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\n \n \n\n \n \n \n \n \n \n A robust approach to estimate relative phytoplankton cell abundances from metagenomes.\n \n \n \n \n\n\n \n Pierella Karlusich, J. J.; Pelletier, E.; Zinger, L.; Lombard, F.; Zingone, A.; Colin, S.; Gasol, J. M.; Dorrell, R. G.; Henry, N.; Scalco, E.; Acinas, S. G.; Wincker, P.; de Vargas, C.; and Bowler, C.\n\n\n \n\n\n\n Molecular Ecology Resources, 23(1): 16–40. 2023.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13592\n\n\n\n
\n\n\n\n \n \n![\"A](\"//bibbase.org/img/filetypes/link.svg\"\n\t "\\"Paper\\"\n\t")
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\n\n\n@article{pierella_karlusich_robust_2023,\n\ttitle = {A robust approach to estimate relative phytoplankton cell abundances from metagenomes},\n\tvolume = {23},\n\tissn = {1755-0998},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13592},\n\tdoi = {10.1111/1755-0998.13592},\n\tabstract = {Phytoplankton account for {\\textgreater}45\\% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of {\\textgreater}18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2022-12-06},\n\tjournal = {Molecular Ecology Resources},\n\tauthor = {Pierella Karlusich, Juan José and Pelletier, Eric and Zinger, Lucie and Lombard, Fabien and Zingone, Adriana and Colin, Sébastien and Gasol, Josep M. and Dorrell, Richard G. and Henry, Nicolas and Scalco, Eleonora and Acinas, Silvia G. and Wincker, Patrick and de Vargas, Colomban and Bowler, Chris},\n\tyear = {2023},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13592},\n\tkeywords = {18S rRNA, Tara Oceans, metabarcoding, metagenomics, metatranscriptomics, photosynthesis, phytoplankton, psbO},\n\tpages = {16--40},\n}\n\n\n\n Phytoplankton account for \\textgreater45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of \\textgreater18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.\n
\n\n\n\n \n\n \n \n \n \n \n \n Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.\n \n \n \n \n\n\n \n Veglia, A. J.; Bistolas, K. S. I.; Voolstra, C. R.; Hume, B. C. C.; Ruscheweyh, H.; Planes, S.; Allemand, D.; Boissin, E.; Wincker, P.; Poulain, J.; Moulin, C.; Bourdin, G.; Iwankow, G.; Romac, S.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, M.; Forcioli, D.; Furla, P.; Galand, P. E.; Gilson, E.; Lombard, F.; Pesant, S.; Reynaud, S.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Zoccola, D.; Correa, A. M. S.; and Vega Thurber, R. L.\n\n\n \n\n\n\n Communications Biology, 6(1): 1–13. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{veglia_endogenous_2023,\n\ttitle = {Endogenous viral elements reveal associations between a non-retroviral {RNA} virus and symbiotic dinoflagellate genomes},\n\tvolume = {6},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2399-3642},\n\turl = {https://www.nature.com/articles/s42003-023-04917-9},\n\tdoi = {10.1038/s42003-023-04917-9},\n\tabstract = {Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Communications Biology},\n\tauthor = {Veglia, Alex J. and Bistolas, Kalia S. I. and Voolstra, Christian R. and Hume, Benjamin C. C. and Ruscheweyh, Hans-Joachim and Planes, Serge and Allemand, Denis and Boissin, Emilie and Wincker, Patrick and Poulain, Julie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Correa, Adrienne M. S. and Vega Thurber, Rebecca L.},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Microbial ecology, Virology, Water microbiology},\n\tpages = {1--13},\n}\n\n\n\n Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.\n
\n\n\n\n \n\n \n \n \n \n \n \n Pan-Arctic plankton community structure and its global connectivity.\n \n \n \n \n\n\n \n Ibarbalz, F. M.; Henry, N.; Mahé, F.; Ardyna, M.; Zingone, A.; Scalco, E.; Lovejoy, C.; Lombard, F.; Jaillon, O.; Iudicone, D.; Malviya, S.; Tara Oceans Coordinators; Sullivan, M. B.; Chaffron, S.; Karsenti, E.; Babin, M.; Boss, E.; Wincker, P.; Zinger, L.; de Vargas, C.; Bowler, C.; and Karp-Boss, L.\n\n\n \n\n\n\n Elementa: Science of the Anthropocene, 11(1): 00060. April 2023.\n \n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{ibarbalz_pan-arctic_2023,\n\ttitle = {Pan-{Arctic} plankton community structure and its global connectivity},\n\tvolume = {11},\n\tissn = {2325-1026},\n\turl = {https://doi.org/10.1525/elementa.2022.00060},\n\tdoi = {10.1525/elementa.2022.00060},\n\tabstract = {The Arctic Ocean (AO) is being rapidly transformed by global warming, but its biodiversity remains understudied for many planktonic organisms, in particular for unicellular eukaryotes that play pivotal roles in marine food webs and biogeochemical cycles. The aim of this study was to characterize the biogeographic ranges of species that comprise the contemporary pool of unicellular eukaryotes in the AO as a first step toward understanding mechanisms that structure these communities and identifying potential target species for monitoring. Leveraging the Tara Oceans DNA metabarcoding data, we mapped the global distributions of operational taxonomic units (OTUs) found on Arctic shelves into five biogeographic categories, identified biogeographic indicators, and inferred the degree to which AO communities of unicellular eukaryotes share members with assemblages from lower latitudes. Arctic/Polar indicator OTUs, as well as some globally ubiquitous OTUs, dominated the detection and abundance of DNA reads in the Arctic samples. OTUs detected only in Arctic samples (Arctic-exclusives) showed restricted distribution with relatively low abundances, accounting for 10–16\\% of the total Arctic OTU pool. OTUs with high abundances in tropical and/or temperate latitudes (non-Polar indicators) were also found in the AO but mainly at its periphery. We observed a large change in community taxonomic composition across the Atlantic-Arctic continuum, supporting the idea that advection and environmental filtering are important processes that shape plankton assemblages in the AO. Altogether, this study highlights the connectivity between the AO and other oceans, and provides a framework for monitoring and assessing future changes in this vulnerable ecosystem.},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Elementa: Science of the Anthropocene},\n\tauthor = {Ibarbalz, Federico M. and Henry, Nicolas and Mahé, Frédéric and Ardyna, Mathieu and Zingone, Adriana and Scalco, Eleonora and Lovejoy, Connie and Lombard, Fabien and Jaillon, Olivier and Iudicone, Daniele and Malviya, Shruti and {Tara Oceans Coordinators} and Sullivan, Matthew B. and Chaffron, Samuel and Karsenti, Eric and Babin, Marcel and Boss, Emmanuel and Wincker, Patrick and Zinger, Lucie and de Vargas, Colomban and Bowler, Chris and Karp-Boss, Lee},\n\tmonth = apr,\n\tyear = {2023},\n\tpages = {00060},\n}\n\n\n\n The Arctic Ocean (AO) is being rapidly transformed by global warming, but its biodiversity remains understudied for many planktonic organisms, in particular for unicellular eukaryotes that play pivotal roles in marine food webs and biogeochemical cycles. The aim of this study was to characterize the biogeographic ranges of species that comprise the contemporary pool of unicellular eukaryotes in the AO as a first step toward understanding mechanisms that structure these communities and identifying potential target species for monitoring. Leveraging the Tara Oceans DNA metabarcoding data, we mapped the global distributions of operational taxonomic units (OTUs) found on Arctic shelves into five biogeographic categories, identified biogeographic indicators, and inferred the degree to which AO communities of unicellular eukaryotes share members with assemblages from lower latitudes. Arctic/Polar indicator OTUs, as well as some globally ubiquitous OTUs, dominated the detection and abundance of DNA reads in the Arctic samples. OTUs detected only in Arctic samples (Arctic-exclusives) showed restricted distribution with relatively low abundances, accounting for 10–16% of the total Arctic OTU pool. OTUs with high abundances in tropical and/or temperate latitudes (non-Polar indicators) were also found in the AO but mainly at its periphery. We observed a large change in community taxonomic composition across the Atlantic-Arctic continuum, supporting the idea that advection and environmental filtering are important processes that shape plankton assemblages in the AO. Altogether, this study highlights the connectivity between the AO and other oceans, and provides a framework for monitoring and assessing future changes in this vulnerable ecosystem.\n
\n\n\n\n \n\n \n \n \n \n \n \n Predicting global distributions of eukaryotic plankton communities from satellite data.\n \n \n \n \n\n\n \n Kaneko, H.; Endo, H.; Henry, N.; Berney, C.; Mahé, F.; Poulain, J.; Labadie, K.; Beluche, O.; El Hourany, R.; Chaffron, S.; Wincker, P.; Nakamura, R.; Karp-Boss, L.; Boss, E.; Chris Bowler; de Vargas, C.; Tomii, K.; and Ogata, H.\n\n\n \n\n\n\n ISME Communications, 3(1): 1–9. September 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \nPaper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{kaneko_predicting_2023,\n\ttitle = {Predicting global distributions of eukaryotic plankton communities from satellite data},\n\tvolume = {3},\n\tcopyright = {2023 ISME Publications B.V},\n\tissn = {2730-6151},\n\turl = {https://www.nature.com/articles/s43705-023-00308-7},\n\tdoi = {10.1038/s43705-023-00308-7},\n\tabstract = {Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67\\% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {ISME Communications},\n\tauthor = {Kaneko, Hiroto and Endo, Hisashi and Henry, Nicolas and Berney, Cédric and Mahé, Frédéric and Poulain, Julie and Labadie, Karine and Beluche, Odette and El Hourany, Roy and Chaffron, Samuel and Wincker, Patrick and Nakamura, Ryosuke and Karp-Boss, Lee and Boss, Emmanuel and {Chris Bowler} and de Vargas, Colomban and Tomii, Kentaro and Ogata, Hiroyuki},\n\tmonth = sep,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Biooceanography, Microbial ecology},\n\tpages = {1--9},\n}\n\n\n\n Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.\n
\n\n\n\n \n\n \n \n \n \n \n \n Different environmental response strategies in sympatric corals from Pacific Islands.\n \n \n \n \n\n\n \n Porro, B.; Zamoum, T.; Forcioli, D.; Gilson, E.; Poquet, A.; Di Franco, E.; Barnay-Verdier, S.; Lombard, F.; Voolstra, C. R.; Hume, B. C. C.; Galand, P. E.; Moulin, C.; Boissin, E.; Bourdin, G.; Iwankow, G.; Poulain, J.; Romac, S.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, M.; Pesant, S.; Reynaud, S.; Sullivan, M. B.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Wincker, P.; Zoccola, D.; Planes, S.; Allemand, D.; Röttinger, E.; and Furla, P.\n\n\n \n\n\n\n Communications Earth & Environment, 4(1): 1–17. September 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{porro_different_2023,\n\ttitle = {Different environmental response strategies in sympatric corals from {Pacific} {Islands}},\n\tvolume = {4},\n\tcopyright = {2023 Springer Nature Limited},\n\tissn = {2662-4435},\n\turl = {https://www.nature.com/articles/s43247-023-00946-8},\n\tdoi = {10.1038/s43247-023-00946-8},\n\tabstract = {Coral reefs are severely threatened by global and local environmental changes. However, susceptibility to perturbations and subsequent mortality varies among coral species. In this study, we tested the contribution of genetic and environmental conditions to coral’s phenotypic response in Pocillopora spp. and Porites spp. sampled together at a large ecological and temporal scale throughout the Pacific Ocean. We assessed coral phenotype signatures using a multi-biomarker approach (animal and symbiont biomasses, protein carbonylation and ubiquitination and total antioxidant capacities). In both genera, we highlighted a strong anticorrelation between the redox state and the animal and symbiont biomasses. In addition, Pocillopora exhibited high phenotypic plasticity, responding to various environmental variables such as temperature, nutrients, phosphate, and carbonate chemistry. In contrast, Porites displayed more robust phenotypes influenced by both genetics and past climate events. In conclusion, co-located coral species display different phenotypic response strategies that are influenced by different environmental conditions.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Communications Earth \\& Environment},\n\tauthor = {Porro, Barbara and Zamoum, Thamilla and Forcioli, Didier and Gilson, Eric and Poquet, Adrien and Di Franco, Eugenio and Barnay-Verdier, Stéphanie and Lombard, Fabien and Voolstra, Christian R. and Hume, Benjamin C. C. and Galand, Pierre E. and Moulin, Clémentine and Boissin, Emilie and Bourdin, Guillaume and Iwankow, Guillaume and Poulain, Julie and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, Michel and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Zoccola, Didier and Planes, Serge and Allemand, Denis and Röttinger, Eric and Furla, Paola},\n\tmonth = sep,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Ecophysiology, Marine biology},\n\tpages = {1--17},\n}\n\n\n\n Coral reefs are severely threatened by global and local environmental changes. However, susceptibility to perturbations and subsequent mortality varies among coral species. In this study, we tested the contribution of genetic and environmental conditions to coral’s phenotypic response in Pocillopora spp. and Porites spp. sampled together at a large ecological and temporal scale throughout the Pacific Ocean. We assessed coral phenotype signatures using a multi-biomarker approach (animal and symbiont biomasses, protein carbonylation and ubiquitination and total antioxidant capacities). In both genera, we highlighted a strong anticorrelation between the redox state and the animal and symbiont biomasses. In addition, Pocillopora exhibited high phenotypic plasticity, responding to various environmental variables such as temperature, nutrients, phosphate, and carbonate chemistry. In contrast, Porites displayed more robust phenotypes influenced by both genetics and past climate events. In conclusion, co-located coral species display different phenotypic response strategies that are influenced by different environmental conditions.\n
\n\n\n\n \n\n \n \n \n \n \n \n Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.\n \n \n \n \n\n\n \n Lombard, F.; Bourdin, G.; Pesant, S.; Agostini, S.; Baudena, A.; Boissin, E.; Cassar, N.; Clampitt, M.; Conan, P.; Da Silva, O.; Dimier, C.; Douville, E.; Elineau, A.; Fin, J.; Flores, J. M.; Ghiglione, J.; Hume, B. C. C.; Jalabert, L.; John, S. G.; Kelly, R. L.; Koren, I.; Lin, Y.; Marie, D.; McMinds, R.; Mériguet, Z.; Metzl, N.; Paz-García, D. A.; Pedrotti, M. L.; Poulain, J.; Pujo-Pay, M.; Ras, J.; Reverdin, G.; Romac, S.; Rouan, A.; Röttinger, E.; Vardi, A.; Voolstra, C. R.; Moulin, C.; Iwankow, G.; Banaigs, B.; Bowler, C.; de Vargas, C.; Forcioli, D.; Furla, P.; Galand, P. E.; Gilson, E.; Reynaud, S.; Sunagawa, S.; Sullivan, M. B.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Wincker, P.; Zoccola, D.; Allemand, D.; Planes, S.; Boss, E.; and Gorsky, G.\n\n\n \n\n\n\n Scientific Data, 10(1): 324. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{lombard_open_2023,\n\ttitle = {Open science resources from the {Tara} {Pacific} expedition across coral reef and surface ocean ecosystems},\n\tvolume = {10},\n\tcopyright = {2022 The Author(s)},\n\tissn = {2052-4463},\n\turl = {https://www.nature.com/articles/s41597-022-01757-w},\n\tdoi = {10.1038/s41597-022-01757-w},\n\tabstract = {The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Scientific Data},\n\tauthor = {Lombard, Fabien and Bourdin, Guillaume and Pesant, Stéphane and Agostini, Sylvain and Baudena, Alberto and Boissin, Emilie and Cassar, Nicolas and Clampitt, Megan and Conan, Pascal and Da Silva, Ophélie and Dimier, Céline and Douville, Eric and Elineau, Amanda and Fin, Jonathan and Flores, J. Michel and Ghiglione, Jean-François and Hume, Benjamin C. C. and Jalabert, Laetitia and John, Seth G. and Kelly, Rachel L. and Koren, Ilan and Lin, Yajuan and Marie, Dominique and McMinds, Ryan and Mériguet, Zoé and Metzl, Nicolas and Paz-García, David A. and Pedrotti, Maria Luiza and Poulain, Julie and Pujo-Pay, Mireille and Ras, Joséphine and Reverdin, Gilles and Romac, Sarah and Rouan, Alice and Röttinger, Eric and Vardi, Assaf and Voolstra, Christian R. and Moulin, Clémentine and Iwankow, Guillaume and Banaigs, Bernard and Bowler, Chris and de Vargas, Colomban and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Reynaud, Stéphanie and Sunagawa, Shinichi and Sullivan, Matthew B. and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Zoccola, Didier and Allemand, Denis and Planes, Serge and Boss, Emmanuel and Gorsky, Gaby},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Biodiversity, Ecosystem ecology},\n\tpages = {324},\n}\n\n\n\n The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.\n
\n\n\n\n \n\n \n \n \n \n \n \n Ocean-wide comparisons of mesopelagic planktonic community structures.\n \n \n \n \n\n\n \n Rigonato, J.; Budinich, M.; Murillo, A. A.; Brandão, M. C.; Pierella Karlusich, J. J.; Soviadan, Y. D.; Gregory, A. C.; Endo, H.; Kokoszka, F.; Vik, D.; Henry, N.; Frémont, P.; Labadie, K.; Zayed, A. A.; Dimier, C.; Picheral, M.; Searson, S.; Poulain, J.; Kandels, S.; Pesant, S.; Karsenti, E.; Bork, P.; Bowler, C.; Cochrane, G.; de Vargas, C.; Eveillard, D.; Gehlen, M.; Iudicone, D.; Lombard, F.; Ogata, H.; Stemmann, L.; Sullivan, M. B.; Sunagawa, S.; Wincker, P.; Chaffron, S.; and Jaillon, O.\n\n\n \n\n\n\n ISME Communications, 3(1): 1–11. August 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{rigonato_ocean-wide_2023,\n\ttitle = {Ocean-wide comparisons of mesopelagic planktonic community structures},\n\tvolume = {3},\n\tcopyright = {2023 ISME Publications B.V},\n\tissn = {2730-6151},\n\turl = {https://www.nature.com/articles/s43705-023-00279-9},\n\tdoi = {10.1038/s43705-023-00279-9},\n\tabstract = {For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3− and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70\\% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {ISME Communications},\n\tauthor = {Rigonato, Janaina and Budinich, Marko and Murillo, Alejandro A. and Brandão, Manoela C. and Pierella Karlusich, Juan J. and Soviadan, Yawouvi Dodji and Gregory, Ann C. and Endo, Hisashi and Kokoszka, Florian and Vik, Dean and Henry, Nicolas and Frémont, Paul and Labadie, Karine and Zayed, Ahmed A. and Dimier, Céline and Picheral, Marc and Searson, Sarah and Poulain, Julie and Kandels, Stefanie and Pesant, Stéphane and Karsenti, Eric and Bork, Peer and Bowler, Chris and Cochrane, Guy and de Vargas, Colomban and Eveillard, Damien and Gehlen, Marion and Iudicone, Daniele and Lombard, Fabien and Ogata, Hiroyuki and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Chaffron, Samuel and Jaillon, Olivier},\n\tmonth = aug,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Community ecology, Microbial ecology},\n\tpages = {1--11},\n}\n\n\n\n For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3− and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.\n
\n\n\n\n \n\n \n \n \n \n \n \n Mirusviruses link herpesviruses to giant viruses.\n \n \n \n \n\n\n \n Gaïa, M.; Meng, L.; Pelletier, E.; Forterre, P.; Vanni, C.; Fernandez-Guerra, A.; Jaillon, O.; Wincker, P.; Ogata, H.; Krupovic, M.; and Delmont, T. O.\n\n\n \n\n\n\n Nature, 616(7958): 783–789. April 2023.\n Number: 7958 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{gaia_mirusviruses_2023,\n\ttitle = {Mirusviruses link herpesviruses to giant viruses},\n\tvolume = {616},\n\tcopyright = {2023 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/s41586-023-05962-4},\n\tdoi = {10.1038/s41586-023-05962-4},\n\tabstract = {DNA viruses have a major influence on the ecology and evolution of cellular organisms1–4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria6, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.},\n\tlanguage = {en},\n\tnumber = {7958},\n\turldate = {2023-10-25},\n\tjournal = {Nature},\n\tauthor = {Gaïa, Morgan and Meng, Lingjie and Pelletier, Eric and Forterre, Patrick and Vanni, Chiara and Fernandez-Guerra, Antonio and Jaillon, Olivier and Wincker, Patrick and Ogata, Hiroyuki and Krupovic, Mart and Delmont, Tom O.},\n\tmonth = apr,\n\tyear = {2023},\n\tnote = {Number: 7958\nPublisher: Nature Publishing Group},\n\tkeywords = {Evolutionary genetics, Marine biology, Metagenomics, Phylogenetics, Viral genetics},\n\tpages = {783--789},\n}\n\n\n\n DNA viruses have a major influence on the ecology and evolution of cellular organisms1–4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria6, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.\n
\n\n\n\n \n\n \n \n \n \n \n \n Diversity of the Pacific Ocean coral reef microbiome.\n \n \n \n \n\n\n \n Galand, P. E.; Ruscheweyh, H.; Salazar, G.; Hochart, C.; Henry, N.; Hume, B. C. C.; Oliveira, P. H.; Perdereau, A.; Labadie, K.; Belser, C.; Boissin, E.; Romac, S.; Poulain, J.; Bourdin, G.; Iwankow, G.; Moulin, C.; Armstrong, E. J.; Paz-García, D. A.; Ziegler, M.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, M.; Forcioli, D.; Furla, P.; Gilson, E.; Lombard, F.; Pesant, S.; Reynaud, S.; Thomas, O. P.; Troublé, R.; Zoccola, D.; Voolstra, C. R.; Thurber, R. V.; Sunagawa, S.; Wincker, P.; Allemand, D.; and Planes, S.\n\n\n \n\n\n\n Nature Communications, 14(1): 3039. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{galand_diversity_2023,\n\ttitle = {Diversity of the {Pacific} {Ocean} coral reef microbiome},\n\tvolume = {14},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38500-x},\n\tdoi = {10.1038/s41467-023-38500-x},\n\tabstract = {Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Nature Communications},\n\tauthor = {Galand, Pierre E. and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Hochart, Corentin and Henry, Nicolas and Hume, Benjamin C. C. and Oliveira, Pedro H. and Perdereau, Aude and Labadie, Karine and Belser, Caroline and Boissin, Emilie and Romac, Sarah and Poulain, Julie and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Armstrong, Eric J. and Paz-García, David A. and Ziegler, Maren and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Voolstra, Christian R. and Thurber, Rebecca Vega and Sunagawa, Shinichi and Wincker, Patrick and Allemand, Denis and Planes, Serge},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Microbial ecology, Microbiome},\n\tpages = {3039},\n}\n\n\n\n Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.\n
\n\n\n\n \n\n \n \n \n \n \n \n Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals.\n \n \n \n \n\n\n \n Rouan, A.; Pousse, M.; Djerbi, N.; Porro, B.; Bourdin, G.; Carradec, Q.; Hume, B. C.; Poulain, J.; Lê-Hoang, J.; Armstrong, E.; Agostini, S.; Salazar, G.; Ruscheweyh, H.; Aury, J.; Paz-García, D. A.; McMinds, R.; Giraud-Panis, M.; Deshuraud, R.; Ottaviani, A.; Morini, L. D.; Leone, C.; Wurzer, L.; Tran, J.; Zoccola, D.; Pey, A.; Moulin, C.; Boissin, E.; Iwankow, G.; Romac, S.; de Vargas, C.; Banaigs, B.; Boss, E.; Bowler, C.; Douville, E.; Flores, M.; Reynaud, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Planes, S.; Allemand, D.; Pesant, S.; Galand, P. E.; Wincker, P.; Sunagawa, S.; Röttinger, E.; Furla, P.; Voolstra, C. R.; Forcioli, D.; Lombard, F.; and Gilson, E.\n\n\n \n\n\n\n Nature Communications, 14(1): 3038. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{rouan_telomere_2023,\n\tseries = {\\#26},\n\ttitle = {Telomere {DNA} length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals},\n\tvolume = {14},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38499-1},\n\tdoi = {10.1038/s41467-023-38499-1},\n\tabstract = {Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-03},\n\tjournal = {Nature Communications},\n\tauthor = {Rouan, Alice and Pousse, Melanie and Djerbi, Nadir and Porro, Barbara and Bourdin, Guillaume and Carradec, Quentin and Hume, Benjamin CC and Poulain, Julie and Lê-Hoang, Julie and Armstrong, Eric and Agostini, Sylvain and Salazar, Guillem and Ruscheweyh, Hans-Joachim and Aury, Jean-Marc and Paz-García, David A. and McMinds, Ryan and Giraud-Panis, Marie-Josèphe and Deshuraud, Romane and Ottaviani, Alexandre and Morini, Lycia Die and Leone, Camille and Wurzer, Lia and Tran, Jessica and Zoccola, Didier and Pey, Alexis and Moulin, Clémentine and Boissin, Emilie and Iwankow, Guillaume and Romac, Sarah and de Vargas, Colomban and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and Douville, Eric and Flores, Michel and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Planes, Serge and Allemand, Denis and Pesant, Stephane and Galand, Pierre E. and Wincker, Patrick and Sunagawa, Shinichi and Röttinger, Eric and Furla, Paola and Voolstra, Christian R. and Forcioli, Didier and Lombard, Fabien and Gilson, Eric},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Cell biology, Ecology, Evolution},\n\tpages = {3038},\n}\n\n\n\n Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.\n
\n\n\n\n \n\n \n \n \n \n \n \n Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.\n \n \n \n \n\n\n \n Belser, C.; Poulain, J.; Labadie, K.; Gavory, F.; Alberti, A.; Guy, J.; Carradec, Q.; Cruaud, C.; Da Silva, C.; Engelen, S.; Mielle, P.; Perdereau, A.; Samson, G.; Gas, S.; Voolstra, C. R.; Galand, P. E.; Flores, J. M.; Hume, B. C. C.; Perna, G.; Ziegler, M.; Ruscheweyh, H.; Boissin, E.; Romac, S.; Bourdin, G.; Iwankow, G.; Moulin, C.; Paz García, D. A.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Forcioli, D.; Furla, P.; Gilson, E.; Lombard, F.; Pesant, S.; Reynaud, S.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Zoccola, D.; Scarpelli, C.; Jacoby, E. K.; Oliveira, P. H.; Aury, J.; Allemand, D.; Planes, S.; and Wincker, P.\n\n\n \n\n\n\n Scientific Data, 10(1): 326. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{belser_integrative_2023,\n\tseries = {\\#21},\n\ttitle = {Integrative omics framework for characterization of coral reef ecosystems from the {Tara} {Pacific} expedition},\n\tvolume = {10},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2052-4463},\n\turl = {https://www.nature.com/articles/s41597-023-02204-0},\n\tdoi = {10.1038/s41597-023-02204-0},\n\tabstract = {Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-03},\n\tjournal = {Scientific Data},\n\tauthor = {Belser, Caroline and Poulain, Julie and Labadie, Karine and Gavory, Frederick and Alberti, Adriana and Guy, Julie and Carradec, Quentin and Cruaud, Corinne and Da Silva, Corinne and Engelen, Stefan and Mielle, Paul and Perdereau, Aude and Samson, Gaelle and Gas, Shahinaz and Voolstra, Christian R. and Galand, Pierre E. and Flores, J. Michel and Hume, Benjamin C. C. and Perna, Gabriela and Ziegler, Maren and Ruscheweyh, Hans-Joachim and Boissin, Emilie and Romac, Sarah and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Paz García, David A. and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Zoccola, Didier and Scarpelli, Claude and Jacoby, E’ Krame and Oliveira, Pedro H. and Aury, Jean-Marc and Allemand, Denis and Planes, Serge and Wincker, Patrick},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Data processing, Marine biology, Metagenomics, Next-generation sequencing},\n\tpages = {326},\n}\n\n\n\n Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.\n
\n\n\n\n \n\n \n \n \n \n \n \n Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.\n \n \n \n \n\n\n \n Armstrong, E. J.; Lê-Hoang, J.; Carradec, Q.; Aury, J.; Noel, B.; Hume, B. C. C.; Voolstra, C. R.; Poulain, J.; Belser, C.; Paz-García, D. A.; Cruaud, C.; Labadie, K.; Da Silva, C.; Moulin, C.; Boissin, E.; Bourdin, G.; Iwankow, G.; Romac, S.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, M.; Forcioli, D.; Furla, P.; Galand, P. E.; Gilson, E.; Lombard, F.; Pesant, S.; Reynaud, S.; Sullivan, M. B.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Zoccola, D.; Planes, S.; Allemand, D.; and Wincker, P.\n\n\n \n\n\n\n Nature Communications, 14(1): 3056. June 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{armstrong_host_2023,\n\tseries = {\\#27},\n\ttitle = {Host transcriptomic plasticity and photosymbiotic fidelity underpin {Pocillopora} acclimatization across thermal regimes in the {Pacific} {Ocean}},\n\tvolume = {14},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38610-6},\n\tdoi = {10.1038/s41467-023-38610-6},\n\tabstract = {Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-03},\n\tjournal = {Nature Communications},\n\tauthor = {Armstrong, Eric J. and Lê-Hoang, Julie and Carradec, Quentin and Aury, Jean-Marc and Noel, Benjamin and Hume, Benjamin C. C. and Voolstra, Christian R. and Poulain, Julie and Belser, Caroline and Paz-García, David A. and Cruaud, Corinne and Labadie, Karine and Da Silva, Corinne and Moulin, Clémentine and Boissin, Emilie and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Zoccola, Didier and Planes, Serge and Allemand, Denis and Wincker, Patrick},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Ecophysiology, Gene expression, Marine biology},\n\tpages = {3056},\n}\n\n\n\n Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.\n
\n\n\n\n \n\n \n \n \n \n \n \n Pervasive tandem duplications and convergent evolution shape coral genomes.\n \n \n \n \n\n\n \n Noel, B.; Denoeud, F.; Rouan, A.; Buitrago-López, C.; Capasso, L.; Poulain, J.; Boissin, E.; Pousse, M.; Da Silva, C.; Couloux, A.; Armstrong, E.; Carradec, Q.; Cruaud, C.; Labadie, K.; Lê-Hoang, J.; Tambutté, S.; Barbe, V.; Moulin, C.; Bourdin, G.; Iwankow, G.; Romac, S.; Agostini, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, J. M.; Forcioli, D.; Furla, P.; Galand, P. E.; Lombard, F.; Pesant, S.; Reynaud, S.; Sullivan, M. B.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Allemand, D.; Planes, S.; Gilson, E.; Zoccola, D.; Wincker, P.; Voolstra, C. R.; and Aury, J.\n\n\n \n\n\n\n Genome Biology, 24(1): 123. June 2023.\n \n\n\n\n
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\n\n\n@article{noel_pervasive_2023,\n\ttitle = {Pervasive tandem duplications and convergent evolution shape coral genomes},\n\tvolume = {24},\n\tissn = {1474-760X},\n\turl = {https://doi.org/10.1186/s13059-023-02960-7},\n\tdoi = {10.1186/s13059-023-02960-7},\n\tabstract = {Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-03},\n\tjournal = {Genome Biology},\n\tauthor = {Noel, Benjamin and Denoeud, France and Rouan, Alice and Buitrago-López, Carol and Capasso, Laura and Poulain, Julie and Boissin, Emilie and Pousse, Mélanie and Da Silva, Corinne and Couloux, Arnaud and Armstrong, Eric and Carradec, Quentin and Cruaud, Corinne and Labadie, Karine and Lê-Hoang, Julie and Tambutté, Sylvie and Barbe, Valérie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Allemand, Denis and Planes, Serge and Gilson, Eric and Zoccola, Didier and Wincker, Patrick and Voolstra, Christian R. and Aury, Jean-Marc},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {123},\n}\n\n\n\n Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.\n
\n\n\n\n \n\n \n \n \n \n \n \n Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation.\n \n \n \n \n\n\n \n Voolstra, C. R.; Hume, B. C. C.; Armstrong, E. J.; Mitushasi, G.; Porro, B.; Oury, N.; Agostini, S.; Boissin, E.; Poulain, J.; Carradec, Q.; Paz-García, D. A.; Zoccola, D.; Magalon, H.; Moulin, C.; Bourdin, G.; Iwankow, G.; Romac, S.; Banaigs, B.; Boss, E.; Bowler, C.; de Vargas, C.; Douville, E.; Flores, M.; Furla, P.; Galand, P. E.; Gilson, E.; Lombard, F.; Pesant, S.; Reynaud, S.; Sullivan, M. B.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; Thurber, R. V.; Wincker, P.; Planes, S.; Allemand, D.; and Forcioli, D.\n\n\n \n\n\n\n npj Biodiversity, 2(1): 1–16. July 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{voolstra_disparate_2023,\n\ttitle = {Disparate genetic divergence patterns in three corals across a pan-{Pacific} environmental gradient highlight species-specific adaptation},\n\tvolume = {2},\n\tcopyright = {2023 The Author(s)},\n\tissn = {2731-4243},\n\turl = {https://www.nature.com/articles/s44185-023-00020-8},\n\tdoi = {10.1038/s44185-023-00020-8},\n\tabstract = {Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla—across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-07-10},\n\tjournal = {npj Biodiversity},\n\tauthor = {Voolstra, Christian R. and Hume, Benjamin C. C. and Armstrong, Eric J. and Mitushasi, Guinther and Porro, Barbara and Oury, Nicolas and Agostini, Sylvain and Boissin, Emilie and Poulain, Julie and Carradec, Quentin and Paz-García, David A. and Zoccola, Didier and Magalon, Hélène and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and de Vargas, Colomban and Douville, Eric and Flores, Michel and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Planes, Serge and Allemand, Denis and Forcioli, Didier},\n\tmonth = jul,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Conservation biology, Ecological genetics, Evolutionary genetics, Genetic variation, Population genetics},\n\tpages = {1--16},\n}\n\n\n\n Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla—across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.\n
\n\n\n\n \n\n \n \n \n \n \n \n Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.\n \n \n \n \n\n\n \n Dorrell, R. G.; Kuo, A.; Füssy, Z.; Richardson, E. H.; Salamov, A.; Zarevski, N.; Freyria, N. J.; Ibarbalz, F. M.; Jenkins, J.; Karlusich, J. J. P.; Steindorff, A. S.; Edgar, R. E.; Handley, L.; Lail, K.; Lipzen, A.; Lombard, V.; McFarlane, J.; Nef, C.; Vanclová, A. M. N.; Peng, Y.; Plott, C.; Potvin, M.; Vieira, F. R. J.; Barry, K.; Vargas, C. d.; Henrissat, B.; Pelletier, E.; Schmutz, J.; Wincker, P.; Dacks, J. B.; Bowler, C.; Grigoriev, I. V.; and Lovejoy, C.\n\n\n \n\n\n\n Life Science Alliance, 6(3). March 2023.\n Publisher: Life Science Alliance Section: Research Articles\n\n\n\n
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\n\n\n@article{dorrell_convergent_2023,\n\ttitle = {Convergent evolution and horizontal gene transfer in {Arctic} {Ocean} microalgae},\n\tvolume = {6},\n\tcopyright = {© 2022 Dorrell et al.. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).},\n\tissn = {2575-1077},\n\turl = {https://www.life-science-alliance.org/content/6/3/e202201833},\n\tdoi = {10.26508/lsa.202201833},\n\tabstract = {Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.},\n\tlanguage = {en},\n\tnumber = {3},\n\turldate = {2022-12-17},\n\tjournal = {Life Science Alliance},\n\tauthor = {Dorrell, Richard G. and Kuo, Alan and Füssy, Zoltan and Richardson, Elisabeth H. and Salamov, Asaf and Zarevski, Nikola and Freyria, Nastasia J. and Ibarbalz, Federico M. and Jenkins, Jerry and Karlusich, Juan Jose Pierella and Steindorff, Andrei Stecca and Edgar, Robyn E. and Handley, Lori and Lail, Kathleen and Lipzen, Anna and Lombard, Vincent and McFarlane, John and Nef, Charlotte and Vanclová, Anna MG Novák and Peng, Yi and Plott, Chris and Potvin, Marianne and Vieira, Fabio Rocha Jimenez and Barry, Kerrie and Vargas, Colomban de and Henrissat, Bernard and Pelletier, Eric and Schmutz, Jeremy and Wincker, Patrick and Dacks, Joel B. and Bowler, Chris and Grigoriev, Igor V. and Lovejoy, Connie},\n\tmonth = mar,\n\tyear = {2023},\n\tpmid = {36522135},\n\tnote = {Publisher: Life Science Alliance\nSection: Research Articles},\n}\n\n\n\n Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.\n
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\n \n \n\n \n \n \n \n \n Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome.\n \n \n \n\n\n \n Zayed, A. A.; Wainaina, J. M.; Dominguez-Huerta, G.; Pelletier, E.; Guo, J.; Mohssen, M.; Tian, F.; Pratama, A. A.; Bolduc, B.; Zablocki, O.; Cronin, D.; Solden, L.; Delage, E.; Alberti, A.; Aury, J.; Carradec, Q.; da Silva, C.; Labadie, K.; Poulain, J.; Ruscheweyh, H.; Salazar, G.; Shatoff, E.; Tara Oceans Coordinators‡; Bundschuh, R.; Fredrick, K.; Kubatko, L. S.; Chaffron, S.; Culley, A. I.; Sunagawa, S.; Kuhn, J. H.; Wincker, P.; Sullivan, M. B.; Acinas, S. G.; Babin, M.; Bork, P.; Boss, E.; Bowler, C.; Cochrane, G.; de Vargas, C.; Gorsky, G.; Guidi, L.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels, S.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Poulton, N.; Pesant, S.; Sardet, C.; Speich, S.; Stemmann, L.; Sullivan, M. B.; Sungawa, S.; and Wincker, P.\n\n\n \n\n\n\n Science, 376(6589): 156–162. April 2022.\n \n\n\n\n
