Phylogeny and diversity of Rigidoporus (Hymenochaetales, Basidiomycota), including three new species from Asia.

Phylogenetic and morphological analyses on Rigidoporus were carried out. The genus Rigidoporus (Hymenochaetales, Basidiomycota), typified by R. microporus (Fr.) Overeem. (synonym Polyporus micromegas Mont.), was established by Murrill in 1905. The genus is mainly characterized by annual to perennial, resupinate, effused-reflexed to pileate or stipitate basidiomata with azonate or concentrically zonate and sulcate upper surface, a monomitic to pseudo-dimitic hyphal structure, simple-septate generative hyphae, and ellipsoid to globose basidiospores. Phylogeny on species of the genus is reconstructed with two loci DNA sequences including the internal transcribed spacer regions and the large subunit. Three new species in Rigidoporus are described and illustrated from Asia, and one new combination in the genus is proposed. The main morphological characteristics of the currently accepted species of Rigidoporus are provided.

Two new species of Scytinostroma (Russulales, Basidiomycota) in Southwest China.

Two new species of Scytinostroma viz. S. acystidiatum and S. macrospermum, are described from southwest China. Phylogeny based on ITS + nLSU dataset demonstrates that samples of the two species form two independent lineages and are different in morphology from the existing species of Scytinostroma. Scytinostroma acystidiatum is characterized by resupinate, coriaceous basidiomata with cream to pale yellow hymenophore, a dimitic hyphal structure with generative hyphae bearing simple septa, the absence of cystidia, and amyloid, broadly ellipsoid basidiospores measuring 4.7-7 × 3.5-4.7 µm. Scytinostroma macrospermum is characterized by resupinate, coriaceous basidiomata with cream to straw yellow hymenophore, a dimitic hyphal structure with generative hyphae bearing simple septa, numerous cystidia embedded or projecting from hymenium, and inamyloid, ellipsoid basidiospores measuring 9-11 × 4.5-5.5 µm. The differences between the new species and morphologically similar and phylogenetically related species are discussed.

[The Structure, Expression, and Non-Canonical Functions of Human rDNA: The Role of Non-Coding Regions].

The genes coding for the rRNAs seem evolutionary conserved on the first glance, but astonish one with their variability in the structure and a variety of functions on closer examination. The non-coding parts of rDNA contain regulatory elements, protein binding sites, pseudogenes, repetitive sequences, and microRNA genes. Ribosomal intergenic spacers are not only in charge with the nucleolus morphology and functioning, namely, the rRNA expression and ribosome biogenesis, but also control nuclear chromatin formation thus mediating cell differentiation. The alterations in the expression of these non-coding regions of rDNA in response to environmental stimuli underlie the keen sense of a cell to various types of stressors. Malfunctioning of this process may result in a wide range of pathologies from oncology to neurodegenerative disease and mental illness. Here, we observe to-date materials on the structure and transcription of the ribosomal intergenic spacer in humans and its role in rRNA expression, in-born disease development, and cancer.

Two new species of Haploporus (Polyporales, Basidiomycota) from China and Ecuador based on morphology and phylogeny.

At present, 25 species are accepted in Haploporus and are distributed in Asia, Europe, North America, South America, Australia, and Africa. In this study, two new species, Haploporus ecuadorensis from Ecuador and H. monomitica from China, are described and illustrated based on morphological examination and phylogenetic analyses. H. ecuadorensis is characterized by annual, resupinate basidiomata with pinkish buff to honey yellow hymenophore when dry, round to angular pores of 2-4 per mm, a dimitic hyphal structure with generative hyphae bearing clamp connections, hyphae at dissepiment edge usually with one or two simple septa, the presence of dendrohyphidia and cystidioles, and oblong to ellipsoid basidiospores measuring 14.9-17.9 × 6.9-8.8 µm. Haploporus monomitica differs from other Haploporus species in that it has a monomitic hyphal system and strongly dextrinoid basidiospores. The differences between the new species and morphologically similar and phylogenetically related species are discussed. In addition, an updated key to 27 species of Haploporus is provided.

Constrictifilum karadense gen. et sp. nov., a new Nostocalean genus from Maharashtra, India.

