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Bacterial biofilms can form in porous media that are of interest in industrial and particularly environmental applications such as in situ groundwater remediation. The presence of biofilms modifies pore-scale and bulk hydrodynamics and consequently solutes transport and reaction kinetics. Porous media consist of highly heterogeneous flow fields and thus biofilm growth is also highly variable resulting in spatially variable biofilm permeabilities. Random processes are often invoked in hydrogeology to model variable quantities. Geo-statistical simulations require numerous realizations of a stochastic process over a grid. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore scale flow and solute transport on a fine grid by considering various realizations of the biofilm permeability field. Using a conservative tracer experiment we first validate our flow and transport model which is then used to understand the impact of a heterogeneous permeability field on fluid-fluid and biologically driven reactions.

© 2018 Elsevier Ltd This study investigates the functional correspondence between porescale hydrodynamics, mass transfer, pore structure and biofilm morphology during progressive biofilm colonization of a porous medium. Hydrodynamics and the structure of both the porous medium and the biofilm are experimentally measured with 3D particle tracking velocimetry and micro X-ray Computed Tomography, respectively. The analysis focuses on data obtained in a clean porous medium after 36 h of biofilm growth. Registration of the particle tracking and X-ray data sets allows to delineate the interplay between porous medium geometry, hydrodynamic and mass transfer processes on the morphology of the developing biofilm. A local analysis revealed wide distributions of wall shear stresses and concentration boundary layer thicknesses. The spatial distribution of the biofilm patches uncovered that the wall shear stresses controlled the biofilm development. Neither external nor internal mass transfer limitations were noticeable in the considered system, consistent with the excess supply of nutrient and electron acceptors. The wall shear stress remained constant in the vicinity of the biofilm but increased substantially elsewhere.

Biofilms are ubiquitous bacterial communities that grow in various porous media including soils, trickling, and sand filters. In these environments, they play a central role in services ranging from degradation of pollutants to water purification. Biofilms dynamically change the pore structure of the medium through selective clogging of pores, a process known as bioclogging. This affects how solutes are transported and spread through the porous matrix, but the temporal changes to transport behavior during bioclogging are not well understood. To address this uncertainty, we experimentally study the hydrodynamic changes of a transparent 3‐D porous medium as it experiences progressive bioclogging. Statistical analyses of the system's hydrodynamics at four time points of bioclogging (0, 24, 36, and 48 h in the exponential growth phase) reveal exponential increases in both average and variance of the flow velocity, as well as its correlation length. Measurements for spreading, as mean‐squared displacements, are found to be non‐Fickian and more intensely superdiffusive with progressive bioclogging, indicating the formation of preferential flow pathways and stagnation zones. A gamma distribution describes well the Lagrangian velocity distributions and provides parameters that quantify changes to the flow, which evolves from a parallel pore arrangement under unclogged conditions, toward a more serial arrangement with increasing clogging. Exponentially evolving hydrodynamic metrics agree with an exponential bacterial growth phase and are used to parameterize a correlated continuous time random walk model with a stochastic velocity relaxation. The model accurately reproduces transport observations and can be used to resolve transport behavior at intermediate time points within the exponential growth phase considered., Key Points Experimental three‐dimensional particle tracking of flow tracers provides pore‐scale hydrodynamics in a progressively bioclogged porous mediumBiofilm growth induces formation of preferential flow paths and stagnation zones, leading to an increase of anomalous transportA continuous time random walk model based on a gamma distribution of the pore‐scale velocities captures transport dynamics