We examined the phylogenetic relationships of two species that mimic Chaetosphaeria in teleomorph and anamorph morphologies, Chaetosphaeriatulasneorum with a Cylindrotrichum anamorph and Australiasca queenslandica with a Dischloridium anamorph. Four data sets were analysed: a) the internal transcribed spacer region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c) nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal polymerase B2). The traditional placement of Ch. tulasneorum in the Microascales based on ncLSU sequences is unsupported and Australiasca does not belong to the Chaetosphaeriaceae. Both holomorph species are nested within the Glomerellales. A new genus, Reticulascus, is introduced for Ch. tulasneorum with associated Cylindrotrichum anamorph; another species of Reticulascus and its anamorph in Cylindrotrichum are described as new. The taxonomic structure of the Glomerellales is clarified and the name is validly published. As delimited here, it includes three families, the Glomerellaceae and the newly described Australiascaceae and Reticulascaceae. Based on ITS and ncLSU rDNA sequence analyses, we confirm the synonymy of the anamorph genera Dischloridium with Monilochaetes. Consequently Dischloridium laeënse, type species of the genus, and three related species are transferred to the older genus Monilochaetes. The teleomorph of D. laeënse is described in Australiasca as a new species. The Plectosphaerellaceae, to which the anamorph genus Stachylidium is added, is basal to the Glomerellales in the three-gene phylogeny. Stilbella annulata also belongs to this family and is newly combined in Acrostalagmus. Phylogenetic analyses based on ncLSU, ncSSU, and combined ncLSU-ncSSU-RPB2 sequences clarify family relationships within the Microascales. The family Ceratocystidaceae is validated as a strongly supported monophyletic group consisting of Ceratocystis, Cornuvesica, Thielaviopsis, and the type species of Ambrosiella. The new family Gondwanamycetaceae, a strongly supported sister clade to the Ceratocystidaceae, is introduced for the teleomorph genus Gondwanamyces and its Custingophora anamorphs. Four families are accepted in the Microascales, namely the Ceratocystidaceae, Gondwanamycetaceae, Halosphaeriaceae, and Microascaceae. Because of a suggested affinity of a Faurelina indica isolate to the Microascales, the phylogenetic position of the Chadefaudiellaceae is reevaluated. Based on the results from a separate ncLSU analysis of the Dothideomycetes, Faurelina is excluded from the Microascales and placed in the Pleosporales.

Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.

Phylogenetic analyses of DNA sequences from nuclear ribosomal and protein-coding loci support the placement of several perithecial ascomycetes and dematiaceous hyphomycetes from freshwater and terrestrial environments in two monophyletic clades closely related to the Savoryellales. One clade formed by five species of Conioscypha and a second clade containing several genera of uncertain taxonomic status centred on Pleurothecium, represent two distinct taxonomic groups at the ordinal systematic rank. They are proposed as new orders, the Conioscyphales and Pleurotheciales. Several taxonomic novelties are introduced in the Pleurotheciales, i.e. two new genera (Adelosphaeria and Melanotrigonum), three novel species (A. catenata, M. ovale, Phaeoisaria fasciculata) and a new combination (Pleurotheciella uniseptata). A new combination is proposed for Savoryella limnetica in Ascotaiwania s.str. based on molecular data and culture characters. A strongly supported lineage containing a new genus Plagiascoma, species of Bactrodesmiastrum and Ascotaiwania persoonii, was identified as a sister to the Conioscyphales/Pleurotheciales/Savoryellales clade in our multilocus phylogeny. Together, they are nested in a monophyly in the Hypocreomycetidae, significantly supported by Bayesian inference and Maximum Likelihood analyses. Members of this clade share a few morphological characters, such as the absence of stromatic tissue or clypeus, similar anatomies of the 2-layered ascomatal walls, thin-walled unitunicate asci with a distinct, non-amyloid apical annulus, symmetrical, transversely septate ascospores and holoblastic conidiogenesis. They represent the only fungi in the Hypocreomycetidae with apically free, filiform to cylindrical, persistent or partially disintegrating paraphyses. The systematic placement of two other dematiaceous hyphomycetes was resolved based on DNA sequences; Phragmocephala stemphylioides is a member of the Pleurotheciales and Triadelphia uniseptata is within the Savoryellales.

