Damage and recovery of flagella in soil bacteria exposed to shear within long microchannels

The swimming motility of bacteria is driven by the action of bacterial flagellar motors, whose outermost structure is a long and thin helicoidal filament. When rotated, the fluid medium exerts an anisotropic viscous drag on the flagellar filaments, ultimately leading to bacterial propulsion. The flagellar filaments are protein-based flexible structures that can break due to interactions with fluid flows. Here, we study the evolution of flagellar filaments in the soil bacterium $\textit{Bradyrhizobium diazoefficiens}$ after being exposed to shear flows created in long microchannels, for shear rates between $1$ s$^{-1}$ and $10^5$ s$^{-1}$, and for durations between tens of milliseconds and minutes. We demonstrate that the average swimming speed and fraction of swimming cells decrease after exposition to shear, but both parameters can recover, at least partially, with time. These observations support the hypothesis that shear flows cut flagellar filaments but that reversibly damaged bacterial flagellar motors can be restored thanks to filament regeneration. By fitting our observations with phenomenological expressions, we obtain the individual growth rates of the two different flagellar filaments that $\textit{B. diazoefficiens}$ possesses, showing that the lateral filaments have a recovery time of about 40 min while the subpolar one requires more than 4.5 h to regrow. Our work demonstrates that simple monitoring of bacterial motility after exposition to shear can be used to characterize the process of flagellar filament breakup and growth, a phenomenon widely present in bacteria swimming in porous soil and exposed to shear flows due to rainfall and watering systems.