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United States Department of Agriculture

Agricultural Research Service

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

Authors
item Davelos, Anita - UNIVERSITY OF MINNESOTA
item Xiao, Kun - UNIVERSITY OF MINNESOTA
item SAMAC, DEBORAH
item Martin, Andrew - UNIVERSITY OF COLORADO
item Kinkel, Linda - UNIVERSITY OF MINNESOTA

Submitted to: Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 1, 2004
Publication Date: December 1, 2004
Citation: Davelos, A.L., Xiao, K., Samac, D.A., Martin, A.P., Kinkel, L.L. 2004. Spatial variation in Streptomyces genetic composition and diversity in a prairie soil. Microbial Ecology. 48:601-612.

Interpretive Summary: The soil contains highly diverse bacterial communities that affect plant health. One commonly occurring group of soil bacteria is the streptomycetes. These bacteria produce many antibiotics that increase the ability of the streptomycetes to compete for nutrients. In addition, introduction of specific streptomycetes into soil may reduce the number of plant pathogenic organisms and promote plant health. The genetic diversity of streptomycetes was studied in an undisturbed native prairie soil. Colonies were isolated from three locations at four soil depths. The DNA sequence of a gene encoding a portion of the protein synthesis apparatus was obtained for all isolates and used to identify each isolate to the closest known species. Each location varied in the number of streptomycete species. However, at each location, a single species dominated at shallow depths while a diversity of species was found in deeper samples. These results indicate that each location and soil depth exerts different selective pressures to vary the species composition at that location. The repetitive DNA pattern was visualized for each isolate resulting in a DNA fingerprint. Within the same species, many different DNA fingerprints were obtained. DNA fingerprints did not correspond closely to species designations. Each location varied in the number of related isolates. The greatest diversity of isolates by DNA fingerprinting was seen at shallow depths. The large number of DNA fingerprints obtained suggests that the streptomycete chromosome is unstable and is capable of various rearrangements. Understanding the range in diversity and the factors driving diversity of streptomycetes in native soils will aid in developing strategies for using streptomycetes to control plant diseases in agricultural soils. Development of such biological controls will give growers more choices for ecologically sound crop production.

Technical 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 strains isolated from prairie soil among 3 locations and 4 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 square meter). 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.

Last Modified: 8/27/2014
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