Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

Linz, Alexandra M.; He, Shaomei; Stevens, Sarah L. R.; Anantharaman, Karthik; Rohwer, Robin R.; Malmstrom, Rex R.; Bertilsson, Stefan; McMahon, Katherine D.

doi:10.7717/peerj.6075

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

Journal Article · Mon Dec 10 00:00:00 EST 2018 · PeerJ

DOI:https://doi.org/10.7717/peerj.6075· OSTI ID:1510750

^[1]; He, Shaomei ^[1];

^[1]; Anantharaman, Karthik ^[1];

^[1]; Malmstrom, Rex R. ^[2]; Bertilsson, Stefan ^[3]; McMahon, Katherine D. ^[1]

Univ. of Wisconsin-Madison, Madison, WI (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Uppsala Univ., Uppsala (Sweden)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1510750

Journal Information:: PeerJ, Vol. 6, Issue 12; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 39 works

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Time‐series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems Linz, Alexandra M.; Aylward, Frank O.; Bertilsson, Stefan Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11306	journal	January 2020
Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake Xing, Peng; Tao, Ye; Luo, Jianhua Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11346	journal	January 2020
Think global, act local: The small‐scale environment mainly influences microbial community development and function in lake sediment Orland, Chloé; Yakimovich, Kurt M.; Mykytczuk, Nadia C. S. Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11370	journal	January 2020
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles Grossart, Hans‐Peter; Massana, Ramon; McMahon, Katherine D. Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11382	journal	January 2020
Expansion of known ssRNA phage genomes: From tens to over a thousand Callanan, J.; Stockdale, S. R.; Shkoporov, A. Science Advances, Vol. 6, Issue 6 https://doi.org/10.1126/sciadv.aay5981	journal	February 2020
Think global, act local: The small-scale environment mainly influences microbial community development and function in lake sediment Orland, C.; Yakimovich, Km; Mykytczuk, Ncs Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.44763	text	January 2020
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes Alneberg, Johannes; Bennke, Christin; Beier, Sara Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-0856-x	journal	March 2020
Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation Chen, Lin-Xing; Méheust, Raphaël; Crits-Christoph, Alexander Goldschmidt Abstracts https://doi.org/10.46427/gold2020.389	conference	January 2020

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