Skip to main content
Log in

Detection, identification and disease diagnosis of soilborne pathogens

  • ASDS Keynote Address Session 5
  • Published:
Australasian Plant Pathology Aims and scope Submit manuscript

Abstract

Recent advances in the detection of plant pathogens using immunological and nucleic acid-based techniques has enabled the major genera and species of disease-causing organisms to be quickly and reliably identified. Methods that are based on the use of monoclonal antibodies or the polymerase chain reaction (PCR) are highly sensitive and specific and have the potential to replace traditional technologies. Detection and identification of pathogens that are soilbome presents a number of difficulties such as sampling and reaction inhibition that are beginning to be overcome. New approaches to antibody production such as that of phage display, the combination of immunoassays with PCR and the development of species-specific PCR primers will allow versatile and wide-scale use of these new techniques.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Aujame, L., Sodoyer, R. and Teillaud, J-L. (1997) — Phage display and antibody engineering: a French overview. Trends in Biotechnology 15: 155–157.

    Article  CAS  PubMed  Google Scholar 

  • Avila, F.J., Yeun, G.Y. and Klopfenstein, N.B. (1995) — Characterization of a Pythium ultimum-specific antigen and factors that affect its detection using a monoclonal antibody. Phytopathology 85: 1378–1387.

    Article  CAS  Google Scholar 

  • Balesdent, M.H., Jedryczka, M., Jain, L., Mendes-Pereira, E., Bertrandy, J and Rouxel, T. (1998) — Conidia as a substrate for internal transcribed spacer-based PCR identification of members of Leptosphaeria maculans species complex. Phytopathology 88: 1210–1217.

    Article  CAS  PubMed  Google Scholar 

  • Barker, K.R. and Davis, E.L. (1996) — Assessing plant nematode infestations and infections. Advances in Botanical Research 23: 103–136.

    Article  Google Scholar 

  • Barry, K., Hu, J.S., Kuehnle, A.R. and Sughii, N. (1996) — Sequence analysis and detection using immunocapture-PCR of Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus in Hawaiian orchids. Joumal of Phytopathologv 144: 179–186.

    Article  CAS  Google Scholar 

  • Cahill, D.M. and Hardham, A.R. (1994a)— Exploitation of zoospore taxis in the development of a novel dipstick immunoassay for the specific detection of Phytophthora cinnamomi. Phytopathologv 84: 193–200.

    Article  Google Scholar 

  • Cahill, D.M. and Hardham, A.R. (1994b) — A dipstick immunoassay for the specific detection of Phytophthora cinnamomi in soils. Phytopathology 84: 1284–1292.

    Article  Google Scholar 

  • Cenis, J.L. (1992) — Rapid extraction of fungal DNA for PCR amplification. Nucleic Acid Research 20: 2380.

    Article  CAS  Google Scholar 

  • Clausen, C.A. (1997) — Immunological detection of wood decay fungi — An overview of techniques developed from 1986 to the present. International Biodeterioration and Biodegradation 39: 133–143.

    Article  Google Scholar 

  • Cullen, D.W. and Hirsch, P.R. (1998) — Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biologv and Biochemistry 30: 983–993.

    Article  CAS  Google Scholar 

  • Davies, K.G., Curtis, R.H. and Evens, K. (1996) — Serologically based diagnostic and quantification tests for nematodes. Pesticide Science 47: 81–87.

    Article  Google Scholar 

  • De Boer, S.H., Cuppels, D.A. and Gitaitis, R.D. (1996) — Detecting latent bacterial infections. Advances in Botanical Research 23: 27–49.

    Article  Google Scholar 

  • Dewey, F.M., Thornton, C.R. and Gilligan, C.A. (1997) —Use of monoclonal antibodies to detect, quantify and visualise fungi in soils. Advances in Botanical Research 24: 276–308.

    Article  Google Scholar 

  • Dinesen, I.G. and van Zaayan, A. (1996) — Potential of pathogen detection technology for management of diseases in glasshouse ornamental crops. Advances in Botanical Research 23: 137–170.

    Article  Google Scholar 

  • Dobrowolski, M.P. and O’Brien, P.A. (1993) — Use of RAPD-PCR to isolate a species-specific DNA probe for Phytophthora cinnamomi. FEMS Microbiology Letters 113: 43–48.

    Article  CAS  PubMed  Google Scholar 

  • Dobrowolski, M.P., Tommerup, I.C. and O’Brien, P.A. (1998) — Microsatellites in the mitochondria1 genome of Phytophthora cinnamomi failed to provide highly polymorphic markers for population genetics. FEMS Microbiology Letters 163: 243–248.

