Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era

Insights into the antifungal properties and modes of action of a recombinant hepcidin, rAd-Hep from the shrimp scad, Alepes djedaba (Forsskål, 1775)

Antimicrobial peptides are short, mostly cationic and amphipathic molecules crucial for host defence. Among these, hepcidins are a family of cysteine rich peptides, with HAMP1 hepcidins playing a dual role in iron metabolism and antimicrobial defense. Recently, recombinantly produced Alepes djedaba hepcidin, rAd-Hep was characterized and its antibacterial potential against various pathogens have been discerned. Herein, we investigated the antifungal nature and modes of action of rAd-Hep against some fungal pathogens. The peptide was found to be active against both filamentous fungi and yeasts viz., Aspergillus flavus, Aspergillus sydowii, Fusarium solani, Penicillium citrinum, Candida albicans and Saccharomyces cerevisiae. The peptide acted via membrane permeabilization creating pores of ∼0.7-1.4 nm radii, ROS generation, chromatin condensation and DNA binding. The recombinant hepcidin, rAd-Hep can be considered as a promising candidate for future endeavors in antifungal therapies.

Taxonomy of Chemical Bondings: Opportunities and Challenges

The concept of the chemical bond is fundamental to chemistry, governing atomic interactions that define all known matter. Despite this central role, the classification and most convenient naming of chemical bonds remain subjects of debate due to the diverse theoretical models and experimental observations. Modelings from quantum mechanical calculations and heuristic principles from experimental observations offer valuable and complementary insights, but sometimes the match and coalescence of these different approaches into a common terminology is not immediate. This paper describes a hierarchical categorization of noncovalent interactions based on the electrophilic atom involved, aligning with IUPAC definitions of hydrogen bonding (HB), halogen bonding (HaB), chalcogen bonding (ChB), and pnictogen bonding (PnB). The resulting taxonomy may avoid some ambiguities that arise from naming interactions based on single chemical/physical features. The proposed categorization that moves from more general and comprehensive terms to more specific and descriptive terms may ensure clarity, comprehensiveness, consistency with periodic trends, and invariancy over evolving understanding of the chemical bonds so that findings can be communicated and stored effectively via both human and machine based protocols.

Two new species of Penicillium (Eurotiales, Aspergillaceae) from China based on morphological and molecular analyses

Penicillium is a large and significant genus of fungi, exhibiting widespread distribution across diverse substrates. Ongoing taxonomic and nomenclatural revisions have led to an annual increase in the number of newly described species. This study described two new Penicillium species, i.e., P.lentum and P.tibetense, discovered in China. They have been identified and characterized through morphological examination and both single gene and multigene phylogenetic analyses. Based on these analyses, P.lentum was classified within the section Brevicompacta, while P.tibetense was placed in the section Lanata-Divaricata. Both species exhibited the morphological features typical of their respective sections. Penicilliumlentum is characterized by restricted growth with dense colonies on agar media and predominantly generates terverticillate conidiophores. Penicilliumtibetense demonstrates rapid growth on media and has vigorous growth on CYA at 30 °C, producing biverticillate conidiophores. Comprehensive descriptions and detailed illustrations of these new species were presented. A morphological comparison between the new species and their closely related taxa was provided.

Introducing Melanocucurbitariauktampratovii sp. nov. and the sexual morph of Melanocamarosporioidesugamica in Melanommataceae (Dothideomycetes, Pleosporales)

Most species of Melanommataceae are saprobic on decayed parts of various plants in tropical and temperate terrestrial habitats. During a survey of microfungi associated with terrestrial plants in Uzbekistan, two melanommataceous taxa were collected from dead branches of Rosaecae (Rosaceae) and Salviakarelinii (Lamiaceae). This study introduces a new species, Melanocucurbitariauktampratovii, and provides a new host and sexual morph record for Melanocamarosporioidesugamica, based on morphological observations and multi-gene phylogenetic analyses of concatenated LSU, SSU, ITS, and TEF-1 sequence data. Melanocucurbitariauktampratovii is the second species described within this genus and differs from the type species of Melanocucurbitaria in having smaller ascomata, smaller asci, smaller ascospores, and a different number of septa. The sexual morph of Melanocamarosporioidesugamica is characterized by globose to ovoid ascomata, cylindrical-clavate asci, ellipsoidal, muriform ascospores with 5-7 transversely septate, and 5-11 vertical septa. Illustrations and descriptions are provided, along with ecological and morphological comparisons of similar species within their respective genera.

