Influence of pore geometry on motility and trapping of metal reducing bacteria

Diverse processes such as bioremediation, biofertilization, and microbial drug delivery
rely on bacterial migration in porous media. However, how pore-scale confinement alters
bacterial motility is unknown due to the inherent heterogeneity in porous media. As a
result, models of migration are limited and often employ ad hoc assumptions.
We aim to determine the impact of pore confinement in the spreading dynamics of two
populations of motile metal reducing bacteria by directly visualizing individual Acidovorax
and Pelosinus in an unconfined liquid medium and in a microfluidic chip containing regular
placed pillars. We observe that the length of runs of the two species differs from the
unconfined and confined medium. Results show that bacteria in the confined medium
display a systematic shorter jumps due to grain obstacles when compared to the open
porous medium. Close inspection of the trajectories reveals that cells are intermittently
and transiently trapped, which produces superdiffusive motion at early and subdiffusion
behavior at late times, as they navigate through the confined pore space. While in the open
medium, we observe a linearly increasing variance with respect to time for Acidovorax, and
for Pelosinus the variance increases at a much faster rate showing super diffusive behavior
at early times. At late times, the rate of growth in spreading increases for Acidovorax while
it reduces for Pelosinus. We finally discuss that the paradigm of run-and-tumble motility
is dramatically altered in the confined porous medium and its practical applications of
these effects on large-scale transport.