Plant Virus Identification and Virus-Vector-Host Interactions
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Plant virus identification and virus-vector-host interactions Yahya Zakaria Abdou Gaafar ORCID 0000-0002-7833-1542 Plant virus identification and virus- vector-host interactions Dissertation for the award of the degree "Doctor rerum naturalium" (Dr.rer.nat.) "Doctor of Philosophy" Ph.D. Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the International PhD Programme for Agricultural Sciences in Göttingen (IPAG) of the Graduate School Forest and Agricultural Sciences (GFA) submitted by Yahya Zakaria Abdou Gaafar from Cairo, Egypt Göttingen, 2019 Thesis committee Prof. Dr. Stefan Vidal Georg-August University Göttingen, Department for Crop Sciences, Agricultural Entomology Prof. Dr. Edgar Maiss Leibniz Universität Hannover, The Institute of Horticultural Production Systems, Section of Phytomedicine Dr. Heiko Ziebell Julius Kühn-Institut (JKI), Federal Research Institute for Cultivated Plants, Institute for Epidemiology and Plant Diagnostics Members of the Examination Board Reviewer Prof. Dr. Michael Rostás Georg-August University Göttingen, Department for Crop Sciences, Agricultural Entomology II | P a g e Plant virus identification and virus-vector-host interactions Copyright © 2019 by Yahya Zakaria Abdou Gaafar. All rights reserved. Printed in Germany. No part of this book may be used or reproduced in any manner whatsoever without written permission except in the case of brief quotations embodied in critical articles or reviews. For information contact; [email protected] Book layout and cover were designed by the author. November 2019 III | P a g e Dedicated to my family IV | P a g e Contents Chapter 1: General introduction ___________________________________________________________ 1 Part one: Plant virus identification ________________________________________________________ 13 Chapter 2: Plant disease aetiology _________________________________________________________ 15 Chapter 3: Investigating the pea virome in Germany – old friends and new players in the field(s) _____ 88 Part two: Virus-vector-host interactions ___________________________________________________ 161 Chapter 5: Aphid transmission of nanoviruses: a review ______________________________________ 163 Chapter 6: Probing and feeding behaviours of Acyrthosiphon pisum change on nanoviruses-infected faba beans ______________________________________________________________________________ 174 Chapter 7: General discussion ___________________________________________________________ 192 Summary ____________________________________________________________________________ 199 References ___________________________________________________________________________ 202 Acknowledgments _____________________________________________________________________ 232 Curriculum vitae ______________________________________________________________________ 234 V | P a g e Chapter 1: General introduction 1.1. Plant viruses Plant viruses are the cause of many crop diseases worldwide, leading to both yield and quality losses e.g., reduction in growth, vigour and market value (Bos, 1982; Hull, 2014). The type and severity of the host reactions to virus infections are very variable (Hull, 2014). They depend greatly on the virus strains, sources of infection, the time of infection, the crop genotypes and also influenced by environmental conditions (Hull, 2014). Several plant viruses are highly contagious and their effects on plants are often drastic. The losses caused by plant virus infections can have severe financial implications or have socio-economic effects (Anderson et al., 2004; Hull, 2009; Patil et al., 2015; Pechinger et al., 2019). introductionChapter General 1: Virus infection can cause histological changes to the cells and the intracellular structure (Hull, 2009). The symptoms caused by virus infection vary from necrotic or chlorotic lesions on inoculated leaves to systemic e.g., mosaic, mottle, stunting and leaves distortions (Hull, 2014). Nevertheless, some virus infections cause mild or no symptoms. Infection agents e.g., viroids and phytoplasma can induce diseases that resemble virus infections (Hull, 2014). Also, virus associated nucleic acids can alter the disease symptoms (Roossinck et al., 1992; Ziebell & Carr, 2010). Some virus-like symptoms e.g., yellowing and necrosis, can easily be confused with non-viral disorders. Additionally, complex or multiple infections in plants are very common (Bos, 1982; Al Rwahnih et al., 2009; Carvajal-Yepes et al., 2014). These can consist of different viruses, or viruses with other pathogens, pests or abiotic factors. Such infections generally alter the plant physiology and in consequence the susceptibility and sensitivity to other