|
|
|
|
|
| Pesant, Stephane; Not, Fabrice; Picheral, Marc; Kandels-lewis, Stefanie; Le Bescot, Noan; Gorsky, Gabriel; Iudicone, Daniele; Karsenti, Eric; Speich, Sabrina; Trouble, Romain; Dimier, Celine; Searson, Sarah. |
| 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... |
| Tipo: Text |
|
| Ano: 2015 |
URL: https://archimer.ifremer.fr/doc/00600/71209/69583.pdf |
| |
|
|
| Caputi, Luigi; Carradec, Quentin; Eveillard, Damien; Kirilovsky, Amos; Pelletier, Eric; Karlusich, Juan J. Pierella; Vieira, Fabio Rocha Jimenez; Villar, Emilie; Chaffron, Samuel; Malviya, Shruti; Scalco, Eleonora; Acinas, Silvia G.; Alberti, Adriana; Aury, Jean-marc; Benoiston, Anne-sophie; Bertrand, Arnaud; Biard, Tristan; Bittner, Lucie; Boccara, Martine; Brum, Jennifer R.; Brunet, Cedric; Busseni, Greta; Carratala, Anna; Claustre, Herve; Coelho, Luis Pedro; Colin, Sbastien; D'Aniello, Salvatore; Da Silva, Corinne; Del Core, Marianna; Dore, Hugo; Gasparini, Stephane; Kokoszka, Florian; Jamet, Jean-louis; Lejeusne, Christophe; Lepoivre, Cyrille; Lescot, Magali; Lima-mendez, Gipsi; Lombard, Fabien; Lukes, Julius; Maillet, Nicolas; Madoui, Mohammed-amin; Martinez, Elodie; Mazzocchi, Maria Grazia; Neou, Mario B.; Paz-yepes, Javier; Poulain, Julie; Ramondenc, Simon; Romagnan, Jean-baptiste; Roux, Simon; Manta, Daniela Salvagio; Sanges, Remo; Speich, Sabrina; Sprovieri, Mario; Sunagawa, Shinichi; Taillandier, Vincent; Tanaka, Atsuko; Tirichine, Leila; Trottier, Camille; Uitz, Julia; Veluchamy, Alaguraj; Vesela, Jana; Vincent, Flora; Yau, Sheree; Kandels-lewis, Stefanie; Searson, Sarah; Dimier, Cline; Picheral, Marc; Bork, Peer; Boss, Emmanuel; De 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'Alcala, Maurizio Ribera; Wincker, Patrick; Bowler, Chris; Iudicone, Daniele; Gorsky, Gabriel; Jaillon, Olivier; Karp-boss, Lee; Krzic, Uros; Ogata, Hiroyuki; Pesant, Stephane; Raes, Jeroen; Reynaud, Emmanuel G.; Sardet, Christian; Sieracki, Mike; Velayoudon, Didier; Weissenbach, Jean. |
| 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 ‐omics datasets 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 towards iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole sub‐communities co‐varying with... |
| Tipo: Text |
|
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00475/58680/61184.pdf |
| |
|
|
| Gorsky, Gabriel; Bourdin, Guillaume; Lombard, Fabien; Pedrotti, Maria Luiza; Audrain, Samuel; Bin, Nicolas; Boss, Emmanuel; 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; Haentjens, Nils; Hertau, Martin; John, Seth G.; Kelly, Rachel L.; Koren, Ilan; Lin, Yajuan; Marie, Dominique; Moulin, Clementine; Moucherie, Yohann; Pesant, Stephane; Picheral, Marc; Poulain, Julie; Pujo-pay, Mireille; Reverdin, Gilles; Romac, Sarah; Sullivan, Mathew B.; Trainic, Miri; Tressol, Marc; Trouble, 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.; Thurber, Rebecca Lisette Vega; Zoccola, Didier; Planes, Serge; Allemand, Denis; Karsenti, Eric; Planes, S.; Banaig, B.; Boissin, E.; Iwankow, G.; Allemand, D.; Zoccola, D.; Reynaud, S.; Beraud, E.; Djerbi, N.; Forcioli, D.; Furla, P.; Gilson, E.; Mcmind, R.; Ottaviani, A.; Rottinger, E.; Rouan, A.; Zamoum, T.; Flume, B. C. C.; Pogoreutz, C.; Voolstra, C. R.; Rothig, T.; Ziegler, M.; Paoli, L.; Ruscheweyh, H-j; Salazar, G.; Sunagawa, S.; Flores, J. M.; Koren, I; Trainic, M.; Lang-yona, N.; Vardi, A.; Conan, P.; Ghiglione, J-f; Pujo-pay, M.; Galand, P. E.; Hochart, C.; Audrain, S.; Bourgois, E.; Hertau, M.; Lancelot, J.; Monmarche, D.; Moulin, C.; Moucherie, Y.; Trouble, R.; Boss, E.; Bourdin, G.; Haentjens, N.; Karp-boss, L.; Douville, Eric; Agostini, S.; Mitsuhashi, G.; Kitano, Y.; Da Silva, O.; Dolan, J. R.; Gorsky, G.; Lemee, R.; Lombard, F.; Pedrotti, M-l; Cronin, D.; Sullivan, M.; Armstrong, E.; Aury, J-m; Barbe, V; Belser, C.; Carradec, Q.; Labadie, K.; Le-hoang, J.; Noel, B.; Poulain, J.; Wincker, P.; Klinges, G.; Vega-thunder, R.; Bonnival, E.; De Vargas, C.; Henry, N.; Marie, D.; Romac, S.; Pesant, S.; Miguel-gorda, M.; Thomas, O. P.; Bowler, C.; Friedrich, R.; Cassar, N.; Lin, Y.; John, S. G.; Kelly, R. L.; Cohen, N. R.; Reverdin, G.; Filee, J.. |
| 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... |
| Tipo: Text |
