New Approaches to the Detection of Microbial Plant Pathogens

Early and rapid detection of potato's fungal infection by Fourier transform infrared microscopy

Fungi are considered serious pathogens to many plants and can cause severe economic damage. Early detection of these pathogens is very important and might be critical for their control. The available methods for detection of fungi are time consuming and not always very specific. Fourier transform infrared (FT-IR) microscopy has proved to be a reliable and sensitive method for detection of molecular changes in cells. Fungi pathogens display typical infrared spectra that differ from the spectra of substrate material such as potato. In the present study we used FT-IR microscopy for early and rapid detection of the potato fungal pathogen Colletotrichum coccodes on the surface of potato tubers. Infected potatoes with this fungal pathogen and uninfected potatoes were examined and correctly classified as infected or not infected by FT-IR microscopy at very early stages of infection when no morphological signs of infection could be seen. Unique spectral biomarkers were found in naturally infected potatoes compared to disease-free control potatoes.

A PCR-based method for detection of potato pathogen, Helminthosporium solani, in silver scurf infected tuber tissue and soils

Silver scurf caused by Helminthosporium solani causes significant economic losses in table stock, seed and processing potatoes. Specific polymerase chain reaction (PCR) primers, Hs1F1/Hs2R1, from H. solani were used for the amplification of a 447-bp product from 20 tissue samples and 54 single spore H. solani isolates, from eastern Canada (27 isolates), western Canada (13 isolates) and North Dakota in USA (14 isolates), but not from other potato fungal pathogens. In addition to PCR analysis, all 54 isolates were studied using conventional detection methods, visual disease symptoms and/or colony morphology and microscopic examination of the morphology of conidiophores and conidia. The PCR assay successfully detected H. solani and the PCR results correlated well with assessments based on conventional techniques. The detection of H. solani by PCR (1 day) is rapid and offers an alternative to the time consuming conventional diagnostic techniques (4-5 weeks). Nested PCR assay was necessary for the detection of H. solani in soils and thus can provide a sensitive technique to study the epidemiology of silver scurf in soils.

Impacts of Molecular Diagnostic Technologies on Plant Disease Management

Detection and diagnosis of plant viruses has included serological laboratory tests since the 1960s. Relatively little work was done on serological detection of plant pathogenic bacteria and fungi prior to the development of ELISA and monoclonal antibody technologies. Most applications for laboratory-based tests were directed at virus detection with relatively little emphasis on fungal and bacterial pathogens, though there was some good work done with other groups of plant pathogens. With the advent of molecular biology and the ability to compare regions of genomic DNA representing conserved sequences, the development of laboratory tests increased at an amazing rate for all groups of plant pathogens. Comparison of ITS regions of bacteria, fungi, and nematodes has proven useful for taxonomic purposes. Sequencing of conserved genes has been used to develop PCR-based detection with varying levels of specificity for viruses, fungi, and bacteria. Combinations of ELISA and PCR technologies are used to improve sensitivity of detection and to avoid problems with inhibitors or PCR often found in plants. The application of these technologies in plant pathology has greatly improved our ability to detect plant pathogens and is increasing our understanding of, their ecology and epidemiology.

Comparison of Techniques for Detection of Barley Yellow Dwarf Virus-PAV-IL

Detection of barley yellow dwarf virus (BYDV)-PAV-IL by an improved nucleic acid hybridization technique, using a nonradioactive probe with chromogenic and chemiluminescent substrates, was compared with detection by polymerase chain reaction (PCR), double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with polyclonal antibodies, and triple antibody sandwich ELISA with polyclonal and monoclonal antibodies. Each method was used to detect purified virus and virus in sap extracts from infected oat leaves. The detection limits for both ELISA procedures were 1 ng of purified BYDV-PAV-IL and the equivalent of 78 ng of infected tissue. Nucleic acid hybridization with either chemiluminescent or chromogenic substrates also detected as little as 1 ng of purified BYDV-PAV-IL, but it was slightly more sensitive at detecting virus in tissue extracts (25 ng of infected tissue). The most sensitive detection technique was PCR amplification, which could detect as little as 0.1 pg of RNA extracted from purified virus and detected viral RNA in the equivalent of 0.5 pg of infected leaf tissue.

Identification of root rot fungi in nursery seedlings by nested multiplex PCR

The internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) subunit repeat was sequenced in 12 isolates of Cylindrocladium floridanum and 11 isolates of Cylindrocarpon destructans. Sequences were aligned and compared with ITS sequences of other fungi in GenBank. Some intraspecific variability was present within our collections of C. destructans but not in C. floridanum. Three ITS variants were identified within C. destructans, but there was no apparent association between ITS variants and host or geographic origin. Two internal primers were synthesized for the specific amplification of portions of the ITS for C. floridanum, and two primers were designed to amplify all three variants of C. destructans. The species-specific primers amplified PCR products of the expected length when tested with cultures of C, destructans and C. floridanum from white spruce, black spruce, Norway spruce, red spruce, jack pine, red pine, and black walnut from eight nurseries and three plantations in Quebec. No amplification resulted from PCR reactions on fungal DNA from 26 common contaminants of conifer roots. For amplifications directly from infected tissues, a nested primer PCR using two rounds of amplification was combined with multiplex PCR approach resulting in the amplification of two different species-specific PCR fragments in the same reaction. First, the entire ITS was amplified with one universal primer and a second primer specific to fungi; a second round of amplification was carried out with species-specific primers that amplified a 400-bp PCR product from C. destructans and a 328-bp product from C. floridanum. The species-specific fragments were amplified directly from infected roots from which one or the two fungi had been isolated.

An appraisal of different methods for the detection of the walnut strain of cherry leafroll virus

Three methods were evaluated for the detection of cherry leafroll virus: ELISA, dot-blot and reverse transcriptional polymerase chain reaction (RT-PCR). Dot-blot and RT-PCR were carried out in crude plant extracts without any further RNA purification. Dot-blot hybridization using a 32P-labelled DNA probe was as sensitive as previously reported ELISA results for cherry leafroll virus detection. The most sensitive method was RT-PCR, which amplified a specific fragment of 448 bp from the 3' untranslated region of both viral genomic RNAs. RT-PCR was used to detect cherry leafroll virus in infected walnut buds and twigs.