Biological and Phylogenetic Analyses Suggest that Two Cryphonectria spp. Cause Cankers of Eucalyptus in Africa

Fungal Communities of Eucalyptus grandis Leaves Are Influenced by the Insect Pest Leptocybe invasa

Fungal communities in above-ground tree tissues are hyperdiverse and are influenced by biotic interactions with other organisms living in or on these tissues. These biotic interactions are, however, still poorly understood. In this study, we aimed to understand how insect-associated gall formation on Eucalyptus foliage correlates with the diversity of foliar fungal communities in surrounding healthy leaf tissue, as well as the co-occurrence patterns among the members of the fungal community. We used ITS metabarcoding to characterise the foliar fungal communities of 179 individual E. grandis trees. These trees were assigned to infestation levels of the wasp Leptocybe invasa (Eulophidae: Hymenoptera), which causes gall formation on shoot tips and leaves of its host. Fungal community networks were calculated using a Pearson correlation coefficient. The composition and diversity of fungal communities were influenced by the severity of L. invasa infestations. We identified potential Eucalyptus pathogens with high sequence abundance at all disease severity levels, but network analysis indicated that the co-occurrence of potential pathogens between no to mild and medium to heavy infestation differed significantly. A better understanding of microbial interactions, especially the role of pathogens, can be useful for controlling disease- and beneficial host-associated microbial communities.

eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors

Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the Eucalyptus grandis genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed E. grandis genes in common among responses to the insect pest Leptocybe invasa, oomycete pathogen Phytophthora cinnamomi and fungus Chrysoporthe austroafricana. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with NITRATE TRANSPORTER 2.5 (NRT2.5) being a key gene, up-regulated under susceptible interactions and down-regulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of NRT2.5 in plant defense is unclear. The T-DNA mutants of AtNRT2.5 were more resistant to Pseudomonas syringae pv. tomato pv tomato DC3000 inoculation than the wild-type counterpart, supporting a direct role for NRT2.5 in plant defense. Future studies will focus on characterizing the Eucalyptus ortholog of NRT2.5.

Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors

Chrysoporthe austroafricana is a fungal pathogen that causes the development of stem cankers on susceptible Eucalyptus grandis trees. Clones of E. grandis that are partially resistant and highly susceptible have been identified based on the extent of lesion formation on the stem upon inoculation with C. austroafricana. These interactions have been used as a model pathosystem to enhance our understanding of interactions between pathogenic fungi and woody hosts, which may be different to herbaceous hosts. In previous research, transcriptomics of host responses in these two clones to C. austroafricana suggested roles for salicylic acid and gibberellic acid phytohormone signaling in defense. However, it is unclear how the pathogen infiltrates host tissue and which pathogenicity factors facilitate its spread in the two host genotypes. The aim of this study was to investigate these two aspects of the E. grandis-C. austroafricana interaction and to test the hypothesis that the pathogen possesses mechanisms to modulate the tree phytohormone-mediated defenses. Light microscopy showed that the pathogen occurred in most cell types and structures within infected E. grandis stem tissue. Notably, the fungus appeared to spread through the stem by penetrating cell wall pits. In order to understand the molecular interaction between these organisms and predict putative pathogenicity mechanisms of C. austroafricana, fungal gene expression was studied in vitro and in planta. Fungal genes associated with cell wall degradation, carbohydrate metabolism and phytohormone manipulation were expressed in planta by C. austroafricana. These genes could be involved in fungal spread by facilitating cell wall pit degradation and manipulating phytohormone mediated defense in each host environment, respectively. Specifically, the in planta expression of an ent-kaurene oxidase and salicylate hydroxylase in C. austroafricana suggests putative mechanisms by which the pathogen can modulate the phytohormone-mediated defenses of the host. These mechanisms have been reported in herbaceous plant-pathogen interactions, supporting the notion that these aspects of the interaction are similar in a woody species. This study highlights ent-kaurene oxidase and salicylate hydroxylase as candidates for further functional characterization.

