Pseudomonas sp. UW4 promotes garlic growth through systemic integration of auxin and ethylene pathways

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable strategy to enhance crop productivity, the multi-omics regulatory mechanisms underlying their growth-promoting effects in garlic remain poorly understood. In this study, we integrated physiological, phytohormone metabolomic, and transcriptomic analyses to systematically elucidate the growth-promoting mechanism of Pseudomonas sp. strain UW4 in garlic. Our results demonstrated that UW4 inoculation significantly improved aboveground morphological traits, including plant height, leaf length, leaf width, and pseudostem thickness, and optimized root system architecture by increasing total root length, root surface area, and root tip number. These morphological improvements were accompanied by enhanced photosynthetic pigment accumulation and increased biomass production. Phytohormone profiling revealed that UW4 inoculation elevated the levels of auxin (indole-3-acetic acid, IAA) and its precursors (L-tryptophan and tryptamine), while significantly reducing the content of 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene biosynthesis. Transcriptomic analysis identified 687 differentially expressed genes (DEGs), which were significantly enriched in auxin and ethylene signaling pathways. Mechanistically, UW4 upregulated the expression of SAUR (Small auxin-up RNA) to promote IAA synthesis, and suppressed the transcription of ethylene biosynthesis-related genes. Additionally, the downregulation of PYL (Pyrabactin resistance 1-like) genes indicated that UW4 also modulates the abscisic acid (ABA) signaling pathway. Quantitative real-time PCR (qRT-PCR) validation confirmed that the expression of ACO (ACC oxidase), a key rate-limiting enzyme in ethylene synthesis, was significantly downregulated in UW4 groups. Collectively, our findings demonstrate that UW4 optimizes garlic growth and yield potential by coordinately regulating auxin, ethylene, and ABA metabolism and gene expression, providing a theoretical foundation and elite microbial resource for the green and high-yield cultivation of garlic.