Wissenschaftliche Publikationen ¶

Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.

Biological invasions, driven mainly by human activities, pose significant threats to global ecosystems and economies, with fungi and fungal-like oomycetes playing a pivotal role. Ink disease, caused by Phytophthora cinnamomi and P. × cambivora, is a growing concern for sweet chestnut stands (Castanea sativa) in Europe. Since both pathogens are thermophilic organisms, ongoing climate change will likely exacerbate their impact. In this study, we applied species distribution modeling techniques to identify potential substitutive species for sweet chestnut in the light of future climate scenarios SSP126 and SSP370 in southern Switzerland. Using the presence-only machine learning algorithm MaxEnt and leveraging occurrence data from the global dataset GBIF, we delineated the current and projected (2070–2100) distribution of 28 tree species. Several exotic species emerged as valuable alternatives to sweet chestnut, although careful consideration of all potential ecological consequences is required. We also identified several native tree species as promising substitutes, offering ecological benefits and potential adaptability to climatic conditions. Since species diversification fosters forest resilience, we also determined communities of alternative species that can be grown together. Our findings represent a valuable decision tool for forest managers confronted with the challenges posed by ink disease and climate change. Given that, even in absence of disease, sweet chestnut is not a future-proof tree species in the study region, the identified species could offer a pathway toward resilient and sustainable forests within the entire chestnut belt.

Since the early 1990s, the invasive pathogen Hymenoscyphus fraxineus has been spreading in Europe causing severe dieback of common ash (Fraxinus excelsior) and narrow-leaved ash (Fraxinus angustifolia). H. fraxineus also causes necrotic lesions at the stem base and on roots of ash trees, which frequently serve as an entry point of secondary wood decay fungi, like Armillaria spp. Rot of the stem base and roots leads to structural weaknesses of ash trees, which makes them prone to uprooting or stem fracturing during storm events. To prevent fatalities and damage to infrastructure it is crucial to timely identify and remove potentially hazardous ash trees. Here, we investigated the synergistic effects of H. fraxineus and Armillaria spp. on the health status (crown defoliation, presence, and extent of basal stem necroses) of mature trees of common ash in ten mixed forest stands in Switzerland over a four-year period (2018–2022). In addition, we conducted non-destructive static load tests on a set of 30 ash trees to assess their breaking and tipping stability so that stability weakness at the stem base could be related to tree health data. The health of the monitored ash trees declined rapidly during the monitoring period, indicating that also mature ash trees in mixed forests may be heavily impacted by ash dieback after prolonged exposure to H. fraxineus (here 12–13 years) and subsequent colonization by root rot pathogens. At the end of the monitoring, only 4.1 % of ash trees with a healthy crown (defoliation ≤ 25 %) remained and 75.4 % of ash trees showed basal stem necroses, which were, with a few exceptions, all colonized by Armillaria. Although the results from the static load tests indicated that predicting tree stability based on crown defoliation level and stem base damage level is not straightforward, i.e. also trees with advanced crown defoliation and stem necrosis can still be stable, our study shows that ash trees with necroses affecting at least 20 % of the basal stem circumference and trees with more than 75 % crown defoliation are likely to suffer from a weakness at the stem base. Building on the new findings and previous research, guidelines for the management of mature ash trees affected by ash dieback are suggested.

The European Commission requested the EFSA Panel on Plant Health to deliver a risk assessment on the likelihood of pest freedom from regulated EU quarantine pests, with emphasis on Bursaphelenchus xylophilus and its vectors Monochamus spp. of debarked conifer wood chips fumigated with sulfuryl fluoride as proposed by the United States (US) and as outlined in ISPM 28 - PT23 of sulfuryl fluoride (SF) fumigation treatment for nematodes and insects in debarked wood. The assessment considered the different phases in the wood chips' production, with special emphasis on the SF treatment. In addition to B. xylophilus and its vectors Monochamus spp., 22 EU quarantine pests and protected zone quarantine pests, some of which are regulated as groups of pests by the Commission Implementing Regulation (EU) 2019/2072, are present in the US and are potentially associated with the commodity. For these pests an expert judgement is given on the likelihood of pest freedom taking into consideration the available scientific information and technical information provided by the US, including uncertainties associated with the assessment. The likelihood of pest freedom varies among the pests evaluated, with B. xylophilus being the pest most frequently expected on the commodity. The Expert Knowledge Elicitation (EKE) indicated with 95% certainty that between 9491 and 10,000 m³ of debarked conifer wood chips treated with SF per 10,000 m³ will be free from B. xylophilus, and that between 9987 and 10,000 m³ of wood chips per 10,000 m³ will be free from Monochamus spp. Technical elements which are critical for a successful treatment and for minimising the presence of Union quarantine pests on the commodity are identified and described in the opinion. In particular, it is important to note that SF treatments are generally less effective in eliminating fungi than insects, the required parameters of the fumigation should be met at all points of the pile of wood chips and the time of storage of wood chips before treatment should be kept as short as possible because B. xylophilus can easily reproduce and spread throughout the pile under conducive conditions.

