Bio fuels will occupy an important acreage of worldwide production in the future. Some land will come from agriculture, and some will be from soils not now intensively cultivated. Since this is a new venture, it is imperative that we, as scientists, strive to ensure that this is done in the most environmentally friendly manner. We need to ensure that there is net C sequestration in the soil, a minimum of applied chemicals, no soil erosion and maximum ecosystem sustainability. This will include both wildlife and societal benefits involving effects on the landscape and bio diversity. Nitrogen must be an important planning-research component. There should be a closed N cycle that involves no loss of radiative N gases to the atmosphere, no leaching of N to groundwater and a closed cycle of movement of nutrients from the field to the processing plant back to the field to maximize nutrient efficiency. Our own studies with Miscanthus and switchgrass in Illinois show deep rooting of the Miscanthus, which has three to four times the production capacity of switchgrass. This produces sequestered C at depth and appears to mine mineral soil N from depth in former agricultural fields. Extended laboratory incubations and measurement of CO₂ fluxes show a build up of the active and slow pool of carbon with an associated increase in soil N pools. Pyrolysis molecular beam mass spectrometry shows unique chemical soil constituents in the tested Miscanthus, switchgrass, and associated soybean fields and may be useful in measuring root production.