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37 results on '"Troublé, Romain"'

1. Comparison of macrolitter and meso- and microplastic pollution on French riverbanks and coastal beaches using citizen science with schoolchildren

Author: Philip, Léna, Le Picard, Maëla, Lavergne, Edouard, Bourgain, Pascaline, Sabard, Brigitte, Troublé, Romain, Meistertzheim, Anne-Leila, Ludwig, Wolfgang, ter Halle, Alexandra, Lacroix, Camille, and Ghiglione, Jean-François
Published: 2024
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2. Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Author: Canesi, Marine, Douville, Eric, Montagna, Paolo, Bordier, Louise, Caquineau, Sandrine, Pons-Branchu, Edwige, Iwankow, Guillaume, Stolarski, Jarosław, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie
Published: 2024
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3. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Author: Reddy, Maggie M., Goossens, Corentine, Zhou, Yuxiang, Chaib, Slimane, Raviglione, Delphine, Nicolè, Florence, Hume, Benjamin C. C., Forcioli, Didier, Agostini, Sylvain, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Voolstra, Christian R., Allemand, Denis, Planes, Serge, Thomas, Olivier P., and Banaigs, Bernard
Published: 2023
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4. Different environmental response strategies in sympatric corals from Pacific Islands

Author: Porro, Barbara, Zamoum, Thamilla, Forcioli, Didier, Gilson, Eric, Poquet, Adrien, Di Franco, Eugenio, Barnay-Verdier, Stéphanie, Lombard, Fabien, Voolstra, Christian R., Hume, Benjamin C. C., Galand, Pierre E., Moulin, Clémentine, Boissin, Emilie, Bourdin, Guillaume, Iwankow, Guillaume, Poulain, Julie, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Planes, Serge, Allemand, Denis, Röttinger, Eric, and Furla, Paola
Published: 2023
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5. Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Author: Canesi, Marine, Douville, Eric, Montagna, Paolo, Taviani, Marco, Stolarski, Jarosław, Bordier, Louise, Dapoigny, Arnaud, Coulibaly, Gninwoyo Eric Hermann, Simon, Anne-Catherine, Agelou, Mathieu, Fin, Jonathan, Metzl, Nicolas, Iwankow, Guillaume, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie
Published: 2023
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6. An integrative assessment of the plastic debris load in the Mediterranean Sea

Author: Pedrotti, Maria Luiza, Lombard, Fabien, Baudena, Alberto, Galgani, François, Elineau, Amanda, Petit, Stephanie, Henry, Maryvonne, Troublé, Romain, Reverdin, Gilles, Ser-Giacomi, Enrico, Kedzierski, Mikaël, Boss, Emmanuel, and Gorsky, Gabriel
Published: 2022
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7. Comparison of the macro-, meso- and microplastic pollution in French riverbanks and beaches using citizen science with schoolchildren

Author: Philip, Léna, primary, Picard, Maela Le, additional, Lavergne, Edouard, additional, Bourgain, Pascaline, additional, Sabard, Brigitte, additional, Troublé, Romain, additional, Meistertzheim, Anne-Leila, additional, Ludwig, Wolfgang, additional, Halle, Alexandra ter, additional, Lacroix, Camille, additional, and Ghiglione, Jean-Francois, additional
Published: 2024
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8. A Roadmap for Using the UN Decade of Ocean Science for Sustainable Development in Support of Science, Policy, and Action

