Molecular approaches for assessing fungal diversity in marine substrata

Botanica Marina

Volumn 48, Issue 5-6, 2005, Pages 332-347

  Pang, Ka Lai ^a   Mitchell, Julian I ^a  

^a UNIVERSITY OF PORTSMOUTH   (United Kingdom)

Author keywords

Ecology; Marine fungi; PCR primers; rRNA

Indexed keywords

FUNGUS; MARINE ENVIRONMENT; MOLECULAR ANALYSIS; SPECIES DIVERSITY; SUBSTRATE;

FUNGI;

EID: 29244442961     PISSN: 00068055     EISSN: 14374323     Source Type: Journal    
DOI: 10.1515/BOT.2005.046     Document Type: Conference Paper

References (139)

1. Alker, A.P., G.W. Smith and K. Kim. 2001. Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean sea fan corals. Hydrobiologia 460: 105-111.
2. Allen, T.R., T. Millar, S.M. Berch and M.L. Berbee. 2003. Culturing and direct DNA extraction find different fungi from the same ericoid mycorrhizal roots. New Phytol. 160: 255-272.
3. Amann, R.I., W. Ludwig and K.H. Schliefer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
4. Ander, P. and K. Eriksson. 1976. The importance of phenol oxidase activity in lignin degradation by the white rot fungus Sporotrichum pulverulentum. Archiv. Microbiol. 109: 1-8.
5. Anderson, I.C. and J.W.G. Cairney. 2004. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ. Microbiol. 6: 769-779.
6. Anderson, I.C., C.D. Campbell and J.I. Prosser. 2003a. Potential bias of fungal SSU rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ. Microbiol. 5: 36-47.
7. Anderson, I.C., C.D. Campbell and J.I. Prosser. 2003b. Diversity of fungi in organic soils under a moorland-Scots pine (Pinus sylvestris L.) gradient. Environ. Microbiol. 5: 1121-1132.
8. Bakker, P.A.H.M., D.C.M. Glandorf, M. Viebahn, T.W.M. Ouwens, E. Smit, P. Leeflang, K. Wernars, L.S. Thomashow, J.E. Thomas-Oates and L.C. van Loon. 2002. Effects of Pseudomonas putida modified to produce phenazine-1-carboxylic acid and 2,4-diacetylphloroglucinol on the microflora of field grown wheat. Anton. Leeuw. Int. J. G. 81: 617-624.
9. Bebout, B., S. Schatz, J. Kohlmeyer and M. Haibach. 1987. Temperature-dependent growth in isolates of Corollospora maritima Werderm. (Ascomycetes) from different geographical regions. J. Exp. Mar. Biol. Ecol. 106: 203-210.
10. Berch, S.M., T.R. Allen and M.L. Berbee. 2002. Molecular detection, community structure and phylogeny of ericoid mycorrhizal fungi. Plant Soil 244: 55-66.
11. Bertilsson, S., C.M. Cavanaugh and M.F. Polz. 2002. Sequencing- independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers. Appl. Environ. Microbiol. 68: 6077-6086.
12. Booth, T. 1979. Strategies for study of fungi in marine and marine influenced ecosystems. Rev. Microbiol. 10: 123-138.
13. Borneman, J. and R.J. Hartin. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66: 4356-4360.
14. Bridge, P. and B. Spooner. 2001. Soil fungi: diversity and detection. Plant Soil 232: 147-154.
15. Bridge, P.D., P.J. Roberts, B.M. Spooner and G. Panchal. 2003. On the unreliability of published DNA sequences. New Phytol. 160: 43-48.
16. Brodie, E., S. Edwards and N. Clipson. 2003. Soil community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45: 105-114.
17. Bruns, T.D. 2001. ITS reality. Inoculum 52: 2-3.
18. Buchan, A., S.Y. Newell, J.I.J. Moreta and M.A. Moran. 2002. Analysis of internal transcribed spacer (ITS) regions of rRNA genes in fungal communities in a southeastern U.S. salt marsh. Microbial Ecol. 43: 329-340.
