Results for Author Santi Ioulia :
2025 |
Daraghmeh, Nauras; Exter, Katrina; Pagnier, Justine; Balazy, Piotr; Cancio, Ibon; Chatzigeorgiou, Giorgos; Chatzinikolaou, Eva; Chelchowski, Maciej; Chrismas, Nathan Alexis Mitchell; Comtet, Thierry; Dailianis, Thanos; Deneudt, Klaas; Cerio, Oihane Diaz De; Digenis, Markos; Gerovasileiou, Vasilis; González, José; Kauppi, Laura; Kristoffersen, Jon Bent; Kukliński, Piotr; Lasota, Rafał; Levy, Liraz; Małachowicz, Magdalena; Mavrič, Borut; Mortelmans, Jonas; Paredes, Estefania; Poćwierz‐Kotus, Anita; Reiss, Henning; Santi, Ioulia; Sarafidou, Georgia; Skouradakis, Grigorios; Solbakken, Jostein; Staehr, Peter A U; Tajadura, Javier; Thyrring, Jakob; Troncoso, Jesus S; Vernadou, Emmanouela; Viard, Frederique; Zafeiropoulos, Haris; Zbawicka, Małgorzata; Pavloudi, Christina; Obst, Matthias A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020 Journal Article Molecular Ecology Resources, pp. e14073, 2025, ISSN: 1755-098X, 1755-0998. @article{daraghmeh_longterm_2025, title = {A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020}, author = {Nauras Daraghmeh and Katrina Exter and Justine Pagnier and Piotr Balazy and Ibon Cancio and Giorgos Chatzigeorgiou and Eva Chatzinikolaou and Maciej Chelchowski and Nathan Alexis Mitchell Chrismas and Thierry Comtet and Thanos Dailianis and Klaas Deneudt and Oihane Diaz De Cerio and Markos Digenis and Vasilis Gerovasileiou and José González and Laura Kauppi and Jon Bent Kristoffersen and Piotr Kukliński and Rafał Lasota and Liraz Levy and Magdalena Małachowicz and Borut Mavrič and Jonas Mortelmans and Estefania Paredes and Anita Poćwierz‐Kotus and Henning Reiss and Ioulia Santi and Georgia Sarafidou and Grigorios Skouradakis and Jostein Solbakken and Peter A U Staehr and Javier Tajadura and Jakob Thyrring and Jesus S Troncoso and Emmanouela Vernadou and Frederique Viard and Haris Zafeiropoulos and Małgorzata Zbawicka and Christina Pavloudi and Matthias Obst}, url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.14073 /wp-content/uploads/2025/02/2025-Daraghmeh-MolEcoRes-6.pdf}, doi = {10.1111/1755-0998.14073}, issn = {1755-098X, 1755-0998}, year = {2025}, date = {2025-02-05}, urldate = {2025-02-05}, journal = {Molecular Ecology Resources}, pages = {e14073}, abstract = {ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols. |
Pavloudi, Christina; Santi, Ioulia; Azua, Iñigo; Baña, Zuriñe; Bastianini, Mauro; Belser, Caroline; Bilbao, Jone; Bitz-Thorsen, Julie; Broudin, Caroline; Camusat, Mathieu; Cancio, Ibon; Caray-Counil, Louis; Casotti, Raffaella; Castel, Jade; Comtet, Thierry; Cox, Cymon; Daguin, Claire; Cerio, Oihane Díaz De; Exter, Katrina; Fauvelot, Cécile; Frada, Miguel; Galand, Pierre; Garczarek, Laurence; Fernández, Jose González; Guillou, Laure; Hablützel, Pascal; Heynderickx, Hanneloor; Houbin, Céline; Kervella, Anne; Krystallas, Apostolos; Lagaisse, Rune; Laroquette, Arnaud; Lescure, Lyvia; Lopes, Eva; Loulakaki, Melina; Louro, Bruno; Magalhaes, Catarina; Maidanou, Maria; Margiotta, Francesca; Montresor, Marina; Not, Fabrice; Paredes, Estefanía; Percopo, Isabella; Péru, Erwan; Poulain, Julie; Præbel, Kim; Rigaut-Jalabert, Fabienne; Romac, Sarah; Stavroulaki, Melanthia; Troncoso, Jesús Souza; Thiébaut, Eric; Thomas, Wilfried; Tkacz, Andrzej; Trano, Anna Chiara; Wincker, Patrick; Pade, Nicolas First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Journal Article Biodiversity Data Journal, 13 , pp. e143585, 2025, ISSN: 1314-2828, 1314-2836. @article{pavloudi_first_2025, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples}, author = {Christina Pavloudi and Ioulia Santi and Iñigo Azua and Zuriñe Baña and Mauro Bastianini and Caroline Belser and Jone Bilbao and Julie Bitz-Thorsen and Caroline Broudin and Mathieu Camusat and Ibon Cancio and Louis Caray-Counil and Raffaella Casotti and Jade Castel and Thierry Comtet and Cymon Cox and Claire Daguin and Oihane Díaz De Cerio and Katrina Exter and Cécile Fauvelot and Miguel Frada and Pierre Galand and Laurence Garczarek and Jose González Fernández and Laure Guillou and Pascal Hablützel and Hanneloor Heynderickx and Céline Houbin and Anne Kervella and Apostolos Krystallas and Rune Lagaisse and Arnaud Laroquette and Lyvia Lescure and Eva Lopes and Melina Loulakaki and Bruno Louro and Catarina Magalhaes and Maria Maidanou and Francesca Margiotta and Marina Montresor and Fabrice Not and Estefanía Paredes and Isabella Percopo and Erwan Péru and Julie Poulain and Kim Præbel and Fabienne Rigaut-Jalabert and Sarah Romac and Melanthia Stavroulaki and Jesús Souza Troncoso and Eric Thiébaut and Wilfried Thomas and Andrzej Tkacz and Anna Chiara Trano and Patrick Wincker and Nicolas Pade}, url = {https://bdj.pensoft.net/article/143585/ /wp-content/uploads/2025/04/2025-Pavloudi-BDJ-17.pdf}, doi = {10.3897/BDJ.13.e143585}, issn = {1314-2828, 1314-2836}, year = {2025}, date = {2025-01-01}, urldate = {2025-04-03}, journal = {Biodiversity Data Journal}, volume = {13}, pages = {e143585}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place. |
2023 |
Zafeiropoulos, Haris; Beracochea, Martin; Ninidakis, Stelios; Exter, Katrina; Potirakis, Antonis; De Moro, Gianluca; Richardson, Lorna; Corre, Erwan; Machado, João; Pafilis, Evangelos; Kotoulas, Georgios; Santi, Ioulia; Finn, Robert D; Cox, Cymon J; Pavloudi, Christina metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data Journal Article GigaScience, 12 , pp. giad078, 2023, ISSN: 2047-217X. @article{zafeiropoulos_metagoflow_2022, title = {metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data}, author = {Haris Zafeiropoulos and Martin Beracochea and Stelios Ninidakis and Katrina Exter and Antonis Potirakis and Gianluca De Moro and Lorna Richardson and Erwan Corre and João Machado and Evangelos Pafilis and Georgios Kotoulas and Ioulia Santi and Robert D Finn and Cymon J Cox and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/10/2023-Zafeiropoulos-GiGa-57.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad078/7321054}, doi = {10.1093/gigascience/giad078}, issn = {2047-217X}, year = {2023}, date = {2023-10-19}, urldate = {2023-10-23}, journal = {GigaScience}, volume = {12}, pages = {giad078}, abstract = {Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data. |
Meyer, Raïssa; Davies, Neil; Pitz, Kathleen J; Meyer, Chris; Samuel, Robyn; Anderson, Jane; Appeltans, Ward; Barker, Katharine; Chavez, Francisco P; Duffy, Emmett J; Goodwin, Kelly D; Hudson, Maui; Hunter, Margaret E; Karstensen, Johannes; Laney, Christine M; Leinen, Margaret; Mabee, Paula; Macklin, James A; Muller-Karger, Frank; Pade, Nicolas; Pearlman, Jay; Phillips, Lori; Provoost, Pieter; Santi, Ioulia; Schigel, Dmitry; Schriml, Lynn M; Soccodato, Alice; Suominen, Saara; Thibault, Katherine M; Ung, Visotheary; van de Kamp, Jodie; Wallis, Elycia; Walls, Ramona; Buttigieg, Pier Luigi The founding charter of the Omic Biodiversity Observation Network (Omic BON) Journal Article GigaScience, 12 , pp. giad068, 2023, ISSN: 2047-217X. @article{meyer_founding_2022, title = {The founding charter of the Omic Biodiversity Observation Network (Omic BON)}, author = {Raïssa Meyer and Neil Davies and Kathleen J Pitz and Chris Meyer and Robyn Samuel and Jane Anderson and Ward Appeltans and Katharine Barker and Francisco P Chavez and Emmett J Duffy and Kelly D Goodwin and Maui Hudson and Margaret E Hunter and Johannes Karstensen and Christine M Laney and Margaret Leinen and Paula Mabee and James A Macklin and Frank Muller-Karger and Nicolas Pade and Jay Pearlman and Lori Phillips and Pieter Provoost and Ioulia Santi and Dmitry Schigel and Lynn M Schriml and Alice Soccodato and Saara Suominen and Katherine M Thibault and Visotheary Ung and Jodie van de Kamp and Elycia Wallis and Ramona Walls and Pier Luigi Buttigieg}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Meyer-GigaSci-49.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad068/7252077}, doi = {10.1093/gigascience/giad068}, issn = {2047-217X}, year = {2023}, date = {2023-09-20}, urldate = {2023-09-20}, journal = {GigaScience}, volume = {12}, pages = {giad068}, abstract = {Abstract Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities. |
Santi, Ioulia; Beluche, Odette; Beraud, Mélanie; Buttigieg, Pier Luigi; Casotti, Raffaella; Cox, Cymon J; Cunliffe, Michael; Davies, Neil; Cerio, Oihane Diaz De; Exter, Katrina; Kervella, Anne Emmanuelle; Kotoulas, Georgios; Lagaisse, Rune; Laroquette, Arnaud; Louro, Bruno; Not, Fabrice; Obst, Matthias; Pavloudi, Christina; Poulain, Julie; Præbel, Kim; Vanaverbeke, Jan; Pade, Nicolas European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation Journal Article Frontiers in Marine Science, 10 , pp. 1118120, 2023, ISSN: 2296-7745. @article{santi_european_2023, title = {European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation}, author = {Ioulia Santi and Odette Beluche and Mélanie Beraud and Pier Luigi Buttigieg and Raffaella Casotti and Cymon J Cox and Michael Cunliffe and Neil Davies and Oihane Diaz De Cerio and Katrina Exter and Anne Emmanuelle Kervella and Georgios Kotoulas and Rune Lagaisse and Arnaud Laroquette and Bruno Louro and Fabrice Not and Matthias Obst and Christina Pavloudi and Julie Poulain and Kim Præbel and Jan Vanaverbeke and Nicolas Pade}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Santi-Frontiers-MarSci-24.pdf https://www.frontiersin.org/articles/10.3389/fmars.2023.1118120/full}, doi = {10.3389/fmars.2023.1118120}, issn = {2296-7745}, year = {2023}, date = {2023-05-29}, urldate = {2023-06-06}, journal = {Frontiers in Marine Science}, volume = {10}, pages = {1118120}, abstract = {Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address. |
2022 |
Foundation, Tara Ocean; Abreu, Andre; Bourgois, Etienne; Gristwood, Adam; Troublé, Romain; Oceans, Tara; Acinas, Silvia G; Bork, Peer; Boss, Emmanuel; Bowler, Chris; Budinich, Marko; Chaffron, Samuel; de Vargas, Colomban; Delmont, Tom O; Eveillard, Damien; Guidi, Lionel; Iudicone, Daniele; Kandels, Stephanie; Morlon, Hélène; Lombard, Fabien; Pepperkok, Rainer; Karlusich, Juan José Pierella; Piganeau, Gwenael; Régimbeau, Antoine; Sommeria-Klein, Guilhem; Stemmann, Lars; Sullivan, Matthew B; Sunagawa, Shinichi; Wincker, Patrick; Zablocki, Olivier; (EMBL), European Molecular Biology Laboratory; Arendt, Detlev; Bilic, Josipa; Finn, Robert; Heard, Edith; Rouse, Brendan; Vamathevan, Jessica; (EMBRC-ERIC), European Marine Biological Resource Centre European Research Infrastructure Consortium -; Casotti, Raffaella; Cancio, Ibon; Cunliffe, Michael; Kervella, Anne Emmanuelle; Kooistra, Wiebe H C F; Obst, Matthias; Pade, Nicolas; Power, Deborah M; Santi, Ioulia; Tsagaraki, Tatiana Margo; Vanaverbeke, Jan Priorities for ocean microbiome research Journal Article Nature Microbiology, 7 (7), pp. 937–947, 2022, ISSN: 2058-5276. @article{tara_ocean_foundation_priorities_2022, title = {Priorities for ocean microbiome research}, author = {Tara Ocean Foundation and Andre Abreu and Etienne Bourgois and Adam Gristwood and Romain Troublé and Tara Oceans and Silvia G Acinas and Peer Bork and Emmanuel Boss and Chris Bowler and Marko Budinich and Samuel Chaffron and Colomban de Vargas and Tom O Delmont and Damien Eveillard and Lionel Guidi and Daniele Iudicone and Stephanie Kandels and Hélène Morlon and Fabien Lombard and Rainer Pepperkok and Juan José Pierella Karlusich and Gwenael Piganeau and Antoine Régimbeau and Guilhem Sommeria-Klein and Lars Stemmann and Matthew B Sullivan and Shinichi Sunagawa and Patrick Wincker and Olivier Zablocki and European Molecular Biology Laboratory (EMBL) and Detlev Arendt and Josipa Bilic and Robert Finn and Edith Heard and Brendan Rouse and Jessica Vamathevan and European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC) and Raffaella Casotti and Ibon Cancio and Michael Cunliffe and Anne Emmanuelle Kervella and Wiebe H C F Kooistra and Matthias Obst and Nicolas Pade and Deborah M Power and Ioulia Santi and Tatiana Margo Tsagaraki and Jan Vanaverbeke}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Sandi-et-al.-Priorities_for_ocean_microbiome_research-51.pdf https://www.nature.com/articles/s41564-022-01145-5}, doi = {10.1038/s41564-022-01145-5}, issn = {2058-5276}, year = {2022}, date = {2022-07-01}, urldate = {2022-07-29}, journal = {Nature Microbiology}, volume = {7}, number = {7}, pages = {937--947}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dimitriou, Panagiotis D; Santi, Ioulia; Moraitis, Manos L; Tsikopoulou, Irini; Pitta, Paraskevi; Karakassis, Ioannis Benthic–Pelagic Coupling in the Oligotrophic Eastern Mediterranean: A Synthesis of the HYPOXIA Project Results Journal Article Frontiers in Marine Science, 9 , pp. 886335, 2022, ISSN: 2296-7745. @article{dimitriou_benthicpelagic_2022, title = {Benthic–Pelagic Coupling in the Oligotrophic Eastern Mediterranean: A Synthesis of the HYPOXIA Project Results}, author = {Panagiotis D Dimitriou and Ioulia Santi and Manos L Moraitis and Irini Tsikopoulou and Paraskevi Pitta and Ioannis Karakassis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Dimitriou-FMS-47.pdf https://www.frontiersin.org/articles/10.3389/fmars.2022.886335/full}, doi = {10.3389/fmars.2022.886335}, issn = {2296-7745}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Frontiers in Marine Science}, volume = {9}, pages = {886335}, abstract = {Benthic–pelagic coupling studies have shown that the response of the benthic system to eutrophication is subject to complex nonlinear dynamics with specific thresholds beyond which abrupt changes in the response of the ecosystem occur and time lags between inputs and responses. The “HYPOXIA: Benthic–pelagic coupling and regime shifts ” project aimed to investigate how nutrient input in the water column results in ecological processes of eutrophication, which may lead to significant, irreversible changes in the eastern Mediterranean marine ecosystems within a short period of time. The project included analysis of historical water and benthic data, field sampling, and mesocosm experiments. From the project results, it can be concluded that nutrient inputs are quickly capitalized by small phytoplankton species in the water column resulting in the bloom of specific species with high nutrient uptake capabilities. When Eutrophic Index values (calculated using nutrient and chlorophyll- a concentrations) cross the moderate-to-poor threshold, the precipitating organic matter can cause observable effects on the benthic system. Depending on eutrophication intensity and persistence, the effects can start from microbenthos, meiofauna, and macrofauna increase in abundance and biomass to significant changes in the community structure. The latter includes the proliferation of macrofaunal opportunistic species, an increase in deposit feeders, and the high risk of ecosystem quality degradation. However, contrary to other regions of the world, no water hypoxia or benthic dead zones were observed as chlorophyll- a and O 2 concentrations showed a positive correlation. This is caused by the high photosynthetic activity of the phytoplankton and microphytobenthos, the increased bioturbation of macrofauna, and the increased abundance of sediment deposit-feeding species, which quickly consume the excess organic matter. Eastern Mediterranean coastal ecosystems show high resilience to the adverse effects of eutrophication, preventing hypoxia and azoic conditions when eutrophication is the only source of environmental disturbance.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Benthic–pelagic coupling studies have shown that the response of the benthic system to eutrophication is subject to complex nonlinear dynamics with specific thresholds beyond which abrupt changes in the response of the ecosystem occur and time lags between inputs and responses. The “HYPOXIA: Benthic–pelagic coupling and regime shifts ” project aimed to investigate how nutrient input in the water column results in ecological processes of eutrophication, which may lead to significant, irreversible changes in the eastern Mediterranean marine ecosystems within a short period of time. The project included analysis of historical water and benthic data, field sampling, and mesocosm experiments. From the project results, it can be concluded that nutrient inputs are quickly capitalized by small phytoplankton species in the water column resulting in the bloom of specific species with high nutrient uptake capabilities. When Eutrophic Index values (calculated using nutrient and chlorophyll- a concentrations) cross the moderate-to-poor threshold, the precipitating organic matter can cause observable effects on the benthic system. Depending on eutrophication intensity and persistence, the effects can start from microbenthos, meiofauna, and macrofauna increase in abundance and biomass to significant changes in the community structure. The latter includes the proliferation of macrofaunal opportunistic species, an increase in deposit feeders, and the high risk of ecosystem quality degradation. However, contrary to other regions of the world, no water hypoxia or benthic dead zones were observed as chlorophyll- a and O 2 concentrations showed a positive correlation. This is caused by the high photosynthetic activity of the phytoplankton and microphytobenthos, the increased bioturbation of macrofauna, and the increased abundance of sediment deposit-feeding species, which quickly consume the excess organic matter. Eastern Mediterranean coastal ecosystems show high resilience to the adverse effects of eutrophication, preventing hypoxia and azoic conditions when eutrophication is the only source of environmental disturbance. |
Martin, Jon Lapeyra; Santi, Ioulia; Pitta, Paraskevi; John, Uwe; Gypens, Nathalie Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias Journal Article Metabarcoding and Metagenomics, 6 , pp. e85794, 2022, ISSN: 2534-9708. @article{martin_towards_2022, title = {Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias}, author = {Jon Lapeyra Martin and Ioulia Santi and Paraskevi Pitta and Uwe John and Nathalie Gypens}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Santi_MBMG-60.pdf https://mbmg.pensoft.net/article/85794/}, doi = {10.3897/mbmg.6.85794}, issn = {2534-9708}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-26}, journal = {Metabarcoding and Metagenomics}, volume = {6}, pages = {e85794}, abstract = {Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor. |
2021 |
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. |
2020 |
