Structure and function of the global ocean microbiome

Abstract

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…http://dx.doi.org/10.1101/053090 doi: bioRxiv preprint first posted online May. 12, 2016; as described in 21 , (ii) all reads not mapping (Bowtie 2 56 , options --sensitive, -X 2000, and --nondeterministic, other parameters at default) to a MOCAT contig (by which we denote 'scaftigs', that is, contigs that were extended and linked using the paired-end information of sequencing read 57 ) were assembled sample by sample with Idba_ud (iterative k-mer assembly, with k-mer increasing from 20 to 100 by step of 20), (iii) all reads remaining unmapped to any contig were then pooled by Longhurst province (i.e. unmapped reads from samples corresponding to the same Longhurst province were gathered) and assembled with Idba_ud (with the same parameters as above), and (iv) all remaining reads unmapped from every samples were gathered for a final cross-assembly (using Idba_ud).…”

“…A genome database of putative hosts for the epi-and mesopelagic GOV viruses was generated, including all archaea and bacteria genomes annotated as "marine" from NCBI RefSeq and WGS (both times only sequences ≥5kb, 184,663 sequences from 4,452 genomes, downloaded in August 2015), and all contigs ≥5kb from the 139 Tara Oceans microbial metagenomes corresponding to the bacteria and archaea size fraction (791,373 sequences) 21 . For these microbial metagenomic contigs, a first blastn was computed to compare them to all GOV contigs, and exclude from the putative host dataset all metagenomic contigs with a significant similarity to a viral GOV sequence (thresholds of 50 on bit score, 0.001 on e-value, and 70% on identity percentage) on ≥90% of their length, as these are likely sequences of viral origin sequenced in the bacteria and archaea size fraction (these represented 2.2% of the contigs in the assembled microbial metagenomes).…”

“…The taxonomic affiliation of NCBI genomes was taken from the NCBI taxonomy. For Tara Oceans contigs, a last common ancestor (LCA) affiliation was generated for each contig based on genes affiliation 21 , if 3 genes or more on the contig were affiliated. Three different approaches were then used to link viral contigs and putative host genomes (see Supplementary Text and ref.…”

“…Diversity and richness indexes for putative host populations were based on the OTU abundance matrix generated from the analysis of miTAGs in Tara Oceans microbial metagenomes 21 . These indexes were computed for each host group at the same taxonomic level as the host prediction, i.e.…”

“…The hosts of the 38 globally abundant VCs were largely restricted to abundant and widespread epipelagic-ocean microbes identified from miTag-based OTU counts in Tara Oceans microbial metagenomes 21 . Notably, the 4 ubiquitous and abundant VCs were predicted to infect 7 of the 8 globally abundant microbial groups (Actinobacteria, Alpha-, Delta-, and Gamma-proteobacteria, Bacteroidetes, Cyanobacteria, Deferribacteres; Fig.…”