Plant Beneficial Features and Application of Paraburkholderia sp. NhPBG1 Isolated from Pitcher of Nepenthes hamblack


Pitchers are the unique structures of carnivorous plants used for the trapping of insects and other small invertebrates. The digestion of captured prey here is assisted by the bacteria, which have been associated with pitchers. These bacterial communities can therefore expect to have a variety of plant beneficial functions. In this study, the bacterial isolate NhPBG1 from the pitcher of Nepenthes hamblack was screened for activity against Pythium aphanidermatum, Rhizoctonia solani, Fusarium oxysporum, and Colletotrichum accutatum and was found to have the inhibitory activity towards all the tested phytopathogens. Interestingly, the isolate was found to have hyper-inhibitory effect against P. aphanidermatum. Further to this, the isolate was also shown to be positive for plant beneficial traits such as indole-3-acetic acid (IAA) and ammonia production, phosphate, potassium and zinc solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. BLAST analysis of the 16S rDNA sequence of NhPBG1 has identified it as Paraburkholderia sp. Also, the Zingiber officinale rhizome pre-treated with NhPBG1 was found to get protected from P. aphanidermatum induced infection, whereas the control showed symptoms of infection. This was further confirmed by the microscopic evaluation of the presence of fungal mycelia in the tissues of control. However, the mycelial invasion could not be detected in the NhPBG1 treated rhizome. The metabolite profiling of NhPBG1 by GC–MS has identified variety of general metabolites, while the antifungal compounds pyocyanin and 1-hydroxyphenazine could be identified by the LC–MS/MS analysis.

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  1. 1.

    Pandey A, Tripathi A, Srivastava P, Choudhary KK, Dikshit A (2019) Plant growth-promoting microorganisms in sustainable agriculture. In: Kumar A, Singh AK, Choudhary KK (eds) Role of plant growth promoting microorganisms in sustainable agriculture and nanotechnology, 1st edn. Elsevier, Woodhead Publishing pp 1–19.

  2. 2.

    Kumar J, Singh D, Ghosh P, Kumar A (2017) Endophytic and epiphytic modes of microbial interactions and benefits. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives, Vol 2: microbial interactions and agro-ecological impacts. Springer NatureSingapore Pvt Ltd., Singapore, pp 227–253.

    Google Scholar 

  3. 3.

    Patel NR, Krishnamurthy R (2014) Carnivory in pitcher plants: an enigmatic meat eating plant. Res Rev Biosci 8:94–106

    Google Scholar 

  4. 4.

    Glick BR (2012) Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:1–15.

    CAS  Article  Google Scholar 

  5. 5.

    Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V (2012) Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 63(2):249–266.

    Article  PubMed  Google Scholar 

  6. 6.

    Hassan KI, Rafik SA, Mussum K (2012) Molecular identification of Pseudomonas aeruginosa isolated from hospitals in kurdistan region. J Adv Res 2(3):90–98

    CAS  Google Scholar 

  7. 7.

    Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Rahman A, Sitepu IR, Tang SY, Hashidoko Y (2010) Salkowski’s reagent test as a primary screening index for functionalities of rhizobacteria isolated from wild dipterocarp saplings growing naturally on medium-strongly acidic tropical peat soil. Biosci Biotechnol Biochem 74(11):2202–2208.

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Jasim B, John Jimtha C, Jyothis M, Radhakrishnan EK (2013) Plant growth promoting potential of endophytic bacteria isolated from Piper nigrum. Plant Growth Regul 71(1):1–11.

    CAS  Article  Google Scholar 

  10. 10.

    Intorne AC, de Oliveira MVV, Lima ML, da Silva JF, Olivares FL, de Souza Filho GA (2009) Identification and characterization of Gluconacetobacter diazotrophicus mutants defective in the solubilization of phosphorus and zinc. Arch Microbiol 191(5):477–483.

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Dinesh R, Anandaraj M, Kumar A, Bini YK, Subila KP, Aravind R (2015) Isolation, characterization, and evaluation of multi-trait plant growth promoting rhizobacteria for their growth promoting and disease suppressing effects on ginger. Microbiol Res 173:34–43.

    Article  PubMed  Google Scholar 

  12. 12.

    Cappuccino JC, Sherman N (1992) Microbiology: a laboratory manual (third ed). Benjamin/cummings Pub. Co., New York, pp 125–179

    Google Scholar 

  13. 13.

    Sabu R, Aswani R, Jishma P, Jasim B, Mathew J, Radhakrishnan EK (2019) Plant growth promoting endophytic Serratia sp. ZoB14 protecting ginger from fungal pathogens. Proc Natl Acad Sci, India, Sect B Biol Sci 89(1):213–220.

    Article  Google Scholar 

  14. 14.

    Buch F, Rott M, Rottloff S, Paetz C, Hilke I, Raessler M, Mithöfer A (2013) Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth. Ann Bot 111(3):375–383.

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Ismail NA, Kamariah AS, Lim LBL, Ahmad N (2015) Phytochemical and pharmacological evaluation of methanolic extracts of the leaves of Nepenthes bicalcarata Hook. F Int J Pharmacogn Phytochem Res 7(6):1127–1138

    Google Scholar 

  16. 16.

    Eilenberg H, Pnini-Cohen S, Rahamim Y, Sionov E, Segal E, Carmeli S, Zilberstein A (2010) Induced production of antifungal naphthoquinones in the pitchers of the carnivorous plant Nepenthes khasiana. J Exp Bot 61(3):911–922.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Caballero-Mellado J, Onofre-Lemus J, Estrada-de los Santos P, Martínez-Aguilar L (2007) The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation. Appl Environ Microbiol 73:5308–5319.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Mannaa M, Park I, Seo YS (2019) Genomic features and insights into the taxonomy, virulence, and benevolence of plant-associated Burkholderia species. Int J Mol Sci 20(1):121.

    CAS  Article  Google Scholar 

  19. 19.

    Carrión VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VC, Raaijmakers JM (2018) Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. ISME J 9:2307–2321.

    CAS  Article  Google Scholar 

  20. 20.

    Elshafie HS, Racioppi R, Bufo SA, Camele I (2017) In vitro study of biological activity of four strains of Burkholderia gladioli pv. agaricicola and identification of their bioactive metabolites using GC–MS. Saudi J Biol Sci 24(2):295–301.

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    Timmermann T, Armijo G, Donoso R, Seguel A, Holuigue L, González B (2017) Paraburkholderia phytofirmans PsJN protects Arabidopsis thaliana against a virulent strain of Pseudomonas syringae through the activation of induced resistance. Mol Plant-Microbe Interact 30(3):215–230.

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Esmaeel Q, Miotto L, Rondeau M, Leclère V, Clément C, Jacquard C, Barka EA (2018) Paraburkholderia phytofirmans PsJN-plant interaction: from perception to the induced mechanisms. Front Microbiol 9:2093.

    Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Shirakawa M, Uehara I, Tanaka M (2019) Mycorrhizosphere bacterial communities and their sensitivity to antibacterial activity of ectomycorrhizal fungi. Microbes Environ 34(2):191–198.

    Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Iqbal U, Jamil N, Ali I, Hasnain S (2010) Effect of zinc-phosphate-solubilizing bacterial isolates on growth of Vigna radiata. Ann Microbiol 60(2):243–248.

    Article  Google Scholar 

  25. 25.

    Zahir ZA, Munir A, Asghar HN, Shaharoona B, Arshad M (2008) Effectiveness of rhizobacteria containing ACC deaminase for growth promotion of peas (Pisum sativum) under drought conditions. J Microbiol Biotechnol 18(5):958–963

    CAS  PubMed  Google Scholar 

  26. 26.

    Gusain YS, Singh US, Sharma AK (2015) Bacterial mediated amelioration of drought stress in drought tolerant and susceptible cultivars of rice (Oryza sativa L.). Afr J Biotechnol 14(9):764–773.

    CAS  Article  Google Scholar 

  27. 27.

    Fankem H, TChakounte GVT, Nkot LN, Mafokoua HL, Dondjou DT, Simo C, Etoa FX (2015) Common bean (Phaseolus vulgaris L.) and soya bean (Glycine max) growth and nodulation as influenced by rock phosphate solubilising bacteria under pot grown conditions. Int J Agric Pol Res 5:242–250.

    Article  Google Scholar 

  28. 28.

    Faridha Begum I, Mohankumar R, Jeevan M, Ramani K (2016) GC-MS analysis of bio-active molecules derived from Paracoccus pantotrophus FMR19 and the antimicrobial activity against bacterial pathogens and MDROs. Indian J Microbiol 56(4):426‐432.

  29. 29.

    Varsha KK, Devendra L, Shilpa G, Priya S, Pandey A, Nampoothiri KM (2015) 2, 4-Di-tert-butyl phenol as the antifungal, antioxidant bioactive purified from a newly isolated Lactococcus sp. Int J Food Microbiol 211:44–50.

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    Bhimba BV, Meenupriya J, Joel EL, Naveena DE, Kumar S, Thangaraj M (2010) Antibacterial activity and characterization of secondary metabolites isolated from mangrove plant Avicennia officinalis. Asian Pac J Trop Med 3(7):544–546.

    Article  Google Scholar 

  31. 31.

    Begum IF, Mohankumar R, Jeevan M, Ramani K (2016) GC–MS analysis of bio-active molecules derived from Paracoccus pantotrophus FMR19 and the antimicrobial activity against bacterial pathogens and MDROs. Indian J Microbiol 56(4):426–432.

    CAS  Article  Google Scholar 

  32. 32.

    Kushwaha M, Jain S K, Sharma N, Abrol V, Jaglan S, Vishwakarma R A (2018) Establishment of LCMS based platform for discovery of quorum sensing inhibitors: Signal detection in Pseudomonas aeruginosa PAO1. ACS chem biol 13(3):657-665.

  33. 33.

    Kerr JR, Taylor GW, Rutman A, Hoiby N, Cole PJ, Wilson R (1999) Pseudomonas aeruginosa pyocyanin and 1-hydroxyphenazine inhibit fungal growth. J Clin Pathol 52(5):385–387.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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The authors acknowledge Kerala State Plan Fund Project and DST-PURSE P II programme.


This study is supported by the Kerala State Council for Science, Technology and Environment—Kerala Biotechnology Commission—Young Investigators Programme in Biotechnology (673/2017/KSCSTE dated October 13, 2017) and JAIVAM project, Mahatma Gandhi University Kottayam (3972/AD A7/2019 dated August 17, 2019).

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Correspondence to Radhakrishnan Edayileveettil Krishnankutty.

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Ravi, A., Theresa, M., Nandayipurath, V.V.T. et al. Plant Beneficial Features and Application of Paraburkholderia sp. NhPBG1 Isolated from Pitcher of Nepenthes hamblack. Probiotics & Antimicro. Prot. (2020).

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  • Paraburkholderia sp.
  • Nepenthes hamblack
  • Rhizome protection
  • Biocontrol properties
  • Plant beneficial traits
  • Zingiber officinale