Abstract
In the present work PCR technology was used as a tool to detect the early stages of wood decay and was compared with microscopic evaluation. The wood decay fungi Postia placenta and Coniophora puteana were detectable in interior wood samples by terminal restriction fragment length polymorphism (T-RFLP) after 2weeks of incubation with monocultures, while microscopic detection of hyphae was not possible until after 7 weeks. A potential problem when fungal communities are studied with T-RFLPs of rDNA is that intra-specific variation complicates data analysis. In this work, we show that intra-specific sequence variation in the internal transcribed spacer of the rDNA in Coniophora puteana allows T-RFLP identification of this species. This is due to intra-specific variations in fragment length, in combination with the absence of point mutations in the selected restriction sites.
References
Adair, S., Kim, S.H., Breuil, C. (2002) A molecular approach for early monitoring of decay basidiomycetes in wood chips. FEMS Microbiol. Lett.211:117–122.10.1111/j.1574-6968.2002.tb11212.xSearch in Google Scholar
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.25:3389–3402.10.1093/nar/25.17.3389Search in Google Scholar
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.69:926–932.10.1128/AEM.69.2.926-932.2003Search in Google Scholar
Boddy, L. (2000) Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiol. Ecol.31: 185–194.10.1111/j.1574-6941.2000.tb00683.xSearch in Google Scholar
Bridge, P. (2002) The history and application of molecular mycology. Mycologist16:90–99.10.1017/S0269915X0200201XSearch in Google Scholar
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. Methods31:135–142.10.1016/S0167-7012(97)00105-XSearch in Google Scholar
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.156:527–535.10.1046/j.1469-8137.2002.00535.xSearch in Google Scholar
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.Search in Google Scholar
Down, G. (2002) Fungal family trees – finding relationships from molecular data. Mycologist16:51–58.10.1017/S0269915X02002045Search in Google Scholar
Findley, W.P.K. (1965) Ecology of wood-destroying and wood-inhabiting fungi. Holz Organismen1:199–211.Search in Google Scholar
Gardes, M., Bruns, T.D. (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Mol. Ecol.2:113–118.10.1111/j.1365-294X.1993.tb00005.xSearch in Google Scholar
Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., Gibson, T.J. (1998) Multiple sequence alignment with Clustal X. Trends Biochem. Sci.23:403–405.10.1016/S0968-0004(98)01285-7Search in Google Scholar
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. Holzforschung58:199–204.10.1515/HF.2004.030Search in Google Scholar
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. Genetics157:149–161.10.1093/genetics/157.1.149Search in Google Scholar PubMed PubMed Central
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.66:4725–4734.10.1128/AEM.66.11.4725-4734.2000Search in Google Scholar PubMed PubMed Central
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. 346–357.10.1021/bk-2003-0845.ch020Search in Google Scholar
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. 129–174.10.1016/B978-0-12-215001-2.50011-8Search in Google Scholar
Käärik, A., Lundström, H., Ahlström, K. (1976) Försök till analys av luftens svampsporer [An attempt to analyse fungal spores in the air]. Fauna Flora71:9–14.Search in Google Scholar
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.13:3137–3146.10.1111/j.1365-294X.2004.02307.xSearch in Google Scholar PubMed
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.63:4516–4522.10.1128/aem.63.11.4516-4522.1997Search in Google Scholar PubMed PubMed Central
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.42:327–337.10.1111/j.1574-6941.2002.tb01022.xSearch in Google Scholar PubMed
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.Search in Google Scholar
Moreth, U., Schmidt, O. (2000) Identification of indoor rot fungi by taxon-specific priming polymerase chain reaction. Holzforschung54:1–8.10.1515/HF.2000.001Search in Google Scholar
Mounce, I. (1929) Studies in Forest Pathology II. The Biology of Fomes pinicola (Fr.) Cooke. Canadian Department of Agriculture Bulletin No. 111.Search in Google Scholar
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.Search in Google Scholar
Schmidt, O. (2000) Molecular methods for the characterization and identification of the dry rot fungus Serpula lacrymans. Holzforschung54:221–228.10.1515/HF.2000.038Search in Google Scholar
Schmidt, O., Moreth, U. (2000) Species-specific PCR primers in the rDNA-ITS region as a diagnostic tool for Serpula lacrymans. Mycol. Res.104:69–72.10.1017/S0953756299001562Search in Google Scholar
Schmidt, O., Moreth, U. (2002) Data bank of rDNA-ITS sequences from building-rot fungi for their identification. Wood Sci. Technol.36:429–433.10.1007/s00226-002-0152-6Search in Google Scholar
Schmidt, O., Moreth, U. (2003) Molecular identity of species and isolates of internal pore fungi Antrodia spp. and Oligoporus placenta. Holzforschung57:120–126.Search in Google Scholar
Schmidt, O., Grimm, K., Moreth, U. (2002) Molecular identity of species and isolates of the Coniophora cellar fungi. Holzforschung56:563–571.10.1515/HF.2002.086Search in Google Scholar
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.51:83–88.10.1007/s10086-004-0617-3Search in Google Scholar
Swofford, D.L. (1998) PAUP* 4.0 – Phylogenetic Analysis Using Parsimony (*and other methods). Sinauer Associates, Sunderland, MA.Search in Google Scholar
Taylor, J.W., Geiser, D.M., Burt, A., Koufopanou, V. (1999) The evolutionary biology and population genetics underlying fungal strain typing. Clin. Microbiol. Rev.12:126–146.10.1128/CMR.12.1.126Search in Google Scholar PubMed PubMed Central
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.[el12]10.1016/B978-0-12-372180-8.50042-1Search in Google Scholar
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