360 results on '"Grimsley, Nigel"'
Search Results
2. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
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Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C, Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A, Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, and Wincker, Patrick
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Genetics ,Climate Action ,Gene Expression Regulation ,Geography ,Metagenome ,Microbiota ,Molecular Sequence Annotation ,Oceans and Seas ,RNA ,Messenger ,Seawater ,Temperature ,Transcriptome ,Tara Oceans Coordinators ,Tara Oceans ,biogeochemistry ,community turnover ,eco-systems biology ,gene expression change ,global ocean microbiome ,metagenome ,metatranscriptome ,microbial ecology ,ocean warming ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - 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.
- Published
- 2019
3. Marine DNA Viral Macro- and Microdiversity from Pole to Pole
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Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon
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Genetics ,Infection ,Life Below Water ,Aquatic Organisms ,Biodiversity ,DNA Viruses ,DNA ,Viral ,Metagenome ,Water Microbiology ,Tara Oceans Coordinators ,community ecology ,diversity gradients ,marine biology ,metagenomics ,population ecology ,species ,viruses ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - 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 ∼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.
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- 2019
4. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
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Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, and Pelletier, Eric
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- 2022
- Full Text
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5. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
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Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier
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Genetics ,Life Below Water ,Atmospheric Sciences ,Geochemistry ,Oceanography ,Meteorology & Atmospheric Sciences - Abstract
Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.
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- 2019
6. Population genomics of picophytoplankton unveils novel chromosome hypervariability
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Blanc-Mathieu, Romain, Krasovec, Marc, Hebrard, Maxime, Yau, Sheree, Desgranges, Elodie, Martin, Joel, Schackwitz, Wendy, Kuo, Alan, Salin, Gerald, Donnadieu, Cecile, Desdevises, Yves, Sanchez-Ferandin, Sophie, Moreau, Hervé, Rivals, Eric, Grigoriev, Igor V, Grimsley, Nigel, Eyre-Walker, Adam, and Piganeau, Gwenael
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Microbiology ,Biological Sciences ,Ecology ,Genetics ,Biotechnology ,Human Genome ,Life Below Water ,Chromosomes ,Disease Susceptibility ,Evolution ,Molecular ,Genetic Variation ,Genetics ,Population ,Genomics ,Mutation ,Phenotype ,Phylogeny ,Phytoplankton ,Polymorphism ,Single Nucleotide ,Selection ,Genetic ,GC content evolution ,chromothripsis ,evolutionary genomics ,linkage disequilbrium ,mating type locus ,multiple nucleotide mutation events ,picophytoplankton ,population genomics ,prasinovirus ,sex evolution - Abstract
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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- 2017
7. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes
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Benites, L. Felipe, Poulton, Nicole, Labadie, Karine, Sieracki, Michael E., Grimsley, Nigel, and Piganeau, Gwenael
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- 2019
8. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
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Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M., Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C., Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, and Poulain, Julie
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- 2019
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9. Global Trends in Marine Plankton Diversity across Kingdoms of Life
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Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pelletier, Eric, Bopp, Laurent, Lombard, Fabien, and Zinger, Lucie
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- 2019
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10. Marine DNA Viral Macro- and Microdiversity from Pole to Pole
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Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Gregory, Ann C., Zayed, Ahmed A., Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Culley, Alexander I., Dutilh, Bas E., and Roux, Simon
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- 2019
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11. Phycodnaviruses (Phycodnaviridae)
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Van Etten, James L., primary, Dunigan, David D., additional, Nagasaki, Keizo, additional, Schroeder, Declan C., additional, Grimsley, Nigel, additional, Brussaard, Corina P.D., additional, and Nissimov, Jozef I., additional
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- 2021
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12. Typical Features of Genomes in the Mamiellophyceae
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Grimsley, Nigel, Yau, Sheree, Piganeau, Gwenaël, Moreau, Hervé, Ohtsuka, Susumu, editor, Suzaki, Toshinobu, editor, Horiguchi, Takeo, editor, Suzuki, Noritoshi, editor, and Not, Fabrice, editor
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- 2015
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13. Predicting global distributions of eukaryotic plankton communities from satellite data
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Kaneko, Hiroto, Endo, Hisashi, Henry, Nicolas, Berney, Cédric, Mahe, Frédéric, Poulain, Julie, Labadie, Karine, Beluche, Odette, El Hourany, Roy, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Pesant, Stéphane, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Chaffron, Samuel, Wincker, Patrick, Nakamura, Ryosuke, Karp-Boss, Lee, Boss, Emmanuel, Tomii, Kentaro, Ogata, Hiroshi Y., Kaneko, Hiroto, Endo, Hisashi, Henry, Nicolas, Berney, Cédric, Mahe, Frédéric, Poulain, Julie, Labadie, Karine, Beluche, Odette, El Hourany, Roy, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Pesant, Stéphane, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Chaffron, Samuel, Wincker, Patrick, Nakamura, Ryosuke, Karp-Boss, Lee, Boss, Emmanuel, Tomii, Kentaro, and Ogata, Hiroshi Y.
