10 research outputs found
Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland
No full textNewly discovered Phytophthora species include invasive pathogens that threaten trees and shrubs. We present draft genome assemblies for three isolates of Phytophthora kernoviae and one isolate of the EU2 lineage of Phytophthora ramorum, collected from outbreak sites in Scotland
Population studies on Phytophthora infestans on potatoes and tomatoes in southern Germany
No full textFifty-seven isolates of Phytophthora infestans from blighted potato foliage were collected in 1995 in southern Germany and analysed for mating type and sensitivity to metalaxyl. Fifty-six of them were characterised as A1 and one as A2 mating types. Resistance to metalaxyl was observed frequently: 53 isolates were resistant, three were partially sensitive, and one was sensitive. In a subsequent field study in 1999, 84 isolates collected from blighted potato and tomato foliage were analysed for mating type. Seventy-two were characterised as A1 and twelve as A2 mating types. The response of 76 isolates to metalaxyl and to propamocarb was tested. The majority (42) of the 76 isolates was classified as resistant to metalaxyl; 31 were partially sensitive and only three isolates were sensitive. The results with propamocarb were less discrete; 10 isolates were classified as resistant and three were clearly sensitive. AFLP fingerprinting was used to examine the genetic structure of the southern German P. infestans population collected in 1999 and indicated that the tested population can be sub-divided into a tomato group, a potato group and a mixed group containing isolates collected from both crops. The presence of Ia and IIa mitochondrial DNA haplotypes indicates that the German P. infestans isolates belong to the new pathogen population that has also been reported in neighbouring regions of Europe. The present study indicates that at the beginning of the season only a few genotypes were present, and the population became genetically more variable at the end of the growing season
The epidemiology of Phytophthora ramorum and P.Kernoviae at two historic gardens in Scotland
No full textThis study looked at the factors that facilitated the spread of Phytophthora ramorum and P. kernoviae at two locations in the west of Scotland. Spore traps, river baiting, bait plants, and soil sampling were used to both confirm the presence of, and measure the amount of, inoculum in the environment in order to quantify the relationship between inoculum levels and disease development. Phytophthora ramorum was detected in spore traps at high levels under a sporulating host, but also at sites where hosts were not present, leading to the conclusion that inocula in low-level spore traps were the result of soil splash. Rhododendron and Vaccinium bait plants were also infected with P. ramorum via soil splash at sites where there was no sporulating host present. Phytophthora kernoviae was only detected in spore traps where there was a sporulating host overhead. Water baiting confirmed the presence of P. ramorum in two streams in one of the gardens, but P. kernoviae was not detected using this method at the other garden despite the large-scale P. kernoviae infection there. Inoculum continued to be detected in soil in areas where infected hosts had been removed 2 years ago, confirming that both of these pathogens can survive in soil for a considerable period. Evidence of the movement of infested mulch during horticultural activity was found. These findings have clear implications for the control of disease spread within the garden setting
Phyto-threats : addressing threats to UK forests and woodlands from phytophthora; identifying risks of spread in trade and methods for mitigation
No full textThe multidisciplinary ‘Phyto-threats’ project was initiated in 2016 to address the increasing risks to UK forest and woodland ecosystems from trade-disseminated Phytophthora. A major component of this project was to examine the risk of Phytophthora spread through nursery and trade practices. Close to 4000 water and root samples were collected from plant nurseries located across the UK over a three-year period. Approximately half of the samples tested positive for Phytophthora DNA using a metabarcoding approach with 63 Phytophthora species identified across nurseries, including quarantine-regulated pathogens and species not previously reported in the UK. Phytophthora diversity within nurseries was linked to high-risk management practices such as use of open rather than closed water sources. Analyses of global Phytophthora risks identified biological traits and trade pathways that explained global spread and host range, and which may be of value for horizon-scanning. Phytophthoras having a higher oospore wall index and faster growth rates had wider host ranges, whereas cold-tolerant species had broader geographic and latitudinal ranges. Annual workshops revealed how stakeholder and sector ‘appetite’ for nursery accreditation increased over three years, although an exploratory cost-benefit analysis indicated that the predicted benefits of introducing best practice expected by nurseries outweigh their costs only when a wider range of pests and diseases (for example, Xylella) is considered. However, scenario analyses demonstrated the significant potential carbon costs to society from the introduction and spread of a new tree-infecting Phytophthora: Thus, the overall net benefit to society from nurseries adopting best practice could be substantial
Phylogeny, phylogeography and movement of Kirramyces spp. associated with leaf blight diseases of plantation eucalypts
No full textWhen this study commenced in early 2004, only five Phaeophleospora species. had been reported from eucalypts of which only two; P. destructans (STE-U 1336) and P. epicoccoides (STE-U 1346) had been sequenced. In a former study, Phaeophleospora species emerged in two separate clades suggesting that Phaeophelospora is polyphyletic. The appearance and severity of lesions on eucalypt leaves are generally used to recognise the species of Phaeophleospora responsible for disease. However, depending on host and climate, the symptoms associated with infection by P. epicoccoides, P. eucalypti and P. destructans can be almost identical and incorrect diagnosis is a common problem. Thus, Phaeophleospora species were compared based on DNA sequences and multi gene genealogies were constructed. In addition species- specific primers were designed and tested on leaf material.