Palavras-chave: Neuston/plankton genomics/taxonomy/imaging; Aerosols; NCP; IOP; Trace metals; Microplastic. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00599/71083/69390.pdf |
| |
|
|
| De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Frederic; Logares, Ramiro; Lara, Enrique; Berney, Cedric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sebastien; Aury, Jean-marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Guidi, Lionel; Horak, Ales; Jaillon, Olivier; Lima-mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Vincent, Flora; Zingone, Adriana; Dimier, Celine; Picheral, Marc; Searson, Sarah; Kandels-lewis, Stefanie; Acinas, Silvia G.; Bork, Peer; Bowler, Chris; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Raes, Jeroen; Sieracki, Michael E.; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Weissenbach, Jean; Wincker, Patrick; Karsenti, Eric. |
| Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, > 0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at similar to 150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups.... |
| Tipo: Text |
|
| Ano: 2015 |
URL: http://archimer.ifremer.fr/doc/00270/38135/37217.pdf |
| |
|
|
| Ibarbalz, Federico M.; Henry, Nicolas; Costa Brandao, Manoela; 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; Kandels, 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; Bopp, Laurent; Lombard, Fabien; Zinger, Lucie. |
| 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 Glades 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... |
| Tipo: Text |
|
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00597/70911/69146.pdf |
| |
|
|
| Picheral, Marc; Guidi, Lionel; Stemmann, Lars; Karl, David M.; Iddaoud, Ghizlaine; Gorsky, Gabriel. |
| The Underwater Vision Profiler (UVP) was developed to quantify the vertical distribution of macroscopic particles and zooplankton > 100 mu m in size. The smaller size limit is fixed by optical resolution, whereas the larger size limit is determined by the volume of water illuminated per image. The new fifth generation instrument (UVP5) is compact (30 kg in air) and operates either as a stand-alone instrument with an independent power supply for use on a mooring or free-drifting array, or as a component of a Conductivity, Temperature, and Depth (CTD)-rosette package. Images are recorded at a frequency up to 6 Hz. If the UVP5 is interfaced with a CTD, these images are acquired and analyzed in real time. Images are recorded every 20 cm at the 1 m s(-1)... |
| Tipo: Text |
Palavras-chave: Video plankton recorder; Marine snow; MU-M; Vertical distribution; Aggregate dynamics; In situ; System; Ocean; Flux; Phytoplankton. |
| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00133/24413/22426.pdf |
| |
|
|
| Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frederick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'Krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaelle; Wessner, Mark; Acinas, Silvia G.; Royo-llonch, Marta; Cornejo-castillo, Francisco M.; Logares, Ramiro; Fernandez-gomez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Ten Hoopen, Petra; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E.; Stepanauskas, Ramunas; Sullivan, Matthew B.; Brum, Jennifer R.; Duhaime, Melissa B.; Poulos, Bonnie T.; Hurwitz, Bonnie L.; Pesant, Stephane; Karsenti, Eric; Wincker, Patrick; Bork, Peer; Boss, Emmanuel; Follows, Michael; Gorsky, Gabriel; Hingamp, Pascal; Iudicone, Daniele; Karp-boss, Lee; Not, Fabrice; Raes, Jeroen; Sardet, Christian; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Bazire, Pascal; Beluche, Odette; Besnard-gonnet, Marielle; Bordelais, Isabelle; Boutard, Magali; Dubois, Maria; Dumont, Corinne; Ettedgui, Evelyne; Fernandez, Patricia; Garcia, Esperance; Aiach, Nathalie Giordanenco; Guerin, Thomas; Hamon, Chadia; Brun, Elodie; Lebled, Sandrine; Lenoble, Patricia; Louesse, Claudine; Mahieu, Eric; Mairey, Barbara; Martins, Nathalie; Megret, Catherine; Milani, Claire; Muanga, Jacqueline; Orvain, Celine; Payen, Emilie; Perroud, Peggy; Petit, Emmanuelle; Robert, Dominique; Ronsin, Murielle; Vacherie, Benoit. |
| A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the... |
| Tipo: Text |
|
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00600/71256/69634.pdf |
| |
|
|
|
