Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium

Phenotypic and chemotaxonomic characteristics of five isolates of acetylenereducing (nitrogen-fixing) oligotrophic bacteria from a paddy soil were investigated. They showed similar phenotypic characteristics: they were aerobic, asporogenous, gram-negative, motile by a polar flagellum, and irregular rods. On full strength nutrient broth (NB) growth was severely suppressed, but well supported on 10-to 10000-fold diluted NB. They consumed glucose but produced no acid, and also utilized phenolic acids such as ferulic acid or p-coumaric acid. The cellular fatty acid composition, quinone system and DNA base composition of the isolates were investigated. Cellular fatty acids mainly consisted of straightchain unsaturated C_{18 : 1} (62–81% of total fatty acids). Ubiquinone Q-10 and a high guanine-plus-cytosine content (65.1–66.0 mol%) were found. The taxonomic status of the isolates is discussed and a new genus, Agromonas, with a single species Agromonas oligotrophica sp. nov., is proposed for these isolates. The type strain of A. oligotrophica is JCM 1494.     

Molecular and morphological data reveal two new species of Scolecobasidium

Two species of Scolecobasidium were isolated from soil in Hainan and Hebei Provinces, China. The two taxa develop broadly ellipsoid conidia and ellipsoidal to oblong conidia, respectively. Their taxonomic placement in Scolecobasidium was confirmed by morphological similarity and phylogenetic analysis of the RNA polymerase II subunit b (RPB2) sequence data. The two fungi, which are morphologically distinct to previously described species, and occupy unique positions in the phylogenetic tree, are thus introduced as the new species Scolecobasidium terricola and S. ellipsoideum. They are described and illustrated and compared with similar species in the genus.     

Cookeina cremeirosea,a new species of cup fungus from the South Pacific

A new species in the Sarcoscyphaceae from the Samoan Islands, Cookeina cremeirosea, is described and illustrated. This species is morphologically and phylogenetically distinct from the other eight species that are currently accepted for the genus. It is closely related to the Asian species Cookeina indica from which it can be separated by color and spore morphology.     

A new species of the genus Trematosphaeria from China

A new species of the genus Trematosphaeria was isolated and identified from the soil in Jiuzhaigou Nature Reserve, southwestern China. The new taxon was studied based on morphological characters and phylogenetic analyses of three nuclear loci, i.e., the internal transcribed spacer rDNA operon (ITS), and large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA). The analyzed Trematosphaeria species were clustered in several clades within the Pleosporales and the genus was shown to be polyphyletic. The new species is introduced as Trematosphaeria terricola, and it is characterized by short-papillate ascomata with suborbicular ostiolum, 3-septate, cinnamon-brown, fusiform ascospores with narrowly rounded ends, verruculose at maturity. Trematosphaeria terricola is compared with morphologically similar species T. confusa, T. mangrovis, and T. pertusa, which differ from the former species in the number of septa, and the shape and size of the ascospores with or without a sheath. This is the first report of a Trematosphaeria isolate from alpine soil in China.     

Polyphasic characterisation of three novel species of <Emphasis Type="Italic">Paraboeremia</Emphasis>

Paraboeremia was recently introduced for a distinct lineage in the family Didymellaceae. Currently, three species are included, i.e. P. adianticola, P. putaminum and P. selaginellae, all of which are plant pathogens. Paraboeremia is morphologically similar to Phoma but phylogenetically distinct. In this paper, three new species, i.e. Paraboeremia camelliae isolated from Camellia sp., P. litseae from Litsea sp., and P. oligotrophica from cave limestone, are described, illustrated and compared with closely related taxa. Phylogenetic analysis based on the multi-locus sequences of the internal transcribed spacer regions 1 and 2 and 5.8S nuclear ribosomal RNA gene (ITS), partial large subunit 28S nrDNA region (LSU), partial β-tubulin (TUB2) gene and RNA polymerase II (RPB2) gene regions confirmed the distinction of these species in Paraboeremia. These three new species were discovered from habitats and hosts that are previously unknown from this genus.     

Molecular systematics and taxonomic overview of the bird's nest fungi (Nidulariaceae)

Fungi in the Nidulariaceae, otherwise known as ‘bird's nest fungi’, are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.     

Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats,India

A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members—R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8–2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats.     

Molecular evidence of cryptic diversity in Paracaryophyllaeus (Cestoda: Caryophyllidea), parasites of loaches (Cobitidae) in Eurasia,including description of P. vladkae n. sp.

