The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

The huge land areas in China provide highly diverse habitats for macrofungi. Of these macrofungi, many are directly related to people’s daily life and have been utilized by ancient Chinese for at least 6800 years. In this study, we evaluate the current known resource diversity of Chinese macrofungi. A total of 1662 taxa are summarized, and all species names and their authorities have been checked and corrected according to authentic mycological databases. Among the 1662 taxa, 1020, 692, and 480 are considered to be edible, medicinal and poisonous mushrooms, respectively. A few of edible macrofungi in China are commonly used for commercial production. All known medicinal functions are labeled for medicinal species. The most common medicinal functions possessed by Chinese macrofungi are antitumor or anticancer, followed by antioxidant and antimicrobial. A total of 277 Chinese macrofungi are edible simultaneously with certain medicinal functions and without known toxicity. These species could be treated as “Gold Mushrooms”. Contrarily, 193 edible and/or medicinal species are also recognized as poisonous mushrooms. To avoid poisoning caused by these species, ingestion either in a proper way or in small amounts is important. However, the mycotoxins metabolized by these poisonous species could be a huge wealth of natural products yet to be explored. How to utilize these Chinese macrofungal resources is a critical to benefit humans worldwide.

Fungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.

Micropeltidaceae species are flyspeck fungi which have been subjected to few systematic studies. We re-examined 27 genera which were accepted in the Micropeltidaceae and re-described them based on herbaria materials and protologues. Based on morphology and phylogenetic investigations, we transfer Micropeltidaceae to a new order, Micropeltidales (Lecanoromycetes). Genera with bluish or greenish upper walls (Dictyopeltella, Dictyothyriella, Dictyothyrina, Dictyothyrium, Haplopeltheca, Micropeltis, Scolecopeltidium and Stomiopeltopsis) are accepted in the new taxonomic concept for Micropeltidaceae. A molecular clock approach estimated the divergence time of the Micropeltidaceae crown group at 130 (165–104) Mya, which also supports its rank as an order (diverging from 220–100 Mya). The evolutionary histories between Micropeltidaceae species and host plants are interpreted by cophylogenetic analyses calibrated by their divergence times. The result indicates that the diversification of Angiospermae (130–80 Mya) fosters the formation of genera of Micropeltidaceae mainly via cospeciation events, and this codivergent period would be an important reference when establishing generic boundaries of epifoliar fungi.

Polyporaceae is one of the most important families of Basidiomycota. Investigations on the species diversity, taxonomy and phylogeny of Polyporaceae in China are carried out. So far 217 species belonging to 42 genera are reported from China. Two new genera: Amylosporia gen. nov. and Murinicarpus gen. nov., twelve new species: Coriolopsis dendriformis sp. nov., C. hainanensis sp. nov., Funalia cystidiata sp. nov., Haploporus microsporus sp. nov., Perenniporia citrinoalba sp. nov., P. yinggelingensis sp. nov., Picipes hainanensis sp. nov., P. jiajinensis sp. nov., P. pseudovarius sp. nov., Trametes duplexa sp. nov., T. ellipsoidea sp. nov. and T. stiptica sp. nov., and six new combinations, Amylosporia hattorii comb. nov., Hornodermoporus latissimus comb. nov., Murinicarpus subadustus comb. nov., Picipes pumilus comb. nov., Vanderbylia delavayi comb. nov. and Vanderbylia robiniophila comb. nov., are proposed. All the species are described based on the Chinese collections. Keys to genera of Polyporaceae occurring in China and keys to species of each genus are provided. This monograph provides a revised classification of Polyporaceae in China according to the modern taxonomy. The phylogeny of Polyporaceae from China are reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit nuclear ribosomal RNA gene (nSSU), the small subunit mitochondrial rRNA gene sequences (mtSSU), the translation elongation factor 1-α gene (TEF1), the β-tubulin gene (TBB1), the RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2) genes. In addition, full morphological descriptions, illustrations, color photographs, taxonomic notes, ecology and all the available sequences of Polyporaceae species found from China are provided.

Index Fungorum, Species Fungorum and MycoBank are the key fungal nomenclature and taxonomic databases that can be sourced to find taxonomic details concerning fungi, while DNA sequence data can be sourced from the NCBI, EBI and UNITE databases. Nomenclature and ecological data on freshwater fungi can be accessed on http://fungi.life.illinois.edu/, while http://www.marinespecies.org/provides a comprehensive list of names of marine organisms, including information on their synonymy. Previous websites however have little information on marine fungi and their ecology, beside articles that deal with marine fungi, especially those published in the nineteenth and early twentieth centuries may not be accessible to those working in third world countries. To address this problem, a new website www.marinefungi.org was set up and is introduced in this paper. This website provides a search facility to genera of marine fungi, full species descriptions, key to species and illustrations, an up to date classification of all recorded marine fungi which includes all fungal groups (Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota and fungus-like organisms e.g. Thraustochytriales), and listing recent publications. Currently, 1257 species are listed in the marine fungi website (www.marinefungi.org), in 539 genera, 74 orders, 168 families, 20 classes and five phyla, with new taxa continuing to be described. The website has curators with specialist mycological expertise who help to provide update data on the classification of marine fungi. This article also reviews knowledge of marine fungi covering a wide range of topics: their higher classification, ecology and world distribution, role in energy transfer in the oceans, origin and new chemical structures. An updated classification of marine fungi is also included. We would like to invite all mycologists to contribute to this innovative website.

This article is the tenth series of the Fungal Diversity Notes, where 114 taxa distributed in three phyla, ten classes, 30 orders and 53 families are described and illustrated. Taxa described in the present study include one new family (viz. Pseudoberkleasmiaceae in Dothideomycetes), five new genera (Caatingomyces, Cryptoschizotrema, Neoacladium, Paramassaria and Trochilispora) and 71 new species, (viz. Acrogenospora thailandica, Amniculicola aquatica, A. guttulata, Angustimassarina sylvatica, Blackwellomyces lateris, Boubovia gelatinosa, Buellia viridula, Caatingomyces brasiliensis, Calophoma humuli, Camarosporidiella mori, Canalisporium dehongense, Cantharellus brunneopallidus, C. griseotinctus, Castanediella meliponae, Coprinopsis psammophila, Cordyceps succavus, Cortinarius minusculus, C. subscotoides, Diaporthe italiana, D. rumicicola, Diatrypella delonicis, Dictyocheirospora aquadulcis, D. taiwanense, Digitodesmium chiangmaiense, Distoseptispora dehongensis, D. palmarum, Dothiorella styphnolobii, Ellisembia aurea, Falciformispora aquatic, Fomitiporia carpinea, F. lagerstroemiae, Grammothele aurantiaca, G. micropora, Hermatomyces bauhiniae, Jahnula queenslandica, Kamalomyces mangrovei, Lecidella yunnanensis, Micarea squamulosa, Muriphaeosphaeria angustifoliae, Neoacladium indicum, Neodidymelliopsis sambuci, Neosetophoma miscanthi, N. salicis, Nodulosphaeria aquilegiae, N. thalictri, Paramassaria samaneae, Penicillium circulare, P. geumsanense, P. mali-pumilae, P. psychrotrophicum, P. wandoense, Phaeoisaria siamensis, Phaeopoacea asparagicola, Phaeosphaeria penniseti, Plectocarpon galapagoense, Porina sorediata, Pseudoberkleasmium chiangmaiense, Pyrenochaetopsis sinensis, Rhizophydium koreanum, Russula prasina, Sporoschisma chiangraiense, Stigmatomyces chamaemyiae, S. cocksii, S. papei, S. tschirnhausii, S. vikhrevii, Thysanorea uniseptata, Torula breviconidiophora, T. polyseptata, Trochilispora schefflerae and Vaginatispora palmae). Further, twelve new combinations (viz. Cryptoschizotrema cryptotrema, Prolixandromyces australi, P. elongatus, P. falcatus, P. longispinae, P. microveliae, P. neoalardi, P. polhemorum, P. protuberans, P. pseudoveliae, P. tenuistipitis and P. umbonatus), an epitype is chosen for Cantharellus goossensiae, a reference specimen for Acrogenospora sphaerocephala and new synonym Prolixandromyces are designated. Twenty-four new records on new hosts and new geographical distributions are also reported (i.e. Acrostalagmus annulatus, Cantharellus goossensiae, Coprinopsis villosa, Dothiorella plurivora, Dothiorella rhamni, Dothiorella symphoricarposicola, Dictyocheirospora rotunda, Fasciatispora arengae, Grammothele brasiliensis, Lasiodiplodia iraniensis, Lembosia xyliae, Morenoina palmicola, Murispora cicognanii, Neodidymelliopsis farokhinejadii, Neolinocarpon rachidis, Nothophoma quercina, Peroneutypa scoparia, Pestalotiopsis aggestorum, Pilidium concavum, Plagiostoma salicellum, Protofenestella ulmi, Sarocladium kiliense, Tetraploa nagasakiensis and Vaginatispora armatispora).

Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears to be around 30%, even higher than previously estimated. Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species (when BLAST top scores were equally high for different species), all belonging to Agaricomycotina. This paper dissects for the first time a number of sequence-based identifications, thereby showing in every detail—particularly to the user community of taxonomic information—why sequence-based identification in the context of a fungal inventory can easily go wrong. Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories: we spent two months on verification of approx. 20 identifications. Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification, it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata. While checking the original publications associated with top score sequences for the few examples that were here re-examined, a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank. Advantages and pitfalls of sequence-based identification are discussed, particularly in the light of undertaking fungal inventories. Recommendations are made to avoid or reduce some of the major problems with sequence-based identification. Nevertheless, the prospects for a more reliable sequence-based identification of fungi remain quite dim, unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.

Inaccurate taxonomic placement of fossils can lead to the accumulation of errors in molecular clock studies and their generated evolutionary lineages. There are limited fossil data that can be used in divergence time estimations. Therefore, reliable morphological characterization and taxonomical identification of fossil fungi are extremely important. Most fossils of Dothideomycetes and Sordariomycetes are from the early Cenozoic (66–23 Mya), with fewer from the late Mesozoic (174–145 Mya). However, it is hard to distinguish some fossil descriptions as photographs and illustrations are unclear; thus, the validity of using these fossils in calibrations of molecular clocks is problematic. This study brings scattered paleobiological data on selected fossil Ascomycota, using descriptions, fossil images and illustrations, coupled with recent age estimations, and taxonomic and phylogenetic affinity of extant species. As an integrated approach, this study summarizes a historical fossil outline with a reliable minimum age for 16 calibrating points viz. crown of Aigialus, Anzia, Aspergillus, Asterina, Calicium chlorosporum–C. nobile, Capnodiales, Chaenotheca, Colletotrichum, Diaporthales, Meliola, Ophiocordyceps, Microthyriales, Microthyrium, Muyocopron, Pezizomycotina and Stigmatomyces. A scheme of Ascomycota ancient lineages is also provided in order to improve divergence time estimations.

