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A 68-year-old woman was submitted to our hospital because of erythematous and scaly skin lesions. To exclude tinea samples of stratum corneum were collected and used for mycological investigations. In this material, no fungal elements were detected microscopically, but inoculation on Sabouraud agar with cycloheximide yielded a presumptive dermatophyte fungus. Subsequent detailed investigations with conventional morphological and physiological methods and a phylogenetic analysis of the combined LSU rRNA gene (D1/D2 domains) and ITS region sequences suggested that the fungus represents a hitherto undescribed species of the genus Arthroderma. Here, we describe this species as Arthroderma chiloniense sp. nov., EMBL accession no. LT992885. This new species can be distinguished from phylogenetically related Arthroderma species using ribosomal ITS and LSU genes, and 60S L10 protein sequences; specific macroscopic, microscopic and physiological features are lacking. Our attempts to re-isolate this fungus from the patient's skin failed although her skin lesions persisted. Most likely A. chiloniense is a geophilic species that incidentally contaminated or transiently colonised the patient's skin. To avoid diagnostic misinterpretations, it is necessary to distinguish A. chiloniense from truly pathogenic dermatophytes like Trichophyton (T.) rubrum and T. interdigitale which can easily be confused with A. chiloniense based on similar mycelium morphology., (© 2018 Blackwell Verlag GmbH.)

An alarming pan Indian increase in the incidence of superficial dermatophytosis has been noticed over the past 5-6 years. Recent studies have demonstrated emerging predominance of Trichophyton (T.) mentagrophytes as the causative organism in such cases. Interestingly, a distinct Indian genotype of T. mentagrophytes has been identified and recognised with the help of sequencing of the ITS region of the rDNA. That has, however, led to a basic confusion owing to the newly introduced taxonomy of dermatophytes in 2017. According to this most recently suggested classification and new taxonomy of dermatophytes, the former "T. mentagrophytes complex" is differentiated into T. mentagrophytes (zoophilic strains) and T. interdigitale (anthropophilic strains). We have noticed that in some recent studies the causative agent of the chronic, relapsing dermatophytosis outbreak in India has been described as T. interdigitale. In our opinion, it is very likely that these T. interdigitale strains isolated in Delhi and Chennai in India are indeed strains more closely related to the neotype of T. mentagrophytes and not strains of T. interdigitale. We therefore want to underscore the importance of a common nomenclature of species in accordance with the new taxonomy of dermatophytes. This would most likely facilitate better understanding of the issue amongst dermatologists and microbiologists in general. Mistaken identification of Trichophyton isolates not limited to India is very likely to occur due to the lack of appropriate molecular diagnosis which in turn is based on the already published data that presumably wrongly identify one species instead of the other., (© 2018 Blackwell Verlag GmbH.)

The fungal community of six sand samples from Saudi Arabia and Jordan deserts was characterized by culture-independent analysis via next generation sequencing of the 18S rRNA genes and by culture-dependent methods followed by sequencing of internal transcribed spacer (ITS) region. By 18S sequencing were identified from 163 to 507 OTUs per sample, with a percentage of fungi ranging from 3.5% to 82.7%. The identified fungal Phyla were Ascomycota, Basal fungi, and Basidiomycota and the most abundant detected classes were Dothideomycetes, Pezizomycetes, and Sordariomycetes. A total of 11 colonies of filamentous fungi were isolated and cultured from six samples, and the ITS sequencing pointed toward five different species of the class Sordariomycetes, belonging to genera Fusarium (F. redolens, F. solani, F. equiseti), Chaetomium (C. madrasense), and Albifimbria (A. terrestris). The results of this study show an unexpectedly large fungal biodiversity in the Middle East desert sand and their possible role and implications on human health., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets., (© 2018 John Wiley & Sons Ltd.)

Plant deaths had been observed in the sub-alpine and alpine areas of Australia. Although no detailed aetiology was established, patches of dying vegetation and progressive thinning of canopy suggested the involvement of root pathogens. Baiting of roots and associated rhizosphere soil from surveys conducted in mountainous regions New South Wales and Tasmania resulted in the isolation of eight Phytophthora species; Phytophthora cactorum, Phytophthora cryptogea, Phytophthora fallax, Phytophthora gonapodyides, Phytophthora gregata, Phytophthora pseudocryptogea, and two new species, Phytophthora cacuminis sp. nov and Phytophthora oreophila sp. nov, described here. P. cacuminis sp. nov is closely related to P. fallax, and was isolated from asymptomatic Eucalyptus coccifera and species from the family Proteaceae in Mount Field NP in Tasmania. P. oreophila sp. nov, was isolated from a disturbed alpine herbfield in Kosciuzsko National Park. The low cardinal temperature for growth of the new species suggest they are well adapted to survive under these conditions, and should be regarded as potential threats to the diverse flora of sub-alpine/alpine ecosystems. P. gregata and P. cryptogea have already been implicated in poor plant health. Tests on a range of alpine/subalpine plant species are now needed to determine their pathogenicity, host range and invasive potential., (Copyright © 2018 British Mycological Society. All rights reserved.)

