To cross or not to cross: the collective swimming of bacteria in two-dimensional confinement

The natural habitats of microorganisms often involve confined geometries, which alter their swimming behavior and mutual interactions. To explore the effect of confinement on the collective behavior of bacteria, we image a suspension of swimming E. coli in a Hele-Shaw cell using bright-field microscopy. By slightly varying the thickness of our cell, we create two closely related confined geometries: a 2D cell where bacteria are strictly confined to a monolayer and unable to cross over each other, and a quasi-2D cell where they can cross over each other out of the plane. We find that the emergent collective behaviors of bacteria are qualitatively different depending on the geometry of the cell. For the quasi-2D geometry, we observe the nematic alignment of bacteria with long-range orientational order. However, for the 2D geometry, the long-range nematic order is replaced by short-range polar order with transient clusters of co-moving bacteria. We show that individual swimming bacterium experiences stronger velocity fluctuations in the 2D geometry, which interrupt the growth of bacterial clusters. Our experiments reveal how a subtle change in the geometric confinement strongly affects the collective swimming of bacteria.