SSU rDNA Gene Research Articles

Giardia duodenalis multi-locus genotypes in dogs with different levels of synanthropism and clinical signs

BackgroundIn dogs, infections with Giardia duodenalis are mainly caused by assemblages C and D, but also by the potentially zoonotic assemblages A and B. The aims of this study were to assess differences in assemblages (i) between dogs living mainly in close proximity to humans (synanthropic dogs) versus dogs living mainly among other dogs, (ii) between samples of dogs with or without loose stool, and (iii) related to the amount of cysts shedding.MethodsOne hundred eighty-nine qPCR Giardia positive fecal samples of dogs originating from four groups (household, sheltered, hunting, and dogs for which a veterinarian sent a fecal sample to a diagnostic laboratory) were used for genotyping. For this, multi-locus genotyping of beta-giardin, triose phosphate isomerase, and glutamate dehydrogenase and genotyping of SSU rDNA gene fragments were performed. Fecal consistency was scored (loose or non-loose stool), and cysts per gram of feces were determined with qPCR.ResultsAssemblage D was the most prevalent in all groups, followed by the other canid assemblage C. Also, mixed C/D was common. In two (synanthropic) household dogs, the potentially zoonotic assemblage AI was present. Although occurrence of assemblage AI in household dogs was not significantly different from dogs living among other dogs (sheltered and hunting dogs), it was significantly higher compared to dogs for which a sample was sent to a diagnostic laboratory. Dogs with assemblage D shed significantly more cysts than dogs with other assemblages (except for mixed C/D results) or dogs in which no assemblage could be determined. None of the assemblages was significantly associated with loose stool.ConclusionNot only do dogs mainly shed the canid Giardia duodenalis assemblages D and/or C, the numbers of cysts per gram for the canid assemblage D were also higher than for the potential zoonotic assemblage AI. Based on the assemblages shed by dogs, the risk to public health posed by dogs is estimated to be low, even though the dogs that shed AI were synanthropic household dogs. Loose stool in infected dogs was not associated with any particular Giardia assemblage.

Morphology and molecular phylogeny of two new soil ciliates, Hemiurosomoida warreni nov. spec. and Hemiurosoma clampi nov. spec. (Ciliophora, Hypotrichia) from Tibet

Two novel hypotrichous ciliates, Hemiurosomoida warreni nov. spec. and Hemiurosoma clampi nov. spec., isolated from soil in the Lhalu Wetland and Motuo Virgin Forest in Tibet, respectively, were investigated using live observation and protargol staining. Hemiurosomoida warreni nov. spec. strongly resembles the type species H. longa but can be distinguished by its body size in vivo (110–145 × 30–40 μm vs. 50–100 × 18–40 μm), number of adoral membranelles (25–38 vs. 15–22), and numbers of right (29–39 vs. 14–23) and left (26–35 vs. 13–23) marginal cirri, transverse cirri (3 vs. 4 or 5) and macronuclear nodules (4–8 vs. 2). Hemiurosoma clampi nov. spec. is characterized by its vermiform body shape, colourless cortical granules distributed in irregular rows, two macronuclear nodules, three frontal cirri, one buccal cirrus, four frontoventral cirri ranged in a line, two transverse cirri, lacking postoral ventral and pretransverse ventral cirri, and marginal rows that are not posteriorly confluent. Phylogenetic analyses based on SSU rDNA gene sequences suggest that Hemiurosomoida is not monophyletic. A close relationship is revealed between Hemiurosomoida warreni nov. spec., Parakahilella macrostoma, Hemiurosoma clampi nov. spec., and the type species Hemiurosoma terricola. As expected, all these species are classified within the “non-oxytrichid Dorsomarginalia”.

