of dietary administered praziquantel in greater amberjack, Seriola dumerili}, author = {Dimitra Kogiannou and Chrysanthi Nikoloudaki and George Rigos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848621000168}, doi = {10.1016/j.aquaculture.2021.736354}, issn = {00448486}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Aquaculture}, volume = {535}, pages = {736354}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mandalakis, Manolis; Anastasiou, Thekla I; Martou, Natalia; Keisaris, Sofoklis; Greveniotis, Vasileios; Katharios, Pantelis; Lazari, Diamanto; Krigas, Nikos; Antonopoulou, Efthimia Molecules, 26 (9), pp. 2731, 2021. @article{mandalakis_antibacterial_2021, title = {Antibacterial Effects of Essential Oils of Seven Medicinal-Aromatic Plants Against the Fish Pathogen Aeromonas veronii bv. sobria: To Blend or Not to Blend?}, author = {Manolis Mandalakis and Thekla I Anastasiou and Natalia Martou and Sofoklis Keisaris and Vasileios Greveniotis and Pantelis Katharios and Diamanto Lazari and Nikos Krigas and Efthimia Antonopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Mandalakis-molecules-37.pdf https://www.mdpi.com/1420-3049/26/9/2731}, doi = {10.3390/molecules26092731}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {Molecules}, volume = {26}, number = {9}, pages = {2731}, abstract = {Despite progress achieved, there is limited available information about the antibacterial activity of constituents of essential oils (EOs) from different medicinal-aromatic plants (MAPs) against fish pathogens and the complex interactions of blended EOs thereof. The present study aimed to investigate possible synergistic antimicrobial effects of EOs from seven Greek MAPs with strong potential against Aeromonas veronii bv. sobria, a fish pathogen associated with aquaculture disease outbreaks. The main objective was to evaluate whether blending of these EOs can lead to increased antimicrobial activity against the specific microorganism. A total of 127 combinations of EOs were prepared and their effect on A. veronii bv. sobria growth was tested in vitro. We examined both the inhibitory and bactericidal activities of the individual EOs and compared them to those of the blended EOs. The vast majority of the investigated combinations exhibited significant synergistic and additive effects, while antagonistic effects were evident only in a few cases, such as the mixtures containing EOs from rosemary, lemon balm and pennyroyal. The combination of EOs from Greek oregano and wild carrot, as well as the combinations of those two with Spanish oregano or savoury were the most promising ones. Overall, Greek oregano, savoury and Spanish oregano EOs were the most effective ones when applied either in pure form or blended with other EOs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Despite progress achieved, there is limited available information about the antibacterial activity of constituents of essential oils (EOs) from different medicinal-aromatic plants (MAPs) against fish pathogens and the complex interactions of blended EOs thereof. The present study aimed to investigate possible synergistic antimicrobial effects of EOs from seven Greek MAPs with strong potential against Aeromonas veronii bv. sobria, a fish pathogen associated with aquaculture disease outbreaks. The main objective was to evaluate whether blending of these EOs can lead to increased antimicrobial activity against the specific microorganism. A total of 127 combinations of EOs were prepared and their effect on A. veronii bv. sobria growth was tested in vitro. We examined both the inhibitory and bactericidal activities of the individual EOs and compared them to those of the blended EOs. The vast majority of the investigated combinations exhibited significant synergistic and additive effects, while antagonistic effects were evident only in a few cases, such as the mixtures containing EOs from rosemary, lemon balm and pennyroyal. The combination of EOs from Greek oregano and wild carrot, as well as the combinations of those two with Spanish oregano or savoury were the most promising ones. Overall, Greek oregano, savoury and Spanish oregano EOs were the most effective ones when applied either in pure form or blended with other EOs. |
