Caves, characterized by enclosed, unique, and stable environments, provide favorable conditions for fungal growth and harbor high levels of fungal diversity. Although Yunnan Province is home to more than 200 caves, studies on cave-associated fungi in this region remain scarce. To address this knowledge gap, we surveyed six accessible karst caves in the eastern, western, and southeastern Yunnan. A total of 34 fungal strains representing 17 species were isolated. Morphological characteristics and multi-gene phylogenetic analyses revealed taxonomic diversity among culturable fungi isolated from the sampled Yunnan caves, including numerous previously undescribed taxa. This study introduces one new genus ( Neoachaetomiella ), 12 novel species ( Aspergillus dehongensis , Cosmospora cavernicola , Neoachaetomiella cavernicola , Pithoascus cavernicola , Trichoderma dehongense , T. hongheense , T. mangshiense , T. neogongcheniae , T. neopyramidale , T. nujiangense , T. yingjiangense , and Trichocladium cavernicola ), and reports five species ( Aspergillus baeticus , Chaetomium subaffine , Daldinia eschscholtzii , Mucor phayaoensis , and Trichoderma obovatum ) as new records for caves in Yunnan, China. Detailed descriptions, illustrations, and phylogenetic analyses of all 17 taxa are provided. Additionally, a global checklist of cave-associated fungi is presented.
The phylogenetic affiliations of anaerobic gut fungi ( Neocallimastigomycota ) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.
Taphrina, a genus within the family Taphrinaceae and the order Taphrinales, is a globally distributed group of plant-associated fungi. However, only three species of this genus have been previously reported in China. To enhance the understanding of species diversity within the Taphrina genus in China, sixteen yeast strains, isolated from leaf surfaces across various locations in China and initially identified as members of Taphrina, were examined from both phylogenetic and phenotypic perspectives. From these isolates, one new genus, Srisukozyma, is described to accommodate two new species, Srisukozyma ovata and Sr. musae, along with five additional new species Taphrina aspidistrae, T. cunninghamiae, T. foliicola, T. fujianensis, and T. guizhouensis which we describe. The descriptions of these taxa are supplemented by illustrations and results from phylogenetic analyses. Additionally, phenotypic comparisons with related genus and species are provided. This study contributes to the broader understanding of ascomycetous yeast diversity in natural environments and sets the stage for future taxonomic and ecological investigations.
Wood-inhabiting fungal (WIF) communities are strongly structured by host tree species and environmental gradients. However, how WIF communities are structured among deadwood substrates when such drivers are minimized remains less clear, as do the implications for eDNA-based monitoring. We addressed these questions in a mono-dominant and unmanaged old Beech (Fagus sylvatica) forest, using long-read community profiling. Sampling followed a cross-fraction, tree-linked design that linked four deadwood substrate types to their source tree: logs, snags, attached fine woody debris (aFWD), and fallen fine woody debris (fFWD). Across three analytical scopes, we quantified (1) stand-scale substrate structuring, (2) within-substrate variation, and (3) directed cross-substrate transitions. Alpha diversity was comparable across all substrates, but total richness did not approach saturation. In contrast, dominant diversity (Hill q2) saturated rapidly. Communities were strongly turnover-driven, indicating species replacement rather than nestedness. Tree identity explained a consistent fraction of compositional variance at the stand scale and remained the strongest predictor within coarse woody debris. In fine woody fractions, tree-identity effects weakened and substrate characteristics gained relative importance. Substrate differentiation was stronger in abundance-weighted than in presence-absence space, indicating that substrates primarily reorganize dominance within partially shared species pools. These results show that tree-level legacy persists across fragmented deadwood fractions, while substrate context modulates competitive outcomes. Given these patterns, long-read eDNA efficiently captures dominant and recurrent components of WIF communities, whereas recovery of total richness is unrealistic under typical sampling effort. Monitoring should therefore prioritize sampling many trees with pooled cores per tree and broad coverage of substrate types and characteristics, including decay stage, size, and depth gradients, rather than intensive within-object stratification.
