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International audience; Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

Chilli (Capsicum annuum L.) is one of the most important crops in Bhutan, but currently production is seriously affected by a wilt disease. Although chilli wilt was first reported in Bhutan in 1995, the causal pathogen has never been formally identified. The aim of this study was to identify the causative agent of wilt epidemics on chilli in Bhutan and to investigate the morphological and genetic variations in the pathogen. A survey of the disease was conducted in all three chilli growing regions of Bhutan in 2018 and the pathogen isolated from 54 diseased plants. Morphological and PCR evidence identified the pathogen as Phytophthora capsici in 100% of the diseased plants. All isolates were of the A1 mating type. Four random amplified micro-satellite (RAMS) markers were employed to assess genetic variation among the 54 isolates of P. capsici collected. Genetic analysis showed 26 loci from all four primers and 65.4% of the isolates were polymorphic. Shannon’s index of diversity (I) for the P. capsici isolates collected was 0.42, indicating that the pathogen population is highly clonal. These findings have significant implications for the development of sustainable disease management strategies including resistant genotypes in Bhutan.

Fusarium solani f. sp. cucurbitae (syn. Neocosmosporum cucurbitae) is one of the most devastating soilborne pathogens affecting the production of cucurbits worldwide. Since its first detection in Almería Province in Spain in the spring of 2007, it has become one of the main soilborne pathogens affecting zucchini production. It has also been reported on melon, watermelon, and squash rootstocks in Spain, representing a high risk of dissemination in the area. The objectives of this study were to investigate the incidence and distribution of this disease in southeastern Spain and characterize isolates collected over 5 years. These strains were characterized on the basis of greenhouse aggressiveness assays on a range of cucurbit hosts, morphological characteristics, and elongation factor 1-α and RNA polymerase II second largest subunit phylogenies. All pathogenic isolates were highly aggressive on zucchini plants, causing a high mortality rate a few weeks after inoculation. The rest of the cucurbit hosts showed differential susceptibility to the pathogen, with cucumber being the least susceptible. Plants belonging to other families remained asymptomatic. Morphological characterization revealed the formation of verticilate monophialides and chlamydospores forming long chains, characteristics not described for this forma specialis. Phylogenetic studies of both the individual loci and combined datasets revealed that all pathogenic isolates clustered together with strong monophyletic support, nested within clade 3 in the F. solani species complex.

Phytophthora root rot is one of the most devastating diseases of perennial plants worldwide, affecting plants in food production, amenity plantings and in natural ecosystems. The impact of these diseases in botanic gardens can be substantial and can affect how a site may be used for months and years ahead. Management is critically dependent on avoidance of the introduction of the pathogen and effective hygiene protocols are key to achieving this. Additionally, botanic gardens have a key role to play in protecting plants and enhancing conservation outcomes through surveillance, education and ex situ conservation programmes, as well as through the recognition that they can be critical as sentinel sites to detect new incursions of pests anddiseases. The impact of several Phytophthora species on the in situ and ex situ management of the critically endangered Wollemia nobilis (Wollemi pine), which is highly susceptible to phytophthora root rot, is used to highlight the need to ensure management of these pathogens is a critical component of threatened species recovery and management.

Pepper blight caused by Phytophthora capsici Leonian is one of the most economically important plant diseases worldwide. In East Asia, pepper blight is a serious disease that is capable of decimating entire chili crops resulting in high economic losses. Management strategies undertaken to control the disease include the use of chemical and biological agents alongside soil fumigation and improved cultural practices. In recent years, biological agents are considered to be preferable to the use of chemicals due to the lower risk of resistance evolution and harm to the environment. Using meta-analysis, we synthesised the literature on the efficacy of different types of controls on pepper blight in East Asia. The studies were almost all conducted in Korea and China. We found that phenylamides (FRAC group 4), Xenorhabdus sp., Pseudomonas sp., and plant extracts were generally more effective against the pathogen in pepper; while soil amendments, Bacillus sp., Chryseobacterium sp., unidentified antagonists, and carboxylic acid amides (FRAC group 11) tend to be less effective. Overall, chemical agents were 50% more effective than biological agents. However, the benefits of using biological agents may outweigh the reduction in efficacy, particularly if used as a part of mixed treatments. Interestingly, control agents were 58% more effective on the disease in Korea compared to China, highlighting potential differences among pathogen genotypes or the resistance of cultivars to disease. Avenues for future research on biological forms of control and novel control strategies for plant pathogens are discussed.