Cryphonectria parasitica, the causal agent of chestnut blight, was officially found in Azerbaijan in 2004. Currently, the disease is widespread and causes severe damage in seven out of eight forest districts where sweet chestnut (Castanea sativa) is native. Studies conducted in 2015 and 2023 showed that the local fungal population is dominated by a single vegetative compatibility type which is also widespread in neighboring Georgia. All 296 sampled and analysed bark cankers were caused by virus-free C. parasitica strains suggesting that the hypovirulence-inducing virus CHV1 is still not present in Azerbaijan. Here we discuss the possibility of artificially introducing this virus in the Azerbaijani C. parasitica population by treating virulent cankers with CHV1-infected fungal strains. 

In 2023, the invasive black twig borer Xylosandrus compactus (Eichhoff, 1875) (Coleoptera: Scolytinae) was found for the first time in Switzerland. Outbreaks of this non-native species have been recorded during phytosanitary survey activities in four municipalities south of the Alps in the Canton of Ticino. Conducting genetic analyses using the mitochondrial COI barcode region, specimens found in Switzerland were identical with those from France, Italy, and Spain, suggesting a European source of invasion. So far, only ornamental plants in urban areas were found to be affected by attacks of X. compactus. However, because of the increasing proportion of broadleaved evergreen plant species, the availability of suitable host plants such as Laurus nobilis may also favour the spread of X. compactus into insubric forest systems. Three previously undescribed host plant species, Argyrocytisus battandieri, Mahonia aquifolium, and Wisteria sp., were identified. In addition, fungal isolations from adult beetles and breeding galleries revealed eight fungal species likely or potentially associated with X. compactus. These include Ambrosiella xylebori (Ascomycota: Ceratocystidaceae), the obligate ambrosia fungus of X. compactus, and a Thyridium species (Ascomycota: Thyridiaceae) that has been found as an associated fungus in previous studies.

In May 2024, symptoms consistent with those caused by an Exobasidium species were observed on Camellia sasanqua in a private garden in the Maggia Valley, southern Switzerland (46.25°N, 8.7°E). Affected leaves became swollen, deformed, and spongy, with a light green hue and red tones, in contrast to the original dark green appearance and the leathery, coriaceous texture (Figure. 1). The galls formed due to the intercellular growth of the fungus within the leaf epidermis, causing the leaf thickness to more than double. These symptoms and the host plant C. sasanqua are in agreement with previous reports of Exobasidium gracile in Asia (Shirai, 1896; Akai, 1939; Mims et al., 2007; Lee et al., 2015). The total rainfall in May was 305.9 mm, which is higher than the mean of 189.6 mm calculated between 1991 and 2020; the temperature ranged from 10.6 – 18.7°C in May, where a temperature deviation of -1,3°C from the 1991–2020 mean was observed (Locarno Monti; Federal Office of Meteorology and Climatology, 2022). A month later, the leaves showed signs of rot at fungal proliferation sites (Figure. 2). As the season progressed, the cool, humid conditions favourable to Exobasidium declined (Chen et al., 2023).

Armillaria is a soil-borne genus of basidiomycetes whose species can cause stem and root rot in woody plants. The effects of plant-pathogenic Armillaria species are well known in forests, but are underestimated in urban areas, where cases causing damage to trees and shrubs in green spaces have been steadily increasing in Switzerland since the 1980s. In this study, we present a simple, rapid, and cost-effective protocol for high-throughput diagnostics of the two primary pathogens A. mellea and A. ostoyae based on partial PCR amplification of the RPB2 gene. The specificity and sensitivity of the presented duplex PCR-I and single-plex PCR-II were evaluated using different methods: (i) testing both PCRs on tree pathogenic or soil-borne fungi of genera other than Armillaria, (ii) using dilution series of Armillaria-DNA to determine a minimum detection limit, and (iii) sequencing the selected RPB2 region to verify the primer sequences and positions. The utility of PCR-I and PCR-II as a high-throughput method was successfully tested on 65 DNA samples of Armillaria from Switzerland. Finally, an uninvolved person compared both classical methods, pairing test and sequencing, with PCR-I and PCR-II in a blind test. This study provides a reliable and alternative protocol for the rapid diagnosis of A. mellea and A. ostoyae causing root rot of woody plants.

