Evidence that Austropuccinia psidii may complete its sexual life cycle on Myrtaceae

Development and validation of a rapid loop-mediated isothermal amplification assay for the detection of Chrysomyxa and characterization of Chrysomyxa woroninii overwintering on Picea in China

Chrysomyxa rusts cause significant damage to spruce in both natural forests and plantations. Particularly, Three Chrysomyxa species, Chrysomyxa deformans, Chrysomyxa qilianensis, and Chrysomyxa rhododendri, listed as National Forest Dangerous Pests in China, have severely affected many economically and ecologically important spruce native species in China. Also, Chrysomyxa arctostaphyli, an important plant quarantine fungus, causes a damaging broom rust disease on spruce. Therefore, rapid, and efficient detection tools are urgently needed for proper rust disease detection and management. In this study, a sensitive, genus-specific loop-mediated isothermal amplification (LAMP) assay targeting the ITS-28S rRNA region was developed to detect the presence of Chrysomyxa in spruce needle and bud samples. After optimization and validation, the LAMP assay was found to be sensitive to detect as low as 5.2 fg/µL DNA, making it suitable for rapid on-site testing for rust infection. The assay was also specific to Chrysomyxa species, with no positive signals from other rust genus/species. The application of LAMP in the early detection of rust infections in spruce needles and buds was investigated, and spatial colonization profiles as well as the means of overwintering of Chrysomyxa woroninii in infected buds and branches were verified using the LAMP assay. This LAMP detection method will facilitate further studies on the characteristics of the life cycle and inoculation of other systemic rusts.

Phylogenetics of the rust fungi (Pucciniales) of South Africa, with notes on their life histories and possible origins

South Africa has an indigenous rust (Pucciniales) funga of approximately 460 species. This funga was sampled with species from as many genera as possible. The nuclear ribosomal large subunit (28S) region was amplified from samples representing 110 indigenous species, as well as the small subunit (18S) region and the cytochrome c oxidase subunit 3 (CO3) in some cases, and these were used in phylogenetic analyses. One new species is described, 12 new combinations made, six names reinstated, and two life history connections made. The life histories of this funga were summarized; it is dominated by species with contracted life histories. The majority of species are autoecious, with a small proportion being heteroecious. Of the autoecious species, many will likely be homothallic with no spermagonia. A shortened life history with homothallism allows for a single basidiospore infection to initiate a local population buildup under the prevailing unpredictable climatic conditions. Suggestions are made as to the possible origin of this funga based on the development of the modern South African flora. It is postulated that the rusts of South Africa are of relatively recent origin, consisting of three groups. Firstly, there is an African tropical element with members of the Mikronegerineae (Hemileia), the Sphaerophragmiaceae (Puccorchidium, Sphaerophragmium), and certain Uredinineae (Stomatisora). Their immediate ancestors likely occurred in the tropical forests of Africa during the Paleogene. Secondly, there is a pantropical element including the Raveneliaceae (e.g., Diorchidium, Maravalia, Ravenelia sensu lato, Uropyxis). This likely diversified during the Neogene, when the mimosoids became the dominant trees of the developing savannas. Thirdly, the Pucciniaceae invaded Africa as this continent pushed northward closing the Tethys Sea. They diversified with the development of the savannas as these become the dominant habitat in most of Africa, and are by far the largest component of the South African rust funga.

Austropuccinia licaniae, first congeneric with the myrtle rust pathogen A. psidii

In 1895 and 2001, rust fungi affecting Licania trees (Chrysobalanchaceae) in Brazil were described as Uredo licaniae by Hennings in the state of Goiás and as Phakopsora tomentosae by Ferreira et al. in the state of Amazonas, respectively. Recently, a Licania rust fungus collected close to the Amazonian type location sharing symptoms with the former two species was subjected to morphological examinations and molecular phylogenetic analyses using 28S nuc rDNA (ITS2-28S) and cytochrome c oxidase subunit III (CO3) gene sequences. Since the original type specimen of Ph. tomentosae is considered lost, we carefully reviewed the type description and questioned the identity of the telium, which justified the description of the fungus as a Phakopsora species. Furthermore, the additional revision of the type material described by Hennings revealed that Ph. tomentosae is a synonym of U. licaniae. Based on the morphological examinations, disease symptoms, and shared hosts, we concluded that the newly collected material is conspecific with U. licaniae. However, the phylogenetic analyses rejected allocation in Phakopsora and instead assigned the Licania rust fungus in a sister relationship with Austropuccinia psidii (Sphaerophragmiaceae), the causal agent of the globally invasive myrtle rust pathogen. We therefore favored a recombination of U. licaniae (syn. Ph. tomentosae) into Austropuccinia and proposed the new name Austropuccina licaniae for the second species now identified for this genus. The fungus shares conspicuous symptoms with A. psidii, causing often severe infections of growing leaves and shoots that lead to leaf necrosis, leaf shedding, and eventually to the dieback of entire shoots. In view of the very similar symptoms of its aggressively invasive sister species, we briefly discuss the current state of knowledge about A. licaniae and the potential risks, and the opportunity of its identification.