Despite decades of recommendations from the scientific community, fungi have yet to be included in any international legal instruments that regulate wildlife species conservation in the European Union (EU), such as the Bern Convention. However, several EU member states include lists of protected non-lichenized and lichenized fungal species in their national legislation. Most of these legal documents are available only in local languages and are dispersed across national legal databases. To increase the visibility of fungi protected across the EU and facilitate comparisons of these regulations, the first consolidated list of 884 non-lichenized and 787 lichenized fungal taxa protected under the national laws of 18 EU member states is presented. The shortcomings of the current framework for protecting fungal species are highlighted, the distinction between non-binding Red Lists and legally binding species protection is clarified, and improvements to enhance the effectiveness of fungal conservation laws in the EU and beyond are proposed.
Ultramafic substrates impose severe edaphic stress characterised by metal toxicity, nutrient imbalance, and extreme microclimatic conditions, creating spatially fragmented habitats that can shape evolutionary and ecological dynamics of associated organisms. Together with climatic variation, such factors may also influence the structure of holobiont communities of lichenized fungi. Here we investigated the ultramafic specialist lichen Solenopsora liparina across its entire range. We contextualized its symbiotic associations using calcicolous congeners (S. candicans and S. cesatii), as ecological reference taxa representing contrasting substrate-associated lineages within the sampled dataset, to assess how climatic filtering acting within a specialised edaphic niche structures symbiotic partner diversity and composition. Photobionts and endolichenic fungi displayed climate-associated compositional turnover and lineage-level diversity. Variation in the composition of these symbionts was most strongly associated with precipitation during the warmest quarter and, in photobionts, with altitude and temperature seasonality. In photobionts, dominant lineages differed in their relative occurrence among host taxa, whereas low-abundance lineages were broadly shared across samples within the dataset. Despite this turnover, alpha diversity remained generally stable across environmental gradients, indicating that climatic variation most strongly affects community composition rather than within-sample diversity. The results are consistent with a model of mixed host- and substrate- associated symbiont assembly, in which dominant photobiont lineages exhibit host- or substrate-linked preferences, whereas low-abundance associates show weaker specificity and broader ecological overlap across environmental and host contexts. Overall, the findings indicate that climatic factors structure the composition of symbiotic partners without strongly altering their overall diversity, while variation among host taxa is reflected in lineage turnover of dominant symbionts. The persistence of the ultramafic specialist lichen S. liparina thus appears to rely on flexible, compositionally dynamic symbiotic associations shaped by climatic variation within a spatially and edaphically constrained niche, rather than obligate partner specificity. Substrate effects are interpreted here as host-associated lineage patterns rather than independently quantified drivers. More broadly, the results suggest that climatic variation can in some cases strongly influence symbiotic assembly within environmentally extreme and spatially heterogeneous systems. Substrate specialisation provides the ecological context in which such interactions occur. Together, the findings highlight the importance of climatic variation in shaping symbiotic assembly within an edaphically specialised system, emphasizing that patterns associated with host and substrate context are expressed mainly through lineage turnover rather than wholesale community replacement.
The genus Phytophthora (Oomycota) comprises highly destructive and widely distributed plant pathogens that threaten global agriculture and forest ecosystems; however, the evolutionary significance of intraspecific and interspecific mitogenomic variation within this genus remains poorly understood. In this study, complete mitochondrial genomes of 11 Phytophthora species, isolated from forest tree rhizospheres in the Qinling Mountains of China, were sequenced, assembled, and annotated to resolve their genetic diversity and evolutionary patterns. All 11 mitogenomes possess typical circular topologies, ranging in size from 37,502 bp ( P. citrophthora ) to 41,542 bp ( P. cryptogea ), with a uniform GC content averaging approximately 21.96%. The gene repertoire was highly conserved across all genomes, containing 34 core protein-coding genes (PCGs), two rRNA genes, 24–25 tRNA genes, and no introns. Selective pressure analysis showed that Ka/Ks ratios for all 34 core PCGs were significantly below 1 (ranging from 0.0096 to 0.1737), demonstrating that purifying selection drives mitochondrial genome evolution in Phytophthora . Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence. Overall, this work enriches the mitogenomic resources of Phytophthora from pristine natural ecosystems and establishes a critical genomic baseline for accurate species identification, taxonomic revisions, and the study of evolutionary dynamics in oomycetes.
