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\n \n 2024\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates.\n \n \n \n \n\n\n \n Novak Vanclova, A. M., Nef, C., Fussy, Z., Vancl, A., Liu, F., Bowler, C., & Dorrell, R. G.\n\n\n \n\n\n\n EMBO Rep. 2024.\n \n\n\n\n
\n\n\n\n \n \n $\"New$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN297,\r\n   author = {Novak Vanclova, A. M. and Nef, C. and Fussy, Z. and Vancl, A. and Liu, F. and Bowler, C. and Dorrell, R. G.},\r\n   title = {New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates},\r\n   journal = {EMBO Rep},\r\n   abstract = {Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.},\r\n   keywords = {Automated Tree Sorting\r\nMyzozoa\r\nPost-Endosymbiotic Organelle Evolution\r\nProtists\r\nShopping Bag Model},\r\n   ISSN = {1469-3178 (Electronic)\r\n1469-221X (Linking)},\r\n   DOI = {10.1038/s44319-024-00103-y},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/38499810},\r\n   year = {2024},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Linking satellites to genes with machine learning to estimate phytoplankton community structure from space.\n \n \n \n\n\n \n El Hourany, R., Pierella Karlusich, J. J., Zinger, L., Loisel, H., Levy, M., & Bowler, C.\n\n\n \n\n\n\n EGU Ocean Science, 20(1): 217-239. 2024.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN296,\r\n   author = {El Hourany, R. and Pierella Karlusich, J. J. and Zinger, L. and Loisel, H. and Levy, M. and Bowler, C.},\r\n   title = {Linking satellites to genes with machine learning to estimate phytoplankton community structure from space},\r\n   journal = {EGU Ocean Science},\r\n   volume = {20},\r\n   number = {1},\r\n   pages = {217-239},\r\n   DOI = {https://doi.org/10.5194/os-20-217-2024},\r\n   year = {2024},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2023\n \n \n (7)\n \n \n

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\n \n\n \n \n \n \n \n \n Genomic adaptation of giant viruses in polar oceans.\n \n \n \n \n\n\n \n Meng, L., Delmont, T. O., Gaia, M., Pelletier, E., Fernandez-Guerra, A., Chaffron, S., Neches, R. Y., Wu, J., Kaneko, H., Endo, H., & Ogata, H.\n\n\n \n\n\n\n Nat Commun, 14(1): 6233. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\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

@article{RN295,\r\n   author = {Meng, L. and Delmont, T. O. and Gaia, M. and Pelletier, E. and Fernandez-Guerra, A. and Chaffron, S. and Neches, R. Y. and Wu, J. and Kaneko, H. and Endo, H. and Ogata, H.},\r\n   title = {Genomic adaptation of giant viruses in polar oceans},\r\n   journal = {Nat Commun},\r\n   volume = {14},\r\n   number = {1},\r\n   pages = {6233},\r\n   abstract = {Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.},\r\n   keywords = {*Giant Viruses/genetics\r\nGenome, Viral/genetics\r\nEcosystem\r\nOceans and Seas\r\nPhylogeny\r\nDNA Viruses/genetics\r\nGenomics\r\n*Viruses/genetics\r\nEukaryota/genetics},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/s41467-023-41910-6},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/37828003},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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., Mahe, F., Poulain, J., Labadie, K., Beluche, O., El Hourany, R., Tara Oceans, C., Chaffron, S., Wincker, P., Nakamura, R., Karp-Boss, L., Boss, E., Bowler, C., de Vargas, C., Tomii, K., & Ogata, H.\n\n\n \n\n\n\n ISME Commun, 3(1): 101. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Predicting$ Paper\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

@article{RN294,\r\n   author = {Kaneko, H. and Endo, H. and Henry, N. and Berney, C. and Mahe, F. and Poulain, J. and Labadie, K. and Beluche, O. and El Hourany, R. and Tara Oceans, Coordinators and Chaffron, S. and Wincker, P. and Nakamura, R. and Karp-Boss, L. and Boss, E. and Bowler, C. and de Vargas, C. and Tomii, K. and Ogata, H.},\r\n   title = {Predicting global distributions of eukaryotic plankton communities from satellite data},\r\n   journal = {ISME Commun},\r\n   volume = {3},\r\n   number = {1},\r\n   pages = {101},\r\n   abstract = {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.},\r\n   ISSN = {2730-6151 (Electronic)\r\n2730-6151 (Print)\r\n2730-6151 (Linking)},\r\n   DOI = {10.1038/s43705-023-00308-7},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/37740029},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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., Brandao, M. C., Pierella Karlusich, J. J., Soviadan, Y. D., Gregory, A. C., Endo, H., Kokoszka, F., Vik, D., Henry, N., Fremont, P., Labadie, K., Zayed, A. A., Dimier, C., Picheral, M., Searson, S., Poulain, J., Kandels, S., Pesant, S., Karsenti, E., Tara Oceans, c., Bork, P., Bowler, C., de Vargas, C., Eveillard, D., Gehlen, M., Iudicone, D., Lombard, F., Ogata, H., Stemmann, L., Sullivan, M. B., Sunagawa, S., Wincker, P., Chaffron, S., & Jaillon, O.\n\n\n \n\n\n\n ISME Commun, 3(1): 83. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Ocean-wide$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN293,\r\n   author = {Rigonato, J. and Budinich, M. and Murillo, A. A. and Brandao, M. C. and Pierella Karlusich, J. J. and Soviadan, Y. D. and Gregory, A. C. and Endo, H. and Kokoszka, F. and Vik, D. and Henry, N. and Fremont, P. and Labadie, K. and Zayed, A. A. and Dimier, C. and Picheral, M. and Searson, S. and Poulain, J. and Kandels, S. and Pesant, S. and Karsenti, E. and Tara Oceans, coordinators and Bork, P. and Bowler, C. and de Vargas, C. and Eveillard, D. and Gehlen, M. and Iudicone, D. and Lombard, F. and Ogata, H. and Stemmann, L. and Sullivan, M. B. and Sunagawa, S. and Wincker, P. and Chaffron, S. and Jaillon, O.},\r\n   title = {Ocean-wide comparisons of mesopelagic planktonic community structures},\r\n   journal = {ISME Commun},\r\n   volume = {3},\r\n   number = {1},\r\n   pages = {83},\r\n   abstract = {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, NO(3)(-) 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.},\r\n   ISSN = {2730-6151 (Electronic)\r\n2730-6151 (Print)\r\n2730-6151 (Linking)},\r\n   DOI = {10.1038/s43705-023-00279-9},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/37596349},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

\n\n\n\n\n\n

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\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., Sullivan, M. B., Chaffron, S., Karsenti, E., Babin, M., Boss, E., Wincker, P., Zinger, L., de Vargas, C., Bowler, C., Karp-Boss, L., & Coordinators, T. O.\n\n\n \n\n\n\n Elementa-Science of the Anthropocene, 11(1). 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Pan-Arctic$ Paper\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\n\n

@article{RN292,\r\n   author = {Ibarbalz, F. M. and Henry, N. and Mahé, F. and Ardyna, M. and Zingone, A. and Scalco, E. and Lovejoy, C. and Lombard, F. and Jaillon, O. and Iudicone, D. and Malviya, S. and Sullivan, M. B. and Chaffron, S. and Karsenti, E. and Babin, M. and Boss, E. and Wincker, P. and Zinger, L. and de Vargas, C. and Bowler, C. and Karp-Boss, L. and Coordinators, Tara Oceans},\r\n   title = {Pan-Arctic plankton community structure and its global connectivity},\r\n   journal = {Elementa-Science of the Anthropocene},\r\n   volume = {11},\r\n   number = {1},\r\n   abstract = {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.},\r\n   keywords = {marine protists\r\nunicellular\r\nphytoplankton\r\nglobal change\r\nadvection\r\nenvironmental filtering\r\nspecies richness\r\nsea-ice\r\nocean\r\nbiodiversity\r\nbiogeography\r\ndiversity\r\ninsights\r\ntrends\r\ninflow\r\nwater},\r\n   ISSN = {2325-1026},\r\n   DOI = {10.1525/elementa.2022.00060},\r\n   url = {<Go to ISI>://WOS:001173935900002},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition.\n \n \n \n \n\n\n \n Inomura, K., Pierella Karlusich, J. J., Dutkiewicz, S., Deutsch, C., Harrison, P. J., & Bowler, C.\n\n\n \n\n\n\n Microbiol Spectr, 11(3): e0331122. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"High$ Paper\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

@article{RN291,\r\n   author = {Inomura, K. and Pierella Karlusich, J. J. and Dutkiewicz, S. and Deutsch, C. and Harrison, P. J. and Bowler, C.},\r\n   title = {High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition},\r\n   journal = {Microbiol Spectr},\r\n   volume = {11},\r\n   number = {3},\r\n   pages = {e0331122},\r\n   abstract = {The rapid growth of diatoms makes them one of the most pervasive and productive types of plankton in the world's ocean, but the physiological basis for their high growth rates remains poorly understood. Here, we evaluate the factors that elevate diatom growth rates, relative to other plankton, using a steady-state metabolic flux model that computes the photosynthetic C source from intracellular light attenuation and the carbon cost of growth from empirical cell C quotas, across a wide range of cell sizes. For both diatoms and other phytoplankton, growth rates decline with increased cell volume, consistent with observations, because the C cost of division increases with size faster than photosynthesis. However, the model predicts overall higher growth rates for diatoms due to reduced C requirements and the low energetic cost of Si deposition. The C savings from the silica frustule are supported by metatranscriptomic data from Tara Oceans, which show that the abundance of transcripts for cytoskeleton components in diatoms is lower than in other phytoplankton. Our results highlight the importance of understanding the origins of phylogenetic differences in cellular C quotas, and suggest that the evolution of silica frustules may play a critical role in the global dominance of marine diatoms. IMPORTANCE This study addresses a longstanding issue regarding diatoms, namely, their fast growth. Diatoms, which broadly are phytoplankton with silica frustules, are the world's most productive microorganisms and dominate in polar and upwelling regions. Their dominance is largely supported by their high growth rate, but the physiological reasoning behind that characteristic has been obscure. In this study, we combine a quantitative model and metatranscriptomic approaches and show that diatoms' low carbon requirements and low energy costs for silica frustule production are the key factors supporting their fast growth. Our study suggests that the effective use of energy-efficient silica as a cellular structure, instead of carbon, enables diatoms to be the most productive organisms in the global ocean.},\r\n   keywords = {*Diatoms\r\nCarbon/metabolism\r\nSilicon Dioxide/metabolism\r\nPhylogeny\r\nPhytoplankton\r\nTara Oceans\r\ncomputer modeling\r\ndiatom\r\necosystem\r\ngrowth\r\nmicrobiology\r\noceanography\r\nphotosynthesis\r\nsilica frustule},\r\n   ISSN = {2165-0497 (Electronic)\r\n2165-0497 (Linking)},\r\n   DOI = {10.1128/spectrum.03311-22},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/37010412},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

\n\n\n

\n The rapid growth of diatoms makes them one of the most pervasive and productive types of plankton in the world's ocean, but the physiological basis for their high growth rates remains poorly understood. Here, we evaluate the factors that elevate diatom growth rates, relative to other plankton, using a steady-state metabolic flux model that computes the photosynthetic C source from intracellular light attenuation and the carbon cost of growth from empirical cell C quotas, across a wide range of cell sizes. For both diatoms and other phytoplankton, growth rates decline with increased cell volume, consistent with observations, because the C cost of division increases with size faster than photosynthesis. However, the model predicts overall higher growth rates for diatoms due to reduced C requirements and the low energetic cost of Si deposition. The C savings from the silica frustule are supported by metatranscriptomic data from Tara Oceans, which show that the abundance of transcripts for cytoskeleton components in diatoms is lower than in other phytoplankton. Our results highlight the importance of understanding the origins of phylogenetic differences in cellular C quotas, and suggest that the evolution of silica frustules may play a critical role in the global dominance of marine diatoms. IMPORTANCE This study addresses a longstanding issue regarding diatoms, namely, their fast growth. Diatoms, which broadly are phytoplankton with silica frustules, are the world's most productive microorganisms and dominate in polar and upwelling regions. Their dominance is largely supported by their high growth rate, but the physiological reasoning behind that characteristic has been obscure. In this study, we combine a quantitative model and metatranscriptomic approaches and show that diatoms' low carbon requirements and low energy costs for silica frustule production are the key factors supporting their fast growth. Our study suggests that the effective use of energy-efficient silica as a cellular structure, instead of carbon, enables diatoms to be the most productive organisms in the global ocean.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae.\n \n \n \n \n\n\n \n Arrigoni, R., Stolarski, J., Terraneo, T. I., Hoeksema, B. W., Berumen, M. L., Payri, C., & Montano, S.\n\n\n \n\n\n\n Contributions to Zoology, 92(2): 130-171. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Phylogenetics$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN290,\r\n   author = {Arrigoni, R. and Stolarski, J. and Terraneo, T. I. and Hoeksema, B. W. and Berumen, M. L. and Payri, C. and Montano, S.},\r\n   title = {Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae},\r\n   journal = {Contributions to Zoology},\r\n   volume = {92},\r\n   number = {2},\r\n   pages = {130-171},\r\n   abstract = {The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensiverevision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.},\r\n   keywords = {coral reefs\r\nhard corals\r\nindo-pacific ocean\r\nintegrative systematics\r\nmitochondrial markers\r\nmorphology\r\ncnidaria anthozoa scleractinia\r\nribosomal-rna gene\r\nreef coral\r\nmolecular phylogeny\r\nuniversal primers\r\nclassification\r\ninference\r\nevolution\r\nalignment\r\njakarta},\r\n   ISSN = {1383-4517},\r\n   DOI = {10.1163/18759866-bja10041},\r\n   url = {<Go to ISI>://WOS:001010716700001},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Mirusviruses link herpesviruses to giant viruses.\n \n \n \n \n\n\n \n Gaia, M., Meng, L., Pelletier, E., Forterre, P., Vanni, C., Fernandez-Guerra, A., Jaillon, O., Wincker, P., Ogata, H., Krupovic, M., & Delmont, T. O.\n\n\n \n\n\n\n Nature, 616(7958): 783-789. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Mirusviruses$ Paper\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

@article{RN289,\r\n   author = {Gaia, M. and Meng, L. and Pelletier, E. and Forterre, P. and Vanni, C. and Fernandez-Guerra, A. and Jaillon, O. and Wincker, P. and Ogata, H. and Krupovic, M. and Delmont, T. O.},\r\n   title = {Mirusviruses link herpesviruses to giant viruses},\r\n   journal = {Nature},\r\n   volume = {616},\r\n   number = {7958},\r\n   pages = {783-789},\r\n   abstract = {DNA viruses have a major influence on the ecology and evolution of cellular organisms(1-4), but their overall diversity and evolutionary trajectories remain elusive(5). 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 Duplodnaviria(6), 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.},\r\n   keywords = {Animals\r\nEcosystem\r\nEukaryota/virology\r\nGenome, Viral/genetics\r\n*Giant Viruses/classification/genetics\r\n*Herpesviridae/classification/genetics\r\n*Phylogeny\r\n*Plankton/virology\r\nMetagenomics\r\nMetagenome\r\nSunlight\r\n*Oceans and Seas\r\nTranscription, Genetic/genetics\r\n*Aquatic Organisms/virology},\r\n   ISSN = {1476-4687 (Electronic)\r\n0028-0836 (Print)\r\n0028-0836 (Linking)},\r\n   DOI = {10.1038/s41586-023-05962-4},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/37076623},\r\n   year = {2023},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2022\n \n \n (17)\n \n \n

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\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. A., Pelletier, E., & Bowler, C.\n\n\n \n\n\n\n PLoS Biol, 20(11): e3001893. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Whole-genome$ Paper\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

@article{RN288,\r\n   author = {Nef, C. and Madoui, M. A. and Pelletier, E. and Bowler, C.},\r\n   title = {Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros},\r\n   journal = {PLoS Biol},\r\n   volume = {20},\r\n   number = {11},\r\n   pages = {e3001893},\r\n   abstract = {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.},\r\n   keywords = {*Diatoms/genetics\r\nEcosystem\r\nGenomics\r\nMetagenomics},\r\n   ISSN = {1545-7885 (Electronic)\r\n1544-9173 (Print)\r\n1544-9173 (Linking)},\r\n   DOI = {10.1371/journal.pbio.3001893},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/36441816},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 Guerin, N., Ciccarella, M., Flamant, E., Fremont, 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. M., & Carradec, Q.\n\n\n \n\n\n\n Commun Biol, 5(1): 983. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\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

@article{RN281,\r\n   author = {Guerin, N. and Ciccarella, M. and Flamant, E. and Fremont, P. and Mangenot, S. and Istace, B. and Noel, B. and Belser, C. and Bertrand, L. and Labadie, K. and Cruaud, C. and Romac, S. and Bachy, C. and Gachenot, M. and Pelletier, E. and Alberti, A. and Jaillon, O. and Wincker, P. and Aury, J. M. and Carradec, Q.},\r\n   title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},\r\n   journal = {Commun Biol},\r\n   volume = {5},\r\n   number = {1},\r\n   pages = {983},\r\n   abstract = {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.},\r\n   keywords = {Acclimatization/genetics\r\nChromosomes\r\nGenomics\r\n*Iron/metabolism\r\nNitrates/metabolism\r\nOceans and Seas\r\nPhytoplankton/genetics/metabolism\r\n*Stramenopiles/genetics},\r\n   ISSN = {2399-3642 (Electronic)\r\n2399-3642 (Linking)},\r\n   DOI = {10.1038/s42003-022-03939-z},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/36114260},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Phytoplankton DNA metabarcoding in four sectors of the SW Atlantic in the context of the global ocean.\n \n \n \n\n\n \n F. M. Ibarbalz, J. J. K. P., S. V. Ayuso, N. V., & L. Guidi, C. B.\n\n\n \n\n\n\n Ecologia Austral, 32: 835-848. 2022.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN287,\r\n   author = {F. M. Ibarbalz, J. J. Karlusich Pierella, S. V. Ayuso, N. Visintini, L. Guidi, C. Bowler, P. Flombaum},\r\n   title = {Phytoplankton DNA metabarcoding in four sectors of the SW Atlantic in the context of the global ocean},\r\n   journal = {Ecologia Austral},\r\n   volume = {32},\r\n   pages = {835-848},\r\n   DOI = {https://doi.org/10.25260/EA.22.32.3.0.1812},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Mathias Penot, Joel B. Dacks, Betsy Read and Richard G. Dorrell.\n \n \n \n\n\n \n Penot, M., Dacks, J., Read, B., & Dorrell, R.\n\n\n \n\n\n\n Applied Phycology, 3(1): 340-359. 2022.\n \n\n\n\n
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@article{RN286,\r\n   author = {Penot, M. and Dacks, J.B. and Read, B. and Dorrell, R.G.},\r\n   title = {Mathias Penot, Joel B. Dacks, Betsy Read and Richard G. Dorrell},\r\n   journal = {Applied Phycology},\r\n   volume = {3},\r\n   number = {1},\r\n   pages = {340-359},\r\n   DOI = {https://doi.org/10.1080/26388081.2022.2103732},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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., Fremont, P., Reygondeau, G., Maillet, N., Henry, N., Benoit, G., Da Silva, O., Delmont, T. O., Fernandez-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, C., Pesant, S., Aury, J. M., 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'Alcala , M., Iudicone, D., & Jaillon, O.\n\n\n \n\n\n\n Elife, 11. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\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 6 downloads\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 \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 \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

@article{RN280,\r\n author = {Richter, D. J. and Watteaux, R. and Vannier, T. and Leconte, J. and Fremont, P. and Reygondeau, G. and Maillet, N. and Henry, N. and Benoit, G. and Da Silva, O. and Delmont, T. O. and Fernandez-Guerra, A. and Suweis, S. and Narci, R. and Berney, C. and Eveillard, D. and Gavory, F. and Guidi, L. and Labadie, K. and Mahieu, E. and Poulain, J. and Romac, S. and Roux, S. and Dimier, C. and Kandels, S. and Picheral, M. and Searson, S. and Tara Oceans, Coordinators and Pesant, S. and Aury, J. M. and Brum, J. R. and Lemaitre, C. and Pelletier, E. and Bork, P. and Sunagawa, S. and Lombard, F. and Karp-Boss, L. and Bowler, C. and Sullivan, M. B. and Karsenti, E. and Mariadassou, M. and Probert, I. and Peterlongo, P. and Wincker, P. and de Vargas, C. and Ribera d'Alcala, M. and Iudicone, D. and Jaillon, O.},\r\n title = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems},\r\n journal = {Elife},\r\n volume = {11},\r\n abstract = {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.\r\nOceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These 'marine plankton' are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth's oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.\r\neng},\r\n keywords = {*Ecosystem\r\nGenomics\r\nGeography\r\nOceans and Seas\r\n*Plankton/genetics\r\necology\r\ngenetics\r\nmetabarcoding\r\nmetagenomics\r\nmicrobial oceanography\r\nplankton biogeography\r\nJP, SR, SR, CD, SK, MP, SS, SP, JA, JB, CL, EP, PB, SS, FL, LK, CB, MS, EK, MM,\r\nIP, PP, PW, Cd, MR, DI, OJ No competing interests declared},\r\n ISSN = {2050-084X (Electronic)\r\n2050-084X (Linking)},\r\n DOI = {10.7554/eLife.78129},\r\n url = {https://www.ncbi.nlm.nih.gov/pubmed/35920817},\r\n year = {2022},\r\n type = {Journal Article}\r\n}\r\n\r\n

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\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. Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These 'marine plankton' are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth's oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography. eng\n

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\n \n\n \n \n \n \n \n Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions.\n \n \n \n\n\n \n Pierella Karlusich, J. J., Lombard, F., Irisson, J., Bowler, C., & Foster, R. A.\n\n\n \n\n\n\n Frontiers in Marine Science, 9: 878803. 2022.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN285,\r\n   author = {Pierella Karlusich, J. J. and Lombard, F. and Irisson, J.O. and Bowler, C. and Foster, R. A.},\r\n   title = {Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions},\r\n   journal = {Frontiers in Marine Science},\r\n   volume = {9},\r\n   pages = {878803},\r\n   DOI = {https://doi.org/10.3389/fmars.2022.878803},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Vernette, C., Lecubin, J., Sanchez, P., Tara Oceans, C., Sunagawa, S., Delmont, T. O., Acinas, S. G., Pelletier, E., Hingamp, P., & Lescot, M.\n\n\n \n\n\n\n Nucleic Acids Res. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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 12 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN274,\r\n   author = {Vernette, C. and Lecubin, J. and Sanchez, P. and Tara Oceans, Coordinators and Sunagawa, S. and Delmont, T. O. and Acinas, S. G. and Pelletier, E. and Hingamp, P. and Lescot, M.},\r\n   title = {The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes},\r\n   journal = {Nucleic Acids Res},\r\n   abstract = {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/.},\r\n   ISSN = {1362-4962 (Electronic)\r\n0305-1048 (Linking)},\r\n   DOI = {10.1093/nar/gkac420},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35687095},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \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. M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Tara Oceans Coordinators section , s., Bowler, C., Eveillard, D., Guidi, L., Karsenti, E., Kuhn, J. H., Ogata, H., Wincker, P., Culley, A., Chaffron, S., & Sullivan, M. B.\n\n\n \n\n\n\n Science, 376(6598): 1202-1208. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Diversity$ Paper\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\n\n

@article{RN284,\r\n   author = {Dominguez-Huerta, G. and Zayed, A. A. and Wainaina, J. M. and Guo, J. and Tian, F. and Pratama, A. A. and Bolduc, B. and Mohssen, M. and Zablocki, O. and Pelletier, E. and Delage, E. and Alberti, A. and Aury, J. M. and Carradec, Q. and da Silva, C. and Labadie, K. and Poulain, J. and Tara Oceans Coordinators section, sign and Bowler, C. and Eveillard, D. and Guidi, L. and Karsenti, E. and Kuhn, J. H. and Ogata, H. and Wincker, P. and Culley, A. and Chaffron, S. and Sullivan, M. B.},\r\n   title = {Diversity and ecological footprint of Global Ocean RNA viruses},\r\n   journal = {Science},\r\n   volume = {376},\r\n   number = {6598},\r\n   pages = {1202-1208},\r\n   abstract = {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.},\r\n   keywords = {Carbon Cycle\r\nEcosystem\r\nOceans and Seas\r\n*Plankton/classification/metabolism/virology\r\n*RNA Viruses/classification/genetics/isolation & purification\r\n*Seawater/virology\r\n*Virome/genetics},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.abn6358},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35679415},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 Delmont, T., Gaia, M., Hinsinger, D., Fremont, P., Vanni, C., Fernandez Guerra, A., Eren, A., Kourlaiev, A., d'Agata , L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Silva, C., Wessner, M., Noel, B., Aury, J., Coordinators, T. O., de Vargas, C., Bowler, C., Karsenti, E., Pelletier, E., Wincker, P., & Jaillon, O.\n\n\n \n\n\n\n Cell Genomics, 2: 100123. 2022.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 5 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN275,\r\n   author = {Delmont, T.O. and Gaia, M. and Hinsinger, D.D. and Fremont, P. and Vanni, C. and Fernandez Guerra, A. and Eren, A.M. and Kourlaiev, A. and d'Agata, L. and Clayssen, Q. and Villar, E. and Labadie, K. and Cruaud, C. and Poulain, J. and Da Silva, C. and Wessner, M. and Noel, B. and Aury, J.M. and Coordinators, Tara Oceans and de Vargas, C. and Bowler, C. and Karsenti, E. and Pelletier, E. and Wincker, P. and Jaillon, O.},\r\n   title = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean},\r\n   journal = {Cell Genomics},\r\n   volume = {2},\r\n   pages = {100123},\r\n   DOI = {https://doi.org/10.1016/j.xgen.2022.100123},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Priorities for ocean microbiome research.\n \n \n \n \n\n\n \n Tara Ocean, F., Tara, O., European Molecular Biology, L., & European Marine Biological Resource Centre - European Research Infrastructure, C.\n\n\n \n\n\n\n Nat Microbiol, 7(7): 937-947. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Priorities$ Paper\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 13 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN283,\r\n   author = {Tara Ocean, Foundation and Tara, Oceans and European Molecular Biology, Laboratory and European Marine Biological Resource Centre - European Research Infrastructure, Consortium},\r\n   title = {Priorities for ocean microbiome research},\r\n   journal = {Nat Microbiol},\r\n   volume = {7},\r\n   number = {7},\r\n   pages = {937-947},\r\n   abstract = {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.},\r\n   keywords = {Ecology\r\n*Microbiota/genetics\r\nOceans and Seas\r\nSustainable Development},\r\n   ISSN = {2058-5276 (Electronic)\r\n2058-5276 (Linking)},\r\n   DOI = {10.1038/s41564-022-01145-5},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35773399},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Biosynthetic potential of the global ocean microbiome.\n \n \n \n \n\n\n \n Paoli, L., Ruscheweyh, H. J., Forneris, C. C., Hubrich, F., Kautsar, S., Bhushan, A., Lotti, A., Clayssen, Q., Salazar, G., Milanese, A., Carlstrom, C. I., Papadopoulou, C., Gehrig, D., Karasikov, M., Mustafa, H., Larralde, M., Carroll, L. M., Sanchez, 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., & Sunagawa, S.\n\n\n \n\n\n\n Nature, 607(7917): 111-118. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Biosynthetic$ Paper\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 22 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN282,\r\n   author = {Paoli, L. and Ruscheweyh, H. J. and Forneris, C. C. and Hubrich, F. and Kautsar, S. and Bhushan, A. and Lotti, A. and Clayssen, Q. and Salazar, G. and Milanese, A. and Carlstrom, C. I. and Papadopoulou, C. and Gehrig, D. and Karasikov, M. and Mustafa, H. and Larralde, M. and Carroll, L. M. and Sanchez, P. and Zayed, A. A. and Cronin, D. R. and Acinas, S. G. and Bork, P. and Bowler, C. and Delmont, T. O. and Gasol, J. M. and Gossert, A. D. and Kahles, A. and Sullivan, M. B. and Wincker, P. and Zeller, G. and Robinson, S. L. and Piel, J. and Sunagawa, S.},\r\n   title = {Biosynthetic potential of the global ocean microbiome},\r\n   journal = {Nature},\r\n   volume = {607},\r\n   number = {7917},\r\n   pages = {111-118},\r\n   abstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups(1), this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds(2,3). However, studying this diversity to identify genomic pathways for the synthesis of such compounds(4) 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.},\r\n   keywords = {Bacteria/classification/genetics\r\n*Biosynthetic Pathways/genetics\r\nGenomics\r\n*Microbiota/genetics\r\nMultigene Family/genetics\r\n*Oceans and Seas\r\nPhylogeny},\r\n   ISSN = {1476-4687 (Electronic)\r\n0028-0836 (Linking)},\r\n   DOI = {10.1038/s41586-022-04862-3},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35732736},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\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 \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. M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Ruscheweyh, H. J., Salazar, G., Shatoff, E., Tara Oceans Coordinatorsdouble, d., 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., & Wincker, P.\n\n\n \n\n\n\n Science, 376(6589): 156-162. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Cryptic$ Paper\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 15 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN272,\r\n   author = {Zayed, A. A. and Wainaina, J. M. and Dominguez-Huerta, G. and Pelletier, E. and Guo, J. and Mohssen, M. and Tian, F. and Pratama, A. A. and Bolduc, B. and Zablocki, O. and Cronin, D. and Solden, L. and Delage, E. and Alberti, A. and Aury, J. M. and Carradec, Q. and da Silva, C. and Labadie, K. and Poulain, J. and Ruscheweyh, H. J. and Salazar, G. and Shatoff, E. and Tara Oceans Coordinatorsdouble, dagger and Bundschuh, R. and Fredrick, K. and Kubatko, L. S. and Chaffron, S. and Culley, A. I. and Sunagawa, S. and Kuhn, J. H. and Wincker, P. and Sullivan, M. B. and Acinas, S. G. and Babin, M. and Bork, P. and Boss, E. and Bowler, C. and Cochrane, G. and de Vargas, C. and Gorsky, G. and Guidi, L. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels, S. and Karp-Boss, L. and Karsenti, E. and Not, F. and Ogata, H. and Poulton, N. and Pesant, S. and Sardet, C. and Speich, S. and Stemmann, L. and Sullivan, M. B. and Sungawa, S. and Wincker, P.},\r\n   title = {Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome},\r\n   journal = {Science},\r\n   volume = {376},\r\n   number = {6589},\r\n   pages = {156-162},\r\n   abstract = {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 approximately 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 >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.},\r\n   keywords = {Ecosystem\r\nGenome, Viral\r\nPhylogeny\r\nRna\r\n*RNA Viruses/genetics\r\nVirome/genetics\r\n*Viruses/genetics},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.abm5847},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35389782},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 Fremont, P., Gehlen, M., Vrac, M., Leconte, J., Delmont, T. O., Wincker, P., Iudicone, D., & Jaillon, O.\n\n\n \n\n\n\n Nature Climate Change, 12(4): 393-+. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Restructuring$ Paper\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 26 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN264,\r\n   author = {Fremont, P. and Gehlen, M. and Vrac, M. and Leconte, J. and Delmont, T. O. and Wincker, P. and Iudicone, D. and Jaillon, O.},\r\n   title = {Restructuring of plankton genomic biogeography in the surface ocean under climate change},\r\n   journal = {Nature Climate Change},\r\n   volume = {12},\r\n   number = {4},\r\n   pages = {393-+},\r\n   abstract = {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 degrees 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.\r\nThe authors define the global environmental niches of plankton from nano- (viruses) to meso-zooplankton (small metazoans) using metagenomic data. They assess reorganizations under climate change and the environmental drivers of change, with focus on the impacts on nitrogen and carbon fluxes.},\r\n   keywords = {export production\r\nnorth-atlantic\r\ncarbon\r\nzooplankton\r\ncommunity\r\nmicrobes\r\nshifts\r\nmodel\r\nwater\r\nflux},\r\n   ISSN = {1758-678x},\r\n   DOI = {10.1038/s41558-022-01314-8},\r\n   url = {<Go to ISI>://WOS:000778096800004},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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., & Bowler, C.\n\n\n \n\n\n\n Mol Ecol Resour. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\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 8 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN263,\r\n   author = {Pierella Karlusich, J. J. and Pelletier, E. and Zinger, L. and Lombard, F. and Zingone, A. and Colin, S. and Gasol, J. M. and Dorrell, R. G. and Henry, N. and Scalco, E. and Acinas, S. G. and Wincker, P. and de Vargas, C. and Bowler, C.},\r\n   title = {A robust approach to estimate relative phytoplankton cell abundances from metagenomes},\r\n   journal = {Mol Ecol Resour},\r\n   abstract = {Phytoplankton account for >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 >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.},\r\n   keywords = {psbO\r\n18S rRNA\r\nTara Oceans\r\nmetabarcoding\r\nmetagenomics\r\nmetatranscriptomics\r\nphotosynthesis\r\nphytoplankton},\r\n   ISSN = {1755-0998 (Electronic)\r\n1755-098X (Linking)},\r\n   DOI = {10.1111/1755-0998.13592},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35108459},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Giant Viruses Encode Actin-Related Proteins.\n \n \n \n \n\n\n \n Da Cunha, V., Gaia, M., Ogata, H., Jaillon, O., Delmont, T. O., & Forterre, P.\n\n\n \n\n\n\n Mol Biol Evol, 39(2). 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Giant$ Paper\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 \n\n\n\n