Fungi of the genus Cryphonectria are of special interest to tree pathologists because they cause bark disease in numerous species of the Fagaceae and Betulaceae. Despite this special attention, several Cryphonectria species were not recognized as such for a long time. This also affected the identity of eight isolates with outdated names that have been deposited in our laboratory since 1954. The present study reconstructs the history of the Cryphonectria cultures M282–M289 using primary bibliographic sources. To verify the species identity, all isolates were DNA barcoded and taxonomic affiliation was assessed using a phylogenetic approach. The taxonomic identity combined with the history of the isolates confirms that the chestnut blight epidemic (Cryphonectria parasitica) in Spain was caused by the planting of Asian chestnuts and that the first documented case of bark canker in 1940 was caused by Cryphonectria radicalis on Japanese chestnuts imported from France. The history of isolate M289 could be traced back to CBS 165.32, which proved to be the oldest preserved isolate of the rare Cryphonectria naterciae, confirming the presence of this fungus in Europe for at least 100 years. Based on the ITS barcoding of the 32-year-old type specimen, Cryphonectria decipiens must be reclassified as a later synonym of Cryphonectria radicalis. The reconstruction of the history of isolates M282–M289 takes us on a scientific journey from Italy to France, Spain and Portugal in the early twentieth century and offers new insights into the historical context of the invasion of Cryphonectria parasitica in Europe.

Bacterial tree diseases have been mainly studied in agriculture and horticulture. For forest trees, damage due to bacterial diseases is understudied. Moreover, bacterial tree diseases often appear in the context of so-called complex diseases, which are dependent on other factors, such as multiple microorganisms, insects or abiotic factors which weaken the host. In recent years, outbreaks of bacterial tree diseases, such as Xylella fastidiosa in the Mediterranean region or acute oak decline (AOD) in the United Kingdom, raised the awareness of bacterial diseases on forest trees. In this review, we aim to summarise the current issues and available knowledge about bacterial diseases of forest trees in Central Europe. Furthermore, we identify potential bacterial pathogens that could gain importance in the future for central European forests. The methods used were a systematic literature search and the analysis of the data collected over the last 10 years on bacterial diseases by the Swiss forest protection service. We conclude that, on one side, complex bacterial diseases could increase in importance, especially considering ongoing climate change. Therefore, the bacterial community of diseased trees (the pathobiome) needs to be studied more in depth to understand the emergence of complex bacterial diseases. On the other side, host ranges of highly pathogenic invasive genera and species, such as Xylella, need to be investigated experimentally for common central European tree species and varieties, to implement proactive risk management strategies against bacterial diseases in forest trees. Finally, urban trees and green spaces should be monitored more closely, as they could serve as starting points for bacterial disease outbreaks in forests, similarly to other emerging diseases and pathogens.

The European Commission requested the EFSA Panel on Plant Health to deliver a risk assessment on the likelihood of pest freedom from Union quarantine pests and pests subject to measures adopted pursuant to Article 30 of Regulation (EU) No 2016/2031 for the maple veneer sheets manufactured according to the process set out by Canada, with emphasis on the freedom from Davidsoniella virescens and Phytophthora ramorum (non-EU isolates). The assessment was conducted for veneer sheets of up to 0.7 mm and up to 6 mm thickness, taking into account the different phases in the veneer production in a systems approach. Some of those phases, taken alone, including the heat treatment of logs in a water bath, the cutting into thin veneer sheets and the final high heat drying of veneer sheets are expected to be effective against some of the pests, without uncertainties, making the system approach fully effective. The panel considers that no insects would survive cutting of logs into thin veneer sheets of 0.7 mm and that Xylella fastidiosa will not survive the temperatures in the water bath and final drying of veneers. The degree of pest freedom for the different groups of organisms is generally very high with slightly lower degree of pest freedom for veneer sheets of 6 mm thickness because of lower temperatures reached in the final drying of veneer sheets compared to thinner sheets. P. ramorum is not expected to survive the high heat drying of thin veneer sheets, but it may survive the lower temperatures inside thicker veneer sheets. The Expert Knowledge Elicitation (EKE) indicated, with 95% certainty, that between 9989 and 10,000 veneer sheets (thickness 6 mm) per 10,000 will be free from living P. ramorum. For D. virescens, the EKE indicated, with 95% certainty, that between 9984 and 10,000 veneer sheets (0.7 mm) per 10,000 and that between 9954 and 10,000 veneer sheets (6 mm) per 10,000 will be free from living inoculum. For other relevant groups of pests, the greatest likelihood of pest presence was observed for wood decay fungi. The EKE indicated, with 95% certainty, that between 9967 and 10,000 veneer sheets (0.7 mm) per 10,000 and that between 9911 and 10,000 veneer sheets (6 mm) per 10,000 will be free from living wood decay fungi.
 