Aided by a host of bioinformatics tools, primary and secondary structural analyses of the internal transcribed spacer 2 (ITS2) from the eukaryotic ribosomal RNA repeat have a long and enviable record of service to diversity studies of fungi, plants and protists. Automation of annotation, secondary structure estimation and sequence alignment have become routine for the vast majority of ITS2 sequences. Challenges to the bioinformatics pipeline for ITS2 analysis generally arise in cases where the sequence length lies well outside the norm. These sequences generally defy protocols for annotation and secondary structure prediction. The long ITS2 sequences (ca. 600 nucleotides) from the green alga, Jenufa, offered an opportunity to explore this problem. Custom BLAST parameters revealed the presence of 4-helix structures (200-250 nucleotides) embedded in the 5' portion of several long ITS2 sequences of Jenufa. Of special note is the ITS2 sequence of J. lobulosa where a 4-helix structure was obtained for both the embedded ITS2 and for the complete sequence. Phylogenetic analysis of these typically-sized sequences resolved Golenkinia longispicula as the sister to Jenufa. Our observations indicate that other long ITS2 sequences should be examined for evidence of expansion or duplication. In addition, if the embedded ITS2 sequences are functional, then ribogenesis is almost certainly more diverse than is already apparent from studies of humans and yeast., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The protozoan parasite Sarcocystis falcatula is an important cause of clinical disease in several avian intermediate hosts. The host range of S. falcatula is wide, and numerous outbreaks of acute sarcocystosis have been reported in passerine and psittacine birds in captivity in the Americas. Previous diagnosis was performed by serologic methods, light, and/or electron microscopic examinations with limited molecular confirmation. Here, we report histological and molecular diagnosis of acute, fatal S. falcatula infections in rainbow lorikeets ( Trichoglossus moluccanus) at the Philadelphia Zoo. Pulmonary sarcocystosis was suspected antemortem in 3 lorikeets (3-5 yr old); these birds died despite antiprotozoal therapy. The predominant lesion was pneumonia associated with S. falcatula-like schizonts in pulmonary vascular endothelium. The multilocus PCR-DNA sequencing ( 18S rDNA, 28S rDNA, ITS-1, and cox1) of frozen lung tissue confirmed S. falcatula infections in all 3 birds. Our results and previous studies suggest that acute pulmonary form of sarcocystosis is a major contributor of death to Old World psittacine birds.

A novel biflagellate protist that consumed chloroplasts inside material of the invasive marine green alga Codium fragile was reported from the U.S. east coast in 2003. We observed a similar association in C. fragile from five sites in Nova Scotia, Canada during 2013 and 2014. After incubating Codium fragments for 2-3 days, some utricles and filaments contained numerous chloroplast-consuming cells. Transmission electron microscopy (TEM) confirmed that these were kinetoplastids with a pankinetoplast, large electron-dense droplets in the cytoplasm and a connective between the paraxonemal rod bases, but no conspicuous para-cytopharyngeal rod, all consistent with U.S. material observed in 2003. The ITS1-5.8S rRNA-ITS2 sequences from 13 Nova Scotia isolates were identical. SSU rRNA gene phylogenies placed the Codium-associated kinetoplastid in neobodonid clade '1E'. Clade 1E likely contains no previously described species, and branches outside all other major neobodonid groups, either as their sister or as a separate lineage, depending on rooting. These results indicate that the kinetoplastid represents a single species that merits a new genus (and family), and we describe it as Allobodo chlorophagus n. gen., n. sp. The lack of evidence for food sources other than Codium is consistent with a parasitic association, but other possibilities exist (e.g. necrotrophy)., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

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 β-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, β-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., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

This study was carried out to determine the pathogen-causing diarrhoea in sheep Ovis aries in the Qinghai Tibetan Plateau Area, China. A trophozoite was identified as species of ciliate alveolates infecting the sheep based on morphological characteristics examined by microscope. It was mostly spherical, colourless and transparent, with many vesicles. Macronucleus and contractile vacuoles could not be distinguished. Size of the trophozoite was 80-180 × 70-150 μm and its surface was covered with cilia. Molecular analysis based on sequences of 18S rRNA and ITS genes confirmed the ciliate species as Balantidium coli. According to the literature, there have been many epidemiological investigations of B. coli infection in pigs, monkeys and humans. To our knowledge, this was the first report of B. coli infections in sheep in the Qinghai Tibetan Plateau Area of China, or eleswhere around the world. Importantly, the sheep case was rare but raised our concern that B. coli may spread across species and expand its host range.

Ophiostoma spp. (Ophiostomatales, Ascomycota) are well-known fungi associated with bark and ambrosia beetles (Curculionidae: Scolytinae, Platypodinae). Fungi in the Ophiostomatales include serious tree pathogens as well as agents of timber blue-stain. Although these fungi have been extensively studied in the northern hemisphere, very little is known regarding their occurrence on hardwoods in Europe. The aims of the present study were to identify and characterize new Ophiostoma spp. associated with bark and ambrosia beetles infesting hardwoods in Norway and Poland, and to resolve phylogenetic relationships of Ophiostoma spp. related to the Norwegian and Polish isolates, using multigene phylogenetic analyses. Results obtained from five gene regions (ITS, LSU, β-tubulin, calmodulin, translation elongation factor 1-α) revealed four new Ophiostoma spp. These include Ophiostoma hylesinum sp. nov., O. signatum sp. nov., and O. villosum sp. nov. that phylogenetically are positioned within the Ophiostoma ulmi complex. The other new species, Ophiostoma pseudokarelicum sp. nov. reside along with Ophiostoma karelicum in a discrete, well-supported phylogenetic group in Ophiostoma s. stricto. The results of this study clearly show that the diversity and ecology of Ophiostoma spp. on hardwoods in Europe is poorly understood and that further studies are required to enrich our knowledge about these fungi., (Copyright © 2018. Published by Elsevier Ltd.)

Chromoblastomycosis is one of the most prevalent implantation fungal infections caused by melanized fungi, affecting individuals with certain risk factors with high morbidity due to its recalcitrant nature. It is difficult to identify the etiological agents and thus a suitable reproductive molecular identification method applicable in developing countries has been investigated. We report the identification of four different fungal causative agents of chromoblastomycosis by reverse line blotting hybridization (RLB) based on biotin-labeled PCR products and amine labeled probes to hybridize. Sixty five reference strains, including type strains, i.e. Fonsecaea pedrosoi, F. monophora, F. nubica, and Phialophora verrucosa, obtained from the CBS-KNAW were included in this study. Internal transcribed spacer 1 (ITS1) regions of relevant species were aligned and adjusted using BIONUMERICS v. 4.61 in order to design four specific probes to identify informative nucleotide polymorphisms. The final identification of these species by RLB assay was concordant with ITS sequencing and showed 100% specificity with no cross hybridization, able to identify all tested strains. The time and cost were less compare to other routine identification methods such as sequencing. This assay allows sensitive and specific simultaneous detection and identification of a different fungal species., (Copyright © 2018. Published by Elsevier Ltd.)

