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Title: Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

Abstract

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 datamore » into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.« less

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [2];  [3];  [1]
  1. Univ. of Wisconsin-Madison, Madison, WI (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Uppsala Univ., Uppsala (Sweden)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1510750
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 6; Journal Issue: 12; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; Freshwater; Metabolism; Carbon cycling; Nutrient cycling; Microbial communities

Citation Formats

Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, and McMahon, Katherine D. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. United States: N. p., 2018. Web. doi:10.7717/peerj.6075.
Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, & McMahon, Katherine D. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. United States. doi:10.7717/peerj.6075.
Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, and McMahon, Katherine D. Mon . "Freshwater carbon and nutrient cycles revealed through reconstructed population genomes". United States. doi:10.7717/peerj.6075. https://www.osti.gov/servlets/purl/1510750.
@article{osti_1510750,
title = {Freshwater carbon and nutrient cycles revealed through reconstructed population genomes},
author = {Linz, Alexandra M. and He, Shaomei and Stevens, Sarah L. R. and Anantharaman, Karthik and Rohwer, Robin R. and Malmstrom, Rex R. and Bertilsson, Stefan and McMahon, Katherine D.},
abstractNote = {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.},
doi = {10.7717/peerj.6075},
journal = {PeerJ},
issn = {2167-8359},
number = 12,
volume = 6,
place = {United States},
year = {2018},
month = {12}
}

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Works referenced in this record:

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