Dual origin of recent Dutch elm disease outbreaks in Europe

Ganoderma lucidum: Insights on host range, diagnosis, and management strategies

Forest ecosystems play an important role in upholding life on our planet. However, the onslaught of fungal pathogens like Ganoderma lucidum, poses a threat by decimating numerous tree species. G. lucidum identified as a root pathogen, causing root rot in numerous tree species of horticulture and forestry importance. The fungus initiates infection through basidiospores, which germinate and penetrate within roots and start to degrade lignocellulosic components of plant cells. Early-stage detection of G. lucidum, is challenging, while in advance stages, the wood undergoes softening and a loss of tensile strength, rendering the disease incurable. Hence, effective management of G. lucidum necessitates a pivotal role of disease diagnostic techniques, which are currently underutilized or inadequately accessible. Subsequent implementation of suitable control measures becomes imperative to thwart disease occurrence and mitigate its impact in early stages, thus preserving the vitality of forest ecosystems. This study provides comprehensive overview of G. lucidum, covering taxonomy, pathogenicity, disease cycle, diagnosis and effective control measures, which will be helpful in formulating effective diagnostic techniques for early management of root rot disease.

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.

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.

Ophiostomatales Associated with Mediterranean Pine Engraver, Orthotomicus erosus (Coleoptera, Curculionidae) in Dalmatia, Croatia

Mediterranean pine engraver, Orthotomicus erosus was never considered as a significant pest in Croatia and did not appear in high population densities until 2017, when it reached outbreak level in Aleppo pine stands. The beetle was first detected in Marjan Forest Park, Split, and was soon recorded in other parts of the Dalmatian coast. Soon after the outbreak occurred, we observed that all of the attacked trees exhibit severe blue staining in the sapwood which indicated fungal infection caused by the Ophiostomatales group of fungi. This raised the need to investigate their relationship with O. erosus and the pine decline, and the main aim of this study was to isolate and identify them. Isolates were obtained from adult O. erosus beetles, their galleries, and blue-stained sapwood, and identified according to the morphological characteristics and DNA sequencing. A total of six Ophiostomatales (Ophiostoma ips, O. piceae, Graphilbum cf. rectangulosporium, O. floccosum, Sporothrix pseudoabietina and Ceratocystiopsis cf. minuta) were identified in the study. This is the first record of Ophiostomatales as organisms associated with the pest O. erosus and pine species in Croatia.

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.

Microclimates hold the key to spatial forest planning under climate change: Cyanolichens in temperate rainforest

There is deepening interest in how microclimatic refugia can reduce species threat, if suitable climatic conditions are maintained locally, despite global climate change. Microclimates are a particularly important consideration in topographically heterogeneous landscapes, while in some habitats, such as forests and woodlands, microclimates are also extremely labile and affected by management practices that could consequently be used to offset climate change impact. This study explored a conservation priority guild-cyanolichen epiphytes in temperate rainforest-quantifying the niche response to macroclimate, and landscape or woodland stand structures that determine the microclimate. Based on epiphyte survey in a core region of European temperate rainforest (western Scotland), a 'random forest' machine-learning model confirmed a strong cyanolichen response to summer dryness, as well as the effects of distance to running water, topographic heatload and tree species identity, which modify the local moisture regime and/or lichen growth rates. By quantifying this response to macroclimate, landscape and stand structures, it was possible to estimate an extent to which woodland may be expanded in the future, to offset a negative effect of increasing summer dryness projected through to the 2080s. Using current policy as a yardstick, sufficient woodland expansion could be delivered relatively quickly for median impacted sites, but with times to woodland delivery extending over 10, 20 and 25 years for sites at the 75th, 90th and 95th percentiles of cyanolichen decline. Furthermore, the extent of new woodland required, and delivery times, increase almost threefold on average, as new woodland becomes distributed over wider riparian zones. These contrasting implications emphasize an urgent need for afforestation that achieves targeted spatial planning responsive to microclimates as refugia.