@article{RN262,\r\n   author = {Da Cunha, V. and Gaia, M. and Ogata, H. and Jaillon, O. and Delmont, T. O. and Forterre, P.},\r\n   title = {Giant Viruses Encode Actin-Related Proteins},\r\n   journal = {Mol Biol Evol},\r\n   volume = {39},\r\n   number = {2},\r\n   abstract = {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.},\r\n   keywords = {Actins/genetics\r\nEukaryota/genetics\r\nEukaryotic Cells\r\nEvolution, Molecular\r\n*Giant Viruses/genetics\r\nPhylogeny\r\n*NucleoCytoplasmic Large DNA virus\r\n*actin and actin-related proteins\r\n*viral eukaryogenesis},\r\n   ISSN = {1537-1719 (Electronic)\r\n0737-4038 (Linking)},\r\n   DOI = {10.1093/molbev/msac022},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35150280},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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. A., 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., & Pawlowski, J.\n\n\n \n\n\n\n Sci Adv, 8(5): eabj9309. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Patterns$ Paper\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 21 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN261,\r\n   author = {Cordier, T. and Angeles, I. B. and Henry, N. and Lejzerowicz, F. and Berney, C. and Morard, R. and Brandt, A. and Cambon-Bonavita, M. A. and Guidi, L. and Lombard, F. and Arbizu, P. M. and Massana, R. and Orejas, C. and Poulain, J. and Smith, C. R. and Wincker, P. and Arnaud-Haond, S. and Gooday, A. J. and de Vargas, C. and Pawlowski, J.},\r\n   title = {Patterns of eukaryotic diversity from the surface to the deep-ocean sediment},\r\n   journal = {Sci Adv},\r\n   volume = {8},\r\n   number = {5},\r\n   pages = {eabj9309},\r\n   abstract = {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.},\r\n   ISSN = {2375-2548 (Electronic)\r\n2375-2548 (Linking)},\r\n   DOI = {10.1126/sciadv.abj9309},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/35119936},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Patterns of mesozooplankton community composition and vertical fluxes in the global ocean.\n \n \n \n \n\n\n \n Soviadan, Y. D., Benedetti, F., Brandao, M. C., Ayata, S., Irisson, J., Jamet, J. L., Kiko, R., Lombard, F., Gnandi, K., & Stemmann, L.\n\n\n \n\n\n\n Progress in Oceanography, 200: 102717. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Patterns$ Paper\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 31 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN259,\r\n   author = {Soviadan, Yawouvi Dodji and Benedetti, Fabio and Brandao, Manoela C. and Ayata, Sakina-Dorothee and Irisson, Jean-Olivier and Jamet, Jean Louis and Kiko, Rainer and Lombard, Fabien and Gnandi, Kissao and Stemmann, Lars},\r\n   title = {Patterns of mesozooplankton community composition and vertical fluxes in the global ocean},\r\n   journal = {Progress in Oceanography},\r\n   volume = {200},\r\n   pages = {102717},\r\n   abstract = {Vertical variations in physical and chemical conditions drive changes in marine zooplankton community composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000 m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (<5µmol O2.kg−1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the temperature, on the phytoplankton size distribution and the surface large particulate organic matter while oxygen was an additional important factor for structuring zooplankton in the mesopelagic. Our results further suggest that future changes in surface phytoplankton size and taxa composition and mesopelagic oxygen loss might lead to profound shift in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump.},\r\n   keywords = {Zooplankton\r\nBiological carbon pump\r\nEpipelagic\r\nMesopelagic\r\nCommunity structure\r\nParticle flux\r\nAttenuation rates\r\nOxygen Minimum Zone},\r\n   ISSN = {0079-6611},\r\n   DOI = {https://doi.org/10.1016/j.pocean.2021.102717},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S0079661121002007},\r\n   year = {2022},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n Vertical variations in physical and chemical conditions drive changes in marine zooplankton community composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000 m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (<5µmol O2.kg−1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the temperature, on the phytoplankton size distribution and the surface large particulate organic matter while oxygen was an additional important factor for structuring zooplankton in the mesopelagic. Our results further suggest that future changes in surface phytoplankton size and taxa composition and mesopelagic oxygen loss might lead to profound shift in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump.\n

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\n \n 2021\n \n \n (14)\n \n \n

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\n \n\n \n \n \n \n \n \n Global drivers of eukaryotic plankton biogeography in the sunlit ocean.\n \n \n \n \n\n\n \n Sommeria-Klein, G., Watteaux, R., Ibarbalz, F. M., Pierella Karlusich, J. J., Iudicone, D., Bowler, C., & Morlon, H.\n\n\n \n\n\n\n Science, 374(6567): 594-599. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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 17 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN260,\r\n   author = {Sommeria-Klein, G. and Watteaux, R. and Ibarbalz, F. M. and Pierella Karlusich, J. J. and Iudicone, D. and Bowler, C. and Morlon, H.},\r\n   title = {Global drivers of eukaryotic plankton biogeography in the sunlit ocean},\r\n   journal = {Science},\r\n   volume = {374},\r\n   number = {6567},\r\n   pages = {594-599},\r\n   abstract = {Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity, yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. In this work, we use Tara Oceans metabarcoding data, which cover all major ocean basins, combined with a probabilistic model of taxon co-occurrence to compare the biogeography of 70 major groups of eukaryotic plankton. We uncover two main axes of biogeographic variation. First, more-diverse groups display clearer biogeographic patterns. Second, large-bodied consumers are structured by oceanic basins, mostly through the main current systems, whereas small-bodied phototrophs are structured by latitude and follow local environmental conditions. Our study highlights notable differences in biogeographies across plankton groups and investigates their determinants at the global scale.},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.abb3717},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34709919},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Royo-Llonch, M., Sanchez, P., Ruiz-Gonzalez, C., Salazar, G., Pedros-Alio, C., Sebastian, M., Labadie, K., Paoli, L., F, M. I., Zinger, L., Churcheward, B., Tara Oceans, C., Chaffron, S., Eveillard, D., Karsenti, E., Sunagawa, S., Wincker, P., Karp-Boss, L., Bowler, C., & Acinas, S. G.\n\n\n \n\n\n\n Nat Microbiol, 6(12): 1561-1574. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Compendium$ Paper\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 11 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

@article{RN258,\r\n   author = {Royo-Llonch, M. and Sanchez, P. and Ruiz-Gonzalez, C. and Salazar, G. and Pedros-Alio, C. and Sebastian, M. and Labadie, K. and Paoli, L. and F, M. Ibarbalz and Zinger, L. and Churcheward, B. and Tara Oceans, Coordinators and Chaffron, S. and Eveillard, D. and Karsenti, E. and Sunagawa, S. and Wincker, P. and Karp-Boss, L. and Bowler, C. and Acinas, S. G.},\r\n   title = {Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean},\r\n   journal = {Nat Microbiol},\r\n   volume = {6},\r\n   number = {12},\r\n   pages = {1561-1574},\r\n   abstract = {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.},\r\n   keywords = {Archaea/classification/*genetics/isolation & purification\r\nArctic Regions\r\nBacteria/classification/*genetics/isolation & purification\r\nEcosystem\r\nGenome, Archaeal\r\nGenome, Bacterial\r\nMetagenome\r\nPhylogeny\r\nSeawater/*microbiology},\r\n   ISSN = {2058-5276 (Electronic)\r\n2058-5276 (Linking)},\r\n   DOI = {10.1038/s41564-021-00979-9},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34782724},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Brandao, M. C., Benedetti, F., Martini, S., Soviadan, Y. D., Irisson, J. O., Romagnan, J. B., 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, C., Stemmann, L., & Lombard, F.\n\n\n \n\n\n\n Sci Rep, 11(1): 15714. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Macroscale$ Paper\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 6 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN257,\r\n   author = {Brandao, M. C. and Benedetti, F. and Martini, S. and Soviadan, Y. D. and Irisson, J. O. and Romagnan, J. B. and Elineau, A. and Desnos, C. and Jalabert, L. and Freire, A. S. and Picheral, M. and Guidi, L. and Gorsky, G. and Bowler, C. and Karp-Boss, L. and Henry, N. and de Vargas, C. and Sullivan, M. B. and Tara Oceans Consortium, Coordinators and Stemmann, L. and Lombard, F.},\r\n   title = {Macroscale patterns of oceanic zooplankton composition and size structure},\r\n   journal = {Sci Rep},\r\n   volume = {11},\r\n   number = {1},\r\n   pages = {15714},\r\n   abstract = {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.},\r\n   ISSN = {2045-2322 (Electronic)\r\n2045-2322 (Linking)},\r\n   DOI = {10.1038/s41598-021-94615-5},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34344925},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \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, c., Acinas, S. G., Babin, M., Iudicone, D., Jaillon, O., Karsenti, E., Wincker, P., Karp-Boss, L., Sullivan, M. B., Bowler, C., de Vargas, C., & Eveillard, D.\n\n\n \n\n\n\n Sci Adv, 7(35). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Environmental$ Paper\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 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN256,\r\n   author = {Chaffron, S. and Delage, E. and Budinich, M. and Vintache, D. and Henry, N. and Nef, C. and Ardyna, M. and Zayed, A. A. and Junger, P. C. and Galand, P. E. and Lovejoy, C. and Murray, A. E. and Sarmento, H. and Tara Oceans, coordinators and Acinas, S. G. and Babin, M. and Iudicone, D. and Jaillon, O. and Karsenti, E. and Wincker, P. and Karp-Boss, L. and Sullivan, M. B. and Bowler, C. and de Vargas, C. and Eveillard, D.},\r\n   title = {Environmental vulnerability of the global ocean epipelagic plankton community interactome},\r\n   journal = {Sci Adv},\r\n   volume = {7},\r\n   number = {35},\r\n   abstract = {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.},\r\n   ISSN = {2375-2548 (Electronic)\r\n2375-2548 (Linking)},\r\n   DOI = {10.1126/sciadv.abg1921},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34452910},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n efam: an expanded, metaproteome-supported HMM profile database of viral protein families.\n \n \n \n \n\n\n \n Zayed, A. A., Lucking, D., Mohssen, M., Cronin, D., Bolduc, B., Gregory, A. C., Hargreaves, K. R., Piehowski, P. D., White, R. A., Huang, E. L., Adkins, J. N., Roux, S., Moraru, C., & Sullivan, M. B.\n\n\n \n\n\n\n Bioinformatics. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"efam:$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN255,\r\n   author = {Zayed, A. A. and Lucking, D. and Mohssen, M. and Cronin, D. and Bolduc, B. and Gregory, A. C. and Hargreaves, K. R. and Piehowski, P. D. and White, R. A. and Huang, E. L. and Adkins, J. N. and Roux, S. and Moraru, C. and Sullivan, M. B.},\r\n   title = {efam: an expanded, metaproteome-supported HMM profile database of viral protein families},\r\n   journal = {Bioinformatics},\r\n   abstract = {MOTIVATION: Viruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. RESULTS: Here we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from "conservative" to "eXtremely Conservative" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by approximately 24% on average (up to approximately 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. AVAILABILITY: The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},\r\n   ISSN = {1367-4811 (Electronic)\r\n1367-4803 (Linking)},\r\n   DOI = {10.1093/bioinformatics/btab451},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34132786},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n MOTIVATION: Viruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. RESULTS: Here we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from \"conservative\" to \"eXtremely Conservative\" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by approximately 24% on average (up to approximately 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. AVAILABILITY: The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.\n

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\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 \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., & Foster, R. A.\n\n\n \n\n\n\n Nat Commun, 12(1): 4160. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN254,\r\n   author = {Pierella Karlusich, J. J. and Pelletier, E. and Lombard, F. and Carsique, M. and Dvorak, E. and Colin, S. and Picheral, M. and Cornejo-Castillo, F. M. and Acinas, S. G. and Pepperkok, R. and Karsenti, E. and de Vargas, C. and Wincker, P. and Bowler, C. and Foster, R. A.},\r\n   title = {Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods},\r\n   journal = {Nat Commun},\r\n   volume = {12},\r\n   number = {1},\r\n   pages = {4160},\r\n   abstract = {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 >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). 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 (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). 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 (>10 mum) 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.},\r\n   keywords = {Aquatic Organisms\r\nBacteria/genetics/metabolism\r\nCyanobacteria/genetics/metabolism\r\nMolecular Imprinting/*methods\r\nNitrogen/*metabolism\r\nNitrogen Fixation/*genetics/physiology\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/metabolism\r\nSeawater/*chemistry/microbiology\r\nSymbiosis/genetics/physiology},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/s41467-021-24299-y},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34230473},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Kijima, S., Delmont, T. O., Miyazaki, U., Gaia, M., Endo, H., & Ogata, H.\n\n\n \n\n\n\n Front Microbiol, 12: 683294. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Discovery$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN253,\r\n   author = {Kijima, S. and Delmont, T. O. and Miyazaki, U. and Gaia, M. and Endo, H. and Ogata, H.},\r\n   title = {Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton},\r\n   journal = {Front Microbiol},\r\n   volume = {12},\r\n   pages = {683294},\r\n   abstract = {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.},\r\n   keywords = {Ncldv\r\nNucleocytoviricota\r\ngiant viruses\r\nmyosin\r\nphylogeny\r\nviral diversity\r\ncommercial or financial relationships that could be construed as a potential\r\nconflict of interest.},\r\n   ISSN = {1664-302X (Print)\r\n1664-302X (Linking)},\r\n   DOI = {10.3389/fmicb.2021.683294},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/34163457},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Phylogenomics of Porites from the Arabian Peninsula.\n \n \n \n \n\n\n \n Terraneo, T. I., Benzoni, F., Arrigoni, R., Baird, A. H., Mariappan, K. G., Forsman, Z. H., Wooster, M. K., Bouwmeester, J., Marshell, A., & Berumen, M. L.\n\n\n \n\n\n\n Mol Phylogenet Evol, 161: 107173. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Phylogenomics$ Paper\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

@article{RN251,\r\n   author = {Terraneo, T. I. and Benzoni, F. and Arrigoni, R. and Baird, A. H. and Mariappan, K. G. and Forsman, Z. H. and Wooster, M. K. and Bouwmeester, J. and Marshell, A. and Berumen, M. L.},\r\n   title = {Phylogenomics of Porites from the Arabian Peninsula},\r\n   journal = {Mol Phylogenet Evol},\r\n   volume = {161},\r\n   pages = {107173},\r\n   abstract = {The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.},\r\n   keywords = {Corals\r\nSpecies delimitation\r\nSpecies tree\r\nSystematics\r\ndDocent\r\nezRAD},\r\n   ISSN = {1095-9513 (Electronic)\r\n1055-7903 (Linking)},\r\n   DOI = {10.1016/j.ympev.2021.107173},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/33813021},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans.\n \n \n \n \n\n\n \n Pierella Karlusich, J. J., Bowler, C., & Biswas, H.\n\n\n \n\n\n\n Frontiers in Plant Science, 12(659). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Carbon$ Paper\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 1 download\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 \n \n\n\n\n

@article{RN252,\r\n   author = {Pierella Karlusich, Juan José and Bowler, Chris and Biswas, Haimanti},\r\n   title = {Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans},\r\n   journal = {Frontiers in Plant Science},\r\n   volume = {12},\r\n   number = {659},\r\n   abstract = {Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO<sub>2</sub> to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO<sub>2</sub>, which is vital information toward modeling their response to future CO<sub>2</sub> levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO<sub>2</sub> variability. The current study investigates the interlink between the environmental variability of CO<sub>2</sub> and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO<sub>2</sub> concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8–5 μm, 5–20 μm, 20–180 μm, and 180–2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO<sub>2</sub> levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.},\r\n   keywords = {tara oceans,Diatoms,Carbon Metabolism,carbon dioxide concentration mechanism,Metagenomics,metatranscriptomics},\r\n   ISSN = {1664-462X},\r\n   DOI = {10.3389/fpls.2021.657821},\r\n   url = {https://www.frontiersin.org/article/10.3389/fpls.2021.657821},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO₂ to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO₂, which is vital information toward modeling their response to future CO₂ levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO₂ variability. The current study investigates the interlink between the environmental variability of CO₂ and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO₂ concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8–5 μm, 5–20 μm, 20–180 μm, and 180–2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO₂ levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.\n

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\n \n\n \n \n \n \n \n \n Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses.\n \n \n \n \n\n\n \n Meng, L., Endo, H., Blanc-Mathieu, R., Chaffron, S., Hernandez-Velazquez, R., Kaneko, H., & Ogata, H.\n\n\n \n\n\n\n mSphere, 6(2). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\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

@article{RN250,\r\n   author = {Meng, L. and Endo, H. and Blanc-Mathieu, R. and Chaffron, S. and Hernandez-Velazquez, R. and Kaneko, H. and Ogata, H.},\r\n   title = {Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses},\r\n   journal = {mSphere},\r\n   volume = {6},\r\n   number = {2},\r\n   abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments.IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.},\r\n   keywords = {Ncldv\r\nTara Oceans\r\nassessment\r\nco-occurrence\r\nhost prediction},\r\n   ISSN = {2379-5042 (Electronic)\r\n2379-5042 (Linking)},\r\n   DOI = {10.1128/mSphere.01298-20},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/33883262},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments.IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.\n

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\n \n\n \n \n \n \n \n \n Integrative systematics of the scleractinian coral genera Caulastraea, Erythrastrea and Oulophyllia.\n \n \n \n \n\n\n \n Arrigoni, R., Huang, D., Berumen, M. L., Budd, A. F., Montano, S., Richards, Z. T., Terraneo, T. I., & Benzoni, F.\n\n\n \n\n\n\n Zoologica Scripta. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Integrative$ Paper\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

@article{RN246,\r\n author = {Arrigoni, Roberto and Huang, Danwei and Berumen, Michael L. and Budd, Ann F. and Montano, Simone and Richards, Zoe T. and Terraneo, Tullia I. and Benzoni, Francesca},\r\n title = {Integrative systematics of the scleractinian coral genera Caulastraea, Erythrastrea and Oulophyllia},\r\n journal = {Zoologica Scripta},\r\n abstract = {Abstract Modern systematics integrating molecular and morphological data has greatly improved our understanding of coral evolutionary relationships during the last two decades and led to a deeply revised taxonomy of the order Scleractinia. The family Merulinidae (Cnidaria: Scleractinia) was recently subjected to a series of revisions following this integrated approach but the phylogenetic affinities of several genera ascribed to it remain unknown. Here, we partially fill this gap through the study of 89 specimens belonging to all 10 valid species from four genera (Caulastraea, Erythrastrea, Oulophyllia and Dipsastraea) collected from 14 localities across the Indo-Pacific realm. Four molecular loci (histone H3, COI, ITS and IGR) were sequenced, and a total of 44 skeletal morphological characters (macromorphology, micromorphology and microstructure) were analysed. Molecular phylogenetic analyses revealed that the phaceloid Caulastraea species are split into two distinct lineages. A species previously ascribed to the genus Dipsastraea, Dipsastraea maxima, is also recovered in one on these lineages. Furthermore, Erythrastrea is nested within Oulophyllia. The molecular reconstructions of evolutionary relationships are further corroborated by multiscale morphological evidence. To resolve the taxonomy of these genera, Astraeosmilia is resurrected to accommodate Astraeosmilia connata, Astraeosmilia curvata, Astraeosmilia tumida and Astraeosmilia maxima, with Caulastraea retaining Caulastraea furcata and Caulastraea echinulata. Based on the examination of type material, Erythrastrea flabellata is considered an objective synonym of Lobophyllia wellsi, which is transferred to Oulophyllia following the obtained morpho-molecular results. This work further confirms that an integrated morpho-molecular approach based on a rigorous phylogenetic framework is fundamental for an objective classification that reflects the evolutionary history of scleractinian corals.},\r\n keywords = {cladistics\r\nCOI\r\nhistone H3\r\nIGR\r\nIndo-Pacific\r\nITS\r\nmacromorphology\r\nmicromorphology\r\nmicrostructure\r\ntaxonomic revision},\r\n ISSN = {0300-3256},\r\n DOI = {10.1111/zsc.12481},\r\n url = {https://doi.org/10.1111/zsc.12481},\r\n year = {2021},\r\n type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability.\n \n \n \n \n\n\n \n Kotabova, E., Malych, R., Pierella Karlusich, J. J., Kazamia, E., Eichner, M., Mach, J., Lesuisse, E., Bowler, C., Prasil, O., & Sutak, R.\n\n\n \n\n\n\n mSystems, 6(1). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Complex$ Paper\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

@article{RN215,\r\n author = {Kotabova, E. and Malych, R. and Pierella Karlusich, J. J. and Kazamia, E. and Eichner, M. and Mach, J. and Lesuisse, E. and Bowler, C. and Prasil, O. and Sutak, R.},\r\n title = {Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability},\r\n journal = {mSystems},\r\n volume = {6},\r\n number = {1},\r\n abstract = {The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.},\r\n keywords = {Bigelowiella natans\r\niron\r\nmetagenomics\r\nmetatranscriptomics\r\nphotosynthesis\r\nphytoplankton\r\nproteomics},\r\n ISSN = {2379-5077 (Print)\r\n2379-5077 (Linking)},\r\n DOI = {10.1128/mSystems.00738-20},\r\n url = {https://www.ncbi.nlm.nih.gov/pubmed/33563784},\r\n year = {2021},\r\n type = {Journal Article}\r\n}\r\n\r\n

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\n The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.\n

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\n \n\n \n \n \n \n \n \n The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms.\n \n \n \n \n\n\n \n Vernette, C., Henry, N., Lecubin, J., de Vargas, C., Hingamp, P., & Lescot, M.\n\n\n \n\n\n\n Mol Ecol Resour. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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 8 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN218,\r\n   author = {Vernette, C. and Henry, N. and Lecubin, J. and de Vargas, C. and Hingamp, P. and Lescot, M.},\r\n   title = {The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms},\r\n   journal = {Mol Ecol Resour},\r\n   abstract = {The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.},\r\n   keywords = {biogeography\r\ndiversity\r\nmarine ecology\r\nmetabarcoding\r\nmetadata\r\nplankton},\r\n   ISSN = {1755-0998 (Electronic)\r\n1755-098X (Linking)},\r\n   DOI = {10.1111/1755-0998.13322},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/33434383},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean.\n \n \n \n \n\n\n \n Kaneko, H., Blanc-Mathieu, R., Endo, H., Chaffron, S., Delmont, T. O., Gaia, M., Henry, N., Hernandez-Velazquez, R., Nguyen, C. H., Mamitsuka, H., Forterre, P., Jaillon, O., de Vargas, C., Sullivan, M. B., Suttle, C. A., Guidi, L., & Ogata, H.\n\n\n \n\n\n\n iScience, 24(1): 102002. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Eukaryotic$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN216,\r\n   author = {Kaneko, H. and Blanc-Mathieu, R. and Endo, H. and Chaffron, S. and Delmont, T. O. and Gaia, M. and Henry, N. and Hernandez-Velazquez, R. and Nguyen, C. H. and Mamitsuka, H. and Forterre, P. and Jaillon, O. and de Vargas, C. and Sullivan, M. B. and Suttle, C. A. and Guidi, L. and Ogata, H.},\r\n   title = {Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean},\r\n   journal = {iScience},\r\n   volume = {24},\r\n   number = {1},\r\n   pages = {102002},\r\n   abstract = {The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.},\r\n   keywords = {Biogeoscience\r\nCarbon Cycle\r\nGlobal Carbon Cycle\r\nOceanography\r\nViral Microbiology\r\nVirology},\r\n   ISSN = {2589-0042 (Electronic)\r\n2589-0042 (Linking)},\r\n   DOI = {10.1016/j.isci.2020.102002},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/33490910},\r\n   year = {2021},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2020\n \n \n (14)\n \n \n

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\n \n\n \n \n \n \n \n Exploration of marine phytoplankton: From their historical appreciation to the omics era.\n \n \n \n\n\n \n Pierella Karlusich, J. J., Ibarbalz, F., & Bowler, C.\n\n\n \n\n\n\n Journal of Plankton Research, 42. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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

