Transcriptomic and comprehensive analysis of salt stress–alleviating mechanisms by Ensifer sesbaniae DY22 in soybean

Soil salinization poses a major constraint to crop productivity worldwide. Cultivated soybean (Glycine max) is a major oilseed crop with moderate salt tolerance. Accumulating evidence indicates that plant growth-promoting rhizobacteria (PGPR) can promote crop growth and reduce the negative impacts of salt stress on crops. In the present study, we isolated DY22, a newly identified strain of Ensifer sesbaniae, from saline soil and determined that it showed high tolerance to 4 % NaCl. DY22 treatment enhanced the tolerance of soybean to salt stress compared to salt-treated control seedlings. We analyzed the mechanism underlying DY22-mediated salt tolerance in soybean via physiological, biochemical, and transcriptomic analyses. DY22 inoculation significantly increased chlorophyll accumulation and soluble sugar and proline contents in soybean under salt stress. Moreover, inoculation with DY22 enhanced antioxidant enzyme activity and reduced malondialdehyde contents compared with non-inoculation treatment under salt stress. Transcriptomic analysis revealed 8911 differentially expressed genes (4412 upregulated and 4499 downregulated) in DY22-inoculated plants under high-salinity conditions compared with the salt-treated control. GO and KEGG pathway analysis suggested that DY22 affects the transcriptional responses of genes involved in photosynthesis, oxidation-reduction, and plant hormone-mediated pathways, especially auxin, jasmonic acid, and abscisic acid signaling under salt stress. Overall, these findings highlight the important contribution of DY22 in mitigating the deleterious effects of salinity on soybean growth and development and provide valuable insights into the mechanisms underlying plant–microbes interactions.