Comprehensive genomic and pan-genomic analysis of the drought-tolerant Bacillus halotolerans strain OM-41 isolated from Olive rhizosphere, reveals potential plant growth-promoting and biocontrol traits.

Abiotic and biotic stresses increasingly threaten plant health and productivity, causing substantial yield losses in vital crops. In this study, 99 rhizobacteria isolated from Moroccan olive rhizospheres, OM-41 was selected as the most potent strain, exhibiting exceptional drought tolerance (thriving at Aw 0.859), thermotolerance (up to 55 °C), and halotolerance (15% NaCl), alongside plant growth-promoting (PGP) traits such as phosphate solubilization, indole-acetic acid (IAA), gibberellic acid, siderophore production, and hydrolytic enzyme secretion. The strain suppressed V. dahliae via diffusible and volatile antifungal compounds, achieving 76% and 69% inhibition rates, respectively. Whole-genome sequencing revealed a 4.2 Mbp genome (43.5% GC content) with 4362 protein-coding genes. Phylogenetic analyses confirmed its classification as B. halotolerans. Genomic annotation identified 11 secondary metabolite clusters and stress-related genes, including those linked to phosphate solubilization (phy, pho, pst family), IAA synthesis (dhaS, trp operon), siderophores (dhb cluster), nitrogen fixation (nif, suf, urt genes), ammonia production (gudB, nasD/E), biofilm formation (tasA, bsl genes), antifungal volatiles (alsD, ilv operon), hydrolytic enzymes (e.g., amyE, eglS), and vitamin biosynthesis (thiamine/riboflavin operons). Pangenome analysis of 79 B. halotolerans strains highlighted an open pangenome with 12,679 total genes (2270 core, 2382 accessory and 8027 unique); OM-41 harbored 98 unique genes. These findings underscore potential of OM-41 as a biofertilizer and biocontrol agent, leveraging antibiosis, resource competition, and plant defense induction to mitigate pathogens and abiotic stresses. Up to our knowledge, this is the first work that evaluates the pangenome features of B. halotolerans, offering insights into its genomic plasticity and adaptive traits. The strain's multifunctional PGP capabilities and stress resilience position it as a promising solution for sustainable agriculture in challenging environments.