Browsing by Author "Xu, Xiangming"

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    Cladosporium species: the predominant species present on raspberries from the U.K. and Spain and their ability to cause skin and stigmata infections
    (MDPI, 2023-01-17) Farwell, Lauren Helen; Deakin, Greg; Harris, Adrian Lee; Fagg, Georgina; Passey, Thomas; Verheecke-Vaessen, Carol; Magan, Naresh; Xu, Xiangming
    Raspberry (Rosales: Rosaceae) production in the U.K. has moved rapidly in the last 10 years to under polythene, combined with a reduced availability of broad-spectrum fungicides. Hence, the incidence of previously less prevalent diseases, such as Cladosporium (Capnodiales: Cladosporiaceae), has largely increased. This study aimed to identify the predominant Cladosporium species on raspberry and to understand the nature of its infection on raspberry fruit. Raspberries were collected from farms across the U.K. and Spain and incubated; fungal isolates were then isolated from typical Cladosporium lesions and identified to the species level based on the sequences of the trans elongation factor α and actin genes. Cladosporium cladosporioides (Fres) de Vries was confirmed as the predominant species responsible for infecting raspberry fruit close to harvest on fruit from the U.K. and Spain, being present on 41.5% of U.K. fruit and 84.6% of Spanish fruit. Raspberries were subsequently inoculated at different developmental stages with C. cladosporioides isolates to determine the susceptibility to Cladosporium skin lesions and stigmata infections in relation to the developmental stage. Only the ripening and ripe raspberries were susceptible to Cladosporium, resulting in skin lesions. Cladosporium can colonise the stigmata of raspberries earlier in fruit development and future research is required to determine if such stigmata infections could cause subsequent skin lesion infections. This study has provided the necessary epidemiological information to develop effective management measures against the Cladosporium species.
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    Conditions for infection of strawberry fruit by M. piriformis and Rhizopus spp.
    (Springer, 2020-05-09) Agyare, Solomon; Magan, Naresh; Xu, Xiangming
    Botrytis cinerea, Mucor piriformis and Rhizopus spp. are mainly responsible for post-harvest fruit rot in strawberry in the UK. However, research to date has been focused on the epidemiology and management of B. cinerea in strawberry (i.e., grey mould). A number of experiments were carried out to study the epidemiology of M. piriformis and Rhizopus on strawberry, including flower/fruit susceptibility, inoculum dose, in vitro spore germination and infection of both detached and attached fruit. The results showed that M. piriformis and Rhizopus had very similar epidemiological characteristics. Both pathogens were unable to infect flowers, but fruit became increasingly susceptible from the green development stage onwards. In vitro germination required near-saturation humidity conditions and was reduced in both low and high temperatures. However, infection of attached ripe fruit and subsequent rot development were relatively unaffected by temperature and relative humidity conditions that commonly occur under field conditions in the UK. On detached ripe fruit, a high spore infection potency was observed for both pathogens. Infection of fruit was completed within 9 to 24 h. Thus, the most important factor determining the level of infection of fruit by M. piriformis and Rhizopus in UK commercial crops is probably the number of spores deposited on the fruit. Management strategies should be targeted at reducing inoculum concentrations within crops in order to minimise the risk of fruit infection by M. piriformis and Rhizopus.
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    Critical evaluation of two commercial biocontrol agents for their efficacy against B. cinerea under in vitro and in vivo conditions in relation to different abiotic factors
    (MDPI, 2021-09-17) Tut, Gurkan; Magan, Naresh; Brain, Philp; Xu, Xiangming
    The study evaluated the dose–response relationship of two commercial microbial biocontrol agents, Bacillus subtilis and Gliocladium catenulatum, against Botrytis cinerea both in vitro and in vivo. Inoculum doses, formulation, temperature and foliar leaf part all affected the control achieved by the two BCAs. In vitro competition assays on modified PDA plates tested a range of BCA doses (log10 3–10 CFUs or spores/droplet) at 4, 10 and 20 °C on the development of B. cinerea colonies. The dose–response relationship was influenced by both the BCA formulation and temperature. In vivo studies on lettuce plants in semi-commercial greenhouses examined the BCA dose (log10 5–9 CFUs or spores/mL) for controlling B. cinerea with a high inoculum (log10 6 spores/mL). Leaf disc assays showed that the dose–response relationship was influenced by the leaf parts sampled. These results suggest that the dose–response relationship between a BCA and specific pathogen will be significantly influenced by environmental conditions, formulation and plant phyllosplane tissue.