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\n\n\n@article{zayed_cryptic_2022,\n\ttitle = {Cryptic and abundant marine viruses at the evolutionary origins of {Earth}'s {RNA} virome},\n\tvolume = {376},\n\tissn = {1095-9203},\n\tdoi = {10.1126/science.abm5847},\n\tabstract = {Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding {\\textgreater}50\\% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.},\n\tlanguage = {eng},\n\tnumber = {6589},\n\tjournal = {Science},\n\tauthor = {Zayed, Ahmed A. and Wainaina, James M. and Dominguez-Huerta, Guillermo and Pelletier, Eric and Guo, Jiarong and Mohssen, Mohamed and Tian, Funing and Pratama, Akbar Adjie and Bolduc, Benjamin and Zablocki, Olivier and Cronin, Dylan and Solden, Lindsey and Delage, Erwan and Alberti, Adriana and Aury, Jean-Marc and Carradec, Quentin and da Silva, Corinne and Labadie, Karine and Poulain, Julie and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Shatoff, Elan and {Tara Oceans Coordinators‡} and Bundschuh, Ralf and Fredrick, Kurt and Kubatko, Laura S. and Chaffron, Samuel and Culley, Alexander I. and Sunagawa, Shinichi and Kuhn, Jens H. and Wincker, Patrick and Sullivan, Matthew B. and Acinas, Silvia G. and Babin, Marcel and Bork, Peer and Boss, Emmanuel and Bowler, Chris and Cochrane, Guy and de Vargas, Colomban and Gorsky, Gabriel and Guidi, Lionel and Grimsley, Nigel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Kandels, Stefanie and Karp-Boss, Lee and Karsenti, Eric and Not, Fabrice and Ogata, Hiroyuki and Poulton, Nicole and Pesant, Stéphane and Sardet, Christian and Speich, Sabrinia and Stemmann, Lars and Sullivan, Matthew B. and Sungawa, Shinichi and Wincker, Patrick},\n\tmonth = apr,\n\tyear = {2022},\n\tpmid = {35389782},\n\tkeywords = {Biological Evolution, Ecosystem, Genome, Viral, Oceans and Seas, Phylogeny, RNA, RNA Viruses, Virome, Viruses},\n\tpages = {156--162},\n}\n\n\n\n Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding \\textgreater50% new classes) and evolutionary understanding. \"Species\"-rank abundance determination revealed that viruses of the new phyla \"Taraviricota,\" a missing link in early RNA virus evolution, and \"Arctiviricota\" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.\n
\n\n\n\n \n\n \n \n \n \n \n \n Restructuring of plankton genomic biogeography in the surface ocean under climate change.\n \n \n \n \n\n\n \n Frémont, P.; Gehlen, M.; Vrac, M.; Leconte, J.; Delmont, T. O.; Wincker, P.; Iudicone, D.; and Jaillon, O.\n\n\n \n\n\n\n Nature Climate Change, 12(4): 393–401. April 2022.\n Number: 4 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{fremont_restructuring_2022,\n\ttitle = {Restructuring of plankton genomic biogeography in the surface ocean under climate change},\n\tvolume = {12},\n\tcopyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited},\n\tissn = {1758-6798},\n\turl = {https://www.nature.com/articles/s41558-022-01314-8},\n\tdoi = {10.1038/s41558-022-01314-8},\n\tabstract = {The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here environmental niches are evidenced for plankton communities at the genomic scale for six size fractions from viruses to meso-zooplankton. The spatial extrapolation of these niches portrays ocean partitionings south of 60° N into climato-genomic provinces characterized by signature genomes. By 2090, under the RCP8.5 future climate scenario, provinces are reorganized over half of the ocean area considered, and almost all provinces are displaced poleward. Particularly, tropical provinces expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50\\%), followed by phosphate (11\\%) and salinity (10\\%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease, on average, by 4\\% in response to biogeographical restructuring.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2022-04-29},\n\tjournal = {Nature Climate Change},\n\tauthor = {Frémont, Paul and Gehlen, Marion and Vrac, Mathieu and Leconte, Jade and Delmont, Tom O. and Wincker, Patrick and Iudicone, Daniele and Jaillon, Olivier},\n\tmonth = apr,\n\tyear = {2022},\n\tnote = {Number: 4\nPublisher: Nature Publishing Group},\n\tkeywords = {Biogeochemistry, Biogeography, Climate-change ecology, Marine biology, Molecular ecology},\n\tpages = {393--401},\n}\n\n\n\n The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here environmental niches are evidenced for plankton communities at the genomic scale for six size fractions from viruses to meso-zooplankton. The spatial extrapolation of these niches portrays ocean partitionings south of 60° N into climato-genomic provinces characterized by signature genomes. By 2090, under the RCP8.5 future climate scenario, provinces are reorganized over half of the ocean area considered, and almost all provinces are displaced poleward. Particularly, tropical provinces expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%), followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease, on average, by 4% in response to biogeographical restructuring.\n
\n\n\n\n \n\n \n \n \n \n \n \n Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.\n \n \n \n \n\n\n \n Richter, D. J; Watteaux, R.; Vannier, T.; Leconte, J.; Frémont, P.; Reygondeau, G.; Maillet, N.; Henry, N.; Benoit, G.; Da Silva, O.; Delmont, T. O; Fernàndez-Guerra, A.; Suweis, S.; Narci, R.; Berney, C.; Eveillard, D.; Gavory, F.; Guidi, L.; Labadie, K.; Mahieu, E.; Poulain, J.; Romac, S.; Roux, S.; Dimier, C.; Kandels, S.; Picheral, M.; Searson, S.; Tara Oceans Coordinators; Pesant, S.; Aury, J.; Brum, J. R; Lemaitre, C.; Pelletier, E.; Bork, P.; Sunagawa, S.; Lombard, F.; Karp-Boss, L.; Bowler, C.; Sullivan, M. B; Karsenti, E.; Mariadassou, M.; Probert, I.; Peterlongo, P.; Wincker, P.; de Vargas, C.; Ribera d'Alcalà , M.; Iudicone, D.; and Jaillon, O.\n\n\n \n\n\n\n eLife, 11: e78129. August 2022.\n Publisher: eLife Sciences Publications, Ltd\n\n\n\n
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\n\n\n@article{richter_genomic_2022,\n\ttitle = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems},\n\tvolume = {11},\n\tissn = {2050-084X},\n\turl = {https://doi.org/10.7554/eLife.78129},\n\tdoi = {10.7554/eLife.78129},\n\tabstract = {Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.},\n\turldate = {2022-08-29},\n\tjournal = {eLife},\n\tauthor = {Richter, Daniel J and Watteaux, Romain and Vannier, Thomas and Leconte, Jade and Frémont, Paul and Reygondeau, Gabriel and Maillet, Nicolas and Henry, Nicolas and Benoit, Gaëtan and Da Silva, Ophélie and Delmont, Tom O and Fernàndez-Guerra, Antonio and Suweis, Samir and Narci, Romain and Berney, Cédric and Eveillard, Damien and Gavory, Frederick and Guidi, Lionel and Labadie, Karine and Mahieu, Eric and Poulain, Julie and Romac, Sarah and Roux, Simon and Dimier, Céline and Kandels, Stefanie and Picheral, Marc and Searson, Sarah and {Tara Oceans Coordinators} and Pesant, Stéphane and Aury, Jean-Marc and Brum, Jennifer R and Lemaitre, Claire and Pelletier, Eric and Bork, Peer and Sunagawa, Shinichi and Lombard, Fabien and Karp-Boss, Lee and Bowler, Chris and Sullivan, Matthew B and Karsenti, Eric and Mariadassou, Mahendra and Probert, Ian and Peterlongo, Pierre and Wincker, Patrick and de Vargas, Colomban and Ribera d'Alcalà, Maurizio and Iudicone, Daniele and Jaillon, Olivier},\n\teditor = {Louca, Stilianos and Schuman, Meredith C},\n\tmonth = aug,\n\tyear = {2022},\n\tnote = {Publisher: eLife Sciences Publications, Ltd},\n\tkeywords = {metabarcoding, metagenomics, microbial oceanography, plankton biogeography},\n\tpages = {e78129},\n}\n\n\n\n Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.\n
\n\n\n\n \n\n \n \n \n \n \n \n Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans.\n \n \n \n \n\n\n \n Lang-Yona, N.; Flores, J. M.; Haviv, R.; Alberti, A.; Poulain, J.; Belser, C.; Trainic, M.; Gat, D.; Ruscheweyh, H.; Wincker, P.; Sunagawa, S.; Rudich, Y.; Koren, I.; and Vardi, A.\n\n\n \n\n\n\n Communications Earth & Environment, 3(1): 1–10. May 2022.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{lang-yona_terrestrial_2022,\n\ttitle = {Terrestrial and marine influence on atmospheric bacterial diversity over the north {Atlantic} and {Pacific} {Oceans}},\n\tvolume = {3},\n\tcopyright = {2022 The Author(s)},\n\tissn = {2662-4435},\n\turl = {https://www.nature.com/articles/s43247-022-00441-6},\n\tdoi = {10.1038/s43247-022-00441-6},\n\tabstract = {The diversity of microbes and their transmission between ocean and atmosphere are poorly understood despite the implications for microbial global dispersion and biogeochemical processes. Here, we survey the genetic diversity of airborne and surface ocean bacterial communities sampled during springtime transects across the northwest Pacific and subtropical north Atlantic as part of the Tara Pacific Expedition. We find that microbial community composition is more variable in the atmosphere than in the surface ocean. Bacterial communities were more similar between the two surface oceans than between the ocean and the overlying atmosphere. Likewise, Pacific and Atlantic atmospheric microbial communities were more similar to each other than to those in the ocean beneath. Atmospheric community composition over the Atlantic was dominated by terrestrial and specifically, dust-associated bacteria, whereas over the Pacific there was a higher prevalence and differential abundance of marine bacteria. Our findings highlight regional differences in long-range microbial exchange and dispersal between land, ocean, and atmosphere.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-10-25},\n\tjournal = {Communications Earth \\& Environment},\n\tauthor = {Lang-Yona, Naama and Flores, J. Michel and Haviv, Rotem and Alberti, Adriana and Poulain, Julie and Belser, Caroline and Trainic, Miri and Gat, Daniella and Ruscheweyh, Hans-Joachim and Wincker, Patrick and Sunagawa, Shinichi and Rudich, Yinon and Koren, Ilan and Vardi, Assaf},\n\tmonth = may,\n\tyear = {2022},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Air microbiology, Microbial ecology, Molecular ecology},\n\tpages = {1--10},\n}\n\n\n\n The diversity of microbes and their transmission between ocean and atmosphere are poorly understood despite the implications for microbial global dispersion and biogeochemical processes. Here, we survey the genetic diversity of airborne and surface ocean bacterial communities sampled during springtime transects across the northwest Pacific and subtropical north Atlantic as part of the Tara Pacific Expedition. We find that microbial community composition is more variable in the atmosphere than in the surface ocean. Bacterial communities were more similar between the two surface oceans than between the ocean and the overlying atmosphere. Likewise, Pacific and Atlantic atmospheric microbial communities were more similar to each other than to those in the ocean beneath. Atmospheric community composition over the Atlantic was dominated by terrestrial and specifically, dust-associated bacteria, whereas over the Pacific there was a higher prevalence and differential abundance of marine bacteria. Our findings highlight regional differences in long-range microbial exchange and dispersal between land, ocean, and atmosphere.\n
\n\n\n\n \n\n \n \n \n \n \n \n Patterns of eukaryotic diversity from the surface to the deep-ocean sediment.\n \n \n \n \n\n\n \n Cordier, T.; Angeles, I. B.; Henry, N.; Lejzerowicz, F.; Berney, C.; Morard, R.; Brandt, A.; Cambon-Bonavita, M.; Guidi, L.; Lombard, F.; Arbizu, P. M.; Massana, R.; Orejas, C.; Poulain, J.; Smith, C. R.; Wincker, P.; Arnaud-Haond, S.; Gooday, A. J.; de Vargas, C.; and Pawlowski, J.\n\n\n \n\n\n\n Science Advances, 8(5): eabj9309. February 2022.\n Publisher: American Association for the Advancement of Science\n\n\n\n
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\n\n\n@article{cordier_patterns_2022,\n\ttitle = {Patterns of eukaryotic diversity from the surface to the deep-ocean sediment},\n\tvolume = {8},\n\turl = {https://www.science.org/doi/full/10.1126/sciadv.abj9309},\n\tdoi = {10.1126/sciadv.abj9309},\n\tabstract = {Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.},\n\tnumber = {5},\n\turldate = {2023-10-25},\n\tjournal = {Science Advances},\n\tauthor = {Cordier, Tristan and Angeles, Inès Barrenechea and Henry, Nicolas and Lejzerowicz, Franck and Berney, Cédric and Morard, Raphaël and Brandt, Angelika and Cambon-Bonavita, Marie-Anne and Guidi, Lionel and Lombard, Fabien and Arbizu, Pedro Martinez and Massana, Ramon and Orejas, Covadonga and Poulain, Julie and Smith, Craig R. and Wincker, Patrick and Arnaud-Haond, Sophie and Gooday, Andrew J. and de Vargas, Colomban and Pawlowski, Jan},\n\tmonth = feb,\n\tyear = {2022},\n\tnote = {Publisher: American Association for the Advancement of Science},\n\tpages = {eabj9309},\n}\n\n\n\n Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.\n
\n\n\n\n \n\n \n \n \n \n \n \n Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence.\n \n \n \n \n\n\n \n Guérin, N.; Ciccarella, M.; Flamant, E.; Frémont, P.; Mangenot, S.; Istace, B.; Noel, B.; Belser, C.; Bertrand, L.; Labadie, K.; Cruaud, C.; Romac, S.; Bachy, C.; Gachenot, M.; Pelletier, E.; Alberti, A.; Jaillon, O.; Wincker, P.; Aury, J.; and Carradec, Q.\n\n\n \n\n\n\n Communications Biology, 5(1): 1–14. September 2022.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
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\n\n\n@article{guerin_genomic_2022,\n\ttitle = {Genomic adaptation of the picoeukaryote {Pelagomonas} calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},\n\tvolume = {5},\n\tcopyright = {2022 The Author(s)},\n\tissn = {2399-3642},\n\turl = {https://www.nature.com/articles/s42003-022-03939-z},\n\tdoi = {10.1038/s42003-022-03939-z},\n\tabstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2022-09-17},\n\tjournal = {Communications Biology},\n\tauthor = {Guérin, Nina and Ciccarella, Marta and Flamant, Elisa and Frémont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin},\n\tmonth = sep,\n\tyear = {2022},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Biogeography, Comparative genomics, Metagenomics, Water microbiology},\n\tpages = {1--14},\n}\n\n\n\n The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.\n
\n\n\n\n \n\n \n \n \n \n \n Diversity and ecological footprint of Global Ocean RNA viruses.\n \n \n \n\n\n \n Dominguez-Huerta, G.; Zayed, A. A.; Wainaina, J. M.; Guo, J.; Tian, F.; Pratama, A. A.; Bolduc, B.; Mohssen, M.; Zablocki, O.; Pelletier, E.; Delage, E.; Alberti, A.; Aury, J.; Carradec, Q.; da Silva, C.; Labadie, K.; Poulain, J.; Tara Oceans Coordinators§; Bowler, C.; Eveillard, D.; Guidi, L.; Karsenti, E.; Kuhn, J. H.; Ogata, H.; Wincker, P.; Culley, A.; Chaffron, S.; and Sullivan, M. B.\n\n\n \n\n\n\n Science, 376(6598): 1202–1208. June 2022.\n \n\n\n\n
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\n\n\n@article{dominguez-huerta_diversity_2022,\n\ttitle = {Diversity and ecological footprint of {Global} {Ocean} {RNA} viruses},\n\tvolume = {376},\n\tissn = {1095-9203},\n\tdoi = {10.1126/science.abn6358},\n\tabstract = {DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.},\n\tlanguage = {eng},\n\tnumber = {6598},\n\tjournal = {Science},\n\tauthor = {Dominguez-Huerta, Guillermo and Zayed, Ahmed A. and Wainaina, James M. and Guo, Jiarong and Tian, Funing and Pratama, Akbar Adjie and Bolduc, Benjamin and Mohssen, Mohamed and Zablocki, Olivier and Pelletier, Eric and Delage, Erwan and Alberti, Adriana and Aury, Jean-Marc and Carradec, Quentin and da Silva, Corinne and Labadie, Karine and Poulain, Julie and {Tara Oceans Coordinators§} and Bowler, Chris and Eveillard, Damien and Guidi, Lionel and Karsenti, Eric and Kuhn, Jens H. and Ogata, Hiroyuki and Wincker, Patrick and Culley, Alexander and Chaffron, Samuel and Sullivan, Matthew B.},\n\tmonth = jun,\n\tyear = {2022},\n\tpmid = {35679415},\n\tkeywords = {Carbon Cycle, Ecosystem, Oceans and Seas, Plankton, RNA Viruses, Seawater, Virome},\n\tpages = {1202--1208},\n}\n\n\n\n DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and \"species\"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.\n
\n\n\n\n \n\n \n \n \n \n \n \n Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.\n \n \n \n \n\n\n \n Nef, C.; Madoui, M.; Pelletier, É.; and Bowler, C.\n\n\n \n\n\n\n PLOS Biology, 20(11): e3001893. November 2022.\n Publisher: Public Library of Science\n\n\n\n
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\n\n\n@article{nef_whole-genome_2022,\n\ttitle = {Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom {Chaetoceros}},\n\tvolume = {20},\n\tissn = {1545-7885},\n\turl = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001893},\n\tdoi = {10.1371/journal.pbio.3001893},\n\tabstract = {Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.},\n\tlanguage = {en},\n\tnumber = {11},\n\turldate = {2022-12-02},\n\tjournal = {PLOS Biology},\n\tauthor = {Nef, Charlotte and Madoui, Mohammed-Amin and Pelletier, Éric and Bowler, Chris},\n\tmonth = nov,\n\tyear = {2022},\n\tnote = {Publisher: Public Library of Science},\n\tkeywords = {Arctic Ocean, Diatoms, Genetic loci, Genomics, Metagenomics, Oceans, Phosphates, Population genetics},\n\tpages = {e3001893},\n}\n\n\n\n Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.\n
\n\n\n\n \n\n \n \n \n \n \n \n Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea.\n \n \n \n \n\n\n \n Da Silva, O.; Ayata, S.; Ser-Giacomi, E.; Leconte, J.; Pelletier, E.; Fauvelot, C.; Madoui, M.; Guidi, L.; Lombard, F.; and Bittner, L.\n\n\n \n\n\n\n Environmental Microbiology, n/a(n/a). September 2022.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.16171\n\n\n\n
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\n\n\n@article{da_silva_genomic_2022,\n\ttitle = {Genomic differentiation of three pico-phytoplankton species in the {Mediterranean} {Sea}},\n\tvolume = {n/a},\n\tissn = {1462-2920},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16171},\n\tdoi = {10.1111/1462-2920.16171},\n\tabstract = {For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.},\n\tlanguage = {en},\n\tnumber = {n/a},\n\turldate = {2022-09-07},\n\tjournal = {Environmental Microbiology},\n\tauthor = {Da Silva, Ophélie and Ayata, Sakina-Dorothée and Ser-Giacomi, Enrico and Leconte, Jade and Pelletier, Eric and Fauvelot, Cécile and Madoui, Mohammed-Amin and Guidi, Lionel and Lombard, Fabien and Bittner, Lucie},\n\tmonth = sep,\n\tyear = {2022},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.16171},\n}\n\n\n\n For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.\n
\n\n\n\n \n\n \n \n \n \n \n Giant Viruses Encode Actin-Related Proteins.\n \n \n \n\n\n \n Da Cunha, V.; Gaia, M.; Ogata, H.; Jaillon, O.; Delmont, T. O.; and Forterre, P.\n\n\n \n\n\n\n Molecular Biology and Evolution, 39(2): msac022. February 2022.\n \n\n\n\n