A freshwater dwelling cyanobacterium (strain MKW3) was isolated from a sample collected from a water logged sugarcane field located in Malkapur, Karad, Maharashtra, India, and was characterized using a polyphasic approach. In the 16S rRNA gene phylogenetic analysis, strain MKW3 clustered with two misidentified strains-Nostoc sp. CENA239 and Calothrix sp. NIES2100. The phylogenetically related members included strains identified as Nostoc, Aulosira, Calothrix, Tolypothrix, Camptylonemopsis and Microchaete. The phylogenetic and the morphological analysis of the strain MKW3 indicated that it does not belong to any of the above mentioned genera. Furthermore, the 16S-23S ITS secondary structure analysis provided clear evidence indicating that strain MKW3 is different from Nostoc sp. CENA239 and Calothrix sp. NIES2100. Based on the morphological, phylogenetic and 16S-23S ITS secondary structure analysis we describe our strain as Constrictifilum karadense gen. et sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.

Concordance of Giardia duodenalis assemblages determined by different PCR methodologies in three observational studies in Cuba.

Giardia duodenalis is one of the most important intestinal parasites globally, especially in children, and in Cuba is the leading cause of chronic paediatric diarrhoea in this population. G. duodenalis is composed of eight genetic groups (or assemblages), two of which (A and B) are apparently zoonotic, occurring in both humans and other animals. However, consensus on the most appropriate genotyping scheme for optimal characterization of G. duodenalis isolates is lacking. In this article we present the results of three descriptive observational studies conducted in Havana, Cuba between 2010 and 2013, with the aim of comparing the results from molecular (PCR) approaches targeting different genes in order to assign with confidence 224 isolates of G. duodenalis to the correct assemblages. In each sub-study, following DNA isolation by the phenol/chloroform/isoamyl alcohol extraction method, PCR targeting the triose phosphate isomerase (tpi) gene was used for molecular characterization, as well as one additional PCR-method targeting another gene or pair of genes. DNA amplification was obtained in 87%, 83%, and 80% in the three sub-studies. Although excellent agreement (kappa index = 1) was recorded between results from some pairs of genes, for other combinations only moderate or substantial agreement was achieved. These results highlight the importance of interpretation of genotyping data, especially when single genetic markers are used. From the results of our studies, PCR targeting a combination of the tpi gene and the intergenic spacer region of rDNA may be a useful approach for the molecular characterization of G. duodenalis isolates.

An overview of Antrodiella and related genera of Polyporales from the Neotropics.

The genus Antrodiella includes resupinate and pileate species of polypores with a dimitic hyphal system, small, globose to cylindrical basidiospores, absence of cystidia, tetrapolar mating system, and haplo-dikaryotic nuclear behavior. Recent studies, however, indicate that Antrodiella is highly polyphyletic, so many of its species have been transferred to other genera. This study reviews the systematic status and diversity of Antrodiella from the Neotropics based, in part, on studies of type specimens. Collections from Brazil were used for molecular analysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), nuc 28S rDNA (28S), and portions of genes encoding translation elongation factor 1-α (tef1) and the second largest subunit of RNA polymerase II (rpb2). Eight genera are confirmed to include Neotropical species treated as Antrodiella in a broad sense: Aegis, Antrodiella s. str., Flaviporus, Metuloidea, Mycorrhaphium, Rickiopora, Trametopsis, and Trullella. Molecular data reveal the occurrence of two new species, described as Antrodiella trivialis, the only Neotropical species of Antrodiella s. str. known so far, and Mycorrhaphium hispidum. In addition, Antrodiella luteocontexta was found to nest in the genus Aegis, close to the Grifolaceae and Polyporaceae; therefore, the new combination Aegis luteocontexta is proposed. Comments on the eight Antrodiella-related genera as well as species with uncertain taxonomic position are provided, together with a key to their identification.

Observations on Texas hypoxylons, including two new Hypoxylon species and widespread environmental isolates of the H. croceum complex identified by a polyphasic approach.