19. Buchan, A., S.Y. Newell, M. Butler, E.J. Biers, J.T. Hollibaugh and M.A. Moran. 2003. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl. Environ. Microbiol. 69: 6676-6687.
20. Byrne, P.J. and E.B.G. Jones. 1974. Lignicolous marine fungi. Veröff. Inst. Meeresforsch. Bremerhaven Suppl. 5: 301-320.
21. Daniell, T.J., R. Husband, A.H. Fitter and J.P.W. Young. 2001. Molecular diversity of arbuscular mycorrhizal fungi colonising arable crops. FEMS Microbiol. Ecol. 36: 203-209.
22. Davidson, D.E. 1974. Wood-inhabiting and marine fungi from a saline lake in Wyoming. Trans. Br. Mycol. Soc. 63: 143-149.
23. De Souza, F.A., G.A. Kowalchuk, P. Leeflang, J.A. van Veen and E. Smit. 2004. PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies SSU rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Appl. Environ. Microbiol. 70: 1413-1424.
24. Dickie, I.A., B. Xu and R.T. Koide. 2002. Vertical distribution of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol. 156: 527-224.
25. Dunbar, J., L.O. Ticknor and C.R. Kuske. 2001. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66: 2943-2950.
26. Edwards, I.P., J.L. Cripliver, A.R. Gillespie, K.H. Johnsen, M. Scholler and R.F. Turco. 2004. Nitrogen availability alters macrofungal basidiomycete community structure in optimally fertilized loblolly pine forests. New Phytol. 162: 755-770.
27. Eggert, C., U. Temp and K. Eriksson. 1997. Laccase is essential for lignin degradation by the white rot fungus Pycnoporus cinnabarinus. FEMS Lett. 407: 89-92.
28. Elwood, H.J., G.J. Olsen and M.L. Sogin. 1985. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2: 399-410.
29. Fell, J.W. and S.Y. Newell. 1998. Biochemical and molecular methods for the study of marine fungi. In: (K. Cooksey, ed.) Molecular approaches to the study of the oceans. Chapman & Hall, London, pp. 259-272.
30. Fernández, A., S. Huang, S. Seston, J. Xing, R. Hickey, C. Criddle and J. Tiedje. 1999. How stable is stable? Function versus community composition. Appl. Environ. Microbiol. 65: 3697-3704.
31. Fuhrman, J.A. and L. Campbell. 1998. Microbial microdiversity. Nature 393: 410-411.
32. Gardes, M. and T.D. Bruns. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol. 2: 113-118.
33. Geiser, D.M., J.W. Taylor, K.B. Ritchie and G.W. Smith. 1998. Cause of sea fan death in the West Indies. Nature 394: 137-138.
34. Girvan, M.S., J. Bullimore, A.S. Ball, J.N. Pretty and A.M. Osborn. 2004. Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens. Appl. Environ. Microbiol. 70: 2692-2701.
35. Gomes, N.C.M., O. Fagbola, R. Costa, N.G. Rumjanek, A. Buchner, L. Mendona-Hagler and K. Smalla. 2003. Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl. Environ. Microbiol. 69: 3758-3766.
36. Green, S.J., S. Freeman, Y. Hadar and D. Minz. 2004. Molecular tools for isolate and community studies of Pyrenomycete fungi. Mycologia 96: 439-451.
37. Helgason, T., A.H. Fitter and J.P.W. Young. 1999. Molecular diversity of arbuscular mycorrhizal fungi colonising Hyacinthoides non-scripta (Bluebell) in a seminatural woodland. Mol. Ecol. 8: 659-666.
38. Herndl, G.L. and M.G. Weinbauer. 2003. Marine microbial food web structure and function. In: (G. Wefer, F. Lamy and F. Mantoura, eds) Marine science frontiers for Europe. Springer-Verlag, Berlin. pp. 265-277.
