Search

Your search keyword '"Bittner, Lucie"' showing total 246 results
Start Over Author "Bittner, Lucie"
246 results on '"Bittner, Lucie"'

4. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier

Subjects
Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

5. A resource-frugal probabilistic dictionary and applications in bioinformatics

Author

Marchet, Camille, Lecompte, Lolita, Limasset, Antoine, Bittner, Lucie, and Peterlongo, Pierre

Subjects
Computer Science - Data Structures and Algorithms, Quantitative Biology - Quantitative Methods
Abstract

Indexing massive data sets is extremely expensive for large scale problems. In many fields, huge amounts of data are currently generated, however extracting meaningful information from voluminous data sets, such as computing similarity between elements, is far from being trivial. It remains nonetheless a fundamental need. This work proposes a probabilistic data structure based on a minimal perfect hash function for indexing large sets of keys. Our structure out-compete the hash table for construction, query times and for memory usage, in the case of the indexation of a static set. To illustrate the impact of algorithms performances, we provide two applications based on similarity computation between collections of sequences, and for which this calculation is an expensive but required operation. In particular, we show a practical case in which other bioinformatics tools fail to scale up the tested data set or provide lower recall quality results., Comment: Submitted to Journal of Discrete Algorithms. arXiv admin note: substantial text overlap with arXiv:1605.08319

Published
2017

6. A resource-frugal probabilistic dictionary and applications in (meta)genomics

Author

Marchet, Camille, Limasset, Antoine, Bittner, Lucie, and Peterlongo, Pierre

Subjects
Computer Science - Data Structures and Algorithms, Quantitative Biology - Genomics
Abstract

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure., Comment: Submitted to PSC 2016

Published
2016

8. Plankton networks driving carbon export in the oligotrophic ocean

Author

Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Subjects
Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus, Tara Oceans coordinators, General Science & Technology
Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

13. Functional trait-based approaches as a common framework for aquatic ecologists: Synthesis and recent results

Author

Martini, Séverine, Larras, Floriane, Boyé, Aurélien, Faure, Emile, Aberle, Nicole, Archambault, Philippe, Bacouillard, Lise, Beisner, Beatrix, Bittner, Lucie, Castella, Emmanuel, Danger, Michael, Gauthier, Olivier, Karp-Boss, Lee, Lombard, Fabien, Maps, Frédéric, Stemmann, Lars, Thiébaut, Éric, Usseglio-Polatera, Philippe, Vogt, Meike, Laviale, Martin, Ayata, Sakina‐dorothée, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université du Québec à Montréal = University of Québec in Montréal (UQAM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Laboratoire d'Ecologie et de Biologie Aquatique - LEBA (Genève, Suisse), Université de Genève = University of Geneva (UNIGE), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Maine, 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), 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, Takuvik International Research Laboratory, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Institute of Biogeochemistry and Pollutant Dynamics [ETH Zürich] (IBP), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Zone Atelier du Bassin de la Moselle [LTSER France] (ZAM), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Association for the Sciences of Limnology and Oceanography (ASLO)

Subjects
aquatic ecology, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, functional traits
Abstract

International audience; Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. In a recent review paper published in Limnology and Oceanography (Martini et al., 2021), we advocated the use of functional trait-based approaches (FTBAs) for aquatic ecologists and proposed concrete paths to go forward. In this presentation, we will first present an overview of this synthesis work. Then, using a few examples of recent results, including from quantitative imaging, genomics, and machine learning, we will then concretely illustrate how FTBAs can allow aquatic ecologists to tackle some of the scientific challenges identified in the paper.

Published
2023

18. A communal catalogue reveals Earths multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]

Published
2017
Full Text
View/download PDF

19. Blue-Cloud Virtual Labs in support of Sustainable Development Goals

Author

Drago, Federico, Cabrera, Patricia, Irisson, Jean-Olivier, Bittner, Lucie, Schickele, Alexandre, Drudi, Massimiliano, Balem, Kevin, Noteboom, Jan Willem, Castaño-Primo, Rocío, Jones, Steve, Taconet, Marc, Ellenbroek, Anton, Vallejo, Bryan R., Haberle, Ines, Hackenberger, Domagoj K, Djerdj, Tamara, Hackenberger, Branimir K., Ćaleta, Bruno, Purgar, Marija, Kapetanović, Damir, Marn, Nina, Pečar Ilić, Jadranka, Klanjšček, Tin, Gómez Navarro, Laura, Jongedijk, Cleo, Kaandorp, Mikael, Lobelle, Delphine, Manral, Darshika, Onink, Victor, Pierard, Claudio, Richardson, Joey, and Zavala-Romero, Olmo

Abstract

The Blue-Cloud thematic Virtual Labs (VLabs) are the main test beds for users to get the hang of the Blue-Cloud framework, exploiting the 10+ million datasets available via the Data Discovery and Access Service (DD&AS), as well as the easy access to the collaborative VLabs via D4Science and the EOSC federated login. These collaborative workspaces hosted in the Blue-Cloud Virtual Research Environment (VRE) are serving more than 1,300 users in total spread across more than 20 countries. Five Virtual Labs were developed and deployed in the Blue-Cloud pilot project, making use of the analytical tools and generic services as provided through the VRE, and the data repositories, as made accessible via the DD&AS and through external data services. The Blue-Cloud VLabs are real-life demonstrators for web-based open science and are open and available for testing by different research communities. Each VLab comprises a series of applications for data processing, publishing of data results, and managing computation routines as well as services for collaboration, this way providing open science-friendly working environments for its users to analyse datasets and (re)generate research products. Zoo & Phytoplankton EOV Products Plankton Genomics Marine Environmental Indicators Fish, a matter of scales Aquaculture Monitor 12 thematic marine services are included in the VLabs and make extensive use of the Blue-Cloud framework and its rich set of resources. These services illustrate the wide range of subjects that can be addressed using such resources, from genomics to wildlife as well as environmental data coming from multiple disciplines and repositories, and all together demonstrate Blue-Cloud’s potential in different fields of marine research,ranging from biodiversity to environmental science, as well as fisheries and aquaculture. In addition to these, this document also features factsheets for the three top teams awarded at the Blue-Cloud Hackathon 2022, providing additional examples of applications for Blue-Cloud assets in the blue economy. Sea Clearly- A tool to assess ocean plastic impacts on and by aquaculture farms PerfeCt- Performance of Aquaculture under Climate change Wildlife Tracker for Oceans- MPA assessment with real-time wildlife tracking & ocean monitoring data

Published
2023
Full Text
View/download PDF

21. From TARA Oceans metagenomics to carbon fixation biogeography in picoeukaryotes

Author

Schickele, Alexandre, Debeljak, Pavla, Sakina-Dorothée Ayata, Bittner, Lucie, Pelletier, Eric, Guidi, Lionel, and Irisson, Jean Olivier

Subjects
carbon concentration mechanisms, metagenomic, biogeography, picoeukaryotes
Abstract

Flash talk presentation at the Tara Oceans Retreat, from June 7th - 10th, 2022, presenting the Plankton Genomics VLab from the Blue-Cloud project.

