The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.

在农业土壤中施用有机改良剂可以提高作物产量，同时改善受体土壤的理化和生物特性。然而，使用粪便改良剂作为肥料会带来环境风险，例如抗生素残留、抗生素抗性基因（ARG）和移动遗传元件（MGE）污染土壤和作物。为了深入研究这些风险，我们将从传统农场和有机农场获得的奶牛粪便改良剂（泥浆、新鲜粪便、陈化粪便）施用于土壤。随后，在改良后的土壤中种植了生菜和小麦。收获后，通过高通量 qPCR 测定改良土壤和植物中 95 个 ARG 和 MGE 基因的丰度。通过 16S rRNA 扩增子测序和 qPCR 确定土壤原核生物群落的结构。ARG 和 MGE 基因的绝对丰度在处理（改良与未改良）、改良来源（传统与有机）和改良类型（浆料与新鲜粪便与陈化粪便）之间有所不同。关于改良剂本身中的 ARG 绝对丰度，与新鲜或陈化粪便相比，通常在浆液中发现更高的值。土壤中的这些丰度通常高于植物样品中的丰度，小麦籽粒中的丰度通常高于生菜植物中的丰度。与用有机改良剂施肥的生菜植物相比，用传统改良剂施肥的生菜植物显示出更高的四环素抗性基因绝对丰度。对于土壤和植物样品中抗生素耐药性的风险，没有一种处理方法可以被确定为最佳或最差的处理方法。在同一处理中，改良剂、改良土壤和最终作物之间的抗药性风险有所不同。换句话说，根据我们的数据，粪便改良作物的抗药性风险不能从改良本身的分析中直接推断出来。我们的结论是，根据所研究的具体问题，抗性风险分析应特别关注修正、修正的土壤或作物。