Åke Olson

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.

Scots pine blister rust is one of the most devastating diseases in the Swedish pine forest. Its causal agent, Cronartium pini , has two forms. The autoecious form only infects pine, while the heteroecious form is macrocyclic and infects pine as the aecial host and many herbaceous plants as telial hosts. Both forms cause similar symptoms on pine and produce aecia with aeciospores, which are morphologically indistinguishable. Distinguishing the two forms relies on inoculation tests, which are time‐consuming and low‐throughput, and microsatellite (SSR) genotyping, which provides limited resolution. In this study, we developed a more efficient identification method using a digital PCR (dPCR)‐based protocol targeting three markers: the housekeeping gene TEF1‐α and two mating‐type genes, bW1‐HD1 and bE1‐HD2 . We applied this protocol to 20 samples representing both autoecious and heteroecious forms and compared the results with those from inoculation tests and SSR genotyping. The accuracy of the dPCR protocol was examined using C. pini samples identified previously. Additionally, we analysed the morphology and nuclear behaviour during the autoecious and heteroecious aeciospores germination. Heteroecious aeciospores have non‐septate germ tubes with two nuclei, while the germ tube of autoecious aeciospores forms a vesicle and septa, producing one to four uninucleate buds. The microscopic observations provide additional insight into the biology of each life cycle form. To the best of our knowledge, this protocol with mating‐type gene markers is the first application of dPCR to differentiate lineages within a single species and provide a simple and cost‐effective method to differentiate the two forms.

Reproductive systems are central to the evolutionary and ecological processes shaping population structure and adaptability. Rust fungi are a large group of obligate plant pathogens with complex life cycles and diverse reproductive modes. In the rust fungus Cronartium pini, which exists in both macrocyclic heteroecious and microcyclic autoecious forms, transitions between reproductive modes can be studied within a single species. Here, we used comparative genomics to analyse the structure, diversity, and organization of mating-type (MAT) loci across both forms of C. pini. We identified a canonical tetrapolar system in the heteroecious form, characterized by unlinked, multiallelic homeodomain (HD) and pheromone/receptor (P/R) loci, consistent with obligate outcrossing. In contrast, the autoecious form displayed distinct reproductive signatures, including MAT gene homozygosity in some samples—indicative of clonal reproduction—and MAT gene duplications in others, suggesting self-fertility or altered mating pathways. Three HD loci were detected, but only one exhibited high allelic diversity and was consistently present, indicating functional divergence. Expanded allelic diversity at the STE3.2 pheromone receptor further suggests plasticity at the P/R locus. Although allele sharing between life cycle forms was rare, isolated cases of shared MAT alleles suggest limited historical connectivity and possible trans-specific polymorphism. Together, our findings reveal flexibility in the mating system architecture of C. pini and suggest that transitions between sexual and asexual reproduction may be facilitated by retained, functionally ambiguous MAT structures. This work highlights C. pini as a powerful model for studying life cycle evolution and mating system transitions in rust fungi.

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. IMPORTANCE: Fungal 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.

In Europe, Pinus sylvestris and Picea abies are the most common coniferous tree species used in commercial forestry, which rely on high‐quality reproductive material for successful reforestation. Clear‐cut harvested forest sites are often replanted using tree seedlings, which are produced in forest nurseries using seeds from seed orchards. However, incidences of fungal diseases in seedling production show that a better knowledge of seedborne fungi, including fungal pathogens, is needed to manage diseases in forest nurseries. This study aimed to assess seedborne fungal communities associated with commercial seeds of P. abies, P. sylvestris and Larix sp. seeds originated from geographically separated regions in Sweden, Belarus, Finland and Poland. Fungal communities were obtained first from the seed surface and then from the seed tissue. These were analysed using high‐throughput sequencing of the ITS2 rDNA region. The results showed that fungal diversity and community composition differed between the seed surface and the seed tissue. Picea abies accommodated a higher fungal diversity than P. sylvestris. In addition, a strong host affinity of the fungal community composition on the seed surface and a weaker association in the seed tissue was found. Fungal communities on P. abies and P. sylvestris seed surface differed significantly between geographical regions, whereas no regional differences were found in the seed tissue. The seedborne fungal communities included a high proportion of plant pathogens, among which the most abundant were Sydowia polyspora (13.3%), Phoma herbarum (11.2%) and Sirococcus conigenus (3.8%). In conclusion, the results showed (a) characteristic fungal diversity and community composition between the seed surface and the seed tissue; (b) a host‐specific fungal community composition on the seed surface and in the seed tissue; (c) regional difference in fungal communities on P. abies and P. sylvestris seed surface, thus the movement of seeds between different regions can contribute to the spread of fungal diseases; and (d) the presence of a high incidence of seedborne fungal pathogens which suggest a potential need of preventative or control measures to reduce the occurrence of these fungi on the seed surface.

Introduction: Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.Methods: In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.Results and Discussion: Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.

