Spatial Organization of Biomass Controls Intrinsic Permeability of Porous Systems

Biofilms alter the hydraulic properties of porous media, impacting processes ranging from groundwater remediation to industrial filtration. While biomass accumulation is known to reduce permeability, a quantitative link between its spatial organization and system-scale hydraulics remains missing. Here, using microfluidics, time-lapse microscopy, and a novel mechanistic model, we demonstrate that biofilm spatial organization is the key control for the resultant permeability decline. With independent experiments, we show that motile Pseudomonas putida sp. and its nonmotile mutant grow biofilm, attaining identical total biomass, yet cause permeability reductions of 78% and 94%, respectively. This divergence arises because motile cells, escaping nutrient-depleted zones, colonize the porous system differently in space, confining significant biomass upstream, whereas nonmotile cells persistently colonize homogeneously the entire system. Our model, conceptualizing the medium as a series of pores with different sizes and biomass-modified permeability, accurately predicts these dynamics. We conclude that biomass spatial distribution, not simply its abundance, is the primary control of permeability, offering a new framework to predict and manage clogging in environmental and engineered systems.