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    Effect on microbial communities in apple orchard soil when exposed short-term to climate change abiotic factors and different orchard management practices
    (Oxford University Press, 2023-01-11) Cook, Chris; Magan, Naresh; Robinson-Boyer, Louisa; Xu, Xiangming
    Aim We assessed the effect of exposing apple orchard soil to different temperatures and CO2 levels on the resident microbiome of soils from a conventionally managed and an organically managed apple orchard. The key difference between these two orchards was that synthetic fertilizers and pesticides are routinely used in the former one. Methods and results To investigate the effect of CO2 and temperature soil samples from each site at two depths were exposed to elevated temperature (29°C) at either 5,000 or 10,000 ppm for 5 weeks or control conditions (25°C + 400 ppm). Both bacterial and fungal communities were profiled with amplicon-sequencing. The differences between the two orchards were the most significant factor affecting bacterial and fungal communities contributing to 53.7% and 14.0% of variance in Bray-Curtis β diversity respectively. Elevated CO2 concentration and increased temperature affected organic orchard microbial diversity more than the conventionally managed orchard. A number of candidate beneficial and pathogenic microorganisms had differential abundance when temperature and CO2 were elevated, but their effect on the plant is unclear. Conclusions This study has highlighted that microbial communities in bulk soils are most significantly influenced by crop management practice compared to the climate conditions used in the study. The studied climate conditions had a more limited effect on microbial communitiy diversity in conventionally managed soil samples than in organically managed soils.
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    Influence of abiotic factors on kinetics of viable populations of biocontrol agents in the phyllosphere of lettuce and strawberry leaves
    (Wiley, 2023-02-28) Tut, Gurkan; Magan, Naresh; Xu, Xiangming
    There is little information on the effect of temperature, relative humidity (RH) and vapour pressure deficit (VPD) on the viable populations of two commercial biocontrol strains, Bacillus subtilis QST 713 (recently classified as B. velezensis) and Gliocladium catenulatum J1446 (syn. Clonostachys rosea). The PMAxx-qPCR molecular assay was used to quantify the viable biocontrol agent (BCA) populations on fully extended lettuce and strawberry leaves under a range of temperature and RH combinations. Overall, there was a small decline in the population size of viable cells for the two biocontrol organisms on strawberry and lettuce leaves within 10 days of application. However, for most experimental runs, which contained general UK agronomy climates, such a decline was not statistically significant. Moreover, for a few runs, the viable populations increased significantly in optimal BCA growth temperatures with high RH. Only temperature (ambient) and dew point significantly affected the rate of temporal changes in the viable biocontrol population size. Thus, an increasing temperature led to decreased daily mortality. It should be noted that much of the variability in the estimated daily mortality rates remains unaccounted for, thus unless under extreme conditions, the biocontrol efficacy in practice is less likely to be affected by the survival of biocontrol microbes but more likely by other factors that influence the density of biocontrol cells in the phyllosphere, especially dilution due to rapid host leaf expansion, spray coverage and rain wash-off.
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    Inter-row cropping and rootstock genotype selection in a UK cider orchard to combat apple replant disease
    (BioMed Central, 2023-07-04) Cook, Chris; Magan, Naresh; Xu, Xiangming
    Apple rootstock genotypes confer different levels of tolerance to apple replant disease (ARD) and vigour to a newly replanted apple tree. A hybrid management system of rotating the rootstock genotype planted between successive generations and inter-row planting in the alleyways of orchards may minimise the severity of ARD symptoms. High-throughput sequencing of the fungal ITS and bacterial 16S rDNA regions was used to investigate the diversity, and differential taxa present in soils displaying symptoms of ARD. Candidate pathogens and beneficial microorganisms were correlated with the above-ground establishment of each rootstock genotype in a UK cider orchard. Our results suggest that the same rootstock or rootstock with closely related parentage to the previous rootstock had more severe ARD symptoms. Planting in the alleyway appeared an effective strategy to minimise the severity of symptoms irrespective of rootstock genotype. The planting location effect had a higher contribution to the variation in the rhizosphere microbiome than that of the rootstock genotype. No predicted causal agents for ARD could be identified to a taxonomic level to predict their function but two species associated with mycorrhizae, Pteridiospora spinosispora and Paraglomus laccatum were identified as inversely correlated with ARD severity and could be candidate beneficial species for apple, warranting further investigation and research. Our findings suggest that planting in the alleyways and planting rootstocks genetically dissimilar to the previously planted rootstock can be beneficial for tree establishment. We have also identified species inversely associated with ARD severity, making candidates for future research to test the antagonistic effect of the species against ARD pathogens in apple roots.