Two new species and a new combination of Hypoxylon from Texas were identified and described based on morphological, multigene phylogenetic (ITS [nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2], 28S [5' 1200 bp of nuc 28S rDNA], RPB2 [partial second largest subunit of the DNA-directed RNA polymerase II], TUB2 [partial ß-tubulin]), and chemotaxonomic data. Hypoxylon olivaceopigmentum is characterized by its pulvinate to glomerate stromata, olivaceous KOH-extractable pigments, equilateral ascospores, and indehiscent perispore. Hypoxylon texense can be distinguished from morphologically similar species by its rust to dark brick KOH-extractable pigments and the high-performance liquid chromatography (HPLC) profile of its stromatal secondary metabolites. Hypoxylon hinnuleum is proposed as the sexual morph of Nodulisporium hinnuleum, featuring dark vinaceous glomerate stromata with dark brick KOH-extractable pigments composed of cohaerin-type azaphilones and smooth equilateral ascospores with indehiscent perispore. Based on these diagnostic characters, H. hinnuleum forms a complex with H. croceum and H. minicroceum. More than 50 ITS sequences with high identity originating from North American and East Asian environmental isolates formed a well-supported clade with the type of N. hinnuleum, demonstrating the widespread distribution of the species complex. In addition, updated descriptions and comprehensive illustrations with detailed information on the diagnostic features of H. fendleri and H. perforatum are provided. The multilocus phylogenetic reconstruction of Hypoxylon supported the status of the new species and broadened the knowledge about intergeneric relationships.

Morphological plasticity in brown-rot fungi: Antrodia is redefined to encompass both poroid and corticioid species.

Most known brown rot-producing species of Polyporales belong to the so-called "Antrodia clade" that largely consists of poroid species. In this study, we use three genetic markers to revise Antrodia s. str., the core group of this clade. We show that a corticioid species with a smooth hymenophore, Phlebia griseoflavescens, belongs to Antrodia s. str. Accordingly, we revise the generic concept of Antrodia s. str. to accommodate this species and two recently described poroid taxa, A. tenerifensis and A. multiformis. In addition, we describe two new poroid species within Antrodia s. str., A. latebrosa from Africa and A. peregrina from East Asia, and provide new documentation for the Southeast Asian species A. parvula based on recent collections from the type location.

Molecular Identification of Anisakis Larvae Extracted by Gastrointestinal Endoscopy from Health Check-up Patients in Korea.

Anisakiasis is a zoonotic disease induced by anisakid nematodes, and endoscopic inspection is used for a diagnosis or remedy for it. Anisakis simplex, Anisakis physeteris, and Pseudoterranova decipiens had been reported to be the major species causing human infections, particularly, in Japan. However, in Korea, recent studies strongly suggested that Anisakis pegreffii is the major species of human infections. To support this suggestion, we collected anisakid larvae (n=20) from 20 human patients who were undergone gastrointestinal endoscopy at a health check-up center in Korea, and molecular identification was performed on the larvae using PCR-RFLP analysis and gene sequencing of rDNA ITS regions and mtDNA cox2. In addition, anisakid larvae (n=53) collected from the sea eel (Astroconger myriaster) were also examined for comparison with those extracted from humans. The results showed that all human samples (100%) were identified as A. pegreffii, whereas 90.7% of the samples from the sea eel were A. pegreffii with the remaining 9.3% being Hysterothylacium aduncum. Our study confirmed that A. pegreffii is the predominant species causing human anisakiasis in Korea, and this seems to be due to the predominance of this larval type in the fish (sea eels) popularly consumed by the Korean people. The possibility of human infection with H. aduncum in Korea is also suggested.

Natural occurrence in Argentina of a new fungal pathogen of cockroaches, Metarhizium argentinense sp. nov.

