From plant auxin to antibiotic resistance genes dissemination: Comparative insights into indole-3-acetic acid-enhanced horizontal gene transfer and underlying mechanisms between soil microbiomes and pure cultures

The spread of antibiotic resistance genes (ARGs) in plant-soil systems threatens human health. Indole-3-acetic acid (IAA), an auxin secreted by plants and microorganisms, can be released into the soil during plant growth. However, little is known about whether IAA affects the spread of ARGs in soil microbiomes, which possess broad-host-range plasmids that potentially affect ARGs transmission more substantially than pure bacterial cultures. Here, we systematically investigated contributions of environmental-level IAA on the horizontal transfer of ARGs and the underlying mechanisms in soil microbiomes and pure cultures. Our results demonstrated that IAA enhanced both conjugative and transformative transfer of ARGs in soil microbial communities, in contrast to the limited effects in pure cultures. Integrated phenotypic, genotypic, transcriptomic, and proteomic analyses revealed that the enhanced ARGs transmission in the soil microbial community was affiliated with over-produced reactive oxygen species (ROS), increased cell membrane permeability, enhanced biofilm formation, activated quorum sensing, and promoted bacterial competence. Different biofilm formation capacities and ROS-induced stress responses resulted in different ARGs transfer frequencies in soil microbiomes and pure cultures. Our study highlights IAA's important role in ARGs dissemination in microbiomes of plant-soil systems and underscores the need to evaluate the potential risks of IAA application in agriculture.