Background: Candida parapsilosis is a common agent of fungaemia, but few outbreaks of Candida parapsilosis infection have been reported in China., Aim: To elaborate an outbreak of nosocomial Candida parapsilosis sensu stricto fungaemia in a neonatal intensive care unit (NICU) of a comprehensive hospital in China from July to October 2017., Methods: Epidemics and characteristics of fungaemia cases were investigated. Surveillance samples were collected. Vitek 2 Compact System, internal transcribed spacer sequencing, and random amplified polymorphic DNA (RAPD) typing were conducted to identify the isolates. Antifungal susceptibility test was performed for all bloodstream isolates., Findings: Sixteen neonates were diagnosed as Candida parapsilosis sensu stricto fungaemia during this period. Presenting symptoms included leucopenia, thrombocytopenia, and respiratory crackles. Fifteen cases were cured whereas one case who suffered from severe concomitant diseases died. The isolates were susceptible to fluconazole, amphotericin B, itraconazole, voriconazole, and 5-fluorocytosine. A total of 313 surveillance samples were collected, and Candida parapsilosis sensu stricto was identified from 16 environmental samples and one sample from an ultrasonographer's hand. The colonized locations included wiping cloths, faucets, sinks, operating table, puddles in the bathroom, a ventilator, and an ultrasonic probe. The RAPD patterns of all the Candida parapsilosis sensu stricto isolates from bloodstream and surveillance samples were identical. The outbreak was controlled after a series of infection control measures., Conclusion: Contaminated environment was associated with this outbreak. Close attention to immunocompromised patients, thorough environmental disinfection and hand hygiene should be strengthened in NICU., (Copyright © 2018 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

In 1983, Hasle and colleagues removed cymatosiroid diatoms from the pennates, and erected a new centric diatom family, the Cymatosiraceae, mainly to accommodate for their newly discovered mode of sexual reproduction. The new family consisted of two subfamilies differing in frustule structure. The family was later elevated to the rank of Order Cymatosirales Round and Crawford. We revisited intra-ordinal relationships within Cymatosirales using combined genetic (DNA sequences), morphological (valve and frustule structure), and reproductive (auxospore type) characters. In total, 36 cymatosiroid strains from 19 species representing 13 genera (80% of the total number of extant genera; nine of them represented by their generitypes) were used in this study. Instead of only the commonly used loci (18S rRNA and plastidal genes) to infer diatom phylogeny, we developed a consensus secondary structure model of the Internal Transcribed Spacer 2 (ITS2) for this order and applied it to aid in sequence alignments for ITS2. This improved the alignment and thus the robustness of the phylogenetic framework. The compensatory base changes (CBCs) found in ITS2 secondary structures were mapped onto the multi-gene (18S rRNA + ITS2 + rbcL) phylogenetic tree topology. In all these trees, all species grouped into two morphologically and genetically distinct clades. Each clade was supported by multiple CBCs, as did all the clades representing genera. However, these clades did not correspond to the previously established subfamilies. Consequently, we amend the Order Cymatosirales and family Cymatosiraceae, and propose a new family, the Leyanellaceae. The structure of the auxospore was an additional synapomorphic character for Cymatosirales. Overall, we demonstrate a novel approach to study diatom phylogeny across a broader taxonomic range using ITS2 secondary structural information. Our results suggest that this approach might be useful in establishing higher taxonomic relationships in other groups of diatoms., (Copyright © 2018 Elsevier Inc. All rights reserved.)

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.

Anopheles (Anopheles) lindesayi Giles consists of 5 subspecies. In Japan, only one subspecies, An. l. japonicus Yamada, has been reported. Its geographical populations are morphologically diverse; however, they are regarded as a single subspecies. In this study, we re-evaluated the taxonomic status of An. l. japonicus in Japan, and that of another subspecies, An. l. pleccau, distributed in Taiwan, by comparative morphological and molecular analyses based on the gene sequences of mitochondrial DNA cytochrome c oxidase I (COI) and ribosomal DNA internal transcribed spacer 2 (ITS2). Nucleotide sequence divergence was calculated using the Kimura-two-parameter (K2P) distance model. Phylogenetic trees based on COI and ITS2 sequences showed 3 distinct clades: Eastern Japan, Western Japan, and the Ryukyus. The sequences of the Ryukyu specimens were located within the same clade as that of the sequences of the Taiwanese specimens. Regarding the COI sequences, the 3 geographical groups in Japan were genetically distinct. The following morphological characteristics distinguished the groups: larval seta 1-S, pupal setae 5 through segments IV-VII, and pupal setae 6 on segments IV-VII. Based on these results, it was revealed that An. l. japonicus included 3 genetically and morphologically distinct groups: 2 groups of An. l. japonicus and a group in the Ryukyus, which was a synonym of An. l. pleccau.

Members of the genus Uvulifer are distributed worldwide and infect aquatic snails and freshwater fishes as first and second intermediate hosts, respectively, and fish-eating birds (kingfishers) as definitive hosts. Metacercariae of Uvulifer spp. were collected from the fins and skin of 20 species of freshwater fishes in Mexico, Guatemala, Honduras, Nicaragua and Costa Rica, and the adults were recovered from the intestine of kingfishers in four localities of Mexico. The genetic divergence among 76 samples (64 metacercariae and 12 adults) was estimated by sequencing the 28S and 5.8S nuclear genes, as well as the internal transcribed spacers ITS1 and ITS2, and one mitochondrial gene (cox1). Maximum likelihood and Bayesian inference analyses inferred with each dataset showed a high genetic diversity within the genus Uvulifer across Middle America, revealing the existence of four genetic lineages that exhibit some level of host specificity to their second intermediate hosts. The metacercariae of lineage 1 were associated with characids and cyprinids in central and northern Mexico. Metacercariae of lineages 2 and 3 were associated with cichlids distributed widely across Middle America. The lack of adults of these lineages in kingfishers, in lineages 2 and 3, or the fact that just a few adult specimens were recovered, as in lineage 1, prevented a formal description of these species. The metacercariae of lineage 4 were found in poeciliids, across a distribution range comprising Mexico, Guatemala, Honduras and Nicaragua, and the adult was found in the green kingfisher in Mexico. The number of specimens sampled for lineage 4, for both gravid adults and metacercariae, allowed us to describe a new species, Uvulifer spinatus n. sp. We describe the new species herein and we discuss briefly the genetic diversity in Uvulifer spp. and the importance of using DNA sequences to properly characterize parasite diversity.

