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Diagnosis of Fungal Plant Pathogens Using Conventional and Molecular Approaches

Authors:
Monika Dayarathne at University of Manitoba
Monika Dayarathne
Amin Uddin Mridha at University of Chittagong
Amin Uddin Mridha
Yong Wang at Guizhou University
Yong Wang
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Fungi are a large group of eukaryotes found as saprophytes, pathogens or endophytes, which distribute in every corner of our planet. As the main pathogens, fungi can cause 70–80% of total plant diseases, leading to huge crop yield reduction and economic loss. For identification of fungal plant pathogens, mycologists and plant pathologists have mainly gone through two stages, viz. morphological observation and morphology/phylogeny, and the next era might be utilizing DNA barcodes as the tool for rapid identification. This chapter accounts i) the brief history of development for fungal identification tools and main concepts, ii) the importance and confusion of “One fungus, one name” for pathogen identification, iii) more or fewer species that we need in agricultural practice, and iv) the foreground of fungal plant pathogen identification. These will help to solve the practical problems of identification of fungal pathogens in agricultural production.
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... Losses in S. lycopersicum L. production range between 30% and 40%, but it can sometimes reach up to 80% [4]. Fusarium oxysporum (Fo) soil-borne fungus is one of the most devastating diseases, ranking fifth among phytopathogenic fungi, which can significantly reduce the production of S. lycopersicum L. [4]. The Fusarium oxysporum f. sp. ...
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Article
Full-text available
  • Jul 2023
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... Some of them are highly specialized to closely related plants, while others have a large spectrum of plant hosts (Newman and Derbyshire, 2020). The majority of plant infections that cause substantial crop and economic suppression are fungi, which account for around 80% of all plant pathogens that are destructive and widely disseminated (Dayarathne et al., 2020). ...
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Chapter
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Article
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Article
Full-text available
  • Jul 2022
  • J. Fungi
Plant growth-promoting fungi (PGPF) improve plant health and resist plant pathogens. The present study was carried out to biocontrol tomato Fusarium wilt using PGPF through antifungal activity and enhance tomato plant immune response. Four PGPF were identified genetically as Aspergillus flavus, Aspergillus niger, Mucor circinelloides and Pencillium oxalicum. In vitro antagonistic activity assay of PGPF against Fusariumoxysporum was evaluated, where it exhibited promising antifungal activity where MIC was in the range 0.25–0.5 mg/mL. Physiological markers of defense in a plant as a response to stimulation of induced systemic resistance (ISR) were recorded. Our results revealed that A. niger, M. circinelloides, A. flavus and P. oxalicum strains significantly reduced percentages of disease severity by 16.60% and 20.83% and 37.50% and 45.83 %, respectively. In addition, they exhibited relatively high protection percentages of 86.35%, 76.87%, 56.87% and 59.06 %, respectively. With concern to the control, it is evident that the percentage of disease severity was about 87.50%. Moreover, the application of M. circinelloides, P. oxalicum, A. niger and A. flavus successfully recovered the damage to morphological traits, photosynthetic pigments’ total carbohydrate and total soluble protein of infected plants. Moreover, the application of tested PGPF enhanced the growth of healthy and infected tomato plants. View Full-Text
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Revolutionizing Potato Farming: Dynamic Innovations Reshaping Late Blight Control in Pakistan: Revolutionizing Potato Farming
Article
Full-text available
  • Dec 2023
Potato (Solanum tuberosum L.) is one of the most extensively cultivated crops around the world, and Pakistan’s weather favor production and cultivation. Despite the ease of cultivating potatoes and the nominal labor supplies, Pakistan’s output of potatoes has not yet achieved a promising level when compared to nearby nations like India and Bangladesh. The crop's low production in Pakistan is caused by several biotic and abiotic stresses that instigated several pathogenic diseases such as early blight, bacterial wilt, viral infections, nematode infestations and late blight. Late blight disease is one of the most dreaded diseases of potatoes globally. It is caused by the fungus Phytophthora infestans which is highly adaptive to fungicides. Several fungicides have been in use against this disease for a long time, however, it has developed a high degree of resistant strains to these fungicides due to their unselective use over time and ultimately may cause colossal losses to the crop. In response, scientists have developed different potato varieties like Setanta, Nicola, Cara and Acoustic that are highly resistant to late blight. Similarly, cultural methods are also employed to combat late blight disease. This article provides an overview of the implications of late blight disease in potato cultivation and explores various strategies to reduce yield losses brought on by this disease via the application of synthetic fungicides.
