Detection and species discrimination using rDNA T-RFLP for identification of wood decay fungi

Holzforschung

Volumn 59, Issue 6, 2005, Pages 696-702

  Råberg, Ulrika ^a   Högberg, Nils O S ^a   Land, Carl Johan ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Brown rot; Coniophora; Fungal colonisation; Fungi; Polymerase chain reaction (PCR); Sequencing; Terminal restriction fragment length polymorphism (T RFLP); Wood

Indexed keywords

DECAY (ORGANIC); DNA; MICROSCOPIC EXAMINATION; WOOD;

BROWN ROOT; CONIOPHORA; FUNGAL COLONIZATION; POLYMERASE CHAIN REACTION (PCR); TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM (T-RELP);

FUNGI;

DECAY; FUNGI; MICROSCOPY; NUCLEIC ACIDS; SEQUENCING; WOOD;

CONIOPHORA; CONIOPHORA PUTEANA; FUNGI; POSTIA PLACENTA;

EID: 29244484833     PISSN: 00183830     EISSN: 1437434X     Source Type: Trade Journal    
DOI: 10.1515/HF.2005.111     Document Type: Article

References (34)

1. Adair, S., Kim, S.H., Breuil, C. (2002) A molecular approach for early monitoring of decay basidiomycetes in wood chips. FEMS Microbiol. Lett. 211:117-122.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Blackwood, C.B., Marsh, T., Kim, S.-H., Paul, E.A. (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69:926-932.
4. Boddy, L. (2000) Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiol. Ecol. 31:185-194.
5. Bridge, P. (2002) The history and application of molecular mycology. Mycologist 16:90-99.
6. Clement, B.G., Kehl, L.E., DeBord, K.L., Kitts, C.L. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31:135-142.
7. Dickie, I.A., Xu, B., Koide, R.T. (2002) Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol. 156:527-535.
8. Diehl, S.V., McElroy, T.C., Prewitt, M.L. (2004) Development and implementation of a DNA-RFLP database for wood decay and wood associated fungi. Document No. IRG/WP 04-10527. IRG Secretariat, Stockholm, Sweden. pp. 1-18.
9. Down, G. (2002) Fungal family trees - finding relationships from molecular data. Mycologist 16:51-58.
10. Findley, W.P.K. (1965) Ecology of wood-destroying and wood-inhabiting fungi. Holz Organismen 1:199-211.
11. Gardes, M., Bruns, T.D. (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol. 2:113-118.
12. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., Gibson, T.J. (1998) Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23:403-405.
13. Högberg, N., Land, C.J. (2004) Identification of Serpula lacrymans and other decay fungi in construction timber by sequencing of ribosomal DNA - a practical approach. Holzforschung 58:199-204.
14. James, T.Y., Moncalvo, J.M., Li, S., Vilgalys, R. (2001) Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics 157:149-161.
15. Jasalavich, C.A., Ostrofsky, A., Jellison, J. (2000) Detection and identification of decay fungi in spruce wood by restriction fragment length polymorphism analysis of amplified genes encoding rRNA. Appl. Environ. Microbiol. 66:4725-4734.
16. Jellison, J., Jasalavich, C., Ostrofsky, A. (2003) Detecting and identifying wood decay fungi using DNA analysis. In: Wood Deterioration and Preservation: Advances in Our Changing World. Eds. Goodell, B., Nicholas, D.D., Schultz, T.P. American Chemical Society, Washington, DC. pp. 346-357.
17. Käärik, A. (1974) Decomposition of wood. In: Biology of Plant Litter Decomposition. Eds. Dickinson, C.H., Pugh, G.J.F. Academic Press, New York. pp. 129-174.
18. Käärik, A., Lundström, H., Ahlström, K. (1976) Försök till analys av luftens svampsporer [An attempt to analyse fungal spores in the air]. Fauna Flora 71:9-14.
19. Kauserud, H., Högberg, N., Knudsen, H., Elborne, S.A., Schumacher, T. (2004) Molecular phylogenetics suggest a North American link between the anthropogenic dry rot fungus Serpula lacrymans and its wild relative S. himantioides. Mol. Ecol. 13:3137-3146.
20. Liu, W.-T., Marsh, T.L., Cheng, H., Forney, L.J. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
21. Lord, N.S., Kaplan, C.W., Shank, P., Kitts, C.L., Elrod, S.L. (2002) Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of 18S and ITS ribosomal regions. FEMS Microbiol. Ecol. 42:327-337.
22. McElroy, T.C., Prewitt, M., Diehl, S.V. (2003) A comparison of fatty acid and molecular profiles for identification of wood colonizing Basidiomycota. Document No. IRG/WP 03-20278. IRG Secretariat, Stockholm, Sweden. pp. 1-12.
23. Moreth, U., Schmidt, O. (2000) Identification of indoor rot fungi by taxon-specific priming polymerase chain reaction. Holzforschung 54:1-8.
24. Mounce, I. (1929) Studies in Forest Pathology II. The Biology of Fomes pinicola (Fr.) Cooke. Canadian Department of Agriculture Bulletin No. 111.
25. Ray, M.J., Dickinson, D.J., Buck, M. (2004) Aureobasidium or Hormonema? A genetic approach. Document No. IRG/WP 04-10529. IRG Secretariat, Stockholm, Sweden. pp. 1-13.
26. Schmidt, O. (2000) Molecular methods for the characterization and identification of the dry rot fungus Serpula lacrymans. Holzforschung 54:221-228.
27. Schmidt, O., Moreth, U. (2000) Species-specific PCR primers in the rDNA-ITS region as a diagnostic tool for Serpula lacrymans. Mycol. Res. 104:69-72.
28. Schmidt, O., Moreth, U. (2002) Data bank of rDNA-ITS sequences from building-rot fungi for their identification. Wood Sci. Technol. 36:429-433.
29. Schmidt, O., Moreth, U. (2003) Molecular identity of species and isolates of internal pore fungi Antrodia spp. and Oligoporus placenta. Holzforschung 57:120-126.
30. Schmidt, O., Grimm, K., Moreth, U. (2002) Molecular identity of species and isolates of the Coniophora cellar fungi. Holzforschung 56:563-571.
31. Suhara, H., Maekawa, N., Kubayashi, T., Kondo, R. (2005) Specific detection of a basidiomycete, Phlebia brevispora associated with butt rot of Chamaecyparis obtusa, by PCR-based analysis. J. Wood Sci. 51:83-88.
32. Swofford, D.L. (1998) PAUP* 4.0 - Phylogenetic Analysis Using Parsimony (*and other methods). Sinauer Associates, Sunderland, MA.
33. Taylor, J.W., Geiser, D.M., Burt, A., Koufopanou, V. (1999) The evolutionary biology and population genetics underlying fungal strain typing. Clin. Microbiol. Rev. 12:126-146.
34. White, T.J., Bruns, T., Lee, S., Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols. A guide to Methods and Applications. Eds. Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J. Academic Press, San Diego, USA. pp. 315-322.