Diseases in natural and agricultural systems have been linked to species of the Oomycete genus Phytophthora, around the world. Direct detection of the pathogen requires sampling of soil or plant material, which can be expensive, difficult to obtain and error-prone. As an alternative, reflectance spectroscopy provides a potential indirect method for detecting symptoms of infection by P. cinnamomi. Here we evaluate the use of reflectance spectroscopy to detect physiological changes associated with infection in host plants using spectral indices designed to quantify changes in plant pigments (pigment indices), leaf water content (water indices) and fluorescence (fluorescence indices). Two grasses and two tree species with different susceptibilities to P. cinnamomi were inoculated and/or exposed to water stress in a glasshouse experiment. Inoculated plants were detected using pigment and fluorescence indices, which also had the capacity to separate inoculated plants from water stressed uninoculated plants. While inoculation may have caused an opposing spectral response to water stress in some indices, plants that were both water stressed and inoculated then demonstrated an intermediate response. Water stress was detected using the water indices in all four species, and spectroscopic changes associated with inoculation were often greater in the susceptible species. Our results indicate that reflectance spectroscopy at the leaf scale detects the effects of P. cinnamomi infection in native vegetation. Extending these results has the potential to improve early detection of disease in natural vegetation and avoiding manual sampling, thus improving management of the disease.

Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi. P. cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a phylogeographic analysis of populations of this pathogen sampled in Asia, Australia, Europe, southern and northern Africa, South America, and North America. Based on genotyping-by-sequencing, we observed the highest genotypic diversity in Taiwan and Vietnam, followed by Australia and South Africa. Mating type ratios were in equal proportions in Asia as expected for a sexual population. Simulations based on the index of association suggest a partially sexual, semi-clonal mode of reproduction for the Taiwanese and Vietnamese populations while populations outside of Asia are clonal. Ancestral area reconstruction provides new evidence supporting Taiwan as the ancestral area, given our sample, indicating that this region might be near or at the centre of origin for this pathogen as speculated previously. The Australian and South African populations appear to be a secondary centre of diversity following migration from Taiwan or Vietnam. Our work also identified two panglobal, clonal lineages PcG1-A2 and PcG2-A2 of A2 mating type found on all continents. Further surveys of natural forests across Southeast Asia are needed to definitively locate the actual centre of origin of this important plant pathogen. Agricultural Research Service, Grant/Award Number: 2072-22000-041-00-D; National Institute of Food and Agriculture, Grant/Award Number: 2011-68004-30154 and 2018-67013-27823 info:eu-repo/semantics/publishedVersion

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the

Phytophthora species are associated with disease in horticulture, agriculture and natural vegetation worldwide but are not well known in cold areas. In Australia, alpine regions have been regarded as unsuitable for the survival and disease expression of Phytophthora cinnamomi, which has caused catastrophic damage to vegetation in other parts of the country. Phytophthora cambivora, on the other hand, has been detected recently in the roots of an endemic alpine shrub (Nematolepis ovatifolia) and may already be exerting pressure on alpine vegetation. We conducted glasshouse susceptibility trials on nine Australian alpine and subalpine shrub species to P. cambivora and P. cinnamomi. The pathogens were re-isolated from the roots of most test species but for some species, few replicates were infected and few died. One species (Phebalium squamulosum) was regarded as highly susceptible with most plants in inoculated pots dying and both pathogens being commonly isolated from roots. The climatic conditions of most populations of the test species are currently unsuitable for disease expression from P. cinnamomi. However, the projected change in temperature in the Australian Alps with climate change will expose most populations of eight of the species to P. cinnamomi activity by 2070. Pathogens are likely to be important drivers of future vegetation in many mountainous areas which are currently not within their range of survival and pathogenesis. Management of these areas should include hygiene and pathogen monitoring, and minimise disturbances that heighten stress for susceptible species.

Mango malformation (MMD) is an economically significant disease of mango growing regions and a notifiable disease in Australia. Following an incursion of the disease in the Northern Territory (NT) in 2007, numerous Fusarium species were isolated from mango samples during surveillance activities in growing regions within the country between 2007 and 2013, including reported MMD pathogens (Fusarium mangiferae, F. proliferatum and F. pseudocircinatum), established pathogens of other hosts (e.g. F. fujikuroi, F. oxysporum, F. parvisorum, F. solani and F. verticillioides) and several undescribed species. In this paper we review the status of all species of Fusarium isolated from mango tissue associated with putative malformation symptoms in Australia since 2007, documenting location origins and diagnostic methods and re-assessing their identification based on phylogenetic analysis of available DNA sequences. Their taxonomic affiliations and pathogenicity in particular are discussed with implications for disease management including quarantine, while knowledge gaps are highlighted.