The newly discovered systematic placement of Bactrodesmium abruptum, the lectotype species of the genus, prompted a re-evaluation of the traditionally broadly conceived genus Bactrodesmium. Fresh material, axenic cultures and new DNA sequence data of five gene regions of six species, i.e. B. abruptum, B. diversum, B. leptopus, B. obovatum, B. pallidum and B. spilomeum, were studied. Bactrodesmium is a strongly resolved lineage in the Savoryellales (Sordariomycetes), supported by Bayesian and Maximum Likelihood methods. The genus Bactrodesmium is emended and delimited to hyphomycetes characterised by sporodochial conidiomata, mononematous often fasciculate conidiophores, holoblastic conidiogenesis and acrogenous, solitary, dry, pigmented, transversely or rarely longitudinally septate conidia. The conidia are seceding rhexolytically, exhibiting multiple secession patterns. An identification key to 35 species accepted in Bactrodesmium is given, providing the most important diagnostic characters. Novel DNA sequence data of B. longisporum and B. stilboideum confirmed their placement in the Sclerococcales (Eurotiomycetes). For other Bactrodesmium, molecular data are available for B. cubense and B. gabretae, which position them in the Dothideomycetes and Leotiomycetes, respectively. All four species are excluded from Bactrodesmium and segregated into new genera, Aphanodesmium, Gamsomyces and Kaseifertia. Classification of 20 other species and varieties not recognised in the genus is discussed. Based on new collections of Dematiosporium aquaticum, the type species of Dematiosporium, the genus is emended to accommodate monodictys-like freshwater lignicolous fungi of the Savoryellales characterised by effuse colonies, holoblastic conidiogenous cells and dictyosporous, pigmented conidia with a pore in each cell. Study of additional new collections, cultures and DNA sequence data revealed several unknown species, which are proposed as taxonomic novelties in the Savoryellales and closely related Pleurotheciales. Ascotaiwania latericolla, Helicoascotaiwania lacustris and Pleurotheciella erumpens are described from terrestrial, lentic and lotic habitats from New Zealand and France, respectively. New combinations are proposed for Helicoascotaiwania farinosa and Neoascotaiwania fusiformis. Relationships and systematics of the Savoryellales are discussed in the light of recent phylogenies and morphological patterns newly linked with the order through cultural studies.

Seagrasses provide invaluable ecosystem services yet very little is known about their root mycobiont diversity and distribution. Here we focused on the dominant Mediterranean seagrass Posidoniaoceanica and assessed its root mycobiome at 32 localities covering most of the ecoregions in the NW Mediterranean Sea using light and scanning electron microscopy and tag-encoded 454-pyrosequencing. Microscopy revealed that the recently discovered dark septate endophytic association specific for P.oceanica is present at all localities and pyrosequencing confirmed that the P.oceanica root mycobiome is dominated by a single undescribed pleosporalean fungus, hitherto unknown from other hosts and ecosystems. Its numerous slow-growing isolates were obtained from surface-sterilised root segments at one locality and after prolonged cultivation, several of them produced viable sterile mycelium. To infer their phylogenetic relationships we sequenced and analysed the large (LSU) and small (SSU) subunit nrDNA, the ITS nrDNA and the DNA-directed RNA polymerase II (RPB2). The fungus represents an independent marine biotrophic lineage in the Aigialaceae (Pleosporales) and is introduced here as Posidoniomycesatricolorgen. et sp. nov. Its closest relatives are typically plant-associated saprobes from marine, terrestrial and freshwater habitats in Southeast Asia and Central America. This study expands our knowledge and diversity of the Aigialaceae, adds a new symbiotic lifestyle to this family and provides a formal name for the dominant root mycobiont of the dominant Mediterranean seagrass.

The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.