Endophytic Cryphonectriaceae on native Myrtales: Possible origin of Chrysoporthe canker on plantation-grown Eucalyptus

Chrysoporthe austroafricana (Cryphonectriaceae) is a damaging canker pathogen on Eucalyptus species in Southern Africa. Recent studies have shown that the fungus occurs on native Syzygium species and that it has apparently undergone a host range expansion from these native trees to infect non-native Eucalyptus. The aim of this study was to consider whether Chr. austroafricana and other Cryphonectriaceae might exist as endophytes in native Myrtaceae, providing a source of inoculum to infect non-native Myrtales. Healthy branches were collected from Myrtaceae in Mozambique, incubated in florist foam, allowed to dry gradually and monitored for the appearance of fruiting bodies resembling species in the Cryphonectriaceae. Isolates were identified based on DNA sequence data. Two species in the Cryphonectriaceae were obtained, representing the first evidence that species in the Cryphonectriaceae occur as endophytes on native Myrtales, thus providing a source of inoculum to infect non-native and susceptible trees. This has important implications regarding the movement of planting stock used by ornamental tree and forestry enterprises.

Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana

BACKGROUND

Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. The aim of this study was to characterize the defence response of E. grandis against C. austroafricana.

RESULTS

Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction.

CONCLUSION

The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials.

New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp. nov

The Cryphonectriaceae accommodates some of the world's most important tree pathogens, including four genera known from native and introduced Myrtales in Africa. Surveys in the past 3 y in southern Africa have led to the discovery of cankers with fruiting structures resembling those of the Cryphonectriaceae on trees in the Myrtales in Namibia, South Africa, Swaziland and Zambia. These fungi were identified with morphological characteristics and DNA sequence data. For the first time we report Chrysoporthe austroafricana from Namibia and on Syzygium guineense and Holocryphia eucalypti in Swaziland on a Eucalyptus grandis clone. The host and geographic ranges of Celoporthe dispersa are expanded to include S. legatti in South Africa and S. guineense in Zambia. In addition a monotypic genus, Latruncellus aurorae gen. sp. nov., is described from Galpinia transvaalica (Lythraceae, Myrtales) in Swaziland. The present and other recent studies clearly emphasize the limited understanding of the diversity and distribution of fungi in the Cryphonectriaceae in Africa.

Multigene phylogenetic and population differentiation data confirm the existence of a cryptic species within Chrysoporthe cubensis

Chrysoporthe cubensis is one of the most important pathogens of Eucalyptus. Based on phylogenetic evidence and geographic origin, isolates of this fungus are known to reside in distinct 'South America' and 'Southeast Asia' clades. In this study, reproductive isolation amongst these isolates of C. cubensis was tested using gene flow statistics for 12 polymorphic loci, and to support these data, phylogenetic affiliations based on gene trees and a multigene phylogeny were used. Gene flow statistics between populations, and relative to the closely related Chrysoporthe austroafricana, were low and not significantly different (P<0.05). Additionally, phylogenetic analyses of DNA sequence data for four gene regions convincingly distinguished the two subclades of C. cubensis. Isolates in the Southeast Asian subclade are described in the new species, Chrysoporthe deuterocubensis. Chrysoporthe cubensis and C. deuterocubensis represent closely related fungi that are thought to be native to South America and Southeast Asia, respectively. A technique is presented that allows for rapid differentiation between these species and that will aid in quarantine procedures to limit their spread to new environments.

