Microbial communities provide an excellent study system to explore the integration of ecology and evolution. At one end of the spectrum, the composition of microbial communities (assessed at broad taxonomic levels) dramatically shifts in response to environmental changes. At the other end, laboratory studies demonstrate the potential for rapid evolution in response to the similar environmental changes. In between these two extremes, very closely related bacterial and fungal strains coexist in natural communities, and this standing variation results in allele frequency shifts within microbial taxa. New advances in microbial population genomics allow us to investigate these blurry eco-evo boundaries. I will present our recent approaches to investigate ecological and evolutionary processes simultaneously in soil microbial communities and solicit feedback about new directions.