Adults of Skrjabinolecithum spinosum n. sp. were discovered in Mugil cephalus from the Gulf of Peter the Great in southern Far-East Russia. Additionally, adults of Unisaccus tonkini n. sp. were found in the intestine of Moolgarda cunnesius and Moolgarda seheli from the coastal waters of Cat Ba Island, Tonkin Bay, northern Vietnam. Skrjabinolecithum spinosum n. sp. possesses a larger body, and ventral and oral sucker size in comparison with Skrjabinolecithum vitellosum, a smaller pharynx size and body length/width rate ratio in comparison to Skrjabinolecithum pyriforme, a smaller body length and prepharynx size in comparison to Skrjabinolecithum lobolecitum and a smaller pharynx length and egg size in comparison to Skrjabinolecithum indicum and S. lobolecitum. The new species also differs from S. indicum, S. lobolecitum and S. vitellosum by the form of the testis, and from the last two species by the presence of a two-branched intestine. The morphometric parameters of S. spinosum n. sp. are similar to those of Skrjabinolecithum spasskii. However, S. spinosum n. sp., unlike S. spasskii, has an armed hermaphroditic duct. Unisaccus tonkini n. sp. is similar to Unisaccus spinosus (Martin, 1973), Unisaccus brisbanensis (Martin, 1973) and Unisaccus overstreeti (Ahmad, 1987) in body size but differs in oral sucker, pharynx and hermaphroditic sac size from U. spinosus, and in ventral sucker and ovary size from U. brisbanensis and U. overstreeti. Bayesian phylogenetic analysis, based on combined data of internal transcribed spacer 2 (ITS2) and partial 28S rRNA gene sequences, confirmed the validity of S. spinosum n. sp. and U. tonkini n. sp. Analysis of interrelationships of the family Haploporidae, including molecular data on new species, showed that the Waretrematinae subfamily is more heterogeneous in comparison with Haploporinae and Forticulcitinae, and includes U. tonkini n. sp.

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.

Paracoccidioides brasiliensis and the related species P. americana, P. restrepiensis, P. venezuelensis, and P. lutzii (Ascomycota, Ajellomycetaceae) are the etiological agents of paracoccidoidoimycosis (PCM), one of the most important systemic mycoses in Latin America. They are dimorphic fungi, with a mycelial life cycle in soil and a yeast phase associated with tissues of mammalian hosts. This study aimed to detect Paracoccidioides spp. in armadillo tissues and associated soil samples in three well-defined geographic areas, including the Alta Floresta, an area not only endemic for PCM in the central region of Brazil but also of probable P. lutzii occurrence, whose ecology and geographic distribution are poorly elucidated. The isolates were genotyped by sequencing ITS-rDNA and the gp43-exon-2 region, and by PCR-RFLP of alpha tubulin (tub1) gene; mycological aspects such as yeast-to-mycelial transition, growth and conidial production in soil extract agar were also evaluated. We confirmed that while armadillos are highly infected by P. brasiliensis, including multiple infections by distinct genotypes or species (P. brasiliensis and P. americana) in the same animal, the same does not hold true for P. lutzii, which in turn seems to present less capacity for mycelial growth and conidial production, when developing in a soil-related condition.

A rare ascaridoid species, Mawsonascaris australis (Johnston & Mawson, 1943), is reported from the Taiwan Strait for the first time, and the brown guitarfish Rhinobatos schlegelii Müller & Henle (Rhinopristiformes: Rhinobatidae) represents a new fish host. The detailed morphology of M. australis was studied using light and scanning electron microscopy (SEM) based on the newly collected specimens. The results revealed some important, but previously unreported or erroneous, morphological features, including the lateral alae starting well posterior to the base of the ventrolateral lips, the presence of one pair of double paracloacal papillae and a single, small precloacal median papilla on the anterior margin of the cloaca. In addition, in order to determine whether the morphometric difference in the relative lengths of the right and left spicules represents intraspecific or interspecific variation, specimens of M. australis were characterized using molecular approaches by sequencing and analysing the ribosomal internal transcribed spacer (ITS) and mitochondrial cox1 genes. The results indicate that this morphometric difference represents intraspecific variability.

Enterocytozoon bieneusi, which has recently been re-classified as a fungus, was identified in 5.2% (3/58) bat intestinal tissues and 1.9% (4/210) bat feces collected in South Korea. The positive cases were classified into six genotypes including four novel genotypes, KBAT1-KBAT4, based on sequence analysis of the E. bieneusi internal transcribed spacer (ITS) region. In addition, a novel genotype, KBAT3, belonged to group 1, which is considered having zoonotic potential by phylogenetic analysis of the E. bieneusi ITS region. This study expands our knowledge of the host range of E. bieneusi.

DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short-read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long-read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly., (© 2018 John Wiley & Sons Ltd.)

Two new species of Andracantha (Polymorphidae) are described from the intestine of the shags Leucocarbo chalconotus (Gray) and Phalacrocorax punctatus (Sparrman), and the penguin Eudyptula minor (Forster) from southern South Island, New Zealand. Andracantha leucocarboi n. sp. is distinguished from its congeners by having no genital or ventral trunk spines, but possessing a scattering of small spines between the anterior fields of spines. This is the first record of a species of Andracantha from a penguin. Circumbursal papillae are illustrated in a scanning electron micrograph for the first time in the polymorphids. Andracantha sigma n. sp. is distinguished by the sigmoid shape of its largest proboscis hook, hook VIII, and having the ventral field separated from the posterior disc field by an aspinous gap. A Maximum Likelihood tree from cox1 and large ribosomal subunit (LSU) data shows A. leucocarboi n. sp. to be more closely related to A. gravida than A. sigma n. sp. and the genus Andracantha as sister to Corynosoma spp. Genetic distances between species of Andracantha are comparatively large. A key to the species of Andracantha is provided.