A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus

Accurate strain identification is essential for economically significant fungi, as it aids in understanding their diverse agronomic traits, pathogenicity, and other important characteristics. However, traditional methods often face challenges related to limited accuracy, high workloads, and reproducibility issues. Recently, multiple nucleotide polymorphism (MNP) markers have been employed in mushroom strain identification, demonstrating significantly improved accuracy and reproducibility. Nevertheless, the identification of strains across different species still heavily depends on specific and often overly complex MNP markers. In this study, we address these challenges by developing a novel method for constructing high-resolution phylogenomic topologies using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, focusing on Agaricus bisporus (button mushroom). Utilising resequencing data from 213 cultivated and wild strains of A. bisporus, we identified 84 cgMNP markers within 83 core genes from 1011 MNP markers. Phylogenetic analysis based on cgMNP sequences and the genetic distance between strain pairs allowed for precise identification of all strains. Moreover, the successful transferability of these cgMNP markers to an additional 385 A. bisporus strains and other fungal species, including Flammulina filiformis (enoki mushroom) and Saccharomyces cerevisiae (yeast), highlights their cross-species applicability. The high resolution and strong congruence of cgMNP markers with whole-genome data provide a robust and reliable method for strain-level discrimination in fungi. The success of this approach in A. bisporus sets a promising precedent for its application to a broader range of fungal taxa.

Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota)

The Diaporthales includes 32 families, many of which are important plant pathogens, endophytes and saprobes, e.g., members of the families Pseudoplagiostomataceae, Pyrisporaceae and Schizoparmaceae. Nucleotide sequences derived from five genetic loci including: ITS, LSU, TEF1-α, TUB2 and RPB2 were used for Bayesian evolutionary analysis to determine divergence times and evolutionary relationships within the Schizoparmaceae. Molecular clock analyses revealed that the ancestor of Schizoparmaceae split during the Upper Cretaceous period approximately 75.7 Mya (95 % highest posterior density of 60.3-91.3 Mya). Reconstructing ancestral state in phylogenies (RASP) with using the Bayesian Binary Markov chain Monte Carlo (BBM) Method to reconstruct the historical biogeography for the family Schizoparmaceae indicated its most likely origin in Africa. Based on taxonomic and phylogenetic analyses, the Pseudoplagiostomataceae and Pyrisporaceae relationships were clarified and a total of four species described herein. For Pseudoplagiostomataceae, three new species and one known species that include, Pseudoplagiostoma fafuense sp. nov., Ps. ilicis sp. nov., Ps. sanmingense sp. nov. and Ps. bambusae are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered Pseudoplagiostoma castaneae to be a synonym of Pyrispora castaneae. In addition, a new species of Schizoparmaceae, Coniella fujianensis sp. nov. is described and illustrated.

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

BACKGROUND

Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.

RESULTS

Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.

CONCLUSIONS

Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.

Catalogue of fungi in China 3. New taxa of macrofungi from southern Xizang, China

This is the third paper in the series Catalogue of fungi in China that aims to systematically and promptly publish Chinese fungal species. In this paper of the series, we focus on macrofungi from the southern border area of Xizang, a previously less concerned region. A total of 15 new species in six orders, 11 families, and 12 genera from Agaricomycetes, Basidiomycota are described. Both morphological and phylogenetic analyses support the identity of these new species and their taxonomic placements. In addition, one new combination Trechispora cryptomerioides is proposed. We hope that the third paper in the series Catalogue of fungi in China will draw more attention to reporting Chinese fungal diversity in the border areas of Xizang and other special geographic regions besides the aim of this series itself.

Can the concentration of elements in wild-growing mushrooms be deduced from the taxonomic rank?

The mineral composition of wild-growing mushroom species is influenced by various environmental factors, particularly the chemical properties of the soil/substrate. We hypothesised that element uptake might also correlate with taxonomic classification, potentially allowing us to predict contamination levels based on mushrooms within the same taxonomic rank. This study compared the mineral composition (Ag, As, Ba, Ca, Cd, Co, Cu, Fe, Hg, K, Mg, Mn, Mo, Na, Ni, Pb, Se, and Zn) of 16 saprotrophic mushroom species from 11 genera across 4 families and 2 orders. Among these were 13 edible and 3 inedible mushrooms, all collected from natural, wild stands in a forest in central-western Poland between 2017 and 2020. Phallus impudicus exhibited the highest mean content of Ba (together with Phallus hadriani) (6.63 and 8.61 mg kg-1, respectively), Ca (with Paralepista gilva and Stropharia rugosoannulata) (803, 735 and 768 mg kg-1, respectively), Cd (with Lycoperdon perlatum) (3.59 and 3.12 mg kg-1, respectively), Co (0.635 mg kg-1), and Fe (with P. hadriani and S. rugosoannulata) (476, 427 and 477 mg kg-1, respectively), while Macrolepiota mastoidea showed the highest content of Ag (1.96 mg kg-1), As (with Coprinus comatus) (1.56 and 1.62 mg kg-1, respectively) and Cu (with Macrolepiota procera and Chlorophyllum rhacodes) (192, 175 and 180 mg kg-1, respectively). Comparing the content of the analysed elements in the genera represented by at least two species, a similarity was observed, the same as the mean concentration in soil under these species. Soil characteristics could be a superior factor that overshadows the impact of the mushroom genus on the elements accumulation, obscuring its role as a determinant in this process. The results are not definitive evidence that belonging to a particular taxonomic rank is a prerequisite condition affecting the accumulation of all elements. A closer focus on this issue is needed.

