Skip to main content

Advertisement

SpringerLink
Log in

Efficacy of bioinoculants to control of bacterial and fungal diseases of rice (Oryza sativa L.) in northwestern Himalaya

  • Environmental Microbiology - Research Paper
  • Published:
Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

Introduction

Biological control holds great promise for environmentally friendly and sustainable management of the phytopathogens. The multi-function features of plant growth-promoting rhizobacteria (PGPR) enable to protect the plants from disease infections by replacing the chemical inputs. The interaction between the plant root exudates and the microbes stimulates the production of secondary metabolism and enzymes and induces systemic resistance in the plants.

Aim

The aim was to identify the potential PGPR which would show an antagonistic effect against basmati rice fungal and bacterial diseases.

Methods

In the study, native originating microbes have been isolated, characterized using 16S rRNA sequencing, and used as potential antagonistic microbial isolates against diseases of rice plants.

Results

Rhizobacteria isolated from rhizosphere, endo-rhizosphere, and bulk soil samples of Basmati 370 exhibited promising inhibitory activity against rice pathogens. Molecular characterization of bacterial isolates based on 16S rRNA sequencing classified the bacterial isolates into different genera such as Bacillus, Pseudomonas, Streptomyces, Exiguobacterium, Aeromonas, Chryseobacterium, Enterobacter, and Stenotrophomonas. PGPRs exhibited biocontrol activities against various rice diseases like bacterial leaf blight, leaf blast, brown spot, and sheath blight and boost the plant growth traits.

Conclusion

In the study, the potentially identified PGPRs isolates could be used as efficient bioinoculants as bio-fertilizers and biocontrol agents for sustainable rice crop production.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Syed Ab Rahman SF, Singh E, Pieterse CMJ, Schenk PM (2018) Emerging microbial biocontrol strategies for plant pathogens. Plant Sci 267:102–111

    Article  CAS  PubMed  Google Scholar 

  2. Azcon-Aguilar C, Barea J (1997) Arbuscular mycorrhizas and biological control of soilborne plant pathogens–an overview of the mechanisms involved. Mycorrhiza 6:457–464

    Article  Google Scholar 

  3. Bringhurst RM, Cardon ZG, Gage DJ (2001) Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor. Proc Nat Acad Sci U S A 98:4540–4545

    Article  CAS  Google Scholar 

  4. Lee HJ, Jeong SE, Kim PJ, Madsen EL, Jeon CO (2015) High resolution depth distribution of bacteria, archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy. Front Microbiol 6:639. https://doi.org/10.3389/fmicb.2015.00639

    Article  PubMed  PubMed Central  Google Scholar 

  5. Breidenbach B, Pump J, Dumont MG (2016) Microbial community structure in the rhizosphere of rice plants. Front Microbiol 6:1537. https://doi.org/10.3389/fmicb.2015.01537

    Article  PubMed  PubMed Central  Google Scholar 

  6. Goddard VJ, Bailey MJ, Darrah P, Lilley AK, Thompson IP (2001) Monitoring temporal and spatial variation in rhizosphere bacterial population diversity: a community approach for the improved selection of rhizosphere competent bacteria. Plant Soil 232:181–193

    Article  CAS  Google Scholar 

  7. Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319

    Article  CAS  PubMed  Google Scholar 

  8. Timm CM, Campbell AG, Utturkar SM, Jun S-R, Parales RE, Tan WA, Robeson MS, Lu T-YS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA (2015) Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 6:1118. https://doi.org/10.3389/fmicb.2015.01118

    Article  PubMed  PubMed Central  Google Scholar 

  9. Mabjeed A, Abbasi MK, Hameed S, Imran A, Rahim N (2015) Isolation and characterization of plant growth-promoting rhizobacteria from wheat rhizosphere and their effect on plant growth promotion. Front Microbiol 6:198

    Google Scholar 

  10. Sturz A, Christie B (2003) Beneficial microbial allelopathies in the root zone: the management of soil quality and plant disease with rhizobacteria. Soil Tillage Res 72:107–123

    Article  Google Scholar 

  11. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598

    Article  Google Scholar 

  12. Ahemad M, Malik A (2011) Bioaccumulation of heavy metals by zinc resistant bacteria isolated from agricultural soils irrigated with wastewater. Bacteriol J 2:12–21

    Article  Google Scholar 

  13. Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A (2016) Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiol Res 184:13–24

    Article  PubMed  Google Scholar 

  14. Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838

    Article  CAS  PubMed  Google Scholar 

  15. Shoda M (2000) Bacterial control of plant diseases. J Biosci Bioeng 89:515–521

    Article  CAS  PubMed  Google Scholar 

  16. Nihorimbere V, Ongena M, Smargiassi M, Thonart P (2011) Beneficial effect of the rhizosphere microbial community for plant growth and health. Biotechnol Agron Soc 15:327