Morphological and molecular analysis of Henneguya tietensis n. sp. (Cnidaria: Myxosporea), parasitizing the gill filaments of Prochilodus lineatus (Valenciennes, 1837) from Brazil

The present study describes Henneguya tietensis n. sp. parasitizing Prochilodus lineatus (Valenciennes, 1837) from Brazil, through morphological and molecular analysis. Myxospores were found in the gill tissue of P. lineatus with a prevalence of 10%. The myxospores consisted of two elongate, elliptical shell valves each with a long, tapering caudal appendage. The morphology was consistent with Henneguya and the myxospore measured as follows (mean ± SD): total length 55.5 ± 2.1μm, body length 16.2 ± 1.1μm, body width 5.5 ± 0.1μm, caudal appendages length 39.0 ± 2.0μm. The polar capsules were 7.3 ± 0.2μm long, 1.7 ± 0.2μm wide and contained a polar filament coiled 11 to 13 turns. Histological analysis showed the plasmodia developing in the middle region of each gill filament and caused a focally extensive distension by forming a space-occupying mass within the gill filament. The ultrastructural analysis allowed the observation of the presence of mature myxospores throughout the plasmodium. Phylogenetic analysis with the SSU rDNA gene showed Henneguya tietensis n. sp. as a sister species of the subclade formed by Henneguya piaractus and Henneguya brachypomus that infect fishes of the genus Piaractus. The genetically closest species was H. piaractus, which showed a similarity of 82.4%. Using molecular and morphological characterization, the myxozoan parasite described herein represents a new species of the genus Henneguya.

Molecular surveillance reveals bats from eastern Colombia infected with Trypanosoma theileri and Trypanosoma wauwau-like parasites

Several species of trypanosomes can infect bats (Chiroptera), but current information about bat trypanosomes in Colombia is scarce. The objectives of this study were to estimate the infection rate and to characterize the trypanosome species infecting bats from three rural regions near the municipality of Cumaribo in Vichada, Colombia. Blood samples were collected from 39 bats. DNA was extracted from the blood samples and analyzed using nuclear genetic markers (SSU rDNA, ITS rDNA, and cathepsin genes) to discriminate among trypanosome species. Trypanosomes were detected in 66.7 % (26/39) of blood samples using PCR; 61.5 % (24/39) of infections were identified as Trypanosoma theileri and 5.1 % (2/39) as T. wauwau-like parasites. The phylogeographic analysis revealed that our T. theileri sequences were associated with the TthIIB genotype from cattle in Brazil and Venezuela. The T. wauwau-like parasites represent a new genotype of the species and were found in Molossus molossus and Platyrrhinus helleri bats. These data represent the first evidence of this trypanosome in both Colombia, and in these species of bats. Bat infections with T. theileri suggest an important role of these hosts in maintaining this genotype, probably acquired by ingesting insect vectors. The T. wauwau-like genotype in new mammalian host species supports the 'bat seeding' hypothesis of the T. cruzi clade. The epidemiological and evolutionary implications of these findings are discussed.

MOLECULAR IDENTIFICATION OF ENTAMOEBA HISTOLYTICA IN SULAIMANI PEDIATRIC TEACHING HOSPITAL

Background 
 Entamoeba histolytica is a unicellular protozoon that conceder as a common cause of dysentery in human especially in the children under 6 years old. This may be transmitted via the ingestion of cystic stage of the parasite. 
 Objectives 
 This study aimed to investigate the total rate of Entamoeba histolytica infection in children admitted to the Pediatric Teaching Hospital in Sulaimani City, and considering some other aspects such as culturing and detecting subtypes using polymerase chain reaction (PCR). 
 Patients and Methods
 This epidemiologic study includes 1005 stool samples collected from children aged 6 months to 6 years old from the 1st of Jun to the 30th of October 2014. Each stool sample was examined and identified by direct wet mount method using normal physiological saline and iodine solution, followed by culturing and isolation of the parasite for 14 days to elongate life span and then genomic amplification applied from the cultured Entamoeba histolytica by appropriate PCR based method.
 Results
 The result of rapid kit occult blood combined with microscopic wet mount (iodine) showed that the infection with E. histolytica was (12.9%), in which the rate in male (14.18%) was higher than that female (11.42%), with no significant difference between both genders. cultured E. histolytica showed a great ability of this parasite to grow, with detection of the parasite under light microscope (40X). Then two standard kits were used specific primer (1147, F&R), and thus about 1147bp PCR produced. Then, nested PCR was performed for the same PCR products two different primers (246 F&R) which resulted in fragments of approximately 246bp. This fragment coding for the 16S SSUrDNA gene of HM-1IMSS 16s E. histolytica confirms the previous PCR amplification finding. The results of sequence methods identified E. histolytica subtype 1 from PCR positive samples by sequencing alignment (99%) similarity with accession number KB823016. 
 Conclusion
 The prevalence rate of infection with E. histolytica in Pediatric Teaching Hospital in Sulaimani City was (12.9%). Beef extract medium for culturing of E. histolytica showed a great ability for growing of the parasite cystic form. E. histolytica subtype1 can be detected by sequencing method for the first time in molecular genotype of human E .histolytica in Sulaimani city.

