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1. Different environmental response strategies in sympatric corals from Pacific Islands

Author

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

Subjects
Geology, QE1-996.5, Environmental sciences, GE1-350
Abstract

Abstract Coral reefs are severely threatened by global and local environmental changes. However, susceptibility to perturbations and subsequent mortality varies among coral species. In this study, we tested the contribution of genetic and environmental conditions to coral’s phenotypic response in Pocillopora spp. and Porites spp. sampled together at a large ecological and temporal scale throughout the Pacific Ocean. We assessed coral phenotype signatures using a multi-biomarker approach (animal and symbiont biomasses, protein carbonylation and ubiquitination and total antioxidant capacities). In both genera, we highlighted a strong anticorrelation between the redox state and the animal and symbiont biomasses. In addition, Pocillopora exhibited high phenotypic plasticity, responding to various environmental variables such as temperature, nutrients, phosphate, and carbonate chemistry. In contrast, Porites displayed more robust phenotypes influenced by both genetics and past climate events. In conclusion, co-located coral species display different phenotypic response strategies that are influenced by different environmental conditions.

Published
2023
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2. Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Author

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

Subjects
Medicine, Science
Abstract

Abstract With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.

Published
2023
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3. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne Da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, Genoscope Technical Team, Christian R. Voolstra, Pierre E. Galand, J. Michel Flores, Benjamin C. C. Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, David A. Paz García, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier P. Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, E’ Krame Jacoby, Pedro H. Oliveira, Jean-Marc Aury, Denis Allemand, Serge Planes, and Patrick Wincker

Subjects
Science
Abstract

Abstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Published
2023
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4. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author

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

Subjects
Science
Abstract

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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5. Pervasive tandem duplications and convergent evolution shape coral genomes

Author

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

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Published
2023
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6. Diversity of the Pacific Ocean coral reef microbiome

Author

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

Subjects
Science
Abstract

Abstract Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

Published
2023
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7. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Author

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

Subjects
Science
Abstract

Abstract Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.

Published
2023
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8. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author

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

Subjects
Science
Abstract

Abstract Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

Published
2023
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9. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean

Author

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

Subjects
Science
Abstract

Abstract Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.

Published
2023
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10. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author

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

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Published
2023
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11. Recipes for the Derivation of Water Quality Parameters Using the High-Spatial-Resolution Data from Sensors on Board Sentinel-2A, Sentinel-2B, Landsat-5, Landsat-7, Landsat-8, and Landsat-9 Satellites

Author

Juliana Tavora, Binbin Jiang, Thomas Kiffney, Guillaume Bourdin, Patrick Clifton Gray, Lino Sander Carvalho, Gabriel Hesketh, Kristin M. Schild, Luiz Faria Souza, Damian C. Brady, and Emmanuel Boss

Subjects
Environmental sciences, GE1-350, Physical geography, GB3-5030
Abstract

Satellites have provided high-resolution (

Published
2023
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12. Diel cycle of sea spray aerosol concentration

Author

J. Michel Flores, Guillaume Bourdin, Alexander B. Kostinski, Orit Altaratz, Guy Dagan, Fabien Lombard, Nils Haëntjens, Emmanuel Boss, Matthew B. Sullivan, Gabriel Gorsky, Naama Lang-Yona, Miri Trainic, Sarah Romac, Christian R. Voolstra, Yinon Rudich, Assaf Vardi, and Ilan Koren

Subjects
Science
Abstract

Sea spray aerosol (SSA) are an important way through which oceans can influence the atmosphere’s radiative properties. Here, the authors present measurements taken over a 42,000 km ship cruise in the Atlantic and Pacific Ocean and show that SSA number concentrations vary over a 24-hour cycle, possibly linked to surface water bubble-bursting dynamics.

