Soils in silico - solutes, biofilms and structure formation

We assess the complex coupling of biological, chemical and physical processes with the help of a mechanistic modeling approach extending [Rupp 2019] The aim is to study the interplay of relevant mechanisms in silico and consequently gain a model-based understanding of dynamics in soils.
The hybrid discrete-continuum model used explicitly represents the pore structure and allows for dynamic structural organization of the medium at the pore scale. The movement of interacting entities - nutrients, bacteria and possibly charged chemicals - in the fluid is described by means of the diffusion and Nernst-Planck equations with Henry's law at the liquid/gas interfaces. Homogeneous chemical reactions are considered using for instance the mass action law whereas heterogeneous reactions on the solid surface are incorporated via a kinetic Langmuir isotherm. A biomass phase can develop from agglomerations of bacteria and stabilising sticky agents may grow or decay at the solid surfaces. Root cells and an explicit phase of exudate as well as attachment properties of root hairs can be included. In addition to solving the continuous partial differential equations, a discrete cellular automaton method [Ray et al. 2017, Rupp et al 2018, Tang and Valocchi 2013] is used, enabling structural changes in the solid and biomass/mucilage phases at each time step. The partial differential equations are discretised with a local discontinuous Galerkin method which is able to handle discontinuities induced by the evolving geometry. Upscaling techniques enable the incorporation of information from the pore scale into the macroscale.
In this study, we illustrate the ability of the approach to advance the understanding of specific process mechanisms. Microaggregates are the fundamental building blocks of soils and are thus important for soil structure, properties, and functions. Although there has been much research investigating the dynamics, stability, and structure of microaggregates, there is still a substantial lack in quantifying the relationships between the major driving forces (soil fauna, microorganisms, roots, organic and inorganic matter, and physical processes). As an example, we study structure formation of microaggregates as a function of the size and shape of the solid building units taking into account the effect of attraction and repulsion by charges. Biomass development and root exudate can significantly alter the macroscopic soil hydraulic properties. Using the model in hand, this effect can be quantified for different amount and spatial distribution of root exudate with geometries from CT-scans. In the natural environment, microbial communities are highly diverse. We employ the model to investigate the way spatial distribution of organic matter can influence bacterial dynamics.