EBI metagenomics

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Project overview (ERP004168)

Comparative freshwater metagenomics of Swedish and American lakes

Last updated: 18-Feb-2014


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 to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

Contact details

Katarzyna Zaremba-Niedzwiedzka

Associated samples

Sample name Sample ID Collection date Source
American lake Mendota metagenome (spring) ERS362646 12-May-2009 Environmental
American lake Mendota metagenome (summer) ERS362645 23-Aug-2009 Environmental
American lake Sparkling metagenome (spring) ERS362643 28-May-2009 Environmental
American lake Trout Bog metagenome (spring) ERS362642 28-May-2009 Environmental
American lake Damariscotta metagenome (summer) ERS362641 19-Aug-2009 Environmental
American lake Damariscotta metagenome (spring) ERS362640 28-May-2009 Environmental
Swedish lake Vattern metagenome ERS362639 17-Jul-2007 Environmental
Swedish lake Erkoln metagenome ERS362638 31-Jul-2007 Environmental
Swedish lake Erken metagenome ERS362637 20-Jun-2007 Environmental

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