Many isolates of Phaeophleospora spp. were collected and sequenced, and all Phaeophleospora spp. from eucalypts were shown to cluster together and are closely related to the most important leaf pathogens associated with eucalypts namely Colletogloeopsis zuluensis, Mycosphaerella cryptica and M. nubilosa. In contrast, these fungi are distantly related to the type specimen of the genus Phaeophleospora, P. eugeniae. Furthermore, all DNA sequences of isolates of P. destructans examined in this thesis, including the ex-type culture, were identical but different to one previously lodged in GenBank.
This phylogenetic separation led to a morphological study of the species assigned to Phaeophleospora and compared the species from eucalypts with P. eugeniae the type specimen of Phaeophleospora. The phylogenetic and morphological studies show that P. eugeniae is well separated from Phaeophleospora spp. occurring on eucalypts and led to the resurrection of the previous generic name, Kirramyces for Phaeophleospora spp. occurring on eucalypts. Furthermore, phylogenetic analysis and morphological observation of Kirramyces spp. and Colletogloeopsis spp. occurring on eucalypts showed considerable overlap between these two genera. Therefore, Colletogloeopsis was reduced to synonymy with Kirramyces. Consequently, the genus Kirramyces was expanded from five to 14 species, and included the description of two new species, K. angophorae and K. corymbiae. In order to assist with their identification a key based on morphology of conidia for Kirramyces species was developed.
Kirramyces destructans is a devastating pathogen originally described from Indonesia in 1996 and has since been found throughout Asia where all common tropical and subtropical plantation eucalypt species and hybrids are susceptible. K. destructans is considered a major biosecurity threat in Australia, both to native eucalypt forests and the tropical plantation industry. Prior to the current study, there had been no investigation into the origin and movement of this important pathogen. Thus, five gene regions and six microsatellite loci were sequenced for 43 representative isolates of K. destructans from a range of geographical locations and hosts. Two microsatellite markers detected very low nucleotide polymorphism (three haplotypes for each loci); five other gene regions, including four microsatellite region were uniform. This low level of genetic diversity provides strong evidence that K. destructans was introduced into Indonesia as a founder population and that it has subsequently been spread throughout Asia via human-mediated movement of germplasm. Timor and Northern Australia were considered to be a possible source of origin of this fungus, but the high susceptibility of native E. urophylla to K. destructans in Timor indicates that the pathogen is unlikely to be endemic to Timor.
The current distribution of Kirramyces eucalypti is New South Wales, Queensland, Victoria, Tasmania and New Zealand (North Island). The main host of this pathogen is E. nitens which is native to Victoria and New South Wales. Kirramyces eucalypti has not been found in South Africa, yet it causes a severe disease on eucalypt hybrids originating from South Africa growing in New South Wales indicating movement to these hybrids from either native eucalypts or nearby plantations. As such, K. eucalypti poses a threat for the plantation industry in sub-tropical and tropical Australia. The phylogeography of K. eucalypti in Australia and New Zealand was studied by sequencing three gene regions and one microsatellite locus of fifty-seven representative isolates of K. eucalypti from Queensland, New South Wales, Victoria, Tasmania and New Zealand. The highest genetic variation was found among isolates from NSW suggesting that K. eucalypti originates from NSW. Isolates in New Zealand appear to have been introduced from NSW. Isolates from Queensland were consistently different to those from other regions and may in fact represent a cryptic species or a hybrid.
