Dutch elm disease (DED), caused by Ophiostoma fungi, continues to threaten native elm populations in Scandinavia, where natural regeneration and conservation of elms are increasingly at risk. As no curative control methods are available, resistance breeding remains the most effective long-term strategy for mitigating disease impact. Reliable resistance screening requires pathogen inoculum that accurately reflects the genetic composition of natural pathogen populations, including the distribution of subspecies and hybrid genotypes. In this study, symptomatic elms were sampled across Sweden and Norway, yielding Ophiostoma novo-ulmi isolates that were characterised using DNA-based methods. Subspecies assignments were inferred from the col1 gene, and gene,-based concordance was assessed using the cu gene to detect hybrid genotypes. Subspecies americana (SSAM) predominated in both countries, but subspecies composition differed between Sweden and Norway and varied depending on the genetic marker used. Gene-based concordance also differed markedly between countries, with a higher proportion of discordant (hybrid) genotypes (42%) detected among Swedish isolates, while most (91%) Norwegian isolates were classified as pure strains. Hybrid genotypes occurred at low frequency overall and showed no evidence of spatial clustering. These findings demonstrate region-specific differences in subspecies structure and hybridisation dynamics within Scandinavian O. novo-ulmi populations. The results provide an important basis for selecting representative pathogen inoculum for resistance breeding programmes and contribute to improved understanding of the epidemiology and future risk of DED in northern Europe. To our knowledge, this represents the most comprehensive molecular assessment of O. novo-ulmi populations in Scandinavia to date.

Drought weakens tree defenses, predisposing Norway spruce (Picea abies) to spruce bark beetle (Ips typographus) attack. The extreme 2018 summer drought in Sweden triggered an unprecedented bark beetle outbreak. Our objective was to quantify how weather, soil moisture, and tree provenance influence Norway spruce defense capacity to a necrotrophic beetle-associated pathogen. Trees at three sites in Sweden were inoculated with the phytopathogenic fungus Leptographium europhioides on four occasions during each of the 2019 and 2021 growing seasons. At each site, we inoculated spruce provenances of Swedish or East European origin, with early and late spring bud burst, respectively. Tree defense capacity, expressed as the extent of necrotic lesion formation following fungal inoculation, was used as a proxy for resistance to bark beetle attack. Spruce defense capacity (i.e. lesion size) differed with water availability (both precipitation and soil moisture conditions) but not with the timing of spring bud burst. There were within-season differences, with trees having less efficient defenses (producing larger lesions) in the early season (June). On intermediate soil moisture sites, lesions were larger in 2019 than in 2021. In both years, there was a significant negative correlation between lesion size and water availability in the autumn of the previous year. Spruce defense capacity varied with local environmental conditions but not with provenance phenology. Variations between study years reflected the sensitivity of spruce defenses to climatic variability and the partial recovery of tree resistance 3 years after the 2018 drought.

Abstract Airborne environmental DNA (eDNA) is a powerful tool for assessing biodiversity, but its temporal dynamics and applicability to fungi remain poorly understood. Here we discuss how short‐term airborne eDNA variation should be interpreted for fungal communities. We synthesized current knowledge of airborne fungal ecology and aerobiology, comparing it with patterns observed for plants and vertebrates under passive sampling over 1–2‐week periods, focusing on differences in particle accumulation, persistence and the temporal resolution of signals. Unlike plant and vertebrate eDNA, which reflect near‐real‐time changes in community composition, fungal eDNA accumulates over time due to durable, abundant spores. Short‐term fluctuations in airborne fungal eDNA largely reflect deposition dynamics and atmospheric processes rather than immediate changes in source communities. Recognizing sampling differences between taxa groups is essential for designing sampling regimes and interpreting fungal airborne eDNA, enabling fungi to serve as a robust model for calibrating and validating passive eDNA approaches across taxa, and highlighting areas for future research.

