Quambalaria spp. are fungal pathogens originating from Australian eucalypt species that are becoming increasingly important globally. For example, Quambalaria eucalypti, which was once considered a minor pathogen, now poses a significant threat to plantation productivity and forest health across continents. Their spread has been made possible through the expansion of eucalypt plantation forestry outside Australia, the movement of plant material and the increase in travel and trade, which facilitates the intercontinental movement of pathogens. This review summarises current knowledge regarding the taxonomy, distribution, life cycle and ecological and commercial impacts of Quambalaria spp. and some considerations for their control. Recent studies have discovered new species of Quambalaria and there is emerging evidence of host shifts to other genera in the Myrtaceae. Outbreaks in Brazil, China, Indonesia and South Africa illustrate the rapid spread of Quambalaria spp. to new plantation environments. These pathogens threaten eucalypt plantations worldwide because clonal propagation reduces tree diversity and the trade of plant material facilitates their spread. Evidence of sexual reproduction has been identified in one species, Quambalaria pitereka, alluding to a high evolutionary potential. Although new molecular diagnostics and resistance screening tools are emerging, their use in the control of these pathogens remains limited. Quambalaria spp. are important tree pathogens that are increasing their impact beyond their ancestral home in Australia. Their impact on plantation forestry and native forests underscores the broader vulnerabilities of forest ecosystems. Mitigating their impact will require integrated approaches that combine resistance breeding, enhanced surveillance, stringent quarantine measures, integrated disease management and changes to silviculture. Further research into host range, infection biology and pathogen evolution and the development of effective disease control is essential to safeguard global forests and ensure sustainable plantation forestry.

Lemon myrtle (Backhousia citriodora, F. Muell.) is a native Australian myrtaceous species, highly valued for its unique, citral-rich essential oil. The development and success of this Australian industry has been in jeopardy since the detection of myrtle rust (Austropuccinia psidii) in Australia (April 2010). Since the initial invasion, it has spread across the major lemon myrtle growing regions in New South Wales and Queensland. The main commercial clones are highly susceptible to infection, with plantations experiencing up to 70

Macadamia is an evergreen tree grown for its edible kernel in tropical and subtropical regions worldwide. The macadamia nursery industry is faced with graft dieback disease, resulting in the roguing of a large number of grafted plants. These losses are often attributed to Phomopsis graft dieback disease of the clonal root graft (scion) wood. However, the source of scions differs among nurseries, and the identity of the Diaporthe species is unknown. To determine whether the same Diaporthe species is responsible for macadamia graft dieback and whether the primary source of infection is from scion wood, we surveyed five major commercial macadamia nurseries in Australia. From 387 macadamia plants sampled in the nurseries, 86% (n = 337 isolates) of the scions were infected with Diaporthe species compared with 14% (n = 53 isolates) of the rootstock. Based on multigene DNA sequence analyses of internal transcribed spacer, translation elongation factor 1-alpha, β-tubulin, calmodulin, and histone H3, eight Diaporthe species were identified from symptomatic and asymptomatic plants, D. fraxini-angustifoliae was the most dominant species, followed by D. australiana, D. masirevicii, D. litchicola, D. middletonii, D. musigena, D. sojae, and D. arecae. In the in planta pathogenicity assays, D. litchicola was the most aggressive and caused significantly (P < 0.001) larger lesions and more graft dieback than D. australiana, whereas D. middletonii and D. masirevicii produced insignificant lesions and are therefore considered as nonpathogenic to macadamia. Scion wood inoculation with D. litchicola resulted in more significant Phomopsis graft dieback (45%) than rootstock inoculation (25%). Our findings suggest that scion wood is a potential source of infection and cause of Phomopsis graft dieback in macadamia nurseries.

Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Because, cladistically, this renders Phytophthora "paraphyletic," it has been proposed that Phytophthora evolutionary clades be split into multiple genera (Crous et al. 2021; Runge et al. 2011; Thines 2023, 2024). In this letter, we review arguments for the retention of the generic name Phytophthora with a broad circumscription made by Brasier et al. (2022) and by many delegates at an open workshop organized by The American Phytopathological Society. We present our well-considered responses to the genus splitting proposals, both in general terms and in terms of the specific proposals for new genera, alongside new information regarding the biological properties and mode of origin of the Phytophthora clades. We consider that the proposals are mostly non-rigorous and not supported by the scientific evidence. Further, given (i) the apparent lack of any distinguishing biological characteristics (synapomorphies) between the Phytophthora clades; (ii) the fundamental monophyly of Phytophthora in the original Haeckelian sense (Haeckel 1877); (iii) the fact that paraphyly is not a justification for taxonomic splitting; and (iv) the considerable likely damage to effective scientific communication and disease management from an unnecessary breakup of the genus, we report that workshop delegates voted unanimously in favor of preserving the current generic concept and for seeking endorsement of this view by a working group of the International Commission on the Taxonomy of Fungi. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Macadamia is an Australian native tree grown for its edible kernel in tropical and subtropical regions worldwide. However, there is limited knowledge about the fungal leaf pathogens that can infect macadamia nursery plants and potentially reduce productivity. To address this gap, we surveyed major commercial nurseries in Australia to identify leaf diseases affecting macadamia plants in different growing seasons. We identified four main leaf diseases: yellow halo leaf blight, brown leaf blight, anthracnose, and black leaf blight, each caused by multiple fungal species. Leaf anthracnose was the most prevalent disease observed in all the nurseries across the four seasons. From mature leaves with anthracnose symptoms, we isolated eight Colletotrichum spp., but only C. siamense and C. gloeosporioides sensu lato were found to cause infection in pathogenicity assays. In addition, we isolated eleven Neopestalotiopsis and two Pestalotiopsis spp. from yellow halo leaf blight lesions and found that N. clavispora and N. maddoxii were capable of causing disease. We also determined that the A. alternata and A. tenuissima in the Alternaria alternata species complex caused black leaf blight only in non-suberised new leaf flush. For brown leaf blight, Neofusicoccum parvum and Ne. luteum were isolated from symptomatic leaves, both of which caused similar levels of disease. Our findings indicate that several pathogen species are responsible for at least four leaf diseases in macadamia nurseries, suggesting a potential productivity risk when affected plants are planted in the field.

Macadamia cultivation in tropical and subtropical regions is threatened by various pathogens, affecting different parts of the tree. Currently, there is a lack of information about the prevalence of bacterial and fungal pathogens and whether rootstock cultivars influence the occurrence of stem diseases in macadamia nurseries. We examined over 2000 grafted macadamia plants from commercial nurseries in Australia to identify the pathogens associated with diseased plants using multi‐loci DNA sequencing. as well as detached and in planta pathogenicity assays on two major rootstock cultivars (HAES 695 and H2) to confirm the causal pathogens of stem diseases. The results showed that Diaporthe litchicola and Diaporthe australiana were the most dominant and aggressive species, causing Phomopsis graft dieback, in all five nurseries examined. Stem canker (5%–8%) was caused by five Botryosphaeriaceae (three Lasiodiplodia and two Neofusicoccum species) and was more common and severe on H2 (6.0%) than HAES 695 (4.5%) and Daddow (4.0%) rootstocks. Gall canker caused by Nectria pseudotrichia occurred at low frequencies (<3%) in the nursery plants, regardless of the rootstock cultivars. Crown gall caused by Agrobacterium tumefaciens was observed in a few plants (<1%) only on H2 rootstock plants. This study showed that HAES 695 macadamia rootstock is more tolerant to the stem diseases than H2.

Phytophthora cinnamomi stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of P. cinnamomi across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, reverse transcription polymerase chain reaction screening, and Sanger sequencing of selected isolates. Our analysis revealed that virus infections were prevalent across all sampled populations, including RNA viruses associated with the orders Ghabrivirales, Martellivirales, and Tolivirales, and the classes Amabiliviricetes, Bunyaviricetes, and the recently proposed Orpoviricetes. Viruses were mainly found in East and Southeast Asian populations, within the geographic origin of P. cinnamomi but have also spread to new regions where the pathogen has emerged as a clonal destructive pathogen. Among the identified viruses, eight species, including two bunya-like viruses, one narna-like virus, and five ormycoviruses, exhibit a global distribution with some genetic divergence between continents. The interaction between P. cinnamomi and its virome indicates a dynamic coevolution across diverse geographic regions. Indonesia is indicated to be the viral epicentre of P. cinnamomi, with the highest intra- and interspecies diversity of viruses. Viral diversity is significantly enhanced in regions where sexual recombination of P. cinnamomi occurs, while regions with predominantly asexual reproduction harbour fewer viral species. Interestingly, only the partially self-fertile mating type (MAT) A2, associated with the global pandemic, facilitates the spread of viruses across different biogeographic regions, whereas viruses are absent in the self-sterile MAT A1 in its areas of introduction like Australia and South Africa. Intriguingly, the presence of a plant tombusvirus suggests a potential cross-kingdom infection among Chilean isolates and a plant host. This study sheds further light on the geographical origin of P. cinnamomi from a novel virome perspective.