Catalogue of fungi in China 1. New taxa of plant-inhabiting fungi

China has a huge area of diverse landscapes and is believed to conceive incredibly high fungal diversity. To systematically and promptly report Chinese fungal species, we initiate the series of Catalogue of fungi in China here. In the first paper of this series, we focus on plant-inhabiting fungi. A total of 33 new taxa are described all over China. These taxa include two new genera, viz. Cremeoefibula and Nothopucciniastrum, 18 new species, viz. Annulohypoxylon lancangensis, Ascotaiwania coffeae, Clitocella neofallax, Coleopuccinia yunnanensis, Cremeoefibula hengduanensis, Crepidotus furcaticystidiosus, C. tomentellus, Diachea macroverrucosa, Helicogloea hangzhouensis, Hyalopsora caprearum, Nemania polymorpha, Phanerochaetella austrosinensis, Physalacria tianzhongshanensis, Setophaeosphaeria panlongensis, Subulicystidium boreale, Trechispora subaraneosa, Vikalpa dujuanhuensis, and Xylaria pteridicola, and 13 new combinations, viz. Nothopucciniastrum actinidiae, N. boehmeriae, N. coriariae, N. corni, N. coryli, N. fagi, N. kusanoi, N. hikosanense, N. hydrangeae-petiolaris, N. miyabeanum, N. styracinum, N. tiliae, and N. yoshinagae. The morphological characteristics and phylogenetic evidence are used to support the establishment of these new taxa and the accuracy of their taxonomic placements. We hope that the series of Catalogue of fungi in China will contribute to Chinese fungal diversity and promote the significance of recording new fungal taxa from China.

Umbellaceae fam. nov. (Hymenochaetales, Basidiomycota) for Umbellus sinensis gen. et sp. nov. and Three New Combinations

Hymenochaetales, belonging to Agaricomycetes, Basidiomycota, comprises most polypores and corticioid fungi and, also, a few agarics. The latest taxonomic framework accepts 14 families in this order. When further exploring species diversity of Hymenochaetales, two corticioid specimens collected from China producing cystidia with large umbrella-shaped crystalline heads attracted our attention. This kind of cystidia was reported only in three unsequenced species, viz. Tubulicrinis corneri, T. hamatus and T. umbraculus, which were accepted in Tubulicrinaceae, Hymenochaetales. The current multilocus-based phylogeny supports that the two Chinese specimens formed an independent lineage from Tubulicrinaceae as well as the additional 13 families and all sampled genera in Hymenochaetales. Therefore, a monotypic family, Umbellaceae, is newly described with the new genus Umbellus as the type genus to represent this lineage. The two Chinese specimens are newly described as U. sinensis, which differs from T. corneri, T. hamatus, and T. umbraculus in a combination of a smooth to grandinioid hymenophoral surface, not flattened, broadly ellipsoid basidiospores with a tiny apiculus, and growth on angiosperm wood. Due to the presence of the unique cystidia, the three species of Tubulicrinis, even though they lack available molecular sequences, are transferred to Umbellus as U. corneri, U. hamatus, and U. umbraculus. Hereafter, all known species with large umbrella-shaped crystalline-headed cystidia are in a single genus. In summary, the current study provides a supplement to the latest taxonomic framework of Hymenochaetales and will help to further explore species diversity and the evolution of this fungal order.

Preliminary species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi in the Dabie Mountains, Central China reveal unexpected richness

Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.

OMICS and Other Advanced Technologies in Mycological Applications

Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.

Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota)

Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.

Modeling current geographic distribution and future range shifts of Sanghuangporus under multiple climate change scenarios in China

The genus Sanghuangporus is well-known for its edible and medicinal values. In this study, the most comprehensive occurrence records of Sanghuangporus with accurate species identification are subjected to MaxEnt, to model the current geographic distribution and future range shifts under multiple climate change scenarios in China. The current potential distribution model of Sanghuangporus is excellently predicted as indicated by the value of Area Under Receiver Operator Characteristic Curve. The current potential distribution basically corresponds to the known occurrence records of Sanghuangporus, and provides clues to new suitable habitats. The critical environmental variables to the distribution are annual precipitation, host plant, annual mean temperature and elevation. Host plant is not the most critical contribution to the model, but it indeed plays a decisive role in restricting the distribution of Sanghuangporus. This role is further confirmed by the distribution area of the highly suitable habitat increasing by 155.468%, when excluding host plant from environmental variables. For future scenarios, generally the area of highly suitable habitat for Sanghuangporus extremely increases, but the locations do not change a lot. In conclusion, this study provides important ecological information for the utilization and conservation of the edible and medicinal fungus Sanghuangporus.