Molecular and morphological identification of fungal species isolated from bealmijang meju

Bealmijang is a short-term aged paste made from meju, which is a brick of fermented soybeans and other ingredients. Different types of bealmijang are available depending on the geographic region or ingredients used. However, no study has clarified the microbial diversity of these types. We identified 17 and 14 fungal species from black soybean meju (BSM) and buckwheat meju (BWM), respectively, on the basis of morphology, culture characteristics, and internal transcribed spacer and beta-tubulin gene sequencing. In both meju, Aspergillus oryzae, Rhizopus oryzae, Penicillium polonicum, P. steckii, Cladosporium tenuissimum, C. cladosporioides, C. uredinicola, and yeast species Pichia burtonii were commonly found. Moreover, A. flavus, A. niger, P. crustosum, P. citrinum, Eurotium niveoglaucum, Absidia corymbifera, Setomelanomma holmii, Cladosporium spp. and unclassified species were identified from BSM. A. clavatus, Mucor circinelloides, M. racemosus, P. brevicompactum, Davidiella tassiana, and Cladosporium spp. were isolated from BWM. Fast growing Zygomycetous fungi is considered important for the early stage of meju fermentation, and A. oryae and A. niger might play a pivotal role in meju fermentation owing to their excellent enzyme productive activities. It is supposed that Penicillium sp. and Pichia burtonii could contribute to the flavor of the final food products. Identification of this fungal diversity will be useful for understanding the microbiota that participate in meju fermentation, and these fungal isolates can be utilized in the fermented foods and biotechnology industries.     

Molecular identification of a glucose transporter from fish muscle

In mammals and birds, several isoforms of facilitative glucose transporters have been identified (GLUT1-4), but no information is available regarding the molecules involved in glucose transport in other vertebrates. Here we report the cloning of a GLUT molecule from fish muscle with high sequence homology to GLUT4 and containing features characteristic of a functional GLUT. Fish GLUT is expressed predominantly in skeletal muscle, kidney and gill, which are tissues with known high glucose utilization. These results indicate that fish GLUT is structurally, and perhaps functionally, similar to the other known GLUTs expressed in muscle in mammalian and avian species.     

Molecular identification methods of fish species: reassessment and possible applications

Fish species identification is traditionally based on external morphological features. Yet, in many cases fishes and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. This work intends to provide an updated and extensive overview on the PCR-methods for fish species identification. Among the ten main methods developed, three PCR-RFLP, PCR-FINS and PCR-specific primers have been the most used. Two other emerging methods, namely real-time PCR and microarray technology, offer new potential for quantification of DNA and simultaneous detection of numerous species, respectively. Almost 500 species have been targeted in the past decade, among which the most studied belong to gadoids, scombroids, and salmonids. The mitochondrial cytochrome b gene was by far the most targeted DNA markers. The most common applications belonged to the forensic, taxonomic, and ecological fields. At last, some key problems, such as the degradation of DNA, the reliability of sequences, and the use of scientific names, likely to be encountered during the development of molecular identification methods are described. In conclusion, the tremendous advances in molecular biology in the past 10 years has rendered possible the study of DNA from virtually any substrates, offering new perspectives for the development of various applications, which will likely continue to increase in the future.     

Molecular identification of small cetacean samples from Peruvian fish markets

In the last 60 years, incidental entanglement in fishing gears (so called by-catch) became the main cause of mortality worldwide for small cetaceans and is pushing several populations and species to the verge of extinction. Thus, monitoring and quantifying by-catches is an important step towards proper and sustainable management of cetacean populations. Continuous studies indicated that by-catches and directed takes of small cetaceans in Peru greatly increased since 1985. Legal measures banning cetacean takes, enforced in 1994 and 1996, ironically made monitoring highly problematic as fishers continue catching these animals but utilize or dispose of carcasses clandestinely. Hence, in locations where cetaceans are landed covertly or already butchered, molecular genetic methods can provide the only means of identification of the species, sex, and sometimes the population of each sample. Here, we generate and analyse a fragment of the mitochondrial DNA cytochrome b gene and 5 nuclear microsatellite markers from 182 meat and skin samples of unidentified small cetaceans collected at three Peruvian markets between July 2006 and April 2007. Our results, compared to past surveys, indicate that Lagenorhynchus obscurus, Phocoena spinipinnis, Tursiops truncatus, Delphinus capensis, and D. delphis continue to be caught and marketed, but that the relative incidence of P. spinipinnis is highly reduced, possibly because of population depletion. The small number of possible sampling duplicates demonstrates that a high monitoring frequency is required for a thorough evaluation of incidental catches in the area. A wide public debate on by-catch mitigation measures is greatly warranted in Peru.     

Molecular approach to the identification of fish in the South China Sea

Background

DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world''s fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea.

Methodology/Principal Findings

DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species.

Conclusions/Significance

The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy.     

Molecular identification and morphological variations of Dermacentor albipictus collected from two deer species in northern Mexico

Experimental and Applied Acarology - In total, 57 ticks were collected from six white-tailed deer (Odocoileus virginianus) and three mule deer (O. hemionus) in northern Mexico during the 2017, 2018...     