    Article  CAS  PubMed  Google Scholar 

  • Drenth, A,, Irwin, J.A.G. and Maclean, D.J. (1997) — Development of generic DNA-based technologies for identification of Phytophthora pathogens of a wide range of plant species. Rural Industries Research and Development Corporation Research Paper No. 97.

  • Duncan, J.M. and Torrance, L. (1992) — Techniques for the Rapid Detection of Plant Pathogens. Blackwell Scientific Publications, Oxford, UK.

    Google Scholar 

  • Erwin, D.C. and Ribeiro, O.K. (1996) — Phytophthora Diseases Worldwide. APS Press, The American Phytopathological Society, St Paul, Minnesota.

    Google Scholar 

  • Fegan, M., Croft, B.J., Teakle, D.S., Hayward, A.C. and Smith, G.R. (1998) — Sensitive and specific detection of Clavibacter xyli subsp. xyli, causal agent of ratoon stunting disease of sugarcane, with a polymerase chain reaction-based assay. Plant Pathology 47: 495–504.

    Article  CAS  Google Scholar 

  • Fox, R.T.V. (1994) —Principles of Diagnostic Techniques in Plant Pathology. CAB International, Wallingford, UK.

    Google Scholar 

  • Gabor, B.K., O’Gara, E.T., Philip, B.A., Horan, D.P. and Hardham, A.R. (1993) — Specificities of monoclonal antibodies to Phytophthora cinnamomi in two rapid diagnostic assays. Plant Disease 77: 1189–1197.

    Article  Google Scholar 

  • Galbraith, D.N. and Palfreyman, J.W. (1994) — Detection of Heterobasidium annosum using monoclonal antibodies. In Modem Assays for PIant Pathogenic Fungi. (Eds A. Schots, F.M. Dewey and R.P. Oliver), pp. 105–110. CAB International, Wallingford, UK.

    Google Scholar 

  • Goodwin, P.H., Kirkpatrick, B.C. and Duniway, J.M. (1989) — Cloned DNA probes for identification of Phytophthora parasitica. Phytopathology 79: 716–721.

    Article  CAS  Google Scholar 

  • Goodwin, P.H., Kirkpatrick, B.C. and Duniway, J.M. (1990a) — Identification of Phytophthora citrophthora with cloned DNA probes. Applied and Environmental Microbiology 56: 669–674.

    CAS  PubMed  Google Scholar 

  • Goodwin, P.H., English, J.T., Neher, D.A., Duniway, J.M., and Kirkpatrick, B.C. (1990b) — Detection of Phytophthora parasitica from soil and host tissue with a species-specific DNA probe. Phytopathology 80: 277–281.

    Article  Google Scholar 

  • Goodwin, PH., Hsiang, T., Xue, B.G. and Liu, H.W. (1995) — Differentiation of Gaeumannomyces graminis from other turf-grass fungi by amplification with primers from ribosomal internal transcribed spaces. Plant Pathology 44: 384–391.

    Article  CAS  Google Scholar 

  • Griep, R.A., van Twisk, C., van Beckhoven, J.R.C.M., van der Wolf, J.M. and Schots, A. (1998) — Development of specific recombinant monoclonal antibodies against the lipopolysaccharide of Ralstonia solanacearum Race 3. Phytopathology 88: 795–803.

    Article  CAS  PubMed  Google Scholar 

  • Hardham, A.R., Suzaki, E. and Perkin, J.L. (1986) — Monoclonal antibodies to isolate-, species- and genus-specific components on the surface of zoospores and cysts of the fungus Phytophthora cinnamomi. Canadian Journal of Botany 64: 311–321.

    Article  Google Scholar 

  • Hardham, A.R., Cahill, D.M., Cope, M., Gabor, B.K., Gubler, E and Hyde, G.J. (1994) — Cell surface antigens of Phytophthora spores: biological and taxonomic characterization. Protoplasma 181: 213–232.

    Article  Google Scholar 

  • Hardham, A.R., Gubler, F., Duniec, J. and Elliott, J. (1991) — A review of methods for the production and use of monoclonal antibodies to study zoosporic plant pathogens. Journal of Microscopy 162: 305–318.

    Google Scholar 

  • Harrison, J.G., Lowe, R., Wallace, A. and Williams, N.A. (1994) — Detection of Spongospora subterranea by ELISA using monoclonal antibodies. In Modern Assays for Plant Pathogenic Fungi. (Eds A. Schots, F.M. Dewey and R.P. Oliver), pp. 23–28. CAB International, Wallingford, UK.