infecting agents in an additive or synergistic effect or non-additive effect resulting in changes in the displayed symptoms (Bos, 1982; Syller, 2012). Furthermore, there are no simple relationships between virus content within a plant or virus incidence within a crop and the yield losses (Bos, 1982). Thus, detecting and identifying the exact virus causing the disease can be difficult. However, determining the exact disease causative agent (known viruses, new viruses or virus strains) is necessary to decide which management strategy (e.g., insect vector control, resistance breeding, provision of virus-free germplasm etc) could be applied. In addition, it is important to detect quarantine viruses and prevent them from entering a country and becoming established. Therefore, it helps also in deciding on monitoring and preventive strategies, and in the prediction of plant diseases in annual crops. 1.2. Plant virus diagnostics: Plant virus diagnosis often starts with spotting suspicious plants with "virus-like" symptoms in a field or greenhouse and sending it to diagnostics laboratories for analysis. 1 | P a g e A range of techniques are available to detect and confirm the aetiology of the disease (Hamilton et al., 1981; Hull, 2009). Important factors are taken in consideration when choosing the detection methods i.e., the sensitivity of the method to small amounts of viruses, accuracy, reproducibility, cost, time required, level of expertise needed and ability to perform in field (Hull, 2009). Additionally, the choice of test will determine the outcome i.e., whether only a virus family can be determined or a virus species or if strain-specific detection is possible. 1.2.1. Conventional detection methods: Conventional detection methods have been developed and successfully implemented for a long time as virus detection tools and are widely used in many laboratories. Virus diagnosis has been relying on experienced specialists who can recognize and describe the disease causal agent from the symptoms on hosts, complemented with methods e.g., bioassays on indicator plants and electron microscopy (Boonham et al., 2014). Conventional methods include bioassays, electron microscopy (EM), enzyme-linked immunosorbent assay (ELISA), Western, Northern and Southern blotting and polymerase chain reaction (PCR)-based methods. They provide rapid and inexpensive diagnoses for known viruses and viroids (Wu et al., 2015). The following are descriptions of the commonly used methods in virus/viroid diagnosis. 1.2.1.1. Bioassays Indicator plants have been used from the early ages of plant virology for propagation of plant viruses. Based on symptoms and host range reactions, differential host plants were used for the identification and classification of a number of plant viruses (Kirby et al., 2001; Hull, 2014). However, a correct diagnosis based on symptoms is not possible and these days indicator plants are mainly used for virus propagation and enrichment for the subsequent use in different tests (e.g., electron microscopy). 1.2.1.2. Electron microscopy Due to the small size of plant viruses, EM is the only technology that can directly Chapter 1: General introductionChapter General 1: visualise virus particles. The high resolution power of EM provides direct images at nanometre scale for virus diagnosis and research (Richert-Pöggeler et al., 2018). Transmission electron microscopy (TEM) can be used as initial step in virus diagnosis from crud plant extracts without the necessity of viral enrichment (Bawden & Nixon, 1951; Gentile & Gelderblom, 2014; Richert-Pöggeler et al., 2018). A main advantage of EM for viral diagnosis is that it does not require virus-specific reagents thus it provides an open view on the sample (Goldsmith & Miller, 2009). EM may not be able to identify a virus beyond the family level, thus additional assays can be performed which require virus- specific reagents e.g., antibodies. Immunosorbent electron microscopy (ISEM), as an example, increases the sensitivity of EM by virus trapping (Debrick, 1973; Roberts & Harrison, 1979). If specific antibodies are available, they can be used to “decorate” the virus particles and therefore differentiate between different species depending on the specificity of these antibodies. However, not always are specific antibodies available for all viruses. Additionally, an enrichment step is required for phloem restricted and low titre viruses, viruses without virions and viroids e.g., ultracentrifugation (Richert-Pöggeler et 2 | P a g e al., 2018). Moreover, EM requires expertise, and EM facilities are not widely available (Naidu & Hughes, 2003). Thus, other methods such as serological or molecular assays can be performed additionally for specific virus identification and characterisation e.g., ELISA and PCR-based methods.