Ophiostoma novo-ulmi sp. nov., causative agent of current Dutch elm disease pandemics

Arthropods as Vectors of Grapevine Trunk Disease Pathogens: Quantification of Phaeomoniella chlamydospora on Arthropods and Mycobiome Analysis of Earwig Exoskeletons

Viticulture worldwide is challenged by grapevine trunk diseases (GTDs). Involvement of arthropods in the dissemination process of GTD pathogens, notably esca pathogens, is indicated after detection of associated pathogens on arthropod exoskeletons, and demonstration of transmission under artificial conditions. The present study is the first to quantify spore loads via qPCR of the esca-relevant pathogen Phaeomoniella chlamydospora on arthropods collected in German vineyards, i.e., European earwigs (Forficula auricularia), ants (Formicidae), and two species of jumping spiders (Marpissa muscosa and Synageles venator). Quantification of spore loads showed acquisition on exoskeletons, but most arthropods carried only low amounts. The mycobiome on earwig exoskeletons was described for the first time to reveal involvement of earwigs in the dispersal of GTDs in general. Metabarcoding data support the potential risk of earwigs as vectors for predominantly Pa. chlamydospora and possibly Eutypa lata (causative agent of Eutypa dieback), as respective operational taxonomical unit (OTU) assigned genera had relative abundances of 6.6% and 2.8% in total reads, even though with great variation between samples. Seven further GTD-related genera were present at a very low level. As various factors influence the successful transmission of GTD pathogens, we hypothesize that arthropods might irregularly act as direct vectors. Our results highlight the importance of minimizing and protecting pruning wounds in the field.

Unraveling the transcriptional features and gene expression networks of pathogenic and saprotrophic Ophiostoma species during the infection of Ulmus americana

American elm (Ulmus americana), highly prized for its ornamental value, has suffered two successive outbreaks of Dutch elm disease (DED) caused by ascomycete fungi belonging to the genus Ophiostoma. To identify the genes linked to the pathogenicity of different species and lineages of Ophiostoma, we inoculated 2-year-old U. americana saplings with six strains representing three species of DED fungi, and one strain of the saprotroph Ophiostoma quercus. Differential expression analyses were performed following RNA sequencing of fungal transcripts recovered at 3- and 10-days post-infection. Based on a total of 8,640 Ophiostoma genes, we observed a difference in fungal gene expression depending on the strain inoculated and the time of incubation in host tissue. Some genes overexpressed in the more virulent strains of Ophiostoma encode hydrolases that possibly act synergistically. A mutant of Ophiostoma novo-ulmi in which the gene encoding the ogf1 transcription factor had been deleted did not produce transcripts for the gene encoding the hydrophobin cerato-ulmin and was less virulent. Weighted gene correlation network analyses identified several candidate pathogenicity genes distributed among 13 modules of interconnected genes.IMPORTANCEOphiostoma is a genus of cosmopolitan fungi that belongs to the family Ophiostomataceae and includes the pathogens responsible for two devastating pandemics of Dutch elm disease (DED). As the mechanisms of action of DED agents remain unclear, we carried out the first comparative transcriptomic study including representative strains of the three Ophiostoma species causing DED, along with the phylogenetically close saprotrophic species Ophiostoma quercus. Statistical analyses of the fungal transcriptomes recovered at 3 and 10 days following infection of Ulmus americana saplings highlighted several candidate genes associated with virulence and host-pathogen interactions wherein each strain showed a distinct transcriptome. The results of this research underscore the importance of investigating the transcriptional behavior of different fungal taxa to understand their pathogenicity and virulence in relation to the timeline of infection.

Characterization of Trichoderma species from forest ecosystems by high-throughput phenotypic microarray

The use of beneficial organisms for the biocontrol of soil-borne pathogens in forestry is still poor explored. In this work, the nutritional demands of 10 previously selected isolates of Trichoderma for the biocontrol of forest soil-borne pathogens have been tested by Phenotype Microarray technology, to investigate about their C-source utilization and exploring the possibility to obtain a microbial consortia (SynCom), an innovative strategy for the biocontrol of plant disease. All Trichoderma isolates tested in this study showed a high spore germination percentage within 3 d and evidenced nutritional preference regardless of the species they belong to, and unrelated to their soil of origin. Results of growth curve analysis and MANOVA test revealed that all isolates assimilate a broad range of substrates, generally preferring complex compounds such as monosaccharides related compounds, nitrogen compounds, carboxylic acids and esters. No evidence of competition for nutritional resources have been observed among isolates of this study. As a result, a combination of different isolates could be proposed to obtain a SynCom useful for the practice of phytopathogen biocontrol in forestry. The addition of i-erythritol, adenosine and turanose to a growth substrate could be suggested as stimulating compounds for the growth of the selected Trichoderma isolates.

Vaccination of Elms against Dutch Elm Disease—Are the Associated Epiphytes and Endophytes Affected?

Dutch elm disease (DED) is causing extensive mortality of ecologically and culturally valuable elm trees (Ulmus spp.). Treatment of elms with the biological vaccine Dutch Trig® has been found to provide effective protection against DED by stimulating the defensive mechanisms of the trees. We hypothesized that the same mechanisms could also affect non-target organisms associated with elms. We explored the possible effects of vaccination on epiphytes (mainly lichens) and fungal endophytes living in the bark and young xylem of treated elms. Epiphyte cover percentage was assessed visually using a grid placed on the trunks, and a culture-based approach was used to study endophytes. Epiphyte cover was lower on the trunks of vaccinated trees as compared with unvaccinated trees, but the difference was not statistically significant. The presence of slow-growing and uncommon endophytes seemed to be reduced in continuously vaccinated elms; however, the highest endophyte diversity was found in elms four years after cessation of the vaccination treatments. Our findings suggest that although vaccination may shape epiphyte and endophyte communities in elms, its impacts are not straightforward. More detailed studies are, therefore, needed to inform the sustainable application of the vaccine as a part of the integrated management of DED.