Published
2022
Full Text
View/download PDF

24. Coverage and SNP datasets for Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata in the Mediteranean Sea, studied with Tara Oceans metagenomic samples

Author

Da Silva, Ophélie, Ayata, Sakina-Dorothée, Ser-Giacomi, Enrico, Leconte, Jade, Pelletier, Eric, Amin, Mohammed-Amin, Guidi, Lionel, Lombard, Fabien, and Bittner, Lucie

Abstract

Files for Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata SNP dataset: VCF files Coverage dataset: STATION: Tara Oceans station SAMPLE: Tara Oceans metagenomic sample TOT: Total length of the reference H_SUM: Total number of position covered V_SUM: Total length of aligned aligned H_COV: Horizontal coverage V_COV: Vertical coverage

Published
2022
Full Text
View/download PDF

25. Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea

Author

Da Silva, Ophélie, Ayata, Sakina‐dorothée, Ser‐giacomi, Enrico, Leconte, Jade, Pelletier, Eric, Fauvelot, Cécile, Madoui, Mohammed‐amin, Guidi, Lionel, Lombard, Fabien, Bittner, Lucie, Da Silva, Ophélie, Ayata, Sakina‐dorothée, Ser‐giacomi, Enrico, Leconte, Jade, Pelletier, Eric, Fauvelot, Cécile, Madoui, Mohammed‐amin, Guidi, Lionel, Lombard, Fabien, and Bittner, Lucie

Abstract

For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a FAIR pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos whereas P. cordata is impacted by geographic distance (i.e., isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations, and paves the way for future protist population metagenomic studies.

Published
2022
Full Text
View/download PDF

26. Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites

Author

Rizos, Iris, Debeljak, Pavla, Finet, Thomas, Klein, Dylan, Ayata, Sakina-dorothée, Not, Fabrice, Bittner, Lucie, Rizos, Iris, Debeljak, Pavla, Finet, Thomas, Klein, Dylan, Ayata, Sakina-dorothée, Not, Fabrice, and Bittner, Lucie

Abstract

Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2 171 unassigned clusters exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 38 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community’s variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.

Published
2022
Full Text
View/download PDF

29. Exploring and mapping plankton genomics data with Blue-Cloud

Author

Debeljak, Pavla, Schickele, Alexandre, Ayata, Sakina-Dorothée, Bittner, Lucie, Irisson, Jean-Olivier, Drago, Federico, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Trust-IT, and European Project: 862409,Blue-Cloud

Subjects
[SDE]Environmental Sciences
Abstract

Recent metagenomic studies have revealed that marine plankton is far more diverse than previously thought (Carradec et al. 2018, Salazar et al. 2019, Duarte et al. 2020), with hundreds of thousands of genetically distinct taxa and more than 116 million genes documented for eukaryotic plankton and 47 million genes for prokaryotes. However, the taxonomy and/or function of more than half of the planktonic ‘omic’ sequences is still unknown. These unprecedented amounts of data on planktonic communities call for innovative, data-driven approaches to quantify and observe their biogeographic importance (Faure et al. 2021).Marine plankton play a fundamental role in the global biogeochemical cycles and marine food webs. They are also a sentinel of environmental changes. Gathering more information about their genomics can help us better describe plankton distributions at global scale and further understand their response to environmental changes. The Blue-Cloud demonstrator Plankton Genomics responds to this challenge by mining the rich metagenomic and metatranscriptomic data collected during the Tara Oceans mission and combining it with in situ or climatological environmental information to infer the function, taxonomy and distribution of the large portion of unknown sequences. In this article, we are going to explore the main results of the demonstrator and its intended evolution.The demonstrator is led by the European Bioinformatics Institute (EMBL-EBI) and created by the Faculty of Sciences at Sorbonne University.

Published
2022

30. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Author

Massana, Ramon, Gobet, Angélique, Audic, Stéphane, Bass, David, Bittner, Lucie, Boutte, Christophe, Chambouvet, Aurélie, Christen, Richard, Claverie, Jean-Michel, Decelle, Johan, Dolan, John R., Dunthorn, Micah, Edvardsen, Bente, Forn, Irene, Forster, Dominik, Guillou, Laure, Jaillon, Olivier, Kooistra, Wiebe H. C. F., Logares, Ramiro, Mahé, Frédéric, Not, Fabrice, Ogata, Hiroyuki, Pawlowski, Jan, Pernice, Massimo C., Probert, Ian, Romac, Sarah, Richards, Thomas, Santini, Sébastien, Shalchian-Tabrizi, Kamran, Siano, Raffaele, Simon, Nathalie, Stoeck, Thorsten, Vaulot, Daniel, Zingone, Adriana, and de Vargas, Colomban

