3rd ISMC Conference ─ Advances in Modeling Soil Systems
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Evaluating the interaction of biofilms, organic matter and soil structures at the pore scale

Alexander Prechtel, Simon Zech, Alice Lieu, Raphael Schulz, and Nadja Ray
Alexander Prechtel et al.
  • University of Erlangen-Nürnberg, Department of Mathematics, Erlangen, Germany (

Key functions of soils, such as permeability or habitat for microorganisms, are determined by structures at the microaggregate scale. The evolution of elemental distributions and dynamic processes can often not be assessed experimentally. So mechanistic models operating at the pore scale are needed.
We consider the complex coupling of biological, chemical, and physical processes in a hybrid discrete-continuum modeling approach. It integrates dynamic wetting (liquid) and non-wetting (gas) phases including biofilms, diffusive processes for solutes, mobile bacteria transforming into immobile biomass, and ions which are prescribed by means of partial differential equations. Furthermore the growth of biofilms as, e.g., mucilage exuded by roots, or the distribution of particulate organic matter in the system, is incorporated in a cellular automaton framework (CAM) presented in [1, 2]. It also allows for structural changes of the porous medium itself (see, e.g. [3]). As the evolving computational domain leads to discrete discontinuities, we apply the local discontinuous Galerkin (LDG) method for the transport part. Mathematical upscaling techniques incorporate the information from the pore to the macroscale [1,4].
The model is applied for two research questions: We model the incorporation and turnover of particulate OM influencing soil aggregation, including ‘gluing’ hotspots, and show scenarios varying of OM input, turnover, or particle size distribution.
Second, we quantify the effective diffusivity on 3D geometries from CT scans of a loamy and a sandy soil. Conventional models cannot account for natural pore geometries and varying phase properties. Upscaling allows also to quantify how root exudates (mucilage) can significantly alter the macroscopic soil hydraulic properties.

[1]  Ray, Rupp, Prechtel (2017). AWR (107), 393-404.
[2] Rupp, Totsche, Prechtel, Ray (2018). Front. Env. Sci. (6) 96.
[3] Zech, Dultz, Guggenberger, Prechtel, Ray (2020). Appl. Clay Sci. 198, 105845.
[4] Ray, Rupp, Schulz, Knabner (2018). TPM 124(3), 803-824.

How to cite: Prechtel, A., Zech, S., Lieu, A., Schulz, R., and Ray, N.: Evaluating the interaction of biofilms, organic matter and soil structures at the pore scale, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-59,, 2021.