@article{RN249,\r\n   author = {Pierella Karlusich, Juan José and Ibarbalz, Federico and Bowler, Chris},\r\n   title = {Exploration of marine phytoplankton: From their historical appreciation to the omics era},\r\n   journal = {Journal of Plankton Research},\r\n   volume = {42},\r\n   DOI = {10.1093/plankt/fbaa049},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions.\n \n \n \n \n\n\n \n Endo, H., Blanc-Mathieu, R., Li, Y., Salazar, G., Henry, N., Labadie, K., de Vargas, C., Sullivan, M. B., Bowler, C., Wincker, P., Karp-Boss, L., Sunagawa, S., & Ogata, H.\n\n\n \n\n\n\n Nat Ecol Evol, 4(12): 1639-1649. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Biogeography$ Paper\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\n\n

@article{RN181,\r\n   author = {Endo, H. and Blanc-Mathieu, R. and Li, Y. and Salazar, G. and Henry, N. and Labadie, K. and de Vargas, C. and Sullivan, M. B. and Bowler, C. and Wincker, P. and Karp-Boss, L. and Sunagawa, S. and Ogata, H.},\r\n   title = {Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions},\r\n   journal = {Nat Ecol Evol},\r\n   volume = {4},\r\n   number = {12},\r\n   pages = {1639-1649},\r\n   abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara Oceans pole-to-pole metagenomic data set, we investigated the distribution of NCLDVs across size fractions, depths and biomes, as well as their associations with eukaryotic communities. Our analyses reveal a heterogeneous distribution of NCLDVs across oceans, and a higher proportion of unique NCLDVs in the polar biomes. The community structures of NCLDV families correlate with specific eukaryotic lineages, including many photosynthetic groups. NCLDV communities are generally distinct between surface and mesopelagic zones, but at some locations they exhibit a high similarity between the two depths. This vertical similarity correlates to surface phytoplankton biomass but not to physical mixing processes, which suggests a potential role of vertical transport in structuring mesopelagic NCLDV communities. These results underscore the importance of the interactions between NCLDVs and eukaryotes in biogeochemical processes in the ocean.},\r\n   keywords = {DNA Viruses\r\nEukaryota\r\n*Giant Viruses/genetics\r\nHumans\r\nOceans and Seas\r\nPhylogeny},\r\n   ISSN = {2397-334X (Electronic)\r\n2397-334X (Linking)},\r\n   DOI = {10.1038/s41559-020-01288-w},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32895519},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Diversity and distribution of marine heterotrophic bacteria from a large culture collection.\n \n \n \n \n\n\n \n Sanz-Saez, I., Salazar, G., Sanchez, P., Lara, E., Royo-Llonch, M., Sa, E. L., Lucena, T., Pujalte, M. J., Vaque, D., Duarte, C. M., Gasol, J. M., Pedros-Alio, C., Sanchez, O., & Acinas, S. G.\n\n\n \n\n\n\n BMC Microbiol, 20(1): 207. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Diversity$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN209,\r\n   author = {Sanz-Saez, I. and Salazar, G. and Sanchez, P. and Lara, E. and Royo-Llonch, M. and Sa, E. L. and Lucena, T. and Pujalte, M. J. and Vaque, D. and Duarte, C. M. and Gasol, J. M. and Pedros-Alio, C. and Sanchez, O. and Acinas, S. G.},\r\n   title = {Diversity and distribution of marine heterotrophic bacteria from a large culture collection},\r\n   journal = {BMC Microbiol},\r\n   volume = {20},\r\n   number = {1},\r\n   pages = {207},\r\n   abstract = {BACKGROUND: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. RESULTS: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. CONCLUSIONS: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.},\r\n   keywords = {*Bacterial isolates\r\n*Deep ocean\r\n*Diversity\r\n*Photic ocean},\r\n   ISSN = {1471-2180 (Electronic)\r\n1471-2180 (Linking)},\r\n   DOI = {10.1186/s12866-020-01884-7},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32660423},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n BACKGROUND: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. RESULTS: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. CONCLUSIONS: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.\n

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\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 \n Laso-Jadart, R., Sugier, K., Petit, E., Labadie, K., Peterlongo, P., Ambroise, C., Wincker, P., Jamet, J. L., & Madoui, M. A.\n\n\n \n\n\n\n Ecol Evol, 10(16): 8894-8905. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Investigating$ Paper\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

@article{RN182,\r\n   author = {Laso-Jadart, R. and Sugier, K. and Petit, E. and Labadie, K. and Peterlongo, P. and Ambroise, C. and Wincker, P. and Jamet, J. L. and Madoui, M. A.},\r\n   title = {Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)},\r\n   journal = {Ecol Evol},\r\n   volume = {10},\r\n   number = {16},\r\n   pages = {8894-8905},\r\n   abstract = {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 < 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 x 10(-30)), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .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.},\r\n   keywords = {Arctic seas\r\nTara Oceans\r\nZooplankton\r\nallelic expression\r\ncopepod\r\nmetagenomics\r\nmetatranscriptomics\r\nselection\r\nstructure},\r\n   ISSN = {2045-7758 (Print)\r\n2045-7758 (Linking)},\r\n   DOI = {10.1002/ece3.6588},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32884665},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters.\n \n \n \n \n\n\n \n Lucena, T., Sanz-Saez, I., Arahal, D. R., Acinas, S. G., Sanchez, O., Pedros-Alio, C., Aznar, R., & Pujalte, M. J.\n\n\n \n\n\n\n Int J Syst Evol Microbiol, 70(7): 4329-4338. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Mesonia$ Paper\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 \n\n\n\n

@article{RN186,\r\n   author = {Lucena, T. and Sanz-Saez, I. and Arahal, D. R. and Acinas, S. G. and Sanchez, O. and Pedros-Alio, C. and Aznar, R. and Pujalte, M. J.},\r\n   title = {Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters},\r\n   journal = {Int J Syst Evol Microbiol},\r\n   volume = {70},\r\n   number = {7},\r\n   pages = {4329-4338},\r\n   abstract = {Strain ISS653(T), isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15 % NaCl) and mesophilic (4-37 degrees C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653(T) in a clade with species of the genus Mesonia. We conclude that strain ISS653(T) represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653(T) (=CECT 9532(T)=LMG 31236(T)) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.},\r\n   keywords = {Atlantic Ocean\r\nBacterial Typing Techniques\r\nBase Composition\r\nDNA, Bacterial/genetics\r\nFatty Acids/chemistry\r\nFlavobacteriaceae/*classification/isolation & purification\r\nPacific Ocean\r\n*Phylogeny\r\nPigmentation\r\nRNA, Ribosomal, 16S/genetics\r\nSeawater/*microbiology\r\nSequence Analysis, DNA\r\nVitamin K 2/analogs & derivatives\r\nFlavobacteriaceae\r\nMesonia\r\nMesonia oceanica\r\nmarine bacteria\r\nmesopelagic zone\r\ntaxogenomics},\r\n   ISSN = {1466-5034 (Electronic)\r\n1466-5026 (Linking)},\r\n   DOI = {10.1099/ijsem.0.004296},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32589567},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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., Annamale, A., Wincker, P., & Pelletier, E.\n\n\n \n\n\n\n Genome Res, 30(4): 647-659. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Transcriptome$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN195,\r\n   author = {Vorobev, A. and Dupouy, M. and Carradec, Q. and Delmont, T. O. and Annamale, A. and Wincker, P. and Pelletier, E.},\r\n   title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics},\r\n   journal = {Genome Res},\r\n   volume = {30},\r\n   number = {4},\r\n   pages = {647-659},\r\n   abstract = {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 approximately 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 approximately 12,000 co-abundant gene groups (CAGs), encompassing approximately 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.},\r\n   ISSN = {1549-5469 (Electronic)\r\n1088-9051 (Linking)},\r\n   DOI = {10.1101/gr.253070.119},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32205368},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific.\n \n \n \n\n\n \n Arrigoni, R., Berumen, M., Mariappan, K., Beck, P., Hulver, A., Montano, S., Pichon, M., Strona, G., Terraneo, T. I., & Benzoni, F.\n\n\n \n\n\n\n Coral Reefs, 39. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN248,\r\n   author = {Arrigoni, Roberto and Berumen, Michael and Mariappan, Kiruthiga and Beck, Pieter and Hulver, Ann and Montano, Simone and Pichon, Michel and Strona, Giovanni and Terraneo, Tullia Isotta and Benzoni, Francesca},\r\n   title = {Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific},\r\n   journal = {Coral Reefs},\r\n   volume = {39},\r\n   DOI = {10.1007/s00338-020-01924-8},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Diatoms Are Selective Segregators in Global Ocean Planktonic Communities.\n \n \n \n \n\n\n \n Vincent, F., & Bowler, C.\n\n\n \n\n\n\n mSystems, 5(1). 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Diatoms$ Paper\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

@article{RN198,\r\n   author = {Vincent, F. and Bowler, C.},\r\n   title = {Diatoms Are Selective Segregators in Global Ocean Planktonic Communities},\r\n   journal = {mSystems},\r\n   volume = {5},\r\n   number = {1},\r\n   abstract = {Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups.IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.},\r\n   keywords = {cooccurrence networks\r\nenvironmental microbiology\r\nmarine microbiology\r\nphytoplankton\r\nprotists},\r\n   ISSN = {2379-5077 (Print)\r\n2379-5077 (Linking)},\r\n   DOI = {10.1128/mSystems.00444-19},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31964765},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

\n\n\n

\n Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups.IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.\n

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\n \n\n \n \n \n \n \n \n Diversity and evolution of bacterial bioluminescence genes in the global ocean.\n \n \n \n \n\n\n \n Vannier, T., Hingamp, P., Turrel, F., Tanet, L., Lescot, M., & Timsit, Y.\n\n\n \n\n\n\n NAR Genom Bioinform, 2(2): lqaa018. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Diversity$ Paper\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 5 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN208,\r\n   author = {Vannier, T. and Hingamp, P. and Turrel, F. and Tanet, L. and Lescot, M. and Timsit, Y.},\r\n   title = {Diversity and evolution of bacterial bioluminescence genes in the global ocean},\r\n   journal = {NAR Genom Bioinform},\r\n   volume = {2},\r\n   number = {2},\r\n   pages = {lqaa018},\r\n   abstract = {Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.},\r\n   ISSN = {2631-9268 (Electronic)\r\n2631-9268 (Linking)},\r\n   DOI = {10.1093/nargab/lqaa018},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/33575578},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Tara Oceans: towards global ocean ecosystems biology.\n \n \n \n \n\n\n \n Sunagawa, S., Acinas, S. G., Bork, P., Bowler, C., Tara Oceans, C., Eveillard, D., Gorsky, G., Guidi, L., Iudicone, D., Karsenti, E., Lombard, F., Ogata, H., Pesant, S., Sullivan, M. B., Wincker, P., & de Vargas, C.\n\n\n \n\n\n\n Nat Rev Microbiol, 18(8): 428-445. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Tara$ Paper\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 20 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN190,\r\n   author = {Sunagawa, S. and Acinas, S. G. and Bork, P. and Bowler, C. and Tara Oceans, Coordinators and Eveillard, D. and Gorsky, G. and Guidi, L. and Iudicone, D. and Karsenti, E. and Lombard, F. and Ogata, H. and Pesant, S. and Sullivan, M. B. and Wincker, P. and de Vargas, C.},\r\n   title = {Tara Oceans: towards global ocean ecosystems biology},\r\n   journal = {Nat Rev Microbiol},\r\n   volume = {18},\r\n   number = {8},\r\n   pages = {428-445},\r\n   abstract = {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.},\r\n   keywords = {Animals\r\nBiodiversity\r\nBiology/methods\r\nClimate Change\r\n*Ecosystem\r\nHumans\r\nOceans and Seas\r\nPlankton/*growth & development},\r\n   ISSN = {1740-1534 (Electronic)\r\n1740-1526 (Linking)},\r\n   DOI = {10.1038/s41579-020-0364-5},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/32398798},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Genome Resolved Biogeography of Mamiellales.\n \n \n \n \n\n\n \n Leconte, J., Benites, L. F., Vannier, T., Wincker, P., Piganeau, G., & Jaillon, O.\n\n\n \n\n\n\n Genes (Basel), 11(1). 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN173,\r\n   author = {Leconte, J. and Benites, L. F. and Vannier, T. and Wincker, P. and Piganeau, G. and Jaillon, O.},\r\n   title = {Genome Resolved Biogeography of Mamiellales},\r\n   journal = {Genes (Basel)},\r\n   volume = {11},\r\n   number = {1},\r\n   abstract = {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.},\r\n   keywords = {Base Sequence\r\nChlorophyta/*genetics\r\nDemography/methods\r\nGenome\r\nOceans and Seas\r\nPhylogeny\r\nPhylogeography/*methods\r\nPhytoplankton\r\nPopulation Density\r\nSeawater\r\n*Mamiellales\r\n*Tara Oceans\r\n*biogeography\r\n*ecogenomics\r\n*mating-type\r\n*sexual reproduction},\r\n   ISSN = {2073-4425 (Electronic)\r\n2073-4425 (Linking)},\r\n   DOI = {10.3390/genes11010066},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31936086},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability.\n \n \n \n \n\n\n \n Sordino, P., D'Aniello, S., Pelletier, E., Wincker, P., Nittoli, V., Stemmann, L., Mazzocchi, M. G., Lombard, F., Iudicone, D., & Caputi, L.\n\n\n \n\n\n\n Mol Ecol, 29(2): 292-307. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Into$ Paper\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

@article{RN204,\r\n   author = {Sordino, P. and D'Aniello, S. and Pelletier, E. and Wincker, P. and Nittoli, V. and Stemmann, L. and Mazzocchi, M. G. and Lombard, F. and Iudicone, D. and Caputi, L.},\r\n   title = {Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability},\r\n   journal = {Mol Ecol},\r\n   volume = {29},\r\n   number = {2},\r\n   pages = {292-307},\r\n   abstract = {The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.},\r\n   keywords = {Animals\r\nDNA Barcoding, Taxonomic/*methods\r\nEcology\r\nEcosystem\r\nTranscriptome/genetics\r\nUrochordata/classification/*genetics\r\n*DNA barcoding\r\n*community ecology\r\n*ecological genetics\r\n*metagenomics\r\n*population ecology\r\n*transcriptomics},\r\n   ISSN = {1365-294X (Electronic)\r\n0962-1083 (Linking)},\r\n   DOI = {10.1111/mec.15321},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31793138},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Ecological and functional capabilities of an uncultured Kordia sp.\n \n \n \n \n\n\n \n Royo-Llonch, M., Sanchez, P., Gonzalez, J. M., Pedros-Alio, C., & Acinas, S. G.\n\n\n \n\n\n\n Syst Appl Microbiol, 43(1): 126045. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Ecological$ Paper\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 \n \n \n \n \n\n\n\n

@article{RN203,\r\n   author = {Royo-Llonch, M. and Sanchez, P. and Gonzalez, J. M. and Pedros-Alio, C. and Acinas, S. G.},\r\n   title = {Ecological and functional capabilities of an uncultured Kordia sp},\r\n   journal = {Syst Appl Microbiol},\r\n   volume = {43},\r\n   number = {1},\r\n   pages = {126045},\r\n   abstract = {Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.},\r\n   keywords = {Bacterial Proteins/genetics\r\nDNA, Bacterial/genetics\r\nEcosystem\r\nFlavobacteriaceae/*classification/*genetics\r\nGenome, Bacterial/genetics\r\nIndian Ocean\r\nMetagenomics\r\nMicrobiota/genetics\r\nNucleic Acid Hybridization\r\nPhylogeny\r\nRNA, Ribosomal, 16S/genetics\r\nRhodopsins, Microbial/genetics\r\nSeawater/microbiology\r\nSequence Analysis, DNA\r\nCo-assembly\r\nKordia\r\nPhotoheterotrophy\r\nSag},\r\n   ISSN = {1618-0984 (Electronic)\r\n0723-2020 (Linking)},\r\n   DOI = {10.1016/j.syapm.2019.126045},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31831198},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Phytoplankton in the Tara Ocean.\n \n \n \n\n\n \n Pierella Karlusich, J. J., Ibarbalz, F., & Bowler, C.\n\n\n \n\n\n\n Annual Review of Marine Science, 12: 233-265. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 7 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN243,\r\n   author = {Pierella Karlusich, Juan José and Ibarbalz, Federico and Bowler, Chris},\r\n   title = {Phytoplankton in the Tara Ocean},\r\n   journal = {Annual Review of Marine Science},\r\n   volume = {12},\r\n   pages = {233-265},\r\n   DOI = {10.1146/annurev-marine-010419-010706},\r\n   year = {2020},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems.\n \n \n \n \n\n\n \n Capotondi, A., Jacox, M., Bowler, C., Kavanaugh, M., Lehodey, P., Barrie, D., Brodie, S., Chaffron, S., Cheng, W., Dias, D. F., Eveillard, D., Guidi, L., Iudicone, D., Lovenduski, N. S., Nye, J. A., Ortiz, I., Pirhalla, D., Pozo Buil, M., Saba, V., Sheridan, S., Siedlecki, S., Subramanian, A., de Vargas, C., Di Lorenzo, E., Doney, S. C., Hermann, A. J., Joyce, T., Merrifield, M., Miller, A. J., Not, F., & Pesant, S.\n\n\n \n\n\n\n Frontiers in Marine Science, 6(623). 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Observational$ Paper\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 2 downloads\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\n\n\n

@article{RN244,\r\n   author = {Capotondi, Antonietta and Jacox, Michael and Bowler, Chris and Kavanaugh, Maria and Lehodey, Patrick and Barrie, Daniel and Brodie, Stephanie and Chaffron, Samuel and Cheng, Wei and Dias, Daniela F. and Eveillard, Damien and Guidi, Lionel and Iudicone, Daniele and Lovenduski, Nicole S. and Nye, Janet A. and Ortiz, Ivonne and Pirhalla, Douglas and Pozo Buil, Mercedes and Saba, Vincent and Sheridan, Scott and Siedlecki, Samantha and Subramanian, Aneesh and de Vargas, Colomban and Di Lorenzo, Emanuele and Doney, Scott C. and Hermann, Albert J. and Joyce, Terrence and Merrifield, Mark and Miller, Arthur J. and Not, Fabrice and Pesant, Stephane},\r\n   title = {Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems},\r\n   journal = {Frontiers in Marine Science},\r\n   volume = {6},\r\n   number = {623},\r\n   abstract = {Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.},\r\n   keywords = {Marine Ecosystems,Modeling and forecasting,Seascapes,Genetics,Acoustics},\r\n   ISSN = {2296-7745},\r\n   DOI = {10.3389/fmars.2019.00623},\r\n   url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00623},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H. J., 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., Sanchez, P., Uehara, H., Zayed, A. A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Tara Oceans, C., 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., & Sunagawa, S.\n\n\n \n\n\n\n Cell, 179(5): 1068-1083 e21. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Gene$ Paper\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 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN130,\r\n   author = {Salazar, G. and Paoli, L. and Alberti, A. and Huerta-Cepas, J. and Ruscheweyh, H. J. and Cuenca, M. and Field, C. M. and Coelho, L. P. and Cruaud, C. and Engelen, S. and Gregory, A. C. and Labadie, K. and Marec, C. and Pelletier, E. and Royo-Llonch, M. and Roux, S. and Sanchez, P. and Uehara, H. and Zayed, A. A. and Zeller, G. and Carmichael, M. and Dimier, C. and Ferland, J. and Kandels, S. and Picheral, M. and Pisarev, S. and Poulain, J. and Tara Oceans, Coordinators and Acinas, S. G. and Babin, M. and Bork, P. and Bowler, C. and de Vargas, C. and Guidi, L. and Hingamp, P. and Iudicone, D. and Karp-Boss, L. and Karsenti, E. and Ogata, H. and Pesant, S. and Speich, S. and Sullivan, M. B. and Wincker, P. and Sunagawa, S.},\r\n   title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome},\r\n   journal = {Cell},\r\n   volume = {179},\r\n   number = {5},\r\n   pages = {1068-1083 e21},\r\n   abstract = {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.},\r\n   keywords = {*Gene Expression Regulation\r\nGeography\r\n*Metagenome\r\nMicrobiota/genetics\r\nMolecular Sequence Annotation\r\n*Oceans and Seas\r\nRNA, Messenger/genetics/metabolism\r\nSeawater/microbiology\r\nTemperature\r\nTranscriptome/*genetics\r\nTara Oceans\r\nbiogeochemistry\r\ncommunity turnover\r\neco-systems biology\r\ngene expression change\r\nglobal ocean microbiome\r\nmetagenome\r\nmetatranscriptome\r\nmicrobial ecology\r\nocean warming},\r\n   ISSN = {1097-4172 (Electronic)\r\n0092-8674 (Linking)},\r\n   DOI = {10.1016/j.cell.2019.10.014},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31730850},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Ibarbalz, F. M., Henry, N., Brandao, M. C., Martini, S., Busseni, G., Byrne, H., Coelho, L. P., Endo, H., Gasol, J. M., Gregory, A. C., Mahe, F., Rigonato, J., Royo-Llonch, M., Salazar, G., Sanz-Saez, 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, C., 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., & Zinger, L.\n\n\n \n\n\n\n Cell, 179(5): 1084-1097 e21. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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 8 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN129,\r\n   author = {Ibarbalz, F. M. and Henry, N. and Brandao, M. C. and Martini, S. and Busseni, G. and Byrne, H. and Coelho, L. P. and Endo, H. and Gasol, J. M. and Gregory, A. C. and Mahe, F. and Rigonato, J. and Royo-Llonch, M. and Salazar, G. and Sanz-Saez, I. and Scalco, E. and Soviadan, D. and Zayed, A. A. and Zingone, A. and Labadie, K. and Ferland, J. and Marec, C. and Kandels, S. and Picheral, M. and Dimier, C. and Poulain, J. and Pisarev, S. and Carmichael, M. and Pesant, S. and Tara Oceans, Coordinators and Babin, M. and Boss, E. and Iudicone, D. and Jaillon, O. and Acinas, S. G. and Ogata, H. and Pelletier, E. and Stemmann, L. and Sullivan, M. B. and Sunagawa, S. and Bopp, L. and de Vargas, C. and Karp-Boss, L. and Wincker, P. and Lombard, F. and Bowler, C. and Zinger, L.},\r\n   title = {Global Trends in Marine Plankton Diversity across Kingdoms of Life},\r\n   journal = {Cell},\r\n   volume = {179},\r\n   number = {5},\r\n   pages = {1084-1097 e21},\r\n   abstract = {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 21(st) 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.},\r\n   keywords = {*Biodiversity\r\nGeography\r\nModels, Theoretical\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/*physiology\r\nSeawater/*microbiology\r\n*Tara Oceans\r\n*climate warming\r\n*high-throughput imaging\r\n*high-throughput sequencing\r\n*latitudinal diversity gradient\r\n*macroecology\r\n*plankton functional groups\r\n*temperature\r\n*trans-kingdom diversity},\r\n   ISSN = {1097-4172 (Electronic)\r\n0092-8674 (Linking)},\r\n   DOI = {10.1016/j.cell.2019.10.008},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31730851},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics.\n \n \n \n \n\n\n \n Castillo, Y. M., Mangot, J. F., Benites, L. F., Logares, R., Kuronishi, M., Ogata, H., Jaillon, O., Massana, R., Sebastian, M., & Vaque, D.\n\n\n \n\n\n\n Mol Ecol, 28(18): 4272-4289. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Assessing$ Paper\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

@article{RN140,\r\n   author = {Castillo, Y. M. and Mangot, J. F. and Benites, L. F. and Logares, R. and Kuronishi, M. and Ogata, H. and Jaillon, O. and Massana, R. and Sebastian, M. and Vaque, D.},\r\n   title = {Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics},\r\n   journal = {Mol Ecol},\r\n   volume = {28},\r\n   number = {18},\r\n   pages = {4272-4289},\r\n   abstract = {Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single-cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2-3 microm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single-cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity.},\r\n   keywords = {Base Sequence\r\nCells, Cultured\r\nContig Mapping\r\nEukaryotic Cells/*virology\r\nGenetic Variation\r\nGenome, Viral\r\n*Genomics\r\n*Oceans and Seas\r\nPhylogeography\r\n*Single-Cell Analysis\r\nViruses/*genetics\r\n*protists\r\n*single-cell genomics\r\n*uncultured stramenopiles\r\n*viral associations\r\n*virophages\r\n*viruses},\r\n   ISSN = {1365-294X (Electronic)\r\n0962-1083 (Linking)},\r\n   DOI = {10.1111/mec.15210},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31448836},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes.\n \n \n \n \n\n\n \n Benites, L. F., Poulton, N., Labadie, K., Sieracki, M. E., Grimsley, N., & Piganeau, G.\n\n\n \n\n\n\n Philos Trans R Soc Lond B Biol Sci, 374(1786): 20190089. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Single$ Paper\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

@article{RN136,\r\n   author = {Benites, L. F. and Poulton, N. and Labadie, K. and Sieracki, M. E. and Grimsley, N. and Piganeau, G.},\r\n   title = {Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes},\r\n   journal = {Philos Trans R Soc Lond B Biol Sci},\r\n   volume = {374},\r\n   number = {1786},\r\n   pages = {20190089},\r\n   abstract = {Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 microm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.},\r\n   keywords = {Chlorophyta/genetics/*physiology/virology\r\nDNA Viruses/*physiology\r\n*Genome\r\n*Tara-Oceans\r\n*cross-contamination\r\n*mating type\r\n*picoeukaryotes\r\n*single amplified genome\r\n*virus},\r\n   ISSN = {1471-2970 (Electronic)\r\n0962-8436 (Linking)},\r\n   DOI = {10.1098/rstb.2019.0089},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31587637},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \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'Alcala , M. R., Caputi, L., & Iudicone, D.\n\n\n \n\n\n\n Mol Biol Evol. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Meta-omics$ Paper\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

@article{RN145,\r\n   author = {Busseni, G. and Vieira, F. R. J. and Amato, A. and Pelletier, E. and Pierella Karlusich, J. J. and Ferrante, M. I. and Wincker, P. and Rogato, A. and Bowler, C. and Sanges, R. and Maiorano, L. and Chiurazzi, M. and d'Alcala, M. R. and Caputi, L. and Iudicone, D.},\r\n   title = {Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes},\r\n   journal = {Mol Biol Evol},\r\n   abstract = {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.},\r\n   ISSN = {1537-1719 (Electronic)\r\n0737-4038 (Linking)},\r\n   DOI = {10.1093/molbev/msz157},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31259367},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The Earth Is Small for \"Leviathans\": Long Distance Dispersal of Giant Viruses across Aquatic Environments.\n \n \n \n \n\n\n \n Li, Y., Endo, H., Gotoh, Y., Watai, H., Ogawa, N., Blanc-Mathieu, R., Yoshida, T., & Ogata, H.\n\n\n \n\n\n\n Microbes Environ, 34(3): 334-339. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN143,\r\n   author = {Li, Y. and Endo, H. and Gotoh, Y. and Watai, H. and Ogawa, N. and Blanc-Mathieu, R. and Yoshida, T. and Ogata, H.},\r\n   title = {The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments},\r\n   journal = {Microbes Environ},\r\n   volume = {34},\r\n   number = {3},\r\n   pages = {334-339},\r\n   abstract = {Giant viruses of 'Megaviridae' have the ability to widely disperse around the globe. We herein examined 'Megaviridae' communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.},\r\n   keywords = {DNA-Directed DNA Polymerase/genetics\r\n*Ecosystem\r\nFresh Water/virology\r\nGeography\r\nGiant Viruses/classification/genetics/isolation & purification/*physiology\r\nMetagenome\r\nPhylogeny\r\nSeawater/virology\r\nViral Proteins/genetics\r\n*Water Microbiology\r\nDNA polymerase\r\nMegaprimer\r\nMimiviridae\r\nrichness\r\n'Megaviridae'},\r\n   ISSN = {1347-4405 (Electronic)\r\n1342-6311 (Linking)},\r\n   DOI = {10.1264/jsme2.ME19037},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31378760},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Sieracki, M. E., Poulton, N. J., Jaillon, O., Wincker, P., de Vargas, C., Rubinat-Ripoll, L., Stepanauskas, R., Logares, R., & Massana, R.\n\n\n \n\n\n\n Sci Rep, 9(1): 6025. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Single$ Paper\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

