Four new species of Entoloma s.l. (Agaricales) from southern China

Four new Entoloma s.l. species (E. azureosquamulosum, E. caeruleoflavum, E. hainanense, and E. subtenuicystidiatum) are described from southern China. E. azureosquamulosum fits well within the section Rhamphocystotae, E. caeruleoflavum belongs to the section Entoloma, E. hainanense is placed in the section Calliderma, and E. subtenuicystidiatum is a species in the section Cyanula. Preliminary phylogenetic analyses for the four new species are provided based on ITS and LSU sequences in this paper.     

Characterization of virulence factors and phylogenetic group determination of <Emphasis Type="Italic">Escherichia coli</Emphasis> isolated from diarrheic and non-diarrheic calves from Brazil

This study aimed to detect virulence factors, pathovars, and phylogenetic groups of Escherichia coli strains obtained from feces of calves with and without diarrhea up to 70 days old and to determine the association between occurrence of diarrhea, phylogenetic groups, and pathovars. Phylo-typing analysis of the 336 E. coli strains isolated from calves with Clermont method showed that 21 (6.25 %) belong to phylogroup A, 228 (67.85 %) to phylogroup B1, 2 (0.6 %) to phylogroup B2, 5 (1.49 %) to phylogroup C, 57 (16.96 %) to phylogroup E, and 3 (0.9 %) to phylogroup F. Phylogroup D was not identified and 20 strains (5.95 %) were assigned as “unknown.” The distribution of phylogenetic groups among pathovars showed that NTEC belong to phylogroups B1 (17) and C (4); EPEC to phylogroups B1 (6) and E (8); STEC to phylogroups A (5), B1 (56), B2 (2), C (1), and E (15); EHEC to phylogroups B1 (95) and E (5); and ETEC to phylogroups A (3), B1 (7), and E (10). The EAST-1 strains were phylogroups A (13), B1 (47), E (19), and F (3); E. coli strains of “unknown” phylogroups belonged to pathovars EPEC (1), EHEC (2), STEC (7), and EAST-1 strains (6). ETEC was associated with diarrhea (P = 0.002). Our study did not find association between the phylogenetic background and occurrence of diarrhea (P = 0.164) but did find some relationship in phylogenetic group and pathovar. The study showed that EHEC and STEC are classified as phylogroup B1, EAST-1 phylogroup A, ETEC, and EPEC phylogroup E.     

Phylogenetic analysis of rDNA sequences indicates that the sequestrate Amogaster viridiglebus is derived from within the agaricoid genus Lepiota (Agaricaceae)

The rare sequestrate fungus Amogaster viridiglebus is known from only one collection in California where it was discovered among Populus roots. Based on sporocarp coloration and spore morphology, this sequestrate taxon was putatively considered to be an ectomycorrhizal member of the Boletales. However, no molecular data were previously available to definitively determine the closest relatives of this fungus. Here we revisit the morphology of Amogaster viridiglebus and present a phylogenetic analysis based on ITS and 28S ribosomal DNA. Our phylogeny indicates that Amogaster viridiglebus is nested in the genus Lepiota, suggesting that this rare species has a saprobic trophic mode and does not form ectomycorrhizae with plants. A new combination, L. viridigleba, is made based on these phylogenetic results.     

Molecular detection,community structure and phylogeny of ericoid mycorrhizal fungi

Through traditional culturing and molecular characterization, we have determined that five putative species and 2 polyphyletic assemblages of fungi produce ericoid mycorrhizae in Gaultheria shallon, other Ericaceae and Epacridaceae. Using phylogenetic analysis of ITS2 sequences in GenBank, we have confirmed that most of these fungi occur in North America, Europe, and Australia. The low recovery rate of culturable ericoid mycorrhizal fungi from Gaultheria shallon may partly be explained by the fact that most mycorrhizal root segments contain an unculturable basidiomycete, revealed by direct amplification, cloning, and sequencing of LSU fungal DNA from root. Molecular characterization and phylogenetic analysis are powerful tools in revealing the geographic distribution and identity of ericoid mycorrhizal fungi.     