Author: Claudet, Joachim, Bopp, Laurent, Cheung, William W.L., Devillers, Rodolphe, Escobar-Briones, Elva, Haugan, Peter, Heymans, Johanna J., Masson-Delmotte, Valérie, Matz-Lück, Nele, Miloslavich, Patricia, Mullineaux, Lauren, Visbeck, Martin, Watson, Robert, Zivian, Anna Milena, Ansorge, Isabelle, Araujo, Moacyr, Aricò, Salvatore, Bailly, Denis, Barbière, Julian, Barnerias, Cyrille, Bowler, Chris, Brun, Victor, Cazenave, Anny, Diver, Cameron, Euzen, Agathe, Gaye, Amadou Thierno, Hilmi, Nathalie, Ménard, Frédéric, Moulin, Cyril, Muñoz, Norma Patricia, Parmentier, Rémi, Pebayle, Antoine, Pörtner, Hans-Otto, Osvaldina, Silva, Ricard, Patricia, Santos, Ricardo Serrão, Sicre, Marie-Alexandrine, Thiébault, Stéphanie, Thiele, Torsten, Troublé, Romain, Turra, Alexander, Uku, Jacqueline, and Gaill, Françoise
Published: 2020
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9. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Author: Voolstra, Christian R., primary, Hume, Benjamin C. C., additional, Armstrong, Eric J., additional, Mitushasi, Guinther, additional, Porro, Barbara, additional, Oury, Nicolas, additional, Agostini, Sylvain, additional, Boissin, Emilie, additional, Poulain, Julie, additional, Carradec, Quentin, additional, Paz-García, David A., additional, Zoccola, Didier, additional, Magalon, Hélène, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Planes, Serge, additional, Allemand, Denis, additional, and Forcioli, Didier, additional
Published: 2023
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10. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Author: Rouan, Alice, primary, Pousse, Melanie, additional, Djerbi, Nadir, additional, Porro, Barbara, additional, Bourdin, Guillaume, additional, Carradec, Quentin, additional, Hume, Benjamin CC., additional, Poulain, Julie, additional, Lê-Hoang, Julie, additional, Armstrong, Eric, additional, Agostini, Sylvain, additional, Salazar, Guillem, additional, Ruscheweyh, Hans-Joachim, additional, Aury, Jean-Marc, additional, Paz-García, David A., additional, McMinds, Ryan, additional, Giraud-Panis, Marie-Josèphe, additional, Deshuraud, Romane, additional, Ottaviani, Alexandre, additional, Morini, Lycia Die, additional, Leone, Camille, additional, Wurzer, Lia, additional, Tran, Jessica, additional, Zoccola, Didier, additional, Pey, Alexis, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, de Vargas, Colomban, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Douville, Eric, additional, Flores, Michel, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Planes, Serge, additional, Allemand, Denis, additional, Pesant, Stephane, additional, Galand, Pierre E., additional, Wincker, Patrick, additional, Sunagawa, Shinichi, additional, Röttinger, Eric, additional, Furla, Paola, additional, Voolstra, Christian R., additional, Forcioli, Didier, additional, Lombard, Fabien, additional, and Gilson, Eric, additional
Published: 2023
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11. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author: Veglia, Alex J., primary, Bistolas, Kalia S. I., additional, Voolstra, Christian R., additional, Hume, Benjamin C. C., additional, Ruscheweyh, Hans-Joachim, additional, Planes, Serge, additional, Allemand, Denis, additional, Boissin, Emilie, additional, Wincker, Patrick, additional, Poulain, Julie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Correa, Adrienne M. S., additional, and Vega Thurber, Rebecca L., additional
Published: 2023
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12. Pervasive tandem duplications and convergent evolution shape coral genomes

Author: Noel, Benjamin, primary, Denoeud, France, additional, Rouan, Alice, additional, Buitrago-López, Carol, additional, Capasso, Laura, additional, Poulain, Julie, additional, Boissin, Emilie, additional, Pousse, Mélanie, additional, Da Silva, Corinne, additional, Couloux, Arnaud, additional, Armstrong, Eric, additional, Carradec, Quentin, additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Lê-Hoang, Julie, additional, Tambutté, Sylvie, additional, Barbe, Valérie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, J. Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Allemand, Denis, additional, Planes, Serge, additional, Gilson, Eric, additional, Zoccola, Didier, additional, Wincker, Patrick, additional, Voolstra, Christian R., additional, and Aury, Jean-Marc, additional
Published: 2023
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13. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean

Author: Armstrong, Eric J., primary, Lê-Hoang, Julie, additional, Carradec, Quentin, additional, Aury, Jean-Marc, additional, Noel, Benjamin, additional, Hume, Benjamin C. C., additional, Voolstra, Christian R., additional, Poulain, Julie, additional, Belser, Caroline, additional, Paz-García, David A., additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Da Silva, Corinne, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Zoccola, Didier, additional, Planes, Serge, additional, Allemand, Denis, additional, and Wincker, Patrick, additional
Published: 2023
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14. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, primary, Bourdin, Guillaume, additional, Pesant, Stéphane, additional, Agostini, Sylvain, additional, Baudena, Alberto, additional, Boissin, Emilie, additional, Cassar, Nicolas, additional, Clampitt, Megan, additional, Conan, Pascal, additional, Da Silva, Ophélie, additional, Dimier, Céline, additional, Douville, Eric, additional, Elineau, Amanda, additional, Fin, Jonathan, additional, Flores, J. Michel, additional, Ghiglione, Jean-François, additional, Hume, Benjamin C. C., additional, Jalabert, Laetitia, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, McMinds, Ryan, additional, Mériguet, Zoé, additional, Metzl, Nicolas, additional, Paz-García, David A., additional, Pedrotti, Maria Luiza, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Ras, Joséphine, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Rouan, Alice, additional, Röttinger, Eric, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Moulin, Clémentine, additional, Iwankow, Guillaume, additional, Banaigs, Bernard, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Sullivan, Matthew B., additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Boss, Emmanuel, additional, and Gorsky, Gaby, additional
Published: 2023
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15. Diversity of the Pacific Ocean coral reef microbiome

