Nitrification is a biological oxidation of NH3 to NO2- and then to NO3-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO3- leaching, and reducing NO and N2O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The study site was a long-term (>40 years) continuous maize (Zea mays L.) experiment with three N fertilization rates (0, 168, and 336 kg ha-1) and either no-tillage (NT) or plow tillage (PT). Most Probable Number method was used to estimate the density of AOB and NOB; the shaken slurry method was used to measure potential nitrification rates; PCR-denaturing gradient gel electrophoresis (DGGE) was used to analyze nitrifier communities. Tillage, fertilization, and their interaction all significantly influenced the AOB and NOB densities, the ratio of AOB to NOB, and potential nitrification rate. Nitrifier densities and potential nitrification rates increased with increased N fertilization; NOB density increased faster than AOB density with fertilization. The influence of tillage on nitrification was different for different fertilization rates. The trends for nitrifier density and potential nitrification rate were not consistent. Nitrifier community structure was influenced by sample season, N fertilization rates, tillage, and their interaction. Different nitrifier groups had different responses to the treatments. The AOB became more diverse with increasing N input; tillage rather than N fertilizer played a dominant role affecting the AOA community; two NOB genera had different responses to N fertilization rates: Nitrobacter diversity increased with more N applied; Nitrospira was the opposite. Unique bands/members were discovered in different treatments, manifesting environmental selection. Long-term field trials were useful in better understanding how soil management influenced the relationship between nitrifier densities, nitrification rates, and community structure, which may facilitate new approaches to optimize nitrification and provide new clues to discover which environmental factors most influence the nitrifier community in agroecosystems.

In an effort to develop cost-effective technologies for the removal of ammonium nitrogen from dairy waste, a novel biological wastewater treatment process, utilizing anaerobic ammonium oxidation (anammox), referred to as Oxygen-Limited Autotrophic Nitrification and Denitrification (OLAND) was examined. Due to the potential use of OLAND-based systems in dairy manure management, a detailed water quality assessment of a modern dairy farm manure treatment-system was conducted. The Johnson Highland Dairy Farm, Glade Spring, Virginia, was selected for this assessment and a comprehensive analysis of the wastewater characteristics throughout the confined animal feeding operation was completed. The results suggest that ammonia concentrations in the anaerobic storage facility was high enough to justify use of treatment technologies that reduce ammonia loads in stored dairy waste. A lightly loaded Fixed Film Bioreactor (FFBR), in which the OLAND process was desired to occur, was then constructed in the laboratory and monitored over 51 days. Of particular interest was the time taken to achieve stable performance of this OLAND system. Furthermore, a protocol was developed to determine whether OLAND based metabolism was occurring. Ammonium nitrogen removal efficiency in the FFBR throughout the 51-day monitoring period was high, averaging approximately 95 % for the length of the study. From day 32 to 51, simultaneous removal of both ammonium and nitrite with a low level of concomitant nitrate production was observed, a key indicator of possible anammox activity. Stoichiometric ratios calculated for the FFBR compared favorably with those already established for OLAND systems. The developed protocol, incorporating anaerobic and aerobic batch experiments, to verify the occurrence of OLAND based metabolism did not yield expected results and described poorly what was being observed in the FFBR. Volatilization of ammonia during the experimental test was suspected and should be controlled when the protocol is performed in the future. / Master of Science