39. Hopple, J.S. and R. Vilgalys. 1999. Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups and monophyly. Mol. Phylogenet. Evol. 13: 1-19.
40. Horton, T.R. and T.D. Bruns. 2001. The molecular revolution in ectomycorrhizal ecology: peeking into the black box. Mol. Ecol. 10: 1855-1871.
41. Hyde, K.D. 1992. The effect of incubation on the occurrence of marine fungi on randomly collected lignocellulose samples. Sydowia 44: 131-136.
42. Hyde, K.D. and E.B.G. Jones. 1989. Marine mangrove fungi. P. S. Z. N. I. Mar. Ecol. 9: 15-33.
43. Hyde, K.D., E.B.G. Jones, E. Leaño, S.B. Pointing, A.D. Poonyth and L.L.P. Vrijmoed. 1998. Role of fungi in marine ecosystems. Biodivers. Conserv. 7: 1147-1161.
44. Hyde, K.D., V.V. Sarma and E.B.G. Jones. 2000. Morphology and taxonomy of higher marine fungi. In: (K.D. Hyde and S.B. Pointing, eds) Marine mycology: a practical approach. Fungal Diversity Press, Hong Kong. pp. 172-204.
45. Inderbitzin, P., S.R. Lim, B. Volkmann-Kohlmeyer, J. Kohlmeyer and M.L. Berbee. 2004. The phylogenetic position of Spathulospora based on DNA sequences from dried herbarium material. Mycol. Res. 108: 737-748.
46. Jansa, J., A. Mozafar, G. Kuhn, T. Anken, R. Ruh, I.R. Sanders and E. Frossard. 2003. Soil tillage affects the community structure of mycorrhizal fungi in maize roots. Ecol. Appl. 13: 1164-1176.
47. Jones, E.B.G. 1963. Observations on the fungal succession on wood test blocks submerged in the sea. J. Inst. Wood Sci. 11: 14-23.
48. Jones, E.B.G. 1968. The distribution of marine fungi on wood submerged in the sea. In: (J.J. Elphick and A.H. Walters, eds) Biodeterioration of materials. Vol. 1. Elesvier, New York. pp. 460-485.
49. Jones, E.B.G. 1985. Wood-inhabiting marine fungi from San Juan Island with special reference to ascospore appendages. Bot. J. Linn. Soc. 91: 219-231.
50. Jones, E.B.G. 1993. Tropical marine fungi. In: (S. Issac, J.C. Frankland, R. Watling and A.J.S. Whalley, eds) Aspects of tropical mycology. Cambridge University Press, Cambridge. pp. 73-89.
51. Jones, E.B.G. 2000. Marine fungi: some factors influencing biodiversity. Fungal Divers. 4: 53-73.
52. Jones, E.B.G. and K.D. Hyde. 1988. Methods for the study of mangrove marine fungi. In: (A.D. Agate, C.V. Subramanian and M. Vannucci, eds) Mangrove microbiology: role of microorganisms in nutrient cycling of mangrove soils and waters. UNDP/UNESCO, Delhi. pp. 9-27.
53. Jones, E.B.G. and K.D. Hyde. 2002. Succession: where do we go from here? Fungal Divers. 10: 241-253.
54. Jones, E.B.G., L.L.P. Vrijmoed and S.A. Alias. 1998. Intertidal marine fungi from San Juan Island and comments on temperate water species. Bot. J. Scotl. 50: 177-187.
55. Jumpponen, A. 2003. Soil fungal community assembly in a primary successional glacier forefront ecosystem as inferred from rDNA sequence analysis. New Phytol. 158: 569-578.
56. Kent, A.D., D.J. Smith, B.J. Benson and E.W. Triplett. 2003. Web-based phylogenetic assignment tool for analysis of terminal restriction fragment polymorphism profiles of microbial communities. Appl. Environ. Microbiol. 69: 6768-6776.