Impacts of Dutch elm disease-causing fungi on foliage photosynthetic characteristics and volatiles in Ulmus species with different pathogen resistance

Global warming affects the abiotic and biotic growth environment of plants, including the spread of fungal diseases such as Dutch elm disease (DED). Dutch elm disease-resistance of different Ulmus species varies, but how this is reflected in leaf-level physiological pathogen responses has not been investigated. We studied the impacts of mechanical injury alone and mechanical injury plus inoculation with the DED-causing pathogens Ophiostoma novo-ulmi subsp. novo-ulmi and O. novo-ulmi subsp. americana on Ulmus glabra, a more vulnerable species, and U. laevis, a more resistant species. Plant stress responses were evaluated for 12 days after stress application by monitoring leaf net CO2 assimilation rate (A), stomatal conductance (gs), ratio of ambient to intercellular CO2 concentration (Ca/Ci) and intrinsic water-use efficiency (A/gs), and by measuring biogenic volatile (VOC) release by plant leaves. In U. glabra and U. laevis, A was not affected by time, stressors or their interaction. Only in U. glabra, gs and Ca/Ci decreased in time, yet recovered by the end of the experiment. Although the emission compositions were affected in both species, the stress treatments enhanced VOC emission rates only in U. laevis. In this species, mechanical injury especially when combined with the pathogens increased the emission of lipoxygenase pathway volatiles and dimethylallyl diphosphate and geranyl diphosphate pathway volatiles. In conclusion, the more resistant species U. laevis had a more stable photosynthesis, but stronger pathogen-elicited volatile response, especially after inoculation by O. novo-ulmi subsp. novo-ulmi. Thus, stronger activation of defenses might underlay higher DED-resistance in this species.

Independent Evolution Has Led to Distinct Genomic Signatures in Dutch Elm Disease-Causing Fungi and Other Vascular Wilts-Causing Fungal Pathogens

Vascular wilts are important diseases caused by plant pathogenic fungi that result in the rapid death of their plant hosts. This is due to a systemic defense mechanism whereby the plant induces the compartmentalization of the infected vascular system in order to reduce the propagation of the fungus. The ascomycete class Sordariomycetes contains several species that cause vascular wilts in diverse plant hosts, and they can be classified into four taxonomic orders. The genetic mechanisms of pathogenesis have already been investigated in Fusarium and Verticillium species, but they have not yet been compared with other well-known wilt-causing species, especially fungi causing oak wilt or Dutch elm disease (DED). Here we analyzed 20 whole genome assemblies of wilt-causing fungi together with 56 other species using phylogenetic approaches to trace expansions and contractions of orthologous gene families and gene classes related to pathogenicity. We found that the wilt-causing pathogens evolved seven times, experiencing the largest fold changes in different classes of genes almost every time. However, some similarities exist across groups of wilt pathogens, particularly in Microascales and Ophiostomatales, and these include the common gains and losses of genes that make up secondary metabolite clusters (SMC). DED pathogens do not experience large-scale gene expansions, with most of the gene classes, except for some SMC families, reducing in number. We also found that gene family expansions in the most recent common ancestors of wilt pathogen groups are enriched for carbohydrate metabolic processes. Our study shows that wilt-causing species evolve primarily through distinct changes in their repertoires of pathogenicity-related genes and that there is the potential importance of carbohydrate metabolism genes for regulating osmosis in those pathogens that penetrate the plant vascular system.

Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra

The aim of this study was to investigate fungal communities associated with leaves and roots of healthy-looking and declining U. glabra trees. The study was expected to demonstrate whether and how the diversity and composition of fungal communities change in these functional tissues following the infection by Dutch elm disease-causing fungi. The study sites included six U. glabra sites in Lithuania, where leaves and roots were sampled. DNA was isolated from individual samples, amplified using ITS2 rRNA as a marker, and subjected to high-throughput sequencing. The sequence analysis showed the presence of 32,699 high-quality reads, which following clustering, were found to represent 520 non-singleton fungal taxa. In leaves, the fungal species richness was significantly higher in healthy-looking trees than in diseased ones (p < 0.05). In roots, a similar comparison showed that the difference was insignificant (p > 0.05). The most common fungi in all samples of roots were Trichocladium griseum (32.9%), Penicillium restrictum (21.2%), and Unidentified sp. 5238_7 (12.6%). The most common fungi in all samples of leaves were Trichomerium sp. 5238_8 (12.30%), Aureobasidium pullulans (12.03%), Cladosporium sp. 5238_5 (11.73%), and Vishniacozyma carnescens (9.86%). The results showed that the detected richness of fungal taxa was higher in samples collected from healthy-looking trees than from diseased ones, thereby highlighting the negative impact of the Dutch elm disease on the overall fungal diversity.

No priming, just fighting-endophytic yeast attenuates the defense response and the stress induced by Dutch elm disease in Ulmus minor Mill

One century after the first report of Dutch elm disease (DED), there is still no practical solution for this problem threatening European and American elms (Ulmus spp.). The long breeding cycles needed to select resistant genotypes and the lack of efficient treatments keep disease incidence at high levels. In this work, the expression of defense-related genes to the causal agent of DED, Ophiostoma novo-ulmi Brasier, was analyzed in in vitro clonal plantlets from two DED-resistant and two DED-susceptible Ulmus minor Mill. trees. In addition, the effect of the inoculation of an endophytic pink-pigmented yeast (Cystobasidium sp.) on the plant's defense system was tested both individually and in combination with O. novo-ulmi. The multifactorial nature of the resistance to DED was confirmed, as no common molecular response was found in the two resistant genotypes. However, the in vitro experimental system allowed discrimination of the susceptible from the resistant genotypes, showing higher levels of oxidative damage and phenolic compounds in the susceptible genotypes after pathogen inoculation. Inoculation of the endophyte before O. novo-ulmi attenuated the plant molecular response induced by the pathogen and moderated oxidative stress levels. Niche competition, endophyte-pathogen antagonism and molecular crosstalk between the host and the endophyte are discussed as possible mechanisms of stress reduction. In sum, our results confirm the complex and heterogeneous nature of DED resistance mechanisms and highlight the possibility of using certain endophytic yeasts as biological tools to improve tree resilience against biotic stress.

