Morpho-Molecular Features and Phylogenetic Relationships of Metorchis butoridi Oschmarin, 1963 (Trematoda: Opisthorchiidae) from East Asia

Adult trematodes of the genus Metorchis were found in the gallbladders of ducklings that had been experimentally fed freshwater fishes of the genera Rhynchocypris and Rhodeus that were naturally infected by Metorchis metacercariae. Some of the trematodes were identified as Metorchis ussuriensis, whose morphology of developmental stages and molecular data had previously been described in detail. The other trematodes were confirmed as species Metorchis butoridi on the basis of morphological features: subterminal oral sucker, vitelline follicles with interrupted bands, and rosette-shaped testes. An analysis of phylogenetic relationships within Opisthorchiidae using nuclear and mitochondrial markers confirmed that the obtained trematodes were actually from the genus Metorchis. The morphological and molecular features indicated that a number of trematodes found in East Asia and described as Metorchis orientalis belong to M. butoridi. Also, the M. orientalis individuals from Europe are, in fact, representatives of another Metorchis species.

Detailed Protocol to Perform Direct PCR Using Filamentous Fungal Biomass-Tips and Considerations

The precise and rapid detection of fungi is important in various fields, including clinics, industry, and agriculture. While sequencing universal DNA barcodes remains the standard method for species identification and phylogenetic analysis, a significant bottleneck has been the labor-intensive and time-consuming sample preparation for genomic DNA extraction. To address this, we developed a direct PCR method that bypasses the DNA extraction steps, facilitating efficient target DNA amplification. Instead of extracting genomic DNA from fungal mycelium, our method involves adding a small quantity of mycelium directly to the PCR mixture, followed by a heat shock and vortexing. We found these simple adjustments to be sufficient to lyse many filamentous fungal cells, enabling target DNA amplification. This paper presents a comprehensive protocol for executing direct PCR in filamentous fungi. Beyond species identification, this direct PCR approach holds promise for diverse applications, such as diagnostic PCR for genotype screening without fungal DNA extraction. We anticipate that direct PCR will expedite research on filamentous fungi and diagnosis of fungal diseases. Key features • Eliminates the time-consuming genomic DNA extraction step for PCR, enhancing the speed of molecular identification. • Adds a small quantity of mycelium directly into the PCR mix. • Emphasizes the crucial role of heat shock and vortexing in achieving efficient target DNA amplification. • Accelerates the molecular identification of filamentous fungi and rapid diagnosis of fungal diseases.

Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage

Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. We studied alveolate diversity in soil under the undisturbed steppe (US) and cropped for wheat using two tillage practices (conventional, CT, and no-till, NT) by amplifying the ITS2 marker with ITS3_KYO2/ITS4 primers and sequencing amplicons using Illumina MiSeq. A total of 198 Alveolata OTUs were identified, with 158 OTUs attributed to the Ciliophora phylum, containing five classes: Litostomatea, Spirotrichea and Oligohymenophorea, Nassophorea and Phyllopharyngea. Litostomatea and Phyllopharyngea were more abundant in US as compared with CT and NT. The observed OTU richness was higher in US than in CT and NT. The β-biodiversity of soil ciliates also very distinctly differentiated the US field from CT and NT. In the US, Nassophorea and Spirotrichea correlated positively with sand and negatively with clay, silt and SOM contents. This is the first report about soil ciliates diversity in Siberia as assessed by metabarcoding technique. The revealed clear effect of land use on the relative abundance of some taxa and a lack of tillage effect suggest the importance of the quantity and quality of plant material input for shaping the prey for ciliates. The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.

Phytochemical and metabolic profiling of the different Podocarpus species in Egypt: Potential antimicrobial and antiproliferative activities

Podocarpus is the most dominant genus of Podocarpaceae, with higher taxonomical proximity to the Taxaceae, having numerous pharmaceutical applications, however, scarce studies dealing with the physiological and metabolic criteria of Podocarpus in Egypt were reported. Thus, the objective of this work was to assess the physiological and metabolical patterns of the different species of Podocarpus; P. gracilior, P. elongates, P. macrophyllus and P. neriifolius. The highest terpenoids contents were reported in P. neriifolius, followed by P. elongatus, and P. macrophyllus. P. gracilior had the highest antioxidants amount, followed by P. macrophyllus, P. neriifolius and P. elongatus. From the GC/MS metabolic profiling, caryophyllene, β-cadinene, β-cuvebene, vitispirane, β-cadinene and amorphene were the most dominant metabolites in P. gracilior. β-Caryophyllene was the common in P. gracilior, P. elongatus, P. macrophyllus and P. neriifolius with an obvious fluctuation. The plant methanolic extracts have an obvious activity against the multidrug resistant bacteria; E. coli, P. aeruginosa, S. pyogenes and S. aureus, and fungi; A. fumigatus, A. flavus, A. niger and C. albicans in a concentration-dependent manner. The highest Taxol yield was assessed in the extracts of P. elongatus (16.4 μg/gdw), followed by P. macrophyllus, and P. neriifolius. The chemical identity of Taxol derived from P. elongatus was resolved by LC/MS, with molecular mass 854.6 m/z, and similar structural fragmentation pattern of the authentic one. The highest antitumor activity of P. elongatus extracted Taxol was assessed towards HCT-116 (30.2 μg/ml), HepG-2 (53.7 μg/ml) and MCF-7 (71.8 μg/ml). The ITS sequence of P. elongatus "as potent Taxol producer" was deposited on Genbank with accession #ON540734.1, that is the first record of Podocarpus species on Genbank.

Redefining the Genus Corollospora Based on Morphological and Phylogenetic Approaches

The present study, initially to resolve the cryptic species within Corollospora maritima, is to determine how to attain taxonomic discrimination at species and generic levels. Multiple sequence alignments (MSAs) of the ITS, 28S, and 18S regions of the nuclear ribosomal cistron were separately subjected to pairwise distance assessments, Bayesian, and Maximum likelihood phylogenetic analyses. Morphological descriptions of 15 type strains of Corollospora species, along with MSAs involving representatives of the whole genus Corollospora (268 isolates, many from C. maritima sensu lato) totaling 355 published sequences, allowed phylogenetic assessments conducted to the following p-distance thresholds in the ITS/28S regions: ≥3%/1% for species segregation and ≥8%/2% for generic segregation. This resulted in the introduction of 10 new genera encompassing 13 new combinations of current Corollospora species: Ajigaurospora pseudopulchella, Corollosporella anglusa, Corollosporella ramulosa, Corollosporopsis portsaidica, Garethelia parvula, Honshuriella fusca, Keraliethelia pulcehlla, Nakagariella filiformis, Paracorollospora angusta, Paracorollospora luteola, Paracorollospora marina, Shirahamella gracilis, and Tokuratelia colossa. Furthermore, seven undefined genera considered putative new genera (pNGenus A to G), and 16 undefined putative new species (seven spp. come from the resolution of the C. maritima complex), await re-assessment of their morphology and additional molecular data, which may result in the recognition of new taxa.

The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera

Reducing the use of fungicides, insecticides, and herbicides in order to limit environmental pollution and health risks for agricultural operators and consumers is one of the goals of European regulations. In fact, the European Commission developed a package of measures (the European Green Deal) to promote the sustainable use of natural resources and strengthen the resilience of European agri-food systems. As a consequence, new plant protection products, such as biostimulants, have been proposed as alternatives to agrochemicals. Their application in agroecosystems could potentially open new scenarios regarding the microbiota. In particular, the vineyard microbiota and the microbiota on the grape surface can be affected by biostimulants and lead to different wine features. The aim of this work was to assess the occurrence of a possible variation in the mycobiota due to the biostimulant application. Therefore, our attention has been focused on the yeast community of grape bunches from vines subjected to the phytostimulant BION®50WG treatment. This work was carried out in the CREA-VE experimental vineyard of Vitis vinifera cv. Barbera in Asti (Piedmont, Italy). The composition of fungal communities on grapes from three experimental conditions such as IPM (integrated pest management), IPM+BION®50WG, and IPM+water foliar nebulization was compared by a metabarcoding approach. Our results revealed the magnitude of alpha and beta diversity, and the microbial biodiversity index and specific fungal signatures were highlighted by comparing the abundance of yeast and filamentous fungi in IPM and BION®50WG treatments. No significant differences in the mycobiota of grapevines subjected to the three treatments were detected.

