A pore-scale study of bacterial chemotaxis with segregated and controlled nutrient sources

Natural porous systems, like soils and aquifers, are physically and chemically highly heterogeneous. Microorganisms inhabiting these environments are therefore exposed to heterogeneous fluid flow velocities and nutrient landscapes. Bacteria capable of biasing their motion to swim along chemical gradients – known as chemotaxis – profit from their ability to localize and navigate towards nutrient hot spots, such as soil aggregates or plant roots.
We propose a novel experimental microfluidic platform to study chemotaxis at the pore-scale, allowing full optical access to the pore space and simultaneously enabling control over the spatio-temporal availability of nutrients. The microfluidic device contains hydrogel features, acting as nutrient hotspots, embedded in a porous medium, made out of transparent polydimethylsiloxane (PDMS) pillars. Nutrients are transported by diffusion from the access channels through the hydrogel into the porous medium, where they are released. The generated nutrient gradients downstream of the hotspots under flow conditions drive the swimming of chemotactic bacteria.
This approach enables the study of subsurface processes at the pore-scale under more realistic conditions, and shed new light onto the influence of physical and chemical heterogeneity on bacterial dispersion and residence time in the subsurface.

Keywords: porous media, soil, chemotaxis, microfluidics, heterogeneity