Corriero, Aldo; Zupa, Rosa; Mylonas, Constantinos C; Passantino, Letizia Atresia of ovarian follicles in fishes, and implications and uses in aquaculture and fisheries Journal Article Journal of Fish Diseases, 44 (9), pp. 1271–1291, 2021, ISSN: 0140-7775, 1365-2761. @article{corriero_atresia_2021, title = {Atresia of ovarian follicles in fishes, and implications and uses in aquaculture and fisheries}, author = {Aldo Corriero and Rosa Zupa and Constantinos C Mylonas and Letizia Passantino}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Corriero-JFD-59.pdf https://onlinelibrary.wiley.com/doi/10.1111/jfd.13469}, doi = {10.1111/jfd.13469}, issn = {0140-7775, 1365-2761}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {Journal of Fish Diseases}, volume = {44}, number = {9}, pages = {1271--1291}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ragaza, Janice Alano; Hossain, Md. Sakhawat; Koshio, Shunsuke; Ishikawa, Manabu; Yokoyama, Saichiro; Kotzamanis, Yannis; Brezas, Andreas; Kumar, Vikas Aquaculture Nutrition, 27 (4), pp. 1052–1064, 2021, ISSN: 1353-5773, 1365-2095. @article{ragaza_brown_2021, title = {Brown seaweed ( textitSargassum fulvellum ) inclusion in diets with fishmeal partially replaced with soy protein concentrate for Japanese flounder ( textitParalichthys olivaceus ) juveniles}, author = {Janice Alano Ragaza and Md. Sakhawat Hossain and Shunsuke Koshio and Manabu Ishikawa and Saichiro Yokoyama and Yannis Kotzamanis and Andreas Brezas and Vikas Kumar}, url = {https://onlinelibrary.wiley.com/doi/10.1111/anu.13246}, doi = {10.1111/anu.13246}, issn = {1353-5773, 1365-2095}, year = {2021}, date = {2021-01-01}, urldate = {2021-07-26}, journal = {Aquaculture Nutrition}, volume = {27}, number = {4}, pages = {1052--1064}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Stavrakidis-Zachou, Orestis; Sturm, Astrid; Lika, Konstadia; Wätzold, Frank; Papandroulakis, Nikos ClimeGreAq: A software-based DSS for the climate change adaptation of Greek aquaculture Journal Article Environmental Modelling & Software, 143 , pp. 105121, 2021, ISSN: 13648152. @article{stavrakidis-zachou_climegreaq_2021, title = {ClimeGreAq: A software-based DSS for the climate change adaptation of Greek aquaculture}, author = {Orestis Stavrakidis-Zachou and Astrid Sturm and Konstadia Lika and Frank Wätzold and Nikos Papandroulakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Stavrakidis-EnvModSoft-56.pdf https://linkinghub.elsevier.com/retrieve/pii/S136481522100164X}, doi = {10.1016/j.envsoft.2021.105121}, issn = {13648152}, year = {2021}, date = {2021-01-01}, urldate = {2021-07-26}, journal = {Environmental Modelling & Software}, volume = {143}, pages = {105121}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mladineo, Ivona; Hrabar, Jerko; Trumbić, Željka; Manousaki, Tereza; Tsakogiannis, Alexandros; Taggart, John B; Tsigenopoulos, Costas S Pathogens, 10 (2), pp. 100, 2021, ISSN: 2076-0817. @article{mladineo_community_2021, title = {Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish}, author = {Ivona Mladineo and Jerko Hrabar and Željka Trumbić and Tereza Manousaki and Alexandros Tsakogiannis and John B Taggart and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2020-Mladineo-Pathogens-7.pdf https://www.mdpi.com/2076-0817/10/2/100}, doi = {10.3390/pathogens10020100}, issn = {2076-0817}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Pathogens}, volume = {10}, number = {2}, pages = {100}, abstract = {Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides. |
Charalampous, Georgia; Fragkou, Efsevia; Kormas, Konstantinos A; Menezes, Alexandre De B; Polymenakou, Paraskevi N; Pasadakis, Nikos; Kalogerakis, Nicolas; Antoniou, Eleftheria; Gontikaki, Evangelia Energies, 14 (8), pp. 2246, 2021. @article{charalampous_comparison_2021, title = {Comparison of Hydrocarbon-Degrading Consortia from Surface and Deep Waters of the Eastern Mediterranean Sea: Characterization and Degradation Potential}, author = {Georgia Charalampous and Efsevia Fragkou and Konstantinos A Kormas and Alexandre De B Menezes and Paraskevi N Polymenakou and Nikos Pasadakis and Nicolas Kalogerakis and Eleftheria Antoniou and Evangelia Gontikaki}, url = {https://www.mdpi.com/1996-1073/14/8/2246 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Charalampous-ENERGIES-30-1.pdf}, doi = {10.3390/en14082246}, year = {2021}, date = {2021-01-01}, urldate = {2021-04-27}, journal = {Energies}, volume = {14}, number = {8}, pages = {2246}, abstract = {The diversity and degradation capacity of hydrocarbon-degrading consortia from surface and deep waters of the Eastern Mediterranean Sea were studied in time-series experiments. Microcosms were set up in ONR7a medium at in situ temperatures of 25 °C and 14 °C for the Surface and Deep consortia, respectively, and crude oil as the sole source of carbon. The Deep consortium was additionally investigated at 25 °C to allow the direct comparison