Phylogenetic analysis based on the ITS, matK and rbcL DNA barcodes and comparison of chemical contents of twelve Paeonia taxa in Türkiye

BACKGROUD

Twelve taxa of herbaceous Paeonia species were recorded in Türkiye. All definitions were performed morphologically and/or anatomically and there is no study based on DNA barcode sequences. Three barcode regions were sequenced to determine the phylogenetic relationships of Turkish Paeonia taxa. The chemical comparison of roots was also investigated.

METHODS AND RESULTS

The taxons were collected between May and June 2021 from nine cities. Leaf materials were used for DNA isolation and ITS, matK and rbcL regions were amplified and sequenced. There was no difference among taxa in terms of rbcL sequences. But the ITS and matK regions distinguished 12 taxa and structured them in two groups. ITS region distinguished P. peregrina, P. arietina, and P. tenuifolia from other taxa, while matK region distinguished P. arietina and P. witmanniana from other taxa. Both barcode sequences actually showed that the registration of P. mascula subsp. arasicola was actually 100% similar to P. arietina. ITS was the most polymorphic region (n = 54) followed by matK (n = 9). These sequences could successfully discriminate Paoenia species from each other and diploid P. tenuifolia. The methanolic root (100 gr) extracts were examined for total phenolic and flavonoid content, and antioxidant activities. Significant variation was found for polyphenolic content, and antioxidant properties (TPC from 204.23 to 2343.89 mg, TFC from 7.73 to 66.16 mg, and FRAP from 523.81 to 4338.62 mg). SC₅₀ values of ABTS and DPPH were ranged from 115.08 to 1115.52 μg/ml and 73.83 to 963.59 μg/ml, respectively.

CONCLUSION

It was concluded that 11 of 12 taxa had differences in terms of ITS and matK sequences and these region must be used for the correct identification of Turkish Paeonia.

Crocus speciosus (Iridaceae)-A New Species for the Bulgarian Flora

This is the first report on the autumn-flowering species Crocus speciosus, belonging to C. ser. Speciosi from the Bulgarian flora. The species was found in Southeastern Bulgaria, in the area between Ahtopol and Rezovo. Re-examining the Bulgarian collections, the earliest specimen was collected in 1975, was probably overlooked, and most likely determined as C. pulchellus. The nearest known localities of the species are on the territory of Türkiye. In this study, we compared C. pulchellus and C. ibrahimii using DNA sequence data from the nuclear ITS1/2 region and morphological features. Our study showed a close relationship between the specimens from Bulgaria and the recently deposited data of C. speciosus and their separation from the closely related C. pulchellus. Together with the previously cited white anthers as a key feature for determination, the molecular data confirmed a clear distinction between the samples with white anthers in the two species. The morphological data of our taxon overlapped with the description of C. ibrahimii. The molecular data strongly supported the affiliation of C. speciosus s.l., but did not support the recognition of C. ibrahimii as a separate species and it should be referred to as a subspecies of C. speciosus subsp. ibrahimii Rukšāns.

Unique Rhizobial Communities Dominated by Bradyrhizobium liaoningense and Bradyrhizobium ottawaense were Found in Vegetable Soybean Nodules in Osaka Prefecture, Japan

Vegetable soybean (Glycine max [L.]) is mainly consumed in Asian countries, but has recently attracted attention worldwide due to its high nutritional value. We aimed to identify the indigenous rhizobia of vegetable soybean in Yao City, Osaka Prefecture, Japan, and to clarify the relationships between the rhizobial community and soil environmental factors. Soil samples were collected from 12 vegetable soybean cultivation fields under two different conditions (six greenhouses and six open fields) in Yao City with different varieties of vegetable soybean. A total of 217 isolates were obtained from the nodules and clustered into nine operational taxonomic units (OTUs) with 97% homology based on the 16S-23S rRNA internal transcribed spacer (ITS) region. A phylogenetic ana-lysis showed that OTUs were closely related to Bradyrhizobium liaoningense, B. ottawaense, B. elkanii, and other Bradyrhizobium species and were dominant in this order. B. liaoningense was widely found in sampled sites and accounted for 50.7% of all isolates, while B. ottawaense was mostly limited to open fields. This rhizobial community differed from Japanese soybean rhizobia, in which B. diazoefficiens, B. japonicum, and B. elkanii were dominant. These results imply the characteristic differences among host plants or regional specialties. A non-metric multidimensional scaling (NMDS) ana-lysis revealed the significant impact of soil pH and the contents of Ca, Mg, Mn, total nitrogen (TN), and total carbon (TC) on the distribution of rhizobia. B. liaoningense was detected in soils with a neutral pH, and high TN and low Mn contents increased its abundance. The present study provides novel insights into Japanese rhizobia and potentially novel resources for sustainable agriculture.

Genetic and population diversity of Toxocara cati (Schrank, 1788) Brumpt, 1927, on the basis of the internal transcribed spacer (ITS) region

The present investigation was aimed to study the sequence, phylogenetic and haplotype analyses of Toxocara cati based on the ITS region, along with the genetic diversity, demographic history and population-genetic structure. The maximum likelihood tree based on Kimura 2-parameter model was constructed using the complete ITS region of all the nucleotide sequences (n = 57) of Toxocara spp. and other related ascarid worms available in the GenBank™. It placed all the sequences of T. cati into four major clades designated as T. cati genotypes 1-4 (TcG1-G4). A total of 66 signature nucleotides were identified in the ITS region between genotypes. The median-joining haplotype network displayed a total of 24 haplotypes, with China exhibiting the highest number of haplotypes (h = 20) followed by India (h = 4), and Japan and Russia (h = 1). It indicated a clear distinction between all the four genotypes. The pairwise F_ST values between all the genotypes indicated huge genetic differentiation (> 0.25) between different T. cati genotypes. Moreover, the gene flow (Nm) between T. cati genotypes was very low. Results of AMOVA revealed higher genetic variation between genotypes (92.82%) as compared to the variation within genotypes (7.18%). The neutrality indices and mismatch distributions for the G1-G4 genotypes, Indian isolates and the overall dataset of T. cati indicated either a constant population size or a slight population increase. The geographical distribution of all the genotypes of T. cati is also reported. This is the first report of genotyping of T. cati on the basis of the ITS region.

Enterocytozoon bieneusi in patients with diarrhea and in animals in the northeastern Chinese city of Yichun: genotyping and assessment of potential zoonotic transmission

Enterocytozoon bieneusi is a common microsporidia species in humans and animals. Due to lack of effective vaccines and drugs, understanding of its epidemiological status and characteristics in different hosts is an important step in controlling the infection. The present study aimed at determining the prevalence of E. bieneusi in humans with diarrhea and animals in Yichun, in northeastern China, and assessing the epidemiological role of animals in the transmission of microsporidiosis. A total of 540 fecal samples were collected from diarrheal patients (n = 222) and 11 animal species (n = 318). Enterocytozoon bieneusi was identified and genotyped by polymerase chain reaction (PCR) and sequencing of the internal transcribed spacer (ITS) region of the rRNA gene. Enterocytozoon bieneusi was detected in 1.4% (3/222) of diarrheal patients, and genotype D and novel genotypes YCHH1 and YCHH2 were identified. Enterocytozoon bieneusi was detected in wild boars (7.7%), sika deer (8.2%), dogs (3.2%), and ostriches (10.7%), and genotypes D, Type IV, Peru6, BEB6 and novel genotypes YCHA1, YCHA2 and YCHA3 were identified. Genotypes YCHH1, YCHH2 and YCHA1 were phylogenetically assigned to group 1, while YCHA2 and YCHA3 to groups 2 and 11, respectively. The finding of genotype D in humans and animals, and the identification of zoonotic genotypes Peru6, Type IV, BEB6 in animal-derived E. bieneusi isolates indicate the potential of zoonotic transmission of microsporidiosis in the investigated area. The observation of the three novel genotypes in group 1 indicates their zoonotic potential.

