Fungal Diversity最新文献

The Microsporidia, an often overlooked fungal lineage, exhibit increasing diversity and taxonomic understanding with the use of genomic techniques. They are obligate parasites infecting a diversity of hosts, including crustaceans. Crustacea are, in essence, ancient insects and their relationship with the Microsporidia is both diverse and convoluted. Relationships between crayfish and their microsporidian parasites display geospatial and taxonomic diversity. Through classical (histological, ultrastructural, developmental) and genomic (phylogenetic, phylogenomic) approaches, we expand the known diversity of crayfish-infecting microsporidia into the genus Nosema by describing three novel species from North America: Nosema astafloridana n. sp. infecting Procambarus pictus and Procambarus spiculifer, Nosema rusticus n. sp. infecting Faxonius rusticus, and Nosema wisconsinii n. sp. infecting Faxonius propinquus and Faxonius virilis. Additionally, we provide SSU sequence data for further Nosema diversity from Procambarus clarkii and Pacifasticus gambelii. The taxonomy of aquatic crustacean-infecting Nosema have been under scrutiny among microsporidiologists—using genomic data we solidify this systematic relationship. Our genomic data reveal phylogenomic divergence between terrestrial insect-infecting Nosema and aquatic crustacean-infecting Nosema but place our novel species within the Nosema. Comparative genomic analysis reveal that Nosema rusticus n. sp. is a tetraploid organism, making this the first known polyploid from the genus Nosema. Annotation of the genomic data highlight that crayfish-infecting Nosema have distinct proteomic differences when compared to amphipod and insect-infecting microsporidians. Alongside the new diversity uncovered and genome-supported systematics, we consider the role of these new ‘invasive’ parasites in biological invasion systems, exploring their relationship with their invasive hosts.

Estimates of global fungal diversity have varied widely, suggesting a range from fewer than one million to over 10 million species, with each of the estimates drawing data from various criteria. In 2022, Fungal Diversity published a special issue on fungal numbers. It had been hoped that the editorial would provide a more accurate account of the numbers of fungi. Instead, it was concluded that this was not possible based on present evidence and, some of the data necessary for accurate assessments was put forward, and the present paper expands on this short article. The review first looks at estimates of fungal numbers and what these estimates are based on. It then presents future research needs that will help us to gain a more accurate estimate of fungal numbers. This includes work that needs to be done in tropical rainforests, where the greatest diversity is expected, where whole rainforests, canopy diversity, and palm fungi are addressed. Case studies for lichens and associated fungi, soil and litter fungi, evidence from particle filtration, freshwater fungi, marine fungi, mushrooms, and yeasts will also be given. Once we have such information, we can obtain a more accurate estimate of fungal numbers.

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.

Many taxonomic and systematic rearrangements were proposed to Marasmius Fr. since its original concept in 1835, and since 1980 when it became the type of Marasmiaceae. These were based on morphological and/or more recently molecular phylogenetic studies. This study conducted a comprehensive taxonomic and systematic evaluation of Marasmius that benefits the whole family, implementing multilocus (SSU, LSU, ITS, rpb2 and ef1-α) phylogenetic analyses integrated with morphological and other features. The resulting trees support (1) a Marasmiaceae clade-based circumscription within Marasmiineae, (2) a Marasmius clade-based circumscription within Marasmiaceae, and (3) a subgenus-section-subsection-series system. Two subgenera are proposed: Globulares and Marasmius. Marasmius auton. subgen. includes Crinis-eques sect. nov., sect. Marasmius, Sanguirotales sect. nov., Variabilispori sect. nov., and Sicciformes sect. nov., while Globulares subg. nov. groups sect. Globulares and sect. Sicci. Four subsections are proposed in sect. Globulares and three in sect. Marasmius and sect. Sicciformes. Seventeen series were defined in sect. Globulares and three in sect. Sicci. Selected traits were assessed for their phylogenetic signals within Marasmius, providing a robust framework for a natural system. Based on this analysis, Marasmiaceae includes Chaetocalathus, Crinipellis, Marasmius and Moniliophthora/Paramarasmius, and Campanellaceae fam. nov. includes Brunneocorticium, Campanella/Tetrapyrgos, Neocampanella, and Marasmiellus sect. Candidi. New species, names, combinations and epitypes are also proposed.

Diaporthe is an important plant pathogenic genus, which also occurs as endophytes and saprobes. Many Diaporthe species that are morphologically similar proved to be genetically distinct. The current understanding of Diaporthe taxonomy by applying morphological characters, host associations and multi-gene phylogeny are problematic leading to overestimation/underestimation of species numbers of this significant fungal pathogenic genus. Currently, there are no definite boundaries for the accepted species. Hence, the present study aims to re-structure the genus Diaporthe, based on single gene phylogenies (ITS, tef, tub, cal and his), multi-gene phylogeny justified by applying GCPSR (Genealogical Concordance Phylogenetic Species Recognition) methodology as well as the coalescence-based models (PTP—Poisson Tree Processes and mPTP—multi-rate Poisson Tree Processes). Considering all available type isolates of Diaporthe, the genus is divided into seven sections while boundaries for 13 species and 15 species-complexes are proposed. To support this re-assessment of the genus, 82 Diaporthe isolates obtained from woody hosts in Guizhou Province in China were investigated and revealed the presence of two novel species and 17 previously known species. Synonymies are specified for 31 species based on molecular data and morphological studies. Dividing Diaporthe into several specific sections based on phylogenetic analyses can avoid the construction of lengthy phylogenetic trees of the entire genus in future taxonomic studies. In other words, when one conducts research related to the genus, only species from the appropriate section need to be selected for phylogenetic analysis.

Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.

How the four major processes affecting community assembly—selection, dispersal, drift, and diversification—solely or jointly shape co-occurring assemblages of macro- and microorganisms at the same scales remains poorly understood. Here, we delved into the distance pattern of similarity (DPS) in tree and soil fungal communities in three c. 20-hectare forest plots spanning tropical to temperate climates in Yunnan province, Southwest China. Specifically, we decrypted the assembly contribution of individual-based random sampling, selection and/or dispersal using drift-inexplicit ordination and drift-explicit baseline models. Surprisingly, our findings demonstrated that most soil fungal realized distribution ranges (RDR) were shorter than most trees. Because of explicitly integrating drift and the range of DPS is broader than the RDR of most trees and fungi, selection baseline models overwhelmingly captured the DPS structures in trees and fungi across spatial scales in tropical, subtropical, and subalpine forest ecosystems and that for fungi across taxonomic levels and fungal guilds. Under the premise that modeling frameworks, ecosystems, spatial scales, sample intensities, selection variables, and dispersal variables are well unified, the ubiquitous dominance of selection elucidates no fundamental difference in the assembly mechanism between trees and soil fungi.

The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.