Modeling the effect of microscale heterogeneities on soil bacterial dynamics and the impact on soil functions

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly diverse as they are. Mathematically based modeling can facilitate the understanding of their development and function in soils, e.g. with respect to habitat and carbon cycling.

Our mechanistic model is based on [1,2] and allows studying the spatiotemporal dynamics of bacteria in unsaturated soil samples. In this presentation, different levels of saturation are investigated, for which the fluid (liquid and gas) distributions are calculated according to a morphological model. As in [3] various bacteria strains and organic matter are heterogeneously distributed in CT scans of various soil samples.

The bacteria strains grow based on Michaelis-Menten kinetics due to the uptake of oxygen and dissolved organic carbon (DOC) present in the liquid phase. The development of bacterial colonies is realized in a cellular automaton framework (CAM) as presented in [1,2]. DOC is either present as a carbonaceous solution or hydrolized by a first order kinetic from heterogeneously distributed particulate organic matter (POM) sources. The diffusion of both nutrients oxygen and DOC are described by means of reactive transport equations, which include a Henry conditions for the transfer from/into the gas phase. We apply the local discontinuous Galerkin (LDG) method as a discretization scheme.

Our simulations show that the impact heterogeneity in nutrient and bacteria distribution has on overall biodegradation kinetics strongly depends on the scale of interest. On the scale of soil microaggregates (<250 μm), only very specific cases can be distinguished globally, e.g. when nutrient sources are isolated from bacteria due to a disconnected liquid phase. Locally however, heterogeneities in nutrient distribution impact the development of bacteria populations, e.g. a lower geodesic distance of bacteria to nutrient promotes bacteria growth locally. Such local effects can have an important role for competing bacterial species.

On larger scales (millimeter scale), such heterogeneities can also have a large impact. We conclude that the heterogeneous spatial structure must be resolved scale-dependently.

 

 

[1] N. Ray, A. Rupp and A. Prechtel. Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media, Adv. Water Resour. 107, 393-404 (2017), doi:10.1016/j.advwatres.2017.04.001.

[2] A. Rupp, K. Totsche, A. Prechtel and N. Ray. Discrete-continuum multiphase model for structure formation in soils including electrostatic effects, Front. Environ. Sci. 6:96 (2018), doi:10.3389/fenvs.2018.00096.

[3] X. Portell, V. Pot, P. Garnier, W. Otten and P.C. Baveye. Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: insights from computer simulations., Front. Microbiol. 9:1583 (2018), doi:10.3389/fmicb.2018.01583.