Cd

Colomban de Vargas

Research director - DR1 - CNRS
85 %
Libre accès
170
Documents
Affiliations actuelles
  • Station biologique de Roscoff = Roscoff Marine Station (SBR)
  • Adaptation et diversité en milieu marin (AD2M)
  • Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE)
Contact

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Publications

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The southern gap in ocean microbiome science

Hugo Sarmento , Paula Huber , Célio Dias Santos-Júnior , André Abreu , Thulani Makhalanyane et al.

Ocean Microbiology, 2025, 1 (1), pp.6. ⟨10.1186/s44375-025-00006-w⟩

Article dans une revue hal-05334436v1
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Nitrogen concentration shapes the size structure and the functional diversity of phytoplankton communities in the southern Indian Ocean

Hugo Berthelot , Joanna Zukowska , Nicolas Henry , Cyril Noël , Melilotus Thyssen et al.

ISME Communications, 2025, 5 (1), pp.ycaf195. ⟨10.1093/ismeco/ycaf195⟩

Article dans une revue hal-05403677v1

Meiofauna investigation and taxonomic identification through imaging—a game of compromise

Valentin Foulon , Abdesslam Benzinou , Kamal Nasreddine , Abdul Qayyum , Edwin Daché et al.

Limnology and Oceanography: Methods, 2025, 23 (7), pp.482-499. ⟨10.1002/lom3.10690⟩

Article dans une revue hal-05315714v1
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Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Zoltán Füssy , Robert Lampe , Kevin Arrigo , Kerrie Barry , Margaret Brisbin et al.

Nature Communications, 2025, 16 (1), pp.8559. ⟨10.1038/s41467-025-63565-1⟩

Article dans une revue hal-05292826v1
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Omics exploration of deep-sea biodiversity: data from the “Pourquoi Pas les Abysses?” and eDNAbyss projects

Sophie Arnaud-Haond , Blandine Trouche , Cathy Liautard-Haag , Karine Alain , Johanne Aubé et al.

Scientific Data , 2025, 12 (1), pp.1982. ⟨10.1038/s41597-025-06009-1⟩

Article dans une revue hal-05434404v1
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Patterns and drivers of diatom diversity and abundance in the global ocean

Juan Pierella Karlusich , Karen Cosnier , Lucie Zinger , Nicolas Henry , Charlotte Nef et al.

Nature Communications, 2025, 16 (1), pp.3452. ⟨10.1038/s41467-025-58027-7⟩

Article dans une revue hal-05138560v1
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O short'branch Microsporidia, where art thou? Identifying diversity hotspots for future sampling

Megan Gross , Ľubomír Rajter , Frédéric Mahé , David Bass , Cédric Berney et al.

European Journal of Protistology, 2024, 96, pp.126119. ⟨10.1016/j.ejop.2024.126119⟩

Article dans une revue hal-04908383v1

Benthic foraminifera as bio-indicators of natural and anthropogenic conditions in Roscoff Aber Bay (Brittany, France)

Edwin Daché , Pierre-Antoine Dessandier , Ranju Radhakrishnan , Valentin Foulon , Loïc Michel et al.

PLoS ONE, 2024, 19 (10), pp.e0309463. ⟨10.1371/journal.pone.0309463⟩

Article dans une revue hal-04807627v1

How marine are Marine Stramenopiles (MAST)? A cross-system evaluation

Aleix Obiol , Javier del Campo , Colomban de Vargas , Frédéric Mahé , Ramon Massana

FEMS Microbiology Ecology, 2024, 100 (11), pp.fiae130. ⟨10.1093/femsec/fiae130⟩

Article dans une revue hal-04807648v1
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Satellite Data Sharing for Scientific Inter-Group Cooperation Using the Leaflet R Package

Christian Marchese , Emmanuel Boss , Federico Falcini , David Doxaran , Colomban de Vargas et al.

Oceanography, 2024, 37 (3), ⟨10.5670/oceanog.2024.513⟩

Article dans une revue hal-04887465v1
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Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Marine Canesi , Éric Douville , Paolo Montagna , Louise Bordier , Sandrine Caquineau et al.

Chemical Geology, 2024, 645, pp.121884. ⟨10.1016/j.chemgeo.2023.121884⟩

Article dans une revue hal-04337163v1

Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage

Paula Huber , Daniele de Angelis , Hugo Sarmento , Sebastian Metz , Caterina Giner et al.

Microbiome, 2024, 12 (1), pp.162. ⟨10.1186/s40168-024-01874-1⟩

Article dans une revue hal-04908385v1

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Andrew Allen , Zoltán Füssy , Robert Lampe , Kevin Arrigo , Kerrie Barry et al.

Research Square - Preprint, 2024, ⟨10.21203/rs.3.rs-4339559/v1⟩

Article dans une revue hal-04908358v1
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The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton

Raphaël Morard , Kate Darling , Agnes Weiner , Christiane Hassenrück , Chiara Vanni et al.

