Plant growth-promoting bacteria enhance growth and drought resilience in tomato by reprogramming photosynthesis, antioxidant defence, and gene responses

Drought stress is a major constraint on crop productivity, particularly in arid and semi-arid regions where water limitation disrupts photosynthesis, antioxidant balance, and core physiological processes. Here, we isolated three plant growth-promoting bacteria (PGPB) from hypersaline sabkha soil and assessed their capacity to enhance drought resilience in tomato plants. Phylogenomic analysis identified the strains as Lysinibacillus capsica S1, Bacillus paralicheniformis S2, and Bacillus inaquosorum S3. Genome analyses revealed a broad repertoire of plant-beneficial traits, including pathways for phosphate solubilization, siderophore production, auxin biosynthesis, and 1‑aminocyclopropane‑1‑carboxylate (ACC) deaminase activity. Additionally, the presence of key stress-responsive genes such as gsiB , dnaJ , trpA , nifA , accA , dhbF , and cspA indicates strong stress alleviation potential. Consistently, all strains exhibited robust osmotic stress tolerance and growth-promoting activity in vitro . In planta , inoculation under moderate and severe drought significantly improved growth, biomass accumulation, chlorophyll content, photosynthetic efficiency, and osmolyte production. Notably, S1 and S2 conferred the strongest drought tolerance, while S3 also produced a beneficial, albeit less pronounced, effect. These responses were associated with increased survival, improved water status, reduced membrane damage, enhanced antioxidant capacity, and the upregulation of key drought-responsive genes ( SlWRKY4 , SlNCED1 , SlERF024 , and SlAREB1 ). Collectively, these findings identify S1 and S2 as promising biostimulants for enhancing tomato resilience under water-limited conditions, offering a sustainable strategy to mitigate drought stress in arid and semi-arid agricultural systems.