Publications by authors named "Treena I Burgess"

38 Publications

Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests.

Microb Ecol 2021 Jan 2;81(1):122-133. Epub 2020 Aug 2.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.

Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.
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http://dx.doi.org/10.1007/s00248-020-01563-0DOI Listing
January 2021

Association of with Declining Vegetation in an Urban Forest Environment.

Microorganisms 2020 Jun 29;8(7). Epub 2020 Jun 29.

Phytophthora Science and Management, Centre for Climate Impacted Terrestrial Ecosystems, Harry Butler Institute, Murdoch University, Murdoch 6150, Australia.

Urban forests consist of various environments from intensely managed spaces to conservation areas and are often reservoirs of a diverse range of invasive pathogens due to their introduction through the nursery trade. Pathogens are likely to persist because the urban forest contains a mixture of native and exotic plant species, and the environmental conditions are often less than ideal for the trees. To test the impact of different land management approaches on the community, 236 discrete soil and root samples were collected from declining trees in 91 parks and nature reserves in Joondalup, Western Australia (WA). Sampling targeted an extensive variety of declining native trees and shrubs, from families known to be susceptible to . A sub-sample was set aside and DNA extracted for metabarcoding using -specific primers; the remaining soil and root sample was baited for the isolation of We considered the effect on the community of park class and area, soil family, and the change in canopy cover or health as determined through sequential measurements using remote sensing. Of the 236 samples, baiting techniques detected species from 24 samples (18 parks), while metabarcoding detected from 168 samples (64 parks). Overall, forty-four phylotypes were detected. Considering only sampling sites where was detected, species richness averaged 5.82 (range 1-21) for samples and 9.23 (range 2-24) for parks. was the most frequently found species followed by , and While park area and canopy cover had a significant effect on community the R values were very low, indicating they have had little effect in shaping the community. and the two most invasive species, often co-occurring (61% of samples); however, the communities with were more common than those with , reflecting observations over the past decade of the increasing importance of as a pathogen in the urban environment.
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http://dx.doi.org/10.3390/microorganisms8070973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409110PMC
June 2020

A qPCR Assay for the Detection of Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples.

Plant Dis 2019 Sep 16;103(9):2443-2450. Epub 2019 Jul 16.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.

causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against and two closely related clade 7 species, and . From these tests, five primer pairs were selected based on specificity and, with a species-specific probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of DNA and showed no cross-reaction with other species, except for , a very closely related species to , which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with . Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of in recalcitrant environmental samples.
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http://dx.doi.org/10.1094/PDIS-09-18-1641-REDOI Listing
September 2019

Phytophthora Contamination in a Nursery and Its Potential Dispersal into the Natural Environment.

Plant Dis 2018 Jan 26;102(1):132-139. Epub 2017 Oct 26.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University.

A detailed site investigation of a eucalypt nursery suffering disease losses revealed the causal agent to be Phytophthora boodjera. The pathogen was detected in vegetation surrounding the nursery production area, including the lawn, under the production benches during the growing season, and, most importantly, from plant debris in used trays. However, it was not found in the container substrate, water supplies, or production equipment or on the workers themselves. The sterilization methods used by the nursery were shown to be ineffective, indicating that a more rigorous method was required. Boiling trays for 15 min or steaming at 65°C for 60 min eradicated P. boodjera. This pathogen was more pathogenic to the eucalypts tested in their early seedling stage than P. cinnamomi. Tracing of out-planting to revegetation sites showed that P. boodjera was able to spread into the environment. Dispersal via out-planting to native vegetation may affect seedling recruitment and drive long-term shifts in native plant species. Inadequate nursery hygiene increases the risk of an outbreak and can limit the success of biosecurity efforts as well as damage conservation efforts.
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http://dx.doi.org/10.1094/PDIS-05-17-0689-REDOI Listing
January 2018

Phytophthora species isolated from alpine and sub-alpine regions of Australia, including the description of two new species; Phytophthora cacuminis sp. nov and Phytophthora oreophila sp. nov.

