Taxonomy and DNA phylogeny of Diatrypaceae associated with Vitis vinifera and other woody plants in Australia

Taxonomy and pathogenicity of fungi associated with oak decline in northern and central Zagros forests of Iran with emphasis on coelomycetous species

Oak decline is a complex disorder that seriously threatens the survival of Zagros forests. In an extensive study on taxonomy and pathology of fungi associated with oak decline in the central and northern part of Zagros forests, 462 fungal isolates were obtained from oak trees showing canker, gummosis, dieback, defoliation, and partial or total death symptoms. Based on inter-simple sequence repeat (ISSR) fingerprinting patterns, morphological characteristics, and sequences of ribosomal DNA (28S rDNA and ITS) and protein coding loci (acl1, act1, caM, tef-1α, rpb1, rpb2, and tub2), 24 fungal species corresponding to 19 genera were characterized. Forty percent of the isolates were placed in eight coelomycetous species from seven genera, namely, Alloeutypa, Botryosphaeria, Cytospora, Didymella, Gnomoniopsis, Kalmusia, and Neoscytalidium. Of these, four species are new to science, which are introduced here as taxonomic novelties: Alloeutypa iranensis sp. nov., Cytospora hedjaroudei sp. nov., Cytospora zagrosensis sp. nov., and Gnomoniopsis quercicola sp. nov. According to pathogenicity trials on leaves and stems of 2-year-old Persian oak (Quercus brantii) seedlings, Alternaria spp. (A. alternata, A. atra, and A. contlous), Chaetomium globosum, and Parachaetomium perlucidum were recognized as nonpathogenic. All coelomycetous species were determined as pathogenic in both pathogenicity trials on leaves and seedling stems, of which Gnomoniopsis quercicola sp. nov., Botryosphaeria dothidea, and Neoscytalidium dimidiatum were recognized as the most virulent species followed by Biscogniauxia rosacearum.

Characterization and Pathogenicity of Fungal Species Associated with Dieback of Apple Trees in Northern Italy

Severe dieback symptoms were recently observed on apple (Malus × domestica) trees in Northern Italy, representing a growing concern for producers. Surveys were conducted over a 3-year period (2019 to 2021), and five apple orchards, from 5 to 12 years old, were monitored. A total of 33 fungal isolates isolated from symptomatic plants was selected for characterization. The species identification was achieved through multilocus phylogenetic analyses performed on sequences of three genomic loci (ITS, tub2, and tef1). Morphological features were assessed, and the average growth rate at different temperatures was determined. Seven species were identified in association with dieback of apple trees: Botryosphaeria dothidea, Cadophora luteo-olivacea, Diaporthe rudis, Diplodia seriata, Eutypa lata, Kalmusia longispora, and Paraconiothyrium brasiliense. All the species were pathogenic when inoculated on healthy apple plants. B. dothidea resulted in the most aggressive infections. This study provides an insight into the fungal species diversity associated with apple dieback and provides basis for further investigations to assess the phytosanitary status of plant materials to recommend and implement effective management strategies.

Isolation and Reproductive Structures Induction of Fungal Pathogens Associated with Xylem and Wood Necrosis in Grapevine

Grapevine (Vitis vinifera L.) trunk diseases (GTDs) are considered a disease complex including five diseases: esca, Petri disease, black-foot disease, Botryosphaeria dieback, and Eutypa dieback. The main symptom is a general decline in affected plants, which show xylem necrosis and discoloration or sectorial necrosis in the wood. Their diagnosis is tedious due to four main reasons: (i) the wide diversity of internal symptoms that we can find; (ii) the great diversity of fungi that are associated with them; (iii) the high frequency of co-infections in the same plant; and (iv) the different behavior that the fungal species associated with GTDs show in vitro. Here, we describe a detailed protocol to isolate the different fungal trunk pathogens associated with GTDs as well as methods to induce sporulation and formation of fruiting bodies (pycnidia) to make easier their morphological characterization.

Additions to Diatrypaceae (Xylariales): Novel Taxa and New Host Associations

Diatrypaceae members have a broad distribution and are commonly found on decaying wood. Despite taxonomic and morphological challenges within this group, there has been a growing interest in Diatrypaceae in recent years. The dead branches of several plant hosts with fungal fruiting bodies were collected from Doi Tung National Park, Chiang Rai, and the Narathiwat Provinces in Thailand. Their morphological characteristics, coupled with a molecular phylogeny of combined ITS and tub2 sequence data, were used to introduce two novel Allodiatrype species (A. dalbergiae and A. eleiodoxae) and one new Melanostictus species (M. chiangraiensis). Moreover, four new host records, Diatrypella heveae, D. major, Melanostictus thailandicus, and Paraeutypella citricola on Microcos paniculata, Nayariophyton zizyphifolium, Dalbergia cultrata, and M. paniculata, respectively, as well as a new geographical record of D. major are reported. This research provides detailed descriptions of macro- and microcharacteristics, coupled with a phylogenetic tree for the newly introduced species and host records. The morphological features of Allodiatrype and Melanostictus are listed in the synoptic table.

