Date of Award:


Document Type:


Degree Name:

Doctor of Philosophy (PhD)


Plants, Soils, and Climate

Committee Chair(s)

Jeanette M. Norton


Jeanette M. Norton


John M. Stark


Jennifer R. Reeve


Jon Y. takemoto


Paul R. Grossl


The transformations of organic nitrogen to ammonium and nitrate are central processes in the internal soil nitrogen cycle. In most agricultural soils, ammonium is rapidly oxidized to nitrate in the process known as nitrification; often leading to loss of nitrate from the system. Nitrification is mediated by ammonia oxidizing bacteria or archaea, and nitrite oxidizing bacteria. Understanding links between process rates, enzyme activities and the communities of microbes that cycle nitrogen may contribute to sustainable management.

Our main objective was to determine the impacts of contrasting nitrogen management on soil microbial communities, enzyme activities, and functional genes for nitrification and nitrogen mineralization in a Utah agricultural system. Process rates and activities were measured in laboratory potential assays and 15N isotope pool dilution experiments. The abundance and diversity of genes involved in nitrification and nitrogen mineralization were examined using quantitative real-time PCR, pyrosequencing, clone libraries, and metagenomics. Key enzymes and their relevant marker genes included ammonia monooxygenase (amoA), nitrite oxidoreductase (nxrB), protease (npr and sub), chitinase (chiA), and urease (ureC). The overall soil microbial community composition was assessed targeting ribosomal genes.

Ammonia oxidizing bacteria were more responsive than archaea to ammonium fertilizers while the archaea were competitive under low ammonium levels. The relative contribution of ammonia oxidizing archaea to nitrification increased with increasing temperature and their activity had a higher temperature optimum than bacteria. The abundance of ammonia oxidizers in the organic farming system increased with organic nitrogen fertilizers and their activity was higher in manure than in compost treated soil. Nitrogen fertilizers strongly stimulated the rates of potential nitrite oxidation. Nitrospira was the only known nitrite oxidizer genus recovered from any soil sample. The application of organic nitrogen fertilizers, but not inorganic, increased the diversity of the prokaryotic community and the activities of soil enzymes. In the organic farming system, abundances of functional genes for mineralization were increased by organic nitrogen fertilizer and these abundances were significantly correlated with corresponding enzyme activity. Understanding the link between microbial communities and the biogeochemical functions of nitrification and mineralization may allow ecosystem models to incorporate microorganisms as dynamic components driving nitrogen flux.