Fungal Biol 2019 01 1;123(1):29-41. Epub 2018 Nov 1.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia. Electronic address:

Plant deaths had been observed in the sub-alpine and alpine areas of Australia. Although no detailed aetiology was established, patches of dying vegetation and progressive thinning of canopy suggested the involvement of root pathogens. Baiting of roots and associated rhizosphere soil from surveys conducted in mountainous regions New South Wales and Tasmania resulted in the isolation of eight Phytophthora species; Phytophthora cactorum, Phytophthora cryptogea, Phytophthora fallax, Phytophthora gonapodyides, Phytophthora gregata, Phytophthora pseudocryptogea, and two new species, Phytophthora cacuminis sp. nov and Phytophthora oreophila sp. nov, described here. P. cacuminis sp. nov is closely related to P. fallax, and was isolated from asymptomatic Eucalyptus coccifera and species from the family Proteaceae in Mount Field NP in Tasmania. P. oreophila sp. nov, was isolated from a disturbed alpine herbfield in Kosciuzsko National Park. The low cardinal temperature for growth of the new species suggest they are well adapted to survive under these conditions, and should be regarded as potential threats to the diverse flora of sub-alpine/alpine ecosystems. P. gregata and P. cryptogea have already been implicated in poor plant health. Tests on a range of alpine/subalpine plant species are now needed to determine their pathogenicity, host range and invasive potential.
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http://dx.doi.org/10.1016/j.funbio.2018.10.006DOI Listing
January 2019

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems.

FEMS Microbiol Ecol 2018 05;94(5)

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia.

Proper isolation and identification of Phytophthora species is critical due to their broad distribution and huge impact on natural ecosystems throughout the world. In this study, five different sites were sampled and seven methods were compared to determine the Phytophthora community. Three traditional isolation methods were conducted (i) soil baiting, (ii) filtering of the bait water and (iii) isolation from field roots using Granny Smith apples. These were compared to four sources of eDNA used for metabarcoding using Phytophthora-specific primers on (i) sieved field soil, (ii) roots from field, (iii) filtered baiting water and (iv) roots from bait plants grown in the glasshouse in soil collected from these sites. Six Phytophthora species each were recovered by soil baiting using bait leaves and from the filtered bait water. No Phytophthora species were recovered from Granny Smith apples. eDNA extracted from field roots detected the highest number of Phytophthora species (25). These were followed by direct DNA isolation from filters (24), isolation from roots from bait plants grown in the glasshouse (19), and DNA extraction from field soil (13). Therefore, roots were determined to be the best substrate for detecting Phytophthora communities using eDNA.
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http://dx.doi.org/10.1093/femsec/fiy048DOI Listing
May 2018

Lags in the response of mountain plant communities to climate change.

Glob Chang Biol 2018 02 27;24(2):563-579. Epub 2017 Nov 27.

Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, Zürich, Switzerland.

Rapid climatic changes and increasing human influence at high elevations around the world will have profound impacts on mountain biodiversity. However, forecasts from statistical models (e.g. species distribution models) rarely consider that plant community changes could substantially lag behind climatic changes, hindering our ability to make temporally realistic projections for the coming century. Indeed, the magnitudes of lags, and the relative importance of the different factors giving rise to them, remain poorly understood. We review evidence for three types of lag: "dispersal lags" affecting plant species' spread along elevational gradients, "establishment lags" following their arrival in recipient communities, and "extinction lags" of resident species. Variation in lags is explained by variation among species in physiological and demographic responses, by effects of altered biotic interactions, and by aspects of the physical environment. Of these, altered biotic interactions could contribute substantially to establishment and extinction lags, yet impacts of biotic interactions on range dynamics are poorly understood. We develop a mechanistic community model to illustrate how species turnover in future communities might lag behind simple expectations based on species' range shifts with unlimited dispersal. The model shows a combined contribution of altered biotic interactions and dispersal lags to plant community turnover along an elevational gradient following climate warming. Our review and simulation support the view that accounting for disequilibrium range dynamics will be essential for realistic forecasts of patterns of biodiversity under climate change, with implications for the conservation of mountain species and the ecosystem functions they provide.
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http://dx.doi.org/10.1111/gcb.13976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813787PMC
February 2018

Pathways to false-positive diagnoses using molecular genetic detection methods; Phytophthora cinnamomi a case study.

FEMS Microbiol Lett 2017 04;364(7)

Phytophthora cinnamomi is one of the world's most invasive plant pathogens affecting ornamental plants, horticultural crops and natural ecosystems. Accurate diagnosis is very important to determine the presence or absence of this pathogen in diseased and asymptomatic plants. In previous studies, P. cinnamomi species-specific primers were designed and tested using various polymerase chain reaction (PCR) techniques including conventional PCR, nested PCR and quantitative real-time PCR. In all cases, the primers were stated to be highly specific and sensitive to P. cinnamomi. However, few of these studies tested their primers against closely related Phytophthora species (Phytophthora clade 7). In this study, we tested these purported P. cinnamomi-specific primer sets against 11 other species from clade 7 and determined their specificity; of the eight tested primer sets only three were specific to P. cinnamomi. This study demonstrated the importance of testing primers against closely related species within the same clade, and not just other species within the same genus. The findings of this study are relevant to all species-specific microbial diagnosis.
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http://dx.doi.org/10.1093/femsle/fnx009DOI Listing
April 2017

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions.