There were errors in Figs. 1 and 2 in the original publication. Figure panels 1a, 1b, 1h and 1p did not match the legend. The correct Fig. 1 is published below. In Fig. 2, the word Fusion should be Fusional.

This article is the ninth in the series of Fungal Diversity Notes, where 107 taxa distributed in three phyla, nine classes, 31 orders and 57 families are described and illustrated. Taxa described in the present study include 12 new genera, 74 new species, three new combinations, two reference specimens, a re-circumscription of the epitype, and 15 records of sexual-asexual morph connections, new hosts and new geographical distributions. Twelve new genera comprise Brunneofusispora, Brunneomurispora, Liua, Lonicericola, Neoeutypella, Paratrimmatostroma, Parazalerion, Proliferophorum, Pseudoastrosphaeriellopsis, Septomelanconiella, Velebitea and Vicosamyces. Seventy-four new species are Agaricus memnonius, A. langensis, Aleurodiscus patagonicus, Amanita flavoalba, A. subtropicana, Amphisphaeria mangrovei, Baorangia major, Bartalinia kunmingensis, Brunneofusispora sinensis, Brunneomurispora lonicerae, Capronia camelliae-yunnanensis, Clavulina thindii, Coniochaeta simbalensis, Conlarium thailandense, Coprinus trigonosporus, Liua muriformis, Cyphellophora filicis, Cytospora ulmicola, Dacrymyces invisibilis, Dictyocheirospora metroxylonis, Distoseptispora thysanolaenae, Emericellopsis koreana, Galiicola baoshanensis, Hygrocybe lucida, Hypoxylon teeravasati, Hyweljonesia indica, Keissleriella caraganae, Lactarius olivaceopallidus, Lactifluus midnapurensis, Lembosia brigadeirensis, Leptosphaeria urticae, Lonicericola hyaloseptispora, Lophiotrema mucilaginosis, Marasmiellus bicoloripes, Marasmius indojasminodorus, Micropeltis phetchaburiensis, Mucor orantomantidis, Murilentithecium lonicerae, Neobambusicola brunnea, Neoeutypella baoshanensis, Neoroussoella heveae, Neosetophoma lonicerae, Ophiobolus malleolus, Parabambusicola thysanolaenae, Paratrimmatostroma kunmingensis, Parazalerion indica, Penicillium dokdoense, Peroneutypa mangrovei, Phaeosphaeria cycadis, Phanerochaete australosanguinea, Plectosphaerella kunmingensis, Plenodomus artemisiae, P. lijiangensis, Proliferophorum thailandicum, Pseudoastrosphaeriellopsis kaveriana, Pseudohelicomyces menglunicus, Pseudoplagiostoma mangiferae, Robillarda mangiferae, Roussoella elaeicola, Russula choptae, R. uttarakhandia, Septomelanconiella thailandica, Spencermartinsia acericola, Sphaerellopsis isthmospora, Thozetella lithocarpi, Trechispora echinospora, Tremellochaete atlantica, Trichoderma koreanum, T. pinicola, T. rugulosum, Velebitea chrysotexta, Vicosamyces venturisporus, Wojnowiciella kunmingensis and Zopfiella indica. Three new combinations are Baorangia rufomaculata, Lanmaoa pallidorosea and Wojnowiciella rosicola. The reference specimens of Canalisporium kenyense and Tamsiniella labiosa are designated. The epitype of Sarcopeziza sicula is re-circumscribed based on cyto- and histochemical analyses. The sexual-asexual morph connection of Plenodomus sinensis is reported from ferns and Cirsium for the first time. In addition, the new host records and country records are Amanita altipes, A. melleialba, Amarenomyces dactylidis, Chaetosphaeria panamensis, Coniella vitis, Coprinopsis kubickae, Dothiorella sarmentorum, Leptobacillium leptobactrum var. calidus, Muyocopron lithocarpi, Neoroussoella solani, Periconia cortaderiae, Phragmocamarosporium hederae, Sphaerellopsis paraphysata and Sphaeropsis eucalypticola.

Fungicolous fungi are a very large, diverse, ecological and trophic group of organisms that are associated with other fungi. This association occurs with species of different lineages across the fungal kingdom. They are recognized as symbionts, mycoparasites, saprotrophs, and even neutrals. Wherever fungi have been found, fungicolous taxa have also been found. Homogeneous environments favour the development of highly adapted and coevolved fungicolous species, which could have led to host-specificity aspects. As a primary consumer, fungicolous fungi decrease the turnaround time of certain nutrients in food webs, due to their special often-rapid life cycles. They may also significantly affect population dynamics and population sizes of their hosts in aquatic or terrestrial ecosystems. As mycoparasites of pathogenic fungi, some fungicolous fungi have been explored as biocontrol agents. They may also cause serious diseases of cultivated edible and medicinal mushrooms, decreasing both yield and quality. Fungicolous fungi could be used as model organisms that may help determine better understanding of species interactions, fungal evolution and divergence, and fungicolous mechanisms. This review summarizes our current understanding of fungicolous fungi, with a particular focus on the terminology, diversity, global distribution, and interaction with their hosts. We also provide a checklist including 1552 fungicolous fungal taxa so far recorded following the updated classification schemes. There is a need for further investigations on this ecologically important group of fungi to better understand their biology, ecological aspects, origin and divergence, host-specificity and application in biocontrol. Accurate identification of these fungi as pathogens and their significance in quarantine purposes on the mushroom industry need further evaluations so that efficient control measures can be developed for better disease management purposes.

The genus Lactarius Pers. (Russulales) is a cosmopolitan group of Basidiomycota that forms ectomycorrhizal relationships primarily with both deciduous and coniferous trees. Although the genus has been well-studied in Europe and North America, only fragmentary researches have been carried out on Asian species. In particular, the distribution of Lactarius species in South Korea is poorly understood due to insufficient morphological descriptions and a lack of DNA sequence data. In addition, the misuse of European and North American names has added to confusion regarding the taxonomy of Asian Lactarius species. In this study, the diversity of Lactarius in South Korea was evaluated by employing both morphological and phylogenetic approaches. A multi-locus phylogenetic analysis of 729 Lactarius specimens collected between 1960 and 2017 was performed using the internal transcribed spacer (ITS) region, partial nuclear ribosomal large subunit (nrLSU), partial second largest subunit of RNA polymerase II (rpb2), and minichromosome maintenance complex component 7 (mcm7). 49 Lactarius species were identified in three Lactarius subgenera: L. subg. Russularia (17 spp.), L. subg. Lactarius (22 spp.), and L. subg. Plinthogalus (10 spp.). Among them, 28 Lactarius species were identified as new to science, while just 17 were previously described Lactarius species. Four of the taxa remain un-named due to paucity of materials. A key to Korean Lactarius species, molecular phylogenies, a summary of diversity, and detailed description are provided.

Here, we show that Lichinodium (Lichinaceae, Lichinomycetes, Ascomycota) constitutes a formerly unrecognized lineage within the Leotiomycetes, thus being the first lichenized lineage recognized in the superclass Sordariomyceta (Leotiomycetes, Laboulbeniomycetes and Sordariomycetes). To infer the position of Lichinodium, we constructed two multilocus phylogenies based on six and five gene regions (nuLSU rDNA, nuSSU rDNA, mtSSU rDNA, RPB1, RPB2 and MCM7) including main Pezizomycotina groups in the first analysis and focusing secondly on a comprehensive selection of Sordariomyceta. The results show that Lichinodium is sister to Leotiaceae. We discuss the morphological and ecological similarities between Lichinodium and other Leotiomycetes, and describe the new order Lichinodiales and family Lichinodiaceae. The sister relationship between Sordariomycetes and Laboulbeniomycetes is here supported as it is the relationship between this clade and the Leotiomycetes. The results also support the polyphyly of Helotiales, the recognition of the Leotiales in a strict sense or the inclusion of the Triblidiales in Leotiomycetes. The photobionts of Lichinodium were sequenced for two genetic markers (rbcLX and 16S rDNA) and identified as Rhizonema, a recently described genus of filamentous cyanobacteria belonging to Nostocaceae. TEM studies revealed that the mycobiont-cyanobiont interface in Lichinodium does not produce haustoria, thus differing from a typical Lichinomycete (e.g. Ephebe).

This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi. It focuses on 25 phytopathogenic genera: Alternaria, Bipolaris, Boeremia, Botryosphaeria, Calonectria, Coniella, Corticiaceae, Curvularia, Elsinoe, Entyloma, Erythricium, Fomitiporia, Fulviformes, Laetisaria, Limonomyces, Neofabraea, Neofusicoccum, Phaeoacremonium, Phellinotus, Phyllosticta, Plenodomus, Pseudopyricularia, Tilletia, Venturia and Waitea, using recent molecular data, up to date names and the latest taxonomic insights. For each genus a taxonomic background, diversity aspects, species identification and classification based on molecular phylogeny and recommended genetic markers are provided. In this study, varieties of the genus Boeremia have been elevated to species level. Botryosphaeria, Bipolaris, Curvularia, Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries, as many new species have been introduced to these genera.

Botryosphaeriales was introduced in 2006 for a single family Botryosphaeriaceae. Since then the number of families has increased as a result of the transfer of one family (Planistromellaceae) into the order, re-instatement of another (Phyllostictaceae), while others resulted from raising genera to family status (Aplosporellaceae, Endomelanconiopsisaceae, Melanopsaceae, Pseudofusicoccumaceae, Saccharataceae and Septorioideaceae). All these decisions were based solely on phylogenetic analyses of several different loci. There has been no consensus on which loci are suitable markers at this taxonomic level and in some cases the datasets used to construct the phylogenies were incomplete. In this paper, the families of Botryosphaeriales were re-assessed in terms of morphology of the sexual morphs, phylogenetic relationships based on ITS and LSU sequence data, and evolutionary divergence times of lineages in relation to major events in the evolution of their hosts on a geological timescale. Six main lineages were resolved in the phylogenetic analyses and these correspond to six groups as defined on morphology of the sexual morphs. These lineages evolved during the Late epoch of the Cretaceous period and survived the catastrophic event that led to the mass extinction of non-avian dinosaurs and a great loss of plant diversity at the end of the Cretaceous period. They then diversified during the Paleocene and Eocene epochs of the Paleogene period. These six lineages are considered to represent families in Botryosphaeriales. Therefore, six families (Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae) are accepted in Botryosphaeriales, while three (Endomelanconiopsisaceae, Pseudofusicoccumaceae and Septorioideaceae) are reduced to synonymy under existing families.

Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi mainly characterized by perithecial ascomata and inoperculate unitunicate asci. Freshwater Sordariomycetes play an important role in ecosystems and some of them have the potential to produce bioactive compounds. This study documents and reviews the freshwater Sordariomycetes, which is one of the largest and important groups of fungi in aquatic habitats. Based on evidence from DNA sequence data and morphology, we introduce a new order Distoseptisporales, two new families, viz. Ceratosphaeriaceae and Triadelphiaceae, three new genera, viz. Aquafiliformis, Dematiosporium and Neospadicoides, 47 new species, viz. Acrodictys fluminicola, Aquafiliformis lignicola, Aquapteridospora fusiformis, Arthrinium aquaticum, Ascosacculus fusiformis, Atractospora aquatica, Barbatosphaeria lignicola, Ceratosphaeria aquatica, C. lignicola, Chaetosphaeria aquatica, Ch. catenulata, Ch. guttulata, Ch. submersa, Codinaea yunnanensis, Conioscypha aquatica, C. submersa, Cordana aquatica, C. lignicola, Cosmospora aquatica, Cylindrotrichum submersum, Dematiosporium aquaticum, Dictyochaeta cangshanensis, D. ellipsoidea, D. lignicola, D. submersa, Distoseptispora appendiculata, D. lignicola, D. neorostrata, D. obclavata, Hypoxylon lignicola, Lepteutypa aquatica, Myrmecridium aquaticum, Neospadicoides aquatica, N. lignicola, N. yunnanensis, Ophioceras submersum, Peroneutypa lignicola, Phaeoisaria filiformis, Pseudostanjehughesia lignicola, Rhodoveronaea aquatica, Seiridium aquaticum, Sporidesmiella aquatica, Sporidesmium lageniforme, S. lignicola, Tainosphaeria lunata, T. obclavata, Wongia aquatica, two new combinations, viz. Acrodictys aquatica, Cylindrotrichum aquaticum, and 9 new records, viz. Chaetomium globosum, Chaetosphaeria cubensis, Ch. myriocarpa, Cordana abramovii, Co. terrestris, Cuspidatispora xiphiago, Sporidesmiella hyalosperma, Stachybotrys chartarum,S. chlorohalonata. A comprehensive classification of the freshwater Sordariomycetes is presented based on updated literature. Phylogenetic inferences based on DNA sequence analyses of a combined LSU, SSU, RPB2 and TEF1α dataset comprising species of freshwater Sordariomycetes are provided. Detailed information including their habitats distribution, diversity, holotype, specimens collected and classification are provided.

One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Krie-geriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.

In this paper we revisit the Capnodiaceae with notes on selected genera. Type specimens of the ascomycetous genera Aithaloderma, Anopeltis, Callebaea, Capnodaria, Echinothecium, Phragmocapnias and Scorias were re-examined, described and illustrated. Leptoxyphium is anamorphic Capnodiaceae and Polychaeton is a legitimate and earlier name for Capnodium, but in order to maintain nomenclatural stability we propose that the teleomorphic name should be conisdered for the approved lists of names currently in preparation for fungi. Notes are provided on the ascomycetous genus Scoriadopsis. However, we were unable to locate the type of this genus during the time frame of this study. The ascomycetous genera Aithaloderma, Ceramoclasteropsis, Hyaloscolecostroma and Trichomerium are excluded from Capnodiaceae on the basis of having ascostromata and trans-septate hyaline ascospores and should be accommodated in Chaetothyriaceae. Callebaea is excluded as the ascomata are thyriothecia and the genus is placed in Micropeltidaceae. Echinothecium is excluded as synonym of Sphaerellothecium and is transferred to Mycosphaerellaceae. The type specimen of Capnophaeum is lost and this should be considered as a doubtful genus. The coelomycetous Microxiphium is polyphyletic, while the status of Fumiglobus, Polychaetella and Tripospermum is unclear. Fourteen new collections of sooty moulds made in Thailand were isolated and sequenced. The nuclear large and small rDNA was partially sequenced and compared in a phylogeny used to build a more complete understanding of the relationships of genera in Capnodiaceae. Four new species are described and illustrated, while Phragmocapnias and Scorias are epitypified with fresh collections.

The family Microthyriaceae sensuLumbsch and Huhndorf 2010 is a poorly known but interesting family comprising 50 genera consisting of foliar epiphytes or saprobes on dead leaves and stems. We re-visited the family based on examinations of generic types where possible. Members are distributed in Aulographaceae, Asterinaceae, Microthyriaceae, Micropeltidaceae and Palmulariaceae and notes are provided on each of these families. Nine genera are transferred from Microthyriaceae to Asterinaceae, and two to Aulographaceae based on the splitting or dissolving nature of the thyriothecia to release ascospores. New sequence data for a number of species and genera are provided. Microthyriaceous members growing on other fungi and lichens differ from Microthyriaceae sensu stricto and the family Trichothyriaceae is reinstated to accommodate these taxa. Other genera of Microthyriaceae belong in Rhytismataceae, Stictidaceae, Venturiales incertae cedis, Dothideomyetes genera incertae cedis, Hypocreales incertae cedis and Ascomycota genera incertae cedis. The family Microthyriaceae is reduced to seven genera characterised by superficial, flattened thyriothecia, with the cells of the upper wall radiating in parallel arrangement from the distinct central ostiolar opening, while the lower peridium is generally poorly developed. Sequence data is provided for five species with thyriothecia and Paramicrothyrium and Neomicrothyrium are described as new genera and Micropeltis zingiberacicola is introduced as a new species. Our phylogenetic analysis underscores the high genetic diversity for thyriotheciate species and there is no clear clade that can be well defined as Microthyriales. Nuclear ribosomal data support multiple polyphyletic lineages within Microthyriaceae and Micropeltidaceae. Some unexpected DNA based phylogenetic relationships such as those between Muyocopron and Saccardoella will require corroboration with more complete taxon sampling as well as additional non ribosomal markers. There are few differences between Aulographaceae, Asterinaceae and Palmulariaceae and these families may need synonymising.

The Venturiaceae was traditionally assigned to Pleosporales although its diagnostic characters readily distinguish it from other pleosporalean families. These include a parasitic or saprobic lifestyle, occurring on leaves or stems of dicotyledons; small to medium-sized ascomata, often with setae; deliquescing pseudoparaphyses; 8-spored, broadly cylindrical to obclavate asci; 1-septate, yellowish, greenish or pale brown to brown ascospores; and hyphomycetous anamorphs. Phylogenetically, core genera of Venturiaceae form a monophyletic clade within Dothideomycetes, and represent a separate sister lineage from current orders, thus a new order-Venturiales is introduced. A new family, Sympoventuriaceae, is introduced to accommodate taxa of a well-supported subclade within Venturiales, which contains Sympoventuria, Veronaeopsis simplex and Fusicladium-like species. Based on morphology and DNA sequence analysis, eight genera are included in Venturiaceae, viz. Acantharia, Apiosporina (including Dibotryon), Caproventuria, Coleroa, Pseudoparodiella, Metacoleroa, Tyrannosorus and Venturia. Molecular phylogenetic information is lacking for seven genera previously included in Venturiales, namely Arkoola, Atopospora, Botryostroma, Lasiobotrys, Trichodothella, Trichodothis and Rhizogenee and these are discussed, but their inclusion in Venturiaceae is doubtful. Crotone, Gibbera, Lineostroma, Phaeocryptopus, Phragmogibbera, Platychora, Polyrhizon, Rosenscheldiella, Uleodothis and Xenomeris are excluded from Venturiales, and their ordinal placement needs further investigation. Zeuctomorpha is treated as a synonym of Acantharia.

A culture-independent survey of fungal diversity in four arable soils and one grassland in Lower Austria was conducted by RFLP and sequence analysis of clone libraries of the partial ITS/LSU-region. All soils were dominated by the ascomycetous orders Sordariales, Hypocreales and Helotiales, taxa that are known from traditional cultivation approaches to occur in agricultural soils. The most abundant genus in the investigated soils was Tetracladium, a hyphomycete which has been described as occurring predominantly in aquatic habitats, but was also found in agricultural soils. Additionally, soil clone group I (SCGI), a subphylum at the base of the Ascomycota with so far no cultivated members, was identified at high frequency in the grassland soil but was below detection limit in the four arable fields. In addition to this striking difference, general fungal community parameters like richness, diversity and evenness were similar between cropland and grassland soils. The presented data provide a fungal community inventory of agricultural soils and reveal the most prominent species.

The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic key. Trichoderma parareesei and T. effusum are redescribed based on new collections or additional observations. Hypocrea teleomorphs are reported for T. gillesii and T. pinnatum. Previously described species are annotated.

To date 75 species of Hypocrea/Trichoderma forming teleomorphs are recognised in Europe. The 56 hyaline-spored species are here described in detail and illustrated in colour plates, including cultures and anamorphs. This number includes 16 new holomorphs, two new teleomorphs and nine anamorphs of species previously described as teleomorphs. Phylogenetic placement and relationships of the species are shown on the strict consensus tree, based on sequences of RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) exon, comprising 135 species of the genus Hypocrea/Trichoderma. All available holotypes of species described from Europe including some from North America have been examined. A dichotomous key to the species is provided primarily utilising ecological and morphological traits of the teleomorphs and, where necessary, morphology of the anamorphs and cultures, and growth rates. Species descriptions are subdivided among five chapters, arranged primarily according to the larger phylogenetic clades, viz. section Trichoderma with 13 species, the pachybasium core group with 13 species including four species with stipitate stromata ('Podostroma'), species forming large effused stromata with 10 species including the section Hypocreanum, 9 species of the Brevicompactum, Lutea and Psychrophila clades, and 11 residual species of various smaller clades or of unknown phylogenetic placement. Finally, a list comprising dubious names and species excluded from Hypocrea that are relevant for Europe, or species claimed to occur in Europe by other authors is provided. Hypocrea minutispora is by far the most common species in Europe. For H. moravica, H. subalpina and H. tremelloides the anamorphs are newly described. The anamorphs of the latter two species and H. sambuci produce hyaline conidia on unusual structures new to Trichoderma. These three species form a new subclade of the morphologically strikingly different section Longibrachiatum, which is currently only represented by H. schweinitzii in Europe as a holomorph. The subclade is not named yet formally due to low statistical support. H. fungicola f. raduli is described as the new species H. austriaca, while H. hypomycella was found not to belong to Hypocrea. The typification of H. pilulifera, H. tremelloides and H. lutea has been clarified. Gliocladium deliquescens, the anamorph of H. lutea, is combined in Trichoderma. Species are epitypified where appropriate. Anamorph names are established prospectively to avoid numerous new combinations in future when they may be possibly used as holomorphic names if the ICBN is altered accordingly.