    Google Scholar 

  • Hartung, J.S., Pruvost, O.P., Villemot, I. and Alvarez, A. (1996) — Rapid and sensitive colorimetric detection of Xanthomonas axonopodis pv. citri by immunocapture and a nested-polymerase chain reaction assay. Phytopathology 86: 95–101.

    Article  CAS  Google Scholar 

  • Henson, J.M. and French, R. (1993) — The polymerase chain reaction and plant disease diagnosis. Annual Review of Phytopathology 31: 81–109.

    Article  CAS  PubMed  Google Scholar 

  • Henson, J.M., Goins, T., Grey, W., Mathre, D.E. and Elliot, M. (1993) — Use of polymerase chain reaction to detect Gaeumannomyces graminis DNA in plants grown in artificially and naturally infested soil. Phytopathology 83:283–287.

    Article  CAS  Google Scholar 

  • Horner, I.J. and Wilcox, W.R (1995) — SADAMCAP, a technique for quantifying populations of Phytophthora cactorum in apple orchard soils. Phytopathology 85: 1400–1408.

    Article  Google Scholar 

  • Horner, I.J. and Wilcox, W.F. (1996) — Spatial distribution of Phytophthora cactorum in New York apple orchard soils. Phytopathology 86: 1122–1132.

    Article  Google Scholar 

  • Huttinga, H (1996) — Sensitivity of indexing procedures for viruses and viroids. Advances in Botanical Research 23: 59–71.

    Article  Google Scholar 

  • Jacobsen, C.S. (1995) — Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Applied and Environmental Microbiology 61: 3347–3352.

    CAS  PubMed  Google Scholar 

  • Jelkmann, W. and Keim-Konrad, R. (1997) — Immunocapture polymerase chain reaction and plate-trapped ELISA for the detection of Apple Stem Pitting Virus. Journal of Phytopathology 145: 499–503.

    Article  Google Scholar 

  • Judelson, H.S. and Messenger-Routh, B, (1996) — Quantitation of Phytophthora cinnamomi in avocado roots using a species-specific DNA probe. Phytopathology 86: 763–168.

    Article  CAS  Google Scholar 

  • Klassen, G.R., Balcerzak, M. and de Cock, A.W.A.M. (1996) — 5S ribosomal RNA gene spacers as species-specific probes for eight species of Pythium. Phytopathology 86: 581–587.

    Article  CAS  Google Scholar 

  • Kraft, J.M. and Boge, W.L. (1994) — Development of an antiserum to quantify Aphanomyces euteiches in resistant pea lines. Plant Disease 78: 179–183.

    Article  Google Scholar 

  • Kuske, C.R., and Banton, K.L., Adorada, D.L., Stark, PC, Hill, K.K. and Jackson, P.J. (1998) — Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Applied and Environmental Microbiology 64: 2463–2472.

    CAS  PubMed  Google Scholar 

  • Landegren, U., Kaiser, R., Caskey, C.T. and Hood L. (1988) — DNA diagnostics — molecular techniques and automation. Science 242: 229–237.

    Article  CAS  PubMed  Google Scholar 

  • Lee, S.B., White, T.J. and Taylor, J.W. (1993) — Detection of Phytophthora species by oligonucleotide hybridisation to amplified ribosomal DNA spacers. Phytopathology 83: 177–181.

    Article  CAS  Google Scholar 

  • Levesque, M.J., Laboissiere, S., Thomas J.C., Beaudet, R. and Villemur, R. (1997) — Rapid method for detecting Desulfitobacterium frappieri strain PCP-1 in soil by the polymerase chain reaction. Applied Microbiology and Biotechnology 47:719–725.

    Article  CAS  PubMed  Google Scholar 

  • Levesque, C.A., Harlton, C.E. and de Cock, A.W.A.M. (1998) — Identification of some oomycetes by reverse dot blot hybridisation. Phytopathology 88: 213–222.

    Article  CAS  PubMed  Google Scholar 

  • Mahuku, G.S., Hall, R. and Goodwin, PH. (1996) — Distribution of Leptosphaeria maculans in two fields in southern Ontario as determined by polymerase chain reaction. European Journal of Plant Pathology 102: 569–576.

    Article  Google Scholar 

  • Malajczuk, N., McComb, A.J. and Parker, C.A. (1975) — An immunofluorescence technique for detecting Phytophthora cinnamomi Rands. Australian Journal of Botany 23:289–309.

    Article  Google Scholar 

  • MacDonald, J.D., Stites, J. and Kabashima, J. (1990) — Comparison of serological and culture plate methods for detecting species of Phytophthora, Pythium, and Rhizoctonia in ornamental plant species. Plant Disease 74: 655–659.

