Agriculture significantly impacts the global carbon (C) and nitrogen (N) cycles through land use change, soil C loss, greenhouse gas emissions, and increased fixed-N availability. Agriculture occupies a third of the terrestrial biosphere, making understanding its impacts on the C and N cycles critical. I used a novel analytical tool (solid-state 13 C nuclear magnetic resonance spectroscopy) to characterize properties of the C and N cycles in agriculture, including biochemical responses to N fertilizer and agriculture gas fluxes. A central component of the C cycle is the rapid exchange of carbon dioxide (CO 2 ) and oxygen (O 2 ) between the terrestrial biosphere and the atmosphere. Gas flux O 2 /CO 2 ratios (oxidative ratio-OR) vary depending on ecosystem type, plant species, and nutrient status. It is necessary to constrain OR to assess the uptake of anthropogenic CO 2 by the terrestrial biosphere and ocean. I measured the OR of the top three crops in the United States (soybean, corn, and wheat) and found significant variability. I additionally tested the effect of N fertilizer application on corn ecosystem OR and on the difference between respiration and photosynthesis OR and observed no detectable changes. Conversely, soil organic matter OR is different from gas flux OR values, likely due to the influence of past land use and fractionation of OR during decomposition. I also analyzed how anthropogenic inputs to the N cycle (N fertilizer) and sustainable agriculture practices (cover crop) change plant biochemistry. This work has immediate implications for the biofuel industry. A central challenge to cropping for cellulosic ethanol feedstocks is the potential environmental damage from increased fertilizer use. I showed that yield increases in response to fertilization are not uniform across biochemical classes (carbohydrate, protein, lipid, lignin) or tissues (leaf and stem, grain, reproductive support). Heavy fertilizer application yields minimal grain benefits and almost no benefits in residue carbohydrates, while degrading the cellulosic ethanol feedstock quality and soil C sequestration capacity. Further cost analysis of these results showed that it is not cost-effective for farmers to apply high levels of N fertilizer, whether the crop is intended for food or fuel.