J. For. Sci., 2022, 68(5):163-169 | DOI: 10.17221/161/2021-JFS

Development of loop mediated isothermal amplification for rapid species detection of Armillaria ostoyae using assimilating probeOriginal Paper

Tomáš Tonka*, Dagmar Stehlíková, Lucie Walterová, Vladislav Čurn
Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic

We introduced here the first loop mediated isothermal amplification (LAMP) assay for the identification of honey fungus, Armillaria ostoyae, a basidiomycote playing an important role in spruce declines in the Palaearctic region. In total, 101 isolates, representing three Armillaria species, were used to develop a new LAMP assay to determine species specific identification. We have here described LAMP primers enhanced with fluorescent dye that are able to amplify A. ostoyae DNA and detect fungi in a fast single step reaction. The detection limit of LAMP was 1 pg of genomic DNA per reaction. We optimized a new LAMP assay for the rapid detection of A. ostoyae using the translation elongation factor 1-α (tef1) marker and fluorescence labelled oligonucleotide assimilating probe. The LAMP assay does not require any specialized equipment, hence it can be used in the field for the rapid detection of A. ostoyae even using the portable and mobile device. The specificity of the assay was confirmed by the use of A. ostoyae strains and Armillaria cepistipes and Armillaria gallica strains, respectively. In conclusion, the assay could be a rapid, specific, sensitive and low-cost tool for identification of A. ostoyae as well as the first step for expansion of this method in practical applications.

Keywords: detection of fungi; molecular diagnosis; forest pathogen; root rot fungi; spruce decline