First Report of Dutch Elm Disease Caused by Ophiostoma novo-ulmi in South Korea

During a routine survey conducted in July 2021, several dead and dying Ulmus macrocarpa trees were observed in an urban forest located in the Gyeonggi Province of South Korea. The trees had symptoms of wilt with yellowing and browning of leaves, and, in most cases, the trunks of dying trees were infested by bark beetles. Isolations were made from small pieces of wood taken from dying trees, and beetles were collected from the infested stems. Fungal isolates and the beetles were identified using DNA sequence-based phylogenies and morphology, respectively. The results revealed that the fungus was Ophiostoma novo-ulmi, the causal agent of Dutch elm disease, and the associated bark beetle was Scolytus jacobsoni. This study provides the first record of Dutch elm disease in South Korea and suggests that a nationwide survey for the disease should be undertaken.

Are Trees Planted along the Roads Sustainable? A Large-Scale Study in the Czech Republic

Trees provide a wide variety of ecosystem services to society and form the character of the environment and landscape. The analyses of tree populations and their resistance to changing conditions related to climate change typically focus on urban tree communities or forest trees. Similar studies on non-forest trees in the open landscape are largely missing; even the evidence on tree species abundance and distribution is sporadic. The article aims to expand the current evidence by a large-scale study on roadside trees in the Czech Republic. Using an extensive dataset that covers 91.2% of the total tree population along roads in nine NUTS3 regions, we assess the state and observed practices in selecting tree genera for roadside planting and discuss the implications for sustainable tree planning and management. Our survey documented 133,169 tree individuals belonging to 116 species and 40 genera. The results show that 75% of the total roadside plantings along second-class motorways and first-class roads are represented by seven main genera of deciduous trees (Acer, Fraxinus, Tilia, Malus, Betula, Populus, and Quercus), the distribution of which is similar across most Czech regions. New plantings have shifted only a little from the original species distribution. Traditional roadside species are becoming a more popular choice among new plantings, and the effort not to let the invasive trees outgrow into the mature stage is apparent. Most of the original and newly planted species are relatively suitable for emerging risks related to climate change. To achieve more sustainable patterns in roadside tree species composition in the future, especially the susceptibility of some commonly planted roadside tree species to emerging pests and diseases (e.g., Fraxinus excelsior) and to unfavorable site conditions typical for roadside tree stands (Tilia cordata) is of relevance to tree managers. The relative abundance of tree genera was proven to be similar in most studied regions, which makes the recommendations equally relevant for roadside tree managers across the country.

Molecular basis of cycloheximide resistance in the Ophiostomatales revealed

Resistance to the antibiotic Cycloheximide has been reported for a number of fungal taxa. In particular, some yeasts are known to be highly resistant to this antibiotic. Early research showed that this resulted from a transition mutation in one of the 60S ribosomal protein genes. In addition to the yeasts, most genera and species in the Ophiostomatales are highly resistant to this antibiotic, which is widely used to selectively isolate these fungi. Whole-genome sequences are now available for numerous members of the Ophiostomatales providing an opportunity to determine whether the mechanism of resistance in these fungi is the same as that reported for yeast genera such as Kluyveromyces. We examined all the available genomes for the Ophiostomatales and discovered that a transition mutation in the gene coding for ribosomal protein eL42, which results in the substitution of the amino acid Proline to Glutamine, likely confers resistance to this antibiotic. This change across all genera in the Ophiostomatales suggests that the mutation arose early in the evolution of these fungi.

Preinvasion Assessment of Exotic Bark Beetle-Vectored Fungi to Detect Tree-Killing Pathogens

Exotic diseases and pests of trees have caused continental-scale disturbances in forest ecosystems and industries, and their invasions are considered largely unpredictable. We tested the concept of preinvasion assessment of not yet invasive organisms, which enables empirical risk assessment of potential invasion and impact. Our example assesses fungi associated with Old World bark and ambrosia beetles and their potential to impact North American trees. We selected 55 Asian and European scolytine beetle species using host use, economic, and regulatory criteria. We isolated 111 of their most consistent fungal associates and tested their effect on four important southeastern American pine and oak species. Our test dataset found no highly virulent pathogens that should be classified as an imminent threat. Twenty-two fungal species were minor pathogens, which may require context-dependent response for their vectors at North American borders, while most of the tested fungi displayed no significant impact. Our results are significant in three ways; they ease the concerns over multiple overseas fungus vectors suspected of heightened potential risk, they provide a basis for the focus on the prevention of introduction and establishment of species that may be of consequence, and they demonstrate that preinvasion assessment, if scaled up, can support practical risk assessment of exotic pathogens.

