Theoretical Framework to Describe Traveling Waves of Bacteria in Porous Media

How bacteria move in porous media like tissues and soil underlies processes like infection and bioremediation. However, existing models of how bacteria coordinate their motion at the population scale cannot fully explain collective migration inside porous media. To address this gap in knowledge, we use confocal microscopy to directly track bacteria deep inside transparent porous media. Similar to the case of free liquid, we find that the cells move together in directed, traveling waves following self-generated nutrient gradients. However, unlike the case of free liquid, the wave speed and shape are also regulated by the structure of the porous medium itself. By analyzing the single cell tracks, we characterize how biased “hopping and trapping” of the individual cells generates traveling waves; surprisingly, in stark contrast to the case of chemotaxis in free liquid, we find that hop length bias is not the dominant contributor to this mode of collective migration. Further, we show how the statistical features of single cell motion can be used to develop a continuum model that can describe collective migration in a porous medium over large length and time scales. Together, our work provides new principles to predict and possibly control bacterial migration in complex environments.