Livestock manure-based organic fertilization facilitates the transmission of antibiotic resistance genes across the soil-onion continuum: A significant contribution from root exudates

The transmission and transformation patterns of antibiotic resistance genes (ARGs) in the soil-onion continuum under the application of organic fertilizers in actual agricultural cultivation are still unknown. This study systematically analyzed the occurrence characteristics of ARGs in soil and onion (roots and bulbs) under the application of organic fertilizer from livestock manure, and revealed the response mechanism of phenolic metabolites in roots. The results showed that fertilization promoted the enrichment of ARGs in the soil and onions. The abundance of ARGs in the bulbs of the pig manure and sheep manure treatment groups was 4 times and 2 times as high as that in the unfertilized group, respectively. In comparison to the bulbs, a higher abundance of ARGs was observed in the roots of onions. The 11 ARGs, including high-risk variants such as tetX and mexE, were detected co-occurring in both onion tissues and the surrounding soil. Fertilization treatment significantly changed the community composition of ARGs-related host bacteria in onion tissues. Livestock manure-based organic fertilizers elevated the potential exposure risk of ARGs in bulbs by more than 20 %. Five strains of multidrug-resistant endophytic bacteria (including Streptomyces and Fictibacillus) were isolated from the main edible parts of onion bulbs. It is worth noting that this study found that kaempferol (35–140 μg/L) and p-coumaric acid (2.5–10 μg/L) significantly enhanced the conjugation and transfer of the RP4 plasmid in the onion endophytes (Bacillus sp. and Paenibacillus sp.) and soil microbial communities. Root exudates were the predominant factors regulating the transmission of ARGs in the soil-onion system.