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\n\n\n@article{da_cunha_giant_2022,\n\ttitle = {Giant {Viruses} {Encode} {Actin}-{Related} {Proteins}},\n\tvolume = {39},\n\tissn = {1537-1719},\n\tdoi = {10.1093/molbev/msac022},\n\tabstract = {The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.},\n\tlanguage = {eng},\n\tnumber = {2},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Da Cunha, Violette and Gaia, Morgan and Ogata, Hiroyuki and Jaillon, Olivier and Delmont, Tom O. and Forterre, Patrick},\n\tmonth = feb,\n\tyear = {2022},\n\tpmid = {35150280},\n\tpmcid = {PMC8850707},\n\tkeywords = {Actins, Eukaryota, Eukaryotic Cells, Evolution, Molecular, Giant Viruses, NucleoCytoplasmic Large DNA virus, Phylogeny, actin and actin-related proteins, viral eukaryogenesis},\n\tpages = {msac022},\n}\n\n\n\n The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.\n
\n\n\n\n \n\n \n \n \n \n \n Unifying the known and unknown microbial coding sequence space.\n \n \n \n\n\n \n Vanni, C.; Schechter, M. S.; Acinas, S. G.; Barberán, A.; Buttigieg, P. L.; Casamayor, E. O.; Delmont, T. O.; Duarte, C. M.; Eren, A. M.; Finn, R. D.; Kottmann, R.; Mitchell, A.; Sánchez, P.; Siren, K.; Steinegger, M.; Gloeckner, F. O.; and Fernàndez-Guerra, A.\n\n\n \n\n\n\n eLife, 11: e67667. March 2022.\n \n\n\n\n
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\n\n\n@article{vanni_unifying_2022,\n\ttitle = {Unifying the known and unknown microbial coding sequence space},\n\tvolume = {11},\n\tissn = {2050-084X},\n\tdoi = {10.7554/eLife.67667},\n\tabstract = {Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40-60\\% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.},\n\tlanguage = {eng},\n\tjournal = {eLife},\n\tauthor = {Vanni, Chiara and Schechter, Matthew S. and Acinas, Silvia G. and Barberán, Albert and Buttigieg, Pier Luigi and Casamayor, Emilio O. and Delmont, Tom O. and Duarte, Carlos M. and Eren, A. Murat and Finn, Robert D. and Kottmann, Renzo and Mitchell, Alex and Sánchez, Pablo and Siren, Kimmo and Steinegger, Martin and Gloeckner, Frank Oliver and Fernàndez-Guerra, Antonio},\n\tmonth = mar,\n\tyear = {2022},\n\tpmid = {35356891},\n\tkeywords = {Bacteria, Genome, Archaeal, Metagenome, Open Reading Frames, bioinformatics, computational biology, functional metageomics, gene clusters, infectious disease, microbial genomics, microbiology, phylogenomics, systems biology, unknown function},\n\tpages = {e67667},\n}\n\n\n\n Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.\n
\n\n\n\n \n\n \n \n \n \n \n In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.\n \n \n \n\n\n \n Pessi, I. S.; Viitamäki, S.; Virkkala, A.; Eronen-Rasimus, E.; Delmont, T. O.; Marushchak, M. E.; Luoto, M.; and Hultman, J.\n\n\n \n\n\n\n Environmental Microbiome, 17(1): 30. June 2022.\n \n\n\n\n
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\n\n\n@article{pessi_-depth_2022,\n\ttitle = {In-depth characterization of denitrifier communities across different soil ecosystems in the tundra},\n\tvolume = {17},\n\tissn = {2524-6372},\n\tdoi = {10.1186/s40793-022-00424-2},\n\tabstract = {BACKGROUND: In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.\nRESULTS: We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23.\nCONCLUSIONS: By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Environmental Microbiome},\n\tauthor = {Pessi, Igor S. and Viitamäki, Sirja and Virkkala, Anna-Maria and Eronen-Rasimus, Eeva and Delmont, Tom O. and Marushchak, Maija E. and Luoto, Miska and Hultman, Jenni},\n\tmonth = jun,\n\tyear = {2022},\n\tpmid = {35690846},\n\tkeywords = {Arctic, Denitrification, Genome-resolved metagenomics, Nitrous oxide},\n\tpages = {30},\n}\n\n\n\n BACKGROUND: In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. RESULTS: We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. CONCLUSIONS: By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.\n
\n\n\n\n \n\n \n \n \n \n \n Biosynthetic potential of the global ocean microbiome.\n \n \n \n\n\n \n Paoli, L.; Ruscheweyh, H.; Forneris, C. C.; Hubrich, F.; Kautsar, S.; Bhushan, A.; Lotti, A.; Clayssen, Q.; Salazar, G.; Milanese, A.; Carlström, C. I.; Papadopoulou, C.; Gehrig, D.; Karasikov, M.; Mustafa, H.; Larralde, M.; Carroll, L. M.; Sánchez, P.; Zayed, A. A.; Cronin, D. R.; Acinas, S. G.; Bork, P.; Bowler, C.; Delmont, T. O.; Gasol, J. M.; Gossert, A. D.; Kahles, A.; Sullivan, M. B.; Wincker, P.; Zeller, G.; Robinson, S. L.; Piel, J.; and Sunagawa, S.\n\n\n \n\n\n\n Nature, 607(7917): 111–118. July 2022.\n \n\n\n\n
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\n\n\n@article{paoli_biosynthetic_2022,\n\ttitle = {Biosynthetic potential of the global ocean microbiome},\n\tvolume = {607},\n\tissn = {1476-4687},\n\tdoi = {10.1038/s41586-022-04862-3},\n\tabstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.},\n\tlanguage = {eng},\n\tnumber = {7917},\n\tjournal = {Nature},\n\tauthor = {Paoli, Lucas and Ruscheweyh, Hans-Joachim and Forneris, Clarissa C. and Hubrich, Florian and Kautsar, Satria and Bhushan, Agneya and Lotti, Alessandro and Clayssen, Quentin and Salazar, Guillem and Milanese, Alessio and Carlström, Charlotte I. and Papadopoulou, Chrysa and Gehrig, Daniel and Karasikov, Mikhail and Mustafa, Harun and Larralde, Martin and Carroll, Laura M. and Sánchez, Pablo and Zayed, Ahmed A. and Cronin, Dylan R. and Acinas, Silvia G. and Bork, Peer and Bowler, Chris and Delmont, Tom O. and Gasol, Josep M. and Gossert, Alvar D. and Kahles, André and Sullivan, Matthew B. and Wincker, Patrick and Zeller, Georg and Robinson, Serina L. and Piel, Jörn and Sunagawa, Shinichi},\n\tmonth = jul,\n\tyear = {2022},\n\tpmid = {35732736},\n\tpages = {111--118},\n}\n\n\n\n Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.\n
\n\n\n\n \n\n \n \n \n \n \n The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.\n \n \n \n\n\n \n Vernette, C.; Lecubin, J.; Sánchez, P.; Tara Oceans Coordinators; Sunagawa, S.; Delmont, T. O.; Acinas, S. G.; Pelletier, E.; Hingamp, P.; and Lescot, M.\n\n\n \n\n\n\n Nucleic Acids Research,gkac420. June 2022.\n \n\n\n\n
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\n\n\n@article{vernette_ocean_2022,\n\ttitle = {The {Ocean} {Gene} {Atlas} v2.0: online exploration of the biogeography and phylogeny of plankton genes},\n\tissn = {1362-4962},\n\tshorttitle = {The {Ocean} {Gene} {Atlas} v2.0},\n\tdoi = {10.1093/nar/gkac420},\n\tabstract = {Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.},\n\tlanguage = {eng},\n\tjournal = {Nucleic Acids Research},\n\tauthor = {Vernette, Caroline and Lecubin, Julien and Sánchez, Pablo and {Tara Oceans Coordinators} and Sunagawa, Shinichi and Delmont, Tom O. and Acinas, Silvia G. and Pelletier, Eric and Hingamp, Pascal and Lescot, Magali},\n\tmonth = jun,\n\tyear = {2022},\n\tpmid = {35687095},\n\tpages = {gkac420},\n}\n\n\n\n Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.\n
\n\n\n\n \n\n \n \n \n \n \n \n Priorities for ocean microbiome research.\n \n \n \n \n\n\n \n Abreu, A.; Bourgois, E.; Gristwood, A.; Troublé, R.; Acinas, S. G.; Bork, P.; Boss, E.; Bowler, C.; Budinich, M.; Chaffron, S.; de Vargas, C.; Delmont, T. O.; Eveillard, D.; Guidi, L.; Iudicone, D.; Kandels, S.; Morlon, H.; Lombard, F.; Pepperkok, R.; Karlusich, J. J. P.; Piganeau, G.; Régimbeau, A.; Sommeria-Klein, G.; Stemmann, L.; Sullivan, M. B.; Sunagawa, S.; Wincker, P.; Zablocki, O.; Arendt, D.; Bilic, J.; Finn, R.; Heard, E.; Rouse, B.; Vamathevan, J.; Casotti, R.; Cancio, I.; Cunliffe, M.; Kervella, A. E.; Kooistra, W. H. C. F.; Obst, M.; Pade, N.; Power, D. M.; Santi, I.; Tsagaraki, T. M.; Vanaverbeke, J.; Tara Ocean Foundation; Tara Oceans; European Molecular Biology Laboratory (EMBL); and European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)\n\n\n \n\n\n\n Nature Microbiology, 7(7): 937–947. July 2022.\n \n\n\n\n
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\n\n\n@article{abreu_priorities_2022,\n\ttitle = {Priorities for ocean microbiome research},\n\tvolume = {7},\n\tcopyright = {2022 Springer Nature Limited},\n\tissn = {2058-5276},\n\turl = {https://www.nature.com/articles/s41564-022-01145-5},\n\tdoi = {10.1038/s41564-022-01145-5},\n\tabstract = {Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 ‘life below water’. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.},\n\tlanguage = {en},\n\tnumber = {7},\n\turldate = {2022-07-07},\n\tjournal = {Nature Microbiology},\n\tauthor = {Abreu, Andre and Bourgois, Etienne and Gristwood, Adam and Troublé, Romain and Acinas, Silvia G. and Bork, Peer and Boss, Emmanuel and Bowler, Chris and Budinich, Marko and Chaffron, Samuel and de Vargas, Colomban and Delmont, Tom O. and Eveillard, Damien and Guidi, Lionel and Iudicone, Daniele and Kandels, Stephanie and Morlon, Hélène and Lombard, Fabien and Pepperkok, Rainer and Karlusich, Juan José Pierella and Piganeau, Gwenael and Régimbeau, Antoine and Sommeria-Klein, Guilhem and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Zablocki, Olivier and Arendt, Detlev and Bilic, Josipa and Finn, Robert and Heard, Edith and Rouse, Brendan and Vamathevan, Jessica and Casotti, Raffaella and Cancio, Ibon and Cunliffe, Michael and Kervella, Anne Emmanuelle and Kooistra, Wiebe H. C. F. and Obst, Matthias and Pade, Nicolas and Power, Deborah M. and Santi, Ioulia and Tsagaraki, Tatiana Margo and Vanaverbeke, Jan and {Tara Ocean Foundation} and {Tara Oceans} and {European Molecular Biology Laboratory (EMBL)} and {European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)}},\n\tmonth = jul,\n\tyear = {2022},\n\tkeywords = {Environmental sciences, Water microbiology},\n\tpages = {937--947},\n}\n\n\n\n Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 ‘life below water’. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.\n
\n\n\n\n \n\n \n \n \n \n \n \n Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.\n \n \n \n \n\n\n \n Delmont, T. O.; Gaia, M.; Hinsinger, D. D.; Frémont, P.; Vanni, C.; Fernandez-Guerra, A.; Eren, A. M.; Kourlaiev, A.; d'Agata , L.; Clayssen, Q.; Villar, E.; Labadie, K.; Cruaud, C.; Poulain, J.; Da Silva, C.; Wessner, M.; Noel, B.; Aury, J.; Sunagawa, S.; Acinas, S. G.; Bork, P.; Karsenti, E.; Bowler, C.; Sardet, C.; Stemmann, L.; de Vargas, C.; Wincker, P.; Lescot, M.; Babin, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Jaillon, O.; Kandels, S.; Iudicone, D.; Ogata, H.; Pesant, S.; Sullivan, M. B.; Not, F.; Lee, K.; Boss, E.; Cochrane, G.; Follows, M.; Poulton, N.; Raes, J.; Sieracki, M.; Speich, S.; de Vargas, C.; Bowler, C.; Karsenti, E.; Pelletier, E.; Wincker, P.; and Jaillon, O.\n\n\n \n\n\n\n Cell Genomics,100123. April 2022.\n \n\n\n\n
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\n\n\n@article{delmont_functional_2022,\n\ttitle = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean},\n\tissn = {2666-979X},\n\turl = {https://www.sciencedirect.com/science/article/pii/S2666979X22000477},\n\tdoi = {10.1016/j.xgen.2022.100123},\n\tabstract = {Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.},\n\tlanguage = {en},\n\turldate = {2022-04-29},\n\tjournal = {Cell Genomics},\n\tauthor = {Delmont, Tom O. and Gaia, Morgan and Hinsinger, Damien D. and Frémont, Paul and Vanni, Chiara and Fernandez-Guerra, Antonio and Eren, A. Murat and Kourlaiev, Artem and d'Agata, Leo and Clayssen, Quentin and Villar, Emilie and Labadie, Karine and Cruaud, Corinne and Poulain, Julie and Da Silva, Corinne and Wessner, Marc and Noel, Benjamin and Aury, Jean-Marc and Sunagawa, Shinichi and Acinas, Silvia G. and Bork, Peer and Karsenti, Eric and Bowler, Chris and Sardet, Christian and Stemmann, Lars and de Vargas, Colomban and Wincker, Patrick and Lescot, Magali and Babin, Marcel and Gorsky, Gabriel and Grimsley, Nigel and Guidi, Lionel and Hingamp, Pascal and Jaillon, Olivier and Kandels, Stefanie and Iudicone, Daniele and Ogata, Hiroyuki and Pesant, Stéphane and Sullivan, Matthew B. and Not, Fabrice and Lee, Karp-Boss and Boss, Emmanuel and Cochrane, Guy and Follows, Michael and Poulton, Nicole and Raes, Jeroen and Sieracki, Mike and Speich, Sabrina and de Vargas, Colomban and Bowler, Chris and Karsenti, Eric and Pelletier, Eric and Wincker, Patrick and Jaillon, Olivier},\n\tmonth = apr,\n\tyear = {2022},\n\tkeywords = {Oceans, Planktonic eukaryotes, anvi’o, ecology, evolution, functions, genomics, metagenomics},\n\tpages = {100123},\n}\n\n\n\n Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.\n
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\n \n \n\n \n \n \n \n \n \n Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean.\n \n \n \n \n\n\n \n Delmont, T. O.; Pierella Karlusich, J. J.; Veseli, I.; Fuessel, J.; Eren, A. M.; Foster, R. A.; Bowler, C.; Wincker, P.; and Pelletier, E.\n\n\n \n\n\n\n The ISME Journal,1–10. October 2021.\n Bandiera_abtest: a Cg_type: Nature Research Journals Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Biodiversity;Microbial biooceanography;Microbial ecology;Next-generation sequencing Subject_term_id: biodiversity;microbial-biooceanography;microbial-ecology;next-generation-sequencing\n\n\n\n
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\n\n\n@article{delmont_heterotrophic_2021,\n\ttitle = {Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean},\n\tcopyright = {2021 The Author(s), under exclusive licence to International Society for Microbial Ecology},\n\tissn = {1751-7370},\n\turl = {http://www.nature.com/articles/s41396-021-01135-1},\n\tdoi = {10.1038/s41396-021-01135-1},\n\tabstract = {Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92\\% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.},\n\tlanguage = {en},\n\turldate = {2021-10-26},\n\tjournal = {The ISME Journal},\n\tauthor = {Delmont, Tom O. and Pierella Karlusich, Juan José and Veseli, Iva and Fuessel, Jessika and Eren, A. Murat and Foster, Rachel A. and Bowler, Chris and Wincker, Patrick and Pelletier, Eric},\n\tmonth = oct,\n\tyear = {2021},\n\tnote = {Bandiera\\_abtest: a\nCg\\_type: Nature Research Journals\nPrimary\\_atype: Research\nPublisher: Nature Publishing Group\nSubject\\_term: Biodiversity;Microbial biooceanography;Microbial ecology;Next-generation sequencing\nSubject\\_term\\_id: biodiversity;microbial-biooceanography;microbial-ecology;next-generation-sequencing},\n\tkeywords = {Biodiversity, Microbial biooceanography, Microbial ecology, Next-generation sequencing},\n\tpages = {1--10},\n}\n\n\n\n Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.\n
\n\n\n\n \n\n \n \n \n \n \n \n Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection.\n \n \n \n \n\n\n \n Le Luyer, J.; Schull, Q.; Auffret, P.; Lopez, P.; Crusot, M.; Belliard, C.; Basset, C.; Carradec, Q.; Poulain, J.; Planes, S.; and Saulnier, D.\n\n\n \n\n\n\n Animal Microbiome, 3(1): 35. May 2021.\n \n\n\n\n
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\n\n\n@article{le_luyer_dual_2021,\n\ttitle = {Dual {RNAseq} highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection},\n\tvolume = {3},\n\tissn = {2524-4671},\n\turl = {https://doi.org/10.1186/s42523-021-00097-1},\n\tdoi = {10.1186/s42523-021-00097-1},\n\tabstract = {Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154T provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host–pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2022-01-10},\n\tjournal = {Animal Microbiome},\n\tauthor = {Le Luyer, J. and Schull, Q. and Auffret, P. and Lopez, P. and Crusot, M. and Belliard, C. and Basset, C. and Carradec, Q. and Poulain, J. and Planes, S. and Saulnier, D.},\n\tmonth = may,\n\tyear = {2021},\n\tpages = {35},\n}\n\n\n\n Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154T provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host–pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model.\n
\n\n\n\n \n\n \n \n \n \n \n Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms.\n \n \n \n\n\n \n Bulankova, P.; Sekulić, M.; Jallet, D.; Nef, C.; van Oosterhout, C.; Delmont, T. O.; Vercauteren, I.; Osuna-Cruz, C. M.; Vancaester, E.; Mock, T.; Sabbe, K.; Daboussi, F.; Bowler, C.; Vyverman, W.; Vandepoele, K.; and De Veylder, L.\n\n\n \n\n\n\n Current biology: CB, 31(15): 3221–3232.e9. August 2021.\n \n\n\n\n
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\n\n\n@article{bulankova_mitotic_2021,\n\ttitle = {Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms},\n\tvolume = {31},\n\tissn = {1879-0445},\n\tdoi = {10.1016/j.cub.2021.05.013},\n\tabstract = {Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms.},\n\tlanguage = {eng},\n\tnumber = {15},\n\tjournal = {Current biology: CB},\n\tauthor = {Bulankova, Petra and Sekulić, Mirna and Jallet, Denis and Nef, Charlotte and van Oosterhout, Cock and Delmont, Tom O. and Vercauteren, Ilse and Osuna-Cruz, Cristina Maria and Vancaester, Emmelien and Mock, Thomas and Sabbe, Koen and Daboussi, Fayza and Bowler, Chris and Vyverman, Wim and Vandepoele, Klaas and De Veylder, Lieven},\n\tmonth = aug,\n\tyear = {2021},\n\tpmid = {34102110},\n\tkeywords = {Alleles, Cell Division, Chromosomes, DNA Copy Number Variations, Diatoms, copy number variation, diatom, genetic variability, haplotypes diversity, loss of heterozygosity, recombination},\n\tpages = {3221--3232.e9},\n}\n\n\n\n Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms.\n
\n\n\n\n \n\n \n \n \n \n \n Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton.\n \n \n \n\n\n \n Kijima, S.; Delmont, T. O.; Miyazaki, U.; Gaia, M.; Endo, H.; and Ogata, H.\n\n\n \n\n\n\n Frontiers in Microbiology, 12: 683294. 2021.\n \n\n\n\n
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\n\n\n@article{kijima_discovery_2021,\n\ttitle = {Discovery of {Viral} {Myosin} {Genes} {With} {Complex} {Evolutionary} {History} {Within} {Plankton}},\n\tvolume = {12},\n\tissn = {1664-302X},\n\tdoi = {10.3389/fmicb.2021.683294},\n\tabstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Phylogenetic analyses indicate that most viral myosins (named "virmyosins") belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host. Like other viruses that use host motor proteins for their intracellular transport or motility, these viruses may use the virally encoded myosins for the intracellular trafficking of giant viral particles.},\n\tlanguage = {eng},\n\tjournal = {Frontiers in Microbiology},\n\tauthor = {Kijima, Soichiro and Delmont, Tom O. and Miyazaki, Urara and Gaia, Morgan and Endo, Hisashi and Ogata, Hiroyuki},\n\tyear = {2021},\n\tpmid = {34163457},\n\tpmcid = {PMC8215601},\n\tkeywords = {NCLDV, Nucleocytoviricota, giant viruses, myosin, phylogeny, viral diversity},\n\tpages = {683294},\n}\n\n\n\n Nucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Phylogenetic analyses indicate that most viral myosins (named \"virmyosins\") belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host. Like other viruses that use host motor proteins for their intracellular transport or motility, these viruses may use the virally encoded myosins for the intracellular trafficking of giant viral particles.\n