Identification and Pathogenicity of Chrysoporthe cubensis on Eucalyptus and Syzygium spp. in South China

The genus Chrysoporthe includes important pathogens of plantation-grown Eucalyptus spp. and has been reported from several tree genera in the order Myrtales in tropical and subtropical areas of the world. During disease surveys in South China, fruiting structures typical of Chrysoporthe spp. were observed on cankers on Eucalyptus spp. and Syzygium cumini trees. The aim of this study was to confirm the identity of the Chrysoporthe cubensis infecting the Eucalyptus spp. and S. cumini and to test the pathogenicity of the fungus. Following glasshouse trials to select virulent isolates, field inoculations were undertaken to screen different commercial Eucalyptus genotypes for their susceptibility to the fungus. Isolates were characterized based on their morphology and DNA sequence data for the β-tubulin and internal transcribed spacer regions of the ribosomal DNA. Results showed that the putative pathogen represented the Asian form of C. cubensis, which occurred on numerous different Eucalyptus spp. and hybrid clones as well as S. cumini. Field inoculations showed that all six of the Eucalyptus genotypes tested are susceptible to infection by C. cubensis. Significant differences were observed between them, providing prospects to select disease-tolerant planting stock in the future.

Aurifilum, a new fungal genus in the Cryphonectriaceae from Terminalia species in Cameroon

Native Terminalia spp. in West Africa provide a popular source of construction timber as well as medical, spiritual and social benefits to rural populations. Very little is, however, known regarding the diseases that affect these trees. During an investigation into possible diseases of Terminalia spp. in Cameroon, orange to yellow fungal fruiting structures, resembling those of fungi in the Cryphonectriaceae, were commonly observed on the bark of native Terminalia ivorensis, and on dead branches of non-native Terminalia mantaly. In this study the fungus was identified based on morphological features as well as DNA sequence data (ITS and beta-tubulin) and its pathogenicity was tested on T. mantaly seedlings. Our results showed that isolates of this fungus represent a previously undescribed genus in the Cryphonectriaceae, which we describe as Aurifilum marmelostoma gen. et sp. nov. Pathogenicity tests revealed that A. marmelostoma is pathogenic on T. mantaly. These tests, and the association of A. marmelostoma with disease symptoms on T. ivorensis, suggest that the fungus is a pathogen of this important tree.

Novel hosts of the Eucalyptus canker pathogen Chrysoporthe cubensis and a new Chrysoporthe species from Colombia

The pathogen Chrysoporthe cubensis (formerly Cryphonectria cubensis) is best known for the important canker disease that it causes on Eucalyptus species. This fungus is also a pathogen of Syzygium aromaticum (clove), which is native to Indonesia, and like Eucalyptus, is a member of Myrtaceae. Furthermore, C. cubensis has been found on Miconia spp. native to South America and residing in Melastomataceae. Recent surveys have yielded C. cubensis isolates from new hosts, characterized in this study based on DNA sequences for the ITS and beta-tubulin gene regions. These hosts include native Clidemia sericea and Rhynchanthera mexicana (Melastomataceae) in Mexico, and non-native Lagerstroemia indica (Pride of India, Lythraceae) in Cuba. Isolates from these hosts and areas group in the sub-clade of C. cubensis accommodating the South American collections of the fungus. This sub-clade also includes isolates recently collected from Eucalyptus in Cuba, which are used to epitypify C. cubensis. New host records from Southeast Asia include exotic Tibouchina urvilleana from Singapore and Thailand and native Melastoma malabathricum (Melastomataceae) in Sumatra, Indonesia. Consistent with their areas of occurrence isolates from the latter collections group in the Asian sub-clade of C. cubensis. DNA sequence comparisons of isolates from Tibouchina lepidota in Colombia revealed that they represent a new sub-clade within the greater Chrysoporthe clade. Isolates in this clade are described as Chrysoporthe inopina sp. nov., based on distinctive morphological differences.