Biological Reviews, 2024, 99 (4), pp.1218-1241. ⟨10.1111/brv.13065⟩

Article dans une revue hal-04552961v1
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Different environmental response strategies in sympatric corals from Pacific Islands

Barbara Porro , Thamilla Zamoum , Didier Forcioli , Eric Gilson , Adrien Poquet et al.

Communications Earth & Environment, 2023, 4 (1), pp.311. ⟨10.1038/s43247-023-00946-8⟩

Article dans une revue hal-04205154v1
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Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Corentin Hochart , Lucas Paoli , Hans-Joachim Ruscheweyh , Guillem Salazar , Emilie Boissin et al.

Nature Communications, 2023, 14 (1), pp.3037. ⟨10.1038/s41467-023-38502-9⟩

Article dans une revue hal-04176293v1
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Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Maggie M Reddy , Corentine Goossens , Yuxiang Zhou , Slimane Chaib , Delphine Raviglione et al.

Communications Earth & Environment, 2023, 4 (1), pp.281. ⟨10.1038/s43247-023-00942-y⟩

Article dans une revue hal-04184949v1
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Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel et al.

Nature Communications, 2023, 14, pp.3056. ⟨10.1038/s41467-023-38610-6⟩

Article dans une revue cea-04171796v1
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Pervasive tandem duplications and convergent evolution shape coral genomes

Benjamin Noel , France Denoeud , Alice Rouan , Carol Buitrago-López , Laura Capasso et al.

Genome Biology, 2023, 24 (1), pp.123. ⟨10.1186/s13059-023-02960-7⟩

Article dans une revue hal-04117388v1
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Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys

Sebastian Metz , Sarah Itoïz , Aleix Obiol , Evelyne Derelle , Ramon Massana et al.

Scientific Reports, 2023, 13 (1), pp.20111. ⟨10.1038/s41598-023-47378-0⟩

Article dans une revue hal-04298429v1
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Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Christian R Voolstra , Benjamin C C Hume , Eric J Armstrong , Guinther Mitushasi , Barbara Porro et al.

npj Biodiversity, 2023, 2 (1), pp.15. ⟨10.1038/s44185-023-00020-8⟩

Article dans une revue hal-04157744v1
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Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Alice Rouan , Mélanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin et al.

Nature Communications, 2023, 14 (1), pp.3038. ⟨10.1038/s41467-023-38499-1⟩

Article dans une revue cea-04171809v1
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Diversity of the Pacific Ocean coral reef microbiome

Pierre Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry et al.

Nature Communications, 2023, 14 (1), pp.3039. ⟨10.1038/s41467-023-38500-x⟩

Article dans une revue hal-04176291v1
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Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

Isabel Sanz-Sáez , Pablo Sánchez , Guillem Salazar , Shinichi Sunagawa , Colomban de Vargas et al.

ISME Communications, 2023, 3 (1), ⟨10.1038/s43705-023-00290-0⟩

Article dans une revue cea-04481824v1
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Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula

Marie Walde , Cyprien Camplong , Colomban de Vargas , Anne-Claire Baudoux , Nathalie Simon

Frontiers in Marine Science, 2023, 9, ⟨10.3389/fmars.2022.1034235⟩

Article dans une revue hal-04057706v1
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Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti et al.

Scientific Data , 2023, 10 (1), pp.326. ⟨10.1038/s41597-023-02204-0⟩

Article dans une revue hal-04176297v3
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Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Alex Veglia , Kalia Bistolas , Christian Voolstra , Benjamin Hume , Hans-Joachim Ruscheweyh et al.

Communications Biology, 2023, 6 (1), pp.566. ⟨10.1038/s42003-023-04917-9⟩

Article dans une revue hal-04176296v2
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Pan-Arctic plankton community structure and its global connectivity

Federico M Ibarbalz , Nicolas Henry , Frédéric Mahé , Mathieu Ardyna , Adriana Zingone et al.

Elementa: Science of the Anthropocene, 2023, 11 (1), pp.00060. ⟨10.1525/elementa.2022.00060⟩

Article dans une revue hal-04267640v1
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Predicting global distributions of eukaryotic plankton communities from satellite data

Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé et al.

ISME Communications, 2023, 3 (1), pp.101. ⟨10.1038/s43705-023-00308-7⟩

Article dans une revue hal-04394784v1
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Ocean-wide comparisons of mesopelagic planktonic community structures

Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Pierella Karlusich et al.

ISME Communications, 2023, 3 (1), pp.83. ⟨10.1038/s43705-023-00279-9⟩

Article dans une revue hal-04184772v1
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Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Fabien Lombard , Guillaume Bourdin , Stéphane Pesant , Sylvain Agostini , Alberto Baudena et al.

Scientific Data , 2023, 10 (1), pp.324. ⟨10.1038/s41597-022-01757-w⟩

Article dans une revue hal-04164118v1
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Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Marine Canesi , Éric Douville , Paolo Montagna , Marco Taviani , Jarosław Stolarski et al.

