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This is a pivotal time for environmental microbiology. Black box microbially-mediated processes are being pried open by culture-independent techniques that can identify who is responsible for a process and expose the molecular underpinnings of the process. A good case in point is Enhanced Biological Phosphorus Removal (EBPR). Classical culture-based microbiology set researchers off on a 30 year wild goose chase of the wrong organism, then culture-independent methods within a 10 year period identified the real primary agents of the process and metagenomics provided the blue prints of the key metabolic pathways involved in EBPR. Today, instead of 10 years, molecular characterization of microbial community processes can be compressed into a couple of years and should soon include spatial and temporal organization and genome-based predictive models. We propose to characterize important microbially-driven processes using the full ecogenomics toolkit (see key capabilities).