Author: Galand, Pierre E., primary, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Hochart, Corentin, additional, Henry, Nicolas, additional, Hume, Benjamin C. C., additional, Oliveira, Pedro H., additional, Perdereau, Aude, additional, Labadie, Karine, additional, Belser, Caroline, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Armstrong, Eric J., additional, Paz-García, David A., additional, Ziegler, Maren, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Voolstra, Christian R., additional, Thurber, Rebecca Vega, additional, Sunagawa, Shinichi, additional, Wincker, Patrick, additional, Allemand, Denis, additional, and Planes, Serge, additional
Published: 2023
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16. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author: Hochart, Corentin, primary, Paoli, Lucas, additional, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Ziegler, Maren, additional, Porro, Barbara, additional, Armstrong, Eric J., additional, Hume, Benjamin C. C., additional, Aury, Jean-Marc, additional, Pogoreutz, Claudia, additional, Paz-García, David A., additional, Nugues, Maggy M., additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Thurber, Rebecca Vega, additional, Voolstra, Christian R., additional, Sunagawa, Shinichi, additional, and Galand, Pierre E., additional
Published: 2023
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17. Pervasive tandem duplications and convergent evolution shape coral genomes

Author: Noel, Benjamin, Denoeud, France, Rouan, Alice, Buitrago-López, Carol, Capasso, Laura, Poulain, Julie, Boissin, Emilie, Pousse, Mélanie, da Silva, Corinne, Couloux, Arnaud, Armstrong, Eric, Carradec, Quentin, Cruaud, Corinne, Labadie, Karine, Lê-Hoang, Julie, Tambutté, Sylvie, Barbe, Valérie, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew, Sunagawa, Shinichi, Thomas, Olivier, Troublé, Romain, Thurber, Rebecca, Allemand, Denis, Planes, Serge, Gilson, Eric, Zoccola, Didier, Wincker, Patrick, Voolstra, Christian, Aury, Jean-Marc, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), 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), 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), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU]Sciences of the Universe [physics]
Abstract: Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience. † Benjamin Noel and France Denoeud have equal contribution.
Published: 2023
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18. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, Gorsky, Gaby, Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, and Gorsky, Gaby
Abstract: The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
Published: 2023
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19. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Author: Voolstra, Christian R., Hume, Benjamin C. C., Armstrong, Eric J., Mitushasi, Guinther, Porro, Barbara, Oury, Nicolas, Agostini, Sylvain, Boissin, Emilie, Poulain, Julie, Carradec, Quentin, Paz-garcía, David A., Zoccola, Didier, Magalon, Hélène, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Vega Thurber, Rebecca, Wincker, Patrick, Planes, Serge, Allemand, Denis, Forcioli, Didier, Voolstra, Christian R., Hume, Benjamin C. C., Armstrong, Eric J., Mitushasi, Guinther, Porro, Barbara, Oury, Nicolas, Agostini, Sylvain, Boissin, Emilie, Poulain, Julie, Carradec, Quentin, Paz-garcía, David A., Zoccola, Didier, Magalon, Hélène, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Vega Thurber, Rebecca, Wincker, Patrick, Planes, Serge, Allemand, Denis, and Forcioli, Didier
Abstract: Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla—across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.
Published: 2023
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20. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale

Author: Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, de Vargas, Colomban, Le Bescot, Noan, Pollina, Thibaut, Henry, Nicolas, Romac, Sarah, Colin, Sébastien, Haëntjens, Nils, Carmichael, Margaux, Berger, Calixte, Le Guen, David, Decelle, Johan, Mahé, Frédéric, Poulain, Julie, Malpot, Emmanuel, Beaumont, Carole, Hardy, Michel, Guiffant, Damien, Probert, Ian, Gruber, David F, Allen, Andrew E, Gorsky, Gabriel, Follows, Michael J, Pochon, Xavier, Troublé, Romain, Cael, BB, Lombard, Fabien, Boss, Emmanuel, Prakash, Manu, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, de Vargas, Colomban, Le Bescot, Noan, Pollina, Thibaut, Henry, Nicolas, Romac, Sarah, Colin, Sébastien, Haëntjens, Nils, Carmichael, Margaux, Berger, Calixte, Le Guen, David, Decelle, Johan, Mahé, Frédéric, Poulain, Julie, Malpot, Emmanuel, Beaumont, Carole, Hardy, Michel, Guiffant, Damien, Probert, Ian, Gruber, David F, Allen, Andrew E, Gorsky, Gabriel, Follows, Michael J, Pochon, Xavier, Troublé, Romain, Cael, BB, Lombard, Fabien, Boss, Emmanuel, and Prakash, Manu
Abstract: In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modeled at the planetary scale, biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce ‘Plankton Planet’, an initiative whose goal is to engage the curiosity and creativity of researchers, makers, and mariners to (i) co-develop a new generation of cost-effective (frugal) universal scientific instrumentation to measure the genetic and morphological diversity of marine microbiomes in context, (ii) organize their systematic deployment through coastal or open ocean communities of sea-users/farers, to generate uniform plankton data across global and long-term spatio-temporal scales, and (iii) setup tools to flow the data without embargo into public and explorable databases. As proof-of-concept, we show how 20 crews of sailors were able to sample plankton biomass from the world surface ocean in a single year, generating the first seatizen-based, planetary dataset of marine plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. The data unveil significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morph
Published: 2023