Crystallicutis gen. nov. (Irpicaceae,Basidiomycota), including C. damiettensis sp. nov., found on Phoenix dactylifera (date palm) trunks in the Nile Delta of Egypt

The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species, Crystallicutis damiettensis sp. nov. found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit orchards of the Nile Delta region of Egypt is reported. Multigene phylogenetic analyses based on ITS, LSU, EF1α, RPB1 and RPB2 loci place this species in Irpicaceae, and forming a distinct clade with Ceraceomyces serpens and several other hitherto unnamed taxa, which we also incorporate into a new genus Crystallicutis. We name two of these species, Crystallicutis huangshanensis sp. nov. and Crystallicutis rajchenbergii sp. nov. The distinctive feature of Crystallicutis gen. nov. is the presence of crystal-encrusted hyphae in the hymenium and subiculum. Basidiomes are usually honey-yellow with white margins but there is variability in the presence of clamp connections and cystidia, as noted for other genera within Irpicacae. C. damiettensis is hitherto consistently associated with date palms killed by the red palm weevil Rhynchophorus ferrugineus, a highly damaging and invasive pest, recently spread to the Mediterranean region. C. damiettensis causes rapid wood decay by a potentially unusual white-rot mechanism and may play a role in the damage caused by R. ferrugineus.     

Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora

The rare apothecial, cupulate fungus Geopora pellita (Pyronemataceae) is characterized by a uniquely bright yellow-orange excipulum. We here re-examine its affiliations by use of morphological, molecular phylogenetic and ultrastructural analyses. G. pellita appears as phylogenetically rather isolated, being the sister group of a clade comprising Phaeangium, Picoa, the majority of the Tricharina species, and the remaining Geopora species. Based on its phylogenetic position and its unique combination of morphological characters, we assign G. pellita to Hoffmannoscypha, gen. nov., as H. pellita, comb. nov. As in a previous study, analyses of both large subunit (LSU) and internal transcribed spacer (ITS) ribosomal DNA suggest that the remaining genus Geopora is paraphyletic, with the hypogeous, ptychothecial type species more closely related to Picoa and Phaeangium than to the greyish-brownish cupulate and apothecial Geopora spp., indicating that the latter should be reassigned to the genus Sepultaria. The current study also shows that ITS confirm LSU data regarding the polyphyly of Tricharina.     

Molecular detection of <Emphasis Type="Italic">Entoloma</Emphasis> spp. associated with roots of rosaceous woody plants

Seventeen isolates of Entoloma clypeatum, a fungus associated with rosaceous woody plants and suspected to act as a root pathogen, were obtained from fruit-bodies collected at 7 localities in the Czech Republic. The fungus grew best on the medium supplied with cellobiose. The growth of E. clypeatum was inhibited by fungicide preparation Ridomil Gold MZ 68WP. A part of the LSU rRNA gene of 11 selected isolates was sequenced and two reverse primers recognizing the sequence motifs in the LSU rRNA gene of E. clypeatum and other related species associated with rosaceous woody plants were designed. One of these primers, NL4EC2, showed high specificity towards DNA of Entoloma spp. of interest and may be used for detection of these organisms in soil, in roots or in the substrate where the fruit trees are cultivated. The results of in vitro inoculation experiment suggest a resistance of roots of young Prunus domestica plants to colonization by Entoloma clypeatum, and the fungus could be detected only in the surrounding substrate. We were able to detect Entoloma spp. in soil and in roots of Prunus avium but only if the fructification of the fungus occurred at the locality. The method is robust towards the false positive detection caused by nonspecific amplification of DNA of other soil microorganisms.     

Morphological and molecular identification of two new species of Tubulicrinis (Hymenochaetaceae,Hymenochaetales) from southern China

Two new wood-inhabiting fungal species, Tubulicrinis xantha and T. yunnanensis spp. nov., are described based on morphological and molecular characters. Tubulicrinis xantha is characterized by resupinate, furfuraceous basidiomata with buff to yellowish hymenial surface, amyloid lyocystidia and cylindrical to allantoid, hyaline, thin-walled, smooth basidiospores (5.3–6.3 × 1.2–1.6 μm). Tubulicrinis yunnanensis is characterized by pruinose basidiomata with primrose to olivaceous hymenial surface and encrusted lyocystidia and cylindrical, hyaline, thin-walled, smooth basidiospores (4.2–6.2 × 1.2–2 μm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS + nLSU sequences showed that T. xantha grouped with T. martinicensis, and T. yunnanensis grouped with T. glebulosus.     

