Local factors have the potential to generate genetic structure within species if populations respond differently to varying environmental conditions across their geographic range. In this project, spatial genetic structure was examined in the legume, Chamaecrista fasciculata, its symbiotic nitrogen fixing bacteria, and rhizosphere microbiomes. In the first chapter, the aim was to test for genetic structure among populations of C. fasciculata in the Southeast and to evaluate whether phenotypic variation in leaf pubescence is associated with genetic divergence among populations, which would be consistent with local adaptation. My results did not detect a significant association between genetic structure and phenotypic variation in leaf pubescence, but the role of environmental variables in generating the observed patterns of spatial genetic variation in C. fasciculata was demonstrated. In the second project, I analyzed genetic structure within a single population to test for the presence of fine-scale genetic structure of the host plant and to determine if genetic structure of symbiotic nitrogenixing rhizobia is influenced by host plants. Neighboring plants are expected to be more genetically similar than distant plants. If this expectation is supported and genotype x genotype interactions are important in this system, then I anticipated that spatially close host plants would show more genetically similar microbiota in their nodules and rhizospheric soil than distant host plants. The results indicated fine-scale genetic structure for both host plants and nodulating rhizobia, suggesting that the both organisms are influenced by similar mechanisms structuring genetic diversity or shared habitat preferences. In the third project, I characterized fine-scale structure and diversity of microbial communities of the rhizosphere of host plants within a single population. The results revealed significant differences in bacterial and fungal communities among host plants and a significant association between genetic distance of both microbial communities and spatial and plant genetic distances. These data confirm the importance of plant genotype and physical distance in shaping the genetic structure and diversity of bacterial and fungal communities of the rhizosphere. Overall, this study enhances our understanding of the degree to which intraspecific genetic variation in plants influences the diversity and structure of soil microbial communities.

The legume-rhizobia relationship is an important symbiosis. Studies have found variation in specificity and the functionality of symbiotic specificity can vary among plants of the same species and among rhizobia, as well as in concert with geographical variation. Here, we examined the diversity and geographic structure of rhizobia nodulating Chamaecrista fasciculata, which grows throughout the east-central U.S. and is symbiotic with Bradyrhizobium species. We investigated the association of geography and soil variables on rhizobial diversity by sampling plant nodules and soil across Mississippi and evaluated variation in rhizobia housed in different nodules of individual plants. Using nifH and truA, we conducted phylogenetic analyses and mantel tests but did not find that geography correlates with genetic diversity. However, soil variables and genetic distance were significantly correlated. Lastly, we found that rhizobia across nodules of the same plant varied substantially. These results contribute to the knowledge of rhizobial assemblages in natural populations.

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Pine rocklands are endangered ecosystems unique to south Florida, the Bahamas and Cuba. As a result of their karstic calcium carbonate­rich soil, these systems are limited in phosphorus and nitrogen, making symbiotic associations critical to plant growth. Four leguminous species (Cajanus cajan, Chamaecrista fasciculata, Tephrosia angustissima, and Abrus precatorious) were used to determine the relationship between rhizobial partners and plant performance, and the symbiosis related gene nifH was amplified to characterize the diversity of rhizobial symbionts. Plants were grown in soils from four different south Florida pine rocklands, and a salinity treatment was added to determine how storm surge and sea level rise could affect this symbiotic relationship. While plant performance and nodulation were highly impacted by soil type, salinity did not represent a significant effect. Phylogenetic analysis determined that all four plant species were found to associate with Bradyrhizobium spp. and no rhizobial shift between salinity treatment and soil type was found.