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Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed that bacterial motility plays a key role in the transport process. Flow and transport experiments performed in microfluidic chips containing randomly placed obstacles confirmed that the distributions of non-motile particles stays compact, whereas for the motile strains, the distributions are characterized by both significant retention as well as fast downstream motion. For motile bacteria, the detailed microscopic study of individual bacteria trajectories reveals two salient features: (i) the emergence of an active retention process triggered by motility, (ii) enhancement of dispersion due to the exchange between fast flow channels and low flow regions in the vicinity of the solid grains. We propose a physical model based on a continuous time random walk approach. This approach accounts for bacteria dispersion via variable pore-scale flow velocities through a Markov model for equidistant particle speeds. Motility of bacteria is modeled by a two-rate trapping process that accounts for the motion towards and active trapping at the obstacles. This approach captures the forward tails observed for the distribution of bacteria displacements, and quantifies an enhanced hydrodynamic dispersion effect that originates in the interaction between flow at the pore-scale and bacterial motility. The model reproduces the experimental observations, and predicts bacteria dispersion and transport at the macroscale., Comment: 30 pages, 10 figures

The role of activity on the hydrodynamic dispersion of bacteria in a model porous medium is studied by tracking thousands of bacteria in a microfluidic chip containing randomly placed pillars. We first evaluate the spreading dynamics of two populations of motile and non-motile bacteria injected at different flow rates. In both cases, we observe that the mean and the variance of the distances covered by the bacteria vary linearly with time and flow velocity, a result qualitatively consistent with the standard geometric dispersion picture. However, quantitatively, the motiles bacteria display a systematic retardation effect when compared to the non-motile ones. Furthermore, the shape of the traveled distance distribution in the flow direction differs significantly for both the motile and the non-motile strain, hence probing a markedly different exploration process. For the non-motile bacteria, the distribution is Gaussian whereas for the motile ones, the distribution displays a positive skewness and spreads exponentially downstream akin to a Gamma distribution. The detailed microscopic study of the trajectories reveals two salient effects characterizing the exploration process of motile bacteria : (i) The emergence of an "active" retention effect due to an extended exploration of the pore surfaces, (ii) an enhanced spreading at the forefront due to the transport of bacteria along "fast-tracks" where they acquire a velocity larger than the local flow velocity. We finally discuss the practical applications of these effects on the large-scale macroscopic transfer and contamination processes caused by microbes in natural environments., Comment: 10 pages, 10 figures