Abstract
The great majority of the 80 000+ fungal species so far named and described are likely to occur in the soil environment at some stage in their life-cycle. Fungi therefore have many different functions in soils, which include both active roles, such as the degradation of dead plant material, or inactive roles where propagules are present in the soil as resting states. Current knowledge of fungal diversity in soil is based largely on observations of fruiting bodies present in an environment, or from cultures obtained from soil isolation exercises. Both of these approaches have serious limitations for the detection of the true diversity in any chosen environment. An organism that exists only in a mycelial form in the soil is unlikely to be identified from direct observation if a fruiting body is not formed. Therefore, classical observation through direct microscopy will give a greatly reduced measure of the true diversity in the environment. Culturing fungi from soil isolations will only result in the detection of those propagules that are able to grow and sporulate on the isolation medium used. This again will lead to a greatly reduced measure of diversity, as at the present time only about 17% of the known fungal species can be successfully grown in culture. The recovery of a culture from soil also does not distinguish whether the fungus was an active part of the original ecosystem or present in an inactive resting state. The development of molecular techniques has provided a new range of tools that can provide clear insights into specific interactions and activities in soil environments. The combination of broad spectrum polymerase chain reaction (PCR) detection, coupled with single strand conformation polymorphisms (SSCP) or denaturing gradient gel electrophoresis (DGGE), can give more accurate answers to fundamental questions on ecosystem diversity. This technique does not however distinguish between active and resting stages, and in order to interpret results accurately, some a priori knowledge of the ecology and function of the organisms is required.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Anon. 1992 The great fungus. Nature 357, 179.
Ariffin D and Seman I A 1991 A selective medium for the isolation of Ganoderma from disease tissues. In Proceedings of the 1991 International Palm Oil Conference, Progress, Prospects and Challenges Towards the 21st Century. September 1991. Eds. Basiron et al. pp 517–519. PORIM. Selangor, Malaysia.
Bääth E 1991 Tolerance of copper by entomogenous fungi and the use of copper-amended media for isolation of entomogenous fungi from soil. Mycol. Res. 95, 1140–1142.
Bainbridge B W 1994 Modern approaches to the taxonomy of Aspergillus. In The Genus Aspergillus. Eds K A Powell, A Renwick and J F Peberdy. pp 291–301, Plenum, New York.
Barnard J 2000 Oregon’s monster mushroom is world’s biggest living thing. The Independent on Sunday 6 Aug 2000, p 8.
Barron G L 1968 The Genera of Hyphomycetes from Soil. Williams and Wilkins, Baltimore, MD.
Berbee M L, Yoshimura A, Sugiyama J and Taylor J W 1995 Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S, 5.8S and ITS ribosomal DNA sequence data. Mycologia 87, 210–222.
Bridge P D, O’Grady E B, Pilotti C and Sanderson F R 2000 Development of molecular diagnostics for the detection of Ganoderma isolates pathogenic to oil palm. In Ganoderma Disease of Perennial Crops. Eds J Flood, M Holderness and P D Bridge, pp 223–232, CAB International, Wallingford.
Brundrett M, Bougher N, Dell B, Grove T and Malajczuk N 1996 Working with Mycorrhizas in Forestry and Agriculture. ACIAR Monograph 32 ACIAR, Canberra. 374 pp.
Bruns T D, Fogel R and Taylor, J W 1990 Amplification and sequencing of DNA from fungal herbarium specimens. Mycologia 82,175–184.
Bruns T D, White T J and Taylor J W 1991 Fungal molecular systematics. Ann. Rev. Ecol. Systematics 22, 525–564.
Bruns T D, Vilgalys R, Barns S M, Gonzalez, D, Hibbett D S, Lane D J, Simon L, Stickel S, Szaro T M, Weisburg W G and Sogin M L 1992 Evolutionary relationships within the fungi: analysis of nuclear small subunit rRNA sequences. Mol. Phylogenet. Evolut. 1,231–241.
Christensen M 1989 A view of fungal ecology. Mycologia 81, 1–19.
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.
Cravanzola F, Piatti P, Bridge P D and Ozino O I 1997 Detection of genetic polymorphism by RAPD-PCR in strains of the en-tomopathogenic fungus Beauveria bassiana isolated from the European cockchafer (Melolontha spp.). Lett. Appl. Microbiol. 25, 289–294.
Crespo A, Bridge P D and Hawksworth D L 1997 Amplification of fungal rDNA-ITS regions from non-fertile specimens of the lichen-forming genus Parmelia. The Lichenologist 29, 275–282.