- 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.
- Published
- 2023
14. Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability
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Clerissi, Camille, Grimsley, Nigel, Subirana, Lucie, Maria, Eric, Oriol, Louise, Ogata, Hiroyuki, Moreau, Hervé, and Desdevises, Yves
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- 2014
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15. Genomics of Marine Algae
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Coelho, Susana M., Heesch, Svenja, Grimsley, Nigel, Moreau, Hervé, Cock, J. Mark, Cock, J. Mark, editor, Tessmar-Raible, Kristin, editor, Boyen, Catherine, editor, and Viard, Frédérique, editor
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- 2010
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16. Morphology, Genome Plasticity, and Phylogeny in the Genus Ostreococcus Reveal a Cryptic Species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae)
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Subirana, Lucie, Péquin, Bérangère, Michely, Stéphanie, Escande, Marie-Line, Meilland, Julie, Derelle, Evelyne, Marin, Birger, Piganeau, Gwenaël, Desdevises, Yves, Moreau, Hervé, and Grimsley, Nigel H.
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- 2013
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17. GENETIC EXCHANGES OF INTEINS BETWEEN PRASINOVIRUSES (PHYCODNAVIRIDAE)
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Clerissi, Camille, Grimsley, Nigel, and Desdevises, Yves
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- 2013
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18. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
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Delmont, Tom O, Gaia, Morgan, Hinsinger, Damien D, Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Coordinators, Tara Oceans, Sunagawa, Shinichi, Acinas, Silvia G, Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Pelletier, Eric, Delmont, Tom O, Gaia, Morgan, Hinsinger, Damien D, Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Coordinators, Tara Oceans, Sunagawa, Shinichi, Acinas, Silvia G, Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, and Pelletier, Eric
- Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
- Published
- 2022
19. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
- Author
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Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Pelletier, Eric, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, and Pelletier, Eric
- Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
- Published
- 2022
20. Genome diversity in the smallest marine photosynthetic eukaryotes
- Author
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Piganeau, Gwenael, Grimsley, Nigel, and Moreau, Herve
- Published
- 2011
- Full Text
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21. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
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Delmont, Tom O., primary, Gaia, Morgan, additional, Hinsinger, Damien D., additional, Frémont, Paul, additional, Vanni, Chiara, additional, Fernandez-Guerra, Antonio, additional, Eren, A. Murat, additional, Kourlaiev, Artem, additional, d'Agata, Leo, additional, Clayssen, Quentin, additional, Villar, Emilie, additional, Labadie, Karine, additional, Cruaud, Corinne, additional, Poulain, Julie, additional, Da Silva, Corinne, additional, Wessner, Marc, additional, Noel, Benjamin, additional, Aury, Jean-Marc, additional, de Vargas, Colomban, additional, Bowler, Chris, additional, Karsenti, Eric, additional, Pelletier, Eric, additional, Wincker, Patrick, additional, Jaillon, Olivier, additional, Sunagawa, Shinichi, additional, Acinas, Silvia G., additional, Bork, Peer, additional, Sardet, Christian, additional, Stemmann, Lars, additional, Lescot, Magali, additional, Babin, Marcel, additional, Gorsky, Gabriel, additional, Grimsley, Nigel, additional, Guidi, Lionel, additional, Hingamp, Pascal, additional, Kandels, Stefanie, additional, Iudicone, Daniele, additional, Ogata, Hiroyuki, additional, Pesant, Stéphane, additional, Sullivan, Matthew B., additional, Not, Fabrice, additional, Lee, Karp-Boss, additional, Boss, Emmanuel, additional, Cochrane, Guy, additional, Follows, Michael, additional, Poulton, Nicole, additional, Raes, Jeroen, additional, Sieracki, Mike, additional, and Speich, Sabrina, additional
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- 2022
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22. Agroinfection as a tool for the Investigation of Plant-Pathogen Interactions
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Grimsley, Nigel, Jarchow, Elke, Oetiker, Juerg, Schlaeppi, Michael, Hohn, Barbara, Herrmann, R. G., editor, and Larkins, B. A., editor
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- 1991
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23. Macroscale patterns of oceanic zooplankton composition and size structure
