References
-
Hossain, M. S., Islam, M. N., Rahman, M. M., Mostofa, M. G. & Khan, M. A. R. Sorghum: A prospective crop for climatic vulnerability, food and nutritional security. J. Agric. Food Res. 8, 100300 (2022).
-
Rizvi, A., Ahmed, B., Umar, S. & Khan, M. S. Comprehensive insights into sorghum (Sorghum bicolor) defense mechanisms unveiled: Plant growth-promoting rhizobacteria in combating Burkholderia-induced bacterial leaf stripe disease. Plant Stress 11, 100397 (2024).
-
Kulkova, I., Dobrzyński, J., Kowalczyk, P., Bełżecki, G. & Kramkowski, K. Plant growth promotion using *Bacillus cereus*. Int. J. Mol. Sci. 24(11), 9759 (2023).
-
Mahdi, I., Fahsi, N., Hafidi, M., Allaoui, A. & Biskri, L. Plant growth enhancement using rhizospheric halotolerant phosphate solubilizing bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 isolated from Chenopodium quinoa Willd. Microorganisms 8(6), 948 (2020).
-
Ehling-Schulz, M., Lereclus, D. & Koehler, T. M. The *Bacillus cereus* group: *Bacillus* species with pathogenic potential. Microbiol. Spectr. 7(3), 10–1128 (2019).
-
Kumar, C. et al. Sorghum rhizosphere bacteriome studies and generation of multistrain beneficial bacterial consortia. Microbiol. Res. 292, 128036 (2025).
-
Dabban, I. A. et al. Isolation techniques used for molecular characterization of beneficial microorganisms: Cultural, biochemical and molecular characterization. Handb. Agric. Biotechnol. 6, 491–545 (2024).
-
Almasian-Tehrani, N. et al. Overview of typing techniques as molecular epidemiology tools for bacterial characterization. Cell. Mol. Biomed. Rep. 1(2), 69–77 (2021).
-
Flörl, L., Meyer, A. & Bokulich, N. A. Exploring sub-species variation in food microbiomes: A roadmap to reveal hidden diversity and functional potential. Appl. Environ. Microbiol. https://doi.org/10.1128/aem.00524-25 (2025).
-
Prasad, B., Sharma, D., Kumar, P. & Dubey, R. C. Biocontrol potential of Bacillus spp. for resilient and sustainable agricultural systems. Physiol. Mol. Plant Pathol. 128, 102173 (2023).
-
Khan, A. R. et al. Bacillus spp. as bioagents: Uses and application for sustainable agriculture. Biology 11(12), 1763 (2022).
-
Santos-Medellín, C., Edwards, J., Liechty, Z., Nguyen, B. & Sundaresan, V. Drought stress results in a compartment-specific restructuring of the rice root-associated microbiomes. MBio 8, e00764-17 (2017).
-
Etesami, H., Jeong, B. R. & Glick, B. R. Potential use of Bacillus spp. as an effective biostimulant against abiotic stresses in crops—A review. Curr. Res. Biotechnol. 5, 100128 (2023).
-
Huang, Z. et al. Isolation and characterization of *Bacillus cereus* bacteriophage DZ1 and its application in foods. Food Chem. 431, 137128 (2024).
-
She, R. C. & Petti, C. A. Procedures for the storage of microorganisms. Manual Clin. Microbiol. 8, 161–168 (2015).
-
Davis, K. E., Joseph, S. J. & Janssen, P. H. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl. Environ. Microbiol. 71(2), 826–834 (2005).
-
Thomas, P., Sekhar, A. C., Upreti, R., Mujawar, M. M. & Pasha, S. S. Optimization of single plate-serial dilution spotting (SP-SDS) with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples. Biotechnol. Rep. 8, 45–55 (2015).
-
Sousa, A. M., Machado, I., Nicolau, A. & Pereira, M. O. Improvements on colony morphology identification towards bacterial profiling. J. Microbiol. Methods 95(3), 327–335 (2013).
-
Aslim, B., Sağlam, N. & Beyatli, Y. Determination of some properties of Bacillus isolated from soil. Turk. J. Biol. 26(1), 41–48 (2002).
-
Behera, S. Physiochemical and Microbial Analysis of Soil and Water of Dhobiajharan Village (Proposed Coal Mine Site-Tubed). Doctoral dissertation (2013).
