Molecular Taxonomic Analysis Research Articles

Genomic analysis of Strongyloides stercoralis and Strongyloides fuelleborni in Bangladesh.

About 600 million people are estimated to be infected with Strongyloides stercoralis, the species that causes most of the human strongyloidiasis cases. S. stercoralis can also infect non-human primates (NHPs), dogs and cats, rendering these animals putative sources for zoonotic human S. stercoralis infection. S. fuelleborni is normally found in old world NHPs but occasionally also infects humans, mainly in Africa. Dogs in southeast Asia carry at least two types of Strongyloides, only one of which appears to be shared with humans ("dog only" and "human and dog" types). For S. stercoralis with molecular taxonomic information, there is a strong sampling bias towards southeast and east Asia and Australia. In order to extend the geographic range of sampling, we collected human and dog derived Strongyloides spp. and hookworms from two locations in Bangladesh and subjected them to molecular taxonomic and genomic analysis based on nuclear and mitochondrial sequences. All hookworms found were Necator americanus. Contrary to earlier studies in Asia, we noticed a rather high incidence of S. fuelleborni in humans. Also in this study, we found the two types of S. stercoralis and no indication for genetic isolation from the southeast Asian populations. However, we found one genomically "dog only" type S. stercoralis in a human sample and we found two worms in a dog sample that had a nuclear genome of the "dog only" but a mitochondrial genome of the "human and dog" type. S. fuelleborni may play a more prominent role as a human parasite in certain places in Asia than previously thought. The introgression of a mitochondria haplotype into the "dog only" population suggests that rare interbreeding between the two S. stercoralis types does occur and that exchange of genetic properties, for example a drug resistance, between the two types is conceivable.

Biology, distribution, and conservation of the Gamilaroi crayfish Euastacus gamilaroi Morgan, 1997 (Decapoda: Astacidea: Parastacidae), a freshwater crayfish from New South Wales, Australia

Abstract Euastacus gamilaroi Morgan 1997, the Gamilaroi crayfish, was initially described based on specimens collected in 1954 from Hanging Rock, New South Wales, but since then scant subsequent records hinder conservation of this endangered species. Extensive sampling during 2006–2023 delineated the distribution, habitat preferences, biological traits, and conservation status of the species. Together with concurrent molecular taxonomic analyses were extend the species range from headwater regions of highland streams above 960 m altitude of Burrows Creek to include highland streams of Duncan and Dungowan creeks (Peel-Namoi River/western drainage) and Tomalla, Back, and Ben Halls creeks (Barnard-Manning River/eastern drainage). We provide information on the distribution, biology, and ecological associations of the species. Results advocate for the classification of E. gamilaroi as an endangered species, recognizing its distinctive ecological niche and its status as a climate refugee, aiming to protect this rare species from climate-related challenges. We also present a taxonomic key differentiating E. gamilaroi from other species of Parastacidae in the region.

Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms

BackgroundCave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave’s Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave.ResultsThe cave’s biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique “CaveCurd” community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces.ConclusionsThe Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave’s ancient rock paintings.

Comparative cytogenetics of Hemorrhois hippocrepis and Malpolon monspessulanus highlights divergent karyotypes in Colubridae and Psammophiidae (Squamata: Serpentes)

Despite the growing interest in the evolutionary cytogenetics of squamates, chromosomal data are lacking for most taxa. We performed a preliminary molecular taxonomic analysis and a comparative cytogenetic study on Hemorrhois hippocrepis and Malpolon monspessulanus. We used a combination of standard karyotyping, Chromomycin A3/Methyl green staining, C-banding, Ag-NOR staining and NOR-FISH to provide the first karyotype description of H. hippocrepis and a re-description of the karyotype of M. monspessulanus, including chromosome markers, heterochromatin patterns and sex chromosome systems. Our results show that H. hippocrepis has 2 n = 36 chromosomes, with 16 macro- and 20 microchromosomes and NORs on the 6th pair. The 4th pair represents homomorphic (metacentric) ZW sex chromosomes, but the W chromosome is completely heterochromatic. Malpolon monspessulanus has 2 n = 44 chromosomes, with 20 macro- and 24 microchromosomes, NORs on the 6th telocentric pair. The 4th pair represents the sex chromosomes (ZZ/ZW), with a W chromosome smaller than the Z and completely heterochromatic. Comparing our cytogenetic data to those available from the literature, we note the occurrence and distribution of primitive and derived chromosomal characteristics and discuss the chromosome diversification in two snake clades belonging to Colubridae and Psammophiidae, respectively. We highlight that these two families followed different chromosome diversification pathways, characterised by a highly conserved karyotype structure in Colubridae and a higher chromosome variability in Psammophiidae, mostly driven by a progressive reduction of the chromosome number by means of chromosome fusions. We also provide cytotaxonomic insights supporting the distinction between M. monspessulanus and M. insignitus.