The genus Phanerochaete ( Basidiomycota , Polyporales ) is a member of corticioid fungi. Recent phylogenetic studies have reclassified Phanerochaete species into other genera and delimited the core Phanerochaete . However, phylogenetic studies using multi-locus datasets comprising nuclear ribosomal internal transcribed spacer (ITS), nuclear large subunit ribosomal DNA (nLSU), translation elongation factor 1–α ( tef1 ), RNA polymerase II largest subunit ( rpb1 ) and RNA polymerase II second largest subunit ( rpb2 ) are still limited and the divergence time estimation and historical biogeography are under-represented for the genus Phanerochaete . To address this gap, we conducted the first integrative evolutionary study of Phanerochaete using a five-locus dataset. Of the 72 specimens, 14 species were identified, including two novel species: Phanerochaete koreana sp. nov ., characterised by coriaceous basidiome and the absence of leptocystidia and Phanerochaete membranacea sp. nov ., characterised by an ochraceous membranaceous basidiomata and heavily encrusted leptocystidia. Multi-locus phylogenetic analysis, divergence time estimation and historical biogeographic analyses suggest that Phanerochaete originated during the Early Cretaceous, with a mean crown age of 101.66 Mya [95% highest posterior density (HPD): 98.38–104.86 Mya]. This study elucidates the evolutionary relationships between Phanerochaete and allied genera within Polyporales and explains the global diversity, phylogeny and evolution of the genus.
Cordyceps militaris is a prized entomopathogenic fungus with significant medicinal and commercial value, yet its intraspecific genetic diversity has not been thoroughly examined. Mitogenomes from 118 geographically diverse samples were analyzed to trace the evolutionary trajectory of C. militaris and elucidate the diversification of its mitochondrial genome (mitogenome). These mitogenomes are circular DNA molecules with lengths ranging from 26.5 to 40.3 kbp and GC contents ranging from 26.12% to 27.24%. Comparative mitogenomic analyses revealed conserved gene content and syntenic relationships among various samples, with intraspecific divergence primarily driven by dynamic intron turnover (including 18 identified insertion sites, with deletions outnumbering acquisitions) and high variability in intergenic regions. Evidence of mitochondrial-to-nuclear DNA transfer was also detected. Notably, the mitogenome evolved at an accelerated rate, accumulating mutations approximately 2.8-fold faster than the nuclear genome (SNP frequencies: 1.58% vs. 0.57%). Phylogenomic reconstructions based on mitochondrial and nuclear genomes yielded largely congruent topologies but with subtle discordances, reflecting the complex coevolutionary relationship between the two genomic compartments. Collectively, this study provides a comprehensive view of mitogenome architecture and evolutionary dynamics in C. militaris, reveals substantial organellar genetic diversity, and underscores the critical role of mitogenomes in understanding organelle-nuclear coevolution.
Mazosia is one of the most commonly encountered foliicolous genera, regularly present with high species richness in closed rainforest understory communities throughout the tropics. This first comprehensive multi-locus (ITS-nuLSU-mtSSU) phylogenetic analysis indicates a high level of previously unrecognized diversity, with a 50% increase in lineages recognized in this genus. On the basis of combined molecular and phenotypic data, sixteen new species of Mazosia from China are described: Mazosia centrica sp. nov ., M. dimorphoverrucosa sp. nov ., M. gelatinospora sp. nov ., M. intermedia sp. nov ., M. papillosa sp. nov ., M. pruinata sp. nov ., M. pseudoaptrootii sp. nov ., M. pseudocorticola sp. nov ., M. pseudomelanophthalma sp. nov ., M. pseudopapillosa sp. nov ., M. pseudopilosa sp. nov ., M. pseudopruinata sp. nov ., M. pseudotenuissima sp. nov ., M. sinensis sp. nov ., M. straminea sp. nov ., and M. verrucosa sp. nov . A new, world-wide key to the known species of Mazosia is presented.