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    Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air
    (Wiley, 2024-03-01) Farwell, Lauren Helen; Papp-Rupar, Matevz; Deakin, Greg; Magan, Naresh; Xu, Xiangming
    Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.
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    Is it feasible to use mixed orchards to manage apple scab?
    (Maximum Academic Press, 2023-10-10) Stewart, Katie; Passey, Thomas; Verheecke-Vaessen, Carol; Kevei, Zoltan; Xu, Xiangming
    Apple scab, caused by the fungus Venturia inaequalis, is one of the most damaging diseases of cultivated apples (Malus x domestica) worldwide. It results in huge losses as it diminishes fruit quality and impacts tree growth. Current management revolves around application of fungicides, however the number of sprays required per season is unsustainable and expensive. Further to this, populations of V. inaequalis have developed fungicide resistance. Breeding new cultivars with higher levels of resistance to scab is a priority, however, this process is long, so introducing mixed cultivar orchards may be a faster solution. We reviewed the general principles of using mixtures to manage plant diseases, and then considered specifically using mixed cultivars to manage apple scab in commercial production. Limited field studies have demonstrated the potential of using mixture to suppress apple scab development; but scab super-races that could emerge from mixture can pose a significant risk to in commercial production. However, recent research on population genetics of apple scab in monoculture and mixed orchards suggests that the risk of super-race emergence is probably over-stated because assortative mating among lesions on the same leaves is likely to occur rather than commonly assumed random mating. Thus, we conclude that cultivar mixtures can contribute towards sustainable scab management, particularly in commercial cider apple production.
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    Molecular assay development to monitor the kinetics of viable populations of two biocontrol agents, Bacillus subtilis QST 713 and Gliocladium catenulatum J1446, in the phyllosphere of lettuce leaves
    (MDPI, 2021-03-15) Tut, Gurkan; Magan, Naresh; Brain, Philip; Xu, Xiangming
    Optimising the use of biocontrol agents (BCAs) requires the temporal tracking of viable populations in the crop phyllosphere to ensure that effective control can be achieved. No sensitive systems for quantifying viable populations of commercially available BCAs, such as Bacillus subtilis and Gliocladium catenulatum, in the phyllosphere of crop plants are available. The objective of this study was to develop a method to quantify viable populations of these two BCAs in the crop phyllosphere. A molecular tool based on propidium monoazide (PMA) (PMAxx™-qPCR) capable of quantifying viable populations of these two BCAs was developed. Samples were treated with PMAxx™ (12.5–100 μM), followed by 15 min incubation, exposure to a 800 W halogen light for 30 min, DNA extraction, and quantification using qPCR. This provided a platform for using the PMAxx™-qPCR technique for both BCAs to differentiate viable from dead cells. The maximum number of dead cells blocked, based on the DNA, was 3.44 log10 for B. subtilis and 5.75 log10 for G. catenulatum. Validation studies showed that this allowed accurate quantification of viable cells. This method provided effective quantification of the temporal changes in viable populations of the BCAs in commercial formulations on lettuce leaves in polytunnel and glasshouse production systems.
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    Optimising the use of biocontrol agents to improve the control of botrytis cinerea in key vegetable and fruit crops.
    (Cranfield University, 2019-07) Tut, Gurkan; Magan, Naresh; Xu, Xiangming; Medina-Vayá, Ángel
    For sustainable agriculture, efficient usage of biocontrol agents (BCAs) is crucial. As BCAs are living organisms effective biocontrol ability is governed by complex ecological processes. Because of this, biocontrol of plant diseases can become constrained. Research on the ecology, mechanisms of action and population ecology in the phyllopshere environment is critical for modelling the efficacy of BCAs for control of foliar plant pathogens, especially Botrytis cinerea. The aim of the research was to obtain ecological knowledge on Bacillus subtilis QST 713 and Gliocladium catenulatum J1446, and if feasible use this ecological information to apply these two BCAs against B. cinerea. Thus the objective initially was to (i) develop a molecular based assay to quantify viable population changes of the two BCAs, and use this novel assay for investigating: (ii) the dose response relationship of B. cinerea to the bacterial and fungal BCA, (iii) impact of relative humidity (RH) and temperature used in UK agronomic production systems on BCA populations, (iv) produce a simple model to predict BCA fate, (v) identify the colonisation and dispersion kinetics of the two BCAs on expanding foliage, and finally from the collected ecological knowledge (vi) suggest optimisations strategies for the two BCAs. This study successfully developed a PMAxxᵀᴹ-qPCR method for quantifying the kinetics of viable population changes for both the BCAs. The dose response relationship of B. cinerea to the BCAs’ was deciphered and G. catenulatum median effective dose was 1 × 10⁸ spores/ml, while for B. subtilis this was 3 × 10⁸ CFUs/ml⁻¹ . However, this changed with temperature, formulation, and leaf tissue type. Both temperature and humidity impacted on viable population dynamics of the two BCAs, and showed that viable populations were sustained, increased or reduced depending on abiotic factors (temperature, R.H.), with efficacy best at conditions close to the BCAs optimum growth conditions. From the collected data, models were produced and tested for their ability to predict the fate of each BCA in commercial growing sites. The dispersion and colonisation kinetics of the two BCAs were analysed on growing lettuce and strawberry leaves. The two BCAs behaved in different ways, while their ability to disperse and colonise virgin leaf tissue was effective, the rate depended on the season (temperature and RH) and host. This study has developed significant new ecological knowledge on these two BCAs and their behaviour when applied to strawberry and lettuce leaf surfaces, and their establishment to control B. cinerea in these agronomic crop systems.