57. Kiesling, T.L., M.R. Diaz, A. Statzell-Tallman and J.W. Fell. 2002. Identification of yeasts with DNA hybridization macroarrays. In: (K.D. Hyde, ed.) Fungi in marine environments. Fungal Diversity Press, Hong Kong. pp. 69-80.
58. Kjøller, R. and S. Rosendahl. 2000. Detection of arbuscular mycorrhizal fungi (Glomales) in roots by nested PCR and SSCP (single stranded conformation polymorphism). Plant Soil 226: 189-196.
59. 2 on the fungal community in a coastal scrub oak forest soil investigated with terminal-restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 68: 4370-4376.
60. Kline, D.A. and M.W. Paschke. 2004. Filamentous fungi: the indeterminate lifestyle and microbial ecology. Microbial Ecol. 47: 224-235.
61. Koch, J. and K.R.L. Petersen. 1996. A check list of higher marine fungi on wood from Danish coasts. Mycotaxon 15: 397-414.
62. Kohlmeyer, J. 1977. New genera and species of higher fungi from the deep sea (1615-5315 m). Revue de Mycologie 41: 189-206.
63. Kohlmeyer, J. and E. Kohlmeyer. 1979. Marine mycology: the higher fungi. Academic Press, New York. pp. 690.
64. Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 1991. Illustrated key to the filamentous higher marine fungi. Bot. Mar. 34: 1-61.
65. Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 2003a. Marine ascomycetes from algae and animal hosts. Bot. Mar. 46: 285-306.
66. Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 2003b. Fungi from coral reefs: a commentary. Mycol. Res. 107: 386-387.
67. Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1995. Fungi on Juncus memerianus 4. New marine ascomycetes. Mycologia 87: 532-542.
68. Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1996. Fungi on Juncus memerianus. 8. New bitunicate ascomycetes. Can. J. Bot. 74: 1830-1840.
69. Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1997. Fungi on Juncus memerianus 9. New obligate and facultative marine Ascomycotina. Bot. Mar. 40: 291-300.
70. Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1999. Fungi on Juncus memerianus 12. Two new species of Mycosphaerella and Paraphaeosphaeria (Ascomycotina). Bot. Mar. 42: 505-511.
71. Kowalchuk, G.A. 1999. New perspectives towards analysing fungal communities in terrestrial environments. Curr. Opin. Biotechnol. 10: 247-251.
72. Kowalchuk, G.A., S. Gerards and J.W. Woldendorp. 1997. Detection and characterization of fungal infections of Ammophila arenaria (Marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified SSU rDNA. Appl. Environ. Microbiol. 63: 3858-3865.
73. Larena, I., O. Salazar, V. Gonzalez, M.C. Julian and V. Rubio. 1999. Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. J. Biotechnol. 75: 187-194.
74. Loeffler, J., I. Hebart, R. Bialek, L. Hagmeyer, D. Schmidt, F.P. Serey, M. Hartmann, J. Eucker and H. Einsele. 1999. Contaminations occurring in fungal PCR assays. J. Clin. Microbiol. 37: 1200-1202.
75. Lord, N.S., C.W. Kaplan, P. Shark, C.L. Kitts and S.L. Elrod. 2003. Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of SSU and ITS ribosomal regions. FEMS Microbiol. Ecol. 42: 327-337.
76. Lorenz, M.C. 2002. Genomic approaches to fungal pathogenicity. Curr. Opin. Microbiol. 5: 372-378.
77. Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K.-H. Schleifer and M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulphate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68: 5064-5081.
78. Loy, A., C. Schulz, S. Lücker, A. Schöpfer-Wendels, K. Stoecker, C. Baranyi, A. Lehner and M. Wagner. 2005. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl. Environ. Microbiol. 71: 1373-1386.
79. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32: 1363-1371.
80. Lueders, T., B. Wagner, P. Claus and M.W. Friedrich. 2004. Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ. Microbiol. 6: 60-72.
