Whole-Genome analysis of <i>Bacillus subtilis</i> NRCB002 and characterization of its metabolite acetoin as a plant growth stimulant

Yu Song; Rongjun Yin; Hui Shen; Xin Tao; Linmei Li; Nan Gao; Yu Song; Rongjun Yin; Hui Shen; Xin Tao; Linmei Li; Nan Gao

doi:10.3934/microbiol.2025024

AIMS Microbiology

2025, Volume 11, Issue 3: 574-587. doi: 10.3934/microbiol.2025024

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Whole-Genome analysis of Bacillus subtilis NRCB002 and characterization of its metabolite acetoin as a plant growth stimulant

School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China

Received: 15 May 2025 Revised: 30 June 2025 Accepted: 08 July 2025 Published: 21 July 2025

Plant growth-promoting rhizobacteria (PGPR) are instrumental in enhancing crop productivity and resilience to stress. In this study, we characterized Bacillus subtilis subsp. subtilis NRCB002, a PGPR strain isolated from the rice rhizosphere, using genomic and functional analyses. Whole-genome sequencing revealed a circular chromosome of 4,211,270 base pairs with a GC content of 43.51%, encoding genes associated with environmental adaptation, such as antimicrobial resistance, and PGPR-related traits, including the biosynthesis of indole-3-acetic acid. The annotation of key metabolic pathways for acetoin production aligns with its observed role in promoting plant growth. Pot experiments demonstrated that optimal acetoin concentrations significantly enhanced the development of soybean seedlings. These findings elucidate the genetic basis of NRCB002's beneficial traits and underscore its potential for agricultural application.
- Bacillus subtilis,
- whole-genome sequencing,
- acetoin,
- in-silico analysis,
- soybean
Citation: Yu Song, Rongjun Yin, Hui Shen, Xin Tao, Linmei Li, Nan Gao. Whole-Genome analysis of Bacillus subtilis NRCB002 and characterization of its metabolite acetoin as a plant growth stimulant[J]. AIMS Microbiology, 2025, 11(3): 574-587. doi: 10.3934/microbiol.2025024

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Abstract

Plant growth-promoting rhizobacteria (PGPR) are instrumental in enhancing crop productivity and resilience to stress. In this study, we characterized Bacillus subtilis subsp. subtilis NRCB002, a PGPR strain isolated from the rice rhizosphere, using genomic and functional analyses. Whole-genome sequencing revealed a circular chromosome of 4,211,270 base pairs with a GC content of 43.51%, encoding genes associated with environmental adaptation, such as antimicrobial resistance, and PGPR-related traits, including the biosynthesis of indole-3-acetic acid. The annotation of key metabolic pathways for acetoin production aligns with its observed role in promoting plant growth. Pot experiments demonstrated that optimal acetoin concentrations significantly enhanced the development of soybean seedlings. These findings elucidate the genetic basis of NRCB002's beneficial traits and underscore its potential for agricultural application.

Acknowledgments

This study was supported by the National Natural Science Foundation of China (32172673), and Students' Platform for Innovation and Entrepreneurship Training Program of of Jiangsu Province (X2025102911107), and Nanjing Tech University (2025DC1636). We are grateful to the High Performance Computing Center of Nanjing Tech University for supporting the computational resources.

Conflicts of interest

There are no conflicts of interest.

Author contributions

Yu Song (Writing-original draft, Methodology, Data curation, Investigation, Writing - review & editing); Rongjun Yin (Data curation, Formal analysis, Investigation, Writing - review & editing); Hui Shen (Data curation, Investigation, Methodology); Xin Tao (Investigation, Data curation, Software); Linmei Li (Investigation, Resources, Data curation); Nan Gao (Conceptualization, Funding acquisition, Resources, Supervision, Writing–review & editing).