Molecular phylogenetic analysis of an extensive collection of monozoic tapeworms of the genus Paracaryophyllaeus Kulakovskaya, 1961 (Cestoda: Caryophyllidea), parasites of loaches (Cypriniformes: Cobitidae) in Eurasia, has revealed cryptic species diversity within this long-time monotypic genus, especially in the Paracaryophyllaeus gotoi (Motomura, 1927) species complex [syn. Paracaryophyllaeus dubininorum (Kulakovskaya, 1961); type species]. Three independent, well-supported clades were discovered on the basis of molecular data: (i) specimens from Misgurnus anguillicaudatus and Cobitis lutheri from China, Russian Far East and Japan — called herein P. cf. gotoi 1, which may be conspecific with P. gotoi (Motomura, 1927), although in the absence of sequence data for P. gotoi from its type locality (basin of the River Kumkan in Korea), no certain inferences about their identity can currently be made; (ii) specimens from M. anguillicaudatus from China and Japan — P. cf. gotoi 2, which are morphologically indistinguishable from those of P. cf. gotoi 1; and (iii) morphologically distinct tapeworms from the endemic loach Cobitis bilseli from southwestern Turkey (Beyşehir Lake), which are described herein as a new species. Paracaryophyllaeus vladkae Scholz, Oros and Aydoğdu n. sp. differs from the remaining species of the genus in the following characteristics: the testes begin anterior to the first vitelline follicles (versus posterior), the body is short and robust (versus more elongate and slender), and the scolex is wide, rounded or apically tapered (versus claviform to truncate). Species composition of the genus, host specificity of species and geographical distribution are briefly discussed.     

The genus Galumna in Nepalese oribatid mite fauna,with notes on systematic placement of some species (Acari,Oribatida, Galumnidae)

The oribatid mite genus Galumna (Oribatida, Galumnidae) is recorded for the first time in Nepal. A new species, Galumna tetraporosa sp. n., is described from soil of secondary mixed broadleaved forest. It is most similar morphologically to G. tokyoensis Aoki, 1966 and G. valida Aoki, 1994, however, it differs from both by the absence of interlamellar setae and the presence of two pairs of notogastral porose areas Aa. Galumna granalata Aoki, 1984 is redescribed on the basis of specimens from Nepal. Galumna floridae (Jacot, 1929) and G. hexagona Balogh, 1960 are transferred to the genus Notogalumna; G. mauritii Mahunka, 1978 is transferred to the genus Dimidiogalumna.     

Molecular Phylogenetic Analysis Reveals the New Genus Hemisphaericaspora of the Family Debaryomycetaceae

Four strains of a novel ascomycetous yeast species were recovered from the frass of wood-boring beetles collected from the Baotianman Nature Reserve and the Laojieling Nature Reserve in Henan Province, China. This species produced unconjugated and deliquescent asci with hemispheroid or helmet-shaped ascospores. Analysis of gene sequences for the D1/D2 domain of the large subunit (LSU) rRNA, as well as analysis of concatenated gene sequences for the nearly complete small subunit (SSU) rRNA and D1/D2 domain of the large subunit (LSU) rRNA placed the novel species in a small clade including only one recognised species, Candida insectamans, in the family Debaryomycetaceae (Saccharomycotina, Ascomycota). DNA sequence analyses demonstrated that the novel species was distinct from all currently recognised teleomorphic yeast genus. The name Hemisphaericaspora nanyangensis gen nov., sp. nov. is proposed to accommodate the novel genus and species. The new genus can be distinguished from closely related teleomorphic genera Lodderomyces and Spathaspora through sequence comparison and ascospore morphology. The ex-type strain of H. nanyangensis is CBS 13020^T ( = CICC 33021 = NYNU 13717). Furthermore, based on phenotypic and genotypic characteristics, C. insectamans is transferred to the newly described genus as Hemisphaericaspora insectamans comb. nov., in accordance with the changes in the International Code of Nomenclature for algae, fungi and plants.     

Highly diversified fungi are associated with the achlorophyllous orchid Gastrodia flavilabella

Background

Mycoheterotrophic orchids are achlorophyllous plants that obtain carbon and nutrients from their mycorrhizal fungi. They often show strong preferential association with certain fungi and may obtain nutrients from surrounding photosynthetic plants through ectomycorrhizal fungi. Gastrodia is a large genus of mycoheterotrophic orchids in Asia, but Gastrodia species’ association with fungi has not been well studied. We asked two questions: (1) whether certain fungi were preferentially associated with G. flavilabella, which is an orchid in Taiwan and (2) whether fungal associations of G. flavilabella were affected by the composition of fungi in the environment.

