Chemotactic Migration of Bacteria in Porous Media

The chemotactic migration of bacteria—their ability to direct collective motion along chemical gradients—is central to processes ranging from sustaining plant growth, remediating contaminants, sensing and reporting stimuli, and mitigating or causing infection. However, while migration is well-studied in bulk liquid, most bacterial habitats—soils, sediments, and biological gels—are tight and tortuous porous media. Unfortunately, how confinement in a porous medium alters the ability of bacteria to move remains poorly understood: typical media are opaque and have ill-defined pore structures, making systematic studies challenging. Thus, current understanding of migration is based on studies performed in bulk liquid. Here, using confocal microscopy inside three-dimensional (3D) porous media, we elucidate how pore-scale confinement fundamentally alters the chemotactic migration of bacteria. We find that confinement forces the cells to use a completely different mechanism to direct their motion than in bulk liquid: they bias the total extent by which they reorient their bodies, instead of biasing the reorientation frequency—suggesting a revision to the current paradigm of E. coli chemotaxis. Further, we demonstrate that the spatiotemporal dynamics of chemotactic migration can be quantitatively described using a continuum model—but only when conventionally-used motility parameters are altered substantially from their bulk liquid values in a pore-size dependent manner. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous environments.