Santi, I; Kasapidis, P; Psarra, S; Assimakopoulou, G; Pavlidou, A; Protopapa, M; Tsiola, A; Zeri, C; Pitta, P Composition and distribution patterns of eukaryotic microbial plankton in the ultra-oligotrophic Eastern Mediterranean Sea Journal Article Aquatic Microbial Ecology, 84 , pp. 155–173, 2020, ISSN: 0948-3055, (Publisher: Inter-Research Science Center). @article{santi_composition_2020, title = {Composition and distribution patterns of eukaryotic microbial plankton in the ultra-oligotrophic Eastern Mediterranean Sea}, author = {I Santi and P Kasapidis and S Psarra and G Assimakopoulou and A Pavlidou and M Protopapa and A Tsiola and C Zeri and P Pitta}, url = {https://www.int-res.com/abstracts/ame/v84/p155-173/}, doi = {10.3354/ame01933}, issn = {0948-3055}, year = {2020}, date = {2020-06-01}, journal = {Aquatic Microbial Ecology}, volume = {84}, pages = {155--173}, abstract = {Marine microbial eukaryotes play crucial roles in water-column ecosystems; however, there are regional gaps in the investigation of natural microbial eukaryote communities, and uncertainties concerning their distribution persevere. This study combined 18S rRNA metabarcoding, biomass measurements and statistical analyses of multiple environmental variables to examine the distribution of planktonic microbial eukaryotes at different sites and water layers in the ultra-oligotrophic Eastern Mediterranean Sea (Western Levantine Basin). Our results showed that microbial eukaryotic communities were structured by depth. In surface waters, different sites shared high percentages of molecular operational taxonomic units (MOTUs), but this was not the case for deep-sea communities (≥1000 m). Plankton biomass was significantly different among sites, implying that communities of a similar composition may not support the same activity or population size. The deep-sea communities showed high percentages of unassigned MOTUs, highlighting the sparsity of the existing information on deep-sea plankton eukaryotes. Water temperature and dissolved organic matter significantly affected community distribution. Micro-eukaryotic distribution was additionally affected by the nitrogen to phosphorus ratio and viral abundance, while nano- and pico-communities were affected by zooplankton. The present study explores microbial plankton eukaryotes in their natural oligotrophic environment and highlights that, even within restricted oceanic areas, marine plankton may follow distribution patterns that are largely controlled by environmental variables.}, note = {Publisher: Inter-Research Science Center}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine microbial eukaryotes play crucial roles in water-column ecosystems; however, there are regional gaps in the investigation of natural microbial eukaryote communities, and uncertainties concerning their distribution persevere. This study combined 18S rRNA metabarcoding, biomass measurements and statistical analyses of multiple environmental variables to examine the distribution of planktonic microbial eukaryotes at different sites and water layers in the ultra-oligotrophic Eastern Mediterranean Sea (Western Levantine Basin). Our results showed that microbial eukaryotic communities were structured by depth. In surface waters, different sites shared high percentages of molecular operational taxonomic units (MOTUs), but this was not the case for deep-sea communities (≥1000 m). Plankton biomass was significantly different among sites, implying that communities of a similar composition may not support the same activity or population size. The deep-sea communities showed high percentages of unassigned MOTUs, highlighting the sparsity of the existing information on deep-sea plankton eukaryotes. Water temperature and dissolved organic matter significantly affected community distribution. Micro-eukaryotic distribution was additionally affected by the nitrogen to phosphorus ratio and viral abundance, while nano- and pico-communities were affected by zooplankton. The present study explores microbial plankton eukaryotes in their natural oligotrophic environment and highlights that, even within restricted oceanic areas, marine plankton may follow distribution patterns that are largely controlled by environmental variables. |
Tsikopoulou, Irini; Santi, Ioulia; Dimitriou, Panagiotis D; Papageorgiou, Nafsika; Pitta, Paraskevi; Karakassis, Ioannis Response of Microphytobenthos and Benthic Bacteria Viability to Eutrophication in a Benthic–Pelagic Coupling Mesocosm Experiment Journal Article Frontiers in Marine Science, 7 , pp. 270, 2020, ISSN: 2296-7745, (Publisher: Frontiers). @article{tsikopoulou_response_2020, title = {Response of Microphytobenthos and Benthic Bacteria Viability to Eutrophication in a Benthic–Pelagic Coupling Mesocosm Experiment}, author = {Irini Tsikopoulou and Ioulia Santi and Panagiotis D Dimitriou and Nafsika Papageorgiou and Paraskevi Pitta and Ioannis Karakassis}, url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00270/full}, doi = {10.3389/fmars.2020.00270}, issn = {2296-7745}, year = {2020}, date = {2020-04-01}, journal = {Frontiers in Marine Science}, volume = {7}, pages = {270}, abstract = {Excessive primary productivity due to nutrient inputs is a potential problem in coastal areas when resulting in high organic matter sedimentation rates. Microphytobenthos and heterotrophic bacteria are two components of the benthic ecosystem that contribute to nutrient cycling and decomposition of organic matter. In this context, the effects of nutrient addition and the associated in situ produced organic matter on microphytobenthos community composition and benthic bacterial viability were assessed in a mesocosm experiment for 58 days. The experimental setup included triplicate mesocosms filled with sediment and water under three levels of nutrient addition (‘control', ‘low' and ‘high'). Benthic algal community composition was assessed using chemotaxonomy and bacterial viability was estimated using flow cytometry and a double-staining protocol. Multivariate analysis detected a significant effect of treatment and time on microphytobenthic community composition indicating a difference between control and low mesocosms and also between low and high treatments at Day 12 and Day 24 of the experiment. Nonetheless, microphytobenthos implied high resistance and redundancy of benthic algae to disturbance as all three treatments showed no significant difference in community structure between Day 0 and Day 58. Bacterial viability responded quickly to the high nutrient addition and was significantly lower than in the ‘control' and ‘low' treatments at Days 6 and 12. Both pelagic and benthic environmental variables were correlated to these changes in benthic community.}, note = {Publisher: Frontiers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Excessive primary productivity due to nutrient inputs is a potential problem in coastal areas when resulting in high organic matter sedimentation rates. Microphytobenthos and heterotrophic bacteria are two components of the benthic ecosystem that contribute to nutrient cycling and decomposition of organic matter. In this context, the effects of nutrient addition and the associated in situ produced organic matter on microphytobenthos community composition and benthic bacterial viability were assessed in a mesocosm experiment for 58 days. The experimental setup included triplicate mesocosms filled with sediment and water under three levels of nutrient addition (‘control', ‘low' and ‘high'). Benthic algal community composition was assessed using chemotaxonomy and bacterial viability was estimated using flow cytometry and a double-staining protocol. Multivariate analysis detected a significant effect of treatment and time on microphytobenthic community composition indicating a difference between control and low mesocosms and also between low and high treatments at Day 12 and Day 24 of the experiment. Nonetheless, microphytobenthos implied high resistance and redundancy of benthic algae to disturbance as all three treatments showed no significant difference in community structure between Day 0 and Day 58. Bacterial viability responded quickly to the high nutrient addition and was significantly lower than in the ‘control' and ‘low' treatments at Days 6 and 12. Both pelagic and benthic environmental variables were correlated to these changes in benthic community. |
Hopwood, Mark J; Sanchez, Nicolas; Polyviou, Despo; Leiknes, Øystein; Gallego-Urrea, Julián Alberto; Achterberg, Eric P; Ardelan, Murat V; Aristegui, Javier; Bach, Lennart; Besiktepe, Sengul; Heriot, Yohann; Kalantzi, Ioanna; Kurt, Tuba Terbıyık; Santi, Ioulia; Tsagaraki, Tatiana M; Turner, David Experiment design and bacterial abundance control extracellular H2O2 concentrations during four series of mesocosm experiments Journal Article Biogeosciences, 17 (5), pp. 1309–1326, 2020, ISSN: 1726-4189. @article{hopwood_experiment_2020, title = {Experiment design and bacterial abundance control extracellular H2O2 concentrations during four series of mesocosm experiments}, author = {Mark J Hopwood and Nicolas Sanchez and Despo Polyviou and Øystein Leiknes and Julián Alberto Gallego-Urrea and Eric P Achterberg and Murat V Ardelan and Javier Aristegui and Lennart Bach and Sengul Besiktepe and Yohann Heriot and Ioanna Kalantzi and Tuba Terbıyık Kurt and Ioulia Santi and Tatiana M Tsagaraki and David Turner}, url = {https://www.biogeosciences.net/17/1309/2020/}, doi = {10.5194/bg-17-1309-2020}, issn = {1726-4189}, year = {2020}, date = {2020-03-01}, journal = {Biogeosciences}, volume = {17}, number = {5}, pages = {1309--1326}, abstract = {The extracellular concentration of H2O2 in surface aquatic environments is controlled by a balance between photochemical production and the microbial synthesis of catalase and peroxidase enzymes to remove H2O2 from solution. In any kind of incubation experiment, the formation rates and equilibrium concentrations of reactive oxygen species (ROSs) such as H2O2 may be sensitive to both the experiment design, particularly to the regulation of incident light, and the abundance of different microbial groups, as both cellular H2O2 production and catalase–peroxidase enzyme production rates differ between species. Whilst there are extensive measurements of photochemical H2O2 formation rates and the distribution of H2O2 in the marine environment, it is poorly constrained how different microbial groups affect extracellular H2O2 concentrations, how comparable extracellular H2O2 concentrations within large-scale incubation experiments are to those observed in the surface-mixed layer, and to what extent a mismatch with environmentally relevant concentrations of ROS in incubations could influence biological processes differently to what would be observed in nature. Here we show that both experiment design and bacterial abundance consistently exert control on extracellular H2O2 concentrations across a range of incubation experiments in diverse marine environments. During four large-scale (textbackslashtextgreater1000 L) mesocosm experiments (in Gran Canaria, the Mediterranean, Patagonia and Svalbard) most experimental factors appeared to exert only minor, or no, direct effect on H2O2 concentrations. For example, in three of four experiments where pH was manipulated to 0.4–0.5 below ambient pH, no significant change was evident in extracellular H2O2 concentrations relative to controls. An influence was sometimes inferred from zooplankton density, but not consistently between different incubation experiments, and no change in H2O2 was evident in controlled experiments using different densities of the copepod Calanus finmarchicus grazing on the diatom Skeletonema costatum (textbackslashtextless1 % change in [H2O2] comparing copepod densities from 1 to 10 L−1). Instead, the changes in H2O2 concentration contrasting high- and low-zooplankton incubations appeared to arise from the resulting changes in bacterial activity. The correlation between bacterial abundance and extracellular H2O2 was stronger in some incubations than others (R2 range 0.09 to 0.55), yet high bacterial densities were consistently associated with low H2O2. Nonetheless, the main control on H2O2 concentrations during incubation experiments relative to those in ambient, unenclosed waters was the regulation of incident light. In an open (lidless) mesocosm experiment in Gran Canaria, H2O2 was persistently elevated (2–6-fold) above ambient concentrations; whereas using closed high-density polyethylene mesocosms in Crete, Svalbard and Patagonia H2O2 within incubations was always reduced (median 10 %–90 %) relative to ambient waters.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The extracellular concentration of H2O2 in surface aquatic environments is controlled by a balance between photochemical production and the microbial synthesis of catalase and peroxidase enzymes to remove H2O2 from solution. In any kind of incubation experiment, the formation rates and equilibrium concentrations of reactive oxygen species (ROSs) such as H2O2 may be sensitive to both the experiment design, particularly to the regulation of incident light, and the abundance of different microbial groups, as both cellular H2O2 production and catalase–peroxidase enzyme production rates differ between species. Whilst there are extensive measurements of photochemical H2O2 formation rates and the distribution of H2O2 in the marine environment, it is poorly constrained how different microbial groups affect extracellular H2O2 concentrations, how comparable extracellular H2O2 concentrations within large-scale incubation experiments are to those observed in the surface-mixed layer, and to what extent a mismatch with environmentally relevant concentrations of ROS in incubations could influence biological processes differently to what would be observed in nature. Here we show that both experiment design and bacterial abundance consistently exert control on extracellular H2O2 concentrations across a range of incubation experiments in diverse marine environments. During four large-scale (textbackslashtextgreater1000 L) mesocosm experiments (in Gran Canaria, the Mediterranean, Patagonia and Svalbard) most experimental factors appeared to exert only minor, or no, direct effect on H2O2 concentrations. For example, in three of four experiments where pH was manipulated to 0.4–0.5 below ambient pH, no significant change was evident in extracellular H2O2 concentrations relative to controls. An influence was sometimes inferred from zooplankton density, but not consistently between different incubation experiments, and no change in H2O2 was evident in controlled experiments using different densities of the copepod Calanus finmarchicus grazing on the diatom Skeletonema costatum (textbackslashtextless1 % change in [H2O2] comparing copepod densities from 1 to 10 L−1). Instead, the changes in H2O2 concentration contrasting high- and low-zooplankton incubations appeared to arise from the resulting changes in bacterial activity. The correlation between bacterial abundance and extracellular H2O2 was stronger in some incubations than others (R2 range 0.09 to 0.55), yet high bacterial densities were consistently associated with low H2O2. Nonetheless, the main control on H2O2 concentrations during incubation experiments relative to those in ambient, unenclosed waters was the regulation of incident light. In an open (lidless) mesocosm experiment in Gran Canaria, H2O2 was persistently elevated (2–6-fold) above ambient concentrations; whereas using closed high-density polyethylene mesocosms in Crete, Svalbard and Patagonia H2O2 within incubations was always reduced (median 10 %–90 %) relative to ambient waters. |
2019 |
Santi, Ioulia; Tsiola, Anastasia; Dimitriou, Panagiotis D; Fodelianakis, Stilianos; Kasapidis, Panagiotis; Papageorgiou, Nafsika; Daffonchio, Daniele; Pitta, Paraskevi; Karakassis, Ioannis Marine Environmental Research, 150 , pp. 104752, 2019, ISSN: 18790291, (Publisher: Elsevier). @article{santi_prokaryotic_2019, title = {Prokaryotic and eukaryotic microbial community responses to N and P nutrient addition in oligotrophic Mediterranean coastal waters: Novel insights from DNA metabarcoding and network analysis}, author = {Ioulia Santi and Anastasia Tsiola and Panagiotis D Dimitriou and Stilianos Fodelianakis and Panagiotis Kasapidis and Nafsika Papageorgiou and Daniele Daffonchio and Paraskevi Pitta and Ioannis Karakassis}, url = {https://www.sciencedirect.com/science/article/pii/S0141113619302090?dgcid=coauthor https://linkinghub.elsevier.com/retrieve/pii/S0141113619302090}, doi = {10.1016/j.marenvres.2019.104752}, issn = {18790291}, year = {2019}, date = {2019-09-01}, journal = {Marine Environmental Research}, volume = {150}, pages = {104752}, abstract = {The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics.}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics. |
Livanou, Eleni; Lagaria, Anna; Santi, Ioulia; Mandalakis, Manolis; Pavlidou, Alexandra; Lika, Konstadia; Psarra, Stella Deep-Sea Research Part II: Topical Studies in Oceanography, 164 , pp. 100–111, 2019, ISSN: 09670645, (Publisher: Pergamon). @article{livanou_pigmented_2019, title = {Pigmented and heterotrophic nanoflagellates: Abundance and grazing on prokaryotic picoplankton in the ultra-oligotrophic Eastern Mediterranean Sea}, author = {Eleni Livanou and Anna Lagaria and Ioulia Santi and Manolis Mandalakis and Alexandra Pavlidou and Konstadia Lika and Stella Psarra}, url = {https://www.sciencedirect.com/science/article/pii/S096706451930027X?dgcid=coauthor}, doi = {10.1016/j.dsr2.2019.04.007}, issn = {09670645}, year = {2019}, date = {2019-04-01}, journal = {Deep-Sea Research Part II: Topical Studies in Oceanography}, volume = {164}, pages = {100--111}, abstract = {The abundance and grazing effect of small (textbackslashtextless5 μm) pigmented (PNF) and heterotrophic (HNF) nanoflagellates on prokaryotic picoplankton stock (i.e. heterotrophic bacteria (HB) and Synechococcus) were assessed during April 2016 at four stations along a longitudinal transect in the ultra-oligotrophic Eastern Mediterranean Sea and at two selected depths with varying nutrient and light conditions; the 5 m depth representing surface water and the 75 m depth representing the deeper euphotic layer, targeting the Deep Chlorophyll Maximum (DCM) zone at the sampling stations. Cells of size textbackslashtextless3 μm dominated the small nanoflagellate community and accounted for 84 ± 8.2% and 73 ± 12.2% (mean ± sd) of total HNF and PNF, respectively. HNF abundance and their grazing effect on prokaryotic picoplankton did not differ between the two depths, while PNF exhibited higher abundance and grazing effect on prokaryotic picoplankton at 75 m compared to the surface (5 m). HNF dominated prokaryotic picoplankton consumption at 5 m accounting for 67–92% and 71–90% of the HB and Synechococcus consumption, respectively. On the other hand, PNF were the dominant grazers of prokaryotic picoplankton at 75 m accounting for 72–80% of the HB consumption and 60–74% of the Synechococcus consumption. HNF and PNF together consumed 4.4 ± 3.2% d −1 (mean ± sd) of the HB standing stock and 19.7 ± 16% d −1 (mean ± sd) of the Synechococcus standing stock. Moreover, a negative relationship between phosphate concentration and ingestion rates of PNF on prokaryotic picoplankton was observed. Pigment analysis showed that the major PNF groups were Prymnesiophytes followed by Pelagophytes/Chrysophytes. Prymnesiophytes was the group mostly associated with mixotrophy. Overall, our results pinpoint the role of small nanoflagellates as prokaryotic picoplankton consumers and the importance of mixotrophy as a trophic mode for PNF in the ultra-oligotrophic E. Mediterranean Sea.}, note = {Publisher: Pergamon}, keywords = {}, pubstate = {published}, tppubtype = {article} } The abundance and grazing effect of small (textbackslashtextless5 μm) pigmented (PNF) and heterotrophic (HNF) nanoflagellates on prokaryotic picoplankton stock (i.e. heterotrophic bacteria (HB) and Synechococcus) were assessed during April 2016 at four stations along a longitudinal transect in the ultra-oligotrophic Eastern Mediterranean Sea and at two selected depths with varying nutrient and light conditions; the 5 m depth representing surface water and the 75 m depth representing the deeper euphotic layer, targeting the Deep Chlorophyll Maximum (DCM) zone at the sampling stations. Cells of size textbackslashtextless3 μm dominated the small nanoflagellate community and accounted for 84 ± 8.2% and 73 ± 12.2% (mean ± sd) of total HNF and PNF, respectively. HNF abundance and their grazing effect on prokaryotic picoplankton did not differ between the two depths, while PNF exhibited higher abundance and grazing effect on prokaryotic picoplankton at 75 m compared to the surface (5 m). HNF dominated prokaryotic picoplankton consumption at 5 m accounting for 67–92% and 71–90% of the HB and Synechococcus consumption, respectively. On the other hand, PNF were the dominant grazers of prokaryotic picoplankton at 75 m accounting for 72–80% of the HB consumption and 60–74% of the Synechococcus consumption. HNF and PNF together consumed 4.4 ± 3.2% d −1 (mean ± sd) of the HB standing stock and 19.7 ± 16% d −1 (mean ± sd) of the Synechococcus standing stock. Moreover, a negative relationship between phosphate concentration and ingestion rates of PNF on prokaryotic picoplankton was observed. Pigment analysis showed that the major PNF groups were Prymnesiophytes followed by Pelagophytes/Chrysophytes. Prymnesiophytes was the group mostly associated with mixotrophy. Overall, our results pinpoint the role of small nanoflagellates as prokaryotic picoplankton consumers and the importance of mixotrophy as a trophic mode for PNF in the ultra-oligotrophic E. Mediterranean Sea. |
