Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network

Abstract

Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the particle shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and particle attachment is a stochastic process driven by bacterial rheotactic transport across pore space velocity gradients. Over time, we find that gravity-driven flow conditions activate different cell-clustering phentoypes in EPS producing and EPS defective bacteria strains, which subsequently changes the overall spatial distribution of cells across the porous media network as colonies grow and alter the fluid dynamics of their microenvironment.