Reactive Transport in Pore-Scale Biofilms: Model-Based Interpretation of a Microfluidic Experiment

Quantifying solute transport in biofilm-colonized porous media is essential for predicting microbially mediated processes in the hyporheic zone, especially in the presence of anoxic niches. However, our understanding of how pore-scale biofilm structure governs local transport remains limited, posing a significant challenge in developing accurate large-scale reactive transport models. The inherent structural heterogeneity of biofilms makes direct characterization of internal mass transfer technically difficult and complicates the interpretation of experimental observations.

In this study, we combine a high-resolution microfluidic experiment with pore-scale reactive transport modelling to investigate dissolved oxygen transport in biofilm-colonized pore spaces. Transparent planar optical sensors integrated into the microfluidic platform enabled non-invasive imaging of oxygen concentration fields at high spatial resolution, providing direct insight into intra-biofilm transport behaviour. To interpret these observations, we employed a pore-scale micro-continuum modelling framework in which the biofilm is represented as a fluid-filled microporous medium characterized by microscale transport properties, including permeability and effective diffusivity. The numerical model was calibrated against experimental datasets using an optimization-based approach, allowing for the simultaneous estimation of the permeability of the biofilm, effective diffusivity, and metabolic kinetic parameters. Results show strong agreement between simulated and measured oxygen distributions, supporting the suitability of the modelling framework to resolve complex mass transfer mechanisms at the fluid–biofilm interface. Analysis of the inferred parameters suggests that diffusive transport dominates within the biofilm matrix, while biofilm permeability is found to be relatively low. Furthermore, the resolved oxygen consumption rates were found to be significantly lower than those observed in batch reactors, highlighting the role of pore-scale environmental limitations on metabolic activity. This work establishes a robust framework for further exploring the relationship between biofilm morphology and reactive transport, providing a basis for more accurate upscaling in complex porous environments.