    Google Scholar 

  17. Slama HB, Cherif-Silini H, Chenari Bouket A, Qader M, Silini A, Yahiaoui B, Alenezi FN, Luptakova L, Triki MA, Vallat A, Oszako T, Rateb ME, Belbahri L (2019) Screening for Fusarium antagonistic bacteria from contrasting niches designated the endophyte bacillus halotolerans as plant warden against Fusarium. Front Microbiol 9:3236. https://doi.org/10.3389/fmicb.2018.03236

    Article  PubMed  PubMed Central  Google Scholar 

  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(9):1527–1535

    Article  CAS  PubMed  Google Scholar 

  19. Chen D, Liu X, Li C, Tian W, Shen Q, Shen B (2014) Isolation of Bacillus amyloliquefaciens S20 and its application in control of eggplant bacterial wilt. J Environ Manag 137:120–127

    Article  Google Scholar 

  20. Pathak KV, Keharia H (2013) Characterization of fungal antagonistic bacilli isolated from aerial roots of banyan (Ficus benghalensis) using intact-cell MALDI-TOF mass spectrometry (ICMS). J Appl Microbiol 114:1300–1310

    Article  CAS  PubMed  Google Scholar 

  21. Alvarez F, Castro M, Príncipe A, Borioli G, Fischer S, Mori G, Jofré E (2011) 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

    Article  PubMed  Google Scholar 

  22. Raina M, Salgotra RK, Pandotra P, Rathour R, Singh K (2019) Genetic enhancement for semi-dwarf and bacterial blight resistance with enhanced grain quality characteristics in traditional Basmati rice through marker-assisted selection. C R Biolog 342:142–153

    Article  Google Scholar 

  23. Zhao Y, Selvaraj JN, Xing F, Zhou L, Wang Y, Song H, Tan X, Sun L, Sangare L, Folly YME, Liu Y (2014) Antagonistic action of Bacillus subtilis strain SG6 on Fusarium graminearum. PLoS One 9:e92486

    Article  PubMed  PubMed Central  Google Scholar 

  24. Raaijmakers JM, Vlami M, de Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonievan Leeuwenhoek 81:537–547

    Article  CAS  Google Scholar 

  25. Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J (2012) The Top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430

    Article  PubMed  PubMed Central  Google Scholar 

  26. Luster J, Göttlein A, Nowack B, Sarret G (2009) Sampling, defining, characterising and modeling the rhizosphere-the soil science tool box. Plant Soil 321:457–482

    Article  CAS  Google Scholar 

  27. Walkley A, Black IA (1934) An examination of Degtjareff method for determining soil organic matter and a proposed modification of the chromic acid titration method. Soil Sci 37:29–37

    Article  CAS  Google Scholar 

  28. Subbiah BV, Asija GL (1956) A rapid procedure for the estimation of available nitrogen in soils. Curr Sci 25:259–260

    CAS  Google Scholar 

  29. Jackson ML (1962) Soil Chemical Analysis. Prentice Hall, Inc. Eaglewood Cliffs, New York, pp 219–221

  30. Jackson ML (1967) Soil Chemical Analysis. Prentice Hall India Pvt. Ltd. New Delhi, pp 452–85

  31. Chesnin L, Yien CH (1950) Turbidimetric determination of available sulphates. Soil Sci Soc Am Proc 15:149–151

    Article  Google Scholar 

  32. Cheng KL, Bray RH (1951) Determination of calcium and magnesium in soil and plant material. Soil Sci 72:449–458

    Article  Google Scholar 

  33. Lindsay WL, Norvell WA (1978) Development of a DTPA soil test for zinc, iron, manganese, and copper. Soil Sci Soc Amer J 42:421–428

  34. Stotzky G, Mund R, Tsui R (1996) Rapid serial dilution technique with self-filling syringes. Appl Microbiol 14(3):472–473

    Article  Google Scholar 

  35. Bashan Y, de-Bashan LE (2010) How the plant growth-promoting bacterium Azospirillum promotes plant growth–a critical assessment. Adv Agron 108:77–136

    Article  CAS  Google Scholar 

  36. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RG, Wood W, Krieg N (eds) Methods for general and molecular bacteriology. ASM Press, Washington DC, pp 607–654

  37. Cattelan AJ, Hartel PG, Fahurmann JJ (1999) Screening for plant growth promoting rhizobacteria to promote early soybean growth. Soil Sci Soc Am 63:1670–1680