Environmental monitoring for invasive fungal pathogens of ʽŌhiʽa (Metrosideros polymorpha) on the Island of Hawaiʽi

The invasive rust Austropuccina psidii was detected in the Hawaiian Islands in 2005 and has become widely established throughout the archipelago in both native and introduced species of Myrtaceae. Initial predictions about the impacts of the fungus on native ʽōhiʽa lehua (Metrosideros polymorpha), a keystone native tree, have not materialized, but there is ongoing concern that introductions of new genotypes of the fungus could lead to widespread mortality with catastrophic effects on native ecosystems. By contrast, two recently emergent Ascomycete pathogens, Ceratocystis lukuohia (Ceratocystis wilt of ‘ōhi‘a) and C. huliohia (Ceratocystis canker of ‘ōhi‘a), collectively known to cause Rapid ʽŌhiʽa Death (ROD), are causing significant mortality in native forests on Hawaiʻi and Kauaʻi Islands, but pathways of spread are still incompletely understood. We used a network of passive environmental samplers for collecting windblown urediniospores of Austropuccina to evaluate the effectiveness of environmental monitoring to detect seasonal and landscape-scale differences in airborne propagules of this rust on Hawai`i Island. The samplers were also used to determine if windborn ambrosia beetle frass or spores of Ceratocystis can spread long distances. We found frequent detections and regional and seasonal differences in numbers of samplers that were positive for urediniospores of Austropuccinia, but little evidence of long-distance airborne dispersal of the ROD-causing fungi. The simple, inexpensive platform for sampling airborne fungal spores that we used may have value as a monitoring tool for detecting spread of airborne fungal pathogens, evaluating habitats for suitability for restoration efforts, and for detecting new pathogen introductions, particularly new Austropuccinia genotypes both in Hawaiʻi and other parts of the world.

Comparison of the Infection Biology of Teratosphaeria destructans and Teratosphaeria epicoccoides on Eucalyptus

Leaf blight caused by Teratosphaeria destructans is one of the most important diseases of Eucalyptus planted in the subtropics and tropics. In contrast, the better-known T. epicoccoides, though also a primary pathogen of Eucalyptus, causes less damage to trees in these areas. Although T. destructans is an aggressive pathogen, nothing is known about its infection biology. In this study, the conditions for infection and disease development caused by T. destructans and T. epicoccoides were evaluated and compared on a Eucalyptus grandis × E. urophylla hybrid clone. The optimal temperature for germination ranged from 25 to 30°C for T. destructans and 15 to 20°C for T. epicoccoides. The germination of these pathogens was favored under conditions of light and high levels of RH. Penetration by T. destructans and T. epicoccoides occurred via stomata, and the hyphae colonized the intercellular spaces of infected leaves. Symptoms were clearly visible 3 weeks after inoculation by both pathogens, and reproductive structures started to develop in substomatal cavities at 4 weeks after inoculation. The results of this study will facilitate the establishment of rapid screening trials based on artificial inoculations aimed at reducing the impact of disease caused by T. destructans.

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

Efficacy of Fungicides Applied for Protectant and Curative Activity Against Myrtle Rust

Myrtle rust, caused by the pathogen Austropuccinia psidii, affects species of the Myrtaceae, many of which are endemic to Australia and New Zealand. Originating from South America, A. psidii is now present in both countries, necessitating effective chemical control for disease management. Using an artificial inoculation protocol, the efficacy of eight fungicides (tebuconazole/trifloxystrobin, cyproconazole/azoxystrobin, fosetyl aluminum, triforine, triadimenol, oxycarboxin, copper, and tebuconazole) applied as curative or protectant treatments was tested on two native New Zealand species (Lophomyrtus × ralphii and Metrosideros excelsa). The impacts of rate (×2), frequency (single or double), and timing (pre- or postinfection) of fungicide application were investigated. Overall, the most effective fungicides tested across both species were those that included a demethylation inhibitor and strobilurin mix, notably tebuconazole/trifloxystrobin (Scorpio) and cyproconazole/azoxystrobin (Amistar Xtra). These fungicides significantly reduced infection of host plants relative to the water control. Timing of application significantly affected bioefficacy, with applications made 7 days before inoculation or 7 days after inoculation being generally the most effective. The rate of fungicide application was not significant for both host species, with few interaction terms showing overall significance. Key findings from this study will set the foundation for further fungicide bioefficacy research conducted to evaluate formulations and adjuvant mixtures, determine suitable application methods for enhanced retention and coverage, and derive optimum application time for effective protection of native and exotic Myrtaceae species in New Zealand.