Scientific Reports, 2023, 13 (1), pp.11589. ⟨10.1038/s41598-023-37598-9⟩

Article dans une revue cea-04170119v1
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Seasonal dynamics of marine protist communities in tidally mixed coastal waters

Mariarita Caracciolo , Fabienne Rigaut-Jalabert , Sarah Romac , Frédéric Mahé , Samuel Forsans et al.

Molecular Ecology, 2022, 31 (14), pp.3761-3783. ⟨10.1111/mec.16539⟩

Article dans une revue hal-03781932v1
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Basin-Scale Underway Quantitative Survey of Surface Microplankton Using Affordable Collection and Imaging Tools Deployed From Tara

Zoé Mériguet , Anna Oddone , David Le Guen , Thibaut Pollina , Romain Bazile et al.

Frontiers in Marine Science, 2022, 9, ⟨10.3389/fmars.2022.916025⟩

Article dans une revue hal-03877194v1
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Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Tristan Cordier , Inès Barrenechea Angeles , Nicolas Henry , Franck Lejzerowicz , Cédric Berney et al.

Science Advances , 2022, 8 (5), ⟨10.1126/sciadv.abj9309⟩

Article dans une revue hal-03561462v1
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Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Richard Dorrell , Alan Kuo , Zoltan Füssy , Elisabeth Richardson , Asaf Salamov et al.

Life Science Alliance, 2022, 6 (3), pp.e202201833. ⟨10.26508/lsa.202201833⟩

Article dans une revue hal-03859139v1
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Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale

Colomban de Vargas , Noan Le Bescot , Thibaut Pollina , Nicolas Henry , Sarah Romac et al.

Frontiers in Marine Science, 2022, 9, pp.936972. ⟨10.3389/fmars.2022.936972⟩

Article dans une revue hal-03788523v1
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EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

Daniel Richter , Cédric Berney , Jürgen Strassert , Yu-Ping Poh , Emily Herman et al.

Peer Community Journal, 2022, 2, pp.e56. ⟨10.24072/pcjournal.173⟩

Article dans une revue hal-03971621v2
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Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Tom Delmont , Morgan Gaia , Damien Hinsinger , Paul Frémont , Chiara Vanni et al.

Cell Genomics, 2022, 2 (5), pp.100123. ⟨10.1016/j.xgen.2022.100123⟩

Article dans une revue hal-03872935v2
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Exploring the phycosphere of Emiliania huxleyi : from bloom dynamics to microbiome assembly experiments

Mariana Câmara dos Reis , Sarah Romac , Florence Le Gall , Dominique Marie , Miguel Frada et al.

Molecular Ecology, In press, ⟨10.1111/mec.16829⟩

Article dans une revue hal-03596404v3
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PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography

Thibaut Pollina , Adam Larson , Fabien Lombard , Hongquan Li , David Le Guen et al.

Frontiers in Marine Science, 2022, 9, ⟨10.3389/fmars.2022.949428⟩

Article dans une revue hal-03971225v1
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A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Juan José Pierella Karlusich , Eric Pelletier , Lucie Zinger , Fabien Lombard , Adriana Zingone et al.

Molecular Ecology Resources, 2022, 23 (1), pp.16-40. ⟨10.1111/1755-0998.13592⟩

Article dans une revue hal-03559541v1
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Priorities for ocean microbiome research

Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas et al.

Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩

Article dans une revue hal-03781942v1
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Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont et al.

eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩

Article dans une revue hal-02399723v2
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Swarm v3: towards tera-scale amplicon clustering

Frédéric Mahé , Lucas Czech , Alexandros Stamatakis , Christopher Quince , Colomban de Vargas et al.

Bioinformatics, 2022, 38 (1), pp.267-269. ⟨10.1093/bioinformatics/btab493⟩

Article dans une revue hal-03284105v1
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Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front

Pierre Ramond , Raffaele Siano , Sophie Schmitt , Colomban de Vargas , Louis Marié et al.

Scientific Reports, 2021, 11, pp.2682. ⟨10.1038/s41598-021-82071-0⟩

Article dans une revue hal-03127061v1
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Environmental vulnerability of the global ocean epipelagic plankton community interactome

Samuel Chaffron , Erwan Delage , Marko Budinich , Damien Vintache , Nicolas Henry et al.

Science Advances , 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩

Article dans une revue hal-03443359v2
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Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Juan José Pierella Karlusich , Eric Pelletier , Fabien Lombard , Madeline Carsique , Etienne Dvorak et al.

Nature Communications, 2021, 12, pp.4160. ⟨10.1038/s41467-021-24299-y⟩

Article dans une revue hal-03334117v2
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The Ocean Barcode Atlas: a web service to explore the biodiversity and biogeography of marine organisms.

Caroline Vernette , Nicolas Henry , Julien Lecubin , Colomban de Vargas , Pascal Hingamp et al.

Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13322⟩

Article dans une revue hal-03115219v1
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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

Hiroto Kaneko , Romain Blanc-Mathieu , Hisashi Endo , Samuel Chaffron , Tom Delmont et al.

iScience, 2021, 24 (1), pp.102002. ⟨10.1016/j.isci.2020.102002⟩

Article dans une revue hal-03097258v3
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Macroscale patterns of oceanic zooplankton composition and size structure

Manoela Brandão , Fabio Benedetti , Séverine Martini , Yawouvi Dodji Soviadan , Jean-Olivier Irisson et al.

Scientific Reports, 2021, 11 (1), pp.15714. ⟨10.1038/s41598-021-94615-5⟩

Article dans une revue hal-03318806v1
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High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Alexandra Schoenle , Manon Hohlfeld , Karoline Hermanns , Frédéric Mahé , Colomban de Vargas et al.

Communications Biology, 2021, 4 (1), pp.501. ⟨10.1038/s42003-021-02012-5⟩

Article dans une revue hal-03208049v1
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Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems

David Singer , Christophe V W Seppey , Guillaume Lentendu , Micah Dunthorn , David Bass et al.

Environment International, 2021, 146, pp.106262. ⟨10.1016/j.envint.2020.106262⟩

Article dans une revue hal-03028115v1
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Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

Hisashi Endo , Romain Blanc-Mathieu , Yanze Li , Guillem Salazar , Nicolas Henry et al.

Nature Ecology & Evolution, 2020, 4 (12), pp.1639-1649. ⟨10.1038/s41559-020-01288-w⟩

Article dans une revue hal-02974168v1
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Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean

Greta Busseni , Luigi Caputi , Roberta Pirazzini , Paul Fremont , Bruno Hay Mele et al.

Global Ecology and Biogeography, 2020, 29 (11), pp.1915-1928. ⟨10.1111/geb.13161⟩

Article dans une revue hal-02992584v1

Tara Oceans: towards global ocean ecosystems biology

Shinichi Sunagawa , Silvia Acinas , Peer Bork , Chris Bowler , Silvia Acinas et al.

Nature Reviews Microbiology, 2020, 18 (8), pp.428-445. ⟨10.1038/s41579-020-0364-5⟩

Article dans une revue hal-04394809v1
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Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results

J. Flores , G. Bourdin , O. Altaratz , M. Trainic , N. Lang-Yona et al.

Bulletin of the American Meteorological Society, 2020, 101 (5), pp.E536-E554. ⟨10.1175/BAMS-D-18-0224.1⟩

Article dans une revue hal-02967981v1
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Disentangling the mechanisms shaping the surface ocean microbiota

Ramiro Logares , Ina M Deutschmann , Pedro C Junger , Caterina R Giner , Anders K Krabberød et al.

Microbiome, 2020, 8 (1), ⟨10.1186/s40168-020-00827-8⟩

Article dans une revue hal-02557469v1
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An assessment of environmental metabarcoding protocols aiming at favoring contemporary biodiversity in inventories of deep-sea communities

Miriam Brandt , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag , Lois Maignien et al.

Frontiers in Marine Science, 2020, 7, pp.234. ⟨10.3389/fmars.2020.00234⟩

Article dans une revue hal-03410860v1
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Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

Antonietta Capotondi , Michael Jacox , Chris Bowler , Maria Kavanaugh , Patrick Lehodey et al.

Frontiers in Marine Science, 2019, 6, pp.623. ⟨10.3389/fmars.2019.00623⟩

Article dans une revue hal-02316446v1
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Marine DNA viral macro- and microdiversity from Pole to Pole

Ann Gregory , Ahmed Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc et al.

Cell, 2019, 177 (5), pp.1109-1123.e14. ⟨10.1016/j.cell.2019.03.040⟩

Article dans une revue hal-02387010v1
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Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Gabriel Gorsky , Guillaume Bourdin , Fabien Lombard , Maria Luiza Pedrotti , Samuel Audrain et al.

Frontiers in Marine Science, 2019, 6, pp.650. ⟨10.3389/fmars.2019.00750⟩

Article dans une revue hal-02407578v1
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The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

Serge Planes , Denis Allemand , Sylvain Agostini , Bernard Banaigs , Emilie Boissin et al.

PLoS Biology, 2019, 17 (9), pp.e3000483. ⟨10.1371/journal.pbio.3000483⟩

Article dans une revue hal-02402685v1
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Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Éric Pelletier et al.

Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩

Article dans une revue hal-02999805v1
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Global Trends in Marine Plankton Diversity across Kingdoms of Life

Federico Ibarbalz , Nicolas Henry , Manoela Brandão , Severine Martini , Greta Busseni et al.

Cell, 2019, 179 (5), pp.1084-1097.e21. ⟨10.1016/j.cell.2019.10.008⟩

Article dans une revue hal-03094778v1
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Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides

Raphael Morard , Angelina Füllberg , Geert-Jan Brummer , Mattia Greco , Lukas Jonkers et al.

