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} } |