Approximately 950 individual sequences of non-ribosomally biosynthesised peptides are produced by the genus Trichoderma/Hypocrea that belong to a perpetually growing class of mostly linear antibiotic oligopeptides, which are rich in the non-proteinogenic α-aminoisobutyric acid (Aib). Thus, they are comprehensively named peptaibiotics. Notably, peptaibiotics represent ca. 80 % of the total inventory of secondary metabolites currently known from Trichoderma/Hypocrea. Their unique membrane-modifying bioactivity results from amphipathicity and helicity, thus making them ideal candidates in assisting both colonisation and defence of the natural habitats by their fungal producers. Despite this, reports on the in vivo-detection of peptaibiotics have scarcely been published in the past. In order to evaluate the significance of peptaibiotic production for a broader range of potential producers, we screened nine specimens belonging to seven hitherto uninvestigated fungicolous or saprotrophic Trichoderma/Hypocrea species by liquid chromatography coupled to electrospray high resolution mass spectrometry. Sequences of peptaibiotics found were independently confirmed by analysing the peptaibiome of pure agar cultures obtained by single-ascospore isolation from the specimens. Of the nine species examined, five were screened positive for peptaibiotics. A total of 78 peptaibiotics were sequenced, 56 (=72 %) of which are new. Notably, dihydroxyphenylalaninol and O-prenylated tyrosinol, two C-terminal residues, which have not been reported for peptaibiotics before, were found as well as new and recurrent sequences carrying the recently described tyrosinol residue at their C-terminus. The majority of peptaibiotics sequenced are 18- or 19-residue peptaibols. Structural homologies with 'classical representatives' of subfamily 1 (SF1)-peptaibiotics argue for the formation of transmembrane ion channels, which are prone to facilitate the producer capture and defence of its substratum.

During a survey on corticolous Dothideomycetes, several collections with ascospores matching the genera Asteromassaria and Stigmatomassaria (Pleomassariaceae, Pleosporales) were revealed from dead corticated twigs of Acer, Carpinus and Tamarix. Closer morphological examination showed that their ascomata were apothecial, with a hamathecium consisting of septate, branched paraphyses, which are apically swollen at maturity. Several collections were cultured and sequenced, and a Blast search of their nuc 28S rDNA sequences revealed dothideomycetous affiliation, but without a close match to a specific family or order. Phylogenetic analyses of a multigene matrix containing a representative selection of Dothideomycetes from four genes (nuc 18S rDNA, nuc 28S rDNA, rpb2 and tef1) revealed placement within Dothideomycetes but without a supported familial or ordinal affiliation. Based on the phylogenetic analyses and morphological investigations, the new genera Asterodiscus and Stigmatodiscus, with the two new species A. tamaricis and S. enigmaticus, are described and illustrated, and placed in the new family Stigmatodiscaceae and new order Stigmatodiscales.

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.

More than 100 recent collections of Valsaria sensu lato mostly from Europe were used to elucidate the species composition within the genus. Multigene phylogeny based on SSU, LSU, ITS, rpb2 and tef1 sequences revealed a monophyletic group of ten species within the Dothideomycetes, belonging to three morphologically similar genera. This group could not be accommodated in any known family and are thus classified in the new family Valsariaceae and the new order Valsariales. The genus Valsaria sensu stricto comprises V. insitiva, V. robiniae, V. rudis, V. spartii, V. lopadostomoides sp. nov. and V. neotropica sp. nov., which are phylogenetically well-defined, but morphologically nearly indistinguishable species. The new monotypic genus Bambusaria is introduced to accommodate Valsaria bambusae. Munkovalsaria rubra and Valsaria fulvopruinata are combined in Myrmaecium, a genus traditionally treated as a synonym of Valsaria, which comprises three species, with M. rubricosum as its generic type. This work is presented as a basis for additional species to be detected in future.

Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments. In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli, where they persist under the same stressful conditions as their hosts. Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches. The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes, while a minor fraction represents Sordariomycetes and Leotiomycetes. As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages, it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic, extremotolerant fungi within the thalli. Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes, whereas other strains belong to genera of fungi, that are known as lichen colonizers, plant and human pathogens, rock-inhabiting fungi, parasites and saprotrophs. The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi, which potentially benefit from the lichen niche in otherwise hostile habitats.

Trapelioid fungi constitute a widespread group of mostly crust-forming lichen mycobionts that are key to understanding the early evolutionary splits in the Ostropomycetidae, the second-most species-rich subclass of lichenized Ascomycota. The uncertain phylogenetic resolution of the approximately 170 species referred to this group contributes to a poorly resolved backbone for the entire subclass. Based on a data set including 657 newly generated sequences from four ribosomal and four protein-coding gene loci, we tested a series of a priori and new evolutionary hypotheses regarding the relationships of trapelioid clades within Ostropomycetidae. We found strong support for a monophyletic group of nine core trapelioid genera but no statistical support to reject the long-standing hypothesis that trapelioid genera are sister to Baeomycetaceae or Hymeneliaceae. However, we can reject a sister group relationship to Ostropales with high confidence. Our data also shed light on several long-standing questions, recovering Anamylopsoraceae nested within Baeomycetaceae, elucidating two major monophyletic groups within trapelioids (recognized here as Trapeliaceae and Xylographaceae), and rejecting the monophyly of the genus Rimularia. We transfer eleven species of the latter genus to Lambiella and describe the genus Parainoa to accommodate a previously misunderstood species of Trapeliopsis. Past phylogenetic studies in Ostropomycetidae have invoked "divergence order" for drawing taxonomic conclusions on higher level taxa. Our data show that if backbone support is lacking, contrasting solutions may be recovered with different or added data. We accordingly urge caution in concluding evolutionary relationships from unresolved phylogenies.

Since 2007, the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has increased. However, the description style is not consistent and has regional or author-specific patterns. Most recent publications still favour descriptions of spores compared to hymenium and pileipellis elements, and usually only the spore size is provided with statistical support. This study proposes standards for descriptions of the microscopic structure of Russula species (Russulaceae, Agaricomycetes). We present the description template, the template measurements table, the specific terminology and the essential chemical reagents. The proposed standards were tested by mycologists from 11 countries who met at the Russula Microscopy Workshop in Slovakia. Descriptions of 26 species from 9 countries and four continents were prepared, among them R. amarissima, R. castanopsidis, R. seperina and R. subtilis are re-described and 15 species are introduced as new: R. abietiphila, R. amerorecondita, R. aurantioflava, R. echidna, R. flavobrunnescens, R. fluvialis, R. fortunae, R. garyensis, R. gemmata, R. laevis, R. madrensis, R. olivaceohimalayensis, R. purpureogracilis, R. sancti-pauli and R. wielangtae. Seven descriptions for candidate new species are provided without a formal name assignment. Pairwise comparison of species described in this study with available similar descriptions of related species suggests that microscopic characters from all parts of the basidiomata can be equally important for species recognition and they deserve the same treatment including number of measurements and statistics. The majority of recent studies does not recognise differences between the pileus margin and centre, but more than one-third of the species described in this study show distinct differences between the pileus areas, emphasizing the importance to specify the origin of pileipellis observations. This study proved that there is frequently insufficient difference in the ITS barcode between closely related species and that it is necessary to use more genetic markers combined with ecological and geographical data.

Sugarcane (Saccharum officinarum) is one of the oldest crops cultivated by mankind. Numerous fungal taxa have been reported from this host, although most were not identified beyond genus level. In this study, we explored 31 sampling sites in Guangxi and Guangdong Provinces (China), and collected 370 diseased samples from leaves and roots of sugarcane, from which 762 strains were isolated. Our preliminary analysis based on internal transcribed spacer (ITS) sequences suggested that these isolates belonged to 143 species in 51 genera, but we could not assign 129 strains. Bipolaris, Chaetomium, Curvularia, Phoma and Nigrospora represented the top five most common genera identified, while 27 rare genera comprised only one identified species. In this study, we chose above mentioned common genera for in-depth morphological observations and multi-locus analyses, in order to identify these strains to species level. In this paper, we described one new genus, 32 new species, and reported 19 new records for China and the asexual morph of Chaetomium olivaceum. Hitherto, this is the most comprehensive study with molecular identification and illustration of fungi associated with sugarcane, which greatly improves our understanding of culturable mycota associated with this host.

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and organisms. This paper focuses on 25 phytopathogenic genera: Alternaria, Capnodium, Chaetothyrina, Cytospora, Cyphellophora, Cyttaria, Dactylonectria, Diplodia, Dothiorella, Entoleuca, Eutiarosporella, Fusarium, Ilyonectria, Lasiodiplodia, Macrophomina, Medeolaria, Neonectria, Neopestalotiopsis, Pestalotiopsis, Plasmopara, Pseudopestalotiopsis, Rosellinia, Sphaeropsis, Stagonosporopsis and Verticillium. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. A new database (Onestopshopfungi) is established to enhance the current understanding of plant pathogenic genera among plant pathologists.

Symbiotic associations between mammals and fungi have been well documented and are widely regarded as vital to ecosystem functions around the world. Symbioses between birds and fungi are also ecologically vital but have been far less thoroughly studied. This manuscript is the first to review a wide range of symbiotic associations between birds and fungi. We compile the largest list to date of bird species reported to eat fungi (54 bird species in 27 families) and follow up with a discussion of these symbioses and suggestions for how future studies can determine the prevalence of associations between birds and fungi. We review the importance of fungi for cavity-excavating birds and show that at least 30 bird species in three families form varying levels of associations with fungi for cavity excavation. We also review the use of fungal rhizomorphs in nest construction and show that 176 bird species in 37 families use fungal material in their nests. All of these interactions have wide-reaching ecosystem implications, particularly in regard to fungal dispersal and biogeography, plant health, ecosystem function, bird nutrition/fitness and bird behaviour.

