Date of Graduation


Document Type


Degree Name

Master of Science in Cell & Molecular Biology (MS)

Degree Level



Biological Sciences


Mary Savin

Committee Member

Kristen Gibson

Second Committee Member

Burt Bluhm


Nitrifiers, Soil, Sustainable Agriculture


Nitrification is oxidation of ammonia to nitrite and subsequently to nitrate. The rate limiting step of nitrification, ammonia oxidation to nitrite, was thought for many years to be carried out primarily by ammonia oxidizing bacteria (AOB). However, using molecular techniques and investigating the amoA gene, ammonia-oxidizing archaea (AOA) were discovered. Understanding how long-term application of surface ground covers and organic fertilizers to perennial systems affect microbial communities is critical for sustainable soil management. An organically managed experimental apple orchard soil received seven years (2006 – 2013) of annual, surface applications of poultry litter or commercial fertilizer compared to no fertilizer combined with compost (C), wood chips (WC), shredded paper (P), or mow-andblow (MB) ground cover mulches. This research investigates AOB and AOA community composition based on the amoA gene in the soil surface as affected by treatments from 2007, 2009, and 2013, and as related to soil properties. The AOB community exhibited low and variable diversity investigated by using PCR-denaturant gradient gel electrophoresis, and richness ranged between 0.67 and 6.0. The AOB diversity did not consistently change over time and clustering did not distinctly separate communities. The log of the AOB abundance measured using qPCR of the amoA gene fragment ranged from zero to 4.3 with smallest numerical abundances in two of the paper treatments and the largest in compost with poultry litter. The AOA richness ranged from zero to 6.0 across all treatments and years. The AOA community composition clustering suggested that the community shifted from 2009 to 2013. The AOA diversity increased from 2009 to 2013 in compost and wood chip treatments, but diversity decreased in paper with no or poultry litter fertilizer, and in mow-and-blow with poultry litter from 2009 to 2013. Equitability increased with time in compost, decreased in wood chip and paper treatments, and depended on fertilizer in mow-and-blow. Compost supplied the greatest organic matter and dissolved organic N (DON) but the smallest ammonium-N concentration. Poultry litter increased both nitrate and DON. The AOA and AOB were correlated to soil properties, but correlations did not indicate strong linear relationships between communities and particular soil variables.

Included in

Soil Science Commons