Nitrification Under Contrasting Nitrogen Management: From Soils to Genomes and Back Again.

Nitrification changes the form of nitrogen (converting ammonium/ammonia to nitrite and nitrate) and thereby alters the fate of N in agricultural soils. Nitrification provides a link between ammonium (product of mineralization and major fertilizer input) and denitrification, the major biological loss for fixed reactive N and a source of the potent greenhouse gas N₂O. Understanding nitrification is therefore central to the ability to predict and manage soil N losses and to understand impacts of agricultural management on N2O production. Since many of the soil nitrifiers are difficult to culture, molecular tools are used extensively to characterize the community responsible for nitrification in soils. Methods for determining the rates and kinetics of the nitrification process are advancing simultaneously. Genome sequences of soil ammonia oxidizers including Nitrosospira multiformis and Nitrososphaera viennensis and nitrite oxidizers such as Nitrospira spp. have been essential for understanding the physiology of organisms involved in nitrification.  A multi-year replicated randomized block design was initiated in 2011 in both Utah and Georgia USA to examine nitrogen source effects on nitrification and mineralization in agricultural systems. Nitrogen sources include high and low levels of ammonium sulfate fertilizer (100 and 200 kg N/ha) and manure composts. DNA extraction and soil characterization were accomplished for multiple time points. Real-time quantitative PCR targeting amoA for ammonia oxidizers was used to follow changes in bacterial (AOB) and archaeal ammonia oxidizer (AOA) populations. Selective inhibition experiments have allowed differentiation between ammonia oxidation mediated by the two groups. Results from the current experiment will be compared to an earlier experiment from 1997 to 2002 in Utah. The combination of soil process rates, pure culture genomics and soil metagenomics has brought us closer to the goal of linking the capable organisms to the process rate and extent in the environment.