Morphological and phylogenetic characterisation of Unicauda tavaresii n. sp. (Myxosporea: Myxobolidae): a parasite of the circumorbital tissue of the eye of two characiform fishes from the Amazon region of Brazil.

Myxozoans of the family Myxobolidae are common parasites in fish. The diversity and ecology of the species of the genus Unicauda are poorly known, which hampers the understanding of the distribution and prevalence of this group of parasites. In the present study, cysts containing parasites whose morphology was consistent with the genus Unicauda were found in the circumorbital region of the ocular conjunctiva of the freshwater fish Moenkhausia grandisquamis Müller & Troschel, 1845 (Characiformes: Characidae) and Triportheus angulatus Spix & Agassiz, 1829 (Characiformes: Triportheidae). The spores have an oval body and long caudal appendage, with a mean total length of 65.2 ± 5.9μm and width of 5.2 ± 0.7μm, with two oval and symmetrical polar capsules of 4.9 ± 0.5μm in length and 1.4 ± 0.2μm in width, containing polar filaments with five or six coils. An integrated comparative analysis of the morphological characteristics of this parasite and partial sequences of the SSU rDNA gene supported the identification of a new species of histozoic parasite of the genus Unicauda found in fish from the Tocantins River basin, in the eastern Brazilian Amazon region. The new species was denominated by Unicauda tavaresii n. sp.

Comparative genotyping of Blastocystis infecting cattle and human in the south of Iran

BackgroundBlastocystis is a unicellular protozoan and one of the most common parasites found in humans and many animals' intestinal tract. The present study aimed to compare the genotypes of Blastocystis infecting cattle and humans in the south of Iran. MethodsA total of 100 human stool samples and 75 cattle stool samples were microscopically examined for Blastocystis infection. DNA was extracted from thirty-eight microscopically positive samples (13 humans and 25 cattle). PCR was performed on positive samples targeting the Blastocystis-specific SSU rDNA gene. PCR products of eight humans and eleven cattle samples were sequenced and compared with available reference sequences in GenBank by BLAST queries. Genetic diversity was measured for Blastocystis subtypes in human and cattle, based on haplotype and nucleotide diversities. ResultsThe PCR detected Blastocystis in ten humans and twenty-four cattle samples. Blastocystis subtypes 1, 2, and 6 were found in humans whereas subtypes 5 and 10 were found in cattle. Subtype (ST) 2 was the most predominant subtypes in humans whereas, in cattle specimens, the ST5 was the most dominant subtype. Based on the Blastocystis sequences of SSU rDNA, 68 sites were polymorphic and 49 sites were parsimony informative, resulting in the identification of 15 haplotypes, 10 haplotypes in the cattle and 5 in humans. No haplotype was shared between cattle and human parasites. ConclusionHuman-derived Blastocystis subtypes were different from cattle subtypes in southern Iran. Nevertheless, subtype 5 in cattle can be a risk factor for human infection.

Myxozoan hidden diversity: the case of Myxobolus pseudodispar Gorbunova, 1936.

