Cedar Creek Microbial Observatory

Cedar Creek Natural History Area Microbial Observatory

Dr. Linda Kinkel	Cedar Creek LTER
Department of Plant Pathology	University of Minnesota
Genetic and Phenotypic Diversity of Streptomycetes from Prairie Soils

The soil supports a high density and diversity of micro- organisms that perform an amazing array of critical ecosystem functions. Soil microbes are central to nutrient cycling and the decomposition of plant material, and play a significant role in influencing plant health through their abilities to fix nitrogen, cause plant disease, inhibit the development of plant disease, and enhance plant nutrient uptake. Soil microbes exist in a biotically rich environment in which microbial interactions, including resource competition, antibiosis, and parasitism, are hypothesized to be highly significant to fitness.
Streptomycetes *This plate shows 6 Streptomycetes isolated from a soil dilution plate*
In addition, intra- and interspecies communication is believed to have a significant effect on gene expression in many microbes, and can influence a diverse array of microbial functions, including production of antibiotic and wetting agents as well as the initiation of plant infection.
Our work explores the influences of spatial origin, local population and community density, community diversity, microbial nutrient utilization profiles, associated plant species, and carbon and nitrogen inputs on the diversity and intensity of antibiotic activities among soilborne Streptomycetes. In addition, we are evaluating the significance of proximity in soil, genetic relatedness, and nutrient use overlap to predicting the potential for individual Streptomycete isolates to inhibit one another.
Electron micrographs of Streptomycete PonSSII and pathogenic S. scabies isolate Roy.
Finally, we are evaluating the potential effects of different plant species on Streptomycete genetic diversity, whole soil microbial diversity, and Streptomycete phenotype, including both antibiotic activities and nutrient utilization profiles, in prairie soil. Our work strives to develop a comprehensive basis for understanding and predicting the factors that are critical to the generation and maintenance of diversity in antibiotic phenotypes in the soil microbial community, and to identify the relationships between Streptomycete, microbial community, and plant species genetic and phenotypic diversity in prairie soil.
Approach: We developed a small-scale environmental sampler which permits the collection of 12 contiguous soil samples, each of approximately 0.5 g soil. Soil samples were collected at 18 different locations (with 12 contiguous soil samples per location) within a long-term nitrogen input experiment (E001) at Cedar Creek Natural History Area in central Minnesota. Samples have been collected 4 times.
Antibiotic inhibition assays: Each plate has three Streptomycete isolates "dotted" on it, and a fourth isolate (target) spread-plated on top of the dotted isolates. The plate on the right shows three isolates all able to inhibit the target, while the plate on the left shows one isolate inhibiting the target, one partially inhibiting it, and one isolate incapable of inhibiting it.
To date, our work has generated an extensive database of antibiotic activities (including both inhibition and resistance capabilities) for the Streptomycetes from prairie soil, as well as rep-PCR and 16S rRNA data for the Streptomycetes. Further 16S rRNA data for the whole soil microbial community is presently being collected. In addition, nutrient utilization profiles and information on the frequency of interisolate antibiotic induction among Streptomycete isolates are being investigated for a subsample of our Streptomycete collection. We are in the process of developing strategies to make these data available on the web.
Current projects of the Cedar Creek Microbial Observatory Analysis of Streptomycete communities associated with distinct plant species and distinct nitrogen fertilization histories using rep-PCR, 16S rRNA sequencing, antibiotic inhibition profiles, antibiotic resistance profiles, and nutrient utilization abilities. Analysis of soil microbial communities associated with distinct plant species based on 16S rRNA sequencing. Some prairie species we are looking at:

Lithospermum caroliniense
(Hairy Puccoon)

Andropogon gerardii
(Big Bluestem)

Lespedeza capitata
(Round-Headed
Bush-Clover)

Links to the Cedar Creek webpage provide much detail about the prairie plants

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Research supported by the
National Science Foundation
Award #9977907

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