Microbiome-Informed Pathways Linking Nature-Based Treatment Systems to Antimicrobial Resistance Outcomes

Antimicrobial resistance (AMR) is a One Health challenge driven by clinical antibiotic use and environmental processes that shape microbial selection and genetic exchanges. Nature-based solutions (NbS), particularly constructed wetlands, are increasingly used to remove complex contaminant mixtures from aquatic systems. Although these systems often achieve considerable efficiencies, their effects on AMR dynamics remain unclear. This review synthesizes evidence on how aquatic rhizospheres function as microbiome-associated ecological reactors, in which contaminant mixtures, redox gradients and microbial interactions jointly influence resistance. We show that wetlands can function along a continuum between antimicrobial resistance attenuation, persistence, and dissemination, depending on the design, operation, and ecological context. Importantly, the removal of bioactive compounds does not necessarily translate to a reduced resistance risk, as selective pressures may persist within biofilms, sediments, and plant-associated compartments. We propose a microbiome-informed conceptual framework for interpreting AMR in nature-based systems. This perspective identifies potentially modifiable leverage points for understanding, interpreting, and potentially mitigating resistance-related risks and underscores the need for monitoring and risk assessment strategies that extend beyond conventional chemical metrics and incorporate the One Health exposure pathways. Together, these insights reposition wetlands as conditional solutions, whose sustainability depends on explicitly addressing antimicrobial resistance, alongside contaminant removal.