Exploring LSU and ITS rDNA Sequences for Acanthamoeba Identification and Phylogeny

The identification and classification of strains of Acanthamoeba, a potentially pathogenic ubiquitous free-living amoeba, are largely based on the analysis of 18S rDNA sequences, currently delineating 23 genotypes, T1 to T23. In this study, the sequences of the ITS region, i.e., the 5.8S rDNA and the two internal transcribed spacers (ITS-1 and ITS-2), and those of the large subunit (LSU) rDNA of Acanthamoeba were recovered from amoeba genomes; the sequences are available in GenBank. The complete ITS–LSU sequences could be obtained for 15 strains belonging to 7 distinct lineages (T4A, T4D, T4F, T4G, T2, T5, and T18), and the site of the hidden break producing the 26Sα and 26Sβ was identified. For the other lines, either the LSU is partial (T2/T6, T7) or the ITS is fragmentary (T7, T10, T22). It is noteworthy that a number of sequences assigned to fungi turned out to actually be Acanthamoeba, only some of which could be affiliated with known genotypes. Analysis of the obtained sequences indicates that both ITS and LSU are promising for diagnostic and phylogenetic purposes.

Polyphasic Systematics of the Fungicolous Genus Cladobotryum Based on Morphological, Molecular and Metabolomics Data

(1) Background: Species of the anamorphic genus Cladobotryum, are known for their fungicolous lifestyle, making them important mycopathogens in fungiculture. Many morphological, ecological, and molecular phylogenetic studies of the genus have been done to date, but taxonomic uncertainties and challenges still remain. Fungal secondary metabolites, being vastly diverse, are utilised as an extra tool in fungal systematics. Despite being studied for their potentially bioactive compounds, Cladobotryum species are insufficiently investigated regarding metabolomics. (2) Methods: The aim of this study is the identification of Greek strains of Cladobotryum by integrating morphological data, ITS-based phylogeny, and ¹H NMR-based metabolomics into a polyphasic approach. (3) Results: Twenty-three strains, isolated from sporophores of macromycetes inhabiting diverse Greek ecosystems, were morphologically identified as Cladobotryum apiculatum, C. fungicola, C. mycophilum, C. varium, C. verticillatum, and Hypomyces rosellus (anamorph C. dendroides), whereas seven strains, which produced red-pigmented metabolites, presented an ambiguous taxonomic position at the species level. Molecular phylogenetics and metabolomics corroborated the morphological findings. (4) Conclusions: Thorough morphological study, ITS region-based phylogeny, and NMR-based metabolomics contribute complementarily to resolving the genus Cladobotryum systematics.

Soil Mycobiome Diversity under Different Tillage Practices in the South of West Siberia

Managing soil biodiversity by reduced or no tillage is an increasingly popular approach. Soil mycobiome in Siberian agroecosystems has been scarcely studied; little is known about its changes due to tillage. We studied mycobiome in Chernozem under natural steppe vegetation and cropped for wheat by conventional or no tillage in a long-term field trial in West Siberia, Russia, by using ITS2 rDNA gene marker (Illumina MiSeq sequencing). Half of the identified OTUs were Ascomycota with 82% of the total number of sequence reads and showing, like other phyla (Basidiomycota, Zygomycota, Mortierellomycota, Chytridiomycota, Glomeromycota), field-related differential abundance. Several dominant genera (Mortierella, Chaetomium, Clonostachys, Gibberella, Fusarium, and Hypocrea) had increased abundance in both cropped soils as compared with the undisturbed one and therefore can be safely assumed to be associated with wheat residues. Fungal OTUs' richness in cropped soils was less than in the undisturbed one; however, no tillage shifted soil mycobiome composition closer to the latter, albeit, it was still similar to the ploughed soil, despite different organic matter and wheat residue content. The study provided the first inventory of soil mycobiome under different tillage treatments in the south of West Siberia, where wheat production is an important section of the regional economy.

Rapid identification of Amanita citrinoannulata poisoning using colorimetric and real-time fluorescence and loop-mediated isothermal amplification (LAMP) based on the nuclear ITS region

Health concerns and financial losses caused by mushroom poisoning have been reported worldwide. Amanita citrinoannulata, a poisonous mushroom commonly found in China, results in a toxic reaction in humans after mistaken ingestion. To reduce the mistaken ingestion of poisonous mushrooms and to improve clinical diagnosis of mushroom poisoning, a rapid mushroom species identification method is required. Such identification methods could be advantageous in the identification of other poisonous mushroom species. This study developed two rapid and sensitive methods for the detection of A. citrinoannulata utilizing colorimetric and real-time loop-mediated isothermal amplification (LAMP) technology and specifically designed primers for the internal transcribed spacer (ITS) genes of A. citrinoannulata. The methods demonstrated high sensitivity as 0.2 ng of A. citrinoannulata DNA could be detected, with no cross-reaction with 41 non-target mushroom species. The entire detection process could be completed within 40 min without requiring complex instruments and can be observed by the naked eye. Therefore, these novel methods can be used for the identification of fresh and cooked mushroom samples and vomit samples, which contain only 1% A. citrinoannulata. Furthermore, these methods facilitate the detection of mushroom poisoning, and thus, have potential to reduce the number of mushroom poisoning-related deaths worldwide.

Diversity and Identification of Plant-Parasitic Nematodes in Wheat-Growing Ecosystems

Several nematode species can be found in different densities in almost any soil ecosystem, and their diversity in those ecosystems depends on numerous reasons, such as climatic conditions and host presence. Cereals are one of the main hosts of plant-parasitic nematodes (PPN), chiefly root-lesion nematodes (RLN, Pratylenchus spp.) and cereal cyst nematodes (CCN, Heterodera spp.). These nematodes are known as major parasites of the cereal crops; however, agricultural areas accommodate various nematodes showing biological variation. The diversity of parasitic nematodes on cereals in the Sakarya provinces of Türkiye, where cereals are intensively grown and located in the middle of two climatic zones, has not been well studied. Therefore, in this study, we aimed to determine the diversity, identification, and molecular phylogeny of PPNs in wheat-growing ecosystems in the Hendek, Pamukova, Geyve, Akyazı, and Central districts of Sakarya. The diversity of PPNs was calculated using the Shannon diversity index. Thirteen PPN genera were detected in 92% of soil samples. Heterodera filipjevi was identified in 24% of the soil samples using morphological, morphometrical, and molecular tools. In the morphological and molecular analyses, intraspecific polymorphism was observed in H. filipjevi populations. The result indicated that the high infestation rate of H. filipjevi was recorded from Geyve and Pamukova, followed by Hendek and Akyazı; however, a low infestation rate was detected in the Central district. The moderate value of the Shannon index of migratory nematode species was obtained in wheat fields as 2.31, whereas the value of evenness was 0.93, implying moderate diversity and high evenness of nematodes. This study is the first comprehensive report on H. filipjevi from wheat cropping areas in the Sakarya province. Intensified cereal cropping systems with/without non-cereal rotations increased the risk of plant-parasitic nematodes, especially RLNs and H. filipjevi infection of wheat production areas in the province.

Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae

The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.

Study of the diversity of 16S-23S rDNA internal transcribed spacer (ITS) typing of Escherichia coli strains isolated from various biotopes in Tunisia

We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550 bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550 bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.

