Ovipoculum album, a new anamorph with gelatinous cupulate bulbilliferous conidiomata from China and with affinities to the Auriculariales (Basidiomycota)

An anamorphic fungus forming laterally attached, cupulate, gelatinous, hyaline to white conidiomata producing bulbils from clamped hyphae was collected on dead bamboo culms in southwestern China. Though the conidiomatal morphology is similar to that of Dacryoscyphus (anamorphic Dacrymycetales), microscopical and DNA sequence analysis revealed a phylogenetic relationship with members of the Auriculariales. The taxon is therefore described as new and separate from Dacryoscyphus. It is also distinct from other recognized bulbilliferous basidiomycetes. Two recently described anamorphic Dacrymyces species, D. pinacearum and D. subarcticus, were restudied and are transferred to Dacryoscyphus.     

Phylogenetic relationships of five genera of Xylariales and Rosasphaeria gen. nov. (Hypocreales)

Eight inconspicuous non-stromatic perithecial fungi immersed in plant tissue are assessed with respect to their morphology, ecology and phylogenetic position. Emphasis is laid on two genera now and then placed in the family Hyponectriaceae, Xylariales: Leiosphaerella with its type species L. praeclara occurring on Vaccinium, and Pseudomassaria with its type species P. chondrospora occurring on Tilia. In molecular phylogenetic analyses of LSU and ITS sequences, the generic types of these genera are closely related, but their familial affiliation within Xylariales remains unresolved. Pseudomassaria sepincoliformis clusters with P. chondrospora, whereas P. fallax is not congeneric with Pseudomassaria and P. lycopodina is combined in Leiosphaerella despite its apiospores. Three species thought to belong to Leiosphaerella are re-assessed: L. moravica that occurs on Rosa, is disposed in the new genus Rosasphaeria, which is close to Eucasphaeria in the Niessliaceae (Hypocreales), according to multi-gene phylogenetic analyses (ITS, LSU, rpb2 and tef1). For L. vexata the genus Pseudomassariella is revived. A Leiosphaerella-like fungus on Lycopodium is described as the new species Monographella lycopodina. In addition the phylogenetic relationships of two fungi forming superficial stromata are here clarified: Collodiscula japonica belongs to the Xylariaceae, while Melogramma campylosporum may currently be interpreted as representing a family of its own, the Melogrammataceae.     

Echinochlamydosporium variabile, a new genus and species of Zygomycota from soil nematodes

During a recent survey of fungi colonizing juveniles of the soybean cyst nematode, Heterodera glycines, a fungus producing spiny chlamydospores and monosporous sporangia was isolated. Based on morphology and sequences of the rDNA ITS region and 18S and 28S genes, the fungus greatly resembles some species of Mortierella. Although the new isolate’s spiny chlamydospores and delicate arachnoid-like mycelium are very similar to those of Mortierella, it differs significantly from Mortierella in its overall colony appearance and odour, unispored sporangium with a small columella, chlamydospores born laterally on short hyphae, and especially in its phylogenetic position. A new genus and new species, Echinochlamydosporium variabile, in Mortierellaceae (Mortierellales, Zygomycota) are proposed. A key to the genera of Mortierellaceae is provided.     

The new hyphomycete genera Brachyalara and Infundichalara, the similar Exochalara and species of ‘Phialophora sect. Catenulatae’ (Leotiomycetes)

The phylogenetic relationships of five morphologically similar strains labeled Exochalara longissima were studied with sequences of Internal Transcribed Spacer (ITS1-nc5.8S-ITS2) and the small and large subunits of nuclear ribosomal DNA (nc18S and nc28S rDNA) in three different molecular data sets. The phylogenetic analyses, maximum likelihood, maximum parsimony heuristic search and Bayesian approach, revealed that these strains belong to three different genera. Based on the two-gene phylogeny of nc18S-nc28S rDNA, the true relationship of the anamorphic genus Exochalara, typified with E. longissima (strains CBS 393.82 and CBS 980.73), lies within the Helotiales of the Leotiomycetes. Exochalara is characterized by upright, pigmented conidiophores with terminally integrated cylindrical monophialides and hyaline fusiform to drop-shaped conidia, cohering end-to-end in basipetal chains. The holomorph genera Hyphodiscus (anamorph Catenulifera) and Chlorociboria (anamorph Dothiorina) are shown as closest relatives of Exochalara. The strains CBS 622.82 and CBS 114633, which differ from Exochalara in shorter, decumbent conidiophores, ampulliform monophialides, ellipsoidal to obovoidal, 1-celled hyaline conidia straw-yellow in mass and sympodial ramification/branching of conidiophores in vitro also grouped in the Leotiomycetes but on a separate position from Exochalara. The new genus Brachyalara is introduced for them. Subsequently four strains of the morphologically similar Chalara microchona were analysed. Three strains, including the ex-type strain, which formed a strongly supported clade distinct from more typical species of Chalara, Brachyalara and Exochalara, are introduced as a new monotypic genus Infundichalara. Exochalara and the two newly recognized genera are compared with Chalara, Herreromyces and Phialophora. The strain MUCL 40959, according to the ITS (ITS1-ITS2) and three-gene phylogeny (nc18S-nc5.8S-nc28S rDNA) is found to belong to Monilochaetes, which is the anamorph of the holomorph genus Australiasca in the Glomerellales, Sordariomycetes. The fungus is described as a new anamorphic species and compared with the other four species in the genus.     