The aim of this study was to search for entomopathogenic fungi that infect wild cockroaches in forest ecosystems in two protected natural areas of Argentina. Two isolates of Metarhizium argentinense were obtained and identified from wild cockroaches (Blaberidae: Epilamprinae) through the use of morphological characteristics and molecular phylogenetic analyses. This novel species was found in Argentina and is a member of the Metarhizium flavoviride species complex. Phylogenetic analyses, based on sequence similarity analysis using internal transcribed spacer (ITS) and a set of four protein-coding marker sequences (EF1A, RPB1, RPB2 and BTUB), supported the status of this fungus as a new species. In addition, we tested the biological activity of the new species through assays against Blattella germanica nymphs and found that the two evaluated isolates were pathogenic. However, isolate CEP424 was more virulent and caused a confirmed mortality of 76 % with a median lethal time of 7.2 d. This study reports the southernmost worldwide location of a Metarhizium species that infects cockroaches and will help expand the knowledge of the biodiversity of pathogenic fungi of Argentine cockroaches.

Fomitopsis mounceae and F. schrenkii-two new species from North America in the F. pinicola complex.

Two new species, Fomitopsis mounceae and F. schrenkii (Polyporales, Basidiomycota) in the F. pinicola species complex in North America, are described and illustrated. Previous molecular phylogenetic analyses identified three well-delimited lineages that represent F. mounceae and F. ochracea from Canada, the Appalachian Mountains, and the northern United States and F. schrenkii from western and southwestern regions of the United States. Fomitopsis pinicola sensu stricto is restricted to Eurasia and does not occur in North America. Morphological descriptions of basidiocarps and cultures for F. mounceae, F. schrenkii, and F. ochracea are presented. The three species are readily differentiated by nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) sequence, geographic distribution, and basidiospore size. Polyporus ponderosus H. Schrenk is an earlier illegitimate synonym of F. schrenkii. Both F. mounceae and F. schrenkii have a heterothallic multiallelic incompatibility system.

Fungal epidemiology in cystic fibrosis patients with a special focus on Scedosporium species complex.

In this present study, for the first time, we evaluated the cystic fibrosis (CF) patients for the Scedosporium species and their antifungal susceptibility against eight antifungal agents. During one-year period, 90 Sputum samples were collected from Iranian CF patients. All samples were evaluated by direct microscopic examination, culture onto four different media including Malt extract agar, Inhibitory mold agar, Brain Heart Infusion and Scedo-Select III. The mold isolated fungi were identified by PCR-Sequencing of ITS and ß-tubulin genes. In-vitro antifungal susceptibility was performed according to the Clinical & Laboratory Standards Institute (CLSI) M38-A2 guidelines. Out of 90 CF patients, 47 (52.2%) were male. The age of the patients ranged from 1 to 34 years (median of 15.84 ±â€¯7.41 years). Overall, 3 (3.3%) cases were positive for Scedosporium spp. of which two isolates were characterized as Scedosporium boydii and one isolate as S. ellipsoideum. Among Aspergillus genus, A. flavus (29.4%) was the most prevalent species followed by A. tubingensis (24.7%), A. niger (17.0%) and A. fumigatus (14.5%). The minimum effective concentration ranges of micafungin, anidulafungin, and caspofungin were 0.008-0.031 µg/mL, 0.0625-0.25 µg/mL, and 0.0625-0.25 µg/mL, respectively. All isolates of Scedosporium species showed high minimum inhibitory concentration to the triazoles tested, except voriconazole. Our results showed that A. flavus and Scedosporium species are the most prevalent molds isolated from CF patient populations in Iran. Our findings have also showed that Scedo-Select III can be used as a reliable culture media for isolation of Scedosporium spp. in clinical samples.

Allergic Fungal Sinusitis Caused by Exserohilum rostratum and Literature Review.

A case of allergic fungal sinusitis (AFS) caused by Exserohilum rostratum, proven by culture and histopathology of the biopsy material, is described. The identity of the isolate was confirmed by sequencing of ITS region of rDNA. To the best of our knowledge, this is the first report of allergic E. rostratum sinusitis from Kuwait and Arabian Peninsula. Ten previously described cases of AFS have been reviewed. The report highlights the emerging importance of E. rostratum as a human pathogen in this region and role of molecular methods in its accurate identification.

A human subcutaneous infection by Microascus ennothomasiorum sp. nov.

