Abstract
The polymerase chain reaction (PCR) has the ability to amplify specific DNA sequences in an exponentially fashion by in vitro DNA synthesis (Mullis and Faloona, 1987; Saiki et al., 1988). In principle, it is possible from just one or a few copies of target DNA to amplify sufficient amounts of DNA in a few hours to enable visualization of DNA by ethidium bromide staining in gel electrophoresis. Because of these features, PCR is now considered to be a very important technique in molecular biology and has found increasing applications in many different disciplines. In molecular ecology, the technique can be used for producing sensitive and simple methods of detecting and identifying organisms in die environment due to the potential of PCR to detect a few target sequences in a complex mixture. The specificity of the method is dependent on design of oligonucleotide primers, and as with serology, both narrow and broad selectivities are possible. This allows differentiation at many taxonomic levels, and monitoring of specific populations or isolates (Hensou and French, 1993; Ward, 1994).
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References
Barlough, J., East, N., Rowe, J.D., Hoosear, K.V., DeRock, E., Bigornia, L., and Rimstad, E. (1994) Double-nested polymerase chain reaction for detection of caprine arthritis-encephalitis virus proviral DNA in blood, milk, and tissues of infected goats. Journal of Virological Methods 50, 101–114.
Bej, A.K., and Mahbubani, M.H. (1992) Applications of the polymerase chain reaction in environmental microbiology, PCR Methods and Applications 1, 151–159.
Boysen, M., Skouboe, P., Frisvad, J., and Rossen, L. (1996) Reclassification of the Penicillium roqueforti group into three species on the basis of molecular genetic and biochemical profiles, Microbiology, in press.
Brown, A.E., Muhthumeenakshi, S., Sreenivasaprasad, S., Mills, P.R., and Swinburne, T.R. (1993) A PCR primer-specific to Cylindrocarpon heteronema for detection of the pathogen in apple wood, FEMS Microbiology Letters 108, 117–120.
Brown, A.E., Muthumeenakshi S., Swinburne, T.R., and Li, R. (1994) Detection of the source of infection of apple trees by Cylindrocarpon heteronema using DNA polymorphisms, Plant Pathology 43, 338–342.
Bruns, T.D., White, T.J., and Taylor, J. W. (1991) Fungal molecular systematics, Annual Review of Ecology and Systematics 22, 525–564.
Bryan, G.T., Daniels, M.J., and Osbourn, A.E. (1995) Comparison of fungi within the Gaeumannomyces-Phialophora complex by analysis of ribosomal DNA sequences, Applied and Environmental Microbiology 61, 681–689.
Bulat, S.A., and Mironenko, N.V. (1990) Species identity of the phytopathogenic fungi Pyrenophora teres Drechsler and P. graminea Ito and Kuribayashi, Mikologia i Phytopathologia (Russ.) 24, 435–441.
Bulat, S.A., and Mironenko, N.V. (1992) Polymorphism of yeast-like fungus Aureobasidium pullulans (De Bary) revealed by universally primed polymerase chain reaction: species divergence state, Genetika (Russ.) 28, 19–30.
Bulat, S.A., Mironenko, N.V., Lapteva, M.N., and Strelchenko, P.P. (1994) Polymerase chain reaction with universal primers (UP-PCR) and its application to plant genome analysis, in R.P. Adams et al. (eds.), Conservation of Plant Genes II: Utilization of ancient and modern DNA, Missouri Botanical Garden, St. Louis 48. 113–129.
Burgener-Kairuz, P., Zuber, J.P., Jaunin, P., Buchman, T.G., Bille, J., and Rossier, M. (1994) Rapid detection and identification of Candida albicans and Torulopsis (Candida) glabrata in clinical specimens by species-specific nested PCR amplification of a cytochrome P-450 lanosterol-α-demethylase (L1A1) gene fragment, Journal of Clinical Microbiology 32, 1902–1907.
Catalan, V., Moreno, C., Dasi, M.A., Munoz, C., and Apraiz, D. (1994) Nested polymerase chain reaction for detection of Legionella pneumophila in water. Research in Microbiology 145, 603–610.
Chen, W., Hoy, J.W., and Schneider, R.W. (1992) Species-specific polymorphism in transcribed ribosomal DNA of five Pythium species. Experimental Mycology 16, 22–34.
Degrange, V., and Bardin, R. (1995) Detection and counting of Nitrobacter populations in soil by PCR, Applied and Environmental Microbiology 61, 2093–2098.
Doolittle, R.F. (1990) Molecular evolution: computer analysis of protein and nucleic acid sequences, Methods in Enzymology 183
Foster, L.M., Kozak, K.R., Loftus, M.G., Stevens, J.J., and Ross, I.K. (1993) The polymerase chain reaction and its application to filamentous fungi, Mycological Research 97, 769–781.
Gilliland, G., Perrin, S., and Bunn, H. (1990) Competitive PCR for quantitation of mRNA, 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, 60–69.
Henson, J.M., and French, R. (1993) The polymerase chain reaction and plant disease diagnosis, Annual Review of Phytopathology 31, 81–109.
Hillis, D.M., Allard, M.W., and Miyamoto, M.M. (1993) Analysis of DNA sequence data: phylogenetic inference, in E.A. Zimmer, T.J. White, R.L. Cann, and A.C. Wilson (eds.), Molecular Evolution: Producing the Biochemical Data, Methods in Enzymology 224, 456–487.
Holmes, A.R., Cannon, R.D., Shepherd, M.G., and Jenkinson, H.F. (1994) Detection of Candida albicans and other yeasts in blood by PCR, Journal of Clinical Microbiology 32, 228–231.
