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 De Berardinis, Marcel Salanoubat, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, Silvia G. Acinas, Emmanuel BossMichael Follows, Gabriel Gorsky, Nigel Grimsley, Lee Karp-Boss, Uros Krzic, Fabrice Not, Hiroyuki Ogata, Jeroen Raes, Emmanuel G. Reynaud, Christian Sardet, Sabrina Speich, Lars Stemmann, Didier Velayoudon, Jean Weissenbach, Stephane Pesant, Nicole Poulton, Ramunas Stepanauskas, Peer Bork, Chris Bowler, Pascal Hingamp, Matthew Sullivan, Daniele Iudicone, Ramon Massana, Jean Marc Aury, Bernard Henrissat, Eric Karsenti, Olivier Jaillon, Mike Sieracki, Colomban De Vargas, Patrick Wincker

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish (US)
Article number310
JournalNature Communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018
Externally publishedYes

Fingerprint

Stramenopiles
genome
Genomics
Oceans and Seas
oceans
Genes
Genome
cells
prokaryotes
eukaryotes
Expeditions
Gene transfer
Metagenomics
Food
Horizontal Gene Transfer
expeditions
ecology
sequencing
water temperature
locomotion

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E., Wessner, M., ... Wincker, P. (2018). Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications, 9(1), [310]. https://doi.org/10.1038/s41467-017-02235-3

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. / Seeleuthner, Yoann; Mondy, Samuel; Lombard, Vincent; Carradec, Quentin; Pelletier, Eric; Wessner, Marc; Leconte, Jade; Mangot, Jean François; Poulain, Julie; Labadie, Karine; Logares, Ramiro; Sunagawa, Shinichi; De Berardinis, Véronique; Salanoubat, Marcel; Dimier, Céline; Kandels-Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Acinas, Silvia G.; Boss, Emmanuel; Follows, Michael; Gorsky, Gabriel; Grimsley, Nigel; Karp-Boss, Lee; Krzic, Uros; Not, Fabrice; Ogata, Hiroyuki; Raes, Jeroen; Reynaud, Emmanuel G.; Sardet, Christian; Speich, Sabrina; Stemmann, Lars; Velayoudon, Didier; Weissenbach, Jean; Pesant, Stephane; Poulton, Nicole; Stepanauskas, Ramunas; Bork, Peer; Bowler, Chris; Hingamp, Pascal; Sullivan, Matthew; Iudicone, Daniele; Massana, Ramon; Aury, Jean Marc; Henrissat, Bernard; Karsenti, Eric; Jaillon, Olivier; Sieracki, Mike; De Vargas, Colomban; Wincker, Patrick.

In: Nature Communications, Vol. 9, No. 1, 310, 01.12.2018.

Research output: Contribution to journalArticle

Seeleuthner, Y, Mondy, S, Lombard, V, Carradec, Q, Pelletier, E, Wessner, M, Leconte, J, Mangot, JF, Poulain, J, Labadie, K, Logares, R, Sunagawa, S, De Berardinis, V, Salanoubat, M, Dimier, C, Kandels-Lewis, S, Picheral, M, Searson, S, Acinas, SG, Boss, E, Follows, M, Gorsky, G, Grimsley, N, Karp-Boss, L, Krzic, U, Not, F, Ogata, H, Raes, J, Reynaud, EG, Sardet, C, Speich, S, Stemmann, L, Velayoudon, D, Weissenbach, J, Pesant, S, Poulton, N, Stepanauskas, R, Bork, P, Bowler, C, Hingamp, P, Sullivan, M, Iudicone, D, Massana, R, Aury, JM, Henrissat, B, Karsenti, E, Jaillon, O, Sieracki, M, De Vargas, C & Wincker, P 2018, 'Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans', Nature Communications, vol. 9, no. 1, 310. https://doi.org/10.1038/s41467-017-02235-3
Seeleuthner, Yoann ; Mondy, Samuel ; Lombard, Vincent ; Carradec, Quentin ; Pelletier, Eric ; Wessner, Marc ; Leconte, Jade ; Mangot, Jean François ; Poulain, Julie ; Labadie, Karine ; Logares, Ramiro ; Sunagawa, Shinichi ; De Berardinis, Véronique ; Salanoubat, Marcel ; Dimier, Céline ; Kandels-Lewis, Stefanie ; Picheral, Marc ; Searson, Sarah ; Acinas, Silvia G. ; Boss, Emmanuel ; Follows, Michael ; Gorsky, Gabriel ; Grimsley, Nigel ; Karp-Boss, Lee ; Krzic, Uros ; Not, Fabrice ; Ogata, Hiroyuki ; Raes, Jeroen ; Reynaud, Emmanuel G. ; Sardet, Christian ; Speich, Sabrina ; Stemmann, Lars ; Velayoudon, Didier ; Weissenbach, Jean ; Pesant, Stephane ; Poulton, Nicole ; Stepanauskas, Ramunas ; Bork, Peer ; Bowler, Chris ; Hingamp, Pascal ; Sullivan, Matthew ; Iudicone, Daniele ; Massana, Ramon ; Aury, Jean Marc ; Henrissat, Bernard ; Karsenti, Eric ; Jaillon, Olivier ; Sieracki, Mike ; De Vargas, Colomban ; Wincker, Patrick. / Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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