Abstract
BackgroundMicrobes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them.ResultsWe use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world’s largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes’ seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts.ConclusionsWe describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0834-7) contains supplementary material, which is available to authorized users.
Highlights
Microbes are main drivers of biogeochemical cycles in oceans and lakes
Metagenome-assembled genomes We conducted shotgun metagenomic sequencing on 37 surface water samples collected from March to December in 2012 at the Linnaeus Microbial Observatory (LMO), 10 km east of Öland, in the central Baltic Sea
We approved bins having at least 30 of 36 single-copy gene (SCG) present (Additional file 2), of which not more than two were in multiple copies. This resulted in the identification of 83 genomic bins, hereafter referred to as metagenome assembled genomes (MAGs)
Summary
Microbes are main drivers of biogeochemical cycles in oceans and lakes. the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Microorganisms in aquatic environments play a crucial role in determining global fluxes of energy and turnover of elements essential to life To understand these processes through comprehensive analyses of microbial ecology, evolution and metabolism, sequenced reference genomes of representative native prokaryotes are crucial. Despite vast amounts of sequence data allowing inferences on global distribution of phylogenetic lineages and metabolic potentials [11,12,13,14], many biogeochemical, ecological and evolutionary analyses require structuring data into genomes This is critical because, while individual genes or genome fragments provide useful information on the metabolic potential of a community, in practice most biochemical transformations take place inside a cell, involving sets of genes structured in controlled pathways. CONCOCT was previously shown to give high accuracy and recall on both model and real human gut microbial communities [36]
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