A new species and two new Chinese records of Ochroconis from sugarcane and banana rhizosphere in Guangxi,China

Ochroconis guangxiensis isolated from sugarcane and banana rhizosphere, was described as a new species based on morphological characteristics and phylogenetic analysis using sequence data of the nuclear small subunit rRNA gene (SSU), internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene. Taxonomic and phylogenetic remarks are also provided for O. minima and O. ramosa. The latter two species are newly recorded for China. These three Ochroconis species, as dark septate endophytes, inhabit rhizosphere and can form a symbiosis with sugarcane and banana.     

Phylogeny and diversity of Japanese truffles (Tuber spp.) inferred from sequences of four nuclear loci

The genus Tuber, which includes some highly valued truffles, comprises ascomycetous ectomycorrhizal fungi associated with ecologically important tree species. Although the genus is distributed over northern temperate regions, we know little about the phylogeny and diversity of Tuber species in Japan. We have collected 186 new Tuber ascoma samples in Japan over a 10 y period. The identities and phylogenies of the samples were analyzed with sequences of four nuclear loci (i.e. internal transcribed spacer [ITS] and large subunit [LSU] regions of rDNA, elongation factor 1 alpha [EF1-α], and RNA polymerase II large subunit [rpb2] genes). Based on the species delimitation of 95% sequence matches in the ITS region, which is a suitable region for species-level identification of higher fungi, we identified 20 Tuber species. The number of observed species did not reach an asymptote with our maximum sampling localities in a species accumulation curve. The Chao2 species richness estimator indicated that at least 40 Tuber species should be present in Japan. Molecular phylogenetic analyses revealed that Japanese Tuber species belong to five major phylogroups, including Macrosporum, which had not been reported previously in Asia. Two Japanese species were morphologically and phylogenetically distinct from other known phylogroups, and here we propose a new Tuber phylogroup, Japonicum. In addition most of the other Japanese species formed separate clades within individual major phylogroups and deserve to be proposed as new species. Detailed molecular phylogeny within individual phylogroups revealed the existence of phylogeographic structures at both continental and within-Asia scales, indicating that migration and allopatric speciation have occurred even between the mainland and islands in Asia. Although our findings substantially advance current understanding of Tuber diversity and phylogeny, comparable richness estimation and multilocus phylogeny in other geographic regions are necessary to unequivocally address global patterns of Tuber diversity and biogeography.     

Gymnomyces xerophilus sp. nov. (sequestrate Russulaceae), an ectomycorrhizal associate of Quercus in California

Gymnomyces xerophilus sp. nov., a sequestrate species in the Russulaceae, is characterized and described morphologically as a new species from Quercus-dominated woodlands in California. ITS sequences recovered from healthy, ectomycorrhizal roots of Quercus douglasii and Q. wislizeni matched those of G. xerophilus basidiomata, confirming the ectomycorrhizal status of this fungus. Phylogenetic analysis of the ITS region places G. xerophilus in a clade with both agaricoid (Russula in the section Polychromae) and sequestrate (Gymnomyces, Cystangium) relatives. We include a dichotomous key to the species of Gymnomyces associated with Quercus.     

<Emphasis Type="Italic">Cortinarius majestaticus</Emphasis> comb. nov.: phylogenetic evidence for the transfer of <Emphasis Type="Italic">Descolea majestatica</Emphasis> to <Emphasis Type="Italic">Cortinarius</Emphasis>

Descolea majestatica is an agaric with features described as intermediate between the genera Descolea Singer and Rozites P. Karst. (≡ Cortinarius). Molecular phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS), large ribosomal subunit (LSU) and RNA polymerase second largest subunit (RPB2) sequences indicates that D. majestatica is nested within the genus Cortinarius, with its closest relative a sequestrate Cortinarius species from Argentina. Taxonomic recombination is made to restore the monophyly of Cortinarius and Descolea.     