In Papua New Guinea (PNG) cocoa (Theobroma cacao) is one of the most important cash crops grown in the tropical lowland and island regions. As in most cocoa-growing areas, phytophthora black pod and canker cause significant yield losses. Cocoa breeding activities in PNG are focused in East New Britain province where disease control recommendations are also developed. This study tested the hypothesis that there was no diversity in the Phytophthora palmivora population causing black pod on cocoa by characterizing the variation in pathogen populations within and between the five major cocoa-growing areas. Diseased pods were sampled hierarchically from the five locations and additional isolates were collected from soil, stem and leaf lesions, or retrieved from culture collections. Morphological characters showed continuous variation within the range described for P. palmivora. Genetic analysis revealed that the isolates belonged to one dominant clonal lineage, with restricted distributions of several other subpopulations. Lowest diversities were found in the geographically isolated Karkar Island and East Sepik province. Soil isolates showed greater genetic diversity than isolates from cocoa lesions. Intra-farm variation was as much as inter-farm or inter-province variation. Both mating types were detected, although no strong evidence of sexual recombination was observed. The analysis revealed limited geographic, temporal or host specialization, suggesting continuous selection for pathogenicity from a genetic pool of P. palmivora. These findings have significant implications on the deployment of cocoa genotypes, enforcement of inter-province quarantine and sustainable disease management strategies.

The Fusarium oxysporum species complex (FOSC) causes disease in plants and animals, but is also widely dispersed in natural ecosystems without evidence of disease. The present study screened a population representing natural ecosystems across the Australian continent for the putative effector genes pisatin demethylase 1 (PDA1), pectate lyase (pelD), secreted gene expression (SGE1) and secreted in xylem (SIX). The genes pelD and SGE1 were prevalent in the natural isolates, PDA1 was present at an intermediate level, whereas SIX genes were detected at low levels. Phylogenies of these putative effector genes were compared to the EF-1α species phylogeny to determine the likely modes of gene transmission: vertical gene transfer (VGT) and horizontal gene transfer (HGT). There was evidence of both modes of gene transmission within the F. oxysporum isolates. PDA1, pelD and SGE1 were likely to be only vertically inherited, whereas the SIX genes had evidence for both VGT and HGT. The phylogenetic relationships of SIX genes in isolates from natural ecosystems and formae speciales from agro-ecosystems were also established. These findings have important implications for the evolution of effectors in the FOSC.

Fusarium goolgardi, isolated from the grass tree Xanthorrhoea glauca in natural ecosystems of Australia, is closely related to fusaria that produce a subgroup of trichothecene (type A) mycotoxins that lack a carbonyl group at carbon atom 8 (C-8). Mass spectrometric analysis revealed that F. goolgardi isolates produce type A trichothecenes, but exhibited one of two chemotypes. Some isolates (50%) produced multiple type A trichothecenes, including 4,15-diacetoxyscirpenol (DAS), neosolaniol (NEO), 8-acetylneosolaniol (Ac-NEO) and T-2 toxin (DAS-NEO-T2 chemotype). Other isolates (50%) produced only DAS (DAS chemotype). In the phylogenies inferred from DNA sequences of genes encoding the RNA polymerase II largest (RPB1) and second largest (RPB2) subunits as well as the trichothecene biosynthetic genes (TRI), F. goolgardi isolates were resolved as a monophyletic clade, distinct from other type A trichothecene-producing species. However, the relationships of F. goolgardi to the other species varied depending on whether phylogenies were inferred from RPB1 and RPB2, the 12-gene TRI cluster, the two-gene TRI1-TRI16 locus, or the single-gene TRI101 locus. Phylogenies based on different TRI loci resolved isolates with different chemotypes into distinct clades, even though only the TRI1-TRI16 locus is responsible for structural variation at C-8. Sequence analysis indicated that TRI1 and TRI16 are functional in F. goolgardi isolates with the DAS-NEO-T2 chemotype, but non-functional in isolates with DAS chemotype due to the presence of premature stop codons caused by a point mutation.

Six new species of Fusarium associated with soil and plant hosts from ecosystems of minimal anthropogenic disturbance in Australia are described. Fusarium coicis from Coix gasteenii, F. goolgardi from Xanthorrhoea glauca, F. mundagurra from soil and Mangifera indica, F. newnesense from soil, F. tjaetaba from Sorghum interjectum and F. tjaynera from soil, Triodia microstachya, Sorghum interjectum and Sorghum intrans. Morphology and phylogenetic analysis of EF-1α, RPB1 and RPB2 sequence data were used to delineate species boundaries. The new species were phylogenetically dis- tributed in the Fusarium sambucinum, F. fujikuroi ,a nd F. chlamydosporum species complexes, and two novel species complexes. These six new species have particular phylogeo- graphic significance as not only do they provide further insight into the geographic patterns of Fusarium evolution but also challenge current phylogeographic hypotheses.

