Biology, ecology and ultrastructure of Ascobotryozyma and Botryozyma, unique commensal nematode-associated yeasts.

Ascobotryozyma (anamorph Botryozyma) is an ascomycetous yeast genus characterized by its unusual morphology and ability to attach to free-living nematodes in the genus Panagrellus. Other than species descriptions for four taxa little is known about these yeasts. Investigations were carried out to determine the ecological relationship and specificity with nematodes in addition to examining basic cell structure, thallus development and sexual reproduction. Based on previous examinations of the yeast and nematode it was hypothesized the fungus did not parasitize the nematode but instead remained attached to nematodes for dispersal. Electron micrographs supported our hypotheses and revealed a specialized cell wall and mucilage that aid in attachment to the nematode cuticle. Tests to determine the ability of Ascobotryozyma and Botryozyma to attach to different nematode taxa revealed that attachment varies across taxonomic groups. Examinations of thallus cells, thallus growth, cell fusion and ascosporogenesis are presented. This study provides insight into an otherwise cryptic yeast genus.

Reconstructing the early evolution of Fungi using a six-gene phylogeny.

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

New and interesting penzigioid Xylaria species with small, soft stromata.

Six penzigioid Xylaria species that are characterized by small, discoid to pulvinate, soft stromata are included in this study. Xylaria albocinctoides, X. bicampaniformis and X. lechatii are described as new; Nummularia albocincta, Hypoxylon carabayense and H. discolor are moved to the genus Xylaria to form new combinations X. albocincta, X. carabayensis and X. discolor respectively. An identification key is provided for the major aggregates of Xylaria that harbor penzigioid species as well as the species of the X. frustulosa aggregate, to which the six studied penzigioid Xylaria species belong.

Phylogenetic status of Xylaria subgenus Pseudoxylaria among taxa of the subfamily Xylarioideae (Xylariaceae) and phylogeny of the taxa involved in the subfamily.

To infer the phylogenetic relationships of Xylaria species associated with termite nests within the genus Xylaria and among genera of the subfamily Xylarioideae, beta-tubulin, RPB2, and alpha-actin sequences of 131 cultures of 114 species from Xylaria and 11 other genera of the subfamily were analyzed. These 11 genera included Astrocystis, Amphirosellinia, Discoxylaria, Entoleuca, Euepixylon, Kretzschmaria, Nemania, Podosordaria, Poronia, Rosellinia, and Stilbohypoxylon. We showed that Xylaria species were distributed among three major clades, TE, HY, and PO, with clade TE-an equivalent of the subgenus Pseudoxylaria-encompassing exclusively those species associated with termite nests and the other two clades containing those associated with substrates other than termite nests. Xylaria appears to be a paraphyletic genus, with most of the 11 genera submerged within it. Podosordaria and Poronia, which formed a distinct clade, apparently diverged from Xylaria and the other genera early. Species of Entoleuca, Euepixylon, Nemania, and Rosellinia constituted clade NR, a major clade sister to clade PO, while those of Kretzschmaria were inserted within clade HY and those of Astrocystis, Amphirosellinia, Discoxylaria, and Stilbohypoxylon were within clade PO.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

New Annulohypoxylon species from Brazil.

Four new Annulohypoxylon species are described from northeastern Brazil: A. austrobahiense, A. macrodiscum, A. hemicarpum and A. purpureopigmentum. A key is provided.

Xylaria species associated with fallen fruits and seeds.

Twenty-five fructicolous and seminicolous species of Xylaria are classified into three groups by stromatal morphology: (i) the X. ianthinovelutina group; (ii) the X. carpophila group; and (iii) the X. heloidea group. Xylaria reevesiae, X. rossmanae, and X. vivantii are described as new species. Xylaria reevesiae belongs to the X. carpophila group, resembling X. euphorbiicola but differing from it mainly by having conspicuous perithecial mounds and growing on fallen fruits of a different host plant. Xylaria rossmanae and X. vivantii belong to the X. ianthinovelutina group. Xylaria rossmanae differs from the species of the group mainly by larger, paler, fusoid-inequilateral ascospores, and X. vivantii differs by larger ascospores with a slightly oblique germ slit. A dichotomous key is provided for identifying the 25 species. Doubtful names are also listed and annotated.

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny.