of the degradation rates to the Surface consortium. In total, textasciitilde50% of the alkanes and textasciitilde15% of the polycyclic aromatic hydrocarbons were degraded in all treatments by Day 24. Approximately textasciitilde95% of the total biodegradation by the Deep consortium took place within 6 days regardless of temperature, whereas comparable levels of degradation were reached on Day 12 by the Surface consortium. Both consortia were dominated by well-known hydrocarbon-degrading taxa. Temperature played a significant role in shaping the Deep consortia communities with Pseudomonas and Pseudoalteromonas dominating at 25 °C and Alcanivorax at 14 °C. Overall, the Deep consortium showed a higher efficiency for hydrocarbon degradation within the first week following contamination, which is critical in the case of oil spills, and thus merits further investigation for its exploitation in bioremediation technologies tailored to the Eastern Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The diversity and degradation capacity of hydrocarbon-degrading consortia from surface and deep waters of the Eastern Mediterranean Sea were studied in time-series experiments. Microcosms were set up in ONR7a medium at in situ temperatures of 25 °C and 14 °C for the Surface and Deep consortia, respectively, and crude oil as the sole source of carbon. The Deep consortium was additionally investigated at 25 °C to allow the direct comparison of the degradation rates to the Surface consortium. In total, textasciitilde50% of the alkanes and textasciitilde15% of the polycyclic aromatic hydrocarbons were degraded in all treatments by Day 24. Approximately textasciitilde95% of the total biodegradation by the Deep consortium took place within 6 days regardless of temperature, whereas comparable levels of degradation were reached on Day 12 by the Surface consortium. Both consortia were dominated by well-known hydrocarbon-degrading taxa. Temperature played a significant role in shaping the Deep consortia communities with Pseudomonas and Pseudoalteromonas dominating at 25 °C and Alcanivorax at 14 °C. Overall, the Deep consortium showed a higher efficiency for hydrocarbon degradation within the first week following contamination, which is critical in the case of oil spills, and thus merits further investigation for its exploitation in bioremediation technologies tailored to the Eastern Mediterranean Sea. |
Chatziantoniou, Andromachi; Karagaitanakis, Alexandros; Bakopoulos, Vasileios; Papandroulakis, Nikos; Topouzelis, Konstantinos Detection of Biogenic Oil Films near Aquaculture Sites Using Sentinel-1 and Sentinel-2 Satellite Images Journal Article Remote Sensing, 13 (9), pp. 1737, 2021. @article{chatziantoniou_detection_2021, title = {Detection of Biogenic Oil Films near Aquaculture Sites Using Sentinel-1 and Sentinel-2 Satellite Images}, author = {Andromachi Chatziantoniou and Alexandros Karagaitanakis and Vasileios Bakopoulos and Nikos Papandroulakis and Konstantinos Topouzelis}, url = {https://www.mdpi.com/2072-4292/13/9/1737 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatziantoniou-RemoteSensing-36.pdf}, doi = {10.3390/rs13091737}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {Remote Sensing}, volume = {13}, number = {9}, pages = {1737}, abstract = {Biogenic films are very thin surface oils, frequently observed near aquaculture farms, that affect the roughness and the optical properties of the sea surface, making them visible in SAR and multispectral images. The purpose of this study is to investigate the potential of satellite SAR and multispectral sensors in the detection of biogenic oil films near aquaculture farms. Sentinel-1 SAR and Sentinel-2 multispectral data were exploited to detect the films around three aquaculture sites. The study is divided in three stages: (a) preprocessing, (b) main process and (c) accuracy assessment. The preprocessing stage includes subset, filtering, land masking and image corrections. The main process was similar for both datasets, using an adaptive thresholding method to identify dark formations, extract and classify them. Finally, the performance of the algorithm was evaluated based on the estimation of standard classification error statistics. The evaluation of the results was based on empirical photointerpretation and in situ photos. The results are successful and promising, with overall accuracy over 70%, while both sensors are proved to be effective in the detection, with Sentinel-1 SAR presenting slightly better accuracy (81%) than Sentinel-2 MSI (70%). There is no evidence of these films causing stress to the aquaculture farms or the surrounding environment; however, our knowledge on their presence, amount and dissolution is limited and further knowledge could contribute to efficient feeding management and fish welfare.