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

Sankalp Misra; Priti Prasad; Pradeep Semwal; Shashank Kumar Mishra; Mehar Hasan Asif; Puneet Singh Chauhan

doi:10.1007/s13205-024-04164-7

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

3 Biotech. 2024 Dec;14(12):316. doi: 10.1007/s13205-024-04164-7. Epub 2024 Nov 28.

Authors

Sankalp Misra^{1

2}, Priti Prasad^{3

4}, Pradeep Semwal^{1

4}, Shashank Kumar Mishra¹, Mehar Hasan Asif^{3

4}, Puneet Singh Chauhan^{1

4}

Affiliations

¹ Microbial Technologies Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India.
² Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow- Deva Road, Barabanki, Uttar Pradesh 225003 India.
³ Molecular and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India.
⁴ Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India.

PMID: 39619818
PMCID: PMC11604972 (available on 2025-12-01)
DOI: 10.1007/s13205-024-04164-7

Abstract

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04164-7.

Keywords: PGPR; Rhizosphere; Salinity; Whole-genome sequencing.

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