Trichocybe, a new genus for Clitocybe puberula (Agaricomycetes, Agaricales)

Trichocybe, a new genus of Agaricales, is described to accommodate the rare species Clitocybe puberula characterized by an isolated phylogenetic position. Trichocybe is distinguished from its allied clitocyboid genera by a unique combination of macro- and micromorphological characters, including a Gymnopus-like habitus, a pubescent pileus with squamulose flocci, an eccentric stipe growing on wood debris, a putrescent non-reviviscent context, a strongly farinaceous odour, rare but clearly-differentiated cheilocystidia, an unusual, strongly differentiated pileipellis, a subpellis with vesiculose-physaloid elements, a stipitipellis with diverticulate hyphae, and smooth, acyanophilous, inamyloid basidiospores. Trichocybe is so far known only from northwestern Europe. Based on a LSU- and 5.8S-rDNA Bayesian phylogenetic analysis, Trichocybe clusters within the Tricholomatoid clade, where it occupies an isolate position. Furthermore, according to the present analysis, also Clitocybe phaeophthalma seems to represent an independent evolutive line in the clitocyboid fungi, which suggests adopting the genus Singerocybe Harmaja for this taxon as well as similar ones.     

New species of Chalara occupying coniferous needles

Chalara is a genus of anamorphic fungi with typical phialidic conidiogenous cells. Species of Chalara live mostly as litter saprotrophs, many of them on coniferous litter. In this study, the morphology and DNA sequences (ITS rDNA, 28S rDNA and EF-1α) of strains of various species of Chalara isolated from coniferous litter needles were compared with those of strains from public collections. The majority of the isolates belonged to the C. longipes. Other strains represent C. piceae-abietis, C. microspora, C. microchona and four hitherto undescribed species. These are introduced here as C. holubovae sp. nov., C. hyalocuspica sp. nov., C. pseudoaffinis sp. nov. and C. recta sp. nov. Chalara recta is most closely related to C. longipes, which was found to be paraphyletic. However, no correlation of molecular data with the morphology was found. Chalara holubovae is specific among the Chalara species in that it has a synanamorph with fusiform conidia. Together with C. hyalocuspica, C. holubovae likely belong to the anamorphic Hyaloscyphaceae. Chalara piceae-abietis is epitypified. Epitypicifation of C. longipes and C. microspora cannot be done due to absence of a convenient specimen. Chalara austriaca may be re-discovered also after a targeted sampling in the locality of the type specimen. The majority of studied species are saprotrophic and colonise litter needles. An endophytic phase in living needles or other parts of a tree was confirmed for the species C. longipes and C. hyalocuspica. C. holubovae has been recorded only as an endophyte.     

Phylogenetic placement of lichenicolous Phoma species in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes)

More than twenty species of lichenicolous fungi have been described in Phoma, a large anamorphic genus of primarily plant-associated pathogens with broad geographic distributions. We obtained nuclear and mitochondrial rDNA sequences from 19 fungal cultures isolated from specimens representing four described and two undescribed lichenicolous species in the genus. Our multilocus phylogeny indicates that lichenicolous Phoma species represent at least two phylogenetically distinct clades in the Phaeosphaeriaceae, one including a new species, Phoma puncteliae, isolated from a specimen of Punctelia rudecta collected in Maryland, USA, and another group of primarily lichenicolous species. This latter group includes four described lichenicolous Phoma species, an unidentified melanized rock fungus, and a new lichenicolous Phoma species isolated from Xanthomendoza species collected in Canada that we are naming P. xanthomendozae. Some specimens in this clade collected from different lichen genera and species were found to be very similar genetically, which calls into question the recent practice of recognizing lichenicolous Phoma species mainly by differences in host preference.     