@article{RN153,\r\n   author = {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.},\r\n   title = {Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems},\r\n   journal = {Sci Rep},\r\n   volume = {9},\r\n   number = {1},\r\n   pages = {6025},\r\n   abstract = {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 degrees N to 20 degrees 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.},\r\n   keywords = {Biodiversity\r\nDNA/genetics\r\nEcosystem\r\nEukaryota/genetics\r\nGenomics/*methods\r\nIndian Ocean\r\nMediterranean Sea\r\nPhylogeny\r\nPlankton/*genetics\r\nRNA, Ribosomal, 18S/genetics\r\nSingle-Cell Analysis/*methods},\r\n   ISSN = {2045-2322 (Electronic)\r\n2045-2322 (Linking)},\r\n   DOI = {10.1038/s41598-019-42487-1},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30988337},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Gregory, A. C., Zayed, A. A., Conceicao-Neto, N., Temperton, B., Bolduc, B., Alberti, A., Ardyna, M., Arkhipova, K., Carmichael, M., Cruaud, C., Dimier, C., Dominguez-Huerta, G., Ferland, J., Kandels, S., Liu, Y., Marec, C., Pesant, S., Picheral, M., Pisarev, S., Poulain, J., Tremblay, J. E., Vik, D., Tara Oceans, C., Babin, M., Bowler, C., Culley, A. I., de Vargas, C., Dutilh, B. E., Iudicone, D., Karp-Boss, L., Roux, S., Sunagawa, S., Wincker, P., & Sullivan, M. B.\n\n\n \n\n\n\n Cell, 177(5): 1109-1123 e14. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Marine$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN150,\r\n   author = {Gregory, A. C. and Zayed, A. A. and Conceicao-Neto, N. and Temperton, B. and Bolduc, B. and Alberti, A. and Ardyna, M. and Arkhipova, K. and Carmichael, M. and Cruaud, C. and Dimier, C. and Dominguez-Huerta, G. and Ferland, J. and Kandels, S. and Liu, Y. and Marec, C. and Pesant, S. and Picheral, M. and Pisarev, S. and Poulain, J. and Tremblay, J. E. and Vik, D. and Tara Oceans, Coordinators and Babin, M. and Bowler, C. and Culley, A. I. and de Vargas, C. and Dutilh, B. E. and Iudicone, D. and Karp-Boss, L. and Roux, S. and Sunagawa, S. and Wincker, P. and Sullivan, M. B.},\r\n   title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole},\r\n   journal = {Cell},\r\n   volume = {177},\r\n   number = {5},\r\n   pages = {1109-1123 e14},\r\n   abstract = {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 approximately 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.},\r\n   keywords = {Aquatic Organisms/*genetics\r\n*Biodiversity\r\nDNA Viruses/*genetics\r\nDNA, Viral/*genetics\r\n*Metagenome\r\n*Water Microbiology\r\n*community ecology\r\n*diversity gradients\r\n*marine biology\r\n*metagenomics\r\n*population ecology\r\n*species\r\n*viruses},\r\n   ISSN = {1097-4172 (Electronic)\r\n0092-8674 (Linking)},\r\n   DOI = {10.1016/j.cell.2019.03.040},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/31031001},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 Caputi, L., Carradec, Q., Eveillard, D., Kirilovsky, A., Pelletier, E., Pierella Karlusich, J. J., Vieira, F., Villar, E., Chaffron, S., Malviya, S., Scalco, E., Acinas, S., Alberti, A., Aury, J., Benoiston, A., Bertrand, A., Biard, T., Bittner, L., Boccara, M., & Weissenbach, J.\n\n\n \n\n\n\n Global Biogeochemical Cycles, 33. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN242,\r\n   author = {Caputi, Luigi and Carradec, Quentin and Eveillard, Damien and Kirilovsky, Amos and Pelletier, Eric and Pierella Karlusich, Juan José and Vieira, Fabio and Villar, Emilie and Chaffron, Samuel and Malviya, Shruti and Scalco, Eleonora and Acinas, Silvia and Alberti, Adriana and Aury, Jean-Marc and Benoiston, Anne-Sophie and Bertrand, Alexis and Biard, Tristan and Bittner, Lucie and Boccara, Martine and Weissenbach, Jean},\r\n   title = {Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems},\r\n   journal = {Global Biogeochemical Cycles},\r\n   volume = {33},\r\n   DOI = {10.1029/2018GB006022},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Mixotrophic protists display contrasted biogeographies in the global ocean.\n \n \n \n \n\n\n \n Faure, E., Not, F., Benoiston, A. S., Labadie, K., Bittner, L., & Ayata, S. D.\n\n\n \n\n\n\n ISME J, 13(4): 1072-1083. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Mixotrophic$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN125,\r\n   author = {Faure, E. and Not, F. and Benoiston, A. S. and Labadie, K. and Bittner, L. and Ayata, S. D.},\r\n   title = {Mixotrophic protists display contrasted biogeographies in the global ocean},\r\n   journal = {ISME J},\r\n   volume = {13},\r\n   number = {4},\r\n   pages = {1072-1083},\r\n   abstract = {Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.},\r\n   keywords = {Autotrophic Processes\r\nEukaryota/*classification/genetics/isolation & purification\r\nHeterotrophic Processes\r\nOceans and Seas\r\nPhylogeography\r\nPlankton/classification/genetics/isolation & purification\r\nSymbiosis},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/s41396-018-0340-5},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30643201},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Arif, M., Gauthier, J., Sugier, K., Iudicone, D., Jaillon, O., Wincker, P., Peterlongo, P., & Madoui, M. A.\n\n\n \n\n\n\n Mol Ecol Resour, 19(2): 526-535. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Discovering$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN160,\r\n   author = {Arif, M. and Gauthier, J. and Sugier, K. and Iudicone, D. and Jaillon, O. and Wincker, P. and Peterlongo, P. and Madoui, M. A.},\r\n   title = {Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea},\r\n   journal = {Mol Ecol Resour},\r\n   volume = {19},\r\n   number = {2},\r\n   pages = {526-535},\r\n   abstract = {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/).},\r\n   keywords = {Animals\r\nAquatic Organisms/*classification/genetics\r\nAtlantic Ocean\r\n*Genetic Markers\r\nGenetics, Population/*methods\r\nGenotyping Techniques/*methods\r\nMediterranean Sea\r\nMetagenomics/*methods\r\nPlankton/*genetics},\r\n   ISSN = {1755-0998 (Electronic)\r\n1755-098X (Linking)},\r\n   DOI = {10.1111/1755-0998.12985},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30575285},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa.\n \n \n \n \n\n\n \n Cornejo-Castillo, F. M., Munoz-Marin, M. D. C., Turk-Kubo, K. A., Royo-Llonch, M., Farnelid, H., Acinas, S. G., & Zehr, J. P.\n\n\n \n\n\n\n Environ Microbiol, 21(1): 111-124. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"UCYN-A3,$ Paper\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\n\n

@article{RN163,\r\n   author = {Cornejo-Castillo, F. M. and Munoz-Marin, M. D. C. and Turk-Kubo, K. A. and Royo-Llonch, M. and Farnelid, H. and Acinas, S. G. and Zehr, J. P.},\r\n   title = {UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa},\r\n   journal = {Environ Microbiol},\r\n   volume = {21},\r\n   number = {1},\r\n   pages = {111-124},\r\n   abstract = {The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.},\r\n   keywords = {Bacterial Proteins/genetics/metabolism\r\nCyanobacteria/classification/genetics/*isolation & purification/*metabolism\r\nDNA, Bacterial/genetics\r\nHaptophyta/microbiology/physiology\r\nHawaii\r\n*Nitrogen Fixation\r\nNitrogenase/genetics/metabolism\r\nOceans and Seas\r\nPhylogeny\r\nRNA, Ribosomal, 16S/genetics\r\nSeawater/microbiology\r\nSymbiosis},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.14429},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30255541},\r\n   year = {2019},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2018\n \n \n (20)\n \n \n

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\n \n\n \n \n \n \n \n Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.\n \n \n \n\n\n \n Li, Y., Hingamp, P., Watai, H., Endo, H., Yoshida, T., & Ogata, H.\n\n\n \n\n\n\n Viruses, 10: 496. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN241,\r\n   author = {Li, Yanze and Hingamp, Pascal and Watai, Hiroyasu and Endo, Hisashi and Yoshida, Takashi and Ogata, Hiroyuki},\r\n   title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters},\r\n   journal = {Viruses},\r\n   volume = {10},\r\n   pages = {496},\r\n   DOI = {10.3390/v10090496},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Clade-specific diversification dynamics of marine diatoms since the Jurassic.\n \n \n \n \n\n\n \n Lewitus, E., Bittner, L., Malviya, S., Bowler, C., & Morlon, H.\n\n\n \n\n\n\n Nat Ecol Evol, 2(11): 1715-1723. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Clade-specific$ Paper\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

@article{RN101,\r\n   author = {Lewitus, E. and Bittner, L. and Malviya, S. and Bowler, C. and Morlon, H.},\r\n   title = {Clade-specific diversification dynamics of marine diatoms since the Jurassic},\r\n   journal = {Nat Ecol Evol},\r\n   volume = {2},\r\n   number = {11},\r\n   pages = {1715-1723},\r\n   abstract = {Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO2) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.},\r\n   keywords = {*Biodiversity\r\nCarbon Dioxide/chemistry\r\nClimate Change\r\nDNA Barcoding, Taxonomic\r\nDiatoms/*classification\r\nMicrobial Interactions\r\nOceans and Seas\r\n*Phylogeny\r\nPhytoplankton/classification/*physiology\r\nSilicon Dioxide/chemistry},\r\n   ISSN = {2397-334X (Electronic)\r\n2397-334X (Linking)},\r\n   DOI = {10.1038/s41559-018-0691-3},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30349092},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): Too much for one species?.\n \n \n \n\n\n \n Benzoni, F., Arrigoni, R., Berumen, M., Taviani, M., Bongaerts, P., & Frade, P.\n\n\n \n\n\n\n Zootaxa, 4471: 473–492. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN240,\r\n   author = {Benzoni, Francesca and Arrigoni, Roberto and Berumen, Michael and Taviani, Marco and Bongaerts, Pim and Frade, Pedro},\r\n   title = {Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): Too much for one species?},\r\n   journal = {Zootaxa},\r\n   volume = {4471},\r\n   pages = {473–492},\r\n   DOI = {10.11646/zootaxa.4471.3.3},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Decelle, J., Carradec, Q., Pochon, X., Henry, N., Romac, S., Mahe, F., Dunthorn, M., Kourlaiev, A., Voolstra, C. R., Wincker, P., & de Vargas, C.\n\n\n \n\n\n\n Curr Biol, 28(22): 3625-3633 e3. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Worldwide$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN99,\r\n   author = {Decelle, J. and Carradec, Q. and Pochon, X. and Henry, N. and Romac, S. and Mahe, F. and Dunthorn, M. and Kourlaiev, A. and Voolstra, C. R. and Wincker, P. and de Vargas, C.},\r\n   title = {Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean},\r\n   journal = {Curr Biol},\r\n   volume = {28},\r\n   number = {22},\r\n   pages = {3625-3633 e3},\r\n   abstract = {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.},\r\n   keywords = {Animals\r\n*Biodiversity\r\n*Biological Evolution\r\n*Coral Reefs\r\nDNA, Protozoan/analysis/genetics\r\nDinoflagellida/classification/genetics/*physiology\r\nGene Expression Profiling\r\nGenetic Markers\r\nGenetic Variation\r\n*Symbiosis\r\n*Symbiodinium\r\n*Tara Oceans\r\n*marine plankton\r\n*metabarcoding\r\n*metatranscriptomics\r\n*open ocean\r\n*phytoplankton},\r\n   ISSN = {1879-0445 (Electronic)\r\n0960-9822 (Linking)},\r\n   DOI = {10.1016/j.cub.2018.09.024},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30416058},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Coral responses to a repeat bleaching event in Mayotte in 2010.\n \n \n \n \n\n\n \n Obura, D. O., Bigot, L., & Benzoni, F.\n\n\n \n\n\n\n PeerJ, 6: e5305. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Coral$ Paper\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

@article{RN123,\r\n   author = {Obura, D. O. and Bigot, L. and Benzoni, F.},\r\n   title = {Coral responses to a repeat bleaching event in Mayotte in 2010},\r\n   journal = {PeerJ},\r\n   volume = {6},\r\n   pages = {e5305},\r\n   abstract = {Background: High sea surface temperatures resulted in widespread coral bleaching and mortality in Mayotte Island (northern Mozambique channel, Indian Ocean: 12.1 degrees S, 45.1 degrees E) in April-June 2010. Methods: Twenty three representative coral genera were sampled quantitatively for size class distributions during the peak of the bleaching event to measure its impact. Results: Fifty two percent of coral area was impacted, comprising 19.3% pale, 10.7% bleached, 4.8% partially dead and 17.5% recently dead. Acropora, the dominant genus, was the second most susceptible to bleaching (22%, pale and bleached) and mortality (32%, partially dead and dead), only exceeded by Pocillopora (32% and 47%, respectively). The majority of genera showed intermediate responses, and the least response was shown by Acanthastrea and Leptastrea (6% pale and bleached). A linear increase in bleaching susceptibility was found from small colonies (<2.5 cm, 83% unaffected) to large ones (>80 cm, 33% unaffected), across all genera surveyed. Maximum mortality in 2010 was estimated at 32% of coral area or biomass, compared to half that (16%), by colony abundance. Discussion: Mayotte reefs have displayed a high level of resilience to bleaching events in 1983, 1998 and the 2010 event reported here, and experienced a further bleaching event in 2016. However, prospects for continued resilience are uncertain as multiple threats are increasing: the rate of warming experienced (0.1 degrees C per decade) is some two to three times less than projected warming in coming decades, the interval between severe bleaching events has declined from 16 to 6 years, and evidence of chronic mortality from local human impacts is increasing. The study produced four recommendations for reducing bias when monitoring and assessing coral bleaching: coral colony size should be measured, unaffected colonies should be included in counts, quadrats or belt transects should be used and weighting coefficients in the calculation of indices should be used with caution.},\r\n   keywords = {Acropora\r\nClimate change\r\nCoral bleaching\r\nCoral reef\r\nEastern Africa\r\nNorthern Mozambique Channel\r\nRecovery\r\nResilience\r\nWestern Indian Ocean},\r\n   ISSN = {2167-8359 (Print)\r\n2167-8359 (Linking)},\r\n   DOI = {10.7717/peerj.5305},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/30083452},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n Background: High sea surface temperatures resulted in widespread coral bleaching and mortality in Mayotte Island (northern Mozambique channel, Indian Ocean: 12.1 degrees S, 45.1 degrees E) in April-June 2010. Methods: Twenty three representative coral genera were sampled quantitatively for size class distributions during the peak of the bleaching event to measure its impact. Results: Fifty two percent of coral area was impacted, comprising 19.3% pale, 10.7% bleached, 4.8% partially dead and 17.5% recently dead. Acropora, the dominant genus, was the second most susceptible to bleaching (22%, pale and bleached) and mortality (32%, partially dead and dead), only exceeded by Pocillopora (32% and 47%, respectively). The majority of genera showed intermediate responses, and the least response was shown by Acanthastrea and Leptastrea (6% pale and bleached). A linear increase in bleaching susceptibility was found from small colonies (<2.5 cm, 83% unaffected) to large ones (>80 cm, 33% unaffected), across all genera surveyed. Maximum mortality in 2010 was estimated at 32% of coral area or biomass, compared to half that (16%), by colony abundance. Discussion: Mayotte reefs have displayed a high level of resilience to bleaching events in 1983, 1998 and the 2010 event reported here, and experienced a further bleaching event in 2016. However, prospects for continued resilience are uncertain as multiple threats are increasing: the rate of warming experienced (0.1 degrees C per decade) is some two to three times less than projected warming in coming decades, the interval between severe bleaching events has declined from 16 to 6 years, and evidence of chronic mortality from local human impacts is increasing. The study produced four recommendations for reducing bias when monitoring and assessing coral bleaching: coral colony size should be measured, unaffected colonies should be included in counts, quadrats or belt transects should be used and weighting coefficients in the calculation of indices should be used with caution.\n

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\n \n\n \n \n \n \n \n \n Ubiquitous abundance distribution of non-dominant plankton across the global ocean.\n \n \n \n \n\n\n \n Ser-Giacomi, E., Zinger, L., Malviya, S., De Vargas, C., Karsenti, E., Bowler, C., & De Monte, S.\n\n\n \n\n\n\n Nat Ecol Evol, 2(8): 1243-1249. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Ubiquitous$ Paper\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

@article{RN105,\r\n   author = {Ser-Giacomi, E. and Zinger, L. and Malviya, S. and De Vargas, C. and Karsenti, E. and Bowler, C. and De Monte, S.},\r\n   title = {Ubiquitous abundance distribution of non-dominant plankton across the global ocean},\r\n   journal = {Nat Ecol Evol},\r\n   volume = {2},\r\n   number = {8},\r\n   pages = {1243-1249},\r\n   abstract = {Marine plankton populate 70% of Earth's surface, providing the energy that fuels ocean food webs and contributing to global biogeochemical cycles. Plankton communities are extremely diverse and geographically variable, and are overwhelmingly composed of low-abundance species. The role of this rare biosphere and its ecological underpinnings are however still unclear. Here, we analyse the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and use an adaptive algorithm to explore how metabarcoding-based abundance distributions vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant operational taxonomic units, which comprise over 99% of local richness, is commonly governed by a power-law. Despite the high spatial turnover in species composition, the power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Such striking regularity suggests that the assembly of plankton communities in the dynamic and highly variable ocean environment is governed by large-scale ubiquitous processes. Understanding their origin and impact on plankton ecology will be important for evaluating the resilience of marine biodiversity in a changing ocean.},\r\n   keywords = {*Algorithms\r\nDNA Barcoding, Taxonomic\r\n*Models, Theoretical\r\nOceans and Seas\r\nPlankton/*genetics},\r\n   ISSN = {2397-334X (Electronic)\r\n2397-334X (Linking)},\r\n   DOI = {10.1038/s41559-018-0587-2},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29915345},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The Ocean Gene Atlas: exploring the biogeography of plankton genes online.\n \n \n \n \n\n\n \n Villar, E., Vannier, T., Vernette, C., Lescot, M., Cuenca, M., Alexandre, A., Bachelerie, P., Rosnet, T., Pelletier, E., Sunagawa, S., & Hingamp, P.\n\n\n \n\n\n\n Nucleic Acids Res, 46(W1): W289-W295. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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

@article{RN107,\r\n   author = {Villar, E. and Vannier, T. and Vernette, C. and Lescot, M. and Cuenca, M. and Alexandre, A. and Bachelerie, P. and Rosnet, T. and Pelletier, E. and Sunagawa, S. and Hingamp, P.},\r\n   title = {The Ocean Gene Atlas: exploring the biogeography of plankton genes online},\r\n   journal = {Nucleic Acids Res},\r\n   volume = {46},\r\n   number = {W1},\r\n   pages = {W289-W295},\r\n   abstract = {The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.},\r\n   keywords = {Aquatic Organisms/genetics\r\nBiodiversity\r\n*Ecosystem\r\n*Internet\r\nOceans and Seas\r\nPhylogeography\r\nPlankton/*genetics\r\n*Software},\r\n   ISSN = {1362-4962 (Electronic)\r\n0305-1048 (Linking)},\r\n   DOI = {10.1093/nar/gky376},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29788376},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms.\n \n \n \n \n\n\n \n Kazamia, E., Sutak, R., Paz-Yepes, J., Dorrell, R. G., Vieira, F. R. J., Mach, J., Morrissey, J., Leon, S., Lam, F., Pelletier, E., Camadro, J. M., Bowler, C., & Lesuisse, E.\n\n\n \n\n\n\n Sci Adv, 4(5): eaar4536. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Endocytosis-mediated$ Paper\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

@article{RN108,\r\n   author = {Kazamia, E. and Sutak, R. and Paz-Yepes, J. and Dorrell, R. G. and Vieira, F. R. J. and Mach, J. and Morrissey, J. and Leon, S. and Lam, F. and Pelletier, E. and Camadro, J. M. and Bowler, C. and Lesuisse, E.},\r\n   title = {Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms},\r\n   journal = {Sci Adv},\r\n   volume = {4},\r\n   number = {5},\r\n   pages = {eaar4536},\r\n   abstract = {Phytoplankton growth is limited in vast oceanic regions by the low bioavailability of iron. Iron fertilization often results in diatom blooms, yet the physiological underpinnings for how diatoms survive in chronically iron-limited waters and outcompete other phytoplankton when iron becomes available are unresolved. We show that some diatoms can use siderophore-bound iron, and exhibit a species-specific recognition for siderophore types. In Phaeodactylum tricornutum, hydroxamate siderophores are taken up without previous reduction by a high-affinity mechanism that involves binding to the cell surface followed by endocytosis-mediated uptake and delivery to the chloroplast. The affinity recorded is the highest ever described for an iron transport system in any eukaryotic cell. Collectively, our observations suggest that there are likely a variety of iron uptake mechanisms in diatoms besides the well-established reductive mechanism. We show that iron starvation-induced protein 1 (ISIP1) plays an important role in the uptake of siderophores, and through bioinformatics analyses we deduce that this protein is largely diatom-specific. We quantify expression of ISIP1 in the global ocean by querying the Tara Oceans atlas of eukaryotic genes and show a link between the abundance and distribution of diatom-associated ISIP1 with ocean provinces defined by chronic iron starvation.},\r\n   keywords = {Aquatic Organisms/metabolism\r\nChloroplasts/metabolism\r\nDiatoms/*physiology\r\n*Endocytosis\r\nGene Knockdown Techniques\r\nIron/*metabolism\r\nProtein Transport\r\nSiderophores/*metabolism\r\nSpecies Specificity},\r\n   ISSN = {2375-2548 (Electronic)\r\n2375-2548 (Linking)},\r\n   DOI = {10.1126/sciadv.aar4536},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29774236},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean.\n \n \n \n\n\n \n Arrigoni, R., Berumen, M., Stolarski, J., Terraneo, T. I., & Benzoni, F.\n\n\n \n\n\n\n Cladistics, 35. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN239,\r\n   author = {Arrigoni, Roberto and Berumen, Michael and Stolarski, Jarosław and Terraneo, Tullia Isotta and Benzoni, Francesca},\r\n   title = {Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean},\r\n   journal = {Cladistics},\r\n   volume = {35},\r\n   DOI = {10.1111/cla.12346},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Taxon Richness of \"Megaviridae\" Exceeds those of Bacteria and Archaea in the Ocean.\n \n \n \n \n\n\n \n Mihara, T., Koyano, H., Hingamp, P., Grimsley, N., Goto, S., & Ogata, H.\n\n\n \n\n\n\n Microbes Environ, 33(2): 162-171. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Taxon$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

@article{RN122,\r\n   author = {Mihara, T. and Koyano, H. and Hingamp, P. and Grimsley, N. and Goto, S. and Ogata, H.},\r\n   title = {Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean},\r\n   journal = {Microbes Environ},\r\n   volume = {33},\r\n   number = {2},\r\n   pages = {162-171},\r\n   abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early "Big-Bang" radiation of the eukaryotic tree of life.},\r\n   keywords = {Archaea/*classification/genetics\r\nBacteria/*classification/genetics\r\n*Biodiversity\r\nDatabases, Genetic\r\nEvolution, Molecular\r\nGiant Viruses/*classification/genetics\r\nMetagenomics\r\n*Oceans and Seas\r\n*Phylogeny\r\nRNA Polymerase II/genetics\r\nMegaviridae\r\nMimiviridae\r\nRNA polymerase\r\nocean metagenome\r\nspecies richness},\r\n   ISSN = {1347-4405 (Electronic)\r\n1342-6311 (Linking)},\r\n   DOI = {10.1264/jsme2.ME17203},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29806626},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export.\n \n \n \n \n\n\n \n Leblanc, K., Queguiner, B., Diaz, F., Cornet, V., Michel-Rodriguez, M., Durrieu de Madron, X., Bowler, C., Malviya, S., Thyssen, M., Gregori, G., Rembauville, M., Grosso, O., Poulain, J., de Vargas, C., Pujo-Pay, M., & Conan, P.\n\n\n \n\n\n\n Nat Commun, 9(1): 953. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Nanoplanktonic$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN111,\r\n   author = {Leblanc, K. and Queguiner, B. and Diaz, F. and Cornet, V. and Michel-Rodriguez, M. and Durrieu de Madron, X. and Bowler, C. and Malviya, S. and Thyssen, M. and Gregori, G. and Rembauville, M. and Grosso, O. and Poulain, J. and de Vargas, C. and Pujo-Pay, M. and Conan, P.},\r\n   title = {Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export},\r\n   journal = {Nat Commun},\r\n   volume = {9},\r\n   number = {1},\r\n   pages = {953},\r\n   abstract = {Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO2 on Earth. In oceanic models, they are typically represented as large (>20 microm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2-20 microm) and a few species even overlap with the picoplanktonic size-class (<2 microm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.},\r\n   keywords = {Biomass\r\nCarbon/*metabolism\r\nCell Count\r\nChlorophyll/metabolism\r\nDNA Barcoding, Taxonomic\r\nDiatoms/*physiology/ultrastructure\r\nGeography\r\nGeologic Sediments\r\nMediterranean Sea\r\nPhytoplankton/classification/*physiology/ultrastructure\r\n*Seasons},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/s41467-018-03376-9},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29507291},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Competition between Silicifiers and Non-silicifiers in the Past and Present Ocean and Its Evolutionary Impacts.\n \n \n \n \n\n\n \n Hendry, K. R., Marron, A. O., Vincent, F., Conley, D. J., Gehlen, M., Ibarbalz, F. M., Quéguiner, B., & Bowler, C.\n\n\n \n\n\n\n Frontiers in Marine Science, 5(22). 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Competition$ Paper\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 \n\n\n\n

@article{RN238,\r\n   author = {Hendry, Katharine R. and Marron, Alan O. and Vincent, Flora and Conley, Daniel J. and Gehlen, Marion and Ibarbalz, Federico M. and Quéguiner, Bernard and Bowler, Chris},\r\n   title = {Competition between Silicifiers and Non-silicifiers in the Past and Present Ocean and Its Evolutionary Impacts},\r\n   journal = {Frontiers in Marine Science},\r\n   volume = {5},\r\n   number = {22},\r\n   abstract = {Competition is a central part of the evolutionary process, and silicification is no exception: between biomineralized and non-biomineralized organisms, between siliceous and non-siliceous biomineralizing organisms, and between different silicifying groups. Here we discuss evolutionary competition at various scales, and how this has affected biogeochemical cycles of silicon, carbon, and other nutrients. Across geological time we examine how fossils, sediments, and isotopic geochemistry can provide evidence for the emergence and expansion of silica biomineralization in the ocean, and competition between silicifying organisms for silicic acid. Metagenomic data from marine environments can be used to illustrate evolutionary competition between groups of silicifying and non-silicifying marine organisms. Modern ecosystems also provide examples of arms races between silicifiers as predators and prey, and how silicification can be used to provide a competitive advantage for obtaining resources. Through studying the molecular biology of silicifying and non-silicifying species we can relate how they have responded to the competitive interactions that are observed, and how solutions have evolved through convergent evolutionary dynamics.},\r\n   keywords = {Diatoms,Silicifiers,radiolarians,Silicic acid transporters,Silicification},\r\n   ISSN = {2296-7745},\r\n   DOI = {10.3389/fmars.2018.00022},\r\n   url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00022},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria.\n \n \n \n \n\n\n \n Grebert, T., Dore, H., Partensky, F., Farrant, G. K., Boss, E. S., Picheral, M., Guidi, L., Pesant, S., Scanlan, D. J., Wincker, P., Acinas, S. G., Kehoe, D. M., & Garczarek, L.\n\n\n \n\n\n\n Proc Natl Acad Sci U S A, 115(9): E2010-E2019. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Light$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN112,\r\n   author = {Grebert, T. and Dore, H. and Partensky, F. and Farrant, G. K. and Boss, E. S. and Picheral, M. and Guidi, L. and Pesant, S. and Scanlan, D. J. and Wincker, P. and Acinas, S. G. and Kehoe, D. M. and Garczarek, L.},\r\n   title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},\r\n   journal = {Proc Natl Acad Sci U S A},\r\n   volume = {115},\r\n   number = {9},\r\n   pages = {E2010-E2019},\r\n   abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.},\r\n   keywords = {*Acclimatization\r\nChlorophyll/chemistry\r\nColor\r\nComputer Simulation\r\nCyanobacteria/*genetics\r\nEcosystem\r\nEcotype\r\nLight\r\nLikelihood Functions\r\nMetagenome\r\n*Oceans and Seas\r\nPhotosynthesis/physiology\r\nPhycobilisomes/*physiology\r\nPhylogeny\r\nPigmentation\r\nSeawater/*microbiology\r\nSynechococcus/*genetics\r\n*Tara Oceans\r\n*light quality\r\n*marine cyanobacteria\r\n*metagenomics\r\n*phycobilisome},\r\n   ISSN = {1091-6490 (Electronic)\r\n0027-8424 (Linking)},\r\n   DOI = {10.1073/pnas.1717069115},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29440402},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Neobodonids are dominant kinetoplastids in the global ocean.\n \n \n \n \n\n\n \n Flegontova, O., Flegontov, P., Malviya, S., Poulain, J., de Vargas, C., Bowler, C., Lukes, J., & Horak, A.\n\n\n \n\n\n\n Environ Microbiol, 20(2): 878-889. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Neobodonids$ Paper\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\n\n