\n\n\n\n \n\n \n \n \n \n \n Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean.\n \n \n \n\n\n \n Delmont, T. O.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 118(46): e2112355118. November 2021.\n \n\n\n\n
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\n\n\n@article{delmont_discovery_2021,\n\ttitle = {Discovery of nondiazotrophic {Trichodesmium} species abundant and widespread in the open ocean},\n\tvolume = {118},\n\tissn = {1091-6490},\n\tdoi = {10.1073/pnas.2112355118},\n\tabstract = {Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton's primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community's ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.},\n\tlanguage = {eng},\n\tnumber = {46},\n\tjournal = {Proceedings of the National Academy of Sciences of the United States of America},\n\tauthor = {Delmont, Tom O.},\n\tmonth = nov,\n\tyear = {2021},\n\tpmid = {34750267},\n\tpmcid = {PMC8609553},\n\tkeywords = {Carbon, Cyanobacteria, Genome, Metagenomics, Nitrogen, Nitrogen Fixation, Oceans and Seas, Seawater, Tara Oceans, Trichodesmium, ecology and evolution, metagenomics, nitrogen fixation},\n\tpages = {e2112355118},\n}\n\n\n\n Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton's primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community's ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.\n
\n\n\n\n \n\n \n \n \n \n \n Comparative genomics reveals new functional insights in uncultured MAST species.\n \n \n \n\n\n \n Labarre, A.; López-Escardó, D.; Latorre, F.; Leonard, G.; Bucchini, F.; Obiol, A.; Cruaud, C.; Sieracki, M. E.; Jaillon, O.; Wincker, P.; Vandepoele, K.; Logares, R.; and Massana, R.\n\n\n \n\n\n\n The ISME journal, 15(6): 1767–1781. June 2021.\n \n\n\n\n
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\n\n\n@article{labarre_comparative_2021,\n\ttitle = {Comparative genomics reveals new functional insights in uncultured {MAST} species},\n\tvolume = {15},\n\tissn = {1751-7370},\n\tdoi = {10.1038/s41396-020-00885-8},\n\tabstract = {Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.},\n\tlanguage = {eng},\n\tnumber = {6},\n\tjournal = {The ISME journal},\n\tauthor = {Labarre, Aurelie and López-Escardó, David and Latorre, Francisco and Leonard, Guy and Bucchini, François and Obiol, Aleix and Cruaud, Corinne and Sieracki, Michael E. and Jaillon, Olivier and Wincker, Patrick and Vandepoele, Klaas and Logares, Ramiro and Massana, Ramon},\n\tmonth = jun,\n\tyear = {2021},\n\tpmid = {33452482},\n\tpmcid = {PMC8163842},\n\tkeywords = {Genomics, Oceans and Seas, Phylogeny, Plankton, Seawater, Stramenopiles},\n\tpages = {1767--1781},\n}\n\n\n\n Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.\n
\n\n\n\n \n\n \n \n \n \n \n Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods.\n \n \n \n\n\n \n Pierella Karlusich, J. J.; Pelletier, E.; Lombard, F.; Carsique, M.; Dvorak, E.; Colin, S.; Picheral, M.; Cornejo-Castillo, F. M.; Acinas, S. G.; Pepperkok, R.; Karsenti, E.; de Vargas, C.; Wincker, P.; Bowler, C.; and Foster, R. A.\n\n\n \n\n\n\n Nature Communications, 12(1): 4160. July 2021.\n \n\n\n\n
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\n\n\n@article{pierella_karlusich_global_2021,\n\ttitle = {Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods},\n\tvolume = {12},\n\tissn = {2041-1723},\n\tdoi = {10.1038/s41467-021-24299-y},\n\tabstract = {Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining {\\textgreater}2,000,000 images and {\\textgreater}1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions ({\\textless}0.2-2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton ({\\textless}0.2 μm) to mesoplankton (180-2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs ({\\textgreater}20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs ({\\textgreater}10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Nature Communications},\n\tauthor = {Pierella Karlusich, Juan José and Pelletier, Eric and Lombard, Fabien and Carsique, Madeline and Dvorak, Etienne and Colin, Sébastien and Picheral, Marc and Cornejo-Castillo, Francisco M. and Acinas, Silvia G. and Pepperkok, Rainer and Karsenti, Eric and de Vargas, Colomban and Wincker, Patrick and Bowler, Chris and Foster, Rachel A.},\n\tmonth = jul,\n\tyear = {2021},\n\tpmid = {34230473},\n\tpmcid = {PMC8260585},\n\tkeywords = {Aquatic Organisms, Bacteria, Cyanobacteria, Molecular Imprinting, Nitrogen, Nitrogen Fixation, Oceans and Seas, Phylogeny, Plankton, Seawater, Symbiosis},\n\tpages = {4160},\n}\n\n\n\n Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining \\textgreater2,000,000 images and \\textgreater1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (\\textless0.2-2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (\\textless0.2 μm) to mesoplankton (180-2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (\\textgreater20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (\\textgreater10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.\n
\n\n\n\n \n\n \n \n \n \n \n Macroscale patterns of oceanic zooplankton composition and size structure.\n \n \n \n\n\n \n Brandão, M. C.; Benedetti, F.; Martini, S.; Soviadan, Y. D.; Irisson, J.; Romagnan, J.; Elineau, A.; Desnos, C.; Jalabert, L.; Freire, A. S.; Picheral, M.; Guidi, L.; Gorsky, G.; Bowler, C.; Karp-Boss, L.; Henry, N.; de Vargas, C.; Sullivan, M. B.; Tara Oceans Consortium Coordinators; Stemmann, L.; and Lombard, F.\n\n\n \n\n\n\n Scientific Reports, 11(1): 15714. August 2021.\n \n\n\n\n
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\n\n\n@article{brandao_macroscale_2021,\n\ttitle = {Macroscale patterns of oceanic zooplankton composition and size structure},\n\tvolume = {11},\n\tissn = {2045-2322},\n\tdoi = {10.1038/s41598-021-94615-5},\n\tabstract = {Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Scientific Reports},\n\tauthor = {Brandão, Manoela C. and Benedetti, Fabio and Martini, Séverine and Soviadan, Yawouvi Dodji and Irisson, Jean-Olivier and Romagnan, Jean-Baptiste and Elineau, Amanda and Desnos, Corinne and Jalabert, Laëtitia and Freire, Andrea S. and Picheral, Marc and Guidi, Lionel and Gorsky, Gabriel and Bowler, Chris and Karp-Boss, Lee and Henry, Nicolas and de Vargas, Colomban and Sullivan, Matthew B. and {Tara Oceans Consortium Coordinators} and Stemmann, Lars and Lombard, Fabien},\n\tmonth = aug,\n\tyear = {2021},\n\tpmid = {34344925},\n\tpmcid = {PMC8333327},\n\tpages = {15714},\n}\n\n\n\n Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.\n
\n\n\n\n \n\n \n \n \n \n \n Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis.\n \n \n \n\n\n \n Sugier, K.; Laso-Jadart, R.; Vacherie, B.; Käfer, J.; Bertrand, L.; Labadie, K.; Martins, N.; Orvain, C.; Petit, E.; Wincker, P.; Jamet, J.; Alberti, A.; and Madoui, M.\n\n\n \n\n\n\n Biology, 10(7): 657. July 2021.\n \n\n\n\n
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\n\n\n@article{sugier_male_2021,\n\ttitle = {Male {Differentiation} in the {Marine} {Copepod} {Oithona} nana {Reveals} the {Development} of a {New} {Nervous} {Ganglion} and {Lin12}-{Notch}-{Repeat} {Protein}-{Associated} {Proteolysis}},\n\tvolume = {10},\n\tissn = {2079-7737},\n\tdoi = {10.3390/biology10070657},\n\tabstract = {Copepods are among the most numerous animals, and they play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is less mobile and feeds less. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches and revealed the presence of a male-specific nervous ganglion. Transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed in males. Furthermore, some LDPGs coded for proteins with predicted proteolytic activity, and proteases-associated transcripts showed a male-specific enrichment. Using yeast double-hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. We also hypothesized possible roles of the LDPGs in the development of the lateral ganglia through helping in extracellular matrix lysis, neurites growth guidance, and synapses genesis.},\n\tlanguage = {eng},\n\tnumber = {7},\n\tjournal = {Biology},\n\tauthor = {Sugier, Kevin and Laso-Jadart, Romuald and Vacherie, Benoît and Käfer, Jos and Bertrand, Laurie and Labadie, Karine and Martins, Nathalie and Orvain, Céline and Petit, Emmanuelle and Wincker, Patrick and Jamet, Jean-Louis and Alberti, Adriana and Madoui, Mohammed-Amin},\n\tmonth = jul,\n\tyear = {2021},\n\tpmid = {34356512},\n\tpmcid = {PMC8301441},\n\tkeywords = {Lin12-Notch-Repeat, Oithona, copepods, nervous system, protein–protein interaction, sexual differentiation},\n\tpages = {657},\n}\n\n\n\n Copepods are among the most numerous animals, and they play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is less mobile and feeds less. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches and revealed the presence of a male-specific nervous ganglion. Transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed in males. Furthermore, some LDPGs coded for proteins with predicted proteolytic activity, and proteases-associated transcripts showed a male-specific enrichment. Using yeast double-hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. We also hypothesized possible roles of the LDPGs in the development of the lateral ganglia through helping in extracellular matrix lysis, neurites growth guidance, and synapses genesis.\n
\n\n\n\n \n\n \n \n \n \n \n Environmental vulnerability of the global ocean epipelagic plankton community interactome.\n \n \n \n\n\n \n Chaffron, S.; Delage, E.; Budinich, M.; Vintache, D.; Henry, N.; Nef, C.; Ardyna, M.; Zayed, A. A.; Junger, P. C.; Galand, P. E.; Lovejoy, C.; Murray, A. E.; Sarmento, H.; Tara Oceans coordinators; Acinas, S. G.; Babin, M.; Iudicone, D.; Jaillon, O.; Karsenti, E.; Wincker, P.; Karp-Boss, L.; Sullivan, M. B.; Bowler, C.; de Vargas, C.; and Eveillard, D.\n\n\n \n\n\n\n Science Advances, 7(35): eabg1921. August 2021.\n \n\n\n\n
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\n\n\n@article{chaffron_environmental_2021,\n\ttitle = {Environmental vulnerability of the global ocean epipelagic plankton community interactome},\n\tvolume = {7},\n\tissn = {2375-2548},\n\tdoi = {10.1126/sciadv.abg1921},\n\tabstract = {Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.},\n\tlanguage = {eng},\n\tnumber = {35},\n\tjournal = {Science Advances},\n\tauthor = {Chaffron, Samuel and Delage, Erwan and Budinich, Marko and Vintache, Damien and Henry, Nicolas and Nef, Charlotte and Ardyna, Mathieu and Zayed, Ahmed A. and Junger, Pedro C. and Galand, Pierre E. and Lovejoy, Connie and Murray, Alison E. and Sarmento, Hugo and {Tara Oceans coordinators} and Acinas, Silvia G. and Babin, Marcel and Iudicone, Daniele and Jaillon, Olivier and Karsenti, Eric and Wincker, Patrick and Karp-Boss, Lee and Sullivan, Matthew B. and Bowler, Chris and de Vargas, Colomban and Eveillard, Damien},\n\tmonth = aug,\n\tyear = {2021},\n\tpmid = {34452910},\n\tpmcid = {PMC8397264},\n\tpages = {eabg1921},\n}\n\n\n\n Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.\n
\n\n\n\n \n\n \n \n \n \n \n Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.\n \n \n \n\n\n \n Royo-Llonch, M.; Sánchez, P.; Ruiz-González, C.; Salazar, G.; Pedrós-Alió, C.; Sebastián, M.; Labadie, K.; Paoli, L.; M Ibarbalz, F.; Zinger, L.; Churcheward, B.; Tara Oceans Coordinators; Chaffron, S.; Eveillard, D.; Karsenti, E.; Sunagawa, S.; Wincker, P.; Karp-Boss, L.; Bowler, C.; and Acinas, S. G.\n\n\n \n\n\n\n Nature Microbiology, 6(12): 1561–1574. December 2021.\n \n\n\n\n
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\n\n\n@article{royo-llonch_compendium_2021,\n\ttitle = {Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar {Arctic} {Ocean}},\n\tvolume = {6},\n\tissn = {2058-5276},\n\tdoi = {10.1038/s41564-021-00979-9},\n\tabstract = {The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.},\n\tlanguage = {eng},\n\tnumber = {12},\n\tjournal = {Nature Microbiology},\n\tauthor = {Royo-Llonch, Marta and Sánchez, Pablo and Ruiz-González, Clara and Salazar, Guillem and Pedrós-Alió, Carlos and Sebastián, Marta and Labadie, Karine and Paoli, Lucas and M Ibarbalz, Federico and Zinger, Lucie and Churcheward, Benjamin and {Tara Oceans Coordinators} and Chaffron, Samuel and Eveillard, Damien and Karsenti, Eric and Sunagawa, Shinichi and Wincker, Patrick and Karp-Boss, Lee and Bowler, Chris and Acinas, Silvia G.},\n\tmonth = dec,\n\tyear = {2021},\n\tpmid = {34782724},\n\tkeywords = {Archaea, Arctic Regions, Bacteria, Ecosystem, Genome, Archaeal, Genome, Bacterial, Metagenome, Phylogeny, Seawater},\n\tpages = {1561--1574},\n}\n\n\n\n The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.\n
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\n \n \n\n \n \n \n \n \n \n Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.\n \n \n \n \n\n\n \n Vorobev, A.; Dupouy, M.; Carradec, Q.; Delmont, T. O.; Annamalé, A.; Wincker, P.; and Pelletier, E.\n\n\n \n\n\n\n Genome Research, 30(4): 647–659. April 2020.\n Company: Cold Spring Harbor Laboratory Press Distributor: Cold Spring Harbor Laboratory Press Institution: Cold Spring Harbor Laboratory Press Label: Cold Spring Harbor Laboratory Press Publisher: Cold Spring Harbor Lab\n\n\n\n
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\n\n\n@article{vorobev_transcriptome_2020,\n\ttitle = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics},\n\tvolume = {30},\n\tissn = {1088-9051, 1549-5469},\n\turl = {http://genome.cshlp.org/content/30/4/647},\n\tdoi = {10.1101/gr.253070.119},\n\tabstract = {Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2021-09-14},\n\tjournal = {Genome Research},\n\tauthor = {Vorobev, Alexey and Dupouy, Marion and Carradec, Quentin and Delmont, Tom O. and Annamalé, Anita and Wincker, Patrick and Pelletier, Eric},\n\tmonth = apr,\n\tyear = {2020},\n\tpmid = {32205368},\n\tnote = {Company: Cold Spring Harbor Laboratory Press\nDistributor: Cold Spring Harbor Laboratory Press\nInstitution: Cold Spring Harbor Laboratory Press\nLabel: Cold Spring Harbor Laboratory Press\nPublisher: Cold Spring Harbor Lab},\n\tpages = {647--659},\n}\n\n\n\n Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.\n
\n\n\n\n \n\n \n \n \n \n \n Genome Resolved Biogeography of Mamiellales.\n \n \n \n\n\n \n Leconte, J.; Benites, L. F.; Vannier, T.; Wincker, P.; Piganeau, G.; and Jaillon, O.\n\n\n \n\n\n\n Genes, 11(1): E66. January 2020.\n \n\n\n\n
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\n\n\n@article{leconte_genome_2020,\n\ttitle = {Genome {Resolved} {Biogeography} of {Mamiellales}},\n\tvolume = {11},\n\tissn = {2073-4425},\n\tdoi = {10.3390/genes11010066},\n\tabstract = {Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales' biogeography and raise novel testable hypotheses about their life cycle and ecology.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Genes},\n\tauthor = {Leconte, Jade and Benites, L. Felipe and Vannier, Thomas and Wincker, Patrick and Piganeau, Gwenael and Jaillon, Olivier},\n\tmonth = jan,\n\tyear = {2020},\n\tpmid = {31936086},\n\tpmcid = {PMC7016971},\n\tkeywords = {Base Sequence, Chlorophyta, Demography, Genome, Mamiellales, Oceans and Seas, Phylogeny, Phylogeography, Phytoplankton, Population Density, Seawater, Tara Oceans, biogeography, ecogenomics, mating-type, sexual reproduction},\n\tpages = {E66},\n}\n\n\n\n Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales' biogeography and raise novel testable hypotheses about their life cycle and ecology.\n
\n\n\n\n \n\n \n \n \n \n \n Tara Oceans: towards global ocean ecosystems biology.\n \n \n \n\n\n \n Sunagawa, S.; Acinas, S. G.; Bork, P.; Bowler, C.; Tara Oceans Coordinators; Eveillard, D.; Gorsky, G.; Guidi, L.; Iudicone, D.; Karsenti, E.; Lombard, F.; Ogata, H.; Pesant, S.; Sullivan, M. B.; Wincker, P.; and de Vargas, C.\n\n\n \n\n\n\n Nature Reviews. Microbiology, 18(8): 428–445. August 2020.\n \n\n\n\n
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\n\n\n@article{sunagawa_tara_2020,\n\ttitle = {Tara {Oceans}: towards global ocean ecosystems biology},\n\tvolume = {18},\n\tissn = {1740-1534},\n\tshorttitle = {Tara {Oceans}},\n\tdoi = {10.1038/s41579-020-0364-5},\n\tabstract = {A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.},\n\tlanguage = {eng},\n\tnumber = {8},\n\tjournal = {Nature Reviews. Microbiology},\n\tauthor = {Sunagawa, Shinichi and Acinas, Silvia G. and Bork, Peer and Bowler, Chris and {Tara Oceans Coordinators} and Eveillard, Damien and Gorsky, Gabriel and Guidi, Lionel and Iudicone, Daniele and Karsenti, Eric and Lombard, Fabien and Ogata, Hiroyuki and Pesant, Stephane and Sullivan, Matthew B. and Wincker, Patrick and de Vargas, Colomban},\n\tmonth = aug,\n\tyear = {2020},\n\tpmid = {32398798},\n\tkeywords = {Animals, Biodiversity, Biology, Climate Change, Ecosystem, Humans, Oceans and Seas, Plankton},\n\tpages = {428--445},\n}\n\n\n\n A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.\n
\n\n\n\n \n\n \n \n \n \n \n Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866).\n \n \n \n\n\n \n Laso-Jadart, R.; Sugier, K.; Petit, E.; Labadie, K.; Peterlongo, P.; Ambroise, C.; Wincker, P.; Jamet, J.; and Madoui, M.\n\n\n \n\n\n\n Ecology and Evolution, 10(16): 8894–8905. August 2020.\n \n\n\n\n
