Relationship between wood-inhabiting fungi determined by molecular analysis (denaturing gradient gel electrophoresis) and quality of decaying logs

Canadian Journal of Forest Research

Volumn 40, Issue 12, 2010, Pages 2384-2397

  Rajala, Tiina ^a   Peltoniemi, Mikko ^a   Pennanen, Taina ^a   Mäkipää, Raisa ^a  

^a FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

BOREAL FORESTS; COMMUNITY STRUCTURES; DECAYING WOOD; DENATURING GRADIENT GEL ELECTROPHORESIS; FRUIT BODY; FUNGAL COMMUNITY; FUNGAL DIVERSITY; FUNGAL DNA; KLASON LIGNIN; MASS LOSS; MOLECULAR ANALYSIS; NORWAY SPRUCE; PHYSICOCHEMICAL PROPERTY; PICEA ABIES (L.) KARST; PINUS SYLVESTRIS; POLYPORE; POPULUS TREMULA; SCOTS PINE; SPRUCE LOGS; TREE SPECIES; WOOD-INHABITING FUNGI;

DECAY (ORGANIC); DENATURATION; ELECTROPHORESIS; ETHANOL; FORESTRY; FRUITS; GELS; GENE ENCODING; WATER CONTENT; WOOD;

FUNGI;

BOREAL FOREST; DECIDUOUS FOREST; DNA FINGERPRINTING; ELECTROKINESIS; FOREST INVENTORY; FUNGUS; LOGGING (TIMBER); MOLECULAR ANALYSIS; PHYSICOCHEMICAL PROPERTY; SPECIES DIVERSITY; SUCCESSION;

DECAY; DENATURATION; ELECTROPHORESIS; ETHANOL; FORESTRY; FRUITS; FUNGI; GELS; GENES; MOISTURE CONTENT; WOOD;

ASCOMYCOTA; BETULA; FUNGI; PICEA; PICEA ABIES; PINUS SYLVESTRIS; POPULUS TREMULA;

EID: 78650438977     PISSN: 00455067     EISSN: 12086037     Source Type: Journal    
DOI: 10.1139/X10-176     Document Type: Article

References (53)