Molecular detection and identification of Diatrypaceous airborne spores in Australian vineyards revealed high species diversity between regions

The grapevine trunk disease, Eutypa dieback (ED), causes significant vine decline and yield reduction. For many years, the fungus Eutypa lata was considered the main pathogen causing ED of grapevines in Australia. Recent studies showed other Diatrypaceous fungi were also associated with vines exhibiting dieback symptoms but there is limited information on how these fungal pathogens spread in vineyards. Thus, information on the spore dispersal patterns of Diatrypaceous fungi in different wine regions will assist in identifying high-risk infection periods in vineyards. Using more than 6800 DNA samples from airborne spores collected from eight wine regions in south-eastern Australia over 8 years using a Burkard spore trap, this study investigated the diversity and abundance of Diatrypaceous species, using multi-faceted molecular tools. A multi-target quantitative PCR (qPCR) assay successfully detected and quantified Diatrypaceous spores from 30% of the total samples with spore numbers and frequency of detection varying between regions and years. The high-resolution melting analysis (HRMA) coupled with DNA sequencing identified seven species, with E. lata being present in seven regions and the most prevalent species in the Adelaide Hills, Barossa Valley and McLaren Vale. Cryptovalsa ampelina and Diatrype stigma were the predominant species in the Clare Valley and Coonawarra, respectively while Eutypella citricola and Eu. microtheca dominated in the Hunter Valley and the Riverina regions. This study represents the first report of D. stigma and Cryptosphaeria multicontinentalis in Australian vineyards. This study further showed rainfall as a primary factor that triggers spore release, however, other weather factors that may influence the spore release in different climatic regions of Australia still requires further investigation.

Diversity, morphology, and molecular phylogeny of Diatrypaceae from southern China

During an investigation of Diatrypaceae from southern China, 10 xylariales-like taxa have been collected. Morphological and multi-gene analyses confirmed that these taxa reside in Diatrypaceae and represent eight novel taxa and two new records belonging to six genera (viz., Allocryptovalsa, Diatrype, Diatrypella, Paraeutypella, Peroneutypa, and Vasilyeva gen. nov.). Vasilyeva gen. nov. was proposed to accommodate Vasilyeva cinnamomi sp. nov. Among the other collections, seven new species were introduced (viz., Diatrype camelliae-japonicae sp. nov., Diatrype rubi sp. nov., Diatrypella guiyangensis sp. nov., Diatrypella fatsiae-japonicae sp. nov., Paraeutypella subguizhouensis sp. nov., Peroneutypa hainanensis sp. nov., and Peroneutypa qianensis sp. nov.), while two were reported as new records from China (Allocryptovalsa rabenhorstii and Diatrype enteroxantha). For Diatrypaceae, the traditional taxonomic approach based on morphology may not be applicable.

Taxonomic and phylogenetic contributions to Diatrypaceae from southeastern Tibet in China

In this study, we investigated the diversity of diatrypaceous fungi from southeastern Tibet in China. The phylogenetic analyses were carried out based on ITS and β-tubulin sequences of 75 taxa of Diatrypaceae from around the world. Based on a combination of morphological features and molecular evidence, a new genus—Alloeutypa, with three new species—A. milinensis, Diatrype linzhiensis, and Eutypella motuoensis, and a new combination—A. flavovirens, were revealed by the materials in China. Alloeutypa is characterized by stromatal interior olivaceous buff, stromata producing well-developed discrete, and ascospores allantoid, subhyaline. These characteristics separate the new genus from the similar genus Eutypa. Comprehensive morphological descriptions, illustrations, and a phylogenetic tree to show the placement of new taxa are provided. All novelties described herein are morphologically illustrated and phylogeny investigated to better integrate taxa into the higher taxonomic framework and infer their phylogenetic relationships as well as establish new genera and species. Our results indicate that the diatrypaceous fungi harbor higher species diversity in China.

Identification and pathogenicity of six fungal species causing canker and dieback disease on golden rain tree in Beijing, China

Golden rain trees (Koelreuteria paniculata) are largely cultivated because of their important ornamental, medicinal, and economic value. However, they are affected by canker and dieback disease to a large extent. To determine the fungi associated with canker and dieback disease of golden rain trees, isolations were obtained from diseased branches and twigs during 2019 and 2020 in greenbelts and nurseries in Beijing, China. Isolates were identified as six species (Allocryptovalsa castaneicola, Botryosphaeria dothidea, Cytospora koelreutericola sp. nov., Dothiorella acericola, Eutypella citricola, and Peroneutypa scoparia) based on morphological features and phylogenetic analyses of ITS, act, rpb2, tef1-α, and tub2. The results of pathogenicity tests indicated that all fungi produced discoloration and Botryosphaeria dothidea was highly aggressive to golden rain tree. In conclusion, this study explored the taxonomy, phylogeny, and pathogenicity of different fungal species associated with canker and dieback disease on golden rain tree and provided fundamental knowledge to improve disease management.

