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1. An integrative assessment of the plastic debris load in the Mediterranean Sea

Author: Pedrotti, Maria Luiza, Lombard, Fabien, Baudena, Alberto, Galgani, François, Elineau, Amanda, Petit, Stephanie, Henry, Maryvonne, Troublé, Romain, Reverdin, Gilles, Ser-Giacomi, Enrico, Kedzierski, Mikaël, Boss, Emmanuel, and Gorsky, Gabriel
Published: 2022
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2. Quantitative imaging datasets of micro to mesoplankton communities and surface microplastic across the Pacific Ocean from the Tara Pacific Expedition.

Author: Mériguet, Zoé, Bourdin, Guillaume, Kristan, Nathaniel, Jalabert, Laetitia, Bun, Olivier, Picheral, Marc, Caray–Counil, Louis, Maury, Juliette, Pedrotti, Maria-Luiza, Elineau, Amanda, Paz-Garcia, David Arturo, Karp-Boss, Lee, Gorsky, Gabriel, and Lombard, Fabien
Subjects: TERRITORIAL waters, WEB-based user interfaces, BONGO (Musical instrument), WATER pumps, REEFS, LAGOONS
Abstract: This paper presents the quantitative imaging datasets collected during the Tara Pacific Expedition (2016–2018) on the schooner Tara. The datasets cover a wide range of plankton sizes, from micro-phytoplankton > 20 μm to meso-zooplankton of a few cm, as well as non-living particles such as plastic and detrital particles. It consists of surface samples collected across the North and South Pacific Ocean from open ocean stations (a total of 357 samples) and from stations located in coastal waters, lagoons or reefs of 32 Pacific islands (a total of 228 samples). As this expedition involved long distances and long sailing times, we designed two sampling systems to collect plankton while sailing at speeds up to 9 knots. To sample microplankton, surface water was pumped onboard using a customised pumping system and filtered through a 20 µm mesh size plankton net (here after Deck-Net (DN). A High Speed Net (HSN; 330 μm mesh size) was developed to sample the mesoplankton. In addition, a Manta net (330 µm) was also used when possible, to collect mesoplankton and plastics simultaneously. We could not deploy these nets in reef and lagoon stations of islands. Instead, two Bongo nets (20 µm) attached to an underwater scooter were used to sample microplankton. Microplankton (20–200 μm) from the DN and Bongo nets was imaged directly on-board Tara using the FlowCam (Fluid imaging, Inc.) while the mesoplankton (> 200 μm) from the HSN and Manta nets was analyzed in the laboratory with the ZooScan system. Organisms and other particles were taxonomically and morphologically classified using the web application EcoTaxa automatic sorting tools, followed by taxonomic expert validation or correction. More than 300 different taxonomic and morphological groups were identified. The datasets include the metadata with the raw data from which morphological traits such as size (ESD) and biovolume have been calculated for each particle, as well as a number of quantitative descriptors of the surface plankton communities. These include abundance, biovolumes, Shannon diversity index and normalised biovolume size spectra, allowing the study of their structures (e.g. taxonomic, functional, size structure, trophic structure, etc.) according to a wide range of environmental parameters at the basin scale. In addition to describing and presenting the datasets, the complementary aim of this paper is to investigate and quantify the potential sampling biases associated with the two high speed sampling systems and the different net types, in order to improve further ecological interpretations. [ABSTRACT FROM AUTHOR]
Published: 2024
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3. First release of the Pelagic Size Structure database: global datasets of marine size spectra obtained from plankton imaging devices

Author: Dugenne, Mathilde, Corrales-Ugalde, Marco, Luo, Jessica Y., Kiko, Rainer, O'Brien, Todd D., Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, Stock, Charles, Anderson, Clarissa R., Babin, Marcel, Bhairy, Nagib, Bonnet, Sophie, Carlotti, Francois, Cornils, Astrid, Crockford, E. Taylor, Daniel, Patrick, Desnos, Corinne, Drago, Laetitia, Elineau, Amanda, Fischer, Alexis, Grandrémy, Nina, Grondin, Pierre-Luc, Guidi, Lionel, Guieu, Cecile, Hauss, Helena, Hayashi, Kendra, Huggett, Jenny A., Jalabert, Laetitia, Karp-Boss, Lee, Kenitz, Kasia M., Kudela, Raphael M., Lescot, Magali, Marec, Claudie, McDonnell, Andrew, Mériguet, Zoe, Niehoff, Barbara, Noyon, Margaux, Panaïotis, Thelma, Peacock, Emily, Picheral, Marc, Riquier, Emilie, Roesler, Collin, Romagnan, Jean-Baptiste, Sosik, Heidi M., Spencer, Gretchen, Taucher, Jan, Tilliette, Chloé, Vilain, Marion, Dugenne, Mathilde, Corrales-Ugalde, Marco, Luo, Jessica Y., Kiko, Rainer, O'Brien, Todd D., Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, Stock, Charles, Anderson, Clarissa R., Babin, Marcel, Bhairy, Nagib, Bonnet, Sophie, Carlotti, Francois, Cornils, Astrid, Crockford, E. Taylor, Daniel, Patrick, Desnos, Corinne, Drago, Laetitia, Elineau, Amanda, Fischer, Alexis, Grandrémy, Nina, Grondin, Pierre-Luc, Guidi, Lionel, Guieu, Cecile, Hauss, Helena, Hayashi, Kendra, Huggett, Jenny A., Jalabert, Laetitia, Karp-Boss, Lee, Kenitz, Kasia M., Kudela, Raphael M., Lescot, Magali, Marec, Claudie, McDonnell, Andrew, Mériguet, Zoe, Niehoff, Barbara, Noyon, Margaux, Panaïotis, Thelma, Peacock, Emily, Picheral, Marc, Riquier, Emilie, Roesler, Collin, Romagnan, Jean-Baptiste, Sosik, Heidi M., Spencer, Gretchen, Taucher, Jan, Tilliette, Chloé, and Vilain, Marion
Abstract: In marine ecosystems, most physiological, ecological, or physical processes are size dependent. These include metabolic rates, the uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad-scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle normalized biovolume size spectrum (NBSS) and the bulk particle size distribution (PSD), along with their related parameters (slope, intercept, and R2) measured within the epipelagic layer (0–200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP), and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7–10 000 µm size range. A total of 92 472 IFCB samples, 3068 UVP profiles, and 2411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged to 1° × 1° latitude and longitude and by year and month. Our instrument-specific datasets span most major ocean basins, except for the IFCB datasets we have ingested, which were exclusively collected in northern latitudes, and cover decadal time periods (2013–2022 for IFCB, 2008–2021 for UVP, and 1996–2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. The datasets that constitute PSSdb's first release are available at https://doi.org/10.5281/zenodo.11050013 (Dugenne et al., 2024b). In addition, future updates to these data products can be accessed at https://doi.org/10.5281/zenodo.7998799.
Published: 2024
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4. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean

Author: Lombard, Fabien, Guidi, Lionel, Brandão, Manoela C., Coelho Luis, Pedro, Colin, Sébastien, Dolan, John Richard, Elineau, Amanda, Gasol, Josep M, Grondin, Pierre Luc, Henry, Nicolas, Ibarbalz, Federico M, Jalabert, Laetitia, Loreau, Michel, Martini, Séverine, Mériguet, Zoé, Picheral, Marc, Pierella Karlusich, Juan José, Pepperkok, Rainer, Romagnan, Jean-baptiste, Zinger, Lucie, Stemmann, Lars, Acinas, Silvia G, Lee, Karp-boss, Boss, Emmanuel, Sullivan, Matthew B., De Vargas, Colomban, Bowler, Chris, Karsenti, Eric, Gorsky, Gabriel, Lombard, Fabien, Guidi, Lionel, Brandão, Manoela C., Coelho Luis, Pedro, Colin, Sébastien, Dolan, John Richard, Elineau, Amanda, Gasol, Josep M, Grondin, Pierre Luc, Henry, Nicolas, Ibarbalz, Federico M, Jalabert, Laetitia, Loreau, Michel, Martini, Séverine, Mériguet, Zoé, Picheral, Marc, Pierella Karlusich, Juan José, Pepperkok, Rainer, Romagnan, Jean-baptiste, Zinger, Lucie, Stemmann, Lars, Acinas, Silvia G, Lee, Karp-boss, Boss, Emmanuel, Sullivan, Matthew B., De Vargas, Colomban, Bowler, Chris, Karsenti, Eric, and Gorsky, Gabriel
Abstract: Summary paragraph Plankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the ocean’s carbon cycle.
Published: 2024
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5. Statistical Methodology for Identifying Microplastic Samples Collected During TARA Mediterranean Campaign

Author: Falcou-Préfol, Mathilde, Kedzierski, Mikaël, Villain, Jonathan, Kerros, Marie Emmanuelle, Elineau, Amanda, Pedrotti, Maria Luiza, Bruzaud, Stéphane, Cocca, Mariacristina, editor, Di Pace, Emilia, editor, Errico, Maria Emanuela, editor, Gentile, Gennaro, editor, Montarsolo, Alessio, editor, and Mossotti, Raffaella, editor
Published: 2018
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6. TARA Mediterranean Expedition: Assessing the Impact of Microplastics on Mediterranean Ecosystem

Author: Pedrotti, Maria Luiza, Mazzocchi, Maria Grazia, Lombard, Fabien, Galgani, François, Kerros, Marie Emmanuelle, Henry, Maryvonne, Elineau, Amanda, Petit, Stéphanie, Fernandez-de-Puelles, María Luz, Gasparini, Stéphane, Tirelli, Valentina, Jamet, Jean-Louis, Gorsky, Gabriel, Cocca, Mariacristina, editor, Di Pace, Emilia, editor, Errico, Maria Emanuela, editor, Gentile, Gennaro, editor, Montarsolo, Alessio, editor, and Mossotti, Raffaella, editor
Published: 2018
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7. First release of the Pelagic Size Structure database: Global datasets of marine size spectra obtained from plankton imaging devices

Author: Dugenne, Mathilde, primary, Corrales-Ugalde, Marco, additional, Luo, Jessica, additional, Kiko, Rainer, additional, O'Brien, Todd, additional, Irisson, Jean-Olivier, additional, Lombard, Fabien, additional, Stemmann, Lars, additional, Stock, Charles, additional, Anderson, Clarissa R., additional, Babin, Marcel, additional, Bhairy, Nagib, additional, Bonnet, Sophie, additional, Carlotti, Francois, additional, Cornils, Astrid, additional, Crockford, E. Taylor, additional, Daniel, Patrick, additional, Desnos, Corinne, additional, Drago, Laetitia, additional, Elineau, Amanda, additional, Fischer, Alexis, additional, Grandrémy, Nina, additional, Grondin, Pierre-Luc, additional, Guidi, Lionel, additional, Guieu, Cecile, additional, Hauss, Helena, additional, Hayashi, Kendra, additional, Huggett, Jenny A., additional, Jalabert, Laetitia, additional, Karp-Boss, Lee, additional, Kenitz, Kasia M., additional, Kudela, Raphael M., additional, Lescot, Magali, additional, Marec, Claudie, additional, McDonnell, Andrew, additional, Mériguet, Zoe, additional, Niehoff, Barbara, additional, Noyon, Margaux, additional, Panaïotis, Thelma, additional, Peacock, Emily, additional, Picheral, Marc, additional, Riquier, Emilie, additional, Roesler, Collin, additional, Romagnan, Jean-Baptiste, additional, Sosik, Heidi M., additional, Spencer, Gretchen, additional, Taucher, Jan, additional, Tilliette, Chloé, additional, and Vilain, Marion, additional
Published: 2023
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8. Morphological diversity increases with decreasing resources along a zooplankton time series

Author: Beck, Miriam, primary, Cailleton, Caroline, additional, Guidi, Lionel, additional, Desnos, Corinne, additional, Jalabert, Laetitia, additional, Elineau, Amanda, additional, Stemmann, Lars, additional, Ayata, Sakina-Dorothée, additional, and Irisson, Jean-Olivier, additional
Published: 2023
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9. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

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

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

Author: Lilley, Martin K. S., Ferraris, Martina, Elineau, Amanda, Berline, Léo, Cuvilliers, Perrine, Gilletta, Laurent, Thiéry, Alain, Gorsky, Gabriel, and Lombard, Fabien
Published: 2014

12. TARA Mediterranean Expedition: Assessing the Impact of Microplastics on Mediterranean Ecosystem

Author: Pedrotti, Maria Luiza, primary, Mazzocchi, Maria Grazia, additional, Lombard, Fabien, additional, Galgani, François, additional, Kerros, Marie Emmanuelle, additional, Henry, Maryvonne, additional, Elineau, Amanda, additional, Petit, Stéphanie, additional, Fernandez-de-Puelles, María Luz, additional, Gasparini, Stéphane, additional, Tirelli, Valentina, additional, Jamet, Jean-Louis, additional, and Gorsky, Gabriel, additional
Published: 2017
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13. Statistical Methodology for Identifying Microplastic Samples Collected During TARA Mediterranean Campaign

Author: Falcou-Préfol, Mathilde, primary, Kedzierski, Mikaël, additional, Villain, Jonathan, additional, Kerros, Marie Emmanuelle, additional, Elineau, Amanda, additional, Pedrotti, Maria Luiza, additional, and Bruzaud, Stéphane, additional
Published: 2017
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14. First release of the Pelagic Size Structure database: Global datasets of marine size spectra obtained from plankton imaging devices.

