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 Boss; Michael 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 B. Sullivan; Daniele Iudicone; Ramon Massana; Jean Marc Aury; Bernard Henrissat; Eric Karsenti; Olivier Jaillon; Mike Sieracki; Colomban De Vargas; Patrick Wincker

doi:10.1038/s41467-017-02235-3

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 B. Sullivan, Daniele Iudicone, Ramon Massana, Jean Marc Aury, Bernard Henrissat, Eric Karsenti, Olivier Jaillon, Mike Sieracki, Colomban De Vargas, Patrick Wincker

Ecology and Evolutionary Biology

Research output: Contribution to journal › Article › peer-review

78 Scopus citations

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 language	English (US)
Article number	310
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-017-02235-3
State	Published - Dec 1 2018

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-017-02235-3

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Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E., Wessner, M., Leconte, J., Mangot, J. F., Poulain, J., Labadie, K., Logares, R., Sunagawa, S., De Berardinis, V., Salanoubat, M., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Acinas, S. G., ... Wincker, P. (2018). Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature communications, 9(1), Article 310. https://doi.org/10.1038/s41467-017-02235-3

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, MB, 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

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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.",

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AU - Mondy, Samuel

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AU - Carradec, Quentin

AU - Pelletier, Eric

AU - Wessner, Marc

AU - Leconte, Jade

AU - Mangot, Jean François

AU - Poulain, Julie

AU - Labadie, Karine

AU - Logares, Ramiro

AU - Sunagawa, Shinichi

AU - De Berardinis, Véronique

AU - Salanoubat, Marcel

AU - Dimier, Céline

AU - Kandels-Lewis, Stefanie

AU - Picheral, Marc

AU - Searson, Sarah

AU - Acinas, Silvia G.

AU - Boss, Emmanuel

AU - Follows, Michael

AU - Gorsky, Gabriel

AU - Grimsley, Nigel

AU - Karp-Boss, Lee

AU - Krzic, Uros

AU - Not, Fabrice

AU - Ogata, Hiroyuki

AU - Raes, Jeroen

AU - Reynaud, Emmanuel G.

AU - Sardet, Christian

AU - Speich, Sabrina

AU - Stemmann, Lars

AU - Velayoudon, Didier

AU - Weissenbach, Jean

AU - Pesant, Stephane

AU - Poulton, Nicole

AU - Stepanauskas, Ramunas

AU - Bork, Peer

AU - Bowler, Chris

AU - Hingamp, Pascal

AU - Sullivan, Matthew B.

AU - Iudicone, Daniele

AU - Massana, Ramon

AU - Aury, Jean Marc

AU - Henrissat, Bernard

AU - Karsenti, Eric

AU - Jaillon, Olivier

AU - Sieracki, Mike

AU - De Vargas, Colomban

AU - Wincker, Patrick

PY - 2018/12/1

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N2 - 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.

AB - 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.

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

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