Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Screening Plant Growth-Promoting Bacteria with Antimicrobial Properties for Upland Rice

  • Khammool Khamsuk (Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University) ;
  • Bernard Dell (Centre for Crop and Food Innovation, Murdoch University) ;
  • Wasu Pathom-aree (Department of Biology, Faculty of Science, Chiang Mai University) ;
  • Wanwarang Pathaichindachote (Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University) ;
  • Nungruthai Suphrom (Center of Excellence in Biomaterials, Naresuan University) ;
  • Nareeluk Nakaew (Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University) ;
  • Juangjun Jumpathong (Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University)
  • Received : 2024.02.05
  • Accepted : 2024.03.25
  • Published : 2024.05.28
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Abstract

This study explores beneficial bacteria isolated from the roots and rhizosphere soil of Khao Rai Leum Pua Phetchabun rice plants. A total of 315 bacterial isolates (KK001 to KK315) were obtained. Plant growth-promoting traits (phosphate solubilization and indole-3-acetic acid (IAA) production), and antimicrobial activity against three rice pathogens (Curvularia lunata NUF001, Bipolaris oryzae 2464, and Xanthomonas oryzae pv. oryzae) were assessed. KK074 was the most prolific in IAA production, generating 362.6 ± 28.0 ㎍/ml, and KK007 excelled in tricalcium phosphate solubilization, achieving 714.2 ± 12.1 ㎍/ml. In antimicrobial assays using the dual culture method, KK024 and KK281 exhibited strong inhibitory activity against C. lunata, and KK269 was particularly effective against B. oryzae. In the evaluation of antimicrobial metabolite production, KK281 and KK288 exhibited strong antifungal activities in cell-free supernatants. Given the superior performance of KK281, taxonomically identified as Bacillus sp. KK281, it was investigated further. Lipopeptide extracts from KK281 had significant antimicrobial activity against C. lunata and a minimum inhibitory concentration (MIC) of 3.1 mg/ml against X. oryzae pv. oryzae. LC-ESI-MS/MS analysis revealed the presence of surfactin in the lipopeptide extract. The crude extract was non-cytotoxic to the L-929 cell line at tested concentrations. In conclusion, the in vitro plant growth-promoting and disease-controlling attributes of Bacillus sp. KK281 make it a strong candidate for field evaluation to boost plant growth and manage disease in upland rice.

Keywords

Acknowledgement

This work was financially supported by Research and Researcher for industry (RRi), Thailand Science Research and Innovation (TSRI) and Banrai-ioon strawberry farm (Grant No. MSD62I0098). Special thanks are extended to Dr. Sakamon Devahastin for his constructive comments and to Dr. Kumrop Ratanasut for providing the phytopathogenic bacterium.

References

  1. Fageria NK, Baligar VC. 2003. Upland rice and allelopathy. Commun. Soil Sci. Plant Anal. 34: 1311-1329. https://doi.org/10.1081/CSS-120020447
  2. Khotasena S, Sanitchon J, Chankaew S, Monkham T. 2022. The basic vegetative phase and photoperiod sensitivity index as the major criteria for indigenous upland rice production in Thailand under unpredictable conditions. Agronomy 12: 957.
  3. Fitriatin BN, Febriani S, Yuniarti A. 2021. Application of biofertilizers to increase upland rice growth, soil nitrogen and fertilizer use efficiency. In IOP Conference Series: Earth Environ. Sci. 648: 012138. IOP Publishing. https://doi.org/10.1088/1755-1315/648/1/012138
  4. Prashar P, Kapoor N, Sachdeva S. 2014. Rhizosphere: its structure, bacterial diversity and significance. Rev. Environ. Sci. Biotechnol. 13: 63-77. https://doi.org/10.1007/s11157-013-9317-z
  5. Pathan SI, Ceccherini MT, Sunseri F, Lupini A. 2020. Rhizosphere as hotspot for plant-soil-microbe interaction, pp. 17-43. In Datta R, Meena R, Pathan, S, Ceccherini M (eds.), Carbon and Nitrogen Cycling in Soil. Springer, Singapore.