1. Adair, S., Kim, S.H., and Breuil, C. 2002. A molecular approach for early monitoring of decay basidiomycetes in wood chips. FEMS Microbiol. Lett. 211(1): 117-122. doi:10.1111/j.1574-6968.2002.tb11212.x.
2. Allmér, J., Vasiliauskas, R., Ihrmark, K., Stenlid, J., and Dahlberg, A. 2006. Wood-inhabiting fungal communities in woody debris of Norway spruce (Picea abies (L.) Karst.), as reflected by sporocarps, mycelial isolations and T-RFLP identification. FEMS Microbiol. Ecol. 55(1): 57-67. doi:10.1111/j.1574-6941.2005.
3. Allmér, J., Stenlid, J., and Dahlberg, A. 2009. Logging-residue extraction does not reduce the diversity of litter-layer saprotrophic fungi in three Swedish coniferous stands after 25 years. Can. J. For. Res. 39(9): 1737-1748. doi:10.1139/X09-096.
4. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17): 3389-3402. doi:10.1093/nar/25.17. 3389.
5. Anderson, I.C., and Cairney, J.W.G. 2004. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ. Microbiol. 6(8): 769-779. doi:10.1111/j.1462-2920.2004.00675.x.
6. Anderson, I.C., Campbell, C.D., and Prosser, J.I. 2003. Diversity of fungi in organic soils under a moorland - Scots pine (Pinus sylvestris L.) gradient. Environ. Microbiol. 5(11): 1121-1132. doi:10.1046/j.1462-2920.2003.00522.x.
7. Bader, P., Jansson, S., and Jonsson, B.G. 1995. Wood-inhabiting fungi and substratum decline in selectively logged boreal spruce forests. Biol. Conserv. 72(3): 355-362. doi:10.1016/0006-3207(94)00029-P.
8. Boddy, L., Frankland, J.C., and van West, P. 2008. Ecology of Saprotrophic basidiomycetes. 1st ed. Academic Press, London, U.K.
9. Cajander, A.K. 1926. The theory of forest types. Acta For. Fenn. 29: 1-108.
10. Chi, Y., Hatakka, A., and Maijala, P. 2007. Can co-culturing of two white-rot fungi increase lignin degration and the production of lignin-degrading enzymes? Int. Biodeterior. Biodegrad. 59(1): 32-39. doi:10.1016/j.ibiod.2006.06.025.
11. Drummond, A.J., Ashton, B., Cheung, M., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Thierer, T., and Wilson, A. 2009. Geneious version 4.7. Available from www.geneious.com/
12. Fukami, T., Dickie, I.A., Paula Wilkie, J., Paulus, B.C., Park, D., Roberts, A., Buchanan, P.K., and Allen, R.B. 2010. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol. Lett. 13(6): 675-684. doi:10.1111/j.1461-0248.2010.01465.x.
13. Fukasawa, Y., Osono, T., and Takeda, H. 2009a. Dynamics of physicochemical properties and occurrence of fungal fruit bodies during decomposition of coarse woody depris of Fagus crenata. J. For. Res. 14(1): 20-29. doi:10.1007/s10310-008-0098-0.
14. Fukasawa, Y., Osono, T., and Takeda, H. 2009b. Microfungus communities of Japanase beech logs at different stages of decay in a cool temperate decidous forest. Can. J. For. Res. 39(8): 1606-1614. doi:10.1139/X09-080.
15. Gardes, M., and Bruns, T.D. 1993. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol. Ecol. 2(2): 113-118. doi:10.1111/j. 1365-294X.1993.tb00005.x.
16. Hakala, T.K., Maijala, P., Konn, J., and Hatakka, A. 2004. Evaluation of novel wood-rotting polypores and corticoid fungi for the decay and biopulping of Norway spruce (Picea abies) wood. Enzyme Microb. Technol. 34(3-4): 255-263. doi:10.1016/j.enzmictec.2003.10.014.
17. Hotanen, J.-P., Nuosiainen, H., Mäkipää, R., Reinikainen, A., and Tonteri, T. 2008. Metsätyypit-opas kasvupaikkojen luokitteluun. Metsäntutkimuslaitos, Metsäkustannus Oy.
18. Hottola, J., and Siitonen, J. 2008. Significance of woodland key habitats for polypore diversity and red-listed species in boreal forests. Biodivers. Conserv. 17(11): 2559-2577. doi:10.1007/s10531-008-9317-4.
19. Jasalavich, C.A., Ostrofsky, A., and 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(11): 4725-4734. doi:10.1128/AEM.66.11.4725-4734.2000.
20. Johannesson, H., and Stenlid, J. 1999. Molecular identification of wood-inhabiting fungi in an unmanaged Picea abies forest in Sweden. For. Ecol. Manag. 115(2-3): 203-211. doi:10.1016/S0378-1127(98)00399-5.
21. Jönsson, M.T., Edman, M., and Jonsson, B.G. 2008. Colonization and extinction patterns of wood-decaying fungi in a boreal oldgrowth Picea abies forest. J. Ecol. 96(5): 1065-1075. doi:10.1111/j.1365-2745.2008.01411.x.
22. Karsisto, M., Savitski, M., Kitunen, V., Penttilä, T., and Laine, R. 2003. Quantification of organic fractions in litter and peat organic matter. In Proceedings of the Sixth Finnish Conference of Environmental Sciences: Current Perspectives in Environmental Science and Technology. Finnish Society for Environmental Sciences, Lahti, Finland. pp. 135-137.
23. Korkama, T., Pakkanen, A., and Pennanen, T. 2006. Ectomycorrhizal community structure varies among Norway spruce (Picea abies) clones. New Phytol. 171(4): 815-824. doi:10.1111/j.1469-8137.2006.01786.x.
24. Kotiranta, H., Saarenoksa, R., and Kytövuori, I. 2009. Aphyllophoroid fungi of Finland. A check-list with ecology, distribution, and threat categories. Norrlinia 19. Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
25. Kruys, N., Fries, C., Jonsson, B.G., Lämås, T., and Ståhl, G. 1999. Wood-inhabiting cryptogams on dead Norway spruce (Picea abies) trees in managed Swedish boreal forests. Can. J. For. Res. 29(2): 178-186. doi:10.1139/cjfr-29-2-178.
26. Kulhánková, A., Béguiristain, T., Moukoumi, J., Berthelin, J., and Ranger, J. 2006. Spatial and temporal diversity of wood decomposer communities in different forest stands, determined by ITS rDNA targeted TGGE. Ann. For. Sci. 63(5): 547-556. doi:10.1051/forest:2006037.