Novel distribution records and molecular data for species of Macrogyrodactylus Malmberg, 1957 (Monogenea: Gyrodactylidae) from Clarias gariepinus (Burchell) (Siluriformes: Clariidae) in southern Africa

The viviparous gyrodactylid genus Macrogyrodactylus Malmberg, 1957 is endemic to Africa, composed of nine species from hosts of four freshwater fish families, including catfishes (Siluriformes: Clariidae). Three species, Macrogyrodactylus clarii Gussev, 1961; M. congolensis (Prudhoe, 1957) and M. karibae Douëllou et Chishawa, 1995, are primarily known to parasitise the African sharptooth catfish Clarias gariepinus (Burchell) in various African countries. From November 2017 to September 2019, a total of 184 individuals of C. gariepinus were collected from selected localities in southern Africa and their skin, fins and gills were surveyed for monogeneans. Three species of Macrogyrodactylus (M. clarii, M. congolensis and M. karibae) were found parasitising C. gariepinus from five localities in South Africa and Zambia. Overall prevalence was 50% to 100% with intensities of up to 109 parasites per host individual. New locality records in southern Africa, morphological observations and additional molecular data on the complete Internal Transcriber Spacer (ITS-1-5.8S-ITS-2) regions of the rDNA gene for the three gyrodactylid species are presented in this study.

Cultivable Yeast Microbiota from the Marine Fish Species Genypterus chilensis and Seriolella violacea

Because of its outstanding biological and industrial importance, many efforts have been made to characterize the mycobiota of new environments and their biochemical and biotechnological potentials. Gut mycobiota can be a source of novel yeasts with the potential to be used as probiotics or have industrial applications. In this work, we characterized two as-yet unexplored yeast communities from the intestinal content of the cultured marine Chilean fishes Genypterus chilensis (G. chilensis) and Seriolella violacea (S. violacea). Yeasts were isolated through culture, identified by sequencing their ITS region, and characterized their enzymatic profile with API^®ZYM. Rhodotorula mucilaginosa was identified in both fish species. For the first time, Candida palmioleophila, Candida pseudorugosa, Cystobasidium slooffiae, and a member of the Yamadazyma genus were also identified and described as part of the normal fish gut–microbiota. Furthermore, the diverse enzymatic profile exhibited by some of these isolates suggests that it may be possible to develop novel applications for them, such as new probiotics and other biotechnological applications.

Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Characterization of Euplotes lynni nov. spec., E. indica nov. spec. and description of E. aediculatus and E. woodruffi (Ciliophora, Euplotidae) using an integrative approach

Four species belonging to the genus Euplotes have been investigated, namely: E. lynni nov. spec., E. indica nov. spec., E. aediculatus, and E. woodruffi. All populations are from India and were investigated using morphological and molecular markers. The phylogenetic relationships were inferred from small subunit ribosomal rRNA gene (SSU rRNA), internal transcribed spacer (ITS) region, and mitochondrial cytochrome c oxidase subunit I (COI) gene. Predicted secondary structure models for two new species using the hypervariable region of the SSU rRNA gene and ITS2 region support the distinctness of both species. Morphological characters were subjected to principal component analysis (PCA) and genetic variations were studied in-depth to analyze the relatedness of the two new species with their congeners. An integrative approach combining morphological features, molecular analysis, and ecological characteristics was carried out to understand the phylogenetic position of the reported species within the different clades of the genus Euplotes.

Temporal and spatial interactions modulate the soybean microbiome

Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental chamber till seed maturation. Samples from various developmental stages (emergence, growth, flowering and maturation) and compartments (leaf, stem, root and rhizosphere) were collected. Community structure and composition were assessed with 16S rRNA gene and ITS region amplicon sequencing. Overall, the interaction between spatial and temporal dynamics modulated alpha and beta diversity patterns. Time lag analysis on measured diversity indices highlighted a strong temporal dependence of communities. Spatial and temporal interactions influenced the relative abundance of the most abundant genera, whilst random forest predictions reinforced the observed localisation patterns of abundant genera. Overall, our results show that spatial and temporal interactions tend to maintain high levels of biodiversity within the bacterial/archaeal community, whilst in fungal communities OTUs within the same genus tend to have overlapping niches.

Ancylostoma ceylanicum: The Neglected Zoonotic Parasite of Community Dogs in Thailand and Its Genetic Diversity among Asian Countries

Ancylostoma ceylanicum is a zoonotic helminth that is commonly found in domestic dogs and cats throughout Asia but is largely neglected in many countries. This study aimed to confirm the species of hookworm in dogs and soil environments and investigate the evolutionary analyses of A. ceylanicum among Thai and Asian populations. In a total of 299 dog fecal samples and 212 soil samples from 53 temples, the prevalence rates of hookworm infection by microscopic examination were 26.4% (79/299) and 10.4% (22/212) in dog and soil samples, respectively. A PCR-RFLP targeting the ITS region was then utilized to identify the hookworm species. In dogs, A. ceylanicum was the main hookworm species, and the rates of A. ceylanicum and A. caninum infections were 96.6% and 3.5%, respectively. The genetic characterization and diversity indices of the A. ceylanicumcox1 gene among Thai and Asian populations were evaluated. Nine haplotypes were identified from Thai A. ceylanicum, in which the haplotype diversity and the nucleotide diversity were 0.4436 and 0.0036, respectively. The highest nucleotide diversity of Chinese A. ceylanicum populations suggested that it could be the ancestor of the populations. Pairwise fixation indices indicated that Thai A. ceylanicum was closely related to the Malaysian population, suggesting a gene flow between these populations. The temples with hookworm-positive dogs were associated with the presence of hookworm-contaminated soil, as these levels showed an approximately four-fold increase compared with those in temples with hookworm-negative dogs (OR = 4.38, 95% CI: 1.55-12.37). Interestingly, the genotypes of A. ceylanicum in the contaminating soil and infecting dogs were identical. Therefore, increased awareness and concern from the wider public communities with regard to the responsibility of temples and municipal offices to provide proper deworming programs to community dogs should be strongly endorsed to reduce the risk of the transmission of this zoonotic disease. In addition, parasitic examination and treatment should be strongly implemented before dogs are imported and exported worldwide.

Isolation and Characterization of Novel Trichomonas gallinae Ribotypes Infecting Domestic and Wild Birds in Riyadh, Saudi Arabia

Trichomonas gallinae, a single-celled protozoan parasite, is a causative agent of the disease trichomonosis, which is distributed worldwide and has recently been highlighted as a pandemic threat to several wild bird species. The aim of this study was to determine the prevalence and genotypic diversity of T. gallinae in Riyadh, Saudi Arabia. For this purpose, 273 oral swab samples from different bird species (feral pigeon Columba livia, common mynah Acridotheres tristis, chicken Gallus gallus domesticus, turkey Meleagris gallopavo, and ducks Anatidae) were collected and tested for T. gallinae infection with InPouch™ TV culture kits. The results showed that the overall prevalence of T. gallinae in these samples was 26.4% (n = 72). The PCRs were used to detect the internal transcribed spacer (ITS) region of T. gallinae, and the results of the sequence analysis indicated genetic variation. Among 48 sequences, we found 15 different ribotypes, of which 12 were novel. Three had been previously described as ribotypes A, C, and II. To our knowledge, this study demonstrated the presence of T. gallinae strain diversity in Saudi Arabian birds for the first time and revealed that ribotypes A and C are predominant among Riyadh birds.