81. Luo, M., X.Q. Liang, P. Dang, C.C. Holbrook, M.G. Bausher, R.D. Lee and B.Z. Guo. 2005. Microarray-based screening of differentially expressed genes in peanut in response to Aspergillus parasiticus infection and drought stress. Plant Sci. 169: 695-703.
82. Lyons, J.L., S.Y. Newell, A. Buchan and M.A. Moran. 2003. Diversity of ascomycete laccase gene sequences in a southeastern US salt marsh. Microbial Ecol. 45: 270-281.
83. Marshall, M.N., L. Cocolin, D.A. Mills and J.S. VanderGheynst. 2003. Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost. J. Appl. Microbiol. 95: 934-948.
84. Martin, A.P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68: 3673-3682.
85. Martin, K.J. and P.T. Rygiewicz. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol. 5: 28.
86. May, L.A., B. Smiley and M.G. Schmidt. 2001. Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Can. J. Microbiol. 47: 829-841.
87. Miller, S.L. 1995. Functional diversity of fungi. Can. J. Bot. 73 (suppl. 1): S50-S57.
88. Möhlenhoff, P., L. Müller, A.A. Gorbushina and K. Petersen. 2001. Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects. FEMS Microbiol. Lett. 195: 169-173.
89. Naeem, S. and S. Li. 1997. Biodiversity enhances ecosystem reliability. Nature 390: 507-509.
90. Neefs, J.M., Y. Vandepeer, L. Hendriks and R. Dewachter. 1990. Compilation of small ribosomal-subunit RNA sequences. Nucleic Acids Res. 18: 237-2317.
91. Newell, S.Y. 2001. Spore-expulsion rates and extents of blade occupation by ascomycetes of the smooth-cordgrass standing-decay system. Bot. Mar. 44: 321-326.
92. Newell, S.Y., R.D. Fallon and J.D. Miller. 1989. Decomposition and microbial dynamics for standing, naturally positioned leaves of the salt marsh grass Spartina alterniflora. Mar. Biol. 101: 471-481.
93. Nielsen, K.B., R. Kjøller, P.A. Olsson, P.F. Schweiger, F.Ø. Andersen and S. Rosendahl. 2004. Colonisation and molecular diversity of arbuscular mycorrhizal fungi in the aquatic plants Littorella uniflora and Lobelia dortmanna in southern Sweden. Mycol. Res. 108: 616-625.
94. Nikolcheva, L.G. and F. Bärlocher. 2004. Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream. Mycol. Prog. 3: 41-50.
95. Nikolcheva, L.G., A.M. Cockshutt and F. Bärlocher. 2003. Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Appl. Environ. Microbiol. 69: 2548-2554.
96. Öpik, M., M. Moora, J. Liira, U. Kõljalg, M. Zobel and R. Sen. 2003. Divergent arbuscular mycorrhizal fungal communities colonize roots of Pulsatilla spp. in boreal Scots pine forest and grassland soils. New Phytol. 160: 581-593.
97. Osherov, N., J. Mathew, A. Romans and G.S. May. 2002. Identification of conidial-enriched transcripts in Aspergillus nidulans using suppression subtractive hybridisation. Fungal Genet. Biol. 37: 197-204.
98. Panebianco, C., W.Y. Tam and E.B.G. Jones. 2002. The effect of pre-inoculation of balsa wood by selected marine fungi and their effect on subsequent colonisation in the sea. Fungal Divers. 10: 77-88.
99. Patterson, D.J. 1999. The diversity of eukaryotes. Am. Nat. 154: 96-124.
100. Petersen, K.R.L. and J. Koch. 1997. Substrate preference and vertical zonation of lignicolous marine fungi on mooring posts of oak (Quercus sp.) and larch (Larix sp.) in Svanemøllen Harbour, Denmark. Bot. Mar. 40: 451-463.