Published
2021
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13. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale

Author

Colomban de Vargas, Noan Le Bescot, Thibaut Pollina, Nicolas Henry, Sarah Romac, Sébastien Colin, Nils Haëntjens, Margaux Carmichael, Calixte Berger, David Le Guen, Johan Decelle, Frédéric Mahé, Julie Poulain, Emmanuel Malpot, Carole Beaumont, Michel Hardy, Damien Guiffant, Ian Probert, David F. Gruber, Andrew E. Allen, Gabriel Gorsky, Michael J. Follows, Xavier Pochon, Romain Troublé, B. B. Cael, Fabien Lombard, Emmanuel Boss, Manu Prakash, the Plankton Planet core team, Romain Bazile, Guillaume Bourdin, BB Cael, Roberto Casati, Sébastien Colin, Nils Haentjens, Adam Larson, Gilles Mirambeau, Clémentine Moulin, Anna Oddone, Christophe Prazuck, Vincent Raimbault, Clara Trellu, and Romain Troublé

Subjects
planetary biology, citizen oceanography, DNA metabarcoding, plankton, seatizens, sailors, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modeled at the planetary scale, biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce ‘Plankton Planet’, an initiative whose goal is to engage the curiosity and creativity of researchers, makers, and mariners to (i) co-develop a new generation of cost-effective (frugal) universal scientific instrumentation to measure the genetic and morphological diversity of marine microbiomes in context, (ii) organize their systematic deployment through coastal or open ocean communities of sea-users/farers, to generate uniform plankton data across global and long-term spatio-temporal scales, and (iii) setup tools to flow the data without embargo into public and explorable databases. As proof-of-concept, we show how 20 crews of sailors were able to sample plankton biomass from the world surface ocean in a single year, generating the first seatizen-based, planetary dataset of marine plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. The data unveil significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems and microbiomes across the dimensions of the Earth system.

Published
2022
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14. Oyster Aquaculture Site Selection Using High-Resolution Remote Sensing: A Case Study in the Gulf of Maine, United States

Author

Binbin Jiang, Emmanuel Boss, Thomas Kiffney, Gabriel Hesketh, Guillaume Bourdin, Daidu Fan, and Damian C. Brady

Subjects
Landsat 8, Gulf of Maine, oyster aquaculture, Sentinel 2 (ESA), atmospheric correction (AC), Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Aquaculture of the eastern oyster, Crassostrea virginica, is an expanding industry in the US, particularly in the Gulf of Maine. High resolution ocean color satellites launched in the last decade potentially provide aquaculture-relevant water-quality parameters at farm scales. However, these parameters, such as temperature, suspended particulate matter (SPM), and Chlorophyll a (Chl a), need to be derived by interested users. Water quality parameters are derived first by applying an atmospheric correction and then estimating the target parameter with a specific algorithm. Here, we use five atmospheric correction schemes and two algorithms to derive SPM and Chl a from the Sentinel 2A&B satellites’ multispectral instrument data. The best estimates of SPM and Chl a are determined by comparison with in situ observations from buoys. Together with SST from Landsat-8, we estimated an Oyster Suitability Index (OSI) along the transects in five estuaries in the Gulf of Maine as well as applied a novel particulate organic matter algorithm, a function of Chl a and SPM in low turbidity estuaries. We then apply the optimal approaches to derive water quality parameters to study five different estuaries in Maine and find that existing high-yield oyster aquaculture farms are found in areas with elevated OSI values. Additionally, we suggest new areas, currently under-exploited, where oyster aquaculture is likely to succeed, showcasing the utility of the approach.

Published
2022
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15. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Author

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

Subjects
neuston/plankton genomics/taxonomy/imaging, aerosols, NCP, IOP, trace metals, microplastic, Science, General. Including nature conservation, geographical distribution, QH1-199.5
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.

Published
2019
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16. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean.

Author

Serge Planes, Denis Allemand, Sylvain Agostini, Bernard Banaigs, Emilie Boissin, Emmanuel Boss, Guillaume Bourdin, Chris Bowler, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Pierre E Galand, Jean-François Ghiglione, Eric Gilson, Fabien Lombard, Clémentine Moulin, Stephane Pesant, Julie Poulain, Stéphanie Reynaud, Sarah Romac, Matthew B Sullivan, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Colomban de Vargas, Rebecca Vega Thurber, Christian R Voolstra, Patrick Wincker, Didier Zoccola, and Tara Pacific Consortium

Subjects
Biology (General), QH301-705.5
Abstract

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.