    Article  CAS  Google Scholar 

  38. Harrigan W, McCance M (1976) Laboratory methods in food and dairy microbiology. Academic Press Inc. Ltd, London

    Google Scholar 

  39. Sharma S, Kumar V, Tripathi RB (2011) Isolation of phosphate solubilizing microorganism (PSMs) from soil. J Microbiol Biotechnol Res 1(2):90–95

    Google Scholar 

  40. Alexander DB, Zuberer DA (1991) Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fertil Soil 12(1):39–45

    Article  CAS  Google Scholar 

  41. Sachdev DP, Chaudhari HG, Kasture VM, Dhavale DD, Chopra BA (2009) Isolation and characterization of indole acetic acid (IAA) producing Klebsiella pneumonia strains from rhizosphere of wheat (Triticum aestivum) and their effect on plant growth. Indian J Exp Biol 47(12):993–1000

    CAS  PubMed  Google Scholar 

  42. Wilson K (1997) Preparation of genomic DNA from bacteria. Curr Protocols Mol Biol 56(1):241–245

    Google Scholar 

  43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Gram HCJ (1884) Über die isolirte Färbung der Schizomyceten in Schnittund Trockenpräparaten. Fortschritte der Medizin, Berlin 2:185–189

    Google Scholar 

  45. Agostini JP, Timmer LW (1992) Selective isolation procedures for differentiation of two strains of Colletotrichum gloesporiodes from citrus. Plant Dis 76:1176–1178

    Article  Google Scholar 

  46. Smith BJ, Black LL (1990) Morphological, cultural, and pathogenic variation among Colletotrichum species isolated from strawberry. Plant Dis 74:69–76

    Article  Google Scholar 

  47. Valgas C, De Souza SM, Smânia EFA (2007) Screening methods to determine antibacterial activity of natural products. Braz J Microbiol 38:369–380

    Article  Google Scholar 

  48. Kuss AV, Vivian Vicentini Kuss VV, Holtz EV, Lovato T (2007) Inoculation of diazotrophic bacteria and development of flooded rice plants in nutritive solution and greenhouse. Rev FZVA 14:23–33

    Google Scholar 

  49. Kauffman HE, Reddy APK, Hsieh SPY, Merca SD (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 56:537–541

    Google Scholar 

  50. IRRI (1996) Standard Evaluation System Manual. International Rice Research Institute, Manila, p 35

    Google Scholar 

  51. Park DS, Sayler RJ, Hong YG, Nam MH, Yang Y (2008) A method for inoculation and evaluation of rice sheath blight disease. Plant Dis 92:25–29

    Article  PubMed  Google Scholar 

  52. IRRI (2002) Standard Evaluation System for Rice (SES). International Rice Research Institute, Manila, p 19

    Google Scholar 

  53. Panse VG, Sukhatme PV (2000) Statistical Methods for Agricultural Workers. ICAR Publications, New Delhi

    Google Scholar 

  54. Mirzaee H, Shuey L, Schenk PM (2015) Transcriptomics of plants interacting with pathogens and beneficial microbes. In: Genomics, proteomics and metabolomics in nutraceuticals and functional foods, vol 4, pp 525–536

  55. Soderberg KH, Probanza A, Jumpponen A, Baath E (2004) The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil-and cfu-PLFA technique. Appl Soil Ecol 25:135–145

  56. Johansen A, Olsson S (2005) Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere. Microb Ecol 49:272–281

    Article  CAS  PubMed  Google Scholar 

  57. Amara U, Khalid R, Hayat R (2015) Soil bacteria and phytohormones for sustainable crop production. In: Maheshwari D.K. (Ed.), Bacterial metabolites in sustainable agroecosystem. Springer International, pp 87-103

  58. Mwajita MR, Murage H, Tani A, Kahang EM (2013) Evaluation of rhizosphere, rhizoplane and phyllosphere bacteria and fungi isolated from rice in Kenya for plant growth promoters. Springer Plus 2:606

    Article  PubMed  PubMed Central  Google Scholar 

  59. Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lucy M, Reed E, Glick BR (2004) Applications of free living plant growth-promoting rhizobacteria. Antonie Van Leeuwenhoek 86:1–25

    Article  CAS  PubMed  Google Scholar 

  61. Dey R, Pal KK, Bhatt DM, Chauhan SM (2004) Growth promotion and yield enhancement of peanut (Arachis hypogaea L.) by application of plant growth promoting rhizobacteria. Microbiol Res 159:371–394

    Article  CAS  PubMed  Google Scholar 

  62. Calvo P, Ormeno-Orrillo E, Martínez-Romero E, Zuniga D (2010) Characterization of Bacillus isolates of potato rhizosphere from Andean soils of Peru and their potential PGPR characteristics. Braz J Microbiol 41(4):899–906

