In arid and semi-arid ecosystems, dominant tree species create mosaics of tree-islands and barren plant interspaces that exert pressure on ecosystem processes and offer an opportunity to explore the impact of bacterial communities. We evaluated potential links between soil respiration, N mineralization, and community co-occurrence networks and predicted gene function across three tree island microsites (beneath tree canopies, at the canopy edge, and in interspaces) in a replicated field experiment in thirty-eight woodland sites in the Great Basin Desert in UT, USA. We measured a suite of characteristics relating to the metabolic functional state of communities to improve our interpretation of potential links between function and structure. We found that tree islands were the predominant driver, creating highly complex and connected assemblies of bacterial populations and easily discernible differences in abundance and composition of predicted functional genes. Specifically, communities directly beneath Juniperus and Pinus canopies were comprised of at least 5.2-times more connections between bacterial taxa than present in networks from interspace and edge. Tree island communities included 236 predicted genes with many related to the degradation of polyaromatic or polycyclic compounds, while interspace communities included only 66 predicted genes associated with the decomposition of more labile C substrates. Our results identify that tree islands exert enough pressure to create distinct interactions between bacteria and alter gene expression resulting in changes to ecosystem function.