Modeling chemotaxis–biofilm competition during NAPL biodegradation in porous media

Bioremediating non-aqueous phase liquids (NAPLs) in subsurface environments poses a persistent challenge due to their low solubility and the tendency of microbial biofilms to induce pore clogging, both of which limit contaminant accessibility. This study develops a continuum-scale bioreactive transport model to investigate the competitive dynamics between chemotactic motility - defined as the intrinsic ability of bacteria to migrate in response to chemical gradients - and biofilm formation during toluene biodegradation under diffusion-dominated conditions. The model incorporates NAPL dissolution, solute diffusion, chemotactic migration, microbial growth, and biofilm-induced pore clogging. We tested three microbial strategies: a biofilm-only population, a chemotaxis-only population, and a combined system. Our results reveal that competition for feeding alone, even in the absence of physical pore obstruction, limits bacterial mobility. Simulations show that chemotactic bacteria migrate along solute gradients, forming patterns that refresh the contaminant targeting. However, this directed migration toward the aromatic hydrocarbon is progressively restricted in the presence of growing biofilms by a dynamic feeding competition for dissolved toluene. As bacterial activity suppresses the dissolved toluene gradient, the system shifts into a growth-dominated regime, chemotactic activity is suppressed, and continuous biofilm expansion leads to clogging and more reduced substrate accessibility. Our results also show that chemotactic bacteria can mitigate clogging by suppressing biofilm formation through competitive interactions, but this comes at a cost: reduced overall degradation rates compared to biofilm-only systems. While advective transport and shear-induced biofilm detachment are not considered here, the results isolate key microbial competitive mechanisms relevant to diffusion-controlled environments, with implications for bioremediation and other subsurface applications such as underground hydrogen storage, where suppressing microbial activity and bioclogging are desirable.