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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING ALFALFA AND OTHER FORAGE CROPS FOR BIOENERGY, LIVESTOCK PRODUCTION, AND ENVIRONMENTAL PROTECTION

Location: Plant Science Research

Title: Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities

Authors
item Schlatter, Daniel -
item Samac, Deborah
item Tesfaye, Mesfin -
item Kinkel, Linda -

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 6, 2010
Publication Date: March 4, 2010
Repository URL: http://hdl.handle.net/10113/39338
Citation: Schlatter, D.C., Samac, D.A., Tesfaye, M., Kinkel, L.L. 2010. Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities. Applied and Environmental Microbiology. 76(6):2009-2012.

Interpretive Summary: Soils support a multitude of diverse microorganisms with the capacity to produce a wide range of compounds that influence plant growth. These compounds may also influence the microbial communities; however, measuring microbial interactions in soil is difficult to do because of the difficulty in identifying and tracking specific organisms. A method was developed to specifically measure populations of two soil bacteria, a plant pathogen causing potato scab and a related nonpathogenic species that produces antimicrobial compounds. The assay is highly sensitive and specific for measuring the population of each species in a natural soil. When present at lower densities, the two strains appear to compete. The population of the plant pathogen decreased over time. At higher densities the two strains did not differ in population dynamics over time. This assay will be useful in understanding how different agricultural practices influence microbial populations that in turn affect crops and crop productivity.

Technical Abstract: Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative real-time PCR (qPCR) offers a rapid and specific means to assess populations of target microorganisms. SYBR Green and TaqMan-based qPCR assays were developed for quantifying Streptomyces scabies and S. lavendulae strains using primers targeting polymorphisms in the gamma hypervariable region of the 16S rRNA gene. The TaqMan assay was more sensitive than the SYBR Green assay for detecting purified genomic DNA as well as for quantifying strains in native soil. For both strains the lower limit of detection with the TaqMan assay was 0.01 pg genomic DNA and the assay was linear to 10 ng input DNA. The lower detection limit for strains in native soil with the TaqMan assay was 102 colony-forming units/g soil. The utility of qPCR TaqMan assay to accurately and rapidly quantify S. scabies and S. lavenduale strains inoculated together in complex soil communities is demonstrated. This assay will be useful for evaluating the competitive dynamics of Streptomycetes in soil.

Last Modified: 7/28/2014
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