Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

•We modeled macropore topology control on soluble C substrate degradation by bacteria.•A 3D lattice-Boltzmann model was coupled to a compartmental model for biodegradation.•Macropores, water and bacteria distributions were described at submillimeter scale.•Physical and biological effects were quantified on a complete factorial design. Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it.