Results

Using next-generation sequencing, we studied the fungal communities in the tubers of Gastrodia flavilabella and the surrounding soil. We found (1) highly diversified fungi in the G. flavilabella tubers, (2) that Mycena species were the predominant fungi in the tubers but minor in the surrounding soil, and (3) the fungal communities in the G. flavilabella tubers were clearly distinct from those in the surrounding soil. We also found that the fungal composition in soil can change quickly with distance.

Conclusions

G. flavilabella was associated with many more fungi than previously thought. Among the fungi in the tuber of G. flavilabella, Mycena species were predominant, different from the previous finding that adult G. elata depends on Armillaria species for nutritional supply. Moreover, the preferential fungus association of G. flavilabella was not significantly influenced by the composition of fungi in the environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1422-7) contains supplementary material, which is available to authorized users.     

Myxotrichum albicans,a new slowly-growing species isolated from forest litters in China

Myxotrichum albicans sp. nov. is a slowly-growing fungal species that was isolated from forest litters in northeast of China. The new species is morphologically characterized by its white colonies on CMA, PCA, PDA, and YMA, thallic conidiogenous cells, simple, catenate and hyaline conidia. Phylogenetic analysis based on internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences also supported the placement of M. albicans as a new species in the genus Myxotrichum. To compare with related species, the optimal pH and temperature for growth were investigated. The differences among Myxotrichum (Oidiodendron) species producing hyaline conidia were discussed.     

Phylogenetic analysis of <Emphasis Type="Italic">Plectosphaerella</Emphasis> species based on multi-locus DNA sequences and description of <Emphasis Type="Italic">P. sinensis</Emphasis> sp. nov.

Species in Plectosphaerella are well known as pathogens of several plant species causing fruit, root and collar rot and collapse. In an investigation of endophytic fungi associated with cucurbit plants in China, we isolated 77 strains belonging to the genus Plectosphaerella. To identify the isolated strains, we collected the type or reference strains of all currently accepted species in Plectosphaerella except P. oratosquillae and conducted a phylogenetic analysis. Phylogenetic analysis of the partial 28S rDNA sequences showed that all species in Plectosphaerella were located in one clade of Plectosphaerellaceae. Based on multi-locus phylogenetic analysis of the ITS, CaM, EF1, TUB and morphological characteristics, all species in Plectosphaerella were well separated. Three endophytic strains from stems of Cucurbita moschata, Citrullus lanatus and Cucumis melo from North China were assigned to a new species described as P. sinensis in this paper. The new species differs morphologically from other Plectosphaerella species by irregular chlamydospores, and the dimensions of phialides and conidia. The other endophytic strains from several cucurbit plants were identified as P. cucumerina.     

18S rRNA Gene Variation among Common Airborne Fungi, and Development of Specific Oligonucleotide Probes for the Detection of Fungal Isolates

In this study, we sequenced 18S rRNA genes (rDNA) from 49 fungal strains representing 31 species from 15 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence analysis revealed distinct divergence between Zygomycota and Ascomycota. Within Ascomycota, several strongly supported clades were identified that facilitate the taxonomic placement of several little-studied fungi. Wallemia appeared as the group most diverged from all the other Ascomycota species. Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study. After homology searches and DNA hybridization evaluations, 33 probes were verified as genus or species specific. The optimal hybridization temperatures to achieve the best specificity for these 33 probes were determined. These new probes can contribute to the molecular diagnostic research for environmental monitoring.     

Six new species of Pythiogeton in Taiwan,with an account of the molecular phylogeny of this genus

Pythiogeton is a little-studied genus of pythialean Oomycete. The genus is characterized by producing its zoospores outside of the sporangium within an apparently naked protoplasmic mass, which formed from a discharge tube-vesicle complex. A total of nine morphologically distinct Pythiogeton species were identified, of which six were new species (Pythiogeton abundans, Pythiogeton microzoosporum, Pythiogeton oblongilobum, Pythiogeton paucisporum, Pythiogeton proliferatum, and Pythiogeton puliensis). A phylogenetic analysis based on internal transcribed spacer sequences revealed that all isolates of Pythiogeton formed a highly supported clade, nested within the wider clade of Pythium species. Each newly recognized Pythiogeton species that was established on the basis of morphological characters was found to occur in a well-supported subgroup within the Pythiogeton clade, confirming their assignment to new species. Pythiogeton shares a common ancestor with the monophyletic group of Pythium species that have predominantly filamentous sporangia rather than with the separate clade of Pythium species that have predominantly globose or ovoid sporangia. This study confirms that Pythium is an extremely heterogenous and polyphyletic genus containing a number of distinct clades of species, including Pythiogeton, which possess morphologically distinguishable characters. A synoptic key to all the described Pythiogeton species is provided.     

