Date of Graduation


Document Type


Degree Type



Eberly College of Arts and Sciences



Committee Chair

Timothy Driscoll

Committee Co-Chair

Charlene Kelly

Committee Member

Mary Beth Adams

Committee Member

Zachary Freedman

Committee Member

Edward Brzostek


Many forest ecosystems have been receiving elevated nitrogen (N) deposition due to human activity. Increased ecosystem N threatens soil fertility, water and air quality, and modifies the soil microbially-mediated N cycle in complex ways. The current study investigates how the abundance of key functional N cycling genes within soil bacteria is altered by N deposition and further mediated by different dominant tree species at the Fernow Experimental Forest, WV. Soils were analyzed from two watersheds, where watershed 3 (WS 3) has been receiving experimental applications of N fertilizer that are 2x historic ambient N deposition and 5x the current ambient N deposition, relative to a reference watershed (WS 7). Abundance of four N cycling functional genes responsible for nitrate (NO3-) and nitrous oxide (N2O) production (amoA, nirK, nirS, nosZ) were targeted for quantification using qPCR. We hypothesized that the abundance of these N cycling functional genes would be significantly different in soils influenced by elevated N deposition. It was expected that the abundance of genes would reflect the production of NO3- and N2O from soils, measured as soil nitrate content and potential denitrification production from soil samples from beneath four individual tree species (tulip poplar, sweet birch, black cherry, and northern red oak). These tree species represent two mycorrhizal fungal associations (arbuscular and ectomycorrhizal); thus, we also tested whether functional gene abundance can be predicted by mycorrhizal association. It was expected that nitrification would be greatest in WS 3 and beneath arbuscular mycorrhizal trees because AM-associated trees sometimes have relatively more rapid litter decomposition leading to greater N losses than ECM associated tree species. Greater N2O production was also expected in WS 3 due to the acidified soil altering the microbial capacity to reduce N2O to N2 gas. Soil beneath black cherry, an AM-associated species, contained significantly more NH4+ within WS 3. Fertilization has altered gene abundance in WS 3, leading to reduced nirK and nosZ abundance. Tree species did not influence gene abundance in either watershed, although AM-associated trees demonstrated reduced nirK abundance in WS 3. Soil beneath black cherry trees had reduced nirK and nosZ abundance as well as altered nitrification of NH4+ in WS 3, indicating that soils beneath black cherry trees may have altered N processing under fertilization. The reduction of functional gene abundance was not correlated with N transforming processes in either watershed. Gene abundance is not a strong predictor of N transforming rates in this study. Future research of the microbial community, paired with enzymatic activity, will enable better understanding of relationships between structure and function of the microbial community on N cycling processes.