  6. Igiehon NO, Babalola OO. 2018. Rhizosphere microbiome modulators: contributions of nitrogen fixing bacteria towards sustainable agriculture. Int. J. Environ. Res. Public Health 15: 574.
  7. Picot E, Hale CC, Hilton S, Teakle G, Schafer H, Huang YJ, et al. 2021. Contrasting responses of rhizosphere bacterial, fungal, protist, and nematode communities to nitrogen fertilization and crop genotype in field grown oilseed rape (Brassica napus). Front. Sustain. Food Syst. 5: 613269.
  8. Cavite HJM, Mactal AG, Evangelista EV, Cruz JA. 2021. Growth and yield response of upland rice to application of plant growth-promoting rhizobacteria. J. Plant Growth Regul. 40: 494-508. https://doi.org/10.1007/s00344-020-10114-3
  9. Wang Z, Zhu Y, Jing R, Wu X, Li N, Liu H, et al. 2021. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice. Arch. Microbiol. 203: 609-620. https://doi.org/10.1007/s00203-020-02058-9
  10. Vessey JK. 2003. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255: 571-586. https://doi.org/10.1023/A:1026037216893
  11. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW. 1997. Bacterial endophytes in agricultural crops. Can. J. Microbiol. 43: 895-914. https://doi.org/10.1139/m97-131
  12. Kloepper JW, Leong JM, Teintze M, Schroth MN. 1980. Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 286: 885-886. https://doi.org/10.1038/286885a0
  13. Mir MI, Hameeda B, Quadriya H, Kumar BK, Ilyas N, Kee Zuan AT, et al. 2022. Multifarious indigenous diazotrophic rhizobacteria of rice (Oryza sativa L.) rhizosphere and their effect on plant growth promotion. Front. Nutr. 8: 781764.
  14. Sherpa MT, Sharma L, Bag N, Das S. 2021. Isolation, characterization, and evaluation of native rhizobacterial consortia developed from the rhizosphere of rice grown in organic state Sikkim, India, and their effect on plant growth. Front. Microbiol. 12: 713660.
  15. Chaiharn M, Chunhaleuchanon S, Kozo A, Lumyong S. 2008. Screening of rhizobacteria for their plant growth promoting activities. Curr. Appl. Sci. Technol. 8: 18-23.
  16. Romano A, Vitullo D, Di Pietro A, Lima G, Lanzotti V. 2011. Antifungal lipopeptides from Bacillus amyloliquefaciens strain BO7. J. Nat. Prod. 74: 145-151. https://doi.org/10.1021/np100408y
  17. Sharma A, Kaushik N, Sharma A, Bajaj A, Rasane M, Shouche YS, et al. 2021. Screening of tomato seed bacterial endophytes for antifungal activity reveals lipopeptide producing Bacillus siamensis strain NKIT9 as a potential bio-control agent. Front. Microbiol. 12: 1228.
  18. Saechow S, Thammasittirong A, Kittakoop P, Prachya S, Thammasittirong SNR. 2018. Antagonistic activity against dirty panicle rice fungal pathogens and plant growth-promoting activity of Bacillus amyloliquefaciens BAS23. J. Microbiol. Biotechnol. 28: 1527-1535. https://doi.org/10.4014/jmb.1804.04025
  19. Li SB, Xu SR, Zhang RN, Liu Y, Zhou RC. 2016. The antibiosis action and rice-induced resistance, mediated by a lipopeptide from Bacillus amyloliquefaciens B014, in controlling rice disease caused by Xanthomonas oryzae pv. oryzae. J. Microbiol. Biotechnol. 26: 748-756. https://doi.org/10.4014/jmb.1510.10072
  20. Penha R, Vandenberghe L, Faulds C, Soccol V, Soccol C. 2020. Bacillus lipopeptides as powerful pest control agents for a more sustainable and healthy agriculture: recent studies and innovations. Planta 251: 70.
  21. Seenivasagan, R, Babalola, O. 2021. Utilization of microbial consortia as biofertilizers and biopesticides for the production of feasible agricultural product. Biology 10: 1111.
