title: Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.
abstract: 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.
authors.affiliation: Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden.
authors.forename: Alexander
authors.initials: A
authors.lastname: Eiler
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Zaremba-Niedzwiedzka
authors.forename: Manuel
authors.initials: M
authors.lastname: Martínez-García
authors.forename: Katherine D
authors.initials: KD
authors.lastname: McMahon
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
authors.forename: Siv G E
authors.initials: SG
authors.lastname: Andersson
authors.forename: Stefan
authors.initials: S
authors.lastname: Bertilsson
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D057225:Data Mining; D005618:Fresh Water / Q000382:microbiology*; D060106:Lakes / Q000382:microbiology; D053858:Metabolic Networks and Pathways; D054892:Metagenome; D056186:Metagenomics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D054712:Salinity; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D012335:RNA, Ribosomal