2018 |
Tsiola, A; Toncelli, C; Fodelianakis, S; Michoud, G; Bucheli, T D; Gavriilidou, A; Kagiorgi, M; Kalantzi, I; Knauer, K; Kotoulas, G; Mylona, K; Papadopoulou, E; Psarra, S; Santi, I; Tsapakis, M; Daffonchio, D; Pergantis, S A; Pitta, P Low-dose addition of silver nanoparticles stresses marine plankton communities Journal Article Environmental Science: Nano, 5 (8), pp. 1965–1980, 2018, ISSN: 20518153, (Publisher: Royal Society of Chemistry). @article{tsiola_low-dose_2018, title = {Low-dose addition of silver nanoparticles stresses marine plankton communities}, author = {A Tsiola and C Toncelli and S Fodelianakis and G Michoud and T D Bucheli and A Gavriilidou and M Kagiorgi and I Kalantzi and K Knauer and G Kotoulas and K Mylona and E Papadopoulou and S Psarra and I Santi and M Tsapakis and D Daffonchio and S A Pergantis and P Pitta}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85051542012&doi=10.1039%2fc8en00195b&partnerID=40&md5=fbfca29c271ba8fddfd015137b66c273}, doi = {10.1039/c8en00195b}, issn = {20518153}, year = {2018}, date = {2018-01-01}, journal = {Environmental Science: Nano}, volume = {5}, number = {8}, pages = {1965--1980}, abstract = {The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance against AgNPs. However, a realistic evaluation of the toxicity of AgNPs to the marine ecosystem is currently missing. Therefore, we designed a mesocosm experiment to assess the impact of AgNP exposure on natural microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the composition of the planktonic community, from viruses to protists. Further, we analyzed the concentration and properties of AgNPs for the total time of exposure. We found that the addition of AgNPs even at a low dose affected the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition significantly changed. Additionally, the amount of a lysogeny-related gene increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Microbial plankton was significantly affected due to both increased dissolved silver ions and decreased AgNP size. Our results highlight that the release of AgNPs alters the functioning of the marine food web by hampering important viral and bacterial processes. © The Royal Society of Chemistry.}, note = {Publisher: Royal Society of Chemistry}, keywords = {}, pubstate = {published}, tppubtype = {article} } The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance against AgNPs. However, a realistic evaluation of the toxicity of AgNPs to the marine ecosystem is currently missing. Therefore, we designed a mesocosm experiment to assess the impact of AgNP exposure on natural microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the composition of the planktonic community, from viruses to protists. Further, we analyzed the concentration and properties of AgNPs for the total time of exposure. We found that the addition of AgNPs even at a low dose affected the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition significantly changed. Additionally, the amount of a lysogeny-related gene increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Microbial plankton was significantly affected due to both increased dissolved silver ions and decreased AgNP size. Our results highlight that the release of AgNPs alters the functioning of the marine food web by hampering important viral and bacterial processes. © The Royal Society of Chemistry. |
2017 |
Pitta, Paraskevi; Kanakidou, Maria; Mihalopoulos, Nikolaos; Christodoulaki, Sylvia; Dimitriou, Panagiotis D; Frangoulis, Constantin; Giannakourou, Antonia; Kagiorgi, Margarita; Lagaria, Anna; Nikolaou, Panagiota; Papageorgiou, Nafsika; Psarra, Stella; Santi, Ioulia; Tsapakis, Manolis; Tsiola, Anastasia; Violaki, Kalliopi; Petihakis, George Saharan Dust Deposition Effects on the Microbial Food Web in the Eastern Mediterranean: A Study Based on a Mesocosm Experiment Journal Article Frontiers in Marine Science, 4 , pp. 117, 2017, ISSN: 2296-7745, (Publisher: Frontiers). @article{pitta_saharan_2017, title = {Saharan Dust Deposition Effects on the Microbial Food Web in the Eastern Mediterranean: A Study Based on a Mesocosm Experiment}, author = {Paraskevi Pitta and Maria Kanakidou and Nikolaos Mihalopoulos and Sylvia Christodoulaki and Panagiotis D Dimitriou and Constantin Frangoulis and Antonia Giannakourou and Margarita Kagiorgi and Anna Lagaria and Panagiota Nikolaou and Nafsika Papageorgiou and Stella Psarra and Ioulia Santi and Manolis Tsapakis and Anastasia Tsiola and Kalliopi Violaki and George Petihakis}, url = {http://journal.frontiersin.org/article/10.3389/fmars.2017.00117/full}, doi = {10.3389/FMARS.2017.00117}, issn = {2296-7745}, year = {2017}, date = {2017-01-01}, journal = {Frontiers in Marine Science}, volume = {4}, pages = {117}, abstract = {The effect of episodicity of Saharan dust deposition on the pelagic microbial food web was studied in the oligotrophic Eastern Mediterranean by means of a mesocosm experiment in May 2014. Two different treatments in triplicates (addition of natural Saharan dust in a single-strong pulse or in three smaller consecutive doses of the same total quantity), and three unamended controls were employed; chemical and biological parameters were measured during a 10-day experiment. Temporal changes in primary (PP) and bacterial (BP) production, chlorophyll a (Chla) concentration and heterotrophic bacteria, Synechococcus and mesozooplankton abundance were studied. The results suggested that the auto- and hetero-trophic components of the food web (at least the prokaryotes) were enhanced by the dust addition (and by the nitrogen and phosphorus added through dust). Furthermore, a 1-day delay was observed for PP, BP and Chla increases when dust was added in three daily doses; however, the maximal values attained were similar in the two treatments. Although the effect was evident in the first osmotrophic level (phytoplankton and bacteria), it was lost further up the food web, masked under the impact of grazing exerted by predators such as heterotrophic flagellates, ciliates and dinoflagellates. This was partly proved by two dilution experiments. This study demonstrates the important role of atmospheric deposition and protist grazing when evaluating the effect on oligotrophic systems characterised by increased numbers of trophic levels.}, note = {Publisher: Frontiers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of episodicity of Saharan dust deposition on the pelagic microbial food web was studied in the oligotrophic Eastern Mediterranean by means of a mesocosm experiment in May 2014. Two different treatments in triplicates (addition of natural Saharan dust in a single-strong pulse or in three smaller consecutive doses of the same total quantity), and three unamended controls were employed; chemical and biological parameters were measured during a 10-day experiment. Temporal changes in primary (PP) and bacterial (BP) production, chlorophyll a (Chla) concentration and heterotrophic bacteria, Synechococcus and mesozooplankton abundance were studied. The results suggested that the auto- and hetero-trophic components of the food web (at least the prokaryotes) were enhanced by the dust addition (and by the nitrogen and phosphorus added through dust). Furthermore, a 1-day delay was observed for PP, BP and Chla increases when dust was added in three daily doses; however, the maximal values attained were similar in the two treatments. Although the effect was evident in the first osmotrophic level (phytoplankton and bacteria), it was lost further up the food web, masked under the impact of grazing exerted by predators such as heterotrophic flagellates, ciliates and dinoflagellates. This was partly proved by two dilution experiments. This study demonstrates the important role of atmospheric deposition and protist grazing when evaluating the effect on oligotrophic systems characterised by increased numbers of trophic levels. |
Tsiola, Anastasia; Pitta, Paraskevi; Callol, Agnes Junyer; Kagiorgi, Margarita; Kalantzi, Ioanna; Mylona, Kyriaki; Santi, Ioulia; Toncelli, Claudio; Pergantis, Spyros; Tsapakis, Manolis The impact of silver nanoparticles on marine plankton dynamics: Dependence on coating, size and concentration Journal Article Science of The Total Environment, 601-602 , pp. 1838–1848, 2017, ISSN: 0048-9697, (Publisher: Elsevier). @article{tsiola_impact_2017, title = {The impact of silver nanoparticles on marine plankton dynamics: Dependence on coating, size and concentration}, author = {Anastasia Tsiola and Paraskevi Pitta and Agnes Junyer Callol and Margarita Kagiorgi and Ioanna Kalantzi and Kyriaki Mylona and Ioulia Santi and Claudio Toncelli and Spyros Pergantis and Manolis Tsapakis}, url = {http://www.sciencedirect.com/science/article/pii/S0048969717314055#f0030}, doi = {10.1016/J.SCITOTENV.2017.06.042}, issn = {0048-9697}, year = {2017}, date = {2017-01-01}, journal = {Science of The Total Environment}, volume = {601-602}, pages = {1838--1848}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dimitriou, Panagiotis D; Papageorgiou, Nafsika; Geropoulos, Antonios; Kalogeropoulou, Vasiliki; Moraitis, Manolis; Santi, Ioulia; Tsikopoulou, Irini; Pitta, Paraskevi; Karakassis, Ioannis Benthic pelagic coupling in a mesocosm experiment: Delayed sediment responses and regime shifts Journal Article Science of The Total Environment, 605-606 , pp. 637–645, 2017, ISSN: 0048-9697, (Publisher: Elsevier). @article{dimitriou_benthic_2017, title = {Benthic pelagic coupling in a mesocosm experiment: Delayed sediment responses and regime shifts}, author = {Panagiotis D Dimitriou and Nafsika Papageorgiou and Antonios Geropoulos and Vasiliki Kalogeropoulou and Manolis Moraitis and Ioulia Santi and Irini Tsikopoulou and Paraskevi Pitta and Ioannis Karakassis}, url = {http://www.sciencedirect.com/science/article/pii/S0048969717316601}, doi = {10.1016/J.SCITOTENV.2017.06.239}, issn = {0048-9697}, year = {2017}, date = {2017-01-01}, journal = {Science of The Total Environment}, volume = {605-606}, pages = {637--645}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dimitriou, Panagiotis D; Papageorgiou, Nafsika; Geropoulos, Antonios; Kalogeropoulou, Vasiliki; Moraitis, Manolis; Santi, Ioulia; Tsikopoulou, Irini; Pitta, Paraskevi; Karakassis, Ioannis A novel mesocosm setup for benthic‐pelagic coupling experiments Journal Article Limnology and Oceanography: Methods, 15 (4), pp. 349–362, 2017, ISSN: 1541-5856. @article{dimitriou_novel_2017, title = {A novel mesocosm setup for benthic‐pelagic coupling experiments}, author = {Panagiotis D Dimitriou and Nafsika Papageorgiou and Antonios Geropoulos and Vasiliki Kalogeropoulou and Manolis Moraitis and Ioulia Santi and Irini Tsikopoulou and Paraskevi Pitta and Ioannis Karakassis}, url = {http://onlinelibrary.wiley.com/doi/10.1002/lom3.10163/full}, doi = {10.1002/LOM3.10163}, issn = {1541-5856}, year = {2017}, date = {2017-01-01}, journal = {Limnology and Oceanography: Methods}, volume = {15}, number = {4}, pages = {349--362}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2016 |
Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A; Calbet, Albert; Nejstgaard, Jens C; Gasol, Josep M; Isari, Stamatina; Moorthi, Stefanie D; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F; Tsagaraki, Tatiana M; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi A light-induced shortcut in the planktonic microbial loop Journal Article Scientific Reports, 6 (1), pp. 29286, 2016, ISSN: 2045-2322. @article{ptacnik_light-induced_2016, title = {A light-induced shortcut in the planktonic microbial loop}, author = {Robert Ptacnik and Ana Gomes and Sarah-Jeanne Royer and Stella A Berger and Albert Calbet and Jens C Nejstgaard and Josep M Gasol and Stamatina Isari and Stefanie D Moorthi and Radka Ptacnikova and Maren Striebel and Andrey F Sazhin and Tatiana M Tsagaraki and Soultana Zervoudaki and Kristi Altoja and Panagiotis D Dimitriou and Peeter Laas and Ayse Gazihan and Rodrigo A Martínez and Stefanie Schabhüttl and Ioulia Santi and Despoina Sousoni and Paraskevi Pitta}, url = {http://www.nature.com/articles/srep29286}, doi = {10.1038/srep29286}, issn = {2045-2322}, year = {2016}, date = {2016-07-01}, urldate = {2020-08-17}, journal = {Scientific Reports}, volume = {6}, number = {1}, pages = {29286}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2025 |
A, Collective Article New records of introduced species in the Mediterranean (August 2024) Journal Article Mediterranean Marine Science, 2025, ISSN: 1791-6763, 1108-393X. @article{A2025, title = {New records of introduced species in the Mediterranean (August 2024)}, author = {Collective Article A}, url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/34474 /wp-content/uploads/2025/06/2024-Christidis-MMS-51.pdf }, doi = {10.12681/mms.34474}, issn = {1791-6763, 1108-393X}, year = {2025}, date = {2025-06-04}, urldate = {2025-06-04}, journal = {Mediterranean Marine Science}, abstract = {New records of introduced species in the Mediterranean (August 2024) }, keywords = {}, pubstate = {published}, tppubtype = {article} } New records of introduced species in the Mediterranean (August 2024) |
Cascarano, Maria Chiara; Sevasti, Papadogiorgaki; Katharios, Pantelis Ultrastructural Insights Into a textitCandidatus Parilichlamydia sp. Infection of Gill Goblet Cells in Greater Amberjack Journal Article Journal of Fish Diseases, pp. e14146, 2025, ISSN: 0140-7775, 1365-2761. @article{cascarano_ultrastructural_2025, title = {Ultrastructural Insights Into a textitCandidatus Parilichlamydia sp. Infection of Gill Goblet Cells in Greater Amberjack}, author = {Maria Chiara Cascarano and Papadogiorgaki Sevasti and Pantelis Katharios}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jfd.14146 /wp-content/uploads/2025/05/2025-Cascarano-JFD-25.pdf}, doi = {10.1111/jfd.14146}, issn = {0140-7775, 1365-2761}, year = {2025}, date = {2025-05-28}, urldate = {2025-05-28}, journal = {Journal of Fish Diseases}, pages = {e14146}, abstract = {ABSTRACT Despite recent genomic studies and increased molecular data, epitheliocystis remains an enigmatic fish disease with no experimental in vitro or in vivo models to aid the advancement of research. In this study, we revert to a classical microscopical approach and screen with the electron microscope the epitheliocystis lesions caused by a Ca . Parilichlamydia sp., infecting mucus cells in Greater amberjack. We report distinct morphological features of this bacterial family, characterised by Intermediate Bodies that closely resemble those of previously described Candidatus similchlamydia , and Elementary Bodies that exhibit morphological similarities to Chlamydia trachomatis . We describe the characteristics of a novel Chlamydial Inclusion Membrane (IM) type, with abundant interdigitations, possibly shaped by fusion of the IM with cytoplasmic vesicles, and moreover discuss the presence of multivesicular bodies in the infected cell. Our observation of immune cells in the infected areas indicates an interaction of macrophages with infected cells, a role for granular cells as pathogens reservoirs and an active phagoptosis process in the nearby areas, overall shedding light on cellular immune processes characterising these infections in fish hosts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT Despite recent genomic studies and increased molecular data, epitheliocystis remains an enigmatic fish disease with no experimental in vitro or in vivo models to aid the advancement of research. In this study, we revert to a classical microscopical approach and screen with the electron microscope the epitheliocystis lesions caused by a Ca . Parilichlamydia sp., infecting mucus cells in Greater amberjack. We report distinct morphological features of this bacterial family, characterised by Intermediate Bodies that closely resemble those of previously described Candidatus similchlamydia , and Elementary Bodies that exhibit morphological similarities to Chlamydia trachomatis . We describe the characteristics of a novel Chlamydial Inclusion Membrane (IM) type, with abundant interdigitations, possibly shaped by fusion of the IM with cytoplasmic vesicles, and moreover discuss the presence of multivesicular bodies in the infected cell. Our observation of immune cells in the infected areas indicates an interaction of macrophages with infected cells, a role for granular cells as pathogens reservoirs and an active phagoptosis process in the nearby areas, overall shedding light on cellular immune processes characterising these infections in fish hosts. |
