Metagenomics reveals the profiles and drivers of antibiotic resistance genes and virulence factors in Glebionis coronaria L. planting soil

Abstract

Due to the application of contaminated water irrigation and bio-amendments, the emergence and spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soil have become a global problem, thus having potential threats to human health and ecology. However, limited knowledge exists regarding how variations in the soils of Glebionis coronaria L. (previously called Chrysanthemum coronarium L., or the crown daisy) planting sites influence the profiles of ARGs and VFs. In this study, ARGs, VFs, mobile genetic elements (MGEs), and microbial communities were comprehensively characterized using metagenomic methods in the soils from five different Glebionis coronaria L. planting sites in Shanghai. The dominant microbial populations in Glebionis coronaria L. planting soil were not affected by different planting sites, but there were changes in their relative abundance. The abundance and diversity of ARGs, VFs, and MGEs were different among the soils of five planting sites. The overall distribution characteristics of ARGs and VFs in the soils of each planting site remained consistent. Potential hosts shared by ARGs and VFs were present at each site, raising the risk of soil antibiotic resistance. Fe and T were the primary driving factors for the changes in ARGs and VFs, contributing to 11.32 % and 10.74 % of the overall variation in ARGs and VFs, respectively. Taken together, the identification of biological and non-biological factors that affect ARGs and VFs in the soils from different planting sites could provide valuable perspectives for controlling the dissemination of these genes. This study underscored the necessity for accurate and coordinated strategies to tackle the worldwide antibiotic resistance challenge.