THE ROLE OF SPATIAL SCALES IN BIOGEOGRAPHY AND EVOLUTION OF SOIL-BORNE STREPTOMYCES

136 pagesSoil microbes are critical to the sustenance of several nutrient cycles, communities of soil fauna, and ecosystem resilience and stability. Microbial biogeography allows us to understand how communities form and change over evolutionary time. My dissertation investigates the biogeography and population dynamics of soil bacteria using the genus Streptomyces as a model system. Streptomyces form long hyphae, have desiccation-resistant spores, and produce versatile biosynthetic products. Taken together, these traits aid in nutrient acquisition, growth, and competitive ability, and collectively improve their dispersal. In this dissertation, I assess the impact of environmental gradients and geographical separation on Streptomyces community assembly, horizontal gene transfer events, and population differentiation. A combination of amplicon sequencing and comparative genome analyses show that dispersal limitation occurs at local, regional, and continental scales, and is caused by both barriers to dissemination (such as elevation and distance) and inability to establish a population in a new habitat due to local biological conditions. Horizontal gene transfer (HGT) also emerges as an important evolutionary force shaping Streptomyces genomes. Bacterial populations that migrate to new locations show still show evidence of gene flow with their allopatric relatives. Recombination acts as a cohesive force that increases genetic similarity within closely related groups of bacteria, and genes involved in amino acid production, vitamin utilization, and biosynthesis of secondary metabolites are frequently transferred within sympatric strains. Phylogroup-specific actinophage signatures were found in Streptomyces genomes, suggesting that transduction might be an important mechanism of HGT in the environment. The third chapter shows that migration to a new habitat can increase nucleotide-level diversity between conspecific strains even while high gene flow maintains their genetic cohesiveness well above the bacterial species boundary. Finally, the last chapter details the isolation and description of a novel species of soil Streptomyces, Streptomyces apricus. This research expands our understanding of soil microbial ecology and evolution by quantifying the impacts of space and time on bacterial communities. As climates and landscapes change, studying changes in gene content in microbial communities is crucial to understanding how soil ecosystems can be best managed for sustainability and productivity.2023-09-0