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Article
Full-text available
  • Jul 2023
  • INT MICROBIOL
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Article
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Correlation between fine root traits and pathogen richness depends on plant mycorrhizal types
Article
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Root uptake strategies are associated with the strength of negative plant–soil feedback (PSF) induced by soil pathogens. Given the intensified effect of pathogen richness in fine roots on the strength of negative PSF through the synergistic effects of multiple pathogens, researchers have proposed a trade‐off between nutrient acquisition and pathogen defence in roots. However, empirical evidence is lacking. In addition, because the interaction between pathogens and fine roots depends on the mycorrhizal types of tree species, both fine root traits and mycorrhizal types should be incorporated to reveal covariation in pathogen richness and the strength of negative PSF. In this study, we selected 50 arbuscular mycorrhizal (AM) tree species and 7 ectomycorrhizal (ECM) tree species in a subtropical forest to investigate the relationships between fine root traits and pathogen richness in fine roots and determined whether their relationships depended on plant mycorrhizal types. Our results showed that pathogen richness was negatively correlated with fine root diameter but was positively correlated with specific root length for the AM‐associated species, while for the ECM‐associated species, the pathogen richness was only found to have a significant negative relationship with the relative abundance of ECM fungi. These findings highlight the difference between AM‐ and ECM‐associated species in pathogen defence and bridge the gap between root traits and pathogen richness, which is significant for improving our understanding of the potential factors mediating the strength of PSF and thus maintaining tree species diversity.
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Fast and reliable molecular methods to detect fungal pathogens in woody plants
Article
Full-text available
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  • APPL MICROBIOL BIOT
Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.
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Detection and identification of plant pathogens is one of the most important strategies for sustainable plant diseases management. For this reason, the availability of fast, sensitive and accurate methods for detection and identification of plant pathogens is increasingly necessary to improve disease control decision making process. In other words, new technologies and improved methods with reduced/fair cost and improved speed, throughput, multiplexing, accuracy and sensitivity have emerged as an essential strategy for the control of both fungal and bacterial diseases. The development of recombinant DNA technology is also possible to isolate individual genes and incorporate resistance genes into otherwise agronomically acceptable cultivars to develop genetically resistance variety for a particular disease. These advances have been complemented by the development of new nucleic acids extraction methods, increased automation, reliable internal controls, multiplexing assays, online information and on site molecular diagnostics. The different types of polymerase chain reaction (PCR) are the most common DNA amplification technology used for detecting various plant pathogens. With the applications of bioinformatics as a modern technology in plant pathology, identification of specific motifs, DNA sequences has become possible, which ultimately increase the accuracy of modern techniques in plant disease diagnosis. The newly emerged proteomic technology is also a promising tool for providing information about pathogenicity and virulence factors that will open up new possibilities for plant disease diagnosis and appropriate protection measures.
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Article
Full-text available
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First Report of Leaf Black Circular Spots on Dendrobium nobile Caused by Trichoderma longibrachiatum in Guizhou Province, China
Article
Full-text available
  • Aug 2019
  • PLANT DIS
Dendrobium nobile is a conventional Chinese medicinal plant belonging to the family Orchidaceae. Its main medicinal component is dendrobine, which is used for the treatment of problems affecting the cardiovascular, cerebrovascular, digestive, and respiratory systems (Chishui Dendrobium nobile 2018). In November 2018, a research group in Zunyi city, Guizhou Province, China, observed the occurrence of black circular spots on D. nobile seedlings in Chishui city, Guizhou, China, which directly affected the medicinal values and productivity of the plant.