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Biogenic films are very thin surface oils, frequently observed near aquaculture farms, that affect the roughness and the optical properties of the sea surface, making them visible in SAR and multispectral images. The purpose of this study is to investigate the potential of satellite SAR and multispectral sensors in the detection of biogenic oil films near aquaculture farms. Sentinel-1 SAR and Sentinel-2 multispectral data were exploited to detect the films around three aquaculture sites. The study is divided in three stages: (a) preprocessing, (b) main process and (c) accuracy assessment. The preprocessing stage includes subset, filtering, land masking and image corrections. The main process was similar for both datasets, using an adaptive thresholding method to identify dark formations, extract and classify them. Finally, the performance of the algorithm was evaluated based on the estimation of standard classification error statistics. The evaluation of the results was based on empirical photointerpretation and in situ photos. The results are successful and promising, with overall accuracy over 70%, while both sensors are proved to be effective in the detection, with Sentinel-1 SAR presenting slightly better accuracy (81%) than Sentinel-2 MSI (70%). There is no evidence of these films causing stress to the aquaculture farms or the surrounding environment; however, our knowledge on their presence, amount and dissolution is limited and further knowledge could contribute to efficient feeding management and fish welfare. |
Krick, Madoka Vera; Desmarais, Erick; Samaras, Athanasios; Guéret, Elise; Dimitroglou, Arkadios; Pavlidis, Michalis; Tsigenopoulos, Costas; Guinand, Bruno Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.) Journal Article BMC Genomics, 22 (1), pp. 111, 2021, ISSN: 1471-2164. @article{krick_family-effects_2021, title = {Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)}, author = {Madoka Vera Krick and Erick Desmarais and Athanasios Samaras and Elise Guéret and Arkadios Dimitroglou and Michalis Pavlidis and Costas Tsigenopoulos and Bruno Guinand}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Krick-2021_Family-effects-in-sb-BMG-Genomics-14.pdf https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07420-9}, doi = {10.1186/s12864-021-07420-9}, issn = {1471-2164}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-24}, journal = {BMC Genomics}, volume = {22}, number = {1}, pages = {111}, abstract = {Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass ( Dicentrarchus labrax ), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples . This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass ( Dicentrarchus labrax ), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples . This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish. |
Bravakos, Panos; Mandalakis, Manolis; Nomikou, Paraskevi; Anastasiou, Thekla I; Kristoffersen, Jon Bent; Stavroulaki, Melanthia; Kilias, Stephanos; Kotoulas, Georgios; Magoulas, Antonios; Polymenakou, Paraskevi N Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece Journal Article Sci Rep, 11 (1), pp. 1336, 2021, ISSN: 2045-2322. @article{bravakos_genomic_2021, title = {Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece}, author = {Panos Bravakos and Manolis Mandalakis and Paraskevi Nomikou and Thekla I Anastasiou and Jon Bent Kristoffersen and Melanthia Stavroulaki and Stephanos Kilias and Georgios Kotoulas and Antonios Magoulas and Paraskevi N Polymenakou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Bravakos-SciReport-4.pdf http://www.nature.com/articles/s41598-020-79359-y}, doi = {10.1038/s41598-020-79359-y}, issn = {2045-2322}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Sci Rep}, volume = {11}, number = {1}, pages = {1336}, abstract = {Abstract Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO 2 -rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO 2 -rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance. |