Author: Dugenne, Mathilde, Corrales-Ugalde, Marco, Luo, Jessica Y., Kiko, Rainer, O’Brien, Todd D., Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, Stock, Charles, Anderson, Clarissa R., Babin, Marcel, Bhairy, Nagib, Bonnet, Sophie, Carlotti, Francois, Cornils, Astrid, Crockford, E. Taylor, Daniel, Patrick, Desnos, Corinne, Drago, Laetitia, and Elineau, Amanda
Subjects: CARBON cycle, DATABASES, PARTICLE size distribution, IMAGE sensors, CARBON sequestration
Abstract: In marine ecosystems, most physiological, ecological, or physical processes are size-dependent. These include metabolic rates, uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle Normalized Biovolume Size Spectrum (NBSS) and bulk Particle Size Distribution (PSD), along with their related parameters (slope, intercept, and R2) measured within the epipelagic layer (0-200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP) and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7-10,000 µm size range. A total of 92,472 IFCB samples, 3,068 UVP profiles, and 2,411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged in 1x1° latitude/longitude, and by year and month. Our instrument-specific datasets span all major ocean basins, except for the IFCB which was exclusively deployed in northern latitudes, and cover decadal time periods (2013-2022 for IFCB, 2008-2021 for UVP, and 1996-2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. [ABSTRACT FROM AUTHOR]
Published: 2023
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15. Siliceous Rhizaria abundances and diversity in the Mediterranean Sea assessed by combined imaging and metabarcoding approaches

Author: Llopis Monferrer, Natalia, Biard, Tristan, Sandin, Miguel, Lombard, Fabien, Picheral, Marc, Elineau, Amanda, Guidi, Lionel, Leynaert, Aude, Tréguer, Paul, Not, Fabrice, 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), 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), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and ANR-18-CE01-0011,RadiCal,Calibration des isotopes stable du silicium des Radiolaires : Développement d'un nouveau paleo-indicateur du cycle du silicium marin(2018)
Subjects: Ekologi, Global and Planetary Change, imaging technologies, polycystine, Ecology, Ocean Engineering, Aquatic Science, Oceanography, Rhizaria, silicon cycle, metabarcoding, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Science and Technology, Phaeodaria
Abstract: Siliceous Rhizaria (polycystine radiolarians and phaeodarians) are significant contributors to carbon and silicon biogeochemical cycles. Considering their broad taxonomic diversity and their wide size range (from a few micrometres up to several millimetres), a comprehensive evaluation of the entire community to carbon and silicon cycles is challenging. Here, we assess the diversity and contribution of silicified Rhizaria to the global biogenic silica stocks in the upper 500 m of the oligotrophic North-Western Mediterranean Sea using both imaging (FlowCAM, Zooscan and Underwater Vision Profiler) and molecular tools and data. While imaging data (cells m-3) revealed that the most abundant organisms were the smallest, molecular results (number of reads) showed that the largest Rhizaria had the highest relative abundances. While this seems contradictory, relative abundance data obtained with molecular methods appear to be closer to the total biovolume data than to the total abundance data of the organisms. This result reflects a potential link between gene copies number and the volume of a given cell allowing reconciling molecular and imaging data. Using abundance data from imaging methods we estimate that siliceous Rhizaria accounted for up to 6% of the total biogenic silica biomass of the siliceous planktonic community in the upper 500m of the water column.
Published: 2022
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16. AtlantECO Deliverable - D4.2 - Handbook of Standards and Best Practices

Author: Pesant, Stéphane, Muxagatan, Erik, Johns, David, Poulain, Julie, Elineau, Amanda, Huete, Maria, and Schramm, Juliette
Subjects: Standards, Protocols, Best Practice
Abstract: The present deliverable (D4.2) constitutes version 2 of the Handbook of Standards and Best Practices regarding AtlantECO's augmented observations and technological innovations as described in Work Package 4. The Handbook will be developed throughout the project and will be delivered progressively as four revised and augmented deliverables (D4.1-D4.4). The Handbook will address standards and best practices with respect to: Sample collection Sample biobanking Sample analysis Access and Benefits Sharing Provenance reporting Environmental context reporting AtlantECO will generate new observations as part of the activities described in its Grant Agreement and also via a number of synergies with other European and International projects. The Handbook aims to harmonise as much as possible the methodologies used across these projects on some key types of observations, while allowing enough flexibility to adapt methodologies to the different observation programmes, therefore maximising the adoption of the standards and best practices. The present deliverable augments the Handbook with a collection of packages made publicly available on Zenodo (https://doi.org/10.5281/zenodo.4897860). The Handbook includes from the previous version: A short introduction to the Project’s goals, organisation and expected outcomes Guiding principles for the design of AtlantECO's system of standards & best practices The system of base protocols presented in version 1 is augmented with two packages: The Mission Microbiomes handbook of sampling protocols The Continuous Plankton Recorder handbook of sampling protocols The capacity building strategy presented in version 1 is augmented with three packages: A genetic analysis package An imaging analysis package An Access and Benefits Sharing package
Published: 2022
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17. A global marine particle size distribution dataset obtained with the Underwater Vision Profiler 5

Author: Kiko, Rainer, primary, Picheral, Marc, additional, Antoine, David, additional, Babin, Marcel, additional, Berline, Léo, additional, Biard, Tristan, additional, Boss, Emmanuel, additional, Brandt, Peter, additional, Carlotti, Francois, additional, Christiansen, Svenja, additional, Coppola, Laurent, additional, de la Cruz, Leandro, additional, Diamond-Riquier, Emilie, additional, Durrieu de Madron, Xavier, additional, Elineau, Amanda, additional, Gorsky, Gabriel, additional, Guidi, Lionel, additional, Hauss, Helena, additional, Irisson, Jean-Olivier, additional, Karp-Boss, Lee, additional, Karstensen, Johannes, additional, Kim, Dong-gyun, additional, Lekanoff, Rachel M., additional, Lombard, Fabien, additional, Lopes, Rubens M., additional, Marec, Claudie, additional, McDonnell, Andrew M. P., additional, Niemeyer, Daniela, additional, Noyon, Margaux, additional, O'Daly, Stephanie H., additional, Ohman, Mark D., additional, Pretty, Jessica L., additional, Rogge, Andreas, additional, Searson, Sarah, additional, Shibata, Masashi, additional, Tanaka, Yuji, additional, Tanhua, Toste, additional, Taucher, Jan, additional, Trudnowska, Emilia, additional, Turner, Jessica S., additional, Waite, Anya, additional, and Stemmann, Lars, additional
Published: 2022
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18. A global marine particle size distribution dataset obtained with the Underwater Vision Profiler 5