Siaperas, Romanos; Taxeidis, George; Gioti, Anastasia; Nikolaivits, Efstratios; Topakas, Evangelos Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification Journal Article Environmental Pollution, 376 , pp. 126386, 2025, ISSN: 02697491. @article{siaperas_multi-omics_2025, title = {Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification}, author = {Romanos Siaperas and George Taxeidis and Anastasia Gioti and Efstratios Nikolaivits and Evangelos Topakas}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749125007596 /wp-content/uploads/2025/05/2025-Siaperas-EnvPol-24.pdf}, doi = {10.1016/j.envpol.2025.126386}, issn = {02697491}, year = {2025}, date = {2025-05-22}, urldate = {2025-05-22}, journal = {Environmental Pollution}, volume = {376}, pages = {126386}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Díaz-Avello, Ulises G; Skouridou, Vasso; Shkembi, Xhensila; Reverté, Jaume; Mandalakis, Manolis; Peristeraki, Panagiota; Campàs, Mònica; O'Sullivan, Ciara K Aptamer-antibody sandwich lateral flow test for rapid visual detection of tetrodotoxin in pufferfish Journal Article Science of The Total Environment, 978 , pp. 179419, 2025, ISSN: 00489697. @article{diaz-avello_aptamer-antibody_2025, title = {Aptamer-antibody sandwich lateral flow test for rapid visual detection of tetrodotoxin in pufferfish}, author = {Ulises G Díaz-Avello and Vasso Skouridou and Xhensila Shkembi and Jaume Reverté and Manolis Mandalakis and Panagiota Peristeraki and Mònica Campàs and Ciara K O'Sullivan}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969725010563 /wp-content/uploads/2025/05/2025-Díaz-Avello-TTX_LFA-test-DRAFT-SUBMITTED-23.pdf}, doi = {10.1016/j.scitotenv.2025.179419}, issn = {00489697}, year = {2025}, date = {2025-05-20}, urldate = {2025-05-20}, journal = {Science of The Total Environment}, volume = {978}, pages = {179419}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ventriglia, Gianluca; Duncan, Neil; Giménez, Ignacio; Mylonas, Constantinos C; Pousis, Chrysovalentinos; Corriero, Aldo; Zupa, Rosa Spermatogenesis advancement in pre-pubertal meagre Argyrosomus regius treated with recombinant gonadotropins Journal Article Scientific Reports, 15 (1), pp. 15113, 2025, ISSN: 2045-2322. @article{ventriglia_spermatogenesis_2025, title = {Spermatogenesis advancement in pre-pubertal meagre Argyrosomus regius treated with recombinant gonadotropins}, author = {Gianluca Ventriglia and Neil Duncan and Ignacio Giménez and Constantinos C Mylonas and Chrysovalentinos Pousis and Aldo Corriero and Rosa Zupa}, url = {https://www.nature.com/articles/s41598-025-99372-3 /wp-content/uploads/2025/05/2025-Ventriglia-SciRep-22.pdf}, doi = {10.1038/s41598-025-99372-3}, issn = {2045-2322}, year = {2025}, date = {2025-05-13}, urldate = {2025-05-13}, journal = {Scientific Reports}, volume = {15}, number = {1}, pages = {15113}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Papadaki, Maria; Le, Ngoc-Son; Mylonas, Constantinos C; Sarropoulou, Elena Marine Biotechnology, 27 (2), pp. 74, 2025, ISSN: 1436-2228, 1436-2236. @article{papadaki_exploring_2025, title = {Exploring the Fanconi Anemia Gene Expression and Regulation by MicroRNAs in Gilthead Seabream (Sparus aurata) at Different Gonadal Development Stages}, author = {Maria Papadaki and Ngoc-Son Le and Constantinos C Mylonas and Elena Sarropoulou}, url = {https://link.springer.com/10.1007/s10126-025-10444-x /wp-content/uploads/2025/05/2025-Papadaki-MarBioteck-21.pdf}, doi = {10.1007/s10126-025-10444-x}, issn = {1436-2228, 1436-2236}, year = {2025}, date = {2025-05-06}, urldate = {2025-05-06}, journal = {Marine Biotechnology}, volume = {27}, number = {2}, pages = {74}, abstract = {Abstract Fanconi anaemia (FA) is a rare autosomal recessive disease in humans that is distributed worldwide. Fanconi anemia complementation (Fanc) proteins are essential for the appropriate functioning of the FA DNA repair pathway. They are also linked to a number of other biological processes, including oxygen metabolism, cell cycle regulation, haematopoiesis and apoptosis. So far, little research has been conducted on teleosts, but evidence shows that Fanc proteins play a significant role in immune response and sex reversal. For the examination of the expression of three fanc genes ( fancc , fancl, and fancd2 ), as well as the potential regulation of these genes by microRNAs (miRNAs) in gonadal tissues at different stages of development, the present study has selected the gilthead seabream ( Sparus aurata ), a significant aquaculture species that exhibits protandrous hermaphroditism. The obtained data suggested the role of fancl and fancd2 in the maturation of female gonads and the miRNAs miR-210, miR-217 and miR-10926 have been identified as putative regulators of fancd2 , fancc and fancl , respectively. Overall, the data indicated the potential use of fancl and fancd2 genes as sex biomarkers in conjunction with their respective regulation by miRNAs. To the best of our knowledge, this is the first study demonstrating the importance of fanc genes, along with putative regulatory miRNAs, in the reproduction of an important marine aquaculture species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Fanconi anaemia (FA) is a rare autosomal recessive disease in humans that is distributed worldwide. Fanconi anemia complementation (Fanc) proteins are essential for the appropriate functioning of the FA DNA repair pathway. They are also linked to a number of other biological processes, including oxygen metabolism, cell cycle regulation, haematopoiesis and apoptosis. So far, little research has been conducted on teleosts, but evidence shows that Fanc proteins play a significant role in immune response and sex reversal. For the examination of the expression of three fanc genes ( fancc , fancl, and fancd2 ), as well as the potential regulation of these genes by microRNAs (miRNAs) in gonadal tissues at different stages of development, the present study has selected the gilthead seabream ( Sparus aurata ), a significant aquaculture species that exhibits protandrous hermaphroditism. The obtained data suggested the role of fancl and fancd2 in the maturation of female gonads and the miRNAs miR-210, miR-217 and miR-10926 have been identified as putative regulators of fancd2 , fancc and fancl , respectively. Overall, the data indicated the potential use of fancl and fancd2 genes as sex biomarkers in conjunction with their respective regulation by miRNAs. To the best of our knowledge, this is the first study demonstrating the importance of fanc genes, along with putative regulatory miRNAs, in the reproduction of an important marine aquaculture species. |
Thieme, Philipp; Fischbach, Vivian; Papadakis, Ioannis; Moritz, Timo Development of convergent adaptations reveal highly conserved early ontogenetic skull shape in fishes with amphibious vision Journal Article Scientific Reports, 15 (1), pp. 8411, 2025, ISSN: 2045-2322. @article{thieme_development_2025, title = {Development of convergent adaptations reveal highly conserved early ontogenetic skull shape in fishes with amphibious vision}, author = {Philipp Thieme and Vivian Fischbach and Ioannis Papadakis and Timo Moritz}, url = {https://www.nature.com/articles/s41598-025-91563-2 /wp-content/uploads/2025/04/2025-Thieme-SR-20.pdf}, doi = {10.1038/s41598-025-91563-2}, issn = {2045-2322}, year = {2025}, date = {2025-04-28}, urldate = {2025-04-28}, journal = {Scientific Reports}, volume = {15}, number = {1}, pages = {8411}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kapelonis, Zacharias; Chatzigeorgiou, Georgios; Ntoumas, Manolis; Grigoriou, Panos; Pettas, Manos; Michelinakis, Spyros; Correia, Ricardo; Lemos, Catarina Rasquilha; Pinheiro, Luis Menezes; Lomba, Caio; Fortuna, João; Loureiro, Rui; Santos, André; Chatzinikolaou, Eva Flying Robots Teach Floating Robots—A Machine Learning Approach for Marine Habitat Mapping Based on Combined Datasets Journal Article Journal of Marine Science and Engineering, 13 (3), pp. 611, 2025, ISSN: 2077-1312. @article{kapelonis_flying_2025, title = {Flying Robots Teach Floating Robots—A Machine Learning Approach for Marine Habitat Mapping Based on Combined Datasets}, author = {Zacharias Kapelonis and Georgios Chatzigeorgiou and Manolis Ntoumas and Panos Grigoriou and Manos Pettas and Spyros Michelinakis and Ricardo Correia and Catarina Rasquilha Lemos and Luis Menezes Pinheiro and Caio Lomba and João Fortuna and Rui Loureiro and André Santos and Eva Chatzinikolaou}, url = {https://www.mdpi.com/2077-1312/13/3/611 /wp-content/uploads/2025/04/2025-Kapelonis-Mar-Sci-Eng-19.pdf}, doi = {10.3390/jmse13030611}, issn = {2077-1312}, year = {2025}, date = {2025-04-11}, urldate = {2025-04-11}, journal = {Journal of Marine Science and Engineering}, volume = {13}, number = {3}, pages = {611}, abstract = {Unmanned aerial and autonomous surface vehicles (UAVs and ASVs, respectively) are two emerging technologies for the mapping of coastal and marine environments. Using UAV photogrammetry, the sea-bottom composition can be resolved with very high fidelity in shallow waters. At greater depths, acoustic methodologies have far better propagation properties compared to optics; therefore, ASVs equipped with multibeam echosounders (MBES) are better-suited for mapping applications in deeper waters. In this work, a sea-bottom classification methodology is presented for mapping the protected habitat of Mediterranean seagrass Posidonia oceanica (habitat code 1120) in a coastal subregion of Heraklion (Crete, Greece). The methodology implements a machine learning scheme, where knowledge obtained from UAV imagery is embedded (through training) into a classifier that utilizes acoustic backscatter intensity and features derived from the MBES data provided by an ASV. Accuracy and precision scores of greater than 85% compared with visual census ground-truth data for both optical and acoustic classifiers indicate that this hybrid mapping approach is promising to mitigate the depth-induced bias in UAV-only models. The latter is especially interesting in cases where the studied habitat boundaries extend beyond depths that can be studied via aerial devices’ optics, as is the case with P. oceanica meadows.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Unmanned aerial and autonomous surface vehicles (UAVs and ASVs, respectively) are two emerging technologies for the mapping of coastal and marine environments. Using UAV photogrammetry, the sea-bottom composition can be resolved with very high fidelity in shallow waters. At greater depths, acoustic methodologies have far better propagation properties compared to optics; therefore, ASVs equipped with multibeam echosounders (MBES) are better-suited for mapping applications in deeper waters. In this work, a sea-bottom classification methodology is presented for mapping the protected habitat of Mediterranean seagrass Posidonia oceanica (habitat code 1120) in a coastal subregion of Heraklion (Crete, Greece). The methodology implements a machine learning scheme, where knowledge obtained from UAV imagery is embedded (through training) into a classifier that utilizes acoustic backscatter intensity and features derived from the MBES data provided by an ASV. Accuracy and precision scores of greater than 85% compared with visual census ground-truth data for both optical and acoustic classifiers indicate that this hybrid mapping approach is promising to mitigate the depth-induced bias in UAV-only models. The latter is especially interesting in cases where the studied habitat boundaries extend beyond depths that can be studied via aerial devices’ optics, as is the case with P. oceanica meadows. |
Mukiibi, Robert; Ferraresso, Serena; Franch, Rafaella; Peruzza, Luca; Rovere, Giulia Dalla; Babbucci, Massimiliano; Bertotto, Daniela; Toffan, Anna; Pascoli, Francesco; Faggion, Sara; Peñaloza, Carolina; Tsigenopoulos, Costas S; Houston, Ross D; Bargelloni, Luca; Robledo, Diego Integrated functional genomic analysis identifies regulatory variants underlying a major QTL for disease resistance in European sea bass Journal Article BMC Biology, 23 (1), pp. 75, 2025, ISSN: 1741-7007. @article{mukiibi_integrated_2025, title = {Integrated functional genomic analysis identifies regulatory variants underlying a major QTL for disease resistance in European sea bass}, author = {Robert Mukiibi and Serena Ferraresso and Rafaella Franch and Luca Peruzza and Giulia Dalla Rovere and Massimiliano Babbucci and Daniela Bertotto and Anna Toffan and Francesco Pascoli and Sara Faggion and Carolina Peñaloza and Costas S Tsigenopoulos and Ross D Houston and Luca Bargelloni and Diego Robledo}, url = {https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-025-02180-4 /wp-content/uploads/2025/04/2025-Mukiibi-BMC-Biology-18.pdf}, doi = {10.1186/s12915-025-02180-4}, issn = {1741-7007}, year = {2025}, date = {2025-04-07}, urldate = {2025-04-07}, journal = {BMC Biology}, volume = {23}, number = {1}, pages = {75}, abstract = {Abstract Background Viral nervous necrosis (VNN) is an important viral disease threatening global aquaculture sustainability and affecting over 50 farmed and ecologically important fish species. A major QTL for resistance to VNN has been previously detected in European sea bass, but the underlying causal gene(s) and mutation(s) remain unknown. To identify the mechanisms and genetic factors underpinning resistance to VNN in European sea bass, we employed integrative analyses of multiple functional genomics assays in European sea bass. Results The estimated heritability of VNN resistance was high ( h 2 textasciitilde 0.40), and a major QTL explaining up to 38% of the genetic variance of the trait was confirmed on chromosome 3, with individuals with the resistant QTL genotype showing a 90% survivability against a VNN outbreak. Whole-genome resequencing analyses narrowed the location of this QTL to a small region containing 4 copies of interferon alpha inducible protein 27-like 2A ( IFI27L2A ) genes, and one copy of the interferon alpha inducible protein 27-like 2 ( IFI27L2 ) gene. RNA sequencing revealed a clear association between the QTL genotype and the expression of two of the IFI27L2A genes, and the IFI27L2 gene. Integration with chromatin accessibility and histone modification data pinpointed two SNPs in active regulatory regions of two of these genes ( IFI27L2A and IFI27L2 ), and transcription factor binding site gains for the resistant alleles were predicted. These alleles, particularly the SNP variant CHR3:10,077,301, exhibited higher frequencies (0.55 to 0.77) in Eastern Mediterranean Sea bass populations, which show considerably higher levels of resistance to VNN, as compared to susceptible West Mediterranean and Atlantic populations (0.15–0.25). Conclusions The SNP variant CHR3:10,077,301, through modulation of IFI27L2 and IFI27L2A genes, is likely the causative mutation underlying resistance to VNN in European sea bass. This is one of the first causative mutations discovered for disease resistance traits in fish and paves the way for marker-assisted selection as well as biotechnological approaches to enhance resistance to VNN in European sea bass and other susceptible species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background Viral nervous necrosis (VNN) is an important viral disease threatening global aquaculture sustainability and affecting over 50 farmed and ecologically important fish species. A major QTL for resistance to VNN has been previously detected in European sea bass, but the underlying causal gene(s) and mutation(s) remain unknown. To identify the mechanisms and genetic factors underpinning resistance to VNN in European sea bass, we employed integrative analyses of multiple functional genomics assays in European sea bass. Results The estimated heritability of VNN resistance was high ( h 2 textasciitilde 0.40), and a major QTL explaining up to 38% of the genetic variance of the trait was confirmed on chromosome 3, with individuals with the resistant QTL genotype showing a 90% survivability against a VNN outbreak. Whole-genome resequencing analyses narrowed the location of this QTL to a small region containing 4 copies of interferon alpha inducible protein 27-like 2A ( IFI27L2A ) genes, and one copy of the interferon alpha inducible protein 27-like 2 ( IFI27L2 ) gene. RNA sequencing revealed a clear association between the QTL genotype and the expression of two of the IFI27L2A genes, and the IFI27L2 gene. Integration with chromatin accessibility and histone modification data pinpointed two SNPs in active regulatory regions of two of these genes ( IFI27L2A and IFI27L2 ), and transcription factor binding site gains for the resistant alleles were predicted. These alleles, particularly the SNP variant CHR3:10,077,301, exhibited higher frequencies (0.55 to 0.77) in Eastern Mediterranean Sea bass populations, which show considerably higher levels of resistance to VNN, as compared to susceptible West Mediterranean and Atlantic populations (0.15–0.25). Conclusions The SNP variant CHR3:10,077,301, through modulation of IFI27L2 and IFI27L2A genes, is likely the causative mutation underlying resistance to VNN in European sea bass. This is one of the first causative mutations discovered for disease resistance traits in fish and paves the way for marker-assisted selection as well as biotechnological approaches to enhance resistance to VNN in European sea bass and other susceptible species. |
Wei, Xiao-Lei; Hao, Zhi-Wei; Kotzamanis, Yannis P; Zhang, Tian-Hua; Liu, Zhi-Bo; Yang, Hong; Luo, Zhi Aquaculture Reports, 42 , pp. 102739, 2025, ISSN: 23525134. @article{wei_dietary_2025, title = {Dietary iron oxide (Fe2O3) nanoparticles modulate growth performance, body composition, mineral content and intestinal health of yellow catfish juveniles (Pelteobagrus fulvidraco)}, author = {Xiao-Lei Wei and Zhi-Wei Hao and Yannis P Kotzamanis and Tian-Hua Zhang and Zhi-Bo Liu and Hong Yang and Zhi Luo}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2352513425001255 /wp-content/uploads/2025/03/2025-Wei-AquaReports-16.pdf}, doi = {10.1016/j.aqrep.2025.102739}, issn = {23525134}, year = {2025}, date = {2025-03-31}, urldate = {2025-03-31}, journal = {Aquaculture Reports}, volume = {42}, pages = {102739}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Antoniou, Theodora; Dimitriou, Andreas C; Karameta, Emmanouela; Antoniou, Aglaia; Poulakakis, Nikos; Sfenthourakis, Spyros Comparative phylogeography of four lizard taxa within an oceanic island Journal Article Molecular Phylogenetics and Evolution, 205 , pp. 108295, 2025, ISSN: 10557903. @article{antoniou_comparative_2025, title = {Comparative phylogeography of four lizard taxa within an oceanic island}, author = {Theodora Antoniou and Andreas C Dimitriou and Emmanouela Karameta and Aglaia Antoniou and Nikos Poulakakis and Spyros Sfenthourakis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1055790325000120 /wp-content/uploads/2025/03/2025-Antoniou-CompPhylo-pre-print-15.pdf}, doi = {10.1016/j.ympev.2025.108295}, issn = {10557903}, year = {2025}, date = {2025-03-24}, urldate = {2025-03-24}, journal = {Molecular Phylogenetics and Evolution}, volume = {205}, pages = {108295}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Droubogiannis, Stavros; Katharios, Pantelis Phage Therapy in Aquaculture Incollection Elumalai, Preetham; Lakshmi, Sreeja (Ed.): Antimicrobial Resistance in Aquaculture and Aquatic Environments, pp. 229–255, Springer Nature Singapore, Singapore, 2025, ISBN: 9789819773190 9789819773206. @incollection{elumalai_phage_2025, title = {Phage Therapy in Aquaculture}, author = {Stavros Droubogiannis and Pantelis Katharios}, editor = {Preetham Elumalai and Sreeja Lakshmi}, url = {https://link.springer.com/10.1007/978-981-97-7320-6_10 /wp-content/uploads/2025/03/2025-Droumbogiannis-and-Katharios-phage-therapy-in-aquaculture-pre-print-14.pdf}, doi = {10.1007/978-981-97-7320-6_10}, isbn = {9789819773190 9789819773206}, year = {2025}, date = {2025-03-20}, urldate = {2025-03-20}, booktitle = {Antimicrobial Resistance in Aquaculture and Aquatic Environments}, pages = {229--255}, publisher = {Springer Nature Singapore}, address = {Singapore}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Chalmoukis, Charalampos; Droubogiannis, Stavros; Michalopoulou, Vassiliki A; Triga, Adriana; Sarris, Panagiotis F; Katharios, Pantelis Pathogens, 14 (3), pp. 247, 2025, ISSN: 2076-0817. @article{chalmoukis_development_2025, title = {Development and Characterization of Fluorescent Protein-Tagged Vibrio harveyi Strains as a Versatile Tool for Studying Infection Dynamics and Strain Interactions}, author = {Charalampos Chalmoukis and Stavros Droubogiannis and Vassiliki A Michalopoulou and Adriana Triga and Panagiotis F Sarris and Pantelis Katharios}, url = {https://www.mdpi.com/2076-0817/14/3/247 /wp-content/uploads/2025/03/2025-Chalmoukis-pathogens-13.pdf}, doi = {10.3390/pathogens14030247}, issn = {2076-0817}, year = {2025}, date = {2025-03-18}, urldate = {2025-03-18}, journal = {Pathogens}, volume = {14}, number = {3}, pages = {247}, abstract = {Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using triparental mating and evaluated for phenotypic, genomic, and virulence attributes. Genomic analyses revealed strain-specific variations, including mutations in key regulatory and metabolic genes, such as luxO and transketolase. While plasmid acquisition imposed metabolic costs, resulting in altered growth and antibiotic sensitivities in certain transconjugants, others demonstrated robust phenotypic stability. Virulence assays using gilthead seabream larvae revealed that most tagged strains retained moderate pathogenicity, with visualization of co-infections highlighting the potential for studying strain-specific interactions. Furthermore, fluorescent microscopy confirmed the successful colonization and localization of tagged bacteria within host tissues. These findings underscore the utility of GFP- and RFP-tagged Vibrio harveyi as versatile tools for infection dynamics, offering a foundation for future research on strain interactions and pathogen-host relationships.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using triparental mating and evaluated for phenotypic, genomic, and virulence attributes. Genomic analyses revealed strain-specific variations, including mutations in key regulatory and metabolic genes, such as luxO and transketolase. While plasmid acquisition imposed metabolic costs, resulting in altered growth and antibiotic sensitivities in certain transconjugants, others demonstrated robust phenotypic stability. Virulence assays using gilthead seabream larvae revealed that most tagged strains retained moderate pathogenicity, with visualization of co-infections highlighting the potential for studying strain-specific interactions. Furthermore, fluorescent microscopy confirmed the successful colonization and localization of tagged bacteria within host tissues. These findings underscore the utility of GFP- and RFP-tagged Vibrio harveyi as versatile tools for infection dynamics, offering a foundation for future research on strain interactions and pathogen-host relationships. |