AoB Plants 2016 Dec 30. Epub 2016 Dec 30.

Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics, and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand, and manage biological invasions.
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http://dx.doi.org/10.1093/aobpla/plw085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391705PMC
December 2016

Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees.

AoB Plants 2016 Dec 23. Epub 2016 Dec 23.

Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.

Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards, and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilise these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies, and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices.
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http://dx.doi.org/10.1093/aobpla/plw081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499825PMC
December 2016

New cryptic species of on in Australia.

IMA Fungus 2016 Dec 20;7(2):253-263. Epub 2016 Oct 20.

School of Veterinary and Life Sciences, Murdoch University, South St, Murdoch, 6150, Australia;; Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.

and are serious pathogens causing leaf, bud and shoot blight diseases of plantations in the subtropics and tropics of South-East Asia () and North Queensland, Australia (). During disease surveys in northern Western Australia and the Northern Territory of Australia, symptoms resembling those of . were observed on young and adult leaves of native and plantation spp. and its hybrids. Phylogenetic studies revealed species associated with these symptoms are new taxonomic novelties described here as and spp. nov. Isolates from previous records of recorded in Australia were re-examined and based upon the phylogenetic evidence are reassigned to these new taxa. We conclude that is absent from Australia.
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http://dx.doi.org/10.5598/imafungus.2016.07.02.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159596PMC
December 2016

Tree invasions and biosecurity: eco-evolutionary dynamics of hitchhiking fungi.

AoB Plants 2016 2;8. Epub 2017 Jan 2.

Centre of Phytophthora Science and Management, School of Veterinary and Life Science, Murdoch University, Murdoch 6150, Australia.

When non-native plants reach novel environments, they typically arrive with hidden microbiomes. In general, most of these hitchhikers remain on their co-evolved hosts, some contribute to the invasiveness of their hosts, and a small number can undergo host shifts and move onto native hosts. Invasion success can vary depending upon the different categories of fungal associates. When an invader tree relies on a fungal mutualism to survive in the new environment, there is a fundamentally lower likelihood of either the tree, or the fungus, establishing novel associations. In contrast, parasitic hitchhikers could merely use their host plants to move through the landscape and to become established on new hosts (host shifts). Evidence suggests the frequency of these host shifts is low and depends upon the fungal functional group. However, epidemics caused by invasive pathogens in native ecosystems have occurred globally. Thus, elucidating the potential for hidden non-native fungi to form novel host associations in a new environment is important for biodiversity conservation.
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http://dx.doi.org/10.1093/aobpla/plw076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206332PMC
January 2017

Current and projected global distribution of Phytophthora cinnamomi, one of the world's worst plant pathogens.

Glob Chang Biol 2017 04 11;23(4):1661-1674. Epub 2016 Oct 11.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia.

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 was 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 using the large data set from south-west 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.
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http://dx.doi.org/10.1111/gcb.13492DOI Listing
April 2017

Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize.

Fungal Biol 2016 08 14;120(8):975-987. Epub 2016 May 14.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.

During a study on the phylogenetic relationships between species in the Phytophthora cryptogea complex and related species, Phytophthora erythroseptica and Phytophthora sansomeana, 19 hybrid isolates with multiple polymorphisms in the nuclear sequences were observed. Molecular characterization of hybrids was achieved by sequencing three nuclear (internal transcribed spacers, β-tubulin (TUB), heat shock protein 90) and two mitochondrial (cytochrome c oxidase subunit I (coxI), NADH dehydrogenase subunit I (NADH)) gene regions and cloning of the single-copy nuclear gene, TUB. Based on the molecular studies the hybrid isolates belonged to six distinct groups between P. cryptogea, P. erythroseptica, Phytophthora pseudocryptogea, P. sansomeana, and Phytophthora sp. kelmania. In all cases, only a single coxI and NADH allele was detected and nuclear genes were biparentally inherited, suggesting that the hybrids arose from sexual recombination events. Colony morphology, growth rate, cardinal temperatures, breeding system, and morphology of sporangia, oogonia, oospores, and antheridia were also determined. Some morphological differences between the hybrids and the parental species were noted; however, they were not sufficient to reliably distinguish the taxa and DNA markers from nuclear and mitochondrial genes will to be necessary for their identification. The parental species are all important pathogens of agricultural fields that have been transported globally. With the apparent ease of hybridization within this group there is ample opportunity for virulent hybrids to form, perhaps with extended host ranges.
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http://dx.doi.org/10.1016/j.funbio.2016.05.002DOI Listing
August 2016

An overview of Australia's Phytophthora species assemblage in natural ecosystems recovered from a survey in Victoria.

