Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2-3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the 'true fungi' have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Annual surveys of Irish soil samples identified three isolates, CBS 16921 (UCD88), CBS 18246 (UCD443), and CBS 18247 (UCD483), of an apiculate yeast species within the Hanseniaspora genus. The internal transcribed spacer (ITS) and D1/D2 region of the large subunit (LSU) rRNA sequences showed that these are isolates of the recently described species Hanseniaspora menglaensis, first isolated from Southwest China. No genome sequence for H. menglaensis is currently available. The genome sequences of the three Irish isolates were determined using short-read (Illumina) sequencing, and the sequence of one isolate (CBS 16921) was assembled to chromosome level using long-read sequencing (Oxford Nanopore Technologies). Phylogenomic analysis shows that H. menglaensis belongs to the fast-evolving lineage (FEL) of Hanseniaspora. Only one MAT idiomorph (encoding MATα1) was identified in all three sequenced H. menglaensis isolates, consistent with one mating type of a heterothallic species. Genome comparisons showed that there has been a rearrangement near MATα of FEL species compared to isolates from the slowly evolving lineage (SEL).

In this study, we conducted a comprehensive survey aimed at assessing the diversity of yeast species inhabiting the guts of various insect species collected mainly from two Bulgarian National Parks, namely, Rila, and Pirin. The insect specimens encompass a broad taxonomic spectrum, including representatives from Coleoptera, Orthoptera, Lepidoptera, Hymenoptera, Dermaptera, Isopoda, and Collembola. Yeast strains were identified with DNA barcoding using the ribosomal markers, specifically, the D1/D2 domains of the ribosomal large subunit (LSU) and the internal transcribed spacers regions ITS 1 + 2 (ITS). The analysis unveiled the presence of 89 ascomycetous and 18 basidiomycetous yeast isolates associated with the insect specimens. Furthermore, our study identified 18 hitherto unknown yeast species.

A Citizen Science initiative by the Westerdijk Fungal Biodiversity Institute and the Utrecht University Museum gave rise to a project where fungal and yeast isolates were obtained and identified from Dutch soil samples. During the current study, 386 yeast strains were isolated from 157 different locations in the Netherlands. These strains were identified using sequence data of the large-subunit rRNA gene (D1/D2 region) and the internal transcribed spacer 1 and 2 regions. A total of 53 different yeast species were found as well as 15 potentially novel species. Six novel ascomycetous species are described during this study that include Hanseniaspora mollemarum sp. nov., Ogataea degrootiae sp. nov., Pichia gijzeniarum sp. nov., Saccharomycopsis oosterbeekiorum sp. nov., Trichomonascus vanleenenius sp. nov. and Zygoascus flipseniorum sp. nov. This study made it possible to incorporate numerous yeast isolates into the CBS collection without any restrictions, which make these isolates readily available for use by others. Many of the isolates represented species of which only a few isolates or even only a single ex-type strain were available. Therefore, it is a clear indication that such biodiversity-orientated Citizen Science projects can enrich the pool of available yeasts for future research projects.

During studies of the yeast diversity associated with rotting wood in Brazil and fruits, plants and insects in French Guiana, three strains of a new species were isolated. Analysis of the sequences of the internal transcribed spacer (ITS)-5.8S and D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the genus Hyphopichia and its closest relative is Candida homilentoma. These species differ by 44 nucleotide substitutions in D1/D2 sequences. A new species Hyphopichia buzzinii f. a., sp. nov., is proposed to accommodate these isolates. The type strain of Hyphopichia buzzinii sp. nov. is CLIB 1739T (=CBS 14300T = UFMG-CM-Y6121T; MycoBank number is MB 815609). In addition, we isolated 11 strains of C. homilentoma from rotting wood, leaf surfaces, and water bodies in Brazil, and these strains when crossed among one another and with the type strain (CBS 6312T) of this species, produced hat-shaped ascospores typical of the genus Hyphopichia. We describe the teleomorph of C. homilentoma as a new combination, Hyphopichia homilentoma comb. nov. (type strain CBS 6312T; MycoBank number is MB 820009). We also propose to transfer the other six Candida species of the Hyphopichia clade to this genus as new combinations. Hyphopichia homilentoma produced ethanol and xylitol from d-xylose whereas H. buzzinii was only able to convert this pentose to xylitol.