@article{RN120,\r\n   author = {Flegontova, O. and Flegontov, P. and Malviya, S. and Poulain, J. and de Vargas, C. and Bowler, C. and Lukes, J. and Horak, A.},\r\n   title = {Neobodonids are dominant kinetoplastids in the global ocean},\r\n   journal = {Environ Microbiol},\r\n   volume = {20},\r\n   number = {2},\r\n   pages = {878-889},\r\n   abstract = {Kinetoplastid flagellates comprise basal mostly free-living bodonids and derived obligatory parasitic trypanosomatids, which belong to the best-studied protists. Due to their omnipresence in aquatic environments and soil, the bodonids are of ecological significance. Here, we present the first global survey of marine kinetoplastids and compare it with the strikingly different patterns of abundance and diversity in their sister clade, the diplonemids. Based on analysis of 18S rDNA V9 ribotypes obtained from 124 sites sampled during the Tara Oceans expedition, our results show generally low to moderate abundance and diversity of planktonic kinetoplastids. Although we have identified all major kinetoplastid lineages, 98% of kinetoplastid reads are represented by neobodonids, namely specimens of the Neobodo and Rhynchomonas genera, which make up 59% and 18% of all reads, respectively. Most kinetoplastids have small cell size (0.8-5 microm) and tend to be more abundant in the mesopelagic as compared to the euphotic zone. Some of the most abundant operational taxonomic units have distinct geographical distributions, and three novel putatively parasitic neobodonids were identified, along with their potential hosts.},\r\n   keywords = {Biodiversity\r\nDNA, Ribosomal/genetics\r\nKinetoplastida/*classification/*genetics\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/*genetics\r\nRNA, Ribosomal, 18S/genetics},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.14034},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29266706},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean.\n \n \n \n \n\n\n \n Vincent, F. J., Colin, S., Romac, S., Scalco, E., Bittner, L., Garcia, Y., Lopes, R. M., Dolan, J. R., Zingone, A., de Vargas, C., & Bowler, C.\n\n\n \n\n\n\n ISME J, 12(4): 1094-1108. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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

@article{RN118,\r\n   author = {Vincent, F. J. and Colin, S. and Romac, S. and Scalco, E. and Bittner, L. and Garcia, Y. and Lopes, R. M. and Dolan, J. R. and Zingone, A. and de Vargas, C. and Bowler, C.},\r\n   title = {The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean},\r\n   journal = {ISME J},\r\n   volume = {12},\r\n   number = {4},\r\n   pages = {1094-1108},\r\n   abstract = {Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.},\r\n   keywords = {*Ciliophora\r\nDiatoms/classification/cytology/genetics/*physiology\r\nHaplotypes\r\nHeterotrophic Processes\r\nOceans and Seas\r\nPhytoplankton/cytology/genetics/physiology\r\nSymbiosis},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/s41396-017-0029-1},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29348580},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.\n \n \n \n \n\n\n \n Yoshida, T., Nishimura, Y., Watai, H., Haruki, N., Morimoto, D., Kaneko, H., Honda, T., Yamamoto, K., Hingamp, P., Sako, Y., Goto, S., & Ogata, H.\n\n\n \n\n\n\n ISME J, 12(5): 1287-1295. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Locality$ Paper\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

@article{RN94,\r\n   author = {Yoshida, T. and Nishimura, Y. and Watai, H. and Haruki, N. and Morimoto, D. and Kaneko, H. and Honda, T. and Yamamoto, K. and Hingamp, P. and Sako, Y. and Goto, S. and Ogata, H.},\r\n   title = {Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan},\r\n   journal = {ISME J},\r\n   volume = {12},\r\n   number = {5},\r\n   pages = {1287-1295},\r\n   abstract = {Viruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts.},\r\n   keywords = {Bacteriophages/*genetics/metabolism\r\nCyanobacteria/virology\r\nGene Expression Profiling\r\n*Genome, Viral\r\nJapan\r\nMetagenome\r\nMetagenomics\r\nPeriodicity\r\nSeawater/*virology\r\nVirion/genetics},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/s41396-018-0052-x},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29382948},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Influence of diatom diversity on the ocean biological carbon pump.\n \n \n \n \n\n\n \n Tréguer, P., Bowler, C., Moriceau, B., Dutkiewicz, S., Gehlen, M., Aumont, O., Bittner, L., Dugdale, R., Finkel, Z., Iudicone, D., Jahn, O., Guidi, L., Lasbleiz, M., Leblanc, K., Levy, M., & Pondaven, P.\n\n\n \n\n\n\n Nature Geoscience, 11(1): 27-37. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Influence$ Paper\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

@article{RN237,\r\n   author = {Tréguer, Paul and Bowler, Chris and Moriceau, Brivaela and Dutkiewicz, Stephanie and Gehlen, Marion and Aumont, Olivier and Bittner, Lucie and Dugdale, Richard and Finkel, Zoe and Iudicone, Daniele and Jahn, Oliver and Guidi, Lionel and Lasbleiz, Marine and Leblanc, Karine and Levy, Marina and Pondaven, Philippe},\r\n   title = {Influence of diatom diversity on the ocean biological carbon pump},\r\n   journal = {Nature Geoscience},\r\n   volume = {11},\r\n   number = {1},\r\n   pages = {27-37},\r\n   abstract = {Diatoms sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.},\r\n   ISSN = {1752-0908},\r\n   DOI = {10.1038/s41561-017-0028-x},\r\n   url = {https://doi.org/10.1038/s41561-017-0028-x},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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. F., Poulain, J., Labadie, K., Logares, R., Sunagawa, S., de Berardinis, V., Salanoubat, M., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans, C., Pesant, S., Poulton, N., Stepanauskas, R., Bork, P., Bowler, C., Hingamp, P., Sullivan, M. B., Iudicone, D., Massana, R., Aury, J. M., Henrissat, B., Karsenti, E., Jaillon, O., Sieracki, M., de Vargas, C., & Wincker, P.\n\n\n \n\n\n\n Nat Commun, 9(1): 310. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Single-cell$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN92,\r\n   author = {Seeleuthner, Y. and Mondy, S. and Lombard, V. and Carradec, Q. and Pelletier, E. and Wessner, M. and Leconte, J. and Mangot, J. F. and Poulain, J. and Labadie, K. and Logares, R. and Sunagawa, S. and de Berardinis, V. and Salanoubat, M. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Tara Oceans, Coordinators and Pesant, S. and Poulton, N. and Stepanauskas, R. and Bork, P. and Bowler, C. and Hingamp, P. and Sullivan, M. B. and Iudicone, D. and Massana, R. and Aury, J. M. and Henrissat, B. and Karsenti, E. and Jaillon, O. and Sieracki, M. and de Vargas, C. and Wincker, P.},\r\n   title = {Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans},\r\n   journal = {Nat Commun},\r\n   volume = {9},\r\n   number = {1},\r\n   pages = {310},\r\n   abstract = {Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/s41467-017-02235-3},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29358710},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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. A., Meheust, R., Poulain, J., Romac, S., Richter, D. J., Yoshikawa, G., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans, C., Jaillon, O., Aury, J. M., Karsenti, E., Sullivan, M. B., Sunagawa, S., Bork, P., Not, F., Hingamp, P., Raes, J., Guidi, L., Ogata, H., de Vargas, C., Iudicone, D., Bowler, C., & Wincker, P.\n\n\n \n\n\n\n Nat Commun, 9(1): 373. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN116,\r\n   author = {Carradec, Q. and Pelletier, E. and Da Silva, C. and Alberti, A. and Seeleuthner, Y. and Blanc-Mathieu, R. and Lima-Mendez, G. and Rocha, F. and Tirichine, L. and Labadie, K. and Kirilovsky, A. and Bertrand, A. and Engelen, S. and Madoui, M. A. and Meheust, R. and Poulain, J. and Romac, S. and Richter, D. J. and Yoshikawa, G. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Tara Oceans, Coordinators and Jaillon, O. and Aury, J. M. and Karsenti, E. and Sullivan, M. B. and Sunagawa, S. and Bork, P. and Not, F. and Hingamp, P. and Raes, J. and Guidi, L. and Ogata, H. and de Vargas, C. and Iudicone, D. and Bowler, C. and Wincker, P.},\r\n   title = {A global ocean atlas of eukaryotic genes},\r\n   journal = {Nat Commun},\r\n   volume = {9},\r\n   number = {1},\r\n   pages = {373},\r\n   abstract = {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.},\r\n   keywords = {Amino Acid Sequence\r\nAnimals\r\n*Aquatic Organisms\r\nAtlases as Topic\r\nBacteria/classification/genetics\r\nBiodiversity\r\nEcosystem\r\nEukaryota/classification/*genetics\r\nEukaryotic Cells/cytology/*metabolism\r\n*Metagenome\r\nMetagenomics/methods\r\nOceans and Seas\r\n*Phylogeny\r\nPhytoplankton/classification/genetics\r\nSeawater\r\nViruses/classification/genetics\r\nZooplankton/classification/*genetics},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/s41467-017-02342-1},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29371626},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages.\n \n \n \n \n\n\n \n Morard, R., Garet-Delmas, M. J., Mahe, F., Romac, S., Poulain, J., Kucera, M., & de Vargas, C.\n\n\n \n\n\n\n Sci Rep, 8(1): 2539. 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Surface$ Paper\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\n\n

@article{RN90,\r\n   author = {Morard, R. and Garet-Delmas, M. J. and Mahe, F. and Romac, S. and Poulain, J. and Kucera, M. and de Vargas, C.},\r\n   title = {Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages},\r\n   journal = {Sci Rep},\r\n   volume = {8},\r\n   number = {1},\r\n   pages = {2539},\r\n   abstract = {Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009-2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 microm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.},\r\n   keywords = {Atlantic Ocean\r\n*Biodiversity\r\nDNA, Ribosomal/*genetics\r\nEcosystem\r\n*Foraminifera/classification/genetics\r\nHigh-Throughput Nucleotide Sequencing/*methods\r\nIndian Ocean\r\n*Plankton/classification/genetics\r\nRNA, Ribosomal, 18S/*genetics},\r\n   ISSN = {2045-2322 (Electronic)\r\n2045-2322 (Linking)},\r\n   DOI = {10.1038/s41598-018-20833-z},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29416071},\r\n   year = {2018},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2017\n \n \n (13)\n \n \n

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\n \n\n \n \n \n \n \n \n Pan-Arctic optical characteristics of colored dissolved organic matter: Tracing dissolved organic carbon in changing Arctic waters using satellite ocean color data.\n \n \n \n \n\n\n \n Matsuoka, A., Boss, E., Babin, M., Karp-Boss, L., Hafez, M., Chekalyuk, A., Proctor, C. W., Werdell, P. J., & Bricaud, A.\n\n\n \n\n\n\n Remote Sensing of Environment, 200: 89-101. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Pan-Arctic$ Paper\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

@article{RN236,\r\n   author = {Matsuoka, Atsushi and Boss, Emmanuel and Babin, Marcel and Karp-Boss, Lee and Hafez, Mark and Chekalyuk, Alex and Proctor, Christopher W. and Werdell, P. Jeremy and Bricaud, Annick},\r\n   title = {Pan-Arctic optical characteristics of colored dissolved organic matter: Tracing dissolved organic carbon in changing Arctic waters using satellite ocean color data},\r\n   journal = {Remote Sensing of Environment},\r\n   volume = {200},\r\n   pages = {89-101},\r\n   abstract = {Light absorption of the colored fraction of dissolved organic matter (CDOM) is a dominant optical component of the Arctic Ocean (AO). Here we show Pan-Arctic characteristics of CDOM light absorption for various Arctic regions covering both coastal and oceanic waters during the Tara Oceans Polar Circle expedition. The Siberian (or eastern) side of the AO is characterized by higher CDOM absorption values compared to the North American (or western) side. This is due to the difference in watersheds between the eastern and western sides of the AO and is consistent with an Arctic absorption database recently built by Matsuoka et al. (2014). A direct comparison between in situ and satellite data demonstrates that CDOM absorption is derived Arctic-wide from satellite ocean color data with an average uncertainty of 12% (root mean square error of 0.3m−1) using our previously published algorithm. For river-influenced coastal waters, we found a single and highly significant relationship between concentrations of dissolved organic carbon (DOC) and CDOM absorption (r2>0.94) covering major Arctic river mouths. By applying this in situ relationship to satellite-derived CDOM absorption, DOC concentrations in the surface waters are estimated for river-influenced coastal waters with an average uncertainty of 28%. Implications for the monitoring of DOC concentrations in Arctic coastal waters are discussed.},\r\n   keywords = {CDOM\r\nDOC\r\nOcean color\r\nArctic Ocean},\r\n   ISSN = {0034-4257},\r\n   DOI = {https://doi.org/10.1016/j.rse.2017.08.009},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S0034425717303632},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.\n \n \n \n \n\n\n \n Colin, S., Coelho, L. P., Sunagawa, S., Bowler, C., Karsenti, E., Bork, P., Pepperkok, R., & de Vargas, C.\n\n\n \n\n\n\n Elife, 6. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\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

@article{RN74,\r\n   author = {Colin, S. and Coelho, L. P. and Sunagawa, S. and Bowler, C. and Karsenti, E. and Bork, P. and Pepperkok, R. and de Vargas, C.},\r\n   title = {Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes},\r\n   journal = {Elife},\r\n   volume = {6},\r\n   abstract = {We present a 3D-fluorescence imaging and classification tool for high throughput analysis of microbial eukaryotes in environmental samples. It entails high-content feature extraction that permits accurate automated taxonomic classification and quantitative data about organism ultrastructures and interactions. Using plankton samples from the Tara Oceans expeditions, we validate its applicability to taxonomic profiling and ecosystem analyses, and discuss its potential for future integration of eukaryotic cell biology into evolutionary and ecological studies.},\r\n   keywords = {*Ecosystem\r\n*Environmental Microbiology\r\nEukaryota/classification/*cytology/*physiology\r\nImaging, Three-Dimensional/*methods\r\nOptical Imaging/*methods\r\n*Automated microscopy\r\n*Environmental cell biology\r\n*Machine learning\r\n*Marine plankton biodiversity\r\n*Microbial eukaryotes\r\n*Symbioses\r\n*cell biology\r\n*ecology},\r\n   ISSN = {2050-084X (Electronic)\r\n2050-084X (Linking)},\r\n   DOI = {10.7554/eLife.26066},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/29087936},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Biological and physical influences on marine snowfall at the equator.\n \n \n \n \n\n\n \n Kiko, R., Biastoch, A., Brandt, P., Cravatte, S., Hauss, H., Hummels, R., Kriest, I., Marin, F., McDonnell, A. M P, Oschlies, A., Picheral, M., Schwarzkopf, F. U., Thurnherr, A. M., & Stemmann, L.\n\n\n \n\n\n\n Nature Geoscience, 10(11): 852-858. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Biological$ Paper\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

@article{RN235,\r\n   author = {Kiko, R. and Biastoch, A. and Brandt, P. and Cravatte, S. and Hauss, H. and Hummels, R. and Kriest, I. and Marin, F. and McDonnell, A.  M  P and Oschlies, A. and Picheral, M. and Schwarzkopf, F. U. and Thurnherr, A. M. and Stemmann, L.},\r\n   title = {Biological and physical influences on marine snowfall at the equator},\r\n   journal = {Nature Geoscience},\r\n   volume = {10},\r\n   number = {11},\r\n   pages = {852-858},\r\n   abstract = {High primary productivity in the equatorial Atlantic and Pacific oceans is one of the key features of tropical ocean biogeochemistry and fuels a substantial flux of particulate matter towards the abyssal ocean. How biological processes and equatorial current dynamics shape the particle size distribution and flux, however, is poorly understood. Here we use high-resolution size-resolved particle imaging and Acoustic Doppler Current Profiler data to assess these influences in equatorial oceans. We find an increase in particle abundance and flux at depths of 300 to 600 m at the Atlantic and Pacific equator, a depth range to which zooplankton and nekton migrate vertically in a daily cycle. We attribute this particle maximum to faecal pellet production by these organisms. At depths of 1,000 to 4,000 m, we find that the particulate organic carbon flux is up to three times greater in the equatorial belt (1° S–1° N) than in off-equatorial regions. At 3,000 m, the flux is dominated by small particles less than 0.53 mm in diameter. The dominance of small particles seems to be caused by enhanced active and passive particle export in this region, as well as by the focusing of particles by deep eastward jets found at 2° N and 2° S. We thus suggest that zooplankton movements and ocean currents modulate the transfer of particulate carbon from the surface to the deep ocean.},\r\n   ISSN = {1752-0908},\r\n   DOI = {10.1038/ngeo3042},\r\n   url = {https://doi.org/10.1038/ngeo3042},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.\n \n \n \n \n\n\n \n Lopez-Escardo, D., Grau-Bove, X., Guillaumet-Adkins, A., Gut, M., Sieracki, M. E., & Ruiz-Trillo, I.\n\n\n \n\n\n\n Sci Rep, 7(1): 11025. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Evaluation$ Paper\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

@article{RN89,\r\n   author = {Lopez-Escardo, D. and Grau-Bove, X. and Guillaumet-Adkins, A. and Gut, M. and Sieracki, M. E. and Ruiz-Trillo, I.},\r\n   title = {Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis},\r\n   journal = {Sci Rep},\r\n   volume = {7},\r\n   number = {1},\r\n   pages = {11025},\r\n   abstract = {Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.},\r\n   keywords = {Choanoflagellata/classification/*genetics/*isolation & purification\r\nComputational Biology\r\nDNA, Protozoan/*genetics/*isolation & purification\r\nGenomics/*methods\r\nSingle-Cell Analysis/*methods\r\nWhole Genome Sequencing},\r\n   ISSN = {2045-2322 (Electronic)\r\n2045-2322 (Linking)},\r\n   DOI = {10.1038/s41598-017-11466-9},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28887541},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes.\n \n \n \n \n\n\n \n Royo-Llonch, M., Ferrera, I., Cornejo-Castillo, F. M., Sanchez, P., Salazar, G., Stepanauskas, R., Gonzalez, J. M., Sieracki, M. E., Speich, S., Stemmann, L., Pedros-Alio, C., & Acinas, S. G.\n\n\n \n\n\n\n Front Microbiol, 8: 1317. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN88,\r\n   author = {Royo-Llonch, M. and Ferrera, I. and Cornejo-Castillo, F. M. and Sanchez, P. and Salazar, G. and Stepanauskas, R. and Gonzalez, J. M. and Sieracki, M. E. and Speich, S. and Stemmann, L. and Pedros-Alio, C. and Acinas, S. G.},\r\n   title = {Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes},\r\n   journal = {Front Microbiol},\r\n   volume = {8},\r\n   pages = {1317},\r\n   abstract = {Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.},\r\n   keywords = {Bacteroidetes\r\nKordia\r\nMlsa\r\nSAGs\r\nproteorhodopsin},\r\n   ISSN = {1664-302X (Print)\r\n1664-302X (Linking)},\r\n   DOI = {10.3389/fmicb.2017.01317},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28790980},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \n Madoui, M. A., Poulain, J., Sugier, K., Wessner, M., Noel, B., Berline, L., Labadie, K., Cornils, A., Blanco-Bercial, L., Stemmann, L., Jamet, J. L., & Wincker, P.\n\n\n \n\n\n\n Mol Ecol, 26(17): 4467-4482. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"New$ Paper\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

@article{RN79,\r\n   author = {Madoui, M. A. and Poulain, J. and Sugier, K. and Wessner, M. and Noel, B. and Berline, L. and Labadie, K. and Cornils, A. and Blanco-Bercial, L. and Stemmann, L. and Jamet, J. L. and Wincker, P.},\r\n   title = {New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona},\r\n   journal = {Mol Ecol},\r\n   volume = {26},\r\n   number = {17},\r\n   pages = {4467-4482},\r\n   abstract = {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.},\r\n   keywords = {Animals\r\nCopepoda/*genetics\r\nGene Frequency\r\n*Genetics, Population\r\nMale\r\nMediterranean Sea\r\n*Selection, Genetic\r\nZooplankton\r\ngenome\r\nphylogeography\r\nselection},\r\n   ISSN = {1365-294X (Electronic)\r\n0962-1083 (Linking)},\r\n   DOI = {10.1111/mec.14214},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28636804},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The evolution of diatoms and their biogeochemical functions.\n \n \n \n \n\n\n \n Benoiston, A. S., Ibarbalz, F. M., Bittner, L., Guidi, L., Jahn, O., Dutkiewicz, S., & Bowler, C.\n\n\n \n\n\n\n Philos Trans R Soc Lond B Biol Sci, 372(1728). 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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

@article{RN87,\r\n   author = {Benoiston, A. S. and Ibarbalz, F. M. and Bittner, L. and Guidi, L. and Jahn, O. and Dutkiewicz, S. and Bowler, C.},\r\n   title = {The evolution of diatoms and their biogeochemical functions},\r\n   journal = {Philos Trans R Soc Lond B Biol Sci},\r\n   volume = {372},\r\n   number = {1728},\r\n   abstract = {In contemporary oceans diatoms are an important group of eukaryotic phytoplankton that typically dominate in upwelling regions and at high latitudes. They also make significant contributions to sporadic blooms that often occur in springtime. Recent surveys have revealed global information about their abundance and diversity, as well as their contributions to biogeochemical cycles, both as primary producers of organic material and as conduits facilitating the export of carbon and silicon to the ocean interior. Sequencing of diatom genomes is revealing the evolutionary underpinnings of their ecological success by examination of their gene repertoires and the mechanisms they use to adapt to environmental changes. The rise of the diatoms over the last hundred million years is similarly being explored through analysis of microfossils and biomarkers that can be traced through geological time, as well as their contributions to seafloor sediments and fossil fuel reserves. The current review aims to synthesize current information about the evolution and biogeochemical functions of diatoms as they rose to prominence in the global ocean.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.},\r\n   keywords = {*Biological Evolution\r\nCarbon/metabolism\r\nDiatoms/*physiology\r\nOceans and Seas\r\nPhytoplankton/*physiology\r\nbiogeochemistry\r\ncarbon export\r\ndiatom\r\ngenomics\r\ngeological record\r\nphotosynthesis},\r\n   ISSN = {1471-2970 (Electronic)\r\n0962-8436 (Linking)},\r\n   DOI = {10.1098/rstb.2016.0397},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28717023},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells.\n \n \n \n \n\n\n \n Fridman, S., Flores-Uribe, J., Larom, S., Alalouf, O., Liran, O., Yacoby, I., Salama, F., Bailleul, B., Rappaport, F., Ziv, T., Sharon, I., Cornejo-Castillo, F. M., Philosof, A., Dupont, C. L., Sanchez, P., Acinas, S. G., Rohwer, F. L., Lindell, D., & Beja, O.\n\n\n \n\n\n\n Nat Microbiol, 2(10): 1350-1357. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\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 \n\n\n\n

@article{RN76,\r\n   author = {Fridman, S. and Flores-Uribe, J. and Larom, S. and Alalouf, O. and Liran, O. and Yacoby, I. and Salama, F. and Bailleul, B. and Rappaport, F. and Ziv, T. and Sharon, I. and Cornejo-Castillo, F. M. and Philosof, A. and Dupont, C. L. and Sanchez, P. and Acinas, S. G. and Rohwer, F. L. and Lindell, D. and Beja, O.},\r\n   title = {A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells},\r\n   journal = {Nat Microbiol},\r\n   volume = {2},\r\n   number = {10},\r\n   pages = {1350-1357},\r\n   abstract = {Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples (1-4) , viral photosystem I (vPSI) genes have so far only been detected in environmental samples (5,6) . Here, we have used a targeted strategy to isolate a cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition (7) shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans.},\r\n   keywords = {Atlantic Ocean\r\nElectron Transport/*genetics\r\nGene Expression Regulation, Bacterial\r\nGenes, Bacterial/genetics\r\nGenes, Viral/genetics\r\nGenome, Viral/genetics\r\nMyoviridae/classification/*genetics/pathogenicity/ultrastructure\r\nPacific Ocean\r\nPhotosynthesis/genetics\r\nPhotosystem I Protein Complex/*genetics\r\nPhotosystem II Protein Complex/*genetics\r\nPhylogeny\r\nProchlorococcus/*genetics/*virology\r\nViral Proteins/genetics},\r\n   ISSN = {2058-5276 (Electronic)\r\n2058-5276 (Linking)},\r\n   DOI = {10.1038/s41564-017-0002-9},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28785078},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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. M., 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, T., Acinas, S. G., Royo-Llonch, M., Cornejo-Castillo, F. M., Logares, R., Fernandez-Gomez, 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, C., Pesant, S., Karsenti, E., & Wincker, P.\n\n\n \n\n\n\n Sci Data, 4: 170093. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Viral$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN77,\r\n   author = {Alberti, A. and Poulain, J. and Engelen, S. and Labadie, K. and Romac, S. and Ferrera, I. and Albini, G. and Aury, J. M. and Belser, C. and Bertrand, A. and Cruaud, C. and Da Silva, C. and Dossat, C. and Gavory, F. and Gas, S. and Guy, J. and Haquelle, M. and Jacoby, E. and Jaillon, O. and Lemainque, A. and Pelletier, E. and Samson, G. and Wessner, M. and Genoscope Technical, Team and Acinas, S. G. and Royo-Llonch, M. and Cornejo-Castillo, F. M. and Logares, R. and Fernandez-Gomez, B. and Bowler, C. and Cochrane, G. and Amid, C. and Hoopen, P. T. and De Vargas, C. and Grimsley, N. and Desgranges, E. and Kandels-Lewis, S. and Ogata, H. and Poulton, N. and Sieracki, M. E. and Stepanauskas, R. and Sullivan, M. B. and Brum, J. R. and Duhaime, M. B. and Poulos, B. T. and Hurwitz, B. L. and Tara Oceans Consortium, Coordinators and Pesant, S. and Karsenti, E. and Wincker, P.},\r\n   title = {Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition},\r\n   journal = {Sci Data},\r\n   volume = {4},\r\n   pages = {170093},\r\n   abstract = {A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.},\r\n   keywords = {Ecosystem\r\nGenomics\r\nNucleotides\r\nOceans and Seas\r\n*Plankton\r\n*Viruses},\r\n   ISSN = {2052-4463 (Electronic)\r\n2052-4463 (Linking)},\r\n   DOI = {10.1038/sdata.2017.93},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28763055},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation.\n \n \n \n\n\n \n Cózar, A., Marti, E., Duarte, C., Lomas, J., Sebille, E., Ballatore, T., Eguíluz, V., González-Gordillo, J., Pedrotti, M. L., Echevarría, F., Troublè, R., & Irigoien, X.\n\n\n \n\n\n\n Science Advances, 3: e1600582. 2017.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN234,\r\n   author = {Cózar, Andrés and Marti, Elisa and Duarte, Carlos and Lomas, Juan and Sebille, Erik and Ballatore, Thomas and Eguíluz, Víctor and González-Gordillo, Juan and Pedrotti, Maria Luiza and Echevarría, Fidel and Troublè, Romain and Irigoien, Xabier},\r\n   title = {The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation},\r\n   journal = {Science Advances},\r\n   volume = {3},\r\n   pages = {e1600582},\r\n   DOI = {10.1126/sciadv.1600582},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean.\n \n \n \n \n\n\n \n Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M. B., Goto, S., Ogata, H., & Yoshida, T.\n\n\n \n\n\n\n mSphere, 2(2). 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Environmental$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN86,\r\n   author = {Nishimura, Y. and Watai, H. and Honda, T. and Mihara, T. and Omae, K. and Roux, S. and Blanc-Mathieu, R. and Yamamoto, K. and Hingamp, P. and Sako, Y. and Sullivan, M. B. and Goto, S. and Ogata, H. and Yoshida, T.},\r\n   title = {Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean},\r\n   journal = {mSphere},\r\n   volume = {2},\r\n   number = {2},\r\n   abstract = {Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral "dark matter." However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.},\r\n   keywords = {genome\r\nmarine ecosystem\r\nmetabolism\r\nmetagenomics\r\nvirus},\r\n   ISSN = {2379-5042 (Print)\r\n2379-5042 (Linking)},\r\n   DOI = {10.1128/mSphere.00359-16},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28261669},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

\n\n\n

\n Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral \"dark matter.\" However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.\n

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\n \n\n \n \n \n \n \n \n Biogeography and diversity of Collodaria (Radiolaria) in the global ocean.\n \n \n \n \n\n\n \n Biard, T., Bigeard, E., Audic, S., Poulain, J., Gutierrez-Rodriguez, A., Pesant, S., Stemmann, L., & Not, F.\n\n\n \n\n\n\n ISME J, 11(6): 1331-1344. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Biogeography$ Paper\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\n\n