Vanilla stem rot, caused by Fusarium oxysporum f. sp. vanillae (Fov), is the main constraint to increasing vanilla production in the major vanilla-producing countries, including Indonesia. The current study investigated the origin of Fov in Indonesia using a multigene phylogenetic approach. Nineteen Fov isolates were selected to represent Indonesia, the Comoros, Mexico and Reunion Island. The translation elongation factor 1 alpha gene and the mitochondrial small subunit ribosomal RNA gene phylogenies resolved the Fov isolates into three distinct clades in both phylogenetic species of the F. oxysporum species complex, indicating a polyphyletic pattern of evolution. In addition, Fov isolates from Indonesia were also polyphyletic. These results suggest that the vanilla stem rot pathogen in Indonesia has a complex origin. The implications for disease management are discussed.

Fusarium wilt is a serious disease of the date palm Phoenix canariensis, caused by Fusarium oxysporum f. sp. canariensis (Foc). A previous study that characterized and compared the genetic diversity of the Australian Foc population with international strains suggested that the Australian population may have had an independent evolutionary origin. The current study compared the species phylogeny of the Australian and international populations and determined that Foc is not monophyletic, separating into three supported lineages across the two phylogenetic species of the Fusarium oxysporum species complex. This confirms an independent evolutionary origin for Foc in Australia. However, phylogenetic analysis of the putative pathogenicity genes Secreted In Xylem (SIX) did not reveal any separation of the Australian and international Foc strains. Furthermore, there was very low SIX sequence diversity within Foc. Horizontal gene transfer is argued to be the most parsimonious explanation for the incongruence between the species and SIX gene phylogenies.

Phytophthora multivora, a recently described species recovered from declining natural ecosystems in Western Australia, was detected in the natural site of the rare and endangered Wollemi pine in New South Wales. The Phytophthora species was identified based on morphology and sequence analysis of the rDNA ITS and mitochondrial DNA cox1 regions. A pathogenicity trial to test the susceptibility of Wollemi pine to P. multivora resulted in symptoms equal in extent to those caused by P. cinnamomi, a known pathogen of Wollemi pine. Post-trial dry root weight analysis of P. multivora and P. cinnamomi inoculated plants revealed no significant difference between species, as both significantly reduced root mass compared to uninoculated plants. P. multivora was shown to be a pathogen of the Wollemi pine, and the implications on protecting this endangered species in the wild are discussed.

Collar rot associated with the pathogen Phytophthora gregata T. Jung, M.J.C.Stukely & T.Burgess was recently observed on a subalpine wetland shrub, Pimelea bracteata Threlfall, in Kosciuszko National Park, New South Wales. The symptomatic collars of infected plants in the field may mean that P. gregata infects via the collar rather than through roots, as many other Phytophthora species do. In the glasshouse, we tested the susceptibility of seven threatened wetland species to P. gregata. Flooding and stem wound inoculations were applied as treatments. Based on symptoms and reisolations, we found that Boronia deanei ssp. acutifolia Duretto, Correa baeuerlenii F.Muell, Pultenaea parrisiae J.D.Briggs & Crisp and Pimelea bracteata were susceptible to P. gregata. These species were infected following both flood and stem inoculation, and all but C. baeuerlenii displayed very poor health under both treatments; stem wound inoculated C. baeuerlenii plants tended to be less affected than root inoculated plants. The pathogen could not be reisolated from the roots and collars of inoculated plants of Callistemon purpurascens S.M.Douglas & S.David, Grevillea acanthifolia ssp. paludosa Makinson & Albr., and Pultenaea aristata Sieber ex DC. This is the first test of the susceptibility of eastern Australian native plants to P. gregata and the first to investigate the aetiology of the disease caused by this emerging threat. Given the growing body of evidence of the effects of a range of Phytophthora species on native plants, we suggest that the Key Threatening Process listing be broadened to include all destructive Phytophthora species.