IMA Fungus 2016 Jun 2;7(1):47-58. Epub 2016 Mar 2.

Centre for Phytophthora Science & Management, School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia;

Although Phytophthora species cause serious diseases worldwide, until recently the main focus on disease in natural ecosystems in southern Australia has been on the distribution and impact of P. cinnamomi. However, new Phytophthora pathogens have emerged from natural ecosystems, and there is a need to better understand the diversity and distribution of these species in our natural forests, woodlands and heathlands. From a survey along a 70 km pipeline easement in Victoria, Phytophthora species were isolated from 249 rhizosphere samples and 25 bait bags deployed in 21 stream, river, or wetland locations. Of the 186 Phytophthora isolates recovered, 130 were identified to species based on ITS sequence data. Ninety-five isolates corresponded to 13 described Phytophthora species while additionally 35 isolates were identified as Clade 6 hybrids. Phytophthora cinnamomi was the most common species isolated (31 %), followed by P. elongata (6 %), both species were only recovered from soil. Samples from sites with the highest soil moisture at the time of sampling had the highest yield of isolates. Consistent with other studies throughout the world, Clade 6 species and their hybrids dominated water samples, although many of these species were also recovered less frequently from soil samples. Many of the species recovered in this study have not previously been reported from eastern Australia, reinforcing that Phytophthora species are widespread, abundant and diverse in natural ecosystems. We have probably been underestimating Phytophthora diversity in Australia.
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http://dx.doi.org/10.5598/imafungus.2016.07.01.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941687PMC
June 2016

Phytophthora boodjera sp. nov., a damping-off pathogen in production nurseries and from urban and natural landscapes, with an update on the status of P. alticola.

IMA Fungus 2015 Dec 6;6(2):319-35. Epub 2015 Oct 6.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia;

A new homothallic Phytophthora species, isolated in Western Australia (WA), is described as Phytophthora boodjera sp. nov. It produces persistent, papillate sporangia, oogonia with thick-walled oospores, and paragynous antheridia. Although morphologically similar to P. arenaria, phylogenetic analyses of the ITS, cox1, HSP90, β-tubulin and enolase gene regions revealed P. boodjera as a new species. In addition, P. boodjera has a higher optimal temperature for growth and a faster growth rate. Phytophthora boodjera has only recently been found in Western Australia and has mostly been isolated from dead and dying Eucalyptus seedlings in nurseries and from urban tree plantings, and occasionally from disturbed natural ecosystems. It is found in association with declining and dying Agonis flexuosa, Banksia media, B. grandis, Corymbia calophylla, Eucalyptus spp,. and Xanthorrhoea preissii. The status of P. alticola was also reviewed. The loss of all isolates associated with the original description except one; discrepancies in both sequence data and morphology of the remaining isolate with that presented the original description, and inconclusive holotype material places the status of this species in doubt.
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http://dx.doi.org/10.5598/imafungus.2015.06.02.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681256PMC
December 2015

Multiple introductions from multiple sources: invasion patterns for an important Eucalyptus leaf pathogen.

Ecol Evol 2015 Sep 4;5(18):4210-20. Epub 2015 Sep 4.

Department of Genetics Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa ; School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia.

Many population studies on invasive plant pathogens are undertaken without knowing the center of origin of the pathogen. Most leaf pathogens of Eucalyptus originate in Australia and consequently with indigenous populations available, and it is possible to study the pathways of invasion. Teratosphaeria suttonii is a commonly occurring leaf pathogen of Eucalyptus species, naturally distributed in tropical and subtropical regions of eastern Australia where it is regarded as a minor pathogen infecting older leaves; however, repeated infections, especially in exotic plantations, can result in severe defoliation and tree deaths. Nine polymorphic microsatellite markers were used to assess the genetic structure of 11 populations of T. suttonii of which four where from within its native range in eastern Australia and the remaining seven from exotic Eucalyptus plantations. Indigenous populations exhibited high allele and haplotype diversity, predominantly clonal reproduction, high population differentiation, and low gene flow. The diversity of the invasive populations varied widely, but in general, the younger the plantation industry in a country or region, the lower the diversity of T. suttonii. Historical gene flow was from Australia, and while self-recruitment was dominant in all populations, there was evidence for contemporary gene flow, with South Africa being the most common source and Uruguay the most common sink population. This points distinctly to human activities underlying long-distance spread of this pathogen, and it highlights lessons to be learned regarding quarantine.
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http://dx.doi.org/10.1002/ece3.1693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588637PMC
September 2015

Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species.

