Dispersal, Establishment, and Functional Shifts of Runoff-Derived Bacterial Taxa Shaping Microbial Diversity in Infiltration-Based Aquifer Recharge Systems

Stormwater infiltration systems (SIS) are increasingly implemented to mitigate urban flooding and recharge groundwater but can disseminate chemical and biological contaminants, including pathogens. This study assessed the impact of six SIS, differing in vadose zone thickness and runoff transit time, on the microbial composition of the underlying aquifer. Groundwater samples and biofilms collected using passive samplers composed of 8 mm clay beads enclosed in inert pouches were analyzed via a tpm metabarcoding, enabling DNA read allocations at the species level. SIS altered groundwater tpm microbial diversity and community structure, especially in systems with shallow vadose zones and fast transit times. Downstream SIS groundwaters showed higher richness and colonization by potential pathogens such as species from Aeromonas, Pseudomonas, Stenotrophomonas, and Xanthomonas. Biofilms revealed more persistent and pronounced microbial changes than water samples, capturing bacteria with substrate-colonizing capabilities, such as Pseudomonas aeruginosa. Functional predictions from taxonomic allocations indicated a shift toward pollutant degradation and pathogenic traits in fast-transit systems. These findings indicate that SIS can promote waterborne pathogen establishment, threatening groundwater quality and public health. Transit time emerged as a critical factor modulating microbial impacts from tpm-harboring bacteria, underscoring the need to integrate microbial risk assessments into SIS design and management strategies.