Macadamia is a tree producing high-value nuts and is indigenous to subtropical Australia. Macadamia is commercially cultivated across the globe and the macadamia industry is experiencing increased crop losses caused by fungal pathogens. Limited information is available regarding the association of fungal microbes with macadamia nursery plants. Therefore, this study aims to characterise fungal microbes associated with macadamia plants across five growth stages in leaf, stem and root during four seasons. The fungal community in macadamia nursery plants was analysed using a culture-based approach. Fungi were isolated from germinated seedlings, 3-month-old seedlings, non-grafted plants, grafted trees and 2-year-old trees in orchard. A total of 63 fungal species were identified using DNA sequencing, mainly in the phylum Ascomycota, from the different plant organs. The fungal community structure was significantly influenced by the growth stages (P = 0.001) and plant organs (P<0.001). There was no significant seasonal (P = 0.021) effect in the number of fungal genera isolated from the plants. Grafted plants and young orchards had the richest fungal composition and diversity of the 63 fungal species. Alternaria, Arcopilus, Epicoccum, Nigrospora, and Preussia were found in the leaf, Nectria in the stem, and Mortierella and Penicillium in the root organ only. Diaporthe, Neopestalotiopsis, Pestalotiopsis, Fusarium, and Phyllosticta were detected in all three organs. This study revealed that fungal community richness and diversity in macadamia plants depend on the growth stage and organ examined.

In the early decades of British settlement at Sydney Cove in 1788, the struggling colonials tried their hand at growing edible bananas but invariably failed. However, they grew extremely well in the Moreton Bay colony (Brisbane) and over time banana growing became an important agricultural industry there, particularly after the introduction of the Cavendish variety. All was progressing well until a new disease appeared in plantations around Brisbane in the early 1870s. The medical practitioner and naturalist Joseph Bancroft investigated the problem and concluded that a fungus was implicated as the causal agent. In the early 1900s, following serious outbreaks of a disease with similar symptoms in Caribbean countries (where it was called Panama Disease), the American bacteriologist Erwin Frink Smith studied the same disease in Cuba, and named the pathogen Fusarium cubense. Another American scientist, Elmer Walker Brandes, conclusively proved that Fusarium cubense (now called Fusarium oxysporum f.sp. cubense) was the cause of the banana disease. Bancroft's discovery of the disease now called Fusarium Wilt not only predates other reports of the disease in the Caribbean but also represents the first scientific investigation of a plant disease in Australia.

Phytophthora root rot (PRR) of chickpea (Cicer arietinum) caused by Phytophthora medicaginis is an important disease. Partial resistance to PRR is sourced from Cicer echinospermum. In this study, we evaluated if lines with low levels of PRR foliage symptoms in two contrasting recombinant inbred line (RIL) populations parented by chickpea cultivars (Yorker and Rupali) and 04067-81-2-1-1 (C. echinospermum, interspecific breeding line) had a significant drag on yield parameters. For the Yorker × 04067-81-2-1-1 population with the highest level of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly later flowering and podding, lower grain yields, and lighter seed and shorter plant phenotypes than high foliage symptom RIL. A quantitative trait locus analysis identified significant QTL for flowering, height, 100-seed weight, and yield, and there was a significantly higher frequency of alleles for the negative agronomic traits (i.e., drag) from the 04067-81-2-1-1 parent in low foliage symptom RIL than in high foliage symptom RIL. For the Rupali × 04067-81-2-1-1 population with lower levels of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly lighter seed and shorter plants than high foliage symptom RIL. Significant QTL were detected, the majority were for the timing of flowering and podding (n = 18), others were for plant height, yield, and 100-seed weight. For this second population, the frequency of alleles for the negative agronomic traits from the 04067-81-2-1-1 parent did not differ between low and high foliage symptom RIL. The 100 seed weight of RIL under moderate PRR disease pressure showed some promise as a yield component trait to identify phenotypes with both high levels of PRR resistance and grain yield potential for further seed number evaluations. We identified that large population sizes are required to enable selection among chickpea × C. echinospermum crosses for high levels of PRR resistance without a significant drag on yield.