Taxonomy and chemical characterization of new antibiotics produced by Saccharothrix SA198 isolated from a Saharan soil

Actinomycete strain SA198, isolated from a Saharan soil sample of Algeria, exhibited antimicrobial activity against Gram-positive and Gram-negative bacteria, and phytopathogenic and toxinogenic fungi. The morphological and chemotaxonomic characteristics of the strain were consistent with those of the genus Saccharothrix. Analysis of the 16S rRNA gene sequence of strain SA198 showed a similarity level ranging between 97.2 and 98.8% within Saccharothrix species, S. australiensis being the most closely related. Two new active products were isolated by reverse HPLC using a C18 column. The ultraviolet–visible (UV–VIS), infrared (IR), mass, and ¹H and ¹⁴C nuclear magnetic resonance (NMR) spectra showed that these products were new bioactive compounds. The minimum inhibitory concentrations of these antibiotics showed a strong activity against fungi and moderate activities against Gram-positive and Gram-negative bacteria.     

Taxonomy and phylogeny of Ceriporia (Polyporales,Basidiomycota) with an emphasis of Chinese collections

Ceriporia accommodates a kind of wood-inhabiting polypores producing resupinate basidiocarps and causing a white rot. More than 30 species of this genus have been described; however, only a few species were referred to molecular phylogeny. In this study, a total of 203 specimens of Ceriporia were studied morphologically, and the ITS and/or nLSU regions from 42 samples, representing 18 species, were sequenced for phylogenetic analysis. Based on both morphological and phylogenetic analyses, three new species of Ceriporia, C. bubalinomarginata, C. pseudocystidiata and C. variegata, are described and illustrated. An annotated identification key is provided for all 20 species of this genus thus far known in China. Our phylogeny shows that (1) Ceriporia is not monophyletic, (2) C. spissa and C. viridans as morphologically circumscribed are polyphyletic, (3) C. inflata is retained for both C. inflata and C. jiangxiensis, and (4) presence or absence of hymenial cystidia is not a useful character in delimiting species relationships in Ceriporia.     

A new meristematic fungus,Pseudotaeniolina globosa

A new species of Pseudotaeniolina, a genus of anamorphic, melanized fungi with meristematic development, is described. The species is compared to morphologically similar taxa among which are Trimmatostroma and Coniosporium. Its novelty is supported by SSU (small subunit) and ITS (internal transcribed spacer) rDNA sequence data. This revised version was published online in June 2006 with corrections to the Cover Date.     

The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often found to reflect the structure of phylogenies based on molecular data, many species remain of uncertain placement due to a lack of reliable data or conflicting morphological characters. A rigid, darkly pigmented stipe and the production of a Hirsutella-like anamorph in culture were taken as evidence for the transfer of the species Cordyceps cuboidea, Cordyceps prolifica, and Cordyceps ryogamiensis to the genus Ophiocordyceps. Data from ribosomal DNA supported these species as a single group, but were unable to infer deeper relationships in Hypocreales. Here, molecular data for ribosomal and protein coding DNA from specimens of Ophiocordyceps cuboidea, Ophiocordyceps ryogamiensis, Ophiocordyceps paracuboidea, Ophiocordyceps prolifica, Cordyceps ramosopulvinata, Cordyceps nipponica, and isolates of Polycephalomyces were combined with a broadly sampled dataset of Hypocreales. Phylogenetic analyses of these data revealed that these species represent a clade distinct from the other clavicipitoid genera. Applying the recently adopted single system of nomenclature, new taxonomic combinations are proposed for these species in the genus Polycephalomyces, which has been historically reserved for asexual or anamorphic taxa.     

Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil

To take full advantage of biochar as a soil amendment, the objective of this study was to investigate the effects of biochar addition on soil bacterial and fungal diversity and community composition. Incubation experiments with a forest soil (a red oxidized loam soil) with and without biochar amendment were conducted for 96 days. The culture-independent molecular method was utilized to analyze soil bacterial and fungal species after the incubation experiments. Results showed that bacteria and fungi responded differently to the biochar addition during the short-term soil incubation. Twenty four and 18 bacterial genara were observed in the biochar amended and unamended soils, respectively, whereas 11 and 8 fungal genera were observed in the biochar amended and unamended soils, respectively. Microbial taxa analysis indicated that the biochar amendment resulted in significant shifts in both bacterial and fungal taxa during the incubation period. The shift for bacteria occurred at the genus and phylum levels, while for fungi only at the genus level. Specific taxa, such as Actinobacteria of bacteria and Trichoderma and Paecilomyces of fungi, were enriched in the biochar amended soil. The results reveal a pronounced impact of biochar on soil microbial community composition and an enrichment of key bacterial and fungal taxa in the soil during the short time period.