Authors:
Treena I Burgess

PLoS One 2015 6;10(8):e0134225. Epub 2015 Aug 6.

Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.

Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134225PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527719PMC
May 2016

Phosphorus limitation, soil-borne pathogens and the coexistence of plant species in hyperdiverse forests and shrublands.

New Phytol 2015 Apr 10;206(2):507-21. Epub 2014 Dec 10.

School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.

Hyperdiverse forests occur in the lowland tropics, whereas the most species-rich shrublands are found in regions such as south-western Australia (kwongan) and South Africa (fynbos). Despite large differences, these ecosystems share an important characteristic: their soils are strongly weathered and phosphorus (P) is a key growth-limiting nutrient. Soil-borne pathogens are increasingly being recognized as drivers of plant diversity in lowland tropical rainforests, but have received little attention in species-rich shrublands. We suggest a trade-off in which the species most proficient at acquiring P have ephemeral roots that are particularly susceptible to soil-borne pathogens. This could equalize out the differences in competitive ability among co-occurring species in these ecosystems, thus contributing to coexistence. Moreover, effective protection against soil-borne pathogens by ectomycorrhizal (ECM) fungi might explain the occurrence of monodominant stands of ECM trees and shrubs amongst otherwise species-rich communities. We identify gaps in our knowledge which need to be filled in order to evaluate a possible link between P limitation, fine root traits, soil-borne pathogens and local plant species diversity. Such a link may help to explain how numerous plant species can coexist in hyperdiverse rainforests and shrublands, and, conversely, how monodominant stands can develop in these ecosystems.
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http://dx.doi.org/10.1111/nph.13203DOI Listing
April 2015

Phytophthora niederhauserii sp. nov., a polyphagous species associated with ornamentals, fruit trees and native plants in 13 countries.

Mycologia 2014 May-Jun;106(3):431-47. Epub 2014 May 28.

Plant Protection Central Research Institute, Department of Phytopathology, Ankara, Turkey.

A non-papillate, heterothallic Phytophthora species first isolated in 2001 and subsequently from symptomatic roots, crowns and stems of 33 plant species in 25 unrelated botanical families from 13 countries is formally described here as a new species. Symptoms on various hosts included crown and stem rot, chlorosis, wilting, leaf blight, cankers and gumming. This species was isolated from Australia, Hungary, Israel, Italy, Japan, the Netherlands, Norway, South Africa, Spain, Taiwan, Turkey, the United Kingdom and United States in association with shrubs and herbaceous ornamentals grown mainly in greenhouses. The most prevalent hosts are English ivy (Hedera helix) and Cistus (Cistus salvifolius). The association of the species with acorn banksia (Banksia prionotes) plants in natural ecosystems in Australia, in affected vineyards (Vitis vinifera) in South Africa and almond (Prunus dulcis) trees in Spain and Turkey in addition to infection of shrubs and herbaceous ornamentals in a broad range of unrelated families are a sign of a wide ecological adaptation of the species and its potential threat to agricultural and natural ecosystems. The morphology of the persistent non-papillate ellipsoid sporangia, unique toruloid lobate hyphal swellings and amphigynous antheridia does not match any of the described species. Phylogenetic analysis based on sequences of the ITS rDNA, EF-1α, and β-tub supported that this organism is a hitherto unknown species. It is closely related to species in ITS clade 7b with the most closely related species being P. sojae. The name Phytophthora niederhauserii has been used in previous studies without the formal description of the holotype. This name is validated in this manuscript with the formal description of Phytophthora niederhauserii Z.G. Abad et J.A. Abad, sp. nov. The name is coined to honor Dr John S. Niederhauser, a notable plant pathologist and the 1990 World Food Prize laureate.
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http://dx.doi.org/10.3852/12-119DOI Listing
September 2014

Surveys of soil and water reveal a goldmine of Phytophthora diversity in South African natural ecosystems.

IMA Fungus 2013 Jul 10;4(1):123-31. Epub 2013 Jun 10.

Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa ; Current address: E-Planet Co. Ltd. 345-9 Gasandong Gumcheongu, 153-802, Seoul, Republic of Korea.

Phytophthora species are well-known as destructive plant pathogens, especially in natural ecosystems. It is ironic, therefore, how little is known regarding the Phytophthora diversity in South African natural woody ecosystems. In this study, Phytophthora species were isolated using standard baiting techniques from 182 soil and water samples and these were identified based on ITS and coxI sequence data. The 171 resulting Phytophthora isolates resided in 14 taxa including six known species (P. multivora, P. capensis, P. cryptogea, P. frigida, P. cinnamomi, P. cinnamomi var. parvispora), the known but as yet unnamed Phytophthora sp. PgChlamydo, P. sp. emzansi, and P. sp. Kununurra and five novel taxa referred to as P. sp. stellaris, P. sp. Umtamvuna P. sp. canthium, P. sp. xWS, P. sp. xHennops. Four of the new taxa were found exclusively in water and two of these are hybrids. The most commonly isolated species from soil was P. multivora, a species recently described from Western Australia. Phytophthora frigida was isolated for the first time from stream water. With the exception of P. cinnamomi, very little is known regarding the biology, epidemiology or origin of Phytophthora in South Africa.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719200PMC
July 2013

Luteocirrhus shearii gen. sp. nov. (Diaporthales, Cryphonectriaceae) pathogenic to Proteaceae in the South Western Australian Floristic Region.

IMA Fungus 2013 Jul 10;4(1):111-22. Epub 2013 Jun 10.

Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.

Morphological and DNA sequence characteristics of a pathogenic fungus isolated from branch cankers in Proteaceae of the South West Australian Floristic Region elucidated a new genus and species within Cryphonectriaceae (Diaporthales). The pathogen has been isolated from canker lesions in several Banksia species and Lambertia echinata subsp. citrina, and is associated with a serious decline of the rare B. verticillata. Lack of orange pigment in all observed structures except cirrhi, combined with pulvinate to globose black semi-immersed conidiomata with paraphyses, distinguishes the canker fungus from other genera of Cryphonectriaceae. This was confirmed by DNA sequence analysis of the ITS regions, β-tubulin, and LSU genes. The fungus (sexual morph unknown) is described as Luteocirrhus shearii gen. sp. nov. Lesions in seedlings of Banksia spp. following wound inoculation and subsequent recovery confirm Koch's postulates for pathogenicity. This pathogen of native Proteaceae is currently an emerging threat, particularly toward B. baxteri and B. verticillata.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719199PMC
July 2013

Characterization of Phytophthora hybrids from ITS clade 6 associated with riparian ecosystems in South Africa and Australia.

Fungal Biol 2013 May 29;117(5):329-47. Epub 2013 Mar 29.

Department of Genetics, Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa.

Surveys of Australian and South African rivers revealed numerous Phytophthora isolates residing in clade 6 of the genus, with internal transcribed spacer (ITS) gene regions that were either highly polymorphic or unsequenceable. These isolates were suspected to be hybrids. Three nuclear loci, the ITS region, two single copy loci (antisilencing factor (ASF) and G protein alpha subunit (GPA)), and one mitochondrial locus (cytochrome oxidase c subunit I (coxI)) were amplified and sequenced to test this hypothesis. Abundant recombination within the ITS region was observed. This, combined with phylogenetic comparisons of the other three loci, confirmed the presence of four different hybrid types involving the three described parent species Phytophthora amnicola, Phytophthora thermophila, and Phytophthora taxon PgChlamydo. In all cases, only a single coxI allele was detected, suggesting that hybrids arose from sexual recombination. All the hybrid isolates were sterile in culture and all their physiological traits tended to resemble those of the maternal parents. Nothing is known regarding their host range or pathogenicity. Nonetheless, as several isolates from Western Australia were obtained from the rhizosphere soil of dying plants, they should be regarded as potential threats to plant health. The frequent occurrence of the hybrids and their parent species in Australia strongly suggests an Australian origin and a subsequent introduction into South Africa.
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http://dx.doi.org/10.1016/j.funbio.2013.03.004DOI Listing
May 2013

Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

Mol Ecol Resour 2013 Mar 25;13(2):341-3. Epub 2013 Jan 25.

Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.