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Brandão, Manoela, Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea, Picheral, Marc, Henry, Nicolas, Acinas, Silvia, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sullivan, Matthew, Sunagawa, Shinichi, Wincker, Patrick, Stemmann, Lars, Lombard, Fabien, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC)
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[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere ,[SDU]Sciences of the Universe [physics] ,fungi - Abstract
International audience; 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 CO 2 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.
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- 2021
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24. Evolutionary genomics of sex-related chromosomes at the base of the green lineage 2
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Felipe Benites, L, Bucchini, François, Sanchez-Brosseau, Sophie, Grimsley, Nigel, Vandepoele, Klaas, Piganeau, Gwenael, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), and Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics
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mating-type loci ,GC content ,chlorophyta ,recombination suppression ,[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography - Abstract
International audience; Abstract While sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT+ and MT- alleles, spanning 450-650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT+ and MT- alleles. We analysed the phylogenetic profile and GC content of MT gene families in eight different species, whose divergence has been previously estimated at up to 640 million years, and found evidence that the divergence of the two MTs alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT trans-specific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.
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- 2021
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25. Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes
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Clerissi, Camille, Desdevises, Yves, Romac, Sarah, Audic, Stéphane, de Vargas, Colomban, Acinas, Silvia G, Casotti, Raffaella, Poulain, Julie, Wincker, Patrick, Hingamp, Pascal, Ogata, Hiroyuki, and Grimsley, Nigel
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- 2015
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26. ``Agroinfection,'' an Alternative Route for Viral Infection of Plants by Using the Ti Plasmid
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Grimsley, Nigel, Hohn, Barbara, Hohn, Thomas, and Walden, Richard
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- 1986
27. Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage
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Benites, Luis Felipe, primary, Bucchini, François, additional, Sanchez-Brosseau, Sophie, additional, Grimsley, Nigel, additional, Vandepoele, Klaas, additional, and Piganeau, Gwenaël, additional
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- 2021
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28. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean
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Royo-Llonch, Marta, Sánchez, Pablo, Ruiz-González, Clara, Salazar, Guillem, Pedrós-Alió, Carlos, Sebastián, Marta, Labadie, Karine, Paoli, Lucas, M. Ibarbalz, Federico, Zinger, Lucie, Churcheward, Benjamin, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Setmmann, Lars, Sullivan, Matthew B., Chaffron, Samuel, Eveillard, Damien, Karsenti, Eric, Sunagawa, Shinichi, Wincker, Patrick, Karp-Boss, Lee, Bowler, Chris, Acinas, Silvia G., Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Centre National de la Recherche Scientifique (France), European Commission, European Molecular Biology Laboratory, Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Universidad de Granada = University of Granada (UGR), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Microbiology and Swiss Institute of Bioinformatics, Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, European Molecular Biology Laboratory [Heidelberg] (EMBL), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Maine, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), and European Project: 862923,AtlantECO
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Microbiology (medical) ,Environmental change ,SURFACE ,Mesopelagic zone ,education ,Immunology ,DIVERSITY ,PROTEIN ,ECOLOGY ,Applied Microbiology and Biotechnology ,Microbiology ,[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genetics ,Marine ecosystem ,GENE-EXPRESSION ,Science & Technology ,biology ,KINGDOMS ,Ecology ,[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN] ,Cell Biology ,biology.organism_classification ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,READ ALIGNMENT ,Polar circle ,Arctic ,Habitat ,Metagenomics ,SEA-ICE ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,COMMUNITIES ,Life Sciences & Biomedicine ,Archaea ,BIOGEOGRAPHY ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis - Abstract