Background: Oilseed rape (OSR; Brassica napus L.) is a highly valued crop for food, feed and industrial use. It is primarily grown in temperate climates, and over recent decades, its area of production and profitability have increased. Concurrently, several diseases negatively impact OSR production. Diseases caused by soil-borne pathogens, pose a risk of substantial yield loss since crop rotation schemes have become narrow as the time lapse between OSR crops in a field has been shortened. The aims of this paper were to provide an overview of plant protection measures available for OSR production and to identify knowledge gaps and areas where more research is needed. Methods: This systematic map builds on a previously published protocol and follows the ROSES reporting standard. The search strategy was developed in collaboration with stakeholders and designed to cover available scientific evidence for OSR disease management in climate zones relevant for Scandinavian crop production (Dfc, Dfb, Cfb and Cfa in the Köppen-Geiger climate classification). Five scientific databases were used to identify peer-reviewed literature, complemented by additional searches performed in grey literature. Articles were screened at three stages: the title, abstract and full text. The eligible publications included studies of OSR crops, and all measures to control crop disease in agricultural fields were considered eligible interventions. The comparator was intervention and no intervention, and the yield per unit area, disease suppression or an increase in crop quality were determined to be outcomes of interventions. A basic assessment of the experimental design of each study was performed to assess its eligibility. All articles were coded based on the following categories: the location and climate zone, disease, pathogen, intervention and management method, outcome and study design. Articles not reporting original data but judged to be relevant (i.e., review papers, books and notes of registration of cultivars) were saved in a separate category called “books, reviews and reports”. Review findings: A total of 4633 articles were collected through systematic searches. After duplicates were removed, 3513 articles were included in the screening process. After screening at the title and abstract levels, 897 articles were evaluated at the full text level, and 118 articles comprised the studies that met the eligibility criteria of the systematic map. The country (Canada) and region (Europe) with the largest OSR crop production areas also contributed the highest number of articles. In total, 17 different diseases were reported, with black leg (syn. Phoma stem canker) being the most studied disease. Nineteen different intervention methods or management types were examined. Cultivar resistance and pesticide application were the most studied control measures. Conclusion: We report scientific studies on plant disease protection measures for OSR based on field trials where the results are intended to be directly implemented in crop production management. The map clearly provides an overview of research progress throughout the time period chosen, and it identifies knowledge gaps regarding important diseases where only a few studies have been published, for example, diseases caused by viruses.

Emerald Ash Borer (EAB), Agrilus planipennis, is a beetle that originates from East Asia. Upon invasion to North America in the early 2000s, it killed untold millions of ash trees. In European Russia, EAB was first detected in Moscow in 2003 and proved to have the potential to also kill native European ash (Fraxinus excelsior). The beetle has since spread in all geographic directions, establishing itself in eastern Ukraine by 2019 and possessing potential for further westward spread towards the EU. Apart from the approaching EAB, F. excelsior is currently threatened by the dieback disease (ADB) caused by the invasive ascomycete fungus Hymenoscyphus fraxineus. The infestation by EAB combined with ADB infection is expected to be more lethal than either of them alone, yet the potential consequences are unknown. To date, eastern Ukraine represents the geographic area in which both invasions overlap, thus providing the opportunity for related investigations. The aims of the study were to investigate: (i) the EAB expansion range in Ukraine, (ii) the relative susceptibility of F. excelsior and American ash (Fraxinus pennsylvanica) to EAB and ADB, and (iii) the combined effect/impact on ash condition imposed by both the pest and disease in the area subjected to the invasion. The results have demonstrated that (i) the invasion of EAB is currently expanding both in terms of newly infested trees and invaded geographic area; (ii) F. excelsior is more resistant to EAB than F. pennsylvanica, while F. excelsior is more susceptible to ADB than F. pennsylvanica; and (iii) the infection by ADB is likely to predispose F. excelsior to the infestation by EAB. It was concluded that inventory and mapping of surviving F. excelsior, affected by both ADB and EAB, is necessary to acquire genetic resources for the work on strategic, long-term restoration of F. excelsior in devastated areas, thereby tackling a possible invasion of EAB to the EU.

The mitochondrial and nuclear genomes of Eukaryotes are inherited separately and consequently follow distinct evolutionary paths. Nevertheless, the encoding of many mitochondrial proteins by the nuclear genome shows the high level of integration they have reached, which makes mitonuclear genetic interactions all the more conceivable. For each species, natural selection has fostered the evolution of coadapted alleles in both genomes, but a population-wise divergence of such alleles could lead to important phenotypic variation, and, ultimately, to speciation. In this study in the Basidiomycete Heterobasidion parviporum, we have investigated the genetic basis of phenotypic variation among laboratory-designed heterokaryons carrying the same pair of haploid nuclei, but a different mitochondrial genome. Radial growth rate data of thirteen unrelated homokaryotic parents and of their heterokaryotic offspring were combined with SNP data extracted from parental genome sequences to identify nuclear and mitochondrial loci involved in mitonuclear interactions. Two nuclear loci encoding mitochondrial proteins appeared as best candidates to engage in a genetic interaction affecting radial growth rate with a non-conserved mitochondrial open reading frame of unknown function and not reported apart from the Russulales order of Basidiomycete fungi. We believe our approach could be useful to investigate several important traits of fungal biology where mitonuclear interactions play a role, including virulence of fungal pathogens.