Fusarium solani is responsible for leaf yellowing and root and collar rot across a broad range of orchid species. The forma specialis, ‘phalaenopsis’, of Fusarium solani has recently been described using molecular methods as being the causal organism of disease in Phalaenopsis and Cymbidium orchids, and is the predominant pathogen of Taiwanese glasshouse-grown Phalaenopsis orchids. A study in 1996 reported F. solani as the causal agent of root necrosis of Cymbidium in NSW, Australia, but the study did not use molecular methods and predated the forma specialis ‘phalaenopsis’ designation. By comparing the phylogeny of the Australian isolates of F. solani from glasshouse-grown orchids with isolates of F. solani f.sp. phalaenopsis from Taiwan, the current study showed that the Australian and Taiwanese isolates were identical on the basis of the internal transcribed spacer (ITS) and β-tubulin (benA) regions and resulted in the first identification of F. solani f.sp. phalaenopsis in Australia.

Fusarium oxysporum f.sp. niveum is reported for the first time in the Lao PDR. It was isolated from watermelons (Citrullus lanatus) in Songkhon district, Savannahkhet province following a limited ad hoc survey during January and February of 2015. Infected plants showed symptoms of wilt, vascular discolouration, necrosis in the collar region, lower stem base and upper taproot regions, and whole plant death. Identification of the pathogen was confirmed through phylogenetic analysis of the EF1-α locus and a pathogenicity test satisfying Koch’s postulates.

Chestnut rot of Castanea sativa (European chestnut) and C. crenata (Japanese chestnut) × C. sativa hybrids is a significant problem facing the Australian chestnut industry. It affects the chestnut kernel, symptoms occur as pale, medium and dark brown lesions occurring on the endosperm and embryo. Twenty-two orchards in Victoria and New South Wales were surveyed in 2008, and 21 of these were again surveyed in 2009. All 22 orchards were affected by chestnut rot. Incidence at individual orchards up to 72 % was found in 2008, and 35 % in 2009. Incidence varied widely between orchards and within individual orchards between the 2 years. All varieties were affected, including Decoppi Marone, Purton’s Pride and Red Spanish, displaying examples of both high incidence (>1 %) and industry acceptable incidence (0–1 %) depending on orchard and year. In 2008 and 2009, surveys of Sydney Markets showed incidence of >1 % (2008: varieties Decoppi Marone, Purton’s Pride; and in 2009: varieties Purton’s Pride, Red Spanish). The early December flowering Red Spanish had significantly higher average incidence than the early to mid December flowering Decoppi Marone and Purton’s Pride, suggesting that the timing of flowering may be an important factor affecting incidence. There was a mild positive correlation between orchard incidence and December rainfall of the previous year (r2 = 0.4), indicating rainfall during the chestnut flowering period had a mild effect on incidence.

Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Phytophthora capsici is an economically significant pathogen of various important annual and perennial crops in temperate and tropical regions. Not much is known about the genetic diversity of this pathogen worldwide. In Vietnam it is the causal agent of devastating diseases on several hosts, including chilli and black pepper. Crossinfectivity of P. capsici isolates obtained from the two hosts was demonstrated. Analysis of forty-six P. capsici isolates based on Random Amplified Microsatellites (RAMS) and Repetitive Extragenic Palindromic (REP) fingerprinting revealed that isolates from black pepper were genetically distinct from isolates recovered from chilli. Twenty-two isolates from chilli clustered into two clonal groups at a DICE similarity level of >85%, whereas twenty-four isolates from black pepper were separated from these chilli isolates at a similarity level of

Phytophthora foot rot of black pepper caused by Phytophthora capsici is a major disease of black pepper throughout production areas in Vietnam. The disease causes collar, foot and tap root rots and eventual death of the infected vine. Potassium phosphonate was evaluated for the control of this disease in greenhouse and field trials. In greenhouse trials three-month-old vines treated with phosphonate by soil drenching (10–20 g a.i./l) and then inoculated with P. capsici mycelium (2% v/v soil) had significantly less foot rot compared to vines grown in non-treated soil. In field trials mature vines were treated with phosphonate at 50–100 g a.i/pole soil drenching or 10 g a.i./l by root infusion. After 10 days root, stem and leaf specimens were removed for bioassay by inoculation with 5 ml of P. capsici zoospores suspension (106–108 spores/ml). Soil drenching with phosphonate inhibited the colonisation of pathogen on excised leaf, stem and root tissues, significantly more than phosphonate root infusion. Our s...

A new species of Fusarium associated with Australian soils in non-cultivated ecosystems is described as Fusarium burgessii on the basis of morphological and phylogenetic data. Isolates recovered from biogeographical surveys over 26 years were selected for morphological examination. Two distinct morphotypes with morphological affinities to the Fusarium oxysporum, Fusarium redolens and Gibberella fujikuroi species complexes were observed. Phylogenetic resolution based on the translation elongation factor1α (EF-1α) and the second largest subunit of the RNA polymerase II gene (RPB2) separated the two morphotypes into novel phylogenetic Fusarium species, with one morphotype being assigned the species epithet Fusarium burgessii sp. nov. Phylogenetic analysis of the RPB2 locus with representatives of all the major Fusarium species complexes provides evidence that F. burgessii is part of a unique monophyletic lineage of species in the genus Fusarium.

