Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media Applied in a Managed Recharge Scenario

Abstract

Microbial communities play an important role in aquifer systems, as both hazards (e.g., pathogens, carriers of antibiotic resistance genes) and contributors to contaminant remediation. However, monitoring native microbial communities in situ remains challenging. To address this challenge, we developed a passive sampler with that employs removable cartridges containing solid media designed to re-create the aquifer environment in a controlled fashion and support consistent, repeatable, time-series sampling. With a bench-scale, continuous-loop setup circulating advanced-treated wastewater, we compared microbial community dynamics across three candidate porous media: native aquifer sediment, zirconia beads, and laboratory-grade silica sand. 16S rRNA gene amplicon sequencing revealed that native aquifer sediment best reflected influent microbial composition and temporal shifts. Native aquifer sediment also exhibited more spatial consistency in microbial diversity along the sampler. These findings suggest that native aquifer sediment is an optimal porous medium for long-term, in situ monitoring of microbial communities for managed aquifer recharge and other applications in groundwater systems.