First Report of Aspergillus niger causing Black rot of Grapes in Pakistan

In June 2015 & 2016, a postharvest survey of table grapes (Vitis vinifera) cv. King's Ruby, was carried out in five different commercial fruit markets of Rawalpindi (33°38'19.2″N, 73°01'45.0″E) district, Punjab Province. Symptoms appeared as brownish lesions with black sporulation on grapes berries. The incidence of these symptoms on bunches ranged from 12 to 17% at all sites. Symptomatic tissue pieces were surface-sterilized with 0.1% sodium hypochlorite (NaOCl) for 30 seconds, rinsed three times with sterile distilled water, dried on filter paper for 45 seconds, and incubated on potato dextrose agar (PDA) at 25°C. After 3 days, dark brown to black mycelium were formed on PDA media. A total of 24 isolates were examined morphologically. The apex of the conidiophore was observed to be radiate. Vesicles were found to be spherical and covered with irregular metulae and phialides. Conidia were globose or subglobose measured (3.14 μm ± 2.24 in averaged diameter: n=50), dark brown to black, with roughened cell walls. The conidiophores were also smooth-walled, hyaline, and became melanized toward the vesicle. These characteristics of the fungus were similar to those described for Aspergillus niger van Tiegh (de Hoog et al. 2000). For molecular identification, the internal transcribed spacer (ITS) region, beta-tubulin (Bt) gene and partial RNA polymerase II largest subunit (RPB2) gene of representative isolate (Asp.n02) was amplified using primers ITS1/ITS4, BT2a/BT2b and RPB2-6F/RPB2-7R respectively (White et al., 1990; Glass & Donaldson, 1995; Liu et al. 1999). Sequences were deposited in GenBank (ITS, MN658871; Bt2, MT117924; and RPB2, MT318289). Based on BLAST analysis, sequences of the ITS region, Bt2 genes, and RPB2 gene showed 99 to 100% similarity of isolate Asp.n02 to Aspergillus niger (Accession Nos. MK307680.1, MN195121.1, MF078661.1 for ITS gene, MN567299.1, MK451029.1, MK451020.1 for Bt2 gene, and MK450788.1, MK450790.1 for RPB2 gene). To complete Koch's postulates, 10-µl aliquots of spore suspensions (106 spores/ml) of isolate: Asp.n 02 was pipetted onto three non-wounded and four wounded (5 mm diam) asymptomatic grape berries cv. King's Ruby (seven berries per isolate), Sterile distilled water was applied to asymptomatic berries similaries to serve as a negative control (Ghuffar et al. 2018; Jayawardena et al. 2018). Berries were incubated at 25 ± 2°C in sterile moisture chambers, and the experiment was conducted twice. Brownish lesions leading to black sporulation similar to the original symptoms were observed on both wounded and non-wounded inoculated berries after 3 days, whereas no symptoms were recorded on the negative control. The morphology of the fungus that was re-isolated from each of the inoculated berries was identical to that of the original cultures. Aspergillus niger was reported previously in Europe and Israel causing mycotoxin (Ochratoxin A) OTA production on Table grapes (Bau et al. 2006). To our knowledge, this is the first report of Aspergillus niger causing black rot of grapes in Pakistan. This finding will help to plan effective disease management strategies against the black rot of grapes in Pakistan.

First Report of Aspergillus niger causing Black rot of Grapes in Pakistan

In June 2015 & 2016, a postharvest survey of table grapes (Vitis vinifera) cv. King's Ruby, was carried out in five different commercial fruit markets of Rawalpindi (33°38'19.2″N, 73°01'45.0″E) district, Punjab Province. Symptoms appeared as brownish lesions with black sporulation on grapes berries. The incidence of these symptoms on bunches ranged from 12 to 17% at all sites. Symptomatic tissue pieces were surface-sterilized with 0.1% sodium hypochlorite (NaOCl) for 30 seconds, rinsed three times with sterile distilled water, dried on filter paper for 45 seconds, and incubated on potato dextrose agar (PDA) at 25°C. After 3 days, dark brown to black mycelium were formed on PDA media. A total of 24 isolates were examined morphologically. The apex of the conidiophore was observed to be radiate. Vesicles were found to be spherical and covered with irregular metulae and phialides. Conidia were globose or subglobose measured (3.14 μm ± 2.24 in averaged diameter: n=50), dark brown to black, with roughened cell walls. The conidiophores were also smooth-walled, hyaline, and became melanized toward the vesicle. These characteristics of the fungus were similar to those described for Aspergillus niger van Tiegh (de Hoog et al. 2000). For molecular identification, the internal transcribed spacer (ITS) region, beta-tubulin (Bt) gene and partial RNA polymerase II largest subunit (RPB2) gene of representative isolate (Asp.n02) was amplified using primers ITS1/ITS4, BT2a/BT2b and RPB2-6F/RPB2-7R respectively (White et al., 1990; Glass & Donaldson, 1995; Liu et al. 1999). Sequences were deposited in GenBank (ITS, MN658871; Bt2, MT117924; and RPB2, MT318289). Based on BLAST analysis, sequences of the ITS region, Bt2 genes, and RPB2 gene showed 99 to 100% similarity of isolate Asp.n02 to Aspergillus niger (Accession Nos. MK307680.1, MN195121.1, MF078661.1 for ITS gene, MN567299.1, MK451029.1, MK451020.1 for Bt2 gene, and MK450788.1, MK450790.1 for RPB2 gene). To complete Koch's postulates, 10-µl aliquots of spore suspensions (106 spores/ml) of isolate: Asp.n 02 was pipetted onto three non-wounded and four wounded (5 mm diam) asymptomatic grape berries cv. King's Ruby (seven berries per isolate), Sterile distilled water was applied to asymptomatic berries similaries to serve as a negative control (Ghuffar et al. 2018; Jayawardena et al. 2018). Berries were incubated at 25 ± 2°C in sterile moisture chambers, and the experiment was conducted twice. Brownish lesions leading to black sporulation similar to the original symptoms were observed on both wounded and non-wounded inoculated berries after 3 days, whereas no symptoms were recorded on the negative control. The morphology of the fungus that was re-isolated from each of the inoculated berries was identical to that of the original cultures. Aspergillus niger was reported previously in Europe and Israel causing mycotoxin (Ochratoxin A) OTA production on Table grapes (Bau et al. 2006). To our knowledge, this is the first report of Aspergillus niger causing black rot of grapes in Pakistan. This finding will help to plan effective disease management strategies against the black rot of grapes in Pakistan.

Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing

Fungal community analyses in homes have been attracting attention because fungi are now generally considered to be allergens. Currently, these analyses are generally conducted using the culture method, although fungal communities in households often contain species that are difficult to culture. In contrast, next-generation sequencing (NGS) represents a comprehensive, labor- and time-saving approach that can facilitate species identification. However, the reliability of the NGS method has not been compared to that of the culture method. In this study, in an attempt to demonstrate the reliability of this application, we used the NGS method to target the internal transcribed spacer 1 (ITS1) in the fungal genome, conducted fungal community analyses for 18 house-dust samples and analyzed fungal community structures. The NGS method positively correlated with the culture method regarding the relative abundance of Aspergillus, Penicillium, Cladosporium and yeasts, which represent the major fungal components found in houses. Furthermore, several genera, such as Malassezia, could be sensitively detected. Our results imply that the reliability of the NGS method is comparable to that of the culture method and indicates that easily available databases may require modifications, including the removal of registrations that have not been sufficiently classified at the genus level.

Morphological and molecular characterization of a new ciliate Nyctotheroides grimi n. sp. (Armophorea, Clevelandellida) from Chinese frogs

A new species of clevelandellid ciliate, Nyctotheroides grimi n. sp., is described from the frog Fejervarya limnocharis. Light and scanning electron microscopy were used for the morphological studies, and the DNA encoding the SSU rRNA gene (SSU rDNA) and the ITS1-5.8S subunit rRNA-ITS2 region (ITS) were sequenced for genetic comparisons and phylogenetic analysis. The main distinctive morphological feature is a knob-like projection in the left-posterior end; other differential characters are the cell size, the length of the oral groove and the shape of the infundibulum. Nyctotheroides grimi possess an apical suture line in the left and right side of the anterior end and in the left side of the caudal end. In the phylogenetic analyses, the new species engroups with other Nyctotheroides species forming a monophyletic group. The high similarity in the SSU rDNA and ITS sequences between Nyctotheroides species suggests a relative recent divergence. The genetic data and the different host range support the separation of Nyctotheroides and Nyctotherus; however the morphological criterion based on the presence (in Nyctotheroides)/absence (in Nyctothterus) of an apical kinetal suture line should be modified to consider the presence of kinetal suture lines in the apical and/or the caudal left side in Nyctotheroides.

First Report of Root Rot Caused by Phytophthora bilorbang on Olea europaea in Italy

Leaf chlorosis, severe defoliation and wilt associated with root rot were observed on mature olive trees cv. Nera di Gonnos in an experimental orchard at Mirto Crosia (Calabria, southern Italy). An oomycete was consistently isolated from rotten roots of symptomatic olive trees. It was identified as Phytophthora bilorbang by morphological characters and sequencing of Internal Transcribed Spacer (ITS) regions of ribosomal DNA (rDNA). Pathogenicity was verified by inoculating potted two-month-old rooted cuttings of Olea europaea var. Nera di Gonnos in a soil infestation trial. P. bilorbang was re-isolated from roots of symptomatic, artificially inoculated olive cuttings to fulfill Koch's postulates. This is the first report of P. bilorbang on O. europaea L. and on a species of the Oleaceae family worldwide.