14 pages, 6 figures, additional information https://doi.org/10.1038/s41564-021-00979-9.-- Data availability: Accession numbers for the data used and generated in this study can be found in Supplementary Table 12, which includes the Arctic MAGs Catalogue and their functional annotation (European Bioinformatics Institute BioStudies ID: S-BSST451) and the co-assembly of metagenomic samples used to generate the metagenomic bins (European Nucleotide Archive PRJEB41575). Accession numbers for the metagenomic and metatranscriptomic samples used in the fragment recruitment analyses can be found in Supplementary Table 13. Publicly available datasets used in this study include the following: CheckM v.1.0.11 (https://github.com/Ecogenomics/CheckM/releases/tag/v1.1.0), GTDB release 89 (https://data.gtdb.ecogenomic.org/releases/release89/), SILVA 132 (https://www.arb-silva.de/documentation/release-132/), KEGG release 89.1 (https://www.genome.jp/kegg/docs/relnote.html) and Pfam database release 31.0 (http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/). Source data are provided with this paper, 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, This work acknowledges the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). We thank the commitment of the following sponsors and research funding agencies: the Spanish Ministry of Economy and Competitiveness (project MAGGY, grant no. CTM2017-87736-R and Polar EcoGen PID2020-116489RB-I00), Horizon 2020-Research and Innovation Framework Programme (Atlantic ECOsystems assessment, forecasting & sustainability, grant no. H2020-BG-2019-2), Centre National de la Recherche Scientifique (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory, Genoscope/Commissariat à l’Énergie Atomique et aux Énergies Alternatives, the French Ministry of Research and the French Government’s ‘Investissements d’Avenir’ programmes OCEANOMICS (project no. ANR-11-BTBR-0008), FRANCE GENOMIQUE (project no. ANR-10-INBS-09-08), MEMO LIFE (project no. ANR-10-LABX-54), Paris Sciences et Lettres University (project no. ANR-11-IDEX-0001-02), Eidgenössische Technische Hochschule Zürich and Helmut Horten Foundation, the Swiss National Foundation (project no. 205321_184955), MEXT/JSPS/KAKENHI (project nos. 16H06429, 16K21723, 16H06437 and 18H02279)
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- 2021
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29. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence
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Sandaa, Ruth‐Anne, primary, Saltvedt, Marius R., additional, Dahle, Håkon, additional, Wang, Haina, additional, Våge, Selina, additional, Blanc‐Mathieu, Romain, additional, Steen, Ida H., additional, Grimsley, Nigel, additional, Edvardsen, Bente, additional, Ogata, Hiroyuki, additional, and Lawrence, Janice, additional
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- 2021
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30. Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere
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Pinto, Jordan, primary, Lami, Raphaël, additional, Krasovec, Marc, additional, Grimaud, Régis, additional, Urios, Laurent, additional, Lupette, Josselin, additional, Escande, Marie-Line, additional, Sanchez, Frédéric, additional, Intertaglia, Laurent, additional, Grimsley, Nigel, additional, Piganeau, Gwenaël, additional, and Sanchez-Brosseau, Sophie, additional
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- 2021
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31. Tara Oceans: towards global ocean ecosystems biology
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Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Bowler, Chris, Babin, Marcel, Boss, Emmanuel, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Lescot, Magali, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Sieracki, Mike, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Wincker, Patrick, Eveillard, Damien, Lombard, Fabien, Pesant, Stephane, Institute of Microbiology, Department of Biology, ETH Zurich, Institute of Microbiology, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), European Molecular Biology Laboratory [Heidelberg] (EMBL), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Ohio University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ministerio de Ciencia, Innovación y Universidades (España), Centre National de la Recherche Scientifique (France), Fonds Français pour l'Environnement Mondial, National Aeronautics and Space Administration (US), Canada Foundation for Innovation, European Commission, Harvard University, Gordon and Betty Moore Foundation, National Science Foundation (US), ETH Zurich, Helmut Horten Foundation, Swiss National Science Foundation, Agencia Estatal de Investigación (España), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)
