Comprehensive understanding of the microbiome and resistome evolution in compost is crucial for guaranteeing the safety of organic fertilizers. Current studies using different composting systems and sequencing technologies have yielded varying conclusions on the efficacy of exogenous additives (EAs) in reducing antibiotic resistance genes (ARGs) in compost. This study employed metagenomics to investigate the impact of various EAs on microbial communities, ARGs, their coexistence with mobile genetic elements (MGEs), and ARG hosts in co-composting. Our results demonstrated that EAs significantly reshaped the microbial communities and facilitated a notable reduction in total ARG abundance and diversity, primarily by decreasing core ARGs. Cooperative rather than antagonistic relationships among bacteria. The RA changes in total ARGs are mainly caused by a decrease in the prevalence of core ARGs. Furthermore, EAs showed significant efficacy in reducing clinical ARGs, including cfxA, tetX1, cfxA6, vanA, and aac (6′)-Ib', with diatomite (5 %) and zeolite (5 %) being the most effective. The effect of EAs on ARGs and microbial community assembly were stochastic processes. Composting stage and EAs jointly reduced the association between ARGs and MGEs in the composting system. The reduction of ARGs attributed to a decreased abundance of potential pathogenic ARG-associated hosts and diminished associations with MGEs. In conclusion, EAs present a straightforward and effective approach for promoting ARGs reduction in compost, offering crucial insights for assessing the environmental risks associated with the release of agricultural ARGs.

中文翻译：

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外源添加剂重塑微生物组并促进猪粪和蘑菇渣共堆肥中抵抗组的减少


全面了解堆肥中的微生物组和抵抗组进化对于保证有机肥料的安全至关重要。目前使用不同堆肥系统和测序技术的研究对外源添加剂 （EAs） 在减少堆肥中抗生素耐药基因 （ARG） 方面的功效得出了不同的结论。本研究采用宏基因组学研究各种 EA 对微生物群落、ARGs、它们与移动遗传元件 （MGE） 共存以及共堆肥中的 ARG 宿主的影响。我们的结果表明，EAs 显着重塑了微生物群落，并促进了 ARG 总丰度和多样性的显着降低，主要是通过减少核心 ARGs。细菌之间的合作关系而不是拮抗关系。总 ARGs 的 RA 变化主要是由核心 ARGs 患病率的降低引起的。此外，EA 在降低临床 ARGs 方面显示出显着的疗效，包括 cfxA、tetX1、cfxA6、vanA 和 aac （6′）-Ib'，其中硅藻土 （5%） 和沸石 （5%） 是最有效的。EAs 对 ARGs 和微生物群落组装的影响是随机过程。堆肥阶段和 EAs 共同降低了堆肥系统中 ARGs 和 MGEs 之间的关联。ARGs 的减少归因于潜在致病性 ARG 相关宿主的丰度降低以及与 MGEs 的相关性降低。总之，EAs 提出了一种直接有效的方法来促进减少堆肥中的 ARGs，为评估与农业 ARGs 释放相关的环境风险提供了重要的见解。