    Article  Google Scholar 

  • Miller S.A., Bhat, R.G. and Schmitthener, A.R (1994) — Detection of Phytophthora capsici in pepper and cucurbit crops in Ohio with two commercial immunoassay kits. Plant Disease 78: 1042–1046.

    Article  Google Scholar 

  • Miller, S.A. (1996) — Detecting propagules of plant pathogenic fungi. Advances in Botanical Research 23: 73–101.

    Article  Google Scholar 

  • Miller, S.A., Madden, L.V and Schmitthener, A.F. (1997) — Distribution of Phytophthora spp. in field soils determined by immunoassay. Phytopathology 87:101–107.

    Article  CAS  PubMed  Google Scholar 

  • Mitchell, C. and Harley, VR. (1997) — Phage display — A powerful genetic probe of biomolecular interactions. Australasian Biotechnology 7: 218–222.

    CAS  Google Scholar 

  • Moricca, S., Ragazzi, A., Kasuga, T. and Mitchelson, K.R. (1998) — Detection of Fusarium oxysporum f.sp. vasinfectum in cotton tissue by polymerase chain reaction. Plant Pathology 47: 486–494.

    Article  CAS  Google Scholar 

  • Nolasco, G., de Bias, C, Torres, V. and Ponz, F. (1993) — A method combining immunocapture and PCR amplification in a microtiter plate for detection of plant viruses and subviral pathogens. Journal of Virological Methods 45: 210–218.

    Article  Google Scholar 

  • Narayanasamy, P. (1997) — Plant Pathogen Detection and Disease Diagnosis. Marcel Dekker, Inc., New York, USA.

    Google Scholar 

  • Often, W., Gilligan, C.A. and Thornton, C.R. (1997) — Quantification of fungal antigens in soil with a monoclonal antibody-based ELISA: Analysis and reduction of soil-specific bias. Phytopathology 87: 730–736.

    Article  Google Scholar 

  • Parry, D.W. and Nicholson, P. (1996) — Development of a PCR assay to detect Fusarium poae in wheat. Plant Pathology 45: 383–391.

    Article  CAS  Google Scholar 

  • Priestly, R., Mohammed, C. and Dewey, EM. (1994) — The development of monoclonal antibody-based ELISA and dipstick assays for the detection and identification of Armillaria species in infected wood. In Modern Assays for Plant Pathogenic Fungi (Eds A. Schots, F.M. Dewey and R.P Oliver), pp. 149–156. CAB International, Wallingford, UK.

    Google Scholar 

  • Pryor, B.M., Davis, R.M. and Gilbertson, R.L. (1998) — Detection of soilborne Alternaria radicina and its occurrence in California carrot fields. Plant Disease 82: 891–895.

    Article  Google Scholar 

  • Pscheidt, J.W., Burket, J.Z., Fisher, S.L. and Hamm, RB. (1992) — Sensitivity and clinical use of Phytophthora-specific immunoassay kits. Plant Disease 76: 928–932.

    Article  CAS  Google Scholar 

  • Putnam, M.L. (1995) — Evaluation of selected methods of plant disease diagnosis. Crop Protection 14: 517–525.

    Article  Google Scholar 

  • Randies, J.W., Hodgson, R.A.J, and Wefels, E. (1996) — The rapid and sensitive detection of plant pathogens by molecular methods. Australasian Plant Pathology 25: 71–85.

    Article  Google Scholar 

  • Rogers, J.L. and Bendich, A.J. (1985) — Extraction of DNA from milligram amounts of fresh herbarium and mummified plant tissues. Plant Molecular Biology 5:69–76.

    Article  CAS  Google Scholar 

  • Schilling, A.G., Moller, E.M. and Geiger, H.H. (1996) — Polymerase chain reaction-based assays for species-specific detection of Fusarium culmorum, F. graminearum, and F. avenaceum. Phytopathology 86:515–522.

    Article  CAS  Google Scholar 

  • Schots, A., Dewey, F.M. and Oliver, R.P. (1994) — Modern Assays for Plant Pathogenic Fungi. CAB International, Wallingford, UK.

    Google Scholar 

  • Smith, O.P., Peterson, G.L., Beck, R. J., Schaad, N.W and Bonde, M.R. (1996) — Development of a PCR-based method for identification of Tilletia indica, causal agent of carnal bunt of wheat. Phytopathology 86:115–122.

    Article  CAS  Google Scholar 

  • Sreenivasaprasad, S., Sharada, K., Brown, A.E. and Mills, PR. (1996) — PCR-based detection of Colletotrichum acutatum on strawberry. Plant Pathology 45:650–655.