Published
2019
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17. The Impact of Gulf Stream Frontal Eddies on Ecology and Biogeochemistry near Cape Hatteras

Author

Patrick Clifton Gray, Jessica Gronniger, Ivan Sayvelev, Julian Dale, Alexandria K. Niebergall, Nicolas Cassar, Anna E. Windle, Dana E. Hunt, Zackary Johnson, Marina Lévy, Chris Taylor, Guillaume Bourdin, Ashley Blawas, Amanda Lohmann, Greg Silsbe, David W. Johnston, Duke University [Durham], University of Maine, US Naval Research Laboratory, 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)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-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), National Centers for Coastal Ocean Science (NCCOS), National Ocean Service (NOS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of Maryland Center for Environmental Science (UMCES), and University of Maryland System

Subjects
[SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

Ocean physics and biology can interact in myriad and complex ways. Eddies, features found at many scales in the ocean, can drive substantial changes in physical and biogeochemical fields with major implications for marine ecosystems. Mesoscale eddies are challenging to model and difficult to observe synoptically at sea due to their fine-scale variability yet broad extent. In this work we observed a frontal eddy just north of Cape Hatteras via an intensive hydrographic, biogeochemical, and optical sampling campaign. Frontal eddies occur in western boundary currents around the globe and there are major gaps in our understanding of their ecosystem impacts. In the Gulf Stream, frontal eddies have been studied in the South Atlantic Bight, where they are generally assumed to shear apart passing Cape Hatteras. However, we found that the observed frontal eddy had different physical properties and phytoplankton community composition from adjacent water masses, in addition to continued cyclonic rotation. In this work we first synthesize the overall ecological impacts of frontal eddies in a simple conceptual model. This conceptual model led to the hypothesis that frontal eddies could be well timed to supply zooplankton to secondary consumers off Cape Hatteras where there is a notably high concentration and diversity of top predators. Towards testing this hypothesis and our conceptual model we report on the biogeochemical state of this particular eddy connecting physical and biological dynamics, analyze how it differs from Gulf Stream and shelf waters even in “death”, and refine our initial model with this new data.Key PointsIn-depth investigation of a frontal eddy in the Gulf Stream off Cape Hatteras, North CarolinaContinued physical and biogeochemical differences are observed between the eddy and adjacent water masses even as it begins to shear apartWe share a conceptual model of the ecological impact of frontal eddies with a hypothesis that they supply zooplankton to secondary consumersPlain Language SummaryFrontal eddies are spinning masses of water (~30km in diameter) that move along western boundary currents like the Gulf Stream. When they form they carry productive coastal water into the Gulf Stream and drive upwelling within their cores. Together this leads to an increase in the amount of phytoplankton within them - much higher compared to surrounding nutrient-limited Gulf Stream water. On the east coast of the United States one common area of frontal eddy formation is just off Charleston, SC. Eddies then travel up the coast and dissipate near Cape Hatteras, NC. In this work we measured a wide range of physical and biological properties of a frontal eddy just north of Cape Hatteras. We compared these properties within the eddy to the coastal water on one side and the Gulf Stream water on the other, finding clear differences in phytoplankton community composition and other physical and chemical properties. Using the results of these observations together with previous studies we share a simple model for how frontal eddies may impact phytoplankton, zooplankton, and fish – hypothesizing that they may contribute to the high diversity and density of top predators off Cape Hatteras.

Published
2023
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18. From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,PocilloporaandPorites

Author

Romane Deshuraud, Alexandre Ottaviani, Julie Poulain, Marine Leprêtre, Odette Beluche, Eric Mahieu, Sandrine Lebled, Caroline Belser, Alice Rouan, Clementine Moulin, Emilie Boissin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Paola Furla, Pierre Galand, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B Sullivan, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Christian R. Voolstra, Patrick Wincker, Didier Zoccola, Serge Planes, Denis Allemand, Eric Gilson, and Didier Forcioli

Abstract

Coral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera (PoritesandPocillopora). For this purpose, we developed a technique that we called “Divergent Fragment” based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genusPocilloporaand 247 individuals of the genusPoritesto previously identified independent genetic lineages (i.e. species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation.

