Plants select antibiotic resistome in rhizosphere in early stage

Abstract

Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.

Keywords: Antibiotic resistance genes; Metagenome; Multiple generation cultivation; Rhizosphere microbiome; Soil planet health.