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

Yoann Seeleuthner,Céline Dimier,Nicole Poulton,Véronique De Berardinis,Ramunas Stepanauskas,Mike Sieracki,Jade Leconte,Olivier Jaillon,Stéphane Pesant ,Vincent Lombard,Marcel Salanoubat,Ramón Massana ,Quentin Carradec,Daniele Iudicone,Chris Bowler,Marc Wessner,Bernard Henrissat,Shinichi Sunagawa,Sarah Searson,Eric Karsenti,Marc Picheral,Matthew B Sullivan,Jean‐Marc Aury ,Colomban De Vargas,Jean‐François Mangot ,Karine Labadie,Peer Bork,Stefanie Kandels‐Lewis ,Samuel Mondy,Éric Pelletier ,Julie Poulain,Ramiro Logares,Pascal Hingamp,Patrick Wincker

doi:10.1038/s41467-017-02235-3

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.

Highlights

Single-celled eukaryotes are critical players in global biogeochemical cycling of nutrients and energy in the oceans
More than 900 single-cell amplified genomes (SAGs) were generated from small heterotrophic protists selected from eight Tara Oceans sampling stations representing contrasting environments in the Mediterranean Sea and Indian Ocean
The MAST-4A cells were co-assembled as two independent sets of sequences, for use as an internal control for subsequent analyses and because they originated from two different water masses; they were very similar in genome composition (Supplementary Fig. 2) and a single assembly would have been possible[20]

Summary

Introduction

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. An extensive genome-level description of abundant marine heterotrophic protists could be a key step toward understanding their ecological roles. We integrate single-cell genomics with metagenomic and metatranscriptomic sequence data for exploring the ecological and functional complexity of uncultured micro-eukaryotes, key players in the world’s largest ecosystem. We selected for our study 40 single cells representative of three uncultured stramenopile clades that are known to be abundant in marine pico-nano plankton. Assessment of the genes involved in the degradation of organic matter may be relevant for elucidating their roles in marine ecosystems and biogeochemical cycles[17]

Methods

Results

Conclusion