21. From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,PocilloporaandPorites

Author: Deshuraud, Romane, primary, Ottaviani, Alexandre, additional, Poulain, Julie, additional, Leprêtre, Marine, additional, Beluche, Odette, additional, Mahieu, Eric, additional, Lebled, Sandrine, additional, Belser, Caroline, additional, Rouan, Alice, additional, Moulin, Clementine, additional, Boissin, Emilie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Vargas, Colomban de, additional, Douville, Eric, additional, Flores, Michel, additional, Furla, Paola, additional, Galand, Pierre, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B, additional, Sunagawa, Shinichi, additional, Thomas, Olivier, additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Voolstra, Christian R., additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Planes, Serge, additional, Allemand, Denis, additional, Gilson, Eric, additional, and Forcioli, Didier, additional
Published: 2022
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22. Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories

Author: Hume, Benjamin C C, primary, Voolstra, Christian R, additional, Armstrong, Eric, additional, Mitushasi, Guinther, additional, Porro, Barbara, additional, Oury, Nicolas, additional, Agostini, Sylvain, additional, Boissin, Emilie, additional, Poulain, Julie, additional, Carradec, Quentin, additional, Paz-García, David A., additional, Zoccola, Didier, additional, Magalon, Hélène, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Furla, Paola, additional, Galand, Pierre E, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier, additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Planes, Serge, additional, Allemand, Denis, additional, and Forcioli, Didier, additional
Published: 2022
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23. Basin-Scale Underway Quantitative Survey of Surface Microplankton Using Affordable Collection and Imaging Tools Deployed From Tara

Author: Mériguet, Zoé, primary, Oddone, Anna, additional, Le Guen, David, additional, Pollina, Thibaut, additional, Bazile, Romain, additional, Moulin, Clémentine, additional, Troublé, Romain, additional, Prakash, Manu, additional, de Vargas, Colomban, additional, and Lombard, Fabien, additional
Published: 2022
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24. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, primary, Bourdin, Guillaume, additional, Pesant, Stéphane, additional, Agostini, Sylvain, additional, Baudena, Alberto, additional, Boissin, Emilie, additional, Cassar, Nicolas, additional, Clampitt, Megan, additional, Conan, Pascal, additional, Silva, Ophélie Da, additional, Dimier, Céline, additional, Douville, Eric, additional, Elineau, Amanda, additional, Fin, Jonathan, additional, Flores, J. Michel, additional, Ghiglione, Jean François, additional, Hume, Benjamin C.C., additional, Jalabert, Laetitia, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, McMinds, Ryan, additional, Mériguet, Zoé, additional, Metzl, Nicolas, additional, Paz-García, David A., additional, Pedrotti, Maria Luiza, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Ras, Joséphine, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Rouan, Alice, additional, Röttinger, Eric, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Moulin, Clémentine, additional, Iwankow, Guillaume, additional, Banaigs, Bernard, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Sullivan, Matthew B., additional, Thomas, Olivier, additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Boss, Emmanuel, additional, and Gorsky, Gaby, additional
Published: 2022
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25. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale

Author: de Vargas, Colomban, Le Bescot, Noan, Pollina, Thibault, Henry, Nicolas, Romac, Sarah, Colin, Sébastien, Haëntjens, Nils, Carmichael, Margaux, Berger, Calixte, Le Guen, David, Decelle, Johan, Mahe, Frédéric, Poulain, Julie, Malpot, Emmanuel, Beaumont, Carole, Hardy, Michel, Guiffant, Damien, Probert, Ian, Gruber, David F., Allen, Andrew E., Gorsky, Gabriel, Follows, Michael J., Pochon, Xavier, Troublé, Romain, Cael, B.B., Lombard, Fabien, Boss, Emmanuel, Prakash, Manu, de Vargas, Colomban, Le Bescot, Noan, Pollina, Thibault, Henry, Nicolas, Romac, Sarah, Colin, Sébastien, Haëntjens, Nils, Carmichael, Margaux, Berger, Calixte, Le Guen, David, Decelle, Johan, Mahe, Frédéric, Poulain, Julie, Malpot, Emmanuel, Beaumont, Carole, Hardy, Michel, Guiffant, Damien, Probert, Ian, Gruber, David F., Allen, Andrew E., Gorsky, Gabriel, Follows, Michael J., Pochon, Xavier, Troublé, Romain, Cael, B.B., Lombard, Fabien, Boss, Emmanuel, and Prakash, Manu
Abstract: In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modeled at the planetary scale, biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce 'Plankton Planet', an initiative whose goal is to engage the curiosity and creativity of researchers, makers, and mariners to (i) co-develop a new generation of cost-effective (frugal) universal scientific instrumentation to measure the genetic and morphological diversity of marine microbiomes in context, (ii) organize their systematic deployment through coastal or open ocean communities of sea-users/farers, to generate uniform plankton data across global and long-term spatio-temporal scales, and (iii) setup tools to flow the data without embargo into public and explorable databases. As proof-of-concept, we show how 20 crews of sailors were able to sample plankton biomass from the world surface ocean in a single year, generating the first seatizen-based, planetary dataset of marine plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. The data unveil significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems and microbiomes across the dimensions of the Earth system.
Published: 2022

26. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author: Veglia, Alex J., primary, Bistolas, Kalia S.I., additional, Voolstra, Christian R., additional, Hume, Benjamin C. C., additional, Planes, Serge, additional, Allemand, Denis, additional, Boissin, Emilie, additional, Wincker, Patrick, additional, Poulain, Julie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Thomas, Olivier, additional, Troublé, Romain, additional, Zoccola, Didier, additional, Correa, Adrienne M.S., additional, and Vega Thurber, Rebecca L., additional
Published: 2022
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27. Priorities for ocean microbiome research

Author: Tara Ocean Foundation, Abreu, Andre, Bourgois, Etienne, Gristwood, Adam, Troublé, Romain, Tara Oceans, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, Budinich, Marko, Chaffron, Samuel, de Vargas, Colomban, Delmont, Tom O., Eveillard, Damien, Guidi, Lionel, Iudicone, Daniele, Kandels, Stephanie, Morlon, Hélène, Lombard, Fabien, Pepperkok, Rainer, Pierella Karlusich, Juan José, Piganeau, Gwenael, Régimbeau, Antoine, Sommeria-Klein, Guilhem, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Zablocki, Olivier, European Molecular Biology Laboratory (EMBL), Arendt, Detlev, Bilic, Josipa, Finn, Robert, Heard, Edith, Rouse, Brendan, Vamathevan, Jessica, European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC), Casotti, Raffaella, Cancio, Ibon, Cunliffe, Michael, Kervella, Anne Emmanuelle, Kooistra, Wiebe H.C.F., Obst, Matthias, Pade, Nicolas, Power, Deborah M., Santi, Ioulia, Tsagaraki, Tatiana Margo, Vanaverbeke, Jan, European Commission, Agencia Estatal de Investigación (España), Tara Ocean Foundation, Tara Expéditions, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Maine, Institut de biologie de l'ENS Paris (IBENS), 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), 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, Combinatoire et Bioinformatique (LS2N - équipe COMBI), 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)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), 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), and Stazione Zoologica Anton Dohrn (SZN)
Subjects: Microbiology (medical), Genome, Marine, Bacteria, Ecology, Immunology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Cell Biology, Terrestrial, Plankton, Applied Microbiology and Biotechnology, Microbiology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Sequence, Viruses, Genetics, Phages, Biomass, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: This article is contribution number 131 of Tara Oceans.-- 11 pages, 5 figures, 1 table, 1 box, 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, We thank R. Zaayman-Gallant, T. Rauscher and F. Ibarbalz for preparation of the figures, and the European Union’s Horizon 2020 research and innovation project AtlantECO, under grant agreement no. 862923, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2022
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28. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean

