Structure and function of the global ocean microbiome-Reference-Cited by-同舟云学术

Structure and function of the global ocean microbiome

Published:2015-05-22 Issue:6237 Volume:348 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Sunagawa Shinichi¹,Coelho Luis Pedro¹,Chaffron Samuel²³⁴,Kultima Jens Roat¹,Labadie Karine⁵,Salazar Guillem⁶,Djahanschiri Bardya¹,Zeller Georg¹,Mende Daniel R.¹,Alberti Adriana⁵,Cornejo-Castillo Francisco M.⁶,Costea Paul I.¹,Cruaud Corinne⁵,d'Ovidio Francesco⁷,Engelen Stefan⁵,Ferrera Isabel⁶,Gasol Josep M.⁶,Guidi Lionel⁸⁹,Hildebrand Falk¹,Kokoszka Florian¹⁰¹¹,Lepoivre Cyrille¹²,Lima-Mendez Gipsi²³⁴,Poulain Julie⁵,Poulos Bonnie T.¹³,Royo-Llonch Marta⁶,Sarmento Hugo⁶¹⁴,Vieira-Silva Sara²³⁴,Dimier Céline¹⁰¹⁵¹⁶,Picheral Marc⁸⁹,Searson Sarah⁸⁹,Kandels-Lewis Stefanie¹¹⁷,Bowler Chris¹⁰,de Vargas Colomban¹⁵¹⁶,Gorsky Gabriel⁸⁹,Grimsley Nigel¹⁸¹⁹,Hingamp Pascal¹²,Iudicone Daniele²⁰,Jaillon Olivier⁵²¹²²,Not Fabrice¹⁵¹⁶,Ogata Hiroyuki²³,Pesant Stephane²⁴²⁵,Speich Sabrina²⁶²⁷,Stemmann Lars⁸⁹,Sullivan Matthew B.¹³,Weissenbach Jean⁵²¹²²,Wincker Patrick⁵²¹²²,Karsenti Eric¹⁰¹⁷,Raes Jeroen²³⁴,Acinas Silvia G.⁶,Bork Peer¹²⁸,Boss Emmanuel,Bowler Chris,Follows Michael,Karp-Boss Lee,Krzic Uros,Reynaud Emmanuel G.,Sardet Christian,Sieracki Mike,Velayoudon Didier,

Affiliation:

1. Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

2. Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.

3. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium.

4. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

5. CEA–Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.

6. Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.

7. Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France.

8. CNRS, UMR 7093, Laboratoire d’Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.

9. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.

10. Ecole Normale Supérieure, Institut de Biologie de l’ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France.

11. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France.

12. Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France.

13. Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA.

14. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil.

15. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.

16. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.

17. Directors’ Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

18. CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France.

19. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France.

20. Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.

21. CNRS, UMR 8030, CP5706, Evry, France.

22. Université d’Evry, UMR 8030, CP5706, Evry, France.

23. Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan.

24. PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany.

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

26. Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France.

27. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France.

28. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.

Abstract

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Funder

Gordon and Betty Moore Foundation

European Union FP7

Agence Nationale de la Recherche

Japan Society for the Promotion of Science

Università degli Studi di Milano-Bicocca

KU Leuven

VIB

CNRS

Spanish Ministry of Science and Innovation

European Molecular Biology Laboratory

Genoscope/CEA