Modeling coupled nitrification–denitrification in soil with an organic hotspot

The emission of nitrous oxide (N2O) from agricultural soils to the atmosphere is a significant contributor to anthropogenic greenhouse gas emissions. The recycling of organic nitrogen (N) in manure and crop residues may result in spatiotemporal variability in N2O production and soil efflux which is difficult to capture by process-based models. We propose a multi-species, reactive transport model to provide detailed insight into the spatiotemporal variability in nitrogen (N) transformations around such N2O hotspots, which consists of kinetic reactions of soil respiration, nitrification, nitrifier denitrification, and denitrification represented by a system of coupled partial differential equations. The model was tested with results from an incubation experiment at two different soil moisture levels (−30 and −100 hPa) and was shown to reproduce the recorded N2O and dinitrogen (N2) emissions and the dynamics of important carbon (C) and N components in soil reasonably well. The simulation indicated that the four different microbial populations developed in closely connected but separate layers, with denitrifying bacteria growing within the manure-dominated zone and nitrifying bacteria in the well-aerated soil outside the manure zone and with time also within the manure layer. The modeled N2O production within the manure zone was greatly enhanced by the combined effect of oxygen deficit, abundant carbon source, and supply of nitrogenous substrates. In the wetter soil treatment with a water potential of −30 hPa, the diffusive flux of nitrate (NO3-) across the manure–soil interface was the main source of NO3- for denitrification in the manure zone, while at a soil water potential of −100 hPa, diffusion became less dominant and overtaken by the co-occurrence of nitrification and denitrification in the manure zone. Scenarios were analyzed where the diffusive transport of dissolved organic carbon or different mineral N species was switched off, and they showed that the simultaneous diffusion of NO3-, ammonium (NH4+), and nitrite (NO2-) was crucial to simulate the dynamics of N transformations and N2O emissions in the model. Without considering solute diffusion in process-based N2O models, the rapid turnover of C and N associated with organic hotspots can not be accounted for, and it may result in the underestimation of N2O emissions from soil after manure application. The model and its parameters allow for new detailed insights into the interactions between transpor