Image-based model quantification of pore-scale nitrogen diffusion and potential microbial ‘dead zones’ induced by fertilization application

Soil microbial communities contribute many ecosystem services including soil structure maintenance, crop synergy, and carbon sequestration. However, it is not fully understood how the health of microbial communities is effected by fertilization at the pore scale. This study investigates the nature of nitrogen (N) transport and reactions at the soil pore scale in order to better understand the influence of soil structure and moisture content on microbial community health. Using X-ray Computed Tomography (XRCT) scans, we reconstructed a microscale description of a dry soil-pore geometry as a computational mesh. Solving two-phase water/air models produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The model considers ammonium (NH₄⁺), nitrate (NO₃^-) and dissolved organic N (DON), and includes N immobilization, ammonification and nitrification processes, as well as diffusion in soil-solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at the three different water saturation conditions. To aid interpretation of the model results, microbial activity at a range of N concentrations was quantified experimentally using labelled C to infer microbial activity based on CO₂ respiration measurements in bulk soil. The pore-scale model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predicted that the maximum NH₄⁺ and NO₃^- concentrations in soil solution around the pellet under low water saturation conditions (15%) are in the order of 1x10³ and 1x10⁴ mol m^-3 respectively (1-10 M), and under higher water saturation conditions (70%) where on the order of 2x10² and 1x10³ mol m^-3, respectively (0.1-1 M). Supporting experimental evidence regarding microbial respiration suggests that these concentrations at the pore-scale would be sufficient to reduce microbial activity in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm depending on soil moisture status), causing a major loss of soil biological activity by up to 90%. This model demonstrates the importance of pore-scale processes in regulating N movement in soil with special capability to predict the effects of fertilizers on rhizosphere-scale processes and the root microbiome.