Publications by year
In Press
Tyzack TE, Hacker C, Thomas G, Fones HN (In Press). Biofilm formation in<i>Zymoseptoria tritici</i>.
Abstract:
Biofilm formation inZymoseptoria tritici
Zymoseptoria triticiis an economically damaging fungal pathogen of wheat which is able to survive for long periods on the leaf surface. In this environment, the fungus is exposed to many stresses, including fluctuations in temperature, UV radiation, drying, and foliar fungicide applications. We observed biofilm-like cell aggregations on the surface of wheat leaves infected withZ. triticiin both compatible and non-compatible interactions. A literature search revealed few examples of plant pathogenic fungi forming biofilms, but demonstrated that such biofilms have a number of key characteristics, which are shared with other biofilmforming microbes. These include adhesion of cells to the substrate, production of extracellular matrix, altered gene expression and increased tolerance to various stresses. We used a combination of microscopy, qRT-PCR and stress tolerance assays to determine whether putativeZ. triticibiofilms possessed these diagnostic characteristics. We show thatZ. triticibiofilms resemble in form and function those formed by other filamentous and dimorphic fungi, producing extra-cellular matrix in which cells become embedded, creating layers of hyphal bundles and blastospores. These biofilms show increased tolerance to drying and high temperature. There is also isolate-dependent resistance to reactive oxygen stress and the fungicide carboxin. Taken together, these findings demonstrate thatZ. triticiis indeed able to produce genuine biofilms.
Abstract.
Kovács-Simon A, Fones HN (In Press). Use of Chitin:DNA ratio to assess growth form in fungal cells.
Abstract:
Use of Chitin:DNA ratio to assess growth form in fungal cells
Dimorphism, the ability to switch between a ‘yeast-like’ and a hyphal growth form, is an important feature of certain fungi, including important plant and human pathogens. The switch to hyphal growth is often associated with virulence, pathogenicity, biofilm formation and stress resistance. Thus, the ability to accurately and efficiently measure fungal growth form is key to research into these fungi, especially for discovery of potential drug targets. To date, fungal growth form has been assessed microscopically, a process that is both labour intensive and costly. Here, we unite quantification of the chitin in fungal cell walls and the DNA in nuclei to produce a methodology that allows fungal cell shape to be estimated by calculation of the ratio between cell wall quantity and number of nuclei present in a sample of fungus or infected host tissue. Using the wheat pathogenZymoseptoria triticias a test case, with confirmation in the distantly relatedFusarium oxysporum, we demonstrate a close, linear relationship between the chitin:DNA ratio and the average polarity index (length/width) of fungal cells. We show the utility of the method for estimating growth form in infected wheat leaves, differentiating between the timing of germination in two differentZ. triticiisolates using this ratio. We also show that the method is robust to the occurence of thick-walled chlamydospores, which show a chitin:DNA ratio that is distinct from either ‘yeast-like’ blastospores or hyphae.
Abstract.
2023
Fones HN, Soanes D, Gurr SJ (2023). Epiphytic proliferation of Zymoseptoria tritici isolates on resistant wheat leaves.
Fungal Genet Biol,
168Abstract:
Epiphytic proliferation of Zymoseptoria tritici isolates on resistant wheat leaves.
The wheat pathogen Zymoseptoria tritici is capable of a long period of pre-invasive epiphytic growth. Studies have shown that virulent isolates vary in the extent, duration and growth form of this epiphytic growth, and the fungus has been observed to undergo behaviours such as asexual reproduction by budding and vegetative fusion of hyphae on the leaf surface. This epiphytic colonisation has been investigated very little during interactions in which an isolate of Z. tritici is unable to colonise the apoplast, as occurs during avirulence. However, avirulent isolates have been seen to undergo sexual crosses in the absense of leaf penetration, and it is widely accepted that the main point of distinction between virulent and avirulent isolates occurs at the point of attempted leaf penetration or attempted apoplastic growth, which fails in the avirulent case. In this work, we describe extensive epiphytic growth in three isolates which are unable or have very limited ability to invade the leaf, and show that growth form is as variable as for fully virulent isolates. We demonstrate that during certain interactions, Z. tritici isolates rarely invade the leaf and form pycnidia, but induce necrosis. These isolates are able to achieve higher epiphytic biomass than fully virulent isolates during asymptomatic growth, and may undergo very extensive asexual reproduction on the leaf surface. These findings have implications for open questions such as whether and how Z. tritici obtains nutrients on the leaf surface and the nature of its interaction with wheat defences.