This paper provides illustrated descriptions of micro-fungi newly found on Pandanaceae in China and Thailand. The fungi are accommodated in 31 families. New taxa described include a new family, seven new genera, 65 new species, 16 previously known species. A new family: Malaysiascaceae (Glomerellales). New genera are Acremoniisimulans (Plectosphaerellaceae), Pandanaceomyces, Pseudoachroiostachy (Nectriaceae), Pseudohyaloseta (Niessliaceae), Pseudoornatispora (Stachybotriaceae) and Yunnanomyces (Sympoventuriaceae). New species are Acremoniisimulans thailandensis, Beltrania krabiensis, Beltraniella pandanicola, B. thailandicus, Canalisporium krabiense, C. thailandensis, Clonostachys krabiensis, Curvularia chonburiensis, C. pandanicola, C. thailandicum, C. xishuangbannaensis, Cylindrocladiella xishuangbannaensis, Dictyochaeta pandanicola, Dictyocheirospora nabanheensis, D. pandanicola, D. xishuangbannaensis, Dictyosporium appendiculatum, Di. guttulatum, Di. hongkongensis, Di. krabiense, Di. pandanicola, Distoseptispora thailandica, D. xishuangbannaensis, Helicoma freycinetiae, Hermatomyces biconisporus, Lasiodiplodia chonburiensis, L. pandanicola, Lasionectria krabiense, Menisporopsis pandanicola, Montagnula krabiensis, Musicillium pandanicola, Neofusicoccum pandanicola, Neohelicomyces pandanicola, Neooccultibambusa thailandensis, Neopestalotiopsis chiangmaiensis, N. pandanicola, N. phangngaensis, Pandanaceomyces krabiensis, Paracylindrocarpon nabanheensis, P. pandanicola, P. xishuangbannaensis, Parasarcopodium hongkongensis, Pestalotiopsis krabiensis, P. pandanicola, Polyplosphaeria nabanheensis, P. pandanicola, P. xishuangbannaensis, Pseudoachroiostachys krabiense, Pseudoberkleasmium pandanicola, Pseudochaetosphaeronema pandanicola, Pseudohyaloseta pandanicola, Pseudoornatispora krabiense, Pseudopithomyces pandanicola, Rostriconidium pandanicola, Sirastachys phangngaensis, Stictis pandanicola, Terriera pandanicola, Thozetella pandanicola, Tubeufia freycinetiae, T. parvispora, T. pandanicola, Vermiculariopsiella hongkongensis, Volutella krabiense, V. thailandensis and Yunnanomyces pandanicola. Previous studies of micro-fungi on Pandanaceae have not included phylogenetic support. Inspiration for this study came from the book Fungi Associated with Pandanaceae by Whitton, McKenzie and Hyde in 2012. Both studies reveal that the micro-fungi on Pandanaceae is particularly rich in hyphomycetes. All data presented herein are based on morphological examination of specimens, coupled with phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Fungi have been often neglected, despite the fact that they provided penicillin, lovastatin and many other important medicines. They are an understudied, but essential, fascinating and biotechnologically useful group of organisms. The study of fungi in northern Thailand has been carried out by us since 2005. These studies have been diverse, ranging from ecological aspects, phylogenetics with the incorportation of molecular dating, taxonomy (including morphology and chemotaxonomy) among a myriad of microfungi, to growing novel mushrooms, and DNA-based identification of plant pathogens. In this paper, advances in understanding the biodiversity of fungi in the region are discussed and compared with those further afield. Many new species have been inventoried for the region, but many unknown species remain to be described and/or catalogued. For example, in the edible genus Agaricus, over 35 new species have been introduced from northern Thailand, and numerous other taxa await description. In this relatively well known genus, 93% of species novelty is apparent. In the microfungi, which are relatively poorly studied, the percentage of novel species is, surprisingly, generally not as high (55–96%). As well as Thai fungi, fungi on several hosts from Europe have been also investigated. Even with the well studied European microfungi an astounding percentage of new taxa (32–76%) have been discovered. The work is just a beginning and it will be a daunting task to document this astonishingly high apparent novelty among fungi.

An account is provided of the world’s ten most feared fungi. Within areas of interest, we have organized the entries in the order of concern. We put four human pathogens first as this is of concern to most people. This is followed by fungi producing mycotoxins that are highly harmful for humans; Aspergillus flavus, the main producer of aflatoxins, was used as an example. Problems due to indoor air fungi may also directly affect our health and we use Stachybotrys chartarum as an example. Not everyone collects and eats edible mushrooms. However, fatalities caused by mushroom intoxications often make news headlines and therefore we include one of the most poisonous of all mushrooms, Amanita phalloides, as an example. We then move on to the fungi that damage our dwellings causing serious anxiety by rotting our timber structures and flooring. Serpula lacrymans, which causes dry rot is an excellent example. The next example serves to represent all plant and forest pathogens. Here we chose Austropuccinia psidii as it is causing devastating effects in Australia and will probably do likewise in New Zealand. Finally, we chose an important amphibian pathogen which is causing serious declines in the numbers of frogs and other amphibians worldwide. Although we target the top ten most feared fungi, numerous others are causing serious concern to human health, plant production, forestry, other animals and our factories and dwellings. By highlighting ten feared fungi as an example, we aim to promote public awareness of the cost and importance of fungi.

Demarcation of family, genus and species boundaries in the Diaporthales has been tentative due to uninformative illustrations and descriptions, overlapping morphological characteristics, misplacement or poor condition of type specimens and shortage of molecular data from ex-type cultures. In this study, we obtained the type specimens or other authentic specimens of diaporthalean taxa from worldwide fungaria. We examined, described and illustrated them. This study is based on morphological characters from type or authentic specimens, details from protologue and original illustrations and molecular data obtained from GenBank. Combined analyses of nrITS, nrLSU, RPB2 and TEF1-α sequence data were used to construct the molecular phylogeny. Additionally, we provided separate phylogenetic trees for families when necessary to show the generic distribution within these families based on suitable gene markers. Based on morphology and phylogeny, we treat 17 genera previously assigned to Diaporthales genera incertae sedis within several families. For some genera we have designated new generic types as they are lacking type species or type species have affiliations with other families. We exclude Anisomycopsis from Diaporthales and place it in Xylariomycetidae genera incertae sedis. Tirisporellaceae, which was previously placed in Tirisporellales is placed in Diaporthales based on phylogeny and morphology. A new combination, Dendrostoma leiphaemia propose for Amphiporthe leiphaemia (Fr.) Butin. Based on the morphological characters and molecular data we accept 27 families and 138 genera within Diaporthales, 24 genera in Diaporthales genera incertae sedis and one genus in Xylariomycetidae genera incertae sedis. We provide notes for genera in Diaporthales genera incertae sedis, and excluded and doubtful genera are listed with notes on their taxonomy and phylogeny.

Numerous agents of infections in humans and other mammals are found among fungi that are able to survive extreme environmental conditions and to quickly adapt to novel habitats. Nevertheless, the relationship between opportunistic potential and polyextremotolerance was not yet studied systematically in fungi. Here, the link between polyextremotolerance and opportunistic pathogenicity is shown in a kingdom-wide phylogenetic analysis as a statistically significant co-occurrence of extremotolerance (e.g. osmotolerance and psychrotolerance) and opportunism at the level of fungal orders. In addition to extremotolerance, fungal opportunists share another characteristic—an apparent lack of specialised virulence traits. This is illustrated by a comparative genomic analysis of 20 dothideomycetous and eurotiomycetous black fungi. While the genomes of specialised fungal plant pathogens were significantly enriched in known virulence-associated genes that encode secreted proteases, carbohydrate active enzyme families, polyketide synthases, and non-ribosomal peptide synthetases, no such signatures were observed in human opportunists. Together the presented results have several implications. If infection of human hosts is a side effect of fungal stress tolerance and adaptability, the human body is most likely neither the preferred habitat of such species, nor important for their evolutionary success. This defines opportunism as opposed to pathogenicity, where infection is advantageous for the species’ fitness. Since opportunists are generally incapable of the host-to-host transmission, any host-specific adaptations are likely to be lost with the resolution of the infection, explaining the observed lack of specialised virulence traits. In this scenario opportunistic infections should be seen as an evolutionary dead end and unlikely to lead to true pathogenicity.

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (“mgDNA”) from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these ‘dark taxa’ or ‘dark matter fungi’ that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

This study deals with an extensive taxonomic reevaluation focusing on phylogenetic relationships and morphological characterization of Tubeufiales, especially those helicosporous hyphomycetes which are difficult to identify. Based on evidence from DNA sequence data and morphology, we introduce 13 new genera in the family Tubeufiaceae, viz. Acanthotubeufia, Dematiohelicoma, Dematiohelicomyces, Dematiohelicosporum, Dematiotubeufia, Helicoarctatus, Helicohyalinum, Helicotruncatum, Neochlamydotubeufia, Neohelicoma, Pleurohelicosporium, Pseudohelicomyces and Pseudohelicoon; transfer Chaetosphaerulina from Dothideomycetes genera incertae sedis, and Artocarpomyces and Helicodochium from Ascomycetes genera incertae sedis into Tubeufiaceae; introduce 52 new species, viz. Berkleasmium fusiforme, B. longisporum, Chlamydotubeufia cylindrica, Dematiohelicosporum guttulatum, Helicoarctatus aquaticus, Helicodochium aquaticum, Helicohyalinum infundibulum, Helicoma aquaticum, H. brunneisporum, H. cocois, H. rufum, H. fusiforme, H. longisporum, H. multiseptatum, H. rubriappendiculatum, H. septoconstrictum, H. tectonae, Helicomyces hyalosporus, Helicosporium aquaticum, H. flavisporum, H. setiferum, H. vesicarium, H. viridiflavum, Neochlamydotubeufia fusiformis, Neohelicomyces hyalosporus, Neohelicosporium acrogenisporum, N. astrictum, N. ellipsoideum, N. irregulare, N. krabiense, N. laxisporum, N. ovoideum, Pleurohelicosporium parvisporum, Pseudohelicomyces aquaticus, P. hyalosporus, Tubeufia abundata, T. bambusicola, T. brevis, T. brunnea, T. chlamydospora, T. dictyospora, T. eccentrica, T. fangchengensis, T. hechiensis, T. inaequalis, T. krabiensis, T. rubra, T. sessilis, T. sympodihylospora, T. sympodilaxispora, T. taiwanensis and T. tratensis; provide 43 new combinations, viz. Acanthohelicospora guianensis, Acanthotubeufia filiforme, Berkleasmium aquatica, B. guangxiense, B. latisporum, B. thailandicum, Dematiohelicoma perelegans, D. pulchrum, Dematiohelicomyces helicosporus, Dematiotubeufia chiangraiensis, Helicohyalinum aquaticum, Helicoma elinorae, H. gigasporum, H. hongkongense, H. linderi, H. nematosporum, H. pannosum, H. serpentinum, Helicomyces chiayiensis, Helicotruncatum palmigenum, Neochlamydotubeufia khunkornensis, Neohelicoma fagacearum, Neohelicomyces pallidus, Neohelicosporium abuense, N. aurantiellum, N. griseum, N. morganii, N. myrtacearum, N. nizamabadense, N. sympodiophorum, N. taiwanense, N. vesiculiferum, Pseudohelicomyces indicus, P. paludosus, P. talbotii, Pseudohelicoon gigantisporum, P. subglobosum, Tubeufia dentophora, T. geniculata, T. lilliputea, T. machaerinae, T. sympodiophora and T. xylophila; introduce 16 new records, viz. Dictyospora thailandica, Helicomyces colligatus, H. torquatus, Neohelicosporium guangxiense, N. hyalosporum, N. parvisporum, Thaxteriellopsis lignicola, Tubeufia aquatica, T. chiangmaiensis, T. cylindrothecia, T. filiformis, T. guangxiensis, T. laxispora, T. parvispora, T. roseohelicospora and T. tectonae. The taxonomy of Helicoma, Helicomyces and Helicosporium is revisited based on phylogenetic analyses and morphological evidence. Neorhamphoria is transferred to Bezerromycetaceae. Three species are excluded from the genus Chlamydotubeufia, twelve species from Helicoma, four species from Helicomyces, 25 species from Helicosporium, six species from Neoacanthostigma and one species from Tubeufia. A multi-gene phylogenetic tree based on maximum likelihood and Bayesian analyses of ITS, LSU, RPB2 and TEF1α sequence data of species of Tubeufiales is provided. Detailed descriptions and illustrations are provided, as well as the morphological comparison with similar taxa are explored. The checklist of accepted Tubeufiales species and re-organised Tubeufiales species are provided.

