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Nat Commun. 2015 Sep 22;6:8289. doi: 10.1038/ncomms9289.

Exometabolite niche partitioning among sympatric soil bacteria.

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Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, USA.
Climate and Ecosystems Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, USA.
Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California 94720, USA.
School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, Arizona 85287, USA.
Molecular Cell Physiology Department, Faculty of Earth and Life Sciences, VU Amsterdam, de Boelelaan 1085, 1081HV Amsterdam, The Netherlands.
DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California 94598, USA.


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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