Armillaria ostoyae is an economically important forest pathogen whose reproductive development is regulated by environmental cues. Although low temperature is recognized as an important morphogenetic stimulus, the molecular mechanisms underlying the resulting developmental transition-here termed "cryometamorphosis"-remain poorly understood. Using an orthogonal experimental design, we categorized A. ostoyae as a "cold-pressed" species. Induction at 4 °C significantly accelerated primordium formation, reducing the time required for initiation from 25 to 7 days. Transcriptomic profiling across developmental and morphological stages revealed that primordium initiation was associated with the most extensive transcriptional reprograming across the reproductive trajectory. Weighted gene co-expression network analysis identified a core low-temperature-associated module, MEturquoise, and revealed a putative hierarchical regulatory network. Within this network, a group of fungus-specific Zn(II)2Cys6 transcription factors whose promoters contained predicted low-temperature response elements were tightly co-expressed with putative SET-domain histone methyltransferases and F-box proteins. To functionally validate this regulatory model, we established an optimized genetic transformation system for A. ostoyae and overexpressed the leading candidate gene, AoZCy6_17. Overexpression of AoZCy6_17 at a constant temperature of 25 °C was associated with a pronounced morphological transition: no visible rhizomorph formation was observed in the OE strain under the conditions tested, together with increased production of dense aerial mycelia accompanied by abundant surface droplets. Biochemical assays showed that the overexpression strain exhibited enhanced basal antioxidant activity, with significantly higher catalase activity than the wild type (approximately 2,436 versus 2,001 U g-1 fresh weight; P < 0.001). This constitutive physiological reprograming was also associated with increased malondialdehyde accumulation under non-stress conditions (approximately 23.1 versus 9.6 nmol g-1 fresh weight), indicating a potential physiological cost. Notably, activation of AoZCy6_17 alone recapitulated and, for some biochemical traits, exceeded the changes induced by exposure of the wild-type strain to 4 °C. Collectively, our findings provide functional evidence that AoZCy6_17 is a key regulator linking low-temperature signaling to developmental and physiological reprograming in A. ostoyae, thereby establishing a mechanistic framework for investigating fungal cryometamorphosis.
Aureobasidium species are widely distributed fungi commonly associated with diverse ecological niches, including floral environments. However, their diversity in tropical regions, particularly in flower-associated habitats, remains poorly explored. During a survey of fungi associated with flowers from diverse plant hosts in northern Thailand in 2024, a total of 54 Aureobasidium strains were isolated from 31 flower species. Based on a polyphasic approach integrating multilocus phylogenetic analyses, morphological and physiological characteristics, and growth temperature profiles, these strains were identified as 16 novel species ( Aureobasidium anthicola sp. nov ., A. bougainvilleae sp. nov ., A. catharanthi sp. nov ., A. chiangmaiense sp. nov ., A. florale sp. nov ., A. floricola sp. nov ., A. florigenum sp. nov ., A. kwanphayaoense sp. nov ., A. lannaense sp. nov ., A. oroxyli sp. nov ., A. phayaoense sp. nov ., A. plumeriae sp. nov ., A. pollinicola sp. nov ., A. saisamorniae sp. nov ., A. savitreeae sp. nov ., and A. siamense sp. nov .) and five previously known species ( A. albui , A. castaneae , A. melanogenum , A. musti , and A. tremulum ). Species within the A. melanogenum and A. thailandense groups were delimited as novel species based on the genealogical concordance phylogenetic species recognition (GCPSR) concept, supported by pairwise homoplasy index tests and physiological traits. Carbon assimilation profiles represent useful phenotypic characteristics for distinguishing closely related species. Moreover, these are the first geographic records of A. albui , A. castaneae , A. musti , and A. tremulum in Thailand. Full descriptions, color photographs, illustrations, and a phylogenetic tree showing the phylogenetic positions of the Aureobasidium species obtained in this study are provided. This study highlights floral habitats as important and previously underexplored ecological niches for Aureobasidium in tropical ecosystems, providing new insights into its diversity, ecology, and distribution.
The genus Hygrocybe (Hygrocybaceae) exhibits remarkable diversity in the tropical forests of the Dominican Republic, particularly within H. subgenus Hygrocybe . Following over 20 years of fieldwork (2006–2026), seven new taxa are described herein based on morphological, molecular, and ecological analyses. Phylogenetic reconstructions using nuclear ribosomal ITS and LSU sequences resolved four well-supported clades in H. subgenus Hygrocybe (/appalachianensis, /acutoconica, /conica, and /hypohaemacta), each corresponding to a distinct evolutionary lineage. The novel species include H. citrinonigrescens , distinguished by its lemon-yellow pileus, which blackens with age, and the presence of dimorphic basidia in some basidiomata; H. jarabacoensis , a fibrillose, greenish-yellow species associated with coniferous forests; H. perdomoi , a species from the Dominican Republic and Florida that features small, completely viscid, yellow-orange to scarlet-red basidiomata and shares morphological similarities with H. acutoconica ; H. pseudohypohaemacta and H. variecolor , two phylogenetically close yet morphologically divergent taxa within H. section Velosae ; and H. xerophila , a species described from Florida, USA, and the Dominican Republic. Molecular data also revealed cryptic diversity, such as H. parabolica , which is notable for its bisporic basidia and affinity for burned habitats. Dimorphic basidia and spores are reported for the first time in three species of H. subgenus Hygrocybe section Hygrocybe , viz., H. citrinonigrescens , H. parabolica , and H. xerophila . The study highlights the significance of the Dominican Republic as a hub of Hygrocybe diversity, with species exhibiting specialized adaptations to tropical ecosystems, including associations with disturbed or serpentine soils. These findings expand the understanding of Neotropical fungal biodiversity and emphasize the conservation value of Caribbean forests.