In Australia disease caused by Phytophthora cinnamomi can have devastating impacts on native vegetation, especially on plant species with restricted distributions. The identification of susceptible threatened species is a crucial first step in understanding disease aetiology and selecting appropriate management. In a glasshouse trial, plants of 16 rare and threatened New South Wales native species from 10 families were inoculated with the pathogen. Phebalium squamulosum spp. alpinum was included as a susceptible control. We found that three species are highly susceptible to the pathogen (Nematolepis rhytidophylla (Albr. & N.G.Walsh) Paul G.Wilson, Prostanthera marifolia R.Br., Pultenaea sp. ‘Genowlan Point’); four others (Hibbertia spanantha Toelken & A.F.Rob, Phebalium bifidum P.H.Weston & M.J.Turton, Plinthanthesis rodwayi (C.E.Hubb.) S.T.Blake, Pomaderris delicata N.G.Walsh & Coates) are likely to be susceptible based on symptoms. The remaining species had few or no plant deaths and no pathogen recovery from the roots. All of the species regarded as highly susceptible are known from single populations. Following these results, subsequent research will assess the efficacy of prophylactic treatment on highly susceptible threatened species, and test whether glasshouse tests are indicative of field responses. Other threatened species will also be tested for susceptibility.

Fusarium species associated with plants as pathogens, saprobes and endophytes in Australia are listed with notes on their pathogenicity and toxicity provided. A list of Fusarium species not known to occur in Australia also is provided and their quarantine significance evaluated.

Fusarium is a large, complex genus that causes a wide variety of plant diseases, produces a number of mycotoxins and is becoming increasingly recognized as a significant human pathogen. These fungi occur in ecosystems in all parts of the globe, which makes them useful as a model to better understand biogeographic processes affecting the distribution of fungi. Here we review the information available on the biogeography of different species and clades of Fusarium and some of the likely processes affecting dispersal and speciation.

Internal rot of chestnuts is a significant problem facing the Australian chestnut industry. It affects the kernel, manifesting in light, medium and dark brown lesions occurring on the endosperm and embryo. Previous surveys at Melbourne Markets, Victoria, Australia have shown rot incidence up to 40%. Consumer rejection is likely with rot incidence this high. The pathogen responsible has previously been identified as the endophyte, Phomopsis castanea. Recent research has also shown that a significant source of infection occurs during the flowering period via ascospores released from burrs decaying on the orchard floor. Disease incidence has also been observed to be associated with rainfall during the flowering period. P. castanea was recently found to be only a minor pathogen of chestnuts, with Gnomonia pascoe in fact being the major internal rot pathogen. A field survey that was conducted in Victoria (VIC) and New South Wales (NSW) found field rot incidence was significantly different between regions, orchards and cultivars. A market survey in NSW found acceptable industry levels of rot. These field and market surveys, and identification of the chestnut rot pathogen will better inform the Australian and international chestnut industries of the scope of internal rot problem in south-eastern Australia, and provide a basis for improved management of chestnut orchards.

Two new species of Fusarium associated with Australian indigenous grasses in natural ecosystems are described as F. lyarnte and F. werrikimbe on the basis of morphology, DNA fingerprinting and phylogenetic analysis of EF-1α and β-tubulin sequence data. Isolates of these species were initially recovered from soil in the McGraths Creek area of central Australia and subsequently recovered from soil and stems of the indigenous grass Sorghum interjectum from Litchfield National Park in the Northern Territory, and from Sorghum leiocladum from Werrikimbe National Park in New South Wales. The common feature of both of these species is the production of large globose microconidia in false heads on polyphialides. Attempts to apply the biological species concept were unsuccessful.

Cultures morphologically similar to F. brevicatenulatum and F. pseudoanthophilum were recovered from millet collected in Kenya. Morphological characterisation showed that the production of pyriform microconidia and chlamydospores, key characters separating these species from each other and from other Fusarium species, was variable in these cultures. Sexual compatibility studies of these isolates and holotype cultures of F. brevicatenulatum and F. pseudoanthophilum revealed that they belonged to the same biological species. No fertile crosses were observed between putative isolates of F. brevicatenulatum from millet and tester strains of F. verticillioides, F. sacchari, F. proliferatum, F. subglutinans, F. thapsinum, and F. konzum. Neither were fertile crosses obtained from any self-cross tests, indicating that the cultures were heterothallic. Further studies using AFLP, and sequencing of the β-tubulin, calmodulin, and translation elongation factor 1-α genes revealed that the isolates from the millets and those of the ex-holotype cultures of F. brevicatenulatum and F. pseudoanthophilum belonged to the same species. The species epithet F. brevicatenulatum is preferred on the basis of priority.