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\n\n\n@article{laso-jadart_investigating_2020,\n\ttitle = {Investigating population-scale allelic differential expression in wild populations of {Oithona} similis ({Cyclopoida}, {Claus}, 1866)},\n\tvolume = {10},\n\tissn = {2045-7758},\n\tdoi = {10.1002/ece3.6588},\n\tabstract = {Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2\\%) were affected by psADE in at least one population (FDR {\\textless} 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6\\%) were under both selection and psADE (p {\\textless} .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.},\n\tlanguage = {eng},\n\tnumber = {16},\n\tjournal = {Ecology and Evolution},\n\tauthor = {Laso-Jadart, Romuald and Sugier, Kevin and Petit, Emmanuelle and Labadie, Karine and Peterlongo, Pierre and Ambroise, Christophe and Wincker, Patrick and Jamet, Jean-Louis and Madoui, Mohammed-Amin},\n\tmonth = aug,\n\tyear = {2020},\n\tpmid = {32884665},\n\tpmcid = {PMC7452778},\n\tkeywords = {Arctic seas, Tara Oceans, Zooplankton, allelic expression, copepod, metagenomics, metatranscriptomics, selection, structure},\n\tpages = {8894--8905},\n}\n\n\n\n Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR \\textless 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p \\textless .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.\n
\n\n\n\n \n\n \n \n \n \n \n \n Metagenomic Mining for Amine Dehydrogenase Discovery.\n \n \n \n \n\n\n \n Caparco, A. A.; Pelletier, E.; Petit, J. L.; Jouenne, A.; Bommarius, B. R.; Berardinis, V. d.; Zaparucha, A.; Champion, J. A.; Bommarius, A. S.; and Vergne‐Vaxelaire, C.\n\n\n \n\n\n\n Advanced Synthesis & Catalysis, n/a(n/a). 2020.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/adsc.202000094\n\n\n\n
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\n\n\n@article{caparco_metagenomic_2020,\n\ttitle = {Metagenomic {Mining} for {Amine} {Dehydrogenase} {Discovery}},\n\tvolume = {n/a},\n\tcopyright = {© 2020 Wiley‐VCH Verlag GmbH \\& Co. KGaA, Weinheim},\n\tissn = {1615-4169},\n\turl = {http://onlinelibrary.wiley.com/doi/abs/10.1002/adsc.202000094},\n\tdoi = {10.1002/adsc.202000094},\n\tabstract = {Amine dehydrogenases (AmDHs) catalyze the enzymatic reduction of ketones to amines, serving as a suitable biocatalytic route for amine synthesis. A limited number of experimentally validated native AmDHs (nat-AmDHs) have been reported recently, expanding the sequences with this function to complement the small set of engineered enzymes. Since researchers can now probe into the vast diversity of enzymes within niche environments by a metagenomics approach, a tandem metagenomic and bioinformatic approach is a powerful tool to identify new members of limited enzyme families to access new features in an iterative fashion. The previously untapped biocatalytic reservoirs of the ocean environment and human microbiome were screened for potential AmDHs using a hidden Markov model. Among the hundreds of hits, a subset of 18 enzymes was selected for further characterization and were confirmed to display AmDH activity. Additional analysis on six enzymes confirmed altered cofactor specificities and variation in substrate scopes, catalytic efficiencies, and active site residues compared to the reference nat-AmDHs previously described. Particularly, MATOUAmDH2 from an eukaryotic organism demonstrated specific activity of 11.07 and 0.88 U mg−1 toward isobutyraldehyde and 1,2-cyclohexadione respectively. Their abundance among the screened environments was also described. The protein sequence diversity of validated AmDHs reached by this metagenomics mining strategy highlights the success of such an approach. Metagenomically mined proteins, including eukaryotic ones, stand to increase the reach of biocatalysis towards enviromentally benign processes.},\n\tlanguage = {en},\n\tnumber = {n/a},\n\turldate = {2020-04-22},\n\tjournal = {Advanced Synthesis \\& Catalysis},\n\tauthor = {Caparco, Adam A. and Pelletier, Eric and Petit, Jean Louis and Jouenne, Aurélie and Bommarius, Bettina R. and Berardinis, Véronique de and Zaparucha, Anne and Champion, Julie A. and Bommarius, Andreas S. and Vergne‐Vaxelaire, Carine},\n\tyear = {2020},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/adsc.202000094},\n\tkeywords = {biocatalysis, enzyme discovery, metagenome mining},\n}\n\n\n\n Amine dehydrogenases (AmDHs) catalyze the enzymatic reduction of ketones to amines, serving as a suitable biocatalytic route for amine synthesis. A limited number of experimentally validated native AmDHs (nat-AmDHs) have been reported recently, expanding the sequences with this function to complement the small set of engineered enzymes. Since researchers can now probe into the vast diversity of enzymes within niche environments by a metagenomics approach, a tandem metagenomic and bioinformatic approach is a powerful tool to identify new members of limited enzyme families to access new features in an iterative fashion. The previously untapped biocatalytic reservoirs of the ocean environment and human microbiome were screened for potential AmDHs using a hidden Markov model. Among the hundreds of hits, a subset of 18 enzymes was selected for further characterization and were confirmed to display AmDH activity. Additional analysis on six enzymes confirmed altered cofactor specificities and variation in substrate scopes, catalytic efficiencies, and active site residues compared to the reference nat-AmDHs previously described. Particularly, MATOUAmDH2 from an eukaryotic organism demonstrated specific activity of 11.07 and 0.88 U mg−1 toward isobutyraldehyde and 1,2-cyclohexadione respectively. Their abundance among the screened environments was also described. The protein sequence diversity of validated AmDHs reached by this metagenomics mining strategy highlights the success of such an approach. Metagenomically mined proteins, including eukaryotic ones, stand to increase the reach of biocatalysis towards enviromentally benign processes.\n
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\n \n \n\n \n \n \n \n \n \n Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems.\n \n \n \n \n\n\n \n Caputi, L.; Carradec, Q.; Eveillard, D.; Kirilovsky, A.; Karlusich, J. J. P.; Pelletier, E.; Vieira, F. R. J.; Villar, E.; Chaffron, S.; Malviya, S.; Scalco, E.; Acinas, S. G.; Alberti, A.; Aury, J.; Benoiston, A.; Bertrand, A.; Biard, T.; Bittner, L.; Boccara, M.; Brum, J. R.; Brunet, C.; Busseni, G.; Carratalà, A.; Claustre, H.; Coelho, L. P.; Colin, S.; D'Aniello, S.; Silva, C. D.; Core, M. D.; Doré, H.; Gasparini, S.; Kokoszka, F.; Jamet, J.; Lejeusne, C.; Lepoivre, C.; Lescot, M.; Lima-Mendez, G.; Lombard, F.; Lukeš, J.; Maillet, N.; Madoui, M.; Martinez, E.; Mazzocchi, M. G.; Néou, M. B.; Paz-Yepes, J.; Poulain, J.; Ramondenc, S.; Romagnan, J.; Roux, S.; Manta, D. S.; Sanges, R.; Speich, S.; Sprovieri, M.; Sunagawa, S.; Taillandier, V.; Tanaka, A.; Tirichine, L.; Trottier, C.; Uitz, J.; Veluchamy, A.; Veselá, J.; Vincent, F.; Yau, S.; Kandels-Lewis, S.; Searson, S.; Dimier, C.; Picheral, M.; Bork, P.; Boss, E.; Vargas, C. d.; Follows, M. J.; Grimsley, N.; Guidi, L.; Hingamp, P.; Karsenti, E.; Sordino, P.; Stemmann, L.; Sullivan, M. B.; Tagliabue, A.; Zingone, A.; Garczarek, L.; d'Ortenzio , F.; Testor, P.; Not, F.; d'Alcalà , M. R.; Wincker, P.; Bowler, C.; and Iudicone, D.\n\n\n \n\n\n\n Global Biogeochemical Cycles, 33(3): 391–419. January 2019.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2018GB006022\n\n\n\n
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\n\n\n@article{caputi_community-level_2019,\n\ttitle = {Community-{Level} {Responses} to {Iron} {Availability} in {Open} {Ocean} {Plankton} {Ecosystems}},\n\tvolume = {33},\n\tissn = {1944-9224},\n\turl = {http://onlinelibrary.wiley.com/doi/abs/10.1029/2018GB006022},\n\tdoi = {10.1029/2018GB006022},\n\tabstract = {Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.},\n\tlanguage = {en},\n\tnumber = {3},\n\turldate = {2021-09-14},\n\tjournal = {Global Biogeochemical Cycles},\n\tauthor = {Caputi, Luigi and Carradec, Quentin and Eveillard, Damien and Kirilovsky, Amos and Karlusich, Juan J. Pierella and Pelletier, Eric and Vieira, Fabio Rocha Jimenez and Villar, Emilie and Chaffron, Samuel and Malviya, Shruti and Scalco, Eleonora and Acinas, Silvia G. and Alberti, Adriana and Aury, Jean-Marc and Benoiston, Anne-Sophie and Bertrand, Alexis and Biard, Tristan and Bittner, Lucie and Boccara, Martine and Brum, Jennifer R. and Brunet, Christophe and Busseni, Greta and Carratalà, Anna and Claustre, Hervé and Coelho, Luis Pedro and Colin, Sébastien and D'Aniello, Salvatore and Silva, Corinne Da and Core, Marianna Del and Doré, Hugo and Gasparini, Stéphane and Kokoszka, Florian and Jamet, Jean-Louis and Lejeusne, Christophe and Lepoivre, Cyrille and Lescot, Magali and Lima-Mendez, Gipsi and Lombard, Fabien and Lukeš, Julius and Maillet, Nicolas and Madoui, Mohammed-Amin and Martinez, Elodie and Mazzocchi, Maria Grazia and Néou, Mario B. and Paz-Yepes, Javier and Poulain, Julie and Ramondenc, Simon and Romagnan, Jean-Baptiste and Roux, Simon and Manta, Daniela Salvagio and Sanges, Remo and Speich, Sabrina and Sprovieri, Mario and Sunagawa, Shinichi and Taillandier, Vincent and Tanaka, Atsuko and Tirichine, Leila and Trottier, Camille and Uitz, Julia and Veluchamy, Alaguraj and Veselá, Jana and Vincent, Flora and Yau, Sheree and Kandels-Lewis, Stefanie and Searson, Sarah and Dimier, Céline and Picheral, Marc and Bork, Peer and Boss, Emmanuel and Vargas, Colomban de and Follows, Michael J. and Grimsley, Nigel and Guidi, Lionel and Hingamp, Pascal and Karsenti, Eric and Sordino, Paolo and Stemmann, Lars and Sullivan, Matthew B. and Tagliabue, Alessandro and Zingone, Adriana and Garczarek, Laurence and d'Ortenzio, Fabrizio and Testor, Pierre and Not, Fabrice and d'Alcalà, Maurizio Ribera and Wincker, Patrick and Bowler, Chris and Iudicone, Daniele},\n\tmonth = jan,\n\tyear = {2019},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2018GB006022},\n\tkeywords = {iron response, meta-omics, species networks, system biology},\n\tpages = {391--419},\n}\n\n\n\n Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.\n
\n\n\n\n \n\n \n \n \n \n \n Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.\n \n \n \n\n\n \n Arif, M.; Gauthier, J.; Sugier, K.; Iudicone, D.; Jaillon, O.; Wincker, P.; Peterlongo, P.; and Madoui, M.\n\n\n \n\n\n\n Molecular Ecology Resources, 19(2): 526–535. March 2019.\n \n\n\n\n
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\n\n\n@article{arif_discovering_2019,\n\ttitle = {Discovering millions of plankton genomic markers from the {Atlantic} {Ocean} and the {Mediterranean} {Sea}},\n\tvolume = {19},\n\tissn = {1755-0998},\n\tdoi = {10.1111/1755-0998.12985},\n\tabstract = {Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used discosnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. discosnp ++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. discosnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/).},\n\tlanguage = {eng},\n\tnumber = {2},\n\tjournal = {Molecular Ecology Resources},\n\tauthor = {Arif, Majda and Gauthier, Jérémy and Sugier, Kevin and Iudicone, Daniele and Jaillon, Olivier and Wincker, Patrick and Peterlongo, Pierre and Madoui, Mohammed-Amin},\n\tmonth = mar,\n\tyear = {2019},\n\tpmid = {30575285},\n\tkeywords = {Animals, Aquatic Organisms, Atlantic Ocean, Genetic Markers, Genetics, Population, Genotyping Techniques, Mediterranean Sea, Metagenomics, Plankton},\n\tpages = {526--535},\n}\n\n\n\n Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used discosnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. discosnp ++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. discosnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/).\n
\n\n\n\n \n\n \n \n \n \n \n Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.\n \n \n \n\n\n \n Sieracki, M. E.; Poulton, N. J.; Jaillon, O.; Wincker, P.; de Vargas, C.; Rubinat-Ripoll, L.; Stepanauskas, R.; Logares, R.; and Massana, R.\n\n\n \n\n\n\n Scientific Reports, 9(1): 6025. April 2019.\n \n\n\n\n
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\n\n\n@article{sieracki_single_2019,\n\ttitle = {Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems},\n\tvolume = {9},\n\tissn = {2045-2322},\n\tdoi = {10.1038/s41598-019-42487-1},\n\tabstract = {Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15\\% of aplastidic cell sorts, and 7\\% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Scientific Reports},\n\tauthor = {Sieracki, M. E. and Poulton, N. J. and Jaillon, O. and Wincker, P. and de Vargas, C. and Rubinat-Ripoll, L. and Stepanauskas, R. and Logares, R. and Massana, R.},\n\tmonth = apr,\n\tyear = {2019},\n\tpmid = {30988337},\n\tpmcid = {PMC6465268},\n\tkeywords = {Biodiversity, DNA, Ecosystem, Eukaryota, Genomics, Indian Ocean, Mediterranean Sea, Phylogeny, Plankton, RNA, Ribosomal, 18S, Single-Cell Analysis},\n\tpages = {6025},\n}\n\n\n\n Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.\n
\n\n\n\n \n\n \n \n \n \n \n Marine DNA Viral Macro- and Microdiversity from Pole to Pole.\n \n \n \n\n\n \n Gregory, A. C.; Zayed, A. A.; Conceição-Neto, N.; Temperton, B.; Bolduc, B.; Alberti, A.; Ardyna, M.; Arkhipova, K.; Carmichael, M.; Cruaud, C.; Dimier, C.; Domínguez-Huerta, G.; Ferland, J.; Kandels, S.; Liu, Y.; Marec, C.; Pesant, S.; Picheral, M.; Pisarev, S.; Poulain, J.; Tremblay, J.; Vik, D.; Tara Oceans Coordinators; Babin, M.; Bowler, C.; Culley, A. I.; de Vargas, C.; Dutilh, B. E.; Iudicone, D.; Karp-Boss, L.; Roux, S.; Sunagawa, S.; Wincker, P.; and Sullivan, M. B.\n\n\n \n\n\n\n Cell, 177(5): 1109–1123.e14. May 2019.\n \n\n\n\n
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\n\n\n@article{gregory_marine_2019,\n\ttitle = {Marine {DNA} {Viral} {Macro}- and {Microdiversity} from {Pole} to {Pole}},\n\tvolume = {177},\n\tissn = {1097-4172},\n\tdoi = {10.1016/j.cell.2019.03.040},\n\tabstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.},\n\tlanguage = {eng},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Gregory, Ann C. and Zayed, Ahmed A. and Conceição-Neto, Nádia and Temperton, Ben and Bolduc, Ben and Alberti, Adriana and Ardyna, Mathieu and Arkhipova, Ksenia and Carmichael, Margaux and Cruaud, Corinne and Dimier, Céline and Domínguez-Huerta, Guillermo and Ferland, Joannie and Kandels, Stefanie and Liu, Yunxiao and Marec, Claudie and Pesant, Stéphane and Picheral, Marc and Pisarev, Sergey and Poulain, Julie and Tremblay, Jean-Éric and Vik, Dean and {Tara Oceans Coordinators} and Babin, Marcel and Bowler, Chris and Culley, Alexander I. and de Vargas, Colomban and Dutilh, Bas E. and Iudicone, Daniele and Karp-Boss, Lee and Roux, Simon and Sunagawa, Shinichi and Wincker, Patrick and Sullivan, Matthew B.},\n\tmonth = may,\n\tyear = {2019},\n\tpmid = {31031001},\n\tpmcid = {PMC6525058},\n\tkeywords = {Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses},\n\tpages = {1109--1123.e14},\n}\n\n\n\n Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.\n
\n\n\n\n \n\n \n \n \n \n \n Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes.\n \n \n \n\n\n \n Busseni, G.; Vieira, F. R. J.; Amato, A.; Pelletier, E.; Pierella Karlusich, J. J.; Ferrante, M. I.; Wincker, P.; Rogato, A.; Bowler, C.; Sanges, R.; Maiorano, L.; Chiurazzi, M.; d'Alcalà , M. R.; Caputi, L.; and Iudicone, D.\n\n\n \n\n\n\n Molecular Biology and Evolution,msz157. July 2019.\n \n\n\n\n
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\n\n\n@article{busseni_meta-omics_2019,\n\ttitle = {Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes},\n\tissn = {1537-1719},\n\tdoi = {10.1093/molbev/msz157},\n\tabstract = {Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.},\n\tlanguage = {eng},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Busseni, Greta and Vieira, Fabio Rocha Jimenez and Amato, Alberto and Pelletier, Eric and Pierella Karlusich, Juan J. and Ferrante, Maria I. and Wincker, Patrick and Rogato, Alessandra and Bowler, Chris and Sanges, Remo and Maiorano, Luigi and Chiurazzi, Maurizio and d'Alcalà, Maurizio Ribera and Caputi, Luigi and Iudicone, Daniele},\n\tmonth = jul,\n\tyear = {2019},\n\tpmid = {31259367},\n\tpmcid = {PMC6805229},\n\tpages = {msz157},\n}\n\n\n\n Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.\n
\n\n\n\n \n\n \n \n \n \n \n The Tara Pacific expedition-A pan-ecosystemic approach of the \"-omics\" complexity of coral reef holobionts across the Pacific Ocean.\n \n \n \n\n\n \n Planes, S.; Allemand, D.; Agostini, S.; Banaigs, B.; Boissin, E.; Boss, E.; Bourdin, G.; Bowler, C.; Douville, E.; Flores, J. M.; Forcioli, D.; Furla, P.; Galand, P. E.; Ghiglione, J.; Gilson, E.; Lombard, F.; Moulin, C.; Pesant, S.; Poulain, J.; Reynaud, S.; Romac, S.; Sullivan, M. B.; Sunagawa, S.; Thomas, O. P.; Troublé, R.; de Vargas, C.; Vega Thurber, R.; Voolstra, C. R.; Wincker, P.; Zoccola, D.; and Tara Pacific Consortium\n\n\n \n\n\n\n PLoS biology, 17(9): e3000483. September 2019.\n \n\n\n\n
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\n\n\n@article{planes_tara_2019,\n\ttitle = {The {Tara} {Pacific} expedition-{A} pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the {Pacific} {Ocean}},\n\tvolume = {17},\n\tissn = {1545-7885},\n\tdoi = {10.1371/journal.pbio.3000483},\n\tabstract = {Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.},\n\tlanguage = {eng},\n\tnumber = {9},\n\tjournal = {PLoS biology},\n\tauthor = {Planes, Serge and Allemand, Denis and Agostini, Sylvain and Banaigs, Bernard and Boissin, Emilie and Boss, Emmanuel and Bourdin, Guillaume and Bowler, Chris and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Ghiglione, Jean-François and Gilson, Eric and Lombard, Fabien and Moulin, Clémentine and Pesant, Stephane and Poulain, Julie and Reynaud, Stéphanie and Romac, Sarah and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and de Vargas, Colomban and Vega Thurber, Rebecca and Voolstra, Christian R. and Wincker, Patrick and Zoccola, Didier and {Tara Pacific Consortium}},\n\tmonth = sep,\n\tyear = {2019},\n\tpmid = {31545807},\n\tpmcid = {PMC6776362},\n\tkeywords = {Animals, Anthozoa, Coral Reefs, Expeditions, Metabolomics, Metagenomics, Microbiota, Pacific Ocean, Symbiosis},\n\tpages = {e3000483},\n}\n\n\n\n Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the \"-omics\" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.\n
\n\n\n\n \n\n \n \n \n \n \n A thousand plants' phylogeny.\n \n \n \n\n\n \n Wincker, P.\n\n\n \n\n\n\n Nature Plants, 5(11): 1106–1107. November 2019.\n \n\n\n\n
