Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Botanica Marina

Editor-in-Chief: Dring, Matthew J.

6 Issues per year


IMPACT FACTOR 2016: 1.239
5-year IMPACT FACTOR: 1.373

CiteScore 2016: 1.28

SCImago Journal Rank (SJR) 2016: 0.456
Source Normalized Impact per Paper (SNIP) 2016: 0.841

Online
ISSN
1437-4323
See all formats and pricing
More options …
Volume 48, Issue 5-6 (Dec 2005)

Issues

Molecular approaches for assessing fungal diversity in marine substrata

Ka-Lai Pang
  • School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth, Hampshire PO1 2DY, UK
/ Julian I. Mitchell
  • School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth, Hampshire PO1 2DY, UK
Published Online: 2005-12-08 | DOI: https://doi.org/10.1515/bot.2005.046

Abstract

A range of molecular techniques is available to assess fungal diversity in natural environments. These include denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism (SSCP), terminal restriction fragment length polymorphism (T-RFLP), amplified rDNA restriction analysis (ARDRA), amplified ribosomal intergenic spacer analysis (ARISA) and cloning. The techniques, polymerase chain reaction (PCR) primers for environmental work and their potential limitations are discussed in this review, together with applications for describing the diversity of filamentous marine fungi associated with their substrata. It is unlikely that a single technique can be used to assess all aspects of diversity, however the limited number of studies with a molecular approach has demonstrated that marine substrata contain a greater fungal diversity than previously recognised. These studies have also shown that it is important to combine mycological and molecular approaches to accurately assess diversity.

Keywords: ecology; marine fungi; PCR primers; rRNA

References

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • Booth, T. 1979. Strategies for study of fungi in marine and marine influenced ecosystems. Rev. Microbiol. 10 : 123–138.Google Scholar

  • Borneman, J. and R.J. Hartin. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66 : 4356–4360.CrossrefPubMedGoogle Scholar

  • Bridge, P. and B. Spooner. 2001. Soil fungi: diversity and detection. Plant Soil 232 : 147–154.Google Scholar

  • 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.CrossrefGoogle Scholar

  • Brodie, E., S. Edwards and N. Clipson. 2003. Soil community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45 : 105–114.CrossrefGoogle Scholar

  • Bruns, T.D. 2001. ITS reality. Inoculum 52 : 2–3.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • Byrne, P.J. and E.B.G. Jones. 1974. Lignicolous marine fungi. Veröff. Inst. Meeresforsch. Bremerhaven Suppl. 5 : 301–320.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • Davidson, D.E. 1974. Wood-inhabiting and marine fungi from a saline lake in Wyoming. Trans. Br. Mycol. Soc. 63 : 143–149.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • Elwood, H.J., G.J. Olsen and M.L. Sogin. 1985. The small-sub-unit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2 : 399–410.Google Scholar

  • 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.Google Scholar

  • 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.PubMedGoogle Scholar

  • Fuhrman, J.A. and L. Campbell. 1998. Microbial microdiversity. Nature 393 : 410–411.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • Horton, T.R. and T.D. Bruns. 2001. The molecular revolution in ectomycorrhizal ecology: peeking into the black box. Mol. Ecol. 10 : 1855–1871.PubMedCrossrefGoogle Scholar

  • Hyde, K.D. 1992. The effect of incubation on the occurrence of marine fungi on randomly collected lignocellulose samples. Sydowia 44 : 131–136.Google Scholar

  • Hyde, K.D. and E.B.G. Jones. 1989. Marine mangrove fungi. P. S. Z. N. I. Mar. Ecol. 9 : 15–33.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • Jones, E.B.G. 2000. Marine fungi: some factors influencing biodiversity. Fungal Divers. 4 : 53–73.Google Scholar

  • 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.Google Scholar

  • Jones, E.B.G. and K.D. Hyde. 2002. Succession: where do we go from here? Fungal Divers. 10 : 241–253.Google Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • Klamer, M., M.S. Roberts, L.H. Levine, B.G. Drake and J.I. Garland. 2002. Influence of elevated CO2 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.CrossrefGoogle Scholar

  • Kline, D.A. and M.W. Paschke. 2004. Filamentous fungi: the indeterminate lifestyle and microbial ecology. Microbial Ecol. 47 : 224–235.Google Scholar

  • Koch, J. and K.R.L. Petersen. 1996. A check list of higher marine fungi on wood from Danish coasts. Mycotaxon 15 : 397–414.Google Scholar

  • Kohlmeyer, J. 1977. New genera and species of higher fungi from the deep sea (1615–5315 m). Revue de Mycologie 41 : 189–206.Google Scholar

  • Kohlmeyer, J. and E. Kohlmeyer. 1979. Marine mycology: the higher fungi. Academic Press, New York. pp. 690.Google Scholar

  • Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 1991. Illustrated key to the filamentous higher marine fungi. Bot. Mar. 34 : 1–61.CrossrefGoogle Scholar

  • Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 2003a. Marine ascomycetes from algae and animal hosts. Bot. Mar. 46 : 285–306.Google Scholar

  • Kohlmeyer, J. and B. Volkmann-Kohlmeyer. 2003b. Fungi from coral reefs: a commentary. Mycol. Res. 107 : 386–387.PubMedCrossrefGoogle Scholar

  • Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1995. Fungi on Juncus roemerianus 4. New marine ascomycetes. Mycologia 87 : 532–542.CrossrefGoogle Scholar

  • Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1996. Fungi on Juncus roemerianus. 8. New bitunicate ascomycetes. Can. J. Bot. 74 : 1830–1840.CrossrefGoogle Scholar

  • Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1997. Fungi on Juncus roemerianus 9. New obligate and facultative marine Ascomycotina. Bot. Mar. 40 : 291–300.Google Scholar

  • Kohlmeyer, J., B. Volkmann-Kohlmeyer and O.E. Eriksson. 1999. Fungi on Juncus roemerianus 12. Two new species of Mycosphaerella and Paraphaeosphaeria (Ascomycotina). Bot. Mar. 42 : 505–511.Google Scholar

  • Kowalchuk, G.A. 1999. New perspectives towards analysing fungal communities in terrestrial environments. Curr. Opin. Biotechnol. 10 : 247–251.PubMedCrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • Lorenz, M.C. 2002. Genomic approaches to fungal pathogenicity. Curr. Opin. Microbiol. 5 : 372–378.PubMedCrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.PubMedGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • Martin, A.P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68 : 3673–3682.PubMedCrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • Miller, S.L. 1995. Functional diversity of fungi. Can. J. Bot. 73 (suppl. 1): S50–S57.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • Naeem, S. and S. Li. 1997. Biodiversity enhances ecosystem reliability. Nature 390 : 507–509.Google Scholar

  • Neefs, J.M., Y. Vandepeer, L. Hendriks and R. Dewachter. 1990. Compilation of small ribosomal-subunit RNA sequences. Nucleic Acids Res. 18 : 237–2317.Google Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • Patterson, D.J. 1999. The diversity of eukaryotes. Am. Nat. 154 : 96–124.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • 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.Google Scholar

  • Sankaran, M. and S. McNaughton. 1999. Determinants of biodiversity regulate compositional stability of communities. Nature 401 : 691–693.Google Scholar

  • Sarma, V.V. and K.D. Hyde. 2001. A review on frequently occurring fungi in mangroves. Fungal Divers. 8 : 1–34.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • Schmidt, O. and U. Moreth. 1998. Genetic studies on house rot fungi and a rapid diagnosis. Holz Roh. Werkst. 56 : 421–425.CrossrefGoogle Scholar

  • Schmit, J.P. and C.A. Shearer. 2004. Geographic and host distribution of lignicolous mangrove microfungi. Bot. Mar. 47 : 496–500.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.PubMedGoogle Scholar

  • 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.Google Scholar

  • Smith, G.W., L.D. Ives, I.A. Nagelkerken and K.B. Ritchie. 1996. Caribbean sea-fan mortalities. Nature 383 : 487.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.Google Scholar

  • Sterflinger, K., W.E. Krumbein and A. Schweiertz. 1998. A protocol for PCR in situ hybridization of hyphomycetes. Internal Microbiol. 1 : 217–220.Google Scholar

  • 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.CrossrefPubMedGoogle Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • Tubaki, K. 1973. Aquatic sediment as a habitat of Emericellopsis, with a description of an undescribed species of Cephalo-sporium. Mycologia 65 : 938–941.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.PubMedCrossrefGoogle Scholar

  • Vandenkoornhuyse, P., S.L. Baldauf, C. Leyval, J. Straczek and P.W. Young. 2002. Extensive fungal diversity in plant roots. Science 295 : 2051.Google Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • Viaud, M., A. Pasquier and Y. Brygoo. 2000. Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol. Res. 104 : 1027–1032.CrossrefGoogle Scholar

  • Volkmann-Kohlmeyer, B. and J. Kohlmeyer. 1993. Biogeographic observations on Pacific marine fungi. Mycologia 85 : 337–346.Google Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • 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.Google Scholar

  • 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.CrossrefGoogle Scholar

  • 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.Google Scholar

  • Zuccaro, A., B. Schulz and J.I. Mitchell. 2003. Molecular detection of ascomycetes associated with Fucus serratus. Mycol. Res. 107 : 451–1466.Google Scholar

  • 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.Google Scholar

About the article

Corresponding author


Received: 2005-04-01

Accepted: 2005-10-07

Published Online: 2005-12-08

Published in Print: 2005-12-01


Citation Information: Botanica Marina, ISSN (Online) 1437-4323, ISSN (Print) 0006-8055, DOI: https://doi.org/10.1515/bot.2005.046.

Export Citation

©2005 by Walter de Gruyter Berlin New York. Copyright Clearance Center

Comments (0)

Please log in or register to comment.
Log in