Micro-scale determinants of bacterial diversity in soil

Authors

  • Michiel Vos,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
    Current affiliation:
    1. European Centre for Environment and Human Health, University of Exeter, Penryn, UK
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  • Alexandra B. Wolf,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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  • Sarah J. Jennings,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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  • George A. Kowalchuk

    Corresponding author
    1. Department of Ecological Science, Free University of Amsterdam, Amsterdam, The Netherlands
    2. Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
    • Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Correspondence: George A. Kowalchuk, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Tel.: +31 (0) 302536700; fax: +31 (0) 302534526;

e-mail: g.a.kowalchuk@uu.nl

Abstract

Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity.

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