Diversity and ecology of soil fungal communities: Increased understanding through the application of molecular techniques

Environmental Microbiology

Volumn 6, Issue 8, 2004, Pages 769-779

  Anderson, Ian C ^a   Cairney, John W G ^b  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b UNIVERSITY OF WESTERN SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; DNA FINGERPRINTING; DNA SEQUENCE; ECOSYSTEM; FUNGUS; GENETIC PROCEDURES; GENETICS; METHODOLOGY; MICROBIOLOGY; PHYSIOLOGY; SHORT SURVEY;

BIODIVERSITY; DNA FINGERPRINTING; ECOSYSTEM; FUNGI; GENETIC TECHNIQUES; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); FUNGI;

EID: 3543138422     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00675.x     Document Type: Short Survey

References (84)

1. Allen, T.R., Millar, T., Berch, S.M., and Berbee, M.L. (2003) Culturing and direct DNA extraction find different fungi from the same ericoid mycorrhizal roots. New Phytol 160: 255-272.
2. Anderson, I.C., Campbell, C.D., and Prosser, J.I. (2003a) Diversity of fungi in organic soils under a moorland - Scots pine (Pinus sylvestris L.) gradient. Environ Microbiol 5: 1121-1132.
3. Anderson, I.C., Campbell, C.D., and Prosser, J.I. (2003b) Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ Microbiol 5: 36-47.
4. Borneman, J., and Hartin, R.J. (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66: 4356-4360.
5. Bridge, P., and Spooner, B. (2001) Soil fungi: diversity and detection. Plant Soil 232: 147-154.
6. Brodie, E., Edwards, S., and Clipson, N. (2003) Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol Ecol 45: 105-114.
7. Chen, D.M., and Cairney, J.W.G. (2002) Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites. Mycol Res 106: 532-540.
8. Christensen, M. (1989) A view of fungal ecology. Mycologia 81: 1-19.
9. Clapp, J.P., Young, J.P.W., Merryweather, J.W., and Fitter, A.H. (1995) Diversity of fungal symbionts in arbuscular mycorrhizas from a natural community. New Phytol 130: 259-265.
10. Clapp, J.P., Helgason, T., Daniell, T.J., and Young, J.P.W. (2002) Genetic studies of the structure and diversity of arbuscular mycorrhizal communities. In Mycorrhizal Ecology, van der Heijden, M.G.A., and Sanders, I.R. (eds). Berlin: Springer-Verlag, pp. 201-224.
11. Dickie, I.A., Xu, B., and Koide, R.T. (2002) Vertical distribution of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol 156: 527-535.
12. Edel-Hermann, V., Dreumont, C., Pérez-Piqueres, A., and Steinberg, C. (2004) Terminal restriction fragment length polymorphism analysis of ribosomal RNA genes to assess changes in fungal community structure in soils. FEMS Microbiol Ecol 47: 397-404.
13. Edwards, I.P., Cripliver, J.L., Gillespie, A.R., Johnsen, K.H., Scholler, J.M., and Turco, R.F. (2004) Nitrogen availability alters macrofungal basidiomycete community structure in optimally fertilized loblolly pine forests. New Phytol 162: 755-770.
14. Edwards, S.G., Fitter, A.M., and Young, J.P.W. (1997) Quantification of an arbuscular mycorrhizal fungus, Glomus mosseae, within plant roots by competitive polymerase chain reaction. Mycol Res 101: 1440-1444.
15. Egert, M., and Friedrich, M.W. (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69: 2555-2562.
16. van Elsas, J.D., Duarte, G.F., Keijzer-Wolters, A., and Smit, E. (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 Methods 43: 133-151.
17. Filion, M., St-Arnaud, M., and Jabaji-Hare, S.H. (2003) Direct quantification of fungal DNA from soil substrate using real-time PCR. J Microbiol Methods 53: 67-76.
18. Freitag, T.E., and Prosser, J.I. (2003) Community structure of ammonia-oxidising bacteria within anoxic marine sediments. Appl Environ Microbiol 69: 1359-1371.
19. Fromin, N., Hamelin, J., Tarnawski, S., Roesti, D., Jourdain-Miserez, K., Forestier, N., et al. (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4: 634-643.
20. Gardes, M., and Bruns, T.D. (1993) ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhiza and rusts. Mol Ecol 2: 113-118.
21. Gomes, N.C.M., Fagbola, O., Costa, R., Rumjanek, N.G., Buchner, A., Mendona-Hagler, L., and Smalla, K. (2003) Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl Environ Microbiol 69: 3758-3766.
22. Guidot, A., Debaud, J.-C., and Marmeisse, R. (2002) Spatial distribution of the below-ground mycelia of an ectomycorrhizal fungus inferred from specific quantification of its DNA in soil samples. FEMS Microbiol Ecol 42: 477-486.
23. Guidot, A., Debaud, J.-C., Effosse, A., and Marmeisse, R. (2003) Below-ground distribution and persistence of an ectomycorrhizal fungus. New Phytol 161: 539-548.