A 60-year-old woman presented with a nodular granulomatous skin lesion on her right thumb. It had developed after inoculation of a splinter of wood. Because it was resistant to various therapies, the nodule was finally excised. Complete healing followed this surgery and a melanised filamentous fungus with scopulariopsis-like morphology was recovered from the dermal tissue. Fitting with no known species, the fungus was subjected to extensive morphological, physiological and genetic investigations. It was characterised by resistance to cycloheximide, growth at 37°C, branched conidiophores with cylindrical annellides in brush-like groups producing dark conidia in basipetal chains, and cleistothecia with ellipsoidal to slightly reniform ascospores. Genetically it clustered in a well-supported clade together with Microascus (M.) brunneosporus, Microascus chinensis, Microascus intricatus, Microascus longicollis, Microascus micronesiensis and Microascus onychoides, but formed an independent branch distant from the other Microascus species. Based on its unique genetic characteristics and morphological findings, the isolate is proposed as a new species, Microascus ennothomasiorum. Morphologically it differs from its phylogenetically closest species by its branched conidiophores and ascomata with a peridium of textura intricata. Our observation once again emphasises that dermal granulomas can be caused by uncommon fungi; diagnostics should therefore include appropriate mycological investigations.

Molecular Characterization and Identification of Stubby Root Nematode Species From Multiple States in the United States.

Stubby root nematodes (SRN) are important plant parasites infecting many crops and widely distributed in many regions of the United States. SRN transmit Tobacco rattle virus, which causes potato corky ringspot disease, thereby having a significant economic impact on the potato industry. In 2015 to 2017, 184 soil samples and 16 nematode suspensions from North Dakota, Minnesota, Idaho, Oregon, Washington, South Carolina, North Carolina, and Florida were assayed for the presence of SRN. SRN were found in 106 soil samples with population densities of 10 to 320 SRN per 200 g of soil and in eight of the nematode suspensions. Sequencing of ribosomal DNA (rDNA) or species-specific polymerase chain reaction assays revealed the presence of four SRN species, including Paratrichodorus allius, P. minor, P. porosus, and Trichodorus obtusus. Accordingly, their rDNA sequences were characterized by analyzing D2-D3 of 28S rDNA, 18S rDNA, and internal transcribed spacer (ITS) rDNA obtained in this study and retrieved from GenBank. Both intra- and interspecies variations were higher in ITS rDNA than 18S rDNA and D2-D3 of 28S rDNA. Based on phylogenetic analysis, the four SRN species formed a monophyletic group, with P. allius more closely related to P. porosus than P. minor and T. obtusus. Indel variation of ITS2 rDNA was present in P. allius populations from the same geographic regions. This study documented the occurrence of SRN species across multiple states. The intra- and interspecies genetic diversity of rDNA in this study will provide more information for understanding the evolutionary relationships of SRN and will be valuable for future studies of SRN species identification and management.

Taxonomy and phylogeny of Pyrrhoderma: a redefinition, the segregation of Fulvoderma, gen. nov., and identifying four new species.

Previously, Pyrrhoderma accommodated two polypore species, P. adamantinum and P. scaurum; however, phylogenetic studies indicated that these two species were not congeneric within the Hymenochaetaceae and that P. adamantinum formed a clade with Phellinidium noxium. To resolve the relationships among the two species of Pyrrhoderma and other related taxa, specimens from China, Costa Rica, Singapore, and Thailand were studied from both morphological and phylogenetic perspectives. A new genus, Fulvoderma, is erected to accommodate F. scaurum comb. nov., and a new species, F. australe (the generic type). Pyrrhoderma is delimited to include the generic type, P. sendaiense (a later synonym of P. adamantinum); two new combinations, P. lamaënse comb. nov., and P. noxium comb. nov.; and three new species, P. hainanense, P. thailandicum, and P. yunnanense. In addition, an undescribed lineage including several specimens from subtropical and tropical forests in China, Costa Rica, Singapore, and Thailand also nested within the Pyrrhoderma clade. However, as the voucher specimens are sterile or almost so, they are not described. The concept of Pyrrhoderma was emended to also accommodate species bearing resupinate, effuse-reflexed basidiocarps, hymenial or hyphoid setae, and non-subglobose basidiospores. Keys to Fulvoderma and Pyrrhoderma are provided.

Effects of Aged Oil Sludge on Soil Physicochemical Properties and Fungal Diversity Revealed by High-Throughput Sequencing Analysis.

