Impacts of flow on transport of motile microbes in synthetic porous media

Microbial motility is important in a variety of fields, including bioremediation, biogeochemical processes, ecology, and medicine. However, the transport characteristics of self-propelled microbes are not properly understood, particularly in the presence of variable flow, where preferential flow paths may form and the dispersive properties of motile species may lead to exploration of large portions of pore spaces. In this study we use microfluidic devices to investigate the impacts of flow on transport of motile microbes in a quasi-two-dimensional synthetic porous medium. The micro-models were made from polydimethylsiloxane and contain staggered rows of equally sized and spaced pillars that represent grains of a porous medium. The metal-reducing bacterium Paenibacillus strain 300A was injected at a constant concentration, and multiple flow rates transported the bacteria through the micro-models. The experiments were recorded at variable frame rates for 1 to 5 minutes, resulting in thousands of trajectories of individual cells. The trajectories were extracted from videos by subtracting the background image from each frame and then using a particle tracking code to locate and link cells across frames. Bacterial breakthrough curves, velocity distributions, and traveled distance distributions were then computed from the extracted trajectories to characterize the transport of Paenibacillus. The results of this study show how the transport of metal-reducing motile microbes in porous media is affected by different flow rates, which is expected to inform the development of robust bioremediation simulators.