Soils are physically, chemically, and morphologically complex at microscopic scales. Bacterial and fungal communities in soils, likewise, display extreme micro-heterogeneity. This dissertation explores deeper consideration of microscale soil context in studying microbial biogeography. I begin with the assumption that microbial communities are structured by their physical habitats -- microscale soil pores -- and that soil conditions that influence pore size, shape, and connectivity may be significant predictors of microbial communities and interactions at landscape scale. Further, that consideration of microbial traits related to the way they physically navigate soil pores (filamentous growth form, flagellate motility) may predict their individual and collective responses to changes in the soil environment. In my first chapter, I surveyed bacterial and fungal biomass and communities across a landscape with diverse soil characteristics and plant communities. I found that community structures of unicellular and filamentous fungi and bacteria were correlated with distinct soil and plant factors. These communities were sampled from pooled, sieved soils, as is common in microbial ecology. In my second chapter, I investigated the effect of sieving soil samples on patterns of bacterial and fungal biogeography, and the detection and strength of microbial interactions. Sampling microbial communities in individual aggregates revealed distinct distance-decay relationships between fungi and bacteria, and between different bacterial genera. Further, network analysis of soil aggregates revealed distinct positive associations between members of specific fungal genera and putative fungal-mutualist bacteria from genus Burkholderia compared to sieved soil. These bacterial-fungal interactions might be mediated by environmental context, especially degree and frequency of soil saturation. Specifically, flagellate soil bacteria may move along water films surrounding fungal hyphae, exploiting 'fungal highways' to bypass air-filled pores. In my third chapter, I tested the fungal highway mechanism by culturing diverse flagellate bacteria and filamentous fungi from sediment, co-culturing a selected pair in saturated and unsaturated sand, and measuring their distribution and biomass in relationship to each other. The bacterium benefited from exploitation of fungal highways in unsaturated -- but not saturated -- soil media. By investigating the impact of soil morphology on microbial biogeography and interactions, my dissertation shows the potential utility of soil pore-scale considerations in reducing the noise of a seemingly intractably complex system.  [link to publication]