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Background  Salinity is a major threat to the agriculture industry due to the negative impact of salinity stress on crop productivity. In the present study, we isolated rhizobacteria and evaluated their capacities to promote crop growth under salt stress conditions.    Results  We isolated rhizospheric bacteria from sand dune flora of Pohang beach, Korea, and screened them for plant growth-promoting (PGP) traits. Among 55 bacterial isolates, 14 produced indole-3-acetic acid (IAA), 10 produced siderophores, and 12 produced extracellular polymeric and phosphate solubilization. Based on these PGP traits, we selected 11 isolates to assess for salinity tolerance. Among them, ALT29 and ALT43 showed the highest tolerance to salinity stress. Next, we tested the culture filtrate of isolates ALT29 and ALT43 for IAA and organic acids to confirm the presence of these PGP products. To investigate the effects of ALT29 and ALT43 on salt tolerance in soybean, we grew seedlings in 0 mM, 80 mM, 160 mM, and 240 mM NaCl treatments, inoculating half with the bacterial isolates. Inoculation with ALT29 and ALT43 significantly increased shoot length (13%), root length (21%), shoot fresh and dry weight (44 and 35%), root fresh and dry weight (9%), chlorophyll content (16–24%),  Chl a  (8–43%),  Chl b  (13–46%), and carotenoid (14–39%) content of soybean grown under salt stress. Inoculation with ALT29 and ALT43 also significantly decreased endogenous ABA levels (0.77-fold) and increased endogenous SA contents (6–16%), increased total protein (10–20%) and glutathione contents, and reduced lipid peroxidation (0.8–5-fold), superoxide anion (21–68%), peroxidase (12.14–17.97%), and polyphenol oxidase (11.76–27.06%) contents in soybean under salinity stress. In addition, soybean treated with ALT29 and ALT43 exhibited higher K +  uptake (9.34–67.03%) and reduced Na +  content (2–4.5-fold). Genes involved in salt tolerance,  GmFLD19  and  GmNARK , were upregulated under NaCl stress; however, significant decreases in  GmFLD19  (3–12-fold) and  GmNARK  (1.8–3.7-fold) expression were observed in bacterial inoculated plants.    Conclusion  In conclusion, bacterial isolates ALT29 and ALT43 can mitigate salinity stress and increase plant growth, providing an eco-friendly approach for addressing saline conditions in agricultural production systems.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02937-3.

Halotolerant bacteria mitigate the effects of salinity stress on soybean growth by regulating secondary metabolites and molecular responses