Phytotoxic Metabolites Produced by Fungi Involved in Grapevine Trunk Diseases: Progress, Challenges, and Opportunities

Grapevine trunk diseases (GTDs), caused by fungal pathogens, are a serious threat to vineyards worldwide, causing significant yield and economic loss. To date, curative methods are not available for GTDs, and the relationship between the pathogen and symptom expression is poorly understood. Several plant pathologists, molecular biologists, and chemists have been investigating different aspects of the pathogenicity, biochemistry, and chemical ecology of the fungal species involved in GTDs. Many studies have been conducted to investigate virulence factors, including the chemical characterization of phytotoxic metabolites (PMs) that assist fungi in invading and colonizing crops such as grapevines. Moreover, multidisciplinary studies on their role in pathogenicity, symptom development, and plant-pathogen interactions have also been carried out. The aim of the present review is to provide an illustrative overview of the biological and chemical characterization of PMs produced by fungi involved in Eutypa dieback, Esca complex, and Botryosphaeria dieback. Moreover, multidisciplinary investigations on host-pathogen interactions, including those using cutting-edge Omics techniques, will also be reviewed and discussed. Finally, challenges and opportunities in the role of PMs for reliable field diagnosis and control of GTDs in vineyards will also be explored.

Morphology and phylogeny of ascomycetes associated with walnut trees (Juglans regia) in Sichuan province, China

In Sichuan province, walnuts, consisting of Juglans regia, Juglans sigillata, and the hybrid J. regia × J. sigillata, are commercially important edible nuts, and J. regia is the most widespread plant. To date, the diversity and distribution of fungi inhabiting on Juglans have not received enough attention, although there have been studies focusing on pathogens from fruit and stem. In order to update the checklist of fungi associated with Sichuan walnuts, a survey on fungi associated with the three Juglans species from 15 representative regions in Sichuan was conducted. In this article, ten fungi distributed in two classes of Ascomycota (Dothideomycetes and Sordariomycetes) were described based on morpho-molecular analyses, and two novel species, Neofusicoccum sichuanense and Sphaerulina juglandina, a known species of Ophiognomonia leptostyla, and seven new hosts or geographical records of Cladosporium tenuissimum, Diatrypella vulgaris, Helminthosporium juglandinum, Helminthosporium velutinum, Loculosulcatispora hongheensis, Periconia byssoides, and Rhytidhysteron subrufulum were included. Morphological descriptions and illustrations of these fungi are provided.

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.

The road to molecular identification and detection of fungal grapevine trunk diseases

Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.

Brunneosporopsis yunnanensis gen. et sp. nov. and Allocryptovalsa xishuangbanica sp. nov., New Terrestrial Sordariomycetes from Southwest China

Three fungal taxa were collected on dead branches of wood during fieldwork in Sichuan and Yunnan Provinces, China. The new generic name Brunneosporopsis gen. nov. and species B. yunnanensis sp. nov. are introduced for a novel taxon characterized by globose to subglobose and dark olivacous-brown conidia. Phylogenetic analyses based on combined LSU, SSU and tef1-α loci strongly support the monophyly of this taxon and place it in the subclass Diaporthomycetidae. It could not be assigned to any currently recognized families in the subclass and was, therefore, placed in the Diaporthomycetidae genera incertae sedis. A second taxon represents a new species in Allocryptovalsa based on an analysis of the sequence datasets of ITS and btub loci of the novel, brown-spored sexual morphic species. This taxon is described here as A. xishuangbanica sp. nov. An interesting hypocrealean fungus producing synnemata, Stilbocrea gracilipes, was collected from dead wood of an unknown host from Sichuan Province and is reported here, with asexual morph from both the host and culture as well as LSU, ITS, tef1-α, rpb2 and rpb1 sequence data.

Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters

Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata. Despite the relevance of this species to the global wine industry, its genomic diversity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E. lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic diversity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations.

Eutypa dieback of grapevine, caused by the Ascomycete fungus Eutypa lata, is responsible for significant economic losses to the wine industry. Despite the worldwide prevalence of this pathogen, its genomic diversity remains unknown, with only a single publicly available genome assembly. This knowledge gap was addressed by performing whole-genome sequencing of 40 E. lata isolates sourced from different hosts and geographical locations around Australia. Investigation of the genetic diversity of this population showed a high degree of gene-flow and sexual recombination as well as demographic expansion. Through the inspection of signatures of selective sweeps, repeat-mediated chromosomal rearrangements, and pan-genomic elements, it was shown that this species has a highly dynamic secondary metabolite production potential that could have important implications for its pathogenicity and lifestyle. In addition, application of a k-mer based GWAS methodology, identified a potential locus associated with the growth of this species within canes of Vitis vinifera.

Fungal canker agents in apple production hubs of Iran

To identify apple canker casual agents and evaluate their pathogenicity and virulence in apple production hubs including West Azarbaijan, Isfahan and Tehran provinces; samples were collected from symptomatic apple trees. Pathogenic isolates on the detached branches were identified as Cytospora cincta, Diplodia bulgarica, Neoscytalidium dimidiatum and Eutypa cf. lata. E. cf. lata was reported as a potential apple canker causal agent in Iran for the first time based on the pathogenicity test on the detached branches, whereas it caused no canker symptoms in apple trees until 6 months after inoculation. Currently, E. cf. lata seems to be adapted to a single city. C. cincta, D. bulgarica and N. dimidiatum caused canker symptoms in apple trees. “C. cincta” and also “C. cincta and N. dimidiatum” were the most widespread and aggressive apple canker species, respectively, associated with apple canker in Iran. Therefore, they are considered to be the main threat to apple production in Iran and should be carefully monitored. Disease progress curve, area under the disease progress curve and optimum temperatures were determined for mentioned species. It is concluded that the establishment of each species occurs in appropriate areas and times in terms of the optimum temperature for their growth.

