Bio-physical modelling
Modelling provides a powerful and essential tool to understand the consequences of the microscopic heterogeneity of soil. A particular strength of the SIMBIOS Centre is our expertise in modelling and visualization of dynamical soil processes such as water flow and microbial community dynamics.
Internal pore network of soil showing the largest (green) and second largest (red) connected pore clusters through which a fungal invasion front progressesMicro-organisms are major players in soil ecosystem services. Despite their importance little is known regarding the link between microbial diversity and ecosystem services. New interdisciplinary tools are required that will functionally classify microorganism in terms of their essential traits and enable predictions in shifts in microbial populations associated with soil management strategies or climate change. The development of such tools requires integration of physical and microbiological processes. The macroscopic behavior (soil respiration, fungal diversity index, water distribution) emerges as a consequence of microbial interactions which are affected by the local soil environment (soil micro-habitat). Soil structure is crucial in the interaction. For example, on a 2D agar plate (or any structure-less environment) two fungal species will always meet and they will interact. On the other hand, the 3D geometry of the pore space does however provide refuges and separates pathways for fungal spread enabling species to coexist.
We are exploiting recent advances in modern techniques that characterize the soil environment at micro scales, and combine this with parameterized and validated models of fungal growth to develop a predictive framework for fungal growth in heterogeneous soil environments. The micro-environment dynamics are modelled as an emergent consequence of the interactions between pore structure, physical processes (Carbon and water dynamics) and fungal growth and interactions. The physical and biological compartments are integrated in a 3D pore scale representation of soil obtained with X-ray CT. The physical processes in soil use theoretical tools for modelling the reactive flow of multiphase compounds in soil at the pore scale and are based on the Lattice Boltzmann formulism. Our theoretical work is integrated in an experimental program in biophysics to parameterize the models and test model outcomes related to fungal invasion, fungal diversity, and hydraulic properties of soils.
Simulation snapshots
2D and 3d simulations
Deadlock: A simulation of two competing fungi in a 2D environment. Watch Video
Poro033: A simulation of two fungi competing in a 3D soil structure. Due to the limitations on the physical architecture of soil (not shown) the movement of the fungi becomes deadlocked. Watch Video
Microbial distributions in soil: Download Paper