First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary

European beaver (Castor fiber L. 1758) is the biggest rodent species living in Europe. Beavers are semi-aquatic animals; they are defecating directly into the water; thus, they have an important role in spreading parasites related to water (e.g., protozoa and flukes). The first specimens of this once extinct rodent species in Hungary turned up in Szigetköz (upper flow of the Hungarian Danube) in 1991 dispersed from Austria. The reintroduction to Hungary started in 1996, and the population slowly increased in number up to around 4000 individuals, but the knowledge about their parasites is lacking. This is the first report on the metazoan parasites of beavers in Hungary and their molecular taxonomy. In the 5-year study, 47 beavers were trapped in four locations and euthanized with permission. Three different metazoan parasites were collected: larvae and adults of Platypsyllus castoris beetles, nymphs and adults of Schizocarpus sp. mites and eggs and adults of Stichorchis subtriquetrus flukes. From these three parasite species, molecular taxonomic studies were also carried out. The low number of metazoan parasites species detected in Hungarian beavers compared to other European countries (e.g., Poland) might be attributed to host population bottleneck effect during reintroduction. As parasites represent a significant component of the biodiversity and ecosystem, the conservation efforts should focus not only on host species but also on their parasites.

Four new enchytraeid species (Enchytraeidae, Annelida) from a Korean mountain (Jeoksangsan).

In this article, the descriptions of four new enchytraeid species (Enchytraeidae, Clitellata) from Jeoksangsan (Deogyusan National Park, Korea) are presented: Decimodrilus bulbosus sp. n., Fridericia jeoksangsaniensis sp. n., Fridericia sphaericoides sp. n. and Mesenchytraeus globiferus sp. n. Validity of these new species was verified by comparative morphological and molecular taxonomic analyses (based on the ITS region, CO1 and H3 genes). Apart from the new species, 13 other enchytraeid species were recorded in the soil samples of Jeoksangsan. In addition, new reference sequences are provided for the previously described Fridericia seoraksani Christensen Dzsa-Farkas, 2012.

High prevalence of Paramarteilia canceri infecting velvet swimming crabs Necora puber in Ireland.

The velvet swimming crab Necora puber has been fished in Ireland since the early 1980s and contributes significant income to smaller fishing vessels. From 2016 onwards, reduced landings have been reported. We undertook a full pathological investigation of crabs from fishing grounds at 3 sites on the west (Galway), southwest (Castletownbere) and east (Howth) coasts of Ireland. Histopathology, transmission electron microscopy and molecular taxonomic and phylogenetic analyses showed high prevalence and infection level of Paramarteilia canceri, previously only reported from the edible crab Cancer pagurus. This study provides the first molecular data for P. canceri, and shows its phylogenetic position in the order Paramyxida (Rhizaria). Other parasites and symbionts detected in the crabs were also noted, including widespread but low co-infection with Hematodinium sp. and a microsporidian consistent with the Ameson and Nadelspora genera. This is the first histological record of Hematodinium sp. in velvet crabs from Ireland. Four N. puber individuals across 2 sites were co-infected by P. canceri and Hematodinium sp. At one site, 3 velvet crabs infected with P. canceri were co-infected with the first microsporidian recorded from this host; the microsporidian 18S sequence was almost identical to Ameson pulvis, known to infect European shore crabs Carcinus maenas. The study provides a comprehensive phylogenetic analysis of this and all other available Ameson and Nadelspora 18S sequences. Together, these findings provide a baseline for further investigations of N. puber populations along the coast of Ireland.

Streptococcus shenyangsis sp. nov., a New Species Isolated from the Oropharynx of a Healthy Child from Shenyang China

A Gram-positive, catalase-negative, coccus-shaped, chain-forming organism isolated from the oropharynx of a healthy child in Shenyang, China, was subjected to phenotypic and molecular taxonomic analyses. 16S rRNA sequence analysis indicated that this bacterium represents a new member of the genus Streptococcus and is closely related to Streptococcus oralis subsp. dentisani DSM 27088. According to DNA-DNA hybridization analysis, strain D19T was less than 70% similar to other strains with close genetic relationships. Fatty acid analysis, physiological, and biochemical tests showed that strain D19T was different from the published Streptococcus species. The genome of strain D19T is 2,023,003bp long with a GC content of 39.9mol%. It contains 1889 protein-coding genes and 50 RNA genes. These results show that Streptococcus shenyangsis sp. nov. strain D19T is a new species.