Dzyuba, Viktoriya; Cosson, Jacky; Papadaki, Maria; Mylonas, Constantinos C; Steinbach, Christoph; Rodina, Marek; Tučkova, Vladimira; Linhart, Otomar; Shelton, William L; Gela, David; Boryshpolets, Sergii; Dzyuba, Borys Animals, 11 (5), pp. 1417, 2021, ISSN: 2076-2615. @article{dzyuba_influence_2021, title = {Influence of Environmental Temperature and Hormonal Stimulation on the In Vitro Sperm Maturation in Sterlet Acipenser ruthenus in Advance of the Spawning Season}, author = {Viktoriya Dzyuba and Jacky Cosson and Maria Papadaki and Constantinos C Mylonas and Christoph Steinbach and Marek Rodina and Vladimira Tučkova and Otomar Linhart and William L Shelton and David Gela and Sergii Boryshpolets and Borys Dzyuba}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Dzyuba-Animals-45.pdf https://www.mdpi.com/2076-2615/11/5/1417}, doi = {10.3390/ani11051417}, issn = {2076-2615}, year = {2021}, date = {2021-01-01}, urldate = {2021-06-24}, journal = {Animals}, volume = {11}, number = {5}, pages = {1417}, abstract = {Sturgeon sperm maturation occurs outside the testes during the transit of testicular spermatozoa (TS) through the kidneys and the Wolffian ducts. A method of in vitro TS maturation in sterlet Acipenser ruthenus was used to investigate the effects of temperature and hormonal stimulation of spermiation on the ability of TS to complete this process. Spermatozoa motility parameters after in vitro maturation of testicular sperm, concentrations of sex steroid hormones and testis morphology were studied in three groups of sterlet: (1) after overwintering in ponds (OW), (2) adapted to spawning temperature (ST), and (3) adapted to spawning temperature with hormonal induction of spermiation (ST-HI). Blood plasma concentrations of testosterone, 11-ketotestosterone and 17,20β-dihydroxy-pregnenolone increased significantly after hormonal induction of spermiation (group ST-HI). In all groups, TS were not motile. After in vitro sperm maturation, motility was up to 60% only in group ST-HI. The data suggest that the ability of TS to be matured in vitro was not related to the environmental temperature, while hormonal stimulation of spermiation during the spawning season was an absolute requirement for optimal in vitro maturation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sturgeon sperm maturation occurs outside the testes during the transit of testicular spermatozoa (TS) through the kidneys and the Wolffian ducts. A method of in vitro TS maturation in sterlet Acipenser ruthenus was used to investigate the effects of temperature and hormonal stimulation of spermiation on the ability of TS to complete this process. Spermatozoa motility parameters after in vitro maturation of testicular sperm, concentrations of sex steroid hormones and testis morphology were studied in three groups of sterlet: (1) after overwintering in ponds (OW), (2) adapted to spawning temperature (ST), and (3) adapted to spawning temperature with hormonal induction of spermiation (ST-HI). Blood plasma concentrations of testosterone, 11-ketotestosterone and 17,20β-dihydroxy-pregnenolone increased significantly after hormonal induction of spermiation (group ST-HI). In all groups, TS were not motile. After in vitro sperm maturation, motility was up to 60% only in group ST-HI. The data suggest that the ability of TS to be matured in vitro was not related to the environmental temperature, while hormonal stimulation of spermiation during the spawning season was an absolute requirement for optimal in vitro maturation. |
Makridis, Pavlos; Kokou, Fotini; Bournakas, Christos; Papandroulakis, Nikos; Sarropoulou, Elena Microorganisms, 9 (1), pp. 128, 2021, ISSN: 2076-2607. @article{makridis_isolation_2021, title = {Isolation of Phaeobacter sp. from Larvae of Atlantic Bonito (Sarda sarda) in a Mesocosmos Unit, and Its Use for the Rearing of European Seabass Larvae (Dicentrarchus labrax L.)}, author = {Pavlos Makridis and Fotini Kokou and Christos Bournakas and Nikos Papandroulakis and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021_2-Makridis-MICROORGANISMS.pdf https://www.mdpi.com/2076-2607/9/1/128}, doi = {10.3390/microorganisms9010128}, issn = {2076-2607}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {128}, abstract = {The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p textless 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p textless 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p textless 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p textless 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions. |