101. Rand, T.G. 2000. Diseases of animals. In: (K.D. Hyde and S.P. Pointing, eds) Marine mycology: a practical approach. Fungal Diversity Press, Hong Kong. pp. 21-48.
102. Ranjard, L., F. Poly, J.-C. Lata, C. Mougel, J. Thioulouse and S. Nazaret. 2001. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl. Environ. Microbiol. 67: 4479-4487.
103. Roberts, P.L., J.I. Mitchell and E.B.G. Jones. 1996. Morphological and taxonomical identification of marine ascomycetes: detection of races in geographical isolates of Corollospora maritima by RAPD analysis. In: (L. Rossen, M.T. Dawson and J. Frisvad, eds) Fungal identification techniques EU 16510 EN. European Commission, Bruxelles. pp. 103.
104. Sankaran, M. and S. McNaughton. 1999. Determinants of biodiversity regulate compositional stability of communities. Nature 401: 691-693.
105. Sarma, V.V. and K.D. Hyde. 2001. A review on frequently occurring fungi in mangroves. Fungal Divers. 8: 1-34.
106. Schabereiter-Gurtner, C., G. Piñar, W. Lubitz and S. Rölleke. 2001. Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic SSU rDNA sequence analysis. J. Microbiol. Meth. 47: 345-354.
107. Schadt, C.W., A.P. Martin, D.A. Lipson and S.K. Schmidt. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301: 1359-1361.
108. Schloss, P.D., B.R. Larget and J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70: 5485-5492.
109. Schmidt, O. and U. Moreth. 1998. Genetic studies on house rot fungi and a rapid diagnosis. Holz Roh. Werkst. 56: 421-425.
110. Schmit, J.P. and C.A. Shearer. 2004. Geographic and host distribution of lignicolous mangrove microfungi. Bot. Mar. 47: 496-500.
111. Seghers, D., L. Wittebolle, E.M. Top, W. Verstraete and S.D. Siciliano. 2004. Impact of agricultural practices on the Zea mays L. endophytic community. Appl. Environ. Microbiol. 70: 1475-1482.
112. Sequerra, J., R. Marmeisse, G. Valia, P. Normand, A. Capellanio and A. Moiround. 1997. Taxonomic position and interspecific variability of the nodule forming Penicillium nodositatum inferred from RFLP analysis of the ribosomal intergenic spacer and random amplified polymorphic DNA. Mycol. Res. 101: 465-472.
113. Simon, L., M. Lalonde and T.D. Bruns. 1992. Specific amplification of SSU fungal ribosomal genes from vesicular endomycorrhizal fungi colonising roots. Appl. Environ. Microbiol. 58: 291-295.
114. Simon, L., R.C. Lévesque and M. Lalonde. 1993. Identification of endomycorrhizal fungi colonizing roots by fluorescent single-strand conformation polymorphism-polymerase chain reaction. Appl. Environ. Microbiol. 59: 4211-4215.
115. Smit, E., P. Leeflang, B. Glandorf, J.D. van Elas and K. Wernars. 1999. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding SSU rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 2614-2621.
116. Smith, G.W., L.D. Ives, I.A. Nagelkerken and K.B. Ritchie. 1996. Caribbean sea-fan mortalities. Nature 383: 487.
117. Stach, J.E.M., L.A. Maldonado, D.G. Masson, A.C. Ward, M. Goodfellow and A.T. Bull. 2003. Statistical approaches for estimating actinobacterial diversity in marine sediments. Appl. Environ. Microbiol. 69: 6189-6200.
118. Steinke, T.D. and E.B.G. Jones. 1993. Marine and mangrove fungi from the Indian Ocean coast of South Africa. S. Afr. J. Bot. 59: 385-390.
119. Sterflinger, K., W.E. Krumbein and A. Schweiertz. 1998. A protocol for PCR in situ hybridization of hyphomycetes. Internal Microbiol. 1: 217-220.
120. Stoeck, T. and S. Epstein. 2003. Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl. Environ. Microbiol. 69: 2657-2663.