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0303 health sciences ,General Immunology and Microbiology ,030306 microbiology ,business.industry ,Ecology (disciplines) ,Environmental resource management ,[INFO.INFO-OH]Computer Science [cs]/Other [cs.OH] ,Biodiversity ,Climate change ,Plankton ,Biology ,Microbiology ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Environmental data ,03 medical and health sciences ,Infectious Diseases ,13. Climate action ,Anthropocene ,Marine ecosystem ,Ecosystem ,14. Life underwater ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,business ,ComputingMilieux_MISCELLANEOUS ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis - Abstract
This article is contribution number 100 of Tara Oceans.-- 18 pages, 6 figures, 2 boxes, supplementary information https://doi.org/10.1038/s41579-020-0364-5, 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, Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org/). The authors further thank the commitment of the following sponsors: the French CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara GOSEE), the French Facility for Global Environment (FFEM), the European Molecular Biology Laboratory, Genoscope/CEA, the French Ministry of Research and the French Government Investissements d’Avenir programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08) and MEMO LIFE (ANR-10-LABX-54), the PSL research university (ANR-11-IDEX-0001-02) and EMBRC-France (ANR-10-INBS-02). Funding for the collection and processing of the Tara Oceans data set was provided by the NASA Ocean Biology and Biogeochemistry Program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G and NNX15AC08G (to the University of Maine), the Canada Excellence Research Chair in Remote Sensing of Canada’s New Arctic Frontier and the Canada Foundation for Innovation. [...] C.B. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement 835067) as well as the Radcliffe Institute of Advanced Study at Harvard University for a scholar’s fellowship during the 2016–2017 academic year. M.B.S. thanks the Gordon and Betty Moore Foundation (award 3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) as well as the Ohio Supercomputer for computational support. S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). [...] S. Sunagawa is supported by ETH Zürich and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
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- 2020
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32. Macroscale patterns of oceanic zooplankton composition and size structure
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Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, Winckler, Patrick, Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, and Winckler, Patrick
- 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.
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- 2021
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33. Genomics of Algal Host–Virus Interactions
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Grimsley, Nigel H., primary, Thomas, Rozenn, additional, Kegel, Jessica U., additional, Jacquet, Stéphan, additional, Moreau, Hervé, additional, and Desdevises, Yves, additional
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- 2012
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34. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes
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Vandepoele, Klaas, Van Bel, Michiel, Richard, Guilhem, Van Landeghem, Sofie, Verhelst, Bram, Moreau, Hervé, Van de Peer, Yves, Grimsley, Nigel, and Piganeau, Gwenael
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- 2013
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35. Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri
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Thomy, Julie, primary, Sanchez, Frederic, additional, Gut, Marta, additional, Cruz, Fernando, additional, Alioto, Tyler, additional, Piganeau, Gwenael, additional, Grimsley, Nigel, additional, and Yau, Sheree, additional
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- 2021
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36. Acquisition and maintenance of resistance to viruses in eukaryotic phytoplankton populations
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Thomas, Rozenn, Grimsley, Nigel, Escande, Marie-line, Subirana, Lucie, Derelle, Evelyne, and Moreau, Hervé
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- 2011
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37. Responses to iron oxide and zinc oxide nanoparticles in echinoderm embryos and microalgae: uptake, growth, morphology, and transcriptomic analysis
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Genevière, Anne-Marie, primary, Derelle, Evelyne, additional, Escande, Marie-Line, additional, Grimsley, Nigel, additional, Klopp, Christophe, additional, Ménager, Christine, additional, Michel, Aude, additional, and Moreau, Hervé, additional