New contributions to Diatrypaceae from karst areas in China

In this study, fungal specimens of the family Diatrypaceae were collected from karst areas in Guizhou, Hainan and Yunnan Provinces, China. Morpho-molecular analyses confirmed that these new collections comprise a new genus Pseudodiatrype, three new species (Diatrypelancangensis, Diatrypellapseudooregonensis and Eutypacerasi), a new combination (Diatrypellaoregonensis), two new records (Allodiatrypethailandica and Diatrypellavulgaris) from China and two other known species (Neoeutypellabaoshanensis and Paraeutypellacitricola). The new taxa are introduced, based on multi-gene phylogenetic analyses (ITS, β-tubulin), as well as morphological analyses. The new genus Pseudodiatrype is characterised by its wart-like stromata with 5-20 ascomata immersed in one stroma and the endostroma composed of thin black outer and inner layers of large white cells with thin, powdery, yellowish cells. These characteristics separate this genus from two similar genera Allodiatrype and Diatrype. Based on morphological as well as phylogenetic analyses, Diatrypelancangensis is introduced as a new species of Diatrype. The stromata of Diatrypelancangensis are similar to those of D.subundulata and D.undulate, but the ascospores are larger. Based on phylogenetic analyses, Diatrypeoregonensis is transferred to the genus Diatrypella as Diatrypellaoregonensis while Diatrypellapseudooregonensis is introduced as a new species of Diatrypella with 8 spores in an ascus. In addition, multi-gene phylogenetic analyses show that Eutypacerasi is closely related to E.lata, but the ascomata and asci of Eutypacerasi are smaller. The polyphyletic nature of some genera of Diatrypaceae has led to confusion in the classification of the family, thus we discuss whether the number of ascospores per asci can still be used as a basis for classification.

Trunk Surgery as a Tool to Reduce Foliar Symptoms in Diseases of the Esca Complex and Its Influence on Vine Wood Microbiota

In the last few years, trunk surgery has gained increasing attention as a method to reduce foliar symptoms typical of some of the Esca complex diseases. The technique relies on the mechanical removal of decayed wood by a chainsaw. A study on a 14-year-old Cabernet Sauvignon vineyard was carried out to validate the efficacy of trunk surgery and explore possible explanations behind it. Three levels of treatment were applied to three of the most characteristic symptoms associated with some diseases of the Esca complex, such as leaf stripe symptoms (LS), wilted shoots (WS) and apoplexy (APP). The most promising results were obtained by complete trunk surgery, where the larger decay removal allowed lower symptom re-expression. According to the wood types analyzed (decay, medium and sound wood), different changes in microbiota were observed. Alpha-diversity generally decreased for bacteria and increased for fungi. More specifically, main changes were observed for Fomitiporia mediterranea abundance that decreased considerably after trunk surgery. A possible explanation for LS symptom reduction after trunk surgery could be the microbiota shifting caused by the technique itself affecting a microbic-shared biochemical pathway involved in symptom expression.

The Hidden Diversity of Diatrypaceous Fungi in China

In this study, we investigated the diversity of diatrypaceous fungi from six regions in China based on morpho-molecular analyses of combined ITS and tub2 gene regions. We accept 23 genera in Diatrypaceae with 18 genera involved in the phylogram, and the other five genera are lacking living materials with sequences data. Eleven species included in four genera (viz. Allocryptovalsa, Diatrype, Diatrypella, and Eutypella) have been isolated from seven host species, of which nine novel species (viz. Allocryptovalsa castaneae, A. castaneicola, Diatrype betulae, D. castaneicola, D. quercicola, Diatrypella betulae, Da. betulicola, Da. hubeiensis, and Da. shennongensis), a known species of Diatrypella favacea, and a new record of Eutypella citricola from the host genus Morus are included. Current results show the high diversity of Diatrypaceae which are wood-inhabiting fungi in China.

Paraeutypella guizhouensis gen. et sp. nov. and Diatrypella longiasca sp. nov. (Diatrypaceae) from China

Background

In this study, we introduce a novel genus, Paraeutypella, of the family Diatrypaceae comprising three species viz. Paraeutypellaguizhouensis sp. nov. and P.citricola (basionym: Eutypellacitricola) and P.vitis (basionym: Sphaeriavitis). Diatrypellalongiasca sp. nov. is also introduced, which forms a distinct clade in Diatrypella sensu stricto. The discovery of this new genus will contribute to expanding the knowledge and taxonomic framework of Diatrypaceae (Xylariales).

New information

Generic delimitations in Diatrypaceae are unsettled because the phylogeny has yet to be resolved using extensive taxon sampling and sequencing of ex-type cultures. During an investigation of xylarialean fungi, we collected eutypella-like fungi which is distinct from Eutypella sensu stricto in our phylogenetic analyses (ITS and β-tubulin), thus, introduced as Paraeutypellaguizhouensis gen. et sp. nov.. Paraeutypella is characterised by having 4–25 perithecia in a stroma each with 3–6 sulcate, long ostiolar necks. Paraeutypellacitricola comb. nov. (basionym: Eutypellacitricola) is introduced on Acer sp. from China. Diatrypellalongiasca sp. nov. is introduced as a new species in Diatrypella sensu stricto. which has 2–5 ascomata per stroma and long ascospores, unusual when compared to other Diatrypella species and distinct phylogenetically.