Published
2015
Full Text
View/download PDF

31. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Danko, David, primary, Bezdan, Daniela, additional, Afshin, Evan E., additional, Ahsanuddin, Sofia, additional, Bhattacharya, Chandrima, additional, Butler, Daniel J., additional, Chng, Kern Rei, additional, Donnellan, Daisy, additional, Hecht, Jochen, additional, Jackson, Katelyn, additional, Kuchin, Katerina, additional, Karasikov, Mikhail, additional, Lyons, Abigail, additional, Mak, Lauren, additional, Meleshko, Dmitry, additional, Mustafa, Harun, additional, Mutai, Beth, additional, Neches, Russell Y., additional, Ng, Amanda, additional, Nikolayeva, Olga, additional, Nikolayeva, Tatyana, additional, Png, Eileen, additional, Ryon, Krista A., additional, Sanchez, Jorge L., additional, Shaaban, Heba, additional, Sierra, Maria A., additional, Thomas, Dominique, additional, Young, Ben, additional, Abudayyeh, Omar O., additional, Alicea, Josue, additional, Bhattacharyya, Malay, additional, Blekhman, Ran, additional, Castro-Nallar, Eduardo, additional, Cañas, Ana M., additional, Chatziefthimiou, Aspassia D., additional, Crawford, Robert W., additional, De Filippis, Francesca, additional, Deng, Youping, additional, Desnues, Christelle, additional, Dias-Neto, Emmanuel, additional, Dybwad, Marius, additional, Elhaik, Eran, additional, Ercolini, Danilo, additional, Frolova, Alina, additional, Gankin, Dennis, additional, Gootenberg, Jonathan S., additional, Graf, Alexandra B., additional, Green, David C., additional, Hajirasouliha, Iman, additional, Hastings, Jaden J.A., additional, Hernandez, Mark, additional, Iraola, Gregorio, additional, Jang, Soojin, additional, Kahles, Andre, additional, Kelly, Frank J., additional, Knights, Kaymisha, additional, Kyrpides, Nikos C., additional, Łabaj, Paweł P., additional, Lee, Patrick K.H., additional, Leung, Marcus H.Y., additional, Ljungdahl, Per O., additional, Mason-Buck, Gabriella, additional, McGrath, Ken, additional, Meydan, Cem, additional, Mongodin, Emmanuel F., additional, Moraes, Milton Ozorio, additional, Nagarajan, Niranjan, additional, Nieto-Caballero, Marina, additional, Noushmehr, Houtan, additional, Oliveira, Manuela, additional, Ossowski, Stephan, additional, Osuolale, Olayinka O., additional, Özcan, Orhan, additional, Paez-Espino, David, additional, Rascovan, Nicolás, additional, Richard, Hugues, additional, Rätsch, Gunnar, additional, Schriml, Lynn M., additional, Semmler, Torsten, additional, Sezerman, Osman U., additional, Shi, Leming, additional, Shi, Tieliu, additional, Siam, Rania, additional, Song, Le Huu, additional, Suzuki, Haruo, additional, Court, Denise Syndercombe, additional, Tighe, Scott W., additional, Tong, Xinzhao, additional, Udekwu, Klas I., additional, Ugalde, Juan A., additional, Valentine, Brandon, additional, Vassilev, Dimitar I., additional, Vayndorf, Elena M., additional, Velavan, Thirumalaisamy P., additional, Wu, Jun, additional, Zambrano, María M., additional, Zhu, Jifeng, additional, Zhu, Sibo, additional, Mason, Christopher E., additional, Abdullah, Natasha, additional, Abraao, Marcos, additional, Adel, Ait-hamlat, additional, Afaq, Muhammad, additional, Al-Quaddoomi, Faisal S., additional, Alam, Ireen, additional, Albuquerque, Gabriela E., additional, Alexiev, Alex, additional, Ali, Kalyn, additional, Alvarado-Arnez, Lucia E., additional, Aly, Sarh, additional, Amachee, Jennifer, additional, Amorim, Maria G., additional, Ampadu, Majelia, additional, Amran, Muhammad Al-Fath, additional, An, Nala, additional, Andrew, Watson, additional, Andrianjakarivony, Harilanto, additional, Angelov, Michael, additional, Antelo, Verónica, additional, Aquino, Catharine, additional, Aranguren, Álvaro, additional, Araujo, Luiza F., additional, Vasquez Arevalo, Hitler Francois, additional, Arevalo, Jenny, additional, Arnan, Carme, additional, Alvarado Arnez, Lucia Elena, additional, Arredondo, Fernanda, additional, Arthur, Matthew, additional, Asenjo, Freddy, additional, Aung, Thomas Saw, additional, Auvinet, Juliette, additional, Aventin, Nuria, additional, Ayaz, Sadaf, additional, Baburyan, Silva, additional, Bakere, Abd-Manaaf, additional, Bakhl, Katrin, additional, Bartelli, Thais F., additional, Batdelger, Erdenetsetseg, additional, Baudon, François, additional, Becher, Kevin, additional, Bello, Carla, additional, Benchouaia, Médine, additional, Benisty, Hannah, additional, Benoiston, Anne-Sophie, additional, Benson, Joseph, additional, Benítez, Diego, additional, Bernardes, Juliana, additional, Bertrand, Denis, additional, Beurmann, Silvia, additional, Bitard-Feildel, Tristan, additional, Bittner, Lucie, additional, Black, Christina, additional, Blanc, Guillaume, additional, Blyther, Brittany, additional, Bode, Toni, additional, Boeri, Julia, additional, Boldgiv, Bazartseren, additional, Bolzli, Kevin, additional, Bordigoni, Alexia, additional, Borrelli, Ciro, additional, Bouchard, Sonia, additional, Bouly, Jean-Pierre, additional, Boyd, Alicia, additional, Branco, Gabriela P., additional, Breschi, Alessandra, additional, Brindefalk, Björn, additional, Brion, Christian, additional, Briones, Alan, additional, Buczansla, Paulina, additional, Burke, Catherine M., additional, Burrell, Aszia, additional, Butova, Alina, additional, Buttar, Irvind, additional, Bynoe, Jalia, additional, Bönigk, Sven, additional, Bøifot, Kari O., additional, Caballero, Hiram, additional, Cai, Xiao Wen, additional, Calderon, Dayana, additional, Cantillo, Angela, additional, Carbajo, Miguel, additional, Carbone, Alessandra, additional, Cardenas, Anais, additional, Carrillo, Katerine, additional, Casalot, Laurie, additional, Castro, Sofia, additional, Castro, Ana V., additional, Castro, Astred, additional, Castro, Ana Valeria B., additional, Cawthorne, Simone, additional, Cedillo, Jonathan, additional, Chaker, Salama, additional, Chalangal, Jasna, additional, Chan, Allison, additional, Chasapi, Anastasia I., additional, Chatziefthimiou, Starr, additional, Chaudhuri, Sreya Ray, additional, Chavan, Akash Keluth, additional, Chavez, Francisco, additional, Chem, Gregory, additional, Chen, Xiaoqing, additional, Chen, Michelle, additional, Chen, Jenn-Wei, additional, Chernomoretz, Ariel, additional, Chettouh, Allaeddine, additional, Cheung, Daisy, additional, Chicas, Diana, additional, Chiu, Shirley, additional, Choudhry, Hira, additional, Chrispin, Carl, additional, Ciaramella, Kianna, additional, Cifuentes, Erika, additional, Cohen, Jake, additional, Coil, David A., additional, Collin, Sylvie, additional, Conger, Colleen, additional, Conte, Romain, additional, Corsi, Flavia, additional, Cossio, Cecilia