Small Subunit Ribosomal RNA Sequences Research Articles

Description of Bacterial RNA Transcripts Detected in Mycobacterium tuberculosis - Infected Cells from Peripheral Human Granulomas using Single Cell RNA Sequencing.

Mycobacterium tuberculosis (Mtb) remains a global human health threat and a significant cause of human morbidity and mortality. We document here the capture of Mtb transcripts in libraries designed to amplify eukaryotic mRNA. These reads are often considered spurious or nuisance and are rarely investigated. Because of early literature suggesting the possible presence of polyadenylated transcripts in Mtb RNA, we included the H37Rv Mtb reference genome when assembling scRNA seq libraries from fine needle aspirate samples from patients presenting at the TB clinic, Port Moresby General Hospital, Papua New Guinea. We used 10X Genomics single-cell RNA sequencing transcriptomics pipeline, which initiates mRNA amplification with poly-T primers on ~30-micron beads designed to capture, in this case, human mRNA associated with individual cells in the clinical samples. Utilizing the 10X Genomics Cell Ranger tool to align sequencing reads, we consistently detected bacterial small and large ribosomal subunit RNA sequences (rrs and rrl, respectively) and other bacterial gene transcripts in the cell culture and patient samples. We interpret Mtb reads associated with the host cell's unique molecular identifier (UMI) and transcriptome to indicate infection of that individual host cell. The Mtb transcripts detected showed frequent sequence variation from the reference genome, with greater than 90% of the rrs or rrl reads from many clinical samples having at least 1 sequence difference compared to the H37Rv reference genome. The data presented includes only bacterial sequences from patients with TB infections that were confirmed by the hospital pathology lab using acid-fast microscopy and/or GeneXpert analysis. The repeated, non-random nature of the sequence variations detected in Mtb rrs and rrl transcripts from multiple patients, suggests that, even though this appears to be a stochastic process, there is possibly some selective pressure that limits the types and locations of sequence variation allowed. The variation does not appear to be entirely artefactual, and it is hypothesized that it could represent an additional mechanism of adaptation to enhance bacterial fitness against host defenses or chemotherapy.

An insight into the cryptic diversity of Fragilariaceae (Bacillariophyta), with the description of a new Antarctic species, Gedaniella antarctica sp. nov.

ABSTRACT Fragilariaceae is a paraphyletic family of araphid diatoms commonly used as bio-indicators, in environmental assessments and in paleoenvironmental reconstructions, and with various potential industrial applications. Recent molecular taxonomic research has highlighted significant limitations in traditional morphology-based investigations of these diatom species. Most descriptions of species and genera of the Fragilariaceae present broad morphological character definitions and many diagnostic characters are indistinguishable by light microscopy. In this sense, taxon misidentification is common and could have serious implications for environmental surveys and laboratory experiments. To better understand the diversity of the Fragilariaceae, we (1) performed phylogenetic analyses of the small subunit ribosomal RNA (18S rRNA), rbcL and psbC gene sequences, (2) inferred a cladogram from key morphological features used in the traditional identification of Fragilariaceae, (3) tested if the topologies of the tree recovered from the molecular phylogeny, of the tree based on morphology and of the trees constraining to monophyly the genera Sarcophagodes, Pseudostaurosira and Nanofrustulum (together and separately) were significantly different and (4) mapped morphological character states on the ML tree and inferred their evolution based on maximum parsimony. Our results supported the monophyly of a group of Fragilariaceae within small araphid diatoms including the genera Cratericulifera, Plagiostriata, Castoridens, Opephora, Staurosira, Staurosirella, Punctastriata, Psammotaenia, Hendeyella, Stauroforma, Pseudostaurosira sensu Li, Nanofrustulum sensu Li, Serratifera sensu Li and Gedaniella sensu Li. Molecular phylogeny and topology tests suggested that the latest circumscriptions of the genera Sarcophagodes, Pseudostaurosira and Nanofrustulum sensu Morales were not monophyletic. Analyses of the Antarctic strain IMA070A collected during the XXXIV Italian Antarctic Expedition using fine structural features of the frustule and molecular data revealed that this diatom belongs to a distinct lineage within Gedaniella, which we describe here as Gedaniella antarctica sp. nov.

