Bacillus licheniformis GN02 Promotes Cotton Seedling Growth and Alters Phytohormone Levels and Root-Associated Bacterial Communities

The development of novel, efficient, and stable plant growth-promoting bacterial (PGPB) inoculants is crucial for mitigating environmental pollution and ensuring food security. Bacillus licheniformis GN02 has demonstrated significant plant growth-promoting effects. The final nitrogen content of the culture supernatant of GN02 grown in Ashby’s nitrogen-free medium reached 55.8 ± 1.92 mg/L. Genomic annotation of GN02 predicted genes for ammonium assimilation and nitrate reduction, but no canonical nifHDK nitrogenase genes. It also predicted plant growth-promoting potentials, including genes associated with siderophore, L-tryptophan, and polyamine biosynthesis, as well as motility and chemotaxis. Pot experiments on cotton seedlings were conducted with single and double inoculation of GN02 at 104 and 108 CFU/mL. The lower inoculation concentration (104 CFU/mL) exhibited a greater growth-promoting performance: it significantly increased indole-3-acetic acid, brassinosteroid, jasmonic acid, and salicylic acid concentrations and up-regulated YUCCA4, BES1, OPR3, ERF, and NPR1, alongside elevated rhizosphere urease and dehydrogenase activity and enriched root-associated genera such as Opitutus, Aquabacterium, and Hydrogenophaga. These findings demonstrate that GN02-mediated growth promotion is accompanied by root endosphere microbiome shifts and alterations in host hormone signaling. As a promising PGPB candidate, GN02 requires application strategies tailored to strain traits, with a suitable inoculation concentration and frequency.