How E-coli bacteria navigate flow and complex environments

Active fluids consist of self-propelled particles and display properties that differ strongly from their passive counter-parts. Unique physical phenomena, such as enhanced  Brownian diffusivity, viscosity reduction or active transport and mixing, result from particle activity, which locally injects energy into the system. The presence of living and cooperative species may also induce collective motion leading to organization at the macroscopic level. Individual bacteria transported in viscous flows exhibit complex interactions with flows and bounding surfaces, arising from their activity and complex shape. Understanding these transport dynamics is crucial, as they impact soil contamination, transport in biological conduits or catheters, and thus constitute a serious health threat.

Here, we investigate the transport of individual E. coli bacteria under flow and in complex environments, using microfluidic model systems in combination with a novel Lagrangian 3D tracking method. By combining experimental observations and modeling, we elucidate the origin of upstream swimming, lateral drift, persistent transport along edges, as well as bacterial self-focusing. At increasing bacterial concentrations, collective motion emerges, and we characterize the resulting vortex-like structures using PIV. We discuss how the characteristic length scales can be controlled through bounding walls or flows. The understanding gained can, for example, be used to control bacterial transport in complex geometries or to shed light on the role of emergent mesoscopic structures in determining the macroscopic properties of active suspensions.