Myxobolus pseudodispar Gorbunova, 1936 (Myxozoa) was originally described as a parasite of common roach, Rutilus rutilus (Linnaeus), with developing stages in muscles and spores disseminated in macrophage centres of different organs and tissues. Later, this parasite was described from several other cyprinids, but with relatively large intraspecific differences based on SSU rDNA gene sequences. Within our long-term study on myxozoan biodiversity, we performed a broad microscopic and molecular screening of various freshwater fish species (over 450 specimens, 36 species) from different localities. We investigated the cryptic species status of M. pseudodispar. Our analysis revealed four new unique SSU rDNA sequences of M. pseudodispar as well as an infection in new fish host species. Myxobolus pseudodispar sequence analysis showed clear phylogenetic grouping according to fish host criterion forming 13 well-recognised clades. Using 1% SSU rDNA-based genetic distance criterion, at least ten new species of Myxobolus Bütschli, 1882 may be recognised in the group of M. pseudodispar sequences. Our analysis showed the paraphyletic character of M. pseudodispar sequences and the statistical tests rejected hypothetical tree topology with the monophyletic status of the M. pseudodispar group. Myxobolus pseudodispar represents a species complex and it is a typical example of myxozoan hidden diversity phenomenon confirming myxozoans as an evolutionary very successful group of parasites with a great ability to adapt to a new hosts with subsequent speciation events.

Detection of the parasitic nematode, Pseudocapillaria tomentosa, in zebrafish tissues and environmental DNA in research aquaria

Although zebrafish continue to increase in popularity as a vertebrate animal model for biomedical research, chronic infectious diseases in laboratory populations remain prevalent. The presence of pathogens such as Pseudocapillaria tomentosa, a parasitic nematode found in the intestine of infected zebrafish, can significantly influence experimental endpoints and negatively impact reproducibility of research findings. Thus, there is a need for screening tests for zebrafish with the sensitivity to detect even low levels of pathogens present in tissues. Assays based on the detection of DNA are commonly used for such screening tests. Newer technologies such as digital PCR provide an opportunity to improve the sensitivity and precision of these assays, so they can be reliably used to detect pathogen DNA in water, reducing the need for lethal testing. We have designed a qPCR-based assay with the sensitivity to detect less than 5 copies of the P. tomentosa SSU-rDNA gene in tissues of infected zebrafish and environmental DNA from aquarium water housing infected fish. In addition, we adapted this test to a dPCR platform to provide a precise quantification of P. tomentosa DNA and demonstrate the resistance of this assay to inhibitors commonly found in freshwater aquaria.

Phylogenetic relationships of Leptolaimus de Man, 1876 (Plectida: Leptolaimidae) with description of two new species from the Persian Gulf, Iran

Summary Members of the family Leptolaimidae are reported for the first time from Iran with description of two new species of Leptolaimus from the Persian Gulf in the south of the country. Leptolaimus hormozganensis sp. n. is described based upon three populations. It differs from other Leptolaimus species in the position of the pharyngeal supplement and the number of precloacal tubular supplements and has a single sickle-shaped tubular pharyngeal supplement at mid-pharynx level in both sexes, 9-12 male precloacal supplements and one female preanal supplement. Leptolaimus dimorphus sp. n. is characterised by the presence of a pharyngeal tubular supplement only in some adults, one female preanal supplement and four male precloacal supplements. It differs from other species in that the pharyngeal supplement is only present in some specimens, presence of four male precloacal supplements, tail 50-59 μm long and ventrosublateral position of vulva on either the right or left side of the body. Near full length SSU rDNA sequences are provided for L. hormozganensis sp. n. and two different males (one with, and one without, a pharyngeal supplement) of L. dimorphus sp. n. COI sequences for three populations of L. hormozganensis sp. n. from different regions of the Persian Gulf are also obtained. New sequences of two Leptolaimus species formed a clade with other sequenced Leptolaimus spp. and representatives of two genera of Leptolaimidae, i.e., Aphanolaimus and Paraplectonema in a phylogeny based on SSU rDNA gene with 1.00/81 Bayesian posterior probability/maximum likelihood bootstrap (BPP/BS) values. Molecular phylogeny confirmed the synonymy of Leptolaimus and Halaphanolaimus that was formerly proposed based only on morphology. Based on SSU sequences and morphological characters, the presence of a pharyngeal supplement may not be a species-specific character and should not be used to differentiate genera.