Analyses of Xylem Vessel Size on Grapevine Cultivars and Relationship with Incidence of Esca Disease, a Threat to Grape Quality

Esca disease is one of the most important grapevine trunk diseases. It seriously reduces the quality and quantity of grapevine production, and results in a shorter vineyard lifespan. Previous studies have suggested that wide xylem vessel diameter favours development on grapevine of Phaeomoniella chlamydospora, one of the fungi involved in esca, thus affecting disease susceptibility. In this study, cultivars mainly originated from European countries, 27 white-berried and 24 red-berried grapevine cultivars, were grown in the same experimental vineyard and were analysed for xylem vessel sizes (as diameter and frequency) for correlation with esca incidence. In this study, the cultivars showed significant differences in the xylem vessel parameters. However, no relationship was detected between vessel size and esca incidence in the field. Overall, white-berried cultivars showed wider vessel diameters than red-berried cultivars. The relationship between xylem vessel size in the red-berried and white-berried cultivars and incidence of esca symptoms is discussed. We suggest that vessel anatomy profiles can provide useful information for further investigations on grapevine genotype structure–esca incidence relationships.

Morphological and Phylogenetic Analyses Reveal a New Species of Ceratocystiopsis (Ophiostomataceae, Ophiostomatales) Associated with Ips subelongatus in Inner Mongolia (China) with Weak Host Pathogenicity

Ophiostomatoid fungi are known for their associations with bark beetles, and some species are important sources of tree diseases. Ceratocystiopsis is a genus of the ophiostomatoid fungi in order Ophiostomatales. The shortage of DNA barcodes for many species in this genus has resulted in the presence of many unnamed cryptic species. In this study, Ceratocystiopsis subelongati sp. nov. associated with Ips subelongatus infesting Pinus sylvestris var. mongolica in Inner Mongolia, China, was identified and described based on phylogenetic inference of multi-gene DNA sequences and morphological characteristics. The species is characterized by a hyalorhinocladiella- to sporothrix-like asexual state and an optimal growth temperature of 30 °C. Artificial inoculation tests in the field showed that it is mildly pathogenic to five-year-old larch trees, the main host of I. subelongatus. It is also the first described Ceratocystiopsis species associated with I. subelongatus in China. This discovery should provide new avenues for studying the symbiosis between bark beetles and ophiostomatoid fungi.

Abundance and Diversity of Ophiostomatoid Fungi Associated With the Great Spruce Bark Beetle (Dendroctonus micans) in the Northeastern Qinghai-Tibet Plateau

The role of several virulent tree pathogens in host death has been overlooked because of the aggressiveness of their associated bark beetles. The great spruce bark beetle (Dendroctonus micans) is a widely distributed beetle that infests coniferous plants in Eurasia; however, its associated fungi have been poorly studied. Therefore, in this study, we elucidated the diversity of ophiostomatoid fungi associated with D. micans in the northeastern Qinghai-Tibet Plateau through field investigation, laboratory isolation, and culture analyses. A total of 220 strains of ophiostomatoid fungi were isolated from adults and tunnel galleries of D. micans infesting Picea crassifolia. We identified that the isolated strains belonged to eight ophiostomatoid species, including five new species (Ophiostoma huangnanense sp. nov., Ophiostoma maixiuense sp. nov., Ophiostoma sanum sp. nov., Leptographium sanjiangyuanense sp. nov., and Leptographium zekuense sp. nov.), one undefined species (Ophiostoma sp. 1), and two known species (Ophiostoma bicolor and Endoconidiophora laricicola), using phylogenetic analysis of multigene DNA sequences and morphological characteristics. This is the first time that E. laricicola, a pioneer invader and virulent pathogen, has been reported in China. We found that E. laricicola was the dominant species, accounting for 40.91% of the total number of ophiostomatoid communities. This study enriched the knowledge of the fungal associates of D. micans and elucidated that it carried the virulent pathogen E. laricicola at a surprisingly high frequency. Our findings show increased species association between D. micans and ophiostomatoid fungi and provide a basis for understanding the occurrence of forest diseases and pests.

Biological Control of Plant Diseases: An Evolutionary and Eco-Economic Consideration

Biological control is considered as a promising alternative to pesticide and plant resistance to manage plant diseases, but a better understanding of the interaction of its natural and societal functions is necessary for its endorsement. The introduction of biological control agents (BCAs) alters the interaction among plants, pathogens, and environments, leading to biological and physical cascades that influence pathogen fitness, plant health, and ecological function. These interrelationships generate a landscape of tradeoffs among natural and social functions of biological control, and a comprehensive evaluation of its benefits and costs across social and farmer perspectives is required to ensure the sustainable development and deployment of the approach. Consequently, there should be a shift of disease control philosophy from a single concept that only concerns crop productivity to a multifaceted concept concerning crop productivity, ecological function, social acceptability, and economical accessibility. To achieve these goals, attempts should make to develop “green” BCAs used dynamically and synthetically with other disease control approaches in an integrated disease management scheme, and evolutionary biologists should play an increasing role in formulating the strategies. Governments and the public should also play a role in the development and implementation of biological control strategies supporting positive externality.

Priming of Plant Defenses against Ophiostoma novo-ulmi by Elm (Ulmus minor Mill.) Fungal Endophytes

Some fungal endophytes of forest trees are recognized as beneficial symbionts against stresses. In previous works, two elm endophytes from the classes Cystobasidiomycetes and Eurotiomycetes promoted host resistance to abiotic stress, and another elm endophyte from Dothideomycetes enhanced host resistance to Dutch elm disease (DED). Here, we hypothesize that the combined effect of these endophytes activate the plant immune and/or antioxidant system, leading to a defense priming and/or increased oxidative protection when exposed to the DED pathogen Ophiostoma novo-ulmi. To test this hypothesis, the short-term defense gene activation and antioxidant response were evaluated in DED-susceptible (MDV1) and DED-resistant (VAD2 and MDV2.3) Ulmus minor genotypes inoculated with O. novo-ulmi, as well as two weeks earlier with a mixture of the above-mentioned endophytes. Endophyte inoculation induced a generalized transient defense activation mediated primarily by salicylic acid (SA). Subsequent pathogen inoculation resulted in a primed defense response of variable intensity among genotypes. Genotypes MDV1 and VAD2 displayed a defense priming driven by SA, jasmonic acid (JA), and ethylene (ET), causing a reduced pathogen spread in MDV1. Meanwhile, the genotype MDV2.3 showed lower defense priming but a stronger and earlier antioxidant response. The defense priming stimulated by elm fungal endophytes broadens our current knowledge of the ecological functions of endophytic fungi in forest trees and opens new prospects for their use in the biocontrol of plant diseases.