Resistance of New Zealand Provenance Leptospermum scoparium, Kunzea robusta, Kunzea linearis, and Metrosideros excelsa to Austropuccinia psidii

Resistance to the pandemic strain of Austropuccinia psidii was identified in New Zealand provenance Leptospermum scoparium, Kunzea robusta, and K. linearis plants. Only 1 Metrosideros excelsa-resistant plant was found (of the 570 tested) and no resistant plants of either Lophomyrtus bullata or L. obcordata were found. Three types of resistance were identified in Leptospermum scoparium. The first two, a putative immune response and a hypersensitive response, are leaf resistance mechanisms found in other myrtaceous species while on the lateral and main stems a putative immune stem resistance was also observed. Both leaf and stem infection were found on K. robusta and K. linearis plants as well as branch tip dieback that developed on almost 50% of the plants. L. scoparium, K. robusta, and K. linearis are the first myrtaceous species where consistent infection of stems has been observed in artificial inoculation trials. This new finding and the first observation of significant branch tip dieback of plants of the two Kunzea spp. resulted in the development of two new myrtle rust disease severity assessment scales. Significant seed family and provenance effects were found in L. scoparium, K. robusta, and K. linearis: some families produced significantly more plants with leaf, stem, and (in Kunzea spp.) branch tip dieback resistance, and provenances provided different percentages of resistant families and plants. The distribution of the disease symptoms on plants from the same seed family, and between plants from different seed families, suggested that the leaf, stem, and branch tip dieback resistances were the result of independent disease resistance mechanisms.

At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.

Fungal clones win the battle, but recombination wins the war

Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.

Foliar pathogens of eucalypts

Species of eucalypts are commonly cultivated for solid wood and pulp products. The expansion of commercially managed eucalypt plantations has chiefly been driven by their rapid growth and suitability for propagation across a very wide variety of sites and climatic conditions. Infection of foliar fungal pathogens of eucalypts is resulting in increasingly negative impacts on commercial forest industries globally. To assist in evaluating this threat, the present study provides a global perspective on foliar pathogens of eucalypts. We treat 110 different genera including species associated with foliar disease symptoms of these hosts. The vast majority of these fungi have been grown in axenic culture, and subjected to DNA sequence analysis, resolving their phylogeny. During the course of this study several new genera and species were encountered, and these are described. New genera include: Lembosiniella (L. eucalyptorum on E. dunnii, Australia), Neosonderhenia (N. eucalypti on E. costata, Australia), Neothyriopsis (N. sphaerospora on E. camaldulensis, South Africa), Neotrichosphaeria (N. eucalypticola on E. deglupta, Australia), Nothotrimmatostroma (N. bifarium on E. dalrympleana, Australia), Nowamyces (incl. Nowamycetaceae fam. nov., N. globulus on E. globulus, Australia), and Walkaminomyces (W. medusae on E. alba, Australia). New species include (all from Australia): Disculoides fraxinoides on E. fraxinoides, Elsinoe piperitae on E. piperita, Fusculina regnans on E. regnans, Marthamyces johnstonii on E. dunnii, Neofusicoccum corticosae on E. corticosa, Neotrimmatostroma dalrympleanae on E. dalrympleana, Nowamyces piperitae on E. piperita, Phaeothyriolum dunnii on E. dunnii, Pseudophloeospora eucalyptigena on E. obliqua, Pseudophloeospora jollyi on Eucalyptus sp., Quambalaria tasmaniae on Eucalyptus sp., Q. rugosae on E. rugosa, Sonderhenia radiata on E. radiata, Teratosphaeria pseudonubilosa on E. globulus and Thyrinula dunnii on E. dunnii. A new name is also proposed for Heteroconium eucalypti as Thyrinula uruguayensis on E. dunnii, Uruguay. Although many of these genera and species are commonly associated with disease problems, several appear to be opportunists developing on stressed or dying tissues. For the majority of these fungi, pathogenicity remains to be determined. This represents an important goal for forest pathologists and biologists in the future. Consequently, this study will promote renewed interest in foliar pathogens of eucalypts, leading to investigations that will provide an improved understanding of the biology of these fungi.

The Road to Resistance in Forest Trees

In recent years, forests have been exposed to an unprecedented rise in pests and pathogens. This, coupled with the added challenge of climate change, renders forest plantation stock vulnerable to attack and severely limits productivity. Genotypes resistant to such biotic challenges are desired in plantation forestry to reduce losses. Conventional breeding has been a main avenue to obtain resistant genotypes. More recently, genetic engineering has become a viable approach to develop resistance against pests and pathogens in forest trees. Tree genomic resources have contributed to advancements in both these approaches. Genome-wide association studies and genomic selection in tree populations have accelerated breeding tools while integration of various levels of omics information facilitates the selection of candidate genes for genetic engineering. Furthermore, tree associations with non-pathogenic endophytic and subterranean microbes play a critical role in plant health and may be engineered in forest trees to improve resistance in the future. We look at recent studies in forest trees describing defense mechanisms using such approaches and propose the way forward to developing superior genotypes with enhanced resistance against biotic stress.