Hindered Transport of Bacteria in Porous Media Flows

Swimming bacteria play crucial roles in processes ranging from the biodegradation of pollutants in groundwater to the spread of infections in the human body. The environments inhabited by these motile cells are characterized by porous microstructure and dynamic fluid flows. We show that the complex interplay between motility, geometry, and flow can lead to heterogeneous distributions of bacteria and severely hindered bacterial transport properties. Using video microscopy, we track the motion of bacteria (Bacillus subtilis) flowing through a microfluidic porous medium and complement these measurements by Langevin simulations. Cell trajectories reveal filamentous patterns of high cell concentration that result from the orientational coupling of cell elongation to the flow (Jeffery orbits) and steric surface interactions. The effective diffusion coefficient of the bacteria is severely hindered in the transverse flow direction with increasing mean shear rate due to the faster decorrelation of the cells' orientation by shear.