N., additional, Costa, Ana F., additional, Cuebas, Delisia, additional, D’Alessandro, Bruno, additional, Dahlhausen, Katherine E., additional, Darling, Aaron E., additional, Das, Pujita, additional, Davenport, Lucinda B., additional, David, Laurent, additional, Davidson, Natalie R., additional, Dayama, Gargi, additional, Delmas, Stéphane, additional, Deng, Chris K., additional, Dequeker, Chloé, additional, Desert, Alexandre, additional, Devi, Monika, additional, Dezem, Felipe S., additional, Dias, Clara N., additional, Donahoe, Timothy Ryan, additional, Dorado, Sonia, additional, Dorsey, LaShonda, additional, Dotsenko, Valeriia, additional, Du, Steven, additional, Dutan, Alexandra, additional, Eady, Naya, additional, Eisen, Jonathan A., additional, Elaskandrany, Miar, additional, Epping, Lennard, additional, Escalera-Antezana, Juan P., additional, Ettinger, Cassie L., additional, Faiz, Iqra, additional, Fan, Luice, additional, Farhat, Nadine, additional, Faure, Emile, additional, Fauzi, Fazlina, additional, Feigin, Charlie, additional, Felice, Skye, additional, Ferreira, Laís Pereira, additional, Figueroa, Gabriel, additional, Fleiss, Aubin, additional, Flores, Denisse, additional, Velasco Flores, Jhovana L., additional, Fonseca, Marcos A.S., additional, Foox, Jonathan, additional, Forero, Juan Carlos, additional, Francis, Aaishah, additional, French, Kelly, additional, Fresia, Pablo, additional, Friedman, Jacob, additional, Fuentes, Jaime J., additional, Galipon, Josephine, additional, Garcia, Mathilde, additional, Garcia, Laura, additional, García, Catalina, additional, Geiger, Annie, additional, Gerner, Samuel M., additional, Ghose, Sonia L., additional, Giang, Dao Phuong, additional, Giménez, Matías, additional, Giovannelli, Donato, additional, Githae, Dedan, additional, Gkotzis, Spyridon, additional, Godoy, Liliana, additional, Goldman, Samantha, additional, Gonnet, Gaston H., additional, Gonzalez, Juana, additional, Gonzalez, Andrea, additional, Gonzalez-Poblete, Camila, additional, Gray, Andrew, additional, Gregory, Tranette, additional, Greselle, Charlotte, additional, Guasco, Sophie, additional, Guerra, Juan, additional, Gurianova, Nika, additional, Haehr, Wolfgang, additional, Halary, Sebastien, additional, Hartkopf, Felix, additional, Hawkins-Zafarnia, Arya, additional, Hazrin-Chong, Nur Hazlin, additional, Helfrich, Eric, additional, Hell, Eva, additional, Henry, Tamera, additional, Hernandez, Samuel, additional, Hernandez, Pilar Lopez, additional, Hess-Homeier, David, additional, Hittle, Lauren E., additional, Hoan, Nghiem Xuan, additional, Holik, Aliaksei, additional, Homma, Chiaki, additional, Hoxie, Irene, additional, Huber, Michael, additional, Humphries, Elizabeth, additional, Hyland, Stephanie, additional, Hässig, Andrea, additional, Häusler, Roland, additional, Hüsser, Nathalie, additional, Petit, Robert A., additional, Iderzorig, Badamnyambuu, additional, Igarashi, Mizuki, additional, Iqbal, Shaikh B., additional, Ishikawa, Shino, additional, Ishizuka, Sakura, additional, Islam, Sharah, additional, Islam, Riham, additional, Ito, Kohei, additional, Ito, Sota, additional, Ito, Takayuki, additional, Ivankovic, Tomislav, additional, Iwashiro, Tomoki, additional, Jackson, Sarah, additional, Jacobs, JoAnn, additional, James, Marisano, additional, Jaubert, Marianne, additional, Jerier, Marie-Laure, additional, Jiminez, Esmeralda, additional, Jinfessa, Ayantu, additional, De Jong, Ymke, additional, Joo, Hyun Woo, additional, Jospin, Guilllaume, additional, Kajita, Takema, additional, Ahmad Kassim, Affifah Saadah, additional, Kato, Nao, additional, Kaur, Amrit, additional, Kaur, Inderjit, additional, de Souza Gomes Kehdy, Fernanda, additional, Khadka, Vedbar S., additional, Khan, Shaira, additional, Khavari, Mahshid, additional, Ki, Michelle, additional, Kim, Gina, additional, Kim, Hyung Jun, additional, Kim, Sangwan, additional, King, Ryan J., additional, KoLoMonaco, Giuseppe, additional, Koag, Ellen, additional, Kobko-Litskevitch, Nadezhda, additional, Korshevniuk, Maryna, additional, Kozhar, Michael, additional, Krebs, Jonas, additional, Kubota, Nanami, additional, Kuklin, Andrii, additional, Kumar, Sheelta S., additional, Kwong, Rachel, additional, Kwong, Lawrence, additional, Lafontaine, Ingrid, additional, Lago, Juliana, additional, Lai, Tsoi Ying, additional, Laine, Elodie, additional, Laiola, Manolo, additional, Lakhneko, Olha, additional, Lamba, Isha, additional, de Lamotte, Gerardo, additional, Lannes, Romain, additional, De Lazzari, Eleonora, additional, Leahy, Madeline, additional, Lee, Hyunjung, additional, Lee, Yunmi, additional, Lee, Lucy, additional, Lemaire, Vincent, additional, Leong, Emily, additional, Lewandowska, Dagmara, additional, Li, Chenhao, additional, Liang, Weijun, additional, Lin, Moses, additional, Lisboa, Priscilla, additional, Litskevitch, Anna, additional, Liu, Eric Minwei, additional, Liu, Tracy, additional, Livia, Mayra Arauco, additional, Lo, Yui Him, additional, Losim, Sonia, additional, Loubens, Manon, additional, Lu, Jennifer, additional, Lykhenko, Olexandr, additional, Lysakova, Simona, additional, Mahmoud, Salah, additional, Majid, Sara Abdul, additional, Makogon, Natalka, additional, Maldonado, Denisse, additional, Mallari, Krizzy, additional, Malta, Tathiane M., additional, Mamun, Maliha, additional, Manoir, Dimitri, additional, Marchandon, German, additional, Marciniak, Natalia, additional, Marinovic, Sonia, additional, Marques, Brunna, additional, Mathews, Nicole, additional, Matsuzaki, Yuri, additional, Matthys, Vincent, additional, May, Madelyn, additional, McComb, Elias, additional, Meagher, Annabelle, additional, Melamed, Adiell, additional, Menary, Wayne, additional, Mendez, Katterinne N., additional, Mendez, Ambar, additional, Mendy, Irène Mauricette, additional, Meng, Irene, additional, Menon, Ajay, additional, Menor, Mark, additional, Meoded, Roy, additional, Merino, Nancy, additional, Miah, Karishma, additional, Mignotte, Mathilde, additional, Miketic, Tanja, additional, Miranda, Wilson, additional, Mitsios, Athena, additional, Miura, Ryusei, additional, Miyake, Kunihiko, additional, Moccia, Maria D., additional, Mohan, Natasha, additional, Mohsin, Mohammed, additional, Moitra, Karobi, additional, Moldes, Mauricio, additional, Molina, Laura, additional, Molinet, Jennifer, additional, Molomjamts, Orgil-Erdene, additional, Moniruzzaman, Eftar, additional, Moon, Sookwon, additional, de Oliveira Moraes, Isabelle, additional, Moreno, Mario, additional, Mosella, Maritza S., additional, Moser, Josef W., additional, Mozsary, Christopher, additional, Muehlbauer, Amanda