  22. Pang Z, Zhao Y, Xu P, Yu D. 2020. Microbial diversity of upland rice roots and their influence on rice growth and drought tolerance. Microorganisms 8: 1329.
  23. Harahap RT, Azizah IR, Setiawati MR, Herdiyantoro D, Simarmata T. 2023. Enhancing upland rice growth and yield with indigenous plant growth-promoting rhizobacteria (PGPR) isolate at N-fertilizers dosage. Agriculture 13: 1987.
  24. White LJ, Brozel VS, Subramanian S. 2015. Isolation of rhizosphere bacterial communities from soil. Bio-Protoc 5: e1569-e1569. https://doi.org/10.21769/BioProtoc.1569
  25. Defez R, Andreozzi A, Bianco C. 2017. The overproduction of indole-3-acetic acid (IAA) in endophytes upregulates nitrogen fixation in both bacterial cultures and inoculated rice plants. Microb. Ecol. 74: 441-452. https://doi.org/10.1007/s00248-017-0948-4
  26. Pande A, Pandey P, Mehra S, Singh M, Kaushik S. 2017. Phenotypic and genotypic characterization of phosphate solubilizing bacteria and their efficiency on the growth of maize. J. Genet. Eng. Biotechnol. 15: 379-391. https://doi.org/10.1016/j.jgeb.2017.06.005
  27. Murphy JAMES, Riley JP. 1962. A modified single solution method for the determination of phosphate in natural waters. Anal. Chim. Acta 27: 31-36. https://doi.org/10.1016/S0003-2670(00)88444-5
  28. Gordon SA, Weber RP. 1951. Colorimetric estimation of indoleacetic acid. Plant Physiol. 26: 192.
  29. Sev TM, Khai AA, Aung A, Yu SS. 2016. Evaluation of endophytic bacteria from some rice varieties for plant growth promoting activities. Int. J. Innov. Res. Sci. Eng. Technol. 5: 144-148. https://doi.org/10.31254/jsir.2016.5409
  30. Afzal I, Iqrar I, Shinwari ZK, Yasmin A. 2017. Plant growth-promoting potential of endophytic bacteria isolated from roots of wild Dodonaea viscosa L. Plant Growth Regul. 81: 399-408. https://doi.org/10.1007/s10725-016-0216-5
  31. Rangseekaew P, Barros-Rodriguez A, Pathom-Aree W, Manzanera M. 2021. Deep-sea actinobacteria mitigate salinity stress in tomato seedlings and their biosafety testing. Plants 10: 1687.
  32. Raper KB, Thom C. 1949. A manual of the penicillia. The Williams & Wilkins Company, Baltimore.
  33. Balouiri M, Sadiki M, Ibnsouda SK. 2016. Methods for in vitro evaluating antimicrobial activity: a review. J. Pharm. Anal. 6: 71-79. https://doi.org/10.1016/j.jpha.2015.11.005
  34. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703. https://doi.org/10.1128/jb.173.2.697-703.1991
  35. Jumpathong J, Nuengchamnong N, Masin K, Nakaew N, Suphrom N. 2019. Thin layer chromatography-bioautography assay for antibacterial compounds from Streptomyces sp. TBRC 8912, a newly isolated actinomycin D producer. Chiang Mai J. Sci. 46: 839-849.
  36. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  37. Pathak KV, Keharia H. 2014. Identification of surfactins and iturins produced by potent fungal antagonist, Bacillus subtilis K1 isolated from aerial roots of banyan (Ficus benghalensis) tree using mass spectrometry. 3 Biotech 4: 283-295. https://doi.org/10.1007/s13205-013-0151-3
  38. Ma Y, Kong Q, Qin C, Chen Y, Chen Y, Lv R, et al. 2016. Identification of lipopeptides in Bacillus megaterium by two-step ultrafiltration and LC-ESI-MS/MS. AMB Express 6: 79.