Novel Effective Yeast Strains and Their Performance in High Gravity and Very High Gravity Ethanol Fermentations from Sweet Sorghum Juice

Yeasts were isolated from four potential sources, sweet sorghum juice, sugar cane juice, grapes and rambutan. The 27 yeast isolates were tested for their ethanol tolerance (15% v/v of ethanol) and ethanol fermentation performance in a synthetic ethanol production medium (200 g/L of total sugar). Only five isolates, SCJ04KKU, SCJ07KKU, SCJ09KKU, SCJ14KKU and SSJ01KKU could tolerate 15% ethanol and produce ethanol at levels higher than 55 g/L. The ethanol production efficiency from sweet sorghum juice under high gravity (HG, 200 and 240 g/L of total sugar) and very high gravity (VHG, 280 g/L of total sugar) conditions of the five isolates was tested. Saccharomyces cerevisiae NP01 and S. cerevisiae ATCC4132 were used as reference strains. The results showed that the SSJ01KKU isolate gave the highest ethanol production efficiency under all conditions. Ethanol concentration (PE), yield (YP/S) and productivity (QP) values were 98.89 g/L, 0.50 and 1.18 g/L·h, respectively, with sugar consumption (SC) of 98.96% under the HG condition at 200 g/L of total sugar. Under the HG condition at 240 g/L of total sugar, the PE, YP/S and QP values were 118.12 g/L, 0.51 and 1.41 g/L·h, respectively, with the SC of 95.79%. These values were 82.29 g/L, 0.34 and 0.98 g/L·h, respectively, with the SC of 85.59% under the VHG condition. Addition of urea into the sweet sorghum juice under all conditions significantly shortened the fermentation time, resulting in increased QP values. Based on molecular taxonomic analysis of the five isolates using sequence analysis of the D1/D2 domain and the ITS1 and ITS2 regions, SSJ01KKU is S. cerevisiae, whereas SCJ04KKU, SCJ07KKU, SCJ09KKU and SCJ14KKU are Pichia caribbica.

Three new enchytraeid species (Enchytraeidae, Annelida) from mountain soils of Korea and ten species new for the country

In this paper, three new enchytraeid species (Enchytraeidae, Clitellata) are described from different mountains of Korea: Cognettia koreana sp. n., Henlea bidiverticulata sp. n. and Mesenchytraeus longidiverticulatus sp. n. Validity of these new species was confirmed by comparative morphological and molecular taxonomic analyses (based on ITS, CO1 and H3 sequences). In addition, ten enchytraeid species never recorded before from Korea were found in the studied soil samples: Bryodrilus diverticulatus Černosvitov, 1929, Cernosvitoviella atrata Bretscher, 1903, Cernosvitoviella minor Dózsa-Farkas, 1990, Cognettia lapponica Nurminen, 1965, Cognettia varisetosa (Martinsson, Rota & Erséus, 2015), Fridericia cf. sohlenii Rota, Healy & Erséus, 1998, Henlea nasuta Eisen, 1878, Marionina clavata Nielsen & Christensen, 1961, Marionina communis Nielsen & Christensen, 1959, Marionina seminuda Xie & Rota, 2001. Morphological observations and new reference DNA sequences are also provided for the above-mentioned species.

Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis.

The aim of this study was to select a candidate deep-sea amphipod species suitable for connectivity analyses in areas around cobalt-rich ferromanganese crusts (CRCs). We applied DNA barcoding based on the mitochondrial protein-coding gene, cytochrome c oxidase subunit I (COI), to specimens collected from the Xufu Guyot (the JA06 Seamount) off southeastern Minami-Torishima Island in the North Pacific, where CRCs are distributed. We used baited traps to collect 37 specimens. Comparison of COI sequences with public reference databases (GenBank, BOLD) showed that almost all of the specimens belonged to the superfamily Lysianassoidea, which is known to be ubiquitous in deep-sea areas. In a molecular taxonomic analysis of these sequences, we detected 11 clades. One of these clades (group 9) composed of 18 sequences and was identified by DNA barcoding as a putative species belonging to Abyssorchomene, which has been reported from the New Hebrides Trench in the South Pacific. We considered this species to be a candidate for connectivity analysis and analyzed its genome by restriction site–associated DNA sequencing. The results showed that the genetic variation in this species is adequate for analyzing connectivity patterns in CRC areas in the future.