Abstract.
Author URL.
2020
Fones HN, Bebber DP, Chaloner TM, Kay WT, Steinberg G, Gurr SJ (2020). Author Correction: Threats to global food security from emerging fungal and oomycete crop pathogens. Nature Food, 1(7), 455-456.
Fones HN (2020). Presence of ice-nucleating Pseudomonas on wheat leaves promotes Septoria tritici blotch disease (Zymoseptoria tritici) via a mutually beneficial interaction.
Scientific Reports,
10(1).
Abstract:
Presence of ice-nucleating Pseudomonas on wheat leaves promotes Septoria tritici blotch disease (Zymoseptoria tritici) via a mutually beneficial interaction
AbstractZymoseptoria tritici causes Septoria tritici blotch (STB) of wheat, an economically important disease causing yield losses of up to 10% despite the use of fungicides and resistant cultivars. Z. tritici infection is symptomless for around 10 days, during which time the fungus grows randomly across the leaf surface prior to entry through stomata. Wounded leaves show faster, more extensive STB, suggesting that wounds facilitate fungal entry. Wheat leaves also host epiphytic bacteria; these include ice-nucleating (INA+) bacteria, which induce frost damage at warmer temperatures than it otherwise occurs. Here, STB is shown to be more rapid and severe when wheat is exposed to both INA+ bacteria and sub-zero temperatures. This suggests that ice-nucleation-induced wounding of the wheat leaf provides additional openings for fungal entry. INA+ bacterial populations are shown to benefit from the presence of Z. tritici, indicating that this microbial interaction is mutualistic. Finally, control of INA+ bacteria is shown to reduce STB.
Abstract.
Fones HN, Bebber DP, Chaloner TM, Kay WT, Steinberg G, Gurr SJ (2020). Threats to global food security from emerging fungal and oomycete crop pathogens. Nature Food, 1(6), 332-342.
2019
Chaloner TM, Fones HN, Varma V, Bebber DP, Gurr SJ (2019). A new mechanistic model of weather-dependent Septoria tritici blotch disease risk.
Philos Trans R Soc Lond B Biol Sci,
374(1775).
Abstract:
A new mechanistic model of weather-dependent Septoria tritici blotch disease risk.
We present a new mechanistic model for predicting Septoria tritici blotch (STB) disease, parameterized with experimentally derived data for temperature- and wetness-dependent germination, growth and death of the causal agent, Zymoseptoria tritici. The output of this model (A) was compared with observed disease data for UK wheat over the period 2002-2016. In addition, we compared the output of a second model (B), in which experimentally derived parameters were replaced by a modified version of a published Z. tritici thermal performance equation, with the same observed disease data. Neither model predicted observed annual disease, but model a was able to differentiate UK regions with differing average disease risks over the entire period. The greatest limitations of both models are: broad spatial resolution of the climate data, and lack of host parameters. Model B is further limited by its lack of explicitly defined pathogen death, leading to a cumulative overestimation of disease over the course of the growing season. Comparison of models a and B demonstrates the importance of accounting for the temperature-dependency of pathogen processes important in the initiation and progression of disease. However, effective modelling of STB will probably require similar experimentally derived parameters for host and environmental factors, completing the disease triangle. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
Abstract.
Author URL.
Kay WT, Fones HN, Gurr SJ (2019). Rapid loss of virulence during submergence of Z. tritici asexual spores.
Fungal Genet Biol,
128, 14-19.
Abstract:
Rapid loss of virulence during submergence of Z. tritici asexual spores.
Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a notable pathogen of temperate-grown wheat. To better understand the mechanisms underpinning pathogenicity, leaf infection assays are commonly used to compare either the virulence of Z. tritici wildtype or mutant strains, or the susceptibility of wheat cultivars. These assays, which control for many biotic, abiotic and experimental variables, involve the application of known spore numbers to leaves. To achieve this, spore numbers are quantified during a period of aqueous suspension. Published methods rarely state the period in which spores are held in suspension, suggesting that this variable may be uncontrolled. Using simple, agar-based plating experiments, this work firstly demonstrates that blastospore culturability (the ability to form a colony when plated on appropriate agar) decreases rapidly over time during maintenance in aqueous suspension. It is subsequently shown that this reduction in culturability correlates to a reduction in the virulence of the blastospore population. This is shown in three wild type Z. tritici strains. From this, it is concluded that suspension time is a variable of major importance in experimental design and one which, if not controlled, may lead to erroneous conclusions from inter-strain comparisons. The conidia of the unrelated fungus Magnaporthe oryzae also rapidly lose culturability when stored in aqueous suspension, whereas the microspores of Fusarium oxysporum f. sp. cubense do not, suggesting that this phenomenon occurs in some but not all other fungi. Finally, a droplet method of inoculations is proposed to decrease the variability in the numbers of spores applied, within and between experiments.