-
Kones, C., Mwajita, M., Kariuki, L., Kiirika, L. & Kavoo, A. Isolation and characterization of rhizospheric microorganisms from bacterial wilt endemic areas in Kenya. Afr. J. Microbiol. Res. 14(7), 349–360 (2020).
-
Wang, X., Heazlewood, S. P., Krause, D. O. & Florin, T. H. J. Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J. Appl. Microbiol. 95(3), 508–520 (2003).
-
Nikunjkumar, B. D. Molecular Identification of Bacteria Using 16s rDNA Sequencing (Gujarat University, 2012).
-
Janda, J. M. & Abbott, S. L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. J. Clin. Microbiol. 45(9), 2761–2764 (2007).
-
Sting, R., Eisenberg, T. & Hrubenja, M. Rapid and reasonable molecular identification of bacteria and fungi in microbiological diagnostics using rapid real-time PCR and Sanger sequencing. J. Microbiol. Methods 159, 148–156 (2019).
-
Chen, L. et al. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens. PLoS ONE 9(2), e88886 (2014).
-
Crossley, B. M. et al. Guidelines for Sanger sequencing and molecular assay monitoring. J. Vet. Diagn. Invest. 32(6), 767–775 (2020).
-
Buckley, T. R., Simon, C. & Chambers, G. K. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50(1), 67–86 (2001).
-
Mello, B. Estimating timetrees with MEGA and the TimeTree resource. Mol. Biol. Evol. 35(9), 2334–2342 (2018).
-
Tamura, K. et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28(10), 2731–2739 (2011).
-
Soni, R. & Keharia, H. Phytostimulation and biocontrol potential of Gram-positive endospore-forming bacilli. Planta 254(3), 49 (2021).
-
Hernández-Fernández, G., Galán, B., Carmona, M., Castro, L. & García, J. L. Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress. Front. Microbiol. 13, 1009068 (2022).
-
Chen, Y. et al. Current studies of the effects of drought stress on root exudates and rhizosphere microbiomes of crop plant species. Int. J. Mol. Sci. 23(4), 2374 (2022).
-
Wang, Y. et al. Evaluation of Rpf protein of Micrococcus luteus for cultivation of soil actinobacteria. Syst. Appl. Microbiol. 44(5), 126234 (2021).
-
Ansari, F. A., Ahmad, I. & Khan, A. S. Recent molecular tools for analyzing microbial diversity in rhizosphere ecosystem. In Microbial Diversity in the Genomic Era 233–246. (Academic Press, 2024).
-
Soares, M. B. et al. Sporeforming probiotic bacteria: Characteristics, health benefits, and technological aspects for their applications in foods and beverages. Trends Food Sci. Technol. 138, 453–469 (2023).
-
Ma, B. et al. Evaluation of in vitro production capabilities of indole derivatives by lactic acid bacteria. Microorganisms 13(1), 150 (2025).
-
Bal, S. Amelioration of plant biotic stress by mycorrhiza helper bacteria. In Bio-control Agents for Sustainable Agriculture: Diversity, Mechanisms and Applications 359–384 (Springer, 2025).
-
Lies, A., Delteil, A., Prin, Y., and Duponnois, R. (2018). Using mycorrhiza helper microorganisms (MHM) to improve the mycorrhizal efficiency on plant growth. In Role of Rhizospheric Microbes in Soil: Volume 1: Stress Management and Agricultural Sustainability 277–298.
-
Hussain, A. & Ibrahim, M. Molecular characterization of *Bacillus subtilis* OKR isolated from wheat rhizosphere reveals key outer membrane proteins associated with plant growth promotion: A step towards climate-smart agriculture. Int. J. Appl. Exp. Biol. 4(1), 95–106 (2025).
-
Patil, B. L., Gopalkrishna, A. M. & Gm, S. K. Molecular characterization of an endophytic strain of Bacillus subtilis with plant growth-promoting properties from a wild relative of papaya. J. Appl. Microbiol. 136(1), lxaf010 (2025).
-
Ibrahim, R., Aranjani, J. M., Prasanna, N., Biswas, A. & Gayam, P. K. R. Production, isolation, optimization, and characterization of microbial PHA from *Bacillus australimaris*. Sci. Rep. 15(1), 8395 (2025).
-
Liu, Y. et al. Unraveling the ecological interactions between dairy strains Bacillus licheniformis and Bacillus cereus during the dual-species biofilm formation. Food Microbiol. 128, 104716 (2025).