The Use of Ground Penetrating Radar and Microwave Tomography for the Detection of Decay and Cavities in Tree Trunks

Aggressive fungal and insect attacks have reached an alarming level, threatening a variety of tree species, such as ash and oak trees, in the United Kingdom and beyond. In this context, Ground Penetrating Radar (GPR) has proven to be an effective non-invasive tool, capable of generating information about the inner structure of tree trunks in terms of existence, location, and geometry of defects. Nevertheless, it had been observed that the currently available and known GPR-related processing and data interpretation methods and tools are able to provide only limited information regarding the existence of defects and anomalies within the tree inner structure. In this study, we present a microwave tomographic approach for improved GPR data processing with the aim of detecting and characterising the geometry of decay and cavities in trees. The microwave tomographic approach is able to pinpoint explicitly the position of the measurement points on the tree surface and thus to consider the actual geometry of the sections beyond the classical (circular) ones. The robustness of the microwave tomographic approach with respect to noise and data uncertainty is tackled by exploiting a regularised scheme in the inversion process based on the Truncated Singular Value Decomposition (TSVD). A demonstration of the potential of the microwave tomography approach is provided for both simulated data and measurements collected in controlled conditions. First, the performance analysis was carried out by processing simulated data achieved by means of a Finite-Difference Time-Domain (FDTD) in three scenarios characterised by different geometric trunk shapes, internal trunk configurations and target dimensions. Finally, the method was validated on a real trunk by proving the viability of the proposed approach in identifying the position of cavities and decay in tree trunks.

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.

Establishment of invasive and non-invasive reporter systems to investigate American elm-Ophiostoma novo-ulmi interactions

Dutch elm disease (DED), caused by ascomycete fungi in the Ophiostoma genus, is the most devastating disease of American elm (Ulmus americana) trees. Cerato ulmin (CU), a hydrophobin secreted by the fungus, has been implicated in the development of DED, but its role in fungal pathogenicity and virulence remains uncertain and controversial. Here, we describe reporter systems based on the CU promoter and three reporter proteins (GFP, GUS and LUC), developed as research tools for quantitative and qualitative studies of DED in vitro, in vivo and in planta. A strain of the aggressive species Ophiostoma novo-ulmi was transformed with the reporter constructs using Agrobacterium-mediated transformation and the fungal transformants, namely M75-GFP, M75-GUS and M75-LUC, were examined for mitotic stability after repeated subcultures. The intensity of GFP fluorescence was strong in M75-GFP spores and hyphae, allowing microscopic investigations of spore structure, fungal morphogenesis and fungal development. The interaction of M75-GFP and U. americana callus cells was explored with scanning laser confocal microscopy facilitating qualitative studies on fungal strategies for the invasion and penetration of elm cells. M75-GUS was generated to provide an invasive, yet quantitative approach to study fungal-plant interactions in vitro and in planta. The generation of M75-LUC transformants was aimed at providing a non-destructive quantitative approach to study the role of CU in vivo. The sensitivity, low background signal and linearity of LUC assays all predict a very reliable approach to investigate and re-test previously claimed roles of this CU in fungal pathogenicity. These reporter systems provide new tools to investigate plant-pathogen interactions in this complex pathosystem and may aid in better understanding the development of DED.

Interspecific hybridization in plant‐associated fungi and oomycetes: a review

Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.