International audience; Root and stem rot (RSR) is a very detrimental disease of vanilla worldwide. Fusarium oxysporum is frequently associated with the disease but other Fusarium species are also reported. In this international study, 52 vanilla plots were surveyed in three of the most important vanilla producing countries (Madagascar, Reunion Island and French Polynesia) in order to determine the aetiology of RSR disease. Subsets from the 377 single-spored Fusarium isolates recovered from rotten roots and stems in the surveys were characterized by molecular genotyping (EF1α and IGS gene sequences) and pathogenicity assays on Vanilla planifolia and V. ×tahitensis, the two commercially grown vanilla species. Fusarium oxysporum was shown to be the principal species responsible for the disease, representing 79% of the isolates recovered from the RSR tissues, 40% of which induced severe symptoms on inoculated plantlets. Fusarium oxysporum isolates were highly polyphyletic regardless of geographic origin or pathogenicity. Fusarium solani, found in 15% of the samples and inducing only mild symptoms on plantlets, was considered a secondary pathogen of vanilla. Three additional Fusarium species were occasionally isolated in the study (F. proliferatum, F. concentricum and F. mangiferae) but were nonpathogenic. Histopathological preparations observed in wide field and multiphoton microscopy showed that F. oxysporum penetrated the root hair region of roots, then invaded the cortical cells where it induced necrosis in both V. planifolia and V. ×tahitensis. The hyphae never invaded the root vascular system up to 9 days post-inoculation. As a whole, the data demonstrated that RSR of vanilla is present worldwide and that its causal agent should be named F. oxysporum f. sp. radicis-vanillae. (Résumé d'auteur)

The introduction and subsequent impact of Phytophthora cinnamomi within native vegetation is one of the major conservation issues for biodiversity in Australia. Recently, many new Phytophthora species have been described from Australia’s native ecosystems; however, their distribution, origin, and potential impact remain unknown. Historical bias in Phytophthora detection has been towards sites showing symptoms of disease, and traditional isolation methods show variable effectiveness of detecting different Phytophthora species. However, we now have at our disposal new techniques based on the sampling of environmental DNA and metabarcoding through the use of high-throughput sequencing. Here, we report on the diversity and distribution of Phytophthora in Australia using metabarcoding of 640 soil samples and we compare the diversity detected using this technique with that available in curated databases. Phytophthora was detected in 65% of sites, and phylogenetic analysis revealed 68 distinct Phytophthora phylotypes. Of these, 21 were identified as potentially unique taxa and 25 were new detections in natural areas and/or new introductions to Australia. There are 66 Phytophthora taxa listed in Australian databases, 43 of which were also detected in this metabarcoding study. This study revealed high Phytophthora richness within native vegetation and the additional records provide a valuable baseline resource for future studies. Many of the Phytophthora species now uncovered in Australia’s native ecosystems are newly described and until more is known we need to be cautious with regard to the spread and conservation management of these new species in Australia’s unique ecosystems.

Fusarium oxysporum is an important plant and human pathogenic ascomycetous group, with near ubiquity in agricultural and non-cultivated ecosystems. Phylogenetic evidence suggests that F. oxysporum is a complex of multiple morphologically cryptic species. Species boundaries and limits of genetic exchange within this complex are poorly defined, largely due to the absence of a sexual state and the paucity of morphological characters. This study determined species boundaries within the F. oxysporum species complex using Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with eight protein coding loci. GCPSR criteria were used firstly to identify independent evolutionary lineages (IEL), which were subsequently collapsed into phylogenetic species. Seventeen IELs were initially identified resulting in the recognition of two phylogenetic species. Further evidence supporting this delineation is discussed.

