Cessation of manure application diminishes the dissemination potential of antibiotic resistance genes by altering bacterial interaction patterns in soil–lettuce systems

Abstract

The application of livestock manure is a common waste utilization measure that can increase soil fertility and crop yields, but the antibiotics and resistance genes involved result in a potential threat to human health and animal welfare. Here, lettuce, a widely popular edible vegetable, was selected as a model with which to investigate the effects of long-term application (FM) and temporary cessation (cessation) of fresh chicken manure on the distribution and movement of antibiotic resistance genes (ARGs) in the soil-root-plant system to elucidate the bottleneck in assessing the health risks of manure application. ARGs associated with 13 antibiotics and 384 subtypes in soil were quantitatively analyzed via high-throughput qPCR, and the results revealed that cessation treatment significantly affected the patterns of bacteria, mobile genetic elements (MGEs) and ARGs in the soil, leaves and roots in the soil–lettuce cropping system compared with FM treatment. Cessation of manure application reduced the abundance of ARGs by 34.0 %, 53.7 %, and 23.9 % in the bulk soil, rhizosphere soil, and leaves, respectively. Correlation network and source-tracking analyses of ARGs and bacteria within leaves and roots revealed that cessation treatment reduced the diffusion of ARGs and bacteria within leaves and roots into adjacent sites, and partial least squares path model (PLSPM) analysis indicated that FM treatment indirectly affected the pattern of ARGs in soil by influencing the bacterial community and soil properties, which play key roles in the distribution of ARGs. In summary, we investigated the driving mechanism of the effects of manure on the microbial community and ARG spectrum in a soil–lettuce planting system, and the results can support strategies for managing the spread of ARGs in the soil.