Genomic characterization of the salt-tolerant Bacillus and Jeotgalicoccus strains reveals a diverse metabolism relevant to plant growth promotion and salt stress tolerance

Previous research leads have affirmed the crucial role of plant growth-promoting rhizobacteria (PGPR) strains Bacillus safensis (NBRI 12 M), Bacillus subtilis (NBRI 28B, NBRI 33N), and Jeotgalicoccus huakuii (NBRI 13E) in salt stress amelioration and plant growth promotion. In the present study, whole-genome analysis unveiled the underlying molecular mechanisms accounting for phyto-beneficial and stress-mitigating traits of the selected PGPR strains. The genomic characterization has revealed that NBRI 12 M, NBRI 28B, NBRI 33N, and NBRI 13E possessed a single circular chromosome of 3.73 Mb, 4.07 Mb, 4.10 Mb, and 2.17 Mb size, respectively. The genome analysis of these strains demonstrated varied genes such as mrp and yfiY for plant growth promotion, nutrient metabolism, and other secondary metabolites biosynthesis. High salinity tolerance genes (yicL, ydhP_1, spoIIQ, and spoIIID), encoding for membrane transporter, dormancy, and sporulation, were also identified. In addition, several chemotaxis (cheA, cheY, and cheW) and motility gene clusters (motB_1, motB_2) were found in the PGPR strains for successful rhizosphere colonization. Further, NBRI 12 M has significantly increased the shoot and root length and dry weight by 14.13%, 20.63%, and 9.63%, respectively, under salt stress. In addition, NBRI 12 M inoculation reduced defense enzymes by 79.77%, 84.75%, 74.11%, 70.77%, and 57.75% for SOD, APX, GPX, CAT, and PPO, respectively. Overall findings from this study offered a detailed comparative genomic analysis of salt stress ameliorating PGPR of Bacillus genera towards enhancing the deep insights for host-PGPR association.