New cryptic species of Teratosphaeria on Eucalyptus in Australia

Teratosphaeria destructans and T. viscida are serious pathogens causing leaf, bud and shoot blight diseases of Eucalyptus plantations in the subtropics and tropics of South-East Asia (T. destructans) and North Queensland, Australia (T. viscida). During disease surveys in northern Western Australia and the Northern Territory of Australia, symptoms resembling those of T. destructans were observed on young and adult leaves of native and plantation Eucalyptus spp. and its hybrids. Phylogenetic studies revealed Teratosphaeria species associated with these symptoms are new taxonomic novelties described here as T. novaehollandiae and T. tiwiana spp. nov. Isolates from previous records of T. destructans recorded in Australia were re-examined and based upon the phylogenetic evidence are reassigned to these new taxa. We conclude that T. destructans is absent from Australia.The Australian Research Council DPO343600http://www.imafungus.orgam2017Forestry and Agricultural Biotechnology Institute (FABI

Plants for planting ; indirect evidence for the movement of a serious forest pathogen, Teratosphaeria destructans, in Asia

Fungal diseases caused by native pathogens and pathogens introduced with planting stock have a significant impact on exotic plantation forestry in the tropics. Teratosphaeria destructans (formerly Kirramyces destructans) is a serious pathogen causing leaf, bud and shoot blight diseases of Eucalyptus spp. in plantations in the sub-tropics and tropics of south-east Asia. This pathogen was first discovered in Indonesia in 1995 and has subsequently spread to Thailand, China, Vietnam and East Timor. The biology, ecology and genetics of this important pathogen have not been explored yet. The objective of this study was, thus, to determine the genetic diversity and movement of T. destructans throughout south-east Asia using multi-gene phylogenies and microsatellite markers. Out of nine gene regions only two microsatellite markers detected a very low nucleotide polymorphism between isolates; seven other gene regions, ITS, β-tubulin, EF1-α, CHS, ATP6 and two microsatellite loci, reflected genetic uniformity. The two polymorphic molecular markers resolved six haplotypes among isolates from Indonesia and only a single haplotype elsewhere in Asia. The low diversity observed among isolates in the region of the first outbreak is as expected for a small founder population. The spread of a single clone over large distances throughout the region supports the hypothesis of spread via the human-mediated movement of germplasm.Murdoch University Doctoral Research Scholarship, University of Pretoria

Phylogeny, phylogeography and movement of Kirramyces spp. associated with leaf blight diseases of plantation eucalypts

When 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

Multiple gene genealogies reveal important relationships between species of Phaeophleospora infecting Eucalyptus leaves

The majority of Eucalyptus species are native to Australia, but worldwide there are over 3 million ha of exotic plantations, especially in the tropics and subtropics. Of the numerous known leaf diseases, three species of Phaeophleospora can cause severe defoliation of young Eucalyptus; Phaeophleospora destructans, Phaeophleospora eucalypti and Phaeophleospora epicoccoides. Phaeophleospora destructans has a major impact on seedling survival in Asia and has not, as yet, been found in Australia where it is considered a serious threat to the biosecurity of native eucalypts. It can be difficult to distinguish Phaeophleospora species based on symptoms and micromorphology and an unequivocal diagnostic tool for quarantine purposes would be useful. In this study, a multiple gene genealogy of these Phaeophleospora species and designed specific primers has been constructed to detect their presence from leaf samples. The phylogenetic position of these Phaeophleospora species within Mycosphaerella was established. They are closely related to each other and to other important Eucalyptus pathogens, Mycosphaerella nubilosa, Mycosphaerella cryptica and Colletogloeopsis zuluensis. The specific primers developed can now be used for diagnostic and screening purposes within Australia.This work was funded in part by the Australian Research Council DP0343600, 'Population genetics of fungal pathogens that threaten the biosecurity of Australia's eucalypts'. Vera Andjic is a recipient of a Murdoch University Doctoral Research Scholarship. This work also acknowledges funding from various grants to the University of Pretoria linked to tree protection research and a collaborative research agreement linking the University of Pretoria and Murdoch University. Dr Angus Carnegie is thanked for providing samples of various Phaeophloespora species used in this study

Data from: Current and projected global distribution of Phytophthora cinnamomi, one of the world’s worst plant pathogens

Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a CLIMEX model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on the presence and absence of the pathogen. The CLIMEX model captured areas of climatic suitability where P. cinnamomi occurs that is congruent with all available records. The model was validated by the collection of soil samples from asymptomatic vegetation in areas projected to be suitable by the model for which there were few records. DNA was extracted and the presence or absence of P. cinnamomi determined by high throughput sequencing (HTS). While not detected using traditional isolation methods, HTS detected P. cinnamomi at higher elevations in eastern Australia and central Tasmania as projected by the CLIMEX model. Further support for the CLIMEX model was obtained by using the large dataset from southwest Australia where the proportion of positive records in an area is related to the Ecoclimatic Index value for the same area. We provide for the first time a comprehensive global map of the current P. cinnamomi distribution, an improved CLIMEX model of the distribution, and a projection to 2080 of the distribution with predicted climate change. This information provides the basis for more detailed regional scale modelling and supports risk assessment for governments to plan management of this important soil-borne plant pathogen

Colletotrichum species in Australia

Forty-four species of Colletotrichum are confirmed as present in Australia based on DNA sequencing analyses. Many of these species were identified directly as a result of two workshops organised by the Subcommittee on Plant Health Diagnostics in Australia in 2015 that covered morphological and molecular approaches to identification of Colletotrichum. There are several other species of Colletotrichum reported from Australia that remain to be substantiated by DNA sequence-based methods. This body of work aims to provide a basis from which to critically examine a number of isolates of Colletotrichum deposited in Australian culture collections