@article{RN81,\r\n   author = {Biard, T. and Bigeard, E. and Audic, S. and Poulain, J. and Gutierrez-Rodriguez, A. and Pesant, S. and Stemmann, L. and Not, F.},\r\n   title = {Biogeography and diversity of Collodaria (Radiolaria) in the global ocean},\r\n   journal = {ISME J},\r\n   volume = {11},\r\n   number = {6},\r\n   pages = {1331-1344},\r\n   abstract = {Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770+/-1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474+/-17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.},\r\n   keywords = {Animal Distribution\r\nAnimals\r\nDNA, Ribosomal/genetics\r\nGenetic Variation\r\n*Oceans and Seas\r\n*Phylogeny\r\nPlankton\r\nRNA, Ribosomal, 18S/genetics\r\nRhizaria/*genetics/*physiology},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2017.12},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/28338675},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\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 \n Arrigoni, R., Vacherie, B., Benzoni, F., Stefani, F., Karsenti, E., Jaillon, O., Not, F., Nunes, F., Payri, C., Wincker, P., & Barbe, V.\n\n\n \n\n\n\n Mol Ecol Resour, 17(5): 1054-1071. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\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 \n \n \n \n \n\n\n\n

@article{RN69,\r\n   author = {Arrigoni, R. and Vacherie, B. and Benzoni, F. and Stefani, F. and Karsenti, E. and Jaillon, O. and Not, F. and Nunes, F. and Payri, C. and Wincker, P. and Barbe, V.},\r\n   title = {A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications},\r\n   journal = {Mol Ecol Resour},\r\n   volume = {17},\r\n   number = {5},\r\n   pages = {1054-1071},\r\n   abstract = {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.},\r\n   keywords = {Animals\r\nAnthozoa/*classification/*genetics\r\nCluster Analysis\r\nDNA Barcoding, Taxonomic/*methods\r\nDNA, Ribosomal/chemistry/genetics\r\nGenes, rRNA\r\n*Genetic Variation\r\nNucleic Acid Conformation\r\nPhylogeny\r\nRNA, Ribosomal, 18S/genetics\r\nSequence Analysis, DNA\r\ncnidarians\r\ngene structure and function\r\nhard corals\r\nhypervariable region\r\nmolecular evolution\r\nsystematics},\r\n   ISSN = {1755-0998 (Electronic)\r\n1755-098X (Linking)},\r\n   DOI = {10.1111/1755-0998.12640},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27889948},\r\n   year = {2017},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2016\n \n \n (18)\n \n \n

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\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. M., de Vargas, C., Sieracki, M., Iudicone, D., Vaulot, D., Wincker, P., & Jaillon, O.\n\n\n \n\n\n\n Sci Rep, 6: 37900. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Survey$ Paper\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

@article{RN43,\r\n   author = {Vannier, T. and Leconte, J. and Seeleuthner, Y. and Mondy, S. and Pelletier, E. and Aury, J. M. and de Vargas, C. and Sieracki, M. and Iudicone, D. and Vaulot, D. and Wincker, P. and Jaillon, O.},\r\n   title = {Survey of the green picoalga Bathycoccus genomes in the global ocean},\r\n   journal = {Sci Rep},\r\n   volume = {6},\r\n   pages = {37900},\r\n   abstract = {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.},\r\n   keywords = {Chlorophyta/*genetics\r\nEcotype\r\nGenomics/methods\r\nMetagenome/*genetics\r\nMetagenomics/methods\r\nMicroalgae/*genetics\r\nOceans and Seas\r\nPhylogeny\r\nPhytoplankton/*genetics\r\nRNA, Ribosomal, 18S/genetics\r\nSeawater\r\nSurveys and Questionnaires},\r\n   ISSN = {2045-2322 (Electronic)\r\n2045-2322 (Linking)},\r\n   DOI = {10.1038/srep37900},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27901108},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Extreme Diversity of Diplonemid Eukaryotes in the Ocean.\n \n \n \n \n\n\n \n Flegontova, O., Flegontov, P., Malviya, S., Audic, S., Wincker, P., de Vargas, C., Bowler, C., Lukes, J., & Horak, A.\n\n\n \n\n\n\n Curr Biol, 26(22): 3060-3065. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Extreme$ Paper\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 \n \n \n\n\n\n

@article{RN44,\r\n   author = {Flegontova, O. and Flegontov, P. and Malviya, S. and Audic, S. and Wincker, P. and de Vargas, C. and Bowler, C. and Lukes, J. and Horak, A.},\r\n   title = {Extreme Diversity of Diplonemid Eukaryotes in the Ocean},\r\n   journal = {Curr Biol},\r\n   volume = {26},\r\n   number = {22},\r\n   pages = {3060-3065},\r\n   abstract = {The world's oceans represent by far the largest biome, with great importance for the global ecosystem [1-4]. The vast majority of ocean biomass and biodiversity is composed of microscopic plankton. Recent results from the Tara Oceans metabarcoding study revealed that a significant part of the plankton in the upper sunlit layer of the ocean is represented by an understudied group of heterotrophic excavate flagellates called diplonemids [5, 6]. We have analyzed the diversity and distribution patterns of diplonemid populations on the extended set of Tara Oceans V9 18S rDNA metabarcodes amplified from 850 size- fractionated plankton communities sampled across 123 globally distributed locations, for the first time also including samples from the mesopelagic zone, which spans the depth from about 200 to 1,000 meters. Diplonemids separate into four major clades, with the vast majority falling into the deep-sea pelagic diplonemid clade. Remarkably, diversity of this clade inferred from metabarcoding data surpasses even that of dinoflagellates, metazoans, and rhizarians, qualifying diplonemids as possibly the most diverse group of marine planktonic eukaryotes. Diplonemids display strong vertical separation between the photic and mesopelagic layers, with the majority of their relative abundance and diversity occurring in deeper waters. Globally, diplonemids display no apparent biogeographic structuring, with a few hyperabundant cosmopolitan operational taxonomic units (OTUs) dominating their communities. Our results suggest that the planktonic diplonemids are among the key heterotrophic players in the largest ecosystem of our biosphere, yet their roles in this ecosystem remain unknown.},\r\n   keywords = {Aquatic Organisms/physiology\r\n*Biodiversity\r\nDNA Barcoding, Taxonomic\r\n*Ecosystem\r\nEuglenozoa/*classification/genetics\r\nOceans and Seas\r\nPlankton/*classification/genetics\r\nRNA, Protozoan/genetics\r\nRNA, Ribosomal, 18S/genetics\r\nSequence Analysis, RNA\r\n*Tara Oceans\r\n*cosmopolitan\r\n*diplonemids\r\n*diversity\r\n*metabarcoding\r\n*plankton},\r\n   ISSN = {1879-0445 (Electronic)\r\n0960-9822 (Linking)},\r\n   DOI = {10.1016/j.cub.2016.09.031},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27875689},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans.\n \n \n \n \n\n\n \n Boccara, M., Fedala, Y., Bryan, C. V., Bailly-Bechet, M., Bowler, C., & Boccara, A. C.\n\n\n \n\n\n\n Biomed Opt Express, 7(9): 3736-3746. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Full-field$ Paper\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

@article{RN46,\r\n   author = {Boccara, M. and Fedala, Y. and Bryan, C. V. and Bailly-Bechet, M. and Bowler, C. and Boccara, A. C.},\r\n   title = {Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans},\r\n   journal = {Biomed Opt Express},\r\n   volume = {7},\r\n   number = {9},\r\n   pages = {3736-3746},\r\n   abstract = {There is a huge abundance of viruses and membrane vesicles in seawater. We describe a new full-field, incoherently illuminated, shot-noise limited, common-path interferometric detection method that we couple with the analysis of Brownian motion to detect, quantify, and differentiate biotic nanoparticles. We validated the method with calibrated nanoparticles and homogeneous DNA or RNA viruses. The smallest virus size that we characterized with a suitable signal-to-noise ratio was around 30 nm in diameter. Analysis of Brownian motions revealed anisotropic trajectories for myoviruses.We further applied the method for vesicles detection and for analysis of coastal and oligotrophic samples from Tara Oceans circumnavigation.},\r\n   keywords = {(010.0280) Remote sensing and sensors\r\n(110.3175) Interferometric imaging\r\n(120.5820) Scattering measurements\r\n(170.4580) Optical diagnostics for medicine},\r\n   ISSN = {2156-7085 (Print)\r\n2156-7085 (Linking)},\r\n   DOI = {10.1364/BOE.7.003736},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27699134},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species.\n \n \n \n \n\n\n \n Arrigoni, R., Berumen, M. L., Chen, C. A., Terraneo, T. I., Baird, A. H., Payri, C., & Benzoni, F.\n\n\n \n\n\n\n Mol Phylogenet Evol, 105: 146-159. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Species$ Paper\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

@article{RN68,\r\n   author = {Arrigoni, R. and Berumen, M. L. and Chen, C. A. and Terraneo, T. I. and Baird, A. H. and Payri, C. and Benzoni, F.},\r\n   title = {Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species},\r\n   journal = {Mol Phylogenet Evol},\r\n   volume = {105},\r\n   pages = {146-159},\r\n   abstract = {Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.},\r\n   keywords = {Animals\r\nAnthozoa/*classification/genetics\r\nComoros\r\nCoral Reefs\r\nIndian Ocean Islands\r\nPhylogeny\r\n*abgd\r\n*gmyc\r\n*Maldives\r\n*Mayotte\r\n*ptp\r\n*Red Sea},\r\n   ISSN = {1095-9513 (Electronic)\r\n1055-7903 (Linking)},\r\n   DOI = {10.1016/j.ympev.2016.08.023},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27593164},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n When forms meet genes: Revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus.\n \n \n \n\n\n \n Arrigoni, R., Benzoni, F., Huang, D., Fukami, H., Chen, C., Berumen, M., Hoogenboom, M., Thomson, D., Hoeksema, B., Budd, A., Zayasu, Y., Terraneo, T. I., Kitano, Y., & Baird, A.\n\n\n \n\n\n\n Contributions to zoology Bijdragen tot de dierkunde, 85: 387-422. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN232,\r\n   author = {Arrigoni, Roberto and Benzoni, Francesca and Huang, Danwei and Fukami, Hironobu and Chen, Chaolun and Berumen, Michael and Hoogenboom, Mia and Thomson, Damian and Hoeksema, Bert and Budd, Ann and Zayasu, Yuna and Terraneo, Tullia Isotta and Kitano, Yuko and Baird, Andrew},\r\n   title = {When forms meet genes: Revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus},\r\n   journal = {Contributions to zoology Bijdragen tot de dierkunde},\r\n   volume = {85},\r\n   pages = {387-422},\r\n   DOI = {10.1163/18759866-08504002},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \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., Vaque, D., Tara Oceans, C., Bork, P., Acinas, S. G., Wincker, P., & Sullivan, M. B.\n\n\n \n\n\n\n Nature, 537(7622): 689-693. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Ecogenomics$ Paper\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\n\n

@article{RN47,\r\n   author = {Roux, S. and Brum, J. R. and Dutilh, B. E. and Sunagawa, S. and Duhaime, M. B. and Loy, A. and Poulos, B. T. and Solonenko, N. and Lara, E. and Poulain, J. and Pesant, S. and Kandels-Lewis, S. and Dimier, C. and Picheral, M. and Searson, S. and Cruaud, C. and Alberti, A. and Duarte, C. M. and Gasol, J. M. and Vaque, D. and Tara Oceans, Coordinators and Bork, P. and Acinas, S. G. and Wincker, P. and Sullivan, M. B.},\r\n   title = {Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses},\r\n   journal = {Nature},\r\n   volume = {537},\r\n   number = {7622},\r\n   pages = {689-693},\r\n   abstract = {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.},\r\n   keywords = {DNA, Viral/analysis\r\nDatasets as Topic\r\nEcology\r\n*Ecosystem\r\nExpeditions\r\nGenes, Viral\r\n*Genome, Viral\r\nGeographic Mapping\r\nMetagenome\r\n*Metagenomics\r\nNitrogen Cycle\r\nOceans and Seas\r\nSeawater/*virology\r\nSulfur/metabolism\r\nViruses/*genetics/*isolation & purification/metabolism},\r\n   ISSN = {1476-4687 (Electronic)\r\n0028-0836 (Linking)},\r\n   DOI = {10.1038/nature19366},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27654921},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\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

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\n \n\n \n \n \n \n \n \n Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea.\n \n \n \n \n\n\n \n Terraneo, T. I., Benzoni, F., Arrigoni, R., & Berumen, M. L.\n\n\n \n\n\n\n Mol Phylogenet Evol, 102: 278-94. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Species$ Paper\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

@article{RN67,\r\n   author = {Terraneo, T. I. and Benzoni, F. and Arrigoni, R. and Berumen, M. L.},\r\n   title = {Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea},\r\n   journal = {Mol Phylogenet Evol},\r\n   volume = {102},\r\n   pages = {278-94},\r\n   abstract = {Variable skeletal morphology, genotype induced plasticity, and homoplasy of skeletal structures have presented major challenges for scleractinian coral taxonomy and systematics since the 18th century. Although the recent integration of genetic and micromorphological data is helping to clarify the taxonomic confusion within the order, phylogenetic relationships and species delimitation within most coral genera are still far from settled. In the present study, the species boundaries in the scleractinian coral genus Goniopora were investigated using 199 colonies from the Saudi Arabian Red Sea and sequencing of four molecular markers: the mitochondrial intergenic spacer between CytB and NAD2, the nuclear ribosomal ITS region, and two single-copy nuclear genes (ATPsbeta and CalM). DNA sequence data were analyzed using a variety of methods and exploratory species-delimitation tools. The results were broadly congruent in identifying five distinct molecular lineages within the sequenced Goniopora samples: G. somaliensis/G. savignyi, G. djiboutiensis/G. lobata, G. stokesi, G. albiconus/G. tenuidens, and G. minor/G. gracilis. Although the traditional macromorphological characters used to identify these nine morphospecies were not able to discriminate the obtained molecular clades, informative micromorphological and microstructural features (such as the micro-ornamentation and the arrangement of the columella) were recovered among the five lineages. Moreover, unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. This study represents the first attempt to identify species boundaries within Goniopora using a combined morpho-molecular approach. The obtained data establish a basis for future taxonomic revision of the genus, which should include colonies across its entire geographical distribution in the Indo-Pacific.},\r\n   keywords = {Animals\r\nAnthozoa/*classification/genetics\r\nCalmodulin/chemistry/genetics/metabolism\r\nCytochromes b/chemistry/genetics/metabolism\r\nDNA/chemistry/isolation & purification/metabolism\r\nHaplotypes\r\nIndian Ocean\r\nMitochondrial Proton-Translocating ATPases/chemistry/genetics/metabolism\r\nNADH Dehydrogenase/chemistry/genetics/metabolism\r\nPhylogeny\r\nSaudi Arabia\r\nSequence Analysis, DNA\r\n*abgd\r\n*DNA taxonomy\r\n*gmyc\r\n*Haplowebs\r\n*Integrative taxonomy\r\n*ptp},\r\n   ISSN = {1095-9513 (Electronic)\r\n1055-7903 (Linking)},\r\n   DOI = {10.1016/j.ympev.2016.06.003},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27321092},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria.\n \n \n \n \n\n\n \n Farrant, G. K., Dore, H., Cornejo-Castillo, F. M., Partensky, F., Ratin, M., Ostrowski, M., Pitt, F. D., Wincker, P., Scanlan, D. J., Iudicone, D., Acinas, S. G., & Garczarek, L.\n\n\n \n\n\n\n Proc Natl Acad Sci U S A, 113(24): E3365-74. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Delineating$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN51,\r\n   author = {Farrant, G. K. and Dore, H. and Cornejo-Castillo, F. M. and Partensky, F. and Ratin, M. and Ostrowski, M. and Pitt, F. D. and Wincker, P. and Scanlan, D. J. and Iudicone, D. and Acinas, S. G. and Garczarek, L.},\r\n   title = {Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria},\r\n   journal = {Proc Natl Acad Sci U S A},\r\n   volume = {113},\r\n   number = {24},\r\n   pages = {E3365-74},\r\n   abstract = {Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveiled within both genera, even for the most abundant and well-characterized clades, and 136 divergent petB sequences were successfully assembled from metagenomic reads, significantly enriching the reference database. We then defined Ecologically Significant Taxonomic Units (ESTUs)-that is, organisms belonging to the same clade and occupying a common oceanic niche. Three major ESTU assemblages were identified along the cruise transect for Prochlorococcus and eight for Synechococcus Although Prochlorococcus HLIIIA and HLIVA ESTUs codominated in iron-depleted areas of the Pacific Ocean, CRD1 and the yet-to-be cultured EnvB were the prevalent Synechococcus clades in this area, with three different CRD1 and EnvB ESTUs occupying distinct ecological niches with regard to iron availability and temperature. Sharp community shifts were also observed over short geographic distances-for example, around the Marquesas Islands or between southern Indian and Atlantic Oceans-pointing to a tight correlation between ESTU assemblages and specific physico-chemical parameters. Together, this study demonstrates that there is a previously overlooked, ecologically meaningful, fine-scale diversity within some currently defined picocyanobacterial ecotypes, bringing novel insights into the ecology, diversity, and biology of the two most abundant phototrophs on Earth.},\r\n   keywords = {*Aquatic Organisms/classification/genetics\r\nAtlantic Ocean\r\nBacterial Proteins/*genetics\r\n*Genetic Variation\r\nIndian Ocean\r\n*Prochlorococcus/classification/genetics\r\n*Synechococcus/classification/genetics\r\nProchlorococcus\r\nSynechococcus\r\nTara Oceans\r\nmetagenomics\r\nmolecular ecology},\r\n   ISSN = {1091-6490 (Electronic)\r\n0027-8424 (Linking)},\r\n   DOI = {10.1073/pnas.1524865113},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27302952},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Biogeochemical characteristics of a long-lived anticyclonic eddy in the eastern South Pacific Ocean.\n \n \n \n\n\n \n Cornejo-D'Ottone, M., Bravo, L., Ramos, M., Pizarro, O., Karstensen, J., Gallegos, M., Correa-Ramirez, M., Silva, N., Farias, L., & Karp-Boss, L.\n\n\n \n\n\n\n Biogeosciences, 13: 2971-2979. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN247,\r\n   author = {Cornejo-D'Ottone, Marcela and Bravo, Luis and Ramos, Marcel and Pizarro, Oscar and Karstensen, Johannes and Gallegos, Mauricio and Correa-Ramirez, Marco and Silva, Nelson and Farias, Laura and Karp-Boss, Lee},\r\n   title = {Biogeochemical characteristics of a long-lived anticyclonic eddy in the eastern South Pacific Ocean},\r\n   journal = {Biogeosciences},\r\n   volume = {13},\r\n   pages = {2971-2979},\r\n   DOI = {10.5194/bg-13-2971-2016},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Global genetic capacity for mixotrophy in marine picocyanobacteria.\n \n \n \n \n\n\n \n Yelton, A. P., Acinas, S. G., Sunagawa, S., Bork, P., Pedros-Alio, C., & Chisholm, S. W.\n\n\n \n\n\n\n ISME J, 10(12): 2946-2957. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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

@article{RN52,\r\n   author = {Yelton, A. P. and Acinas, S. G. and Sunagawa, S. and Bork, P. and Pedros-Alio, C. and Chisholm, S. W.},\r\n   title = {Global genetic capacity for mixotrophy in marine picocyanobacteria},\r\n   journal = {ISME J},\r\n   volume = {10},\r\n   number = {12},\r\n   pages = {2946-2957},\r\n   abstract = {The assimilation of organic nutrients by autotrophs, a form of mixotrophy, has been demonstrated in the globally abundant marine picocyanobacterial genera Prochlorococcus and Synechococcus. However, the range of compounds used and the distribution of organic compound uptake genes within picocyanobacteria are unknown. Here we analyze genomic and metagenomic data from around the world to determine the extent and distribution of mixotrophy in these phototrophs. Analysis of 49 Prochlorococcus and 18 Synechococcus isolate genomes reveals that all have the transporters necessary to take up amino acids, peptides and sugars. However, the number and type of transporters and associated catabolic genes differ between different phylogenetic groups, with low-light IV Prochlorococcus, and 5.1B, 5.2 and 5.3 Synechococcus strains having the largest number. Metagenomic data from 68 stations from the Tara Oceans expedition indicate that the genetic potential for mixotrophy in picocyanobacteria is globally distributed and differs between clades. Phylogenetic analyses indicate gradual organic nutrient transporter gene loss from the low-light IV to the high-light II Prochlorococcus. The phylogenetic differences in genetic capacity for mixotrophy, combined with the ubiquity of picocyanobacterial organic compound uptake genes suggests that mixotrophy has a more central role in picocyanobacterial ecology than was previously thought.},\r\n   keywords = {Genome, Bacterial\r\nGenomics\r\nOceans and Seas\r\nPhylogeny\r\nProchlorococcus/*genetics/isolation & purification/metabolism\r\nSeawater/*microbiology\r\nSynechococcus/*genetics/isolation & purification/metabolism},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2016.64},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27137127},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n In situ imaging reveals the biomass of giant protists in the global ocean.\n \n \n \n \n\n\n \n Biard, T., Stemmann, L., Picheral, M., Mayot, N., Vandromme, P., Hauss, H., Gorsky, G., Guidi, L., Kiko, R., & Not, F.\n\n\n \n\n\n\n Nature, 532(7600): 504-7. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"In$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN66,\r\n   author = {Biard, T. and Stemmann, L. and Picheral, M. and Mayot, N. and Vandromme, P. and Hauss, H. and Gorsky, G. and Guidi, L. and Kiko, R. and Not, F.},\r\n   title = {In situ imaging reveals the biomass of giant protists in the global ocean},\r\n   journal = {Nature},\r\n   volume = {532},\r\n   number = {7600},\r\n   pages = {504-7},\r\n   abstract = {Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 mum, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.},\r\n   keywords = {Animals\r\n*Biomass\r\n*Biota\r\nCarbon/metabolism\r\nCarbon Sequestration\r\nEarth, Planet\r\nMicroalgae/metabolism\r\n*Oceans and Seas\r\nPhotosynthesis\r\nRhizaria/classification/*isolation & purification/metabolism\r\nSeawater/chemistry\r\nSymbiosis\r\nZooplankton/classification/*isolation & purification/metabolism},\r\n   ISSN = {1476-4687 (Electronic)\r\n0028-0836 (Linking)},\r\n   DOI = {10.1038/nature17652},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27096373},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.\n \n \n \n \n\n\n \n Cornejo-Castillo, F. M., Cabello, A. M., Salazar, G., Sanchez-Baracaldo, P., Lima-Mendez, G., Hingamp, P., Alberti, A., Sunagawa, S., Bork, P., de Vargas, C., Raes, J., Bowler, C., Wincker, P., Zehr, J. P., Gasol, J. M., Massana, R., & Acinas, S. G.\n\n\n \n\n\n\n Nat Commun, 7: 11071. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Cyanobacterial$ Paper\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

@article{RN65,\r\n   author = {Cornejo-Castillo, F. M. and Cabello, A. M. and Salazar, G. and Sanchez-Baracaldo, P. and Lima-Mendez, G. and Hingamp, P. and Alberti, A. and Sunagawa, S. and Bork, P. and de Vargas, C. and Raes, J. and Bowler, C. and Wincker, P. and Zehr, J. P. and Gasol, J. M. and Massana, R. and Acinas, S. G.},\r\n   title = {Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton},\r\n   journal = {Nat Commun},\r\n   volume = {7},\r\n   pages = {11071},\r\n   abstract = {The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean. Both symbiotic systems are lineage specific and differ in the number of UCYN-A cells involved. Our analyses infer a streamlined genome expression towards nitrogen fixation in both UCYN-A lineages. Comparative genomics reveal a strong purifying selection in UCYN-A1 and UCYN-A2 with a diversification process approximately 91 Myr ago, in the late Cretaceous, after the low-nutrient regime period occurred during the Jurassic. These findings suggest that UCYN-A diversified in a co-evolutionary process, wherein their prymnesiophyte partners acted as a barrier driving an allopatric speciation of extant UCYN-A lineages.},\r\n   keywords = {Atlantic Ocean\r\n*Biological Evolution\r\nCyanobacteria/*genetics\r\nGenomics\r\nHaptophyta/*genetics\r\n*Nitrogen Fixation\r\nPhytoplankton/*genetics\r\nSeawater/*microbiology\r\n*Symbiosis},\r\n   ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n   DOI = {10.1038/ncomms11071},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/27002549},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Insights into global diatom distribution and diversity in the world's ocean.\n \n \n \n \n\n\n \n Malviya, S., Scalco, E., Audic, S., Vincent, F., Veluchamy, A., Poulain, J., Wincker, P., Iudicone, D., de Vargas, C., Bittner, L., Zingone, A., & Bowler, C.\n\n\n \n\n\n\n Proc Natl Acad Sci U S A, 113(11): E1516-25. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Insights$ Paper\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

@article{RN54,\r\n   author = {Malviya, S. and Scalco, E. and Audic, S. and Vincent, F. and Veluchamy, A. and Poulain, J. and Wincker, P. and Iudicone, D. and de Vargas, C. and Bittner, L. and Zingone, A. and Bowler, C.},\r\n   title = {Insights into global diatom distribution and diversity in the world's ocean},\r\n   journal = {Proc Natl Acad Sci U S A},\r\n   volume = {113},\r\n   number = {11},\r\n   pages = {E1516-25},\r\n   abstract = {Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of approximately 12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.},\r\n   keywords = {Aquatic Organisms\r\n*Biodiversity\r\nDNA, Ribosomal\r\nDatabases, Factual\r\nDiatoms/classification/*genetics\r\nEcosystem\r\nMicroscopy/methods\r\n*Oceans and Seas\r\nPhytoplankton\r\nReproducibility of Results\r\nTara Oceans\r\nbiodiversity\r\nchoke points\r\ndiatoms\r\nmetabarcoding},\r\n   ISSN = {1091-6490 (Electronic)\r\n0027-8424 (Linking)},\r\n   DOI = {10.1073/pnas.1509523113},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26929361},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Illuminating structural proteins in viral \"dark matter\" with metaproteomics.\n \n \n \n \n\n\n \n Brum, J. R., Ignacio-Espinoza, J. C., Kim, E. H., Trubl, G., Jones, R. M., Roux, S., VerBerkmoes, N. C., Rich, V. I., & Sullivan, M. B.\n\n\n \n\n\n\n Proc Natl Acad Sci U S A, 113(9): 2436-41. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Illuminating$ Paper\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

@article{RN64,\r\n   author = {Brum, J. R. and Ignacio-Espinoza, J. C. and Kim, E. H. and Trubl, G. and Jones, R. M. and Roux, S. and VerBerkmoes, N. C. and Rich, V. I. and Sullivan, M. B.},\r\n   title = {Illuminating structural proteins in viral "dark matter" with metaproteomics},\r\n   journal = {Proc Natl Acad Sci U S A},\r\n   volume = {113},\r\n   number = {9},\r\n   pages = {2436-41},\r\n   abstract = {Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.},\r\n   keywords = {Marine Biology\r\n*Proteomics\r\nViral Structural Proteins/*chemistry\r\nViruses/chemistry\r\nmarine\r\nproteins\r\nviruses},\r\n   ISSN = {1091-6490 (Electronic)\r\n0027-8424 (Linking)},\r\n   DOI = {10.1073/pnas.1525139113},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26884177},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\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 \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, c., 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., & Gorsky, G.\n\n\n \n\n\n\n Nature, 532(7600): 465-470. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Plankton$ Paper\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

@article{RN56,\r\n   author = {Guidi, L. and Chaffron, S. and Bittner, L. and Eveillard, D. and Larhlimi, A. and Roux, S. and Darzi, Y. and Audic, S. and Berline, L. and Brum, J. and Coelho, L. P. and Espinoza, J. C. I. and Malviya, S. and Sunagawa, S. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Poulain, J. and Searson, S. and Tara Oceans, coordinators and Stemmann, L. and Not, F. and Hingamp, P. and Speich, S. and Follows, M. and Karp-Boss, L. and Boss, E. and Ogata, H. and Pesant, S. and Weissenbach, J. and Wincker, P. and Acinas, S. G. and Bork, P. and de Vargas, C. and Iudicone, D. and Sullivan, M. B. and Raes, J. and Karsenti, E. and Bowler, C. and Gorsky, G.},\r\n   title = {Plankton networks driving carbon export in the oligotrophic ocean},\r\n   journal = {Nature},\r\n   volume = {532},\r\n   number = {7600},\r\n   pages = {465-470},\r\n   abstract = {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.},\r\n   keywords = {Aquatic Organisms/genetics/isolation & purification/*metabolism\r\nCarbon/*metabolism\r\nChlorophyll/metabolism\r\nDinoflagellida/genetics/isolation & purification/metabolism\r\n*Ecosystem\r\nExpeditions\r\nGenes, Bacterial\r\nGenes, Viral\r\nGeography\r\nOceans and Seas\r\nPhotosynthesis\r\nPlankton/genetics/isolation & purification/*metabolism\r\nSeawater/*chemistry/microbiology/parasitology\r\nSynechococcus/genetics/isolation & purification/metabolism/virology},\r\n   ISSN = {1476-4687 (Electronic)\r\n0028-0836 (Linking)},\r\n   DOI = {10.1038/nature16942},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26863193},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.).\n \n \n \n \n\n\n \n Mordret, S., Romac, S., Henry, N., Colin, S., Carmichael, M., Berney, C., Audic, S., Richter, D. J., Pochon, X., de Vargas, C., & Decelle, J.\n\n\n \n\n\n\n ISME J, 10(6): 1424-36. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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