Tsagkatakis, G; Roumpakis, S; Nikolidakis, S; Petra, E; Mantes, A; Kapantagakis, A; Grigorakis, K; Katselis, G; Vlahos, N; Tsakalides, P Knowledge distillation from multispectral Images for fish freshness estimation Journal Article Electronic Imaging, 2021 (12), pp. 27–1–27–7, 2021, ISSN: 2470-1173. @article{tsagkatakis_knowledge_2021, title = {Knowledge distillation from multispectral Images for fish freshness estimation}, author = {G Tsagkatakis and S Roumpakis and S Nikolidakis and E Petra and A Mantes and A Kapantagakis and K Grigorakis and G Katselis and N Vlahos and P Tsakalides}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Tsagkatakis-SIST-51.pdf https://www.ingentaconnect.com/content/10.2352/ISSN.2470-1173.2021.12.FAIS-027}, doi = {10.2352/ISSN.2470-1173.2021.12.FAIS-027}, issn = {2470-1173}, year = {2021}, date = {2021-01-01}, urldate = {2021-07-26}, journal = {Electronic Imaging}, volume = {2021}, number = {12}, pages = {27--1--27--7}, abstract = {Fish quality is primarily effected by the number of days elapsed since harvesting, while bad storage conditions can also lead to quality degradation similar to the impact time. Existing approaches require laboratory testing, a laborious and timeconsuming process. In this work, we investigate technologies for quantifying fish quality though the development of deep learning models for analyzing imagery of fish. We first demonstrate that such a quantification is possible, to a certain degree, from multispectral images provided a sufficient number of training examples is available. Given that, we explore how knowledge distillation can be utilized for achieving similar fish quality estimation accuracy, but instead of using high-end multispectral imaging systems, using off-the-shelf RGB cameras. Experimental evaluation on individuals from the Mullus Marbatus family demonstrates that the proposed methodology constitutes a valid approach .}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fish quality is primarily effected by the number of days elapsed since harvesting, while bad storage conditions can also lead to quality degradation similar to the impact time. Existing approaches require laboratory testing, a laborious and timeconsuming process. In this work, we investigate technologies for quantifying fish quality though the development of deep learning models for analyzing imagery of fish. We first demonstrate that such a quantification is possible, to a certain degree, from multispectral images provided a sufficient number of training examples is available. Given that, we explore how knowledge distillation can be utilized for achieving similar fish quality estimation accuracy, but instead of using high-end multispectral imaging systems, using off-the-shelf RGB cameras. Experimental evaluation on individuals from the Mullus Marbatus family demonstrates that the proposed methodology constitutes a valid approach . |
Chatzifotis, Stavros; Gutiérrez, Abraham Gómez; Papadaki, Maria; Caruso, Fabrizio; Sigelaki, Irini; Mylonas, Constantinos C Fish Physiology and Biochemistry, 47 (4), pp. 1257–1270, 2021, ISSN: 0920-1742, 1573-5168. @article{chatzifotis_lack_2021, title = {Lack of negative effects of fasting of gilthead seabream (Sparus aurata) breeders during the spawning period on maternal and egg nutrient composition, fertilization success, and early embryo/larval development}, author = {Stavros Chatzifotis and Abraham Gómez Gutiérrez and Maria Papadaki and Fabrizio Caruso and Irini Sigelaki and Constantinos C Mylonas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Chatzifotis2021_Article_LackOfNegativeEffectsOfFasting-pre-print-57.pdf https://link.springer.com/10.1007/s10695-021-00979-w}, doi = {10.1007/s10695-021-00979-w}, issn = {0920-1742, 1573-5168}, year = {2021}, date = {2021-01-01}, urldate = {2021-07-26}, journal = {Fish Physiology and Biochemistry}, volume = {47}, number = {4}, pages = {1257--1270}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pisera, Andrzej; Gerovasileiou, Vasilis Lithistid Demosponges of Deep-Water Origin in Marine Caves of the North-Eastern Mediterranean Sea Journal Article Frontiers in Marine Science, 8 , 2021, ISSN: 2296-7745. @article{pisera_lithistid_2021, title = {Lithistid Demosponges of Deep-Water Origin in Marine Caves of the North-Eastern Mediterranean Sea}, author = {Andrzej Pisera and Vasilis Gerovasileiou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Gerovasileiou-Frontiers-in-Marine-Science-11.pdf https://www.frontiersin.org/articles/10.3389/fmars.2021.630900/full}, doi = {10.3389/fmars.2021.630900}, issn = {2296-7745}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-05}, journal = {Frontiers in Marine Science}, volume = {8}, abstract = {Desmas-bearing demosponges known as lithistids have heavily silicified skeleton and occur typically in bathyal environments of warm and tropical areas but may be found in certain shallow