The Fusarium oxysporum species complex (FOSC) is a ubiquitous ascomycetous group that includes both pathogenic and non-pathogenic strains, the former being responsible for disease in over 100 cultivated plant species. Previous phylogenetic studies have uncovered at least four major clades within the FOSC, with Clade 1 hypothesised as being ancestral. However, the origin of these clades and pathogenic strains is poorly understood. Due to an emphasis on agricultural isolates in previous studies, the underlying diversity of this species complex in non-cultivated soils is largely unknown. To address this imbalance an extensive survey of isolates associated with native vegetation geographically isolated from cultivation throughout the Australian continent was conducted. A multi-gene phylogenetic analysis of the translation elongation factor (EF-1α) and the mitochondrial small subunit (mtSSU) rDNA loci did not recover any novel clades. However, the Australian isolates had high levels of intra-Clade diversity based on EF-1α sequence type (ST) comparison with a global dataset. The ST diversity was not equally distributed across the four clades, with the majority of novel STs recovered from Clade 1. Implications on the origin of the FOSC are discussed.

The monophyletic status of the genus Massarina was evaluated on the basis of phylogenetic analysis of the partial small subunit gene (SSU), internal transcribed spacers (ITS 12), and 5.8S gene sequences of the ribosomal DNA. Species of Massarina used in the study clustered into two distinct clades with high bootstrap support in trees generated from maximum parsimony, weighted parsimony, maximum likelihood, and neighbor-joining analyses. The hypothesis that Massarina species belong to a phylogenetically monophyletic group is rejected. Species with narrowly fusiform ascospores form a monophyletic clade with Lophiostoma, a genus highly similar in morphology. The five species currently accepted in Massarina with such spore morphology are here transferred into the genus Lophiostoma. Massarina species with broadly fusiform to ellipsoidal ascospores are retained as Massarina s. str., lectotypified by M. eburnea. Massarina walkeri is presently excluded from both Massarina and Lophiostoma. The transfer of M. papulosa to a new genus Oletheriostrigula is verified.

Crown rot, caused by the fungus Fusarium pseudograminearum (teleomorph Gibberella coronicola) is a major disease of wheat in the Australian grain belt. However, there is little information available on the population structure of this pathogen. We measured genetic diversity as assessed with amplified fragment length polymorphism (AFLP) analysis within and between populations of F. pseudograminearum from northeastern, south central, and southwestern regions of the Australian grain belt. Amongst the 217 isolates, 176 haplotypes were identified and grouped into two main clusters. One cluster contained isolates from populations in northeastern Australia, and the other cluster contained isolates from populations in south central and southwestern Australia. The southern populations were distinguished from the northeastern populations by higher levels of population differentiation (Gst) between them and genetic identity amongst the regional populations. We hypothesize that the F. pseudograminearum populations from northeastern and southern Australia are independent, which could result from different founding events or from geographic isolation and the accumulation of genetic differences due to genetic drift and/or selection.

Indonesia is one of the world’s leading producers of vanilla, an important cash crop for smallholders. Stem rot disease is a major constraint to vanilla production in Indonesia and has caused significant economic losses over the last decade. Previous reports of vanilla stem rots in the Asia-Pacific region include those caused by Fusarium, Colletotrichum and Phytophthora species. In this paper, we report Fusarium species associated with the disease. Seven major vanilla-producing provinces were surveyed for disease incidence and 850 samples were collected. Isolates were recovered from diseased stem tissues using a selective medium. Pure cultures on carnation leaf-piece agar and potato dextrose agar were identified based on morphological criteria. Some ambiguous species were verified based on DNA sequences of the translation elongation factor gene.Atotal of 542 Fusarium isolates were recovered, comprising 12 species, namely F. decemcellulare, F. fujikuroi, F. graminearum, F. mangiferae, F. napiforme, F. oxysporum, F. polyphialidicum, F. proliferatum, F. pseudocircinatum, F. semitectum, F. solani and F. subglutinans. F. oxysporum was the most commonly isolated species from all areas surveyed, followed by F. solani and F. semitectum. F. oxysporum, F. solani and F. semitectum were tested for pathogenicity to vanilla but only F. oxysporum was shown to be pathogenic. The vanilla stem rot pathogen in Indonesia is verified to be F. oxysporum f. sp. vanillae.

Black pepper is a high value export crop in Vietnam. The production of black pepper, however, is reduced remarkably by Phytophthora foot rot disease. Although the disease was first reported in 1952, the identity of the causal organism has never been conclusively determined. Hence, the aim of this study was to identify the causal agent associated with Phytophthora foot rot epidemics in black pepper. A national survey of the disease and collection of samples were conducted in four major black pepper growing provinces. Phytophthora isolates obtained from the diseased roots, collars and leaves as well as the root-zone soil were identified by morphological characteristics and verified by ITS-RFLP analysis. Phytophthora capsici was determined as the main pathogen causing Phytophthora foot rot of black pepper in Vietnam based on disease symptoms, morphological characteristics, pathogenicity and ITS-RFLP analysis.