The production of conifer seedlings is an integrated part of forest regeneration in Sweden with over 400 million seedlings produced annually. During recent years, Phoma sp. has emerged as a significant disease in Swedish nurseries, leading to substantial loss of seedlings. Disease symptoms include tissue discolouration, defoliation, stem wounds and decay. The formation of pycnidia on infected tissues is also indicative of infection by Phoma species. The objective of this study was to phylogenetically and phenotypically characterise the species responsible for the disease in Swedish forest nurseries. In total, 181 isolates of Phoma were sampled from Picea abies, Pinus sylvestris and Pinus contorta seedlings from 11 nurseries across Sweden. Cultures were isolated from both shoot and root tissue. Multilocus phylogenetic analyses were performed using ITS, Bt2, CaM, EFA, and G3P markers. The phenotypic assessment included morphological characterisation and measurement of mycelial growth rate. Results showed that a single species, Phoma herbarum, is responsible for this emerging disease in Swedish forest nurseries. Phenotypic variation among the collected isolates was observed, along with genetic variation that revealed multiple clades in the phylogeny of the species. These findings provide valuable insights into the epidemiology of Phoma blight in Swedish forest nurseries.

The emerald ash borer (Agrilus planipennis, EAB) is an invasive wood-boring beetle causing extensive ash mortality, yet little is known about its associated fungal communities in Eurasia. We characterized fungal assemblages associated with adult EAB collected from Fraxinus excelsior and F. pennsylvanica in three regions (Sumy, Kharkiv, and Luhansk) of eastern Ukraine using ITS2 metabarcoding. The final dataset comprised 247 fungal OTUs from 138 samples. Geographic region was the primary factor structuring fungal community composition, whereas the overall host effect was small but depended on geographic context. Fourteen OTUs showed significant regional associations after false-discovery-rate correction. Ecological guild composition also differed geographically, with Sumy communities strongly dominated by yeasts. OTU richness was strongly influenced by sequencing depth, whereas regional differences in Shannon diversity persisted after accounting for depth. The results indicate that EAB-associated fungal assemblages largely reflect geographic context and local fungal pools rather than a uniform specialized microbiota.

Peat is widely recognized for its optimal chemical and physical properties in seedling cultivation, making it a primary constituent of growing media in forest nurseries. However, due to the adverse environmental impacts associated with peat extractions, there is an increasing interest in replacing peat with more sustainable substrates. This study investigates the potential of utilizing by-products from the forestry and paper sectors for Pinus sylvestris seedling cultivation. We also evaluated whether biochar amendments enhance seedling growth and quality. Nine peat-free growing media (GM) were analyzed, all based on sawdust with varying proportions of composted fiber sludge, composted bark, wood fiber, both with and without biochar amendment. Peat-based GM served as the control. The results demonstrated that a GM composed of 70% (v/v) sawdust and 30% (v/v) wood fiber produced seedlings with growth, vitality and Dickson's quality index (DQI) similar to those grown in peat. Additionally, a GM consisting of 50% (v/v) sawdust, 25% (v/v) wood fiber and 25% (v/v) composted bark yielded seedlings with significantly smaller shoots (p <= 0.05), although their DQI did not differ significantly from the control. Conversely, GM containing 15% (v/v) biochar amendment and either 25% (v/v) or 30% (v/v) composted fiber sludge resulted in significantly stunted growth.

Old-growth oak (Quercus robur) forests in Europe are biodiversity hotspots, yet their airborne fungal diversity remains poorly studied. We investigated aeromycobiota in three Lithuanian oak stands (Punia, Dūkštos and Šilinė) using passive spore traps combined with DNA metabarcoding. Weekly sampling between August and September 2022 yielded 75 spore samples, producing 262,755 high-quality fungal sequences clustered into 1,881 operational taxonomic units (OTUs) representing six phyla and 36 classes. Ascomycota (53.1

Rising temperatures attributed to anthropogenic climate change have held a firm grip on European forests for over two decades now and disturbances have increased substantially, mainly from insects and pathogens. Empirical evidence suggests a direct linkage between rising temperatures and increasing damage from native insects. Although the rapid spread of non-native invasive pests and pathogens is mainly driven by globalized trade and lacking tree species adaptation to locally new threats, climate change favors rapid range expansion of some invasive pests. Here, we present some examples of tree-insect-pathogen interactions in native and non-native systems that have experienced climate change-induced severe outbreak dynamics. We document the spread of damaging insects and pathogens into previously climatically unsuitable regions and underscore the severe forest damages such species distribution shifts can cause. Although systematic assessments are still pending, the information provided here by multiple independent empirical evidences is highly valuable for identifying some of the most pressing issues in European forest protection. Our work can guide forest protection agencies in preparing mitigating strategies for upcoming decades.