Enterocytozoon bieneusi in donkeys from Xinjiang, China: prevalence, molecular characterization and the assessment of zoonotic risk

Background

Enterocytozoon bieneusi, a zoonotic pathogen, has the potential to infect both immunocompromised and immunocompetent humans. It is found in large number of animals; however, not much is known regarding its prevalence in equine animals, particularly donkeys. This is the first molecular epidemiological evaluation of E. bieneusi in 178 free-ranging donkeys from five countrysides; and 502 farmed donkeys from 18 farms in 12 cities of Xinjiang, China by Nested PCR.

Results

E. bieneusi was detected in 2.5% (17/680) donkeys, with 2.6% (13/502) in farmed and 2.2% (4/178) in free-ranging ones. Sequence analysis identified eight ITS genotypes, all belonging to zoonotic Groups 1 or 2, including six known genotypes: horse1 (n = 5), D (n = 3), NCD-2 (n = 3), BEB6 (n = 2), BEB4 (n = 1), and NIAI (n = 1); and two new genotypes: XJD1 (n = 1) and XJD2 (n = 1).

Conclusions

This is the first report confirming the presence of E. bieneusi in donkeys in Xinjiang, China, and indicates the possibility of zoonotic transmission of this pathogenic parasite.

Morphological description of Opalina obtrigonoidea Metcalf, 1923 (Heterokonta, Opalinea) from Duttaphrynus melanostictus and evaluation of the ITS region as a suitable genetic marker for inter-species identification in Opalina

The redescription of Opalina obtrigonoidea Metcalf, 1923, collected from the rectum of the toads Duttaphrynus melanostictus, is presented in this paper based on detailed morphological information and molecular data. Our results revealed that O. obtrigonoidea varies greatly in body dimensions. Its morphological characteristics allow its differentiation from Opalina undulata. Surprisingly, we sequenced its SSU rDNA-ITS1-5.8S rDNA-ITS2-LSU rDNA (5' end) and found the SSU rDNA of O. obtrigonoidea is nearly identical to that of O. undulata. However, there are differences in both the ITS1 and ITS2 regions that allow their distinction and confirm the morphological differences. Our results indicate that O. obtrigonoidea and O. undulata are closely related species in which morphological and genetic markers have evolved at different speeds. Due to this, the SSU rDNA gene may not be a valid marker for inter-species identification in Opalina, but the ITS is a valid marker for differentiating species in this genus.

Molecular detection of Enterocytozoon bieneusi in farm-raised pigs in Hainan Province, China: infection rates, genotype distributions, and zoonotic potential

Enterocytozoon bieneusi is a zoonotic fungal pathogen with a high degree of host diversity that can parasitize many animals, including humans. Pigs may play an important role in the epidemiology of E. bieneusi as reservoir hosts. Nevertheless, the genotypes of E. bieneusi in pigs in China remain poorly understood. The aim of this study was to determine the prevalence of E. bieneusi infection amongst pigs raised on farms from four cities of Hainan Province, using nested polymerase chain reaction (PCR) of the partial small subunit of the ribosomal RNA gene, and to identify genotypes of E. bieneusi isolates based on sequence analysis of the ribosomal internal transcribed spacer (ITS) region. Among 188 stool samples, E. bieneusi was detected in 46.8% (88/188). Eight genotypes including four known (EbpA, CS-4, MJ14, and CHG19) and four novel (HNP-I – HNP-IV) genotypes were identified. Using phylogenetic analysis, genotypes EbpA, CS4, CHG19, HNP-III, and HNP-IV were clustered into zoonotic Group 1, while the remaining three genotypes (MJ14, HNP-I, and HNP-II) clustered into Group 10. The high prevalence of zoonotic genotypes of E. bieneusi among pigs suggests that pig farming is a potential source of human infection. Additionally, this is the first identification of genotypes in Group 10 in pigs indicating unique epidemic features of E. bieneusi in pigs in Hainan Province, the southernmost part of China.

Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax. When using the complete k-mer frequency histogram (up to 9 × 105), the programs did not deviate significantly, estimating an average rooibos genome size of 1.03 ± 0.04 Gbp. Differences between the flow cytometry and biocomputational estimates are discussed.

Step-by-Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data

The nuclear ribosomal DNA internal transcribed spacer (ITS) is accepted as the genetic marker or barcode of choice for the identification of fungal samples. Here, we present a protocol to analyze fungal ITS data, from quality preprocessing of raw sequences to identification of operational taxonomic units (OTUs), taxonomic classification, and assignment of functional traits. The pipeline relies on well-established and manually curated data collections, namely the UNITE database and the FUNGuild script. As an example, real ITS data from culturable endophytic fungi were analyzed, providing detailed descriptions for every step, parameter, and downstream analysis, and finishing with a phylogenetic analysis of the sequences and assigned ecological roles. This article constitutes a comprehensive guide for researchers that have little familiarity with bioinformatic analysis of essential steps required in further ecological studies of fungal communities. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Raw sequencing data processing Support Protocol: Building a BLAST database Basic Protocol 2: Obtaining information from databases Basic Protocol 3: Phylogenetic analysis.

Genetic assessment of the internal transcribed spacer region (ITS1.2) in Mangifera indica L. landraces

Mango (Mangifera indica) is one of the most important tropical fruits in the world. Twenty-two genotypes of native mangoes from different regions of southern Iran (Hormozgan and Kerman) were collected and analyzed for the ribosomal genes. GC content was found to be 55.5%. Fu and Li's D* test statistic (0.437), Fu and Li's F* test statistic (0.500) and Tajima's D (1.801) were positive and nonsignificant. A total of 769 positions were identified (319 with insertion or deletion including 250 polymorphic and 69 monomorphic loci; 450 loci without any insertion or deletion including 35 Singletons and 22 haplotypes). Nucleotide diversity of 0.309 and a high genetic differentiation including Chi square of 79.8; P value of 0.3605 and df value of 76 was observed among mango genotypes studied. The numerical value of the ratio dN/dS (0.45) indicated a pure selection in the examined gene and the absence of any key changes. Cluster analysis differentiated the mango used in this research (M. indica L.) into two genotypes but could not differentiate their geographical locations. The results of this study indicated that a high genetic distance exists between HajiGholam (Manojan) and Arbabi (Rodan) genotypes and showed higher genetic diversity in mango of Rodan region. Results of present study suggested that for successful breeding, the genotypes of Rodan region mango especially Arbabi mango can be used as a gene donor and ITS can be a suitable tool for genetic evaluations of inter and intra species.

Genotyping of Enterocytozoon bieneusi among captive long-tailed macaques (Macaca fascicularis) in Hainan Province: High genetic diversity and zoonotic potential

Enterocytozoon bieneusi is a potentially important zoonotic pathogen. However, there is no information on E. bieneusi infection of captive long-tailed macaques (Macaca fascicularis) in Hainan Province, China. Here 193 fecal specimens of M. fascicularis were collected from a breeding base in Hainan Province, China, housing non-human primates for experimental use. E. bieneusi was identified and genotyped by nested PCR analysis of the internal transcribed spacer (ITS) region of the rRNA gene. A total of 59 (30.6%) specimens were PCR-positive for E. bieneusi and 16 ITS genotypes were identified including nine known genotypes: Type IV (n = 19), D (n = 11), CM1 (n = 8), PigEBITS7 (n = 4), Pongo2 (n = 4), Peru8 (n = 3), Peru11 (n = 1), WL21 (n = 1) and CM2 (n = 1) and seven novel genotypes HNM-I to HNM-VII (one each). Importantly, genotypes D, Type IV, Peru8, PigEBITS7, and Peru11, which were the predominant (38/59, 64.4%) genotypes identified among captive M. fascicularis in this study, are also well-known human-pathogenic genotypes. All the genotypes of E. bieneusi identified here, including the seven novel ones, belonged to zoonotic Group 1. This is the first report of the identification of E. bieneusi in M. fascicularis in Hainan Province, China. The finding that the numerous known human-pathogenic types and seven novel genotypes of E. bieneusi all belong to zoonotic Group 1 indicates the possibility of transmission of this important pathogenic parasite between M. fascicularis and humans.

