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Tara Oceans: towards global ocean ecosystems biology

Nature Reviews Microbiology volume 18, pages 428–445 (2020)Cite this article

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Abstract

A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.

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Fig. 1: Tara Oceans sampled the global ocean ecosystem.
Fig. 2: Tara Oceans assessed plankton across taxonomic, organismal and environmental scales to study the whole ecosystem.
Fig. 3: Tara Oceans viral, bacterial and archaeal analysis pipeline and highlighted discoveries.
Fig. 4: Tara Oceans analysis of eukaryotic plankton complexity and highlighted discoveries.
Fig. 5: Eukaryotic shapes and symbioses explored by Tara Oceans plankton imaging.
Fig. 6: Ecosystems biology and integrative analyses of the global oceans.

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Acknowledgements

Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org/). The authors further thank the commitment of the following sponsors: the French CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara GOSEE), the French Facility for Global Environment (FFEM), the European Molecular Biology Laboratory, Genoscope/CEA, the French Ministry of Research and the French Government Investissements d’Avenir programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08) and MEMO LIFE (ANR-10-LABX-54), the PSL research university (ANR-11-IDEX-0001-02) and EMBRC-France (ANR-10-INBS-02). Funding for the collection and processing of the Tara Oceans data set was provided by the NASA Ocean Biology and Biogeochemistry Program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G and NNX15AC08G (to the University of Maine), the Canada Excellence Research Chair in Remote Sensing of Canada’s New Arctic Frontier and the Canada Foundation for Innovation. The authors also thank agnès b. and E. Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier and KAUST for support and commitment. The global sampling effort was made possible by countless scientists and crew who performed sampling aboard the Tara from 2009 to 2013, and the authors thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. The authors are also grateful to the countries that graciously granted sampling permission. The authors thank N. Le Bescot and N. Henry for their help in designing the figures in this article. C.d.V. thanks the Roscoff Bioinformatics platform ABiMS (http://abims.sb-roscoff.fr). S. Sunagawa thanks the European Molecular Biology Laboratory and ETH Zürich’s high-performance computing facilities for computational support. C.B. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement 835067) as well as the Radcliffe Institute of Advanced Study at Harvard University for a scholar’s fellowship during the 2016–2017 academic year. M.B.S. thanks the Gordon and Betty Moore Foundation (award 3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) as well as the Ohio Supercomputer for computational support. S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). F.L. thanks the Institut Universitaire de France as well as the EMBRC platform PIQv for image analysis. S. Sunagawa is supported by ETH Zürich and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955). The authors declare that all data reported herein are fully and freely available from the date of publication, with no restrictions, and that all of the analyses, publications and ownership of data are free from legal entanglement or restriction by the various nations in whose waters the Tara Oceans expeditions conducted sampling. This article is contribution number 100 of Tara Oceans.

Author information

Authors and Affiliations

  1. Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland

    Shinichi Sunagawa & Shinichi Sunagawa

  2. Department of Marine Biology and Oceanography, Institute of Marine Sciences–CSIC, Barcelona, Spain

    Silvia G. Acinas & Silvia G. Acinas

  3. Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany

    Peer Bork, Peer Bork & Stefanie Kandels

  4. Max Delbrück Center for Molecular Medicine, Berlin, Germany

    Peer Bork & Peer Bork

  5. Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany

    Peer Bork & Peer Bork

  6. Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France

    Chris Bowler, Chris Bowler, Eric Karsenti & Eric Karsenti

  7. Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France

    Chris Bowler, Marcel Babin, Chris Bowler, Colomban de Vargas, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Olivier Jaillon, Stefanie Kandels, Eric Karsenti, Magali Lescot, Christian Sardet, Lars Stemmann, Patrick Wincker, Damien Eveillard, Gabriel Gorsky, Lionel Guidi, Eric Karsenti, Fabien Lombard, Patrick Wincker & Colomban de Vargas

  8. Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France

    Damien Eveillard

  9. Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, Villefranche-sur-Mer, France

    Gabriel Gorsky, Lionel Guidi, Christian Sardet, Lars Stemmann, Gabriel Gorsky, Lionel Guidi & Fabien Lombard

  10. Stazione Zoologica Anton Dohrn, Naples, Italy

    Daniele Iudicone & Daniele Iudicone

  11. Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany

    Eric Karsenti & Eric Karsenti

  12. Institute for Chemical Research, Kyoto University, Kyoto, Japan

    Hiroyuki Ogata & Hiroyuki Ogata

  13. PANGAEA, University of Bremen, Bremen, Germany

    Stéphane Pesant & Stephane Pesant

  14. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany

    Stéphane Pesant & Stephane Pesant

  15. Department of Microbiology, The Ohio State University, Columbus, OH, USA

    Matthew B. Sullivan & Matthew B. Sullivan

  16. Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA

    Matthew B. Sullivan & Matthew B. Sullivan

  17. Center for RNA Biology, The Ohio State University, Columbus, OH, USA

    Matthew B. Sullivan & Matthew B. Sullivan

  18. Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France

    Olivier Jaillon, Patrick Wincker & Patrick Wincker

  19. Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France

    Colomban de Vargas, Fabrice Not & Colomban de Vargas

  20. Département de Biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)–CNRS (France), Université Laval, Quebec, QC, Canada