Isoenzyme profiles and phylogenetic analysis of Giardia duodenalis isolates from Iranian patients.

The main objective of this study was to characterize the Giardia duodenalis isolates from Iranian patients in Fars Province, south of Iran by biochemical and molecular methods. Fifteen mass cultivated of G. duodenalis isolates in modified TYI-S-33 medium were analyzed using isoenzyme electrophoresis and PCR genotyping. Polyacrylamide gel electrophoresis (PAGE) of five different enzyme systems was used to characterize isolates: (i) glucose-6-phosphate dehydrogenase, (ii) glucose phosphate isomerase, (iii) malate dehydrogenase, (iv) malic enzyme, and (v) phosphoglucomutase. As well, a fragment of the SSU-rDNA (292bp) gene was amplified by PCR using the primers RH11 and RH4. The sequencing of the PCR products and phylogenetic tree were performed. The isoenzyme electrophoretic profiles divided fifteen G. duodenalis isolates into four zymodemes. G6PD, GPI, MDH, ME, and PGM enzyme systems showed 1, 2, 2, 3, and 3 enzyme pattern, respectively. G6PD isoenzyme pattern had the most homogeneity, while isoenzyme patterns of ME and PGM had the most heterogeneity in our study. Genotyping results indicated that the zymodemes 1-4 were categorized in assemblage A based on the SSU-rDNA gene. Phylogenetic analysis showed that all four zymodemes were distributed within the cluster of assemblage A. Our results indicated that both isoenzyme and DNA analyses were useful to characterize the isolates of Giardia and distinguishing various zymodemes and assemblages. It could be suggested that the genetic diversity among isoenzymes profiles of G. duodenalis may explain the variable clinical manifestations, pathogenicity, host response, drug susceptibility, and treatment efficacy of human giardiasis.

Does the Gonostomum-patterned oral apparatus in hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora, Spirotrichea).

The classification of hypotrichs based on the gonostomatid oral structure is widely accepted, but the phylogenetic signal of this character is unknown. Here, we infer the species phylogeny of those gonostomatids for which molecular data are available, plus 26 new sequences of SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA genes. The results indicate that: (i) the endoral is more phylogenetically informative than the paroral; (ii) the structure of the endoral and the Gonostomum-pattern adoral zone of membranelles are plesiomorphies for the hypotrichs sensu stricto; (iii) the group of species possessing these features is monophyletic in all our phylogenetic analyses, except that for the SSU-rDNA; (iv) Schmidingerotrichidae is monophyletic in all trees, suggesting that it is a well-defined family; (v) the Gonostomatidae is polyphyletic in the SSU-rDNA and ITS1-5.8S-ITS2 trees, with Gonostomum, Cladotricha, Cotterillia, Metagonostomum, Paragonostomum and Wallackia distributed among separate clades, but monophyletic in the LSU-rDNA and concatenated trees; (vi) higher hypotrich taxa such as core urostyloids and core sporadotrichids/stichotrichids might have evolved from species that possessed a gonostomatid oral apparatus.

Evaluation of Different Oocyst DNA Extraction Methods for Cryptosporidium spp. Research in Environmental Samples.