The Sordariomycetes is one of the largest classes in the Ascomycota, and the majority of its species are characterized by perithecial ascomata and inoperculate unitunicate asci. It includes more than 600 genera with over 3000 species and represents a wide range of ecologies including pathogens and endophytes of plants, animal pathogens and mycoparasites. To test and refine the classification of the Sordariomycetes sensu Eriksson (2006), the phylogenetic relationship among 106 taxa from 12 orders out of 16 in the Sordariomycetes was investigated based on four nuclear loci (nSSU and nLSU rDNA, TEF and RPB2), using three species of the Leotiomycetes as outgroups. Three subclasses (i.e. Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae) currently recognized in the classification are well supported with the placement of the Lulworthiales in either a basal group of the Sordariomycetes or a sister group of the Hypocreomycetidae. Except for the Microascales, our results recognize most of the orders as monophyletic groups. Melanospora species form a clade outside of the Hypocreales and are recognized as a distinct order in the Hypocreomycetidae. Glomerellaceae is excluded from the Phyllachorales and placed in Hypocreomycetidae incertae sedis. In the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported clade containing the Boliniales and Chaetosphaeriales. Aspects of morphology, ecology and evolution are discussed.

Some Xylaria species on termite nests.

Xylaria arenicola, X. brasiliensis, X. escharoidea, X. furcata, X. nigripes, X. piperiformis and X. rhizomorpha represent ancient names of fungi known to inhabit abandoned termite nests. We attempt to redescribe them and to reduce the confusion among them. Xylaria tanganyikaensis and X. readeri, species that might be associated with termite nests, are described. We describe a new variety, X. furcata var. hirsuta, and discuss an unnamed fungus that probably represents a new species. Photographs and a key are presented to aid the identification of these taxa.

New Hypoxylon and Nemania species from Costa Rica and Taiwan.

Six xylariaceous fungi, including two Hypoxylon taxa and four Nemania taxa, are described as new. They were collected from either Costa Rica or Taiwan. Two of the Nemania species--N. flavitextura and N. primolutea--were cultured and typical Geniculosporium anamorphs were produced.

Molecular phylogeny of Hypoxylon and closely related genera.

Phylogenetic relationships were inferred among several xylariaceous genera with Nodulisporium or nodulisporium-like anamorphs based on the analyses of beta-tubulin and alpha-actin sequences. One hundred nine cultures and three specimens of 83 representatives of these four genera were included in the study. Biscogniauxia taxa formed a well supported clade that was basal to the other taxa, while taxa of Hypoxylon and Daldinia comprised a large monophyletic group that contained two subclades. The first subclade encompassed Hypoxylon sect. Annulata and is accepted here as the new genus Annulohypoxylon. The second subclade contained taxa of Hypoxylon sect. Hypoxylon and Daldinia. Hypoxylon is restricted to include only those taxa in sect. Hypoxylon. Thirty-three epithets are made in Annulohypoxylon. Hypoxylon cohaerens var. microsporum is raised to the species level and accepted as A. minutellum. Hypoxylon polyporoideum is recognized as distinct from H. crocopeplum. Hypoxylon placentiforme is accepted as Daldinia placentiformis.

New Hypoxylon species and notes on some names associated with or related to Hypoxylon.

These new species of Hypoxylon are described: H. elevatidiscus, H. squamulosum, H. subalbum and H. vinosopulvinatum. A referenced list of all Hypoxylon species known to us described since 1996 is given and a key presented. Names associated with Hypoxylon that were not given in the Ju and Rogers monograph are annotated and diagnostic corrections of taxa discussed in that monograph are given.

Ophiorosellinia costaricensis gen. et sp. nov., a xylariaceous fungus with scolecosporous ascospores.

A pyrenomycete featuring uniperitheciate stromata embedded in a subiculum and asci with iodine-positive apical ascal rings that bear scolecosporous ascospores is described as new. The fungus, Ophiorosellinia costaricensis, is known only from the type location in Costa Rica. It has been cultured, but no anamorph was discovered.

Amphirosellinia gen. nov. and a new species of Entoleuca.

The new genus Amphirosellinia is erected to include five xylariaceous fungi with erumpent or immersed perithecioid stromata. Amphirosellinia fushanensis, A. nigrospora and A. tennesseensis are newly described, whereas A. evansii and A. quercina are new combinations. Synnematous, geniculosporium-like anamorphs are known for A. fushanensis, A. nigrospora, A. tennesseensis and A. evansii; the anamorph of the latter species was produced on natural substratum, whereas those of the former three species were produced in culture. Dichotomous keys are presented for the Amphirosellinia species and for some genera that might be confused with Amphirosellinia. Entoleuca ellisii also is described as new. It readily can be separated from the known species in the genus by its smaller ascospore size range and short ascospore germ slit.

The genus Theissenia: T. pyrenocrata, T. cinerea sp. nov., and T. eurima sp. nov.

The diagnosis of Theissenia is emended to include taxa that lack a definite central perithecial columella and taxa that feature ascospores with a germ slit. Theissenia cinerea is described as a new species that lacks a perithecial columella; T. eurima is described as a new species with ascospores having a germ slit. The type species, T. pyrenocrata, is redescribed and compared with the new species. The taxonomic position of Theissenia is discussed.