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

A new omega-3 rich euglenoid Eutreptiella sp. from the Korean coastal waters

Euglenoids, the primary producers of fatty acids (FAs), are used in functional foods, feeds, and biofuels. Long-chain polyunsaturated FAs (LC-PUFAs) such as eicosapentaenoic acid and docosahexaenoic acid (DHA) are crucial for human health. The primary commercial source of LC-PUFA is fish; however, its heavy metal bioconcentration is concerning. Globally declining wild-harvested fish stocks is another recently recognized serious problem. Herein, the morphology, molecular phylogeny, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectroscopy, and FA compositions of an unspecified euglenoid strain KCTC 19016P isolated from the Korean coastal waters were examined. The vegetative cells were longitudinally spindle-shaped with a truncated apex and a tail-like extension at the anterior and posterior ends, respectively and had two unequal flagella. They had distinct red eyespots, numerous chloroplasts, and paramylon granules. Pellicular cell striations were easily observed using a scanning electron microscope. Phylogenetic analyses based on nuclear and chloroplast small-subunit ribosomal RNA sequences revealed that Eutreptiella sp. KCTC 19016P was nested within the Eutreptiella clade and was closely related to Eutreptiella marina (AY703209). Using the MALDI-TOF spectrum analysis, we differentiated between Eutreptiella sp. KCTC 19016P and the related NIES strains, thereby confirming their taxonomic similarities. Eutreptiella sp. KCTC 19016P growth was observed for 30 days; the maximum growth rate and doubling time was 0.50 ± 0.05 day−1 and 1.40 ± 0.15 day, respectively. Eutreptiella sp. KCTC 19016P had a relatively high monounsaturated FA percentage compared to the other species. The omega-3 FA content in Eutreptiella sp. KCTC 19016P was significantly higher than that of the other strains, as determined using ordinary one-way analysis of variance (P < 0.0001). Among the four euglenoids, Eutreptiella sp. KCTC 19016P had the highest α-linolenic acid and DHA contents. Thus, this new isolate could potentially be used in aquaculture and nutraceuticals without the risks associated with consuming fish.

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

BackgroundMicrobiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life.ResultsWe report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved.ConclusionsThis generic methodology is likely to find wide application in microbiome analysis including diagnostics.

Two new species of Diderma (Physarales, Didymiaceae) from northern China

Diderma is one of the most abundant species in Myxomycetes. Based on the study of morphology and phylogeny, two new species—Diderma liaoningensis (is characterized by grouped sporocarps, the sporocyst with dehiscence lines, capillitium with large brown swelling, spore encircled by a pale line) and Diderma verrucocapillitia (is characterized by depressed plasmodiocarps, verrucose capillitium, red-brown spores)—collected from Liaoning province and Jilin province were introduced. Detailed descriptions and illustrations are presented as well as comparisons to similar species. Phylogenetic analyses were carried out using Maximum Likelihood and Bayesian inference based on small subunit ribosomal RNA sequences (SSU rRNA) of Diderma and related genera. These analyses confirmed the placement of two new species in the genus Diderma. A key to 19 species of Diderma from China is also provided. Holotype specimens have been housed in the Herbarium of the Mycological Institute of Jilin Agricultural University (HMJAU), Changchun, China.

Identification and Genetic Characterization of Blastocystis Species in Patients from Makkah, Saudi Arabia.