Author: Kiko, Rainer, Picheral, Marc, Antoine, David, Babin, Marcel, Berline, Léo, Biard, Tristan, Boss, Emmanuel, Brandt, Peter, Carlotti, Francois, Christiansen, Svenja, Coppola, Laurent, de la Cruz, Leandro, Diamond-Riquier, Emilie, Durrieu de Madron, Xavier, Elineau, Amanda, Gorsky, Gabriel, Guidi, Lionel, Hauss, Helena, Irisson, Jean-Olivier, Karp-Boss, Lee, Karstensen, Johannes, Kim, Dong-gyun, Lekanoff, Rachel M., Lombard, Fabien, Lopes, Rubens M., Marec, Claudie, McDonnell, Andrew M. P., Niemeyer, Daniela, Noyon, Margaux, O'Daly, Stephanie H., Ohman, Mark D., Pretty, Jessica L., Rogge, Andreas, Searson, Sarah, Shibata, Masashi, Tanaka, Yuji, Tanhua, Toste, Taucher, Jan, Trudnowska, Emilia, Turner, Jessica S., Waite, Anya, Stemmann, Lars, Kiko, Rainer, Picheral, Marc, Antoine, David, Babin, Marcel, Berline, Léo, Biard, Tristan, Boss, Emmanuel, Brandt, Peter, Carlotti, Francois, Christiansen, Svenja, Coppola, Laurent, de la Cruz, Leandro, Diamond-Riquier, Emilie, Durrieu de Madron, Xavier, Elineau, Amanda, Gorsky, Gabriel, Guidi, Lionel, Hauss, Helena, Irisson, Jean-Olivier, Karp-Boss, Lee, Karstensen, Johannes, Kim, Dong-gyun, Lekanoff, Rachel M., Lombard, Fabien, Lopes, Rubens M., Marec, Claudie, McDonnell, Andrew M. P., Niemeyer, Daniela, Noyon, Margaux, O'Daly, Stephanie H., Ohman, Mark D., Pretty, Jessica L., Rogge, Andreas, Searson, Sarah, Shibata, Masashi, Tanaka, Yuji, Tanhua, Toste, Taucher, Jan, Trudnowska, Emilia, Turner, Jessica S., Waite, Anya, and Stemmann, Lars
Abstract: Marine particles of different nature are found throughout the global ocean. The term "marine particles" describes detritus aggregates and fecal pellets as well as bacterioplankton, phytoplankton, zooplankton and nekton. Here, we present a global particle size distribution dataset obtained with several Underwater Vision Profiler 5 (UVP5) camera systems. Overall, within the 64 mu m to about 50 mm size range covered by the UVP5, detrital particles are the most abundant component of all marine particles; thus, measurements of the particle size distribution with the UVP5 can yield important information on detrital particle dynamics. During deployment, which is possible down to 6000 m depth, the UVP5 images a volume of about 1 L at a frequency of 6 to 20 Hz. Each image is segmented in real time, and size measurements of particles are automatically stored. All UVP5 units used to generate the dataset presented here were inter-calibrated using a UVP5 high-definition unit as reference. Our consistent particle size distribution dataset contains 8805 vertical profiles collected between 19 June 2008 and 23 November 2020. All major ocean basins, as well as the Mediterranean Sea and the Baltic Sea, were sampled. A total of 19 % of all profiles had a maximum sampling depth shallower than 200 dbar, 38 % sampled at least the upper 1000 dbar depth range and 11 % went down to at least 3000 dbar depth. First analysis of the particle size distribution dataset shows that particle abundance is found to be high at high latitudes and in coastal areas where surface productivity or continental inputs are elevated. The lowest values are found in the deep ocean and in the oceanic gyres. Our dataset should be valuable for more in-depth studies that focus on the analysis of regional, temporal and global patterns of particle size distribution and flux as well as for the development and adjustment of regional and global biogeochemical models. The marine particle size distribution dataset (Kiko et al
Published: 2022
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19. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author: Lombard, Fabien, primary, Bourdin, Guillaume, additional, Pesant, Stéphane, additional, Agostini, Sylvain, additional, Baudena, Alberto, additional, Boissin, Emilie, additional, Cassar, Nicolas, additional, Clampitt, Megan, additional, Conan, Pascal, additional, Silva, Ophélie Da, additional, Dimier, Céline, additional, Douville, Eric, additional, Elineau, Amanda, additional, Fin, Jonathan, additional, Flores, J. Michel, additional, Ghiglione, Jean François, additional, Hume, Benjamin C.C., additional, Jalabert, Laetitia, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, McMinds, Ryan, additional, Mériguet, Zoé, additional, Metzl, Nicolas, additional, Paz-García, David A., additional, Pedrotti, Maria Luiza, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Ras, Joséphine, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Rouan, Alice, additional, Röttinger, Eric, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Moulin, Clémentine, additional, Iwankow, Guillaume, additional, Banaigs, Bernard, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Sullivan, Matthew B., additional, Thomas, Olivier, additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Boss, Emmanuel, additional, and Gorsky, Gaby, additional
Published: 2022
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20. Has the biomass of jellyfish already surpassed small pelagic fish in the NW Mediterranean Sea? Results from an intense spatiotemporal survey during 2011-2014 and comparison with the long-term trend

Author: Lilley, Martin K. S., Berline, Leo, Ferraris, Martina, Elineau, Amanda, Cuvilliers, Perrine, Stemmann, Lars, and Lombard, Fabien
Subjects: Fisheries and aquaculture, Ecosystem observation, processes and dynamics, Pressures, impacts, conservation, and management
Abstract: Jellyfish, especially the scyphozoan Pelagia noctiluca cause recurrent and persistent problems to human activities in the Mediterranean Sea, in particular along the French Riviera. Population oscillations have been observed for over 100 years showing alternative periods of presence and absence; however the spatial and temporal intensity of these blooms remains unclear. By means of year-round night-time transects and intensive spatial surveys during summer months, the abundance and biomass of P. noctiluca was quantified in the Ligurian Sea. Pelagia noctiluca was always found in greatest abundance in the core of the Ligurian current, with lower abundances in the central Ligurian basin and coastal areas. In 2013 the population was observed to grow to a very large size and at high abundance. While population biomass was below one tonne per square kilometre in 2012, in the summer of 2013 this biomass surpassed 10 tonnes km-2., potentially greater than the biomass of small pelagic fishes. Fortunately for tourists, this large population of jellyfish remained offshore and was not pushed to the coast by onshore winds.
Published: 2022
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21. An Integrative Assessment of the Plastic Debris Load in the Mediterranean Sea

Author: Pedrotti, Maria Luiza, primary, Lombard, Fabien, additional, Baudena, Alberto, additional, Galgani, François, additional, Elineau, Amanda, additional, Petit, Stephanie, additional, Henry, Maryvonne, additional, Trouble, Romain, additional, Reverdin, Gilles, additional, Ser-Giacomi, Enrico, additional, Kedzierski, Mikael, additional, Boss, Emmanuel, additional, and Gorsky, Gabriel, additional
Published: 2022
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22. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela, Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea, Picheral, Marc, Henry, Nicolas, Acinas, Silvia, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sullivan, Matthew, Sunagawa, Shinichi, Wincker, Patrick, Stemmann, Lars, Lombard, Fabien, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU]Sciences of the Universe [physics], fungi
Abstract: International audience; Abstract Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO 2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
Published: 2021
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23. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, Vargas, Colomban de, Sullivan, Matthew B., Tara Oceans Coordinators, Acinas, Silvia G., Stemmann, Lars, Lombard, Fabien, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fonds Français pour l'Environnement Mondial, European Commission, and Agencia Estatal de Investigación (España)
Abstract: This article is contribution number 121 of Tara Oceans.-- 19 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41598-021-94615-5.-- Data availability: Median ESD and abundance values by zooplankton groups are available at https://doi.org/10.17632/nwvjwccgvh.1. Zooplankton imaging datasets from the Tara Oceans expeditions are available through the collaborative web Ecotaxa application and repository under the addresses: https://ecotaxa.obs-vlfr.fr/prj/377, https://ecotaxa.obs-vlfr.fr/prj/2245, https://ecotaxa.obs-vlfr.fr/prj/378 for the WP2 net; https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for the Bongo net; https://ecotaxa.obs-vlfr.fr/prj/415, https://ecotaxa.obs-vlfr.fr/prj/409, https://ecotaxa.obs-vlfr.fr/prj/408, https://ecotaxa.obs-vlfr.fr/prj/411, https://ecotaxa.obs-vlfr.fr/prj/412 for the Régent net. Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582, Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump, Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (http://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, The French Ministry of Research, and the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). M.C.B. acknowledges postdoc fellowships from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES) (99999.000487/2016-03) and the Fonds Français pour l'Environnement Mondial (FFEM). F.B. received support from ETH Zürich and from the European Union’s Horizon 2020 research and innovation program under grant agreement n°SEP-210591007, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2021

