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Trichophyton rubrumand T. violaceumare prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrumcomplex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrumand T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrumand T. violaceumwas observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceumcontains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrumand T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrumand T. violaceumunderlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

Melanisation has been considered to be an important virulence factor of Fonsecaea monophora. However, the biosynthetic mechanisms of melanisation remain unknown. We therefore used next generation sequencing technology to investigate the transcriptome and digital gene expression data, which are valuable resources to better understand the molecular and biological mechanisms regulating melanisation in F. monophora. We performed de novotranscriptome assembly and digital gene expression (DGE) profiling analyses of parent (CBS 122845) and albino (CBS 125194) strains using the Illumina RNA-seq system. A total of 17 352 annotated unigenes were found by BLAST search of NR, Swiss-Prot, Gene Ontology, Clusters of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value <1e‒5). A total of 2 283 unigenes were judged to be the differentially expressed between the two genotypes. We identified most of the genes coding for key enzymes involved in melanin biosynthesis pathways, including polyketide synthase (pks), multicopper oxidase (mco), laccase, tyrosinase and homogentisate 1,2-dioxygenase (hmgA). DEG analysis showed extensive down-regulation of key genes in the DHN pathway, while up-regulation was noted in the DOPA pathway of the albino mutant. The transcript levels of partial genes were confirmed by real time RT-PCR, while the crucial role of key enzymes was confirmed by either inhibitor or substrate tests in vitro. Meanwhile, numbers of genes involved in light sensing, cell wall synthesis, morphology and environmental stress were identified in the transcriptome of F. monophora. In addition, 3 353 SSRs (Simple Sequence Repeats) markers were identified from 21 600 consensus sequences. Blocking of the DNH pathway is the most likely reason of melanin deficiency in the albino strain, while the production of pheomelanin and pyomelanin were probably regulated by unknown transcription factors on upstream of both pathways. Most of genes involved in environmental tolerance to oxidants, irradiation and extreme temperatures were also assembled and annotated in transcriptomes of F. monophora. In addition, thousands of identified cSSR (combined SSR) markers will favour further genetic linkage studies. In conclusion, these data will contribute to understanding the regulation of melanin biosynthesis and help to improve the studies of pathogenicity of F. monophora.

The taxonomy of the synnematous genera Cephalotrichum, Doratomycesand Trichurus, and other related genera Gamsia, Wardomycesand Wardomycopsis, has been controversial and relies mainly on morphological criteria. These are microascaceous saprobic fungi mostly found in air and soil and with a worldwide distribution. In order to clarify their taxonomy and to delineate generic boundaries within the Microascaceae, we studied 57 isolates that include clinical, environmental and all the available ex-type strains of a large set of species by means of morphological, physiological and molecular phylogenetic analyses using DNA sequence data of four loci (the ITS region, and fragments of rDNA LSU, translation elongation factor 1α and β-tubulin). The results demonstrate that Cephalotrichum, Doratomycesand Trichurusare congeneric and the genus Cephalotrichumis accepted here with Echinobotryumas a further synonym. The genera Acauliumand Fairmania, typified by A. albonigrescensand F. singularis, respectively, are distinct from Microascusand Scopulariopsis, Gamsiais distinct from Wardomyces, and Wardomycopsisis confirmed as a separate genus in the Microascaceae. Two new species of Cephalotrichumare described as C. brevistipitatumand C. hinnuleum. Nine new combinations are proposed, i.e. Acaulium acremonium, A. caviariforme, Cephalotrichum asperulum, C. columnare, C. cylindricum, C. dendrocephalum, C. gorgonifer, Gamsia columbinaand Wardomyces giganteus. A neotype is designed for C. stemonitis. Lectotypes and epitypes are designated for A. acremonium, A. albonigrescens, C. gorgonifer, C. nanumand W. anomalus. Cephalotrichum cylindricum, C. microsporum, F. singularisand Gamsia columbinaare also epitypified with new specimens. Descriptions of the phenotypic features and dichotomous keys for identification are provided for accepted species in the different genera.

