Bacillus velezensis HR6-1 enhances salt tolerance of soil-cultivated tomatoes via modulating rhizosphere soil health and root metabolic networks

Soil salinization severely suppresses tomato growth and yield, impeding sustainable tomato production. Our previous work confirmed that the plant-growth-promoting rhizobacterium Bacillus velezensis HR6-1 alleviates salt stress in substrate-cultivated tomatoes, whereas the underlying regulatory mechanism of HR6-1 in soil-cultivated systems remains unclear, limiting its practical application in saline soil. Here, multi-omics approaches were used to unravel the regulatory mechanism of HR6-1-mediated salt tolerance in soil-cultivated tomatoes. Physiochemically, HR6-1 could ameliorate the properties of saline rhizosphere soil by reducing soil pH and electrical conductivity, conserving available nutrients and improving soil enzyme activities, thereby alleviating salt stress at the root interface. Meanwhile, HR6-1 improved root physiological performance under salt stress by boosting antioxidant capacity, mitigating membrane damage, maintaining Na + /K + homeostasis, and increasing the accumulation of nitrogen, phosphorus, lignin and melatonin. Transcriptomic and metabolomic analyses further revealed that HR6-1 modulated several core salt-tolerance pathways, including lignin and melatonin biosynthesis, auxin/gibberellin signalling and antioxidant defense, accompanied by the upregulation of key genes for ion transport and stress response. Moreover, HR6-1 reshaped rhizosphere microbial community by modulating tomato root exudates (adenine, sucrose, and amino acids) to recruit beneficial microbial taxa such as Pseudomonas and Nocardiopsis ) under salt stress. Genomic, transcriptomic and in vitro functional assays further validated the growth-promoting and salt-adaptive capacities of HR6-1 under high-salt stress. This study systematically clarifies the multi-level regulatory mechanisms of HR6-1 in enhancing tomato salt tolerance and provides a promising biological strategy for sustainable tomato cultivation in saline soil, with further field validation required.