Carrier-resolved metagenomics suggests the dual “filter–hub” function of a large freshwater lake toward incoming antibiotic resistance genes

Rivers and wastewater-treatment plants (WWTPs) convey antibiotic resistance genes (ARGs) to lakes. Studies simultaneously profiling ARGs and their carriers and tracking their persistence in lakes remain scarce. We collected cell- and virus-size fractions from Lake Biwa, Japan, 11 in-flowing rivers, and one WWTP for shotgun metagenomic sequencing. We reconstructed 326 bacterial metagenome-assembled genomes, 7917 plasmid contigs (472 harboring conjugation genes), and 32,375 viral contigs. The chromosomes contained 1502 ARGs (predominantly fluoroquinolone and glycopeptide resistance). The plasmids encoded efflux- and target-alteration determinants spanning 25 drug classes. Only 3.6 % of the viral genomes carried ARGs, chiefly qnr and dfr. ARG class composition differed among carriers, forming a spatial mosaic unrelated to land use or livestock density. Of the ARG-carrying cells and viruses, 85-97 % were undetectable in the lake, suggesting dilution and adaptation failure. Chromosome comparison identified 1809 putative horizontal gene transfer events, 2.1 % of which bridged lake-resident and external taxa. ARG profiles differed according to carrier type. Thus, Lake Biwa might function simultaneously as a filter, removing incoming ARG-carrying cells and viral particles, and as a "silent hub," potentially integrating external ARGs into lake-resident bacteria through horizontal gene transfer. These data provide a foundation for assessing and managing antimicrobial resistance in large freshwater ecosystems.