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Genera of phytopathogenic fungi: GOPHY 3
Article
Full-text available
  • Jun 2019
p>This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.</p
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Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection
Article
Full-text available
  • Apr 2019
An effective framework for early warning and rapid response is a crucial element to prevent or mitigate the impact of biological invasions of plant pathogens, especially at ports of entry. Molecular detection of pathogens by using PCR-based methods usually requires a well-equipped laboratory. Rapid detection tools that can be applied as point-of-care diagnostics are highly desirable, especially to intercept quarantine plant pathogens such as Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum, three of the most devastating pathogens of trees and ornamental plants in Europe and North America. To this aim, in this study we developed three different loop mediated isothermal amplification (LAMP) assays able to detect each target pathogen both in DNA extracted from axenic culture and in infected plant tissues. By using the portable instrument Genie ® II, the LAMP assay was able to recognize X. fastidi-osa, C. platani and P. ramorum DNA within 30 min of isothermal amplification reaction, with high levels of specific-ity and sensitivity (up to 0.02 pg µL −1 of DNA). These new LAMP-based tools, allowing an on-site rapid detection of pathogens, are especially suited for being used at ports of entry, but they can be also profitably used to monitor and prevent the possible spread of invasive pathogens in natural ecosystems.
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Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom Fungi and reveals thresholds for fungal species and higher taxon delimitation
Article
Full-text available
  • May 2018
Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
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One stop shop III: taxonomic update with molecular phylogeny for important phytopathogenic genera: 51–75 (2019)
Article
  • Sep 2019
This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and organisms. This paper focuses on 25 phytopathogenic genera: Alternaria, Capnodium, Chaetothyrina, Cytospora, Cyphellophora, Cyttaria, Dactylonectria, Diplodia, Dothiorella, Entoleuca, Eutiarosporella, Fusarium, Ilyonectria, Lasiodiplodia, Macrophomina, Medeolaria, Neonectria, Neopestalotiopsis, Pestalotiopsis, Plasmopara, Pseudopestalotiopsis, Rosellinia, Sphaeropsis, Stagonosporopsis and Verticillium. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. A new database (Onestopshopfungi) is established to enhance the current understanding of plant pathogenic genera among plant pathologists.
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One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26–50 (2019)
Article
  • Feb 2019
This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi. It focuses on 25 phytopathogenic genera: Alternaria, Bipolaris, Boeremia, Botryosphaeria, Calonectria, Coniella, Corticiaceae, Curvularia, Elsinoe, Entyloma, Erythricium, Fomitiporia, Fulviformes, Laetisaria, Limonomyces, Neofabraea, Neofusicoccum, Phaeoacremonium, Phellinotus, Phyllosticta, Plenodomus, Pseudopyricularia, Tilletia, Venturia and Waitea, using recent molecular data, up to date names and the latest taxonomic insights. For each genus a taxonomic background, diversity aspects, species identification and classification based on molecular phylogeny and recommended genetic markers are provided. In this study, varieties of the genus Boeremia have been elevated to species level. Botryosphaeria, Bipolaris, Curvularia, Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries, as many new species have been introduced to these genera.
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The Classification of Taphrina and Other Fungi with Yeast-Like Cultural States
Article
  • Mar 1982
TEM studies show that species of Taphrina and Protomyces have cell walls with a thick, electron-transparent inner layer, similar to those of the Endomycetales, e.g., of species of Saccharomyces or Hanseniaspora. The budding is holoblastic at the attenuated end or ends of the cell and is rather similar to that of the apiculate yeasts. Members of the genera Microstroma and Exobasidium have an electron opaque, often multilayered cell wall and show enteroblastic budding, similar to that of the “red yeasts” (Sporobolomycetales) and Ustilaginales. The Taphrinales are consequently classified in the Endomycetes (Ascomycotina), while Microstroma and Exobasidium are placed in the Basidiomycetes. Species of the genera Kabatiella and Aureobasidium have ascomycete-like cell walls, and are therefore not related to Microstroma. The classes of the Ascomycotina and Basidiomycotina are discussed briefly.
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