High-throughput sequencing reveals drastic changes in fungal communities in the phyllosphere of Norway spruce (Picea abies) following invasion of the spruce bud scale (Physokermes piceae)

The aim of this study was to assess the diversity and composition of fungal communities in damaged and undamaged shoots of Norway spruce (Picea abies) following recent invasion of the spruce bud scale (Physokermes piceae) in Lithuania. Sampling was done in July 2013 and included 50 random lateral shoots from ten random trees in each of five visually undamaged and five damaged 40-50-year-old pure stands of P. abies. DNA was isolated from 500 individual shoots, subjected to amplification of the internal transcribed spacer of fungal ribosomal DNA (ITS rDNA), barcoded and sequenced. Clustering of 149,426 high-quality sequences resulted in 1193 non-singleton contigs of which 1039 (87.1 %) were fungal. In total, there were 893 fungal taxa in damaged shoots and 608 taxa in undamaged shoots (p < 0.0001). Furthermore, 431 (41.5 %) fungal taxa were exclusively in damaged shoots, 146 (14.0 %) were exclusively in undamaged shoots, and 462 (44.5 %) were common to both types of samples. Correspondence analysis showed that study sites representing damaged and undamaged shoots were separated from each other, indicating that in these fungal communities, these were largely different and, therefore, heavily affected by P. piceae. In conclusion, the results demonstrated that invasive alien tree pests may have a profound effect on fungal mycobiota associated with the phyllosphere of P. abies, and therefore, in addition to their direct negative effect owing physical damage of the tissue, they may also indirectly determine health, sustainability and, ultimately, distribution of the forest tree species

Exploring Fungal Communities in the Needles of Marginal Conifer Tree Populations

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

Classes and phyla of the kingdom Fungi

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

Survival, growth and mycorrhization of containerised pinus sylvestris and picea abies seedlings of different provenances outplanted in a forest clear-cut

We studied field performance of containerised Pinus sylvestris and Picea abies seedlings of different provenances. Shoot height, needle chemical composition, root collar diameter, root mycorrhization and mycorrhizal species composition were evaluated after four growing seasons following outplanting. The results showed that in general spruce had better survival than pine. Ectomycorrhizas on spruce were dominated by Wilcoxina, Amphinema and Tylospora, while on pine by Suillus and Thelephora species. Spruce and pine showing best growth rates were colonised by ectomycorrhizal fungus Amphinema sp. In conclusion, the results demonstrated that forest nursery practices as well as provenance can significantly impact survival, growth and mycorrhization of the containerised pine and spruce seedlings

Fungal Communities Associated with Siricid Wood Wasps: Focus on Sirex juvencus, Urocerus gigas, and Tremex fuscicornis

We investigated the diversity and occurrence of wood wasps in Lithuania and determined communities of associated fungi. Trapping of wood wasps resulted in three different species, including Sirex juvencus, Urocerus gigas, and Tremex fuscicornis. Fungal culturing from adult females of T. fuscicornis mainly resulted in fungi from the genera Penicillium and Trichoderma. High-throughput sequencing of ITS2 rDNA resulted in 59,797 high-quality fungal sequences, representing 127 fungal OTUs. There were 93 fungal OTUs detected in U. gigas, 66 in S. juvencus, and 10 in T. fuscicornis. The most common fungi were Fusarium sporotrichioides (63.1% of all fungal sequences), Amylostereum chailletii (14.9%), Penicillium crustosum (7.8%), Microascus sp. 2261_4 (5.0%), and Pithoascus ater (2.1%). Among these, only A. chailletii was found in all three insect species with the highest relative abundance in U. gigas (15.2%), followed by S. juvencus (7.7%), and the lowest in T. fuscicornis (0.3%) (

Diversity and Composition of Belowground Fungal Communities Associated with Picea abies L. (H.) Karst. and Larix sp. Mill.: A Comparative Study

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

Fungal Diversity in Fire-Affected Pine Forest Soils at the Upper Tree Line

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 Ku & ccaron;i 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

Fungi Inhabiting Stem Wounds of Quercus robur following Bark Stripping by Deer Animals