24. Benchmark of image classification using several large plankton datasets: Convolutional Neural Networks improve detection of rare taxa

Author: Panaiotis, Thelma, Boniface-Chang, Guillaume, Dulac-Arnold, Gabriel, Blanc, Benjamin, Biard, Tristan, Caray-Counil, Louis, Desnos, Corinne, Elineau, Amanda, Jalabert, Laëtitia, Kiko, Rainer, Lombard, Fabien, Picheral, Marc, Romagnan, Jean-Baptiste, Stemmann, Lars, Irisson, Jean-Olivier, Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Google Research [Paris], 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’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Université du Littoral Côte d'Opale (ULCO), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Sorbonne Université (SU)
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; Plankton imaging instruments generate an ever increasing volume of data which is mostly processed through machine learning algorithms. However, classifying plankton images is a challenging computer science task in its own right: datasets are strongly unbalanced; the dominant classes are often not biologically interesting (artefacts, bubbles) and/or very heterogeneous looking (marine snow); and images span a large size range. Despite a wealth of reports on the performance of automatic plankton images classifiers, we still do not have a definitive idea regarding how methods compare with each other and where they can systematically be trusted. This is mostly because those reports rely on rather small unpublished datasets, not necessarily representative of real-life biological samples in terms of size, number of categories and proportions. Here we report the performance of a classic classification method (Random Forest on handcrafted image features) and a more recent one (a Convoluted Neural Network) on large publicly released datasets, from five widely used plankton imaging instruments. We show that CNN improve classification performance but only noticeably on poorly represented (a few hundred images) classes. Finally, we showcase the difference between the predictions of the two classifiers and a human-checked truth on several real-world datasets, to give insights regarding which ecological questions can or cannot be studied from computer-generated classifications only.
Published: 2021

25. Individual shrinking to enhance population survival: quantifying the reproductive and metabolic expenditures of a starving jellyfish, Pelagia noctiluca

Author: Lilley, Martin K.S., Elineau, Amanda, Ferraris, Martina, Thiéry, Alain, Stemmann, Lars, Gorsky, Gabriel, and Lombard, Fabien
Published: 2014
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26. Occurrence of Eukaryotes in the size fraction >300 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a Multinet and analysed on a ZooScan imaging platform

Author: Romagnan, Jean-Baptiste, Jalabert, Laetitia, Llopis Monferrer, Natalia, Merland, Camille, Trudnowska, Emilia, Brandão, Manoela Costa, Elineau, Amanda, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans Consortium Coordinators, Karsenti, Erik, Pesant, Stéphane, Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, and Gorsky, Gabriel
Subjects: Aetideidae Giesbrecht, 1892, Tomopteridae Grube, 1850, Annelida, Eucalanidae Giesbrecht, 1893, Candaciidae Giesbrecht, 1893, Foraminifera, Hyperiidea, Pyrocystaceae (Schütt, 1896) Lemmermann, 1899, Calocalanus pavo (Dana, 1852), Euchaetidae Giesbrecht, 1893, Laomediidae Borradaile, 1903, Acartiidae Sars G.O., 1903, Centropagidae Giesbrecht, 1893, Copepoda, Eumalacostraca, Pleuromamma Giesbrecht in Giesbrecht & Schmeil, 1898, Gaetanus curvicornis Sars G.O., 1905, Rhizaria, Calanidae Dana, 1849, Heterorhabdidae Sars G.O., 1902, Orbulina d'Orbigny, 1839, +Plankton+>+Zooplankton%22">Biology > Plankton > Zooplankton, Augaptilidae Sars G.O., 1905, Calanoida, Euphausiacea
Abstract: Tara expeditions (2009-2013) sampled the world’s oceans with standardized protocols, putting an exceptional effort into sampling plankton diversity across a large size range, using a combination of water samples and net tows. The efforts to explore the genomic diversity of plankton, through metabarcoding and metagenomics, have led to well publicized papers and have made the renown of Tara. While a similar extensive effort has been put on imaging, the datasets are not public yet. In a limited number of stations, in addition to the usual 5μm -> ~5cm Tara sampling strategy, multinet trawls allowed to sample the vertical distribution of plankton; this is the content of this dataset. Using a 300µm mesh net, it cover organisms from 300µm to ~3cm.
Published: 2021
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27. A global marine particle size distribution dataset obtained with the Underwater Vision Profiler 5

Author: Kiko, R., Picheral, M., Antoine, David, Babin, Marcel, Berline, Léo, Biard, Tristan, Boss, Emmanuel, Brandt, Peter, Carlotti, François, Christiansen, Svenja, Coppola, Laurent, Cruz, Leandro, Diamond-Riquier, Emilie, Madron, Xavier, Elineau, Amanda, Gorsky, Gabriel, Guidi, Lionel, Hauss, Helena, Irisson, Jean-Olivier, Karp-Boss, Lee, Karstensen, Johannes, 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), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), University of Maine - School of Marine Sciences, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Department of Biosciences [Oslo], University of Oslo (UiO), IMPA Jean-Christophe Yoccoz, Instituto Nacional de Matemática Pura e Aplicada (IMPA)-Institut National de Mathématiques Pures-Centre National de la Recherche Scientifique (CNRS), Centre de Formation et de Recherche sur les Environnements Méditérranéens (CEFREM), Université de Perpignan Via Domitia (UPVD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Kiel University, and University of Maine
Subjects: [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2021

28. Occurrence of Eukaryotes in the size fraction >300 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a Bongo net and analysed on a ZooScan imaging platform

Author: Romagnan, Jean-Baptiste, Jalabert, Laetitia, Llopis Monferrer, Natalia, Elineau, Amanda, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans Consortium Coordinators, Karsenti, Erik, Pesant, Stéphane, Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, and Gorsky, Gabriel
Subjects: Oithonidae Dana, 1853, Tomopteridae Grube, 1850, Annelida, Eucalanidae Giesbrecht, 1893, Candaciidae Giesbrecht, 1893, Foraminifera, Hyperiidea, Pyrocystaceae (Schütt, 1896) Lemmermann, 1899, Calocalanus pavo (Dana, 1852), Euchaetidae Giesbrecht, 1893, Penilia Dana, 1852, Acartiidae Sars G.O., 1903, Centropagidae Giesbrecht, 1893, Copepoda, Eumalacostraca, Rhizaria, Calanidae Dana, 1849, Heterorhabdidae Sars G.O., 1902, Temoridae Giesbrecht, 1893, +Plankton+>+Zooplankton%22">Biology > Plankton > Zooplankton, Evadne Lovén, 1836, Augaptilidae Sars G.O., 1905, Calanoida, Euphausiacea, Phaeodaria
Abstract: Tara expeditions sampled the world’s oceans with standardized protocols, putting an exceptional effort into sampling plankton diversity across a large size range, using a combination of water samples and net tows. The efforts to explore the genomic diversity of plankton, through metabarcoding and metagenomics, have led to well publicized papers and have made the renown of Tara. While a similar extensive effort has been put on imaging, the datasets are not public yet. In a limited number of stations, in addition to the usual 5μm -> ~5cm Tara sampling strategy, Bongo net samples were taken during the day and during the night, at the same station; this is the content of this dataset. Using a 300µm mesh net, it cover organisms from 300µm to ~3cm, Bongo net (300μm mesh) hauled vertically from 500m depth to the surface, once during the day, and once during the night. Sample preserved in 4% buffered formalin and stored over the long term at the Centre de Collections Planctoniques de Villefranche (CCPv). Sample scanned on a ZooScan, images processed with ZooProcess and sorted taxonomically on EcoTaxa, within the Plateforme d'Imagerie Quantitative de Villefranche (PIQv). The PIQv and CCPv platforms are part of EMBRC-France, a national Research Infrastructure supported by ANR, under the reference ANR-10-INSB-02.
Published: 2021
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29. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, Winckler, Patrick, Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, and Winckler, Patrick
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
Published: 2021
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30. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fonds Français pour l'Environnement Mondial, European Commission, Agencia Estatal de Investigación (España), Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, Vargas, Colomban de, Sullivan, Matthew B., Tara Oceans Coordinators, Acinas, Silvia G., Stemmann, Lars, Lombard, Fabien, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fonds Français pour l'Environnement Mondial, European Commission, Agencia Estatal de Investigación (España), Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, Vargas, Colomban de, Sullivan, Matthew B., Tara Oceans Coordinators, Acinas, Silvia G., Stemmann, Lars, and Lombard, Fabien
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump
Published: 2021

31. Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere

Author: Scales, Brittan S., primary, Cable, Rachel N., additional, Duhaime, Melissa B., additional, Gerdts, Gunnar, additional, Fischer, Franziska, additional, Fischer, Dieter, additional, Mothes, Stephanie, additional, Hintzki, Lisa, additional, Moldaenke, Lynn, additional, Ruwe, Matthias, additional, Kalinowski, Jörn, additional, Kreikemeyer, Bernd, additional, Pedrotti, Maria-Luiza, additional, Gorsky, Gaby, additional, Elineau, Amanda, additional, Labrenz, Matthias, additional, and Oberbeckmann, Sonja, additional
Published: 2021
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32. Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Lombard, Fabien, Takuvik Joint International Laboratory ULAVAL-CNRS, and Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, Multidisciplinary, Science, Composition (combinatorics), Zooplankton, 03 medical and health sciences, 0302 clinical medicine, Oceanography, [SDE]Environmental Sciences, Medicine, Environmental science, 14. Life underwater, Author Correction, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO
Published: 2021
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33. Occurrence of Eukaryotes in the size fraction >200 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a WPII net and analysed on a ZooScan imaging platform

Author: Romagnan, Jean-Baptiste, Jalabert, Laetitia, Olivier, Marion, Elineau, Amanda, Brandão, Manoela Costa, Caray-Counil, Louis, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans Consortium Coordinators, Karsenti, Erik, Pesant, Stéphane, Irisson, Jean-Olivier, Lombard, Fabien, Stemmann, Lars, and Gorsky, Gabriel
Subjects: Annelida, +Plankton%22">Biology > Plankton, Foraminifera, Ceratiaceae Kofoid, 1907, Oikopleuridae Lohmann, 1915, Eumalacostraca, Calanidae Dana, 1849, Crustacea, Poecilostomatoida, Corycaeidae Dana, 1852, Ophiuroidea, Calanoida, Oncaeidae Giesbrecht, 1893, Oithonidae Dana, 1853, Salpida, Harpacticoida, Collodaria, Acartiidae Sars G.O., 1903, Cirripedia, Spumellaria, Doliolida, Cavoliniidae Gray, 1850 (1815), Thecosomata, Echinodermata, Pterosagitta draco (Krohn, 1853), Diphyidae Quoy & Gaimard, 1827, Ostracoda, Hyperiidea, Bryozoa, Calocalanus pavo (Dana, 1852), Centropagidae Giesbrecht, 1893, Copepoda, Rhopalonematidae Russell, 1953, Siphonophorae, Cnidaria, Limacinidae Gray, 1840, Heterorhabdidae Sars G.O., 1902, Orbulina d'Orbigny, 1839, Temoridae Giesbrecht, 1893, Larvacea, Augaptilidae Sars G.O., 1905, Phaeodaria, Atlanta Lesueur, 1817, Actinopterygii, Creseis acicula (Rang, 1828), Chaetognatha, Eucalanidae Giesbrecht, 1893, Candaciidae Giesbrecht, 1893, Pyrocystaceae (Schütt, 1896) Lemmermann, 1899, Euchaetidae Giesbrecht, 1893, Laomediidae Borradaile, 1903, Bivalvia, Hydrozoa, Rhizaria, Evadne Lovén, 1836, Podon Lilljeborg, 1853, Euphausiacea
Abstract: The Tara Oceans project sampled contrasting ecosystems of the world oceans during a three-year expedition (2009-2013), collecting environmental data and plankton, from viruses to metazoans, on board the 36-metre Tara Schooner. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. Samples were later analysed using modern sequencing and state-of-the-art imaging technologies., We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, 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 Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes
Published: 2020
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34. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Author: Gorsky, Gabriel, Bourdin, Guillaume, Lombard, Fabien, Pedrotti, Maria Luiza, Audrain, Samuel, Bin, Nicolas, Boss, Emmanuel, Bowler, Chris, Cassar, Nicolas, Caudan, Loic, Chabot, Genevieve, Cohen, Natalie R., Cron, Daniel, De Vargas, Colomban, Dolan, John R., Douville, Eric, Elineau, Amanda, Flores, J. Michel, Ghiglione, Jean Francois, Haentjens, Nils, Hertau, Martin, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Moulin, Clementine, Moucherie, Yohann, Pesant, Stephane, Picheral, Marc, Poulain, Julie, Pujo-pay, Mireille, Reverdin, Gilles, Romac, Sarah, Sullivan, Mathew B., Trainic, Miri, Tressol, Marc, Trouble, Romain, Vardi, Assaf, Voolstra, Christian R., Wincker, Patrick, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stephanie, Sunagawa, Shinichi, Thomas, Olivier P., Thurber, Rebecca Lisette Vega, Zoccola, Didier, Planes, Serge, Allemand, Denis, Karsenti, Eric, Planes, S., Banaig, B., Boissin, E., Iwankow, G., Allemand, D., Zoccola, D., Reynaud, S., Beraud, E., Djerbi, N., Forcioli, D., Furla, P., Gilson, E., Mcmind, R., Ottaviani, A., Rottinger, E., Rouan, A., Zamoum, T., Flume, B. C. C., Pogoreutz, C., Voolstra, C. R., Rothig, T., Ziegler, M., Paoli, L., Ruscheweyh, H-j, Salazar, G., Sunagawa, S., Flores, J. M., Koren, I, Trainic, M., Lang-yona, N., Vardi, A., Conan, P., Ghiglione, J-f, Pujo-pay, M., Galand, P. E., Hochart, C., Audrain, S., Bourgois, E., Hertau, M., Lancelot, J., Monmarche, D., Moulin, C., Moucherie, Y., Trouble, R., Boss, E., Bourdin, G., Haentjens, N., Karp-boss, L., Agostini, S., Mitsuhashi, G., Kitano, Y., Da Silva, O., Dolan, J. R., Gorsky, G., Lemee, R., Lombard, F., Pedrotti, M-l, Cronin, D., Sullivan, M., Armstrong, E., Aury, J-m, Barbe, V, Belser, C., Carradec, Q., Labadie, K., Le-hoang, J., Noel, B., Poulain, J., Wincker, P., Klinges, G., Vega-thunder, R., Bonnival, E., De Vargas, C., Henry, N., Marie, D., Romac, S., Pesant, S., Miguel-gorda, M., Thomas, O. P., Bowler, C., Friedrich, R., Cassar, N., Lin, Y., John, S. G., Kelly, R. L., Cohen, N. R., Reverdin, G., Filee, J., Pedrotti, Maria Luiza, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Laboratoires d'excellence - LabexMER Marine Excellence Research: a changing ocean - - LabexMER2010 - ANR-10-LABX-0019 - LABX - OLD, 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), University of Maine, Tara Expéditions, Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Nicholas School of the Environment, Duke University [Durham], Mercator Océan, Société Civile CNRS Ifremer IRD Météo-France SHOM, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Woods Hole Oceanographic Institution (WHOI), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, 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), Processus et interactions de fine échelle océanique (PROTEO), 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), Department of Civil, Environmental and Geodetic Engineering [Columbus], Ohio State University [Columbus] (OSU), Laboratoire d'aérologie (LAERO), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universität Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, 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), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Dpt génétique médicale [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Centre Scientifique de Monaco (CSM), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), European Molecular Biology Laboratory [Heidelberg] (EMBL), TARA, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), 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), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Institut Pierre-Simon-Laplace (IPSL (FR_636)), 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)-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), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), 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), Université Nice Sophia Antipolis (... - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), 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), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, trace metals, Ocean Engineering, neuston, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Oceanography, 01 natural sciences, Pacific ocean, taxonomy, neuston/plankton genomics/taxonomy/imaging, ddc:570, Ecosystem, 14. Life underwater, lcsh:Science, Reef, 0105 earth and related environmental sciences, Water Science and Technology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, geography, geography.geographical_feature_category, aerosols, NCP, IOP, microplastic, plankton genomics, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ACL, 010604 marine biology & hydrobiology, Community structure, imaging, Pelagic zone, Plankton, Inlet, neuston/plankton genomics/taxonomy/imaging, aerosols, NCP, IOP, trace metals, microplastic, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, 13. Climate action, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Neuston
Abstract: Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions. ISSN:2296-7745
Published: 2019
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35. Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)