Published
2022
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19. Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories

Author

Benjamin C C Hume, Christian R Voolstra, Eric Armstrong, Guinther Mitushasi, Barbara Porro, Nicolas Oury, Sylvain Agostini, Emilie Boissin, Julie Poulain, Quentin Carradec, David A. Paz-García, Didier Zoccola, Hélène Magalon, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Paola Furla, Pierre E Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Serge Planes, Denis Allemand, and Didier Forcioli

Abstract

Tropical coral reefs are among the worst affected ecosystems by climate change with predictions ranging between a 70-90% loss of reefs in the coming decades. Effective conservation strategies that maximize ecosystem resilience, and potential for recovery, must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here, we analyzed samples from theTaraPacific Expedition (2016 to 2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals –Pocillopora meandrina, Porites lobata, andMilleporacf.platyphylla– across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data we can show that the sampled transect encompasses multiple morphologically cryptic species that exhibit disparate biogeographic patterns, and most importantly, distinct evolutionary patterns, despite exposure to identical environmental regimes. Our findings demonstrate on a basin-scale that evolutionary trajectories are species-specific and complex, and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to consider the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

Published
2022
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20. Pervasive tandem duplications and convergent evolution shape coral genomes

Author

Corinne DA SILVA, Alice ROUAN, France Denoeud, Benjamin Noel, Guillaume Bourdin, and Carol Buitrago López

Abstract

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to these ecosystems, providing habitat and food to a great diversity of species. In the frame of the Tara Pacific expedition, we generated two coral genomes,Porites lobataandPocillopora meandrinawith vastly improved contiguity that allowed us to study the functional organisation of these genomes. We annotated their gene catalog and report a relatively higher gene number (43,000 and 32,000 genes respectively) than that found in other public coral genome sequences. This finding is explained by a high number of tandemly duplicated genes (almost a third of the predicted genes). We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to immune system and disease-resistance, which we suggest to be functionally linked to coral host resilience. At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Published
2022
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21. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author

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

Subjects
fungi
Abstract

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Published
2022
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22. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, Genoscope Technical Team, Voolstra, Christian R., Galand, Pierre E., Michel Flores, J., Benjamin Cc Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Paz García, David A., Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Éric Douville, Didier Forcioli, Paola Furla, Éric Gilson, Fabien Lombard, Stephane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, Krame Jacoby, E., Oliveira, Pedro H., Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universität Konstanz, Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Weizmann Institute of Science [Rehovot, Israël], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Tara Expéditions, Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), 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), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire 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), 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), Université Côte d'Azur (UCA), 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), European Molecular Biology Laboratory (EMBL), Centre Scientifique de Monaco (CSM), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), Menguy, Caroline, Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), and 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)

Subjects
FOS: Biological sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the host coral organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Published
2022
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23. Diel cycle of sea spray aerosol concentration

Author

Guillaume Bourdin, J. Michel Flores, Sarah Romac, Fabien Lombard, Guy Dagan, Assaf Vardi, Christian R. Voolstra, Alexander B. Kostinski, Ilan Koren, Naama Lang-Yona, Yinon Rudich, Emmanuel Boss, Gabriel Gorsky, Nils Haëntjens, Orit Altaratz, Matthew B. Sullivan, Miri Trainic, Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], University of Maine, Michigan Technological University (MTU), 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 - School of Marine Sciences, and Griffith University [Brisbane]

Subjects
Atmospheric chemistry, 010504 meteorology & atmospheric sciences, Science, General Physics and Astronomy, Sunset, Atmospheric sciences, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Atmosphere, 03 medical and health sciences, ddc:570, Sunrise, 14. Life underwater, Diel vertical migration, 030304 developmental biology, 0105 earth and related environmental sciences, Marine biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Multidisciplinary, fungi, General Chemistry, Sea spray, Aerosol, Sea surface temperature, stomatognathic diseases, 13. Climate action, Environmental chemistry, Environmental science, Surface water
Abstract