During a yeast biodiversity survey conducted in 2009-2011 in Bulgaria (South Eastern Europe) five strains of a novel ascomycetous yeast species were isolated from the beetle Valgus hemipterus (Cetoniinae) collected from two localities, namely Osogovska Planina Mountain and Nature Park Zlatni Pyasatsi. Phylogenetic analysis using combined sequences of the D1/D2 domains of the large subunit ribosomal DNA (LSU rDNA) and the internal transcribed spacers 1 + 2 regions (ITS1+2) placed the novel species on a separate branch near the basal part of the Lodderomyces Glade. The novel species has a unique ascospore morphology distinct from those of the closely related teleomorphic genus Lodderomyces. Based on phylogenetic analysis and morphology of the ascospores we propose Nematodospora valgi gen. nov., sp. nov. to accommodate these isolates (MB811804 D37S(T), MB802458). Two strains of a novel anamorphic yeast species were isolated from the beetles Cetonia aurata and Oxythyreafunesta (Cetoniinae) collected in East Rhodopies and Sofia city, respectively. DNA barcoding analysis placed the new yeast species within the Candida parapsilosis subclade. Here, we present the description of a new yeast species, Candida cetoniae sp. nov. (IMB1R2(T), MB803501) to accommodate these two strains. The ecology and biogeography of the insect-associated yeasts of the Lodderomyces Glade is discussed. (C) 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Yarrowia lipolytica is the only known species in the teleomorph (i.e. sexual) genus Yarrowia and has its anamorph (i.e. asexual state) classified in the genus Candida Berkhout as Candida lipolytica. This species can be found readily in nature, has significant industrial value and is important to the food and medical fields. Candida deformans was first considered a variety of C. lipolytica and was later listed as a synonym of this species. More recent studies based on sequence variation in the nuclear rRNA gene sequences suggested C. deformans to be a separate species with no known teleomorph linked to it. In this study we show that C. deformans strains, obtained from South Africa, can mate with strains present in the CBS yeast collection and produce a Yarrowia teleomorph, described here as Yarrowia deformans. Strains of Candida yakushimensis nom. inval., a species also belonging to the Yarrowia phylogenetic clade, were also studied and described as a novel species of Yarrowia.

Yeast taxonomy and systematics have in recent years been dealt with intensively primarily by a small group of individual researchers with particular expertise. Amongst these was Johannes P. van der Walt, who had a major role in shaping our current understanding of yeast biodiversity and taxonomy. Van der Walt based his taxonomic studies not only on available cultures, but also by going into the field to isolate yeasts from various substrates. This pioneering work led to the discovery of many new genera and species, which were deposited in the Centraalbureau voor Schimmelcultures (CBS) collections for future studies in taxonomy, genomics, and industrial uses. These treasures collected during more than 60 years provide an outstanding legacy to the yeast community and will continue to exist in his absence. This contribution provides a comprehensive overview of the current nomenclatural and taxonomic status of the yeast genera and species introduced by van der Walt during his career.

The present classification of Galactomyces and its anamorph, Geotrichum, is based on various studies that used morphology, ecology, biochemistry, DNA-DNA reassociation comparisons and gene sequencing. In this study, the identities of strains of the Centraalbureau voor Schimmelcultures yeast culture collection, as well as seven strains from South Africa, were examined by analyses of the nucleotide divergence in the internal transcribed spacer regions of the nuclear rRNA gene (nrRNA) operon, the D1/D2 domains of the 26S rRNA gene and partial actin gene sequences as well as compatibility studies. The South African strains were assigned to species in the genus Galactomyces. The phylogenetic analyses and mating studies revealed that Geotrichum silvicola and Geotrichum bryndzae are synonyms of Galactomyces candidus and that Geotrichum vulgare is a synonym of Galactomyces pseudocandidus.

This chapter studies the genus Trichomonascus. In the determination of the asexual reproduction it is seen that colonies are often dry in texture and tannish-white. Asexual reproduction is by multilateral budding and the formation of pseudohyphae and true hyphae, which often produce short chains of blastoconidia that form sympodially. Septa have micropores.The anamorph genus is Blastobotrys. In sexual reproduction it is found that the species may be heterothallic or homothallic. Gametangia may form on hyphal tips or on hyphae after fusion of two intercalary cells by lateral outgrowths. Asci are globose to ellipsoidal with firm, thick walls and contain two to four ascospores. Ascospores are long-ellipsoidal to fusiform or hat- or helmet-shaped. Asci may bear a sterile apical cell. The chapter also discusses physiology/biochemistry and phylogenetic placement of the genus, in which sugars may be fermented, nitrate is not assimilated, and the diazonium blue B reaction is negative. The type species taken is Trichomonascus mycophagus. The fungus is unusual because it is characterized by an ascus that develops from a hyphal tip and is soon accompanied by a slender “trichogyne-like” hypha that arises from the basal cell supporting the ascus. The tip of the trichogyne-like hypha fuses with the top of the ascus, giving the appearance of having completed a fertilization process. The hypha and the apex of the ascus, which becomes a separate cell, broaden and fuse to form an inverted, lipid-filled, claw-like structure that partially enclosed the ascus.

On the basis of nucleotide divergences in the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacers (ITS) domain of the rRNA gene, five novel yeast species, Wickerhamomyces chaumierensis sp. nov. (CBS 8565(T) = JCM 17246(T)), Candida pseudoflosculorum sp. nov. (CBS 8584(T) = JCM 17242(T)), Candida danieliae sp. nov. (CBS 8533(T) = JCM 17247(T)), Candida robnettiae sp. nov. (CBS 8580(T) = JCM 17243(T)) and Candida eppingiae sp. nov. (CBS 8586(T) = JCM 17241(T)), isolated from plants in Thailand and Guyana, are proposed in this study.