  39. Moro GV, Almeida RT, Napp AP, Porto C, Pilau EJ, Ludtke DS, et al. 2018. Identification and ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry characterization of biosurfactants, including a new surfactin, isolated from oil-contaminated environments. Microb. Biotechnol. 11: 759-769. https://doi.org/10.1111/1751-7915.13276
  40. Sriwiriyajan S, Ninpesh T, Sukpondma Y, Nasomyon T, Graidist P. 2014. Cytotoxicity screening of plants of genus piper in breast cancer cell lines. Trop. J. Pharm. Res. 13: 921-928. https://doi.org/10.4314/tjpr.v13i6.14
  41. Sengupta S, Ganguli S, Singh PK. 2017. Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.). Genom. Data 12: 41-43. https://doi.org/10.1016/j.gdata.2017.02.010
  42. Pal SS. 1998. Interactions of an acid tolerant strain of phosphate solubilizing bacteria with a few acid tolerant crops. Plant Soil 198: 169-177. https://doi.org/10.1023/A:1004318814385
  43. Teng Z, Chen Z, Zhang Q, Yao Y, Song M, Li M. 2019. Isolation and characterization of phosphate solubilizing bacteria from rhizosphere soils of the Yeyahu Wetland in Beijing, China. Environ. Sci. Pollut. Res. Int. 26: 33976-33987. https://doi.org/10.1007/s11356-018-2955-5
  44. Paul D, Sinha, SN. 2015. Isolation and characterization of a phosphate solubilizing heavy metal tolerant bacterium from River Ganga, West Bengal, India. Songklanakarin J. Sci. Technol. 37: 651-657.
  45. Chen YP, Rekha PD, Arun AB, Shen FT, Lai WA, Young CC. 2006. Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities. Appl. Soil Ecol. 34: 33-41. https://doi.org/10.1016/j.apsoil.2005.12.002
  46. Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA. 2013. Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. Springerplus 2: 587.
  47. Sun X, Shao C, Chen L, Jin X, Ni H. 2021. Plant growth-promoting effect of the chitosanolytic phosphate-solubilizing bacterium Burkholderia gladioli MEL01 after fermentation with chitosan and fertilization with rock phosphate. J. Plant GrowthRegul. 40: 1674-1686. https://doi.org/10.1007/s00344-020-10223-z
  48. Patten CL, Blakney AJ, Coulson TJ. 2013. Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria. Crit. Rev. Microbiol. 39: 395-415. https://doi.org/10.3109/1040841X.2012.716819
  49. Bose A, Kher MM, Nataraj M, Keharia H. 2016. Phytostimulatory effect of indole-3-acetic acid by Enterobacter cloacae SN19 isolated from Teramnus labialis (L.f.) Spreng rhizosphere. Biocatal. Agric. Biotechnol. 6: 128-137. https://doi.org/10.1016/j.bcab.2016.03.005
  50. Liu Z, Wang H, Xu W, Wang Z. 2020. Isolation and evaluation of the plant growth promoting rhizobacterium Bacillus methylotrophicus (DD-1) for growth enhancement of rice seedling. Arch. Microbiol. 202: 2169-2179. https://doi.org/10.1007/s00203-020-01934-8
  51. Spaepen S, Vanderleyden J, Remans R. 2007. Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol. Rev. 31: 425-448. https://doi.org/10.1111/j.1574-6976.2007.00072.x
  52. Sridevi M, Mallaiah KV. 2007. Production of extracellular polysaccharide by Rhizobium strains from root nodules of Leguminous green manure crop, Sesbania sesban (L.) Merr. Int. J. Soil Sci. 2: 308-313. https://doi.org/10.3923/ijss.2007.308.313
  53. Chiangsin R, Kesee C, Sangchote S. 2018. Biological control of Bipolaris oryzae with Bacillus subtilis and the development of a formulation for rice seed treatment. Thai J. Agric. Sci. 51: 139-151.
