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PeerJ. 2018 Dec 10;6:e6075. doi: 10.7717/peerj.6075. eCollection 2018.

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes.

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Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Department of Geoscience, University of Wisconsin-Madison, Madison, WI, USA.
Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI, USA.
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.


Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.


Carbon cycling; Freshwater; Metabolism; Microbial communities; Nutrient cycling

Conflict of interest statement

The authors declare that they have no competing interests.

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