Date of Graduation


Document Type


Degree Type



Davis College of Agriculture, Natural Resources and Design



Committee Chair

Alan Sexstone


The effect of compost amendment on nitrification rates and ammonia-oxidizing microorganisms in an agricultural soil was examined. Four different rates from 11.2 to 89.6 Mg compost ha-1 of partially composted dairy manure was applied annually from 2000 to 2003 and again in 2005 to 32 plots on a Dormont silt loam that was shifted from long term pasture to crop cultivation. An additional 8 plots were not amended with compost and served as negative controls. Except for lime in the initial year of the experiment, no other fertilizer was used on these plots. Soil physical, chemical, and biochemical measurements were taken from 4 randomly chosen replicate plots of each treatment. Additionally, T-RFLP was used to fingerprint the community of bacteria and archaea responsible for the process of ammonia oxidation using the amoA gene. Extracted DNA concentration and potentially mineralizable nitrogen both significantly increased with increasing rates of compost amendment. There were significant positive correlations between potential ammonia oxidation and potentially mineralizable nitrogen, extracted DNA concentration and potentially mineralizable nitrogen, and extracted DNA and microbial biomass carbon in these plots. Many relationships were stronger when only the three lowest treatments were analyzed. Diversity measures generally did not show strong relationships with compost amendment rates, but there were significant correlations with biochemical variables. Ammonia-oxidizing archaeal (AOA) Shannon diversity and richness negatively correlated with the microbial biomass carbon pool size. Ammonia-oxidizing bacterial (AOB) Shannon evenness and Smith and Wilson evenness negatively correlated with potentially mineralizable nitrogen rate. Analysis of similarity showed that AOB communities with similar rates of nitrogen mineralization were more similar in community composition than would be predicted by chance alone. Nonmetric multidimensional scaling analysis showed that both AOA and AOB communities had nonlinear differences in community similarity based on compost amendment rate. AOA community similarity had a linear relationship with microbial biomass carbon and a nonlinear relationship with potentially mineralizable nitrogen. AOB community similarity had a linear relationship with both potentially mineralizable nitrogen and potential ammonia oxidation, and a weak nonlinear relationship with microbial biomass carbon. Linearity suggests a direct relationship between the two variables, while nonlinearity suggests an indirect relationship between the two variables. This evidence suggests that there is a difference in the ecological niches of the AOA and AOB, with AOB primarily responsible for ammonia oxidation in these plots.