Background/Question/Methods Microbes contribute significantly to plant population and community dynamics in natural habitats and agricultural systems, yet relatively little is understood of the factors that structure microbial communities in the rhizosphere. This research explores the hypothesis that long-lived perennial plant species exert significant selection on their associated soil microbial communities, thus creating rhizosphere-characteristic microbial guilds. Studies were conducted on soil microbial communities associated with vigorous and well- established Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants at the Cedar Creek Ecosystem Science Reserve (CCESR) in east-central Minnesota. Bacterial communities from the rhizosphere of 10 plants of each species (n = 20 plants total) were explored using 1) denaturing gradient gel electrophoresis (DGGE) and 2) targeted sequencing of 16S fragments.

Results/Conclusions Results from DGGE experiments on environmental samples were unable to detect phylogenetic differences in rhizosphere microbial communities associated with the two plant species. Moreover, when distinct bacterial clones were combined and the resulting `communities' analyzed using DGGE, communities were not differentiable. These results highlight the significant limitations of low-resolution molecular analyses for characterizing or differentiating complex communities. In contrast, targeted sequencing of 16S clone libraries revealed differences in microbial communities associated with Ag and Lc, though the data are limited by the small sample sizes possible with traditional cloning approaches. The results from these studies emphasize the limitations of current molecular techniques and available databases , and provide a foundation for the development of 16S sequence-based DNA probes for use in building diversity-enriched 16S clone libraries for analysis of soil microbial communities.