The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection

Abstract

The diversity and geographical distribution of populations within major marine microbial lineages are largely governed by temperature and its co-variables. However, neither the mechanisms by which genomic heterogeneity emerges within a single population nor how it drives the partitioning of ecological niches are well understood.. Here we took advantage of billions of metagenomic reads to study one of the most abundant and widespread microbial populations in the surface ocean. We characterized its substantial amount of genomic heterogeneity using single-amino acid variants (SAAVs), and identified systematic purifying selection and adaptive mechanisms governing non-synonymous variation within this population. Our Deep Learning analysis of SAAVs across metagenomes revealed two main ecological niches that reflect large-scale oceanic current temperatures, as well as six proteotypes demarcating finer-resolved niches. We identified significantly more protein variants in cold currents and an increased number of protein sweeps in warm currents, exposing a global pattern of alternating genomic diversity for this SAR11 population as it drifts along with surface ocean currents. Overall, the geographic partitioning of SAAVs suggests natural selection, rather than neutral evolution, is the main driver of the evolution of SAR11 in surface oceans.

Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic

“…The panels below the trees indicate the % identity (green = 100% while yellow is <100%) and the SNVs of 16S rRNA genes from 21 isolated SAR11 strains and OTUs used in the phylogenetic trees generated from the V4-V5 (B) and the V6-V8 (C) hypervariable regions compared to the reference strain HIMB083 that is widely distributed in the ocean (Delmont et al . 2017).…”

“…The fact that the V6-V8 variable region may be more effective at capturing the taxonomic diversity of the SAR11 clade than the V4V5 variable region is important given the dominance and versatility of this clade in the marine ecosystem (Delmont et al . 2017).…”

Progress in Microbial Ecology in Ice-Covered Seas

“…Metagenomic sequencing efforts have demonstrated bacterial-mediated chemical cycling in frost flowers (Bowman et al 2014) and the importance of select photoreceptors in Antarctic and Arctic sea ice (Koh et al 2010;Vader et al 2018). With increasing throughput of sequence generation and decreasing costs, deep sequencing (i.e., sequencing the same locus multiple times) of the environment should allow comparative studies of full metagenomes to describe the metabolic potential (including uncultured strains) and strain level microbial diversity (e.g., Delmont et al 2017) in sea ice ecosystems.…”

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea

“…Recently, the use of metagenomic data has been proposed to identify natural selection in prokaryotes (Costea et al, 2017;Delmont et al, 2017;Schloissnig et al, 2013). A similar approach has also been applied to the widespread marine copepod Oithona (Madoui et al, 2017) to establish a population genomic analysis at the whole-genome level.…”