Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

PeerJ

卷:6

Karthik Anantharaman¹  Katherine D. McMahon¹  Shaomei He¹  Sarah L.R. Stevens¹  Alexandra M. Linz¹  Stefan Bertilsson²  Rex R. Malmstrom³  Robin R. Rohwer⁴ 

[1] Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA;

[2] Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden;

[3] Department of Energy Joint Genome Institute, Walnut Creek, CA, USA;

[4] Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI, USA;

关键词: Freshwater;    Metabolism;    Carbon cycling;    Nutrient cycling;    Microbial communities;   

DOI  :  10.7717/peerj.6075

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown