Unveiling the genetic basis of biochemical pathways of plant growth promotion in Bacillus pumilus and the first genomic insights into B. pseudomycoides as a biostimulant

Bacillus species are among the most promising plant growth-promoting bacteria (PGPB) due to their adaptability to various environmental niches and extensive biosynthetic capabilities. Despite the available data on the PGP-traits (PGPTs) of Bacillus, the genetic basis underlying their beneficial effects remains largely unexplored. In this study, a comparative genomic analysis of three B. pumilus and one B. pseudomycoides strains, isolated from the maize rhizosphere, is presented to elucidate the molecular mechanisms behind their PGP-traits. All strains exhibited multiple PGP-traits, including phosphate solubilization, phytohormone and siderophore production, growth in nitrogen-free medium, stress tolerance, and biofilm formation. Phylogenomic analysis revealed that plant-associated strains have higher genetic similarity, emphasizing niche-specific evolution. Genome analyses revealed strain- and species-specific adaptations, particularly in relation to nutrient acquisition and abiotic stress response mechanisms. B. pumilus strains encoded alternative sigma factors (SigB, SigM, SigW) enabling enhanced salt tolerance, whereas B. pseudomycoides lacked this system and relied on conventional osmoprotective strategies. The strains utilized different tryptophan-dependent (IAN, IAM or IPyA) pathways for auxin biosynthesis and differed in phosphate solubilization ability, which can be attributed to upstream and missense variants in genes affecting acid metabolism (gltA, acnA, acnB, citM, and citS) and phosphatase (phoA) activity. Iron uptake via bacillibactin-siderophores was exclusive to B. pumilus. The inability of the B. pseudomycoides strain to acquire iron was associated with structural variants (absence of bsaA gene) within the bacillibactin biosynthetic gene cluster. This work provides new insights into the molecular basis of PGP traits in Bacillus and supports the development of Bacillus-based bioinoculants for sustainable agriculture.