Fungal stromata were recently discovered in association with charcoal and burnt soil aggregates during an archaeological survey in the Châtillon-sur-Seine forest massif. The wood and soil in the samples were dated to the medieval period (between 738 and 1411 AD). Light microscopy and scanning electron microscopy revealed that a few of the stromatal fragments still contained ascospores. Their macromorphological characters were described and secondary metabolite profiles were generated using high performance liquid chromatography with diode array and mass spectrometric detection (HPLC–DAD/MS). The combination of these two data lines then allowed species identification. Most of the fragments were assigned to Hypoxylon fragiforme, the type species of the Hypoxylaceae (Xylariales). Two further species whose stromata grew on the fossil charcoal could be tentatively identified as Jackrogersella cohaerens and (more tentatively) as Hypoxylon vogesiacum. These three species are still commonly encountered in the forests of Central Europe today. Furthermore, the HPLC-HRMS data of H. fragiforme suggested the presence of unknown azaphilone dimers and of further new pigments. These archaeological compounds were compared to fresh stromata of H. fragiforme collected in Germany and subjected to the same analytical protocol. While the major components in both samples were identified as the known mitorubrin type azaphilones and orsellinic acid, the chemical structures of seven novel complex azaphilone pigments, for which we propose the trivial names rutilins C-D and fragirubrins A-E, were elucidated using spectral methods (NMR and CD spectroscopy, high resolution mass spectrometry). It appears that these pigments had indeed persisted for millennia in the fossil stromata.

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1–20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced.

Phylogenomic datasets continue to enhance our understanding of evolutionary relationships in many lineages of organisms. However, genome-scale data have not been widely implemented in reconstructing relationships in lichenized fungi. Here we generate a data set comprised of 2556 single-copy protein-coding genes to reconstruct previously unresolved relationships in the most diverse family of lichen-forming fungi, Parmeliaceae. Our sampling included 51 taxa, mainly from the subfamily Parmelioideae, and represented six of the seven previously identified major clades within the family. Our results provided strong support for the monophyly of each of these major clades and most backbone relationships in the topology were recovered with high nodal support based on concatenated dataset and species tree analyses. The alectorioid clade was strongly supported as sister-group to all remaining clades, which were divided into two major sister-groups. In the first major clade the anzioid and usneoid clades formed a strongly supported sister-group relationship with the cetrarioid + hypogymnioid group. The sister-group relationship of Evernia with the cetrarioid clade was also strongly supported, whereas that between the anzioid and usneoid clades needs further investigation. In the second major clade Oropogon and Platismatia were sister to the parmelioid group, while the position of Omphalora was not fully resolved. This study demonstrates the power of genome-scale data sets to resolve long-standing, ambiguous phylogenetic relationships of lichen-forming fungi. Furthermore, the topology inferred in this study will provide a valuable framework for better understanding diversification in the most diverse lineage of lichen-forming fungi, Parmeliaceae.

Mushrooms in the basidiomycete family Amanitaceae are very important both economically and ecologically. However, the delimitation of the family is still controversial, in part due to limited taxon sampling and in part because of insufficient gene fragment employed for molecular phylogenetic analyses. Furthermore, species diversity in the family is likely to have been largely underestimated, due to morphological similarity between taxa and phenotypic plasticity. In this study, we examined 1190 collections, including 1008 Chinese and 182 external ones, and performed the first comprehensive phylogenetic analyses of Amanitaceae using multi-locus sequence data. To test the monophyly of the Amanitaceae, a concatenated (nrLSU, rpb1, and rpb2) dataset of 200 taxa of the order Agaricales was analyzed. To infer the phylogeny of Amanitaceae, a concatenated nrLSU, tef1-α, rpb2 and β-tubulin dataset (3010 sequences from ca. 890 samples with 2309 newly generated sequences) was used. In this dataset, 252 sequences from the types of 77 species were provided. Our results indicate that Amanitaceae is a monophyletic group, and consists of five genera, namely Amanita, Catatrama, Limacella, Limacellopsis and Myxoderma. It is clear that Catatrama is closely related to Limacella, however, the phylogenetic relationships among these genera remain largely unresolved. Amanita contains 95% of the species in the family, and is here divided into three subgenera and eleven sections (subgen. Amanita, containing: sect. Amanita, sect. Amarrendiae, sect. Caesareae and sect. Vaginatae; subgen. Amanitina, containing: sect. Amidella, sect. Arenariae, sect. Phalloideae, sect. Roanokenses, sect. Strobiliformes and sect. Validae; and subgen. Lepidella, containing sect. Lepidella). Subgen. Lepidella occupies the basal position in the genus. One-hundred and sixty-two species of Amanitaceae known from China are treated in this study, including 50 novel species and 112 known taxa. Amanita gleocystidiosa, A. pyriformis, A. atrofusca, A. subjunquillea var. alba and A. areolata are treated as synonyms of A. sychnopyramis f. subannulata, A. orientigemmata, A. umbrinolutea, A. subjunquillea and A. zangii, respectively. 26 extralimital taxa including a novel species, namely Catatrama indica, were included in our study to allow us to make comparisons between these and the Chinese taxa. DNA sequence data for all the species of Amanitaceae in China and keys for identification of the species are provided.

The class Pezizomycetes is monophyletic within the subdivision Pezizomycotina. The main distinguishing character of this class is operculate asci, although in some taxa this character has been lost. The circumscription of the families and generic level delimitation in Pezizomycetes is still controversial, although several molecular phylogenetic studies have been published on this group. This paper reviews 21 families of Pezizomycetes including five new families, which are introduced here, viz. Kallistoskyphaceae, Pseudombrophilaceae, Pulvinulaceae, Strobiloscyphaceae and Tarzettaceae. Moreover, this study provides a modified backbone tree based on phylogenetic analysis of five combined loci. Descriptions and illustrations of representative taxa for the families are provided from collections made in China, Thailand and the UK, herbarium material from international herbaria (FH, FLAS, H, HKAS and MA) and the literature. Pezizales separates into six major clades. Clade 1 of Pezizales includes the families Ascobolaceae and Pezizaceae. Clade 2 is the new family Kallistoskyphaceae. Clade 3 comprises the families Caloscyphaceae, Karstenellaceae and Rhizinaceae. Clade 4 represents the families Discinaceae, Helvellaceae, Morchellaceae, Tuberaceae and Underwoodia columnaris lineage. Clade 5 includes Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae and Clade 6 comprises Ascodesmidaceae, Glaziellaceae, Otideaceae, Pseudombrophilaceae, Pulvinulaceae, Pyronemataceae, Strobiloscyphaceae and Tarzettaceae. New sequence data belonging to ITS, LSU, SSU, TEF, RPB2 gene regions from 40 pezizalian species are provided here. The paper provides a working document for apothecial Pezizomycetes which can be modified as new data comes to light. It is hoped that by illustrating taxa we provide stimulation and interest in the operculate discomycetes, so that further research is carried out on this remarkable, but poorly studied group of fungi.

This study is unique as it compares traditional and high-resolution culture-independent approaches using the same set of samples to study the saprotrophic fungi on Vitis vinifera. We identified the saprotrophic communities of table grape (Red Globe) and wine grape (Carbanate Gernischet) in China using both traditional and culture-independent techniques. The traditional approach used direct observations based on morphology, single spore isolation and phylogenetic analysis yielding 45 taxa which 19 were commonly detected in both cultivars. The same set of samples were then used for Illumina sequencing which analyzed ITS1 sequence data and detected 226 fungal OTUs, of which 176 and 189 belong to the cultivars Carbanate Gernischet and Red Globe, respectively. There were 139 OTUs shared between the two V. vinifera cultivars and 37 and 50 OTUs were specific to Carbanate Gernischet and Red Globe cultivars respectively. In the Carbanate Gernischet cultivar, Ascomycota accounted for 77% of the OTUs and in Red Globe, almost all sequenced were Ascomycota. The fungal taxa overlap at the genus and species level between the traditional and culture-independent approach was relatively low. In the traditional approach we were able to identify the taxa to species level, while in the culture-independent method we were frequently able to identify the taxa to family or genus level. This is remarkable as we used the same set of samples collected in China for both approaches. We recommend the use of traditional techniques to accurately identify taxa. Culture-independent method can be used to get a better understanding about the organisms that are present in a host in its natural environment. We identified primary and secondary plant pathogens and endophytes in the saprotrophic fungal communities, which support previous observations, that dead plant material in grape vineyards can be the primary sources of disease. Finally, based on present and previous findings, we provide a worldwide checklist of 905 fungal taxa on Vitis species, which includes their mode of life and distribution.

A new classification of several clitocyboid taxa is here proposed to accommodate results from multigenic phylogenetic inference. The analysis of ITS rDNA as well as a combined dataset including 18S and 28S rDNA, tef1 and rpb2 data, support significantly a shared monophyletic origin of the genera Pseudoclitocybe, Musumecia and Pogonoloma, and the species Clitocybe alexandri and C. harperi. The new family Pseudoclitocybaceae is here proposed to name this clade, characterized by the presence of loop-like clamp connections in most species, absence of cystidia, and parallel hymenophoral trama with broad, cylindrical hyphae with intracellular granulations. The new genera Clitopaxillus and Harmajaea are proposed to accommodate the type species C. alexandri and H. harperi, as well as the combination H. wellsiae. In addition, two new species are described: C. fibulatus has a differential distribution of clamp connections in the basidiome, while H. guldeniae is, by now, an exclusively European taxon with brownish pileus, somewhat decurrent gills, ovoid spores and basidia longer than those of H. harperi. Finally, the species concept within Pseudoclitocybe and Pogonoloma is discussed and descriptions of the most representative species are provided.

