UC Riverside

Understanding patterns of genotypic abundance and spatial spread is a fundamental objective in studying critically important bacterial strains. Many clinically and agriculturally relevant strains are host-associated, forming either pathogenic or mutualistic symbioses with crops, livestock and humans. Many of these relationships are facilitated by the acquisition of horizontally transferred genomic islands that encompass genes necessary (or beneficial) for association with a host. Genomic islands have been implicated in the clinical epidemic spread of pathogenic strains. However, the impact of genomic islands on natural populations of bacteria has not been well studied.

The legume-rhizobia mutualism is a particularly well studied symbiosis mediated by the acquisition of plasmids or genomic islands and this dissertation research focused on Bradyrhizobium, the most cosmopolitan rhizobial lineage. Like all rhizobia, Bradyrhizobium, exhibit a bipartite lifestyle and the genome reflects this with upregulation in the genomic (symbiosis) island when within a host and upregulation in the rest of the genome (chromosome) when free-living in the soil. Thus, the evolutionary drivers of each lifestyle can be studied through the analysis of their respective genome region.

To examine the effect of symbiosis island acquisition on Bradyrhizobium abundance and spatial spread, the distributions of symbiotic and non-symbiotic Bradyrhizobium were compared. No support was found for an evolutionary association between symbiosis island gain and greater abundance or spatial spread. The frequencies of particular symbiosis island and chromosome genotypes were analyzed in order to examine the role of the host plant versus the soil in structuring Bradyrhizobium populations. Chromosome genotypes exhibited high abundance and spatial spread while symbiosis island genotypes did not. These results taken together suggest that competition within the soil, as opposed to selection by the host plant, is the major driver of population structure.

Antibiotic resistance is a pervasive problem in host-associated pathogens. However, these traits are ancient in environmental populations, where antibiotics are thought to be relevant to intermicrobial communication and conflict. In order to test the degree to which natural populations select for antibiotic resistance, Bradyrhizobium were tested for antibiotic resistance to 17 antibiotics. Resistance traits to all but one antibiotic were recovered and multidrug resistance was ubiquitous.