Diversity of endophytic fungi of Taxus globosa (Mexican yew)

The aim of this work was the isolation and taxonomic characterization of endophytic fungi from Taxus globosa at the Sierra Alta Hidalguense, Mexico. A total of 116 fungi were isolated from the bark, branches, leaves and roots of healthy yew trees. Based on morphological characteristics 57 were selected for taxonomic characterization through phylogenetic analysis of their 28S rDNA sequences. The fungal isolates belonged to Ascomycota (77.2%) and Basidiomycota (22.8%). Twelve different fungal groups were identified: Coniochaetales, Eurotiales, Hypocreales, Phyllachorales, Pleosporales, Pezizales, Sordariomycetidae, Sordariales, Trichosphaeriales, Xylariales, Agaricales and Polyporales. The taxa Alternaria sp. Aspergillus sp., Cochliobolus sp., Coprinellus domesticus, Hypoxylon sp., Polyporus arcularius, Xylaria juruensis and Xylariaceae were the most frequently isolated. The genera Annulohypoxylon, Cercophora, Conoplea, Daldinia, Lecythophora, Letendraea, Massarina, Phialophorophoma, Sporormia, Xylomelasma, Coprinellus, Polyporus and Trametes for the first time were isolated from yews; this suggests that T. globosa harbours novel and highly diverse fungi. The Shannon-Weaver and Simpson diversity index values for the overall fungal community were H′?=?3.139 and 1-D?=?0.941 respectively.     

New Ceratocystis species infecting coffee, cacao, citrus and native trees in Colombia

Ceratocystis fimbriata sensu lato includes a large number of plant and especially tree pathogens. In Colombia, isolates of this fungus cause a serious canker-stain disease on coffee as well as other fruit trees. Large collections of these isolates have been shown to occur in two distinct phylogenetic lineages based on ITS sequence comparisons. The aim of this study was to compare representatives of these two groups of isolates from coffee, citrus, cacao and native trees in Colombia, based on morphology and DNA-sequences for three gene regions. Host-specificity of the fungus was also considered. Representatives of the two groups of isolates were morphologically distinct and could be distinguished based on DNA sequence comparisons. They are also distinct from other species in the C. fimbriata sensu lato species complex and the sweet potato pathogen C. fimbriata sensu stricto and are provided with the names C. colombiana sp. nov and C. papillata sp. nov. There was no evidence for host-specificity amongst isolates of these two fungi that collectively represent a serious threat to coffee production in Colombia.     

Can leaf degrading enzymes provide evidence that endophytic fungi becoming saprobes?

The diversity of endophytic and saprobic fungi from Magnolia liliifera leaves were observed and analyzed to establish relationships. Nine endophytes were morphologically and phylogenetically similar to the saprobes; Colletotrichum gloeosporioides, Colletotrichum sp. 2, Corynespora cassiicola, Fusarium sp. 1, Guignardia mangiferae, Leptosphaeria sp., Phomopsis sp. 2, Phomopsis sp. 6, and Phomopsis sp. 10. The endophytes were found to produce the same degrading enzymes as their saprobic counterparts. The isoform of β-mannanase produced from each of endophyte and saprobe counterparts were similar. Fungal succession and enzyme production patterns during leaf decomposition were correlated. The occurrence of saprobes was found to be related to the enzymes that the fungi produce. The study provides further compelling evidence that endophytes can switch lifestyle to saprobes.     

Phylogenetic diversity of culturable fungi from the deep-sea sediments of the Central Indian Basin and their growth characteristics