Providencia entomophila sp. nov., a new bacterial species associated with major olive pests in Tunisia.

Bioprospection for potential microbial biocontrol agents associated with three major insect pests of economic relevance for olive cultivation in the Mediterranean area, namely the olive fly, Bactrocera oleae, the olive moth, Prays oleae, and the olive psyllid, Euphyllura olivina, led to the isolation of several strains of readily cultivable Gram-negative, rod-shaped bacteria from Tunisian olive orchards. Determination of 16S ribosomal RNA encoding sequences identified the bacteria as members of the taxonomic genus Providencia (Enterobacterales; Morganellaceae). A more detailed molecular taxonomic analysis based on a previously established set of protein-encoding marker genes together with DNA-DNA hybridization and metabolic profiling studies led to the conclusion that the new isolates should be organized in a new species within this genus. With reference to their original insect association, the designation “Providencia entomophila” is proposed here for this hypothetical new taxon.

Two new species of Fridericia (Annelida: Enchytraeidae) from Hungarian caves

Cave research in Hungary has developed a lot in the last decade. As a part of this progress, enchytraeid specimens were collected from Hungarian caves and were subsequently characterized by comparative morphological and molecular taxonomic analyses. Molecular phylogenetic studies based on ITS, CO1 and H3 sequences and morphological results confirmed that these specimens represented two species new to science. The descriptions of Fridericia baradlana sp. nov. and Fridericia spelaeophila sp. nov. are presented in this paper.

Molecular identification of Azolla in the Yangtze River Watershed, China

Seven samples were collected broadly from the Yangtze River watershed of China during a search for Azolla pinnata asiatica, intended as molecular references to identify the subspecies of a new exotic congener in Florida. Molecular taxonomic analysis was carried out using chloroplast trnG-trnR and trnL-trnF, in addition to nuclear ITS1 sequences, which when referenced against NCBI yielded the unexpected result of Azolla caroliniana for all seven samples. In four of five provinces sampled, cold-tolerant A. filiculoides and A. caroliniana would be expected to outcompete A. pinnata due to biological advantages during over-wintering and early spring growth. However, A. caroliniana’s predominance over A. filiculoides in this limited sampling taken widely from the Yangtze watershed was unexpected given the historical predominance of Azolla filiculoides introduction in the literature. The explanation may be A. caroliniana’s use in early rice systems, its intermediate tolerance to heat and cold, and its high biomass production. Azolla caroliniana’s hybrid status is further characterized here using NCBI ITS1 Blasts of an SLA Illumina 2000 dataset.

Decimodrilus, a new enchytraeid genus from Korea (Annelida, Clitellata, Enchytraeidae).

Two new species of the new genus Decimodrilus gen. n. are described in this paper from oak forests of South Korea using a combination of classical morphology and DNA-based molecular taxonomy. A characteristic trait of the new genus is the occurrence of the intestinal diverticula in segments IX-X. The main morphological features of the new genus are: 4-5(6) straight chaetae per bundle, origin of dorsal vessel in clitellar region, anteseptale of nephridia consisting of funnel only, coelomocytes only mucocytes, oesophageal appendages absent, spermathecae united proximally and connected jointly with the oesophagus. Decimodrilus diverticulatus sp. n. has spermathecae with two diverticula-like protrusions and two globular sperm masses. D. globulatus sp. n. has spermathecae with two or three sperm rolls. Molecular taxonomic analysis based on a concatenated phylogenetic tree supports the status of the new genus and that of the two new species.

Reclassification of current Dictyostelium mucoroides strain Dm7 based on rRNA sequences and morphological features

Recent classification and phylogenetic analyses of dictyostelids are based on molecular sequences, but not all strains have been examined using this approach. Since the original identification in 1869, several strains called Dictyostelium mucoroides have been isolated; however, molecular taxonomic analyses of these strains remain insufficient. We therefore attempted to verify classification of one of these strains (Dm7) using rRNA sequences. As a result, strain Dm7 was found to be phylogenetically closer to D. clavatum and D. longosporum than to D. mucoroides. Comparisons of the morphological features of these strains further supported the classification based on sequence data, suggesting that Dm7 should be classified as a strain of D. clavatum.

Bioprospection of Culturable Endophytic Fungi Associated with the Ornamental Plant Pachystachys lutea.