    Article  PubMed  PubMed Central  Google Scholar 

  63. Sabir S, Asghar HN, Kashif SUR, Khan MY, Akhtar MJ (2013) Synergistic effect of plant growth promoting rhizobacteria and kinetin on maize. J Anim Plant Sci 23(6):1750–1755

    CAS  Google Scholar 

  64. Shrestha UB, Shrestha BB (2019) Climate change amplifies plant invasion hotspots in Nepal. Biodivers Res 25:1599–1612. https://doi.org/10.1111/ddi.12963

    Article  Google Scholar 

  65. Bach CC, Bech BH, Nohr EA, Olsen J, Matthiesen NB, Bonefeld-Jorgensen EC, Bossi R, Henriksen TB (2016) Perfluoroalkyl acids in maternal serum and indices of fetal growth: the Aarhus birth cohort Environ. Health Perspect 124:848–854

    Article  CAS  Google Scholar 

  66. Ilsan NA, Nawangsih A, Wahyudi A (2016) Rice phyllosphere actinomycetes as biocontrol agent of bacterial leaf blight disease on rice. Asian J Plant Pathol 10:1–8

    Article  Google Scholar 

  67. Li H, Guan Y, Dong Y, Zhao L, Rong S, Chen W, Lv M, Xu H, Gao X, Chen R, Li L, Xu Z (2018) Isolation and evaluation of endophytic Bacillus tequilensis GYLH001 with potential application for biological control of Magnaporthe oryzae. PLoS ONE 13(10):e0203505

    Article  PubMed  PubMed Central  Google Scholar 

  68. Bendaha MEA, Belaouni HA (2019) Tomato growth and resistance promotion by Enterobacter hormaechei subsp. steigerwaltii EB8D. Arch Phytopathol Plant Protect 52(3-4):318–332

    Article  CAS  Google Scholar 

  69. Anusha BG, Gopalakrishnan S, Naik MK, Sharma M (2019) Evaluation of Streptomyces spp. and Bacillus spp. for biocontrol of Fusarium wilt in chickpea (Cicer arietinum L.). Arch Phytopath Plant Prot. https://doi.org/10.1080/03235408.2019.1635302

  70. Bhattacharyya A, Giri VP, Singh PS, Pande S, Choudhan P, Soni SK, Srivastava S, Singh PC, Mishra A (2019) Intervension of bioactive endophyte Bacillus tequilensis enhance physiolocical strength of tomato during Fusarium wilt infection. Biol Control 139:104074. https://doi.org/10.1016/j.biocontrol.2019.104074

    Article  CAS  Google Scholar 

  71. Wang X, Li Q, Sui J, Zhang J, Liu Z, Du J, Xu R, Zhou Y, Liu Z (2019) Isolation and characterization of antagonistic bacteria Paenibacillus jamilae HS-26 and their effects on plant growth. Biomed Res Int 2019:1–13. https://doi.org/10.1155/2019/3638926

    Article  CAS  Google Scholar 

  72. Kutlu M, Cakmakci R, Hosseinpour A, Karagoz H (2019) The use of plant growth promoting rhizobacteria (PGPR)’s effect on essential oil rate, essential oil content, some morphological parameters and nutrient uptake of Turkish oregano. Appl Ecol Environ Res 17(2):1641–1653

    Article  Google Scholar 

Download references

Acknowledgments

The authors are thankful to the School for Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu, 180009 (J & K), India, for providing infrastructure and other facilities to carry out the study.

Funding

This study was financially supported by the School for Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu-180009 (J & K), India, to carry out the study.

Author information

Authors and Affiliations

  1. School for Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India

    Surabhi Jasrotia, Romesh Kumar Salgotra & Manmohan Sharma

Authors
  1. Surabhi Jasrotia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Romesh Kumar Salgotra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Manmohan Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Experiment design: R.K.S., S.J.; experiments: S.J.; writing original draft: R.K.S., S.J.; conceptualization: R.K.S., funding: R.K.S., supervision: R.K.S., writing, S.J., R.K.S.

Corresponding author

Correspondence to Romesh Kumar Salgotra.

Ethics declarations

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

The authors declare no conflict of interest.

Additional information

Responsible Editor: Ieda Carvalho Mendes

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

ESM 1

(DOC 869 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jasrotia, S., Salgotra, R.K. & Sharma, M. Efficacy of bioinoculants to control of bacterial and fungal diseases of rice (Oryza sativa L.) in northwestern Himalaya. Braz J Microbiol 52, 687–704 (2021). https://doi.org/10.1007/s42770-021-00442-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42770-021-00442-1

Keywords

Search

Navigation