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- 2020
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38. The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies
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Bousquet, Laurie, primary, Hemon, Claire, additional, Malburet, Paul, additional, Bucchini, François, additional, Vandepoele, Klaas, additional, Grimsley, Nigel, additional, Moreau, Hervé, additional, and Echeverria, Manuel, additional
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- 2020
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39. Hervé Moreau 16/10/1958 - 05/07/2020
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Piganeau, Gwenaël, additional and Grimsley, Nigel, additional
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- 2020
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40. Visualization of Viral Infection Dynamics in a Unicellular Eukaryote and Quantification of Viral Production Using Virus Fluorescence in situ Hybridization
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Castillo, Yaiza M., primary, Sebastián, Marta, additional, Forn, Irene, additional, Grimsley, Nigel, additional, Yau, Sheree, additional, Moraru, Cristina, additional, and Vaqué, Dolors, additional
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- 2020
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41. Virus-host coexistence in phytoplankton through the genomic lens
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Yau, Sheree, primary, Krasovec, Marc, additional, Benites, L. Felipe, additional, Rombauts, Stephane, additional, Groussin, Mathieu, additional, Vancaester, Emmelien, additional, Aury, Jean-Marc, additional, Derelle, Evelyne, additional, Desdevises, Yves, additional, Escande, Marie-Line, additional, Grimsley, Nigel, additional, Guy, Julie, additional, Moreau, Hervé, additional, Sanchez-Brosseau, Sophie, additional, Van de Peer, Yves, additional, Vandepoele, Klaas, additional, Gourbiere, Sebastien, additional, and Piganeau, Gwenael, additional
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- 2020
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42. Abundance, spatial distribution and genetic diversity of Ostreococcus tauri viruses in two different environments
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Bellec, Laure, Grimsley, Nigel, Derelle, Evelyne, Moreau, Hervé, and Desdevises, Yves
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- 2010
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43. Cryptic Sex in the Smallest Eukaryotic Marine Green Alga
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Grimsley, Nigel, Péquin, Bérangère, Bachy, Charles, Moreau, Hervé, and Piganeau, Gwenaël
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- 2010
44. Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure
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Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Lombard, Fabien, Takuvik Joint International Laboratory ULAVAL-CNRS, and Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS)
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0303 health sciences ,Multidisciplinary ,Science ,Composition (combinatorics) ,Zooplankton ,03 medical and health sciences ,0302 clinical medicine ,Oceanography ,[SDE]Environmental Sciences ,Medicine ,Environmental science ,14. Life underwater ,Author Correction ,ComputingMilieux_MISCELLANEOUS ,030217 neurology & neurosurgery ,030304 developmental biology - 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 CO
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- 2021
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45. Phylogenetic analysis of new Prasinoviruses (Phycodnaviridae) that infect the green unicellular algae Ostreococcus, Bathycoccus and Micromonas
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Bellec, Laure, Grimsley, Nigel, Moreau, Hervé, and Desdevises, Yves
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- 2009
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46. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
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Salazar Guiral, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca Vera, Miguelangel, Field, Christopher, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C., Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tara Oceans Coordinators, Wincker, Patrick, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy R., de Vargas, Colomban, Follows, Michael J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew, and Sunagawa, Shinichi
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ocean warming ,eco-systems biology ,biogeochemistry ,Tara Oceans ,global ocean microbiome ,metatranscriptome ,metagenome ,microbial ecology ,gene expression change ,community turnover - 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., Cell, 179 (5), ISSN:0092-8674, ISSN:1097-4172
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- 2019
