Rhizosphere-derived Pseudomonas putida EU-36 enhances growth and quality-related metabolite accumulation in Eucommia ulmoides leaves

Sustainable microbial strategies are needed to increase leaf biomass and enhance quality-related metabolite accumulation in Eucommia ulmoides Oliv., a woody medicinal and industrial plant. This study aimed to identify native rhizosphere bacteria, evaluate a selected strain in pot and field experiments, and characterize associated transcriptional and metabolic changes. Thirty-six culturable bacterial isolates were obtained from the rhizosphere soil of E. ulmoides and assigned to 11 taxa by molecular identification. Five representative isolates exhibited at least one putative plant growth-promoting trait in vitro. Among them, Pseudomonas putida EU-36 produced the strongest growth response in E. ulmoides seedlings. Shoot fresh weight, total root length, and net photosynthetic rate were 2.53, 2.29, and 2.07 times the corresponding control values, respectively. The strain was then applied to field-grown E. ulmoides seedlings, and leaves were sampled at 90 and 120 days after inoculation. Metabolomic analysis showed that the relative abundance of chlorogenic acid was 2.63 and 2.37 times that of the control at the two sampling stages, respectively, whereas that of aucubin was 1.42 and 1.17 times that of the control, respectively. RNA sequencing identified 1733 and 1688 differentially expressed genes at 90 and 120 days, respectively; these genes were enriched in phenylpropanoid, flavonoid, and monoterpenoid biosynthesis pathways. Integrated transcriptomic and metabolomic analyses revealed concurrent changes in jasmonate-related gene expression, jasmonic acid (JA) abundance, and secondary metabolic profiles after EU-36 inoculation. These findings support further evaluation of EU-36 as a microbial inoculant for sustainable E. ulmoides leaf production and quality improvement.