Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media

Abstract

Managed aquifer recharge (MAR) with advanced treated wastewater is a promising strategy to combat aquifer depletion; however, its impact on native microbial communities remains insufficiently characterized. Concerns include the potential introduction of pathogens, antibiotic resistance genes (ARGs), and trace organic pollutants, as well as the disruption of native microbial processes critical for contaminant degradation in groundwater. However, it is very challenging to sample aquifer microbes in situ, especially in a representative, time-resolved fashion. With this goal, we developed a passive sampler 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. A bench-scale, continuous-loop study compared microbial community dynamics across three candidate porous media: native aquifer sediment, zirconia beads, and laboratory-grade silica sand. 16S rRNA gene amplicon sequencing was applied to profile microbial communities and revealed that native aquifer sediment from the aquifer of study best reflected influent microbial composition and temporal shifts, particularly among the dominant bacterial phyla Proteobacteria, Bacteroidota, Planctomycetota, and Verrucomicrobiota. Native sediment also exhibited more spatial consistency in microbial diversity. Based on these findings, a full-scale, 3Dprinted sampler using native sediment was developed for long-term monitoring in MAR systems to support future study of the impacts of introduction of advanced treated water into an aquifer.