Costanzo, Di F; Marsico, Di M; Orefice, I; Kristoffersen, J B; Kasapidis, P; Chaumier, T; Ambrosino, L; Miralto, M; Cigliano, Aiese R; Verret, F; Tirichine, L; Trindade, M; Zyl, Van L; Dato, Di V; Romano, G High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida) Journal Article Scientific Data, 12 (1), pp. 310, 2025, ISSN: 2052-4463. @article{di_costanzo_high-quality_2025, title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida)}, author = {F Di Costanzo and M Di Marsico and I Orefice and J B Kristoffersen and P Kasapidis and T Chaumier and L Ambrosino and M Miralto and R Aiese Cigliano and F Verret and L Tirichine and M Trindade and L Van Zyl and V Di Dato and G Romano}, url = {https://www.nature.com/articles/s41597-025-04634-4 /wp-content/uploads/2025/03/2025-Costanzo-SciData-12.pdf}, doi = {10.1038/s41597-025-04634-4}, issn = {2052-4463}, year = {2025}, date = {2025-03-14}, urldate = {2025-03-14}, journal = {Scientific Data}, volume = {12}, number = {1}, pages = {310}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, Elena; Katharios, Pantelis; Kaitetzidou, Elisavet; Scapigliati, Giuseppe; Miccoli, Andrea Circulating miRNAs involved in the immune response of the European seabass (Dicentrarchus labrax) Journal Article Fish & Shellfish Immunology, 160 , pp. 110232, 2025, ISSN: 10504648. @article{sarropoulou_circulating_2025, title = {Circulating miRNAs involved in the immune response of the European seabass (Dicentrarchus labrax)}, author = {Elena Sarropoulou and Pantelis Katharios and Elisavet Kaitetzidou and Giuseppe Scapigliati and Andrea Miccoli}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1050464825001214 /wp-content/uploads/2025/03/2025-Sarropoulou-FishShelImm-11.pdf}, doi = {10.1016/j.fsi.2025.110232}, issn = {10504648}, year = {2025}, date = {2025-03-10}, urldate = {2025-03-11}, journal = {Fish & Shellfish Immunology}, volume = {160}, pages = {110232}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Katharios, Pantelis; Karageorgou, Evangelia Protozoan Co‐Infection Drives Fish Mortality Event in Crete's Karteros River Journal Article Journal of Fish Diseases, pp. e14099, 2025, ISSN: 0140-7775, 1365-2761. @article{katharios_protozoan_2025, title = {Protozoan Co‐Infection Drives Fish Mortality Event in Crete's Karteros River}, author = {Pantelis Katharios and Evangelia Karageorgou}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jfd.14099 /wp-content/uploads/2025/03/2025-Katharios-JFD-10.pdf}, doi = {10.1111/jfd.14099}, issn = {0140-7775, 1365-2761}, year = {2025}, date = {2025-03-07}, urldate = {2025-03-10}, journal = {Journal of Fish Diseases}, pages = {e14099}, abstract = {ABSTRACT In August 2024, a significant fish kill involving hundreds of flathead grey mullet (\textit{Mugil cephalus} ) was reported in the delta region of the Karteros River, Crete, Greece. The investigation identified the primary cause of mortality as severe parasitic infections, specifically from the protozoan parasites Amyloodinium ocellatum and Trichodina sp., both of which heavily affected the gills of the fish. Concurrently, poor water quality in the area, likely due to reduced water volume and limited water renewal, created favourable conditions for parasite proliferation while weakening the fish's natural defences. This event raised concerns due to the location of the fish kill in the Karteros River delta, a highly protected area designated as a small island wetland.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT In August 2024, a significant fish kill involving hundreds of flathead grey mullet (Mugil cephalus ) was reported in the delta region of the Karteros River, Crete, Greece. The investigation identified the primary cause of mortality as severe parasitic infections, specifically from the protozoan parasites Amyloodinium ocellatum and Trichodina sp., both of which heavily affected the gills of the fish. Concurrently, poor water quality in the area, likely due to reduced water volume and limited water renewal, created favourable conditions for parasite proliferation while weakening the fish's natural defences. This event raised concerns due to the location of the fish kill in the Karteros River delta, a highly protected area designated as a small island wetland. |
Brecko, Jonathan; Mathys, Aurore; Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Blettery, Jonathan; Green, Laura; Musson, Alicia; Paton, Alan; Phillips, Sarah; Bastir, Markus; Wiltschke, Karin; Rainer, Heimo; Kroh, Andreas; Haston, Elspeth; Semal, Patrick DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections Journal Article European Journal of Taxonomy, 976 , 2025, ISSN: 2118-9773. @article{brecko_digit-key_2025, title = {DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections}, author = {Jonathan Brecko and Aurore Mathys and Eva Chatzinikolaou and Kleoniki Keklikoglou and Jonathan Blettery and Laura Green and Alicia Musson and Alan Paton and Sarah Phillips and Markus Bastir and Karin Wiltschke and Heimo Rainer and Andreas Kroh and Elspeth Haston and Patrick Semal}, url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2797 /wp-content/uploads/2025/03/2025-Brecko-EuJTax-9.pdf}, doi = {10.5852/ejt.2025.976.2797}, issn = {2118-9773}, year = {2025}, date = {2025-03-04}, urldate = {2025-03-04}, journal = {European Journal of Taxonomy}, volume = {976}, abstract = {Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access. |
Grigorakis, Kriton; Kogiannou, Dimitra; Kotsiri, Mado; Kleidas, Ioannis; Mello, Paulo De H; Habiballah, Salaheldeen; Alshaikhi, Ali; Alhafedh, Youssef S; Mohamed, Asaad H W Freshness and Spoilage Patterns of Wild and Farmed Tropical Fish Species with Major Commercial Importance Originating from Saudi Arabian Waters Journal Article Foods, 14 (4), pp. 690, 2025, ISSN: 2304-8158. @article{grigorakis_freshness_2025, title = {Freshness and Spoilage Patterns of Wild and Farmed Tropical Fish Species with Major Commercial Importance Originating from Saudi Arabian Waters}, author = {Kriton Grigorakis and Dimitra Kogiannou and Mado Kotsiri and Ioannis Kleidas and Paulo H De Mello and Salaheldeen Habiballah and Ali Alshaikhi and Youssef S Alhafedh and Asaad H W Mohamed}, url = {https://www.mdpi.com/2304-8158/14/4/690 /wp-content/uploads/2025/02/2025-Grigorakis-foods-8.pdf}, doi = {10.3390/foods14040690}, issn = {2304-8158}, year = {2025}, date = {2025-02-24}, urldate = {2025-02-24}, journal = {Foods}, volume = {14}, number = {4}, pages = {690}, abstract = {Ice-stored farmed barramundi (Lates calcarifer), snubnose pompano (Trachinotus blochii) and sobaity bream (Sparidentex hasta), as well as wild-caught cobia (Rachycentron canadum), coral trout (Plectropomus leopardus), giant trevally (Caranx ignobilis), milkfish (Chanos chanos) and mangrove red snapper (Lutjanus argentimaculatus), were compared for their freshness/spoilage using sensory, chemical and microbiological methods. Quality Index Method schemes were developed to determine alterations in the sensory freshness. The shelf lives ranged from 8 (coral trout) to 18 days (sobaity bream). The farmed species always exhibited a significantly longer shelf life than the wild-caught species. The adenosine triphosphate (ATP) breakdown followed different patterns in the studied species. The K-values at the time of sensory rejection ranged from 30 to 80% depending on the species, while the microbial load reached or exceeded a level of 6 log cfu/g. Although the shelf life duration was dependent on the origin of the fish (wild or farmed), the ATP breakdown scheme, as well as the K-values and microbial loads at the time of rejection, were species-dependent and independent of the origin.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ice-stored farmed barramundi (Lates calcarifer), snubnose pompano (Trachinotus blochii) and sobaity bream (Sparidentex hasta), as well as wild-caught cobia (Rachycentron canadum), coral trout (Plectropomus leopardus), giant trevally (Caranx ignobilis), milkfish (Chanos chanos) and mangrove red snapper (Lutjanus argentimaculatus), were compared for their freshness/spoilage using sensory, chemical and microbiological methods. Quality Index Method schemes were developed to determine alterations in the sensory freshness. The shelf lives ranged from 8 (coral trout) to 18 days (sobaity bream). The farmed species always exhibited a significantly longer shelf life than the wild-caught species. The adenosine triphosphate (ATP) breakdown followed different patterns in the studied species. The K-values at the time of sensory rejection ranged from 30 to 80% depending on the species, while the microbial load reached or exceeded a level of 6 log cfu/g. Although the shelf life duration was dependent on the origin of the fish (wild or farmed), the ATP breakdown scheme, as well as the K-values and microbial loads at the time of rejection, were species-dependent and independent of the origin. |
Carlot, J; Galobart, C; Gómez-Gras, D; Santamaría, J; Golo, R; Sini, M; Cebrian, E; Gerovasileiou, V; Ponti, M; Turicchia, E; Comeau, S; Rilov, G; Tamburello, L; Mantas, Pulido T; Cerrano, C; Ledoux, J B; Gattuso, J -P; Ramirez-Calero, S; Millan, L; Montefalcone, M; Katsanevakis, S; Bensoussan, N; Garrabou, J; Teixidó, N Vulnerability of benthic trait diversity across the Mediterranean Sea following mass mortality events Journal Article Nature Communications, 16 (1), pp. 1571, 2025, ISSN: 2041-1723. @article{carlot_vulnerability_2025, title = {Vulnerability of benthic trait diversity across the Mediterranean Sea following mass mortality events}, author = {J Carlot and C Galobart and D Gómez-Gras and J Santamaría and R Golo and M Sini and E Cebrian and V Gerovasileiou and M Ponti and E Turicchia and S Comeau and G Rilov and L Tamburello and T Pulido Mantas and C Cerrano and J B Ledoux and J -P Gattuso and S Ramirez-Calero and L Millan and M Montefalcone and S Katsanevakis and N Bensoussan and J Garrabou and N Teixidó}, url = {https://www.nature.com/articles/s41467-025-55949-0 /wp-content/uploads/2025/02/2025-Carlot-Nat-Comm-7.pdf}, doi = {10.1038/s41467-025-55949-0}, issn = {2041-1723}, year = {2025}, date = {2025-02-21}, urldate = {2025-02-20}, journal = {Nature Communications}, volume = {16}, number = {1}, pages = {1571}, abstract = {Abstract Unraveling the functional future of marine ecosystems amid global change poses a pressing challenge. This is particularly critical in the Mediterranean Sea, which is highly impacted by global and local drivers. Utilizing extensive mass mortality events (MMEs) datasets spanning from 1986 to 2020 across the Mediterranean Sea, we investigated the trait vulnerability of benthic species that suffered from MMEs induced by nine distinct mortality drivers. By analyzing changes in ten ecological traits across 389 benthic species—constituting an extensive compendium of Mediterranean ecological traits to date—we identified 228 functional entities (FEs), defined as groups of species sharing the same trait values. Our findings indicate that of these 55 FEs were impacted by MMEs, accentuating a heightened vulnerability within specific trait categories. Notably, more than half of the mortality records showed severe impacts on calcifying and larger species with slower growth which mostly account for tree-like and massive forms. Altogether, we highlight that 29 FEs suffered extreme mortality, leading to a maximum increase of 19.1% of the global trait volume vulnerability over 35 years. We also reveal that 10.8% of the trait volume may have been temporarily lost over the last five years, emphasizing the risk of a rapid ecological transformation in the Mediterranean Sea.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Unraveling the functional future of marine ecosystems amid global change poses a pressing challenge. This is particularly critical in the Mediterranean Sea, which is highly impacted by global and local drivers. Utilizing extensive mass mortality events (MMEs) datasets spanning from 1986 to 2020 across the Mediterranean Sea, we investigated the trait vulnerability of benthic species that suffered from MMEs induced by nine distinct mortality drivers. By analyzing changes in ten ecological traits across 389 benthic species—constituting an extensive compendium of Mediterranean ecological traits to date—we identified 228 functional entities (FEs), defined as groups of species sharing the same trait values. Our findings indicate that of these 55 FEs were impacted by MMEs, accentuating a heightened vulnerability within specific trait categories. Notably, more than half of the mortality records showed severe impacts on calcifying and larger species with slower growth which mostly account for tree-like and massive forms. Altogether, we highlight that 29 FEs suffered extreme mortality, leading to a maximum increase of 19.1% of the global trait volume vulnerability over 35 years. We also reveal that 10.8% of the trait volume may have been temporarily lost over the last five years, emphasizing the risk of a rapid ecological transformation in the Mediterranean Sea. |
Daraghmeh, Nauras; Exter, Katrina; Pagnier, Justine; Balazy, Piotr; Cancio, Ibon; Chatzigeorgiou, Giorgos; Chatzinikolaou, Eva; Chelchowski, Maciej; Chrismas, Nathan Alexis Mitchell; Comtet, Thierry; Dailianis, Thanos; Deneudt, Klaas; Cerio, Oihane Diaz De; Digenis, Markos; Gerovasileiou, Vasilis; González, José; Kauppi, Laura; Kristoffersen, Jon Bent; Kukliński, Piotr; Lasota, Rafał; Levy, Liraz; Małachowicz, Magdalena; Mavrič, Borut; Mortelmans, Jonas; Paredes, Estefania; Poćwierz‐Kotus, Anita; Reiss, Henning; Santi, Ioulia; Sarafidou, Georgia; Skouradakis, Grigorios; Solbakken, Jostein; Staehr, Peter A U; Tajadura, Javier; Thyrring, Jakob; Troncoso, Jesus S; Vernadou, Emmanouela; Viard, Frederique; Zafeiropoulos, Haris; Zbawicka, Małgorzata; Pavloudi, Christina; Obst, Matthias A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020 Journal Article Molecular Ecology Resources, pp. e14073, 2025, ISSN: 1755-098X, 1755-0998. @article{daraghmeh_longterm_2025, title = {A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020}, author = {Nauras Daraghmeh and Katrina Exter and Justine Pagnier and Piotr Balazy and Ibon Cancio and Giorgos Chatzigeorgiou and Eva Chatzinikolaou and Maciej Chelchowski and Nathan Alexis Mitchell Chrismas and Thierry Comtet and Thanos Dailianis and Klaas Deneudt and Oihane Diaz De Cerio and Markos Digenis and Vasilis Gerovasileiou and José González and Laura Kauppi and Jon Bent Kristoffersen and Piotr Kukliński and Rafał Lasota and Liraz Levy and Magdalena Małachowicz and Borut Mavrič and Jonas Mortelmans and Estefania Paredes and Anita Poćwierz‐Kotus and Henning Reiss and Ioulia Santi and Georgia Sarafidou and Grigorios Skouradakis and Jostein Solbakken and Peter A U Staehr and Javier Tajadura and Jakob Thyrring and Jesus S Troncoso and Emmanouela Vernadou and Frederique Viard and Haris Zafeiropoulos and Małgorzata Zbawicka and Christina Pavloudi and Matthias Obst}, url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.14073 /wp-content/uploads/2025/02/2025-Daraghmeh-MolEcoRes-6.pdf}, doi = {10.1111/1755-0998.14073}, issn = {1755-098X, 1755-0998}, year = {2025}, date = {2025-02-05}, urldate = {2025-02-05}, journal = {Molecular Ecology Resources}, pages = {e14073}, abstract = {ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to textasciitilde5500 amplicon sequence variants and textasciitilde1800 operational taxonomic units, and up to textasciitilde250 and textasciitilde50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols. |
Chen, I-Hao; Georgopoulou, Dimitra G; Ebbesson, Lars O E; Voskakis, Dimitris; Munthe-Kaas, Antonella Zanna; Papandroulakis, Nikos Acoustic tags versus camera—a case study on feeding behaviour of European seabass in sea cages Journal Article Frontiers in Marine Science, 11 , pp. 1497336, 2025, ISSN: 2296-7745. @article{chen_acoustic_2025, title = {Acoustic tags versus camera—a case study on feeding behaviour of European seabass in sea cages}, author = {I-Hao Chen and Dimitra G Georgopoulou and Lars O E Ebbesson and Dimitris Voskakis and Antonella Zanna Munthe-Kaas and Nikos Papandroulakis}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2024.1497336/full https://imbbc.hcmr.gr/wp-content/uploads/2025/01/2025-Chen-fmars-5.pdf}, doi = {10.3389/fmars.2024.1497336}, issn = {2296-7745}, year = {2025}, date = {2025-01-30}, urldate = {2025-01-30}, journal = {Frontiers in Marine Science}, volume = {11}, pages = {1497336}, abstract = {Intoduction With the expansion of the aquaculture industry, the need arises for scalable, reliable, and robust methods to assess fish behaviour in sea cages to guide operational management, which includes feeding optimisation and welfare assessments. Fish cage monitoring utilising either acoustic transmitters or underwater cameras is well-studied. However, the relationship between those two different measurement types seems to have not been explored, nor have they been evaluated together in one experimental site. Methods In our 1-month study, we compared the activity of 14 sentinel fish and the artificial intelligence (AI)-inferred speed of individuals from the European seabass ( Dicentrarchus labrax ) sea cage population in three feeding trials. Comparisons include a maximum activity comparison using persistent peaks, fish behavioural pattern establishment and retention, and periodical behavioural patterns. Results Our results demonstrate that under certain circumstances, both technologies are interchangeable from the perspective of persistent peaks and periodicity, but complementary when it comes to behaviour analysis such as food anticipatory behaviour (FAB). Discussion We anticipate that our findings will stimulate advances where multiple sensor types are in use to achieve a more holistic understanding of fish behaviour in the aquaculture sector using underwater technologies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intoduction With the expansion of the aquaculture industry, the need arises for scalable, reliable, and robust methods to assess fish behaviour in sea cages to guide operational management, which includes feeding optimisation and welfare assessments. Fish cage monitoring utilising either acoustic transmitters or underwater cameras is well-studied. However, the relationship between those two different measurement types seems to have not been explored, nor have they been evaluated together in one experimental site. Methods In our 1-month study, we compared the activity of 14 sentinel fish and the artificial intelligence (AI)-inferred speed of individuals from the European seabass ( Dicentrarchus labrax ) sea cage population in three feeding trials. Comparisons include a maximum activity comparison using persistent peaks, fish behavioural pattern establishment and retention, and periodical behavioural patterns. Results Our results demonstrate that under certain circumstances, both technologies are interchangeable from the perspective of persistent peaks and periodicity, but complementary when it comes to behaviour analysis such as food anticipatory behaviour (FAB). Discussion We anticipate that our findings will stimulate advances where multiple sensor types are in use to achieve a more holistic understanding of fish behaviour in the aquaculture sector using underwater technologies. |
