The elucidation of how populations of interest interact in a given community and how the community responds to stress and perturbations can provide insight into the interplay between stress pathways and gene networks that help optimize bacterial biochemistry. The goal of the present study was to characterize the responses of bacterial communities at multiple levels of resolution to understand microbial biochemical capacity at DOE waste sites. The field work at the Field Research Center of the U.S. Department of Energy, Oak Ridge, TN, used a field scale denitrifying fluidized bed reactor (FBR) for nitrate treatment of the groundwater and a series of wells to stimulate microbial growth via ethanol for in situ U(VI) immobilization (Wu et al. ES&T 41:5716-5723). Bacterial community dynamics were investigated during the initial start-up of the FBR while those from the groundwater of the wells were studied over a 1.5-yr period. In addition, the physiology and the genome of the isolate, Anaeromyxobacter Fw109-5, from the site were studied to examine its potential role in U(VI) remediation. The subsurface environment was altered via engineering controls during successive phases to better understand strategies that would improve the remediation process. Within this framework, the interrelationship of bacterial communities and geochemistry was studied at different spatial and temporal scales to characterize the ecosystem ecology of an engineered system. Bacterial communities from both FBR and groundwater samples were analyzed via clone libraries of partial SSU rRNA genes. Multivariate analyses were applied to correlate the changes in the bacterial communities to the measured physicochemical parameters. Our results from the field experiments indicated that there was an important interaction between the engineering controls that altered the subsurface geochemistry over time that influenced bacterial population responses. Growth study experiments and genomic analysis also revealed insights to the physiological potential of an iron-reducing isolate, Anaeromyxobacter Fw109-5. The strong associations between particular environmental variables and certain population distributions will provide insights into establishing practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls.