Identification and Genomic Insights into the Multifunctional Growth-Promoting Traits of Pseudomonas chlororaphis ST2023006 in Rice

Plant growth-promoting rhizobacteria (PGPR) offer a sustainable alternative to chemical fertilizers in rice production, yet the mechanisms underlying multifunctional growth promotion by individual strains remain insufficiently characterized. In this study, strain ST2023006 was isolated from sugarcane rhizosphere and systematically characterized through phenotypic assays and whole-genome sequencing. The strain was identified as Pseudomonas chlororaphis based on morphological, physiological, biochemical, and multilocus sequence analyses. It exhibited tolerance to temperature (25-37 ℃), pH (5.0-9.0), and salinity (≤2% NaCl). ¹⁵N isotope dilution analysis revealed nitrogen fixation contribution rates of 13.4% and 9.72% to rice roots and shoots, respectively. Pot experiments demonstrated that inoculation significantly promoted growth in two rice varieties, increasing plant height by up to 86.6%, while enhancing root surface area, root volume, and biomass accumulation. In vitro antagonism against Rhizoctonia solani and quantitative IAA analysis (59.44 µg·mL⁻¹) provided experimental support for genome-predicted biocontrol and IAA production traits. Whole-genome sequencing revealed genes potentially associated with nitrogen fixation (nifU, fixI), nutrient mobilization (potassium/zinc solubilization, siderophores), phytohormone synthesis (IAA), stress tolerance (heavy metal resistance, heat/cold shock proteins), and complete biosynthetic gene clusters for the antifungal compounds pyrrolnitrin, phenazine, and hydrogen cyanide. These findings indicate that P. chlororaphis ST2023006 is a promising multifunctional PGPR candidate with demonstrated plant growth-promoting effects and experimentally supported genomic potential for biocontrol.