Late Blight, also called Irish blight and brown rot, devastated potato crops in Ireland and countries in Europe in the 1840s, and led to famines, deaths, and the emigration of tens of thousands of poor farmworkers. The outbreaks were blamed on many factors, but finally it was demonstrated that the causal agent was an oomycete (water mould) Phytophthora infestans. The Queensland Government Entomologist and Vegetable Pathologist, Henry Tryon, claimed that he made the first discovery of Late Blight in Australia, on leaves and tubers of potato collected in May 1909 around Brisbane. Within three months, the disease was found in all Australian states. Tryon believed that the Queensland outbreak was caused by Phytophthora-infected planting tubers obtained from Tasmania, which growers and the government in that state initially refused to acknowledge. The Victorian Vegetable Pathologist, Daniel McAlpine, initially agreed with the Tasmanians, but later admitted that he had identified Ph. infestans in Tasmanian potato crops. A herbarium specimen of potato leaves collected in 1900 in Victoria, examined over a century later, was found to be infected with Phytophthora infestans. All the ruckus that ensued after Tryon's discovery was unnecessary; it was really a matter of where and when.

Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.

Magic mushrooms are fungi that produce psilocybin, a compound with breakthrough status for treatment of mental health disorders. Wood-degrading species of Psilocybe , such as P . subaeruginosa and relatives, have high concentrations of psilocybin but are discouraged for clinical production due to a temporary paralytic side effect known as Wood Lover’s Paralysis, the cause of which is unknown. We studied P. subaeruginosa over its partial distribution in Australia based on genomic analyses of 89 isolates to investigate population structure and species boundaries, examine allelic diversity at psilocybin loci, and test its centre of origin. Psilocybe subaeruginosa is structured by geography in Australia, but geographically separated populations are fully sexually compatible. Allelic diversity among populations, such as at mating compatibility loci, is likely a result of genetic drift and minimal gene flow since differentiation from a shared ancestor. Movement of woodchips, mulch, or plants has most likely spread genotypes of P. subaeruginosa locally within Australia and to the northern hemisphere. Species from the northern hemisphere, namely P. azurescens and P. cyanescens , clustered among Australian populations, indicating shared ancestry and supporting a hypothesis these taxa are conspecific with P. subaeruginosa . We identified high allelic diversity in genes of the psilocybin metabolic pathway and haplotypes of P. subaeruginosa with either one or two putatively functional paralogs of psiH , however the functionality of this gene duplication is yet to be determined. Our study provides insights into the evolutionary history and species boundaries of P. subaeruginosa , which has a centre of origin in Australasia.

Since the start of growing bananas in large plantations the industry has been plagued by the introduction of numerous pathogens and none more troublesome than Fusarium wilt of banana (FWB). The introduction of Fusarium race 1 in the Gros Michel plantations in Latin America led to one of the major plant disease epidemics of the 20st century. This chapter outlines the development of the disease, the mode of infection and epidemiology. An account is given of the various disease control methods trialled over the last century and the underlying biological factors are outlined to explain why most of these management options have been ineffective in a monoculture plantation setting to control FWB. At the same time, some of the successful options to manage this disease are explored, together with the challenges around implementing long-term effective disease control measures to combat this disease.

Blood disease of banana is a bacterial wilt caused by Ralstonia syzygii subsp. celebesensis. The symptoms of Blood disease include wilting, chlorosis and necrosis of leaves, red/brown vascular staining, and pulp-rot of the fruit. The disease was first reported in 1905 from southern Sulawesi and was contained in that area, but has in the last 30 years spread across much of Indonesia and more recently to Malaysia. The disease causes significant crop losses where it occurs. This chapter gives an overview of the pathogen, the disease cycle with special emphasis on the mode of transmission. It has been shown that local dispersal is predominantly through mechanical transmission of the bacterium by insects, birds, bats and tools from diseased to healthy banana plants while long-distance dispersal is through the movement of contaminated planting materials. The chapter concludes with an overview of potential disease management and control options.