Author: Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel S., Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-Francois, Gilson, Eric, Lombard, Fabien, Moulin, Clémentine, Pesant, Stephane, Poulain, Julie, Reynaud, Stephanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, de Vargas, Colomban, Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, Tara Pacific Consortium, Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel S., Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-Francois, Gilson, Eric, Lombard, Fabien, Moulin, Clémentine, Pesant, Stephane, Poulain, Julie, Reynaud, Stephanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, de Vargas, Colomban, Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, and Tara Pacific Consortium
Abstract: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Bourdin, G., Bowler, C., Douville, E., Flores, J. M., Forcioli, D., Furla, P., Galand, P. E., Ghiglione, J. F., Gilson, E., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Trouble, R., de Vargas, C., Thurber, R. V., Voolstra, C. R., Wincker, P., Zoccola, D., the Tara Pacific Consortium. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. Plos Biology, 17(9),(2019): e3000483, doi: 10.1371/journal.pbio.3000483., Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and p, We are keen to thank the commitment of the people and the following institutions for their financial and scientific support that made this singular expedition possible: CNRS, PSL, CSM, EPHE, Genoscope/CEA, Inserm, Université Cote d’Azur, ANR, agnès b., UNESCO-IOC, the Veolia Environment Foundation, Région Bretagne, Serge Ferrari, Billerudkorsnas, Amerisource Bergen Company, Lorient Agglomeration, Oceans by Disney, the Prince Albert II de Monaco Foundation, L’Oréal, Biotherm, France Collectivités, Kankyo Station, Fonds Français pour l’Environnement Mondial (FFEM), Etienne BOURGOIS, and the Tara Ocean Foundation teams and crew. Tara Pacific would not exist without the continuous support of the participating institutes. This study has been conducted using E.U. Copernicus Marine Service Information and Mercator Ocean products. We acknowledged funding from the Investissement d’avenir projects France Génomique (ANR-10-INBS-09) and OCEANOMICS (ANR-11-BTBR-0008). RVT was funded by a Dimensions of Biodiversity NSF grant (#1442306) for this work. SS is supported by the ETH Zurich and Helmut Horten Foundation. FL is supported by Sorbonne Université, Institut Universitaire de France, and the Fondation CA-PCA. Finally, we thank the ANR for funding the project CORALGENE, which will support the work the Tara Pacific program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Published: 2020

29. Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)

Author: Gorsky, Gabriel, Bourdin, Guillaume, Lombard, Fabien, Pedrotti, Maria Luiza, Audrain, Samuel, Bin, Nicolas, Boss, Emmanuel S., Bowler, Chris, Cassar, Nicolas, Caudan, Loic, Chabot, Genevieve, Cohen, Natalie R., Cron, Daniel, De Vargas, Colomban, Dolan, John R., Douville, Eric, Elineau, Amanda, Flores, J. Michel, Ghiglione, Jean-Francois, Haëntjens, Nils, Hertau, Martin, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Moulin, Clémentine, Moucherie, Yohann, Pesant, Stephane, Picheral, Marc, Poulain, Julie, Pujo-Pay, Mireille, Reverdin, Gilles, Romac, Sarah, Sullivan, Mathew B., Trainic, Miri, Tressol, Marc, Troublé, Romain, Vardi, Assaf, Voolstra, Christian R., Wincker, Patrick, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stephanie, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Zoccola, Didier, Planes, Serge, Allemand, Denis, Karsenti, Eric, Gorsky, Gabriel, Bourdin, Guillaume, Lombard, Fabien, Pedrotti, Maria Luiza, Audrain, Samuel, Bin, Nicolas, Boss, Emmanuel S., Bowler, Chris, Cassar, Nicolas, Caudan, Loic, Chabot, Genevieve, Cohen, Natalie R., Cron, Daniel, De Vargas, Colomban, Dolan, John R., Douville, Eric, Elineau, Amanda, Flores, J. Michel, Ghiglione, Jean-Francois, Haëntjens, Nils, Hertau, Martin, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Moulin, Clémentine, Moucherie, Yohann, Pesant, Stephane, Picheral, Marc, Poulain, Julie, Pujo-Pay, Mireille, Reverdin, Gilles, Romac, Sarah, Sullivan, Mathew B., Trainic, Miri, Tressol, Marc, Troublé, Romain, Vardi, Assaf, Voolstra, Christian R., Wincker, Patrick, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stephanie, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Zoccola, Didier, Planes, Serge, Allemand, Denis, and Karsenti, Eric
Abstract: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gorsky, G., Bourdin, G., Lombard, F., Pedrotti, M. L., Audrain, S., Bin, N., Boss, E., Bowler, C., Cassar, N., Caudan, L., Chabot, G., Cohen, N. R., Cron, D., De Vargas, C., Dolan, J. R., Douville, E., Elineau, A., Flores, J. M., Ghiglione, J. F., Haentjens, N., Hertau, M., John, S. G., Kelly, R. L., Koren, I., Lin, Y., Marie, D., Moulin, C., Moucherie, Y., Pesant, S., Picheral, M., Poulain, J., Pujo-Pay, M., Reverdin, G., Romac, S., Sullivan, M. B., Trainic, M., Tressol, M., Trouble, R., Vardi, A., Voolstra, C. R., Wincker, P., Agostini, S., Banaigs, B., Boissin, E., Forcioli, D., Furla, P., Galand, P. E., Gilson, E., Reynaud, S., Sunagawa, S., Thomas, O. P., Thurber, R. L. V., Zoccola, D., Planes, S., Allemand, D., Karsenti, E. Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018). Frontiers in Marine Science, 6, (2019): 750, doi: 10.3389/fmars.2019.00750., Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientif, We are thankful for the commitment of the people and the following institutions, for their financial and scientific support that made this singular expedition possible: CNRS, PSL, CSM, EPHE, Genoscope/CEA, Inserm, Université Cote d’Azur, ANR, the Tara Ocean Foundation and its partners agnès b., UNESCO-IOC, the Veolia Environment Foundation, Région Bretagne, Serge Ferrari, Billerudkorsnas, Amerisource Bergen Company, Altran, Lorient Agglomeration, Oceans by Disney, the Prince Albert II de Monaco Foundation, L’Oréal, Biotherm, France Collectivités, Kankyo Station, Fonds Français pour l’Environnement Mondial (FFEM), Etienne Bourgois, the Tara Ocean Foundation teams and crew. Tara Pacific would not exist without the continuous support of the participating institutes. This study has been conducted using E.U. Copernicus Marine Service Information and Mercator Ocean products. We acknowledge funding from the Investissement d’avenir project France Génomique (ANR-10-INBS-09). FL is supported by Sorbonne Université, Institut Universitaire de France and the Fondation CA-PCA. The in-line and atmospheric optics dataset was collected and analyzed with support from NASA Ocean Biology and Biogeochemistry program under grants NNX13AE58G and NNX15AC08G to University of Maine. MF, IK, and AV are supported by a research grant from Scott Jordan and Gina Valdez, the De Botton for Marine Science, the Yeda-Sela center for Basic research, and the Sustainability and Energy Research Initiative (SAERI). NCo was supported by a grant from the Simons Foundation/SFARI (544236). NCa and YL were supported by the “Laboratoire d’Excellence” LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program “Investissements d’Avenir.” The support of Pr. Alan Fuchs, President of CNRS, was crucial for the success of the surface sampling undertaken during the Tara Pacific expedition. We thank A. Gavilli from TECA Inc. France, and E. Tanguy and D. Delhommeau from the Institut de
Published: 2020

30. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Author: Gorsky, Gabriel, primary, Bourdin, Guillaume, additional, Lombard, Fabien, additional, Pedrotti, Maria Luiza, additional, Audrain, Samuel, additional, Bin, Nicolas, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Cassar, Nicolas, additional, Caudan, Loic, additional, Chabot, Genevieve, additional, Cohen, Natalie R., additional, Cron, Daniel, additional, De Vargas, Colomban, additional, Dolan, John R., additional, Douville, Eric, additional, Elineau, Amanda, additional, Flores, J. Michel, additional, Ghiglione, Jean Francois, additional, Haëntjens, Nils, additional, Hertau, Martin, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, Moulin, Clémentine, additional, Moucherie, Yohann, additional, Pesant, Stéphane, additional, Picheral, Marc, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Sullivan, Mathew B., additional, Trainic, Miri, additional, Tressol, Marc, additional, Troublé, Romain, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Wincker, Patrick, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boissin, Emilie, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Thurber, Rebecca Lisette Vega, additional, Zoccola, Didier, additional, Planes, Serge, additional, Allemand, Denis, additional, and Karsenti, Eric, additional
Published: 2019
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31. Open science resources for the discovery and analysis of Tara Oceans data

Author: Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Pesant, Stéphane, Not, Fabrice, Picheral, Marc, Kandels-Lewis, Stefanie, Le Bescot, Noan, Gorsky, Gabriel, Iudicone, Daniele, Karsenti, Eric, Speich, Sabrina, Troublé, Romain, Dimier, Céline, Searson, Sarah, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Grimsley, Nigel, Hingamp, Pascal, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Pesant, Stéphane, Not, Fabrice, Picheral, Marc, Kandels-Lewis, Stefanie, Le Bescot, Noan, Gorsky, Gabriel, Iudicone, Daniele, Karsenti, Eric, Speich, Sabrina, Troublé, Romain, Dimier, Céline, Searson, Sarah, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Grimsley, Nigel, Hingamp, Pascal, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Weissenbach, Jean, and Wincker, Patrick
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.
Published: 2018