L., additional, Muner, Oasima, additional, Munia, Muntaha, additional, Munim, Naimah, additional, Muscat, Maureen, additional, Mustac, Tatjana, additional, Muñoz, Cristina, additional, Nadalin, Francesca, additional, Naeem, Areeg, additional, Nagy-Szakal, Dorottya, additional, Nakagawa, Mayuko, additional, Narce, Ashanti, additional, Nasu, Masaki, additional, Navarrete, Irene González, additional, Naveed, Hiba, additional, Nazario, Bryan, additional, Nedunuri, Narasimha Rao, additional, Neff, Thomas, additional, Nesimi, Aida, additional, Ng, Wan Chiew, additional, Ng, Synti, additional, Nguyen, Gloria, additional, Ngwa, Elsy, additional, Nicolas, Agier, additional, Nicolas, Pierre, additional, Nika, Abdollahi, additional, Noorzi, Hosna, additional, Nosrati, Avigdor, additional, Nunes, Diana N., additional, O’Brien, Kathryn, additional, O’Hara, Niamh B., additional, Oken, Gabriella, additional, Olawoyin, Rantimi A., additional, Oliete, Javier Quilez, additional, Olmeda, Kiara, additional, Oluwadare, Tolulope, additional, Oluwadare, Itunu A., additional, Ordioni, Nils, additional, Orpilla, Jenessa, additional, Orrego, Jacqueline, additional, Ortega, Melissa, additional, Osma, Princess, additional, Osuolale, Israel O., additional, Osuolale, Oluwatosin M., additional, Ota, Mitsuki, additional, Oteri, Francesco, additional, Oto, Yuya, additional, Ounit, Rachid, additional, Ouzounis, Christos A., additional, Pakrashi, Subhamitra, additional, Paras, Rachel, additional, Pardo-Este, Coral, additional, Park, Young-Ja, additional, Pastuszek, Paulina, additional, Patel, Suraj, additional, Pathmanathan, Jananan, additional, Patrignani, Andrea, additional, Perez, Manuel, additional, Peros, Ante, additional, Persaud, Sabrina, additional, Peters, Anisia, additional, Phillips, Adam, additional, Pineda, Lisbeth, additional, Pizzi, Melissa P., additional, Plaku, Alma, additional, Plaku, Alketa, additional, Pompa-Hogan, Brianna, additional, Portilla, María Gabriela, additional, Posada, Leonardo, additional, Priestman, Max, additional, Prithiviraj, Bharath, additional, Priya, Sambhawa, additional, Pugdeethosal, Phanthira, additional, Pugh, Catherine E., additional, Pulatov, Benjamin, additional, Pupiec, Angelika, additional, Pyrshev, Kyrylo, additional, Qing, Tao, additional, Rahiel, Saher, additional, Rahmatulloev, Savlatjon, additional, Rajendran, Kannan, additional, Ramcharan, Aneisa, additional, Ramirez-Rojas, Adan, additional, Rana, Shahryar, additional, Ratnanandan, Prashanthi, additional, Read, Timothy D., additional, Rehrauer, Hubert, additional, Richer, Renee, additional, Rivera, Alexis, additional, Rivera, Michelle, additional, Robertiello, Alessandro, additional, Robinson, Courtney, additional, Rodríguez, Paula, additional, Rojas, Nayra Aguilar, additional, Roldán, Paul, additional, Rosario, Anyelic, additional, Roth, Sandra, additional, Ruiz, Maria, additional, Boja Ruiz, Stephen Eduard, additional, Russell, Kaitlan, additional, Rybak, Mariia, additional, Sabedot, Thais S., additional, Sabina, Mahfuza, additional, Saito, Ikuto, additional, Saito, Yoshitaka, additional, Malca Salas, Gustavo Adolfo, additional, Salazar, Cecilia, additional, San, Kaung Myat, additional, Sanchez, Jorge, additional, Sanchir, Khaliun, additional, Sankar, Ryan, additional, de Souza Santos, Paulo Thiago, additional, Saravi, Zulena, additional, Sasaki, Kai, additional, Sato, Yuma, additional, Sato, Masaki, additional, Sato, Seisuke, additional, Sato, Ryo, additional, Sato, Kaisei, additional, Sayara, Nowshin, additional, Schaaf, Steffen, additional, Schacher, Oli, additional, Schinke, Anna-Lena M., additional, Schlapbach, Ralph, additional, Schori, Christian, additional, Schriml, Jason R., additional, Segato, Felipe, additional, Sepulveda, Felipe, additional, Serpa, Marianna S., additional, De Sessions, Paola F., additional, Severyn, Juan C., additional, Shakil, Maheen, additional, Shalaby, Sarah, additional, Shari, Aliyah, additional, Shim, Hyenah, additional, Shirahata, Hikaru, additional, Shiwa, Yuh, additional, Da Silva, Ophélie, additional, Silva, Jordana M., additional, Simon, Gwenola, additional, Singh, Shaleni K., additional, Sluzek, Kasia, additional, Smith, Rebecca, additional, So, Eunice, additional, Andreu Somavilla, Núria, additional, Sonohara, Yuya, additional, Rufino de Sousa, Nuno, additional, Souza, Camila, additional, Sperry, Jason, additional, Sprinsky, Nicolas, additional, Stark, Stefan G., additional, La Storia, Antonietta, additional, Suganuma, Kiyoshi, additional, Suliman, Hamood, additional, Sullivan, Jill, additional, Supie, Arif Asyraf Md, additional, Suzuki, Chisato, additional, Takagi, Sora, additional, Takahara, Fumie, additional, Takahashi, Naoya, additional, Takahashi, Kou, additional, Takeda, Tomoki, additional, Takenaka, Isabella K., additional, Tanaka, Soma, additional, Tang, Anyi, additional, Man Tang, Yuk, additional, Tarcitano, Emilio, additional, Tassinari, Andrea, additional, Taye, Mahdi, additional, Terrero, Alexis, additional, Thambiraja, Eunice, additional, Thiébaut, Antonin, additional, Thomas, Sade, additional, Thomas, Andrew M., additional, Togashi, Yuto, additional, Togashi, Takumi, additional, Tomaselli, Anna, additional, Tomita, Masaru, additional, Tomita, Itsuki, additional, Toth, Oliver, additional, Toussaint, Nora C., additional, Tran, Jennifer M., additional, Truong, Catalina, additional, Tsonev, Stefan I., additional, Tsuda, Kazutoshi, additional, Tsurumaki, Takafumi, additional, Tuz, Michelle, additional, Tymoshenko, Yelyzaveta, additional, Urgiles, Carmen, additional, Usui, Mariko, additional, Vacant, Sophie, additional, Vann, Laura E., additional, Velter, Fabienne, additional, Ventorino, Valeria, additional, Vera-Wolf, Patricia, additional, Vicedomini, Riccardo, additional, Suarez-Villamil, Michael A., additional, Vincent, Sierra, additional, Vivancos-Koopman, Renee, additional, Wan, Andrew, additional, Wang, Cindy, additional, Warashina, Tomoro, additional, Watanabe, Ayuki, additional, Weekes, Samuel, additional, Werner, Johannes, additional, Westfall, David, additional, Wieler, Lothar H., additional, Williams, Michelle, additional, Wolf, Silver A., additional, Wong, Brian, additional, Wong, Yan Ling, additional, Wong, Tyler, additional, Wright, Rasheena, additional, Wunderlin, Tina, additional, Yamanaka, Ryota, additional, Yang, Jingcheng, additional, Yano, Hirokazu, additional, Yeh, George C., additional, Yemets, Olena, additional, Yeskova, Tetiana, additional, Yoshikawa, Shusei, additional, Zafar, Laraib, additional, Zhang, Yang, additional, Zhang, Shu, additional, Zhang, Amy, additional, Zheng, Yuanting, additional, and Zubenko, Stas, additional