Purpose of review: Because tree seeds have been considered a low-risk pathway for the spread of plant pathogenic fungi, their international movement is not subject to strict phytosanitary regulation. However, recent studies have provided scientific evidence that the biosecurity risk of seed trade may not be as negligible as assumed. This review summarises current knowledge about seed trade activity across the world and seed-borne plant pathogenic fungi and highlights knowledge gaps that need to be filled to mitigate the risk of spreading tree pathogens via seeds.
Recent findings: Several outbreaks of severe tree diseases in natural forests and plantations worldwide have been linked to fungal pathogens spread by seed trade. Indeed, recent studies based on modern sequencing technologies have shown that tree seeds harbour highly diverse fungal communities, including well-known pathogens and fungal taxa belonging to unknown species. While it has become clear that even apparently healthy seeds can carry potentially pathogenic fungi, the likelihood of seed-borne pathogens being introduced and becoming established, spreading and causing impact in the new environment is still unclear which challenges the assessment of the phytosanitary risk posed by seed trade.
Summary: Our analyses show that large amounts of tree seeds have been traded among countries and continents. Based on published literature, the risk of spreading pathogenic fungi via tree seed movement is high. However, the role of the taxonomically and functionally diverse fungal communities associated with seeds is still poorly understood. In particular, more research is needed to assess the likelihood of seed-borne fungi being transmitted to the seedlings and spreading and causing impact in the new environment.

Fungal bioluminescence is mystifying humans since ancient times. Nevertheless, the biosynthetic pathway behind this phenomenon was only very recently resolved. Fungal bioluminescence occurs in five distantly related linages (Omphalotaceae lineage, Armillaria lineage, mycenoid lineage, Lucentipes lineage and Eoscyphella lineage) of the basidiomycete order Agaricales. Recent research suggests fungal bioluminescence has emerged 160 million years ago in the most common ancestor of the mycenoid and marasmioid clade and is maintained since then. Surprisingly, in the mycenoid linage, primarily represented by the genus Mycena, most species are considered non-luminescent, implying that many mycenoid species have lost their bioluminescent ability. Here, we report evidence for bioluminescence in Mycena crocata and show that the genome of this species is fully equipped with the genes associated with fungal bioluminescence. Mycena crocata is a long-known species frequently reported from Europe and Japan, which was considered non-luminescent until now. The low light emission intensity and the restriction of the luminescence to the vegetative mycelium and the base of the basidiome may be reasons why bioluminescence was not perceived earlier. We assume there might be other known Mycena species whose luminescent properties are not yet discovered, and that therefore the number of bioluminescent Mycena species is currently underestimated.

Ambrosia beetles are highly successful as invaders because they are often transported internationally with wood packaging and other wood products and because their inbreeding mating systems facilitates establishment of invading populations. In 2022, two independent insect surveys in canton Ticino (southern Switzerland) revealed the widespread occurrence of the invasive ambrosia beetle Anisandrus maiche (Kurentzov, 1941) from southern to central-upper Ticino. This species is native to east Asia and has previously been found as a non-native invasive species in the United States, Canada, western Russia, Ukraine and, in 2021, in northern Italy. Here, we present the results of several trapping studies using different trap types (bottle traps, funnel traps and Polytrap intercept traps) and attractants and a map of the distribution of the species. In total, 715 specimens of A. maiche, all female, were trapped, and the identity of selected individuals was confirmed by morphological and molecular identification based on three mitochondrial and nuclear markers (COI, 28S and CAD). Trap samples from early April to early September 2022 in intervals of two to four weeks showed that flights of A. maiche occurred mainly from June to mid-August. Isolation of fungal associates of A. maiche from beetles trapped alive revealed the presence of four fungal species, including the ambrosia fungus Ambrosiella cleistominuta, the known mutualist of A. maiche. The identity of A. cleistominuta was confirmed by comparing DNA sequences of its nuclear, internal transcribed spacer (ITS) gene with reference sequences in NCBI and BOLDSYSTEMS. This represents the first record of A. cleistominuta in Europe. Of the other fungal associates isolated from A. maiche in Ticino, Fusarium lateritium is of note as there is a possibility that A. maiche could act as a vector of this plant pathogen. We highlight several research needs that should be addressed to gain insight into the potential impact of these non-native species and to overcome problems with heteroplasmy in COI sequences in studies of invasion and population genetics of ambrosia beetles.