Abstract.
Author URL.
Fones HN, Preston GM, Smith JAC (2019). Variation in defence strategies in the metal hyperaccumulator plant Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence.
R Soc Open Sci,
6(1).
Abstract:
Variation in defence strategies in the metal hyperaccumulator plant Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence.
In the metal hyperaccumulator plant Noccaea caerulescens, zinc may provide a defence against pathogens. However, zinc accumulation is a variable trait in this species. We hypothesize that this variability affects the outcome of interactions between metal accumulation and the various constitutive and inducible defences that N. caerulescens shares with non-accumulator plants. We compare zinc concentrations, glucosinolate concentrations and inducible stress responses, including reactive oxygen species (ROS) and cell death, in four N. caerulescens populations, and relate these to the growth of the plant pathogen Pseudomonas syringae, its zinc tolerance mutants and Pseudomonas pathogens isolated from a natural population of N. caerulescens. The populations display strikingly different combinations of defences. Where defences are successful, pathogens are limited primarily by metals, cell death or organic defences; there is evidence of population-dependent trade-offs or synergies between these. In addition, we find evidence that Pseudomonas pathogens have the capacity to overcome any of these defences, indicating that the arms race continues. These data indicate that defensive enhancement, joint effects and trade-offs between different forms of defence are all plausible explanations for the variation we observe between populations, with factors including metal availability and metal-tolerant pathogen load probably shaping the response of each population to infection.
Abstract.
Author URL.
2018
Fones HN, Littlejohn GR (2018). From sample to data: Preparing, obtaining, and analyzing images of plant-pathogen interactions using confocal microscopy. In (Ed)
Methods in Molecular Biology, 257-262.
Abstract:
From sample to data: Preparing, obtaining, and analyzing images of plant-pathogen interactions using confocal microscopy
Abstract.
2017
Fones HN, Eyles CJ, Kay W, Cowper J, Gurr SJ (2017). A role for random, humidity-dependent epiphytic growth prior to invasion of wheat by Zymoseptoria tritici. Fungal Genetics and Biology, 106, 51-60.
Fones HN, Fisher MC, Gurr SJ (2017). Emerging Fungal Threats to Plants and Animals Challenge Agriculture and Ecosystem Resilience.
Microbiol Spectr,
5(2).
Abstract:
Emerging Fungal Threats to Plants and Animals Challenge Agriculture and Ecosystem Resilience.
While fungi can make positive contributions to ecosystems and agro-ecosystems, for example, in mycorrhizal associations, they can also have devastating impacts as pathogens of plants and animals. In undisturbed ecosystems, most such negative interactions will be limited through the coevolution of fungi with their hosts. In this article, we explore what happens when pathogenic fungi spread beyond their natural ecological range and become invasive on naïve hosts in new ecosystems. We will see that such invasive pathogens have been problematic to humans and their domesticated plant and animal species throughout history, and we will discuss some of the most pressing fungal threats of today.
Abstract.
Author URL.
Fones HN, Fisher MC, Gurr SJ (2017). Emerging fungal threats to plants and animals challenge agriculture and ecosystem resilience. In (Ed)
The Fungal Kingdom, 787-809.
Abstract:
Emerging fungal threats to plants and animals challenge agriculture and ecosystem resilience
Abstract.
Fones HN, Gurr SJ (2017). NOXious gases and the unpredictability of emerging plant pathogens under climate change.
BMC Biol,
15(1).
Abstract:
NOXious gases and the unpredictability of emerging plant pathogens under climate change.
Emerging pathogens of crops threaten food security and are increasingly problematic due to intensive agriculture and high volumes of trade and transport in plants and plant products. The ability to predict pathogen risk to agricultural regions would therefore be valuable. However, predictions are complicated by multi-faceted relationships between crops, their pathogens, and climate change. Climate change is related to industrialization, which has brought not only a rise in greenhouse gas emissions but also an increase in other atmospheric pollutants. Here, we consider the implications of rising levels of reactive nitrogen gases and their manifold interactions with crops and crop diseases.
Abstract.
Author URL.