@article{RN58,\r\n   author = {Mordret, S. and Romac, S. and Henry, N. and Colin, S. and Carmichael, M. and Berney, C. and Audic, S. and Richter, D. J. and Pochon, X. and de Vargas, C. and Decelle, J.},\r\n   title = {The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)},\r\n   journal = {ISME J},\r\n   volume = {10},\r\n   number = {6},\r\n   pages = {1424-36},\r\n   abstract = {Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.},\r\n   keywords = {Animals\r\n*Biodiversity\r\nBiological Evolution\r\nCiliophora/*genetics/physiology\r\nDNA Barcoding, Taxonomic\r\nDNA, Ribosomal/chemistry/genetics\r\nDinoflagellida/*genetics/physiology\r\nEcology\r\nEcosystem\r\nGenotype\r\nGeography\r\nHaplotypes\r\nMetagenomics\r\nOceans and Seas\r\nPhylogeny\r\n*Symbiosis},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2015.211},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26684730},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\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 \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. M., & Ogata, H.\n\n\n \n\n\n\n ISME J, 10(5): 1134-46. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Reverse$ Paper\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

@article{RN39,\r\n   author = {Lescot, M. and Hingamp, P. and Kojima, K. K. and Villar, E. and Romac, S. and Veluchamy, A. and Boccara, M. and Jaillon, O. and Iudicone, D. and Bowler, C. and Wincker, P. and Claverie, J. M. and Ogata, H.},\r\n   title = {Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages},\r\n   journal = {ISME J},\r\n   volume = {10},\r\n   number = {5},\r\n   pages = {1134-46},\r\n   abstract = {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 (>5 mum), 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.},\r\n   keywords = {Eukaryota/enzymology/genetics/isolation & purification\r\n*Metagenome\r\nPhylogeny\r\nPlankton/*enzymology/*genetics/metabolism\r\nProkaryotic Cells/enzymology/metabolism\r\nRNA-Directed DNA Polymerase/*genetics/metabolism\r\nRetroelements\r\nSeawater/*microbiology/virology\r\nTranscription, Genetic},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2015.192},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26613339},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding.\n \n \n \n \n\n\n \n Le Bescot, N., Mahe, F., Audic, S., Dimier, C., Garet, M. J., Poulain, J., Wincker, P., de Vargas, C., & Siano, R.\n\n\n \n\n\n\n Environ Microbiol, 18(2): 609-26. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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 1 download\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\n\n\n

@article{RN63,\r\n   author = {Le Bescot, N. and Mahe, F. and Audic, S. and Dimier, C. and Garet, M. J. and Poulain, J. and Wincker, P. and de Vargas, C. and Siano, R.},\r\n   title = {Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding},\r\n   journal = {Environ Microbiol},\r\n   volume = {18},\r\n   number = {2},\r\n   pages = {609-26},\r\n   abstract = {Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecological scales. Our data and analyses suggest that dinoflagellate diversity has been largely underestimated, representing overall approximately 1/2 of protistan rDNA metabarcode richness assigned at >/= 90% to a reference sequence in the world's surface oceans. Dinoflagellate metabarcode diversity and abundance display regular patterns across the global scale, with different order-level taxonomic compositions across organismal size fractions. While the pico to nano-planktonic communities are composed of an extreme diversity of metabarcodes assigned to Gymnodiniales or are simply undetermined, most micro-dinoflagellate metabarcodes relate to the well-referenced Gonyaulacales and Peridiniales orders, and a lower abundance and diversity of essentially symbiotic Peridiniales is unveiled in the meso-plankton. Our analyses could help future development of biogeochemical models of pelagic systems integrating the separation of dinoflagellates into functional groups according to plankton size classes.},\r\n   keywords = {Base Sequence\r\nBiodiversity\r\n*DNA Barcoding, Taxonomic\r\nDNA, Ribosomal/genetics\r\nDinoflagellida/*classification/*genetics\r\nEcology\r\nOceans and Seas\r\nPhytoplankton/*classification/*genetics\r\nRNA, Ribosomal, 18S/*genetics},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.13039},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26337598},\r\n   year = {2016},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2015\n \n \n (13)\n \n \n

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\n \n\n \n \n \n \n \n \n Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes.\n \n \n \n \n\n\n \n Clerissi, C., Desdevises, Y., Romac, S., Audic, S., de Vargas, C., Acinas, S. G., Casotti, R., Poulain, J., Wincker, P., Hingamp, P., Ogata, H., & Grimsley, N.\n\n\n \n\n\n\n Environ Microbiol Rep, 7(6): 979-89. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Deep$ Paper\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

@article{RN40,\r\n   author = {Clerissi, C. and Desdevises, Y. and Romac, S. and Audic, S. and de Vargas, C. and Acinas, S. G. and Casotti, R. and Poulain, J. and Wincker, P. and Hingamp, P. and Ogata, H. and Grimsley, N.},\r\n   title = {Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes},\r\n   journal = {Environ Microbiol Rep},\r\n   volume = {7},\r\n   number = {6},\r\n   pages = {979-89},\r\n   abstract = {High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a approximately 10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey-predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.},\r\n   keywords = {Biodiversity\r\nChlorophyta/*genetics/*virology\r\nDNA, Viral\r\nEnvironment\r\n*Genotype\r\n*High-Throughput Nucleotide Sequencing\r\nIndian Ocean\r\nPhycodnaviridae/*classification/*genetics/isolation & purification},\r\n   ISSN = {1758-2229 (Electronic)\r\n1758-2229 (Linking)},\r\n   DOI = {10.1111/1758-2229.12345},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26472079},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Closing the gaps on the viral photosystem-I psaDCAB gene organization.\n \n \n \n \n\n\n \n Roitman, S., Flores-Uribe, J., Philosof, A., Knowles, B., Rohwer, F., Ignacio-Espinoza, J. C., Sullivan, M. B., Cornejo-Castillo, F. M., Sanchez, P., Acinas, S. G., Dupont, C. L., & Beja, O.\n\n\n \n\n\n\n Environ Microbiol, 17(12): 5100-8. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Closing$ Paper\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

@article{RN38,\r\n   author = {Roitman, S. and Flores-Uribe, J. and Philosof, A. and Knowles, B. and Rohwer, F. and Ignacio-Espinoza, J. C. and Sullivan, M. B. and Cornejo-Castillo, F. M. and Sanchez, P. and Acinas, S. G. and Dupont, C. L. and Beja, O.},\r\n   title = {Closing the gaps on the viral photosystem-I psaDCAB gene organization},\r\n   journal = {Environ Microbiol},\r\n   volume = {17},\r\n   number = {12},\r\n   pages = {5100-8},\r\n   abstract = {Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF-->C-->A-->B-->K-->E-->D and psaD-->C-->A-->B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD-->C-->A-->B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30 degrees N and 30 degrees S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD-->C-->A-->B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF-->C-->A-->B-->K-->E-->D gene organization and most Prochlorococcus strains. This may indicate a co-evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30 degrees N and 30 degrees S equatorial strip.},\r\n   keywords = {Amino Acid Sequence\r\nAquatic Organisms/genetics/metabolism\r\nAtlantic Ocean\r\nBacteriophages/*genetics\r\nBiological Evolution\r\nGene Order\r\nGenes, Viral/genetics\r\nIndian Ocean\r\nMetagenomics\r\nPacific Ocean\r\nPhotosynthesis/*genetics\r\nPhotosystem I Protein Complex/*genetics\r\nPhotosystem II Protein Complex/genetics\r\nProchlorococcus/*genetics/metabolism/virology\r\nSynechococcus/*genetics/metabolism/virology},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.13036},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26310718},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n A new look at ocean carbon remineralization for estimating deep-water sequestration.\n \n \n \n\n\n \n Guidi, L., Legendre, L., Reygondeau, G., Uitz, J., Stemmann, L., & Henson, S.\n\n\n \n\n\n\n Global Biogeochemical Cycles,n/a-n/a. 2015.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN230,\r\n   author = {Guidi, Lionel and Legendre, Louis and Reygondeau, Gabriel and Uitz, Julia and Stemmann, Lars and Henson, Stephanie},\r\n   title = {A new look at ocean carbon remineralization for estimating deep-water sequestration},\r\n   journal = {Global Biogeochemical Cycles},\r\n   pages = {n/a-n/a},\r\n   DOI = {10.1002/2014GB005063},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Regional ocean-colour chlorophyll algorithms for the Red Sea.\n \n \n \n \n\n\n \n Brewin, R. J. W., Raitsos, D. E., Dall'Olmo, G., Zarokanellos, N., Jackson, T., Racault, M., Boss, E. S., Sathyendranath, S., Jones, B. H., & Hoteit, I.\n\n\n \n\n\n\n Remote Sensing of Environment, 165: 64-85. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Regional$ Paper\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

@article{RN229,\r\n   author = {Brewin, Robert J. W. and Raitsos, Dionysios E. and Dall'Olmo, Giorgio and Zarokanellos, Nikolaos and Jackson, Thomas and Racault, Marie-Fanny and Boss, Emmanuel S. and Sathyendranath, Shubha and Jones, Burt H. and Hoteit, Ibrahim},\r\n   title = {Regional ocean-colour chlorophyll algorithms for the Red Sea},\r\n   journal = {Remote Sensing of Environment},\r\n   volume = {165},\r\n   pages = {64-85},\r\n   abstract = {The Red Sea is a semi-enclosed tropical marine ecosystem that stretches from the Gulf of Suez and Gulf of Aqaba in the north, to the Gulf of Aden in the south. Despite its ecological and economic importance, its biological environment is relatively unexplored. Satellite ocean-colour estimates of chlorophyll concentration (an index of phytoplankton biomass) offer an observational platform to monitor the health of the Red Sea. However, little is known about the optical properties of the region. In this paper, we investigate the optical properties of the Red Sea in the context of satellite ocean-colour estimates of chlorophyll concentration. Making use of a new merged ocean-colour product, from the European Space Agency (ESA) Climate Change Initiative, and in situ data in the region, we test the performance of a series of ocean-colour chlorophyll algorithms. We find that standard algorithms systematically overestimate chlorophyll when compared with the in situ data. To investigate this bias we develop an ocean-colour model for the Red Sea, parameterised to data collected during the Tara Oceans expedition, that estimates remote-sensing reflectance as a function of chlorophyll concentration. We used the Red Sea model to tune the standard chlorophyll algorithms and the overestimation in chlorophyll originally observed was corrected. Results suggest that the overestimation was likely due to an excess of CDOM absorption per unit chlorophyll in the Red Sea when compared with average global conditions. However, we recognise that additional information is required to test the influence of other potential sources of the overestimation, such as aeolian dust, and we discuss uncertainties in the datasets used. We present a series of regional chlorophyll algorithms for the Red Sea, designed for a suite of ocean-colour sensors, that may be used for further testing.},\r\n   keywords = {Phytoplankton\r\nOcean colour\r\nRemote sensing\r\nChlorophyll\r\nRed Sea\r\nValidation\r\nColoured dissolved organic matter},\r\n   ISSN = {0034-4257},\r\n   DOI = {https://doi.org/10.1016/j.rse.2015.04.024},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S0034425715001662},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Open science resources for the discovery and analysis of Tara Oceans data.\n \n \n \n \n\n\n \n Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Trouble, R., Dimier, C., Searson, S., & Tara Oceans Consortium, C.\n\n\n \n\n\n\n Sci Data, 2: 150023. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Open$ Paper\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\n\n

@article{RN27,\r\n   author = {Pesant, S. and Not, F. and Picheral, M. and Kandels-Lewis, S. and Le Bescot, N. and Gorsky, G. and Iudicone, D. and Karsenti, E. and Speich, S. and Trouble, R. and Dimier, C. and Searson, S. and Tara Oceans Consortium, Coordinators},\r\n   title = {Open science resources for the discovery and analysis of Tara Oceans data},\r\n   journal = {Sci Data},\r\n   volume = {2},\r\n   pages = {150023},\r\n   abstract = {The Tara Oceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.},\r\n   keywords = {*Ecosystem\r\n*Expeditions\r\nInformation Dissemination\r\n*Oceans and Seas\r\nPlankton\r\nSeawater\r\nViruses},\r\n   ISSN = {2052-4463 (Print)\r\n2052-4463 (Linking)},\r\n   DOI = {10.1038/sdata.2015.23},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/26029378},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Determinants of community structure in the global plankton interactome.\n \n \n \n \n\n\n \n Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio , F., De Meester, L., Ferrera, I., Garet-Delmas, M. J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sanchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans, c., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., & Raes, J.\n\n\n \n\n\n\n Science, 348(6237): 1262073. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Determinants$ Paper\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\n\n

@article{RN28,\r\n   author = {Lima-Mendez, G. and Faust, K. and Henry, N. and Decelle, J. and Colin, S. and Carcillo, F. and Chaffron, S. and Ignacio-Espinosa, J. C. and Roux, S. and Vincent, F. and Bittner, L. and Darzi, Y. and Wang, J. and Audic, S. and Berline, L. and Bontempi, G. and Cabello, A. M. and Coppola, L. and Cornejo-Castillo, F. M. and d'Ovidio, F. and De Meester, L. and Ferrera, I. and Garet-Delmas, M. J. and Guidi, L. and Lara, E. and Pesant, S. and Royo-Llonch, M. and Salazar, G. and Sanchez, P. and Sebastian, M. and Souffreau, C. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Tara Oceans, coordinators and Gorsky, G. and Not, F. and Ogata, H. and Speich, S. and Stemmann, L. and Weissenbach, J. and Wincker, P. and Acinas, S. G. and Sunagawa, S. and Bork, P. and Sullivan, M. B. and Karsenti, E. and Bowler, C. and de Vargas, C. and Raes, J.},\r\n   title = {Determinants of community structure in the global plankton interactome},\r\n   journal = {Science},\r\n   volume = {348},\r\n   number = {6237},\r\n   pages = {1262073},\r\n   abstract = {Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.},\r\n   keywords = {Animals\r\n*Food Chain\r\nHost Specificity\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/*classification/*physiology\r\nPlatyhelminths/classification/physiology\r\nSunlight\r\n*Symbiosis\r\nViruses/classification},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.1262073},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25999517},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Eukaryotic plankton diversity in the sunlit ocean.\n \n \n \n \n\n\n \n De Vargas, C., Audic, S., Henry, N., Decelle, J., Mahe, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J. M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horak, A., Jaillon, O., Lima-Mendez, G., Lukes, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans, C., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., & Karsenti, E.\n\n\n \n\n\n\n Science, 348(6237): 1261605. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Eukaryotic$ Paper\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 12 downloads\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\n

@article{RN29,\r\n   author = {De Vargas, C. and Audic, S. and Henry, N. and Decelle, J. and Mahe, F. and Logares, R. and Lara, E. and Berney, C. and Le Bescot, N. and Probert, I. and Carmichael, M. and Poulain, J. and Romac, S. and Colin, S. and Aury, J. M. and Bittner, L. and Chaffron, S. and Dunthorn, M. and Engelen, S. and Flegontova, O. and Guidi, L. and Horak, A. and Jaillon, O. and Lima-Mendez, G. and Lukes, J. and Malviya, S. and Morard, R. and Mulot, M. and Scalco, E. and Siano, R. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Tara Oceans, Coordinators and Acinas, S. G. and Bork, P. and Bowler, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Raes, J. and Sieracki, M. E. and Speich, S. and Stemmann, L. and Sunagawa, S. and Weissenbach, J. and Wincker, P. and Karsenti, E.},\r\n   title = {Eukaryotic plankton diversity in the sunlit ocean},\r\n   journal = {Science},\r\n   volume = {348},\r\n   number = {6237},\r\n   pages = {1261605},\r\n   abstract = {Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.},\r\n   keywords = {Animals\r\n*Biodiversity\r\nDNA Barcoding, Taxonomic\r\nDNA, Ribosomal/genetics\r\nEukaryota/*classification/genetics\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/*classification/genetics\r\nRibosomes/genetics\r\nSequence Analysis, DNA\r\nSunlight},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.1261605},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25999516},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Structure and function of the global ocean microbiome.\n \n \n \n \n\n\n \n Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., d'Ovidio , F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans, c., Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G., & Bork, P.\n\n\n \n\n\n\n Science, 348(6237): 1261359. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\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 19 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN32,\r\n   author = {Sunagawa, S. and Coelho, L. P. and Chaffron, S. and Kultima, J. R. and Labadie, K. and Salazar, G. and Djahanschiri, B. and Zeller, G. and Mende, D. R. and Alberti, A. and Cornejo-Castillo, F. M. and Costea, P. I. and Cruaud, C. and d'Ovidio, F. and Engelen, S. and Ferrera, I. and Gasol, J. M. and Guidi, L. and Hildebrand, F. and Kokoszka, F. and Lepoivre, C. and Lima-Mendez, G. and Poulain, J. and Poulos, B. T. and Royo-Llonch, M. and Sarmento, H. and Vieira-Silva, S. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Tara Oceans, coordinators and Bowler, C. and de Vargas, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Not, F. and Ogata, H. and Pesant, S. and Speich, S. and Stemmann, L. and Sullivan, M. B. and Weissenbach, J. and Wincker, P. and Karsenti, E. and Raes, J. and Acinas, S. G. and Bork, P.},\r\n   title = {Structure and function of the global ocean microbiome},\r\n   journal = {Science},\r\n   volume = {348},\r\n   number = {6237},\r\n   pages = {1261359},\r\n   abstract = {Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.},\r\n   keywords = {Databases, Genetic\r\nEcosystem\r\nGastrointestinal Tract/microbiology\r\nGenetic Variation\r\nHumans\r\nMetagenome\r\nMicrobiota/*genetics\r\nOceans and Seas\r\nPlankton/*classification/genetics/isolation & purification\r\nSeawater/*microbiology},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.1261359},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25999513},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Patterns and ecological drivers of ocean viral communities.\n \n \n \n \n\n\n \n Brum, J. R., Ignacio-Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., Gorsky, G., Gregory, A. C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B. T., Schwenck, S. M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans, C., Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E., & Sullivan, M. B.\n\n\n \n\n\n\n Science, 348(6237): 1261498. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Patterns$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN30,\r\n   author = {Brum, J. R. and Ignacio-Espinoza, J. C. and Roux, S. and Doulcier, G. and Acinas, S. G. and Alberti, A. and Chaffron, S. and Cruaud, C. and de Vargas, C. and Gasol, J. M. and Gorsky, G. and Gregory, A. C. and Guidi, L. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Poulos, B. T. and Schwenck, S. M. and Speich, S. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Tara Oceans, Coordinators and Bork, P. and Bowler, C. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Sullivan, M. B.},\r\n   title = {Patterns and ecological drivers of ocean viral communities},\r\n   journal = {Science},\r\n   volume = {348},\r\n   number = {6237},\r\n   pages = {1261498},\r\n   abstract = {Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.},\r\n   keywords = {Biodiversity\r\nDNA, Viral/genetics\r\nEcological and Environmental Phenomena\r\n*Ecosystem\r\nMetagenome/genetics\r\nMicrobiota/genetics\r\nOceans and Seas\r\nPlankton/*classification/genetics\r\nSeawater/*virology\r\nViral Proteins/genetics\r\nViruses/*classification/genetics},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.1261498},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25999515},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Environmental characteristics of Agulhas rings affect interocean plankton transport.\n \n \n \n \n\n\n \n Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., d'Ortenzio , F., Gattuso, J. P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J. L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J. B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans, C., Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., & Iudicone, D.\n\n\n \n\n\n\n Science, 348(6237): 1261447. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Environmental$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

@article{RN31,\r\n   author = {Villar, E. and Farrant, G. K. and Follows, M. and Garczarek, L. and Speich, S. and Audic, S. and Bittner, L. and Blanke, B. and Brum, J. R. and Brunet, C. and Casotti, R. and Chase, A. and Dolan, J. R. and d'Ortenzio, F. and Gattuso, J. P. and Grima, N. and Guidi, L. and Hill, C. N. and Jahn, O. and Jamet, J. L. and Le Goff, H. and Lepoivre, C. and Malviya, S. and Pelletier, E. and Romagnan, J. B. and Roux, S. and Santini, S. and Scalco, E. and Schwenck, S. M. and Tanaka, A. and Testor, P. and Vannier, T. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Tara Oceans, Coordinators and Acinas, S. G. and Bork, P. and Boss, E. and de Vargas, C. and Gorsky, G. and Ogata, H. and Pesant, S. and Sullivan, M. B. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Bowler, C. and Not, F. and Hingamp, P. and Iudicone, D.},\r\n   title = {Environmental characteristics of Agulhas rings affect interocean plankton transport},\r\n   journal = {Science},\r\n   volume = {348},\r\n   number = {6237},\r\n   pages = {1261447},\r\n   abstract = {Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.},\r\n   keywords = {Atlantic Ocean\r\nDNA, Ribosomal/genetics\r\nGenetic Variation\r\nIndian Ocean\r\nMetagenomics\r\nNitrites/metabolism\r\nNitrogen/metabolism\r\nPlankton/genetics/metabolism/*physiology\r\n*Seawater\r\nSelection, Genetic},\r\n   ISSN = {1095-9203 (Electronic)\r\n0036-8075 (Linking)},\r\n   DOI = {10.1126/science.1261447},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25999514},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Comprehensive model of annual plankton succession based on the whole-plankton time series approach.\n \n \n \n \n\n\n \n Romagnan, J. B., Legendre, L., Guidi, L., Jamet, J. L., Jamet, D., Mousseau, L., Pedrotti, M. L., Picheral, M., Gorsky, G., Sardet, C., & Stemmann, L.\n\n\n \n\n\n\n PLoS One, 10(3): e0119219. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Comprehensive$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN18,\r\n   author = {Romagnan, J. B. and Legendre, L. and Guidi, L. and Jamet, J. L. and Jamet, D. and Mousseau, L. and Pedrotti, M. L. and Picheral, M. and Gorsky, G. and Sardet, C. and Stemmann, L.},\r\n   title = {Comprehensive model of annual plankton succession based on the whole-plankton time series approach},\r\n   journal = {PLoS One},\r\n   volume = {10},\r\n   number = {3},\r\n   pages = {e0119219},\r\n   abstract = {Ecological succession provides a widely accepted description of seasonal changes in phytoplankton and mesozooplankton assemblages in the natural environment, but concurrent changes in smaller (i.e. microbes) and larger (i.e. macroplankton) organisms are not included in the model because plankton ranging from bacteria to jellies are seldom sampled and analyzed simultaneously. Here we studied, for the first time in the aquatic literature, the succession of marine plankton in the whole-plankton assemblage that spanned 5 orders of magnitude in size from microbes to macroplankton predators (not including fish or fish larvae, for which no consistent data were available). Samples were collected in the northwestern Mediterranean Sea (Bay of Villefranche) weekly during 10 months. Simultaneously collected samples were analyzed by flow cytometry, inverse microscopy, FlowCam, and ZooScan. The whole-plankton assemblage underwent sharp reorganizations that corresponded to bottom-up events of vertical mixing in the water-column, and its development was top-down controlled by large gelatinous filter feeders and predators. Based on the results provided by our novel whole-plankton assemblage approach, we propose a new comprehensive conceptual model of the annual plankton succession (i.e. whole plankton model) characterized by both stepwise stacking of four broad trophic communities from early spring through summer, which is a new concept, and progressive replacement of ecological plankton categories within the different trophic communities, as recognised traditionally.},\r\n   keywords = {Flow Cytometry\r\nFood Chain\r\nMediterranean Sea\r\n*Models, Biological\r\nPlankton/classification/*physiology\r\nPopulation Dynamics\r\nSeasons},\r\n   ISSN = {1932-6203 (Electronic)\r\n1932-6203 (Linking)},\r\n   DOI = {10.1371/journal.pone.0119219},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25780912},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations.\n \n \n \n \n\n\n \n Acinas, S. G., Ferrera, I., Sarmento, H., Diez-Vives, C., Forn, I., Ruiz-Gonzalez, C., Cornejo-Castillo, F. M., Salazar, G., & Gasol, J. M.\n\n\n \n\n\n\n Environ Microbiol, 17(10): 3557-69. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Validation$ Paper\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 \n \n \n\n\n\n

@article{RN16,\r\n   author = {Acinas, S. G. and Ferrera, I. and Sarmento, H. and Diez-Vives, C. and Forn, I. and Ruiz-Gonzalez, C. and Cornejo-Castillo, F. M. and Salazar, G. and Gasol, J. M.},\r\n   title = {Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations},\r\n   journal = {Environ Microbiol},\r\n   volume = {17},\r\n   number = {10},\r\n   pages = {3557-69},\r\n   abstract = {Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.},\r\n   keywords = {Alteromonadaceae/genetics\r\nBacteroidetes/*classification/genetics\r\nDNA Probes/*genetics\r\nDNA, Bacterial/*genetics\r\nIn Situ Hybridization, Fluorescence/*methods\r\nMediterranean Sea\r\nRNA, Ribosomal, 16S/genetics\r\nRhodobacteraceae/genetics\r\nSeasons\r\nSeawater/microbiology\r\nSequence Analysis, DNA},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.12517},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/24890225},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n An inexpensive, accurate, and precise wet-mount method for enumerating aquatic viruses.\n \n \n \n \n\n\n \n Cunningham, B. R., Brum, J. R., Schwenck, S. M., Sullivan, M. B., & John, S. G.\n\n\n \n\n\n\n Appl Environ Microbiol, 81(9): 2995-3000. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"An$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

@article{RN15,\r\n   author = {Cunningham, B. R. and Brum, J. R. and Schwenck, S. M. and Sullivan, M. B. and John, S. G.},\r\n   title = {An inexpensive, accurate, and precise wet-mount method for enumerating aquatic viruses},\r\n   journal = {Appl Environ Microbiol},\r\n   volume = {81},\r\n   number = {9},\r\n   pages = {2995-3000},\r\n   abstract = {Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely used method to accomplish this with aquatic samples is the "filter mount" method, in which samples are filtered onto costly 0.02-mum-pore-size ceramic filters for enumeration of viruses by epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold-lower materials cost) alternative virus enumeration method in which fluorescently stained samples are wet mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations of <5x10(7) viruses ml(-1). The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained by using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had precision equivalent to, those obtained by the filter mount method across concentrations ranging from 2.17x10(6) to 1.37x10(8) viruses ml(-1) when tested by using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter mount method and is appropriate for rapid, precise, and accurate enumeration of aquatic viruses over a wide range of viral concentrations (>/=1x10(6) viruses ml(-1)) encountered in field and laboratory samples.},\r\n   keywords = {Costs and Cost Analysis\r\nFlocculation\r\nFresh Water/*virology\r\nMicroscopy, Fluorescence/methods\r\nSeawater/*virology\r\nViral Load/economics/*methods\r\nViruses/*isolation & purification},\r\n   ISSN = {1098-5336 (Electronic)\r\n0099-2240 (Linking)},\r\n   DOI = {10.1128/AEM.03642-14},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25710369},\r\n   year = {2015},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2014\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n Evolutionary history of Chaetognatha inferred from molecular and morphological data: a case study for body plan simplification.\n \n \n \n \n\n\n \n Gasmi, S., Neve, G., Pech, N., Tekaya, S., Gilles, A., & Perez, Y.\n\n\n \n\n\n\n Front Zool, 11(1): 84. 2014.\n \n\n\n\n
\n\n\n\n \n \n $\"Evolutionary$ Paper\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

