Biodiversity & Conservation

, Volume 6, Issue 5, pp 669–680 | Cite as

Strategies for rapid assessment of fungal diversity

  • P. F. Cannon


The problems of estimating fungal diversity are considerable, due especially to the large numbers of species even in small study sites, only a small proportion of which are adequately characterized, and the lack of trained staff and appropriate identification manuals. These difficulties are multiplied in the tropics. Strategies for providing preliminary assessments of fungal diversity which can be carried out within short time-frames are discussed, which will allow initial site valuations to be made for conservation purposes. The necessity of identifying all species discovered is considered, and the need emphasized for strictly defined sampling protocols which allow proper comparison between sites. The advantages and disadvantages of preliminary diversity analyses involving different taxonomic and ecological groups, fungus/plant associations, spatial sampling, soil and litter analysis, molecular methods and indirect assessment are considered.

fungi rapid diversity assessment site valuation sampling techniques 


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  1. Abate, T. (1992) Environmental rapid-assessment programmes have appeal and critics. BioSci 42, 486–9.Google Scholar
  2. Abbott, I. (1974) Numbers of plant, insect and land bird species on nineteen remote islands in the Southern Hemisphere. Biol. J. Linnean Soc. 6, 143–52.Google Scholar
  3. Bååth, E. (1988) A critical examination of the soil washing technique with special reference to the effect of the size of the soil particles. Can. J. Bot. 66, 1566–9.Google Scholar
  4. Barkman, J.J., Moravec, J. and Rauschert, S. (1986) Code of phytosociological nomenclature. Vegetatio 67, 145–58.Google Scholar
  5. Beattie, A.J. and Oliver, I. (1994) Taxonomic minimalism. Trends Ecol. Evol. 9, 488–90.Google Scholar
  6. Bendiksen, E. (1994) Sopp og lav-indikatororganismer for gammelskog med stort atrsmangfold. Blyttia 52, 159–66.Google Scholar
  7. Bills, G.F. and Christensen, M. (in press) Evaluating diversity of soil fungi. In Measuring and Monitoring Biological Diversity. Standard Methods for Fungi (G. Mueller et al., eds). Washington and London: Smithsonian University Press.Google Scholar
  8. Bills, G.F. and Polishook, J.D. (1994) Abundance and diversity of microfungi in leaf litter of a lowland rain forest in Costa Rica. Mycologia 86, 187–98.Google Scholar
  9. Bills, G.F. and Polishook, J.D. (in press) Microfungi from decaying leaves of Heliconia mariae (Heliconiaceae). Brenesia.Google Scholar
  10. Brasier, C.M. (1987) The dynamics of fungal speciation. In Evolutionary Biology of the Fungi (A.D.M. Rayner, C.M. Brasier and D. Moore, eds), pp. 231–60. Cambridge: Cambridge University Press.Google Scholar
  11. Cannon, P.F. (1996) Filamentous fungi. In Methods for the Examination of Organismal Diversity in Soils and Sediments (G. Hall, ed.) pp. 127–45. Wallingford, UK: CAB International.Google Scholar
  12. Cannon, P.F. and Hawksworth, D.L. (1995) The diversity of fungi associated with vascular plants: the known, the unknown and the need to bridge the knowledge gap. Adv. Plant Pathol. 11, 277–302.Google Scholar
  13. Cannon, P.F. and Sutton, B.C. (in press) Evaluating diversity of fungi from dead plant parts. In Measuring and Monitoring Biological Diversity. Standard Methods for Fungi (G. Mueller et al., eds). Washington and London: Smithsonian University Press.Google Scholar
  14. Colwell, R.K. and Coddington, J.A. (1994) Estimating terrestrial biodiversity through extrapolation. Phil. Trans. Roy. Soc. London Biological Sciences, Series B, 345(no. 1311), 101–18.Google Scholar
  15. Cornejo, F.H., Varela, A. and Wright, S.J. (1994) Tropical forest litter decomposition under seasonal drought: nutrient release, fungi and bacteria. Oikos 70, 183–90.Google Scholar
  16. Diederich, P. (1996) The lichenicolous heterobasidiomycetes. Bibliotheca Lichenol. 61, 198 pp.Google Scholar
  17. Faith, D.P. and Walker, P.A. (1996) Environmental diversity: on the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas. Biodiv. Conserv. 5, 399–415.Google Scholar