During monitoring of eucalypt taxa trials in far North Queensland, infected leaves resembling symptoms typical of K. destructans were collected and examined. Phylogenetic data based on three gene regions and some morphological characteristics revealed a new taxon described in this study as K. viscidus. Kirramyces viscidus was also shown to be closely related to the devastating pathogen K. destructans. Kirramyces viscidus had been found to cause extensive damage to eucalypt hybrids originating from South America, and less damage to E. grandis from Australia, indicating that this pathogen is probably endemic to Australia. Kirramyces viscidus has the potential to seriously damage tropical eucalypt plantations, especially if clonal and planted off-site.
In conclusion, this study resurrected genus Kirramyces for the Phaeophleospora and Coletoglloeopsis spp. occurring on eucalypts. It also studied the phylogeography and gene flow of the two most important Kirramyces species, K. destructans and K. eucalypti and describes three new Kirramcyes spp. found on eucalypts in Australia. Very recently, K. destructans has been discovered in Northern Australia. This raises a whole series of new issues as there are now several pathogens, K. eucalypti, K. viscidus and K. destructans present in Australia that known to cause serious damage on plantation eucalypts. Recent investigations have also revealed several undescribed Kirramyces spp. in Northern Australia. Their impact, distribution, movement and potential for hybridization now need to be examined
Euphresco Sendo: An international laboratory comparison study of molecular tests for Synchytrium endobioticum detection and identification
No full textAn international test performance study (TPS) was organised to generate validation data for three molecular Synchytrium endobioticum tests: van den Boogert et al. (European Journal of Plant Pathology 113, 47–57, 2005), and van Gent-Pelzer et al. (European Journal of Plant Pathology, 126, 129-133, 2010) for the detection of S. endobioticum, and the pathotype 1(D1) identification test described by Bonants et al. (European Journal of Plant Pathology, 143, 495-506, 2015). Two TPS rounds were organised focussing on different test matrices, i.e. round 1: warted potato tissue, and round 2: resting spore suspensions. When using the tests for detection and identification of S. endobioticum in warted potato tissue, no significant differences were observed for diagnostic sensitivity, diagnostic specificity, overall accuracy, analytical sensitivity and robustness. When using the tests for detection and identification of S. endobioticum in resting spore suspensions, the van den Boogert and van Gent-Pelzer tests significantly outperform the Bonants test for diagnostic sensitivity and diagnostic specificity. For overall accuracy and analytical sensitivity, the van Gent-Pelzer significantly outperforms the van den Boogert and Bonants tests and is regarded as the test of choice when identifying S. endobioticum from resting spores. Tests regarded fit for purpose for routine testing of wart material and resting spore suspensions are proposed for the update of EPPO standard PM7/28(1) Synchytrium endobioticum
Diagnostic methods for Synchytrium endobioticum, especially for pathotype identification (SENDO)
No full textThe main parts of the project consisted of testing new differential cultivars for pathotype identification (bioassays), and the generation of validation data for three molecular S. endobioticum detection and identification assays. As a bioassay, the partners in the project agreed upon the use of the Glynne-Lemmerzahl method to identify pathotypes. In the second year of the project (2013) a test performance study (TPS) was organised. Two different pathotypes were tested, pathotype 6(O1) and 18(T1), and five partners joined in. The cultivars Talent and Logo were chosen to replace cv Miriam in the actual set of differential cultivars (EPPO, 2004). In former research, cv Miriam proved to be less suitable for separating pathotypes 6(O1) and 18(T1), results were inconsistent. As a result, we concluded that cv Talent was the best replacement of cv Miriam in the actual set of differential cultivars. Also, the cultivar Gawin can be added to the set of differentials in a new version of the EPPO Diagnostic Protocol on Synchytrium endobioticum. An international test performance study was organised to generate validation data for three molecular S. endobioticum detection and identification assays: Boogert et al. (2005), van GentPelzer et al. (2010), and Bonants et al. (2015). Two TPS rounds were organised focussing on different test matrices: round 1: wart material, and round 2: winter spore suspensions. When using the