Navigation of magnetotactic bacteria is impaired by porous microstructure: Effects of porosity, pore scale, and geometrical order

Microstructured quiescent environments host a variety of swimming microorganisms, which are crucial to many natural and engineering processes. Using microfluidics to precisely control the porosity, pore scale, and geometrical order of the environment, we systematically study the impact of the microstructure on both the diffusive and directed transport of swimming cells. Magnetotactic bacteria (MTBs) are used as a model biological system, because they share swimming mechanisms with other bacteria of interest, and their swimming direction is easily manipulated via an external magnetic field. We show that the cells’ effective diffusion coefficient without a magnetic field decreases markedly in the presence of porous microstructure compared to bulk fluid. Applying a guiding external field greatly enhances the mobility of the migrating cells through the media, an effect that is enhanced with increasing magnetic field strength. These results are an important step toward understanding the ecology of swimming cells in quiescent porous media as well as for controlling micro-robots in complex environments.