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Title: Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Abstract

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [4];  [4]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Sciences Division
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
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)
OSTI Identifier:
1434034
Grant/Contract Number:  
AC02-05CH11231; S10 OD018174
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Related Information: © 2017 The Author(s).; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; Environmental chemistry; Metabolomics; Microbial ecology; Soil microbiology

Citation Formats

Swenson, Tami L., Karaoz, Ulas, Swenson, Joel M., Bowen, Benjamin P., and Northen, Trent R. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. United States: N. p., 2018. Web. https://doi.org/10.1038/s41467-017-02356-9.
Swenson, Tami L., Karaoz, Ulas, Swenson, Joel M., Bowen, Benjamin P., & Northen, Trent R. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. United States. https://doi.org/10.1038/s41467-017-02356-9
Swenson, Tami L., Karaoz, Ulas, Swenson, Joel M., Bowen, Benjamin P., and Northen, Trent R. Tue . "Linking soil biology and chemistry in biological soil crust using isolate exometabolomics". United States. https://doi.org/10.1038/s41467-017-02356-9. https://www.osti.gov/servlets/purl/1434034.
@article{osti_1434034,
title = {Linking soil biology and chemistry in biological soil crust using isolate exometabolomics},
author = {Swenson, Tami L. and Karaoz, Ulas and Swenson, Joel M. and Bowen, Benjamin P. and Northen, Trent R.},
abstractNote = {Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.},
doi = {10.1038/s41467-017-02356-9},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {1}
}

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