Dr. Simone Prospero

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.

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. 

Nel 2003 è stato scoperto nel Regno Unito il microrganismo Phytophthora kernoviae che danneggia un gran numero di piante. È stato riscontrato con particolare frequenza su faggio comune (Fagus sylvatica) e rododendri (Rhododendron sp.). Il patogeno non è ancora presente in Svizzera ma qualora vi fosse introdotto c'è il rischio che si diffonda in modo simile al Regno Unito e che provochi danni ingenti, soprattutto nelle foreste.

Depuis 1995, une maladie sévit aux États-Unis. Elle fait souvent dépérir les chênes en peu de temps, d'où son nom de «Mort subite du chêne» (en anglais «Sudden Oak Death», SOD). Elle est provoquée par Phytophthora ramorum, un micro-organisme semblable aux champignons. En Suisse, cet agent pathogène a jusqu'à présent été surtout détecté dans les pépinières et n'a pu se propager jusqu'aux forêts. En raison de son fort potentiel de nuisance, il a été classé comme organisme de quarantaine. Sa lutte est donc réglementée par la loi.

Dal 1995 negli Stati Uniti si è diffusa una malattia che può provocare la morte rapida in particolare delle querce e a cui è stato dato il nome di «morte improvvisa delle querce» (in inglese «Sudden Oak Death», SOD). Essa è causata dal microrganismo Phytophthora ramorum. In Svizzera, questo patogeno è stato finora individuato principalmente nei vivai e non è ancora riuscito a diffondersi nelle foreste. A causa del suo elevato potenziale di danno, è stato classificato come organismo di quarantena. Il suo controllo è quindi regolamentato dalla legge.

La Phytophthora degli ontani venne descritta per la prima volta in Gran Bretagna negli anni Novanta. Successivamente, è stato osservato un deperimento di massa di varie specie di ontano in diversi Paesi europei, soprattutto lungo i corsi d'acqua. La malattia è ora presente anche nell'Europa occidentale e centrale. La biodiversità, la produzione di legname e, in particolare, la protezione dalle inondazioni ne risentono. Il deperimento è causato da tre microrganismi, il più aggressivo dei quali è stato individuato per la prima volta in Svizzera nel 2008. Anche se qui non ha ancora causato gravi danni, la sua rapida diffusione in altri Paesi è motivo di preoccupazione.

In den USA grassiert seit 1995 eine Krankheit, die besonders Eichen oftmals innert kurzer Zeit absterben lässt und daher den Namen «Plötzlicher Eichentod» (engl. «Sudden Oak Death», SOD) bekam. Ausgelöst wird sie durch den pilzähnlichen Mikroorganismus Phytophthora ramorum. In der Schweiz wurde dieser Erreger bislang vor allem in Baumschulen nachgewiesen und konnte noch nicht auf den Wald überspringen. Aufgrund seines hohen Schadpotentials wurde er als Quarantäneorganismus eingestuft. Die Bekämpfung ist dementsprechend gesetzlich geregelt.

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.

Vom Triebsterben betroffene Eschen sind zusätzlich oft mit Hallimasch infiziert, was zu einem gefährlichen Stabilitätsverlust führt. In der Schweiz ausgearbeitete Richtlinien sollen dabei helfen, die Kipp- und Bruchgefahr einer Esche einzuschätzen.