BackgroundBlastocystis species (sp.) are gastrointestinal protozoan parasites with high prevalence rates worldwide. Blastocystis sp. show extensive genetic diversity with 17 different subtypes (STs) described to date. A few studies have investigated the prevalence and STs of Blastocystis sp. in Makkah, Saudi Arabia. Therefore, we aimed in this study to identify and characterize subtypes of Blastocystis sp. in the City of Makkah, Saudi Arabia.MethodsStool samples were collected from 140 patients who presented to King Abdulaziz Hospital, Hera General Hospital and Modern Medical Center in Saudi Arabia. Different microscopic examination methods of patients’ stools and molecular analyses (using primers targeting SSU rRNA gene) were performed to identify and characterize STs of Blastocystis sp.ResultsOur microscopic examination of stool samples showed that 96/140 patients (68.6%) had Blastocystis sp. infection. Clinical examination of infected patients revealed that 81 patients were symptomatic, whereas 15 were asymptomatic. Next, we isolated DNA from Blastocystis sp.-positive stool samples followed by PCR amplification of small-subunit ribosomal RNA (SSU rRNA) gene and sequence analysis. Our sequence analysis showed that subtype 3 (ST3) was the most prevalent (53.13%) followed by subtype 1 (ST1) (45.83%), whereas subtype 2 (ST2) was the least prevalent (1.04%). Moreover, our results showed that all three STs resulted in more symptomatic than asymptomatic cases. Finally, we identified novel haplotypes which comprised of 8 ST3, 6 ST1, and one ST2 haplotypes.ConclusionOur identification of several haplotypes in patients’ stools confirms the genetic diversity of Blastocystis sp. and may explain the reported low host specificity and differential pathogenicity of Blastocystis sp. We believe that additional molecular epidemiological and genomic studies are needed to understand the prevalence and pathogenicity of different subtypes in humans and animal hosts.

Two new calcicolous caloplacoid lichens from South Korea, with a taxonomic key to the species of Huriella and Squamulea.

Pyrenodesmiarugosa Lee & Hur and Huriellaaeruginosa Lee & Hur are described as new lichen-forming fungi from a calcareous mountain of South Korea. Pyrenodesmiarugosa is distinguishable from Pyrenodesmiamicromontana (Frolov, Wilk & Vondrák) Hafellner & Türk, the most similar species, by thicker thallus, rugose areoles, larger apothecia, shorter hymenium, shorter hypothecium and narrower tip cells of paraphyses. Huriellaaeruginosa, the second new species, differs from ‘Squamulea’ chelonia Bungartz & Søchting by dark greenish-grey to grey thallus without pruina, gold to yellow-brown epihymenium, larger ascospores and thallus K– and KC– reaction. Molecular analyses employing internal transcribed spacer (ITS), mitochondrial small subunit (mtSSU) and nuclear large subunit ribosomal RNA (LSU) sequences strongly support the two caloplacoid species to be distinct in their genera. A surrogate key is provided to assist in the identification of all 20 taxa in Huriella and Squamulea.

Morphological and genetic description of two new species of philometrid nematodes (Philometridae) parasitic in needlefishes (Belonidae) from estuaries of Florida, USA.

Two new species of philometrid nematodes (Philometridae) from needlefishes (Belonidae) in Florida are described based on morphological and genetic characteristics: Philometra aequispiculata sp. n. (males and females) collected from the ovary of Strongylura marina (Walbaum) (type host) and Strongylura notata (Poey), and Philometra notatae sp. n. (females) from the swimbladder of S. notata. Both species are described and illustrated based on light and scanning electron microscopical examinations. Morphologically, P. aequispiculata sp. n. differs from all congeners mainly in the unique structure of the distal tip of the gubernaculum, whereas P. notatae sp. n. is mainly characterised by the presence of eight markedly large cephalic papillae of the outer circle in gravid and subgravid females, the body length of the gravid female (54 mm) and by the absence of caudal projections. Molecular characterisation of the new species was assessed from phylogenetic analysis of mitochondrial cytochrome c oxidase I (COI) and SSU rRNA small-subunit ribosomal RNA (SSU) sequences among closely related philometrids by way of Bayesian inference. Phylogenetic reconstructions based on COI and SSU sequences show each of the new species comprise discrete ancestor-descendent lineages.

The First Isolation of Microsporidia from Dragonflies in Japan.

Entomopathogenic microsporidia are pathogens of various arthropods and therefore cause disease in important host species ranging from agricultural pests to beneficial insects. Here, we investigated three genera of entomopathogenic microsporidia from dragonflies； these were isolated in Kanagawa, Japan, in 2014. In total, the infection rate was 0.85%（16 of the 1,886 surveyed dragonfly adults）. Four strains of microsporidia selected from infected Orthetrum albistylum speciosum（Uhler）（Odonata: Libellulidae）adults were measured for spore size and analyzed at the molecular level. According to spore size, the four strains were roughly divided into two groups. Analysis of small-subunit ribosomal RNA sequences indicated that the microsporidia strains belonged to the Trachipleistophora, Vavraia, and Paranosema clusters. Microsporidia species that are closely related to the strains isolated in this study have previously been reported to infect insects other than dragonflies. Therefore, we suggest the possibility that the microsporidian strains we isolated in O. albistylum speciosum may also infect other insect species.

Prevalence and Subtype Distribution of Blastocystis Infection in Patients with Diabetes Mellitus in Thailand.

Diabetes mellitus (DM) is a major global public health problem with an increasing prevalence. DM increases the risk of infections caused by bacteria, fungi, viruses, and parasites. We examined the prevalence, subtypes, and risk factors of Blastocystis infection in patients with and without DM in central Thailand. Stool samples and questionnaires were obtained from 130 people in the DM group and 100 people in the non-DM group. Blastocystis infection was identified via a nested polymerase chain reaction and subtyped via sequencing of the partial small-subunit ribosomal RNA (SSU rRNA) gene. Analysis of potential risk factors was conducted via binary logistic regression. The overall prevalence of Blastocystis infection was 10.8%, including rates of 9% and 12.3% in the non-DM and DM groups, respectively. The most prevalent subtype was ST3, followed by ST1, and ST4. Factors that potentially increased the risk of Blastocystis infection include patients being >65 years old, the presence of DM, a DM duration of ≥10 years, a low level of education, and animal ownership. In conclusion, this is the first study of Blastocystis infection in DM, and a high prevalence was found among this population. Therefore, health education promoting sanitation and hygiene is necessary to reduce and prevent infection in the community.

Chylorhabditis epuraeae n. gen., n. sp. (Rhabditida: Rhabditidae) isolated from Epuraea (Haptoncus) ocularis Fairmaire collected from sap on the bark of Ulmus parvifolia Jacq. in Kyoto, Japan

Summary A new rhabditid entomophilic nematode was isolated from adult Epuraea (Haptoncus) ocularis collected from brown to light brown sap on the trunk of Ulmus parvifolia in Kyoto, Japan. The typological characters of the species, anteriorly opened peloderan bursa with nine bursal rays with the first, fifth, and eighth pairs directed dorsally, very long and two-part spicule with broad tip, and elongate conical female tail, do not fit the current nominal rhabditid genera. While phylogenetic analyses based on the near-full-length small subunit (18S) ribosomal RNA sequence tentatively suggest that the species is the sister of Buetschlinema, the typological and biological characters of the new species clearly differ from that genus, and so a new species is described herein as Chylorhabditis epuraeae n. gen., n. sp.

Multilocus genotyping of Giardia duodenalis from pigs in Korea.