Sea spray aerosol (SSA) formation have a major role in the climate system, but measurements at a global-scale of this micro-scale process are highly challenging. We measured high-resolution temporal patterns of SSA number concentration over the Atlantic Ocean, Caribbean Sea, and the Pacific Ocean covering over 42,000 km. We discovered a ubiquitous 24-hour rhythm to the SSA number concentration, with concentrations increasing after sunrise, remaining higher during the day, and returning to predawn values after sunset. The presence of dominating continental aerosol transport can mask the SSA cycle. We did not find significant links between the diel cycle of SSA number concentration and diel variations of surface winds, atmospheric physical properties, radiation, pollution, nor oceanic physical properties. However, the daily mean sea surface temperature positively correlated with the magnitude of the day-to-nighttime increase in SSA concentration. Parallel diel patterns in particle sizes were also detected in near-surface waters attributed to variations in the size of particles smaller than ~1 µm. These variations may point to microbial day-to-night modulation of bubble-bursting dynamics as a possible cause of the SSA cycle., Sea spray aerosol (SSA) are an important way through which oceans can influence the atmosphere’s radiative properties. Here, the authors present measurements taken over a 42,000 km ship cruise in the Atlantic and Pacific Ocean and show that SSA number concentrations vary over a 24-hour cycle, possibly linked to surface water bubble-bursting dynamics.

Published
2021
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24. Author Correction: Airborne microplastic particles detected in the remote marine atmosphere

Author

Iddo Pinkas, Yinon Rudich, Assaf Vardi, Gabriel Gorsky, Guillaume Bourdin, J. Michel Flores, Miri Trainic, Fabien Lombard, Emmanuel Boss, Maria Luiza Pedrotti, and Ilan Koren

Subjects
Atmosphere, General Earth and Planetary Sciences, Environmental science, Atmospheric sciences, General Environmental Science
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s43247-021-00119-5

Published
2021
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25. Airborne microplastic particles detected in the remote marine atmosphere

Author

Maria Luiza Pedrotti, J. Michel Flores, Guillaume Bourdin, Emmanuel Boss, Miri Trainic, Gabriel Gorsky, Fabien Lombard, Yinon Rudich, Iddo Pinkas, Assaf Vardi, Ilan Koren, 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), and 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)

Subjects
Pollutant, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Microplastics, [SDE.MCG]Environmental Sciences/Global Changes, 010501 environmental sciences, 01 natural sciences, Aerosol, Atmosphere, 03 medical and health sciences, Anthropogenic pollution, Oceanography, 13. Climate action, General Earth and Planetary Sciences, Environmental science, Trajectory analysis, Seawater, 14. Life underwater, Transect, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science
Abstract

Anthropogenic pollution from marine microplastic particles is a growing concern, both as a source of toxic compounds, and because they can transport pathogens and other pollutants. Airborne microplastic particles were previously observed over terrestrial and coastal locations, but not in the remote ocean. Here, we collected ambient aerosol samples in the North Atlantic Ocean, including the remote marine atmosphere, during the Tara Pacific expedition in May-June 2016, and chemically characterized them using micro-Raman spectroscopy. We detected a range of airborne microplastics, including polystyrene, polyethylene, polypropylene, and poly-silicone compounds. Polyethylene and polypropylene were also found in seawater, suggesting local production of airborne microplastic particles. Terminal velocity estimations and back trajectory analysis support this conclusion. For technical reasons, only particles larger than 5 µm, at the upper end of a typical marine atmospheric size distribution, were analyzed, suggesting that our analyses underestimate the presence of airborne microplastic particles in the remote marine atmosphere. Airborne microplastic particles with a possible oceanic origin were identified in the marine atmosphere, far from the coast, using micro-Raman spectroscopy analyses of air samples, during a transect across the North Atlantic Ocean in 2016.