Very few studies have addressed the diversity of culturable fungi from deep-sea sediments. We are reporting here the diversity of culturable fungi in deep-sea sediments of the Central Indian Basin obtained from a depth of ～5,000 m. A total of 16 filamentous fungi and 12 yeasts isolated from 20 sediment cores of ～35 cm length were identified by 18S and ITS sequencing of SSU rDNA. Most of the filamentous fungi were Ascomycota, while two were Basidiomycota. Microscopic identification of sporulating cultures mostly matched either with 18S or ITS sequences but seldom with both the sequences. Phylogenetic analysis of ascomycetes using 18S sequence data grouped them into 7 clusters belonging to Aspergillus sp., Sagenomella sp., Exophiala sp., Capronia sp., Cladosporium sp., Acremonium sp. and Tritirachium sp. ITS sequence data grouped isolates into 6 clusters belonging to Aspergillus sp., uncultured member of Hypocreaceae, Exophiala sp., uncultured soil fungus, Hypocreales and Trichothecium sp. The two basidiomycete isolates were a Tilletiopsis sp. evident from 18S as well as ITS sequence data. In contrast, most of the yeast isolates belonged to Basidiomycota and only one isolate belonged to the phylum Ascomycota. Sequences of 18S as well as ITS gave matching identification of most of the yeasts. Filamentous fungi as well as the yeasts grew at 200 bar/5°C indicating their adaptations to deep-sea conditions. This is the first report on isolation of Sagenomella, Exophiala, Capronia and Tilletiopsis spp. from deep-sea sediments. This study reports on the presence of terrestrial fungi as a component of culturable fungi in deep-sea sediments.     

Taxonomy and DNA phylogeny of Diatrypaceae associated with Vitis vinifera and other woody plants in Australia

The Diatrypaceae occur worldwide and comprise a number of pathogens of woody crops, forest and ornamental tree species. Despite the taxonomic difficulties within this family, interest in the Diatrypaceae has increased recently, mainly due to the recent detection of these fungi in the premium grape growing regions of California. In the present study, we investigated the diversity and host range of diatrypaceous fungi from prominent wine grape growing regions in South Australia, New South Wales and Western Australia. Approximately 100 isolates were collected from grapevine and other woody plants and compared with reference collections from the United States and Europe. Phylogenetic analyses of the complete sequence of the internal transcribed spacer (ITS) region of the ribosomal DNA and partial sequence of the β-tubulin gene, combined with morphological analyses separated 12 species. These included the previously described species Cryptovalsa ampelina, C. rabenhorstii, Diatrype brunneospora, Eutypa lata, E. leptoplaca, Eutypella australiensis, E. citricola, a Cryptosphaeria sp. and a Diatrype sp., whereas Diatrypella vulgaris, Eutypella cryptovalsoidea and E. microtheca are described as new. Seven species were isolated from grapevine but the prevalence of Diatrypaceae in grapevine cankers varied among the regions surveyed. In many instances in WA and NSW, these newly reported fungi were more widespread and abundant than E. lata. This study provides new information to assist with diagnosis of the causal agents of dieback and canker diseases in Australia and development of management strategies. Further studies to characterize the pathogenicity of diatrypaceous species to grapevines and to elucidate the biology of these fungi are underway.     

Lethal amanitas of East Asia characterized by morphological and molecular data

This study investigated the morphological characteristics and molecular phylogenetic relationships among lethal Amanita species occurring in East Asia. The results revealed that at least nine phylogenetic taxa exist in the region. Among them, five were identical to previously known morphological taxa including A. exitialis, A. fuliginea, A. subjunquillea, A. subjunquillea var. alba and A. virosa; three new taxa, A. fuligineoides, A. rimosa and A. pallidorosea were described and illustrated here. The remaining one was labeled “A. sp. 1” because no robust morphological evidence was found to distinguish it from A. subjunquillea var. alba. The occurrence of A. virosa in East Asia, a well-known lethally poisonous mushroom originally described from Europe, was confirmed by both ITS sequences and morphology. Another lethal species native to Europe, A. phalloides, was determined as closely related to A. subjunquillea from East Asia. Amanita oberwinklerana was treated in section Phalloideae from a morphological point of view, but appeared to be a member of section Lepidella by the analyses of sequences from both the ITS regions and the large subunit of nuclear ribosomal RNA gene. Distribution features of East Asian Phalloideae and the phylogenetic relationships of these species with their counterparts from Europe and North America were also discussed. A key to species of section Phalloideae in East Asia is furnished.     

Acidiella bohemica gen. et sp. nov. and Acidomyces spp. (Teratosphaeriaceae), the indigenous inhabitants of extremely acidic soils in Europe

Extremely acidic soils (pH?<?3) harbour mycobiota that are different from less acidic habitats and are dominated by a small number of fungal species. During investigation of the mycobiota of highly acidic soils in the Czech Republic and Iceland, a group of melanised fungal isolates was obtained. Based on phenotype and nuclear ribosomal DNA sequences (ITS region, SSU, LSU), the isolates were accommodated by three phylogenetic lineages within the family Teratosphaeriaceae (Capnodiales, Dothideomycetes). The first lineage is here described as a new acidotolerant genus and species Acidiella bohemica gen. nov. et sp. nov. The most closely related species to this new clade are other extremotolerant fungi isolated from rocks and lichens collected in the Alps and Antarctica as well as leaf-spotting species and opportunistic human pathogens. The isolates belonging to the second and the third lineages were identified as the recently described acidophilic fungi Acidomyces acidophilus and Teratosphaeria acidotherma, respectively. The taxonomic status of both sister species is discussed and the latter species is ascribed here to the genus Acidomyces.     

