Manure application enriches phage-associated antimicrobial resistance and reconstructs ecological network of phage-bacteria in paddy soil

Antimicrobial resistance is an urgent threat to global health, causing serious antibiotic-resistant infections and deaths. The phages can serve as genetic reservoirs for bacterial adaptation, facilitating the horizontal transfer of antibiotic resistance genes (ARGs). However, how environmental perturbations impact the variation in viral ARGs via the phage-bacterial ecological network remains obscure. This study applied combined metagenomic and viromic sequencing without amplification bias to investigate the variations in the viral resistome and the ecological phage-bacterial networks in the paddy soils with different fertilizers. Results showed that manure application significantly changed the microbial community composition and increased the abundance of bacterial ARGs. The numbers of shared ARGs between paired virome and metagenome, as well as the diversity of host bacteria for phage-associated ARGs distinctly increased with manure amendment compared to chemical fertilizer treatment and non-fertilizer control. Elevated abundance of genes encoding stress and gene transfer-associated functions was observed in the manured soil viromes. Manure fertilization restructured the phage-bacteria ecological network with increased interactions potentially facilitating the dissemination of ARGs in the manure amended soils.