Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Yoann Seeleuthner, Samuel Mondy, Vincent Lombard, Quentin Carradec, Eric Pelletier, Marc Wessner, Jade Leconte, Jean-François Mangot, Julie Poulain, Karine Labadie, Ramiro Logares, Shinichi Sunagawa, Véronique Berardinis, Marcel Salanoubat, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, Stephane Pesant, Nicole Poulton, Ramunas Stepanauskas, Peer Bork, Chris Bowler, Pascal Hingamp, Matthew B. Sullivan, Daniele Iudicone, Ramon Massana, Jean-Marc Aury, Bernard Henrissat, Eric Karsenti, Olivier Jaillon, Mike Sieracki (), Colomban Vargas () and Patrick Wincker ()
Additional contact information
Yoann Seeleuthner: GENOSCOPE
Samuel Mondy: GENOSCOPE
Vincent Lombard: Centre National de la Recherche Scientifique
Quentin Carradec: GENOSCOPE
Eric Pelletier: GENOSCOPE
Marc Wessner: GENOSCOPE
Jade Leconte: GENOSCOPE
Jean-François Mangot: Institut de Ciències del Mar (CSIC)
Julie Poulain: GENOSCOPE
Karine Labadie: GENOSCOPE
Ramiro Logares: Institut de Ciències del Mar (CSIC)
Shinichi Sunagawa: European Molecular Biology Laboratory
Véronique Berardinis: GENOSCOPE
Marcel Salanoubat: GENOSCOPE
Céline Dimier: CNRS
Stefanie Kandels-Lewis: European Molecular Biology Laboratory
Marc Picheral: UPMC Université Paris 06, CNRS, Laboratoire d’océanographie de Villefranche (LOV), Observatoire Océanologique
Sarah Searson: University of Hawaii
Stephane Pesant: University of Bremen
Nicole Poulton: Bigelow Laboratory for Ocean Sciences
Ramunas Stepanauskas: Bigelow Laboratory for Ocean Sciences
Peer Bork: European Molecular Biology Laboratory
Chris Bowler: PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS)
Pascal Hingamp: Université de Toulon, CNRS, IRD
Matthew B. Sullivan: Ohio State University
Daniele Iudicone: Stazione Zoologica Anton Dohrn
Ramon Massana: Institut de Ciències del Mar (CSIC)
Jean-Marc Aury: GENOSCOPE
Bernard Henrissat: Centre National de la Recherche Scientifique
Eric Karsenti: PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS)
Olivier Jaillon: GENOSCOPE
Mike Sieracki: National Science Foundation
Colomban Vargas: CNRS
Patrick Wincker: GENOSCOPE

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.

Date: 2018
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DOI: 10.1038/s41467-017-02235-3

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