Exometabolite niche partitioning among sympatric soil bacteria

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.

doi:10.1038/ncomms9289

Title: Exometabolite niche partitioning among sympatric soil bacteria

Journal Article · Tue Sep 22 00:00:00 EDT 2015 · Nature Communications

DOI:https://doi.org/10.1038/ncomms9289· OSTI ID:1256039

Baran, Richard ^[1]; Brodie, Eoin L. ^[2]; Mayberry-Lewis, Jazmine ^[3]; Hummel, Eric ^[4]; Da Rocha, Ulisses Nunes ^[5]; Chakraborty, Romy ^[6]; Bowen, Benjamin P. ^[7]; Karaoz, Ulas ^[6]; Cadillo-Quiroz, Hinsby ^[4]; Garcia-Pichel, Ferran ^[4]; Northen, Trent R. ^[7]

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)

© 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.

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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:: 1256039

Alternate ID(s):: OSTI ID: 1513785

Journal Information:: Nature Communications, Vol. 6; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 124 works

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Assessing the influence of soil abiotic and biotic factors on Nostoc commune inoculation success Roncero-Ramos, B.; Román, J. R.; Rodríguez-Caballero, E. Plant and Soil, Vol. 444, Issue 1-2 https://doi.org/10.1007/s11104-019-04239-y	journal	August 2019
Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling Garcia, Joshua; Kao-Kniffin, Jenny Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01516	journal	July 2018
Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest Lee, Tae Kwon; Han, Il; Kim, Min Sung Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01858	journal	August 2019
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas Frainay, Clément; Schymanski, Emma; Neumann, Steffen Metabolites, Vol. 8, Issue 3 https://doi.org/10.3390/metabo8030051	journal	September 2018
Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe Roncero-Ramos, Beatriz; Muñoz-Martín, M. Ángeles; Chamizo, Sonia PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6169	journal	January 2019
Biofilms 2018: a Diversity of Microbes and Mechanisms Fuqua, Clay; Filloux, Alain; Ghigo, Jean-Marc Journal of Bacteriology, Vol. 201, Issue 18 https://doi.org/10.1128/jb.00118-19	journal	February 2019
Learning representations of microbe–metabolite interactions Morton, James T.; Aksenov, Alexander A.; Nothias, Louis Felix Nature Methods, Vol. 16, Issue 12 https://doi.org/10.1038/s41592-019-0616-3	journal	November 2019
Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow Ponomarova, Olga; Gabrielli, Natalia; Sévin, Daniel C. Cell Systems, Vol. 5, Issue 4 https://doi.org/10.1016/j.cels.2017.09.002	journal	October 2017
Patterns and Controls on Nitrogen Cycling of Biological Soil Crusts Barger, Nichole N.; Weber, Bettina; Garcia-Pichel, Ferran Biological Soil Crusts: An Organizing Principle in Drylands https://doi.org/10.1007/978-3-319-30214-0_14	book	January 2016