In Montenegro, coniferous forests play a key ecological role in maintaining ecosystem stability. Root-associated mycorrhizal fungi and saprotrophic fungi inhabiting forest soils are well known for their roles in nutrient cycling, organic matter decomposition, and supporting host tree health. In contrast, the fungal communities residing within conifer needles, despite potentially important ecological functions, remain largely underexplored, particularly in natural and marginal forest ecosystems such as those in the Balkans. This study aimed to investigate the diversity and community composition of needle-associated fungi in three native conifers: Picea abies and Abies alba (at the edge of their native range), and the endemic Pinus heldreichii, from different mountainous regions in Montenegro. High-throughput sequencing was conducted to assess fungal diversity and community composition. Dothideomycetes dominated fungal communities in all three tree species, followed by Leotiomycetes and Tremellomycetes. Multivariate analysis revealed distinct fungal communities in P. heldreichii, whereas fungal communities in A. alba and P. abies were partially overlapping. Functional classification showed a dominance of saprotrophic, pathogenic, and endophytic fungi, with P. heldreichii exhibiting the highest proportion of saprotrophs, while A. alba and P. abies showed a considerable proportion of pathogens. The findings highlight strong host specificity, biogeographical influences, and the ecological importance of fungal communities in coniferous forests. This study provides new insights into the diversity and functional roles of needle-associated fungi, emphasizing the need for conservation efforts to maintain microbial biodiversity in native forests of Montenegro.

Pinus species are extensively abundant in Europe and, as pioneer trees, prominently influence local ecology. However, pine forests in Lithuania, Montenegro, and Ukraine have been significantly damaged by pine bark beetles (Tomicus sp.), which are closely associated with ophiostomatoid and other pathogenic fungi. This study aimed to identify the diversity of ophiostomatoid and other fungi associated with Tomicus sp. in these three countries. Fungi were isolated from beetles and identified. High-throughput sequencing of ITS2 rDNA yielded 285,828 reads, of which 91,141 high-quality reads were retained, representing 561 fungal operational taxonomic units (OTUs). The most important groups of fungi included ophiostomatoids, yeasts, and plant pathogens. While the fungal communities associated with Tomicus spp. were influenced more by environmental factors than by beetle species, the presence of known pathogens such as Ophiostoma spp. indicates that Tomicus spp. could play a significant role in dispersing harmful fungi. Although the virulence of these fungi may vary, their association with potentially pathogenic species suggests that Tomicus spp. may contribute to forest health decline, especially if environmental conditions or host susceptibility change.

In Sweden, reforestation of managed forests relies predominantly on planting nursery-produced tree seedlings. However, the intense production using containerized cultivation systems (e.g., high seedling density, irrigation from above, regular fertilization) creates favorable conditions for fungal infections. Despite the harmful role of diseases in forest nurseries, the origin and dispersal factors of fungal pathogens remain largely unknown. A better understanding of the airborne spread of pathogens could improve the prediction of fungal infection, ultimately optimizing preventative methods and decreasing the use of fungicides. This study investigated the temporal dynamics of airborne fungi in forest nurseries, with a focus on fungal pathogens. Airborne fungi were monitored in four Swedish forest nurseries over two growing seasons using spore traps and high-throughput sequencing. Fungal pathogens were identified using bioinformatics and quantified with quantitative PCR. Results showed strong temporal shifts of airborne fungal diversity and community composition following the growing seasons. The airborne spread included high abundances of important fungal pathogens (e.g., Cladosporium sp., Botrytis cinerea, Alternaria sp., Sydowia polyspora, and Melampsora populnea) with individual temporal and spatial variations. In general, the deposited spore loads of nursery pathogens correlated positively with increased temperature and negatively with higher precipitation. This was expressed the strongest for Cladosporium sp., Alternaria sp., and M. populnea, which suggests a higher availability of fungal inoculum in warm and dry periods. This study highlights the influence of seasonality on the temporal dynamics of economically important fungal pathogens in Swedish forest nurseries, which should be considered in the development of a local decision support system.IMPORTANCEFungal diseases in forest nurseries have significant environmental and economic impacts on the tree seedling production. This study highlights the role of seasonality in the airborne spread of fungal pathogens in Swedish forest nurseries. By analyzing airborne fungal spores using advanced sequencing and monitoring techniques, key fungal pathogens and their dispersal patterns over two growing seasons were identified. The findings indicate that warmer, drier periods may increase the spread of fungal pathogens, emphasizing the need for targeted preventative measures. Understanding these temporal dynamics can help optimize the use of fungicides in forest nurseries, thereby promoting more sustainable and environmentally friendly management practices. This research provides valuable insights for improving disease management in forest nurseries, ultimately supporting sustainable tree seedling production.

