Microbial ammonia oxidation-driven hydroxyl radical generation enables efficient degradation of antibiotic resistance genes.

The environmental dissemination of antibiotic resistance genes (ARGs) poses a significant threat to both ecosystem and human health, yet their efficient removal continues to present considerable challenges. Hydroxyl radicals (•OH), as highly reactive oxidants, are capable of effectively degrading extracellular ARGs (eARGs). However, conventional Fenton reaction systems typically demand substantial chemical inputs and high energy consumption. Here, we report a biologically driven pathway that couples microbial ammonia oxidation with •OH generation to enable sustainable eARGs degradation. Alcaligenes sp. CHO6, a heterotrophic ammonia-oxidizing bacterium, was isolated from aquaculture sediment and shown to couple aerobic ammonia oxidation with Fe(III) reduction, leading to •OH production and subsequent eARGs degradation. During ammonia oxidation, strain CHO6 accumulated hydroxylamine (NH2OH), which acted as a key reductant driving Fe(III)/Fe(II) cycling and iron-mediated •OH formation. Genome sequencing revealed a dnfT1RT2ABCD cluster homologous to the direct ammonia oxidation (Dirammox) pathway. Heterologous expression of dnfABC in Escherichia coli confirmed its functional role in NH2OH accumulation and •OH generation. In vitro, the •OH produced by strain CHO6 degraded >90% of several eARGs (bla, tetA, gmR) within 3 h. This study unveils a previously unrecognized mechanism linking microbial nitrogen metabolism to reactive oxygen species (ROS) formation and offers a proof-of-concept for a biologically driven approach for mitigating eARGs in wastewater and natural systems.