  18. Faliński, J.B. and Mułenko, W. (eds) (1995) Cryptogamous plants in the forest communities of Białowieża National Park. Phytocoenosis n.s. 7 (Archivum Geobotanicum vol. 4): 176 pp.Google Scholar
  19. Farrelly, V., Rainey, F.A. and Stackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61, 2798–801.Google Scholar
  20. Ferris, M.J., Muyzer, G. and Ward, D.M. (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62, 340–6.Google Scholar
  21. Gams, W. and Domsch, K.H. (1969) The spatial and seasonal distribution of microscopic fungi in arable soils. Trans. Br. Mycol. Soc. 52, 301–8.Google Scholar
  22. Gaston, K.J. (1992) Regional numbers of insect and plant species. Funct. Ecol. 6, 243–7.Google Scholar
  23. Hammond, P.M. (1994a) Practical approaches to the estimation of the extent of biodiversity in speciose groups. Phil. Trans. Roy. Soc. Lond. Biological Sciences, Series B, 345(no. 1311): 119–36.Google Scholar
  24. Hammond, P.M. (1994b) Described and estimated species numbers: an objective assessment of current knowledge. In Microbial Diversity and Ecosystem Function (D. Allsopp et al., eds) pp. 29–71. Wallingford, UK: CAB International.Google Scholar
  25. Hammond, P.M. (1995) Magnitude and distribution of biodiversity. In Global Biodiversity Assessment (V. H. Heywood, ed.) pp. 107–91. Cambridge, UK: Cambridge University Press.Google Scholar
  26. Hawksworth, D.L. (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res. 95, 641–55.Google Scholar
  27. Hiss, R.H., Norris, D.E., Dietrich, C.H., Whitcomb, R.F., West, D.F., Bosio, C.F., Kambhampati, S., Piesman, J., Antolin, M.F. and Black, W.C. (1994) Molecular taxonomy using single-stranded conformation polymorphism (SSCP) analysis of mitochondrial ribosomal DNA genes. Insect Mol. Biol. 3, 171–82.Google Scholar
  28. Holben, W.E. (1994) Isolation and purification of bacterial DNA from soil. In Methods of Soil Analysis. Part 2. Microbiological and Biochemical Properties (Anon, ed.), pp. 727–51. Madison, WI: Soil Science Society of America.Google Scholar
  29. Huston, M.A. (1994) Biological Diversity. The Coexistence of Species on Changing Landscapes, 681 pp. Cambridge, UK: Cambridge University Press.Google Scholar
  30. Hyde, K.D. (1994) Fungi from palms. XIII. The genus Oxydothis, a revision. Sydowia 46, 265–314.Google Scholar
  31. Jaeger, R.G. (1995) Patch sampling. In Measuring and Monitoring Biological Diversity. Standard Methods for Amphibians (W.R. Heyer et al., eds) pp. 107–8. Washington and London: Smithsonian University Press.Google Scholar
  32. Janzen, D.H. and Hallwachs, W. (1994) All-Taxa Biodiversity Inventory of Terrestrial Systems, 132 pp. Draft report of an NSF workshop, University of Pennsylvania; available on the Internet at Scholar
  33. Lodge, D.J. and Cantrell, S. (1995) Fungal communities in wet tropical forests: variation in time and space. Can. J. Bot. 73(supplement 1): S1391–8.Google Scholar
  34. Mahoney, D.P. (1972) Soil and Litter Fungi of the Galapagos Islands. PhD thesis, University of Wisconsin.Google Scholar
  35. May, R.M. (1991) A fondness for fungi. Nature 352, 475–6.Google Scholar
  36. Mills, L.S., Soulé, M.E. and Doak, D.F. (1993) The keystone-species concept in ecology and conservation. BioSci. 43, 219–24.Google Scholar
  37. Muyzer, G., De Waal, E. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturating gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695–700.Google Scholar
  38. O'Dell, T.E., Smith, J.E., Castellano, M. and Luoma, D. (1996) Diversity and conservation of forest fungi. In Managing Forest Ecosystems to Conserve Fungus Diversity and Sustain Wild Mushroom Harvests (D. Pilz and R. Molina, eds). USDA Forest Service, Pacific Northwest Research Station General Technical Report PNW-GTR-371.Google Scholar
  39. Okland, B., Bakke, A., Hågvar, S. and Kvamme, T. (1996) What factors influence the diversity of saproxylic beetles? A multiscaled study from a spruce forest in southern Norway. Biodiv. Conserv. 5, 75–100.Google Scholar
  40. Oliver, I. and Beattie, A.J. (1993) A possible method for the rapid assessment of biodiversity. Conserv. Biol. 7, 562–8.Google Scholar
  41. Olsen, G.J., Overbeek, R., Larsen, N. and Woese, C.R. (1991) The ribosomal RNA database project. Nucleic Acid Res. (suppl.) 19, 2017–21.Google Scholar
