Bacillus sp. RA isolated from Sorghum bicolor enhances salt tolerance of tomato in conditions of reduced fertilization

• The salt tolerance-related genes present in genome of PGPR Bacillus sp. RA. • PGPR combined with fertilizer can synergistically on plant salt resistance. • The co-application of PGPR and fertilizer alter soil microbial community assembly. Excessive application of chemical fertilizer in saline soil has posed a significant threat to soil quality and the environment. Plant-growth-promoting rhizobacteria (PGPR) has emerged as a promising complement to conventional fertilization practices. The microbial inoculants used in the study were PGPR strain Bacillus sp. RA that genome consisted of a circular chromosome and three plasmids. Genes responsible for Na + /H + antiporter, potassium transporters and biosynthesis of osmoprotectants that enable bacteria to survive salt environment were identified. The salt resistance of tomato was investigated by integrated application of PGPR under reduced half dose of fertilizers. Based on growth status and physiological indices, in contrast, treatment with PGPR with half a dose of the fertilizer proved to be the best. Under salt condition, PGPR with half a dose of the fertilizer promoted plant growth through modulation of nitrogen metabolism and auxin biosynthesis. In addition, rhizosphere microbial community composition and assembly were affected by PGPR with half a dose of the fertilizer treatment. The relative abundance of bacterial functional groups involved in the nitrogen cycle and symbiotroph fungi significantly increased. Network analysis of microbial communities showed that interactions of between bacterial and fungal were more connected and showed more co-occurrence relationships in PGPR plus half a dose of the fertilizer soil, which strengthen the adaptability of plant to salt stress. We concluded that synergistic use of PGPR and fertilizers could be an effective strategy for improving tomato growth and beneficial in terms of sustainable agricultural production under salt-affected soils.