The oilfield soil was contaminated for years by large quantities of aged oil sludge generated in the petroleum industry. In this study, physicochemical properties, contents of main pollutants, and fungal diversity of the aged oil sludge-contaminated soil were analyzed. Results revealed that aged oil sludge significantly changed physical and chemical properties of the receiving soil and increased the contents of main pollutants (petroleum hydrocarbons and heavy metals) in soil. Meanwhile, the internal transcribed spacer (ITS) sequencing by Illumina Miseq platform at each taxonomic level demonstrated that the toxicological effect of oil pollutants obviously influenced the fungal diversity and community structure in soil. Moreover, it was found that the presence of three genera (Cephalotheca, Lecanicillium, and Septoriella) appeared in aged oil sludge-contaminated soil. And oil pollutants promoted the growth of certain genera in Ascomycota (70.83%) and Basidiomycota (10.78%), such as Venturia, Alternaria, and Piloderma. Nevertheless, the growth of Mortierella (9.16%), Emericella (6.02%), and Bjerkandera (0.00%) was intensively limited. This study would aid thorough understanding of microbial diversity in oil-contaminated soil and thus provide new point of view to soil bioremediation.

An endophytic strain of genus Paenibacillus isolated from the fruits of Noni (Morinda citrifolia L.) has antagonistic activity against a Noni's pathogenic strain of genus Aspergillus.

Endophytes are microbes capable of colonizing the tissues of healthy plants and subsequently establishing a harmonious relationship with their hosts. In this research, the endophytic strain Paenibacillus sp. NEB was isolated from fruits of healthy Noni (Morinda citrifolia L.). Strain NEB was identified as Paenibacillus polymyxa using MALDI-TOF Mass Spectrometry. Pathogenic fungal strain NP-1 was isolated from Noni fruits infected by smut, and was identified as Aspergillus aculeatus by polyphasic taxonomy basing on morphological identification, and ITS-5.8S rDNA and ß-tubulin gene phylogenetic analyses. Through the antagonistic test against the pathogenic strain Aspergillus aculeatus NP-1, the results showed that strain NEB had a good antagonistic activity against smut pathogen of Noni. By sequencing with Illumina HiSeq 2000, the draft genome of Paenibacillus sp. NEB was acquired, and 3 CDSs for glucanases were annotated and potentially correlated to the antagonistic activity of this strain. Using realtime-PCR method with specific primers to amplify the biocontrol gene, ß-1,3-1,4- glucanase gene (gluB), it was found in Paenibacillus polymyxa NEB. This study would provide a theoretical and microbial basis for the rationally developing and using Noni beneficial microbial inoculants against its pathogenic strain in the future.

A Case of Conjunctival Ulcer and Uveitis Caused by Acrophialophora Sp. in an Immunocompromised Patient: a Case Report and Riterature Review.

We report the first case of invasive ophthalmologic infection by Acrophialophora sp. that was successfully treated using voriconazole (VRCZ). Acrophialophora spp., which has been reported to be an opportunistic pathogen, is a rare thermotolerant soil fungus, but its pathogenicity remains unclear. A 77-year-old man had neutropenia and prostate carcinoma and was receiving hemodialysis. His right eye had been infected for 2 days. His conjunctiva was congested, and it partially formed an abscess. Liposomal amphotericin B (L-AMB) was administered following systemic itraconazole. However, the treatment was changed from L-AMB to systemic VRCZ and VRCZ eye drops because his eye symptoms worsened. Subsequently, his symptoms stabilized and his vision was maintained. Acrophialophora sp. was identified by analyzing regions of internal transcribed spacer and domain 1 and 2 of the ribosomal RNA gene. He completed the 7-week systemic VRCZ course. The mean minimum inhibitory concentration of VRCZ for Acrophialophora spp. has been reported to be the lowest among various antifungal agents, and our results indicated the efficacy of VRCZ treatment for Acrophialophora sp. infection. Our results suggest that invasive Acrophialophora sp. infection may require long-term therapy. Further analysis of the clinical spectrum of Acrophialophora spp. infection and adequate treatment methods are required in the future.