Published
2021
Full Text
View/download PDF

32. Functional trait‐based approaches as a common framework for aquatic ecologists

Author

Martini, Séverine, Larras, Floriane, Boye, Aurelien, Faure, Emile, Aberle, Nicole, Archambault, Philippe, Bacouillard, Lise, Beisner, Beatrix E, Bittner, Lucie, Castella, Emmanuel, Danger, Michael, Gauthier, Olivier, Karp‐boss, Lee, Lombard, Fabien, Maps, Frédéric, Stemmann, Lars, Thiébaut, Eric, Usseglio‐polatera, Philippe, Vogt, Meike, Laviale, Martin, Ayata, Sakina‐dorothée, Martini, Séverine, Larras, Floriane, Boye, Aurelien, Faure, Emile, Aberle, Nicole, Archambault, Philippe, Bacouillard, Lise, Beisner, Beatrix E, Bittner, Lucie, Castella, Emmanuel, Danger, Michael, Gauthier, Olivier, Karp‐boss, Lee, Lombard, Fabien, Maps, Frédéric, Stemmann, Lars, Thiébaut, Eric, Usseglio‐polatera, Philippe, Vogt, Meike, Laviale, Martin, and Ayata, Sakina‐dorothée

Abstract

Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. Here, we advocate the use of functional trait‐based approaches (FTBAs) for aquatic ecologists and propose concrete paths to go forward. Firstly, we propose to unify existing definitions in FTBAs to adopt a common language. Secondly, we list the numerous databases referencing functional traits for aquatic organisms. Thirdly, we present a synthesis on traditional as well as recent promising methods for the study of aquatic functional traits, including imaging and genomics. Finally, we conclude with a highlight on scientific challenges and promising venues for which FTBAs should foster opportunities for future research. By offering practical tools, our framework provides a clear path forward to the adoption of trait‐based approaches in aquatic ecology.

Published
2021
Full Text
View/download PDF

33. L’expédition Tara Océans, un rêve de marin, de science et de partage

Author

Bittner, Lucie, Bittner, Lucie, Editions CNRS, Guthleben D, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SHS.EDU]Humanities and Social Sciences/Education, [SHS.EDU] Humanities and Social Sciences/Education, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

34. Functional trait‐based approaches as a common framework for aquatic ecologists

Author

Martini, Séverine, primary, Larras, Floriane, additional, Boyé, Aurélien, additional, Faure, Emile, additional, Aberle, Nicole, additional, Archambault, Philippe, additional, Bacouillard, Lise, additional, Beisner, Beatrix E, additional, Bittner, Lucie, additional, Castella, Emmanuel, additional, Danger, Michael, additional, Gauthier, Olivier, additional, Karp‐Boss, Lee, additional, Lombard, Fabien, additional, Maps, Frédéric, additional, Stemmann, Lars, additional, Thiébaut, Eric, additional, Usseglio‐Polatera, Philippe, additional, Vogt, Meike, additional, Laviale, Martin, additional, and Ayata, Sakina‐Dorothée, additional

Published
2020
Full Text
View/download PDF

35. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Guillou, Laure, Bachar, Dipankar, Audic, Stéphane, Bass, David, Berney, Cédric, Bittner, Lucie, Boutte, Christophe, Burgaud, Gaétan, de Vargas, Colomban, Decelle, Johan, del Campo, Javier, Dolan, John R., Dunthorn, Micah, Edvardsen, Bente, Holzmann, Maria, Kooistra, Wiebe H.C.F., Lara, Enrique, Le Bescot, Noan, Logares, Ramiro, Mahé, Frédéric, Massana, Ramon, Montresor, Marina, Morard, Raphael, Not, Fabrice, Pawlowski, Jan, Probert, Ian, Sauvadet, Anne-Laure, Siano, Raffaele, Stoeck, Thorsten, Vaulot, Daniel, Zimmermann, Pascal, and Christen, Richard