Mit den Revisionen des Pflanzengesundheitsrechts auf EU und Schweizer-Ebene (PgesV,PgesV-WBF-UVEK und VpM-BAFU) müssen seit 2020 prioritäre Quarantäneorganismen (prioQOs) von den Kantonen aktiv und
risikobasiert überwacht werden. Zusätzlich zu den prioQOs müssen auch weitere Quarantäneorganismen (QOs) überwacht werden (VpM-BAFU), für welche vorübergehende Pflanzenschutzmassnahmen vom Bund erlassen wurden. In Zusammenarbeit mit dem BAFU und den elf Kantonen AG, BS, BL, LU, NE, SO, TI, VD, VS, ZG, und ZH wurden 2023 35 kantonale Risikoflächen überwacht. Ausserdem wurden drei EPSD-Risikostandorte am Flughafen Zürich (ZH), am Rheinhafen Birsfelden (BL) und in Chiasso (TI) installiert. Der Kanton Tessin hat auf eigenen Wunsch einen zusätzlichen Risikostandort in Lugano installiert und betreut. Bei den Erhebungen in den Jungpflanzenbetrieben (vom EPSD und beauftragten Kontrollorganisationen ausgeführt) wurden anfällige Wirtspflanzen auf QOs und geregelte Nicht-Quarantäneorganismen (GNQOs) kontrolliert und allfällige Verdachtsproben an der WSL analysiert. Zusätzlich wurden Verdachtsproben aus Importkontrollen von Verpackungsholz (ISPM15 Kontrollen) und aus dem Meldewesen von Waldschutz Schweiz untersucht. [...]

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.

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.

Le châtaignier commun (Castanea sativa) est de plus en plus menacé par la maladie de l'encre en Suisse et sur l'ensemble du continent européen. Cette maladie est principalement causée par deux oomycètes du genre Phytophthora, P. x cambivora et P. cinnamomi. Ces deux espèces sont sensibles au froid et profitent du réchauffement climatique.

Depuis 1995, une maladie sévit aux États-Unis. Elle fait souvent dépérir les chênes en peu de temps, d’où son nom de «Mort subite du chêne» (en anglais «Sudden Oak Death», SOD). Elle est provoquée par Phytophthora ramorum, un micro-organisme semblable aux champignons. En Suisse, cet agent pathogène a jusqu’à présent été surtout détecté dans les pépinières et n’a pu se propager jusqu’aux forêts. En raison de son fort potentiel de nuisance, il a été classé comme organisme de quarantaine. Sa lutte est donc réglementée par la loi.

When a non-native species succeeds in establishing in a new habitat, one of the possible responses is to attempt its eradication. In the present study, we analysed European eradication programmes against non-native pests and pathogens of woody plants (PPWP) from 1945 to date. Our main goal was to identify which factors affect the success of an eradication programme, reinforcing guidelines for future eradication of PPWP. Data on eradication campaigns were obtained from online databases, scientific and grey literature, and Plant Protection Organizations’ reports. Factors influencing eradication success for both arthropods and pathogens were analysed with LASSO regression and decision tree learning.
A total of 848 cases officially declared as eradication attempts were documented in our database (8-fold higher than previous reports). Both the number of programmes and their rate of success increased sharply over the last two decades. Only less than 10% of the non-native organisms affecting woody plants were targeted for attempted eradication despite the high economic and ecological impacts caused by some species for which no efforts were undertaken. Almost one-third of the officially declared cases of eradication concerned organisms that were still restricted to the material with which they were introduced. For these cases the success rate was 100%. The success rate of established species was only 50% for arthropods and 61% for pathogens. The spatial extent of the outbreak was the factor that most affected the outcome of eradication campaigns. The eradication success decreased abruptly above 100 ha for arthropods and 10 ha for pathogens. Additionally, other variables were shown to influence the outcome of eradication programmes, in particular the type of environment, with the highest eradication success rate found in nurseries and glasshouses, with successful outcomes increasing if quarantine measures were applied and when monitoring included asymptomatic plants. Particular species traits may reduce eradication success: parthenogenetic arthropods, saprotrophic pathogens, wind dispersal, the possibility to remain asymptomatic indefinitely, and the existence of resting spores or stages.
In conclusion, small affected areas, quick response, and efficient implementation of quarantine restrictions, together with particular species traits, may allow a high probability of eradication success. Preparedness at the country and European level would allow a larger number of target species to be included in future eradication programmes.