PLoS ONE, 2019, 14 (12), pp.e0225246. ⟨10.1371/journal.pone.0225246⟩

Article dans une revue hal-02412791v1
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Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

M. E Sieracki , N. J Poulton , O. Jaillon , P. Wincker , Colomban de Vargas et al.

Scientific Reports, 2019, 9, pp.6025. ⟨10.1038/s41598-019-42487-1⟩

Article dans une revue hal-02113815v1
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Coupling between taxonomic and functional diversity in protistan coastal communities

Pierre Ramond , Marc Sourisseau , Nathalie Simon , Sarah Romac , Sophie Schmitt et al.

Environmental Microbiology, 2019, 21 (2), pp.730-749. ⟨10.1111/1462-2920.14537⟩

Article dans une revue hal-03971181v1
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EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Javier del Campo , Martin Kolisko , Vittorio Boscaro , Luciana Santoferrara , Serafim Nenarokov et al.

PLoS Biology, 2018, 16 (9), pp.e2005849. ⟨10.1371/journal.pbio.2005849⟩

Article dans une revue hal-03971662v2
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

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Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩

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Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩

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Nature Communications, 2018, 9 (1), pp.953. ⟨10.1038/s41467-018-03376-9⟩

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The International Society of Microbiologial Ecology Journal, 2018, 12 (4), pp.1094 - 1108. ⟨10.1038/s41396-017-0029-1⟩

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Scientific Reports, 2018, 8, pp.2539. ⟨10.1038/s41598-018-20833-z⟩

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Scientific Reports, 2018, 8 (1), pp.18059 (2018). ⟨10.1038/s41598-018-36345-9⟩

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Environmental Microbiology, 2018, 20 (2), pp.878-889. ⟨10.1111/1462-2920.14034⟩

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Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

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Scientific Reports, 2018, 8, pp.9106. ⟨10.1038/s41598-018-27509-8⟩

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Nature Ecology & Evolution, 2017, 1 (4), pp.0091. ⟨10.1038/s41559-017-0091⟩

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Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

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Current Biology, 2016, 26 (22), pp.3060-3065. ⟨10.1016/j.cub.2016.09.031⟩

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Nature Communications, 2016, 7, pp.11071. ⟨10.1038/ncomms11071⟩

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The International Society of Microbiologial Ecology Journal, 2016, 10 (3), pp.693-706. ⟨10.1038/ismej.2015.147⟩

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Frontiers in Marine Science, 2016, 3 (255), pp.1-15. ⟨10.3389/fmars.2016.00255⟩

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Applied and Environmental Microbiology, 2016, 82 (15), pp.4757-4766. ⟨10.1128/AEM.00560-16⟩

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Systematic Biology, 2016, 65 (5), pp.925-940. ⟨10.1093/sysbio/syw031⟩

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Scientific Reports, 2016, 6, pp.37900. ⟨10.1038/srep37900⟩

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Molecular Biology and Evolution, 2016, 12 (12), pp.3226-3248. ⟨10.1093/molbev/msw209⟩

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Biology Letters, 2016, 12 (9), pp.845-871. ⟨10.1098/rsbl.2016.0674⟩

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Scientific Data , 2015, 2, pp.150023. ⟨10.1038/sdata.2015.23⟩

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PeerJ, 2015, 3, pp.e1420. ⟨10.7717/peerj.1420⟩

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Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Peter von Dassow , Uwe John , Hiroyuki Ogata , Ian Probert , El Mahdi Bendif et al.

The International Society of Microbiologial Ecology Journal, 2015, 9 (6), pp.1365-1377. ⟨10.1038/ismej.2014.221⟩

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Johan Decelle , Sarah Romac , Rowena F Stern , El Mahdi Bendif , Adriana Zingone et al.

Molecular Ecology Resources, 2015, 15 (6), pp.1435-1445. ⟨10.1111/1755-0998.12401⟩

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Camille Clerissi , Yves Desdevises , Sarah Romac , Stéphane Audic , Colomban de Vargas et al.

Environmental Microbiology Reports, 2015, 7 (6), pp.979-989. ⟨10.1111/1758-2229.12345⟩

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Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩

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Environmental Microbiology, 2015, 17 (9), pp.3195-3207. ⟨10.1111/1462-2920.12759⟩

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Environmental Microbiology, 2015, 17 (10), pp.4035-4049. ⟨10.1111/1462-2920.12955⟩

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Science, 2015, 348 (6237), pp.873. ⟨10.1126/science.aac5605⟩

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Molecular Biology and Evolution, 2014, 31 (4), pp.993-1009. ⟨10.1093/molbev/msu055⟩

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Comparative Transcriptome of Wild Type and Selected Strains of the Microalgae Tisochrysis lutea Provides Insights into the Genetic Basis, Lipid Metabolism and the Life Cycle

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PLoS ONE, 2014, 9 (1), pp.e86889. ⟨10.1371/journal.pone.0086889⟩

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Patterns of Rare and Abundant Marine Microbial Eukaryotes

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Current Biology, 2014, 24 (8), pp.813-821. ⟨10.1016/j.cub.2014.02.050⟩

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Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

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BMC Microbiology, 2014, 14 (1), pp.110. ⟨10.1186/1471-2180-14-110⟩

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Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)

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Journal of Phycology, 2014, 50 (1), pp.140-148. ⟨10.1111/jpy.12147⟩

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Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Ramiro Logares , Shinichi Sunagawa , Guillem Salazar , Francisco M. Cornejo-Castillo , Isabel Ferrera et al.

