Molecular phylogeny of Hyphoderma and the reinstatement of Peniophorella

Heart Rot Disease of Walnut Caused by Nothophoma juglandis sp. nov. and Its Endophytic Biocontrol Agent

English walnut (Juglans regia L.) is an economically important hardwood tree species cultivated worldwide. Walnut heart rot disease leading to heartwood decay of trees has been frequently observed in a number of plantations in China. To identify the causal agent, 29 diseased stem samples were collected from walnut plantations in Beijing, and 54 fungal isolates were obtained. Koch's postulates were developed, and the results showed that Nothophoma juglandis, a species new to science, was the causal agent of walnut heart rot disease. Granulobasidium vellereum, a notable biocontrol agent, was coisolated with N. juglandis. An antagonistic assay on dual culture and walnut stems (both in the field and detached branches) proved that G. vellereum acted as a potential biocontrol agent against N. juglandis, as it could significantly inhibit the expansion of N. juglandis. The optimal temperature for mycelial growth and pathogenicity of N. juglandis was 26.6 and 27.0°C, respectively, which frequently occur in the summer of the walnut-growing regions in China.

Diversity of Wood-Decaying Fungi in Wuliangshan Area, Yunnan Province, P.R. China

Five surveys were carried out in the Wuliangshan area, Yunnan Province, P.R. China, based on a combination of morphological features and molecular evidence. Around 2454 specimens of wood-decaying fungi were collected. The paper summarizes the obtained results on the wood-decaying fungi of this area, consisting in 95 species distributed in 59 genera, 23 families and 9 orders. Their hosts and substrates were also identified. A checklist of wood-decaying fungi is given. Sequences of the ITS nrRNA gene region of the studied specimens were generated and phylogenetic analysis was performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The present list of wood-decaying fungi enriches the knowledge of fungal diversity worldwide and supplies the basic data for future applications.

Taxonomy of corticioid fungi in Japan : Present status and future prospects

Corticioid fungi form effused basidiomata with various hymenophore configurations, mostly on woody substrates, and they are presently classified into 15 orders in Agaricomycotina in the phylum Basidiomycota. In this review, the corticioid fungi of Japan are treated on the basis of the current classification system, and all currently known species are listed and classified by order. Japanese corticioid fungi number 442 species in 160 genera belonging to 14 orders. Analysis of the distribution of Japanese corticioid species reveals that 375 species (85% of the total) have wide distributions, and that the Japanese corticioid fungal flora is composed of species with diverse patterns of distribution. In the subtropical regions, 146 corticioid species belonging to 77 genera are listed, including 100 species from the Nansei Islands and 76 from the Ogasawara Islands. Although these two island groups are located at similar latitudes, they share only 30 corticioid species-21% of the total reported from the subtropical regions. Along with this summary of the current status, this study presents future directions for the taxonomic research of the Japanese corticioid fungi.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

Reinstatement of the corticioid genus Leifia (Hymenochaetales, Basidiomycota) with a new species L.brevispora from Hubei, Central China

The monotypic genus Leifia was previously considered to be a later synonym of Odonticium. With the morphological and phylogenetic evidence provided by an additional four East Asian specimens, we propose to reinstate Leifia as an independent genus in Hymenochaetales. Leifia morphologically differs from Odonticium by its grandinioid hymenophore with hyphal strands, numerous thick-walled cystidia with an invaginated apical end and narrowly and thick-walled basidia. The phylogeny generated from the current data set of ITS and 28S regions indicates that Leifia forms a sister clade to Odonticium. Besides the generic type Leifiaflabelliradiata in the Leifia clade, two specimens, collected from Hubei, Central China, are newly introduced as Leifiabrevispora. This new species is the second species of Leifia and differs from the generic type by its shorter basidiospores and distribution in warm-temperate to subtropical areas in East Asia. The additional two specimens, collected from Da Lat, Viet Nam, differ morphologically, both from each other and from known species of Leifia, but more samples need to be examined before further taxonomic decisions can be made.