Distribution of Chrysoporthe Canker Pathogens on Eucalyptus and Syzygium spp. in Eastern and Southern Africa

Chrysoporthe cubensis and C. austroafricana, collectively known as Cryphonectria cubensis in the past, are important canker pathogens of Eucalyptus spp. worldwide. Previous studies have suggested that Chrysoporthe austroafricana occurs only in South Africa, whereas C. cubensis occurs in Australia, Cameroon, Tanzania, Democratic Republic of Congo, Republic of Congo, Southeast Asia, and South, Central, and North America. In South Africa, C. austroafricana is a pathogen on nonnative Eucalyptus (Myrtaceae) and Tibouchina (Melastomataceae) spp., both residing in the order Myrtales. Recently, the fungus also has been found on native Syzygium cordatum trees in the country, leading to the hypothesis that it is native to Africa. In contrast, C. cubensis is thought to have been introduced into Africa and is known only on non-native Eucalyptus spp. and S. aromaticum (clove) in four countries. The aim of this study was to consider the distribution of Chrysoporthe spp. on non-native Eucalyptus spp. as well as on native Myrtales in southern and eastern Africa. Isolates were collected from as many trees as possible and characterized based on their morphology and DNA sequence data for two gene regions. Results show, for the first time, that C. cubensis occurs in Kenya, Malawi, and Mozambique on nonnative Eucalyptus spp. C. austroafricana was found for the first time in Mozambique, Malawi, and Zambia on non-native Eucalyptus spp. and native S. cordatum. The known distribution range of C. austroafricana within South Africa also was extended during these surveys.

Discovery of the Canker Pathogen Chrysoporthe austroafricana on Native Syzygium spp. in South Africa

Chrysoporthe canker is one of the most important diseases of plantation-grown Eucalyptus spp. in tropical and subtropical regions worldwide. For many years, the disease was reported to be caused by the fungal pathogen Cryphonectria cubensis. Recent DNA-based studies have shown that the fungus in South Africa is not conspecific with Chr. cubensis and it was recently described in the new genus Chrysoporthe as Chrysoporthe austroafricana. Chr. austroafricana is known only from South Africa, where it causes severe cankers on Eucalyptus spp. and on ornamental Tibouchina trees, both of which have been introduced into South Africa. The origin of Chr. austroafricana is unknown, but it is possible that it expanded its host range from native trees related to Eucalyptus and Tibouchina spp. to these exotic hosts. Subsequent surveys of some indigenous South African Myrtales led to the discovery of fruiting structures resembling those of Chr. austroafricana on native Syzygium cordatum and S. guineense. The fungus from these Syzygium spp. was identified as Chr. austroafricana based on morphological characteristics and β-tubulin gene sequences. Pathogenicity trials showed that Chr. austroafricana is more virulent on exotic Eucalyptus spp. than on native S. cordatum. This study represents the first report of Chr. austroafricana from native hosts in South Africa and adds credence to the view that the fungus could be native to this country.

Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa

In a survey for Cryphonectria and Chrysoporthe species on Myrtales in South Africa, a fungus resembling the stem canker pathogen Chrysoporthe austroafricana was collected from native Syzygium cordatum near Tzaneen (Limpopo Province), Heteropyxis canescens near Lydenburg (Mpumalanga Province) and exotic Tibouchina granulosa in Durban (KwaZulu-Natal Province). The fungus was associated with dying branches and stems on S. cordatum, H.canescens and T.granulosa. However, morphological differences were detected between the unknown fungus from these three hosts and known species of Chrysoporthe. The aim of this study was to characterise the fungus using DNA sequence comparisons and morphological features. Pathogenicity tests were also conducted to assess its virulence on Eucalyptus (ZG 14 clones), H.natalensis and T. granulosa. Plants of H. canescens were not available for inoculation. Results showed distinct morphological differences between the unknown fungus and Chrysoporthe spp. Phylogenetic analysis showed that isolates reside in a clade separate from Chrysoporthe and other related genera. Celoporthe dispersa gen. et sp. nov. is, therefore, described to accommodate this fungus. Pathogenicity tests showed that C.dispersa is not pathogenic to H. natalensis, but that it is a potential pathogen of Eucalyptus and Tibouchina spp.