Engineering auxin degradation into root-associated bacteria promotes plant growth

Overproduction of indole-3-acetic acid (IAA) by rhizosphere bacteria disrupts plant auxin homeostasis and induces root growth inhibition (RGI). Variovorax reverses this effect by degrading IAA, but the underlying pathway remains incompletely resolved. Here, using genetics, metabolomics, and isotope tracing, we define a nine-gene region ( iadCDEFGHIJK2 ) required for IAA catabolism in Variovorax paradoxus CL014, identify a previously uncharacterized intermediate (C₁₀H₉NO₃), and revise the early oxidative steps of the pathway. Although IadDE adopts a Rieske-type oxygenase architecture, our data are consistent with the IadCDE complex functioning as a monooxygenase during IAA degradation. Using these insights, we introduce iad genes into two rhizobacterial chassis, Polaromonas MF047 and Paraburkholderia MF376. These engineered strains degrade IAA and alleviate RGI induced by exogenous IAA, an auxin-producing strain, and a synthetic bacterial community. Engineered Paraburkholderia MF376 delivers the strongest performance, improving plant growth in natural soil. Together, these results establish a framework for engineering auxin-balancing root commensals.