Paramphisphaeria costaricensis gen. et sp. nov. and Pachytrype rimosa sp. nov. from Costa Rica.

Paramphisphaeria is described as a new genus on the basis of the single species, P. costaricensis. It differs from Amphisphaeria spp. primarily in having bicellular ascospores with a germ slit and in having an ascus apical ring that does not become blue in iodine. It resembles Amphisphaeria in its brown color and lack of constriction at the septum of the ascospore. An anamorph is unknown. It tentatively is placed in the Xylariaceae for reasons discussed. Pachytrype rimosa is described as a new species.

Didymella pisi sp. nov., the teleomorph of Ascochyta pisi.

The anamorphic pycnidial fungus Ascochyta pisi is one member of a species complex that causes Ascochyta blight of pea, a potentially devastating disease. The teleomorphic state of this fungus was induced under laboratory conditions. Using morphological and molecular characters, we placed the teleomorph within the genus Didymella as D. pisi and describe a heterothallic mating system using a PCR-based mating type assay and in vitro crosses. We compare D. pisi with other Didymella spp. with which it might be confused.

Coniolariella hispanica sp. nov. and other additions to Coniolariella.

Coniolariella hispanica, isolated as an endophyte from leaves of Eryngium campestre on the Iberian Peninsula, is established as a new cleistocarpous species. The perithecial species Rosellinia limoniispora is transferred to Coniolariella on morphological and molecular evidence. R. australis is transferred to Coniolariella as a variety of C. limoniispora. The type species of Coniolariella, C. gamsii, is considered to be a variety of C. limoniispora. The taxa discussed here have soft stromata, deliquescent asci that lack an iodine-positive apical ring, and more or less symmetrical ascospores. They lack subicula in natural conditions. C. hispanica and C. limoniispora var. limoniispora have Sporothrix- or Geniculosporium-like anamorphs associated with stromata at different stages of development, but anamorphs are not usually evident in cultures. Coniolariella limoniispora var. gamsii produces the anamorph abundantly in culture. It is not known whether or not C. limoniispora var. australis possesses an anamorph. An emendation of the description of Coniolariella is necessitated by these changes.

Chemotaxonomy of Entonaema, Rhopalostroma and other Xylariaceae.

Entonaema, Pulveria, Phylacia, Rhopalostroma, Sarcoxylon and Thamnomyces are relatively small and poorly studied genera of Xylariaceae. Their affinities to the mainstream of the family largely remain to be evaluated. Secondary metabolite profiles of type materials, recently collected specimens, and cultures, were generated to address this problem from a chemotaxonomic point of view. Micro-scale extraction and subsequent analytical HPLC with uv/visual (diode array) and ms detection in the positive and negative Electrospray mode were carried out, employing spectral libraries and standardised gradients that had been optimised to detect characteristic pure compounds in species of allied genera. Surprisingly, the characteristic metabolites had frequently remained stable even in specimens collected up to 190 years ago. Hence, this methodology not only proved valuable to establish the conspecificity of type materials with recent records, but also revealed some interesting correlations: (1) Stromatal pigments of Entonaema cinnabarina, E. globosum and E. liquescens are mitorubrins and other characteristic compounds also prevailing in particular species of Hypoxylon; (2) Rhopalostroma, Phylacia, Pulveria and Thamnomyces contain binapththalenes and other compounds typical of Daldinia and Hypoxylon; (3) Sarcoxylon, as well as E. dengii, E. moluccanum and E. pallida, contained none of these pigments, but characteristic yet unknown lipophilic metabolites were detected in their stromatal extracts; (4) Cultures of E. cinnabarina and Rhopalostroma indicum, obtained for the first time, produced essentially the same secondary metabolites that are also typical of Daldinia, but absent in Biscogniauxia, Hypoxylon and other xylariaceous genera. Hence, chemotaxonomic characters reflected the adaptive radiation of this family. Correlations between the evolution of morphological/anatomical characters are discussed.

Botryozyma mucatilis sp. nov., an anamorphic ascomycetous yeast associated with nematodes in poplar slime flux.

A new species of Botryozyma, Botryozyma mucatilis, was isolated from the surface of free-living nematodes, Panagrellus dubius, inhabiting slime flux from hybrid poplars, Populus deltoidesxtrichocarpa, in Oregon, USA. This species was discovered in relatively close proximity to the teleomorphic species Ascobotryozyma americana and Ascobotryozyma cognata, both collected from P. dubius nematodes inhabiting beetle galleries in Populus spp. and Populus and Salix spp., respectively. B. mucatilis is recognized as a distinct species based on molecular and morphological data. Sequence divergence in both the D1/D2 domain of the nuclear large-subunit rDNA and internal transcribed spacer region rDNA, low DNA reassociation values, notably different amplified fragment-length polymorphic fingerprints, and significantly longer cells all support the designation of a novel species.