32. Open science resources for the discovery and analysis of Tara Oceans data

Author: Pesant, Stéphane, Not, Fabrice, Picheral, Marc, Kandels-Lewis, Stefanie, Le Bescot, Noan, Gorsky, Gabriel, Iudicone, Daniele, Karsenti, Eric, Speich, Sabrina, Troublé, Romain, Dimier, Céline, Searson, Sarah, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Grimsley, Nigel, Hingamp, Pascal, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, Follows, Michael J, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, PANGAEA Consulting Engineers, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Stazione Zoologica Anton Dohrn (SZN), Institut de biologie de l'ENS Paris (IBENS), 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), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Tara Expéditions, Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Grenoble] (EMBL), University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), 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)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), School of Biology & Environmental Science, University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Bigelow Laboratory for Ocean Sciences, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, European Molecular Biology Laboratory, DVIPC, 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), 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), Department of Marine Biology and Oceanography, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Kyoto University [Kyoto], Department of Ecology and Evolutionary Biology, Research Foundation - Flanders, Stazione Zoologica Anton Dohrn, Università degli Studi di Milano-Bicocca, Agence Nationale de la Recherche (France), European Research Council, Ministerio de Ciencia e Innovación (España), Japan Society for the Promotion of Science, Veolia Foundation, Région Bretagne, World Courier, Illumina, Lorient Agglomération, Fondation EDF, Fondation Prince Albert II de Monaco, Centre National de Séquençage (France), Centre National de la Recherche Scientifique (France), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Raes, Jeroen, and Lorient Agglomération (France)
Subjects: [SDE] Environmental Sciences, Statistics and Probability, Open science, Data Descriptor, 010504 meteorology & atmospheric sciences, Oceans and Seas, [SDV]Life Sciences [q-bio], Context (language use), Library and Information Sciences, 01 natural sciences, Education, Environmental data, 03 medical and health sciences, Seawater, 14. Life underwater, Ecosystem, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, business.industry, Information Dissemination, Environmental resource management, Ecological genetics, Biodiversity, Plankton, Biooceanography, Computer Science Applications, [SDV] Life Sciences [q-bio], Oceanography, Geography, Ocean sciences, 13. Climate action, Viruses, [SDE]Environmental Sciences, Expeditions, Statistics, Probability and Uncertainty, business, Information Systems
Abstract: Pesant, Stéphane ... et. al.-- 16 pages, 5 figures, 2 tables.-- This article is contribution number 26 of the Tara Oceans Consortium, 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, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular the Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA- 003, PROMETHEUS/ANR-09-GENM-031, PROMETHEUS/ANR-09-PCS-GENM-217, TARAGIRUS/ANR-09-PCS-GENM-218, OCEANOMICS/ANR-11-BTBR-0008, FRANCE GENOMIQUE/ANR-10-INBS-09-08), EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, MetaCardis/HEALTH-F4-2012-305312), ERC Advanced Grant Awards to CB (Diatomite: 294823) and PB (CancerBiome: 268985), Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to SGA, JSPS KAKENHI Grant Number 26430184 to HO, FWO, BIO5, Biosphere 2, agne`s b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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33. The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation

Author: Cózar, Andrés, Martí, Elisa, Duarte, Carlos M., García-de-Lomas, Juan, van Sebille, Erik, Ballatore, Thomas J., Eguíluz, Victor M., González-Gordillo, J. Ignacio, Pedrotti, Maria L., Echevarría, Fidel, Troublè, Romain, and Irigoien, Xabier
Subjects: SciAdv r-articles, Water Pollution, Arctic waters, North Atlantic, floating plastic debris, thermohaline circulation
Abstract: The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris.
Published: 2017
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34. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean

Author: Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-Francois, Gilson, Eric, Lombard, Fabien, Moulin, Clémentine, Pesant, Stephane, Poulain, Julie, Reynaud, Stéphanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, De Vargas, Colomban, ThurberI, Rebecca V., Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Tara Pacific Consortium
Subjects: 13. Climate action, 14. Life underwater, 15. Life on land, 16. Peace & justice
Abstract: Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., PLoS Biology, 17 (9), ISSN:1544-9173, ISSN:1545-7885

35. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Author: Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, and Wincker P
Subjects: Animals, Biodiversity, Ecosystem, Anthozoa, Coral Reefs
Abstract: Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene., (© 2023. The Author(s).)
Published: 2023
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36. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.

Author: Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, and Zoccola D
Subjects: Animals, Metabolomics, Metagenomics, Pacific Ocean, Symbiosis, Anthozoa microbiology, Coral Reefs, Expeditions, Microbiota
Abstract: Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., Competing Interests: The authors have declared that no competing interests exist.
Published: 2019
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37. Open science resources for the discovery and analysis of Tara Oceans data.

Author: Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C, and Searson S
Subjects: Information Dissemination, Plankton, Seawater, Viruses, Ecosystem, Expeditions, Oceans and Seas
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.
Published: 2015
Full Text: View/download PDF

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