Metagenome-assembled genomes uncover a global brackish microbiome

Microbes are main drivers of biogeochemical cycles in oceans and lakes, yet surprisingly few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Here we used automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea. The genomes represent novel species within freshwater and marine clades, including clades not previously genome-sequenced. Their seasonal dynamics followed phylogenetic patterns, but with fine-grained lineage specific adaptations. Signs of streamlining were evident in most genomes, and estimated genome sizes correlated with abundance variation across filter size fractions. Comparing the genomes with globally distributed aquatic metagenomes suggested the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives >100,000 years ago, hence long before the Baltic Sea was formed (8000 years). This markedly contrasts to most Baltic Sea multicellular organisms that are locally adapted populations of fresh- or marine counterparts.