The taxonomy of the Auriculariaceae (Auriculariales, Basidiomycota) is revised based on morphological data and four- and three-marker datasets, with special emphasis on the Exidia clade. We argue in favor of retaining Exidia as a large genus, encompassing most species previously relegated to it, with an addition of four effused (Exidiopsis-like) species. Phylogenetic data allow us to justify two segregates from Exidia s. lato, namely the reinstated Ulocolla (Exidia saccharina complex) and a newly erected genus Descidia, encompassing Exidia repanda and E. thuretiana. At large, morphological data corroborate this splitting. Exidiopsis effusa, the generic type of Exidiopsis, is typified and redescribed; together with a newly described E. perflua, it constitutes the genus Exidiopsis s. str. The rest of Exidiopsis s. lato species studied by us are redistributed among the redefined genera Adustochaete, Leiostroma, Proterochaete, and Ulocolla, as well as a newly introduced genus, Tegmenticium. Amphistereum is placed among the synonyms of Eichleriella and the single representative of Sclerotrema, Exidiopsis griseobrunnea, is moved into Ulocolla. In total, 52 species are properly redescribed or introduced below, of them twenty are new to science, and twenty new combinations are proposed. Additionally, we detected two single-species lineages: Pholiobasidion senex gen. nov. et sp. nov., from North America, which is recovered as the sister group to all other members of the Auriculariaceae sampled, and Scrupulispora perparvula gen. nov. et sp. nov., from Europe.
Orchidaceae is a highly valuable horticultural and medicinal plant family worldwide; however, large-scale propagation and conservation remain severely limited. Orchid seeds depend on symbiotic fungi for germination, and pre-symbiotic communication is essential for establishing a successful association, a process that remains poorly understood. In this study, exudates were collected from the germination-promoting fungus Ceratobasidium sp. GS2 and applied to seeds of the terrestrial orchid Gymnadenia conopsea to investigate downstream responses. Multi-omics approaches, including RNA-seq, metabolomics, and phylogenetic analysis, combined with biological validation, revealed that the exudates elicited transcriptional and physiological responses in G. conopsea seeds, potentially promoting dormancy release. Exposure to fungal exudates increased the levels of brassinosteroids, cytokinins, and fatty acids in seeds. Exogenous hormone application confirmed that brassinosteroids and cytokinins promote fungal colonization and facilitate symbiotic seed germination. Phylogenetic analysis revealed the conservation of symbiotic genes in partially mycoheterotrophic orchids, and functional characterization confirmed the role of GcRAM2 in G. conopsea. These findings provide new insights into the mechanisms underlying orchid mycorrhizal symbiosis.
The rapid expansion of high-throughput sequencing and environmental DNA (eDNA) studies has led to the introduction of dozens of fungal names based exclusively on molecular data derived from environmental substrates such as soil, dung, or water. In several recent cases, authors and nomenclatural repositories have divergently treated such names as valid or invalid on the grounds that the designated types may or may not constitute specimens under the current wording of the International Code of Nomenclature for algae, fungi, and plants (ICN; Madrid Code). Here, we examine the nomenclatural basis of these treatments by analysing the relevant ICN provisions on specimens, gatherings, admixtures, and typification. We show that while a conservative curatorial approach is defensible under current practice and aligned with the ICN’s objective of nomenclatural stability, the Code does not explicitly address whether preserved environmental samples can serve as types when a taxon is evidenced solely by a molecular signal. We therefore argue that explicit clarification—through formal proposals to amend Chapter F and/or relevant general ICN provisions—is now urgently required to ensure consistent, transparent, and future-ready nomenclatural practice in the face of accelerating detection-driven discovery. Graphical Abstract