This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus argenteus, Pyura sp., Sylvia atricapilla, Teratosphaeria suttonii, Trialeurodes vaporariorum and Trypanosoma brucei. These loci were cross-tested on the following species: Dimorphandra coccicinea, Dimorphandra cuprea, Dimorphandra gardneriana, Dimorphandra jorgei, Dimorphandra macrostachya, Dimorphandra mollis, Dimorphandra parviflora and Dimorphandra pennigera.
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http://dx.doi.org/10.1111/1755-0998.12061DOI Listing
March 2013

Cryptic species, native populations and biological invasions by a eucalypt forest pathogen.

Mol Ecol 2012 Sep 10;21(18):4452-71. Epub 2012 Aug 10.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.

Human-associated introduction of pathogens and consequent invasions is very evident in areas where no related organisms existed before. In areas where related but distinct populations or closely related cryptic species already exist, the invasion process is much harder to unravel. In this study, the population structure of the Eucalyptus leaf pathogen Teratosphaeria nubilosa was studied within its native range in Australia, including both commercial plantations and native forests. A collection of 521 isolates from across its distribution was characterized using eight microsatellite loci, resulting in 112 multilocus haplotypes (MLHs). Multivariate and Bayesian analyses of the population conducted in structure revealed three genetically isolated groups (A, B and C), with no evidence for recombination or hybridization among groups, even when they co-occur in the same plantation. DNA sequence data of the ITS (n = 32), β-tubulin (n = 32) and 27 anonymous loci (n = 16) were consistent with microsatellite data in suggesting that T. nubilosa should be considered as a species complex. Patterns of genetic diversity provided evidence of biological invasions by the pathogen within Australia in the states of Western Australia and New South Wales and helped unravel the pattern of invasion beyond Australia into New Zealand, Brazil and Uruguay. No significant genetic differences in pathogen populations collected in native forests and commercial plantations were observed. This emphasizes the importance of sanitation in the acquisition of nursery stock for the establishment of commercial plantations.
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http://dx.doi.org/10.1111/j.1365-294X.2012.05714.xDOI Listing
September 2012

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum-Neofusicoccum ribis species complex.

Mol Phylogenet Evol 2011 Sep 7;60(3):333-44. Epub 2011 May 7.

Centre of Excellence in Climate Change, Woodland and Forest Health, School of Biological Sciences and Biotechnology, Murdoch University, Perth 6150, Australia.

Neofusicoccum is a recently described genus of common endophytes and pathogens of woody hosts, previously placed in the genus Botryosphaeria. Many morphological characteristics routinely used to describe species overlap in Neofusicoccum, and prior to the use of molecular phylogenetics, isolates from different hosts and locations were often misidentified. Two cryptic species Neofusicoccum ribis and Neofusicoccum parvum were initially described from different continents and recently another four species within this complex were described using fixed nucleotide polymorphisms for differentiation. In a survey of eucalypt cankers in eastern Australia, a collection of morphologically similar Neofusicoccum isolates were obtained. This collection was analysed within the framework of the morphological (MSRC), ecological (ESRC) and phylogenetic (PSRC) species recognition concepts. Morphological data based on spore measurements (MSRC), together with pathogenicity trials (ESRC) were considered alongside molecular analysis (PSRC), which included multiple gene phylogenies constructed from four nuclear gene regions. We also used the Genealogical Sorting Index method to provide objective evidence for the status of terminal taxa in the phylogenetic analysis. The isolates examined exhibited overlapping morphological and culture characteristics, similar pathogenicity to excised stems and shared hosts within the same locations. Phylogenetic analysis separated isolates into 8 clades corresponding to six described species: N. ribis, N. parvum, Neofusicoccum kwambonambiense, Neofusicoccum cordaticola, Neofusicoccum umdonicola, Neofusicoccum batangarum, and two new species. GSI support indicated combined phylogenetic data were monophyletic for all clades and all p-values were significant allowing us to reject the null hypothesis that all groups were from a single mixed group. Consequently the description of Neofusicoccum occulatum is presented.
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http://dx.doi.org/10.1016/j.ympev.2011.04.026DOI Listing
September 2011

Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010.

Mol Ecol Resour 2011 Mar 21;11(2):418-21. Epub 2011 Jan 21.

Department of Biology-University of Padova, via U. Bassi 58/b, Padua, Italy.

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.
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http://dx.doi.org/10.1111/j.1755-0998.2010.02970.xDOI Listing
March 2011

Re-evaluation of Phytophthora Species Isolated During 30 Years of Vegetation Health Surveys in Western Australia Using Molecular Techniques.

Plant Dis 2009 Mar;93(3):215-223

Department of Environment and Conservation, Science Division, Locked Bag 104, Bentley D.C., WA 6983, Australia.

