Nitrogen (N) is the major limiting nutrient in many cropping systems worldwide. In many farming systems and especially in low input, subsistence systems, biological nitrogen fixation serves as the main N source . This study investigates the effect of different agronomic practices including tillage (no-till and tilled), cover crops,  and N fertilization on the population sizes of N cycling bacteria (free living diazotrophs and ammonia oxidizing bacteria) at Jackson, Tennessee. The experiment is  a split split-plot factorial with nitrogen as a whole plot, cover cropping as split plot and tillage as the split-split plot. Real time quantitative polymerase chain reaction (qPCR) will be used to determine the population sizes of these bacterial groups using their functional genes (nifH for diazotrophs and amoA for ammonia oxidizing bacteria) as a target for qPCR primers. Coupled to this objective will be the assessment of net nitrification rates determined through undisturbed soil cores and ion exchange resins to correlate it with the population dynamics of ammonia oxidizing bacteria. There will be four sampling times over the growing season: at planting, flowering, bolling and after harvest. Results from this study will serve as a basis for identifying which management practices promote the diversity and abundance of these beneficial and functional groups of bacteria as they play a vital role in the nutrients (nitrogen) cycling and availability.