Complexities underlying the breeding and deployment of Dutch elm disease resistant elms

Dutch elm disease (DED) is a vascular wilt disease caused by the pathogens Ophiostoma ulmi and Ophiostoma novo-ulmi with multiple ecological phases including pathogenic (xylem), saprotrophic (bark) and vector (beetle flight and beetle feeding wound) phases. Due to the two DED pandemics during the twentieth century the use of elms in landscape and forest restoration has declined significantly. However new initiatives for elm breeding and restoration are now underway in Europe and North America. Here we discuss complexities in the DED 'system' that can lead to unintended consequences during elm breeding and some of the wider options for obtaining durability or 'field resistance' in released material, including (1) the phenotypic plasticity of disease levels in resistant cultivars infected by O. novo-ulmi; (2) shortcomings in test methods when selecting for resistance; (3) the implications of rapid evolutionary changes in current O. novo-ulmi populations for the choice of pathogen inoculum when screening; (4) the possibility of using active resistance to the pathogen in the beetle feeding wound, and low attractiveness of elm cultivars to feeding beetles, in addition to resistance in the xylem; (5) the risk that genes from susceptible and exotic elms be introgressed into resistant cultivars; (6) risks posed by unintentional changes in the host microbiome; and (7) the biosecurity risks posed by resistant elm deployment. In addition, attention needs to be paid to the disease pressures within which resistant elms will be released. In the future, biotechnology may further enhance our understanding of the various resistance processes in elms and our potential to deploy trees with highly durable resistance in elm restoration. Hopefully the different elm resistance processes will prove to be largely under durable, additive, multigenic control. Elm breeding programmes cannot afford to get into the host-pathogen arms races that characterise some agricultural host-pathogen systems.

An Efficient Strategy for Obtaining Mutants by Targeted Gene Deletion in Ophiostoma novo-ulmi

The dimorphic fungus Ophiostoma novo-ulmi is the highly aggressive pathogen responsible for the current, highly destructive, pandemic of Dutch elm disease (DED). Genome and transcriptome analyses of this pathogen previously revealed that a large set of genes expressed during dimorphic transition were also potentially related to plant infection processes, which seem to be regulated by molecular mechanisms different from those described in other dimorphic pathogens. Then, O. novo-ulmi can be used as a representative species to study the lifestyle of dimorphic pathogenic fungi that are not shared by the "model species" Candida albicans and Ustilago maydis. In order to gain better knowledge of molecular aspects underlying infection process and symptom induction by dimorphic fungi that cause vascular wilt disease, we developed a high-throughput gene deletion protocol for O. novo-ulmi. The protocol is based on transforming a Δmus52 O. novo-ulmi mutant impaired for non-homologous end joining (NHEJ) as the recipient strain, and transforming this strain with the latest version of OSCAR plasmids. The latter are used for generating deletion constructs containing the toxin-coding Herpes simplex virus thymidine kinase (HSVtk) gene which prevents ectopic integration of the T-DNA in Ophiostoma DNA. The frequency of gene deletion by homologous recombination (HR) at the ade1 locus associated with purine nucleotide biosynthesis was up to 77.8% in the Δmus52 mutant compared to 2% in the wild-type (WT). To validate the high efficiency of our deletion gene methodology we deleted ade7, which also belongs to the purine nucleotide pathway, as well as bct2, ogf1, and opf2 which encode fungal binuclear transcription factors (TFs). The frequency of gene replacement by HR for these genes reached up to 94%. We expect that our methodology combining the use of NHEJ deficient strains and OSCAR plasmids will function with similar high efficiencies for other O. novo-ulmi genes and other filamentous fungi.

Enhanced Outcrossing, Directional Selection and Transgressive Segregation Drive Evolution of Novel Phenotypes in Hybrid Swarms of the Dutch Elm Disease Pathogen Ophiostoma novo-ulmi

In the 1970s, clones of the two subspecies of Ophiostoma novo-ulmi, subsp. americana (SSAM) and subsp. novo-ulmi (SSNU) began to overlap in Europe, resulting in hybrid swarms. By 1983-1986, hybrids with high, SSAM-like growth and pathogenic fitness comprised ~75% of popula-tions at Limburg, Netherlands and Orvieto, Italy. We resampled these populations in 2008 to examine trends in hybrid fitness traits. Since preliminary sampling in 1979-1980, MAT-1 locus frequency had increased from ~0% to ~32% at Orvieto and 5% to ~43% at Limburg, and vegeta-tive incompatibility type frequency had changed from near clonal to extremely diverse at both sites. This represents an enormous increase in outcrossing and recombination potential, due in part to selective acquisition (under virus pressure) of MAT-1 and vic loci from the resident O. ulmi and in part to SSAM × SSNU hybridisation. Overt virus infection in the 2008 samples was low (~4%), diagnostic SSAM and SSNU cu and col1 loci were recombinant, and no isolates exhib-ited a parental SSAM or SSNU colony pattern. At both sites, mean growth rate and mean patho-genicity to 3-5 m clonal elm were high SSAM-like, indicating sustained directional selection for these characters, though at Orvieto growth rate was slower. The once frequent SSNU-specific up-mut colony dimorphism was largely eliminated at both sites. Perithecia formed by Limburg isolates were mainly an extreme, long-necked SSNU-like form, consistent with transgressive segregation resulting from mismatch of SSAM and SSNU developmental loci. Orvieto isolates produced more parental-like perithecia, suggesting the extreme phenotypes may have been se-lected against. The novel phenotypes in the swarms are remodelling O. novo-ulmi in Europe. Locally adapted genotypes may emerge.

Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans

Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. Using population genomic analyses of 36 full genome sequenced isolates, we demonstrated that European and Japanese isolates are highly divergent and the populations split 3000-19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, probably corresponding to the fungus colonization of the built environment in Europe. The demographic history of these populations, probably lead to low adaptive potential. Only two loci under selection were identified using a F_st outlier approach, and selective sweep analyses identified three loci with extended haplotype homozygosity. The selective sweep analyses found signals in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. Our results suggest that the dry rot fungus independently established in indoor environments in Europe and Japan and that invasive species can potentially establish large populations in new habitats based on a few colonizing individuals.

Comparative transcriptomics reveal different mechanisms for hyphal growth across four plant-associated dimorphic fungi

Fungal dimorphism is a phenomenon by which a fungus can grow both as a yeast form and a hyphal form. It is frequently related to pathogenicity as different growth forms are more suitable for different functions during a life cycle. Among dimorphic plant pathogens, the corn smut fungus Ustilago maydis serves as a model organism to understand fungal dimorphism and its effect on pathogenicity. However, there is a lack of data on whether mechanisms elucidated from model species are broadly applicable to other fungi. In this study, two non-model plant-associated species in the smut fungus subphylum (Ustilaginomycotina), Tilletiopsis washingtonensis and Meira miltonrushii, were selected to compare dimorphic mechanisms in these to those in U. maydis. We sequenced transcriptomic profiles during both yeast and hyphal growth in these two species using Tween40, a lipid mimic, as a trigger for hyphal growth. We then compared our data with previously published data from U. maydis and a fourth but unrelated dimorphic phytopathogen, Ophiostoma novo-ulmi. Comparative transcriptomics was performed to identify common genes upregulated during hyphal growth in all four dimorphic species. Intriguingly, T. washingtonensis shares the least similarities of transcriptomic alteration (hyphal growth versus yeast growth) with the others, although it is closely related to M. miltonrushii and U. maydis. This suggests that phylogenetic relatedness is not correlated with transcriptomic similarity under the same biological phenomenon. Among commonly expressed genes in the four species, genes in cell energy production and conversion, amino acid transport and metabolism and cytoskeleton are significantly enriched. Considering dimorphism genes characterized in U. maydis, as well as hyphal tip-associated genes from the literature, we found only genes encoding the cell end marker Tea4/TeaC and the kinesin motor protein Kin3 concordantly expressed in all four species. This suggests a divergence in species-specific mechanisms for dimorphic transition and hyphal growth.

Continent-Wide Tree Species Distribution Models May Mislead Regional Management Decisions: A Case Study in the Transboundary Biosphere Reserve Mura-Drava-Danube

The understanding of spatial distribution patterns of native riparian tree species in Europe lacks accurate species distribution models (SDMs), since riparian forest habitats have a limited spatial extent and are strongly related to the associated watercourses, which needs to be represented in the environmental predictors. However, SDMs are urgently needed for adapting forest management to climate change, as well as for conservation and restoration of riparian forest ecosystems. For such an operative use, standard large-scale bioclimatic models alone are too coarse and frequently exclude relevant predictors. In this study, we compare a bioclimatic continent-wide model and a regional model based on climate, soil, and river data for central to south-eastern Europe, targeting seven riparian foundation species—Alnus glutinosa, Fraxinus angustifolia, F. excelsior, Populus nigra, Quercus robur, Ulmus laevis, and U. minor. The results emphasize the high importance of precise occurrence data and environmental predictors. Soil predictors were more important than bioclimatic variables, and river variables were partly of the same importance. In both models, five of the seven species were found to decrease in terms of future occurrence probability within the study area, whereas the results for two species were ambiguous. Nevertheless, both models predicted a dangerous loss of occurrence probability for economically and ecologically important tree species, likely leading to significant effects on forest composition and structure, as well as on provided ecosystem services.

Comparison of qPCR and Metabarcoding Methods as Tools for the Detection of Airborne Inoculum of Forest Fungal Pathogens

Forest diseases caused by invasive fungal pathogens are becoming more common, sometimes with dramatic consequences to forest ecosystems. The development of early detection systems is necessary for efficient surveillance and to mitigate the impact of invasive pathogens. Windborne spores are an important pathway for introduction of fungal pathogens into new areas; the design of spore trapping devices adapted to forests, capable of collecting different types of spores, and aligned with development of efficient molecular methods for detection of the pathogen, should help forest managers anticipate new disease outbreaks. Two types of Rotorod samplers were evaluated for the collection of airborne inoculum of forest fungal pathogens with a range of spore sizes in five forest types. Detection was by specific quantitative PCR (qPCR) and by high-throughput sequencing (HTS) of amplified internal transcribed spacer sequences using a new bioinformatic pipeline, FungiSearch, developed for diagnostic purposes. Validation of the pipeline was conducted on mock communities of 10 fungal species belonging to different taxa. Although the sensitivity of the new HTS pipeline was lower than the specific qPCR, it was able to detect a wide variety of fungal pathogens. FungiSearch is easy to use, and the reference database is updatable, making the tool suitable for rapid identification of new pathogens. This new approach combining spore trapping and HTS detection is promising as a diagnostic tool for invasive fungal pathogens.

The mitochondrial genome of Ophiostoma himal-ulmi and comparison with other fungi causing Dutch elm disease

The mitochondrial genome of Ophiostoma himal-ulmi, a species endemic to the Western Himalayas and one of the fungi that cause Dutch elm disease, has been sequenced and characterized. The mitochondrial genome was compared with other available genomes for members of the Ophiostomatales, including other agents of Dutch elm disease (Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi, and Ophiostoma novo-ulmi subspecies americana), and it was observed that gene synteny is highly conserved, and variability among members of the fungi that cause Dutch-elm disease is primarily due to the number of intron insertions. Among the fungi that cause Dutch elm disease that we examined, O. himal-ulmi has the largest mitochondrial genomes (ranging from 94 934 to 111 712 bp), owing to the expansion of the number of introns.