As a result of experimental studies conducted in the Russian southern Far East, adult worms from the genus Metagonimus were obtained. A comparative analysis of the morphometry of these worms with other Metagonimus representatives showed that they are most similar to M. katsuradai Izumi, 1935 and M. otsurui Shimazu & Urabe, 2002 found in Japan, due to the ratio of suckers and the positions of the testicle, uterus and vitellaria. However, Russian worms differ from species in Japan by other metric characters: they differ from M. otsurui by the maximum size of most organs and from M. katsuradai by body width, pharynx length, and maximum size of testes and ovary. At the same time, they are identical to a trematode from the Russian southern Far East, which was previously identified as M. katsuradai. The validity of this species was also confirmed by genetic data. According to the 28S gene and the internal transcribed spacer 2 (ITS2) region of rDNA, as well as the cytochrome c oxidase I (cox1) gene of mtDNA, the Metagonimus specimens found in Russia differ from published genetic data for other members of this genus. However, both morphological similarity and molecular data showed that M. pusillus sp. nov., M. katsuradai and M. otsurui are most likely cryptic species. Furthermore, additional data based on a mitochondrial marker were provided for M. suifunensis Shumenko, Tatonova & Besprozvannykh, 2017 from Russia.

A new genus and species of nematode, Tziminema unachi n. gen., n. sp. is described from the caecum and colon of Baird's tapir Tapirus bairdii (Gill, 1865), found dead in the Reserva de la Biósfera El Triunfo, Chiapas State, in the Neotropical realm of Mexico. Tziminema n. gen. differs from the other nine genera included in the Strongylinae by two main characteristics: having 7-9 posteriorly directed tooth-like structures at the anterior end of the buccal capsule, and the external surface of the buccal capsule being heavily striated. Phylogenetic analyses of the DNA sequences of the mitochondrial cytochrome c oxidase and nuclear DNA, including a partial sequence of the internal transcribed spacer 1, 5.8S and a partial sequence of the internal transcribed spacer 2 of the new taxon, confirmed its inclusion in Strongylinae and its rank as a new genus.

Malassezia furfur is traditionally associated to human skin, although more recent studies have been revealing its presence in a variety of animals. The aim of this study was to analyze phenotypically and genetically the diversity among strains isolated from animals of this species. We have examined 21 strains of M. furfur from domestic and wild animals held in captivity. On the one hand, their phenotypic characteristics were studied, by assessing its growth at different incubation temperatures, their catalase and β-glucosidase activities and the Tween diffusion test on Sabouraud glucose agar (SGA), and on yeast nitrogen base agar (YNBA), a synthetic medium without lipids. On the other hand, the large subunit (LSU) and the internal transcribed spacer (ITS) of ribosomal RNA and the β-tubulin gene were sequenced. Different sequence types were identified for each target gene, and fourteen genotypes were revealed. While several genotypes were obtained from the strains from domestic animals, the strains from zoo animals appeared to be genetically more stable. With ITS and β-tubulin gene, M. furfur strains grouped in two clades. One clade included the strains from domestic animals and the other clade included the strains from zoo animals. The phenotypic tests also revealed a remarkable diversity within this species, which appeared to be more significant among strains from domestic animals. Moreover, the Tween diffusion test using YNBA was more useful to observe differences among strains, which could not be perceived using SGA.

Aspergillosis is a major cause of severe respiratory disease in birds. The prevalence of cryptic section Fumigati and other non-Aspergillus fumigatus species as causative agents is unknown. Species identity was determined in 30 isolates from affected birds from zoos, pet birds and poultry by PCR of the ITS1-5.8S-ITS2 and partial β-tubulin genes. The most prevalent isolate was A. fumigatus sens. str. in 87% (26) cases. Other Aspergillus species were identified in 13% (4) cases, including A. restrictus (1), A. flavus sens. str. (2), and A. nidulans-clade (1). This is the first report of A. restrictus causing avian disease.

Background: Wet biofilms associated with medical devices have been widely studied and their link with healthcare-associated infections (HCAIs) is well recognized. Little attention has been paid to the presence of dry biofilms on environmental surfaces in healthcare settings., Aim: To investigate the occurrence, prevalence, and diversity of dry biofilms on hospital surfaces., Methods: Sixty-one terminally cleaned items were received from three different UK hospitals. The presence of dry biofilm was investigated using culture-based methods and scanning electron microscopy (SEM). Bacterial diversity within biofilms was investigated using ribosomal RNA intergenic spacer analysis (RISA)-polymerase chain reaction and next-generation sequencing., Findings: Multi-species dry biofilms were recovered from 95% of 61 samples. Abundance and complexity of dry biofilms were confirmed by SEM. All biofilms harboured Gram-positive bacteria including pathogens associated with HCAI; 58% of samples grew meticillin-resistant Staphylococcus aureus. Dry biofilms had similar physical composition regardless of the type of items sampled or the ward from which the samples originated. There were differences observed in the dominance of particular species: dry biofilms from two hospitals contained mostly staphylococcal DNA, whereas more Bacillus spp. DNA was found on surfaces from the third hospital., Conclusion: The presence of dry biofilms harbouring bacterial pathogens is virtually universal on commonly used items in healthcare settings. The role of dry biofilms in spreading HCAIs may be underestimated. The risk may be further exacerbated by inefficient cleaning and disinfection practices for hospital surfaces., (Copyright © 2018 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Our understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept, Hesperomyces virescens (Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest that H. virescens could be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades within Hesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.