Published: May 26, 2022  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Tonka T, Stehlíková D, Walterová L, Čurn V. Development of loop mediated isothermal amplification for rapid species detection of Armillaria ostoyae using assimilating probe. J. For. Sci. 2022;68(5):163-169. doi: 10.17221/161/2021-JFS.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Aglietti C., Luchi N., Pepori A.L., Bartolini P., Pecori F., Raio A., Capretti P., Santini A. (2019): Real-time loop-mediated isothermal amplification: An early-warning tool for quarantine plant pathogen detection. AMB Express, 9: 50. Go to original source... Go to PubMed...
    2. Anderson J.B., Stasovski E. (1992): Molecular phylogeny of northern hemisphere species of Armillaria. Mycologia, 84: 505-516. Go to original source...
    3. Antonín V., Tomšovský M., Sedlák P., Májek T., Jankovský L. (2009): Morphological and molecular characterization of the Armillaria cepistipes - A. gallica complex in the Czech Republic and Slovakia. Mycological Progress, 8: 259-271. Go to original source...
    4. Aslam S., Tahir A., Aslam M.F., Alam M.W., Shedayi A.A., Sadia S. (2017): Recent advances in molecular techniques for the identification of phytopathogenic fungi - A mini review. Journal of Plant Interactions, 12: 493-504. Go to original source...
    5. Baumgartner K., Bhat R., Fujiyoshi P. (2010): A rapid infection assay for Armillaria and real-time PCR quantitation of the fungal biomass in planta. Fungal Biology, 114: 107-119. Go to original source... Go to PubMed...
    6. Baumgartner K., Coetzee M.P., Hoffmeister D. (2011): Secrets of the subterranean pathosystem of Armillaria. Molecular Plant Pathology, 12: 515-534. Go to original source... Go to PubMed...
    7. Chillali M., Wipf D., Guillaumin J.J., Mohammed C., Botton B. (1998): Delineation of the European Armillaria species based on the sequences of the internal transcribed spacer (ITS) of ribosomal DNA. The New Phytologist, 138: 553-561. Go to original source...
    8. Cienciala E., Tumajer J., Zatloukal V., Beranová J., Holá Š., Hůnová I., Russ R. (2017): Recent spruce decline with biotic pathogen infestation as a result of interacting climate, deposition and soil variables. European Journal of Forest Research, 136: 307-317. Go to original source...
    9. Coetzee M., Wingfield B.D., Wingfield M.J. (2018): Armillaria root-rot pathogens: Species boundaries and global distribution. Pathogens, 7: 83. Go to original source... Go to PubMed...
    10. Ghosh R., Nagavardhini A., Sengupta A., Sharma M. (2015): Development of loop-mediated isothermal amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - Wilt pathogen of chickpea. BMC Research Notes, 8: 40. Go to original source... Go to PubMed...
    11. Guo T., Wang H.C., Xue W.Q., Zhao J., Yang Z.L. (2016): Phylogenetic analyses of Armillaria reveal at least 15 phylogenetic lineages in China, seven of which are associated with cultivated Gastrodia elata. PLoS ONE, 11: e0154794. Go to original source... Go to PubMed...
    12. Hariharan G., Prasannath K. (2021): Recent advances in molecular diagnostics of fungal plant pathogens: A mini review. Frontiers in Cellular and Infection Microbiology, 10: 600234. Go to original source... Go to PubMed...
    13. He Z., Su Y., Li S., Long P., Zhang P., Chen Z. (2019a): Development and evaluation of isothermal amplification methods for rapid detection of lethal Amanita species. Frontiers in Microbiology, 10: 1523. Go to original source... Go to PubMed...
    14. He M.Q., Zhao R.L., Hyde K.D., Begerow D., Kemler M. et al. (2019b): Notes, outline and divergence times of Basidiomycota. Fungal Diversity, 99: 105-367. Go to original source...
    15. Holuša J., Lubojacký J., Čurn V., Tonka T., Lukášová K., Horák J. (2018): Combined effects of drought stress and Armillaria infection on tree mortality in Norway spruce plantations. Forest Ecology and Management, 427: 434-445. Go to original source...
    16. Jenkins D.M., Kubota R., Dong J., Li Y., Higashiguchi D. (2011): Handheld device for real-time, quantitative, LAMPbased detection of Salmonella enterica using assimilating probes. Biosensors and Bioelectronics, 30: 255-260. Go to original source... Go to PubMed...
    17. Kauserud H., Schumacher T. (2001): Outcrossing or inbreeding: DNA markers provide evidence for type of reproductive mode in Phellinus nigrolimitatus (Basidiomycota). Mycological Research, 105: 676-683. Go to original source...
    18. Keča N., Bodles W.J.A., Woodward S., Karadžić D., Bojović S. (2006): Molecular-based identification and phylogeny of Armillaria species from Serbia and Montenegro. Forest Pathology, 36: 41-57. Go to original source...
    19. King K.M., Hawkins N.J., Atkins S., Dyer P.S., West J.S., Fraaije B.A. (2019): First application of loop-mediated isothermal amplification (LAMP) assays for rapid identification of mating type in the heterothallic fungus Aspergillus fumigatus. Mycoses, 62: 812-817. Go to original source... Go to PubMed...
    20. Kim M.S., Klopfenstein N.B., Hanna J.W., McDonald G.I. (2006): Characterization of North American Armillaria species: Genetic relationships determined by ribosomal DNA sequences and AFLP markers. Forest Pathology, 36: 145-164. Go to original source...
