The structure of microbial communities, shaped by local biotic and abiotic environments, plays a critical role in both ecosystem function and the health of human, agricultural, and natural populations. These communities act as particularly complex networks, with high levels of horizontal gene transfer and multifaceted antagonistic interactions among species. A key challenge is to understand how microbial communities are influenced by interactions with both eukaryotes and viral parasites (bacteriophages), and vice versa. More broadly microbial communities are excellent, tractable model systems with large population sizes and short generations for examining fundamental general problems in evolution and ecology. My approach is to combine studies of natural populations with experimental evolution, both in vitro and in vivo, to examine the trajectory of (co)evolution from the individual population to the community level. In this talk, I first examine the relevant ecological structure of bacteriophage adaptation in natural phyllosphere communities, then present data on the specificity of these natural phages and the potential consequences of phage-mediated selection on bacterial adaptation to plant hosts, and finally explore the importance of historical contingency in shaping fitness trade-offs. I will also discuss my plans to broaden this research to more complex networks and to address the importance, or lack thereof, of specific interactions among species within these networks.