Oikonomou, Stavroula; Tasiouli, Katerina; Tsaparis, Dimitrios; Manousaki, Tereza; Vallecillos, Antonio; Oikonomaki, Katerina; Tzokas, Konstantinos; Katribouzas, Nikolaos; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Genomic evaluation for body weight, length and growth estimates in meagre Argyrosomus regius Journal Article Aquaculture, 595 , pp. 741622, 2025, ISSN: 00448486. @article{oikonomou_genomic_2025, title = {Genomic evaluation for body weight, length and growth estimates in meagre Argyrosomus regius}, author = {Stavroula Oikonomou and Katerina Tasiouli and Dimitrios Tsaparis and Tereza Manousaki and Antonio Vallecillos and Katerina Oikonomaki and Konstantinos Tzokas and Nikolaos Katribouzas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624010846 /wp-content/uploads/2025/01/2025-Oikonomou-AQUA-3.pdf}, doi = {10.1016/j.aquaculture.2024.741622}, issn = {00448486}, year = {2025}, date = {2025-01-24}, urldate = {2025-01-24}, journal = {Aquaculture}, volume = {595}, pages = {741622}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lancerotto, Stefano; Fakriadis, Ioannis; Papadaki, Maria; Giménez, Ignacio; Genovés, José Vicente Roig; Mylonas, Constantinos C Aquaculture, 594 , pp. 741401, 2025, ISSN: 00448486. @article{lancerotto_overcoming_2025, title = {Overcoming dysfunctional gametogenesis in hatchery-produced greater amberjack, Seriola dumerili using recombinant gonadotropins, and spawning induction using gonadotropin releasing hormone agonist-loaded implants}, author = {Stefano Lancerotto and Ioannis Fakriadis and Maria Papadaki and Ignacio Giménez and José Vicente Roig Genovés and Constantinos C Mylonas}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624008627 https://imbbc.hcmr.gr/wp-content/uploads/2025/01/2025-Lancerotto-AQUA-2.pdf}, doi = {10.1016/j.aquaculture.2024.741401}, issn = {00448486}, year = {2025}, date = {2025-01-21}, urldate = {2025-01-21}, journal = {Aquaculture}, volume = {594}, pages = {741401}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kourkouta, Chara; Tsipourlianos, Andreas; Papandroulakis, Nikos; Moutou, Katerina A; Koumoundouros, George Ray‐Resorption Syndrome in European Seabass, textitDicentrarchus labrax (Linnaeus, 1758) Journal Article Journal of Fish Diseases, 48 (2), pp. e14042, 2025, ISSN: 0140-7775, 1365-2761. @article{kourkouta_rayresorption_2025, title = {Ray‐Resorption Syndrome in European Seabass, textitDicentrarchus labrax (Linnaeus, 1758)}, author = {Chara Kourkouta and Andreas Tsipourlianos and Nikos Papandroulakis and Katerina A Moutou and George Koumoundouros}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jfd.14042 https://imbbc.hcmr.gr/wp-content/uploads/2025/01/2025-Kourkouta-JFD-4.pdf}, doi = {10.1111/jfd.14042}, issn = {0140-7775, 1365-2761}, year = {2025}, date = {2025-01-13}, urldate = {2025-01-13}, journal = {Journal of Fish Diseases}, volume = {48}, number = {2}, pages = {e14042}, abstract = {ABSTRACT Fin abnormalities are common in reared fish. They mainly consist of partial to complete lack of rays and severe abnormalities of fin‐supporting skeletal elements, which develop during the larval stage, up to the completion of fin skeleton ontogeny. This study reports a new abnormal condition, ray‐resorption syndrome (RSS), which developed after the completion of fin ontogeny in initially normal European seabass larvae, leading to extensive loss of fin rays. At 49 days post‐fertilisation (dpf) (15 mm standard length, SL) all fish presented normal fins. However, nineteen days later (21 mm SL), significant fin damage, characterised by ray loss or fractures, was observed in all studied populations. The dorsal fin was most affected (55%–84%), followed by the pelvic (27%–53%) and anal fins (7%–17%). Microscopically, multiple non‐mineralised areas resembling resorption lacunae were evident along all fin lepidotrichia. By 98 dpf (40 mm SL), the fin‐ray loss had advanced, reaching its higher frequency in the dorsal (74%–83%) and caudal fins (71%–94%). Gene expression analysis revealed a significant upregulation of bglap (osteoblast maturation marker), acp5a (osteoclast maturation marker) and mmp13a (extracellular‐matrix remodelling marker) in RSS specimens. The results are discussed in respect of the possible causative factors of RSS.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACT Fin abnormalities are common in reared fish. They mainly consist of partial to complete lack of rays and severe abnormalities of fin‐supporting skeletal elements, which develop during the larval stage, up to the completion of fin skeleton ontogeny. This study reports a new abnormal condition, ray‐resorption syndrome (RSS), which developed after the completion of fin ontogeny in initially normal European seabass larvae, leading to extensive loss of fin rays. At 49 days post‐fertilisation (dpf) (15 mm standard length, SL) all fish presented normal fins. However, nineteen days later (21 mm SL), significant fin damage, characterised by ray loss or fractures, was observed in all studied populations. The dorsal fin was most affected (55%–84%), followed by the pelvic (27%–53%) and anal fins (7%–17%). Microscopically, multiple non‐mineralised areas resembling resorption lacunae were evident along all fin lepidotrichia. By 98 dpf (40 mm SL), the fin‐ray loss had advanced, reaching its higher frequency in the dorsal (74%–83%) and caudal fins (71%–94%). Gene expression analysis revealed a significant upregulation of bglap (osteoblast maturation marker), acp5a (osteoclast maturation marker) and mmp13a (extracellular‐matrix remodelling marker) in RSS specimens. The results are discussed in respect of the possible causative factors of RSS. |
Bušelić, Ivana; Trumbić, Željka; Hrabar, Jerko; Lepen-Pleić, Ivana; Šegvić-Bubić, Tanja; Kaitetzidou, Elisavet; Tibaldi, Emilio; Bočina, Ivana; Grubišić, Leon; Sarropoulou, Elena 594 , pp. 741385, 2025, ISSN: 00448486. @article{buselic_unravelling_2025, title = {Unravelling the intricate language of fish guts: Impact of plant-based vs. plant-insect-poultry-based diets on intestinal pathways in European seabass}, author = {Ivana Bušelić and Željka Trumbić and Jerko Hrabar and Ivana Lepen-Pleić and Tanja Šegvić-Bubić and Elisavet Kaitetzidou and Emilio Tibaldi and Ivana Bočina and Leon Grubišić and Elena Sarropoulou}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624008469 https://imbbc.hcmr.gr/wp-content/uploads/2025/01/2025-Buselic-AQUA-1.pdf}, doi = {10.1016/j.aquaculture.2024.741385}, issn = {00448486}, year = {2025}, date = {2025-01-08}, urldate = {2025-01-08}, volume = {594}, pages = {741385}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pavloudi, Christina; Santi, Ioulia; Azua, Iñigo; Baña, Zuriñe; Bastianini, Mauro; Belser, Caroline; Bilbao, Jone; Bitz-Thorsen, Julie; Broudin, Caroline; Camusat, Mathieu; Cancio, Ibon; Caray-Counil, Louis; Casotti, Raffaella; Castel, Jade; Comtet, Thierry; Cox, Cymon; Daguin, Claire; Cerio, Oihane Díaz De; Exter, Katrina; Fauvelot, Cécile; Frada, Miguel; Galand, Pierre; Garczarek, Laurence; Fernández, Jose González; Guillou, Laure; Hablützel, Pascal; Heynderickx, Hanneloor; Houbin, Céline; Kervella, Anne; Krystallas, Apostolos; Lagaisse, Rune; Laroquette, Arnaud; Lescure, Lyvia; Lopes, Eva; Loulakaki, Melina; Louro, Bruno; Magalhaes, Catarina; Maidanou, Maria; Margiotta, Francesca; Montresor, Marina; Not, Fabrice; Paredes, Estefanía; Percopo, Isabella; Péru, Erwan; Poulain, Julie; Præbel, Kim; Rigaut-Jalabert, Fabienne; Romac, Sarah; Stavroulaki, Melanthia; Troncoso, Jesús Souza; Thiébaut, Eric; Thomas, Wilfried; Tkacz, Andrzej; Trano, Anna Chiara; Wincker, Patrick; Pade, Nicolas First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Journal Article Biodiversity Data Journal, 13 , pp. e143585, 2025, ISSN: 1314-2828, 1314-2836. @article{pavloudi_first_2025, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples}, author = {Christina Pavloudi and Ioulia Santi and Iñigo Azua and Zuriñe Baña and Mauro Bastianini and Caroline Belser and Jone Bilbao and Julie Bitz-Thorsen and Caroline Broudin and Mathieu Camusat and Ibon Cancio and Louis Caray-Counil and Raffaella Casotti and Jade Castel and Thierry Comtet and Cymon Cox and Claire Daguin and Oihane Díaz De Cerio and Katrina Exter and Cécile Fauvelot and Miguel Frada and Pierre Galand and Laurence Garczarek and Jose González Fernández and Laure Guillou and Pascal Hablützel and Hanneloor Heynderickx and Céline Houbin and Anne Kervella and Apostolos Krystallas and Rune Lagaisse and Arnaud Laroquette and Lyvia Lescure and Eva Lopes and Melina Loulakaki and Bruno Louro and Catarina Magalhaes and Maria Maidanou and Francesca Margiotta and Marina Montresor and Fabrice Not and Estefanía Paredes and Isabella Percopo and Erwan Péru and Julie Poulain and Kim Præbel and Fabienne Rigaut-Jalabert and Sarah Romac and Melanthia Stavroulaki and Jesús Souza Troncoso and Eric Thiébaut and Wilfried Thomas and Andrzej Tkacz and Anna Chiara Trano and Patrick Wincker and Nicolas Pade}, url = {https://bdj.pensoft.net/article/143585/ /wp-content/uploads/2025/04/2025-Pavloudi-BDJ-17.pdf}, doi = {10.3897/BDJ.13.e143585}, issn = {1314-2828, 1314-2836}, year = {2025}, date = {2025-01-01}, urldate = {2025-04-03}, journal = {Biodiversity Data Journal}, volume = {13}, pages = {e143585}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place. |
2024 |
Voskakis, Dimitris; Kelasidi, Eleni; Papandroulakis, Nikos Design and Development of Underwater Robotic Arm for Automated Camera Calibration for Aquatic Environment Inproceedings 2024 10th International Conference on Automation, Robotics and Applications (ICARA), pp. 50–56, IEEE, Athens, Greece, 2024, ISBN: 9798350394245. @inproceedings{voskakis_design_2024, title = {Design and Development of Underwater Robotic Arm for Automated Camera Calibration for Aquatic Environment}, author = {Dimitris Voskakis and Eleni Kelasidi and Nikos Papandroulakis}, url = {https://ieeexplore.ieee.org/document/10552983/ https://imbbc.hcmr.gr/wp-content/uploads/2025/01/ICARA-2024-Voskakis-pre-print.pdf}, doi = {10.1109/ICARA60736.2024.10552983}, isbn = {9798350394245}, year = {2024}, date = {2024-12-31}, urldate = {2025-01-10}, booktitle = {2024 10th International Conference on Automation, Robotics and Applications (ICARA)}, pages = {50--56}, publisher = {IEEE}, address = {Athens, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Mladineo, Ivona; Hrabar, Jerko; Trumbić, Željka; Rasouli-Dogaheh, Somayeh; Beraldo, Paola; Rigos, George; Palenzuela, Oswado; Sitjà-Bobadilla, Ariadna Aquaculture, 598 , pp. 741997, 2024, ISSN: 00448486. @article{mladineo_mediterranean-wide_2025, title = {Mediterranean-wide transfer of the polyopisthocotylean Sparicotyle chrysophrii between wild sparids and farmed gilthead seabream (Sparus aurata) inferred by ddRAD loci}, author = {Ivona Mladineo and Jerko Hrabar and Željka Trumbić and Somayeh Rasouli-Dogaheh and Paola Beraldo and George Rigos and Oswado Palenzuela and Ariadna Sitjà-Bobadilla}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624014595 https://imbbc.hcmr.gr/wp-content/uploads/2025/01/2024-Mladineo...Rigos-et-al-pre-print-48.pdf}, doi = {10.1016/j.aquaculture.2024.741997}, issn = {00448486}, year = {2024}, date = {2024-12-30}, urldate = {2025-01-08}, journal = {Aquaculture}, volume = {598}, pages = {741997}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Livanou, Eleni; Sauzède, Raphaëlle; Psarra, Stella; Mandalakis, Manolis; Dall’Olmo, Giorgio; Brewin, Robert J W; Raitsos, Dionysios E Evaluating MULTIOBS Chlorophyll-a with Ground-Truth Observations in the Eastern Mediterranean Sea Journal Article Remote Sensing, 16 (24), pp. 4705, 2024, ISSN: 2072-4292. @article{livanou_evaluating_2024, title = {Evaluating MULTIOBS Chlorophyll-a with Ground-Truth Observations in the Eastern Mediterranean Sea}, author = {Eleni Livanou and Raphaëlle Sauzède and Stella Psarra and Manolis Mandalakis and Giorgio Dall’Olmo and Robert J W Brewin and Dionysios E Raitsos}, url = {https://www.mdpi.com/2072-4292/16/24/4705 /wp-content/uploads/2024/12/2024-Livanou-Remote-Sensing-49.pdf}, doi = {10.3390/rs16244705}, issn = {2072-4292}, year = {2024}, date = {2024-12-23}, urldate = {2024-12-23}, journal = {Remote Sensing}, volume = {16}, number = {24}, pages = {4705}, abstract = {Satellite-derived observations of ocean colour provide continuous data on chlorophyll-a concentration (Chl-a) at global scales but are limited to the ocean’s surface. So far, biogeochemical models have been the only means of generating continuous vertically resolved Chl-a profiles on a regular grid. MULTIOBS is a multi-observations oceanographic dataset that provides depth-resolved biological data based on merged satellite- and Argo-derived in situ hydrological data. This product is distributed by the European Union’s Copernicus Marine Service and offers global multiyear, gridded Chl-a profiles within the ocean’s productive zone at a weekly temporal resolution. MULTIOBS addresses the scarcity of observation-based vertically resolved Chl-a datasets, particularly in less sampled regions like the Eastern Mediterranean Sea (EMS). Here, we conduct an independent evaluation of the MULTIOBS dataset in the oligotrophic waters of the EMS using in situ Chl-a profiles. Our analysis shows that this product accurately and precisely retrieves Chl-a across depths, with a slight 1% overestimation and an observed 1.5-fold average deviation between in situ data and MULTIOBS estimates. The deep chlorophyll maximum (DCM) is adequately estimated by MULTIOBS both in terms of positioning (root mean square error}, keywords = {}, pubstate = {published}, tppubtype = {article} } Satellite-derived observations of ocean colour provide continuous data on chlorophyll-a concentration (Chl-a) at global scales but are limited to the ocean’s surface. So far, biogeochemical models have been the only means of generating continuous vertically resolved Chl-a profiles on a regular grid. MULTIOBS is a multi-observations oceanographic dataset that provides depth-resolved biological data based on merged satellite- and Argo-derived in situ hydrological data. This product is distributed by the European Union’s Copernicus Marine Service and offers global multiyear, gridded Chl-a profiles within the ocean’s productive zone at a weekly temporal resolution. MULTIOBS addresses the scarcity of observation-based vertically resolved Chl-a datasets, particularly in less sampled regions like the Eastern Mediterranean Sea (EMS). Here, we conduct an independent evaluation of the MULTIOBS dataset in the oligotrophic waters of the EMS using in situ Chl-a profiles. Our analysis shows that this product accurately and precisely retrieves Chl-a across depths, with a slight 1% overestimation and an observed 1.5-fold average deviation between in situ data and MULTIOBS estimates. The deep chlorophyll maximum (DCM) is adequately estimated by MULTIOBS both in terms of positioning (root mean square error |
Apostolaki, Eugenia T; Lavery, Paul S; Litsi‐Mizan, Victoria; Serrano, Eduard; Inostroza, Karina; Gerakaris, Vasilis; Dailianis, Thanos; Glampedakis, Julius; Holitzki, Tara; Johnson, Erik; Mateo, Miguel A; Serrano, Oscar Patterns of Carbon and Nitrogen Accumulation in Seagrass ( textitPosidonia oceanica ) Meadows of the Eastern Mediterranean Sea Journal Article Journal of Geophysical Research: Biogeosciences, 129 (12), pp. e2024JG008163, 2024, ISSN: 2169-8953, 2169-8961. @article{apostolaki_patterns_2024, title = {Patterns of Carbon and Nitrogen Accumulation in Seagrass ( textitPosidonia oceanica ) Meadows of the Eastern Mediterranean Sea}, author = {Eugenia T Apostolaki and Paul S Lavery and Victoria Litsi‐Mizan and Eduard Serrano and Karina Inostroza and Vasilis Gerakaris and Thanos Dailianis and Julius Glampedakis and Tara Holitzki and Erik Johnson and Miguel A Mateo and Oscar Serrano}, url = {https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2024JG008163 https://imbbc.hcmr.gr/wp-content/uploads/2024/12/2024-Apostolaki-JGR-BiosSci-47-1.pdf}, doi = {10.1029/2024JG008163}, issn = {2169-8953, 2169-8961}, year = {2024}, date = {2024-12-18}, urldate = {2024-12-18}, journal = {Journal of Geophysical Research: Biogeosciences}, volume = {129}, number = {12}, pages = {e2024JG008163}, abstract = {Abstract The variability in stocks and accumulation rates of organic carbon (C org ), nitrogen (N), and carbonate (CaCO 3 ) was studied in fifteen Posidonia oceanica meadows spread throughout the South Aegean Sea (Greece). In addition, the abiotic and biotic drivers determining the pattern of variability in the accumulation rates were assessed by exploring the influence of sediment characteristics, seagrass traits, and environmental settings. The meadows supported on average (±STDEV) 14.6 ± 5.0 kg C org m −2 , 0.47 ± 0.17 kg N m −2 , and 249 ± 210 kg CaCO 3 m −2 in the top meter of their sediments, with mean accumulation rates over the last 500 years of 33.6 ± 23.6 g C org m −2 yr −1 , 1.00 ± 0.62 g N m −2 yr −1 , and 405 ± 336 g CaCO 3 m −2 yr −1 across sites. A redundancy analysis (RDA) explained 70% of the variation in C org , N, and CaCO 3 accumulation rates, with three sediment characteristics (i.e., sediment C org :N and C org :C inorg ratios and P . oceanica contribution to the sediment C org pool) emerging as the primary set of factors shaping the accumulation of matter, followed by seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental variables (i.e., suspended organic matter). The high degree of variability within the region emphasizes the need for fine‐scale assessments to understand the local conditions influencing sequestration. Our findings underscored the critical role of seagrass meadows in carbon and nitrogen sequestration in the region, urging conservation efforts to protect these ecosystems and prevent potential losses of stored carbon and nitrogen following seagrass degradation. , Plain Language Summary In the present study, we explored the abiotic and biotic factors influencing the accumulation patterns of carbon, nitrogen, and carbonate in 15 seagrass ( Posidonia oceanica ) meadows across the South Aegean Sea (Greece). Sediment characteristics (i.e., sediment C org :N and C org :C inorg ratios and P . ocenica contribution to the sediment C org pool) mainly drove the pattern of carbon, nitrogen, and carbonate accumulation, with seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental conditions (i.e., suspended organic matter) contributing to a lesser extent. Overall, seagrass meadows play a crucial role in storing carbon and nitrogen in the studied region, serving as important natural sinks, and thus, protecting these ecosystems is important to prevent the loss of these stored elements. Additionally, understanding the factors that shape the variability in Posidonia oceanica storage capacity is crucial for management and conservation efforts. , Key Points Seagrass ( Posidonia oceanica ) meadows of the South Aegean Sea (Greece) represent important natural sinks for organic carbon, nitrogen, and carbonate. The accumulation pattern of organic carbon, nitrogen, and carbonate in the underlying seagrass sediments was mainly driven by sediment characteristics, followed by seagrass traits and environmental conditions. Fine‐scale assessments are crucial for understanding the local factors shaping the storage capacity of seagrass meadows to support management decisions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The variability in stocks and accumulation rates of organic carbon (C org ), nitrogen (N), and carbonate (CaCO 3 ) was studied in fifteen Posidonia oceanica meadows spread throughout the South Aegean Sea (Greece). In addition, the abiotic and biotic drivers determining the pattern of variability in the accumulation rates were assessed by exploring the influence of sediment characteristics, seagrass traits, and environmental settings. The meadows supported on average (±STDEV) 14.6 ± 5.0 kg C org m −2 , 0.47 ± 0.17 kg N m −2 , and 249 ± 210 kg CaCO 3 m −2 in the top meter of their sediments, with mean accumulation rates over the last 500 years of 33.6 ± 23.6 g C org m −2 yr −1 , 1.00 ± 0.62 g N m −2 yr −1 , and 405 ± 336 g CaCO 3 m −2 yr −1 across sites. A redundancy analysis (RDA) explained 70% of the variation in C org , N, and CaCO 3 accumulation rates, with three sediment characteristics (i.e., sediment C org :N and C org :C inorg ratios and P . oceanica contribution to the sediment C org pool) emerging as the primary set of factors shaping the accumulation of matter, followed by seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental variables (i.e., suspended organic matter). The high degree of variability within the region emphasizes the need for fine‐scale assessments to understand the local conditions influencing sequestration. Our findings underscored the critical role of seagrass meadows in carbon and nitrogen sequestration in the region, urging conservation efforts to protect these ecosystems and prevent potential losses of stored carbon and nitrogen following seagrass degradation. , Plain Language Summary In the present study, we explored the abiotic and biotic factors influencing the accumulation patterns of carbon, nitrogen, and carbonate in 15 seagrass ( Posidonia oceanica ) meadows across the South Aegean Sea (Greece). Sediment characteristics (i.e., sediment C org :N and C org :C inorg ratios and P . ocenica contribution to the sediment C org pool) mainly drove the pattern of carbon, nitrogen, and carbonate accumulation, with seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental conditions (i.e., suspended organic matter) contributing to a lesser extent. Overall, seagrass meadows play a crucial role in storing carbon and nitrogen in the studied region, serving as important natural sinks, and thus, protecting these ecosystems is important to prevent the loss of these stored elements. Additionally, understanding the factors that shape the variability in Posidonia oceanica storage capacity is crucial for management and conservation efforts. , Key Points Seagrass ( Posidonia oceanica ) meadows of the South Aegean Sea (Greece) represent important natural sinks for organic carbon, nitrogen, and carbonate. The accumulation pattern of organic carbon, nitrogen, and carbonate in the underlying seagrass sediments was mainly driven by sediment characteristics, followed by seagrass traits and environmental conditions. Fine‐scale assessments are crucial for understanding the local factors shaping the storage capacity of seagrass meadows to support management decisions. |
