Dual-Functional Rhizobium dioscoreae Q9a for Glyphosate Biodegradation and Plant Growth Promotion: Insights into the Degradation Kinetics, Catabolic Pathways, Beneficial Properties, and Underlying Enzymatic Mechanisms

The extensive and persistent application of glyphosate has led to its accumulation in agricultural soils, creating potential ecological and health risks. In this study, a novel glyphosate-degrading bacterium, Rhizobium dioscoreae Q9a, was isolated and characterized. Strain Q9a effectively degraded glyphosate (50 mg/L) within 9 d in liquid culture. In addition to its degradative ability, strain Q9a exhibited multiple plant growth-promoting traits, including solubilization of up to 150 mg/L insoluble phosphate, production of 45 μg/mL indole-3-acetic acid, and siderophore secretion. Genome sequencing revealed multiple candidate genes potentially responsible for glyphosate metabolism, and heterologous expression validated the glyphosate oxidoreductase function of the key enzyme GoxD encoded by an oxidoreductase gene. Further, molecular docking and site-directed mutagenesis confirmed that Ser38 serves as the critical active site in GoxD for catalyzing glyphosate. These findings highlight the potential of strain Q9a as a promising bioinoculant for the bioremediation of glyphosate-contaminated environments and for enhancing crop growth.