Crespo A, Cubero O F and Grube M 1998 PCR applications in studies on lichen-forming fungi. In Applications of PCR in Mycology. Eds. P D Bridge, D K Arora, C A Reddy and R P Elander. pp 85–106. CAB International, Wallingford.
Cubero O F, Crespo A, Fatehi J and Bridge P D 1999. DNA extraction and PCR amplification method suitable for fresh, herbarium and lichenized fungi. Plant Systematics Evolut. 216, 243–249.
Di Battista C, Bouchard D, Genere B, Martin F and Le Tacon F 1996 Monitoring the persistence of the ectomycorrhizal basidiomycete Laccaria bicolor S238N on Douglas Fir and Norway Spruce in nursery and forest sites by PCR. Abstracts of the First Conference on Mycorrhizae, Berkeley, p 42.
Di Bonito R, Elliot M L and Desjardin E A 1995 Detection of an arbuscular mycorrhizal fungus in roots of different plant species with the PCR. Appl. Environ. Microbiol. 61, 2809–2810.
Domsch K H, Gams W and Anderson T-H 1993 Compendium of Soil Fungi. Vol. 1. IHW-Verlag, Eching.
Driver F and Milner R J 1998 PCR applications to the taxonomy of entomopathogenic fungi. In Applications of PCR in Mycology. Eds P D Bridge, D K Arora, R P Elander and C A Reddy. pp 153–186. CAB International, Wallingford.
Fries N 1983 Basidiospore germination in species of Boletaceae. Mycotaxon 18,345–354.
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, 113–118.
Gardes M and Bruns T D 1996 Community structure of ectomycorrhizal fungi in a Pinus muricata forest: above and below ground views. Can. J. Bot. 74, 1572–1583.
Gilman J C 1957 A Manual of Soil Fungi. 2nd Edn. Iowa State University Press, Inc.
Harley J L and Smith S E 1983 Mycorrhizal Symbiosis. Academic Press, London. 483 p.
Hawksworth D L 1991 The fungal dimension of biodiversity: magnitude, significance and conservation. Mycol. Res. 95, 641–655.
Hawksworth D L, Kirk P M, Sutton B C and Pegler D N 1995 Ainsworth and Bisby’s Dictionary of the Fungi. CAB International, Wallingford. p 424.
Henrion B, Di Battista C, Bouchard D, Vairelles D, Thompson B D, Le Tacon F and Martin F 1994 Monitoring the persistence of Laccaria bicolor as an endomycorrhizal symbiont of nursery-grown Douglas Fir by PCR of the rDNA intergenic spacer. Mol. Ecol. 3,571–580.
Hibbett D S 1992 Ribosomal RNA and fungal systematics. Trans. Mycol. Soc. Jpn. 33, 533–556.
Karen O, Dahlberg A, Finlay R, Jonsson L, Jonsson M and Nylund J E 1996 Diversity of ectomycorrhizal fungi — managed vs. unmanaged forests. Abstracts of the First International conference on Mycorrhizae, Berkeley, p 69.
Keller S 1991 Arthropod-pathogenic Entomophthorales of Switzerland. II. Erynia, Eryniopsis, Neozygites, Zoophthora and Tarichium. Sydowia 43, 39–122.
Kuninaga S, Natsuaki T, Takeuchi T and Yokosawa R 1997 Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani. Curr. Genet. 32, 237–243.
Lanfranco L, Perotto S and Bonfante P 1998 Applications of PCR for studying the biodiversity of mycorrhizal fungi. In Applications of PCR in Mycology. Eds P D Bridge, D K Arora, R P Elander and C A Reddy. pp 107–124. CAB International, Wallingford.
Lee S B and Taylor J W 1992 Phylogeny of five fungus-like protoctistan Phytophthora species, inferred from the internal transcribed spacers of ribosomal DNA. Mol. Biol. Evolut. 9, 636–653.
McLean C B, Cunnington J H and Lawrie A C 1999 Molecular diversity within and between ericoid endophytes from the Ericaceae and Epacridaceae. New Phytol. 144, 351–358.
Miller R N G, Holderness M, Bridge P D and Chung G F 1999 Genetic diversity of Ganoderma in oil palm plantings. Plant Pathol. 48, 595–603.
Moore-Landecker E 1982 Fundamentals of the Fungi. 2nd Edn. Prentice-Hall, New Jersey.
Mordue J E M, Currah R S and Bridge P D 1989 An integrated approach to Rhizoctonia taxonomy: cultural, biochemical and numerical techniques. Mycol. Res. 92, 78–90.
Nankinga C M, Ogenga-Latigo M W and Allard G B 1996 Pathogenicity of indigenous isolates of Beauveria bassiana and Metarrhizium anisopliae to the banana weevil, Cosmopolites sordidus (Germar). Afr. J. Plant Protect. 6, 1–11.