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    The epidemiology and management of cladosporium on raspberry
    (Cranfield University, 2024-01) Farwell, Lauren; Xu, Xiangming; Medina, Angel
    Cladosporium is a genus of fungi that causes dark mycelial lesions on raspberries, rendering fruit unmarketable. As Cladosporium is an opportunistic pathogen, its prevalence varies across years, and there is insufficient research on its epidemiology and management. This study aimed to investigate the epidemiology of Cladosporium on raspberries and to elucidate which management strategies could be effective. Isolates of Cladosporium were obtained from raspberries, with C. cladosporioides being the most predominant, and was therefore used in further experiments. The susceptibility of raspberry fruit development was determined, with ripening and ripe fruit found to be susceptible to skin lesions; this stage of development was subsequently targeted in management studies. The effects of ripening and fruit location (fruit location within a tunnel vs. across a farm) on the inoculum load on the surface of raspberries were investigated using metabarcoding studies. The fungal and bacterial microbiomes were also investigated to better elucidate the ecology of Cladosporium on the fruit surface. Cladosporium was more abundant on green fruit than ripening fruit; perhaps due to organisms such as Rouxiella present on the fruit’s surface. Fungal α diversity increased during ripening while bacterial diversity decreased. The Cladosporium inoculum load in the air was also investigated, with more spores trapped inside a raspberry polytunnel than an open field. The efficacy of commercial Biological Control Agents (BCAs) and resistant varieties to control Cladosporium skin lesions were tested across two years in field applications. The Trichoderma sp. was the most effective at reducing the incidence of Cladosporium on raspberry than compared to the other tested products. The variety resistance study was inconclusive, but results indicate further testing will reveal which varieties are more susceptible. This research will inform potential management strategies against Cladosporium on raspberries that will aid growers in reducing food waste sustainably
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    Understanding the resilience of soil beneficials to combat apple replant disease (ARD).
    (2022-09) Cook, Christopher; Magan, Naresh; Robinson-Boyer, Louisa; Xu, Xiangming; Medina-Vayá, Ángel
    Apple Replant Disease (ARD), caused by an accumulation of soil-borne fungal and oomycete pathogens in the soil, is an economically important disease of apples. Current management relies on the use of broad-spectrum chemical fumigation. Banning of chemical products has seen increased research into biological management strategies for ARD. This study aimed to test the efficacy of a number of commercially available biological soil amendments to improve the establishment of young apple trees in an attempt to minimise the detrimental effects of ARD. It also looked at changes in planting position and rootstock selection at planting to manage ARD and how climate change abiotic factors affect bulk apple soil microbiome communities. The efficacy of single species amendments was variety specific in the field. There was a increased rate of tree girth expansion in Gala trees amended pre-planting with Pseudomonas fluorescens but the same effect was not observed with Braeburn trees. The single species amendments did not increase the establishment of young apple trees either individually or in a consortium of amendments in semi-field conditions. In both field and semi-field conditions pre-plant amendment significantly altered the abundance of individual operational taxonomic units (OTUs) associated with both beneficial and pathogenic taxa of plants. The planting position in the inter-row alleyways and the genetic relationship of the new rootstock to the previously planted rootstock on the site were both identified to minimise ARD severity. In addition, a significant effect of CO₂ concentration and temperature increase on bulk soil microbiome communities was observed but this was not as significant as site management (organic vs conventional) effect. This research will aid with the development of management strategies for ARD by integrating single species biological amendments and cultural approaches with other management practices.