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

Type Article
Date 2018-01
Language English
Author(s) Seeleuthner Yoann1, 2, 3, Mondy SamuelORCID1, 2, 3, Lombard Vincent4, 5, 6, Carradec QuentinORCID1, 2, 3, Pelletier EricORCID1, 2, 3, Wessner Marc1, 2, 3, Leconte JadeORCID1, 2, 3, Mangot Jean-FrancoisORCID7, Poulain JulieORCID1, 2, Labadie Karine1, 2, Logares RamiroORCID7, Sunagawa ShinichiORCID8, 9, De Berardinis Veronique2, 3, Salanoubat Marcel2, 3, Dimier Celine10, 11, 12, Kandels-Lewis Stefanie8, 13, Picheral Marc14, Searson Sarah15, Pesant Stephane16, 17, Poulton NicoleORCID18, Stepanauskas RamunasORCID18, Bork Peer8, Bowler ChrisORCID, Hingamp PascalORCID19, Sullivan Matthew B.20, 21, Iudicone Daniele22, Massana RamonORCID7, Aury Jean-MarcORCID1, Henrissat BernardORCID4, 5, 6, 23, Karsenti Eric12, Jaillon OlivierORCID1, 2, 3, Sieracki Mike24, De Vargas Colomban10, 11, Wincker Patrick1, 2, 3, Tara Oceans Coordinators
Contributor(s) Speich Sabrina
Affiliation(s) 1 : GENOSCOPE, CEA Inst Biol Francois Jacob, 2 Rue Gaston Cremieux, F-91057 Evry, France.
2 : CNRS, UMR 8030, CP5706, Evry, France.
3 : Univ Evry, UMR 8030, CP5706, Evry, France.
4 : CNRS, UMR 7257, F-13288 Marseille, France.
5 : Aix Marseille Univ, UMR 7257, F-13288 Marseille, France.
6 : INRA, USC 1408 AFMB, F-13288 Marseille, France.
7 : CSIC, Inst Ciencies Mar, Dept Marine Biol & Oceanog, E-08003 Barcelona, Catalonia, Spain.
8 : European Mol Biol Lab, Struct & Computat Biol, Meyerhofstr 1, D-69117 Heidelberg, Germany.
9 : Swiss Fed Inst Technol, Inst Microbiol, Dept Biol, Vladimir Prelog Weg 4, CH-8093 Zurich, Switzerland.
10 : CNRS, UMR 7144, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
11 : Sorbonne Univ, UPMC, Univ Paris 06, UMR 7144,Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
12 : PSL Res Univ, Ecole Normale Super, IBENS, CNRS,INSERM,UMR 8197, U1024,46 Rue Ulm, F-75005 Paris, France.
13 : Directors Res European Mol Biol Lab, Meyerhofstr 1, D-69117 Heidelberg, Germany.
14 : Sorbonne Univ, UPMC, Univ Paris 06, CNRS,LOV,Observ Oceanol, F-06230 Villefranche Sur Mer, France.
15 : Univ Hawaii, Dept Oceanog, Honolulu, HI 96815 USA.
16 : Univ Bremen, PANGAEA Data Publisher Earth & Environm Sci, D-28359 Bremen, Germany.
17 : Univ Bremen, MARUM Ctr Marine Environm Sci, D-28359 Bremen, Germany.
18 : Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
19 : Aix Marseille Univ, Univ Toulon, CNRS, IRD,MIO UM 110, F-13288 Marseille, France.
20 : Ohio State Univ, Dept Microbiol, Columbus, OH 43210 USA.
21 : Ohio State Univ, Dept Civil Environm & Geodet Engn, Columbus, OH 43210 USA.
22 : Stn Zool Anton Dohrn, Villa Comunale, I-80121 Naples, Italy.
23 : King Abdulaziz Univ, Dept Biol Sci, Jeddah 21589, Saudi Arabia.
24 : Natl Sci Fdn, Arlington, VA 22230 USA.
Source Nature Communications (2041-1723) (Nature Publishing Group), 2018-01 , Vol. 9 , N. 310 , P. 10p.
DOI 10.1038/s41467-017-02235-3
WOS© Times Cited 32
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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Publisher's official version 10 1 MB Open access
Supplementary Information 18 4 MB Open access
Peer Review File 10 472 KB Open access
Description of Additional Supplementary Files 1 169 KB Open access
Supplementary Data 1 15 KB Open access
Supplementary Data 2 64 KB Open access
Supplementary Data 3 17 KB Open access
Supplementary Data 4 243 3 MB Open access
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Seeleuthner Yoann, Mondy Samuel, Lombard Vincent, Carradec Quentin, Pelletier Eric, Wessner Marc, Leconte Jade, Mangot Jean-Francois, Poulain Julie, Labadie Karine, Logares Ramiro, Sunagawa Shinichi, De Berardinis Veronique, Salanoubat Marcel, Dimier Celine, Kandels-Lewis Stefanie, Picheral Marc, Searson Sarah, Pesant Stephane, Poulton Nicole, Stepanauskas Ramunas, Bork Peer, Bowler Chris, Hingamp Pascal, Sullivan Matthew B., Iudicone Daniele, Massana Ramon, Aury Jean-Marc, Henrissat Bernard, Karsenti Eric, Jaillon Olivier, Sieracki Mike, De Vargas Colomban, Wincker Patrick, Tara Oceans Coordinators (2018). Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications, 9(310), 10p. Publisher's official version : https://doi.org/10.1038/s41467-017-02235-3 , Open Access version : https://archimer.ifremer.fr/doc/00660/77234/