Environmental Microbiology, 2014, 16 (9, SI), pp.2659-2671. ⟨10.1111/1462-2920.12250⟩

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Morphospecies versus phylospecies concepts for evaluating phytoplankton diversity: the case of the Coccolithophores

Jeremy R. Young , Hui Liu , Ian Probert , Stephane Aris-Brosou , Colomban de Vargas

Cryptogamie Algologie, 2014, 35 (4), pp.353-377. ⟨10.7872/crya.v35.iss4.2014.353⟩

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Swarm: robust and fast clustering method for amplicon-based studies

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PeerJ, 2014, 2, pp.e593. ⟨10.7717/peerj.593⟩

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Aurore André , Frédéric Quillévéré , Raphaël Morard , Yurika Ujiié , Gilles Escarguel et al.

PLoS ONE, 2014, 9 (8), pp.e104641. ⟨10.1371/journal.pone.0104641⟩

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Deep relationships of Rhizaria revealed by phylogenomics: A farewell to Haeckel's Radiolaria

Roberto Sierra , Mikhail V. Matz , Galina Aglyamova , Loïc Pillet , Johan Decelle et al.

Molecular Phylogenetics and Evolution, 2013, 67 (1), pp.53-59. ⟨10.1016/j.ympev.2012.12.011⟩

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454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

Elianne Egge , Lucie Bittner , Tom Andersen , Stéphane Audic , Colomban de Vargas et al.

PLoS ONE, 2013, 8 (9), pp.e74371. ⟨10.1371/journal.pone.0074371⟩

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Ecological modeling of the temperature dependence of cryptic species of planktonic Foraminifera in the Southern Hemisphere

Raphael Morard , Frédéric Quillévéré , Gilles Escarguel , Thibault de Garidel-Thoron , Colomban de Vargas et al.

Palaeogeography, Palaeoclimatology, Palaeoecology, 2013, 391, pp.13-33. ⟨10.1016/j.palaeo.2013.05.011⟩

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

Laure Guillou , Dipankar Bachar , Stéphane Audic , David Bass , Cédric Berney et al.

Nucleic Acids Research, 2013, 41 (D1), pp.D597-D604. ⟨10.1093/nar/gks1160⟩

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Bioprospecting Marine Plankton

Heni Abida , Sandrine Ruchaud , Laurent Rios , Anne Humeau , Ian Probert et al.

Marine drugs, 2013, 11 (11), pp.4594-4611. ⟨10.3390/md11114594⟩

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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Pascal Hingamp , Nigel Grimsley , Silvia G Acinas , Camille Clerissi , Lucie Subirana et al.

The International Society of Microbiologial Ecology Journal, 2013, 7 (9), pp.1678-1695. ⟨10.1038/ismej.2013.59⟩

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Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.

Lucie Bittner , Angélique Gobet , Stéphane Audic , Sarah Romac , Elianne S Egge et al.

Molecular Ecology, 2013, 22 (1), pp.87-101. ⟨10.1111/mec.12108⟩

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The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer

Aurore Andre , Agnes Weiner , Frédéric Quillévéré , Ralf Aurahs , Raphaël Morard et al.

Paleobiology, 2013, 39 (1), pp.21-39. ⟨10.1666/0094-8373-39.1.21⟩

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Diversity, ecology and biogeochemistry of cyst-forming acantharia (radiolaria) in the oceans.

Johan Decelle , Patrick Martin , Katsiaryna Paborstava , David W Pond , Geraint Tarling et al.

PLoS ONE, 2013, 8 (1), pp.e53598. ⟨10.1371/journal.pone.0053598⟩

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Global scale same-specimen morpho-genetic analysis of Truncorotalia truncatulinoides: a perspective on the morphological species concept in planktonic foraminifera

Frédéric Quillévéré , Raphaël Morard , Gilles Escarguel , Christophe Jean Douady , Y Ujiie et al.