Phytophthora species are a cause for concern due to their invasive potential and the damage they can cause in agriculture, forestry, and natural ecosystems worldwide. Since water plays a crucial role in their dispersal, stream and river baiting is commonly used to survey risk areas for the presence of quarantine Phytophthora species. However, our understanding of the distribution and diversity of Phytophthora species in European watercourses remains incomplete. This study investigated the presence and diversity of Phytophthora species in Swiss watercourses, with a focus on the highly urbanized Swiss Plateau. Over the period 2012–2016, we sampled 32 watercourses, including major rivers and smaller streams. We isolated Phytophthora on selective media and sequenced the internal transcribed spacer region to identify the species. We recovered 241 Phytophthora isolates, representing 11 species from five major clades. Phytophthora clade 6 prevailed, with P. lacustris being the most common, found in 94.7% of the watercourses. The number of Phytophthora species per watercourse ranged from one to five, with no correlation to watercourse complexity. Our study reveals the presence of six previously unreported species in Switzerland, while known invasive species were not found. Watercourses appear less suited to detect invasive pathogenic Phytophthora species with a still limited distribution in the environment.

The globally distributed basidiomycete genus Armillaria includes wood decomposers that can act as opportunistic parasites, causing deadly root rot on woody plants. To test whether RNA viruses are involved in this opportunistic behaviour, a large isolate collection of five Armillaria species collected over 40 years in Switzerland from trees, dead wood and soil was analysed. De novo assembly of RNA-Seq data revealed 21 viruses, 14 of which belong to putative new species. Two dsRNA viruses and an unclassified Tymovirales are formally described for the first time for Armillaria. One mitovirus occurred with a high prevalence of 71.1%, while all other viruses were much less prevalent (0.6%–16.9%). About half of all viruses were found only in one fungal species, others occurred in 2–6 fungal species. Co-infections of 2–7 viruses per isolate were not uncommon (34.9%), and most viruses persisted circulating within fungal populations for decades. Some viruses were related to viruses associated with other Armillaria species, supporting the hypothesis that virus transmission can occur between different fungal species. Although no specific correlation between viruses and the fungal trophic strategy was found, this study opens new insights into viral diversity hidden in the soil microbiome.

Invasive fungal diseases represent a major threat to forest ecosystems worldwide. As the application of fungicides is often unfeasible and not a sustainable solution, only a few other control options are available, including biological control. In this context, the use of parasitic mycoviruses as biocontrol agents of fungal pathogens has recently gained particular attention. Since the 1990s, the Asian fungus Hymenoscyphus fraxineus has been causing lethal ash dieback across Europe. In the present study, we investigated the biocontrol potential of the mitovirus Hymenoscyphus fraxineus mitovirus 2 (HfMV2) previously identified in Japanese populations of the pathogen. HfMV2 could be successfully introduced via co-culturing into 16 out of 105 HfMV2-free isolates. Infection with HfMV2 had contrasting effects on fungal growth in vitro, from cryptic to detrimental or beneficial. Virus-infected H. fraxineus isolates whose growth was reduced by HfMV2 showed overall a lower virulence on ash (Fraxinus excelsior) saplings as compared to their isogenic HfMV2-free lines. The results suggest that mycoviruses exist in the native populations of H. fraxineus in Asia that have the potential for biological control of ash dieback in Europe.

Since 2015, North American Douglas fir needle midges of the genus Contarinia Rondani (Diptera: Cecidomyiidae) are known to spread across Europe. In 2022, these gall-inducing insects were detected for the first time in Switzerland, where their morphological identification was confirmed by DNA barcoding. Conducting a visual monitoring of Douglas fir stands in northern Switzerland, the current distribution range was delimitated and revealed the presence of Douglas fir needle midges in forest areas close to the borders of France and Germany, where their establishment has been reported earlier. Genetic analyses of five representative populations further proved the presence of two different mitochondrial haplotypes, of which one was only found in the westernmost population, indicating faint population structuring. When assessing co-occurrence of Douglas fir needle midges with other pests and pathogens originating from North America, Douglas fir stands were often found to be infested also by the insect Adelges cooleyi (Gillette) (Hemiptera: Adelgidae) and the fungus Nothophaeocryptopus gaeumannii (T. Rohde) Videira, C. Nakashima, U. Braun, Crous (Mycosphaerellales: Mycosphaerellaceae). The observed abundance of the newly established midges within the invaded area and their co-occurrence with other introduced pests and pathogens are an indication of the increasing biotic stress level on Douglas fir, which should be taken into account when considering Douglas fir as a potential future tree species for European forests.