121. Tan, T.K., W.F. Leong and E.B.G. Jones. 1989. Succession of fungi on wood of Avicennia alba and Avicennia lanata in Singapore. Can. J. Bot. 67: 2686-2691.
122. Tan, T.K., C.L. Teng and E.B.G. Jones. 1995. Substrate type and microbial interactions as factors affecting ascocarp formation by mangrove fungi. Hydrobiologia 295: 127-134.
123. Taylor, D.L and T.D. Bruns. 1999. Community structure of ectomycorrhizal fungi in a Pinus muricata forest: minimal overlap between the mature forest and resistant propagule communities. Mol. Ecol. 8: 1837-1850.
124. Tubaki, K. 1973. Aquatic sediment as a habitat of Emericellopsis, with a description of an undescribed species of Cephalosporium. Mycologia 65: 938-941.
125. Vainio, E.J. and J. Hantula. 2000. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104: 927-936.
126. Valinsky, L., G.D. Vedoa, T. Jiang and J. Borneman. 2002. Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl. Environ. Microbiol. 68: 5999-6004.
127. Vandenkoornhuyse, P., S.L. Baldauf, C. Leyval, J. Straczek and P.W. Young. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.
128. van Elas, J.D., G.F. Duarte, A. Keijzer-Wolters and E. Smit. 2000. Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J. Microbiol. Meth. 43: 33-151.
129. van Tuinen, D., E. Jacquot, B. Zhao, A. Gollotte and V. Gianinazzi-Pearson. 1998. Characterisation of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR. Mol. Ecol. 7: 879-887.
130. Viaud, M., A. Pasquier and Y. Brygoo. 2000. Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol. Res. 104: 1027-1032.
131. Volkmann-Kohlmeyer, B. and J. Kohlmeyer. 1993. Biogeographic observations on Pacific marine fungi. Mycologia 85: 337-346.
132. Vrijmoed, L.L.P. 2000. Isolation and culture of higher filamentous fungi. In: (K.D. Hyde and S.P. Pointing, eds) Marine mycology: a practical approach. Fungal Diversity Press, Hong Kong. pp. 1-20.
133. Vrijmoed, L.L.P., I.J. Hodgkiss and L.B. Thrower. 1986. Occurrence of fungi on submerged pine and teak blocks in Hong Kong coastal waters. Hydrobiologia 135: 109-122.
134. Wagner, M. and M.W. Taylor. 2005. Isotopic-labelling methods for deciphering the function of uncultured microorganisms. In: (G.M. Gadd, K.T. Semple and H.M. Lappin-Scott, eds) SGM symposium 65. Micro-organisms and earth systems: advances in geomicrobiology. Cambridge University Press, Cambridge, UK.
135. White, T.J., T.D. Bruns, S.B. Lee and J.W. Taylor. 1990. Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal DNA genes. In: (M.A. Innis, D.H. Gelfand, J.J. Sninsky and T.J. White, eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego. pp. 315-322.
136. Zhou, G., W.-Z. Whong, T. Ong and B. Chen. 2000. Development of a fungus-specific PCR assay for detecting low-level fungi in an indoor environment. Mol. Cell. Probes 14: 339-348.
137. Zuccaro, A. and J.I. Mitchell. 2005. Fungal communities of seaweeds. In: (J. Dighton, P. Oudemans and J. White, eds) The fungal community: its organisation and role in the ecosystem. Marcel Dekker, New York. pp. 553-579.
138. Zuccaro, A., B. Schulz and J.I. Mitchell. 2003. Molecular detection of ascomycetes associated with Fucus serratus. Mycol. Res. 107: 451-1466.
139. Zuccaro, A., R.C. Summerbell, W. Gams, H.-J. Schroers and J.I. Mitchell. 2004. A new Acremonium species associated with Fucus spp., and its affinity with a phylogenetically distinct marine Emericellopsis clade. Stud. Mycol. 50: 283-297.