Fungi are abundant in wood of living trees, but few studies have compared the diversity of fungi among different tree species and trees of varying age and size, aspects of importance for conservation planning. We investigated if fungal species richness and species composition in wood vary significantly among the temperate broadleaf tree species beech (Fagus sylvatica), linden (Tilia cordata), Norway maple (Acer platanoides) and pedunculate oak (Quercus robur). Each tree species was represented by four stem size classes, and the total sample included 240 trees in southern Norway. Wood cores were collected from individual trees and fungal DNA was amplified using ITS2 rRNA as a marker and subjected to high-throughput sequencing. In total, we detected 1156 fungal OTUs. Oaks had significantly higher richness of fungal OTUs than any of the other tree species and harboured unique communities. Further, oak hosted most species-specific Indicator species (39) and was the only species to host Red-Listed fungal species (five). The circumference (proxy for age) did not significantly affect neither OTU richness nor its overall composition. However, several individual Red List and Indicator species were found only in trees of the largest size class. There was a significant effect of bioclimatic section on species composition. Our results emphasize the important roles of oaks and to some extent large trees as repositories of fungal diversity, which should be considered in conservation planning.

Forest fires represent a significant ecological disturbance in ecosystems that increasingly affects Pinus heldreichii H. Christ forests at the upper tree line in Montenegro, due to climate change and anthropogenic factors. Soil samples were collected from five high-altitude sites in the Kuči Mountains, including three post-fire sites (2-, 4-, and 6-years post-fire) and two unburned control sites. High-throughput sequencing and soil chemical analyses were conducted to assess fungal diversity, community composition, and soil nutrient properties. The results showed that fungal diversity was significantly higher in unburned soils compared to post-fire soils, with the most prominent changes in ectomycorrhizal fungi, which are crucial for pine regeneration. The fungal community composition differed markedly between the post-fire and unburned sites, with specific taxa such as Hygrocybe conica (Schaeff.) P. Kumm. and Solicoccozyma aeria (Saito) Yurkov dominating the post-fire environments. Despite this, the fungal richness did not significantly change over time (2-, 4-, or 6-years post-fire), suggesting the slow recovery of fungal communities in high-altitude environments. In addition to shifts in fungal biodiversity, the post-fire soils exhibited higher levels of available phosphorus, likely due to the conversion of organic phosphorus into soluble forms during combustion. However, the organic matter content remained unchanged. This study provided important insights into the long-term ecological impacts of forest fires on high-altitude P. heldreichii forests and underlined the importance of preserving unburned forest areas to maintain fungal biodiversity and support natural regeneration, as well as the potential need for active restoration strategies in fire-affected regions.

We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica , which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.

The aim of the presented study was to compare the diversity and composition of fungal communities associated with the roots and the rhizosphere soil of P. abies and Larix sp. in mid-age and mature managed forest stands in Lithuania. We also aimed to assess the presence of fungi–host-specific associations, i.e., whether Larix sp. stands could provide habitats for soil fungi currently associated with P. abies. The study sites were 10 Larix sp. and 10 P. abies forest stands in Lithuania. For the study, 100 root samples and 10 organic and 10 mineral soil samples were collected in P. abies stands as well as the same number in Larix sp. stands, and DNA was isolated, amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. The results showed that the Shannon diversity index of fungal communities was similar between the two tree species when compared either between root (H = 4.26 P. abies and H = 3.82 Larix sp.), organic soil (H = 5.12 P. abies and H = 5.13 Larix sp.) or mineral soil (H = 4.71 P. abies and H = 4.29 Larix sp.) samples. Multivariate analysis showed that the fungal community composition in the organic and mineral soil samples of both P. abies and Larix sp. were similar, and thus, overlapping. The analysis also showed that the distribution of fungal species was denser in the roots and organic soil but more scattered in mineral soil. However, several fungi in the roots of either P. abies or Larix sp. showed a certain host specificity.