The Ambrosia Beetle Sueus niisimai (Scolytinae: Hyorrhynchini) is Associated with the Canker Disease Fungus Diatrypella japonica (Xylariales)

Ambrosia beetles in the subtribe Hyorrhynchini are one example of an entire ambrosia beetle lineage whose fungi have never been studied. Here, we identify one dominant fungus associated with a widespread Asian hyorrhynchine beetle Sueus niisimai. This fungus was consistently isolated from beetle galleries from multiple collections. Phylogenetic analyses of combined ITS rDNA and β-tubulin sequences identified the primary fungal symbiont as Diatrypella japonica Higuchi, Nikaido & Hattori (Diatrypaceae, Xylariales, Sordariomycetes), which was recently described as a pathogen of sycamore (Platanus spp.) in Japan. To assess the invasion potential of this beetle-fungus interaction into the U.S., we have investigated the pathogenicity of two D. japonica strains on four species of healthy landscape trees native to the southeastern United States. Only Shumard oak (Quercus shumardii) responded with lesions significantly greater than the control inoculations, but there was no observable dieback or tree mortality. Although disease symptoms were not as prominent as in previous studies of the same fungus in Japan, routine reisolation from the inoculation point suggests that this species is capable of colonizing healthy sapwood of several tree species. Our study shows that the geographical area of its distribution is broader in Asia and potentially includes many hosts of its polyphagous vector. We conclude that the Sueus-Diatrypella symbiosis has high invasion potential but low damage potential, at least on young trees during the growing season.

A Survey of Trunk Disease Pathogens within Citrus Trees in Iran

Citrus trees with cankers and dieback symptoms were observed in Bushehr (Bushehr province, Iran). Isolations were made from diseased cankers and branches. Recovered fungal isolates were identified using cultural and morphological characteristics, as well as comparisons of DNA sequence data of the nuclear ribosomal DNA-internal transcribed spacer region, translation elongation factor 1α, β-tubulin, and actin gene regions. Dothiorellaviticola, Lasiodiplodia theobromae, Neoscytalidiumhyalinum, Phaeoacremonium (P.) parasiticum, P. italicum, P. iranianum, P. rubrigenum, P. minimum, P. croatiense, P. fraxinopensylvanicum, Phaeoacremonium sp., Cadophora luteo-olivacea, Biscogniauxia (B.) mediterranea, Colletotrichum gloeosporioides, C. boninense, Peyronellaea (Pa.) pinodella, Stilbocrea (S.) walteri, and several isolates of Phoma, Pestalotiopsis, and Fusarium species were obtained from diseased trees. The pathogenicity tests were conducted by artificial inoculation of excised shoots of healthy acid lime trees (Citrus aurantifolia) under controlled conditions. Lasiodiplodia theobromae was the most virulent and caused the longest lesions within 40 days of inoculation. According to literature reviews, this is the first report of L. theobromae and N. hyalinum on citrus in Iran. Additionally, we report several Phaeoacremonium species, S. walteri, Pa. pinodella and C. luteo-olivacea on citrus trees for the first time in the world.

Lasiodiplodia mitidjana sp. nov. and other Botryosphaeriaceae species causing branch canker and dieback of Citrus sinensis in Algeria

Several Botryosphaeriaceae species are known to occur worldwide, causing dieback, canker and fruit rot on various hosts. Surveys conducted in ten commercial citrus orchards in the northern region of Algeria revealed five species of Botryosphaeriaceae belonging to three genera associated with diseased trees. Morphological and cultural characteristics as well as phylogenetic analyses of the internal transcribed spacer (ITS) region and the translation elongation factor 1-alpha (tef1-α) identified Diplodia mutila, Diplodia seriata, Dothiorella viticola, Lasiodiplodia mediterranea and a novel species which is here described as Lasiodiplodia mithidjana sp. nov.. Of these, L. mithidjana (14.1% of the samples) and L. mediterranea (13% of the samples) were the most widespread and abundant species. Pathogenicity tests revealed that L. mediterranea and D. seriata were the most aggressive species on citrus shoots. This study highlights the importance of Botryosphaeriaceae species as agents of canker and dieback of citrus trees in Algeria.

Diversity Profiling of Grapevine Microbial Endosphere and Antagonistic Potential of Endophytic Pseudomonas Against Grapevine Trunk Diseases