Rotter, Ana; Varamogianni-Mamatsi, Despoina; Pobirk, Alenka Zvonar; Matjaž, Mirjam Gosenca; Cueto, Mercedes; Díaz-Marrero, Ana R; Jónsdóttir, Rósa; Sveinsdóttir, Kolbrún; Catalá, Teresa S; Romano, Giovanna; Guler, Bahar Aslanbay; Atak, Eylem; Zrimec, Maja Berden; Bosch, Daniel; Deniz, Irem; Gaudêncio, Susana P; Grigalionyte-Bembič, Ernesta; Klun, Katja; Zidar, Luen; Rius, Anna Coll; Baebler, Špela; Bilela, Lada Lukić; Rinkevich, Baruch; Mandalakis, Manolis Marine cosmetics and the blue bioeconomy: From sourcing to success stories Journal Article iScience, 27 (12), pp. 111339, 2024, ISSN: 25890042. @article{rotter_marine_2024, title = {Marine cosmetics and the blue bioeconomy: From sourcing to success stories}, author = {Ana Rotter and Despoina Varamogianni-Mamatsi and Alenka Zvonar Pobirk and Mirjam Gosenca Matjaž and Mercedes Cueto and Ana R Díaz-Marrero and Rósa Jónsdóttir and Kolbrún Sveinsdóttir and Teresa S Catalá and Giovanna Romano and Bahar Aslanbay Guler and Eylem Atak and Maja Berden Zrimec and Daniel Bosch and Irem Deniz and Susana P Gaudêncio and Ernesta Grigalionyte-Bembič and Katja Klun and Luen Zidar and Anna Coll Rius and Špela Baebler and Lada Lukić Bilela and Baruch Rinkevich and Manolis Mandalakis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004224025641 /wp-content/uploads/2024/12/2024-Rotter-iScience-46.pdf}, doi = {10.1016/j.isci.2024.111339}, issn = {25890042}, year = {2024}, date = {2024-12-09}, urldate = {2024-12-10}, journal = {iScience}, volume = {27}, number = {12}, pages = {111339}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Skliros, Dimitrios; Kostakou, Maria; Kokkari, Constantina; Tsertou, Maria Ioanna; Pavloudi, Christina; Zafeiropoulos, Haris; Katharios, Pantelis; Flemetakis, Emmanouil Microorganisms, 12 (11), pp. 2281, 2024, ISSN: 2076-2607. @article{skliros_unveiling_2024, title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries}, author = {Dimitrios Skliros and Maria Kostakou and Constantina Kokkari and Maria Ioanna Tsertou and Christina Pavloudi and Haris Zafeiropoulos and Pantelis Katharios and Emmanouil Flemetakis}, url = {https://www.mdpi.com/2076-2607/12/11/2281 https://imbbc.hcmr.gr/wp-content/uploads/2024/11/2024-Skliros-microorganisms-45.pdf}, doi = {10.3390/microorganisms12112281}, issn = {2076-2607}, year = {2024}, date = {2024-11-12}, urldate = {2024-11-12}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {2281}, abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region. |
Daniso, Enrico; Sarropoulou, Elena; Kaitetzidou, Elisavet; Beraldo, Paola; Tibaldi, Emilio; Cerri, Roberto; Cardinaletti, Gloriana Effect of increasing levels of Hermetia illucens in a fishmeal-free diet at sea bream (Sparus aurata, L.) gastrointestinal level Journal Article Aquaculture Reports, 39 , pp. 102410, 2024, ISSN: 23525134. @article{daniso_effect_2024, title = {Effect of increasing levels of Hermetia illucens in a fishmeal-free diet at sea bream (Sparus aurata, L.) gastrointestinal level}, author = {Enrico Daniso and Elena Sarropoulou and Elisavet Kaitetzidou and Paola Beraldo and Emilio Tibaldi and Roberto Cerri and Gloriana Cardinaletti}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2352513424004988 /wp-content/uploads/2024/10/2024-Daniso-AquaReports-44.pdf}, doi = {10.1016/j.aqrep.2024.102410}, issn = {23525134}, year = {2024}, date = {2024-10-09}, urldate = {2024-10-09}, journal = {Aquaculture Reports}, volume = {39}, pages = {102410}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kotsiri, Mado; Kleidas, Ioannis; Kogiannou, Dimitra; Vryonides, Katerina; Papadouli, Christina; Golomazou, Eleni; Rigos, George Evaluation of the long-term effects of formaldehyde on the physiology of the Mediterranean mussel, Mytilus galloprovincialis Journal Article Chemosphere, 364 , pp. 143190, 2024, ISSN: 00456535. @article{kotsiri_evaluation_2024, title = {Evaluation of the long-term effects of formaldehyde on the physiology of the Mediterranean mussel, Mytilus galloprovincialis}, author = {Mado Kotsiri and Ioannis Kleidas and Dimitra Kogiannou and Katerina Vryonides and Christina Papadouli and Eleni Golomazou and George Rigos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653524020873 https://imbbc.hcmr.gr/wp-content/uploads/2024/10/2024-Kotsiri-43-pre-print.pdf}, doi = {10.1016/j.chemosphere.2024.143190}, issn = {00456535}, year = {2024}, date = {2024-09-30}, urldate = {2024-10-01}, journal = {Chemosphere}, volume = {364}, pages = {143190}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Reverté, Jaume; Rambla-Alegre, Maria; Sanchez-Henao, Andres; Mandalakis, Manolis; Peristeraki, Panagiota; Molgó, Jordi; Diogène, Jorge; Sureda, Francesc X; Campàs, Mònica Toxicity Equivalency Factors for Tetrodotoxin Analogues Determined with Automated Patch Clamp on Voltage-Gated Sodium Channels in Neuro-2a Cells Journal Article Journal of Agricultural and Food Chemistry, 72 (32), pp. 18192–18200, 2024, ISSN: 0021-8561, 1520-5118. @article{reverte_toxicity_2024, title = {Toxicity Equivalency Factors for Tetrodotoxin Analogues Determined with Automated Patch Clamp on Voltage-Gated Sodium Channels in Neuro-2a Cells}, author = {Jaume Reverté and Maria Rambla-Alegre and Andres Sanchez-Henao and Manolis Mandalakis and Panagiota Peristeraki and Jordi Molgó and Jorge Diogène and Francesc X Sureda and Mònica Campàs}, url = {https://pubs.acs.org/doi/10.1021/acs.jafc.4c04321 https://imbbc.hcmr.gr/wp-content/uploads/2024/09/2024-Reverte-JAFC-42-pre-print.pdf}, doi = {10.1021/acs.jafc.4c04321}, issn = {0021-8561, 1520-5118}, year = {2024}, date = {2024-09-26}, urldate = {2024-09-26}, journal = {Journal of Agricultural and Food Chemistry}, volume = {72}, number = {32}, pages = {18192--18200}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Skouradakis, Grigorios; Vernadou, Emmanouela; Koulouri, Panayota; Dailianis, Thanos Mass mortality of the invasive echinoid Diadema setosum (Leske, 1778) in Crete, East Mediterranean Sea Journal Article Mediterranean Marine Science, 25 (2), pp. 480–483, 2024, ISSN: 1791-6763, 1108-393X. @article{skouradakis_mass_2024, title = {Mass mortality of the invasive echinoid Diadema setosum (Leske, 1778) in Crete, East Mediterranean Sea}, author = {Grigorios Skouradakis and Emmanouela Vernadou and Panayota Koulouri and Thanos Dailianis}, url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/36447 https://imbbc.hcmr.gr/wp-content/uploads/2024/09/2024-Skouradakis-MMS-41.pdf}, doi = {10.12681/mms.36447}, issn = {1791-6763, 1108-393X}, year = {2024}, date = {2024-09-23}, urldate = {2024-09-23}, journal = {Mediterranean Marine Science}, volume = {25}, number = {2}, pages = {480--483}, abstract = {Diadema setosum is an echinoid of Indo-Pacific origin that invaded the Mediterranean Sea in 2006. It is an ecosystem engineer with an important ecological function in its native range, but it can have a detrimental effect on Mediterranean reefs. Recently in 2022 a mass mortality event (MME) affecting this species was recorded in the east Aegean Sea in the eastern part of the Mediterranean basin. We are reporting herein a westward progression of the MME in 2023 affecting established populations in various locations around the island of Crete.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diadema setosum is an echinoid of Indo-Pacific origin that invaded the Mediterranean Sea in 2006. It is an ecosystem engineer with an important ecological function in its native range, but it can have a detrimental effect on Mediterranean reefs. Recently in 2022 a mass mortality event (MME) affecting this species was recorded in the east Aegean Sea in the eastern part of the Mediterranean basin. We are reporting herein a westward progression of the MME in 2023 affecting established populations in various locations around the island of Crete. |
Lavecchia, Anna; Virgilio, Caterina De; Mansi, Luigi; Manzari, Caterina; Mylonas, Constantinos C; Picardi, Ernesto; Pousis, Chrysovalentinos; Cox, Sharon N; Ventriglia, Gianluca; Zupa, Rosa; Pesole, Graziano; Corriero, Aldo Comparison of ovarian mRNA expression levels in wild and hatchery-produced greater amberjack Seriola dumerili Journal Article Scientific Reports, 14 (1), pp. 18034, 2024, ISSN: 2045-2322. @article{lavecchia_comparison_2024, title = {Comparison of ovarian mRNA expression levels in wild and hatchery-produced greater amberjack Seriola dumerili}, author = {Anna Lavecchia and Caterina De Virgilio and Luigi Mansi and Caterina Manzari and Constantinos C Mylonas and Ernesto Picardi and Chrysovalentinos Pousis and Sharon N Cox and Gianluca Ventriglia and Rosa Zupa and Graziano Pesole and Aldo Corriero}, url = {https://www.nature.com/articles/s41598-024-69091-2 https://imbbc.hcmr.gr/wp-content/uploads/2024/09/2024-Lavecchia-SciRep-40.pdf}, doi = {10.1038/s41598-024-69091-2}, issn = {2045-2322}, year = {2024}, date = {2024-09-16}, urldate = {2024-09-16}, journal = {Scientific Reports}, volume = {14}, number = {1}, pages = {18034}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Papadaki, Maria; Mylonas, C C; Sarropoulou, Elena MicroRNAs are involved in ovarian physiology of greater amberjack (Seriola dumerili) under captivity Journal Article General and Comparative Endocrinology, 357 , pp. 114581, 2024, ISSN: 00166480. @article{papadaki_micrornas_2024, title = {MicroRNAs are involved in ovarian physiology of greater amberjack (Seriola dumerili) under captivity}, author = {Maria Papadaki and C C Mylonas and Elena Sarropoulou}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0016648024001436 /wp-content/uploads/2024/08/2024-Papadaki-GCE-39.pdf}, doi = {10.1016/j.ygcen.2024.114581}, issn = {00166480}, year = {2024}, date = {2024-08-05}, urldate = {2024-08-13}, journal = {General and Comparative Endocrinology}, volume = {357}, pages = {114581}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kotsakiozi, Panayiota; Antoniou, Aglaia; Psonis, Nikolaos; Sagonas, Κostas; Karameta, Emmanouela; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Jablonski, Daniel; Darriba, Diego; Stamatakis, Alexandros; Lymberakis, Petros; Poulakakis, Nikos Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region Journal Article Molecular Phylogenetics and Evolution, 197 , pp. 108091, 2024, ISSN: 10557903. @article{kotsakiozi_cryptic_2024, title = {Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region}, author = {Panayiota Kotsakiozi and Aglaia Antoniou and Nikolaos Psonis and Κostas Sagonas and Emmanouela Karameta and Çetin Ilgaz and Yusuf Kumlutaş and Aziz Avcı and Daniel Jablonski and Diego Darriba and Alexandros Stamatakis and Petros Lymberakis and Nikos Poulakakis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1055790324000836 /wp-content/uploads/2024/08/2024-Kotsakiozi-MPE-38-pre-print.pdf}, doi = {10.1016/j.ympev.2024.108091}, issn = {10557903}, year = {2024}, date = {2024-08-01}, urldate = {2024-08-12}, journal = {Molecular Phylogenetics and Evolution}, volume = {197}, pages = {108091}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Falconer, Lynne; Sparboe, Lars Olav; Dale, Trine; Hjøllo, Solfrid Sætre; Stavrakidis-Zachou, Orestis; Bergh, Øivind; James, Philip; Papandroulakis, Nikos; Puvanendran, Velmurugu; Siikavuopio, Sten Ivar; Hansen, Øyvind Johannes; Ytteborg, Elisabeth Diversification of marine aquaculture in Norway under climate change Journal Article Aquaculture, 593 , pp. 741350, 2024, ISSN: 00448486. @article{falconer_diversification_2024, title = {Diversification of marine aquaculture in Norway under climate change}, author = {Lynne Falconer and Lars Olav Sparboe and Trine Dale and Solfrid Sætre Hjøllo and Orestis Stavrakidis-Zachou and Øivind Bergh and Philip James and Nikos Papandroulakis and Velmurugu Puvanendran and Sten Ivar Siikavuopio and Øyvind Johannes Hansen and Elisabeth Ytteborg}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624008111 https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Falconer-AQUA-37.pdf}, doi = {10.1016/j.aquaculture.2024.741350}, issn = {00448486}, year = {2024}, date = {2024-07-31}, urldate = {2024-07-31}, journal = {Aquaculture}, volume = {593}, pages = {741350}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zrnčić, Snježana; Katharios, Pantelis; Padrós, Francesc; Fioravanti, Marialetizia; Gustinelli, Andrea; Breton, Alain Le; Toffan, Anna New Challenges and Achievements in Mediterranean Fish Health Management Journal Article Bulletin of the European Association of Fish Pathologists, 2024, ISSN: 3005-4648, 0108-0288. @article{zrncic_new_2024, title = {New Challenges and Achievements in Mediterranean Fish Health Management}, author = {Snježana Zrnčić and Pantelis Katharios and Francesc Padrós and Marialetizia Fioravanti and Andrea Gustinelli and Alain Le Breton and Anna Toffan}, url = {https://eafpbulletin.scholasticahq.com/article/118459-new-challenges-and-achievements-in-mediterranean-fish-health-management https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Katharios-Bulletin-of-EAFP-36.pdf}, doi = {10.48045/001c.118459}, issn = {3005-4648, 0108-0288}, year = {2024}, date = {2024-07-26}, urldate = {2024-07-26}, journal = {Bulletin of the European Association of Fish Pathologists}, abstract = {The European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) are key species in marine aquaculture, cultivated in both EU and North African/Levant Mediterranean regions. Production disparities between these areas emphasize a significant reliance on trade for juveniles, feed, and other resources, posing notable biosecurity risks. Addressing shared health concerns across the Mediterranean requires a regional approach to ensure successful management. A recent workshop delved into pivotal topics, including insights from concluded Horizon 2020 projects, effectiveness of nutraceuticals in combating parasitic infections, legal considerations surrounding autogenous vaccines, updated knowledge in betanodavirus infections, and biosecurity measures in Mediterranean aquaculture. Discussions also explored upcoming challenges such as sustainability in cage-based production, impact of climate change, enhancing diagnostic capabilities, fortifying biosecurity measures, advocating for education, and fostering networking opportunities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) are key species in marine aquaculture, cultivated in both EU and North African/Levant Mediterranean regions. Production disparities between these areas emphasize a significant reliance on trade for juveniles, feed, and other resources, posing notable biosecurity risks. Addressing shared health concerns across the Mediterranean requires a regional approach to ensure successful management. A recent workshop delved into pivotal topics, including insights from concluded Horizon 2020 projects, effectiveness of nutraceuticals in combating parasitic infections, legal considerations surrounding autogenous vaccines, updated knowledge in betanodavirus infections, and biosecurity measures in Mediterranean aquaculture. Discussions also explored upcoming challenges such as sustainability in cage-based production, impact of climate change, enhancing diagnostic capabilities, fortifying biosecurity measures, advocating for education, and fostering networking opportunities. |
