| Summary: | Little is known about the diversity and structuring of freshwater microbial communities beyond
the patterns revealed by tracing their distribution in the landscape with common taxonomic markers
such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were
compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater
metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of
freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial
lineages was also reflected in phylogenies of functional genes, and there were also significant
differences in functional beta-diversity. The pathways and functions that accounted for these
differences are involved in osmoregulation, active transport, carbohydrate and amino acid
metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic
matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes.
This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic-
compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that
strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial
communities.
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