Fusarium wilt of banana (FWB) Tropical Race 4 (TR4) is caused by the plant pathogenic fungus Fusarium odoratissimum. At present, the spread of TR4 has been documented in at least 21 countries throughout all major Cavendish banana-producing regions of the world. It seems inevitable that TR4 will continue to spread to other regions that are currently not affected, as exclusion and field management have failed to contain the fungus. As this chapter shows, breeding for resistance to diversify the banana crop for the export trade and smallholder settings and developing control methods based on the latest insights are essential to manage TR4 to save an essential staple food for millions of people and the world's most favorite fruit.

Freckle disease on banana is becoming more prevalent and in recent years has emerged as a disease of economic importance in some parts of the world. In places where the disease occurs it is a challenge to produce high quality, unblemished banana fruit for export markets. Although freckle disease can be controlled through regular application of fungicides, efforts to manage the disease in a sustainable manner are hampered by limited knowledge about the disease cycle, levels of resistance in different banana varieties, and the presence of diverse pathogen species at different geographic locations. The disease is especially serious in plantations of the Cavendish subgroup where the fruits produced are either downgraded or rejected, adversely affecting the marketable yield. This chapter gives an overview of our current understanding of Freckle disease with regards to its taxonomy, disease cycle, infection biology and epidemiology and discusses the various options to manage the disease.

Global banana production is under threat from the rapidly spreading pathogen Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4), which is pathogenic to Cavendish and many other varieties. Due to the absence of effective control methods and the lack of other market-acceptable resistant cultivars, early diagnostics, containment and quarantine measures are important to limit further spread and impact of this pathogen. Early detection and identification of the pathogen require reliable diagnostic assays. The reliability of a molecular diagnostic assay is directly linked to the rigour applied at validating the assay according to predetermined standards. For specific detection of a target pathogen using molecular diagnostics, a well-resolved taxonomy of the target and related species based on their evolutionary relationships is also required. The advent of sequence-based phylogenetic analysis has given rise to new insights regarding the taxonomic classification of Foc and provided proof for the polyphyletic origin of Foc races, complicating early and reliable detection of the pathogen. Although numerous diagnostic methods for Foc have been developed, choosing a rigorously validated and fit-for-purpose method for adoption is currently challenging as advantages and drawbacks for each assay are not always obvious or put into context with prior methodologies. This review compiles and critically dissects published methods that are reported to detect Foc to date and highlights their benefits and constraints to provide a valuable reference for diagnosticians, researchers and policy makers worldwide.

The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.

Phytophthora root rot caused by Phytophthora medicaginis is an important disease of chickpeas (Cicer arietinum) in Australia with limited management options, increasing reliance on breeding for improved levels of genetic resistance. Resistance based on chickpea-Cicer echinospermum crosses is partial with a quantitative genetic basis provided by C. echinospermum and some disease tolerance traits originating from C. arietinum germplasm. Partial resistance is hypothesised to reduce pathogen proliferation, while tolerant germplasm may contribute some fitness traits, such as an ability to maintain yield despite pathogen proliferation. To test these hypotheses, we used P. medicaginis DNA concentrations in the soil as a parameter for pathogen proliferation and disease assessments on lines of two recombinant inbred populations of chickpea-C. echinospermum crosses to compare the reactions of selected recombinant inbred lines and parents. Our results showed reduced inoculum production in a C. echinospermum backcross parent relative to the C. arietinum variety Yorker. Recombinant inbred lines with consistently low levels of foliage symptoms had significantly lower levels of soil inoculum compared to lines with high levels of visible foliage symptoms. In a separate experiment, a set of superior recombinant inbred lines with consistently low levels of foliage symptoms was tested for soil inoculum reactions relative to control normalised yield loss. The in-crop P. medicaginis soil inoculum concentrations across genotypes were significantly and positively related to yield loss, indicating a partial resistance-tolerance spectrum. Disease incidence and the rankings for in-crop soil inoculum were correlated strongly to yield loss. These results indicate that soil inoculum reactions may be useful to identify genotypes with high levels of partial resistance.