The Farming Systems Project (FSP) in Beltsville, MD. is a long term cropping systems experiment comparing a wide diversity of organic and conventional corn/soybean/wheat production systems. Ecologically, the systems in the FSP represent a gradient of disturbance and plant species diversity and encompass conventional tillage, no-tillage and a range of Organic production practices. We have recently shown that in farming systems with linked carbon and nitrogen inputs (green and animal manures, e.g. Organic systems) soil nitrogen mineralization rates and carbon use efficiency are higher than in conventional tillage, no-tillage systems. What is still unknown is whether the nitrogen liberated during mineralization is re-immobilized by microbes and plants or if it is lost from the system through denitrification and leaching. Determination of the fate of mineralized nitrogen on annual cycles, across this diversity of farming systems is critical for understanding how land management influences agricultural nitrogen use efficiency. We determined the denitrification potential and gene diversity of nirK, nirS and nosZ across farming systems using a combination of quantitive PCR, targeted gene cloning and sequencing. Analysis of functional diversity of the microbial community was coupled with in field greenhouse gas sampling twice a month. Farming systems varied in denitrification potential, in general organic systems showed greater denitrification potential as determined by quantity of nirK, nirS and nosZ copy number. Although denitrification potential did not always result in higher greenhouse gas flux as determined by empirical field measurements. We using this data to develop models that consider soil biogeochemical and physical conditions as well as the functional diversity of soil microbial comminutes to better understand agricultural greenhouse warming potential and nitrogen use efficiency.