Grapevine trunk diseases (GTDs) are a serious problem of grapevines worldwide. The microbiota of the grapevine endosphere comprises prokaryotic and eukaryotic endophytes, which may form varied relationships with the host plant from symbiotic to pathogenic. To explore the interaction between grapevine endophytic bacteria and GTDs, the endomicrobiome associated with grapevine wood was characterized using next-generation Illumina sequencing. Wood samples were collected from grapevine trunks with and without external symptoms of GTD (cankers) from two vineyards in the Hunter Valley and Hilltops, NSW, Australia and metagenomic characterization of the endophytic community was conducted using the 16S rRNA gene (341F/806R) and ITS (1F/2R) sequences. Among the important GTD pathogens, Phaeomoniella, Phaeoacremonium, Diplodia and Cryptovalsa species were found to be abundant in both symptomatic and asymptomatic grapevines from both vineyards. Eutypa lata and Neofusicoccum parvum, two important GTD pathogens, were detected in low numbers in Hilltops and the Hunter Valley, respectively. Interestingly, Pseudomonas dominated the bacterial community in canker-free grapevine tissues in both locations, comprising 56-74% of the total bacterial population. In contrast, the Pseudomonas population in grapevines with cankers was significantly lower, representing 29 and 2% of the bacterial community in Hilltops and the Hunter Valley, respectively. The presence of Pseudomonas in healthy grapevine tissues indicates its ability to colonize and survive in the grapevine. The potential of Pseudomonas spp. as biocontrol agents against GTD pathogens was also explored. Dual culture tests with isolated fluorescent Pseudomonas against mycelial discs of nine Botryosphaeria dieback, three Eutypa dieback, and two Esca/Petri disease pathogens, revealed antagonistic activity for 10 Pseudomonas strains. These results suggest the potential of Pseudomonas species from grapevine wood to be used as biocontrol agents to manage certain GTD pathogens.

Temporal Development of the Culturable, Endophytic Fungal Community in Healthy Grapevine Branches and Occurrence of GTD-Associated Fungi

Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.

Pruning Wound Protection Strategies for Simultaneous Control of Eutypa and Botryosphaeria Dieback in New Zealand

The grapevine trunk diseases Eutypa and Botryosphaeria dieback threaten the sustainability of vineyards worldwide. This study aimed to develop practical and efficient wound protection strategies, which will lead to widespread adoption of preventative control for these diseases and increased longevity of vineyards. Five fungicides (tebuconazole, carbendazim, fluazinam, mancozeb, and flusilazole) were evaluated for efficacy against Eutypa lata and Neofusicoccum luteum infection on pruning wounds of 'Sauvignon blanc' in a New Zealand vineyard. All five fungicides controlled infection by both pathogens to varying degrees, with mean percent disease control of 70 to 90% for E. lata and 33 to 93% for N. luteum. This has led to the first known registration of a fungicide, fluazinam (Gem), for simultaneous control of both Eutypa and Botryosphaeria dieback. Furthermore, application of carbendazim with tractor-driven sprayers provided similar control of E. lata and N. luteum to that when applied by hand with a paintbrush. This constitutes the first report of Botryosphaeria dieback control with fungicides applied with tractor-driven sprayers.

Molecular Methods to Detect and Quantify Botryosphaeriaceae Inocula Associated With Grapevine Dieback in Australia

Botryosphaeria dieback, caused by species of Botryosphaeriaceae, is an important grapevine trunk disease in Australia. Inocula produced by the pathogens are primarily dispersed by rain splash and wind and infect pruning wounds leading to cankers, dieback, and eventually death of vines. The objective of this study was to develop molecular tools to detect and quantify Botryosphaeriaceae inocula from the environment. These tools are essential for investigating spore dispersal patterns of Botryosphaeriaceae pathogens in Australian vineyards. DNA extraction protocols were evaluated and one modified protocol was found suitable for extracting Botryosphaeriaceae DNA from artificially and naturally inoculated Burkard volumetric spore sampler tapes. Multispecies primers and a hydrolysis probe for quantitative PCR (qPCR) were further developed to detect and quantify Botryosphaeriaceae inocula from environmental samples. Specificity tests showed that the multispecies primers were able to amplify the DNA of 10 Botryosphaeriaceae species (58 isolates) found in Australia while none of the 27 nontarget fungal species (90 isolates) tested were amplified. The qPCR assay was suitable for amplifying purified DNA, synthetic DNA fragments (gBlocks), and mixed DNA from spore trap tapes. The qPCR method developed in this study was shown to be rapid and sensitive in detecting Botryosphaeriaceae inocula from the environment using spore traps.

Eutypa, Eutypella, and Cryptovalsa Species (Diatrypaceae) Associated with Prunus Species in South Africa

Stone fruit trees (Prunus spp.) are economically important fruit trees cultivated in South Africa. These trees are often grown in close proximity to vineyards and are to a large extent affected by the same trunk disease pathogens as grapevines. The aim of the present study was to determine whether stone fruit trees are inhabited by Diatrypaceae species known from grapevines and whether these trees could act as alternative hosts for these fungal species. Isolations were carried out from symptomatic wood of Prunus species (almond, apricot, cherry, nectarine, peach, and plum) in stone fruit growing areas in South Africa. Identification of isolates was based on phylogenetic analyses of the internal transcribed spacer region and β-tubulin gene. Forty-six Diatrypaceae isolates were obtained from a total of 380 wood samples, from which five species were identified. All five species have also been associated with dieback of grapevine. The highest number of isolates was found on apricot followed by plum. No Diatrypaceae species were isolated from peach and nectarine. Eutypa lata was the dominant species isolated (26 isolates), followed by Cryptovalsa ampelina (7), Eutypa cremea (5), Eutypella citricola (5), and Eutypella microtheca (3). First reports from Prunus spp. are E. cremea, E. citricola, and E. microtheca. Pathogenicity tests conducted on apricot and plum revealed that all these species are pathogenic to these hosts, causing red-brown necrotic lesions like those typical of Eutypa dieback on apricot.

