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Exometabolite niche partitioning among sympatric soil bacteria

Author

Listed:
  • Richard Baran

    (Lawrence Berkeley National Laboratory)

  • Eoin L. Brodie

    (Lawrence Berkeley National Laboratory
    Policy and Management, University of California Berkeley)

  • Jazmine Mayberry-Lewis

    (Lawrence Berkeley National Laboratory
    School of Life Sciences, Arizona State University)

  • Eric Hummel

    (School of Life Sciences, Arizona State University)

  • Ulisses Nunes Da Rocha

    (Lawrence Berkeley National Laboratory
    Faculty of Earth and Life Sciences, VU Amsterdam)

  • Romy Chakraborty

    (Lawrence Berkeley National Laboratory)

  • Benjamin P. Bowen

    (Lawrence Berkeley National Laboratory
    DOE Joint Genome Institute)

  • Ulas Karaoz

    (Lawrence Berkeley National Laboratory)

  • Hinsby Cadillo-Quiroz

    (School of Life Sciences, Arizona State University)

  • Ferran Garcia-Pichel

    (School of Life Sciences, Arizona State University)

  • Trent R. Northen

    (Lawrence Berkeley National Laboratory
    DOE Joint Genome Institute)

Abstract

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.

Suggested Citation

  • Richard Baran & Eoin L. Brodie & Jazmine Mayberry-Lewis & Eric Hummel & Ulisses Nunes Da Rocha & Romy Chakraborty & Benjamin P. Bowen & Ulas Karaoz & Hinsby Cadillo-Quiroz & Ferran Garcia-Pichel & Tre, 2015. "Exometabolite niche partitioning among sympatric soil bacteria," Nature Communications, Nature, vol. 6(1), pages 1-9, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9289
    DOI: 10.1038/ncomms9289
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    Cited by:

    1. Sarah McLaughlin & Kateryna Zhalnina & Suzanne Kosina & Trent R. Northen & Joelle Sasse, 2023. "The core metabolome and root exudation dynamics of three phylogenetically distinct plant species," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Stefanie Imminger & Dimitri V. Meier & Arno Schintlmeister & Anton Legin & Jörg Schnecker & Andreas Richter & Osnat Gillor & Stephanie A. Eichorst & Dagmar Woebken, 2024. "Survival and rapid resuscitation permit limited productivity in desert microbial communities," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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