The major problem of the PCR method for the search of protozoan cysts/oocysts in environmental samples is the presence of inhibitors. DNA extraction methods capable of removing inhibitory substances of environmental origin and recovering the DNA are decisive for the efficiency of PCR. This study aimed to compare the efficiency of different DNA extraction methods for the search by Cryptosporidium oocysts in water samples by molecular methods. DNA extraction from water samples was performed using four different methods. Two methods use a chaotropic buffer to extract DNA and promote the selective binding of DNA to a silica membrane (GuSCN-silica and GFX Kit). The other method is based on the lysis and digestion of the samples in buffer and proteinase K, adsorption of impurities by an "InhibitEX" insertion matrix and purification of the DNA by a silica column (QIAamp Kit). The fourth method uses ionic and non-ionic detergents and proteinase K, to solubilize and separate the DNA from proteins, and a paramagnetic resin for DNA purification in the presence of high concentrations of guanidine ions (MAGNEX DNA Kit). Nested-PCR was performed, and the Cryptosporidium SSU rDNA gene amplified. The results demonstrated that MAGNEX and GFX commercial kits showed higher sensitivity, with detection of up to 100 oocysts/mL and 104 oocysts/mL respectively. In conclusion, this study confirmed that for low-DNA environmental samples, extraction methods should include an efficient oocyst wall breaking step, and showed that the best Cryptosporidium DNA extraction methods are those that use paramagnetic resins.

Canine Visceral Leishmaniasis in São Paulo, Brazil, the Most Populous City of South America: Isolation, Molecular Diagnosis, and Phylogenetic Inferences.

Background and Objectives: Canine visceral leishmaniasis affects dogs, the main urban reservoirs, which favor the transmission and expansion of this zoonotic disease in areas with high anthropization process and human density. We investigated the occurence of Leishmania infatum based in molecular diagnosis, and phylogenetic analysis of isolates obtained from dogs in metropolitan region of São Paulo. Methods: A total of 201 dogs were tested by parasitological and molecular diagnosis. Phylogenetic analysis based sequences from SSUrDNA and gGAPDH genes were performed. Results: The parasitological diagnosis revealed 5% (10/201) of positivity, and the sequences obtained from seven isolates were clustered with L. infantum in phylogentic analysis based on SSUrDNA and gGAPDH genes. A total of 24.9% (50/201) of dogs were positive in molecular diagnosis based on cathepsin L-like marker. Interpretation and Conclusion: According to this study, it is necessary to implement a surveillance policy of visceral leishmaniasis, intensifying the actions of diagnosis, prevention, and control of this zoonosis.

Identification of Spruce Budworm Natural Enemies Using a qPCR-Based Molecular Sorting Approach

Annual monitoring of mortality agents in the course of a spruce budworm (Choristoneura fumiferana (Clemens) (Lepidoptera: Tortricidae)) population cycle is essential to understanding the factors governing the rise and collapse of outbreaks. To date, assessments of causes of budworm mortality have relied on laboratory rearing of field-collected larvae, followed by visual identification of emerging parasitoids and/or microscopic analysis of pathogens in larval carcasses. Although this approach has provided vital information on the abundance and identity of mortality agents, the procedure is labor-intensive and has limits in terms of accuracy. To overcome these shortcomings, we developed a molecular identification tool that makes use of real-time quantitative PCR (qPCR) and TaqMan® technologies. The tool relies on taxon-specific molecular variants (single nucleotide polymorphism [SNP] markers) found in mitochondrial (COI) and nuclear (28S rDNA) genes, for parasitoids, and in the nuclear SSU rDNA gene for microsporidian pathogens; these are then used as molecular signatures targeted by qPCR primers and TaqMan probes. Thus, the design of several sets of primers and probes deployed in multiplex format enables the identification of natural enemies via a molecular sorting process, bypassing barcode sequencing. Crude budworm DNA extracts are processed through a first module that detects dipteran and hymenopteran parasitoids, and microsporidian infections. Positive samples are then processed for species determination using three additional modules, enabling the identification of 20 common natural enemies of the spruce budworm. The tool has been fully validated using DNA samples from all comprised taxa, and both its sensitivity and accuracy compared favorably with the rearing-based method in an analysis of field-collected budworms. Using this tool, sample processing can be completed within two days, does not require larval rearing, provides accurate species identification, and can be conducted by technical staff without extensive molecular biology or insect taxonomy training.