    21. Klopfenstein N.B., Stewart J.E., Ota Y., Hanna J.W., Richardson B.A., et al. (2017): Insights into the phylogeny of northern hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia, 109: 75-91. Go to original source... Go to PubMed...
    22. Koch R.A., Wilson A.W., Séné O., Henkel T.W., Aime M.C. (2017): Resolved phylogeny and biogeography of the root pathogen Armillaria and its gasteroid relative, Guyanagaster. BMC Evolutionary Biology, 17: 33 Go to original source... Go to PubMed...
    23. Kouguchi Y., Fujiwara T., Teramoto M., Kuramoto M. (2010): Homogenous, real-time duplex loop-mediated isothermal amplification using a single fluorophore-labeled primer and an intercalator dye: Its application to the simultaneous detection of Shiga toxin genes 1 and 2 in Shiga toxigenic Escherichia coli isolates. Molecular and Cellular Probes, 24: 190-195. Go to original source... Go to PubMed...
    24. Kubota R., Alvarez A.M., Su W.W., Jenkins D.M. (2011): FRET-based assimilating probe for sequence-specific realtime monitoring of loop-mediated isothermal amplification (LAMP). Biological Engineering Transactions, 4: 81-100. Go to original source...
    25. Lochman J., Sery O., Mikeš V. (2004): The rapid identification of European Armillaria species from soil samples by nested PCR. FEMS Microbiological Letters, 237: 105-110. Go to original source...
    26. Maphosa L., Wingfield B.D., Coetzee M.P.A., Mwenje E., Wingfield M.J. (2006): Phylogenetic relationships among Armillaria species inferred from partial elongation factor 1-alpha DNA sequence data. Australasian Plant Pathology, 35: 513-520. Go to original source...
    27. Matheny P.B., Wang Z., Binder M., Curtis J.M., Lim Y.W., Nilsson R.H., Hughes K.W., Hofstetter V., Ammirati J.F., Schoch C.L., Langer E., Langer G., McLaughlin D.J., Wilson A.W., Frøslev T., Ge Z.W., Kerrigan R.W., Slot J.C., Yang Z.L., Baroni T.J., Fischer M., Hosaka K., Matsuura K., Seidl M.T., Vauras J., Hibbett D.S. (2007): Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetic and Evolution, 43: 430-451. Go to original source... Go to PubMed...
    28. Mulholland V., MacAskill G.A., Laue B.E., Steele H., Kenyon D., Green, S. (2012): Development and verification of a diagnostic assay based on EF-1 α for the identification of Armillaria species in Northern Europe. Forest Pathology, 42: 229-238. Go to original source...
    29. Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., Amino N., Hase T. (2000): Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28: e63. Go to original source... Go to PubMed...
    30. Ortega S.F., Tomlinson J., Hodgetts J., Spadaro D., Gullino M.L., Boonham N. (2018): Development of loop-mediated isothermal amplification assays for the detection of seedborne fungal pathogens Fusarium fujikuroi and Magnaporthe oryzae in rice seed. Plant Disease, 102: 1549-1558. Go to original source... Go to PubMed...
    31. Panek J., Frac M. (2019): Loop-mediated isothermal amplification (LAMP) approach for detection of heat-resistant Talaromyces flavus species. Scientific Reports, 9: 5846. Go to original source... Go to PubMed...
    32. Park K.H., Oh S.Y., Park M.S., Kim M.S., Klopfenstein N.B., Kim N.K., Park J.Y., Kim J.J., Han S.K., Lee J.K., Lim Y.W. (2018): Re-evaluation of Armillaria and Desarmillaria in South Korea based on ITS/tef1 sequences and morphological characteristics. Forest Pathology, 48: e12447. Go to original source...
    33. Porebski S., Bailey L.G., Baum B.R. (1997): Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Report, 15: 8-15. Go to original source...
    34. Sillo F., Giordano L., Gonthier P. (2018): Fast and specific detection of the invasive forest pathogen Heterobasidion irregulare through a loop-mediated isothermal amplification (LAMP) assay. Forest Pathology, 48: e12396. Go to original source...
    35. Sicoli G., Fatehi J., Stenlid J. (2003): Development of speciesspecific PCR primers on rDNA for the identification of European Armillaria species. Forest Pathology, 33: 287-297. Go to original source...
    36. Stehlíková D., Tonka T., Křížová L., Čurn V. (2019): Detekce Armillaria cepistipes metodou loop-mediated isothermal amplification. Úroda (vědecká příloha časopisu), 12/2019,: 237-241. (in Czech)
    37. Stehlíková D., Luchi N., Aglietti C., Pepori A.L., Diez J.J., Santini A. (2020): Real-time loop-mediated isothermal amplification assay for rapid detection of Fusarium circinatum. Biotechniques, 69: 11-17. Go to original source... Go to PubMed...
    38. Tanner N.A., Zhang Y., Evans Jr. T.C. (2012): Simultaneous multiple target detection in real-time loop-mediated isothermal amplification. Biotechniques, 53: 81-89. Go to original source... Go to PubMed...
    39. Wang X.R., Wu L.F., Wang Y., Ma Y.Y., Chen F.H., Ou H.L. (2015): Rapid detection of Staphylococcus aureus by loopmediated isothermal amplification. Applied Biochemistry and Biotechnology, 175: 882-891. Go to original source... Go to PubMed...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content