The nuclear ribosomal DNA internal transcribed spacer (ITS) has been widely used to assess the fungal composition in different environments by deep sequencing. To evaluate the ITS in the analysis of fungal diversity, comparisons of the clustering and taxonomy generated by sequencing with different portions of the whole fragment were conducted in this study. For a total of 83,120 full-length ITS sequences obtained from the UNITE database, it was found that, on average, ITS1 varied more than ITS2 within the kingdom Fungi; this variation included length and GC content variations and polymorphisms, with some polymorphisms specific to particular fungal groups. The taxonomic accuracy for ITS was higher than that for ITS1 or ITS2. The commonly used operational taxonomic unit (OTU) for evaluating fungal diversity and richness assigned several species to a single OTU even with clustering at 99.00% sequence similarity. The clustering and taxonomic capacities did not differ between ITS1 and ITS2. However, the OTU commonality between ITS1 and ITS2 was very low. To test this observation further, 219,741 pyrosequencing reads, including 39,840 full-length ITS sequences, were obtained from 10 soil samples and were clustered into OTUs. The pyrosequencing results agreed with the results of the in silico analysis. ITS1 might overestimate the fungal diversity and richness. Analyses using ITS, ITS1 and ITS2 yielded several different taxa, and the taxonomic preferences for ITS and ITS2 were similar. The results demonstrated that ITS2 alone might be a more suitable marker for revealing the operational taxonomic richness and taxonomy specifics of fungal communities when the full-length ITS is not available., Competing Interests: The authors declare that there are no conflicts of interest.

Coral-associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral-associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea-associated bacterial and algal communities throughout a natural bleaching event, using full-length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral-associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.

Persistent candidemia refers to the continued isolation of the same Candida species in the blood of a candidemic patient despite appropriate therapy. Despite the clinical importance of persistent candidemia, studies have superficially addressed the biological conditions behind this phenomenon. The aim of this study was to evaluate the correlation between the biofilm-forming ability by Candida bloodstream isolates and the persistence of infection. A total of 55 isolates of Candida were tested and characterized in two groups: (i) group I, which included seven patients with persistent candidemia, and (ii) group II, which included 18 patients with nonpersistent candidemia. Microorganisms were identified at the species level by sequencing the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA). Biofilm quantification was evaluated by the crystal violet staining method and confocal scanning laser microscopy (CSLM). Molecular tests confirmed the identification of Candida albicans (92% group I and 94% group II) and Candida dubliniensis isolates (8% group I and 6% group II). All 55 isolates were able to form biofilms, but a higher biofilm mass was produced by C. albicans/C. dubliniensis strains cultured from the persistent group (P < .05). Our data suggest that Candida sp. biofilm production should be considered a relevant biologic variable in explaining patients who fail to clear a bloodstream infection despite adequate antifungal treatment with triazoles.

In the present study, Neorhadinorhynchus nudus (Harada, 1938) is reported from the frigate tuna Auxis thazard (Lacepéde) (Perciformes: Scombridae), in the South China Sea for the first time. The detailed morphology of N. nudus was studied using light and scanning electron microscopy based on the newly collected material. The results showed some morphometric variability between our specimens and previous studies, including the number of hooks per longitudinal row and the size of copulatory bursa and eggs. Our SEM observations also revealed all proboscis hooks emerged from elevated round rims on proboscis surface. In addition, N. nudus was firstly characterised using molecular methods by sequencing and analysing the ribosomal ITS and mitochondrial cox1 regions. There is no nucleotide divergence found in the ITS sequences, but a low level of nucleotide variability detected in the cox1 regions (the level of intraspecific nucleotide variability being 0.75% to 2.54%). The DNA sequence data obtained herein will indeed be a useful reference for rapid and accurate species identification of Neorhadinorhynchus.

Trematode genus Diplostomum comprises of parasitic species which cause diplostomiasis, the 'white eye' disease in fish and heavy infection can result in mortality. The increasing availability of DNA sequences of accurately identified Diplostomum species on public data base presently enables the rapid identification of species from novel sequences. We report the first molecular evidence of the occurrence of D. pseudospathaceum in the United Kingdom. Two gene regions, nuclear internal transcribed spacer cluster (ITS1-5.8S-ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) of cercariae from infected aquatic snails, Lymnaea stagnalis collected in several locations in Southern England were sequenced. Phylogenetic analysis based on both sequenced genes revealed that the novel sequences were D. pseudospathaceum. Molecular diversity analysis of published D. pseudospathaceum cox1 sequences from seven countries in Europe and the novel sequences from the present study revealed high diversity, but low nucleotide divergence and a lack of gene differentiation between the populations. Haplotype network analysis depicted a star-like pattern and revealed a lack of geographic structure in the population. Fixation indices confirmed gene flow between populations and we suspect high levels of dispersal facilitated by highly mobile second intermediate (fish) and definitive (piscivorous birds) host may be driving gene flow between populations. Neutrality tests and mismatch distribution indicated recent population growth/expansion for D. pseudospathaceum in Europe.

Morphological and molecular identification can pave the way to design the most effective control measures against the Paramphistomum epiclitum in small ruminants. Morphology of the flukes had described the features of Paramphistomum genus. Body was conical with concave ventral and convex dorsal surface, tegumental spines all around the body in the immature stage, terminal funnel shape oral sucker, sub-terminal acetabulum, blind caeca with a serpentine course touching the anterior level of the acetabulum. Vitelline glands were at the lateral margins of the body extended from the pharynx to the posterior sucker. Testes were lobed and tandem, wavy post-testicular uterus and genital pore behind intestinal bifurcation. Sequence analyses of internal transcribed spacer (ITS)-2+ (PCR products of approximately 500 bp) of 10 flukes yielded 2 genotypes, Navsari isolate 1 and 2. In BLAST analysis, ITS-2+ genotypes were 97.3-99% similar with published sequences (KF564870, JF834888, KF642983 and JX678254) of P. epiclitum of Paramphistomatidae. Two genotypes depicted 4 single nucleotide polymorphisms (NPs) in the form of transitions (C-T at 10 and 18; G-A at 255; A-G at 367 locus), 1 triple NPs (CGT-GAA between 21-23 loci) and missing A base at codon 40 in the genotype 1. Average AT and GC content was 49.61% and 50.38%, respectively. Trees topology inferred by Neighbor Joining and Maximum Likelihood methods of ITS2+ of trematodes were similar, with small difference of bootstrap values. Navsari genotypes formed a tight cluster with the P. epiclitum, originated from different location with high bootstrap value and 0.004-0.011 estimated evolutionary divergence.

