Abstract
<jats:p>Biofilms are ubiquitous in natural and engineered porous media, where they structure microbial communities and regulate biogeochemical transformations by altering fluid flow and reactive transport. At pore-scales, biofilm is commonly modeled as a permeable reactive compartment with an evolving morphology but constant intrinsic transport and reaction properties. We leverage time-resolved microscopy data of biomass distribution and dissolved molecular oxygen (O2) to quantify reactive transport in biofilm-colonized porous media. Our dataset allows exploring the pore-scale emergence of O2-depleted microsites, which play a crucial role in biogeochemical processes of well-oxygenated soils and shallow sediments. To this end, we constrain a pore-scale flow and reactive transport model through an inverse modeling approach. Our results show that the measured O2 dynamics can only be reproduced when both biofilm morphology and its intrinsic transport and reaction properties evolve over time. This result quantitatively supports the idea that biofilms actively alter their intrinsic properties (e.g., alteration in microstructure and microbial metabolism), in response to environmental factors and the effects of flow and transport processes. Our framework enables inverse estimation of intrinsic biofilm properties, offering new insight into biofilm microstructure, providing interpretations of experimental observations and establishing new opportunities for modeling and control of biofilm systems.</jats:p>