    Marcel Babin

  21. School of Marine Sciences, University of Maine, Orono, ME, USA

    Emmanuel Boss & Lee Karp-Boss

  22. European Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK

    Guy Cochrane

  23. Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA

    Michael Follows

  24. CNRS UMR 7232, Biologie Intégrative des Organismes Marins, Banyuls-sur-Mer, France

    Nigel Grimsley

  25. Sorbonne Universités Paris 06, OOB UPMC, Banyuls-sur-Mer, France

    Nigel Grimsley

  26. Aix Marseille Universit/e, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France

    Pascal Hingamp & Magali Lescot

  27. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA

    Nicole Poulton & Mike Sieracki

  28. Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium

    Jeroen Raes

  29. Center for the Biology of Disease, VIB KU Leuven, Leuven, Belgium

    Jeroen Raes

  30. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium

    Jeroen Raes

  31. Department of Geosciences, Laboratoire de Météorologie Dynamique, École Normale Supérieure, Paris, France

    Sabrina Speich

  32. Ocean Physics Laboratory, University of Western Brittany, Brest, France

    Sabrina Speich

Authors
  1. Shinichi Sunagawa
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  2. Silvia G. Acinas
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  3. Peer Bork
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  4. Chris Bowler
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  5. Damien Eveillard
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  6. Gabriel Gorsky
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  7. Lionel Guidi
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  8. Daniele Iudicone
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  9. Eric Karsenti
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  10. Fabien Lombard
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  11. Hiroyuki Ogata
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  15. Colomban de Vargas
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Consortia

Tara Oceans Coordinators

  • Silvia G. Acinas
  • , Marcel Babin
  • , Peer Bork
  • , Emmanuel Boss
  • , Chris Bowler
  • , Guy Cochrane
  • , Colomban de Vargas
  • , Michael Follows
  • , Gabriel Gorsky
  • , Nigel Grimsley
  • , Lionel Guidi
  • , Pascal Hingamp
  • , Daniele Iudicone
  • , Olivier Jaillon
  • , Stefanie Kandels
  • , Lee Karp-Boss
  • , Eric Karsenti
  • , Magali Lescot
  • , Fabrice Not
  • , Hiroyuki Ogata
  • , Stéphane Pesant
  • , Nicole Poulton
  • , Jeroen Raes
  • , Christian Sardet
  • , Mike Sieracki
  • , Sabrina Speich
  • , Lars Stemmann
  • , Matthew B. Sullivan
  • , Shinichi Sunagawa
  •  & Patrick Wincker

Contributions

S. Sunagawa and C.d.V. are the lead authors of the article and all other authors contributed to discussion of the content, writing and editing of the article.

Corresponding authors

Correspondence to Shinichi Sunagawa or Colomban de Vargas.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Microbiology thanks David Hutchins, Maria Pachiadaki and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

Artist profiles: https://oceans.taraexpeditions.org/en/m/art/artists/

Plankton chronicles: http://planktonchronicles.org

Tara Ocean Foundation: https://oceans.taraexpeditions.org/en

TaraOceans Sample Registry: https://doi.pangaea.de/10.1594/PANGAEA.875582

TaraOceans Sequencing: https://www.ebi.ac.uk/ena/data/view/PRJEB402

UniEuk: http://unieuk.org

Supplementary information

Glossary

Epipelagic

Referring to uppermost layer of the ocean that receives sunlight, enabling the organisms inhabiting it to perform photosynthesis.

Mesopelagic

Referring to the ocean layer that receives very little to no sunlight, lying beneath the epipelagic layer, ranging from about 200 to 1,000 m in depth.

Heterotrophic

Capable of incorporating organic carbon into biomass.

Remineralized

Derived from the breakdown of organic matter into its simplest inorganic form.

Mixotrophy

Capacity to incorporate carbon into biomass from either inorganic or organic sources.

Photoheterotrophy

Capacity to derive energy from light and carbon from organic matter.

Haptophytes

Group of single-celled photosynthetic planktonic organisms.

Metagenome-assembled genomes

(MAGs). Consensus genome sequences that are reconstructed using sequencing reads of DNA extracted from whole microbial communities.

Eocene epoch

Second geological epoch of the Palaeogene period (66 million to 23 million years ago) that began 56 million years ago and ended 34 million years ago.

Southern Ocean gateways

Pathways of the oceanic circulation that are influenced by the displacement of continents (for example, the Drake Passage, South African gateway and the Tasman gateway between Antarctica and South America, Africa and Australia, respectively).

Bacterivory

Organisms that obtain carbon and energy primarily from the consumption of bacteria.

Miocene epoch

First geological epoch of the Neogene period (2.6 million to 23 million years ago) that extends from about 23 million to 5 million years ago.

Agulhas choke point

Oceanic system south of Africa where warm and salty Indian Ocean waters leak into the South Atlantic Ocean impacting the global oceanic circulation.

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Sunagawa, S., Acinas, S.G., Bork, P. et al. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 18, 428–445 (2020). https://doi.org/10.1038/s41579-020-0364-5

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