Long-term sustainable biofuels production with the concomitant protection and improvement of air, soil and water resources requires a concerted effort by the scientific community to gain knowledge regarding the comparative production potentials and environmental impacts of biofuel cropping systems. U.S. agriculture has extensive experience with intensive maize production and much recent discussion on energy from plants has focused on simply repurposing the existing farming systems towards ethanol instead of or in addition to animal feed. Both the grain and the stover can be used in energy production but removing the majority of the aboveground biomass from a farm field may negatively impact air, soil, and water quality. Alternative annuals, herbaceous perennials including novel species such as Miscanthus imported from Europe and low-input native systems may offer key advantages over maize production. Farmers can use existing farm equipment and these systems are expected to require far fewer energy and financial inputs than maize. However, at present, research on N and C cycling in these candidate biomass systems is fragmented and incomplete, a critical barrier to profitable, sustainable, and environmentally benign on-farm implementation of the U.S. biofuel agenda. Likewise, understanding crop water balance and optimizing water use efficiency will be essential to renewable biofuel success as water is expected to be the single, most limiting factor that transcends the multiple agro-ecozones in which U.S. biofuel production will be pursued. Accompanying this field experimentation will be the creation of a model repository and cyberinfrastructure that provide for curation of a wide variety of data such that archived data can be preserved, retrieved, understood, and accurately repurposed in a user environment that facilitates data mining, integration, and synthesis of disparate datasets. Project results will provide critical baseline knowledge regarding the relevant production and environmental merits of candidate biofuel systems, knowledge also necessary for valid, model-based food and fuel projections and development of informed public policy.