Journal of Korean Society of Forest Science (한국산림과학회지)

Korean Society of Forest Science (한국산림과학회)
권호 표지

Detection of Rhizina undulata in Soil by Nested-PCR Using rDNA ITS-specific Primer

  • Lee, Sun Keun (Department of Forest Resources Protection, College of Forest and Environmental Sciences, Kangwon National University) ;
  • Lee, Jong Kyu (Department of Forest Resources Protection, College of Forest and Environmental Sciences, Kangwon National University) ;
  • Lee, Seung Kyu (Division of Forest Insect Pests and Disease, Korea Forest Research Institute) ;
  • Kim, Kyung Hee (Division of Forest Insect Pests and Disease, Korea Forest Research Institute) ;
  • Lee, Sang Yong (Department of Forest Resources Protection, College of Forest and Environmental Sciences, Kangwon National University)
  • Received : 2007.08.10
  • Accepted : 2007.09.12
  • Published : 2007.10.31
Download PDF
⟨ Previous Next ⟩

Abstract

Rhizina undulata is the fungus, which causes Rhizina root rot on coniferous trees. Nested-PCR using ITS-specific primer was applied to detect R. undulata from the soils of Japanese black pine (Pinus thunbergil) forests infested with the disease in Seocheon, Chungnam Province, South Korea. Soil samples were collected from four different sites, both dead trees and fruit bodies of R. undulata were present, dead trees only present, fruit bodies only present, and both were absent. Nested-PCR products specific to R. undulata ITS-region were amplified. Positive reactions were found in some samples from the sites, where dead trees and fruit bodies of R. undulata were absent as well as where both of those were present. R. undulata was mainly detected in the soil samples from the depth of 5~20 cm under the soil surface. These results show that the nested-PCR could be used to diagnose the presence or potential infestation of R. undulata in the soils of pine forests.

