Despite our ability to characterize diverse microbial communities, we currently lack the capability to identify the mechanisms affecting a given taxon’s response to environmental conditions and its functional consequence. This problem partly stems from the common practice of characterizing microbial communities using conserved marker genes, such as the 16S rRNA region, which mask ecologically-relevant genetic and phenotypic variation. For example, most microbial studies that target the 16S rRNA region, cluster similar sequences into operational taxonomic units (OTUs) that represents millions of years of evolutionary history. My work has explored how much genetic variation may exist within these OTU designations and identified how genetic variation corresponds to phenotypic variation (overview in Chapter 1). Overall, I have focused on the ecological and evolutionary mechanisms driving environmental niche partitioning and speciation within a bacterial taxon to link genotypic variation to functional roles.

Utilizing an abundant soil bacterium, Curtobacterium, I have demonstrated that isolates within this Actinobacteria genus harbored extensive genomic diversity within a single OTU (Chapter 2) that reflected large phenotypic variation even within a single field site. Using extensive isolation efforts with the integration of genomic and metagenomic data, I have identified distinct genomic clusters that would otherwise be masked by traditional microbial analyses (Chapter 3). Further, this vast genomic diversity corresponded to distinct phenotypes denoting fine-scale niche partitioning and the emergence of bacterial ecological populations along a regional climate gradient (Chapter 4). While ecological variation may drive large-scale geographic distributions, the evolutionary mechanisms contributing to microbial speciation and diversity have remained elusive. Selection can drive microbial speciation and later divergence due to barriers to gene flow or mutational adaptations. By analyzing ecologically-similar strains, I demonstrated that Curtobacterium isolates are diverging into independent populations in a heterogeneous soil system (Chapter 5). In conclusion, my research has provided evidence that ecological and evolutionary processes both contribute to the response of bacteria to environmental conditions.