Palaeogeography, Palaeoclimatology, Palaeoecology, 2013, 391, pp.2-12. ⟨10.1016/j.palaeo.2011.03.013⟩

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On the description of Tisochrysis lutea gen. nov sp nov and Isochrysis nuda sp nov in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)

El Mahdi Bendif , Ian Probert , Declan C. Schroeder , Colomban de Vargas

Journal of Applied Phycology, 2013, 25 (6), pp.1763-1776. ⟨10.1007/s10811-013-0037-0⟩

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Two distinct lineages in the radiolarian Order Spumellaria having different ecological preferences

Yoshiyuki Ishitani , Yurika Ujiié , Colomban de Vargas , Fabrice Not , Kozo Takahashi

Deep Sea Research Part II: Topical Studies in Oceanography, 2012, 61-64, pp.172-178. ⟨10.1016/j.dsr2.2011.12.005⟩

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An original mode of symbiosis in open ocean plankton

Johan Decelle , Ian Probert , Lucie Bittner , Yves Desdevises , Sébastien Colin et al.

Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (44), pp.18000-18005. ⟨10.1073/pnas.1212303109⟩

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CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Jan Pawlowski , Stéphane Audic , Sina Adl , David Bass , Lassaâd Belbahri et al.

PLoS Biology, 2012, 10 (11), pp.e1001419. ⟨10.1371/journal.pbio.1001419⟩

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Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria)

Johan Decelle , Noritoshi Suzuki , Frédéric Mahé , Colomban de Vargas , Fabrice Not

Protist, 2012, 163 (3), pp.435-450. ⟨10.1016/j.protis.2011.10.002⟩

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Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

Ramiro Logares , Stéphane Audic , Sébastien Santini , Massimo C. Pernice , Colomban de Vargas et al.

The International Society of Microbiologial Ecology Journal, 2012, 6 (10), pp.1823-1833. ⟨10.1038/ismej.2012.36⟩

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Longitudinal differentiation among pelagic populations in a planktic foraminifer.

Yurika Ujiié , Takahiro Asami , Thibault de Garidel-Thoron , Liu Liu , Yoshiyuki Ishitani et al.

Ecology and Evolution, 2012, 2 (7), pp.1725-37. ⟨10.1002/ece3.286⟩

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In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta)

Miguel J. Frada , Kay D. Bidle , Ian Probert , Colomban de Vargas

Environmental Microbiology, 2012, 14 (6), pp.1558-1569. ⟨10.1111/j.1462-2920.2012.02745.x⟩

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Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms

Antonio Pagarete , Gildas Le Corguille , Bela Tiwari , Hiroyuki Ogata , Colomban de Vargas et al.

FEMS Microbiology Ecology, 2011, 78 (3), pp.555-564. ⟨10.1111/j.1574-6941.2011.01191.x⟩

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Worldwide Genotyping in the Planktonic Foraminifer Globoconella inflata: Implications for Life History and Paleoceanography

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PLoS ONE, 2011, 6 (10), pp.e26665. ⟨10.1371/journal.pone.0026665⟩

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A Holistic Approach to Marine Eco-Systems Biology

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PLoS Biology, 2011, 9 (10), pp.e1001177. ⟨10.1371/journal.pbio.1001177⟩

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Transcriptome Analyses Reveal Differential Gene Expression Patterns Between the Life-Cycle Stages of Emiliania Huxleyi (haptophyta) and Reflect Specialization to Different Ecological Niches1: Gene Expression in E. Huxleyi

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Journal of Phycology, 2011, 47 (4), pp.829-838. ⟨10.1111/j.1529-8817.2011.01014.x⟩

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A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy

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Journal of Nannoplankton Research, 2010, 31 (2), pp.58-112

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Phytoplankton Biogeography and Community Stability in the Ocean

Pedro Cermeno , Colomban de Vargas , Fatima Abrantes , Paul G. Falkowski

PLoS ONE, 2010, 5 (3), pp.e10037. ⟨10.1371/journal.pone.0010037⟩

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Pelagodinium gen. nov and P-beii comb. nov., a Dinoflagellate Symbiont of Planktonic Foraminifera

Raffaele Siano , Marina Montresor , Ian Probert , Fabrice Not , Colomban de Vargas

Protist, 2010, 161 (3), pp.385-399. ⟨10.1016/j.protis.2010.01.002⟩

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A Time line of the Environmental Genetics of the Haptophytes

Hui Liu , Stephane Aris-Brosou , Ian Probert , Colomban de Vargas

Molecular Biology and Evolution, 2010, 27 (1), pp.161-176. ⟨10.1093/molbev/msp222⟩

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Coiling dimorphism within a genetic type of the planktonic foraminifer Globorotalia truncatulinoides

Yurika Ujiié , Thibault de Garidel-Thoron , S Watanabe , P Wiebe , Colomban de Vargas

Micropaleontology, 2010, 77 (3-4), pp.145-153. ⟨10.1016/j.marmicro.2010.09.001⟩

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Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

Adam Monier , Antonio Pagarete , Colomban de Vargas , Michael J. Allen , Betsy Read et al.

Genome Research, 2009, 19 (8), pp.1441-1449. ⟨10.1101/gr.091686.109⟩

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Paleodictyon nodosum: A living fossil on the deep-sea floor

Peter A. Rona , Adolf Seilacher , Colomban de Vargas , Andrew J. Gooday , Joan M. Bernhard et al.