Diversity of Diatrypaceae Species Associated with Dieback of Grapevines in South Africa, with the Description of Eutypa cremea sp. nov

Recent studies in grape-growing areas including Australia, California, and Spain have revealed an extensive diversity of Diatrypaceae species on grapevines showing dieback symptoms and cankers. However, in South Africa, little is known regarding the diversity of these species in vineyards. The aim of this study was, therefore, to identify and characterize Diatrypaceae species associated with dieback symptoms of grapevine in South Africa. Isolates were collected from dying spurs of grapevines aged 4 to 8 years old, grapevine wood showing wedge-shaped necrosis when cut in cross section as well as from perithecia on dead grapevine wood. The collected isolates were identified based on morphological characters and phylogenetic analyses of the internal transcribed spacer region (ITS) and β-tubulin gene. Seven Diatrypaceae species were identified on grapevine, namely Cryptovalsa ampelina, C. rabenhorstii, Eutypa consobrina, E. lata, E. cremea sp. nov., Eutypella citricola, and E. microtheca. The dying spurs yielded the highest diversity of species when compared with the wedge-shaped necrosis and/or perithecia. C. ampelina was the dominant species in the dying spurs, followed by E. citricola, whereas E. lata was the dominant species isolated from the wedge-shaped necroses and perithecia. These results confirm E. lata as an important grapevine canker pathogen in South Africa, but the frequent association of C. ampelina with spur dieback suggests that this pathogen plays a more prominent role in dieback than previously assumed. In some cases, more than one species were isolated from a single symptom, which suggests that interactions may be occurring leading to decline of grapevines. C. rabenhorstii, E. consobrina, E. citricola, E. microtheca, and E. cremea are reported for the first time on grapevine in South Africa.

A Method to Detect and Quantify Eutypa lata and Diplodia seriata-Complex DNA in Grapevine Pruning Wounds

Trunk diseases are factors that limit sustainability of vineyards worldwide. Botryosphaeria and Eutypa diebacks are caused by several fungi belonging to the Botryosphaeriaceae and Diatrypaceae, respectively, with Diplodia seriata and Eutypa lata being two of the most common species. Previous information indicated that the traditional isolation method used to detect these pathogens from plant samples could underestimate their incidence levels. In the present study, we designed two sets of primers that target the β-tubulin gene and that are amenable for quantitative real-time PCR (qPCR) Sybr-Green assays for the detection and quantification of D. seriata-complex (DseCQF/R) and E. lata (ElQF/R) DNA. The design of a species-specific assay was achieved for E. lata. For D. seriata, a species-specific assay could not be designed. The low interspecific diversity across β-tubulin genes resulted in an assay that could not discriminate D. seriata from some closely related species either not yet reported or presenting a low prevalence on grapevine, such as D. intermedia. We validated our technique on grapevine spur samples naturally and artificially infected with D. seriata and E. lata during the dormant season. Experimental grapevines were located in two counties of northern California where the incidence of both pathogens was previously reported. The qPCR assays revealed that a high frequency of pruning wound infections (65%) was achieved naturally by E. lata, while low infection frequency (less than 5%) was observed using the reisolation method. For D. seriata-complex, low (5%) to no natural infection frequencies were observed by the qPCR and the reisolation method, respectively. These results also provided evidence that our qPCR detection methods were more sensitive to assess the incidence of E. lata and D. seriata-complex in plant samples, than traditional isolation techniques. Benefits of molecular methods for the detection of canker pathogens in the field under natural conditions are discussed.

Identification, Distribution, and Pathogenicity of Diatrypaceae and Botryosphaeriaceae Associated with Citrus Branch Canker in the Southern California Desert

Several members of the families Botryosphaeriaceae and Diatrypaceae are known as canker and dieback pathogens of a number of woody hosts. Because desert citrus production in California can occur in proximity to table grape production, it was suspected that fungi associated with grapevine cankers might also be associated with citrus branch canker and dieback decline. To determine the fungi associated with branch canker and dieback disease of citrus in the southern California desert regions, surveys were conducted from 2011 to 2013 in the major citrus-growing regions of Riverside, Imperial, and San Diego Counties. Cankered tissues were collected from branches showing symptoms typical of branch canker and dieback. Various fungal species were recovered from necrotic tissues and species were identified morphologically and by phylogenetic comparison of partial sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), β-tubulin gene, and elongation factor 1-α genes with those of other species in GenBank. Four fungi, including Neoscytalidium hyalinum, Eutypella citricola, E. microtheca, and an unnamed Eutypella sp., were associated with branch canker. N. hyalinum was the most frequently recovered fungus from symptomatic tissues (31%) followed by E. citricola (10%), E. microtheca (4%), and the Eutypella sp. (2%). In pathogenicity tests, all fungi caused lesions when inoculated on 'Lisbon' lemon (citrus) branches. Lesions caused by the Eutypella sp. were significantly longer than those of the other Eutypella spp.; however, they did not differ significantly from those produced by N. hyalinum. The most-parsimonious unrooted trees based on the combined data of ITS and partial β-tubulin gene region sequences showed three distinct clades of Eutypella spp. (E. citricola, E. microtheca, and an unidentified Eutypella sp.). Similarly, ITS and partial translation elongation factor 1-α gene region sequences differentiated two species of Neoscytalidium, N. hyalinum and N. novaehollandiae. Identifying the diversity, distribution, and occurrence of these fungal pathogens is useful for the management of citrus branch canker and dieback disease in the desert citrus-growing regions of California.