    Article  CAS  Google Scholar 

  • Stammler, G. and Seemuller, E. (1993) — Specific and sensitive detection of Phytophthora fragariae var. ruhi in raspberry roots by PCR amplification. Journal of Plant Diseases and Protection 100: 394–400.

    Google Scholar 

  • Susi, P., Ziegler, A. and Torrance L. (1998) — Selection of single-chain variable fragment antibodies to black currant reversion associated virus from a synthetic phage display library. Phytopathology 88: 230–233.

    Article  CAS  PubMed  Google Scholar 

  • Takahashi, Y, Omura, T., Hibino, H. and Sato, M. (1996) — Detection and identification of Pseudomonas syringae pv. atropurpurea by PCR amplification of specific fragments from an indigenous plasmid. Plant Disease 80: 783–788.

    Article  CAS  Google Scholar 

  • 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 a yeast. Applied and Environmental Microbiology 59: 2657–2665.

    CAS  PubMed  Google Scholar 

  • Thornton, C.R., Dewey, F.M. and Gilligan, C.A. (1994) — Development of monoclonal antibody-based immunological assays for the detection of live propagules of Rhizoctonia solani in the soil. In Modern Assays for Plant Pathogenic Fungi. (Eds A. Schots, F.M. Dewey and R.P. Oliver), pp. 23–28. CAB International, Wallingford, UK.

    Google Scholar 

  • Timmer, L.W., Menge, J.A., Zitko, S.E., Miller, S.A. and Johnson, E.L.V. (1993) — Comparison of ELISA techniques and standard isolation methods for Phytophthora detection in citrus orchards in Florida and California. Plant Disease 11: 791–796.

    Article  Google Scholar 

  • Tisserat, N.A., Hulbert, S.H. and Sauer, K.M. (1994) — Selective amplification of rDNA transcribed spacer regions to detect Ophiosphaerella korrae and O. herpotricha. Phytopathology 84:478–482.

    Article  CAS  Google Scholar 

  • Turner, A.S., Lees, A.K, Rezanoor, H.N. and Nicholson, P. (1998) — Refinement of PCR detection of Fusarium avenaceum and evidence from DNA marker studies for the phenetic relatedness to Fusarium tricineturn. Plant Pathology 47:278–288.

    Article  CAS  Google Scholar 

  • Volossiouk, T, Robb, E.J. and Nazar, R.N. (1995) — Direct DNA extraction for PCR-mediated assays of soil organisms. Applied and Environmental Microbiology 61:3972–3976.

    CAS  PubMed  Google Scholar 

  • Ward, E. and Bateman, G.L. (1994) — Identification of fungi in the Gaeumannomyces-Phialophora complex associated with Take-all of cereals and grasses using DNA probes. In Modern Assays for Plant Pathogenic Fungi. (Eds A. Schots, F.M. Dewey and R.P Oliver), pp. 127–133. CAB International, Wallingford, UK.

    Google Scholar 

  • Weising, K., Nyboom, H, Wolff, K, and Meyer, W. (1995) — DNA Fingerprinting in Plants and Fungi. CRC Press Inc.

  • Wilkstrom, P., Wiklund, A., Andersson, A.C. and Forsman, M. (1996) — DNA recovery and PCR quantification of catechol 2,3-dioxygmase genes from different soil types. Journal of Biotechnology 52: 107–120.

    Article  Google Scholar 

  • Wilson, I.G. (1997) — Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology 63:3741–3751.

    CAS  PubMed  Google Scholar 

  • Wilson, D.R. and Finlay, B.B. (1998) — Phage display: applications, innovations, and issues in phage and host biology. Canadian Journal of Microbiology 44: 313–329.

    Article  CAS  PubMed  Google Scholar 

  • Yeates, C. and Gillings, M.R. (1998) — Rapid purification of DNA from soil for molecular biodiversity analysis. Letters in Applied Microbiology 27:49–53.

    Article  CAS  Google Scholar 

  • Yuen, G.Y, Xia, J.Q. and Sutula, C.L. (1998) — A sensitive ELISA fox Pythium ultimum using polyclonal and species-specific monoclonal antibodies. Plant Disease 82: 1029–1032.

    Article  Google Scholar 

  • Zijlstra, C. (1997) — A fast PCR assay to identify Meloidogyne hapla, M. chitwoodi, and M. fallax, and to sensitively differentiate them from each other and from M. incognita in mixtures. Fundamental and Applied Nematology 20: 505–511.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cahill, D.M. Detection, identification and disease diagnosis of soilborne pathogens. Australasian Plant Pathology 28, 34–44 (1999). https://doi.org/10.1071/AP99005

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1071/AP99005

Keywords

Navigation