Deep Sea Research Part II: Topical Studies in Oceanography, 2009, 56 (19-20), pp.1700-1712. ⟨10.1016/j.dsr2.2009.05.015⟩

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Morphological recognition of cryptic species in the planktonic foraminifer Orbulina universa

Raphael Morard , Frédéric Quillévéré , Gilles Escarguel , Y Ujiie , Thibault de Garidel-Thoron et al.

Micropaleontology, 2009, 71 (3-4), pp.148-165. ⟨10.1016/j.marmicro.2009.03.001⟩

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Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest

Antonio Pagarete , Michael J. Allen , William H. Wilson , Susan A. Kimmance , Colomban de Vargas

Environmental Microbiology, 2009, 11 (11), pp.2840-2848. ⟨10.1111/j.1462-2920.2009.02006.x⟩

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First observations of heterococcolithophore-holococcolithophore life cycle combinations in the family Pontosphaeraceae (Calcihaptophycideae, Haptophyta)

Miguel Frada , Isabella Percopo , Jeremy Young , Adriana Zingone , Colomban de Vargas et al.

Marine Micropaleontology, 2009, 71 (1-2), pp.20-27. ⟨10.1016/j.marmicro.2009.01.001⟩

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New Insights into the Diversity of Marine Picoeukaryotes

Fabrice Not , Javier Del Campo , Vanessa Balague , Colomban de Vargas , Ramon Massana

PLoS ONE, 2009, 4 (9), pp.e7143. ⟨10.1371/journal.pone.0007143⟩

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Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans

Hui Liu , Ian Probert , Julia Uitz , Hervé Claustre , Stephane Aris-Brosou et al.

Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (31), pp.12803-12808. ⟨10.1073/pnas.0905841106⟩

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Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

Peter Von Dassow , Hiroyuki Ogata , Ian Probert , Patrick Wincker , Corinne da Silva et al.

Genome Biology, 2009, 10 (10), pp.R114. ⟨10.1186/gb-2009-10-10-r114⟩

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Light-Dependent Transcriptional Regulation of Genes of Biogeochemical Interest in the Diploid and Haploid Life Cycle Stages of Emiliania huxleyi

Sophie Richier , Marie-Emmanuelle Kerros , Colomban de Vargas , Liti Haramaty , Paul G. Falkowski et al.

Applied and Environmental Microbiology, 2009, 75 (10), pp.3366-3369. ⟨10.1128/AEM.02737-08⟩

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Acquired phototrophy in aquatic protists

Diane K. Stoecker , Matthew D. Johnson , Colomban de Vargas , Fabrice Not

Aquatic Microbial Ecology, 2009, 57 (3, 3), pp.279-310. ⟨10.3354/ame01340⟩

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Causal or casual link between the rise of nannoplankton calcification and a tectonically-driven massive decrease in Late Triassic atmospheric CO2 ?

Y. Godderis , Y. Donnadieu , C. de Vargas , Raymond T. Pierrehumbert , Gilles Dromart et al.

Earth and Planetary Science Letters, 2008, 267, pp.247-265

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Causal or casual link between the rise of nannoplankton calcification and a tectonically-driven massive decrease in Late Triassic atmospheric CO2?

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Earth and Planetary Science Letters, 2008, 267 (1-2), pp.247-255. ⟨10.1016/J.EPSL.2007.11.051⟩

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Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

J. Pawlowski , I. Bolivar , J.F. Fahrni , C. de Vargas , Manolo Gouy et al.

Molecular Biology and Evolution, 1997, 14 (5), pp.498-505. ⟨10.1093/oxfordjournals.molbev.a025786⟩

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Find the good imaging technique for automatic identification of meiofauna - Part of the Blue Revolution project.

Valentin Foulon , Daniela Zeppilli , Catherine Borremans , Valentine Foulquier , Edwin Dache et al.

4th Marine Imaging Workshop (MIW'22), Oct 2022, Brest, France

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Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change

Nayat Sanchez-Pi , Luis Marti , André Abreu , Olivier Bernard , Colomban de Vargas et al.

NeurIPS 2020 Workshop - Tackling Climate Change with Machine Learning, Dec 2020, Santiago / Virtual, Chile

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Plankton networks correlated to the biological carbon pump in the global ocean

A.S. Benoiston , L. Bittner , Lionel Guidi , S. Chaffron , D. Eveillard et al.

Journée analyse des réseaux, GDR génomique environnementale, 2017, Nantes, France

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Rethinking the Ocean: Conceptual Engineering for the Next 10,000 Years

Roberto Casati , Sacha Bourgeois-Gironde , Emilie Flamme , Alberto Gallace , Quentin Hiernaux et al.

New Perspectives on Conceptual Engineering - Volume 3, 515, Springer Nature Switzerland, pp.69-93, 2025, Synthese Library, ⟨10.1007/978-3-031-98535-5_4⟩

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