47. Global Trends in Marine Plankton Diversity across Kingdoms of Life
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Ibarbalz, Federico M, Henry, Nicolas, Brandao, Manoela C, Martini, Verine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M, Gregory, Ann C, Mahe, Frederic, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Saez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A, Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Celine, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stephane, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Bopp, Laurent, Lombard, Fabien, and Zinger, Lucie
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Biochemistry & Molecular Biology ,Science & Technology ,CLIMATE-CHANGE ,fungi ,Cell Biology ,ECOLOGY ,LATITUDINAL GRADIENTS ,OCEAN ,PHYTOPLANKTON ,PATTERNS ,DISTRIBUTIONS ,BIODIVERSITY ,Life Sciences & Biomedicine ,TEMPERATURE ,human activities ,MICROBIAL DIVERSITY - 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 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT. ispartof: CELL vol:179 issue:5 pages:1084-+ ispartof: location:United States status: published
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- 2019
48. Virus-host coexistence in phytoplankton through the genomic lens
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Yau, Sheree, Krasovec, Marc, Benites, L. Felipe, Rombauts, Stephane, Groussin, Mathieu, Vancaester, Emmelien, Aury, Jean-marc, Derelle, Evelyne, Desdevises, Yves, Escande, Marie-line, Grimsley, Nigel, Guy, Julie, Moreau, Hervé, Sanchez-brosseau, Sophie, Van De Peer, Yves, Vandepoele, Klaas, Gourbiere, Sebastien, Piganeau, Gwenael, Yau, Sheree, Krasovec, Marc, Benites, L. Felipe, Rombauts, Stephane, Groussin, Mathieu, Vancaester, Emmelien, Aury, Jean-marc, Derelle, Evelyne, Desdevises, Yves, Escande, Marie-line, Grimsley, Nigel, Guy, Julie, Moreau, Hervé, Sanchez-brosseau, Sophie, Van De Peer, Yves, Vandepoele, Klaas, Gourbiere, Sebastien, and Piganeau, Gwenael
- Abstract
Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.
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- 2020
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49. Responses to iron oxide and zinc oxide nanoparticles in echinoderm embryos and microalgae: uptake, growth, morphology, and transcriptomic analysis
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Genevière, Anne-marie, Derelle, Evelyne, Escande, Marie-line, Grimsley, Nigel, Klopp, Christophe, Ménager, Christine, Michel, Aude, Moreau, Hervé, Genevière, Anne-marie, Derelle, Evelyne, Escande, Marie-line, Grimsley, Nigel, Klopp, Christophe, Ménager, Christine, Michel, Aude, and Moreau, Hervé
- Abstract
We investigated the toxicity of Iron oxide and Zinc oxide engineered nanoparticles (ENPs) on Paracentrotus lividus sea urchin embryos and three species of microalgae. Morphological responses, internalization, and potential impacts of Fe2O3 and ZnO ENPs on physiology and metabolism were assessed. Both types of ENPs affected P. lividus larval development, but ZnO ENPs had a much stronger effect. While growth of the alga Micromonas commoda was severely impaired by both ENPs, Ostreococcus tauri or Nannochloris sp. were unaffected. Transmission electron microscopy showed the internalization of ENPs in sea urchin embryonic cells while only nanoparticle interaction with external membranes was evidenced in microalgae, suggesting that marine organisms react in diverse ways to ENPs. Transcriptome-wide analysis in P. lividus and M. commoda showed that many different physiological pathways were affected, some of which were common to both species, giving insights about the mechanisms underpinning toxic responses
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- 2020
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50. Virus-host coexistence in phytoplankton through the genomic lens
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Agence Nationale de la Recherche (France), European Commission, Agencia Estatal de Investigación (España), Yau, Sheree, Rombauts, Stéphane, Benites, L. Felipe, Groussin, Mathieu, Vancaester, Emmelien, Aury, Jean‐Marc, Derelle, Evelyne, Desdevises, Yves, Escande, Marie-Line, Grimsley, Nigel, Guy, Julie, Moreau, Hervé, Sanchez-Brosseau, Sophie, Van de Peer, Yves, Vandepoele, Klaas, Gourbiere, Sebastien, Piganeau, Gwenael, Agence Nationale de la Recherche (France), European Commission, Agencia Estatal de Investigación (España), Yau, Sheree, Rombauts, Stéphane, Benites, L. Felipe, Groussin, Mathieu, Vancaester, Emmelien, Aury, Jean‐Marc, Derelle, Evelyne, Desdevises, Yves, Escande, Marie-Line, Grimsley, Nigel, Guy, Julie, Moreau, Hervé, Sanchez-Brosseau, Sophie, Van de Peer, Yves, Vandepoele, Klaas, Gourbiere, Sebastien, and Piganeau, Gwenael
- Abstract
Virus-microbe interactions in the ocean are commonly described by “boom and bust”dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.
- Published
- 2020
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