Microbial communities are at the heart of important ecosystem functions such as decomposition and the mineralization of nutrients. Thus, understanding the factors that shape the spatial distribution of microbial communities is important in order to predict the ecosystem services they support and biogeochemical feedbacks to climate change. Both edaphic factors and plants shape microbial communities, yet the integrated influence of these factors on microbial community dynamics is largely unknown. The goal of this research was to quantify how edaphic conditions affect microbial abundance, composition and diversity and subsequent changes in microbial activity under different cropping systems. To address this goal, I conducted studies at the Landscape Biomass Project, Boone County, IA, using an annual (continuous corn) and perennial (switchgrass) cropping systems replicated at three landscape positions along a topographic gradient. In addition, I investigated the effect of land use on variation in microbial variables along a transect across a cultivated corn field and an uncultivated switchgrass monoculture.

Cropping system was found to be a stronger driver of microbial diversity and activity than landscape position, with consequences for rates of decomposition. In contrast, microbial community abundance and composition were most strongly shaped by landscape position. This disparity between drivers of microbial communities and activity suggests an important, but often overlooked, temporal component to our predictions of microbial parameters - where the soil environment over longer temporal scales shapes community membership and shorter temporal dynamics associated with plants shape a small but consistent group of microbes and community activity. Spatial modeling using wavelet analysis indicated microbial communities and enzyme activity were structured by fine-scale environmental heterogeneity, both within and across land use. We also detected a distinct signature of homogenization of microbial communities and stochastic community assembly in the cultivated soil. Correlations between microbial communities and enzyme activity revealed scale-specific relationships, suggesting the importance of microbial abundance to nitrogen and phosphorus cycling enzymes and microbial community structure to carbon cycling enzymes. Results highlight the importance of scale to understanding the biological mechanisms regulating ecosystem functions, which has implications for predicting biogeochemical cycling.