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\n\n\n\n@article{wincker_thousand_2019,\n\ttitle = {A thousand plants' phylogeny},\n\tvolume = {5},\n\tissn = {2055-0278},\n\tdoi = {10.1038/s41477-019-0555-0},\n\tlanguage = {eng},\n\tnumber = {11},\n\tjournal = {Nature Plants},\n\tauthor = {Wincker, Patrick},\n\tmonth = nov,\n\tyear = {2019},\n\tpmid = {31712759},\n\tkeywords = {Biodiversity, Genes, Plant, Molecular Typing, Multigene Family, Phylogeny, Transcriptome, Viridiplantae},\n\tpages = {1106--1107},\n}\n\n\n\n \n\n \n \n \n \n \n Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.\n \n \n \n\n\n \n Salazar, G.; Paoli, L.; Alberti, A.; Huerta-Cepas, J.; Ruscheweyh, H.; Cuenca, M.; Field, C. M.; Coelho, L. P.; Cruaud, C.; Engelen, S.; Gregory, A. C.; Labadie, K.; Marec, C.; Pelletier, E.; Royo-Llonch, M.; Roux, S.; Sánchez, P.; Uehara, H.; Zayed, A. A.; Zeller, G.; Carmichael, M.; Dimier, C.; Ferland, J.; Kandels, S.; Picheral, M.; Pisarev, S.; Poulain, J.; Tara Oceans Coordinators; Acinas, S. G.; Babin, M.; Bork, P.; Bowler, C.; de Vargas, C.; Guidi, L.; Hingamp, P.; Iudicone, D.; Karp-Boss, L.; Karsenti, E.; Ogata, H.; Pesant, S.; Speich, S.; Sullivan, M. B.; Wincker, P.; and Sunagawa, S.\n\n\n \n\n\n\n Cell, 179(5): 1068–1083.e21. November 2019.\n \n\n\n\n
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\n\n\n@article{salazar_gene_2019,\n\ttitle = {Gene {Expression} {Changes} and {Community} {Turnover} {Differentially} {Shape} the {Global} {Ocean} {Metatranscriptome}},\n\tvolume = {179},\n\tissn = {1097-4172},\n\tdoi = {10.1016/j.cell.2019.10.014},\n\tabstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.},\n\tlanguage = {eng},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Salazar, Guillem and Paoli, Lucas and Alberti, Adriana and Huerta-Cepas, Jaime and Ruscheweyh, Hans-Joachim and Cuenca, Miguelangel and Field, Christopher M. and Coelho, Luis Pedro and Cruaud, Corinne and Engelen, Stefan and Gregory, Ann C. and Labadie, Karine and Marec, Claudie and Pelletier, Eric and Royo-Llonch, Marta and Roux, Simon and Sánchez, Pablo and Uehara, Hideya and Zayed, Ahmed A. and Zeller, Georg and Carmichael, Margaux and Dimier, Céline and Ferland, Joannie and Kandels, Stefanie and Picheral, Marc and Pisarev, Sergey and Poulain, Julie and {Tara Oceans Coordinators} and Acinas, Silvia G. and Babin, Marcel and Bork, Peer and Bowler, Chris and de Vargas, Colomban and Guidi, Lionel and Hingamp, Pascal and Iudicone, Daniele and Karp-Boss, Lee and Karsenti, Eric and Ogata, Hiroyuki and Pesant, Stephane and Speich, Sabrina and Sullivan, Matthew B. and Wincker, Patrick and Sunagawa, Shinichi},\n\tmonth = nov,\n\tyear = {2019},\n\tpmid = {31730850},\n\tpmcid = {PMC6912165},\n\tkeywords = {Gene Expression Regulation, Geography, Metagenome, Microbiota, Molecular Sequence Annotation, Oceans and Seas, RNA, Messenger, Seawater, Tara Oceans, Temperature, Transcriptome, biogeochemistry, community turnover, eco-systems biology, gene expression change, global ocean microbiome, metagenome, metatranscriptome, microbial ecology, ocean warming},\n\tpages = {1068--1083.e21},\n}\n\n\n\n Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.\n
\n\n\n\n \n\n \n \n \n \n \n Global Trends in Marine Plankton Diversity across Kingdoms of Life.\n \n \n \n\n\n \n Ibarbalz, F. M.; Henry, N.; Brandão, M. C.; Martini, S.; Busseni, G.; Byrne, H.; Coelho, L. P.; Endo, H.; Gasol, J. M.; Gregory, A. C.; Mahé, F.; Rigonato, J.; Royo-Llonch, M.; Salazar, G.; Sanz-Sáez, I.; Scalco, E.; Soviadan, D.; Zayed, A. A.; Zingone, A.; Labadie, K.; Ferland, J.; Marec, C.; Kandels, S.; Picheral, M.; Dimier, C.; Poulain, J.; Pisarev, S.; Carmichael, M.; Pesant, S.; Tara Oceans Coordinators; Babin, M.; Boss, E.; Iudicone, D.; Jaillon, O.; Acinas, S. G.; Ogata, H.; Pelletier, E.; Stemmann, L.; Sullivan, M. B.; Sunagawa, S.; Bopp, L.; de Vargas, C.; Karp-Boss, L.; Wincker, P.; Lombard, F.; Bowler, C.; and Zinger, L.\n\n\n \n\n\n\n Cell, 179(5): 1084–1097.e21. November 2019.\n \n\n\n\n
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\n\n\n@article{ibarbalz_global_2019,\n\ttitle = {Global {Trends} in {Marine} {Plankton} {Diversity} across {Kingdoms} of {Life}},\n\tvolume = {179},\n\tissn = {1097-4172},\n\tdoi = {10.1016/j.cell.2019.10.008},\n\tabstract = {The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.},\n\tlanguage = {eng},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Ibarbalz, Federico M. and Henry, Nicolas and Brandão, Manoela C. and Martini, Séverine and Busseni, Greta and Byrne, Hannah and Coelho, Luis Pedro and Endo, Hisashi and Gasol, Josep M. and Gregory, Ann C. and Mahé, Frédéric and Rigonato, Janaina and Royo-Llonch, Marta and Salazar, Guillem and Sanz-Sáez, Isabel and Scalco, Eleonora and Soviadan, Dodji and Zayed, Ahmed A. and Zingone, Adriana and Labadie, Karine and Ferland, Joannie and Marec, Claudie and Kandels, Stefanie and Picheral, Marc and Dimier, Céline and Poulain, Julie and Pisarev, Sergey and Carmichael, Margaux and Pesant, Stéphane and {Tara Oceans Coordinators} and Babin, Marcel and Boss, Emmanuel and Iudicone, Daniele and Jaillon, Olivier and Acinas, Silvia G. and Ogata, Hiroyuki and Pelletier, Eric and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Bopp, Laurent and de Vargas, Colomban and Karp-Boss, Lee and Wincker, Patrick and Lombard, Fabien and Bowler, Chris and Zinger, Lucie},\n\tmonth = nov,\n\tyear = {2019},\n\tpmid = {31730851},\n\tpmcid = {PMC6912166},\n\tkeywords = {Biodiversity, Geography, Models, Theoretical, Oceans and Seas, Phylogeny, Plankton, Seawater, Tara Oceans, climate warming, high-throughput imaging, high-throughput sequencing, latitudinal diversity gradient, macroecology, plankton functional groups, temperature, trans-kingdom diversity},\n\tpages = {1084--1097.e21},\n}\n\n\n\n The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.\n
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\n \n \n\n \n \n \n \n \n \n Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.\n \n \n \n \n\n\n \n Seeleuthner, Y.; Mondy, S.; Lombard, V.; Carradec, Q.; Pelletier, E.; Wessner, M.; Leconte, J.; Mangot, J.; Poulain, J.; Labadie, K.; Logares, R.; Sunagawa, S.; Berardinis, V. d.; Salanoubat, M.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Pesant, S.; Poulton, N.; Stepanauskas, R.; Bork, P.; Bowler, C.; Hingamp, P.; Sullivan, M. B.; Iudicone, D.; Massana, R.; Aury, J.; Henrissat, B.; Karsenti, E.; Jaillon, O.; Sieracki, M.; Vargas, C. d.; and Wincker, P.\n\n\n \n\n\n\n Nature Communications, 9(1): 310. January 2018.\n \n\n\n\n
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\n\n\n@article{seeleuthner_single-cell_2018,\n\ttitle = {Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans},\n\tvolume = {9},\n\tcopyright = {2018 The Author(s)},\n\tissn = {2041-1723},\n\turl = {http://www.nature.com/articles/s41467-017-02235-3},\n\tdoi = {10.1038/s41467-017-02235-3},\n\tabstract = {The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.},\n\tlanguage = {En},\n\tnumber = {1},\n\turldate = {2019-02-19},\n\tjournal = {Nature Communications},\n\tauthor = {Seeleuthner, Yoann and Mondy, Samuel and Lombard, Vincent and Carradec, Quentin and Pelletier, Eric and Wessner, Marc and Leconte, Jade and Mangot, Jean-François and Poulain, Julie and Labadie, Karine and Logares, Ramiro and Sunagawa, Shinichi and Berardinis, Véronique de and Salanoubat, Marcel and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Pesant, Stephane and Poulton, Nicole and Stepanauskas, Ramunas and Bork, Peer and Bowler, Chris and Hingamp, Pascal and Sullivan, Matthew B. and Iudicone, Daniele and Massana, Ramon and Aury, Jean-Marc and Henrissat, Bernard and Karsenti, Eric and Jaillon, Olivier and Sieracki, Mike and Vargas, Colomban de and Wincker, Patrick},\n\tmonth = jan,\n\tyear = {2018},\n\tkeywords = {Genomics, Marine biology, Microbial ecology, Water microbiology},\n\tpages = {310},\n}\n\n\n\n The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.\n
\n\n\n\n \n\n \n \n \n \n \n Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean.\n \n \n \n\n\n \n Decelle, J.; Carradec, Q.; Pochon, X.; Henry, N.; Romac, S.; Mahé, F.; Dunthorn, M.; Kourlaiev, A.; Voolstra, C. R.; Wincker, P.; and de Vargas, C.\n\n\n \n\n\n\n Current biology: CB, 28(22): 3625–3633.e3. November 2018.\n \n\n\n\n
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\n\n\n@article{decelle_worldwide_2018,\n\ttitle = {Worldwide {Occurrence} and {Activity} of the {Reef}-{Building} {Coral} {Symbiont} {Symbiodinium} in the {Open} {Ocean}},\n\tvolume = {28},\n\tissn = {1879-0445},\n\tdoi = {10.1016/j.cub.2018.09.024},\n\tabstract = {The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1\\% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.},\n\tlanguage = {eng},\n\tnumber = {22},\n\tjournal = {Current biology: CB},\n\tauthor = {Decelle, Johan and Carradec, Quentin and Pochon, Xavier and Henry, Nicolas and Romac, Sarah and Mahé, Frédéric and Dunthorn, Micah and Kourlaiev, Artem and Voolstra, Christian R. and Wincker, Patrick and de Vargas, Colomban},\n\tmonth = nov,\n\tyear = {2018},\n\tpmid = {30416058},\n\tkeywords = {Animals, Biodiversity, Biological Evolution, Coral Reefs, DNA, Protozoan, Dinoflagellida, Gene Expression Profiling, Genetic Markers, Genetic Variation, Symbiodinium, Symbiosis, Tara Oceans, coral reefs, marine plankton, metabarcoding, metatranscriptomics, open ocean, phytoplankton, symbiosis},\n\tpages = {3625--3633.e3},\n}\n\n\n\n The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.\n
\n\n\n\n \n\n \n \n \n \n \n \n A global ocean atlas of eukaryotic genes.\n \n \n \n \n\n\n \n Carradec, Q.; Pelletier, E.; Da Silva, C.; Alberti, A.; Seeleuthner, Y.; Blanc-Mathieu, R.; Lima-Mendez, G.; Rocha, F.; Tirichine, L.; Labadie, K.; Kirilovsky, A.; Bertrand, A.; Engelen, S.; Madoui, M.; Méheust, R.; Poulain, J.; Romac, S.; Richter, D. J.; Yoshikawa, G.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Jaillon, O.; Aury, J.; Karsenti, E.; Sullivan, M. B.; Sunagawa, S.; Bork, P.; Not, F.; Hingamp, P.; Raes, J.; Guidi, L.; Ogata, H.; Vargas, C. d.; Iudicone, D.; Bowler, C.; and Wincker, P.\n\n\n \n\n\n\n Nature Communications, 9(1): 373. January 2018.\n Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Genomics;Marine biology;Microbial ecology;Water microbiology Subject_term_id: genomics;marine-biology;microbial-ecology;water-microbiology\n\n\n\n
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\n\n\n@article{carradec_global_2018,\n\ttitle = {A global ocean atlas of eukaryotic genes},\n\tvolume = {9},\n\tcopyright = {2018 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-017-02342-1},\n\tdoi = {10.1038/s41467-017-02342-1},\n\tabstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2021-07-16},\n\tjournal = {Nature Communications},\n\tauthor = {Carradec, Quentin and Pelletier, Eric and Da Silva, Corinne and Alberti, Adriana and Seeleuthner, Yoann and Blanc-Mathieu, Romain and Lima-Mendez, Gipsi and Rocha, Fabio and Tirichine, Leila and Labadie, Karine and Kirilovsky, Amos and Bertrand, Alexis and Engelen, Stefan and Madoui, Mohammed-Amin and Méheust, Raphaël and Poulain, Julie and Romac, Sarah and Richter, Daniel J. and Yoshikawa, Genki and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Jaillon, Olivier and Aury, Jean-Marc and Karsenti, Eric and Sullivan, Matthew B. and Sunagawa, Shinichi and Bork, Peer and Not, Fabrice and Hingamp, Pascal and Raes, Jeroen and Guidi, Lionel and Ogata, Hiroyuki and Vargas, Colomban de and Iudicone, Daniele and Bowler, Chris and Wincker, Patrick},\n\tmonth = jan,\n\tyear = {2018},\n\tnote = {Bandiera\\_abtest: a\nCc\\_license\\_type: cc\\_by\nCg\\_type: Nature Research Journals\nNumber: 1\nPrimary\\_atype: Research\nPublisher: Nature Publishing Group\nSubject\\_term: Genomics;Marine biology;Microbial ecology;Water microbiology\nSubject\\_term\\_id: genomics;marine-biology;microbial-ecology;water-microbiology},\n\tkeywords = {Genomics, Marine biology, Microbial ecology, Water microbiology},\n\tpages = {373},\n}\n\n\n\n While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.\n
\n\n\n\n \n\n \n \n \n \n \n Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy.\n \n \n \n\n\n \n Sugier, K.; Vacherie, B.; Cornils, A.; Wincker, P.; Jamet, J.; and Madoui, M.\n\n\n \n\n\n\n PeerJ, 6: e4685. 2018.\n \n\n\n\n
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\n\n\n@article{sugier_chitin_2018,\n\ttitle = {Chitin distribution in the {Oithona} digestive and reproductive systems revealed by fluorescence microscopy},\n\tvolume = {6},\n\tissn = {2167-8359},\n\tdoi = {10.7717/peerj.4685},\n\tabstract = {Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.},\n\tlanguage = {eng},\n\tjournal = {PeerJ},\n\tauthor = {Sugier, Kevin and Vacherie, Benoit and Cornils, Astrid and Wincker, Patrick and Jamet, Jean-Louis and Madoui, Mohammed-Amin},\n\tyear = {2018},\n\tpmid = {29780666},\n\tpmcid = {PMC5957050},\n\tkeywords = {Anatomy, Biology marine, Chitin, Copepod, Microscopy, Oithona},\n\tpages = {e4685},\n}\n\n\n\n Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.\n
\n\n\n\n \n\n \n \n \n \n \n An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region.\n \n \n \n\n\n \n Hume, B. C. C.; Ziegler, M.; Poulain, J.; Pochon, X.; Romac, S.; Boissin, E.; de Vargas, C.; Planes, S.; Wincker, P.; and Voolstra, C. R.\n\n\n \n\n\n\n PeerJ, 6: e4816. 2018.\n \n\n\n\n
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\n\n\n@article{hume_improved_2018,\n\ttitle = {An improved primer set and amplification protocol with increased specificity and sensitivity targeting the {Symbiodinium} {ITS2} region},\n\tvolume = {6},\n\tissn = {2167-8359},\n\tdoi = {10.7717/peerj.4816},\n\tabstract = {The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM\\_VAR\\_5.8S2/SYM\\_VAR\\_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM\\_VAR\\_5.8S2/SYM\\_VAR\\_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol's ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.},\n\tlanguage = {eng},\n\tjournal = {PeerJ},\n\tauthor = {Hume, Benjamin C. C. and Ziegler, Maren and Poulain, Julie and Pochon, Xavier and Romac, Sarah and Boissin, Emilie and de Vargas, Colomban and Planes, Serge and Wincker, Patrick and Voolstra, Christian R.},\n\tyear = {2018},\n\tpmid = {29844969},\n\tpmcid = {PMC5970565},\n\tkeywords = {Coral Reef, Metabarcoding, Metagenomics, Microbial Biology, Next-generation sequencing, Symbiodinium},\n\tpages = {e4816},\n}\n\n\n\n The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol's ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.\n
\n\n\n\n \n\n \n \n \n \n \n A de novo approach to disentangle partner identity and function in holobiont systems.\n \n \n \n\n\n \n Meng, A.; Marchet, C.; Corre, E.; Peterlongo, P.; Alberti, A.; Da Silva, C.; Wincker, P.; Pelletier, E.; Probert, I.; Decelle, J.; Le Crom, S.; Not, F.; and Bittner, L.\n\n\n \n\n\n\n Microbiome, 6(1): 105. June 2018.\n \n\n\n\n
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\n\n\n@article{meng_novo_2018,\n\ttitle = {A de novo approach to disentangle partner identity and function in holobiont systems},\n\tvolume = {6},\n\tissn = {2049-2618},\n\tdoi = {10.1186/s40168-018-0481-9},\n\tabstract = {BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.\nRESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.\nCONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Microbiome},\n\tauthor = {Meng, Arnaud and Marchet, Camille and Corre, Erwan and Peterlongo, Pierre and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Pelletier, Eric and Probert, Ian and Decelle, Johan and Le Crom, Stéphane and Not, Fabrice and Bittner, Lucie},\n\tmonth = jun,\n\tyear = {2018},\n\tpmid = {29885666},\n\tpmcid = {PMC5994019},\n\tkeywords = {Animals, Cnidaria, Computational Biology, Coral Reefs, De novo assembly, Holobiont, Marine, Meta-transcriptomic, Microalgae, Plankton, Porifera, Rhizaria, Symbiosis, Transcriptome, k-mer based similarity},\n\tpages = {105},\n}\n\n\n\n BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept. RESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited. CONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.\n
\n\n\n\n \n\n \n \n \n \n \n Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains.\n \n \n \n\n\n \n Farhat, S.; Florent, I.; Noel, B.; Kayal, E.; Da Silva, C.; Bigeard, E.; Alberti, A.; Labadie, K.; Corre, E.; Aury, J.; Rombauts, S.; Wincker, P.; Guillou, L.; and Porcel, B. M.\n\n\n \n\n\n\n Frontiers in Microbiology, 9: 2251. 2018.\n \n\n\n\n