Molecular identification of Bacteria and Eukarya inhabiting an Antarctic cryoconite hole

Inhabitants of a cryoconite hole formed in the Canada Glacier in the McMurdo Dry Valley region of Antarctica have been isolated and identified by small subunit (16S/18S) rDNA amplification, cloning, and sequencing. The sequences obtained revealed the presence of members of eight bacterial lineages (Acidobacterium, Actinobacteria, Cyanobacteria, Cytophagales, Gemmimonas, Planctomycetes, Proteobacteria, and Verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (Choiromyces), ciliate (Spathidium), and green algal (Pleurastrium) Eukarya. Bacterial recovery was approximately 20-fold higher at 4 degrees C and 15 degrees C than at 22 degrees C, and obligately psychrophilic bacteria were identified and isolated. Several of the rDNA molecules amplified from isolates and directly from cryoconite DNA preparations had sequences similar to rDNA molecules of species present in adjacent lake ice and microbial mat environments. This cryoconite hole community was therefore most likely seeded by particulates from these local environments. Cryoconite holes may serve as biological refuges that, on glacial melting, can repopulate the local environments.     

Molecular tools for the detection and identification of Ichthyobodo spp. (Kinetoplastida), important fish parasites

Ichthyobodo spp. are ectoparasitic flagellates of fish that may cause disease (ichthyobodosis), a common problem affecting the aquaculture industry worldwide. Ichthyobodosis in farmed fish is often associated with a range of other infectious agents and diagnosis in for example gill disease may be difficult. Sensitive and effective methods for detection and identification of Ichthyobodo spp. are needed to aid diagnosis of ichthyobodosis and epizootiological studies on Ichthyobodo spp. We have designed a specific quantitative real-time PCR assay targeting SSU rDNA for the detection of Ichthyobodo spp. infections. Also, several novel primer sets are presented for use in identification of Ichthyobodo spp. through PCR and sequencing. These PCR methods have been optimized and tested on samples from wild caught and farmed fish from different geographical areas in Norway. The real-time PCR assay has been tested for sensitivity and efficiency, and we present data demonstrating its use for absolute quantification of Ichthyobodo salmonis in tissue samples through RT-qPCR and qPCR. We demonstrate the use of the described set of molecular tools for the detection and sequencing of Ichthyobodo spp. from farmed and wild fish, and also show that they may aid the discovery of new Ichthyobodo species. The detection of light Ichthyobodo spp. infections through microscopy is time consuming and less sensitive compared to PCR methods. Initial real-time PCR testing and subsequent sequencing of positive samples is a powerful method that will increase diagnostic precision, aid carrier detection and promote species discoveries in the Ichthyobodonidae. Our preliminary observations indicate a high Ichthyobodo spp. diversity.     

Molecular identification and phylogeny of an aquatic moss species in Antarctic lakes

Due to the morphological variability, the identification of moss species can be difficult when the plant grows in submerged environments. The taxonomic status of an aquatic moss found in lakes of the Sôya Coast region, East Antarctica, had been controversial, and then, it was investigated by molecular phylogenetic and haplotype network analysis of two chloroplast regions (rps4 and trnL-F) and/or the nuclear ribosomal ITS region. Based on the results of the analyses, the moss was assigned to the genus Leptobryum and determined to be conspecific with Leptobryum wilsonii (Mitt.) Broth. described from South America. Almost no genetic variation was observed between all samples from Antarctic lakes and some samples of L. wilsonii from Chile. Molecular and geohistorical evidence suggests that immigration of L. wilsonii into Antarctic lakes took place during the Holocene via long-distance dispersal from South America. This study gives a clear example of the widespread assumption that most of the Antarctic moss species are post-glacial immigrants.     

Molecular and morphological differentiation in Limonium dufourii (Plumbaginaceae), an endangered Mediterranean plant

We have analyzed the morphological andmolecular variation in individuals from aLimonium dufourii population in which we hadpreviously described the presence of twomarkedly different molecular haplotypes bymeans of RAPDs and AFLPs. Ten differentmorphological variables were scored in each of72 individuals and their molecular haplotypegroup was established by RAPD analysis. Thevariation observed in the 10 morphometricvariables was explained by four dimensions in aprincipal components analysis, and a plot ofeach individual in the plane defined by the twofirst dimensions did not show any significantgrouping until the molecular haplotype wasincorporated into the plot. A discriminantanalysis performed using the molecularhaplotype as the grouping variable resulted in88.9% of correctly classified cases, thusreflecting a high correlation betweenmorphometric and molecular variation in theseindividuals. We discuss the relevance of thiscorrelation for the conservation strategypreviously proposed for this species.     

Molecular and morphological characterization of Pyricularia and allied genera

The phylogenetic relationships of Pyricularia species and species from related genera were established from sequences of the internal transcribed spacer ribosomal RNA gene. Phylogenetic analysis disclosed a consistent correlation with spore morphology. Most Pyricularia species studied, and two species of Dactylaria that have obpyriform conidia, fell within the Magnaporthaceae cluster with high bootstrap support. Pyricularia variabilis was more related to Dactylaria, Tumularia or Ochroconis species than to the Magnaporthaceae. Dactylaria and species of Nakataea, Ochroconis, Pyriculariopsis and Tumularia were distinct from the Magnaporthaceae, and the genus Dactylaria is polyphyletic. The combination of morphological and molecular characters, such as spore morphology and ITS ribosomal DNA sequences data, suggested that conidial shape could be a primary character to distinguish Pyricularia from related genera.     

Methylation - an uncommon modification of glycans

Abstract A methyl (Me) group on a sugar residue is a rarely reported event. Until now, this type of modification has been found in the animal kingdom only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. The monosaccharides involved as well as the positions of the Me groups on the sugar vary with species. Methylation appears to play a role in some recognition events, but details are still unknown. This review summarises the current knowledge on methylation of sugars in all types of organism.     

Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.     

Molecular and morphological identification of the alfalfa weevil larval parasitoids Bathyplectes anura and Bathyplectes curculionis to estimate the rate of parasitism

BioControl - The alfalfa weevil (Hypera postica Gyllenhal, Coleoptera: Curculionidae) is a major pest of alfalfa crops. Chemical control measures are inefficient, but the larvae are often infested...