The interplay between porous medium structure and bacterial biofilms in a microfluidic flow cell

Enhancing plants' ability to deal with climate change consequences requires adopting new measures to improve soil viability. Using beneficial bacteria to enhance plant resilience is a promising approach. Understanding the interplay between bacterial biofilm and water flow and distribution after drainage is crucial to achieving sustainable positive effects. However, the impact of soil structure and various biofilm extracellular components on water flow is still largely unknown. Here, we study the effects of biofilm characteristics and porous medium structure on water retention during drainage. We use microfluidic porous medium devices with prescribed structures and inoculate them with a common soil bacterium, Bacillus Velezensis. We use a wild-type strain and two mutants – a ΔtasA strain mutant in extracellular protein fibers formations and a ΔepsH mutant in forming extracellular sugar polymers. The model porous medium microfluidic devices are fabricated with PDMS and contain an array of circular pillars in a rectangular channel. The porous medium structure is controlled by two parameters: the pillar diameter distribution variance and their spatial correlation. The distribution variance controls the pore-scale heterogeneity of the porous medium, while the spatial correlation controls its macroscopic heterogeneity. We begin our experiments by inoculating the porous medium with a bacterial culture solution. Then, we inject nutrient broth into the microfluidic chip at a constant flow rate while periodically capturing images of biofilm development using a microscope in Brightfield mode. We also compare the biofilm images to a numerical solution of pore-scale velocity by solving Stokes flow in OpenFOAM for the specific geometry of the microfluidic cell. Preliminary results show biofilm accumulates in a heterogeneous porous medium in regions of narrower pore apertures with lower flow velocities. In contrast, biofilm accumulation is not preferential to specific areas in a homogeneous porous medium. Using ΔtasA and Δepsh mutants resulted in reduced biofilm accumulation. In the next stage, we will perform drainage experiments to assess the simultaneous effect of structure and biofilm on water retention and distribution. The fundamental understanding gained from this study will help facilitate upscaled experiments that could indicate the preferred saturation conditions for increasing plant-available water content under different structural and biological soil features.