27. Lindblad, I. 1998. Wood-inhabiting fungi on fallen logs of Norway spruce: relations to forest management and substrate quality. Nord. J. Bot. 18(2): 243-255. doi:10.1111/j.1756-1051.1998. tb01877.x.
28. Lumley, T.C., Gignac, L.D., and Currah, R.S. 2001. Microfungus communities of white spruce and trembling aspen logs at different stages of decay in disturbed and undisturbed sites in the boreal mixedwood region of Alberta. Can. J. Bot. 79(1): 76-92. doi:10.1139/cjb-79-1-76.
29. Mäkinen, H., Hynynen, J., Siitonen, J., and Sievänen, R. 2006. Predicting the decomposition of Scots pine, Norway spruce, and birch stems in Finland. Ecol. Appl. 16(5): 1865-1879. doi:10. 1890/1051-0761(2006)016[1865:PTDOSP]2.0.CO;2.
30. Muyzer, G., and Smalla, K. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek, 73(1): 127-141. doi:10.1023/A:1000669317571.
31. Novinscak, A., DeCoste, N.J., Surette, C., and Filion, M. 2009. Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis. Can. J. Microbiol. 55(4): 375-387. doi:10.1139/W08-152.
32. Oksanen, J., Kindt, R., Legendre, P., O'Hara, B., Simpson, G.L., Solymos, P., Stevens, M.H.H., and Wagner, H. 2009. Vegan: community ecology package. R package version 1.15-2. Available from https://r-forge.r-project.org/.
33. Olesen, P.O. 1971. The water displacement method. For. Tree Improv. 3: 3-23.
34. Olsson, J. 2008. Colonization patterns of wood-inhabiting fungi in boreal forest. Doctoral dissertation, Department of Ecology and Environmental Science, Umea° University, Umea°, Sweden.
35. Ovaskainen, O., Nokso-Koivisto, J., Hottola, J., Rajala, T., Pennanen, T., Ali-Kovero, H., Miettinen, O., Oinonen, P., Auvinen, P., Paulin, L., Larsson, K.-H., and Mäkipää, R. 2010. Identifying wood-inhabiting fungi with 454 sequencing -what is the probability that BLAST gives the correct species? Fungal Ecol. 3(4): 274-283. doi:10.1016/j.funeco.2010.01.001.
36. Palviainen, M., Laiho, R., Mäkinen, H., and Finér, L. 2008. Do decomposing Scots pine, Norway spruce, and silver birch stems retain nitrogen? Can. J. For. Res. 38(12): 3047-3055. doi:10.1139/X08-147.
37. Penttilä, R., Siitonen, J., and Kuusinen, M. 2004. Polypore diversity in managed and old-growth boreal Picea abies forests in southern Finland. Biol. Conserv. 117(3): 271-283. doi:10.1016/j.biocon.2003.12.007.
38. R Development Core Team. 2009. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
39. Rassi, P., Alanen, A., Kanerva, T., and Mannerkoski, I. 2001. The 2000 Red list of Finnish species. Ministry of the Environmental and Finnish Environment Institute, Helsinki, Finland.
40. Rayner, A.D.M., and Boddy, L. 1988. Fungal decomposition of wood: its biology and ecology. John Wiley & Sons, Bath, U.K.
41. Renvall, P. 1995. Community structure and dynamics of wood-rotting basidiomycetes on decomposing conifer trunks in northern Finland. Karstenia, 35: 1-51.
42. Ryan, M.G., Melillo, J.M., and Ricca, A. 1990. A comparison of methods for determining proximate carbon fractions of forest litter. Can. J. For. Res. 20(2): 166-171. doi:10.1139/x90-023.
43. Siitonen, J. 2001. Forest management, coarse woody debris and saproxylic organisms: Fennoscandian boreal forest as an example. Ecol. Bull. 49: 231-242.
44. Stenlid, J., Penttilä, R., and Dahlberg, A. 2008. Wood-decay basidiomycetes in boreal forests: distribution and community development. In Ecology of saprotrophic basidiomycetes. Edited by L. Boddy, J.C. Frankland, and P. van West. Academic Press, London, U.K. pp. 239-262.
45. Tiunov, A.V., and Scheu, S. 2005. Facilitative interactions rather than resource partitioning drive diversity-functioning relationships in laboratory fungal communities. Ecol. Lett. 8(6): 618-625. doi:10.1111/j.1461-0248.2005.00757.x.
46. Toljander, Y., Lindahl, B., Holmer, L., and Högberg, N. 2006. Environmental fluctuations facilitate species co-existence and increase decomposition in communities of wood decay fungi. Oecologia (Berl.), 148(4): 625-631. doi:10.1007/s00442-006-0406-3.
47. Vainio, E.J., and Hantula, J. 2000a. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104(8): 927-936. doi:10.1017/S0953756200002471.
48. Vainio, E.J., and Hantula, J. 2000b. Genetic differentiation between European and North American populations of Phlebiopsis gigantea. Mycologia, 92(3): 436-446. doi:10.2307/3761502.
49. Vainio, E., Korhonen, K., and Hantula, J. 1998. Genetic variation in Phlebiopsis gigantea as detected with random amplified microsatellite (RAMS) markers. Mycol. Res. 102(2): 187-192. doi:10.1017/S0953756297004577.
50. Vávřová, P., Penttilä, T., and Laiho, R. 2009. Decomposition of Scots pine fine woody debris in boreal conditions: implications for estimating carbon pools and fluxes. For. Ecol. Manag. 257(2): 401-412. doi:10.1016/j.foreco.2008.09.017.
51. White, T.J., Bruns, T., Lee, S., and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: a guide to methods and applications. Edited by M.A. Innis, D.H. Gelfaud, J.J. Sninsky, and T.J. White. Academic Press, San Diego, Calif. pp. 315-322.
52. Wieder, R.K., and Starr, S.T. 1998. Quantitative determination of organic fractions in highly organic, Sphagnum peat soils. Commun. Soil. Sci. Plant Anal. 29(7): 847-857. doi:10.1080/00103629809369990.
53. Worrall, J.J., Anagnost, S.E., and Zabel, R.A. 1997. Comparison of wood decay among diverse lignicolous fungi. Mycologia, 89(2): 199-219. doi:10.2307/3761073.