Confinement controls bacterial spreading at all scales

Abstract: In many natural environments such as in soils or in physiological ducts bacterial motion often alternates between three-dimensional (3D) swimming in the bulk and a quite distinct two-dimensional (2D) kinematics at surfaces. This interplay is crucial to assess large-scale transport and contamination properties but still remains poorly understood. Here, using a prototypical setup, we address this fundamental question for motile E. coli bacteria undergoing run-and-tumble (R&T) exploration under confinement. We report the first experimental measurements of the emergent large-scale diffusivity revealing its explicit dependence on the confinement height. In addition, we provide a theoretical framework showing how the diffusion coefficient is governed by the interplay between 2D and 3D motion coupled to an internal biochemical process that induces large scale memory in the exploration dynamics. These findings offer general and critical insights into how microswimmers explore complex environments where their motion is bound to alternate between bulk and surfaces.