Objective This study aimed to isolate and screen highly efficient saline-alkali tolerant, plant growth-promoting bacteria, to analyze their saline and alkali tolerances, growth-promoting traits, action mechanisms, and to identify candidate strains for developing microbial fertilizers to restore saline-alkali soil.

Method Salt-tolerant, plant growth-promoting bacterial strains were isolated from the rhizosphere soil of Suaeda salsa, a kind of halophyte. Morphological analysis and 16S rDNA gene sequencing were used for bacterial strain classification. Then, the ability of bacterial strains in nitrogen fixation, phosphate solubilization, potassium release, iron chelation, and IAA production were qualitatively assessed. Finally, the whole genome of bacterial strain was sequenced and then annotated in different database to elucidate its salt tolerance and plant growth promotion mechanisms.

Result A saline-alkali tolerant strain, NMGSB13, was identified as a bacterium of Kushneria sp. based on 16S rDNA gene sequencing. The NMGSB13 strain could grow at 5% - 15% of salinity and pH 7.0 - 9.0, and exhibit the plant growth-promoting abilities with nitrogen fixation, phosphorus and potassium solubilization, siderophore production, and IAA production. Whole genome sequencing indicated that NMGSB13 possessed the complete pathways to ectoine and proline biosynthesis and a series of genes encoding Na ⁺ /H ⁺ exchangers, which regulated the balance of intracellular and extracellular osmotic pressure, helping bacterium to resist salt stress. In addition, several biosynthesis pathways or regulating genes were also identified for involving in nitrogen fixation, phosphate solubilization, potassium release, siderophore production, and IAA production.

Conclusion A saline-alkali tolerant, plant growth-promoting Kushneria sp. NMGSB13 was obtained, which exhibited abilities of nitrogen fixation, phosphorus and potassium solubilization, siderophore production, and IAA production. The salt tolerance and plant growth-promoting mechanisms for this strain were elucidated at the genomic level. This study provided a theoretical insight as well as an elite strain resource for further developing microbial fertilizers to restore saline-alkali soil.