Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions

Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.