marine caves. Here we report, for the first time two lithistid species, i.e. Neophrissospongia endoumensis, and N. cf. nana, that were earlier known from Western Mediterranean marine caves, from four marine caves in the Aegean Sea (north-eastern Mediterranean), and their congener N. nolitangere from deep waters (ca. 300 m) of the same ecoregion. All marine caves, and sections within these caves, where lithistids occur, have freshwater springs. We interpret this surprising association between lithistids and freshwater input by elevated concentration of silica in water in cave sections where such springs occur, being 8–11 times higher in comparison with shallow water outside caves, and comparable to that of deep waters, that promoted lithistids’ development. One of the studied caves harbored an abundant population of N. endoumensis which formed large masses. The age estimation of these lithistids, based on known growth rate of related deep-water sponges, suggest that they could be 769–909 years old in the case of the largest specimen observed, about 100 cm large. These sponges could have colonized the caves from adjacent deep-water areas not earlier than 7,000–3,000 years ago, after the last glaciation, because earlier they were emerged. High variability of spicules, especially microscleres, and underdevelopment of megascleres may be related to silicic acid concentration.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Desmas-bearing demosponges known as lithistids have heavily silicified skeleton and occur typically in bathyal environments of warm and tropical areas but may be found in certain shallow marine caves. Here we report, for the first time two lithistid species, i.e. Neophrissospongia endoumensis, and N. cf. nana, that were earlier known from Western Mediterranean marine caves, from four marine caves in the Aegean Sea (north-eastern Mediterranean), and their congener N. nolitangere from deep waters (ca. 300 m) of the same ecoregion. All marine caves, and sections within these caves, where lithistids occur, have freshwater springs. We interpret this surprising association between lithistids and freshwater input by elevated concentration of silica in water in cave sections where such springs occur, being 8–11 times higher in comparison with shallow water outside caves, and comparable to that of deep waters, that promoted lithistids’ development. One of the studied caves harbored an abundant population of N. endoumensis which formed large masses. The age estimation of these lithistids, based on known growth rate of related deep-water sponges, suggest that they could be 769–909 years old in the case of the largest specimen observed, about 100 cm large. These sponges could have colonized the caves from adjacent deep-water areas not earlier than 7,000–3,000 years ago, after the last glaciation, because earlier they were emerged. High variability of spicules, especially microscleres, and underdevelopment of megascleres may be related to silicic acid concentration. |
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. |
Fioravanti, Maria Letizia; Gustinelli, Andrea; Rigos, George; Buchmann, Kurt; Caffara, Monica; Pascual, Santiago; Pardo, Miguel Ángel Negligible risk of zoonotic anisakid nematodes in farmed fish from European mariculture, 2016 to 2018 Journal Article Eurosurveillance, 26 (2), 2021, ISSN: 1560-7917. @article{fioravanti_negligible_2021, title = {Negligible risk of zoonotic anisakid nematodes in farmed fish from European mariculture, 2016 to 2018}, author = {Maria Letizia Fioravanti and Andrea Gustinelli and George Rigos and Kurt Buchmann and Monica Caffara and Santiago Pascual and Miguel Ángel Pardo}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Fioravanti-Eurosurv-5.pdf https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.2.1900717}, doi = {10.2807/1560-7917.ES.2021.26.2.1900717}, issn = {1560-7917}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Eurosurveillance}, volume = {26}, number = {2}, abstract = {Background The increasing demand for raw or undercooked fish products, supplied by both aquaculture and fisheries, raises concerns about the transmission risk to humans of zoonotic fish parasites. This has led to the current European Union (EU) Regulation No 1276/2011 amending Annex III of Regulation (EC) No 853/2004 and mandating a freezing treatment of such products. Zoonotic parasites, particularly anisakid larvae, have been well documented in wild fish. Data on their presence in European aquaculture products, however, are still scarce, except for Atlantic salmon ( Salmo