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Motility is a fundamental survival strategy of bacteria to navigate porousenvironments. Swimming cells thrive in quiescent wetlands and sediments at thebottom of the marine water column, where they mediate many essentialbiogeochemical processes. While swimming motility in bulk fluid is now wellestablished, a comprehensive understanding of the mechanisms regulatingself-transport in the confined interstices of porous media is lacking, anddetermining the interactions between cells and surfaces of the solid matrixbecomes paramount. Here, we precisely track the movement of bacteria(\emph{Magnetococcus marinus}) through a series of microfluidic porous mediawith broadly varying geometries and show that cell motility results in asuccession of scattering events from the porous microstructure. Order ordisorder can impact the cells' motility over short ranges, but we directlydemonstrate that their large-scale transport properties are regulated by thecutoff of their persistent swimming, which is dictated primarily by theporosity and scale of the porous geometry. The effective mean free path isestablished as the key geometrical parameter controlling transport, and alongwith with minimal knowledge of cell swimming motility and surface scatteringproperties, we implement a theoretical model that universally predicts theeffective diffusion of cells for the geometries studied here. These results arean important step toward predicting the physical ecology of swimming cells inquiescent porous media and understanding their role in environmental and healthhazards in stagnant water.

Self-transport of swimming bacteria is impaired by porous microstructure