Olson A and Stenlid J 2000 Functional units in root diseases: lessons from Heterobasidion annosum. In Ganoderma Diseases of Perennial Crops Eds. J Flood, P D Bridge and M Holderness. pp 137–154. CAB International, Wallingford.
Perotto S, Actis-Perino E, Perugini J and Bonfante P 1996 Molecular diversity of fungi from ericoid mycorrhizal roots. Mol. Ecol. 5, 123–131.
Piatti P, Cravanzola F, Bridge P D and Ozino O I 1998 Molecular characterization of Beauveria brongniartii isolates obtained from Melolontha melolontha in Valle d’Aosta (Italy) by RAPD-PCR. Lett. Appl. Microbiol. 26, 317–324.
Pugh G J F 1969 Some problems in the classification of soil fungi. In The Soil Ecosystem, A Symposium. Ed. J G Sheals. pp 119–130. Systematics Association Publication No. 8, Academic Press, London.
Roberts P J 1999 Rhizoctonia-forming fungi. Royal Botanic Gardens, Kew.
Rogers S O and Bendich A J 1994 Extraction of total cellular DNA from plants, algae and fungi. Plant Mol. Biol. Manual DI, 1–8.
Sanders I R, Alt M, Groppe K, Boiler T and Wiemken A 1995 Identification of ribosomal DNA polymorphisms among and within spores of the Glomales: application to studies on the genetic diversity of arbuscular mycorrhizal fungal communities. New Phytol. 130,419–427.
Seifert K A, Wingfield B D and Wingfield M J 1995 A critique of DNA sequence analysis in the taxonomy of filamentous ascomycetes and ascomycetous anamorphs. Can. J. Bot. 73 (Suppl 1), S760–767.
Selosse M-A, Costa G, Di Battista C, Le Tacon F and Martin F 1996. Meiotic segregation and recombination of the intergenic spacer of the ribosomal DNA in the ectomycorrhizal basidiomycete Laccaria bicolor. Curr. Genet. 30, 332–337.
Singh G 1991 Ganoderma: the scourge of oil palms in the coastal areas. In Proceedings of Ganoderma Workshop, 1990, Bamgi, Selangor, Malaysia. Eds D. Ariffin and J. Sukaimi. pp 81–97. Palm Oil Research Institute of Malaysia, Kuala Lumpur.
Smith M L, Bruhn J N and Anderson J B 1992 The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nature 356, 428–431.
Stenlid J, Karlsson J-0 and Hogberg N 1994 Interspecific genetic variation in Heterobasidion annosum revealed by amplification of minisatellite DNA. Mycol. Res. 98, 57–63.
Tisserat N A, Hulbert S H and Sauer K M 1994 Selective amplification of rDNA internal transcribed spacer region to detect Ophiosphaerella korrae and O. herpotricha. Phytopathology 84, 478–482.
Wainwright M 1988 Metabolic diversity of fungi in relation to growth and mineral cycling in soil — a review. Trans. Br. Mycol. Soc. 90, 159–170.
Warcup J H 1951 The ecology of soil fungi. Trans. Br. Mycol. Soc. 34, 376–399.
Warcup J H 1957 Studies on the occurrence and activity of fungi in a wheat-field soil. Trans. Br. Mycol. Soc. 40, 237–262.
Watanabe T 1994 Pictorial Atlas of Soil and Seed Fungi. Lewis Publishers, Boca Raton, FL.
Waterhouse G M and Brady B L 1982 Key to the species of Entomophthora sensu lato. Bull. Br. Mycol. Soc. 16, 113–143.
White T J, Bruns T D, Lee S and Taylor J 1990 Amplification and direct sequencing of fungal ribosomal DNA genes for phylogenetics. In PCR Protocols. Eds. M A Innis, D H Sninsky and T J White, pp 315–322. Academic Press, London.
Zolan M E and Pukkila P J 1986 Inheritance of DNA methylation in Coprinus cinereus. Mol. Cell. Biolo. 6, 195–200.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2002 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Bridge, P., Spooner, B. (2002). Soil fungi: diversity and detection. In: Powlson, D.S., Bateman, G.L., Davies, K.G., Gaunt, J.L., Hirsch, P.R. (eds) Interactions in the Root Environment: An Integrated Approach. Developments in Plant and Soil Sciences, vol 96. Springer, Dordrecht. https://doi.org/10.1007/978-94-010-0566-1_15
Download citation
DOI: https://doi.org/10.1007/978-94-010-0566-1_15
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-3925-3
Online ISBN: 978-94-010-0566-1
eBook Packages: Springer Book Archive