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2-3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the 'true fungi' have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Plant production systems worldwide are struggling to meet the diverse and increasing needs of humankind while also facing challenges such as climate change and biodiversity loss. This, combined with the desirable transition from the use of conventional pesticides to more sustainable plant protection solutions, has led to an urgent, and increasing, need for low-risk plant protection products (PPPs) to be developed, applied, and integrated into management practices across all types of plant production systems. Despite a high demand from end users and consumers together with joint political goals at the EU level to replace conventional pesticides, the number of low-risk PPPs on the European market remains low, in comparison to synthetic agrochemicals. In this review, we summarize knowledge about the policy, technical, and administrative issues hampering the process of bringing new low-risk PPPs to the European market. We present an overview of the challenges in using the low-risk PPPs that are currently available within the EU agricultural, horticultural, and forestry sectors. We describe the variation in modes of action and the limitations associated with different application techniques and give concrete examples of problems and solutions from Swedish plant production sectors, in contrast to global perspectives as demonstrated by examples from African agriculture. Finally, we conclude that trans-sectoral, multi-actor approaches are required and provide suggestions on how to address the remaining knowledge gaps related to efficiency, application, and economics of low-risk PPP use in Integrated Pest Management (IPM) solutions for plant protection to improve future food security in Europe.

Silver birch Betula pendula Roth is a widely distributed tree species in northern Europe, the wood of which is extensively used to produce plywood and veneer. However, birch wood is highly susceptible to fungal decay and discoloration. This study investigated the effectiveness of urea treatment against fungi causing discoloration in birch logs. The effect of urea treatment was evaluated in two settings, i.e. in the forest and in the log yard. In the forest, 80 one-meter-long stem segments were produced and half of them were treated with 35% urea solution and the other half with water. To simulate mechanical bark injury, half of the segments were deliberately damaged before storage. In the log yard, 60 stem segments were similarly prepared to assess fungal species colonizing wood during long-term storage. The results showed that urea-treated and bark-damaged logs exhibit the highest rate of wood discoloration, which increased with prolonged storage. Fungal isolation from wood samples identified a higher diversity of fungal species in samples from the log yard. The most frequently isolated fungi were ascomycetes from the genus Ophiostoma. In conclusion, the results demonstrated that the urea treatment is an ineffective measure against fungi causing discoloration in birch wood.

It is assumed that climate change (global warming) worsens the living conditions for conifers and at the same time favours the cultivation of deciduous trees, including oaks. In fact, in Poland, for example, many more oaks are now being planted as forest-forming tree species than in the 1980s and 1990s. However, the monitoring of the health status of European forests (according to the International Co-operation Project) does not confirm these optimistic assumptions, and oak has been cited as one of the most damaged tree species in terms of defoliation in recent decades. The prospects for oak cultivation in European forestry are therefore a combination of abiotic conditions and biotic damage factors. This review article focuses in particular on the new threats posed by pathogenic organisms causing emerging diseases. These include newly identified bacteria responsible for the so-called Acute Oak Decline (AOD), oomycetes (especially those specialised in damaging fine roots, such as Phytophthora quercina T.Jung) and semi-parasites of the genus Loranthus. At the same time, the pressure from commonly observed insects and fungi described in connection with the complex syndrome of oak decline, which is divided into predisposing, inciting, and contributing factors (according to Manion’s disease spiral), has not abated. Therefore, international, interdisciplinary research (such as that proposed in Oakland) is needed, using modern technologies (RS remote sensing) based on the comparison of satellite images (from different years), not only to inventory the most valuable oak stands in Europe (microrefugia) but also to identify trends in changes in their condition and biodiversity. As RS has its limitations (e.g., resolution), aerial monitoring should be complemented by quantitative and qualitative inventory from the ground, e.g., monitoring of the presence of soil microorganisms using effective molecular biological methods (e.g., Next-Generation Sequencing NGS).