salar ), where the zoonotic risk was assessed as negligible, exempting it from freezing treatment. Aim To evaluate the zoonotic Anisakidae parasite risk in European farmed marine fish other than Atlantic salmon. Methods From 2016 to 2018 an observational parasitological survey was undertaken on 6,549 farmed fish including 2,753 gilthead seabream ( Sparus aurata ), 2,761 European seabass ( Dicentrarchus labrax ) and 1,035 turbot ( Scophthalmus maximus ) from 14 farms in Italy, Spain and Greece. Furthermore, 200 rainbow trout ( Oncorhynchus mykiss ) sea-caged in Denmark, as well as 352 seabream and 290 seabass imported in Italy and Spain from other countries were examined. Fish were subjected to visual inspection and candling. Fresh visceral organs/fillet samples were artificially digested or UV pressed and visually examined for zoonotic anisakid larvae. Results No zoonotic parasites were found in any of the fish investigated. Conclusions The risk linked to zoonotic Anisakidae in the examined fish species from European mariculture appears negligible. This study laid the groundwork for considerations to amend the current EU regulation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background The increasing demand for raw or undercooked fish products, supplied by both aquaculture and fisheries, raises concerns about the transmission risk to humans of zoonotic fish parasites. This has led to the current European Union (EU) Regulation No 1276/2011 amending Annex III of Regulation (EC) No 853/2004 and mandating a freezing treatment of such products. Zoonotic parasites, particularly anisakid larvae, have been well documented in wild fish. Data on their presence in European aquaculture products, however, are still scarce, except for Atlantic salmon ( Salmo salar ), where the zoonotic risk was assessed as negligible, exempting it from freezing treatment. Aim To evaluate the zoonotic Anisakidae parasite risk in European farmed marine fish other than Atlantic salmon. Methods From 2016 to 2018 an observational parasitological survey was undertaken on 6,549 farmed fish including 2,753 gilthead seabream ( Sparus aurata ), 2,761 European seabass ( Dicentrarchus labrax ) and 1,035 turbot ( Scophthalmus maximus ) from 14 farms in Italy, Spain and Greece. Furthermore, 200 rainbow trout ( Oncorhynchus mykiss ) sea-caged in Denmark, as well as 352 seabream and 290 seabass imported in Italy and Spain from other countries were examined. Fish were subjected to visual inspection and candling. Fresh visceral organs/fillet samples were artificially digested or UV pressed and visually examined for zoonotic anisakid larvae. Results No zoonotic parasites were found in any of the fish investigated. Conclusions The risk linked to zoonotic Anisakidae in the examined fish species from European mariculture appears negligible. This study laid the groundwork for considerations to amend the current EU regulation. |
Digenis, Markos; Ragkousis, Michail; Vasileiadou, Katerina; Gerovasileiou, Vasilis; Katsanevakis, Stelios New records of the Indo-Pacific shrimp Urocaridella pulchella Yokeş & Galil, 2006 from the Eastern Mediterranean Sea Journal Article BIR, 10 (2), pp. 295–303, 2021, ISSN: 22421300. @article{digenis_new_2021, title = {New records of the Indo-Pacific shrimp Urocaridella pulchella Yokeş & Galil, 2006 from the Eastern Mediterranean Sea}, author = {Markos Digenis and Michail Ragkousis and Katerina Vasileiadou and Vasilis Gerovasileiou and Stelios Katsanevakis}, url = {https://www.reabic.net/journals/bir/2021/Issue2.aspx https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Digenis-BioInvasions-Records-35.pdf}, doi = {10.3391/bir.2021.10.2.07}, issn = {22421300}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {BIR}, volume = {10}, number = {2}, pages = {295--303}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Fanini, Lucia; Guittard, Alice On single use plastic straws: Pre-ban findings on touristic beaches in Crete Journal Article Marine Pollution Bulletin, 171 , pp. 112790, 2021, ISSN: 0025326X. @article{fanini_single_2021, title = {On single use plastic straws: Pre-ban findings on touristic beaches in Crete}, author = {Lucia Fanini and Alice Guittard}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Fanini-MarPollBull-58-pre-print.pdf https://linkinghub.elsevier.com/retrieve/pii/S0025326X21008249 }, doi = {10.1016/j.marpolbul.2021.112790}, issn = {0025326X}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {Marine Pollution Bulletin}, volume = {171}, pages = {112790}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