Published
2020
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26. Diel cycle of sea spray aerosol concentration over vast areas of the tropical Pacific Ocean and the Caribbean Sea

Author

Ilan Koren, Guillaume Bourdin, Gabriel Gorsky, Sarah Romac, J. Michel Flores, Nils Haëntjens, Fabien Lombard, Guy Dagan, Yinon Rudich, Orit Altaratz, Assaf Vardi, Alexander B. Kostinski, Naama Lang-Yona, Matthew B. Sullivan, Miri Trainic, Emmanuel Boss, and Christian R. Voolstra

Subjects
Tropical pacific, Oceanography, Environmental science, Sea spray, Diel vertical migration, Aerosol
Abstract

Ocean-atmosphere interactions such as sea spray aerosol (SSA) formation have a major role in the climate system, but a global-scale assessment of this micro-scale process is highly challenging. We measured high-resolution temporal patterns of SSA number concentration over the Atlantic Ocean, Caribbean Sea, and the Pacific Ocean covering 42,000 km of open ocean waters. We discovered a ubiquitous 24-hour rhythm to the number concentration, clearly seen for particle diameters > ~ 0.58 µm, with spikes at dawn and drops at dusk throughout the Pacific Ocean and Caribbean Sea, showing more than doubling of the SSA number concentration during the day than at night. No correlation with surface winds, atmospheric radiation, pollution nor oceanic physical properties were found. Instead, parallel diel patterns in particle sizes detected in near-surface waters, attributed to variations in the size of particles smaller than ~ 1 µm, point to microbial day-to-night modulation of bubble-bursting dynamics as the cause of the SSA cycle.

Published
2020
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27. Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results

Author

Paola Furla, Naama Lang-Yona, Matthew B. Sullivan, Miri Trainic, Guillaume Bourdin, Sarah Romac, Patrick Wincker, Stephane Pesant, Eric Douville, Ilan Koren, Romain Troublé, Chris Bowler, Clémentine Moulin, F. Tettich, Stéphanie Reynaud, Olivier P. Thomas, Yinon Rudich, J. M. Flores, Eric Gilson, Emmanuel Boss, Julie Poulain, C. de Vargas, Assaf Vardi, Emilie Boissin, Sylvain Agostini, E. Dzimban, Bernard Banaigs, Didier Zoccola, Christian R. Voolstra, Orit Altaratz, Denis Allemand, Serge Planes, Fabien Lombard, G. Gorsky, Didier Forcioli, Shinichi Sunagawa, R. Vega Thurber, S. Steinau, Pierre E. Galand, 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), Laboratoire d'Excellence CORAIL (LabEX CORAIL), 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), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), 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), Géochrononologie Traceurs Archéométrie (GEOTRAC), 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), Service de Réanimation Médicale, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Université de Lyon, Lyon, France, Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Department of Environmental Sciences Weizmann Institute, Department of Environmental Sciences, Weizmann Institute, Weizmann Institute of Science [Rehovot, Israël], PSL Research University, EPHE-UPVDCNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, Centre Scientifique de Monaco (CSM), CSM, Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), 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), 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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, Atmospheric sciences, 01 natural sciences, Atmosphere, 03 medical and health sciences, Atmospheric measurements, 13. Climate action, Particle dynamics, ddc:570, [SDE]Environmental Sciences, Radiative transfer, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences
Abstract

Marine aerosols play a significant role in the global radiative budget, in clouds’ processes, and in the chemistry of the marine atmosphere. There is a critical need to better understand their production mechanisms, composition, chemical properties, and the contribution of ocean-derived biogenic matter to their mass and number concentration. Here we present an overview of a new dataset of in situ measurements of marine aerosols conducted over the 2.5-yr Tara Pacific Expedition over 110,000 km across the Atlantic and Pacific Oceans. Preliminary results are presented here to describe the new dataset that will be built using this novel set of measurements. It will characterize marine aerosols properties in detail and will open a new window to study the marine aerosol link to the water properties and environmental conditions.