-
Sousa, E. G. et al. The research on the identification, taxonomy, and comparative genomics analysis of nine Bacillus velezensis strains significantly contributes to microbiology, genetics, bioinformatics, and biotechnology. Front. Microbiol. 16, 1544934 (2025).
-
da Silva, P. T. L. et al. Biological modulatorns with Bacillus licheniformis and Bacillus subtilis in compost barn. Cad. Pedagog. 22(5), e14872–e14872 (2025).
-
Das, S. et al. Bacillus ayatagriensis sp. nov., a novel plant growth-promoting rhizobacteria strain isolated from mulberry rhizosphere. Sci. Rep. 15, 26693 (2025).
-
Murag, S. et al. Molecular analysis of Bacillus anthracis isolates from Karnataka’s ruminant Anthrax outbreaks reveals genetic relationships and environmental factors Influencing spore persistence. Res. Microbiol. 8, 104343 (2025).
-
Nikolaidis, M. et al. A comparative analysis of the core proteomes within and among the Bacillus subtilis and Bacillus cereus evolutionary groups reveals the patterns of lineage-and species-specific adaptations. Microorganisms 10(9), 1720 (2022).
-
Gonçalves, L. B. et al. Microbial inoculants and fertilizer reduction in Sorghum cultivation: Implications for sustainable agriculture. Microbiol. Res. 16, 115 (2025).
-
Petkar, G. V., Giri, G. K. & Charpe, A. M. Antagonistic potential of phylloplane Bacillus subtilis PBs4 isolate against grain mold fungi of sorghum in India. Int. J. Environ. Agric. Biotechnol. 10(3), 619305 (2025).
-
Uchegbu, N., Adepeju, A. B. & Fasuan, T. O. Bio-nutritional and microbiological quality assessment of tiger-nut-enriched instant sorghum kunu-zaki beverage as potential milk-analogue. Nutr. Food Sci. 55(7), 1202–1211 (2025).
-
Muhammad, S. A. et al. Effect of phosphate solubilizing Bacillus on the growth of Sorghum (Sorghum bicolor [L.] Moench). Niger. J. Basic Appl. Sci. 32(2), 58–66 (2024).
-
Adeleke, B. S., Ayangbenro, A. S. & Babalola, O. O. Genomic analysis of endophytic Bacillus cereus T4S and its plant growth-promoting traits. Plants 10(9), 1776 (2021).
-
Imtiyaz, T. Bioprospecting of Bacterial Endophytes Isolated from Himalayan Cold Desert for Abiotic Stress Tolerance in Plants. Doctoral dissertation, University of Agricultural Sciences, GKVK, Bangalore (2022). https://krishikosh.egranth.ac.in/server/api/core/bitstreams/3bcba48a-b721-4845-a0a8-f0c62d47047e/content
-
Aehsas, S. et al. Morpho-biochemical and molecular characterization of Bacillus subtilis and Priestia megaterium isolates from eastern Indian farmlands. Mol. Biol. Rep. 52(1), 706 (2025).
-
Satapathy, S. S., Priyadarshini, B., Subhadarshini, S., Nayak, J., Kuldip, R. & Sahoo, J. P. Pangenomics for studying plant-microbe interactions. In Plant Pangenomes and Pangenomics 347–360. (Academic Press, 2025).
-
Mishra, A. P., Sahoo, J. P., Padhi, P. P., Pattnaik, S. & Jena, L. Applications of horizontal gene transfer in soil bioremediation. In Bioremediation and Phytoremediation Technologies in Sustainable Soil Management 171–203. (Apple Academic Press, 2022).
-
Raimi, A. & Adeleke, R. 16S rRNA gene-based identification and plant growth-promoting potential of cultivable endophytic bacteria. Agron. J. 115(3), 1447–1462 (2023).
-
Okechukwu, E. C. et al. Pea-saving partners: Bacillus and pseudomonas combat downy mildew in pea crops. Plant Pathol. 75(1), e70095 (2026).
-
Patra, D., Mishra, S., Mohanty, J., Subhadarsani, S. & Sahoo, J. P. Harnessing the plant microbiome: a genomic and metagenomic perspective for sustainable agriculture. Acad. Mol. Biol. Genom. https://doi.org/10.20935/AcadMolBioGen7892 (2025).
