Cessation of manure application alters bacterial symbiosis patterns in soil-Lettuce systems, diminishing the dissemination potential of antibiotic resistance genes

Application of livestock manure is a common waste utilization measure that can enhance soil fertility and increase crop yields, but the antibiotics and resistance genes result in a potential threat to human and ecological health. Here, lettuce, a widely popular edible vegetable, was selected as a model to investigated the effect of long-term manure application on the distribution and movement of antibiotics resistance genes (ARGs) and potential host microorganisms in the soil-inter-root-plant system to decipher the bottleneck in assessing the health risks of manure application. To this end, we conducted field experiments to study the distribution of ARGs and microorganisms in soil and lettuce tissues after long-term application and cessation of fresh chicken manure. The ARGs of 384 subtypes and 13 antibiotics in soil were quantitatively analyzed by high-throughput qPCR chip. The results showed that fresh chicken manure inputs significantly affected the pattern of bacteria, mobile genetic elements (MEGs) and ARGs in soil, leaves and roots in the soil-lettuce cropping system. The cessation of manure application reduced the abundance of ARGs by 34.0%, 53.7%, and 23.9% in bulk soil, rhizosphere, and leaf, respectively. Correlation network and source-tracking analyses of ARGs and bacteria within leaves and roots of plants showed the ceasing manure input reducing the diffusion of ARGs and bacteria within leaves and roots into adjacent compartments. Partial least squares path model analysis (PLSPM) indicating the fresh chicken manure input indirectly affected the pattern of ARGs in soil by influencing the bacterial community and soil properties, which played a key role in the distribution of ARGs. In this study, we investigated the driving mechanism of the effects of manure on microbial community and ARG spectrum in soil-lettuce planting system, and the results can support the management strategy of soil ARGs spread.