2016
Fones HN, McCurrach H, Mithani A, Smith JAC, Preston GM (2016). Local adaptation is associated with zinc tolerance in Pseudomonas endophytes of the metal-hyperaccumulator plant Noccaea caerulescens.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES,
283(1830).
Author URL.
2015
Kilaru S, Schuster M, Latz M, Das Gupta S, Steinberg N, Fones H, Gurr SJ, Talbot NJ, Steinberg G (2015). A gene locus for targeted ectopic gene integration in Zymoseptoria tritici.
Fungal Genet Biol,
79, 118-124.
Abstract:
A gene locus for targeted ectopic gene integration in Zymoseptoria tritici.
Understanding the cellular organization and biology of fungal pathogens requires accurate methods for genomic integration of mutant alleles or fluorescent fusion-protein constructs. In Zymoseptoria tritici, this can be achieved by integrating of plasmid DNA randomly into the genome of this wheat pathogen. However, untargeted ectopic integration carries the risk of unwanted side effects, such as altered gene expression, due to targeting regulatory elements, or gene disruption following integration into protein-coding regions of the genome. Here, we establish the succinate dehydrogenase (sdi1) locus as a single "soft-landing" site for targeted ectopic integration of genetic constructs by using a carboxin-resistant sdi1(R) allele, carrying the point-mutation H267L. We use various green and red fluorescent fusion constructs and show that 97% of all transformants integrate correctly into the sdi1 locus as single copies. We also demonstrate that such integration does not affect the pathogenicity of Z. tritici, and thus the sdi1 locus is a useful tool for virulence analysis in genetically modified Z. tritici strains. Furthermore, we have developed a vector which facilitates yeast recombination cloning and thus allows assembly of multiple overlapping DNA fragments in a single cloning step for high throughput vector and strain generation.
Abstract.
Author URL.
Fones HN, Steinberg G, Gurr SJ (2015). Measurement of virulence in Zymoseptoria tritici through low inoculum-density assays.
Fungal Genet Biol,
79, 89-93.
Abstract:
Measurement of virulence in Zymoseptoria tritici through low inoculum-density assays.
Hitherto, pathogenicity assays with mutants or wildtype variants of Zymoseptoria tritici have been based on pycnidial counts, following inoculation of host leaves with high density inoculum. Here, we present data which suggest that high inoculum densities may mask deficiencies in virulence due to symptom saturation. We describe a low inoculum-density method which obviates this problem. This method can also be used to (i) interrogate the process of lesion formation in Z. tritici (ii) determine whether individuals of the same or different genotypes co-operate or compete during the establishment of apoplastic infections (iii) dissect the determinants of virulence, by assessing a given strain's stomatal penetration efficiency (SPE), its ability to spread within the apoplast and its pycnidiation efficiency. Such methodology can thus be used to investigate the reasons underpinning attenuated virulence in mutant or avirulent wildtype strains.
Abstract.
Author URL.
Jiménez-Guerrero I, Pérez-Montaño F, Monreal JA, Preston GM, Fones H, Vioque B, Ollero FJ, López-Baena FJ (2015). The <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>fredii</i> HH103 Type 3 Secretion System Suppresses Early Defense Responses to Effectively Nodulate Soybean.
Molecular Plant-Microbe Interactions®,
28(7), 790-799.
Abstract:
The Sinorhizobium (Ensifer) fredii HH103 Type 3 Secretion System Suppresses Early Defense Responses to Effectively Nodulate Soybean
Plants that interact with pathogenic bacteria in their natural environments have developed barriers to block or contain the infection. Phytopathogenic bacteria have evolved mechanisms to subvert these defenses and promote infection. Thus, the type 3 secretion system (T3SS) delivers bacterial effectors directly into the plant cells to alter host signaling and suppress defenses, providing an appropriate environment for bacterial multiplication. Some rhizobial strains possess a symbiotic T3SS that seems to be involved in the suppression of host defenses to promote nodulation and determine the host range. In this work, we show that the inactivation of the Sinorhizobium (Ensifer) fredii HH103 T3SS negatively affects soybean nodulation in the early stages of the symbiotic process, which is associated with a reduction of the expression of early nodulation genes. This symbiotic phenotype could be the consequence of the bacterial triggering of soybean defense responses associated with the production of salicylic acid (SA) and the impairment of the T3SS mutant to suppress these responses. Interestingly, the early induction of the transcription of GmMPK4, which negatively regulates SA accumulation and defense responses in soybean via WRKY33, could be associated with the differential defense responses induced by the parental and the T3SS mutant strain.
