Temporal progression of treatment performance in soil aquifer treatment systems: Role of microbial communities

Soil aquifer treatment (SAT) is a nature-based solution for wastewater reuse and aquifer recharge in which subsurface passage attenuates biological and chemical hazards. Here, we monitored the performance of two pilot SAT systems fed by secondary WWTP effluent. The unsaturated-zone (USZ) consisted of sand in both systems, whereas one of them included woodchips, compost, and mineral amendments in its composition (reactive barrier). The study began shortly after complete replacement of both USZ media and spanned two years across five recharge campaigns, allowing evaluation of system maturation. Semi-quantitative analysis of 127 contaminants of emerging concern (CECs) by UHPLC-HRMS, quantification of antibiotic-resistance markers by qPCR, and zebrafish eleuthero embryo qPCR-based toxicity bioassays showed a progressive improvement in effluent quality over time. Overall reductions of 95% to >99% were reached in bacterial loads, ARG markers, and toxic responses after about one year of operation, whereas CEC levels decreased more gradually. Both systems showed similar efficiencies in reducing microbial and toxic hazards, while the reactive-barrier system systematically outperformed the sand-only one in CEC removal. 16S rRNA gene sequencing and functional inference of USZ microbiomes revealed a substitution of influent-derived taxa predominant in newly replaced systems by communities with distinct predicted metabolic potentials, describing a taxonomic succession concomitant with the improvement in effluent water quality. These results indicate that SAT performance after media replacement is strongly time-dependent and highlight the value of tracking the microbiome composition for interpreting and optimizing treatments. They also suggest that inoculation or seeding strategies may help shorten system maturation periods.