Ascaridia (A.) galli is one of the most commonly occurring nematodes in poultry worldwide, often in hens and broiler chickens. The infection with Ascaridia galli in free-range chickens was even 70%. There is not much information about A. galli genetic features. The present study was conducted to assess the genetic diversity of A. galli isolated from hens in Poland by analyzing the nucleotide sequence of the region ITS1-5.8rRNA-ITS2 and to define its homology within the family Ascaridiidae. Adult A. galli were collected from the intestines of naturally infected hens from two flocks of free-run laying hens from the Wielkopolska region in Poland. From all parasites an identical ITS1-5.8rRNA-ITS2 sequence was obtained, which was homologous in 99% with A. columbae (JQ995321.1) sequence. The high homology sequences of A. galli (KX683286) from Poland and A. columbae (JQ995321.1) isolate from the USA, support the observations of other authors suggesting that A. galli and A. columbae might be closely related. It is the first whole ITS1-5.8rRNA-ITS2 of A. galli in the GenBank database, so there is not enough data for detailed phylogenetic analysis of A. galli. Detailed genetic analysis is necessary to get better insight into the birds' Ascaridia species.

Fasciolosis in ruminants in India is caused by the liver fluke Fasciola gigantica. Radix (Lymnaea) spp. are known to carry the infective stages of this parasite. Understanding the seasonal prevalence of F. gigantica infection in the intermediate host is of extreme importance in order to elucidate the transmission dynamics of the parasite. So the present study was designed to determine the bioclimatic distribution of larval stages of F. gigantica in Radix spp. snails as well as to explore the genetic diversity of F. gigantica in three geographical regions (Deccan plateau, Western Ghats and coastal region) of Karnataka. The lymnaeid snails were sampled (n = 2077) for a period of one year (June 2015 to May 2016) at 24 sites. The snails were morphologically identified and the infection status was established through cercarial shedding and nested polymerase chain reaction (PCR) based technique targeting second internal transcribed spacers (ITS-2) of nuclear ribosomal DNA. The sensitivity of PCR (8.2%) for detection of F. gigantica infection within snail is significantly higher than cercarial shedding (4.3%) with an overall prevalence of 5.1%. The prevalence of infection was higher in winter than in the rainy and summer seasons (6.2% instead of 4.6% and 4.3% respectively). Deccan plateau (5.8%) showed a higher prevalence of infection compared to Western Ghats (5.2%) and Coastal region (3.6%). The sequencing ITS-2 region permitted the identification of the parasite as F. gigantica which is having high implication in studying the population genetic structure of the parasite in the country. In conclusion, overall results indicated that Radix spp. snails harboured F. gigantica developmental stages throughout the year and nested PCR was found to be sensitive and specific for detection of F. gigantica infection in snails compared to routine parasitological techniques.

Here, we used multilocus sequence typing (MLST) to evaluate 3 intergenic genes (16S rRNA, ospA, and 5S-23S IGS) in Borrelia isolated from South Korea to analyze the relationships between host, vector, and molecular background. We identified B. afzelii, B. yangtzensis, B. garinii, and B. bavariensis. This study is the first report for the identification of B. yangtzensis using MLST in South Korea.

Background: Whipworms (Nematoda: Trichuridae), among the most common soil-transmitted helminths (STHs), can cause the socioeconomically important disease trichuriasis in various mammalian hosts including humans and non-human primates. For many years, Trichuris from non-human primates has been assigned to the same species as the one infecting humans Trichuris trichiura. More recently, several molecular reports challenged this assumption following recognition of a Trichuris species complex observed in humans and non-human primates. A refined concept for species limits within Trichuris contributes to an understanding of diversity and the potential (zoonotic) transmission among humans and non-human primates. In this study, we expanded previous investigations by exploring the diversity of Trichuris among eight primates including three Asian autochthonous species (i.e. Rhinopithecus roxellana, Rhinopithecus bieti and Nomascus leucogenys). Species-level identification, whether novel or assignable to known lineages of Trichuris, was based on analyses of nuclear internal transcribed spacers (ITS) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes., Results: In total, seven genetically distinct subgroups of whipworms were determined to be present among the primates sampled. Most Trichuris lineages, including Subgroups 1, 1', 3, 5 and 6, showed a broad host range and were not restricted to particular primate species; in addition to T. trichiura, a complex of Trichuris species was shown infecting primates. Furthermore, it was assumed that Trichuris spp. from either N. leucogenys and P. hamadryas or R. roxellana and R. bieti, respectively, were conspecific. Each pair was indicated to be a discrete lineage of Trichuris, designated, respectively, as Subgroups 1 or 1' and 2, based on integrated genetic and phylogenetic evidence., Conclusion: These results emphasise that the taxonomy and genetic variations of Trichuris are more complicated than previously acknowledged. These cumulative molecular and phylogenetic data provide a better understanding of the taxonomy, genetics and evolutionary biology of the whipworms.

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.

We describe Isorchis cannoni n. sp. from the rabbitfishes Siganus fuscescens (Houttuyn) and Siganus lineatus (Valenciennes) (Siganidae) collected off Heron Island, southern Great Barrier Reef, Australia and, using molecular data, demonstrate that 'Cercariae queenslandae II' of Cannon (1978) from the gastropod Clypeomorus batillariaeformis Habe & Kosuge (Cerithiidae) is the larval form of this new species. The cercariae of I. cannoni n. sp. develop in rediae, encyst in the environment after emergence, and are inferred to then be consumed by grazing rabbitfish. Additionally, we provide a new report of Isorchis currani Andres, Pulis & Overstreet, 2016 from the type host, Selenotoca multifasciata (Richardson) (Scatophagidae) collected in Moreton Bay, south-east Queensland, Australia, greatly expanding the known geographical range of this species. Molecular sequence data (ITS1, ITS2 and 28S rDNA) generated for I. cannoni n. sp. and the new specimens of I. currani, confirm the identification of I. currani and demonstrate a distinct genotype for I. cannoni n. sp. relative to other species of Isorchis Durio & Manter, 1969, for which molecular data are available. Isorchis cannoni n. sp. is morphologically distinct from all other species in the genus, and is further distinguished by utilizing species of Siganidae as definitive hosts, rather than species of Chanidae or Scatophagidae. Because haploporid and atractotrematid cercariae have well-developed reproductive organs, we find cercariae of these closely related families morphologically distinguishable in the same way as adult trematodes: atractotrematids have two symmetrical testes and haploporids have a single testis or, rarely, two tandem or oblique testes.