24. Hattori, T., Mitsui, H., Haga, H., Wakao, N., Shikano, S., Gorlach, K., et al. (1997) Advances in soil microbial ecology and biodiversity. Antonie Van Leeuwenhoek 71: 21-28.
25. Helgason, T., Daniell, T.J., Husband, R., Fitter, A.H., and Young, J.P.W. (1998) Ploughing up the wood-wide web? Nature 394: 431.
26. Hibbett, D.S. (1992) Ribosomal RNA and fungal systematics. Trans Mycol Soc Japan 33: 533-556.
27. Hitchcock, C.J., Chambers, S.M., Anderson, I.C., and Cairney, J.W.G. (2003) Development of markers for simple sequence repeat-rich regions that discriminate between Pisolithus albus and P. microcarpus. Mycol Res 107: 699-706.
28. Horton, T.R., and Bruns, T.D. (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black box. Mol Ecol 10: 1855-1871.
29. Hugenholtz, P., and Pace, N.R. (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol 14: 190-197.
30. Hunt, J., Boddy, L., Randerson, P.F., and Rogers, H.J. (2004) An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microb Ecol (in press).
31. Johnsen, K., Jacobsen, C.S., Torsvik, V., and Sørensen, J. (2001) Pesticide effects on bacterial diversity in agricultural soils - a review. Biol Fertil Soils 33: 443-453.
32. Johnson, D., Vandenkoornhuyse, P.J., Leake, J.R., Gilbert, L., Booth, R.E., Grime, J.P., et al. (2003) Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms. New Phytol 161: 503-515.
33. 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.
34. Kårén, O., Högberg, N., Dahlberg, A., Jonsson, L., and Nylund, J.E. (1997) Inter- and intraspecific variation in the ITS region of rDNA of ectomycorrhizal fungi in Fennoscandia as detected by endonuclease analysis. New Phytol 136: 313-325.
35. Kent, A.D., and Triplett, E.W. (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56: 211-236.
36. Klamer, M., Roberts, M.S., Levine, L.H., Drake, B.G., and Garland, J.L. (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.
37. Kowalchuk, G.A., Gerards, S., and Woldendorp, J.W. (1997) Detection and characterisation of fungal infections of Ammophila arenaria (Marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl Environ Microbiol 63: 3858-3865.
38. Kowalchuk, G.A., de Souza, F.A., and van Veen, J.A. (2002) Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria. Dutch coastal sand dunes. Mol Ecol 11: 571-581.
39. Kozdrój, J., and van Elsas, J.D. (2001) Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches. J Microbiol Methods 43: 197-212.
40. Landeweert, R., Leeflang, P., Kuyper, T.W., Hoffland, E., Rosling, A., Wernars, K., and Smit, E. (2003a) Molecular identification of ectomycorrhizal mycelium in soil horizons. Appl Environ Microbiol 69: 327-333.
41. Landeweert, R., Veenman, C., Kuyper, T.W., Fritze, H., Wernars, K., and Smit, E. (2003b) Quantification of ectomycorrhizal mycelium in soil by real-time PCR compared to conventional quantification techniques. FEMS Microbiol Ecol 45: 283-292.
42. Landeweert, R., Leeflang, P., Smit, E., and Kuyper, T.W. (2004) Diversity of an ectomycorrhizal fungal community studied by a root tip and total soil DNA approach. Mycorrhiza (in press).
43. Larena, I., Salazar, O., González, V., Julián, M.C., and Rubio, V. (1999) Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. J Biotechnol 75: 187-194.
44. Leckie, S.E., Prescott, C.E., Grayston, S.J., Neufeld, J.D., and Mohn, W.W. (2004) Characterisation of humus microbial communities in adjacent forest types that differ in nitrogen availability. Microb Ecol (in press).
45. Lord, N.S., Kaplan, C.W., Shank, P., Kitts, C.L., and 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.
46. Lowell, J.L., and Klein, D.A. (2001) Comparative single-stranded conformation polymorphism (SSCP) and microscopy-based analysis of nitrogen cultivation interactive effects on the fungal community of a semiarid steppe soil. FEMS Microbiol Ecol 36: 85-92.
47. Lueders, T., Wagner, B., Claus, P., and Friedrich, M.W. (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.
48. Maidak, B.L., Cole, J.R., Parker, C.T., Jr, Garrity, G.M., Larsen, N., Li, B., et al. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27: 171-173.
49. Marsh, T.L. (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2: 323-327.
50. Martin-Laurent, F., Philippot, L., Hallet, S., Chaussod, R., Germon, J.C., Soulas, G., and Catroux, G. (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67: 2354-2359.
51. Morris, S.A., Radajewski, S., Willison, T.W., and Murrell, J.C. (2002) Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol 68: 1446-1453.
52. Muyzer, G. (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2: 317-322.
53. Muyzer, G., De Waal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