assays for detection and identification of S. endobioticum in warted potato tissue, no significant differences were observed for diagnostic sensitivity, diagnostic specificity, overall accuracy, analytical sensitivity and robustness. After applying a Ct cut-off value for the GentPelzer assay, all assays are regarded equal. When using the assays for detection and identification of S. endobioticum in winter spore suspensions, the Boogert and Gent-Pelzer assays significantly outperform the Bonants assay for diagnostic sensitivity and diagnostic specificity. For overall accuracy and analytical sensitivity, the Gent-Pelzer assay significantly outperforms the Boogert and Bonants assays and is regarded as the assay of choice when identifying S. endobioticum winter spores. The tests included in this TPS are regarded fit for purpose for routine testing of wart material and winter spore suspensions with ≥ 500 spores per sample.Report of the Euphresco project 'Diagnostic methods for Synchytrium endobioticum, especially for pathotype identification (SENDO)
The prevalence of Phytophthora in British plant nurseries; high‐risk hosts and substrates and opportunities to implement best practice
No full textInvasive Phytophthora species infect a very broad range of herbaceous and woody hosts globally. The UK alone has experienced a particularly damaging series of outbreaks and epidemics of new, invasive Phytophthora species affecting the nation's trees over the last 30 years. The link between Phytophthora outbreaks and the importation and spread of infected nursery stock is well established across many countries worldwide. To understand better the pathways of spread of Phytophthora in the nursery trade in Britain, we applied a standardized nursery sampling method combined with a refined metabarcoding detection method to capture the diversity of Phytophthora species at 134 British plant nurseries representing a range of biosecurity and trading practices over multiple sampling years between 2016 and 2022. This included root and water samples collected from 17 nurseries sampled seasonally and root samples collected from 117 nurseries sampled once as part of plant health inspections. Based on analyses of 1894 pooled samples, DNA barcodes of 85 Phytophthora species or complexes were detected, with variation in species' relative frequencies across nurseries. We present the top 20 host– Phytophthora associations ranked by relative frequency and report five novel Phytophthora records for the UK. We identified surprisingly high‐risk hosts (such as Douglas fir) with the greatest number of Phytophthora associations and revealed Phytophthora nursery niche preferences for water or roots. We discuss the implications of our findings in terms of pathogen diversity and abundance, high‐risk hosts, our information dissemination approach and resulting advice on nursery practices aimed at reducing risk
The prevalence of Phytophthora in British plant nurseries : high-risk hosts and substrates and opportunities to influence practice
No full textInvasive Phytophthora species infect a very broad range of herbaceous and woody hosts globally. The UK alone has experienced a particularly damaging series of outbreaks and epidemics of new, invasive Phytophthora species affecting the nation's trees over the last 30 years. The link between Phytophthora outbreaks and the importation and spread of infected nursery stock is well established across many countries worldwide. To understand better the pathways of spread of Phytophthora in the nursery trade in Britain, we applied a standardized nursery sampling method combined with a refined metabarcoding detection method to capture the diversity of Phytophthora species at 134 British plant nurseries representing a range of biosecurity and trading practices over multiple sampling years between 2016 and 2022. This included root and water samples collected from 17 nurseries sampled seasonally and root samples collected from 117 nurseries sampled once as part of plant health inspections. Based on analyses of 1894 pooled samples, DNA barcodes of 85 Phytophthora species or complexes were detected, with variation in species' relative frequencies across nurseries. We present the top 20 host–Phytophthora associations ranked by relative frequency and report five novel Phytophthora records for the UK. We identified surprisingly high-risk hosts (such as Douglas fir) with the greatest number of Phytophthora associations and revealed Phytophthora nursery niche preferences for water or roots. We discuss the implications of our findings in terms of pathogen diversity and abundance, high-risk hosts, our information dissemination approach and resulting advice on nursery practices aimed at reducing risk