When the ribosomal DNA does not tell the truth: The case of the taxonomic position of Kurtia argillacea, an ericoid mycorrhizal fungus residing among Hymenochaetales

The nuclear ribosomal DNA (nuc-rDNA) is widely used for the identification and phylogenetic reconstruction of Agaricomycetes. However, nuc-rDNA-based phylogenies may sometimes be in conflict with phylogenetic relationships derived from protein coding genes. In this study, the taxonomic position of the basidiomycetous mycobiont that forms the recently discovered sheathed ericoid mycorrhiza was investigated, because its nuc-rDNA is highly dissimilar to any other available fungal sequences in terms of nucleotide composition and length, and its nuc-rDNA-based phylogeny is inconclusive and significantly disagrees with protein coding sequences and morphological data. In the present work, this mycobiont was identified as Kurtia argillacea (= Hyphoderma argillaceum) residing in the order Hymenochaetales (Basidiomycota). Bioinformatic screening of the Kurtia ribosomal DNA sequence indicates that it represents a gene with a non-standard substitution rate or nucleotide composition heterogeneity rather than a deep paralogue or a pseudogene. Such a phenomenon probably also occurs in other lineages of the Fungi and should be taken into consideration when nuc-rDNA (especially that with unusual nucleotide composition) is used as a sole marker for phylogenetic reconstructions. Kurtia argillacea so far represents the only confirmed non-sebacinoid ericoid mycorrhizal fungus in the Basidiomycota and its intriguing placement among mostly saprobic and parasitic Hymenochaetales begs further investigation of its eco-physiology.

A revised family-level classification of the Polyporales (Basidiomycota)

Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia + amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea, and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological, and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.

Novel root-fungus symbiosis in Ericaceae: sheathed ericoid mycorrhiza formed by a hitherto undescribed basidiomycete with affinities to Trechisporales

Ericaceae (the heath family) are widely distributed calcifuges inhabiting soils with inherently poor nutrient status. Ericaceae overcome nutrient limitation through symbiosis with ericoid mycorrhizal (ErM) fungi that mobilize nutrients complexed in recalcitrant organic matter. At present, recognized ErM fungi include a narrow taxonomic range within the Ascomycota, and the Sebacinales, basal Hymenomycetes with unclamped hyphae and imperforate parenthesomes. Here we describe a novel type of basidiomycetous ErM symbiosis, termed 'sheathed ericoid mycorrhiza', discovered in two habitats in mid-Norway as a co-dominant mycorrhizal symbiosis in Vaccinium spp. The basidiomycete forming sheathed ErM possesses clamped hyphae with perforate parenthesomes, produces 1- to 3-layer sheaths around terminal parts of hair roots and colonizes their rhizodermis intracellularly forming hyphal coils typical for ErM symbiosis. Two basidiomycetous isolates were obtained from sheathed ErM and molecular and phylogenetic tools were used to determine their identity; they were also examined for the ability to form sheathed ErM and lignocellulolytic potential. Surprisingly, ITS rDNA of both conspecific isolates failed to amplify with the most commonly used primer pairs, including ITS1 and ITS1F + ITS4. Phylogenetic analysis of nuclear LSU, SSU and 5.8S rDNA indicates that the basidiomycete occupies a long branch residing in the proximity of Trechisporales and Hymenochaetales, but lacks a clear sequence relationship (>90% similarity) to fungi currently placed in these orders. The basidiomycete formed the characteristic sheathed ErM symbiosis and enhanced growth of Vaccinium spp. in vitro, and degraded a recalcitrant aromatic substrate that was left unaltered by common ErM ascomycetes. Our findings provide coherent evidence that this hitherto undescribed basidiomycete forms a morphologically distinct ErM symbiosis that may occur at significant levels under natural conditions, yet remain undetected when subject to amplification by 'universal' primers. The lignocellulolytic assay suggests the basidiomycete may confer host adaptations distinct from those provisioned by the so far investigated ascomycetous ErM fungi.

Re-thinking the classification of corticioid fungi

Corticioid fungi are basidiomycetes with effused basidiomata, a smooth, merulioid or hydnoid hymenophore, and holobasidia. These fungi used to be classified as a single family, Corticiaceae, but molecular phylogenetic analyses have shown that corticioid fungi are distributed among all major clades within Agaricomycetes. There is a relative consensus concerning the higher order classification of basidiomycetes down to order. This paper presents a phylogenetic classification for corticioid fungi at the family level. Fifty putative families were identified from published phylogenies and preliminary analyses of unpublished sequence data. A dataset with 178 terminal taxa was compiled and subjected to phylogenetic analyses using MP and Bayesian inference. From the analyses, 41 strongly supported and three unsupported clades were identified. These clades are treated as families in a Linnean hierarchical classification and each family is briefly described. Three additional families not covered by the phylogenetic analyses are also included in the classification. All accepted corticioid genera are either referred to one of the families or listed as incertae sedis.