54. Ogram, A. (2000) Soil molecular microbial ecology at age 20: methodological challenges for the future. Soil Biol Biochem 32: 1499-1504.
55. Polz, M.F., and Cavanaugh, C.M. (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
56. Radajewski, S., Ineson, P., Parekh, N.R., and Murrell, J.C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646-649.
57. Ranjard, L., Poly, F., and Nazaret, S. (2000) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol 151: 167-177.
58. Ranjard, L., Poly, F., Lata, J.C., Mougel, C., Thioulouse, J., and Nazaret, S. (2001) Characterisation of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67: 4479-4487.
59. Ranjard, L., Lejon, D.P.H., Mougel, C., Scheher, L., Merdinoglu, D., and Chaussod, R. (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting of fungal and bacterial communities. Environ Microbiol 5: 1111-1120.
60. Rodriguez-Valera, F. (2004) Environmental genomics, the big picture? FEMS Microbiol Lett 231: 153-158.
61. Schmalenberger, A., and Tebbe, C.C. (2003) Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies. Mol Ecol 12: 251-262.
62. Schüßler, A., Schwarzott, D., and Walker, C. (2001) A new phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105: 1413-1421.
63. Sequerra, J., Marmeisse, R., Valla, G., Normand, P., Capellano, A., and Moiroud, A. (1997) taxonomic position and intraspecific 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.
64. Simon, L., Levesque, R.C., and Lalonde, M. (1993) Identification of endomycorrhizal fungi colonising roots by fluorescent single-strand conformation polymorphism-polymerase chain reaction. Appl Environ Microbiol 59: 4211-4215.
65. Smit, E., Leeflang, P., Glandorf, B., van Elsas, J.D., and Wernars, K. (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65: 2614-2621.
66. Smit, E., Veenman, C., and Baar, J. (2003) Molecular analysis of ectomycorrhizal basidiomycete communities in a Pinus sylvestris L. stand reveals long-term increased diversity after removal of litter and humus layers. FEMS Microbiol Ecol 45: 49-57.
67. Stephen, J.R., Kowalchuk, G.A., Bruns, M.-A.V., McCaig, A.E., Phillips, C.J., Embley, T.M., and Prosser, J.I. (1998) Analysis of γ-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis and hierarchical phylogenetic probing. Appl Environ Microbiol 64: 2958-2965.
68. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
69. Taroncher-Oldenburg, G., Griner, E.M., Francis, C.A., and Ward, B.B. (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69: 1159-1171.
70. Tebbe, C.C., and Vahjen, W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast. Appl Environ Microbiol 59: 2657-2665.
71. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
72. Vainio, E.J., and Hantula, J. (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104: 927-936.
73. Valinsky, L., Della Vedova, G., Jiang, T., and Borneman, J. (2002) Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl Environ Microbiol 68: 5999-6004.
74. Vandenkoornhuyse, P., and Leyval, C. (1998) SSU rDNA sequencing and PCR fingerprinting reveal genetic variation within Glomus mosseae. Mycologia 90: 791-797.
75. Vandenkoornhuyse, P., Baldauf, S.L., Leyval, C., Straczek, J., and Young, J.P.W. (2002a) Extensive fungal diversity in plant roots. Science 295: 2051.
76. Vandenkoornhuyse, P., Husband, R., Daniell, T.J., Watson, I.J., Duck, J.M., Fitter, A.H., and Young, J.P.W. (2002b) Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Mol Ecol 11: 1555-1564.
77. Vandenkoornhuyse, P., Ridgway, K.P., Watson, I.J., Fitter, A.H., and Young, J.P.W. (2003) Co-existing grass species have distinct arbuscular mycorrhizal communities. Mol Ecol 12: 3085-3095.
78. Viaud, M., Pasquier, A., and Brygoo, Y. (2000) Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol Res 104: 1027-1032.
79. White, T.J., Bruns, T.D., Lee, S., and Taylor, J. (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In PCR Protocols: a Guide to Methods and Applications. Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.J. (eds). New York: Academic Press, pp. 315-322.
80. Wintzingerode, F.V., Göbel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
81. Ye, R.W., Wang, T., Bedzyk, L., and Kroker, K.M. (2001) Applications of DNA microarrays in microbial systems. J Microbiol Methods 47: 257-272.
82. Yeates, C., and Gillings, M.R. (1998) Rapid purification of DNA from soil for molecular biodiversity analysis. Lett Appl Microbiol 27: 49-53.
83. Zak, J.C., and Visser, S. (1996) An appraisal of soil fungal biodiversity: the crossroads between taxonomic and functional biodiversity. Biodivers Conserv 5: 169-183.
84. Zelles, L. (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fertil Soils 29: 111-129.