TY - JOUR T1 - Metagenome-assembled genomes uncover a global brackish microbiome JF - bioRxiv DO - 10.1101/018465 SP - 018465 AU - Luisa W. Hugerth AU - John Larsson AU - Johannes Alneberg AU - Markus V. Lindh AU - Catherine Legrand AU - Jarone Pinhassi AU - Anders F. Andersson Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/04/23/018465.abstract N2 - Microbes are main drivers of biogeochemical cycles in oceans and lakes. Yet an understanding of the regulation of such processes is hampered by limited genome-context insight into the metabolic potential of bacterial populations. Here we explored an automatic binning approach to reconstruct representative bacterioplankton genomes from metagenomic samples across a time-series in the Baltic Sea. The 30 unique genomes assembled represent novel species within typical marine and freshwater clades. Analysis of the first genomes for abundant lineages entirely lacking reference genomes, such as OM182, acIV and LD19, uncovered divergent ecological adaptations. While phylogenetic patterns in the seasonal succession of the investigated genomes were evident, closely related genomes sometimes displayed distinct seasonal patterns, that could to some extent be explained by gene content. Signs of streamlining were evident in most genomes; and genome sizes correlated with abundance variation across filter size fractions. Comparisons of 86 aquatic metagenomes against the assembled genomes revealed significant fragment recruitment from brackish waters in North America, but little from lakes or oceans, suggesting the existence of a global brackish microbiome. Current estimates of evolutionary rates imply brackish bacteria diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 ya) - markedly contrasting the evolutionary history of Baltic Sea macro-organisms, which are locally adapted populations of nearby meta-populations. We have thus demonstrated how metagenome-assembled genomes enable an integrated analysis of ecological patterns, functional potential and evolutionary history of several relevant genomes at a time in natural communities.Significance statement Prokaryotes are main drivers of biogeochemical cycles in oceans and lakes. However, a majority of the most abundant populations are still uncharacterized due to difficulties in retrieving cultures and genome information. Here, we used isolation-free metagenomic sequencing and automatic binning to reconstruct genomes from abundant prokaryotic populations of the Baltic Sea, one of world’s largest brackish environments. Results showed genome features influencing functional potential and seasonal progression of 30 strains of Bacteria and Archaea. Comparisons to global metagenomic data placed these populations in biogeographic and evolutionary contexts, revealing brackish prokaryotes have a worldwide distribution, having diverged from marine and freshwater representatives long before current brackish water bodies formed. This suggests a global reservoir of brackish lineages that colonise new environments over geological time. ER -