The family Ajellomycetaceae (Onygenales) includes mammal-associated pathogens within the genera Blastomyces, Emmonsia, Histoplasma and Paracoccidioides, as well as the recently described genera, Emergomyces that causes disease in immunocompromised hosts, and Emmonsiellopsis, known only from soil. To further assess the phylogenetic relationships among and between members of these genera and several previously undescribed species, we sequenced and analyzed the DNA-directed RNA polymerase II (rPB2), translation elongation factor 3-α (TEF3), β-tubulin (TUB2), 28S large subunit rDNA (LSU) and the internal transcribed spacer regions (ITS) in 68 strains, in addition to morphological and physiological investigations. To better understand the thermal dimorphism among these fungi, the dynamic process of transformation from mycelial to yeast-like or adiaspore-like forms was also assessed over a range of temperatures (6–42 °C). Molecular data resolved the relationships and recognized five major well-supported lineages that correspond largely to the genus level. Emmonsia, typified by Emmonsia parva, is a synonym of Blastomyces that also accommodates Blastomyces helicus (formerly Emmonsia helica). Emmonsia crescens is phylogenetically distinct, and found closely related to a single strain from soil without known etiology. Blastomyces silverae, Emergomyces canadensis, Emergomyces europaeus and Emmonsia sola are newly described. Almost all of the taxa are associated with human and animal disease. Emmonsia crescens, B. dermatitidis and B. parvus are prevalently associated with pulmonary disease in humans or animals. Blastomyces helicus, B. percursus, Emergomyces africanus, Es. canadensis, Es. europaeus, Es. orientalis and Es. pasteurianus (formerly Emmonsia pasteuriana) are predominantly found in human hosts with immune disorders; no animal hosts are known for these species except B. helicus.

Grapevines (Vitis vinifera) are colonized by ubiquitous microorganisms known as endophytes, which may have advantageous or neutral effects without causing disease symptoms. Certain endophytes are uncultivable, so culture-independent approaches such as next generation sequencing (NGS) can help for a better understanding of their ecology and distribution. To date, there are no studies which directly link NGS results with taxa derived from a culturing approach, integrating morphological and multi-gene phylogenetic analysis of endophytes. In this study, a culture-dependent and high-resolution culture-independent approach (next generation sequencing) were used to identify endophytes in grapevine stems. In the culture-dependent approach, a total of 94 isolates were recovered from 84 of 144 healthy grapevine stem fragments (colonization rate = 58.3%). The study is unique as we used subsets of combined multi-gene regions to identify the endophytes to species level. Based on each multi-gene phylogenetic analysis, 28 species belong to 19 genera (Acremonium, Alternaria, Arthrinium, Ascorhizoctonia, Aspergillus, Aureobasidium, Bipolaris, Botryosphaeria, Botrytis, Chaetomium, Cladosporium, Curvularia, Hypoxylon, Lasiodiplodia, Mycosphaerella, Nigrospora, Penicillium, Phoma, Scopulariopsis) were identified. A higher number of culturable fungi were obtained from 13 year-old vines, followed by eight and three year-old vines. In the culture-independent approach, a fungal richness of 59 operational taxonomic units (OTU) was detected, being highest in 13 year-old grapevines, followed by eight and three years. Even though the cultivation approach detected lower fungal richness, the results related to stem are consistent for fungal community composition and richness. Comparison of the fungal taxa identified by the two approaches resulted in an overlap of 53% of the fungal genera. Due to interspecific variability of the sequences from NGS, in many cases the OTUs (even with the highly abundant ones) were only assignable to order, family or genus level. Incorporating multi-gene phylogenies we successfully identified many of the NGS derived OTUs with poor taxonomic information in reference databases to the genus or species levels. Hence, this study signifies the importance of applying both culture-dependent and culture-independent approaches to study the fungal endophytic community composition in Vitis vinifera. This principle could also be applied to other host species and ecosystem level studies.

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

For the very first time, morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi (Russula, Russulales) as an example. In this first of two papers, the authors focus more specifically on below-ground structures. Our five-gene phylogeny divides the genus in five main clades, here interpreted as representing seven subgenera, all significantly supported. Although more conserved than features of fruiting bodies, the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis, but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus. Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification. Tropical taxa mostly nest in ancient lineages, but are also present in some terminal clades of otherwise temperate species groups. The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics, and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere. Available data as well as our own observations on below ground structures of several Lactifluus species suggests that this genus shares with Russula the absence of lactifers in ECM mantles and rhizomorphs, contrary to species of Lactarius where lactifers are always present. First observations on rhizomorphs of species in Multifurca confirm the presence of vessel-like and ladder-like hyphae, also found in the other agarioid genera of this family, while distinct lactifers are only present in the lactarioid, but not in russuloid members of this genus.

This paper is the seventh in the Fungal Diversity Notes series, where 131 taxa accommodated in 28 families are mainly described from Rosa (Rosaceae) and a few other hosts. Novel fungal taxa are described in the present study, including 17 new genera, 93 new species, four combinations, a sexual record for a species and new host records for 16 species. Bhatiellae, Cycasicola, Dactylidina, Embarria, Hawksworthiana, Italica, Melanocucurbitaria, Melanodiplodia, Monoseptella, Uzbekistanica, Neoconiothyrium, Neopaucispora, Pararoussoella, Paraxylaria, Marjia, Sporormurispora and Xenomassariosphaeria are introduced as new ascomycete genera. We also introduce the new species Absidia jindoensis, Alternaria doliconidium, A. hampshirensis, Angustimassarina rosarum, Astragalicola vasilyevae, Backusella locustae, Bartalinia rosicola, Bhatiellae rosae, Broomella rosae, Castanediella camelliae, Coelodictyosporium rosarum, Comoclathris rosae, C. rosarum, Comoclathris rosigena, Coniochaeta baysunika, C. rosae, Cycasicola goaensis, Dactylidina shoemakeri, Dematiopleospora donetzica, D. rosicola, D. salsolae, Diaporthe rosae, D. rosicola, Endoconidioma rosae-hissaricae, Epicoccum rosae, Hawksworthiana clematidicola, H. lonicerae, Italica achilleae, Keissleriella phragmiticola, K. rosacearum, K. rosae, K. rosarum, Lophiostoma rosae, Marjia tianschanica, M. uzbekistanica, Melanocucurbitaria uzbekistanica, Melanodiplodia tianschanica, Monoseptella rosae, Mucor fluvius, Muriformistrickeria rosae, Murilentithecium rosae, Neoascochyta rosicola, Neoconiothyrium rosae, Neopaucispora rosaecae, Neosetophoma rosarum, N. rosae, N. rosigena, Neostagonospora artemisiae, Ophiobolus artemisiicola, Paraconiothyrium rosae, Paraphaeosphaeria rosae, P. rosicola, Pararoussoella rosarum, Parathyridaria rosae, Paraxylaria rosacearum, Penicillium acidum, P. aquaticum, Phragmocamarosporium rosae, Pleospora rosae, P. rosae-caninae, Poaceicola agrostina, P. arundinicola, P. rosae, Populocrescentia ammophilae, P. rosae, Pseudocamarosporium pteleae, P. ulmi-minoris, Pseudocercospora rosae, Pseudopithomyces rosae, Pseudostrickeria rosae, Sclerostagonospora lathyri, S. rosae, S. rosicola, Seimatosporium rosigenum, S. rosicola, Seiridium rosarum, Setoseptoria arundelensis, S. englandensis, S. lulworthcovensis, Sigarispora agrostidis, S. caryophyllacearum, S. junci, S. medicaginicola, S. rosicola, S. scrophulariae, S. thymi, Sporormurispora atraphaxidis, S. pruni, Suttonomyces rosae, Umbelopsis sinsidoensis, Uzbekistanica rosae-hissaricae, U. yakutkhanika, Wojnowicia rosicola, Xenomassariosphaeria rosae. New host records are provided for Amandinea punctata, Angustimassarina quercicola, Diaporthe rhusicola, D. eres, D. foeniculina, D. rudis, Diplodia seriata, Dothiorella iberica, Lasiodiplodia theobromae, Lecidella elaeochroma, Muriformistrickeria rubi, Neofusicoccum australe, Paraphaeosphaeria michotii, Pleurophoma pleurospora, Sigarispora caulium and Teichospora rubriostiolata. The new combinations are Dactylidina dactylidis (=Allophaeosphaeria dactylidis), Embarria clematidis (=Allophaeosphaeria clematidis), Hawksworthiana alliariae (=Dematiopleospora alliariae) and Italica luzulae (=Dematiopleospora luzulae). This study also provides some insights into the diversity of fungi on Rosa species and especially those on Rosa spines that resulted in the characterisation of eight new genera, 45 new species, and nine new host records. We also collected taxa from Rosa stems and there was 31% (20/65) overlap with taxa found on stems with that on spines. Because of the limited and non-targeted sampling for comparison with collections from spines and stems of the same host and location, it is not possible to say that the fungi on spines of Rosa differ from those on stems. The study however, does illustrate how spines are interesting substrates with high fungal biodiversity. This may be because of their hard structure resulting in slow decay and hence are suitable substrates leading to fungal colonisation. All data presented herein are based on morphological examination of specimens, coupled with phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Obligate anaerobic fungi of the phylum Neocallimastigomycota play a key role in digesting fibrous feeds in the gut of herbivores, but little is known about their global diversity. In this study, the collective diversity of gut anaerobic fungi was examined using all curated internal transcribed spacer 1 (ITS1) sequences of anaerobic gut fungi available in GenBank. The 262,770 quality-checked fungal ITS1 sequences downloaded from GenBank were assigned to 274 operational taxonomic units (OTUs) at the approximate species level. Of these approximate species-equivalent (Sp-eq) OTUs, 119 were represented by at least five ITS1 sequences, with 38 containing known species and 81 containing no known species. Based on a rarefaction analysis, the currently available ITS1 sequences represent nearly all the major species of gut anaerobic fungi, but much more sequencing effort is needed to assess the actual richness of minor OTUs. One dataset of ITS1 reference sequences (referred to as AF-RefSeq) and one comprehensive taxonomic framework are also presented, and they are shown to be suitable for taxonomic classification of most of the ITS1 sequences in GenBank. The results of the present study may help guide future studies involving taxonomic and phylogenetic analysis of ITS1 sequences of anaerobic fungi and targeted isolation and characterization of new anaerobic fungi.

