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

Seeleuthner, Yoann ... et al.-- This article is contribution number 63 of Tara Oceans.-- 10 pages, 4 figures, 1 table, data availability, supplementary material https://dx.doi.org/10.1038/s41467-017-02235-3Single-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 ecologyWe thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Governement ‘Investissement d’Avenir’ programs Oceanomics (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), Fund for Scientific Research-Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects ‘PHYTBACK/ANR-2010-1709-01’, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No. 287589, IHMS/HEALTH-F4-2010-261376), ERC Advanced Grant Award to CB (Diatomite: 294823), US NSF grant DEB-1031049 to M.E.S. and R.S., FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)Peer Reviewe