Abstract.
Fones H, Gurr S (2015). The impact of Septoria tritici Blotch disease on wheat: an EU perspective. Fungal Genetics and Biology, 79, 3-7.
2014
O'Leary BM, Rico A, McCraw S, Fones HN, Preston GM (2014). The Infiltration-centrifugation Technique for Extraction of Apoplastic Fluid from Plant Leaves Using <em>Phaseolus vulgaris</em> as an Example. Journal of Visualized Experiments(94).
2013
Hörger AC, Fones HN, Preston GM (2013). The current status of the elemental defense hypothesis in relation to pathogens. Frontiers in Plant Science, 4
Fones H, Preston GM (2013). The impact of transition metals on bacterial plant disease. FEMS Microbiology Reviews, 37(4), 495-519.
Fones HN, Preston GM (2013). Trade‐offs between metal hyperaccumulation and induced disease resistance in metal hyperaccumulator plants.
Plant Pathology,
62(S1), 63-71.
Abstract:
Trade‐offs between metal hyperaccumulation and induced disease resistance in metal hyperaccumulator plants
Metal hyperaccumulation is an unusual trait involving the uptake and storage of high concentrations of metals in the aerial tissues of plants. A number of hypotheses have been proposed to explain the evolution of the metal hyperaccumulation trait, of which the hypothesis that accumulated metal provides a defence against herbivores or pathogens has received most attention and support. Metal hyperaccumulation requires a range of physiological adaptations that enable plants to take up, transport, sequester and tolerate high concentrations of metal. Such adaptations may confer a fitness cost, and it has been suggested that metal hyperaccumulator plants may compensate for this cost by reducing investment in other traits such as induced disease resistance. This is supported by recent work that shows that metal hyperaccumulators such as Noccaea spp. show reduced or altered production of key components of induced disease resistance. However, an alternative explanation exists, which is that the physiological adaptations involved in metal hyperaccumulation require alterations to, or compromise, functional aspects of plant defence mechanisms. Here, the evidence for trade‐offs between metal hyperaccumulation and disease resistance mechanisms is reviewed, and the nature of the physiological adaptations involved in metal hyperaccumulation and their potential to impact other forms of plant defence is discussed. It is suggested that defensive trade‐offs may have been key to the evolution of the metal hyperaccumulation trait, resulting in increased dependence upon the protection conferred by metals.
Abstract.
Fones HN, Eyles CJ, Bennett MH, Smith JAC, Preston GM (2013). Uncoupling of reactive oxygen species accumulation and defence signalling in the metal hyperaccumulator plant Noccaea caerulescens.
New Phytologist,
199(4), 916-924.
Abstract:
Uncoupling of reactive oxygen species accumulation and defence signalling in the metal hyperaccumulator plant Noccaea caerulescens
The metal hyperaccumulator plant Noccaea caerulescens is protected from disease by the accumulation of high concentrations of metals in its aerial tissues, which are toxic to many pathogens. As these metals can lead to the production of damaging reactive oxygen species (ROS), metal hyperaccumulator plants have developed highly effective ROS tolerance mechanisms, which might quench ROS-based signals. We therefore investigated whether metal accumulation alters defence signalling via ROS in this plant. We studied the effect of zinc (Zn) accumulation by N. caerulescens on pathogen-induced ROS production, salicylic acid accumulation and downstream defence responses, such as callose deposition and pathogenesis-related (PR) gene expression, to the bacterial pathogen Pseudomonas syringae pv. maculicola. The accumulation of Zn caused increased superoxide production in N. caerulescens, but inoculation with P. syringae did not elicit the defensive oxidative burst typical of most plants. Defences dependent on signalling through ROS (callose and PR gene expression) were also modified or absent in N. caerulescens, whereas salicylic acid production in response to infection was retained. These observations suggest that metal hyperaccumulation is incompatible with defence signalling through ROS and that, as metal hyperaccumulation became effective as a form of elemental defence, normal defence responses became progressively uncoupled from ROS signalling in N. caerulescens. © 2013 the Authors © 2013 New Phytologist Trust.
Abstract.
2011
Fones H, Preston GM (2011). Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas. FEMS Microbiology Letters, 327(1), 1-8.
2010
Fones H, Davis CAR, Rico A, Fang F, Smith JAC, Preston GM (2010). Metal Hyperaccumulation Armors Plants against Disease. PLoS Pathogens, 6(9), e1001093-e1001093.
