Organic Fertiliser Additions Promote Transformation of Extracellular Antibiotic Resistance Genes to Soil Bacteria

The spread of antibiotic resistance genes (ARGs) through horizontal gene transfer (HGT) poses a serious risk to public health. Natural transformation of extracellular ARGs (eARGs) to bacterial competent cells is a HGT pathway, but its frequency in soil and the influencing factors remain largely unknown. Here, we show that organic fertiliser amendment significantly increased the transformation frequency of plasmid-borne eARGs to both the model species Acinetobacter baylyi ADP1 inoculated into a sterile soil and to diverse native bacteria in an unsterile soil. During incubation in unsterile soil, eARGs were transformed into six bacterial phyla, especially Pseudomonadota and Actinobacteria, including opportunistic pathogens in the genera Stenotrophomonas, Acinetobacter and Pseudomonas. Most (87.5%) of the detected transformants belong to bacterial taxa previously unknown to be capable of acquiring extracellular DNA by natural transformation. Organic fertiliser amendments, likely through enriched metals (e.g., Mn and Zn), promoted reactive oxygen species (ROS) production, triggered oxidative stress responses, increased membrane permeability and ATP synthesis and enhanced bacterial competence for the uptake of eARGs. Our findings indicate that natural transformation of eARGs represents an important HGT pathway in soils and organic fertiliser additions can substantially promote the eARG spreads within the soil bacterial community through natural transformation.