Mycobiota associated with the ambrosia beetle Scolytodes unipunctatus (Coleoptera: Curculionidae, Scolytinae)

Ambrosia beetles (Coleoptera: Scolytinae) are associated with strictly entomochoric and mutualistic fungi. We studied the mycobiota associated with Scolytodes unipunctatus, ambrosia beetles that infest Cecropia trees in Central America. Isolates were characterized using morphology and rDNA sequences (ITS region, LSU, and SSU rDNA). Four species are described here: Raffaelea scolytodis sp. nov. (Ophiostomatales), Gondwanamyces scolytodis sp. nov., Custingophora cecropiae sp. nov., and Graphium sp. (Microascales). The genus Custingophora is emended to include Knoxdaviesia anamorphs of Gondwanamyces based on uniformity of DNA sequences and phenotype.     

Mycena species can be opportunist-generalist plant root invaders

Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of ¹³C/¹⁵N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published ¹³C/¹⁵N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.     

The phylogeny and taxonomy of genera Cystoderma and Cystodermella (Agaricales) based on nuclear ITS and LSU sequences

Species delimitation in Cystoderma and Cystodermella was evaluated based on ITS and LSU rDNA sequences as well as morphological data. Two species of Cystoderma are synonymised with C. carcharias and three species with C. jasonis, distinguishing the synonymised taxa as varieties of these accepted species. Analyses of partial LSU rDNA sequences revealed Cystoderma and Cystodermella as distinct monophyletic genera, with Ripartitella representing a well-supported sister group of the latter. Phaeolepiota aurea represents either an unsupported sister group or member of Cystoderma in the phylogenies based on LSU and ITS sequences rDNA data, respectively. The tribe Cystodermateae sensu Singer did not appear monophyletic according to analyses of LSU sequences. On the basis of these data, the phylogenetic relationships among most of the analyzed genera could not be resolved unequivocally.     

Mrakia terrae sp. nov. and Mrakia soli sp. nov., Two Novel Basidiomycetous Yeast Species Isolated from Soil in Korea

Three strains, YP416^T, YP421^T, and Y422, were isolated from soil samples in Pocheon City, Gyeonggi province, South Korea. The strains belong to two novel yeast species in the genus Mrakia. Molecular phylogenetic analysis showed that the strain YP416^T was closely related to Mrakia niccombsii. Still, it differed by 9 nucleotide substitutions with no gap (1.51%) in the D1/D2 domain of the LSU rRNA gene and 14 nucleotide substitutions with 7 gaps (2.36%) in the ITS region. The strain YP421^T differed from the type strain of the most closely related species, Mrakia aquatica, by 5 nucleotide substitutions with no gap (0.81%) in the D1/D2 domain of the LSU rRNA gene and 9 nucleotide substitutions with one gap (1.43%) in the ITS region. The names Mrakia terrae sp. nov. and Mrakia soli sp. nov. are proposed, with type strains YP416^T (KCTC 27886^T) and YP421^T (KCTC 27890^T), respectively. MycoBank numbers of the strains YP416^T and YP421^T are MB 836844 and MB 836847, respectively.     

A new species of Leptobacillim,L. symbioticum,isolated from mites and sori of soybean rust

A verticillium-like fungus forming a whitish colony and mainly solitary phialides that produced fusiform to cylindrical conidia in chains was isolated from uredinia of Phakopsora pachyrhizi, a causal agent of soybean rust. In addition, two similar looking isolates were obtained from Prostigmata mites. Our taxonomic study based on morphology and phylogenetic analysis using ITS rDNA and LSU rDNA D1/D2 region sequences revealed that the three isolates were the same species and assigned to the genus Leptobacillium. These isolates represent a new species, morphologically and phylogenetically distinguished from the type species, L. leptobactrum, and we propose L. symbioticum sp. nov. In addition, Simplicillium chinense and S. coffeanum are assigned to the genus Leptobacillium.