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.

中文翻译：

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肥料施用丰富了噬菌体相关的抗菌药物耐药性并重建了水稻土中噬菌体-细菌的生态网络


抗生素耐药性是对全球健康的紧迫威胁，导致严重的抗生素耐药性感染和死亡。噬菌体可以作为细菌适应的遗传库，促进抗生素抗性基因（ARG）的水平转移。然而，环境扰动如何通过噬菌体-细菌生态网络影响病毒 ARG 的变化仍然不清楚。本研究应用无扩增偏倚的宏基因组和病毒组学组合测序来研究不同肥料水稻土中病毒抗性组和生态噬菌体-细菌网络的变化。结果表明，粪便施用显着改变了微生物群落组成并增加了细菌 ARG 的丰度。与化肥处理和非肥料对照相比，粪便改良后配对病毒组和宏基因组之间共享的 ARG 数量以及噬菌体相关 ARG 的宿主细菌多样性明显增加。在施肥土壤病毒体中观察到编码应激和基因转移相关功能的基因丰度升高。粪肥施肥重建了噬菌体-细菌生态网络，增加了相互作用，有可能促进 ARG 在粪肥改良土壤中的传播。