Journal
FEMS MICROBIOLOGY REVIEWS
Volume 37, Issue 6, Pages 936-954Publisher
OXFORD UNIV PRESS
DOI: 10.1111/1574-6976.12023
Keywords
biodiversity; soil heterogeneity; bacterial interactions; microcosm experimentation; soil ecology; soil imaging
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Funding
- Vici grant of GAK from the Dutch Science Foundation (NWO)
- European Regional Development Fund
- European Social Fund Convergence Programme for Cornwall
- Isles of Scilly
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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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