Over 200 new sequences are generated for members of the genus Acremoniumand related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremoniumspecies. One clade contains Acremonium sclerotigenum,the genus Emericellopsis,and the genus Geosmithiaas prominent elements. The second clade contains the genera Gliomastix sensu strictoand Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictumand the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breveand related species plus Acremonium curvulumand related species. This sequence information allows the revision of three genera. Gliomastixis revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea,and G. masseei. Sarocladiumis extended to include all members of the phylogenetically distinct A. strictumclade including the medically important A. kilienseand the protective maize endophyte A. zeae. Also included in Sarocladiumare members of the phylogenetically delimited Acremonium bacillisporumclade, closely linked to the A. strictumclade. The genus Trichotheciumis revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichotheciumfor the tightly interrelated Acremonium crotocinigenum, Spicellum roseum,and teleomorph Leucosphaerina indica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseumfalls into the Cephalothecaceae.

Coniosporium epidermidissp. nov. is described from a superficial skin lesion with blackish discolouration in an 80-yr-old Chinese patient. The species produces dark, thick-walled, inflated, reluctantly liberating arthroconidia without longitudinal septa. Sequences of the ribosomal operon, as well as of the translation elongation factor 1-α support its novelty. The species is found in a lineage basal to the order Chaetothyriales, amidst relatives from rock, but also species repeatedly isolated from human skin and nails and eventually causing mild cutaneous infections. Coniosporium epidermidisis consistently found on humans, either asymptomatic or symptomatic. The species indicates a change of life style towards human pathogenicity, which is a recurrent type of ecology in derived Chaetothyriales. Superficial and cutaneous infection by melanized fungi is a new category in dermatology.

The black yeast Exophiala dermatitidisis known as a rare etiologic agent of neurotropic infections in humans, occurring particularly in East and Southeast Asia. In search of its natural habitat, a large sampling was undertaken in temperate as well as in tropical climates. Sampling sites were selected on the basis of the origins of previously isolated strains, and on the basis of physiological properties of the species, which also determined a selective isolation protocol. The species was absent from outdoor environments in the temperate climate, but present at low abundance in comparable habitats in the tropics. Positive outdoor sites particularly included faeces of frugivorous birds and bats, in urban as well as in natural areas. Tropical fruits were found E. dermatitidispositive at low incidence. Of the human-made environments sampled, railway ties contaminated by human faeces and oily debris in the tropics were massively positive, while the known abundance of the fungus in steam baths was confirmed. On the basis of the species' oligotrophy, thermotolerance, acidotolerance, moderate osmotolerance, melanization and capsular yeast cells a natural life cycle in association with frugivorous animals in foci in the tropical rain forest, involving passage of living cells through the intestinal tract was hypothesized. The human-dominated environment may have become contaminated by ingestion of wild berries carrying fungal propagules

Using media with low water activity, a large numbers of aureobasidium-like black yeasts were isolated from glacial and subglacial ice of three polythermal glaciers from the coastal Arctic environment of Kongsfjorden (Svalbard, Spitsbergen), as well as from adjacent sea water, sea ice and glacial meltwaters. To characterise the genetic variability of Aureobasidium pullulansstrains originating from the Arctic and strains originating pan-globally, a multilocus molecular analysis was performed, through rDNA (internal transcribed spacers, partial 28 S rDNA), and partial introns and exons of genes encoding β-tubulin (TUB), translation elongation factor (EF1α) and elongase (ELO). Two globally ubiquitous varieties were distinguished: var. pullulans, occurring particularly in slightly osmotic substrates and in the phyllosphere; and var. melanogenum, mainly isolated from watery habitats. Both varieties were commonly isolated from the sampled Arctic habitats. However, some aureobasidium-like strains from subglacial ice from three different glaciers in Kongsfjorden (Svalbard, Spitsbergen), appeared to represent a new variety of A. pullulans.A strain from dolomitic marble in Namibia was found to belong to yet another variety. No molecular support has as yet been found for the previously described var. aubasidani. A partial elongase-encoding gene was successfully used as a phylogenetic marker at the (infra-)specific level.

