The Environmental Remediation & Water Resources Program's bioenergy research, which is primarily sponsored by the BP Energy Bioscience Institute and by the DOE JBEI Bioenergy Center, focuses on improving the understanding of microbial genomics associated with biofuels and enhanced oil recovery and investigating feedbacks between long term biomass production and ecosystem processes. Research advances are needed along many fronts to efficiently and sustainably harness the potential of bioenergy as a transportation fuel.