Control of plant pathogens with viruses and related agents

Cytoplasmically transmissible agents causing diseases of plant pathogenic fungi characterized by reductions in pathogenicity, ability to form sexual and asexual spores, spore viability and growth rate, are often associated with the presence of one or more specific segments of virus-like double-stranded RNA (dsRNA). In Italy, hypovirulent dsRNA-containing strains of the chestnut blight fungus,Endothia(Cryphonectria)parasitica, have become predominant in many areas where blight is no longer a serious problem. dsRNA-containing strains of other pathogens, with various degrees of debilitation, survive in natural populations but have not become predominant or resulted in any great reduction in disease. Examples include the Dutch elm disease fungus,Ophiostoma(Ceratocystis)ulmi, and the wheat take-all fungus,Gaeumannomyces graminisvar.tritici. Successful biological control of such pathogens could probably be achieved, however, if methods could be developed to suppress the loss of dsRNA that occurs during the sexual and other stages of their life cycles, and to suppress the vegetative incompatibility reactions that reduce the cytoplasmic transmission of dsRNA. Systemic infection with attenuated strains of plant viruses can protect plants from later infection by virulent strains of the same or closely related viruses. Despite some notable successes, e.g. control of citrus tristeza and tomato mosaic viruses, such ‘cross-protection’ has not been widely applied because of the cost and difficulty of application, and caution about the widespread distribution of infectious agents in the environment. These problems could be overcome if cross-protection could be achieved by the expression of a single viral gene rather than infection with intact virus, and consideration of possible mechanisms of cross protection suggests novel ways of producing virus-resistant plants.

A comparison of the nucleotide sequence of the cerato-ulmin gene and the rDNA ITS between aggressive and non-aggressive isolates of Ophiostoma ulmi sensu lato, the causal agent of Dutch elm disease

Little genetic information exists comparing aggressive and non-aggressive isolates of the causal agent of Dutch elm disease, Ophiostoma ulmi. Two genetic elements were compared between the subgroups. The ceratoulmin cu gene product has been associated with disease symptoms. Nucleotide-sequence analysis of cu and the internal transcribed spacer (ITS) region of the rDNA were made from three aggressive and three non-aggressive isolates of the pathogen. Our results suggested uniformity within, and unique differences between, subgroups. Differences were detected for cu in the promoter, coding, and transcription termination regions. Sequence data for the ITS clearly distinguish the subgroups.

Episodic selection as a force in fungal microevolution, with special reference to clonal speciation and hybrid introgression

Episodic selection encompasses any sudden environmental disturbance likely to lead to a significant alteration in a species' population structure. Such disturbances include geographical transposition, a change in substrate availability, exposure to a new host or a new vector, climate change, and pollution stress. Today, such events may often be brought about by man. Their role in the promotion of fungal microevolution is discussed. In some circumstances, episodic selection may result in the emergence of a highly fitted clone from an originally heterogeneous population, and sustained disturbance may lead to clonal speciation. Clonal speciation accompanied by loss of sexual function, whether under episodic selection or under less intensive but analagous environmental conditions, could account for the origin of many of today's imperfect taxa (Deuteromycotina). Geographical transposition, a special form of episodic selection, can lead to hybridization between previously allopatric species. This may result in modifications to existing species via the acquisition of new loci or cytoplasmic elements, in the production of new taxa via secondary speciation, or in the emergence of hybrid swarms. Episodic selection will also favour survival of novel genotypes by providing new habitats for exploitation, so encouraging novel evolutionary development. Key words: episodic selection, fungal speciation, hybridization, introgression.

Electrophoretic karyotypes of the elm tree pathogen Ophiostoma ulmi (sensu lato)

Pulsed field gel electrophoresis using OFAGE, TAFE, and CHEF systems has been used to more fully characterize karyotypic variation within the two closely related fungal species of Ophiostoma ulmi sensu lato. Twelve wild-type and laboratory strains, representing the less aggressive species O. ulmi and both of the biotypes of the more aggressive species O. novo-ulmi were studied and their karyotypes determined. Depending on the strain, a minimum of four to a minimum of eight chromosomal DNA bands were present that fall into three distinct size classes, with one exception. Strain CESS16K (O. novo-ulmi, North American aggressive subgroup) contains a unique chromosomal DNA band which comigrated near a Saccharomyces cerevisiae chromosome of 0.95 Mb. This unique band was the smallest O. ulmi s. l. chromosomal DNA observed. Seven of the twelve strains shared a common chromosomal DNA banding pattern, whereas each of the other five had a unique karyotype. There was no correlation between chromosome profile and species, as some O. novo-ulmi and O. ulmi strains shared common electrophoretic karyotypes.