Auxarthron alboluteum related to non-dermatophytic toenail infection in Kurdistan region, Iraq: A case report

We report a rare case of non-dermatophytic onychomycosis of the big toenail caused by Auxarthron alboluteum in a 63-years old Iraqi female with a history of diabetes. The big toenail showed distal subungual onychomycosis with extensive yellow-white discoloration. Identification of the causative agent was confirmed by morphological and microscopical characteristics in culture and analysis of ITS-rDNA region. To the best of our knowledge, the isolated Auxarthron alboluteum reported here is a new etiologic species of nail infection in Iraq and this is the first case of its kind to be reported in the world.

Evolutionary Origin and Host Range of Plagiotoma lumbrici (Ciliophora, Hypotrichia), an Obligate Gut Symbiont of Lumbricid Earthworms

Four common earthworm species, the anecic Lumbricus terrestris, the endogeic Octolasion tyrteum as well as the epigeic Eisenia fetida and Dendrobaena veneta, were examined for the presence of the microbial gut symbiont Plagiotoma lumbrici. The evolutionary origin of this endobiotic microbe was reconstructed, using the 18S rRNA gene, the ITS1-5.8S-ITS2 region, and the first two domains of the 28S rRNA gene. Plagiotoma lumbrici was exclusively detected in the anecic Lumbricus terrestris. Multigene analyses and the ITS2 secondary structure robustly determined the phylogenetic home of Plagiotoma lumbrici populations within the oxytrichid Dorsomarginalia (Spirotrichea: Hypotrichia) as a sister taxon of the free-living Hemiurosomoida longa. This indicates that earthworms obtained their gut endosymbiont by ingesting soil/leaf litter containing oxytrichine ciliates that became adapted to the intestinal tract of earthworms. Interestingly, according to the literature data, Plagiotoma lumbrici was detected in multiple anecic and some epigeic but never in endogeic earthworms. These observations suggest that Plagiotoma lumbrici might be adapted to certain gut conditions and the lifestyle of anecic Lumbricidae, such as Lumbricus, Aporrectodea, and Scherotheca, as well as of some co-occurring epigeic Lumbricus species.

Identification of medically important yeasts by sequence analysis of the internal transcribed spacer and D1/D2 region of the large ribosomal subunit

BACKGROUND

The prevalence of opportunistic yeast infections has increased in recent decades as the result of an increasing immunocompromised patient population.

AIMS

To evaluate ribosomal RNA (rRNA) gene sequence to identify medically important yeast species, to investigate the performance of both the rRNA gene internal transcribed spacer (ITS) and D1/D2 region in identifying clinically relevant yeasts, and to compare these results with those of a standard phenotypic method.

METHODS

Both regions from 50 yeast strains, comprising 45 clinical isolates and 5 reference strains, were amplified using PCR and then sequenced. The sequences were compared to reference data available from the GenBank database of the National Center for Biotechnology Information using the BLASTn tool.

RESULTS

Using ID32C, 88% (44/50) of all strains were identified accurately at the species level, although 6% were misidentified; two Candida eremophila isolates were identified as Candida glabrata and Candida tropicalis, and one Saprochaete clavata isolate was identified as Saprochaete capitata. Two of the four isolates identified by phenotypic methods as Trichosporon asahii were defined so by analyzing the ITS region, but the remaining two were not distinguishable from closely related species. Based on the D1/D2 region, these four isolates had 100% sequence identity with T. asahii, Trichosporon japonicum, and Trichosporon asteroides. The isolate identified as Trichosporon inkin using ID32C could not be distinguished from Trichosporon ovoides by analyzing the ITS and D1/D2 regions.

CONCLUSIONS

Identifying medically important yeasts by sequencing the ITS and D1/D2 region is a rapid and reliable alternative to conventional identification methods. For a diagnostic algorithm, we suggest a two-step procedure integrating conventional methods (e.g. microscopic morphology on corn meal agar with Tween® 80 and API ID32C®) and sequence analysis of the ITS and D1/D2 region.

Genotype identification and phylogenetic analysis of Enterocytozoon bieneusi in farmed black goats (Capra hircus) from China's Hainan Province

Enterocytozoon bieneusi is an important pathogen commonly found in humans and animals. Farmed animals with close contact to humans are important hosts of E. bieneusi. The role of goats in the transmission of E. bieneusi, however, remains unclear. In this study, 341 fresh fecal samples of black goats were collected from five locations in Hainan Province, China. Enterocytozoon bieneusi was identified and genotyped by sequences of the internal transcribed spacer (ITS) region. Phylogenetic analysis was performed by constructing a neighbor-joining tree of the ITS gene sequences. The average prevalence of E. bieneusi in black goats was 24.0% (82/341) with rates ranging from 6.3% (4/63) to 37.2% (32/86) across the locations (χ² = 17.252, p < 0.01). Eight genotypes of E. bieneusi were identified, including six known genotypes: CHG5 (n = 47); CHG3 (n = 23); CHG2 (n = 4); CM21 (n = 3); D (n = 2); and AHG1 (n = 1), and two novel genotypes termed HNG-I (n = 1) and HNG-II (n = 1). In the phylogenetic tree, genotype D was clustered into Group 1 and the other identified genotypes were included in Group 2. This represents the first report identifying E. bieneusi in black goats from Hainan Province, with a high prevalence and wide occurrence demonstrated. The two new genotypes identified provide additional insights into the genotypic variations in E. bieneusi. Due to the small percentage of zoonotic genotypes in these animals, there is minimal risk of zoonotic transmission of E. bieneusi.

Russula swatica: A new species of Russula based on molecular, light microscopy, and scanning electron microscopy analyses from Swat Valley of Khyber Pakhtunkhwa province of Pakistan

Himalayan range of Pakistan is one of the diversity rich hotspots of the world. Many areas are yet to be explored here to discover new species of organisms including fungi. During present research, Swat District of Pakistan was explored for fungal diversity. One new species of mushroom Russula swatica (Russulales) is described from Himalayan range of Pakistan and analyzed by light microscopy and scanning electron microscopy as well as by molecular markers. A comprehensive description, photographs, and comparisons with morphologically similar and phylogenetically related species are provided. Conclusions of its phylogenetic relationships within the genus are provided based on the sequence of the nuclear internal transcribed spacer region.

Hybrid identification in Nothofagus subgenus using high resolution melting with ITS and trnL approach

The genus Nothofagus is the main component of southern South American temperate forests. The 40 Nothofagus species, evergreen and deciduous, and some natural hybrids are spread among Central and Southern Chile, Argentina, New Zealand, Australia, New Guinea and New Caledonia. Nothofagus nervosa, Nothofagus obliqua and Nothofagus dombeyi are potentially very important timber producers due to their high wood quality and relative fast growth; however, indiscriminate logging has degraded vast areas the Chilean forest causing a serious state of deterioration of their genetic resource. The South of Chile has a large area covered by secondary forests of Nothofagus dombeyi. These forests have a high diversity of species, large amount of biomass and high silvicultural potential. This work shows a case of hybrid identification in Nothofagus subgenus in different secondary forests of Chile, using high resolution melting. Unknown samples of Nothofagus subgenus are genetically distinguishable with the ITS region of Nothofagus antarctica, Nothofagus nitida and N. obliqua species. It was not possible to distinguish between unknown samples of Andean versus coastal origin. Melting curves with ITS approach of unknown material are genetically similar, positioned between N. dombeyi and N. antarctica and distant from N. nitida. The unknown samples are genetically very close to Nothofagus dombeyi. This suggests the presence of hybrid individuality between species (N. dombeyi × N. antarctica) with the possibility of introgression towards the gene pool of N. antarctica, producing the deciduous foliage that is both present. The trnL locus has no distinction between the N. dombeyi and N. antarctica species, since a similar melting curve is present and equal Tm (80.00 °C). The trnL locus cannot be genetically distinguished from one unknown sample of Nothofagus to another, as highlighted in this study.

