PUNCS: Towards Predictive Understanding of Nitrogen Cycling in Soils
In anoxic environments, the major nitrate/nitrite-consuming processes are respiratory ammonification (also known as dissimilatory nitrate reduction to ammonium) and denitrification (i.e., the formation of the gaseous products N 2 O and N 2 ). Respiratory ammonification oxidizes more carbon per mole of nitrate than denitrification and generates a cation (NH 4+ ), which is retained in soils and bioavailable for plants. Thus, these processes have profoundly different impacts on N retention and greenhouse gas (CO 2 , N 2 O) emissions. Microbes capable of respiratory ammonification or denitrification coexist but the environmental controls over these competing nitrate/nitrite-reducing processes are largely unknown. With the current level of understanding, predictions under what environmental conditions respiratory ammonification activity predominates leading to N-retention rather than N-loss are tenuous. Further, the diversity of genes encoding the ammonium-forming nitrite reductase NrfA is poorly defined hampering the development of tools to assess and monitor this activity in environmental systems. Incomplete denitrification leads to N 2 O, a gas implicated in ozone layer destruction and climate change. The conversion of the greenhouse gas N 2 O to benign N 2 is catalyzed by N 2 O reductase, the characteristic enzyme system of complete denitrifiers. Thus, efforts to estimate N 2 O conversion to N 2 have focused on the well-characterized denitrifier nosZ genes; however, our understanding of the diversity of genes and organisms contributing to N 2 O consumption is incomplete. This paucity of information limits the development of more accurate, predictive models for C- and N-fluxes and greenhouse gas emissions. A comprehensive analysis of the key catalyst of respiratory ammonification, ammonia-forming nitrite reductase NrfA, revealed the evolutionary history of nrfA and identified novel diagnostic features, allowing optimized primer design for nrfA monitoring. Further, a novel group of functional “atypical” nosZ genes was found indicating that a much broader diversity of genes and organisms contribute to consumption of N 2 O. The atypical nosZ genes are distributed in soil ecosystems and often outnumber their typical counterparts, emphasizing their potential role in N 2 O consumption in soils and possibly other environments. Kinetic studies revealed that organisms with atypical NosZ exhibit significantly higher affinity to N 2 O, indicating that the relative activity of bacteria with typical versus atypical NosZ control N 2 O emissions and determine a soil’s N 2 O sink capacity. Collectively, the discoveries made under the PUNCS project improve understanding of N- and associated C-cycling processes in soils, enable the design of enhanced monitoring tools, and allow a larger research community to generate comprehensive datasets required to generate Earth System Models with higher predictive power.