Exometabolite niche partitioning among sympatric soil bacteria
Abstract
© 2015 Macmillan Publishers Limited. All rights reserved. Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Sciences Division; Univ. of California, Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Arizona State Univ., Mesa, AZ (United States)
- Arizona State Univ., Mesa, AZ (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Sciences Division; Vrije Univ., Amsterdam (Netherlands)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Sciences Division
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; DOE Joint Genome Institute, Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1256039
- Alternate Identifier(s):
- OSTI ID: 1513785
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Baran, Richard, Brodie, Eoin L., Mayberry-Lewis, Jazmine, Hummel, Eric, Da Rocha, Ulisses Nunes, Chakraborty, Romy, Bowen, Benjamin P., Karaoz, Ulas, Cadillo-Quiroz, Hinsby, Garcia-Pichel, Ferran, and Northen, Trent R.. Exometabolite niche partitioning among sympatric soil bacteria. United States: N. p., 2015.
Web. doi:10.1038/ncomms9289.
Baran, Richard, Brodie, Eoin L., Mayberry-Lewis, Jazmine, Hummel, Eric, Da Rocha, Ulisses Nunes, Chakraborty, Romy, Bowen, Benjamin P., Karaoz, Ulas, Cadillo-Quiroz, Hinsby, Garcia-Pichel, Ferran, & Northen, Trent R.. Exometabolite niche partitioning among sympatric soil bacteria. United States. https://doi.org/10.1038/ncomms9289
Baran, Richard, Brodie, Eoin L., Mayberry-Lewis, Jazmine, Hummel, Eric, Da Rocha, Ulisses Nunes, Chakraborty, Romy, Bowen, Benjamin P., Karaoz, Ulas, Cadillo-Quiroz, Hinsby, Garcia-Pichel, Ferran, and Northen, Trent R.. Tue .
"Exometabolite niche partitioning among sympatric soil bacteria". United States. https://doi.org/10.1038/ncomms9289. https://www.osti.gov/servlets/purl/1256039.
@article{osti_1256039,
title = {Exometabolite niche partitioning among sympatric soil bacteria},
author = {Baran, Richard and Brodie, Eoin L. and Mayberry-Lewis, Jazmine and Hummel, Eric and Da Rocha, Ulisses Nunes and Chakraborty, Romy and Bowen, Benjamin P. and Karaoz, Ulas and Cadillo-Quiroz, Hinsby and Garcia-Pichel, Ferran and Northen, Trent R.},
abstractNote = {© 2015 Macmillan Publishers Limited. All rights reserved. Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.},
doi = {10.1038/ncomms9289},
journal = {Nature Communications},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {9}
}
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Figures / Tables:
Figure 1: Two scenarios for substrate preferences in sympatric soil bacteria. (a) Metabolites have a weak effect in supporting diversity due to substrate generalism among heterotrophs. (b) Metabolite diversity contributes to niche differentiation and supports diversity due to strong substrate preferences among heterotrophs.
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Challenges and Approaches in Microbiome Research: From Fundamental to Applied
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