Published
2013
Full Text
View/download PDF

36. Functional trait-based approaches as a common framework for freshwater and marine ecologists

Author

Martini, Severine, Larras, Floriane, Boyé, Aurélien, Faure, Emile, Aberle, Nicole, Archambault, Philippe, Bacouillard, Lise, Beisner, Beatrix, Bittner, Lucie, Castella, Emmanuel, Danger, Michael, Gauthier, Olivier, Karp-Boss, Lee, Lombard, Fabien, Maps, Frédéric, Stemmann, Lars, Thiébaut, Éric, Usseglio-Polatera, Philippe, Vogt, Meike, Laviale, Martin, Ayata, Sakina-Dorothée, 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), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Takuvik International Research Laboratory, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université du Québec à Montréal = University of Québec in Montréal (UQAM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Institute for Environmental Sciences [Geneva] (ISE), University of Geneva [Switzerland], Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Zone Atelier du Bassin de la Moselle [LTSER France] (ZAM), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université de Genève = University of Geneva (UNIGE), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

37. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Karp‐Boss, Lee, Wincker, Patrick, Kandels‐Lewis, Stefanie, Jaillon, Olivier, Iudicone, Daniele, Hingamp, Pascal, Grimsley, Nigel, Gorsky, Gabriel, Follows, Michael J., Vargas, Colomban, Bowler, Chris, Boss, Emmanuel, Bork, Peer, Acinas, Silvia G., Karsenti, Eric, Weissenbach, Jean, Velayoudon, Didier, Sunagawa, Shinichi, Sullivan, Matthew B., Stemmann, Lars, Speich, Sabrina, Sieracki, Mike, Sardet, Christian, Reynaud, Emmanuel G., Raes, Jeroen, Pesant, Stéphane, Ogata, Hiroyuki, Not, Fabrice, Krzic, Uros, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Sprovieri, Mario, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Searson, Sarah, Dimier, Céline, Picheral, Marc, Guidi, Lionel, Sordino, Paolo, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, d'Alcalà, Maurizio Ribera, Stazione Zoologica Anton Dohrn (SZN), 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), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Oceanography and Coastal Sciences, Louisiana State University (LSU), 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), Instituto de Engenharia de Sistemas e Computadores (INESC), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Istituto per l'Ambiente Marino Costiero, Sezione Ecologia Marina Integrata, European Molecular Biology Laboratory [Heidelberg] (EMBL), National Cardiovascular Center, 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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), University of Maine, Department of Earth and Environment [Boston], Boston University [Boston] (BU), Department of Earth Ocean and Ecological Sciences [Liverpool], University of Liverpool, Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, National Science Foundation [Arlington] (NSF), DVIPC, ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), 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), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), 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), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Consiglio Nazionale delle Ricerche [Roma] (CNR), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Vrije Universiteit Brussel (VUB), Department of Structural Biology, 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), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, and JAMET, Jean-Louis

Subjects
0106 biological sciences, Atmospheric Science, PROCHLOROCOCCUS, 010504 meteorology & atmospheric sciences, Iron fertilization, species networks, DIVERSITY, PROTEIN, Oceanography, 01 natural sciences, CARBON, Settore BIO/13 - Biologia Applicata, oxidative stress, Meteorology & Atmospheric Sciences, Geosciences, Multidisciplinary, OXIDATIVE STRESS, ComputingMilieux_MISCELLANEOUS, GENE-EXPRESSION, General Environmental Science, Global and Planetary Change, LIMITATION, Ecology, IN-SITU, system biology, Geology, Plankton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], iron response, meta-omics, MARINE-PHYTOPLANKTON, in-situ, limitation, Physical Sciences, Life Sciences & Biomedicine, Biogeochemical cycle, PACIFIC, Environmental Sciences & Ecology, Context (language use), prochlorococcus, Biology, Zooplankton, marine-phytoplankton, diversity, Atmospheric Sciences, Phytoplankton, pacific, Genetics, Environmental Chemistry, Ecosystem, 14. Life underwater, Life Below Water, 0105 earth and related environmental sciences, Science & Technology, 010604 marine biology & hydrobiology, carbon, fungi, Pelagic zone, gene-expression, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, Cardiovascular and Metabolic Diseases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, protein, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

29 pages, 9 figures, supporting information https://doi.org/10.1029/2018GB006022, Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280, the Mission Pour l'Interdisciplinarité – Project MEGALODOM, and the Fédération de Recherche GO‐SEE FR2022), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government “Investissements d'Avenir” programs Oceanomics (ANR‐11‐BTBR‐0008), MEMO LIFE (ANR‐10‐LABX‐54), PSL* Research University (ANR‐11‐IDEX‐0001‐02), and FRANCE GENOMIQUE (ANR‐10‐INBS‐09), Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects “PHYTBACK/ANR‐2010‐1709‐01,” POSEIDON/ANR‐09‐BLAN‐0348, PROMETHEUS/ANR‐09‐PCS‐GENM‐217, TARA‐GIRUS/ANR‐09‐PCS‐GENM‐218, SAMOSA/ANR‐13‐ADAP‐0010, CINNAMON/ANR‐17‐CE02‐0014‐01), EU FP7 (MicroB3/No. 287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to C. B., JSPS/MEXT KAKENHI (26430184, 16H06437, and 16KT0020), The Canon Foundation (203143100025), Gordon and Betty Moore Foundation (award #3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) to MBS, agnès 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 Fonds Français pour l'Environnement Mondial, the TARA schooner and its captain and crew.

Published
2019

38. Genetic diversity and species boundaries of corallinales (Rhodophyta) in south Pacific Ocean

Author

Bittner, Lucie, Flecher, C., de Reviers, Bruno, Le Gall, Line, Payri, Claude, Ishida, Ken-Ichiro, Nozaki, Hisayoshi, Miyashita, Hideaki, Horiguchi, Takeo, Kawai, Hiroshi, and Marani, Gilberto

Subjects
[SDV] Life Sciences [q-bio], [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Published
2019

39. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J., Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, Weissenbach, Jean, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J., Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, and Weissenbach, Jean

Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. © 2019. American Geophysical Union. All Rights Reserved.

