Plant growth-promoting bacteria Bacillus amyloliquefaciens NBRISN13 modulates gene expression profile of leaf and rhizosphere community in rice during salt stress

► PGPR Bacillus amyloliquefaciens NBRISN13 (SN13) promotes growth of rice plants under salt stress. ► SN13 modulates gene expression in rice under salt-stressed condition. ► Salt stress leads to changes in microbial diversity of the rice rhizosphere which can be neutralized by SN13. ► SN13 alters rice rhizosphere by increasing the osmoprotectant utilizing microflora in the soil under normal and salt stress.