Coupled C and N turnover in a dynamic pore scale model reveal the impact of exudate quality on microbial necromass formation

Abstract. The adequate quantification of soil organic carbon (SOC) turnover is a pressing need for improving soil health and understanding climate dynamics. It is controlled by the complex interplay of microbial activity, availability of carbon (C) and nitrogen (N) sources, and the dynamic restructuring of the soil's architecture. Accurate modeling of SOC dynamics requires the representation of these processes at small spatial scales.

We present a mechanistic, spatially explicit model at the pore scale, which couples enzymatic degradation of particulate organic matter (POM), microbial necromass and root exudates with microbial growth and turnover, C respiration and N cycling depending on the C/N ratios of the different organic carbon sources. It is combined with a cellular automaton model for simulating soil structure dynamics including the stabilization of soil particles, POM or microbial necromass via organo‐mineral associations.

The virtual soil simulations use µCT data of aggregates and parameters from rhizosphere experiments without parameter fitting to explore the influence of (i) soil structural heterogeneity and connectivity, (ii) N limitation, and (iii) necromass formation on SOC storage.

Our results highlight that evolving soil architecture and pore connectivity control substrate accessibility, creating micro‐scale hot and cold spots for microbes. N availability consistently co-limits microbial growth, while a favorable C/N ratio of root exudates substantially reduces respiration and increases CUE over extended periods. Necromass emerges as long‐term SOC pool, as N from short‐term root exudation pulses promotes biomass growth and is converted into slowly degradable necromass, which can be physically protected through occlusion. The findings align with lab experiments and additionally allow us to elucidate the spatial and temporal dynamics of the drivers of carbon turnover.