Giardia duodenalis (syn. G. intestinalis, G. lamblia) is an important zoonotic parasite infecting livestock (including pigs) through ingesting cysts in contaminated food or water. This parasite has been classified into eight different genetic assemblages, A to H. Here, we examined the individual-level prevalence of G. duodenalis in domestic pig farms and confirmed host specificity by genotype comparisons. Samples were collected from southern and central Korea, between May 2017 and January 2019. DNA directly extracted from 745 pig fecal specimens were tested by PCR for G. duodenalis small subunit ribosomal RNA (ssu rRNA), glutamate dehydrogenase (gdh), and β-giardin gene sequences. Based on ssu rRNA PCR, 110 (14.8%) were positive for G. duodenalis. Infection risk was the highest in the fattener group (31/139, 22.3%) and during the autumn season (52/245, 21.2%: p<.001). No statistically significant differences in risk for infection were observed between fecal types (normal versus diarrheal). Fifty ssu rRNA samples, three gdh samples, and five β-giardin samples were successfully sequenced and genotyped. Ssu rRNA assemblage sequence analysis identified E (40.0%, 20/50), D (34.0%, 17/50), C (24.0%, 12/50), and A (2.0%, 1/50). The gdh locus identified three samples as assemblage E, and the β-giardin locus identified four samples as assemblage E and one as assemblage C. Assemblage A sequences obtained (ssu rRNA; MK430919) had 100% identity with Giardia sequences isolated from a Korean individual (AJ293301), indicating the potential of zoonotic transmission. Continuous management and monitoring for prevention of transmission and protection of animal and human health are essential.

PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

BackgroundPhylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building.ResultsHere, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree.ConclusionsTogether with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).

Isolation and Molecular Identification of Microsporidian Pathogen Causing Nosemosis in Muga Silkworm, Antheraea assamensis Helfer (Lepidoptera: Saturniidae).

Microsporidia are intracellular fungal parasites and they are the most common pathogens for sericulture. Microsporidian sp. can cause pebrine, a dreadful disease and lead to destructive disorder in Muga silkworm, Antheraea assamensis Helfer by vertical and horizontal transmission. This disease is the key factor obstructing the developmental progress of Muga culture in India. Nevertheless, molecular identification and characterization of pathogen associated with pebrine disease in A. assamensis is not yet established. Insect bioassay studies revealed that microsporidian infection in Muga silkworm, A. assamensis Helfer significantly reduced (P < 0.005) cocoon weight, pupal weight, shell weight and silk ratios. A new set of PCR primers suitable for amplification of small subunit ribosomal RNA (SSU-rRNA) of microsporidia infecting A. assamensis have been designed. The amplicon was cloned, sequenced and analysed. Microsporidia pathogen of wild silk moth A. assamensis has been identified at genus level as Nosema sp. AA1. Phylogeny of Nosema sp. AA1 was constructed on the basis of SSU-rRNA sequence and it has a close evolutionary relationship with microsporidian pathogens of other wild silkmoths. The arrangement and organization of the rRNA genes inferred that Nosema sp. AA1 belongs to true Nosema group and not to members of the Nosema/Vairimorpha group.

Morphological and molecular characterization of avian trypanosomes in raptors from Thailand.

From September 2012 to May 2018, blood samples from 364 raptors (mostly adults) were collected and screened for trypanosomes and haemosporidians by microscopic examination and nested polymerase chain reactions (PCR). Trypanosoma spp. were identified in 15 birds from eight different species. Light microscopy revealed 14 cases of infection with Trypanosoma cf. corvi, including one each in black-shouldered kite (Elanus caeruleus, n = 49), Brahminy kite (Haliastur indus, n = 50), and spotted owlet (SO, Athene brama, n = 27); two mountain hawk-eagles (Spizaetus nipalensis, n = 3); and three each in Asian barred owlets (ABO, Glaucidium cuculoides, n = 27), barn owls (BO, Tyto alba, n = 65) and collared scops owls (CSO, Otus lettia, n = 41). In addition, one case of infection with T. avium was identified in an oriental scops owl (OSO, Otus sunia, n = 2). All infected raptors showed very low parasitemia levels. The PCR detected more three positives in one CSO, one Japanese sparrowhawk (Accipiter gularis), and one OSO. The sensitivity and specificity of the PCR method were 93.3% and 99.1%, respectively. The overall infection rate was very low (4.9%). The highest infection rate was recorded in cold-dry season (9.9%). Coinfection of Plasmodium with trypanosomes was found in all three ABOs. Coinfection with Haemoproteus spp. was found in one BO, three CSOs, and one SO. Coinfection with Haemoproteus spp. and Leucocytozoon danilewskyi was found in the OSO. Microfilarias were detected in one ABO and one CSO. The ultrastructure of trypomastigotes of T. cf. corvi in an ABO revealed fine structures. All small subunit ribosomal RNA (SSU rRNA) sequences belong to two clades: T. avium and T. corvi-culicavium complex/group. SSU rRNA gene amplification was not successful in one BO. The raptors with trypanosome infections showed normal hematological values and healthy appearance. Furthermore, this is the first report of T. avium in a nocturnal raptor from Thailand.

Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China

A new species (Comatricha macrospora) has been collected from the Changbai Mountain National Nature Reserve, Jilin Province, China. Comatricha macrospora has smaller sporocarps and larger spores (about 15–18 μm in diameter) than other species of Comatricha as well as a persistent peridium at the base of the sporotheca. In addition, two newly recorded species of Comatricha—C. tenerrima (M.A. Curtis) G. Lister and C. afroalpina Rammeloo—have been documented in China for the first time, based on material collected from northeast China and the campus of East China Normal University, Fuzhou City, Jiangxi Province. Comatricha tenerrima is characterised by fusiform long-stalked sporocarps and warted pinkish brown spores (about 7–8 μm in diameter)., whereas C. afroalpina occurs on rotting logs and has spores marked by larger warts with an irregular reticulation at their base. Descriptions and scanning electron micrographs for these members of the genus Comatricha are provided. Phylogenetic analyses, based on small subunit ribosomal RNA sequences (SSUrRNA) of Comatricha and related genera, were carried out using Bayesian inference. These analyses confirmed the placement of the new species in the genus Comatricha.

Morphology and phylogeny of a new species, Uroleptus (Caudiholosticha) antarctica n. sp. (Ciliophora, Hypotricha) from Greenwich Island in Antarctica.

This paper describes the morphological features based on standard methods and estimates their phylogenetic position using small subunit ribosomal RNA (SSU rRNA) sequences of a Uroleptus (Caudiholosticha) antarctica n. sp. population investigated from moss of the Greenwich Island, Antarctica. The morphology of Uroleptus (Caudiholosticha) antarctica n. sp. is characterized as follows: 213.0-238.0×67.5-74.5 μm size in vivo; contractile vacuole located slightly above left of mid-body; cortical granules lacking; three frontal and two frontoterminal cirri; five to six transverse cirri; one pretransverse cirri; one right and one left marginal rows; six to seven dorsal kineties; three caudal cirri.

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method.

Intertidal mudflats are land–sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.

Pseudotrichonympha leei, Pseudotrichonympha lifesoni, and Pseudotrichonympha pearti, new species of parabasalian flagellates and the description of a rotating subcellular structure

Pseudotrichonympha is a large and structurally complex genus of parabasalian protists that play a key role in the digestion of lignocellulose in the termite hindgut. Like many termite symbionts, it has a conspicuous body plan that makes genus-level identification relatively easy, but species-level diversity of Pseudotrichonympha is understudied. Molecular surveys have suggested the diversity is much greater than the current number of described species, and that many “species” described in multiple hosts are in fact different, but gene sequences from formally described species remain a rarity. Here we describe three new species from Coptotermes and Prorhinotermes hosts, including small subunit ribosomal RNA (SSU rRNA) sequences from single cells. Based on host identification by morphology and DNA barcoding, as well as the morphology and phylogenetic position of each symbiont, all three represent new Pseudotrichonympha species: P. leei, P. lifesoni, and P. pearti. Pseudotrichonympha leei and P. lifesoni, both from Coptotermes, are closely related to other Coptotermes symbionts including the type species, P. hertwigi. Pseudotrichonympha pearti is the outlier of the trio, more distantly related to P. leei and P. lifesoni than they are to one another, and contains unique features, including an unusual rotating intracellular structure of unknown function.