Phenomena affecting aquifer clogging by microorganisms during in-situ bioremediation or groundwater recharge in water reuse are poorly understood. To gain basic understanding of these clogging phenomena, two-dimensional micromodels representative of fine sand, called Silicon Pore Imaging Elements (SPIEs), were constructed to visualize biological growth. This apparatus allows both short and long time-lapse observations to be made at both the pore micrometer scale and the SPIE centimeter mesoscale.;The SPIEs were seeded with mixed cultures and fed a mineral salt solution amended with acetate. Microscale observations revealed a variety of biological growth morphologies (biofilms, aggregates, filaments, "pearl necklaces", and biowebs) with different attaching properties and different colonization patterns (spreading, attachment and detachment, chemotropism and/or rheotropism, and cell motility). Clogging occurred within millimeters of an injection well, even with flow velocities of several meters per day. Permeability reductions were similar to that observed in field operations: an initial slow decrease, followed by a rapid drop, with sudden periodic permeability increases correlated to biomass sloughing in preferential flow paths.;Chlorine disinfection with 40 mg/L for 8 to 14 hr opened flow paths through a uniformly colonized SPIE by initial sloughing of biofilms and single colonies along preferential paths, then by erosion of larger biological masses. Permeability was partially recovered. Following restoration of acetate feeding however, the open flow paths rapidly recolonized. Within two to seven days, permeability decreased to pre-disinfection values. Disinfection with 5mg/L chlorine for 6 hr of a fungi colonized SPIE caused no detachment as the filaments were woven between the SPIE grains. Spores released in the preexisting flow channel separating mycelia sprouted once normal feed was restored and led to rapid colonization.;Aggregate growth, modeled in network models, showed that aggregates can lead to much greater permeability reductions for a given porosity reduction than biofilms, closer to the observed permeability reductions in fine porous media. The narrowest pores clog faster than the widest pores but to a lesser extent.;The experimental and modeling results suggest the need for multi-species model assumptions for improved predictions of substrate consumption and biological clogging.
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