@article{RN17,\r\n   author = {Gasmi, S. and Neve, G. and Pech, N. and Tekaya, S. and Gilles, A. and Perez, Y.},\r\n   title = {Evolutionary history of Chaetognatha inferred from molecular and morphological data: a case study for body plan simplification},\r\n   journal = {Front Zool},\r\n   volume = {11},\r\n   number = {1},\r\n   pages = {84},\r\n   abstract = {BACKGROUND: Chaetognatha are a phylum of marine carnivorous animals which includes more than 130 extant species. The internal systematics of this group have been intensively debated since it was discovered in the 18(th) century. While they can be traced back to the earlier Cambrian, they are an extraordinarily homogeneous phylum at the morphological level - a fascinating characteristic that puzzled many a scientist who has tried to clarify their taxonomy. Recent studies which have attempted to reconstruct a phylogeny using molecular data have relied on single gene analyses and a somewhat restricted taxon sampling. Here, we present the first large scale phylogenetic study of Chaetognatha based on a combined analysis of nearly the complete ribosomal RNA (rRNA) genes. We use this analysis to infer the evolution of some morphological characters. This work includes 36 extant species, mainly obtained from Tara Oceans Expedition 2009/2012, that represent 16 genera and 6 of the 9 extant families. RESULTS: Cladistic and phenetic analysis of morphological characters, geometric morphometrics and molecular small subunit (SSU rRNA) and large subunit (LSU rRNA) ribosomal genes phylogenies provided new insights into the relationships and the evolutionary history of Chaetognatha. We propose the following clade structure for the phylum: (((Sagittidae, Krohnittidae), Spadellidae), (Eukrohniidae, Heterokrohniidae)), with the Pterosagittidae included in the Sagittidae. The clade (Sagittidae, Krohnittidae) constitutes the monophyletic order of Aphragmophora. Molecular analyses showed that the Phragmophora are paraphyletic. The Ctenodontina/Flabellodontina and Syngonata/Chorismogonata hypotheses are invalidated on the basis of both morphological and molecular data. This new phylogeny also includes resurrected and modified genera within Sagittidae. CONCLUSIONS: The distribution of some morphological characters traditionally used in systematics and for species diagnosis suggests that the diversity in Chaetognatha was produced through a process of mosaic evolution. Moreover, chaetognaths have mostly evolved by simplification of their body plan and their history shows numerous convergent events of losses and reversions. The main morphological novelty observed is the acquisition of a second pair of lateral fins in Sagittidae, which represents an adaptation to the holoplanktonic niche.},\r\n   keywords = {Body plan simplification\r\nChaetognatha\r\nHomoplasy\r\nPhylogenetics\r\nProcrustes surimposition\r\nSystematics},\r\n   ISSN = {1742-9994 (Print)\r\n1742-9994 (Linking)},\r\n   DOI = {10.1186/s12983-014-0084-7},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/25473413},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n BACKGROUND: Chaetognatha are a phylum of marine carnivorous animals which includes more than 130 extant species. The internal systematics of this group have been intensively debated since it was discovered in the 18(th) century. While they can be traced back to the earlier Cambrian, they are an extraordinarily homogeneous phylum at the morphological level - a fascinating characteristic that puzzled many a scientist who has tried to clarify their taxonomy. Recent studies which have attempted to reconstruct a phylogeny using molecular data have relied on single gene analyses and a somewhat restricted taxon sampling. Here, we present the first large scale phylogenetic study of Chaetognatha based on a combined analysis of nearly the complete ribosomal RNA (rRNA) genes. We use this analysis to infer the evolution of some morphological characters. This work includes 36 extant species, mainly obtained from Tara Oceans Expedition 2009/2012, that represent 16 genera and 6 of the 9 extant families. RESULTS: Cladistic and phenetic analysis of morphological characters, geometric morphometrics and molecular small subunit (SSU rRNA) and large subunit (LSU rRNA) ribosomal genes phylogenies provided new insights into the relationships and the evolutionary history of Chaetognatha. We propose the following clade structure for the phylum: (((Sagittidae, Krohnittidae), Spadellidae), (Eukrohniidae, Heterokrohniidae)), with the Pterosagittidae included in the Sagittidae. The clade (Sagittidae, Krohnittidae) constitutes the monophyletic order of Aphragmophora. Molecular analyses showed that the Phragmophora are paraphyletic. The Ctenodontina/Flabellodontina and Syngonata/Chorismogonata hypotheses are invalidated on the basis of both morphological and molecular data. This new phylogeny also includes resurrected and modified genera within Sagittidae. CONCLUSIONS: The distribution of some morphological characters traditionally used in systematics and for species diagnosis suggests that the diversity in Chaetognatha was produced through a process of mosaic evolution. Moreover, chaetognaths have mostly evolved by simplification of their body plan and their history shows numerous convergent events of losses and reversions. The main morphological novelty observed is the acquisition of a second pair of lateral fins in Sagittidae, which represents an adaptation to the holoplanktonic niche.\n

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\n \n\n \n \n \n \n \n Taxonomy and phylogenetic relationships of the coral genera Australomussa and Parascolymia (Scleractinia, Lobophylliidae).\n \n \n \n\n\n \n Arrigoni, R., Z.T, R., Chen, C., Baird, A., & Benzoni, F.\n\n\n \n\n\n\n Contributions to Zoology Bijdragen tot de dierkunde, 83: 195-215. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN228,\r\n   author = {Arrigoni, Roberto and Z.T, Richards and Chen, Chaolun and Baird, Andrew and Benzoni, Francesca},\r\n   title = {Taxonomy and phylogenetic relationships of the coral genera Australomussa and Parascolymia (Scleractinia, Lobophylliidae)},\r\n   journal = {Contributions to Zoology Bijdragen tot de dierkunde},\r\n   volume = {83},\r\n   pages = {195-215},\r\n   DOI = {10.1163/18759866-08303004},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications.\n \n \n \n\n\n \n Arrigoni, R., Kitano, Y., Stolarski, J., Hoeksema, B., Fukami, H., Stefani, F., Galli, P., Montano, S., Castoldi, E., & Benzoni, F.\n\n\n \n\n\n\n Zoologica Scripta, 43: 661-688. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN227,\r\n   author = {Arrigoni, Roberto and Kitano, Yuko and Stolarski, Jarosław and Hoeksema, Bert and Fukami, Hironobu and Stefani, Fabrizio and Galli, Paolo and Montano, Simone and Castoldi, Elisa and Benzoni, Francesca},\r\n   title = {A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications},\r\n   journal = {Zoologica Scripta},\r\n   volume = {43},\r\n   pages = {661-688},\r\n   DOI = {10.1111/zsc.12072},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n Phylogenetic relationships and revision of the genus Blastomussa (Cnidaria: Anthozoa: Scleractinia) with description of a new species.\n \n \n \n\n\n \n Benzoni, F., Arrigoni, R., Waheed, Z., Stefani, F., & Hoeksema, B.\n\n\n \n\n\n\n The Raffles bulletin of zoology, 62: 358-378. 2014.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

@article{RN226,\r\n   author = {Benzoni, Francesca and Arrigoni, Roberto and Waheed, Zarinah and Stefani, Fabrizio and Hoeksema, Bert},\r\n   title = {Phylogenetic relationships and revision of the genus Blastomussa (Cnidaria: Anthozoa: Scleractinia) with description of a new species},\r\n   journal = {The Raffles bulletin of zoology},\r\n   volume = {62},\r\n   pages = {358-378},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes.\n \n \n \n \n\n\n \n Clerissi, C., Grimsley, N., Ogata, H., Hingamp, P., Poulain, J., & Desdevises, Y.\n\n\n \n\n\n\n Appl Environ Microbiol, 80(10): 3150-60. 2014.\n \n\n\n\n
\n\n\n\n \n \n $\"Unveiling$ Paper\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

@article{RN13,\r\n   author = {Clerissi, C. and Grimsley, N. and Ogata, H. and Hingamp, P. and Poulain, J. and Desdevises, Y.},\r\n   title = {Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes},\r\n   journal = {Appl Environ Microbiol},\r\n   volume = {80},\r\n   number = {10},\r\n   pages = {3150-60},\r\n   abstract = {Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.},\r\n   keywords = {*Biodiversity\r\nCapsid Proteins/*genetics\r\nDNA-Directed DNA Polymerase/*genetics\r\nHigh-Throughput Nucleotide Sequencing\r\nMolecular Sequence Data\r\nPhycodnaviridae/classification/enzymology/genetics/*isolation & purification\r\nPhylogeny\r\nPolymerase Chain Reaction\r\nSeawater/*virology\r\nViral Proteins/*genetics},\r\n   ISSN = {1098-5336 (Electronic)\r\n0099-2240 (Linking)},\r\n   DOI = {10.1128/AEM.00123-14},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/24632251},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.\n \n \n \n \n\n\n \n Logares, R., Sunagawa, S., Salazar, G., Cornejo-Castillo, F. M., Ferrera, I., Sarmento, H., Hingamp, P., Ogata, H., de Vargas, C., Lima-Mendez, G., Raes, J., Poulain, J., Jaillon, O., Wincker, P., Kandels-Lewis, S., Karsenti, E., Bork, P., & Acinas, S. G.\n\n\n \n\n\n\n Environ Microbiol, 16(9): 2659-71. 2014.\n \n\n\n\n
\n\n\n\n \n \n $\"Metagenomic$ Paper\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 1 download\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\n\n\n

@article{RN9,\r\n   author = {Logares, R. and Sunagawa, S. and Salazar, G. and Cornejo-Castillo, F. M. and Ferrera, I. and Sarmento, H. and Hingamp, P. and Ogata, H. and de Vargas, C. and Lima-Mendez, G. and Raes, J. and Poulain, J. and Jaillon, O. and Wincker, P. and Kandels-Lewis, S. and Karsenti, E. and Bork, P. and Acinas, S. G.},\r\n   title = {Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities},\r\n   journal = {Environ Microbiol},\r\n   volume = {16},\r\n   number = {9},\r\n   pages = {2659-71},\r\n   abstract = {Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mi tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454 tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.},\r\n   keywords = {Archaea/genetics\r\nBacteria/genetics\r\nDNA Primers/genetics\r\nDNA, Ribosomal/*genetics\r\n*Metagenome\r\nMetagenomics/*methods\r\nPolymerase Chain Reaction\r\nRNA, Ribosomal, 16S/genetics\r\nSequence Analysis, DNA/*methods},\r\n   ISSN = {1462-2920 (Electronic)\r\n1462-2912 (Linking)},\r\n   DOI = {10.1111/1462-2920.12250},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/24102695},\r\n   year = {2014},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Decomposition of in situ particulate absorption spectra.\n \n \n \n \n\n\n \n Chase, A., Boss, E., Zaneveld, R., Bricaud, A., Claustre, H., Ras, J., Dall’Olmo, G., & Westberry, T. K.\n\n\n \n\n\n\n Methods in Oceanography, 7: 110-124. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Decomposition$ Paper\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 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN225,\r\n   author = {Chase, Alison and Boss, Emmanuel and Zaneveld, Ronald and Bricaud, Annick and Claustre, Herve and Ras, Josephine and Dall’Olmo, Giorgio and Westberry, Toby K.},\r\n   title = {Decomposition of in situ particulate absorption spectra},\r\n   journal = {Methods in Oceanography},\r\n   volume = {7},\r\n   pages = {110-124},\r\n   abstract = {A global dataset of in situ particulate absorption spectra has been decomposed into component functions representing absorption by phytoplankton pigments and non-algal particles. The magnitudes of component Gaussian functions, used to represent absorption by individual or groups of pigments, are well correlated with pigment concentrations determined using High Performance Liquid Chromatography. We are able to predict the presence of chlorophylls a,b, and c, as well as two different groups of summed carotenoid pigments with percent errors between 30% and 57%. Existing methods of analysis of particulate absorption spectra measured in situ provide for only chlorophyll a; the method presented here, using high spectral resolution particulate absorption, shows the ability to obtain the concentrations of additional pigments, allowing for more detailed studies of phytoplankton ecology than currently possible with in-situ spectroscopy.},\r\n   keywords = {Bio-optics\r\nParticulate absorption\r\nPhytoplankton pigments\r\nSpectral decomposition},\r\n   ISSN = {2211-1220},\r\n   DOI = {https://doi.org/10.1016/j.mio.2014.02.002},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S2211122014000036},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The characteristics of particulate absorption, scattering and attenuation coefficients in the surface ocean; Contribution of the Tara Oceans expedition.\n \n \n \n \n\n\n \n Boss, E., Picheral, M., Leeuw, T., Chase, A., Karsenti, E., Gorsky, G., Taylor, L., Slade, W., Ras, J., & Claustre, H.\n\n\n \n\n\n\n Methods in Oceanography, 7: 52-62. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN224,\r\n   author = {Boss, Emmanuel and Picheral, Marc and Leeuw, Thomas and Chase, Alison and Karsenti, Eric and Gorsky, Gabriel and Taylor, Lisa and Slade, Wayne and Ras, Josephine and Claustre, Herve},\r\n   title = {The characteristics of particulate absorption, scattering and attenuation coefficients in the surface ocean; Contribution of the Tara Oceans expedition},\r\n   journal = {Methods in Oceanography},\r\n   volume = {7},\r\n   pages = {52-62},\r\n   abstract = {A dataset consisting of AC-S measurements of (hyper-) spectral particulate absorption, scattering and attenuation coefficients were obtained from measurements performed on the flow-through system of the R/V Tara during its 2.5-year long expedition. The AC-S instruments were robust, working continuously with weekly maintenance for about 3 months at a time, and provided absorption (attenuation) data for 454 (375) days, or 90% (75%) of total possible days during the expedition. This dataset has been mapped to 1 km×1 km bins to avoid over emphasizing redundant data, and to match the spatial scale of typical ocean color satellite sensors. It consists of nearly 70,000 particulate absorption spectra and about 60,000 particulate scattering and attenuation spectra. These data are found to be consistent with chlorophyll extraction and with the published average shapes of particulate absorption and scattering spectra and bio-optical relationships. This dataset is richer than previous ones in the data from open-ocean (oligotrophic) environments making it more representative of global distributions and of utility for global algorithm development.},\r\n   keywords = {Bio-optics\r\nParticle absorption coefficient\r\nParticle scattering coefficient\r\nParticle attenuation coefficient},\r\n   ISSN = {2211-1220},\r\n   DOI = {https://doi.org/10.1016/j.mio.2013.11.002},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S2211122013000467},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Bioprospecting marine plankton.\n \n \n \n \n\n\n \n Abida, H., Ruchaud, S., Rios, L., Humeau, A., Probert, I., De Vargas, C., Bach, S., & Bowler, C.\n\n\n \n\n\n\n Mar Drugs, 11(11): 4594-611. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Bioprospecting$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN12,\r\n   author = {Abida, H. and Ruchaud, S. and Rios, L. and Humeau, A. and Probert, I. and De Vargas, C. and Bach, S. and Bowler, C.},\r\n   title = {Bioprospecting marine plankton},\r\n   journal = {Mar Drugs},\r\n   volume = {11},\r\n   number = {11},\r\n   pages = {4594-611},\r\n   abstract = {The ocean dominates the surface of our planet and plays a major role in regulating the biosphere. For example, the microscopic photosynthetic organisms living within provide 50% of the oxygen we breathe, and much of our food and mineral resources are extracted from the ocean. In a time of ecological crisis and major changes in our society, it is essential to turn our attention towards the sea to find additional solutions for a sustainable future. Remarkably, while we are overexploiting many marine resources, particularly the fisheries, the planktonic compartment composed of zooplankton, phytoplankton, bacteria and viruses, represents 95% of marine biomass and yet the extent of its diversity remains largely unknown and underexploited. Consequently, the potential of plankton as a bioresource for humanity is largely untapped. Due to their diverse evolutionary backgrounds, planktonic organisms offer immense opportunities: new resources for medicine, cosmetics and food, renewable energy, and long-term solutions to mitigate climate change. Research programs aiming to exploit culture collections of marine micro-organisms as well as to prospect the huge resources of marine planktonic biodiversity in the oceans are now underway, and several bioactive extracts and purified compounds have already been identified. This review will survey and assess the current state-of-the-art and will propose methodologies to better exploit the potential of marine plankton for drug discovery and for dermocosmetics.},\r\n   keywords = {Animals\r\nBiomass\r\nHumans\r\nMarine Biology/methods\r\nOceans and Seas\r\nPlankton/*physiology},\r\n   ISSN = {1660-3397 (Electronic)\r\n1660-3397 (Linking)},\r\n   DOI = {10.3390/md11114594},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/24240981},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Underway sampling of marine inherent optical properties on the Tara Oceans expedition as a novel resource for ocean color satellite data product validation.\n \n \n \n \n\n\n \n Werdell, P. J., Proctor, C. W., Boss, E., Leeuw, T., & Ouhssain, M.\n\n\n \n\n\n\n Methods in Oceanography, 7: 40-51. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Underway$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN223,\r\n   author = {Werdell, P. Jeremy and Proctor, Christopher W. and Boss, Emmanuel and Leeuw, Thomas and Ouhssain, Mustapha},\r\n   title = {Underway sampling of marine inherent optical properties on the Tara Oceans expedition as a novel resource for ocean color satellite data product validation},\r\n   journal = {Methods in Oceanography},\r\n   volume = {7},\r\n   pages = {40-51},\r\n   abstract = {Developing and validating data records from operational ocean color satellite instruments requires substantial volumes of high quality in situ data. In the absence of broad, institutionally supported field programs, organizations such as the NASA Ocean Biology Processing Group seek opportunistic datasets for use in their operational satellite calibration and validation activities. The publicly available, global biogeochemical dataset collected as part of the two and a half year Tara Oceans expedition provides one such opportunity. We showed how the inline measurements of hyperspectral absorption and attenuation coefficients collected onboard the R/V Tara can be used to evaluate near-surface estimates of chlorophyll-a, spectral particulate backscattering coefficients, particulate organic carbon, and particle size classes derived from the NASA Moderate Resolution Imaging Spectroradiometer onboard Aqua (MODISA). The predominant strength of such flow-through measurements is their sampling rate—the 375 days of measurements resulted in 165 viable MODISA-to-in situ match-ups, compared to 13 from discrete water sampling. While the need to apply bio-optical models to estimate biogeochemical quantities of interest from spectroscopy remains a weakness, we demonstrated how discrete samples can be used in combination with flow-through measurements to create data records of sufficient quality to conduct first order evaluations of satellite-derived data products. Given an emerging agency desire to rapidly evaluate new satellite missions, our results have significant implications on how calibration and validation teams for these missions will be constructed.},\r\n   keywords = {Ocean color\r\nBio-optics\r\nRemote sensing\r\nParticle absorption},\r\n   ISSN = {2211-1220},\r\n   DOI = {https://doi.org/10.1016/j.mio.2013.09.001},\r\n   url = {https://www.sciencedirect.com/science/article/pii/S2211122013000315},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Echinophyllia tarae sp. n. (Cnidaria, Anthozoa, Scleractinia), a new reef coral species from the Gambier Islands, French Polynesia.\n \n \n \n \n\n\n \n Benzoni, F.\n\n\n \n\n\n\n Zookeys, (318): 59-79. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Echinophyllia$ Paper\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 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN8,\r\n   author = {Benzoni, F.},\r\n   title = {Echinophyllia tarae sp. n. (Cnidaria, Anthozoa, Scleractinia), a new reef coral species from the Gambier Islands, French Polynesia},\r\n   journal = {Zookeys},\r\n   number = {318},\r\n   pages = {59-79},\r\n   abstract = {A new shallow water scleractinian coral species, Echinophyllia tarae sp. n., is described from the Gambier Islands, French Polynesia. It is characterized by an encrusting corallum, a few large and highly variable corallites with protruding walls, and distinctive costosepta. This coral was observed in muddy environments where several colonies showed partial mortality and re-growth. The new species has morphological affinities with both Echinophyllia echinata and with Echinomorpha nishihirai, from which it can be distinguished on the basis of the diameter and the protrusion of the largest corallite, the thickness of the septa, and the development of the size of the crown of paliform lobes.},\r\n   keywords = {Echinomorpha nishihirai\r\nEchinophyllia echinata\r\nLobophylliidae\r\nTara Oceans Expedition},\r\n   ISSN = {1313-2989 (Print)\r\n1313-2970 (Linking)},\r\n   DOI = {10.3897/zookeys.318.5351},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23950677},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.\n \n \n \n \n\n\n \n Swan, B. K., Tupper, B., Sczyrba, A., Lauro, F. M., Martinez-Garcia, M., Gonzalez, J. M., Luo, H., Wright, J. J., Landry, Z. C., Hanson, N. W., Thompson, B. P., Poulton, N. J., Schwientek, P., Acinas, S. G., Giovannoni, S. J., Moran, M. A., Hallam, S. J., Cavicchioli, R., Woyke, T., & Stepanauskas, R.\n\n\n \n\n\n\n Proc Natl Acad Sci U S A, 110(28): 11463-8. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Prevalent$ Paper\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

@article{RN6,\r\n   author = {Swan, B. K. and Tupper, B. and Sczyrba, A. and Lauro, F. M. and Martinez-Garcia, M. and Gonzalez, J. M. and Luo, H. and Wright, J. J. and Landry, Z. C. and Hanson, N. W. and Thompson, B. P. and Poulton, N. J. and Schwientek, P. and Acinas, S. G. and Giovannoni, S. J. and Moran, M. A. and Hallam, S. J. and Cavicchioli, R. and Woyke, T. and Stepanauskas, R.},\r\n   title = {Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean},\r\n   journal = {Proc Natl Acad Sci U S A},\r\n   volume = {110},\r\n   number = {28},\r\n   pages = {11463-8},\r\n   abstract = {Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.},\r\n   keywords = {Bacteria/*classification/genetics\r\n*Genome, Bacterial\r\nGeography\r\n*Marine Biology\r\nOceans and Seas\r\nPlankton/*classification/genetics\r\n*Water Microbiology\r\ncomparative genomics\r\nmarine microbiology\r\nmicrobial ecology\r\nmicrobial microevolution\r\noperational taxonomic unit},\r\n   ISSN = {1091-6490 (Electronic)\r\n0027-8424 (Linking)},\r\n   DOI = {10.1073/pnas.1304246110},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23801761},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Sequencing platform and library preparation choices impact viral metagenomes.\n \n \n \n \n\n\n \n Solonenko, S. A., Ignacio-Espinoza, J. C., Alberti, A., Cruaud, C., Hallam, S., Konstantinidis, K., Tyson, G., Wincker, P., & Sullivan, M. B.\n\n\n \n\n\n\n BMC Genomics, 14: 320. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Sequencing$ Paper\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\n\n

@article{RN5,\r\n   author = {Solonenko, S. A. and Ignacio-Espinoza, J. C. and Alberti, A. and Cruaud, C. and Hallam, S. and Konstantinidis, K. and Tyson, G. and Wincker, P. and Sullivan, M. B.},\r\n   title = {Sequencing platform and library preparation choices impact viral metagenomes},\r\n   journal = {BMC Genomics},\r\n   volume = {14},\r\n   pages = {320},\r\n   abstract = {BACKGROUND: Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10 pg of DNA. RESULTS: Using %G+C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1 mug), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields. CONCLUSIONS: These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.},\r\n   keywords = {Base Composition\r\nDNA, Viral/genetics\r\n*Gene Library\r\nGenome, Viral/*genetics\r\nHigh-Throughput Nucleotide Sequencing\r\nMetagenome/*genetics\r\nNucleic Acid Amplification Techniques\r\n*Sequence Analysis, DNA},\r\n   ISSN = {1471-2164 (Electronic)\r\n1471-2164 (Linking)},\r\n   DOI = {10.1186/1471-2164-14-320},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23663384},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses.\n \n \n \n \n\n\n \n Brum, J. R., Schenck, R. O., & Sullivan, M. B.\n\n\n \n\n\n\n ISME J, 7(9): 1738-51. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\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

@article{RN4,\r\n   author = {Brum, J. R. and Schenck, R. O. and Sullivan, M. B.},\r\n   title = {Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses},\r\n   journal = {ISME J},\r\n   volume = {7},\r\n   number = {9},\r\n   pages = {1738-51},\r\n   abstract = {Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.},\r\n   keywords = {*Biodiversity\r\nCapsid/ultrastructure\r\nEnvironment\r\nGeography\r\nMicroscopy, Electron, Transmission\r\nOceans and Seas\r\nSalinity\r\nSeawater/*virology\r\nViruses/classification/*ultrastructure\r\n*Water Microbiology},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2013.67},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23635867},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.\n \n \n \n \n\n\n \n Hingamp, P., Grimsley, N., Acinas, S. G., Clerissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, E., Lima-Mendez, G., Faust, K., Sunagawa, S., Claverie, J. M., Moreau, H., Desdevises, Y., Bork, P., Raes, J., de Vargas, C., Karsenti, E., Kandels-Lewis, S., Jaillon, O., Not, F., Pesant, S., Wincker, P., & Ogata, H.\n\n\n \n\n\n\n ISME J, 7(9): 1678-95. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\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\n\n

@article{RN3,\r\n   author = {Hingamp, P. and Grimsley, N. and Acinas, S. G. and Clerissi, C. and Subirana, L. and Poulain, J. and Ferrera, I. and Sarmento, H. and Villar, E. and Lima-Mendez, G. and Faust, K. and Sunagawa, S. and Claverie, J. M. and Moreau, H. and Desdevises, Y. and Bork, P. and Raes, J. and de Vargas, C. and Karsenti, E. and Kandels-Lewis, S. and Jaillon, O. and Not, F. and Pesant, S. and Wincker, P. and Ogata, H.},\r\n   title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes},\r\n   journal = {ISME J},\r\n   volume = {7},\r\n   number = {9},\r\n   pages = {1678-95},\r\n   abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 mum size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.},\r\n   keywords = {Animals\r\n*Biodiversity\r\nCell Nucleus/virology\r\nCytoplasm/virology\r\nDNA Viruses/*classification/genetics/*physiology\r\nEukaryota/virology\r\nGene Transfer, Horizontal\r\nGenes, Viral/genetics\r\nGenome, Viral/genetics\r\nIndian Ocean\r\n*Metagenome\r\nOceans and Seas\r\nOomycetes/virology\r\nPhycodnaviridae/classification/genetics/physiology\r\nPhylogeny\r\nPopulation Density\r\nProkaryotic Cells/physiology},\r\n   ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n   DOI = {10.1038/ismej.2013.59},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23575371},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data.\n \n \n \n \n\n\n \n Corse, E., Rampal, J., Cuoc, C., Pech, N., Perez, Y., & Gilles, A.\n\n\n \n\n\n\n PLoS One, 8(4): e59439. 2013.\n \n\n\n\n
\n\n\n\n \n \n $\"Phylogenetic$ Paper\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 1 download\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\n\n\n

@article{RN2,\r\n   author = {Corse, E. and Rampal, J. and Cuoc, C. and Pech, N. and Perez, Y. and Gilles, A.},\r\n   title = {Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data},\r\n   journal = {PLoS One},\r\n   volume = {8},\r\n   number = {4},\r\n   pages = {e59439},\r\n   abstract = {Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy.},\r\n   keywords = {Animals\r\nBayes Theorem\r\nDatabases, Genetic\r\nElectron Transport Complex IV/genetics\r\nEvolution, Molecular\r\nGastropoda/*anatomy & histology/*classification\r\n*Phylogeny\r\nRNA, Ribosomal, 28S/genetics},\r\n   ISSN = {1932-6203 (Electronic)\r\n1932-6203 (Linking)},\r\n   DOI = {10.1371/journal.pone.0059439},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/23593138},\r\n   year = {2013},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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\n \n 2011\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n A holistic approach to marine eco-systems biology.\n \n \n \n \n\n\n \n Karsenti, E., Acinas, S. G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J. M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E. G., Sardet, C., Sieracki, M. E., Speich, S., Velayoudon, D., Weissenbach, J., Wincker, P., & Tara Oceans, C.\n\n\n \n\n\n\n PLoS Biol, 9(10): e1001177. 2011.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\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 22 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

@article{RN1,\r\n   author = {Karsenti, E. and Acinas, S. G. and Bork, P. and Bowler, C. and De Vargas, C. and Raes, J. and Sullivan, M. and Arendt, D. and Benzoni, F. and Claverie, J. M. and Follows, M. and Gorsky, G. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels-Lewis, S. and Krzic, U. and Not, F. and Ogata, H. and Pesant, S. and Reynaud, E. G. and Sardet, C. and Sieracki, M. E. and Speich, S. and Velayoudon, D. and Weissenbach, J. and Wincker, P. and Tara Oceans, Consortium},\r\n   title = {A holistic approach to marine eco-systems biology},\r\n   journal = {PLoS Biol},\r\n   volume = {9},\r\n   number = {10},\r\n   pages = {e1001177},\r\n   abstract = {The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.},\r\n   keywords = {Animals\r\n*Ecosystem\r\n*Expeditions\r\n*Marine Biology\r\nOceans and Seas\r\nPlankton/*growth & development},\r\n   ISSN = {1545-7885 (Electronic)\r\n1544-9173 (Linking)},\r\n   DOI = {10.1371/journal.pbio.1001177},\r\n   url = {https://www.ncbi.nlm.nih.gov/pubmed/22028628},\r\n   year = {2011},\r\n   type = {Journal Article}\r\n}\r\n\r\n

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