Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
This article is Tara Oceans contribution number 87.-- 11 pages, 6 figures, 1 table, supplemental material https://dx.doi.org/10.1038/s41598-019-42487-1 ; Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered ; Funding was provided by the following sponsors: U.S. NSF grant DEB-1031049; CNRS (in particular Groupement de Recherche GDR3280); European Molecular Biology Laboratory (EMBL), Genoscope/CEA; the French Government 'Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08; Agence Nationale de la Recherche; European Union FP7 (MicroB3/No.287589); and EU project SINGEK (H2020-MSCA-ITN-2015-675752). RL was supported by a RyC fellowship (RYC-2013-12554, MINECO, Spain). We also thank the support and commitment of agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions ; Peer Reviewed