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Research article2022Peer reviewedOpen access

Scenario modelling of carbon mineralization in 3D soil architecture at the microscale: Toward an accessibility coefficient of organic matter for bacteria

Mbe, Bruno; Monga, Olivier; Pot, Valerie; Otten, Wilfred; Hecht, Frederic; Raynaud, Xavier; Nunan, Naoise; Chenu, Claire; Baveye, Philippe C.; Garnier, Patricia


The microscale physical characteristics of microbial habitats considerably affect the decomposition of organic matter in soils. One of the challenges is to identify microheterogeneities in soil that can explain the extent of carbon mineralization. The aim of this study was therefore to identify descriptors of mu m-scale soil heterogeneity that can explain CO2 fluxes obtained at the mm scale. A suite of methods and models that visualize soil heterogeneity at scales relevant to microorganisms has been developed over the last decade. Among the existing 3D models that simulate microbial activity in soils, Mosaic is able to simulate, within a short computation time, the microbial degradation of organic matter at the microhabitat scale in soil using real 3D images of soil porosity. Our approach was to generate scenarios of carbon mineralization for various microscale environmental conditions and determine how the descriptors of soil structure could explain CO2 evolution. First, we verified that the simulated diffusion of solutes in the soil samples obtained with Mosaic were the same as those obtained using the same parameter set from a robust 3D model based on a lattice Boltzmann approach. Then, we ran scenarios considering different soil pore architectures, water saturations and microorganism and organic matter placements. We found that the CO2 emissions simulated for the different scenarios could be explained by the distance between microorganisms and organic matter, the diffusion of the substrate and the concentration of the available substrate. For some of the scenarios, we proposed a descriptor of accessibility based on the geodesic distance between microorganisms and organic matter weighted by the amount of organic matter. This microscale descriptor is correlated to the simulated CO2 flux with a correlation coefficient of 0.69. Highlights Does the microscopic soil organisation explain the macroscopic mineralisation fluxes ? We present a new descriptor based on the geodesic distances between organic matter and microorganisms. We found a correlation between the descriptor of mu m-heterogeneity and the mineralization fluxes. Other scenarios should be carried out under wider environmental mu m-conditions to confirm our results.


decomposition; diffusion; model scenarios; soil structure; tomography

Published in

European Journal of Soil Science
2022, Volume: 73, number: 1
Publisher: WILEY

    UKÄ Subject classification

    Soil Science

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