Published
2020
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28. Dynamics of transparent exopolymeric particles and their precursors during a mesocosm experiment: Impact of ocean acidification

Author

Maria Luiza Pedrotti, Guillaume Bourdin, Marie-Emmanuelle Kerros, Frédéric Gazeau, Sophie Marro, 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), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, chemistry.chemical_classification, Total organic carbon, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, 010604 marine biology & hydrobiology, chemistry.chemical_element, Ocean acidification, Aquatic Science, Oceanography, 01 natural sciences, Mesocosm, chemistry, 13. Climate action, Nanophytoplankton, Environmental chemistry, [SDE]Environmental Sciences, Phytoplankton, Organic matter, Seawater, 14. Life underwater, Carbon, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract

The dissolution of anthropogenic atmospheric CO 2 in seawater is suspected to exert a strong pressure on biological processes as well as on carbon and nutrient cycles. Transparent exopolymeric particles (TEP) are polysaccharide particles, formed by aggregation of polymers exuded by phytoplankton and strongly involved in organic matter sedimentation. A mesocosm experiment was performed from February to March 2013 in the coastal waters of the Northwestern Mediterranean Sea, a region characterised by low-nutrient low-chlorophyll (LNLC) levels. We aimed to determine the effect of ocean acidification on the organic carbon pool of TEP produced by a natural phytoplankton community. The experiment was conducted in nine mesocosms of 50 m 3 deployed for 12 days, and subjected to seven partial pressures of CO 2 ( p CO 2 ) levels: one control level in triplicate and six elevated levels between 450 and 1250 μatm. The use of different analytical methods allowed the assessment of TEP density, volume concentration and size distribution as well as both TEP and TEP precursors carbon content. TEP contributed vastly to the particulate organic carbon pool (∼62%), and were mainly produced by small-sized phytoplankton such as pico- and nanophytoplankton. TEP precursors carbon content represented three times the carbon content of particulate TEP, showing that this pool has to be considered in experiments focused on the environmental control of TEP production. There was no evidence that TEP and TEP precursors were dependent on p CO 2 . These parameters exhibited clear temporal dynamics, with tight links to community composition, nutrient availability and other environmental parameters.

Published
2017
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29. Ocean acidification and viral replication cycles: Frequency of lytically infected and lysogenic cells during a mesocosm experiment in the NW Mediterranean Sea

Author

Guillaume Bourdin, Paraskevi Pitta, Anastasia Tsiola, Maria Luiza Pedrotti, Antonia Giannakourou, Sophie Marro, Laure Maugendre, Frédéric Gazeau, Hellenic Centre for Marine Research (HCMR), 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), and 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)

Subjects
0106 biological sciences, Chlorophyll a, 010504 meteorology & atmospheric sciences, Ecology, 010604 marine biology & hydrobiology, Ocean acidification, Aquatic Science, Bacterial growth, Biology, Plankton, Oceanography, 01 natural sciences, Mesocosm, chemistry.chemical_compound, Mediterranean sea, chemistry, 13. Climate action, Lysogenic cycle, Phytoplankton, [SDE]Environmental Sciences, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract

The frequency of lytically infected and lysogenic cells (FLIC and FLC, respectively) was estimated during an in situ mesocosm experiment studying the impact of ocean acidification on the plankton community of a low nutrient low chlorophyll (LNLC) system in the north-western Mediterranean Sea (Bay of Villefranche, France) in February/March 2013. No direct effect of elevated partial pressure of CO2 (pCO2) on viral replication cycles could be detected. FLC variability was negatively correlated to heterotrophic bacterial and net community production as well as the ambient bacterial abundance, confirming that lysogeny is a prevailing life strategy under unfavourable-for-the-hosts conditions. Further, the phytoplankton community, assessed by chlorophyll a concentration and the release of >0.4 μm transparent exopolymeric particles, was correlated with the occurrence of lysogeny, indicating a possible link between photosynthetic processes and bacterial growth. Higher FLC was found occasionally at the highest pCO2-treated mesocosm in parallel to subtle differences in the phytoplankton community. This observation suggests that elevated pCO2 could lead to short-term alterations in lysogenic dynamics coupled to phytoplankton-derived processes. Correlation of FLIC with any environmental parameter could have been obscured by the sampling time or the synchronization of lysis to microbial processes not assessed in this experiment. Furthermore, alterations in microbial and viral assemblage composition and gene expression could be a confounding factor. Viral-induced modifications in organic matter flow affect bacterial growth and could interact with ocean acidification with unpredictable ecological consequences.

Published
2017
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