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

36. The Seasonal and Inter-Annual Fluctuations of Plankton Abundance and Community Structure in a North Atlantic Marine Protected Area

Author: Benedetti, Fabio, primary, Jalabert, Laëtitia, additional, Sourisseau, Marc, additional, Becker, Beatriz, additional, Cailliau, Caroline, additional, Desnos, Corinne, additional, Elineau, Amanda, additional, Irisson, Jean-Olivier, additional, Lombard, Fabien, additional, Picheral, Marc, additional, Stemmann, Lars, additional, and Pouline, Patrick, additional
Published: 2019
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37. The Seasonal and Inter-Annual Fluctuations of Plankton Abundance and Community Structure in a North Atlantic Marine Protected Area

Author: Benedetti, Fabio, Jalabert, Laëtitia, Sourisseau, Marc, Becker, Beatriz, Cailliau, Caroline, Desnos, Corinne, Elineau, Amanda, Irisson, Jean-olivier, Lombard, Fabien, Picheral, Marc, Stemmann, Lars, Pouline, Patrick, Benedetti, Fabio, Jalabert, Laëtitia, Sourisseau, Marc, Becker, Beatriz, Cailliau, Caroline, Desnos, Corinne, Elineau, Amanda, Irisson, Jean-olivier, Lombard, Fabien, Picheral, Marc, Stemmann, Lars, and Pouline, Patrick
Abstract: Marine Protected Areas have become a major tool for the conservation of marine biodiversity and resources. Yet our understanding of their efficacy is often limited because it is measured for a few biological components, typically top predators or species of commercial interest. To achieve conservation targets, marine protected areas can benefit from ecosystem-based approaches. Within such an approach, documenting the variation of plankton indicators and their covariation with climate is crucial as plankton represent the base of the food webs. With this perspective, we sought to document the variations in the emerging properties of the plankton to better understand the dynamics of the pelagic fishes, mammals and seabirds that inhabit the region. For the first time, we analyze the temporal variations of the entire plankton community of one of the widest European protected areas, the Parc Naturel Marin de la Mer d’Iroise. We used data from several sampling transects carried out in the Iroise Sea from 2011 to 2015 to explore the seasonal and inter-annual variations of phytoplankton and mesozooplankton abundance, composition and size, as well as their covariation with abiotic variables, through multiple multivariate analyses. Overall, our observations are coherent with the plankton dynamics that have been observed in other regions of the North-East Atlantic. We found that both phytoplankton and zooplankton show consistent seasonal patterns in taxonomic composition and size structure but also display inter-annual variations. The spring bloom was associated with a higher contribution of large chain-forming diatoms compared to nanoflagellates, the latter dominating in fall and summer. Dinoflagellates show marked inter-annual variations in their relative contribution. The community composition of phytoplankton has a large impact on the mesozooplankton together with the distance to the coast. The size structure of the mesozooplankton community, examined through the ratio of s
Published: 2019
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38. Poster presentation: Statistical Methodology for Identifying Microplastic Samples Collected During TARA Mediterranean Campaign

Author: Falcou-Préfol, Mathilde, Mikaël Kedzierski, Villain, Jonathan, Kerros, Marie Emmanuelle, Elineau, Amanda, Pedrotti, Maria Luiza, and Bruzaud, Stéphane
Published: 2017
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39. Spatio-temporal variations of the planktonic communities in a North Atlantic Marine Protected Area and their potential links with Sardina pilchardus (Walbaum, 1792) catches

Author: Benedetti, Fabio, Jalabert, Laëtitia, Sourisseau, Marc, Beker, Beatriz, Elineau, Amanda, Cailliau, Caroline, Irisson, Jean-Olivier, Picheral, Marc, Stemmann, Lars, Pouline, Patrick, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), and Agence Française pour la Biodiversité (AFB)
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2017

40. Tara mediterranean expedition : Assessing the impact of microplastics on Mediterranean ecosystem

Author: Pedrotii, Maria Luiza, Mazzocchi, Maria Grazia, Lombard, Fabien, Galgani, François, Kerros, Marie Emanuelle, Henri, Maryvonne, Elineau, Amanda, Petit, S., Fernández-de-Puelles, María Luz, Pedrotii, Maria Luiza, Mazzocchi, Maria Grazia, Lombard, Fabien, Galgani, François, Kerros, Marie Emanuelle, Henri, Maryvonne, Elineau, Amanda, Petit, S., and Fernández-de-Puelles, María Luz
Published: 2017

41. Changes in the Floating Plastic Pollution of the Mediterranean Sea in Relation to the Distance to Land

Author: Pedrotti, Maria Luiza, primary, Petit, Stéphanie, additional, Elineau, Amanda, additional, Bruzaud, Stéphane, additional, Crebassa, Jean-Claude, additional, Dumontet, Bruno, additional, Martí, Elisa, additional, Gorsky, Gabriel, additional, and Cózar, Andrés, additional
Published: 2016
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42. Individual shrinking to enhance population survival: quantifying the reproductive and metabolic expenditures of a starving jellyfish, Pelagia noctiluca.

