Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.

中文翻译：

---

长期无抗生素施肥下土壤抗生素抗性组患病率的田间证据


越来越多的证据表明，使用含有残留抗生素的粪便普遍会导致土壤抗生素耐药基因 （ARG） 的增加。然而，对于长期无抗生素施肥的影响以及无抗生素粪肥和化肥对土壤 ARG 的差异，人们的了解有限。本研究旨在通过原位探测长期暴露于化学肥料和/或未经抗生素改良的动物粪便的田间土壤中的细菌群落和环境变化来量化抗生素耐药组的组装模式。长期受精略微影响抗生素耐药组的多样性，85.5% 的总 ARG 和移动遗传元件 （MGE） 在所有治疗类型中都很常见，同时它们的丰度从 0.68 个显着增加到最大 0.90 拷贝/16S rRNA。与化肥相比，使用无抗生素粪肥时，ARG 丰度的增加不那么明显，尤其是 II 级 ARGs。然而，当无抗生素粪污和化肥混合施用时，养分（如有效氮和有机质）和基质强化因子显著增加，导致土壤微生物种群富集，尤其是某些抗性物种和I.级和II.级耐药性物质。尽管受到细菌群落、土壤特性、重金属和 MGEs 等多种因素的影响，但 MGEs 通过直接和间接途径对塑造 ARGs 具有最显着的标准化影响。 我们的研究结果表明，虽然不含抗生素的粪便可以降低抗生素残留的风险并促进可持续农业实践，但它可能无法完全消除 ARGs 的流行，这凸显了需要更全面的策略来解决农业中的抗生素耐药性，而不是简单地禁止使用抗生素。