We investigated fungal communities in oak wounds to determine how fungal species richness and community composition changes depending on the age of wounds. The sampling of wood cores was carried out from 10-, 20-, 30-, 40-, and 50-year-old wounds. The fungal community was analyzed using high-throughput sequencing of ITS2 rDNA. Sequence analysis showed the presence of 534 fungal OTUs, which were 83.4% Ascomycota, 16.3% Basidiomycota, and 0.3% Mucoromycota. The fungal OTU richness changed over time: it increased as compared between 10- and 20-year-old wounds, remained similar in 20- to 40-year-old wounds, and decreased in 50-year-old wounds. The fungal community composition also changed over time with the largest differences detected between 10-year-old and older wounds (p < 0.001). The most common representatives of Basidiomycota were Laetiporus sulphureus (34.7%), Mycena galericulata (17.0%), and Cylindrobasidium evolvens (6.5%), and the most common of Ascomycota were Aposphaeria corallinolutea (13.6%), Sclerostagonospora cycadis (7.6%), and Cadophora malorum (5.8%). In conclusion, oak wounds of different ages were colonized by a high diversity of fungi including oak-associated species. Fungal communities in oak wounds underwent qualitative and quantitative changes over time, which led to the gradual shift from fungal generalists in young wounds to oak specialists in older wounds

The 2024 Outline of Fungi and fungus-like taxa

With the simultaneous growth in interest from the mycological community to discover fungal species and classify them, there is also an important need to assemble all taxonomic information onto common platforms. Fungal classification is facing a rapidly evolving landscape and organizing genera into an appropriate taxonomic hierarchy is central to better structure a unified classification scheme and avoid incorrect taxonomic inferences. With this in mind, the Outlines of Fungi and fungus-like taxa (2020, 2022) were published as an open-source taxonomic scheme to assist mycologists to better understand the taxonomic position of species within the Fungal Kingdom as well as to improve the accuracy and consistency of our taxonomic language. In this paper, the third contribution to the series of Outline of Fungi and fungus-like taxa prepared by the Global Consortium for the Classification of Fungi and fungus-like taxa is published. The former is updated considering our previous reviews and the taxonomic changes based on recent taxonomic work. In addition, it is more comprehensive and derives more input and consensus from a larger number of mycologists worldwide. Apart from listing the position of a particular genus in a taxonomic level, nearly 1000 notes are provided for newly established genera and higher taxa introduced since 2022. The notes section emphasizes on recent findings with corresponding references, discusses background information to support the current taxonomic status and some controversial taxonomic issues are also highlighted. To elicit maximum taxonomic information, notes/taxa are linked to recognized databases such as Index Fungorum, Faces of Fungi, MycoBank and GenBank, Species Fungorum and others. A new feature includes links to Fungalpedia, offering notes in the Compendium of Fungi and fungus-like Organisms. When specific notes are not provided, links are available to webpages and relevant publications for genera or higher taxa to ease data accessibility. Following the recent synonymization of Caulochytriomycota under Chytridiomycota, with Caulochytriomycetes now classified as a class within the latter, based on formally described and currently accepted data, the Fungi comprises 19 Phyla, 83 classes, 1,220 families, 10,685 genera and ca 140,000 species. Of the genera, 39.5% are monotypic and this begs the question whether mycologists split genera unnecessarily or are we going to find other species in these genera as more parts of the world are surveyed? They are 433 speciose genera with more than 50 species. The document also highlights discussion of some important topics including number of genera categorized as incertae sedis status in higher level fungal classification. The number of species at the higher taxonomic level has always been a contentious issue especially when mycologists consider either a lumping or a splitting approach and herein we provide figures. Herein a summary of updates in the outline of Basidiomycota is provided with discussion on whether there are too many genera of Boletales, Ceratobasidiaceae, and speciose genera such as Colletotrichum. Specific case studies deal with Cortinarius, early diverging fungi, Glomeromycota, a diverse early divergent lineage of symbiotic fungi, Eurotiomycetes, marine fungi, Myxomycetes, Phyllosticta, Hymenochaetaceae and Polyporaceae and the longstanding practice of misapplying intercontinental conspecificity.The outline will aid to better stabilize fungal taxonomy and serves as a necessary tool for mycologists and other scientists interested in the classification of the Fungi

Prospects for Oak Cultivation in Europe Under Changing Environmental Conditions and Increasing Pressure from Harmful Organisms

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)