The ecological significance of fungi occurring asymptomatically inside living plant leaves is poorly understood. Given the broad saprotrophic potential of many endophytic fungi, we hypothesized that they persist in decaying litter for an extended period of time after leaf abscission. Fungal assemblages were assessed by high-throughput sequencing in autumn leaves of beech (Fagus sylvatica) and in the corresponding leaf litter in 388 samples from 22 beech forest plots in three widely distant regions of Germany. A considerable proportion of the leaf-endophytic fungi was also found in 1-year-old litter. Co-occurrence networks revealed that the fungi formed unstructured assemblages inside the living leaves, rather than well-structured communities. Previously endophytic fungi constituted an integral part of the fungal litter community and were by far the most active fungi in 1-year-old litter. We therefore consider these endophytic occurrences to represent transient stages. Composition of the aboveground microbiome appears therefore to be closely connected to the process of litter decomposition. Considering the respective linked fungal habitat will facilitate predicting nutrient and carbon cycling and storage in forest ecosystems as well as elucidating the ecology of leaf microbiomes.

Species and generic recognition in the order Xylariales has been uncertain due to lack of molecular data from authentic cultures, as well as overlapping morphological characteristics. In this study, we revise the families Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae in Xylariales. Our study is based on DNA sequence data derived from living cultures of fresh isolates, data from GenBank and morphological observation of type and worldwide herbarium specimens. We also collected new specimens from Germany, Italy and Thailand. Combined analyses of ITS, LSU, RPB2 and β-tubulin sequence data were used to reconstruct the molecular phylogeny of the above families. Generic and familiar boundaries between these families are revised and presented in an updated combined phylogenetic tree. We accept six genera in Graphostromataceae, 19 genera in Hypoxylaceae, four in Lopadostomataceae and 37 genera in Xylariaceae. Five genera previously treated in Xylariaceae are placed in Amphisphaeriales genera incertae sedis and seven genera are placed in Xylariales genera incertae sedis. Two genera are placed in Sordariomycetes genera incertae sedis, while four genera are placed as Xylariomycetidae genera incertae sedis. Three genera are considered as doubtful. Barrmaelia and Cannonia, presently included in Xylariaceae are transferred to Diatrypaceae and Coniochaetales respectively, based on their morphology and phylogeny. Areolospora and Myconeesia are excluded from Xylariaceae and synonymized with Phaeosporis and Anthostomella respectively. Updated descriptions and illustrations are provided for all taxa with notes provided on each genus. Excluded and doubtful genera are listed with notes on their taxonomy and phylogeny. Taxonomic keys are provided for all revised families with morphological details for genera within the families.

Taxonomic placement of genera have been changing rapidly as taxonomists widely use DNA sequence data in phylogenetic and evolutionary studies. It is essential to update existing databases/outlines based on recent studies, since these sources are widely used as a foundation for other research. In this outline, we merge both asexual and sexual genera into one outline. The phylum Ascomycota comprises of three subphyla viz. Pezizomycotina (including 13 classes, 124 orders and 507 families), Saccharomycotina (including one class, one order and 13 families) and Taphrinomycotina (five classes, five orders and six families). Approximately, 6600 genera have been listed under different taxonomic ranks including auxiliary (intermediate) taxonomic ranks.

Ophiobolus is a large genus of Phaeosphaeriaceae comprising more than 350 possible species, most of which are saprobes on herbaceous plants in Europe and North America. Ophiobolus species are polyphyletic and the type of Ophiobolus is not represented in GenBank. Therefore, an increased taxon sampling of ophiobolus-like taxa and epitypification of the type species, O. disseminans is reported. Multigene phylogenetic analyses of combined LSU, SSU, TEF1-α and ITS sequence data position O. disseminans in a sister clade with O. ponticus and several Entodesmium species in Phaeosphaeriaceae with high support. Therefore, Entodesmium is synonymized under Ophiobolus. Premilcurensis with it type species, P. senecionis also clusters within the Ophiobolus clade and is synonymized under Ophiobolus. Ophiobolus rossicus sp. nov. is introduced and a reference specimen is designated for O. ponticus. Other ophiobolus-like taxa (Ophiobolus sensu lato) can be distinguished as three main groups, which are introduced as new genera. Ophiobolopsis is introduced to accommodate the new species, Ophiobolopsis italica. The new genus Paraophiobolus is introduced to accommodate P. arundinis sp. nov. and P. plantaginis comb. nov. This genus is characterized by hyaline to pale yellowish ascospores, some green-yellowish at maturity, with a swollen cell, terminal appendages and ascospores not separating into part spores. Pseudoophiobolus gen. nov. is introduced to accommodate six new species and two new combinations, viz. Ps. achilleae, Ps. erythrosporus, Ps. galii, Ps. italicus, Ps. mathieui, Ps. rosae, Ps. subhyalinisporus and Ps. urticicola. Pseudoophiobolus is characterized by subhyaline to pale yellowish or yellowish ascospores, with a swollen cell, lack of terminal appendages and ascospores that do not separate into part spores and is related to Nodulosphaeria. An updated tree for Phaeosphaeriaceae based on multigene analysis is also provided.

Discomycetes are an artificial grouping of apothecia-producing fungi in the phylum Ascomycota. Molecular-based studies have revealed that the discomycetes can be found among ten classes of Ascomycota. The classification of discomycetes has been a major challenge due to the lack of a clear understanding of the important morphological characters, as well as a lack of reference strains. In this review, we provide a historical perspective of discomycetes, notes on their morphology (including both asexual and sexual morphs), ecology and importance, an outline of discomycete families and a synoptical cladogram of currently accepted families in Ascomycota showing their systematic position. We also calculated evolutionary divergence times for major discomycetous taxa based on phylogenetic relationships using a combined LSU, SSU and RPB2 data set from 175 strains and fossil data. Our results confirm that discomycetes are found in two major subphyla of the Ascomycota: Taphrinomycotina and Pezizomycotina. The taxonomic placement of major discomycete taxa is briefly discussed. The most basal group of discomycetes is the class Neolectomycetes, which diverged from other Taphrinomycotina around 417 MYA (216–572), and the most derived group of discomycetes, the class Lecanoromycetes, diverged from Eurotiomycetes around 340 MYA (282–414). Further clarifications based on type specimens, designation of epitypes or reference specimens from fresh collections, and multi-gene analyses are needed to determine the taxonomic arrangement of many discomycetes.

This is the sixth in a series of papers where we bring collaborating mycologists together to produce a set of notes of several taxa of fungi. In this study we introduce a new family Fuscostagonosporaceae in Dothideomycetes. We also introduce the new ascomycete genera Acericola, Castellaniomyces, Dictyosporina and Longitudinalis and new species Acericola italica, Alternariaster trigonosporus, Amarenomyces dactylidis, Angustimassarina coryli, Astrocystis bambusicola, Castellaniomyces rosae, Chaetothyrina artocarpi, Chlamydotubeufia krabiensis, Colletotrichum lauri, Collodiscula chiangraiensis, Curvularia palmicola, Cytospora mali-sylvestris, Dictyocheirospora cheirospora, Dictyosporina ferruginea, Dothiora coronillae, Dothiora spartii, Dyfrolomyces phetchaburiensis, Epicoccum cedri, Epicoccum pruni, Fasciatispora calami, Fuscostagonospora cytisi, Grandibotrys hyalinus, Hermatomyces nabanheensis, Hongkongmyces thailandica, Hysterium rhizophorae, Jahnula guttulaspora, Kirschsteiniothelia rostrata, Koorchalomella salmonispora, Longitudinalis nabanheensis, Lophium zalerioides, Magnibotryascoma mali, Meliola clerodendri-infortunati, Microthyrium chinense, Neodidymelliopsis moricola, Neophaeocryptopus spartii, Nigrograna thymi, Ophiocordyceps cossidarum, Ophiocordyceps issidarum, Ophiosimulans plantaginis, Otidea pruinosa, Otidea stipitata, Paucispora kunmingense, Phaeoisaria microspora, Pleurothecium floriforme, Poaceascoma halophila, Periconia aquatica, Periconia submersa, Phaeosphaeria acaciae, Phaeopoacea muriformis, Pseudopithomyces kunmingnensis, Ramgea ozimecii, Sardiniella celtidis, Seimatosporium italicum, Setoseptoria scirpi, Torula gaodangensis and Vamsapriya breviconidiophora. We also provide an amended account of Rhytidhysteron to include apothecial ascomata and a J+ hymenium. The type species of Ascotrichella hawksworthii (Xylariales genera incertae sedis), Biciliopsis leptogiicola (Sordariomycetes genera incertae sedis), Brooksia tropicalis (Micropeltidaceae), Bryochiton monascus (Teratosphaeriaceae), Bryomyces scapaniae (Pseudoperisporiaceae), Buelliella minimula (Dothideomycetes genera incertae sedis), Carinispora nypae (Pseudoastrosphaeriellaceae), Cocciscia hammeri (Verrucariaceae), Endoxylina astroidea (Diatrypaceae), Exserohilum turcicum (Pleosporaceae), Immotthia hypoxylon (Roussoellaceae), Licopolia franciscana (Vizellaceae), Murispora rubicunda (Amniculicolaceae) and Doratospora guianensis (synonymized under Rizalia guianensis, Trichosphaeriaceae) were re-examined and descriptions, illustrations and discussion on their familial placement are given based on phylogeny and morphological data. New host records or new country reports are provided for Chlamydotubeufia huaikangplaensis, Colletotrichum fioriniae, Diaporthe subclavata, Diatrypella vulgaris, Immersidiscosia eucalypti, Leptoxyphium glochidion, Stemphylium vesicarium, Tetraploa yakushimensis and Xepicula leucotricha. Diaporthe baccae is synonymized under Diaporthe rhusicola. A reference specimen is provided for Periconia minutissima. Updated phylogenetic trees are provided for most families and genera. We introduce the new basidiomycete species Agaricus purpurlesquameus, Agaricus rufusfibrillosus, Lactifluus holophyllus, Lactifluus luteolamellatus, Lactifluus pseudohygrophoroides, Russula benwooii, Russula hypofragilis, Russula obscurozelleri, Russula parapallens, Russula phoenicea, Russula pseudopelargonia, Russula pseudotsugarum, Russula rhodocephala, Russula salishensis, Steccherinum amapaense, Tephrocybella constrictospora, Tyromyces amazonicus and Tyromyces angulatus and provide updated trees to the genera. We also introduce Mortierella formicae in Mortierellales, Mucoromycota and provide an updated phylogenetic tree.