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\n\n\n@article{farhat_comparative_2018,\n\ttitle = {Comparative {Time}-{Scale} {Gene} {Expression} {Analysis} {Highlights} the {Infection} {Processes} of {Two} {Amoebophrya} {Strains}},\n\tvolume = {9},\n\tissn = {1664-302X},\n\tdoi = {10.3389/fmicb.2018.02251},\n\tabstract = {Understanding factors that generate, maintain, and constrain host-parasite associations is of major interest to biologists. Although little studied, many extremely virulent micro-eukaryotic parasites infecting microalgae have been reported in the marine plankton. This is the case for Amoebophrya, a diverse and highly widespread group of Syndiniales infecting and potentially controlling dinoflagellate populations. Here, we analyzed the time-scale gene expression of a complete infection cycle of two Amoebophrya strains infecting the same host (the dinoflagellate Scrippsiella acuminata), but diverging by their host range (one infecting a single host, the other infecting more than one species). Over two-thirds of genes showed two-fold differences in expression between at least two sampled stages of the Amoebophrya life cycle. Genes related to carbohydrate metabolism as well as signaling pathways involving proteases and transporters were overexpressed during the free-living stage of the parasitoid. Once inside the host, all genes related to transcription and translation pathways were actively expressed, suggesting the rapid and extensive protein translation needed following host-cell invasion. Finally, genes related to cellular division and components of the flagellum organization were overexpressed during the sporont stage. In order to gain a deeper understanding of the biological basis of the host-parasitoid interaction, we screened proteins involved in host-cell recognition, invasion, and protection against host-defense identified in model apicomplexan parasites. Very few of the genes encoding critical components of the parasitic lifestyle of apicomplexans could be unambiguously identified as highly expressed in Amoebophrya. Genes related to the oxidative stress response were identified as highly expressed in both parasitoid strains. Among them, the correlated expression of superoxide dismutase/ascorbate peroxidase in the specialist parasite was consistent with previous studies on Perkinsus marinus defense. However, this defense process could not be identified in the generalist Amoebophrya strain, suggesting the establishment of different strategies for parasite protection related to host specificity.},\n\tlanguage = {eng},\n\tjournal = {Frontiers in Microbiology},\n\tauthor = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.},\n\tyear = {2018},\n\tpmid = {30333799},\n\tpmcid = {PMC6176090},\n\tkeywords = {amoebophrya, dinoflagellates, gene expression, infection, oxidative stress response, parasite, plankton, syndiniales},\n\tpages = {2251},\n}\n\n\n\n Understanding factors that generate, maintain, and constrain host-parasite associations is of major interest to biologists. Although little studied, many extremely virulent micro-eukaryotic parasites infecting microalgae have been reported in the marine plankton. This is the case for Amoebophrya, a diverse and highly widespread group of Syndiniales infecting and potentially controlling dinoflagellate populations. Here, we analyzed the time-scale gene expression of a complete infection cycle of two Amoebophrya strains infecting the same host (the dinoflagellate Scrippsiella acuminata), but diverging by their host range (one infecting a single host, the other infecting more than one species). Over two-thirds of genes showed two-fold differences in expression between at least two sampled stages of the Amoebophrya life cycle. Genes related to carbohydrate metabolism as well as signaling pathways involving proteases and transporters were overexpressed during the free-living stage of the parasitoid. Once inside the host, all genes related to transcription and translation pathways were actively expressed, suggesting the rapid and extensive protein translation needed following host-cell invasion. Finally, genes related to cellular division and components of the flagellum organization were overexpressed during the sporont stage. In order to gain a deeper understanding of the biological basis of the host-parasitoid interaction, we screened proteins involved in host-cell recognition, invasion, and protection against host-defense identified in model apicomplexan parasites. Very few of the genes encoding critical components of the parasitic lifestyle of apicomplexans could be unambiguously identified as highly expressed in Amoebophrya. Genes related to the oxidative stress response were identified as highly expressed in both parasitoid strains. Among them, the correlated expression of superoxide dismutase/ascorbate peroxidase in the specialist parasite was consistent with previous studies on Perkinsus marinus defense. However, this defense process could not be identified in the generalist Amoebophrya strain, suggesting the establishment of different strategies for parasite protection related to host specificity.\n
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\n \n \n\n \n \n \n \n \n A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications.\n \n \n \n\n\n \n Arrigoni, R.; Vacherie, B.; Benzoni, F.; Stefani, F.; Karsenti, E.; Jaillon, O.; Not, F.; Nunes, F.; Payri, C.; Wincker, P.; and Barbe, V.\n\n\n \n\n\n\n Molecular Ecology Resources, 17(5): 1054–1071. September 2017.\n \n\n\n\n
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\n\n\n@article{arrigoni_new_2017,\n\ttitle = {A new sequence data set of {SSU} {rRNA} gene for {Scleractinia} and its phylogenetic and ecological applications},\n\tvolume = {17},\n\tissn = {1755-0998},\n\tdoi = {10.1111/1755-0998.12640},\n\tabstract = {Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.},\n\tlanguage = {eng},\n\tnumber = {5},\n\tjournal = {Molecular Ecology Resources},\n\tauthor = {Arrigoni, Roberto and Vacherie, Benoît and Benzoni, Francesca and Stefani, Fabrizio and Karsenti, Eric and Jaillon, Olivier and Not, Fabrice and Nunes, Flavia and Payri, Claude and Wincker, Patrick and Barbe, Valérie},\n\tmonth = sep,\n\tyear = {2017},\n\tpmid = {27889948},\n\tkeywords = {Animals, Anthozoa, Cluster Analysis, DNA Barcoding, Taxonomic, DNA, Ribosomal, Genes, rRNA, Genetic Variation, Nucleic Acid Conformation, Phylogeny, RNA, Ribosomal, 18S, Sequence Analysis, DNA, cnidarians, gene structure and function, hard corals, hypervariable region, molecular evolution, systematics},\n\tpages = {1054--1071},\n}\n\n\n\n Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.\n
\n\n\n\n \n\n \n \n \n \n \n Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.\n \n \n \n\n\n \n Mangot, J.; Logares, R.; Sánchez, P.; Latorre, F.; Seeleuthner, Y.; Mondy, S.; Sieracki, M. E.; Jaillon, O.; Wincker, P.; Vargas, C. d.; and Massana, R.\n\n\n \n\n\n\n Scientific Reports, 7: 41498. January 2017.\n \n\n\n\n
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\n\n\n@article{mangot_accessing_2017,\n\ttitle = {Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells},\n\tvolume = {7},\n\tissn = {2045-2322},\n\tdoi = {10.1038/srep41498},\n\tabstract = {Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features {\\textgreater}74\\% of genome recovery, against about 20\\% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.},\n\tlanguage = {eng},\n\tjournal = {Scientific Reports},\n\tauthor = {Mangot, Jean-François and Logares, Ramiro and Sánchez, Pablo and Latorre, Fran and Seeleuthner, Yoann and Mondy, Samuel and Sieracki, Michael E. and Jaillon, Olivier and Wincker, Patrick and Vargas, Colomban de and Massana, Ramon},\n\tmonth = jan,\n\tyear = {2017},\n\tpmid = {28128359},\n\tpmcid = {PMC5269757},\n\tkeywords = {Aquatic Organisms, Base Sequence, Eukaryota, Genome, Genomics, Oceans and Seas, Phylogeny, Ribosomes, Sequence Analysis, DNA, Single-Cell Analysis},\n\tpages = {41498},\n}\n\n\n\n Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features \\textgreater74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.\n
\n\n\n\n \n\n \n \n \n \n \n New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona.\n \n \n \n\n\n \n Madoui, M.; Poulain, J.; Sugier, K.; Wessner, M.; Noel, B.; Berline, L.; Labadie, K.; Cornils, A.; Blanco-Bercial, L.; Stemmann, L.; Jamet, J.; and Wincker, P.\n\n\n \n\n\n\n Molecular Ecology, 26(17): 4467–4482. September 2017.\n \n\n\n\n
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\n\n\n@article{madoui_new_2017,\n\ttitle = {New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod {Oithona}},\n\tvolume = {26},\n\tissn = {1365-294X},\n\tdoi = {10.1111/mec.14214},\n\tabstract = {In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12-Notch-repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male-specific gene. The variation in the B-allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.},\n\tlanguage = {eng},\n\tnumber = {17},\n\tjournal = {Molecular Ecology},\n\tauthor = {Madoui, Mohammed-Amin and Poulain, Julie and Sugier, Kevin and Wessner, Marc and Noel, Benjamin and Berline, Leo and Labadie, Karine and Cornils, Astrid and Blanco-Bercial, Leocadio and Stemmann, Lars and Jamet, Jean-Louis and Wincker, Patrick},\n\tmonth = sep,\n\tyear = {2017},\n\tpmid = {28636804},\n\tkeywords = {Animals, Copepoda, Gene Frequency, Genetics, Population, Male, Mediterranean Sea, Selection, Genetic, Zooplankton, genome, phylogeography, selection},\n\tpages = {4467--4482},\n}\n\n\n\n In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12-Notch-repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male-specific gene. The variation in the B-allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.\n
\n\n\n\n \n\n \n \n \n \n \n \n Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.\n \n \n \n \n\n\n \n Alberti, A.; Poulain, J.; Engelen, S.; Labadie, K.; Romac, S.; Ferrera, I.; Albini, G.; Aury, J.; Belser, C.; Bertrand, A.; Cruaud, C.; Da Silva, C.; Dossat, C.; Gavory, F.; Gas, S.; Guy, J.; Haquelle, M.; Jacoby, E.; Jaillon, O.; Lemainque, A.; Pelletier, E.; Samson, G.; Wessner, M.; Genoscope Technical Team; Bazire, P.; Beluche, O.; Bertrand, L.; Besnard-Gonnet, M.; Bordelais, I.; Boutard, M.; Dubois, M.; Dumont, C.; Ettedgui, E.; Fernandez, P.; Garcia, E.; Aiach, N. G.; Guerin, T.; Hamon, C.; Brun, E.; Lebled, S.; Lenoble, P.; Louesse, C.; Mahieu, E.; Mairey, B.; Martins, N.; Megret, C.; Milani, C.; Muanga, J.; Orvain, C.; Payen, E.; Perroud, P.; Petit, E.; Robert, D.; Ronsin, M.; Vacherie, B.; Acinas, S. G.; Royo-Llonch, M.; Cornejo-Castillo, F. M.; Logares, R.; Fernández-Gómez, B.; Bowler, C.; Cochrane, G.; Amid, C.; Hoopen, P. T.; De Vargas, C.; Grimsley, N.; Desgranges, E.; Kandels-Lewis, S.; Ogata, H.; Poulton, N.; Sieracki, M. E.; Stepanauskas, R.; Sullivan, M. B.; Brum, J. R.; Duhaime, M. B.; Poulos, B. T.; Hurwitz, B. L.; Tara Oceans Consortium Coordinators; Acinas, S. G.; Bork, P.; Boss, E.; Bowler, C.; De Vargas, C.; Follows, M.; Gorsky, G.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels-Lewis, S.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Pesant, S.; Raes, J.; Sardet, C.; Sieracki, M. E.; Speich, S.; Stemmann, L.; Sullivan, M. B.; Sunagawa, S.; Wincker, P.; Pesant, S.; Karsenti, E.; and Wincker, P.\n\n\n \n\n\n\n Scientific Data, 4: 170093. 2017.\n \n\n\n\n
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\n\n\n\n@article{alberti_viral_2017,\n\ttitle = {Viral to metazoan marine plankton nucleotide sequences from the {Tara} {Oceans} expedition},\n\tvolume = {4},\n\turl = {https://doi.org/10.1038/sdata.2017.93},\n\tjournal = {Scientific Data},\n\tauthor = {Alberti, Adriana and Poulain, Julie and Engelen, Stefan and Labadie, Karine and Romac, Sarah and Ferrera, Isabel and Albini, Guillaume and Aury, Jean-Marc and Belser, Caroline and Bertrand, Alexis and Cruaud, Corinne and Da Silva, Corinne and Dossat, Carole and Gavory, Frédérick and Gas, Shahinaz and Guy, Julie and Haquelle, Maud and Jacoby, E'krame and Jaillon, Olivier and Lemainque, Arnaud and Pelletier, Eric and Samson, Gaëlle and Wessner, Mark and {Genoscope Technical Team} and Bazire, Pascal and Beluche, Odette and Bertrand, Laurie and Besnard-Gonnet, Marielle and Bordelais, Isabelle and Boutard, Magali and Dubois, Maria and Dumont, Corinne and Ettedgui, Evelyne and Fernandez, Patricia and Garcia, Espérance and Aiach, Nathalie Giordanenco and Guerin, Thomas and Hamon, Chadia and Brun, Elodie and Lebled, Sandrine and Lenoble, Patricia and Louesse, Claudine and Mahieu, Eric and Mairey, Barbara and Martins, Nathalie and Megret, Catherine and Milani, Claire and Muanga, Jacqueline and Orvain, Céline and Payen, Emilie and Perroud, Peggy and Petit, Emmanuelle and Robert, Dominique and Ronsin, Murielle and Vacherie, Benoit and Acinas, Silvia G. and Royo-Llonch, Marta and Cornejo-Castillo, Francisco M. and Logares, Ramiro and Fernández-Gómez, Beatriz and Bowler, Chris and Cochrane, Guy and Amid, Clara and Hoopen, Petra Ten and De Vargas, Colomban and Grimsley, Nigel and Desgranges, Elodie and Kandels-Lewis, Stefanie and Ogata, Hiroyuki and Poulton, Nicole and Sieracki, Michael E. and Stepanauskas, Ramunas and Sullivan, Matthew B. and Brum, Jennifer R. and Duhaime, Melissa B. and Poulos, Bonnie T. and Hurwitz, Bonnie L. and {Tara Oceans Consortium Coordinators} and Acinas, Silvia G. and Bork, Peer and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Follows, Michael and Gorsky, Gabriel and Grimsley, Nigel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Kandels-Lewis, Stefanie and Karp-Boss, Lee and Karsenti, Eric and Not, Fabrice and Ogata, Hiroyuki and Pesant, Stéphane and Raes, Jeroen and Sardet, Christian and Sieracki, Michael E. and Speich, Sabrina and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Pesant, Stéphane and Karsenti, Eric and Wincker, Patrick},\n\tyear = {2017},\n\tpages = {170093},\n}\n\n\n\n
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\n \n \n\n \n \n \n \n \n Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.\n \n \n \n\n\n \n Lescot, M.; Hingamp, P.; Kojima, K. K.; Villar, E.; Romac, S.; Veluchamy, A.; Boccara, M.; Jaillon, O.; Iudicone, D.; Bowler, C.; Wincker, P.; Claverie, J.; and Ogata, H.\n\n\n \n\n\n\n The ISME journal, 10(5): 1134–1146. May 2016.\n \n\n\n\n
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\n\n\n@article{lescot_reverse_2016,\n\ttitle = {Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages},\n\tvolume = {10},\n\tissn = {1751-7370},\n\tdoi = {10.1038/ismej.2015.192},\n\tabstract = {Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes ({\\textgreater}5 μm), where they reached a maximum of 13.5\\% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.},\n\tlanguage = {eng},\n\tnumber = {5},\n\tjournal = {The ISME journal},\n\tauthor = {Lescot, Magali and Hingamp, Pascal and Kojima, Kenji K. and Villar, Emilie and Romac, Sarah and Veluchamy, Alaguraj and Boccara, Martine and Jaillon, Olivier and Iudicone, Daniele and Bowler, Chris and Wincker, Patrick and Claverie, Jean-Michel and Ogata, Hiroyuki},\n\tmonth = may,\n\tyear = {2016},\n\tpmid = {26613339},\n\tpmcid = {PMC5029228},\n\tkeywords = {Eukaryota, Metagenome, Phylogeny, Plankton, Prokaryotic Cells, RNA-Directed DNA Polymerase, Retroelements, Seawater, Transcription, Genetic},\n\tpages = {1134--1146},\n}\n\n\n\n Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (\\textgreater5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.\n
\n\n\n\n \n\n \n \n \n \n \n Plankton networks driving carbon export in the oligotrophic ocean.\n \n \n \n\n\n \n Guidi, L.; Chaffron, S.; Bittner, L.; Eveillard, D.; Larhlimi, A.; Roux, S.; Darzi, Y.; Audic, S.; Berline, L.; Brum, J.; Coelho, L. P.; Espinoza, J. C. I.; Malviya, S.; Sunagawa, S.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Poulain, J.; Searson, S.; Tara Oceans coordinators; Stemmann, L.; Not, F.; Hingamp, P.; Speich, S.; Follows, M.; Karp-Boss, L.; Boss, E.; Ogata, H.; Pesant, S.; Weissenbach, J.; Wincker, P.; Acinas, S. G.; Bork, P.; de Vargas, C.; Iudicone, D.; Sullivan, M. B.; Raes, J.; Karsenti, E.; Bowler, C.; and Gorsky, G.\n\n\n \n\n\n\n Nature, 532(7600): 465–470. April 2016.\n \n\n\n\n
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\n\n\n@article{guidi_plankton_2016,\n\ttitle = {Plankton networks driving carbon export in the oligotrophic ocean},\n\tvolume = {532},\n\tissn = {1476-4687},\n\tdoi = {10.1038/nature16942},\n\tabstract = {The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.},\n\tlanguage = {eng},\n\tnumber = {7600},\n\tjournal = {Nature},\n\tauthor = {Guidi, Lionel and Chaffron, Samuel and Bittner, Lucie and Eveillard, Damien and Larhlimi, Abdelhalim and Roux, Simon and Darzi, Youssef and Audic, Stephane and Berline, Léo and Brum, Jennifer and Coelho, Luis Pedro and Espinoza, Julio Cesar Ignacio and Malviya, Shruti and Sunagawa, Shinichi and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Poulain, Julie and Searson, Sarah and {Tara Oceans coordinators} and Stemmann, Lars and Not, Fabrice and Hingamp, Pascal and Speich, Sabrina and Follows, Mick and Karp-Boss, Lee and Boss, Emmanuel and Ogata, Hiroyuki and Pesant, Stephane and Weissenbach, Jean and Wincker, Patrick and Acinas, Silvia G. and Bork, Peer and de Vargas, Colomban and Iudicone, Daniele and Sullivan, Matthew B. and Raes, Jeroen and Karsenti, Eric and Bowler, Chris and Gorsky, Gabriel},\n\tmonth = apr,\n\tyear = {2016},\n\tpmid = {26863193},\n\tpmcid = {PMC4851848},\n\tkeywords = {Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus},\n\tpages = {465--470},\n}\n\n\n\n The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.\n
\n\n\n\n \n\n \n \n \n \n \n Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.\n \n \n \n\n\n \n Roux, S.; Brum, J. R.; Dutilh, B. E.; Sunagawa, S.; Duhaime, M. B.; Loy, A.; Poulos, B. T.; Solonenko, N.; Lara, E.; Poulain, J.; Pesant, S.; Kandels-Lewis, S.; Dimier, C.; Picheral, M.; Searson, S.; Cruaud, C.; Alberti, A.; Duarte, C. M.; Gasol, J. M.; Vaqué, D.; Tara Oceans Coordinators; Bork, P.; Acinas, S. G.; Wincker, P.; and Sullivan, M. B.\n\n\n \n\n\n\n Nature, 537(7622): 689–693. September 2016.\n \n\n\n\n
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\n\n\n@article{roux_ecogenomics_2016,\n\ttitle = {Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses},\n\tvolume = {537},\n\tissn = {1476-4687},\n\tdoi = {10.1038/nature19366},\n\tabstract = {Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1\\% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.},\n\tlanguage = {eng},\n\tnumber = {7622},\n\tjournal = {Nature},\n\tauthor = {Roux, Simon and Brum, Jennifer R. and Dutilh, Bas E. and Sunagawa, Shinichi and Duhaime, Melissa B. and Loy, Alexander and Poulos, Bonnie T. and Solonenko, Natalie and Lara, Elena and Poulain, Julie and Pesant, Stéphane and Kandels-Lewis, Stefanie and Dimier, Céline and Picheral, Marc and Searson, Sarah and Cruaud, Corinne and Alberti, Adriana and Duarte, Carlos M. and Gasol, Josep M. and Vaqué, Dolors and {Tara Oceans Coordinators} and Bork, Peer and Acinas, Silvia G. and Wincker, Patrick and Sullivan, Matthew B.},\n\tmonth = sep,\n\tyear = {2016},\n\tpmid = {27654921},\n\tkeywords = {DNA, Viral, Datasets as Topic, Ecology, Ecosystem, Expeditions, Genes, Viral, Genome, Viral, Geographic Mapping, Metagenome, Metagenomics, Nitrogen Cycle, Oceans and Seas, Seawater, Sulfur, Viruses},\n\tpages = {689--693},\n}\n\n\n\n Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.\n
\n\n\n\n \n\n \n \n \n \n \n \n Survey of the green picoalga Bathycoccus genomes in the global ocean.\n \n \n \n \n\n\n \n Vannier, T.; Leconte, J.; Seeleuthner, Y.; Mondy, S.; Pelletier, E.; Aury, J.; de Vargas, C.; Sieracki, M.; Iudicone, D.; Vaulot, D.; Wincker, P.; and Jaillon, O.\n\n\n \n\n\n\n Scientific Reports, 6: 37900. November 2016.\n \n\n\n\n
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\n\n\n@article{vannier_survey_2016,\n\ttitle = {Survey of the green picoalga \\textit{{Bathycoccus}} genomes in the global ocean},\n\tvolume = {6},\n\tissn = {2045-2322},\n\turl = {http://www.nature.com/articles/srep37900},\n\tdoi = {10.1038/srep37900},\n\tabstract = {Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.},\n\tlanguage = {en},\n\turldate = {2019-02-19},\n\tjournal = {Scientific Reports},\n\tauthor = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier},\n\tmonth = nov,\n\tyear = {2016},\n\tpages = {37900},\n}\n\n\n Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.\n
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