Polypore fungi as a flagship group to indicate changes in biodiversity - a test case from Estonia

Polyporous fungi, a morphologically delineated group of Agaricomycetes (Basidiomycota), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia, Physisporinus, Sidera and Sistotrema). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3-5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.

Beetles as Plant Pathogen Vectors

Herbivorous insects, likewise, other organisms, are exposed to diverse communities of microbes from the surrounding environment. Insects and microorganisms associated with them share a range of relationships, including symbiotic and pathogenic. Insects damage plants by feeding on them and delivering plant pathogens to wounded places, from where pathogens spread over the plant. Thus insects can be considered as both pests and reservoirs or vectors of plant pathogens. Although beetles are not mentioned in the first place as plant pathogen vectors, their transmission of pathogens also takes place and affects the ecosystem. Here we present an overview of beetles as vectors of plant pathogens, including viruses, bacteria, fungi, nematodes, and Oomycota, which are responsible for developing plant diseases that can have a significant impact on crop yield and quality.

Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis

BACKGROUND

Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated from Asia; however, there is no report of laurel wilt causing widespread mortality on native Lauraceae trees in Asia. To gain insight into why R. lauricola is a tree-killing plant pathogen in North America, we generated and compared high quality draft genome assemblies of R. lauricola and its closely related non-pathogenic species R. aguacate.

RESULTS

Relative to R. aguacate, the R. lauricola genome uniquely encodes several small-secreted proteins that are associated with virulence in other pathogens and is enriched in secondary metabolite biosynthetic clusters, particularly polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit significant differences in secreted proteins including CAZymes that are associated with polysaccharide binding including the chitin binding CBM50 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and in vitro-grown fungal cultures further revealed a number of secreted protein genes, secondary metabolite clusters and alternative sulfur uptake and assimilation pathways that are coordinately up-regulated during infection.

CONCLUSIONS

Through these comparative analyses we have identified potential adaptations of R. lauricola that may enable it to colonize and cause disease on susceptible hosts. How these adaptations have interacted with co-evolved hosts in Asia, where little to no disease occurs, and non-co-evolved hosts in North America, where lethal wilt occurs, requires additional functional analysis of genes and pathways.

Ophiostomatoid fungi associated with mites phoretic on bark beetles in Qinghai, China

Bark beetle galleries are complex ecosystems where many microbes and other arthropods co-exist with the beetles. Fungi isolated from these galleries are often referred to as ‘beetle associates’, but the nature of these associations are poorly understood. The possibility that many of these fungi might in fact be mite associates is often overlooked. Several recent studies explored the diversity of fungi from conifer-infesting bark beetles and their galleries in China, but only one study considered phoretic mites and their fungi from conifer-infesting bark beetles in Yunnan, southwestern China. We studied the mites and fungi from galleries of four spruce-infesting bark beetle species in the high altitude forests of Qinghai province, western China. Mites were identified based on morphological characteristics, and fungi based on DNA sequences of four gene regions. In total, 173 mite individuals were collected belonging to 18 species in 11 genera. A total of 135 fungal isolates were obtained from the mites, representing 14 taxa from the Ophiostomatales. The most frequently isolated fungus was Ophiostoma nitidum, which represented 23.5% of the total isolates. More fungal species were found from fewer mites and bark beetle species than from the study in Yunnan. Although we could not elucidate the exact nature of interactions between mites and their fungi, our results re-enforce that these organisms should not be ignored in pest risk assessments of bark beetles, that often focus only on the beetles and their fungi. Three new species are described: Grosmannia zekuensis, O. manchongi, and O. kunlunense spp. nov., and our data revealed that O. typographi, recently described from China, is a synonym of O. ainoae.

Hybridization and introgression drive genome evolution of Dutch elm disease pathogens

Hybridization and the resulting introgression can drive the success of invasive species via the rapid acquisition of adaptive traits. The Dutch elm disease pandemics in the past 100 years were caused by three fungal lineages with permeable reproductive barriers: Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana. Using whole-genome sequences and growth phenotyping of a worldwide collection of isolates, we show that introgression has been the main driver of genomic diversity and that it impacted fitness-related traits. Introgressions contain genes involved in host-pathogen interactions and reproduction. Introgressed isolates have enhanced growth rate at high temperature and produce different necrosis sizes on an in vivo model for pathogenicity. In addition, lineages diverge in many pathogenicity-associated genes and exhibit differential mycelial growth in the presence of a proxy of a host defence compound, implying an important role of host trees in the molecular and functional differentiation of these pathogens.

The threat of emerging and re-emerging pathogenic Sporothrix species

Sporotrichosis is a neglected subcutaneous mycosis of humans and animals acquired by traumatic inoculation of soil and plant material (classical route) contaminated with infectious propagules of the pathogen or being bitten/scratched by infected cats (alternative route). Within a genus composed of 53 species displaying an essentially environmental core, there are only a few members which have considerable impacts on human or animal health. Infections are typically caused by S. brasiliensis, S. schenckii or S. globosa. Rare mammal pathogens include members of the S. pallida and S. stenocereus complexes. To illustrate the tremendous impact of emerging zoonotic sporotrichosis on public health, we discuss the main features of the expanding epidemics driven by S. brasiliensis in cats and humans. The cat entry in the transmission chain of sporotrichosis, causing epizooties (cat-cat) or zoonosis (cat-human), has contributed to the definition of new paradigms in Sporothrix transmission, reaching epidemic levels, making the disease a serious public health problem. Indeed, S. brasiliensis infection in humans and animals is likely to become even more important in the future, with projections of its expansion in biogeographic domains and host range, as well as greater virulence in mammals. Therefore, lessons from a long-standing outbreak in the state of Rio de Janeiro about the source and distribution of the etiological agents among outbreak areas can be used to create better control and prevention plans and increase awareness of sporotrichosis as a serious emerging zoonotic disease.

