Plasmid–Host Networks Reveal Persistent Mobile Elements Across Wastewater Treatment

Abstract

Plasmids drive horizontal gene transfer and antimicrobial resistance spread in water resource recovery facilities, yet their in situ dynamics in complex microbial communities remain poorly characterized. We apply Hi-C metagenomics to resolve plasmid–host associations across influent, activated sludge, and effluent at three facilities. We identify 944 plasmid clusters with facility- and stage-specific distributions. Plasmid host range narrows from influent to effluent, indicating that treatment selectively constrains plasmid–host associations. Persistent plasmid clusters with detectable mobility markers show a trend toward broader, less modular host networks than those with no detected markers. Hi-C-supported antibiotic resistance gene associations highlight Burkholderiaceae and Rhodocyclaceae as prominent hosts of beta-lactam, tetracycline and sulfonamide resistance genes across facilities. These findings indicate that wastewater treatment narrows plasmid host range while maintaining dominant plasmid-carrying taxa and adaptive mobile elements, providing a framework for understanding plasmid persistence across treatment systems. Using Hi-C metagenomics, this study maps how plasmids associate with bacterial hosts across wastewater treatment. They find that plasmid host range narrows from influent to effluent, and a few bacterial families act as persistent plasmid reservoir.