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Dissolved organic carbon (DOC) depicts a key component in the aquatic carbon cycle as well as for drinking water production from surface waters. DOC concentrations increased in water bodies of the northern hemisphere in the last decades, posing ecological consequences and water quality problems. Within the pelagic zone of lakes and reservoirs, the DOC pool is greatly affected by biological activity as DOC is simultaneously produced and decomposed. This thesis aimed for a conceptual understanding of organic carbon cycling and DOC quality changes under differing hydrological and trophic conditions. Further, the occurrence of aquatic priming was investigated, which has been proposed as a potential process facilitating the microbial decomposition of stable allochthonous DOC within the pelagic zone. To study organic carbon cycling under different hydrological conditions, quantitative and qualitative investigations were carried out in three pre-dams of drinking water reservoirs exhibiting a gradient in DOC concentrations and trophic…

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. ; This work was supported by the Swedish Foundation for Strategic Research (Grant Number ICA10-0015 to AE), the Swedish Research Council (Grant Numbers 349-2007-831, 621-2008-3259 and 621-2011-4669 to SGEA; 2009-3784, 2008-1923 and 2012-3892 to SB), the National Science Foundation [Awards CBET-0644949 (CAREER), MCB-0702653 (Microbial Observatories Program) to KD and DEB-841933 to RS], DEB-0822700 (Long Term Ecological Research, NTL LTER to KDM), the European Union (grant to SGEA), the Göran Gustafsson Foundation (grant to SGEA), the Knut and Alice Wallenberg Foundation (Grant Numbers KAW-2011.0148 and KAW-2012.0075 to SGEA), and the Swedish Wennergren Foundation (to KDM and SB).