Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

中文翻译：

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与受稻田生态系统稻田养鱼一体化影响的古菌、细菌和病毒群落相关的抗生素耐药性变化

抗生素抗性基因（ARG）作为一种新认​​识的污染物，对全球人类健康构成潜在风险，而稻田土壤中的抗生素抗性基因可能会因不同的农业生产模式而发生改变。为了阐明广泛使用的可持续农业生产模式（即稻田养鱼一体化）对抗生素抗性组的影响和机制，我们应用宏基因组测序来评估ARG、移动遗传元件（MGE）、细菌、古细菌和病毒。水稻土。水稻土中鉴定出20个类型、359个亚型的ARG。稻田养鱼一体化降低了 ARG 和 MGE 的多样性以及优势 ARG 和 MGE 的丰度。显着减少的ARG主要是抗生素失活和调节剂类型，并且根据其对人类健康的潜在威胁主要排名IV级。稻田养鱼一体化降低了阿尔法多样性并改变了微生物群落组成。 MGE、细菌、古细菌和病毒与 ARG 表现出显着的相关性，而稻田养鱼一体化有效地改变了它们之间的相互关系。病毒、细菌和 MGE 在影响稻田养鱼综合农业的 ARG 方面发挥着至关重要的作用。稻田养鱼一体化影响 ARG 的最关键途径是通过调节病毒群落，从而直接或间接影响 ARG 丰度。我们的研究有助于从新的角度控制和修复ARGs污染，为清洁可持续农业生产的发展提供理论支撑。