Microbial carbon use efficiency emerges from interactions between soil structure and life-history strategies

Microbial carbon use efficiency (CUE) is believed to be a key regulator of the accumulation of persistent soil organic carbon. Microbial processing of organic carbon in soil occurs in the pore network, the properties of which are known to affect microbial activity. However, the effects of interactions between pore architecture and microbial life-history strategies on carbon dynamics, and how these interactions are modulated by moisture conditions, remain poorly understood. Here, we use a spatially explicit model based on a cellular automaton, applied to realistic soil pore networks derived from X-ray tomographic images, to investigate how pore geometry and organic matter distribution shape microbial dynamics and CUE. The model explicitly represents r- and K-strategists that are either motile or immobile, and have different resource requirements for growth, maintenance and motility. The constraints imposed by the moisture conditions on substrate diffusion and the spatial domain in which motile bacteria can effectively disperse are explicitly represented in the model, in order to capture how moisture regulates decomposer access to resources. The simulations show that pore architecture has a significant effect on microbial CUE. Micropores promoted high CUE and a dominance of K-strategists by limiting substrate diffusion, reducing pore connectivity, and constraining microbial access to spatially isolated resources. In contrast, macropores with high connectivity and greater substrate accessibility favour r-strategists, rapid biomass turnover and lower CUE. Motility emerges as advantageous in connected, carbon-rich macropores, but energetically unfavourable in confined or poorly connected micropores, where immobile strategies outperform motile ones. Overall, our results indicate that microbial CUE is not an intrinsic property of life-strategies alone, but emerges from the interaction between microbial life-strategies and pore-scale physical constraints. This study suggests that soil structure influences microbial strategies by limiting resource availability and dispersal.