On the occurrence and molecular identification of Contracaecum larvae (Nematoda: Anisakidae) in Mugil cephalus from Turkish waters

Anisakis and Contracaecum species are fish borne zoonotic nematodes. In our previous studies, other larval anisakid and raphidascarid nematodes, Anisakis and Hysterothylacium species, were genetically identified in marine fish from Turkish waters. However, there is no information on molecular identification of larval Contracaecum species in marine fish from Turkey. Therefore, the aim of this study was only to investigate the presence and molecular identification of Contracaecum species in commonly commercialized marine fish from Turkish waters. A total of 475 marine fish, which belong to 21 different species, were sampled from the Aegean (FAO 37.3.1), Mediterranean (FAO 37.3.2), and Black Sea (FAO 37.4.2). The prevalence of Contracaecum L3 larvae in the Aegean Sea was identified as 10% in Mugil cephalus. All Contracaecum L3 larvae were molecularly characterized with RFLP targeting the ITS region and rrnS gene. Moreover, all larvae were analyzed by sequencing of ITS region, rrnS and cox2 gene. All Contracaecum larvae were identified as C. overstreeti based on the cox2 sequence analysis. This is the first report of C. overstreeti larvae in M. cephalus as paratenic and intermediate hosts. Furthermore, the analysis reveals novel information on ITS region. Additionally, the rrnS gene of C. overstreeti was also achieved and deposited in Genbank for the first time. The PCR-RFLP patterns of the ITS region and rrnS gene from C. overstreeti were presented in the present study. Consequently, the presence of C. overstreeti larvae in M. cephalus from the Aegean Sea may also potentially capable of inducing allergic sensitization in humans.

Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition

Copper-based fungicides are routinely used for wood and plant protection, which can lead to an enrichment of copper-tolerant microbial communities in soil. To investigate the effect of such wood preservatives on the soil fungal and bacterial community compositions, five different vineyard and fruit-growing soil environments were evaluated using incubation studies over time. Pine sapwood specimens were impregnated with either water or different biocide treatment solutions containing a mixture of copper, triazoles, and quaternary ammonium compounds (CuTriQAC), a mixture of triazoles and quaternary ammonium compounds (TriQAC), or copper alone (Cu). Specimens were incubated in soil from each sample site for 8, 16, 24, and 32 weeks. The effects of preservative treatment on the modulus of elasticity (MOE) of the wood specimens and on the soil fungal as well as bacterial community composition at the soil-wood interface were assessed by quantitative PCR and amplicon sequencing of the fungal internal transcribed spacer (ITS) region and bacterial 16S rRNA gene. Specimens impregnated with CuTriQAC and Cu showed decreased MOE and reduced fungal and bacterial copy numbers over time compared to those impregnated with water and TriQAC. Fungal but not bacterial community composition was significantly affected by wood preservative treatment. The relative abundance of members of the family Trichocomaceae compared to other genera increased in the presence of the Cu and CuTriQAC treatments at three sites, suggesting these to be Cu-tolerant fungi. In conclusion, the copper-containing treatments resulted in marginally increased MOE, lowered microbial gene copy numbers compared to those in the TriQAC and water treatments, and thus enhanced wood protection against soil microbial wood degradation.IMPORTANCE Copper-containing rather than TRIQAC formulations are efficient wood preservatives irrespective of the origin and composition of the soil microbial communities. However, some fungi appear to be naturally insensitive to copper and should be the focus of future wood preservative formulations to facilitate the life span of wooden construction in contact with soil while also minimizing the overall environmental impact.

Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods

Fungal endophytes are the most ubiquitous plant symbionts on earth and are phylogenetically diverse. Studies on the fungal endophytes in tobacco have shown that they are widely distributed in the leaves, stems, and roots, and play important roles in the composition of the microbial ecosystem of tobacco. Herein, we analyzed and quantified the endophytic fungi of healthy tobacco leaves at the seedling stage (SS), resettling growth stage (RGS), fast-growing stage (FGS), and maturing stage (MS) at three altitudes (600, 1000, and 1300 m). We sequenced the internal transcribed spacer (ITS) region of fungal samples to delimit operational taxonomic units (OTUs) and phylogenetically characterize the communities. The results showed that the numbers of clustering OTUs at SS, RGS, FGS, and MS were 516, 709, 469, and 428, respectively. At the phylum level, species in Ascomycota and Basidiomycota had absolute predominance, representing 97.8% and 2.0% of the total number of species, respectively. We also found the number of fungi at the RGS and FGS stages was higher than those at the other two stages. Additionally, OTU richness was determined by calculating the Observed Species, Shannon, Simpson, Chao1, abundance-based coverage estimator (ACE), Good's coverage and phylogenetic distance (PD)_whole_tree indices based on the total number of species. Our results showed RGS samples had the highest diversity indices. Furthermore, we found that the diversity of fungal communities tended to decrease with increasing altitude. The results from this study indicated that tobacco harbors an abundant and diverse endophytic fungal community, which provides new opportunities for exploring their potential utilization.

Evaluation of six regions for their potential as DNA barcodes in epiphyllous liverworts from Thailand

PREMISE OF THE STUDY

Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms.

METHODS

With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers (rbcL, matK, trnL-F, psbA, ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance-based and tree-based approaches with nucleotide data.

RESULTS

The amplification success was relatively high (70-90%) with all of the markers, except for matK, which yielded no success. The barcoding gap, as calculated from the difference between inter- and intraspecific genetic distances, was the highest in ITS2, whereas the highest numbers of monophyletic groups were found with ITS2 and rbcL.

DISCUSSION

rbcL should be used as a main barcoding marker with the addition of ITS2 for epiphyllous species. The development of DNA barcoding as a tool for quantifying species diversity will provide a rapid and reliable identification tool for epiphyllous bryophytes.

Evidence of cryptic species in the genus Tinaminyssus (Acari: Rhinonyssidae) based on morphometrical and molecular data

The study of cryptic species allows to describe and to understand biodiversity, and the evolutionary processes shaping it. Mites of the family Rhinonyssidae are permanent parasites of the nasal cavities of birds, currently including about 500 described species and 12 genera. Here, we tested the hypothesis that mites from five populations of the genus Tinaminyssus-three isolated from European turtle doves (Streptopelia turtur), and two from Eurasian collared doves (Streptopelia decaocto; Aves: Columbiformes)-are, in fact, two cryptic species inhabiting different hosts. First, we performed a morphometrical study on 16 traits. Then, we used the ITS1-5.8S rDNA-ITS2 nuclear region (ITS region), and a fragment of the mitochondrial cytochrome c-oxidase 1 (COI) to carry out phylogenetic and species delimitation analyses on Tinaminyssus species. Morphological analyses revealed a lack of biometric differentiation among Tinaminyssus populations from the two host species. However, molecular analyses indicated a high degree of genetic differentiation between populations of Tinaminyssus sp. from S. turtur and S. decaocto. Overall, results show that they can be considered as different cryptic species, suggesting a case of evolutionary stasis, likely because of the anatomical similarity between closely-related bird host species.

Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing

Microcystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (HTS) method was developed to detect the internal transcribed spacer (ITS) regions between 16S and 23S rRNA region of Microcystis populations along a typical water system in Yuqiao Reservoir-Haihe River in Tianjin, northern China. A total of 629,341 reads were obtained and clustered into 2005 operational taxonomic units (OTUs). Analysis of alpha diversity indices showed that the Haihe River is more diverse than Yuqiao Reservoir. In general, the two water areas exhibit a clear differentiation pattern in OTU abundance, sharing genotypes from a small part of Yuqiao Reservoir with those in the Haihe River. Phylogenetic analysis further indicated the possible flexible evolution of Microcystis genotypes occurring in the research areas. This study provides the first exhaustive description of HTS method for detection of ITS region to evaluate Microcystis intra-species diversity and relationship.