Life in a tight spot: Transport and collective behavior of bacteria in heterogeneous media

Diverse processes in healthcare, agriculture, and the environment rely on bacterial motility in porous media; indeed, most bacterial habitats—e.g. biological gels, tissues, soils, and sediments—are heterogeneous porous media. However, while bacterial motility is well-studied in homogeneous environments, how confinement in a porous environment impacts bacterial transport remains poorly understood. To address this gap in knowledge, we combine microscopy, materials fabrication, and microbiology to investigate how E. coli moves in 3D porous media. By probing single cells, we demonstrate that the paradigm of run-and-tumble motility is dramatically altered by pore-scale confinement. Instead, we find a new mode of motility in which cells are intermittently and transiently trapped as they navigate the pore space; analysis of these dynamics enables prediction of bacterial transport over large length and time scales. Further, by developing a new 3D printing approach, we design multi-cellular communities with precise control over the spatial distribution of bacteria. Using this approach, we show that concentrated populations can collectively migrate through a porous medium—despite being strongly confined—and develop principles to predict and direct this behavior.