For 30 years, large-scale aerial photography has been used to map the extent of Phytophthora dieback disease in native forests in the southwest of Western Australia, with validation of the observations involving routine testing of soil and root samples for the presence of Phytophthora cinnamomi. In addition to P. cinnamomi, six morpho-species have been identified using this technique: P. citricola, P. megasperma, P. cryptogea, P. drechsleri, P. nicotianae, and P. boehmeriae. In recent years, many new Phytophthora species have been described worldwide, often with similar morphology to existing species; thus, as many of the isolates collected in Western Australia have been difficult to identify based on morphology, molecular identification of the morpho-species is required. Based on amplification of the internal transcribed spacer (ITS) region of the rDNA gene, sequence data of more than 230 isolates were compared with those of existing species and undescribed taxa. P. inundata, P. asparagi, P. taxon PgChlamydo, P. taxon personii, and P. taxon niederhauserii were identified based on sequence data. Phylogenetic analysis revealed that nine potentially new and undescribed taxa can be distinguished. Several of the new taxa are morphologically indistinguishable from species such as P. citricola, P. drechsleri, and P. megasperma. In some cases, the new taxa are closely related to species with similar morphology (e.g., P.sp.4 and P. citricola). However, the DNA sequences of other new taxa such as P.sp.3 and P.sp.9 show that they are not closely related to morphologically similar species P. drechsleri and P. megasperma, respectively. Most of the new taxa have been associated with dying Banksia spp., while P.sp.2 and P.sp.4 have also been isolated from dying Eucalyptus marginata (jarrah). Some taxa (P.sp.3, 6, and 7) appear to have limited distribution, while others like P.sp.4 are widespread.
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http://dx.doi.org/10.1094/PDIS-93-3-0215DOI Listing
March 2009

Seven new species of the Botryosphaeriaceae from baobab and other native trees in Western Australia.

Mycologia 2008 Nov-Dec;100(6):851-66

Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, 0002, South Africa.

In this study seven new species of the Botryosphaeriaceae are described from baobab (Adansonia gibbosa) and surrounding endemic tree species growing in the Kimberley region of northwestern Australia. Members of the Botryosphaeriaceae were predominantly endophytes isolated from apparently healthy sapwood and bark of endemic trees; others were isolated from dying branches. Phylogenetic analyses of ITS and EF1-alpha sequence data revealed seven new species: Dothiorella longicollis, Fusicoccum ramosum, Lasiodiplodia margaritacea, Neoscytalidium novaehollandiae, Pseudofusicoccum adansoniae, P. ardesiacum and P. kimberleyense.
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http://dx.doi.org/10.3852/08-020DOI Listing
April 2009

Botryosphaeriaceae from tuart (Eucalyptus gomphocephala) woodland, including descriptions of four new species.

Mycol Res 2009 Mar 6;113(Pt 3):337-53. Epub 2008 Dec 6.

Faculty of Sustainability, Environmental and Life Sciences, Murdoch University, Murdoch 6150, WA, Australia.

Eucalyptus gomphocephala (tuart) is a tree native to the southwest coast of Western Australia, where, in some areas, there is a significant decline in the health of tuart. Botryosphaeriaceous taxa have been isolated as endophytes and canker pathogens from numerous hosts in many parts of the world and have been implicated in the decline of E. gomphocephala. In the present study, endophytic fungi were isolated from a wide variety of native woody plant species (Acacia cochlearis, A. rostellifera, Allocasuarina fraseriana, Agonis flexuosa, Banksia grandis, E. gomphocephala, E. marginata and Santalum acuminatum), at two locations in native E. gomphocephala woodland; a site in decline at Yalgorup National Park and a healthy site at Woodman Point Regional Park. Of the 226 isolates obtained, 154 were botryosphaeriaceous taxa, 80% of which were found to be Neofusicoccum australe, isolated from all hosts at both collection sites. Four new species are described, Dothiorella moneti, Dothiorella santali, Neofusicoccum pennatisporum, and a species belonging to a genus only recently included in the Botryosphaeriaceae, Aplosporella yalgorensis. The other species isolated were Botryosphaeria dothidea on the new hosts A. rostellifera, A. cochlearis and E. marginata and Dichomera eucalypti, on the new host E. marginata. None of the new species formed lesions on excised stems of their host species, E. gomphocephala, or a common plantation species, E. globulus. However, Neofusicoccum australe formed lesions on excised stems of E. globulus and E. gomphocephala.
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http://dx.doi.org/10.1016/j.mycres.2008.11.010DOI Listing
March 2009