References

[1]	Zainuddin N, Keni MF, Ibrahim SAS, et al. (2022) Effect of integrated biofertilizers with chemical fertilizers on the oil palm growth and soil microbial diversity. Biocatal Agric Biotechnol 39: 102237. https://doi.org/10.1016/j.bcab.2021.102237
[2]	Liu-Xu L, González-Hernández AI, Camañes G, et al. (2024) Harnessing green helpers: nitrogen-fixing bacteria and other beneficial microorganisms in plant–microbe interactions for sustainable agriculture. Horticulturae 10: 621. https://doi.org/10.3390/horticulturae10060621
[3]	Wang T, Xu J, Chen J, et al. (2024) Progress in microbial fertilizer regulation of crop growth and soil remediation research. Plants 13: 346. https://doi.org/10.3390/plants13030346
[4]	Zhao Y, Hong Y, Wang P, et al. (2023) Assembly of tomato rhizobacteria from different functional groups improves seedling photosynthesis and growth. Plants 12: 4000. https://doi.org/10.3390/plants12234000
[5]	Shi JW, Lu LX, Shi HM, et al. (2022) Effects of plant growth-promoting rhizobacteria on the growth and soil microbial community of Carya illinoinensis. Curr Microbiol 79: 352. https://doi.org/10.1007/s00284-022-03027-9
[6]	Liu J, Zhang J, Zhu M, et al. (2022) Effects of plant growth promoting rhizobacteria (PGPR) strain Bacillus licheniformis with biochar amendment on potato growth and water use efficiency under reduced irrigation regime. Agronomy 12: 1031. https://doi.org/10.3390/agronomy12051031
[7]	Maina S, Prabhu AA, Vivek N, et al. (2022) Prospects on bio-based 2,3-butanediol and acetoin production: Recent progress and advances. Biotechnol Adv 54: 107783. https://doi.org/10.1016/j.biotechadv.2021.107783
[8]	Rath M, Mitchell TR, Gold SE (2018) Volatiles produced by Bacillus mojavensis RRC101 act as plant growth modulators and are strongly culture-dependent. Microbiol Res 208: 76-84. https://doi.org/10.1016/j.micres.2017.12.014
[9]	Zhou C, Shen H, Yan S, et al. (2024) Acetoin promotes plant growth and alleviates saline stress by activating metabolic pathways in lettuce seedlings. Plants 13: 3312. https://doi.org/10.3390/plants13233312
[10]	Du J, Ji Y, Li Y, et al. (2024) Microbial volatile organic compounds 2-heptanol and acetoin control Fusarium crown and root rot of tomato. J Cell Physiol 239: e30889. https://doi.org/10.1002/jcp.30889
[11]	Ryu CM, Farag MA, Hu CH, et al. (2003) Bacterial volatiles promote growth in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 100: 4927-4932. https://doi.org/10.1073/pnas.0730845100
[12]	Li L, Liu N, Ma C, et al. (2024) Growth promoting effects of fermentation broth and optimization of high-yield acetoin fermentation conditions of Bacillus subtilis NRCB002 (in Chinese). J Nanjing Agricultural University 47: 1105-1112.
[13]	Zhu Z, Zhang H, Leng J, et al. (2020) Isolation and characterization of plant growth-promoting rhizobacteria and their effects on the growth of Medicago sativa L. under salinity conditions. Antonie van Leeuwenhoek 113: 1263-1278. https://doi:10.1007/s10482-020-01434-1
[14]	Ma C, Li S, Gong J, et al. (2023) Mechanism of growth promotion by acetoin and Bacillus subtilis NRCB002 (in Chinese). J Plant Nutr Fert 29: 582-590.
[15]	Jabborova D, Kannepalli A, Davranov K, et al. (2021) Co-inoculation of rhizobacteria promotes growth, yield, and nutrient contents in soybean and improves soil enzymes and nutrients under drought conditions. Sci Rep 11: 22081. https://doi.org/10.1038/s41598-021-01337-9
[16]	Bakhshandeh E, Gholamhosseini M, Yaghoubian Y, et al. (2020) Plant growth promoting microorganisms can improve germination, seedling growth and potassium uptake of soybean under drought and salt stress. Plant Growth Regul 90: 123-136. https://doi.org/10.1007/s10725-019-00556-5
[17]	Guardado-Fierros BG, Tuesta-Popolizio DA, Lorenzo-Santiago MA, et al. (2024) Comparative study between Salkowski reagent and chromatographic method for auxins quantification from bacterial production. Front Plant Sci 15: 1378079. https://doi.org/10.3389/fpls.2024.1378079
[18]	Krishnamurthi VR, Niyonshuti II, Chen J, et al. (2021) A new analysis method for evaluating bacterial growth with microplate readers. Plos One 16: e0245205. https://doi.org/10.1371/journal.pone.0245205
[19]	Zhou C, Li S, Zheng Y, et al. (2022) An energy-rich phosphate compound enhances the growth of lettuce through the activation of photosynthesis, growth, and induced systemic resistance-related processes. J Soil Sci Plant Nutr 22: 1955-1969. https://doi.org/10.1007/s42729-022-00786-z
[20]	Zhou C, Shen H, Yan S, et al. (2024) Acetoin promotes plant growth and alleviates saline stress by activating metabolic pathways in lettuce seedlings. Plants 13: 3312. https://doi.org/10.3390/plants13233312
[21]	Galperin MY, Wolf YI, Makarova KS, et al. (2020) COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 49: D274-D281. https://doi.org/10.1093/nar/gkaa1018
[22]	Koua SH, N'golo DC, Alloue-Boraud WM, et al. (2020) Bacillus subtilis strains isolated from cocoa trees (Theobroma cacao L.) rhizosphere for their use as potential plant growth promoting rhizobacteria in Côte d'Ivoire. Curr Microbiol 77: 2258-2264. https://doi.org/10.1007/s00284-020-02027-x
[23]	Thiruvengadam R, Gandhi K, Vaithiyanathan S, et al. (2022) Complete genome sequence analysis of Bacillus subtilis Bbv57, a promising biocontrol agent against phytopathogens. Int J Mol Sci 23: 9732. https://doi.org/10.3390/ijms23179732
[24]	Iqbal S, Ullah N, Janjua HA (2021) In vitro evaluation and genome mining of Bacillus subtilis strain RS10 reveals its biocontrol and plant growth-promoting potential. Agriculture 11: 1273. https://doi.org/10.3390/agriculture11121273
[25]	Franco-Sierra ND, Posada LF, Santa-María G, et al. (2020) Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture. Funct Integr Genomics 20: 575-589. https://doi.org/10.1007/s10142-020-00736-x
[26]	Chen XH, Koumoutsi A, Scholz R, et al. (2007) Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25: 1007-1014. https://doi.org/10.1038/nbt1325
[27]	Fincheira P, Parra L, Mutis A, et al. (2017) Volatiles emitted by Bacillus sp. BCT9 act as growth modulating agents on Lactuca sativa seedlings. Microbiol Res 203: 47-56. https://doi.org/10.1016/j.micres.2017.06.007
[28]	Peng G, Zhao X, Li Y, et al. (2019) Engineering Bacillus velezensis with high production of acetoin primes strong induced systemic resistance in Arabidopsis thaliana. Microbiol Res 227: 126297. https://doi.org/10.1016/j.micres.2019.126297

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