The phylogenetic position of the lichenicolous ascomycete Capronia peltigerae

The genus Capronia includes a number of lichenicolous (lichen-inhabiting) species, none of which have previously been characterized in vitro or considered in molecular phylogenetic studies. We cultured Capronia peltigerae from Peltigera rufescens and report here the growth of this species on a variety of media and its phylogenetic position based on the analyses of nuclear ribosomal RNA, mitochondrial ribosomal RNA, and RNA polymerase II (RPB1) gene sequences. This species differs from the majority of Capronia studied in axenic culture in lacking a conidial anamorph. Phylogenetic analyses position C. peltigerae outside the Herpotrichiellaceae within a robustly supported basal lineage of the Chaetothyriales composed primarily of melanized, rock-inhabiting anamorphic fungi. Our results demonstrate that Capronia, as circumscribed currently, is polyphyletic, but they do not resolve the relationship of C. peltigerae with members of the Chaetothyriaceae.     

Deciphering mycorrhizal fungi in cultivated Phalaenopsis microbiome with next-generation sequencing of multiple barcodes

Ochroconis is a genus of ascomycete fungi that includes oligotrophic saprobes and some opportunistic species causing infections in vertebrates. The most important of these opportunists is the neurotropic species Ochroconis gallopava, which occurs in birds and occasionally in immunocompromised humans. Other Ochroconis species have been isolated from superficial infections of cats, dogs and fish. In their natural environment, these species are found in litter, soil, and on moist surfaces. Some thermophilic species have been isolated from hot springs, industrial effluents, and self-heated plant material. Although their ecology and epidemiology has been investigated, their classification within the ascomycetes is still unknown. Here, the phylogenetic placement of Ochroconis is investigated using a four-gene phylogeny (nuLSU, nuSSU, mtSSU and RPB2). The results show that Ochroconis and its recently described sister genus Verruconis belong to the order Venturiales (Dothideomycetes) and are nested within the Sympoventuriaceae, a family recently erected for a group of plant-saprobes or -pathogens sister to the Venturiaceae. They form a well-supported monophyletic group together with five species of the anamorphic genus Fusicladium isolated from leaf and needle litters.     

A taxonomic revision and phylogenetic reconstruction of the Jahnulales (Dothideomycetes), and the new family Manglicolaceae

Genera assigned to the Jahnulales are morphologically diverse, especially in ascospores equipped with or without appendages, sheaths or apical caps. They are predominantly freshwater fungi occurring on woody substrata, with Manglicola guatemalensis, Xylomyces chlamydosporus and X. rhizophorae the only species known from marine habitats. The order Jahnulales with 4 teleomorphic genera: Jahnula (15 species), Aliquandostipite (5), Megalohypha (1), Manglicola (2) and the anamorphic genera Brachiosphaera (2), Speiropsis (9), Xylomyces (8), amounting to a total of 42 species, is reviewed and nomenclatural changes are proposed. Twenty species are treated at the molecular level, with 94 sequences, 13 of which are newly generated for this review. Three species are rejected (Speiropsis irregularis, Xylomyces aquaticus, X. elegans) while the phylogenetic placement of 6 Xylomyces, 7 Speiropsis, 1 Brachiosphaera and 1 Manglicola require molecular data to confirm their placement in the order. Sequences are derived from ex-holotype isolates and new collections made in Thailand. Most taxa are included in the family Aliquandostipitaceae and a new family Manglicolaceae is erected for the marine ascomycete Manglicola guatemalensis with its large ascomata (1,100–1,750?×?290–640 μm), wide ostioles and ascospores that are fusiform, unequally one-septate with the apical cell larger than the turbinate basal cell and bear apical gelatinous appendages. The genus Jahnula is polyphyletic grouping in three clades with J. aquatica, J. granulosa, J. rostrata, J. potamophila and Megalohypha aqua-dulces in the Jahnula sensu stricto clade. No taxonomical changes are proposed for Jahnula species not grouping in the Jahnula sensu stricto clade, until further species are isolated and sequenced.