This chapter focuses on Dipodascus genus and its constituent species. The colonies of this genus are white or cream-colored, farinose or hairy, and are usually dry. Its hyphae are hyaline, mostly disarticulating into rectangular arthroconidia and the asci are acicular, cylindrical, ellipsoidal or subglobose, formed after fusion of gametangia located laterally on hyphae. The asci have persistent walls and open by rupture at the apex. The ascospores are 4–128 per ascus, hyaline, ellipsoidal, with smooth walls and surrounded by regular slime sheaths. Fermentation is mostly absent and extracellular starch is not produced. The constituent species of this genus include Dipodascus aggregatus, Dipodascus albidus, Dipodascus ambrosiae, and Dipodascus armillariae. Hyphae in Dipodascus aggregatus locally becomedensely septate and form clusters of isogamic gametangia. Asci are aggregated in small groups, cylindrical with rounded apex, mostly with 10–30 ascospores, which are liberated by apical rupture of the ascus. In Dipodascus albidus, gametangia are mostly identical, and mostly formed on opposite sides of a septum. The ascospores of this species are up to 128 per ascus, and are hyaline or subhyaline and broadly ellipsoidal.

Publisher Summary This chapter describes Ascobotryozyma, which was erected as a new genus to accommodate the teleomorphic state of Botryozyma. The type species, A. americana, was considered novel because of its North American distribution, in addition to molecular, morphological, and physiological comparisons. A second species, A. cognata, was found in similar habitats and in close proximity to A. americana, but was considered novel based on molecular, morphological, and physiological criteria. All Ascobotryozyma and Botryozyma strains are discovered on Panagrellus nematodes, which typically inhabit fermenting and acidic environments such as slime fluxes from trees or associated with Drosophila flies. Insects attracted to these fermenting environments because of their scent presumably vector the nematodes. Ascbotryozyma appears to be widely, but not densely, dispersed. Asci are evanescent with passively discharged ascospores. Asci and ascospore production of Ascobotryozyma cannot be maintained in pure agar culture.

Publisher Summary This chapter focuses on Geotrichum genus and its member species. The colonies of this genus are white, farinose or hairy, usually dry, and consist of true hyphae which disarticulate into rectangulararthroconidia. Mostly sympodially produced conidia may be present. Budding is absent. The member species of this genus include Geotrichum candidum , Geotrichum capitatum, Geotrichum citri-aurantii , and Geotrichum clavatum . When the cells of these four species undergo growth on 4% malt extract or 0.5% yeast extract agar for 10 days at 20–22° C, the colonies become 15–17 mm in diameter, glassy-white, flat, smooth, and tough.When the cells of Geotrichum decipiens and Geotrichum fermentans undergo growth on 4% malt extract or 0.5% yeast extract agar for 10 days at 20–22° C, colonies become 35–40 mm in diameter, whitish, moist and somewhat raised, with straight and sharp margins that later become fimbriate margins.

Publisher Summary This chapter studies the genus Saprochaete. In the asexual reproduction it is seen that thallus growth is initially mostly pseudohyphal with inflated cells. Hyphae are branched at acute angles with acuminate apices and disarticulate into arthroconidia. Additional sympodial and annellidic blastoconidiogenesis may be present. Chlamydospores are mostly absent. Septa have micropores. In sexual reproduction it is found that Magnusiomyces represents the teleomorph state of Saprochaete. The chapter also discusses physiology/biochemistry and phylogenetic placement of the genus in which assimilation of D-xylose is mostly absent, nitrate is not assimilated, urease activity is absent, and extracellular starch is not produced. The diazonium blue B reaction is negative and small subunit rRNA genes have deletions in domains V2, V3, and V8. The type species taken is Saprochaete saccharophila. Several Saprochaete species produce remarkably large, somewhat alga-like thalli, which are strictly hyphal and do not produce budding cells. Most species have only rarely been isolated, and thus it is difficult to establish any ecological trends in each species.

This chapter focuses on Lipomyces genus and its member species. Cells are ellipsoidal or globose, and reproduction takes place through multilateral budding. Oval to cylindrical giant cells may occur in this genus, and pseudomycelium is absent. The cells of most strains are surrounded by a thick mucoid capsule and most strains form starch-like polysaccharides in this capsule. Asci develop in various ways where an "active bud" is mostly involved in formation of the ascus. When the asci develop from active buds only, they often enlarge to an elongate pear shape. The entire ascus may liberate itself from the cell when they mature and the number of spores may reach up to 16 or more for each ascus. When the ascus results from the conjugation of an active bud and a protuberance of a cell, the ascus wall is thicker. The ascospores are globose, ellipsoidal to oblong-ellipsoidal, and generally liberated at maturity. The pigmented walls are of a light amber to brown color and the ascospore wall may be warty, smooth, or it bears ridges running longitudinally on the surface. The member species of this genus include Lipomyces japonicus, Lipomyces kononenkoae, Lipomyces lipofer, and Lipomyces starkeyi.