Trunk Disease Fungi Associated With Diospyros kaki in South Africa

Persimmon trees with dieback symptoms and cankers were observed in three production areas in Western Cape Province in South Africa. Isolations were made from diseased branches, cankers, and pruning wounds as well as fungal fruiting bodies on dead branches and old pruning wounds. Several trunk disease pathogens were identified based on morphological characteristics and by molecular methods, including Diaporthe eres, D. infecunda, Eutypella citricola, E. microtheca, Phaeoacremonium parasiticum, P. scolyti, P. australiense, P. minimum, Fomitiporia capensis, Fomitiporia sp., Fomitiporella sp., and Inocutis sp., which were isolated from persimmon for the first time in the world. Other first reports from persimmon in South Africa include D. foeniculina, D. ambigua, D. mutila, Diaporthe sp., Neofusicoccum australe, N. parvum, Diplodia seriata, and Eutypa lata. Pathogenicity tests conducted with all species, except the basidiomycetes, confirmed their status as possible persimmon pathogens. This is the first study to determine and identify fungi associated with diseased persimmon in South Africa. The knowledge gained in this study forms the basis for further research to determine the impact of these fungi on persimmon productivity.

Seasonal Susceptibility of Grapevine Pruning Wounds and Cane Colonization in Catalonia, Spain Following Artificial Infection with Diplodia seriata and Phaeomoniella chlamydospora

Diplodia seriata and Phaeomoniella chlamydospora are two fungal pathogens associated with grapevine trunk diseases worldwide. This study aimed to evaluate the period during which grapevine pruning wounds remain susceptible to fungal infection and to describe the colonization of canes artificially inoculated with these pathogens. In the first experiment, pruning wounds made in either fall or winter were separately inoculated with each pathogen at different times after pruning. Wound susceptibility to both pathogens decreased as the period between pruning and inoculation increased, from high percentages recorded in the first inoculation round (D. seriata, 97.5% and P. chlamydospora, 75%) down to approximately 10% 12 weeks after pruning. Pruning wounds remained more susceptible to D. seriata after a late pruning in winter whereas no overall seasonal changes in wound susceptibility were detected for P. chlamydospora. In the second experiment, canes were pruned by leaving two different lengths between the top node and the pruning wound before inoculations. Pathogens were recovered at different incubation periods and from different sites along the canes to estimate fungal cane colonization. A longer pruned internode made cane colonization by P. chlamydospora difficult, as indicated by fungal recoveries lower than 10% at the lowest recovery site, whereas D. seriata was less inhibited.

Identification of Eutypa spp. Causing Eutypa Dieback of Grapevine in Eastern North America

Eutypa dieback of grapevine is caused by Eutypa lata in production areas with Mediterranean climates in California, Australasia, Europe, and South Africa. Eutypa dieback has also been described in the colder, eastern North American vineyards where cultivars adapted from native Vitis spp. (e.g., Vitis × labruscana 'Concord') are primarily grown. However, the causal agents associated with the diseases in this region have not been conclusively identified. Examination of 48 vineyards showing symptoms of dieback in the northeastern United States (Connecticut, Massachusetts, Michigan, New York, Ohio, and Rhode Island) and Ontario, Canada revealed that vineyards were mainly infected by Eutypa spp. other than E. lata. Multigene phylogenies (internal transcribed spacer ribosomal DNA, β-tubulin, and RNA polymerase II) of isolates recovered from these vineyards indicated that Eutypa dieback is caused primarily by an undescribed Eutypa sp. and E. laevata. Eutypa sp. was recovered from 56% of the vineyards examined, whereas E. laevata and E. lata were less far common (17 and 6%, respectively). Fruiting body morphology and spore dimensions supported phylogenetic separation of the three taxa. Pathogenicity tests conducted on Vitis vinifera 'Chardonnay' in the greenhouse and in the field verified that all three species were able to cause wood canker and to infect pruning wounds, respectively.

Identification of New Fungal Pathogens of Coast Live Oak in California

A decline of coast live oak (Quercus agrifolia) has been observed throughout southern California. In this study, the identity and pathogenicity of non-Botryosphaeriaceae fungal species consistently recovered from necrotic tissues of branch and bleeding trunk canker samples from these locations were assessed. Species were identified morphologically and by comparison of the complete sequence of the internal transcribed spacer (ITS) of the ribosomal DNA to sequences available in GenBank. Phylogenetic analyses were then conducted using ITS and partial sequences of the β-tubulin and mitochondrial small ribosomal subunit genes for unknown species. Fungi recovered and identified included Fusarium solani, Phaeoacremonium mortoniae, Diatrypella verrucaeformis, and a fungus described herein as Cryptosporiopsis querciphila sp. nov. One-year-old coast live oak seedlings were wound inoculated under controlled conditions to test pathogenicity of the fungal species. Each fungal species was successfully reisolated from necrotic tissue at 70 and 100% for P. mortoniae and all other species, and xylem necrosis was significantly different between all treatments and controls (P < 0.0001 at α = 0.05). Isolates of F. solani were the most aggressive tested. These species represent new records of fungal pathogens of coast live oak in California. Results from the pathogenicity test suggest that these fungi play a role in the decline of southern California coast live oak trees.