Nitrification in Agricultural Soils Under Contrasting N Management.

Nitrification changes the form of nitrogen (converting ammonium/ammonia to nitrite and nitrate) and provides a link between ammonium (product of mineralization and major fertilizer input) and denitrification, the major biological loss for fixed reactive N. 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 soil nitrifiers are difficult to culture, molecular tools are used in combination with process kinetics to characterize the community responsible for nitrification in soils. Genome sequences of soil ammonia oxidizers including Nitrosospira multiformis C71, Nitrosospira briensis C128 and Nitrososphaera viennensis EN 76 (Stieglmeier et al. 2014) have improved our understanding of ammonia oxidizer physiology. A field plot experiment (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. Amplicon pyrosequencing of amoA characterized community and selective inhibition differentiated ammonia oxidation mediated by AOB versus AOA.   Changes in population size for the AO in response to N treatments were found in the first year based on potentials and by the second season treatment effects were significant for gene abundance. Differential inhibition and quantitative PCR revealed that while AOA gene counts were higher, AOB populations were more dynamic and responsible for an equal or greater fraction of the ammonium oxidized under fertilization. The combination of soil ecology, genomics and environmental metagenomics has brought us closer to the goal of linking the capable organisms to the process rate and extent in the soil environment.