  54. Chen O, Yi L, Deng L, Ruan C, Zeng K. 2020. Screening antagonistic yeasts against citrus green mold and the possible biocontrol mechanisms of Pichia galeiformis (BAF03). J. Sci. Food Agric. 100: 3812-3821. https://doi.org/10.1002/jsfa.10407
  55. Lee KJ, Kamala-Kannan S, Sub HS, Seong CK, Lee GW. 2008. Biological control of Phytophthora blight in red pepper (Capsicum annuum L.) using Bacillus subtilis. World J. Microbiol. Biotechnol. 24: 1139-1145. https://doi.org/10.1007/s11274-007-9585-2
  56. Kefi A, Slimene IB, Karkouch I, Rihouey C, Azaeiz S, Bejaoui M, et al. 2015. Characterization of endophytic Bacillus strains from tomato plants (Lycopersicon esculentum) displaying antifungal activity against Botrytis cinerea Pers. World J. Microbiol. Biotechnol. 31: 1967-1976. https://doi.org/10.1007/s11274-015-1943-x
  57. Fira D, Dimkic I, Beric T, Lozo J, Stankovic S. 2018. Biological control of plant pathogens by Bacillus species. J. Biotechnol. 285: 44-55. https://doi.org/10.1016/j.jbiotec.2018.07.044
  58. Ye YF, Li QQ, Gang FU, Yuan GQ, Miao JH, Wei LIN. 2012. Identification of antifungal substance (Iturin A2) produced by Bacillus subtilis B47 and its effect on southern corn leaf blight. J. Integr. Agric. 11: 90-99. https://doi.org/10.1016/S1671-2927(12)60786-X
  59. You W, Ge C, Jiang Z, Chen M, Li W, Shao Y. 2021. Screening of a broad-spectrum antagonist-Bacillus siamensis, and its possible mechanisms to control postharvest disease in tropical fruits. Biological Control 157: 104584.
  60. Alvarez F, Castro M, Principe A, Borioli G, Fischer S, Mori G, et al. 2012. The plant-associated Bacillus amyloliquefaciens strains MEP218 and ARP23 capable of producing the cyclic lipopeptides iturin or surfactin and fengycin are effective in biocontrol of sclerotinia stem rot disease. J. Appl. Microbiol. 112: 159-174. https://doi.org/10.1111/j.1365-2672.2011.05182.x
  61. Torres MJ, Brandan CP, Petroselli G, Erra-Balsells R, Audisio MC. 2016. Antagonistic effects of Bacillus subtilis subsp. subtilis and Bacillu amyloliquefaciens against Macrophomina phaseolina: SEM study of fungal changes and UV-MALDI-TOF MS analysis of their bioactive compounds. Microbiol. Res. 182: 31-39. https://doi.org/10.1016/j.micres.2015.09.005
  62. Ongena M, Jacques P. 2008. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol. 16: 115-125 https://doi.org/10.1016/j.tim.2007.12.009
  63. Tang JS, Zhao F, Gao H, Dai Y, Yao ZH, Hong K, et al. 2010. Characterization and online detection of surfactin isomers based on HPLC-MSn analyses and their inhibitory effects on the overproduction of nitric oxide and the release of TNF-α and IL-6 in LPS-induced macrophages. Mar. Drugs 8: 2605-2618. https://doi.org/10.3390/md8102605
  64. Li YM, Haddad NI, Yang SZ, Mu BZ. 2008. Variants of lipopeptides produced by Bacillus licheniformis HSN221 in different medium components evaluated by a rapid method ESI-MS. Int. J. Pept. Res. Ther. 14: 229-235. https://doi.org/10.1007/s10989-008-9137-0
  65. De Faria AF, Teodoro-Martinez DS, de Oliveira Barbosa GN, Vaz BG, Silva IS, Garcia JS, et al. 2011. Production and structural characterization of surfactin (C14/Leu7) produced by Bacillus subtilis isolate LSFM-05 grown on raw glycerol from the biodiesel industry. Process Biochem. 46: 1951-1957. https://doi.org/10.1016/j.procbio.2011.07.001
  66. Chen Y, Liu SA, Mou H, Ma Y, Li M, Hu X. 2017. Characterization of lipopeptide biosurfactants produced by Bacillus licheniformis MB01 from marine sediments. Front. Microbiol. 8: 871.