Genetic Variation Explains Changes in Susceptibility in a Naïve Host Against an Invasive Forest Pathogen: The Case of Alder and the Phytophthora alni Complex

Predicting whether naïve tree populations have the potential to adapt to exotic pathogens is necessary owing to the increasing rate of invasions. Adaptation may occur as a result of natural selection when heritable variation in terms of susceptibility exists in the naïve population. We searched for signs of selection on black alder (Alnus glutinosa) stands growing on riverbanks invaded by two pathogens differing in aggressiveness, namely, Phytophthora uniformis (PU) and Phytophthora × alni (PA). We compared the survival and heritability measures from 72 families originating from six invaded and uninvaded (naïve) sites by performing in vitro inoculations. The results from the inoculations were used to assess the relative contribution of host genetic variation on natural selection. We found putative signs of natural selection on alder exerted by PU but not by PA. For PU, we found a higher survival in families originating from invaded sites compared with uninvaded sites. The narrow sense heritability of susceptibility to PU of uninvaded populations was significantly higher than to PA. Simulated data supported the role of heritable genetic variation on natural selection and discarded a high aggressiveness of PA decreasing the transmission rate as an alternative hypothesis for a slow natural selection. Our findings expand on previous attempts of using heritability as a predictor for the likelihood of natural adaptation of naïve tree populations to invasive pathogens. Measures of genetic variation can be useful for risk assessment purposes or when managing Phytophthora invasions.

Ophiostomatoid fungi associated with Ips subelongatus, including eight new species from northeastern China

Ips subelongatus is a major pest that infects larch plantations over large areas of northern and northeastern China. Ips species are closely associated with ophiostomatoid fungi that are morphologically well-adapted for dispersal by beetles. These associations result in important threat for coniferous forests worldwide. The aim of this study was to characterize the ophiostomatoid communities associated with I. subelongatus infesting Larix species and sympatric Pinus sylvestris var. mongolica in northeastern China forests. Morphological and multilocus phylogenetic approaches (based on six markers: ITS, LSU, 60S, β-tubulin, EF-1α, and CAL gene regions) allowed identifying 14 species of four genera (Ceratocystiopsis, Endoconidiophora, Leptographium and Ophiostoma). Eight species are showed to be new to science. Most strains resided in two Ophiostoma species complexes, viz. the O. clavatum and the O. ips complexes, all together accounting for 76.8% of all isolates. Ophiostoma hongxingense sp. nov., O. peniculi sp. nov., and O. subelongati sp. nov. (O. clavatum complex) and O. pseudobicolor sp. nov. (O. ips complex) were the four dominant species. The ophiostomatoid communities associated with larch bark beetles, I. cembrae and I. subelongatus, in Europe and Asia, China and Japan, also were compared. These comparisons showed distinct, specific assemblage patterns.

Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum

The sudden oak and sudden larch death pathogen Phytophthora ramorum emerged simultaneously in the United States on oak and in Europe on Rhododendron in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for P. ramorum have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of P. ramorum in Asia provide renewed impetus for research on the sudden oak death pathogen.

Complex Insect-Pathogen Interactions in Tree Pandemics

Tree pandemics are a major cause of economic and ecological loss in forest and urban ecosystems. They often depend on the introduction of a non-native pathogen, which is occupying the niche of a native, non-aggressive organism. Complex interactions with native insects carrying fungi and nematodes can be established based on the proximity of the aggressive pathogenic agents. Here we review three major pandemics of forest and urban trees in temperate ecosystems at world scale, i.e., the Dutch elm disease, the cypress canker, and the pine wilt disease. For each system, the relationships between aggressive and non-aggressive fungi and nematodes with the native insect vectors are presented. Hidden players such as insects, microorganisms or plants, which may have the role of facilitating or contrasting the performance of the agents, are also considered. Results suggest that pandemics rely on the introduction of a non-native pathogen that exploits well-developed interactions between native non-aggressive organisms and insects associated with trees. The success of the invaders depends on the morpho-physiological proximity of the players and on the mutual benefits resulting from the associations. Deciphering such interactions in native systems may help to predict the outcome of the introduction of new pathogens and the development of new tree pandemics.

The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.

Geosmithia-Ophiostoma: a New Fungus-Fungus Association

In Europe as in North America, elms are devastated by Dutch elm disease (DED), caused by the alien ascomycete Ophiostoma novo-ulmi. Pathogen dispersal and transmission are ensured by local species of bark beetles, which established a novel association with the fungus. Elm bark beetles also transport the Geosmithia fungi genus that is found in scolytids' galleries colonized by O. novo-ulmi. Widespread horizontal gene transfer between O. novo-ulmi and Geosmithia was recently observed. In order to define the relation between these two fungi in the DED pathosystem, O. novo-ulmi and Geosmithia species from elm, including a GFP-tagged strain, were grown in dual culture and mycelial interactions were observed by light and fluorescence microscopy. Growth and sporulation of O. novo-ulmi in the absence or presence of Geosmithia were compared. The impact of Geosmithia on DED severity was tested in vivo by co-inoculating Geosmithia and O. novo-ulmi in elms. A close and stable relation was observed between the two fungi, which may be classified as mycoparasitism by Geosmithia on O. novo-ulmi. These results prove the existence of a new component in the complex of organisms involved in DED, which might be capable of reducing the disease impact.