Holsinger, K.E., and Jansen, R.K. (1993) Phylogenetic analysis of restriction site data, in E.A. Zimmer, T.J. White, R.L. Cann, and A.C. Wilson (eds.), Molecular Evolution: Producing the Biochemical Data, Methods in Enzymology 224, 439–455.
Hu, X., Nazar, R.N., and Robb, J. (1993) Quantification of Verticillium biomass in wilt disease development, Physiological and Molecular Plant Pathology 42, 23–36.
Lamar, R.T., Schoenike, B., Vanden Wymelenberg, A., Stewart, P., Dietrich, D.M., and Cullen, D. (1995) Quantitation of fungal mRNAs in complex substrates by reverse transcription PCR and its application to Phanerochaete chrysosporium-colonized soil. Applied and Environmental Microbiology 61, 2122–2126.
Lanfranco, L., Wyss, P., Marzachi, C., and Bonfante, P. (1993) DNA probes for identification of the ectomycorrhizal fungus Tuber magnatum Pico, FEMS Microbiology Letters 114, 245–252.
Li, K.-N., Rouse, D.I., and German, T.L. (1994) PCR primers that allow intergeneric differentiation of ascomycetes and their application to Verticillium spp., Applied and Environmental Microbiology 60, 4324–4331.
Liu, Z.L., and Sinclair, J.B. (1992) Genetic diversity of Rhizoctonia solani anastomosis Group 2, Phytopathology 82, 778–787.
Lübeck, M., Bulat, S.A., Lübeck, P.S., Mironenko, N., and Jensen, D.F. (1996) Identification and characterization of isolates of Trichoderma and Gliocladium by PCR-based methods, this volume
Ménard, C., Gosselin, P., Duhaime, J.-F., and Mouton, C. (1994) Polymerase chain reaction using arbitrary primer for the design and construction of a DNA probe specific for Porphyromonas gingivalis, Research in Microbiology 145, 595–602.
Mills, P.R., Sreenivasaprasad, S., and Brown, A.E. (1992) Detection and differentiation of Colletotrichum gloeosporioides isolates using PCR, FEMS Microbiology Letters 98, 137–144.
Morton, A., Garder, J.H., and Barbara, D.J. (1995) Sequences of the internal transcribed spacers of the ribosomal RNA genes and relationships between isolates of Verticillium alboatrum and Verticillium dahliae, Plant Pathology 44, 183–190.
Mullis, K.B., and Faloona, F.A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction, Methods in Enzymology 155, 335–351.
Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B., and Erlich, H.A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase, Science 239, 487–491.
Schaad, N.W., Cheong, S.S., Tamaki, S., Hatziloukas, and Panopoulos, N.J. (1995) A combined biological and enzymatic amplification (BIO-PCR) technique to detect Pseudomonas syringae pv. phaseolicola in bean seed extracts. Phytopathology 85, 243–248.
Schraft, H., and Griffiths, M.W. (1995) Specific oligonucleotide primers for detection of lecithinase-positive Bacillus spp. by PCR, Applied and Environmental Microbiology 61, 98–102.
Simon, L., Lalonde, M., and Bruns, T.D. (1992) Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots, Applied and Environmental Microbiology 58, 291–295.
Steffan, R.J., and Atlas, R.M. (1988) DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Applied and Environmental Microbiology 54, 2185–2191.
Steffan, R.J., and Atlas, R.M. (1991) Polymerase chain reaction: applications in environmental microbiology, Annual Review of Microbiology 45, 137–162.
Straub, T.M., Pepper, I.L., Abbaszadegan, M., and Gerba, C.P. (1994) A method to detect enteroviruses in sewage sludge-amended soil using the PCR, Applied and Environmental Microbiology 60, 1014–1017.
Tisserat, N.A., Hulbert, S.H., and Sauer, K.M. (1994) Selective amplification of rDNA internal transcribed spacer regions to detect Ophiosphaeralla korrae and O. herpotricha, Phytopathology 84, 478–482.
Tsushima, S., Hasebe, A., Komoto, Y., Carter, J.P., Miyashita, K., Yokoyama, K., and Pickup, R.W. (1995) Detection of genetically engineered microorganisms in paddy soil using a simple and rapid “nested” polymerase chain reaction method, Soil Biology and Biochemistry 27, 219–227.
Ward, E. (1994) Use of the polymerase chain reaction for identifying plant pathogens, in J. P. Blakeman and B. Williamsen (eds.), Ecology of Plant Pathogens, CAB International, 143–160.
Ward, E. (1995) Improved polymerase chain reaction (PCR) detection of Gaumannomyces graminis including a safeguard against false negatives, European Journal of Plant Pathology 101, 561–566.
Welsh, J., and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers, Nucleic Acids Research 18, 7213–7218.
Wheeler, W.C. (1994) Sources of ambiguity in nucleic acid sequence alignment, in B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle (eds.) Molecular Ecology and Evolution: Approaches and Applications, Birkhäuser Verlag, Basel, 323–352.
White, T.J., Bruns, T.D., Lee, S., and Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, in M. 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.
Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers, Nucleic Acids Research 18, 6531–6535.
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Lubeck, M., Lubeck, P.S. (1996). PCR-Based Methods — A Promising Tool for Detection and Identification of Fungi in Soil. In: Jensen, D.F., Jansson, HB., Tronsmo, A. (eds) Monitoring Antagonistic Fungi Deliberately Released into the Environment. Developments in Plant Pathology, vol 8. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-1698-2_16
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DOI: https://doi.org/10.1007/978-94-009-1698-2_16
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