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Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

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Abstract

Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

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Acknowledgments

Funding for this research was provided by the National Science Foundation through Microbial Observatories project no. 9977907. We thank Jennifer Flor for technical assistance and production of graphics and Elizabeth Brodeen for assistance with 16S sequencing. Mary Brown and Lee Ann Johnson provided support for fingerprint analyses. This paper is a joint contribution from the Plant Science Research Unit, USDA, Agricultural Research Service and the Minnesota Agricultural Experiment Station. Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the USDA, and it does not imply its approval to the exclusion of other products and vendors that might also be suitable.

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  1. A.L. Davelos

    Present address: Department of Biology, The University of Texas-Pan American, 1201 W. University Dr., Edinburg, TX 78541, USA

Authors and Affiliations

  1. Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA

    A.L. Davelos, K. Xiao, D.A. Samac & L.L. Kinkel

  2. USDA-ARS-Plant Science Research Unit, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA

    D.A. Samac

  3. Department of E.P.O. Biology, University of Colorado, Boulder, CO, 80309-0334, USA

    A.P. Martin

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Davelos, A., Xiao, K., Samac, D. et al. Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil. Microb Ecol 48, 601–612 (2004). https://doi.org/10.1007/s00248-004-0031-9

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