Buck, Bela H; Bjelland, Hans V; Bockus, Abigail; Chambers, Michael; Costa-Pierce, Barry Antonio; Dewhurst, Tobias; Ferreira, Joao G; Føre, Heidi Moe; Fredriksson, David W; Goseberg, Nils; Holmyard, John; Isbert, Wolf; Krause, Gesche; Markus, Till; Papandroulakis, Nikos; Sclodnick, Tyler; Silkes, Bill; Strand, Åsa; Troell, Max; Wieczorek, Daniel; Burg, Sander Van Den W K; Heasman, Kevin G Resolving the term “offshore aquaculture” by decoupling “exposed” and “distance from the coast” Journal Article Frontiers in Aquaculture, 3 , pp. 1428056, 2024, ISSN: 2813-5334. @article{buck_resolving_2024, title = {Resolving the term “offshore aquaculture” by decoupling “exposed” and “distance from the coast”}, author = {Bela H Buck and Hans V Bjelland and Abigail Bockus and Michael Chambers and Barry Antonio Costa-Pierce and Tobias Dewhurst and Joao G Ferreira and Heidi Moe Føre and David W Fredriksson and Nils Goseberg and John Holmyard and Wolf Isbert and Gesche Krause and Till Markus and Nikos Papandroulakis and Tyler Sclodnick and Bill Silkes and Åsa Strand and Max Troell and Daniel Wieczorek and Sander W K Van Den Burg and Kevin G Heasman}, url = {https://www.frontiersin.org/articles/10.3389/faquc.2024.1428056/full https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Buck-Frontiers-35.pdf}, doi = {10.3389/faquc.2024.1428056}, issn = {2813-5334}, year = {2024}, date = {2024-07-22}, urldate = {2024-07-22}, journal = {Frontiers in Aquaculture}, volume = {3}, pages = {1428056}, abstract = {The terms “offshore” and “open ocean” have been used to describe aquaculture sites that are further from the coast or in higher energy environments. Neither term has been clearly defined in the scientific literature nor in a legal context, and the terms are often used interchangeably. These and other related terms (for example “exposed”, “high-energy”) variously refer to aspects of a site such as the geographic distance from shore or infrastructure, the level of exposure to large waves and strong currents, the geographic fetch, the water depth, or some combination of these parameters. The ICES Working Group (ICES, 2024) on Open Ocean Aquaculture (WGOOA) therefore identified a need to define the terminology to reduce ambiguity for these types of aquaculture sites or more precisely, to: (1) promote a common understanding and avoid misuse for different classifications; (2) enable regulators to identify the characteristics of a marine site; (3) allow farmers to be able to assess or quantitatively compare sites for development; (4) equip developers and producers to identify operational parameters in which the equipment and vessels will need to operate; (5) provide insurers and investors with the terminology to consistently assess risk and premiums; and (6) circumvent the emergence of narratives that root in different cognitive interpretations of the terminology in public discourse. This paper describes the evolution of the use of the term “offshore aquaculture” and define the most relevant parameters to shift to a more definitive and robust term “exposed aquaculture” that can inherently relay clearer information. Adoption of this more definitive definition of “exposed” will allow the user to define a site with more than just distance from shore. Key differences and the importance of these terms are discussed that affect various interest groups. Follow-up articles in this compilation from scientific members of the WGOOA as well as other scientists outside ICES are incorporated that develop a set of definitions and a rigorous exposure index.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The terms “offshore” and “open ocean” have been used to describe aquaculture sites that are further from the coast or in higher energy environments. Neither term has been clearly defined in the scientific literature nor in a legal context, and the terms are often used interchangeably. These and other related terms (for example “exposed”, “high-energy”) variously refer to aspects of a site such as the geographic distance from shore or infrastructure, the level of exposure to large waves and strong currents, the geographic fetch, the water depth, or some combination of these parameters. The ICES Working Group (ICES, 2024) on Open Ocean Aquaculture (WGOOA) therefore identified a need to define the terminology to reduce ambiguity for these types of aquaculture sites or more precisely, to: (1) promote a common understanding and avoid misuse for different classifications; (2) enable regulators to identify the characteristics of a marine site; (3) allow farmers to be able to assess or quantitatively compare sites for development; (4) equip developers and producers to identify operational parameters in which the equipment and vessels will need to operate; (5) provide insurers and investors with the terminology to consistently assess risk and premiums; and (6) circumvent the emergence of narratives that root in different cognitive interpretations of the terminology in public discourse. This paper describes the evolution of the use of the term “offshore aquaculture” and define the most relevant parameters to shift to a more definitive and robust term “exposed aquaculture” that can inherently relay clearer information. Adoption of this more definitive definition of “exposed” will allow the user to define a site with more than just distance from shore. Key differences and the importance of these terms are discussed that affect various interest groups. Follow-up articles in this compilation from scientific members of the WGOOA as well as other scientists outside ICES are incorporated that develop a set of definitions and a rigorous exposure index. |
Waterhouse, Robert M; Adam-Blondon, Anne-Françoise; Balech, Bachir; Barta, Endre; Chua, Physilia Ying Shi; Cola, Valeria Di; Heil, Katharina F; Hughes, Graham M; Jermiin, Lars S; Kalaš, Matúš; Lanfear, Jerry; Pafilis, Evangelos; Palagi, Patricia M; Papageorgiou, Aristotelis C; Paupério, Joana; Psomopoulos, Fotis; Raes, Niels; Burgin, Josephine; Gabaldón, Toni The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity Journal Article F1000Research, 12 , pp. 499, 2024, ISSN: 2046-1402. @article{waterhouse_elixir_2024, title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity}, author = {Robert M Waterhouse and Anne-Françoise Adam-Blondon and Bachir Balech and Endre Barta and Physilia Ying Shi Chua and Valeria Di Cola and Katharina F Heil and Graham M Hughes and Lars S Jermiin and Matúš Kalaš and Jerry Lanfear and Evangelos Pafilis and Patricia M Palagi and Aristotelis C Papageorgiou and Joana Paupério and Fotis Psomopoulos and Niels Raes and Josephine Burgin and Toni Gabaldón}, url = {https://f1000research.com/articles/12-499/v2 /wp-content/uploads/2024/07/2024-Waterhouse-F1000-Research-34.pdf}, doi = {10.12688/f1000research.133724.2}, issn = {2046-1402}, year = {2024}, date = {2024-07-16}, urldate = {2024-07-15}, journal = {F1000Research}, volume = {12}, pages = {499}, abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders. |
Loufi, Katerina; Papadakis, Ioannis E; Makridis, Pavlos Aquaculture Nutrition, 2024 , pp. 1–15, 2024, ISSN: 1365-2095, 1353-5773. @article{loufi_use_2024, title = {The Use of Acartia tonsa Nauplii during the First Days of Feeding on the Ontogeny of the Digestive System of Greater Amberjack (Seriola dumerili Risso, 1810)}, author = {Katerina Loufi and Ioannis E Papadakis and Pavlos Makridis}, editor = {Yanjiao Zhang}, url = {https://www.hindawi.com/journals/anu/2024/1826300/ https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Loufi-AquaNutri-33.pdf}, doi = {10.1155/2024/1826300}, issn = {1365-2095, 1353-5773}, year = {2024}, date = {2024-07-10}, urldate = {2024-07-10}, journal = {Aquaculture Nutrition}, volume = {2024}, pages = {1--15}, abstract = {The effect of feeding greater amberjack with copepod nauplii (Acartia tonsa) on the ontogeny of the digestive system was observed until 40 days after hatching (DAH). Copepods are part of the diet of fish larvae in nature, and they are rich in highly unsaturated fatty acids and free amino acids that enhance the digestive capacity of the fish. In a marine hatchery, four cylindroconical tanks of 2,700 L were stocked with about 150 × 103 greater amberjack larvae (Seriola dumerili) in each. The larvae were initially fed from 3 to 17 DAH in two tanks with copepod nauplii and rotifers (Brachionus sp.; Copepods group), while in the other two tanks, they were fed only with rotifers (Control group) during the same period. All the tanks were fed with rotifers (3–27 DAH), Artemia nauplii (12–22 DAH), enriched Artemia metanauplii (20–30 DAH), and formulated diet (25–40 DAH). Fish samples were taken regularly (every 2 or 4 days) for histological analysis and every day for the measurement of total length (TL). The TL was 3.7, 4.5 ± 0.1, 6.1, 11, 17.3 ± 0.1 and 20.3 ± 2.3 mm at 4, 10, 16, 22, 30, and 40 DAH, respectively. Copepod-fed fish showed higher TL in the last 2 days of the trial ( p textless 0.05 ), while mortality rates were lower in the beginning of the trial 10–17 DAH, ( p textless 0.05 ). In addition, copepods-fed fish had less skeletal deformities ( p textless 0.05 ). Pyloric caeca appeared earlier in the Copepods group compared with the Control, while the length and surface of the villi, the abundance of goblet cells/100 μm of intestine length, and the area covered with lipid vacuoles in the liver were significantly higher in the Copepods group ( p textless 0.05 ). We can conclude that the use of copepods in the diet of the greater amberjack larvae can improve the ontogeny of the digestive system.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of feeding greater amberjack with copepod nauplii (Acartia tonsa) on the ontogeny of the digestive system was observed until 40 days after hatching (DAH). Copepods are part of the diet of fish larvae in nature, and they are rich in highly unsaturated fatty acids and free amino acids that enhance the digestive capacity of the fish. In a marine hatchery, four cylindroconical tanks of 2,700 L were stocked with about 150 × 103 greater amberjack larvae (Seriola dumerili) in each. The larvae were initially fed from 3 to 17 DAH in two tanks with copepod nauplii and rotifers (Brachionus sp.; Copepods group), while in the other two tanks, they were fed only with rotifers (Control group) during the same period. All the tanks were fed with rotifers (3–27 DAH), Artemia nauplii (12–22 DAH), enriched Artemia metanauplii (20–30 DAH), and formulated diet (25–40 DAH). Fish samples were taken regularly (every 2 or 4 days) for histological analysis and every day for the measurement of total length (TL). The TL was 3.7, 4.5 ± 0.1, 6.1, 11, 17.3 ± 0.1 and 20.3 ± 2.3 mm at 4, 10, 16, 22, 30, and 40 DAH, respectively. Copepod-fed fish showed higher TL in the last 2 days of the trial ( p textless 0.05 ), while mortality rates were lower in the beginning of the trial 10–17 DAH, ( p textless 0.05 ). In addition, copepods-fed fish had less skeletal deformities ( p textless 0.05 ). Pyloric caeca appeared earlier in the Copepods group compared with the Control, while the length and surface of the villi, the abundance of goblet cells/100 μm of intestine length, and the area covered with lipid vacuoles in the liver were significantly higher in the Copepods group ( p textless 0.05 ). We can conclude that the use of copepods in the diet of the greater amberjack larvae can improve the ontogeny of the digestive system. |
Hartle-Mougiou, Katherine; Gubili, Chrysoula; Xanthopoulou, Panagiota; Kasapidis, Panagiotis; Valiadi, Martha; Gizeli, Electra Frontiers in Marine Science, 11 , pp. 1358793, 2024, ISSN: 2296-7745. @article{hartle-mougiou_development_2024, title = {Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfish Pterois miles from environmental DNA}, author = {Katherine Hartle-Mougiou and Chrysoula Gubili and Panagiota Xanthopoulou and Panagiotis Kasapidis and Martha Valiadi and Electra Gizeli}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Hartle-Mougiou-fmars-32.pdf https://www.frontiersin.org/articles/10.3389/fmars.2024.1358793/full}, doi = {10.3389/fmars.2024.1358793}, issn = {2296-7745}, year = {2024}, date = {2024-07-08}, urldate = {2024-07-08}, journal = {Frontiers in Marine Science}, volume = {11}, pages = {1358793}, abstract = {The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles , has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles , has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field. |
Kovačić, Marcelo; Gerovasileiou, Vasilis; Patzner, Robert A Fishes in Marine Caves Journal Article Fishes, 9 (6), pp. 243, 2024, ISSN: 2410-3888. @article{kovacic_fishes_2024, title = {Fishes in Marine Caves}, author = {Marcelo Kovačić and Vasilis Gerovasileiou and Robert A Patzner}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Kovacic-fishes-31.pdf https://www.mdpi.com/2410-3888/9/6/243}, doi = {10.3390/fishes9060243}, issn = {2410-3888}, year = {2024}, date = {2024-07-04}, urldate = {2024-07-04}, journal = {Fishes}, volume = {9}, number = {6}, pages = {243}, abstract = {Fishes in marine caves have attracted limited attention by the scientific community in comparison to subterranean fishes which have lost eyes and pigmentation. They constitute a largely unexplored component of marine fish diversity, except for the relatively well-studied marine caves of the Mediterranean Sea. These habitats are characterized by steep environmental gradients of decreasing light and decreasing water exchange. The fishes recorded so far in marine caves are not exclusive residents of this habitat and they are also present at least in the other mesolithial habitats. In the Mediterranean marine caves, 132 fishes have been recorded to date, representing about 17% of the total Mediterranean fish species richness. Most of these species are reported from the anterior cave zones where some light still exists, while a smaller number of species are known from the totally dark zones. Among them, 27.3% are accidental visitors, 53.8% are the regular mesolithial visitors and switchers between mesolithion and open water, 5.3% are permanent residents of the mesolithion, but also occur in other habitats, and 13.6% are exclusive permanent residents of mesolithion. Some mesolithial exclusive permanent residents recorded in marine caves share similar morphology, probably as adaptations to these habitats.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fishes in marine caves have attracted limited attention by the scientific community in comparison to subterranean fishes which have lost eyes and pigmentation. They constitute a largely unexplored component of marine fish diversity, except for the relatively well-studied marine caves of the Mediterranean Sea. These habitats are characterized by steep environmental gradients of decreasing light and decreasing water exchange. The fishes recorded so far in marine caves are not exclusive residents of this habitat and they are also present at least in the other mesolithial habitats. In the Mediterranean marine caves, 132 fishes have been recorded to date, representing about 17% of the total Mediterranean fish species richness. Most of these species are reported from the anterior cave zones where some light still exists, while a smaller number of species are known from the totally dark zones. Among them, 27.3% are accidental visitors, 53.8% are the regular mesolithial visitors and switchers between mesolithion and open water, 5.3% are permanent residents of the mesolithion, but also occur in other habitats, and 13.6% are exclusive permanent residents of mesolithion. Some mesolithial exclusive permanent residents recorded in marine caves share similar morphology, probably as adaptations to these habitats. |
Superio, Joshua; Resseguier, Julien; Nobrega, Rafael Henrique; Grebstad, Caroline M; Fakriadis, Ioannis; Foss, Atle; Hagen, Ørjan; Zhang, Meiling; García-Hernández, Maria Del Pilar; Galindo-Villegas, Jorge Aquaculture, 592 , pp. 741214, 2024, ISSN: 00448486. @article{superio_unravelling_2024, title = {Unravelling spermatogenesis in spotted wolffish: Insights from the ultrastructure of juvenile male testes to the cryopreservation of broodstock sperm}, author = {Joshua Superio and Julien Resseguier and Rafael Henrique Nobrega and Caroline M Grebstad and Ioannis Fakriadis and Atle Foss and Ørjan Hagen and Meiling Zhang and Maria Del Pilar García-Hernández and Jorge Galindo-Villegas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Superio-AQUA-30.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848624006756}, doi = {10.1016/j.aquaculture.2024.741214}, issn = {00448486}, year = {2024}, date = {2024-07-01}, urldate = {2024-07-01}, journal = {Aquaculture}, volume = {592}, pages = {741214}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bolanakis, Giannis; Paragkamian, Savvas; Chatzaki, Maria; Kotitsa, Nefeli; Kardaki, Liubitsa; Trichas, Apostolos The conservation status of the Cretan endemic Arthropods under Natura 2000 network Journal Article Biodiversity and Conservation, 2024, ISSN: 0960-3115, 1572-9710. @article{bolanakis_conservation_2024, title = {The conservation status of the Cretan endemic Arthropods under Natura 2000 network}, author = {Giannis Bolanakis and Savvas Paragkamian and Maria Chatzaki and Nefeli Kotitsa and Liubitsa Kardaki and Apostolos Trichas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Bolanakis-Biodiv-b-Conservation-pre-print-29.pdf https://link.springer.com/10.1007/s10531-024-02877-y}, doi = {10.1007/s10531-024-02877-y}, issn = {0960-3115, 1572-9710}, year = {2024}, date = {2024-06-26}, urldate = {2024-06-26}, journal = {Biodiversity and Conservation}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Roussos, Efstratios; Triantaphyllidis, George; Ilia, Vassiliki; Tsagarakis, Konstantinos; Machias, Athanasios; Tziveleka, Leto-Aikaterini; Roussis, Vassilios; Ioannou, Efstathia; Kotzamanis, Yannis Status of Fishery Discards and By-Products in Greece and Potential Valorization Scenarios towards a National Exploitation Master Plan Journal Article Marine Drugs, 22 (6), pp. 264, 2024, ISSN: 1660-3397. @article{roussos_status_2024, title = {Status of Fishery Discards and By-Products in Greece and Potential Valorization Scenarios towards a National Exploitation Master Plan}, author = {Efstratios Roussos and George Triantaphyllidis and Vassiliki Ilia and Konstantinos Tsagarakis and Athanasios Machias and Leto-Aikaterini Tziveleka and Vassilios Roussis and Efstathia Ioannou and Yannis Kotzamanis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Roussos-Marinedrugs-28.pdf https://www.mdpi.com/1660-3397/22/6/264}, doi = {10.3390/md22060264}, issn = {1660-3397}, year = {2024}, date = {2024-06-17}, urldate = {2024-06-17}, journal = {Marine Drugs}, volume = {22}, number = {6}, pages = {264}, abstract = {The valorization of aquaculture/fishery processing by-products, as well as unavoidable/unwanted catches and discards in Greece, is currently an underutilized activity despite the fact that there are several best practices in Northern Europe and overseas. One of the main challenges is to determine whether the available quantities for processing are sufficient to warrant the valorization of discards and fish side streams. This is the first attempt to systematically record and analyze the available quantities of fish by-products and discards in Greece spatially and temporally in an effort to create a national exploitation Master Plan for the valorization of this unavoidable and unwanted biomass. A thorough survey conducted within the VIOAXIOPIO project unveiled a substantial biomass of around 19,000 tonnes annually that could be harnessed for valorization. Furthermore, the production of various High-Added-Value Biomolecules (HAVBs) was investigated and experimental trials were conducted to assess the potential yields, with the collected data used to formulate four valorization scenarios.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The valorization of aquaculture/fishery processing by-products, as well as unavoidable/unwanted catches and discards in Greece, is currently an underutilized activity despite the fact that there are several best practices in Northern Europe and overseas. One of the main challenges is to determine whether the available quantities for processing are sufficient to warrant the valorization of discards and fish side streams. This is the first attempt to systematically record and analyze the available quantities of fish by-products and discards in Greece spatially and temporally in an effort to create a national exploitation Master Plan for the valorization of this unavoidable and unwanted biomass. A thorough survey conducted within the VIOAXIOPIO project unveiled a substantial biomass of around 19,000 tonnes annually that could be harnessed for valorization. Furthermore, the production of various High-Added-Value Biomolecules (HAVBs) was investigated and experimental trials were conducted to assess the potential yields, with the collected data used to formulate four valorization scenarios. |
Papadaki, Maria; Karamanlidis, Dimitris; Sigelaki, Eirini; Fakriadis, Ioannis; Mylonas, Constantinos C Evolution of sex ratio and egg production of gilthead seabream (Sparus aurata) over the course of five reproductive seasons Journal Article Aquaculture and Fisheries, 9 (4), pp. 534–542, 2024, ISSN: 2468550X. @article{papadaki_evolution_2024, title = {Evolution of sex ratio and egg production of gilthead seabream (Sparus aurata) over the course of five reproductive seasons}, author = {Maria Papadaki and Dimitris Karamanlidis and Eirini Sigelaki and Ioannis Fakriadis and Constantinos C Mylonas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Papadaki-AquaFish-27.pdf https://linkinghub.elsevier.com/retrieve/pii/S2468550X22001836}, doi = {10.1016/j.aaf.2022.10.006}, issn = {2468550X}, year = {2024}, date = {2024-06-13}, urldate = {2024-06-13}, journal = {Aquaculture and Fisheries}, volume = {9}, number = {4}, pages = {534--542}, keywords = {}, pubstate = {published}, tppubtype = {article} } |