  42. Pankhurst, C.E., Ophel-Keller, K., Doube, B.M. and Gupta, V.V.S.R. (1996) Biodiversity of soil microbial communities in agricultural systems. Biodiv. Conserv. 5, 197–209.Google Scholar
  43. Prendergast, J.R., Quinn, R.M., Lawton, J.H., Eversham, B.C. and Gibbons, D.W. (1993) Rare species, the coincidence of diversity hotspots and conservation strategies. Nature 365, 335–7.Google Scholar
  44. Rambelli, A., Persiani, A.M., Maggi, O., Lunghini, D., Onofri, S., Riess, S., Dowgiallo, G. and Puppi, G. (1983) Comparative Studies on Microfungi in Tropical Ecosystems, 102 pp. Rome: UNESCO.Google Scholar
  45. Rees, C.J.C. (1983) Microclimate and the flying Hemiptera fauna of a primary lowland rainforest in Sulawesi. In Tropical Rainforest. Ecology and Management (S.L. Sutton et al., eds) pp. 121–36. Oxford, UK: Blackwell Scientific Publications.Google Scholar
  46. Reysenbach, A.L., Giver, L.J., Wickham, G.S. and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58, 3417–8.Google Scholar
  47. Rose, F. (1976) Lichenological indicators of age and environmental continuity in woodlands. In Lichenology: Progress and Problems (D.H. Brown et al., eds) pp. 279–307. London: Academic Press.Google Scholar
  48. Stackebrandt, E., Liesack, W. and Goebel, B.M. (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S RNA analysis. FASEB J. 7, 232–6.Google Scholar
  49. States, J.S. (1978) Soil fungi of cool-desert plant communities in northern Arizona and southern Utah. J. Arizona-Nevada Acad. Sci. 13, 13–7.Google Scholar
  50. Strong, D.R. and Levin, D.A. (1979) Species richness of plant parasites and growth form of their hosts. Am. Nat. 114, 1–22.Google Scholar
  51. Tibell, L. (1992) Crustose lichens as indicators of forest continuity in boreal coniferous forests. Nordic J. Bot. 12, 427–50.Google Scholar
  52. Tokumasu, S., Tubaki, K. and Manoch, L. (in press) Microfungal communities on decaying pine needles in Thailand. In Tropical Mycology (K.K. Janardhanan et al., eds) pp. 93–106. New Delhi: Oxford and IBH.Google Scholar
  53. Torsvik, V., Goksoyr, J. and Daae, F.L. (1990a) High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56, 782–7.Google Scholar
  54. Torsvik, V., Salte, K., Sorheim, R. and Goksoyr, J. (1990b) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl. Environ. Microbiol. 56, 776–81.Google Scholar
  55. Visser, S. and Parkinson, D. (1975) Fungal succession on aspen poplar leaf litter. Can. J. Bot. 53, 1640–51.Google Scholar
  56. Vrijmoed, L.L.P., Sadaba, R.B., Jones, E.B.G. and Hodgkiss, I.J.H. (1995) An ecological study of fungi colonising decayed Acanthus ilicifolius at Mai Po mangroves, Hong Kong. In Abstracts of the Seventh International Symposium of Microbial Ecology (Anon, ed.) p. 65. Santos, Brazil.Google Scholar
  57. Wang, G. C.-Y. and Wang, Y. (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142, 1107–14.Google Scholar
  58. Ward, D.M., Weller, R. and Bateson, M.M. (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–5.Google Scholar
  59. Ward, D.M., Bateson, M.M., Weller, R. and Ruff-Roberts, A. (1992) Ribosomal analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12, 219–86.Google Scholar
  60. Ward, N., Rainey, F.A., Goebel, B. and Stackebrandt, E. (1994) Identifying and culturing the ‘unculturables’: a challenge for microbiologists. In Microbial Diversity and Ecosystem Function (D. Allsopp et al., eds) pp. 89–110. Wallingford, UK: CAB International.Google Scholar
  61. Watson, E.S., McClurkin, D.C. and Huneycutt, M.B. (1974) Fungal succession on loblolly pine and upland hardwood foliage and litter in North Mississippi. Ecol. 55, 1128–34.Google Scholar
  62. Yen, A.L. (1987) A preliminary assessment of the correlation between plant, vertebrate and Coleoptera communities in the Victorian mallee. In The Role of Invertebrates in Conservation and Biological Survey (J.D. Majer, ed.) pp. 73–88. Perth: Department of Conservation and Land Management.Google Scholar

Copyright information

© Chapman and Hall 1997

Authors and Affiliations

  • P. F. Cannon
    • 1
  1. 1.International Mycological InstituteSurreyUK

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