Cutaneous leishmaniasis in Cavia porcellus (guinea pig): case report

ABSTRACT Leishmaniasis is a parasitic disease of worldwide spread. It is caused by protozoa of the genus Leishmania and is transmitted to animals and humans through the bite of sand flies. In Brazil, leishmaniasis is one of the zoonoses of major importance and expansion. The objective of this work is to describe the clinical, pathological, immunohistochemical and molecular findings of cutaneous leishmaniasis by Leishmania enriettii in guinea pig (Cavia porcellus). Three animals had nodular and alopecia lesions on the muzzle, ears and ulcerated lesions on the distal extremities of the pelvic limbs. The males (2) also had diffuse thickening of the scrotal skin. Samples of the ulcerated cutaneous lesions were evaluated by cytology which were observed as amastigote forms of Leishmania. One of the animals was euthanized and necropsied. Histopathology showed abundant dermal infiltrate of macrophages, plasma cells, lymphocytes and multinucleated giant cells. Numerous macrophages contained parasitoid vacuoles with amastigote forms, evidenced by immunohistochemical examination. The molecular characterization based on the SSUrDNA gene identified the species as L. enrietti. The diagnosis of cutaneous leishmaniasis in these cases was based on pathological findings and confirmed by immunohistochemistry, PCR and sequencing.

High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon-specific Primers.

Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2-10, 10-35, 35-100, and 100-300μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized by DNA (i.e. active+quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life-history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.

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.

Phenotypic masquerade: Polymorphism in the life cycle of the centrohelid heliozoan Raphidiophrys heterophryoidea (Haptista: Centroplasthelida)

The life cycle of the centrohelid heliozoan Raphidiophrys heterophryoidea Zlatogursky, 2012 was studied with light and electron microscopy in clonal cultures from the type locality. The alternation of two types of trophozoites, having contrastingly different morphology, was observed. Type 1 trophozoites morphology matched the original description. Type 2 trophozoites tended to form colonies usually of 6–8 individuals, connected with cytoplasmic bridges and their cell size was noticeably bigger, namely 43−45 μm compared to 24.5 μm on average in type 1 trophozoites. Some colonies were forming stalks composed of three or four axopodia covered with scales. Spicules were lacking completely, while plate-scales differed from those of type 1 trophozoites: they had oblong-elliptical shape, larger (5.9–14.1 × 2.4–5.8 μm) size, non-branching septa always reaching scale centre, solid upper plate. The conspecificity of the two trophozoite types was confirmed with the comparison of SSU rDNA gene sequence data. Both types of trophozoites were capable of encystment and excysted individuals always were type 1 trophozoites. A new type of cyst-scales (cup-scales) was described. Transitions between cysts and the two trophozoites types were documented. The diagnosis of R. heterophryoidea was improved accordingly. The possible functions, driving forces, and taxonomic consequences of the polymorphism were discussed.

Taxonomy and SSU rDNA-based phylogeny of three new Euplotes species (Protozoa, Ciliophora) from China seas

As widely accepted, Euplotid ciliates, a unique mono-cellular organisms, play important roles in ecological, environmental, evolutionary and basic biological studies. We investigate the living morphology, infraciliature and silverline system of three new marine Euplotes found from China in this study: Euplotes bergeri n. sp., E. weissei n. sp. and E. shini n. sp. The new species Euplotes bergeri is characterized by its dominant adoral zone of membranelles, ten frontoventral cirri, three or four caudal cirri, 12–14 dorsal kineties with 14–20 dikinetids in the mid-dorsal row, and a dorsal silverline system of the double-eurystomus type. Euplotes weissei can be recognized by its tiny size, having two conspicuous dorsal grooves, nine frontoventral cirri, one marginal cirri, six or seven dorsal kineties, ca. 10 basal bodies in the mid-dorsal row and a mix single-double silverline system. Euplotes shini is a medium-sized form with the ciliary and silverline pattern of the well-known E. minuta but differs from the latter mainly in SSU rDNA gene sequences and usually different-sized marginal cirri. Phylogenetic analyses based on molecular data documented the systematic positions of those new taxa and support the validity of all three organism as distinct species.