Endophytes are fungi and bacteria that inhabit plant tissues without causing disease. Endophytes have characteristics that are important for the health of the plant and have been isolated from several plants of economic and medicinal interest but rarely from ornamental plants. The current study isolates and identifies endophytic fungi from the leaves of Pachystachys lutea and evaluates the antagonistic activity of these endophytes as well as cellulase production by the endophytes. Fungi were isolated by fragmentation from surface-disinfected leaves and were identified by the sequencing of the ITS gene and the genes coding for EF 1-α and β-tubulin followed by multilocus sequence analysis. Molecular taxonomic analysis revealed that 78% of the identified fungi belonged to the genus Diaporthe. We also identified strains belonging to the genera Colletotrichum, Phyllosticta, Xylaria, Nemania, and Alternaria. Most of the strains tested were able to inhibit the growth of pathogenic fungi, especially PL09 (Diaporthe sp.), which inhibited the growth of Colletotrichum sp., and PL03 (Diaporthe sp.), which inhibited the growth of Fusarium oxysporum. The production of cellulase ranged from 0.87 to 1.60μmol/min. Foliar endophytic fungal isolates from P. lutea showed promising results for the in vitro control of plant pathogens and for cellulase production. This paper is the first report on culturable endophytic fungi isolated from the ornamental plant P. lutea.

Molecular investigations of the bat tick Argas vespertilionis (Ixodida: Argasidae) and Babesia vesperuginis (Apicomplexa: Piroplasmida) reflect "bat connection" between Central Europe and Central Asia.

Argas vespertilionis is a geographically widespread haematophagous ectoparasite species of bats in the Old World, with a suspected role in the transmission of Babesia vesperuginis. The aims of the present study were (1) to molecularly screen A. vespertilionis larvae (collected in Europe, Africa and Asia) for the presence of piroplasms, and (2) to analyze mitochondrial markers of A. vespertilionis larvae from Central Asia (Xinjiang Province, Northwestern China) in a phylogeographical context. Out of the 193 DNA extracts from 321 A. vespertilionis larvae, 12 contained piroplasm DNA (10 from Hungary, two from China). Sequencing showed the exclusive presence of B. vesperuginis, with 100% sequence identity between samples from Hungary and China. In addition, A. vespertilionis cytochrome oxidase c subunit 1 (cox1) and 16S rRNA gene sequences had 99.1-99.2 and 99.5-100% similarities, respectively, between Hungary and China. Accordingly, in the phylogenetic analyses A. vespertilionis from China clustered with haplotypes from Europe, and (with high support) outside the group formed by haplotypes from Southeast Asia. This is the first molecular evidence on the occurrence of B. vesperuginis in Asia. Bat ticks from hosts in Vespertilionidae contained only the DNA of B. vesperuginis (in contrast with what was reported on bat ticks from Rhinolophidae and Miniopteridae). Molecular taxonomic analyses of A. vespertilionis and B. vesperuginis suggest a genetic link of bat parasites between Central Europe and Central Asia, which is epidemiologically relevant in the context of any pathogens associated with bats.

A new Cernosvitoviella species (Clitellata: Enchytraeidae) and its comparison with other Cernosvitoviella species from Sphagnum mires in Hungary.

Results of a comparative investigation on five Cernosvitoviella species from Hungarian Sphagnum mires including their distribution and the description of a new species, Cernosvitoviella farkasi sp. n., are presented in this paper. Cernosvitoviella atrata, C. aggtelekiensis, C. crassoductus and C. farkasi sp. n. could be easily distinguished from each other based on both morphological and molecular taxonomic analyses. However, C. minor seems to be a species complex on the basis of these investigations, so it was referred as C. minor sensu lato. The status of the C. minor variants requires further studies.

Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana.

Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five Marmota himalayana animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus Streptococcus, being phylogenetically closest to Streptococcus marmotae DSM 101995T (98.4 % similarity). The groEL, sodA and rpoB sequence analysis showed interspecies similarity values between HTS2T and Streptococcus. marmotae DSM 101995T, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus Streptococcus validated that HTS2T forms a distinct subline and exhibits specific phylogenetic affinity with S. marmotae. In silico DNA-DNA hybridization of HTS2T showed an estimated DNA reassociation value of 40.5 % with Streptococcus. marmotae DSM 101995T. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus Streptococcus, Streptococcus himalayensis sp. nov. The type strain is HTS2T (=DSM 101997T=CGMCC 1.15533T). The genome of Streptococcus himalayensis sp. nov. strain HTS2T contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.