Published
2019

40. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sebastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, Iudicone, Daniele, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sebastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, and Iudicone, Daniele

Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment

Published
2019

43. Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

Author

Lopez Philippe, de Reviers Bruno, Cruaud Corinne, Payri Claude, Halary Sébastien, Bittner Lucie, and Bapteste Eric

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution. Presentation of the hypothesis We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments. Testing the hypothesis We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies. Implications of the hypothesis Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data. Reviewers This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon).

Published
2010
Full Text
View/download PDF

44. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network

Author

Meng, Arnaud, Corre, Erwan, Probert, Ian, Gutierrez-rodriguez, Andres, Siano, Raffaele, Annamale, Anita, Alberti, Adriana, Da Silva, Corinne, Wincker, Patrick, Le Crom, Stephane, Not, Fabrice, Bittner, Lucie, Meng, Arnaud, Corre, Erwan, Probert, Ian, Gutierrez-rodriguez, Andres, Siano, Raffaele, Annamale, Anita, Alberti, Adriana, Da Silva, Corinne, Wincker, Patrick, Le Crom, Stephane, Not, Fabrice, and Bittner, Lucie

Abstract

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.

Published
2018
Full Text
View/download PDF

45. Plankton networks driving carbon export in the oligotrophic ocean

Author

Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R., Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B., Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Gorsky, Gabriel, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R., Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B., Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2018

46. Tara Oceans : de l’odyssée à l’étude systémique de l’océan

Author

Bittner, Lucie, Bowler, Chris, Evolution Paris-Seine (EPS), Institut de Recherche pour le Développement (IRD)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Sorbonne Paris Cité (USPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Editions CNRS, Euzen A, Gaill F, Lacroix D, Cury P, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université des Antilles (UA)-Université Sorbonne Paris Cité (USPC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, and 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)

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

National audience

Published
2017

47. Tara Océans et son flot de données : vers une compréhension multi-échelle de l'écosystème océan

Author

Bowler, Chris, Bittner, Lucie, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Evolution Paris-Seine (EPS), Institut de Recherche pour le Développement (IRD)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Sorbonne Paris Cité (USPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Editions CNRS, Bouzeghoub M, Mosseri R, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université des Antilles (UA)-Université Sorbonne Paris Cité (USPC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

National audience

Published
2017

48. Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass lowering

Author

Botebol, Hugo, Lelandais, Gaelle, Six, Christophe, Lesuisse, Emmanuel, Meng, Arnaud, Bittner, Lucie, Lecrom, Stéphane, Sutak, Robert, Lozano, Jean-Claude, Schatt, Philippe, Vergé, Valérie, Blain, Stéphane, Bouget, François-Yves, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), 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), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), MArine Phototrophic Prokaryotes (MAPP), 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), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Charles University [Prague] (CU), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Evolution Paris Seine, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Université des Antilles et de la Guyane (UAG), and Charles University [Prague]

Subjects
Chlorophyta, Science, Acclimatization, Gene Expression Profiling, Iron, Medicine, Biomass, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Article, Trace Elements
Abstract

International audience; Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophytoplankton does contribute significantly to primary production and carbon transfer to higher trophic levels. In particular, metagenomic studies of the green picoalga Ostreococcus have revealed the occurrence of two main clades distributed along coast-offshore gradients, suggesting niche partitioning in different nutrient regimes. Here, we present a study of the response to iron limitation of four Ostreococcus strains isolated from contrasted environments. Whereas the strains isolated in nutrient-rich waters showed high iron requirements, the oceanic strains could cope with lower iron concentrations. The RCC802 strain, in particular, was able to maintain high growth rate at low iron levels. Together physiological and transcriptomic data indicate that the competitiveness of RCC802 under iron limitation is related to a lowering of iron needs though a reduction of the photosynthetic machinery and of protein content, rather than to cell size reduction. Our results overall suggest that iron is one of the factors driving the differentiation of physiologically specialized Ostreococcus strains in the ocean.

Published
2017

49. Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

Author

Chust, Guillem, Vogt, Meike, Benedetti, Fabio, Nakov, Teofil, Villeger, Sebastien, Aubert, Anais, Vallina, Sergio M., Righetti, Damiano, Not, Fabrice, Biard, Tristan, Bittner, Lucie, Benoiston, Anne-sophie, Guidi, Lionel, Villarino, Ernesto, Gaborit, Charlie, Cornils, Astrid, Buttay, Lucie, Irisson, Jean-olivier, Chiarello, Marlene, Vallim, Alessandra L., Blanco-bercial, Leocadio, Basconi, Laura, Guilhaumon, Francois, Ayata, Sakina-dorothee, Eusko Jaurlaritza, Centre National de la Recherche Scientifique (France), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), 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), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Ecology (disciplines), Climate change, Plankton, Macroecology, Species distribution, Functional diversity, Habitat modeling, Ocean Engineering, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Marine ecosystem, Ecosystem, natural sciences, Marine Science, 14. Life underwater, Water Science and Technology, Grand Challenges, 2. Zero hunger, Global and Planetary Change, Ecology, 010604 marine biology & hydrobiology, Global warming, fungi, Geography, 13. Climate action
Abstract

Chust, Guillem ... et al.-- 9 pages, 1 figure.-- Corrigendum: Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research, Frontiers in Marine Science 4: 122 (2017) https://doi.org/10.3389/fmars.2017.00122, With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of climate change on the distribution of plankton functional and phylogenetic diversity” (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: (1) What can we learn about plankton communities from the new wealth of high-throughput “omics” data? (2) What is the link between plankton diversity and ecosystem function? (3) How can species distribution models be adapted to represent plankton biogeography? (4) How will plankton biogeography be altered due to anthropogenic climate change? and (5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way, This research was funded by the EuroMarine Network (http://www.euromarinenetwork.eu), through the organization of the PlankDiv EuroMarine Foresight workshop, held at the Observatoire Océanographique de Villefranche-sur-mer, Villefranche-sur-mer, France, in March 2016, and cofounded by the Basque Government (Department Deputy of Agriculture, Fishing and Food Policy). The PlankDiv workshop was also supported by the Laboratoire d'Océanographie de Villefranche-sur-mer (LOV, UPMC/CNRS), the PlankMed action of WP5 MERMEX/MISTRAL, and by the French national programme EC2CO-LEFE (FunOmics project).

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results