Abstract

Plant growth-promoting rhizobacteria (PGPR) can rebalance growth–defense trade-offs in plants. However, the temporal molecular mechanisms underlying sustained growth promotion in woody fruit crops, particularly cherry (Prunus avium), remain largely unclear. This study inoculated Gisela 6 sweet cherry seedlings with three PGPR strains (RahnellaY17,ArthrobacterY37, andBacillus megateriumP6). Phenotypic and physiological traits were assessed at 60 days (d), while targeted phytohormone metabolomics and root transcriptomes were profiled at 30 and 40 d post-treatment. Our results demonstrated that all three PGPR strains enhanced plant growth, photosynthetic capacity, and root architecture, with Y37 demonstrating superior biomass promotion. Phytohormone dynamics featured consistent ABA (abscisic acid) suppression, coupled with an early elevation of GA (gibberellin) and auxin followed by subsequent cytokinin accumulation. Notably, Y37 uniquely enriched jasmonate intermediates. Comparative transcriptomic analysis uncovered strain-specific trajectories, with integrated co-expression analysis defining modules associated with early metabolism and later structural remodeling. Key hub genes were identified as involved in hormone regulation and cell wall synthesis. Collectively, these findings suggest that Y37 drives a temporal partitioning from metabolic priming to architectural reinforcement by reallocating carbon and tuning hormone pathways, thereby underpinning superior growth and resilience. This study provides novel insights into PGPR-based strategies for sustainable cherry production.