Author: Thiéry, Alain, Lilley, Martin K.S., Elineau, Amanda, Ferraris, Martina, Stemmann, Lars, Gorsky, Gabriel, and Lombard, Fabien
Subjects: JELLYFISHES, METABOLISM, RESPIRATION, OPTODES, REPRODUCTION
Abstract: The holoplanktonic jellyfish Pelagia noctiluca is renowned for periods of high abundance, causing considerable problems to tourism and aquaculture. Little is understood about the drivers of its periodic presence and absence or how it survives unfavourable periods. Studying the effect of starvation, we evaluated the main metabolic expenses (reproduction, respiration and excretion) during those periods. P. noctiluca could shrink in size, losing up to 85% of their mass (6.6–7.1% loss day−1), while continuing to release eggs quasi-daily over a 28-day period. Egg production was proportional to size (mean 759 eggs day−1 at 6 cm bell diameter), with up to 19 526 eggs released in a single spawn, thereby providing huge potential for population growth despite undergoing starvation. Small food rations decreased the rate of shrinking to 3.1% day−1, prolonging life (49 days), potentially enhancing the chances of encountering more prey and regrowing. Metabolism increased with wet mass (allometric exponent: 0.93 for respiration, 0.82 for ammonium), however reproduction was the greatest carbon expenditure for individuals larger than 9 cm bell diameter. Temperature (9–29°C) also significantly increased both respiration and, to a greater extent, excretion (Q10 = 2.25 and 4.76). Consequentially a warming ocean may negatively affect survival rates unless prey abundance balances the increased metabolic demands. [ABSTRACT FROM PUBLISHER]
Published: 2014

43. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Tara Oceans Consortium Coordinators, Stemmann, Lars, and Lombard, Fabien
Subjects: Ocean sciences, Ecology, 13. Climate action, FOS: Biological sciences, fungi, 14. Life underwater, 15. Life on land
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump., Scientific Reports, 11 (1), ISSN:2045-2322

44. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, and Lombard, Fabien
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45. The Seasonal and Inter-Annual Fluctuations of Plankton Abundance and Community Structure in a North Atlantic Marine Protected Area

Author: Benedetti, Fabio, Jalabert, Laëtitia, Sourisseau, Marc, Becker, Beatriz, Cailliau, Caroline, Desnos, Corinne, Elineau, Amanda, Irisson, Jean-Olivier, Lombard, Fabien, Picheral, Marc, Stemmann, Lars, and Pouline, Patrick
Subjects: size structure, 13. Climate action, fungi, 14. Life underwater, Seasonality, 15. Life on land, Plankton, Copepod, Life sciences, Marine Protected Area
Abstract: Marine Protected Areas have become a major tool for the conservation of marine biodiversity and resources. Yet our understanding of their efficacy is often limited because it is measured for a few biological components, typically top predators or species of commercial interest. To achieve conservation targets, marine protected areas can benefit from ecosystem-based approaches. Within such an approach, documenting the variation of plankton indicators and their covariation with climate is crucial as plankton represent the base of the food webs. With this perspective, we sought to document the variations in the emerging properties of the plankton to better understand the dynamics of the pelagic fishes, mammals and seabirds that inhabit the region. For the first time, we analyze the temporal variations of the entire plankton community of one of the widest European protected areas, the Parc Naturel Marin de la Mer d’Iroise. We used data from several sampling transects carried out in the Iroise Sea from 2011 to 2015 to explore the seasonal and inter-annual variations of phytoplankton and mesozooplankton abundance, composition and size, as well as their covariation with abiotic variables, through multiple multivariate analyses. Overall, our observations are coherent with the plankton dynamics that have been observed in other regions of the North-East Atlantic. We found that both phytoplankton and zooplankton show consistent seasonal patterns in taxonomic composition and size structure but also display inter-annual variations. The spring bloom was associated with a higher contribution of large chain-forming diatoms compared to nanoflagellates, the latter dominating in fall and summer. Dinoflagellates show marked inter-annual variations in their relative contribution. The community composition of phytoplankton has a large impact on the mesozooplankton together with the distance to the coast. The size structure of the mesozooplankton community, examined through the ratio of small to large copepods, also displays marked seasonal patterns. We found that larger copepods (members of the Calanidae) are more abundant in spring than in summer and fall. We propose several hypotheses to explain the observed temporal patterns and we underline their importance for understanding the dynamics of other components of the food-web (such as sardines). Our study is a first step toward the inclusion of the planktonic compartment into the planning of the resources and diversity conservation within the Marine Protected Area., Frontiers in Marine Science, 6, ISSN:2296-7745

46. The Seasonal and Inter-Annual Fluctuations of Plankton Abundance and Community Structure in a North Atlantic Marine Protected Area

Author: Benedetti, Fabio, Jalabert, Laëtitia, Sourisseau, Marc, Becker, Beatriz, Cailliau, Caroline, Desnos, Corinne, Elineau, Amanda, Irisson, Jean-Olivier, Lombard, Fabien, Picheral, Marc, Stemmann, Lars, Pouline, Patrick, 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), 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), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Unité Dyneco, Laboratoire Pelagos, Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), Agence Française pour la Biodiversité (AFB), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), European Project: 654410,H2020,H2020-INFRAIA-2014-2015,JERICO-NEXT(2015), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), 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)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, size structure, temporal variability, ACL, fungi, plankton, Ocean Engineering, Aquatic Science, Oceanography, Life sciences, Plankton, Marine Protected Area, Seasonality, Copepod, MPA, ddc:570, community composition, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Iroise Sea, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Water Science and Technology
Abstract: International audience; Marine Protected Areas have become a major tool for the conservation of marine biodiversity and resources. Yet our understanding of their efficacy is often limited because it is measured for a few biological components, typically top predators or species of commercial interest. To achieve conservation targets, marine protected areas can benefit from ecosystem-based approaches. Within such an approach, documenting the variation of plankton indicators and their covariation with climate is crucial as plankton represent the base of the food webs. With this perspective, we sought to document the variations in the emerging properties of the plankton to better understand the dynamics of the pelagic fishes, mammals and seabirds that inhabit the region. For the first time, we analyze the temporal variations of the entire plankton community of one of the widest European protected areas, the Parc Naturel Marin de la Mer d’Iroise. We used data from several sampling transects carried out in the Iroise Sea from 2011 to 2015 to explore the seasonal and inter-annual variations of phytoplankton and mesozooplankton abundance, composition and size, as well as their covariation with abiotic variables, through multiple multivariate analyses. Overall, our observations are coherent with the plankton dynamics that have been observed in other regions of the North-East Atlantic. We found that both phytoplankton and zooplankton show consistent seasonal patterns in taxonomic composition and size structure but also display inter-annual variations. The spring bloom was associated with a higher contribution of large chain-forming diatoms compared to nanoflagellates, the latter dominating in fall and summer. Dinoflagellates show marked inter-annual variations in their relative contribution. The community composition of phytoplankton has a large impact on the mesozooplankton together with the distance to the coast. The size structure of the mesozooplankton community, examined through the ratio of small to large copepods, also displays marked seasonal patterns. We found that larger copepods (members of the Calanidae) are more abundant in spring than in summer and fall. We propose several hypotheses to explain the observed temporal patterns and we underline their importance for understanding the dynamics of other components of the food-web (such as sardines). Our study is a first step toward the inclusion of the planktonic compartment into the planning of the resources and diversity conservation within the Marine Protected Area.
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