Soil microorganisms are largely responsible for biogeochemical fluxes in the terrestrial biosphere that effect ecosystem productivity and alter global climate patterns. Though the importance of soil microorganisms is easy to state, little is known about interactions between microbes necessary for the production of ecosystem-scale fluxes. Furthermore, measurement of biogeochemical fluxes at the scale of microorganisms or ecosystems is far from straightforward; the lack of understanding regarding linkages between these two scales (microbial habitat and ecosystem) remains as an important knowledge gap in ecology. For my dissertation I focused on studying microbial communities among soil aggregates, aggregate-scale fluxes of soil carbon, and the scaling of greenhouse gas fluxes from single measurements to ecosystem-level experiments in order to understand how agriculture alters microbially driven biogeochemical fluxes. In the following chapters I did not attempt to find a direct link between particular microorganisms and a specific flux; rather I aimed to fill this knowledge gap regarding linkages between microbes and ecosystems in order to inform models predicting microbial and ecosystem-scale function. My dissertation is broken into four chapters: exploring potential microbial interactions across ecosystems, observing differences in microbial communities within aggregates from bioenergy cropping systems, and the scaling of carbon fluxes and greenhouse gas emissions from small scales (i.e., aggregates or square meter) to ecosystem scales. The main conclusions drawn from these chapters are that our understanding of soil microbes and terrestrial fluxes of carbon must begin at the aggregate-scale rather than whole soil, and understanding uncertainty about fluxes, whether it be soil carbon or greenhouse gases, is necessary for agroecosystem ecology. By taking care to sample microorganisms at the scale of soil aggregates and addressing the uncertainty around biogeochemical fluxes measured at larger, ecosystem scales, we may begin to finally design testable models that explain both microbial and ecosystem functioning in order to understand the effects of land-use and climate change on the terrestrial biosphere.