Identifying ecological differentiation in microbial communities across taxonomic scales

Microbial diversity, both genetic and phenotypic, is a product of evolutionary and ecological processes interacting at multiple levels of biological organization. High-throughput sequencing is providing a means to resolve the vast amount of genetic diversity in microbial assemblages. However, a current fundamental challenge is associating genetic diversity, whether at the community or population scale, to phenotypic variation that defines ecological roles and dictates how microbial community diversity and ecosystem functioning respond to environmental change. In this body of work, I have used sequencing-based techniques to identify ecological differentiation at taxonomic scales ranging from a whole bacterial community to a single population of methanogenic archaea. At the broadest taxonomic scale, I used a whole-ecosystem disturbance along with 16S rRNA 454-pyrosequencing to identify ecologically relevant distinctions among taxonomic groups defined at various taxonomic scales. The findings showed that bacterial lineages require different taxonomic definitions to capture ecological patterns. At a more refined taxonomic breadth, I used a culture-independent approach to elucidate how methanogen community diversity was distributed within and between a set of freshwater lakes and also identified the ecological processes dictating this spatial distribution of diversity. Finally, at the highest resolution, I employed a comparative genomics approach to identify genomic signals of adaptive evolution in a Methanosarcina mazei population in order to link genetic variation to the ecological processes that define spatial and temporal distributions of methanogen populations. Together, this work has helped to resolve the interdependencies between genetic diversity and ecological processes, which concomitantly act to create and maintain microbial diversity across time and space