Cladophialophora carrioniiis one of the four major etiologic agents of human chromoblastomycosis in semi-arid climates. This species was studied using sequence data of the internal transcribed spacer region of rDNA, the partial β-tubulin gene and an intron in the translation elongation factor 1-alpha gene, in addition to morphology. With all genes a clear bipartition was observed, which corresponded with minute differences in conidiophore morphology. A new species, C. yegresii, was introduced, which appeared to be, in contrast to C. carrionii, associated with living cactus plants. All strains from humans, and a few isolates from dead cactus debris, belonged to C. carrionii,for which a lectotype was designated. Artificial inoculation of cactus plants grown from seeds in the greenhouse showed that both fungi are able to persist in cactus tissue. When reaching the spines they produce cells that morphologically resemble the muriform cells known as the “invasive form” in chromoblastomycosis. The tested clinical strain of C. carrioniiproved to be more virulent in cactus than the environmental strain of C. yegresiithat originated from the same species of cactus, Stenocereus griseus. The muriform cell expressed in cactus spines can be regarded as the extremotolerant survival phase, and is likely to play an essential role in the natural life cycle of these organisms.

Although morphologically similar, species of Cladophialophora (Herpotrichiellaceae) were shown to be phylogenetically distinct from Pseudocladosporium(Venturiaceae), which was revealed to be synonymous with the older genus, Fusicladium. Other than being associated with human disorders, species of Cladophialophorawere found to also be phytopathogenic, or to occur as saprobes on organic material, or in water, fruit juices, or sports drinks, along with species of Exophiala. Caproventuriaand Metacoleroawere confirmed to be synonyms of Venturia, which has Fusicladium(= Pseudocladosporium) anamorphs. Apiosporina, based on A. collinsii, clustered basal to the Venturiaclade, and appears to represent a further synonym. Several species with a pseudocladosporium-like morphology in vitrorepresent a sister clade to the Venturiaclade, and are unrelated to Polyscytalum. These taxa are newly described in Fusicladium, which is morphologically close to Anungitea, a heterogeneous genus with unknown phylogenetic affinity. In contrast to the Herpotrichiellaceae, which were shown to produce numerous synanamorphs in culture, species of the Venturiaceaewere morphologically and phylogenetically more uniform. Several new species and new combinations were introduced in Cladophialophora, Cyphellophora (Herpotrichiellaceae), Exophiala, Fusicladium, Venturia(Venturiaceae), and Cylindrosympodium(incertae sedis).

The Cladosporium herbarumcomplex comprises five species for which Davidiellateleomorphs are known. Cladosporium herbarum s. str.(D. tassiana), C. macrocarpum(D. macrocarpa) and C. bruhnei(D. allicina) are distinguishable by having conidia of different width, and by teleomorph characters. Davidiella variabileis introduced as teleomorph of C. variabile, a homothallic species occurring on Spinacia, and D. macrosporais known to be the teleomorph of C. iridison Irisspp. The C. herbarumcomplex combines low molecular distance with a high degree of clonal or inbreeding diversity. Entities differ from each other by multilocus sequence data and by phenetic differences, and thus can be interpreted to represent individual taxa. Isolates of the C. herbarumcomplex that were formerly associated with opportunistic human infections, cluster with C. bruhnei. Several species are newly described from hypersaline water, namely C. ramotenellum, C. tenellum, C. subinflatum, and C. herbaroides. Cladosporium pseudiridiscollected from Irissp. in New Zealand, is also a member of this species complex and shown to be distinct from C. iridisthat occurs on this host elsewhere in the world. A further new species from New Zealand is C. sinuosumon Fuchsia excorticata. Cladosporium antarcticumis newly described from a lichen, Caloplaca regalis, collected in Antarctica, and C. subtilissimumfrom grape berries in the U.S.A., while the new combination C. ossifragi, the oldest valid name of the Cladosporiumknown from Nartheciumin Europe, is proposed. Standard protocols and media are herewith proposed to facilitate future morphological examination of Cladosporiumspp. in culture, and neotypes or epitypes are proposed for all species treated.