Keywords

References

  1. Binnicker, M.J., Buckwalter, S.P., Eisberner, J.J., Stewart, R.A., McCullough, A.E., Wohlfiel, S.L. and Wengenack, N.L. 2007. Detection of Coccidioides species in clinical specimens by real-time PCR. Journal of Clinical Microbiology 45: 173-178 https://doi.org/10.1128/JCM.01776-06
  2. Chao, C.C., Lee, J.T. and Tsung, C.C. 2004. Identification of clinically relevant Viridans group Streptococci by sequence analysis of the 16s-23s ribosome DNA spacer region. Journal of Clinical Microbiology 42: 2651-2657 https://doi.org/10.1128/JCM.42.6.2651-2657.2004
  3. Chiang, Y.C., Chou, C.H., Lee, P.R. and Chiang, T.Y. 2001. Detection of leaf-associated fungi based on PCR and nucleotide sequence of the ribosomal internal transcribed spacer (ITS) in Miscanthus. Botanical Bulletin of Academia Sinica 42: 39-44
  4. Cullen S.W. and Hirsch P.R. 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biology and Biochemistry 30: 983-993 https://doi.org/10.1016/S0038-0717(98)00001-7
  5. Egger, K.N. 1996. Molecular systematics of E-strain mycorrhizal fungi: Wilcoxina and its relationship to Tricharina (Pezizales). Canadian Journal of Botany 74: 773-779 https://doi.org/10.1139/b96-096
  6. George, M.S., Johanne M. and Paul M.K. 2000. Genetic similarity among Cercospora apii - group species and their detection in host plant tissue by PCR/RFLP analyses of the rDNA internal transcribed spacer (ITS). The Journal of General and Applied Microbiology 46: 69-78 https://doi.org/10.2323/jgam.46.69
  7. Hayasaki, M., Toshinobu, M. and Leggett, J.M. 2001. Intraspecific variation of 18S-5.8S-26S rDNA sites revealed by FISH and RFLP in wild oat, Avena agadiriana. Genes and Genetic Systems 76: 9-14 https://doi.org/10.1266/ggs.76.9
  8. Jacquot, E., van Tuinen, D., Gianinazzi, S. and Gianinazzi-Pearson, V. 2000. Monitoring species of arbuscular mycorrhizal fungi in plant and soil by nested PCR : application to the study of the impact of sewage sludge. Plant and Soil 226: 179-188 https://doi.org/10.1023/A:1026475925703
  9. Jaeger, E.E.M., Carroll, N.M., Choudhury, S., Dunlop, A.A.S., Towler, H.M.A., Matheson, M.M., Adamson, P., Okahravi, N. and Lightman, S. 2000. Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR. Journal of Clinical Microbiology 38: 2902-2908
  10. Jung, J.S., Han, H.S, Jo, Y.S. and Koh, Y.J. 2003. Nested PCR detection of Pseudomonas syringae pv. actinidiae, the causal bacterium of kiwifruit canker. Research in Plant Disease 9: 116-120 https://doi.org/10.5423/RPD.2003.9.3.116
  11. Kageyama, K., Komatsu, T. and Suga, H. 2003. Refilled PCR protocol for detection of plant pathogens in soil. The Phytopathological Society of Japan 69: 153-160
  12. Kikuchi, K., Matsushita, N., Guerin-Laguette, A., Ota A. and Suzuki, K. 2000. Detection of Tricholoma matsutake by specific ITS primers. Mycological Research 104: 1427-1430 https://doi.org/10.1017/S0953756200002653
  13. Kreader, C.A. 1996. Relief of amplification inhibition in PCR with bovine serum albumin of T4 gene 32 protein. Applied and Environmental Microbiology 62: 1102-1106
  14. Lundquist, J.E. 1984. The occurrence and distribution of Rhizina root rot in South Africa and Swaziland. The South African Journal of Sociology 131: 22-24
  15. Lee, I.M., Lukaesko, L.A. and Maroon, C.J.M. 2001. Comparison of dig-labeled PCR, nested PCR, and ELISA for the detection of Clavibacter michiganensis subsp. sepedonicus in field-grown potatoes. Plant Disease 85: 261-266 https://doi.org/10.1094/PDIS.2001.85.3.261
  16. Lee, J.K., Lee, S.Y, Lee, S.J. and Kim, K.H. 2005. Fruiting body development of a root pathogenic fungus, Rhizina undulata, after forest fire in eastern coastal pine forests of Korea. Forest Research 1: 33-37
  17. Lee, S.K., Lee, J.K., Kim, K.H., Lee, S.K. and Lee, S.Y. 2007. PCR detection and sequence analysis of the rDNA ITS regions of Rhizina undulata. Journal of Korean Forest Society 96: (in press)
  18. Lee, S.Y. and Kim, W.K. 1990. Studies on Rhizina root rot disease of Pinus densiflora : Physiological characteristics and pathogenicity of Rhizina undulata. Journal of Korean Forest Society 79: 322-329
  19. Lu, L., Li, J. and Cang, Y. 2002. PCR-based sensitive detection of dedicinal fungi Hericium species from ribosomal internal transcribed spacer(ITS) sequences. Pharmaceutical Society of Japan 25: 975-980
  20. Norman, J.E. and Egger, K.N. 1996. Phylogeny of the genus Plicaria and its relationship to Peziza inferred from ribosomal DNA sequence analysis. Mycologia 88: 986-995 https://doi.org/10.2307/3761062
  21. Murray, J.S. and Young, C. 1961. Group dying of conifers. Forestry Commission Forest Record No. 46. 19pp
  22. Porteus, L.A., Armstrong, J.L., Seidler, R.J. and Watrud, L.S. 1994. An effective method to extract DNA from environmental samples for polymerase chain reaction amplification. Journal of Applied Bacteriology 74: 78-85
  23. Ranjard, L., Poly, F., Lata, J.C., Mougel, C., Thioulouse, J. and Nazaret, S. 2001. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Applied and Environmental Microbiology 67: 4479-4487 https://doi.org/10.1128/AEM.67.10.4479-4487.2001
  24. Robert, E. and Farrell, Jr. 2005. RT-PCR In : RNA methodologies. A laboratory guide for isolation and characterization (3rd. edition). p.478-481. Elsevier Academic Press, USA
  25. Sato, K., Yokozawa, Y. and Shoji, T. 1974. Studies on Rhizina root rot causing group dying of pine trees. Bulletin of the Government Forest Experiment Station 268: 13-48
  26. Sugita, T., Nakajima, M., Ikeda, R., Niki, Y., Matsushima, T. and Shinoda, T. 2001. A nested PCR assay to detect DNA in sera for the diagnosis of deep-seated Trichosporonosis. Microbiology and Immunology 45: 143-148 https://doi.org/10.1111/j.1348-0421.2001.tb01282.x
  27. White, P.L., Barton, R., Guiver, M., Linton, C.J., Wilson, S., Smith, M., Gomez, L.B., Carr, M.J., Kimmitt, P.T., Seaton, S., Rajakumar, K., Holyoake, T., Kibbler, C.C., Johnson, E., Hobson, R.P., Jones, B. and Barnes, R.A. 2006. A consensus on fungal polymerase chain reaction diagnosis? A United Kingdom-Ireland evaluation of polymerase chain reaction methods for detection of systemic fungal infections. Journal of Molecular Diagnostics 8(3): 376-384 https://doi.org/10.2353/jmoldx.2006.050120
  28. White, T.J., Bruns, T. Lee, S. and Taylor, J. 1990. Ampilification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In : PCR Protocols by M.A. Innis, D.H. Gelfand, J.J. Snisky & T.J. White, eds., p.315-322. Academic Press, London
  29. Zinno, T. and Shoji, T. 1981. Studies on Rhizina root rot of pine trees(II). Relation between occurrence of the disease and detection of the causal fungus in soil. Proceedings of the 92nd Meeting of the Japanese Forest Society. p.399-400