- Physiology and metabolism of anaerobic bacteria (e.g., anaerobic hydrocarbon degradation via benzylsuccinate synthase; nitrate-dependent metabolism in chemolithoautotrophic bacteria; biotransformation of contaminants like chromate and the high-explosive RDX),
- Exploration of bacterial metabolic diversity through enzyme discovery [e.g., a novel glycyl radical enzyme that catalyzes anaerobic toluene biosynthesis; novel c-type cytochromes that catalyze nitrate-dependent U(IV) oxidation],
- Metagenomic and metatranscriptomic studies of subsurface biogeochemical cycling,
- Design and engineering of novel biofuel pathways in model and non-model bacteria,
- Development of mass spectrometric and biomolecular techniques to document in situ metabolism.