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.

Timoniella spp. are cryptogonimid flukes (Digenea: Cryptogonimidae) that parasitize the guts of fish in brackish waters. Timoniella imbutiforme, a species from the Mediterranean Sea, is recorded in the Black Sea, while T. balthica has been described from the Baltic Sea. In this paper, we clarify the taxonomic status of Timoniella populations in the Baltic and Black seas. Adults and metacercariae of Timoniella spp. were sampled from localities in the Mediterranean Sea (France), Black Sea (Ukraine) and Baltic Sea (Germany) and subjected to molecular and morphological analysis, including Bayesian phylogenetic reconstruction based on concatenated sequences of ITS1-ITS2-28S. This allowed us to construct a new key to species of the genus Timoniella. Our results suggest that T. balthica forms part of the Boreal-Atlantic relict fauna of the Black Sea and should now be considered a junior synonym of T. imbutiforme.

The ectomycorrhizal milkcap genus Lactifluus (Russulaceae) is commonly found in tropical and subtropical forests of Southeast Asia. During several sampling expeditions in Thailand, multiple collections of Lactifluus (Lf.) species with pleurotoid or small agaricoid basidiocarps were found. A molecular study was combined with a morphological study, in which the collections were compared with herbarium material. The molecular study indicated that four Thai collections belonged to undescribed species within Lactifluus section Gerardii, as was also the case for herbarium collections of a pleurotoid species from Nepal. One other collection from Thailand appeared closely related to Lf. uyedae, known only from Japan. Five species are described as new in the genus: Lf. auriculiformis, Lf. gerardiellus, Lf. bhandaryi, Lf. pulchrellus, and Lf. raspei.

Species of tropical tar spot fungi (Phyllachorales, Ascomycota) are obligate biotrophic plant parasitic fungi associated with living leaves of a wide range of families of host plants, mainly in tropical and subtropical regions. In this study, samples of tropical tar spot fungi were collected in forests in Costa Rica and Panamá. To identify taxa, we used morphology and information on host plants and combined multigene phylogeny of four genes: the large subunit nuclear ribosomal DNA (28S rDNA), the small subunit nuclear ribosomal DNA (18S rDNA), the complete internal transcribed spacer region of ribosomal DNA (nuc rDNA ITS1-5.8S-ITS2; ITS), and the translation elongation factor 1-α (tef1). Here we propose one new species in the genus Camarotella and eight new species in Telimena with their morphological descriptions, illustrations, and sequence data. The newly described species are Camarotella licaniae on Licania arborea (Chrysobalanaceae) and in the genus Telimena: T. billiae on Billia rosea (Sapindaceae), T. drymoniae on Drymonia multiflora (Gesneriaceae), T. hydrangeae on Hydrangea sp. (Hydrangeaceae), T. miravallensis on Symplocos panamensis (Symplocaceae), T. protii on Protium sp. (Burseraceae), T. rinoreae on Rinorea sp. (Violaceae), T. semialarii on Semialarium mexicanum (Celastraceae), and T. triseptata on Tapirira mexicana (Anacardiaceae). The new name Telimena nitens on Schlegelia brachyanta (Schlegeliaceae) is presented and 10 species of Phyllachora are transferred to Telimena, leading to the new combinations T. canarii, T. galavisii, T. insueta, T. ruelliae, T. scutiformis, T. serjaniicola, T. spicatae, T. subrepens, T. symploci, and T. symplocicola. Additionally, revisions of tar spot fungi on host families Burseraceae, Sapindaceae, and Symplocaceae are provided, and four new synonyms are proposed.

In this study, 49 species of Hydnum are recognized worldwide. Twenty-two of them are described here as new species. Epitypes are proposed for H. repandum and H. rufescens. The majority of the species are currently known only from a single continent. The barcodes produced in this study are deposited in the RefSeq database and used as a basis to name species hypotheses in UNITE. Eleven infrageneric clades recovered in a phylogenetic analysis are supported by morphological characteristics and formally recognized: subgenera Alba, Hydnum, Pallida, and Rufescentia; sections Hydnum, Olympica, Magnorufescentia, and Rufescentia; and subsections Mulsicoloria, Rufescentia, and Tenuiformia.

Members of the genus Drepanocephalus are endoparasites of fish-eating birds of the families Phalacrocoracidae and Sulidae distributed across the Americas. Currently, Drepanocephalus contains three species, i.e. D. spathans (type species), D. olivaceus and D. auritus. Two additional species, D. parvicephalus and D. mexicanus were transferred to the genus Petasiger. In the current study, available DNA sequences of D. spathans, D. auritus and Drepanocephalus sp., were aligned with newly generated sequences of D. spathans and Petasiger mexicanus. Phylogenetic analyses inferred with three nuclear (LSU, SSU and ITS1, 5.8S, ITS2) and two mitochondrial (cox1, nad1) molecular markers showed that the sequences of D. spathans and D. auritus are nested together in a single clade with very low genetic divergence, with Petasiger mexicanus as its sister species. Additionally, P. mexicanus was not a close relative of other members of the genus Petasiger, showing that P. mexicanus actually belongs to the genus Drepanocephalus, suggesting the need to re-allocate Petasiger mexicanus back into the genus Drepanocephalus, as D. mexicanus. Morphological observations of the newly sampled individuals of D. spathans showed that the position of the testes is variable and testes might be contiguous or widely separated, which is one of the main diagnostic traits for D. auritus. Our results suggest that D. auritus might be considered a synonym of D. spathans and, as a result, the latter represents a species with a wide geographic range across the Americas, parasitizing both the Neotropical and the double-crested cormorant in Argentina, Brazil, Paraguay, Venezuela, Colombia, Mexico, USA and Canada.