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The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxa Urocentrum and Paranassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques. Phylogenomic analysis was performed based on expanded taxon sampling of 85 taxa, including 157 nuclear genes encoding 36,953 amino acids. The results indicate that: (1) urocentrids form an independent branch that is sister to the clade formed by Scuticociliatia and Hymenostomatia, which, together with the morphological data, supports the establishment of a new subclass, Urocentria n. subcl., within Oligohymenophorea; (2) phylogenomic analysis and ortholog comparison reveal a close relationship between Paranassula and peniculines, providing corroborative evidence for removing Paranassula from Nassulida and elevating it as an order, Paranassulida, within the subclass Peniculia; (3) based on the phylogenomic analyses and morphological data, we hypothesize that Peritrichia is the earliest diverging clade within Oligohymenophorea while Scuticociliatia and Hymenostomatia share the most common ancestor, followed successively by Urocentria and Peniculia. In addition, stop codon analyses indicate that oligohymenophoreans widely use UGA as the stop codon, while UAR are reassigned to glutamate (peritrichs) or glutamine (others), supporting the evolutionary hypothesis., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Two poorly known tintinnine ciliates collected from the coastal waters of PR China, viz., Codonellopsis mobilis Wang, 1936 and Tintinnopsis chinglanensis Nie & Ch'eng, 1947, were redescribed and neotypified using live observation, protargol staining and SSU rRNA gene sequencing. Ciliature information and SSU rRNA gene sequence data of both species were revealed for the first time and improved diagnoses were given based on the original descriptions and data from the present study. Further phylogenetic analyses inferred from SSU rRNA gene sequences and morphological data suggested that the genus Tintinnopsis is polyphyletic and that the genus Codonellopsis is non-monophyletic. The approximately unbiased test, however, does not reject the possibility that Codonellopsis is monophyletic.

The morphology of two new scuticociliates, Uronema apomarinum sp. nov. and Homalogastra parasetosa sp. nov., isolated from a mangrove wetland in Shenzhen, PR China, was studied using live observation and the protargol impregnation method. Uronema apomarinum is characterized by a body size of about 20-35×10-15 µm in vivo , a partly two-rowed membranelle 1, and 12 or 13 somatic kineties. Homalogastra parasetosa is distinguished by a membranelle 1 comprising two longitudinal rows of basal bodies. Three Homalogastra setosa populations are suggested as subjective synonyms of the new species. Improved diagnoses of the genus Homalogastra Kahl, 1926 and its type species Homalogastra setosa Kahl, 1926 are provided. Results of phylogenetic analyses based on 18S rRNA gene and ITS1-5.8S-ITS2 region sequences indicate that U. apomarinum is most closely related to U. marinum , while the closest relative of H. parasetosa is H. setosa .

The general morphology and ultrastructure of two soil hypotrichous ciliates, Urosoma emarginata and U. salmastra, were investigated using light microscopy, scanning electron microscopy and transmission electron microscopy. Phylogenetic analyses, based on the newly sequenced small subunit ribosomal (SSU) rRNA genes, were conducted on three U. emarginata populations and one U. salmastra population. Our findings support for the validity of Perilemmaphora Berger, 2008, a rankless taxon comprising spirotrich ciliates having a perilemma. The cortical granules of both species are extrusomes representing a new type of mucocyst in U. emarginata and possibly a new type of pigmentocyst in U. salmastra. Additionally, the lithosomes were revealed as subglobose structures composed of a low electron-dense, homogeneous inner part and an electron-dense outer part. The ultrastructural features of the cortical granules, together with ontogenetic and molecular phylogenetic data, suggest that the genus Urosoma might need to be divided. It is posited that ultrastructural features of hypotrichous ciliates in general may have important taxonomic value warranting further investigation., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

The morphology and phylogeny of four oligotrichid ciliates, Parallelostrombidium paraellipticum sp. n., P. dragescoi sp. n., P. jankowskii (Xu et al. 2009) comb. n., and P. kahli (Xu et al. 2009) comb. n., are described or redescribed based on live observation, protargol stained material, and SSU rRNA gene sequences. The new species P. paraellipticum sp. n. is characterized by its obovoidal cell shape, adoral zone composed of 17-21 collar, 9-11 buccal, and two thigmotactic membranelles, and extrusomes attached in one row along the girdle kinety. The new species P. dragescoi sp. n. is distinguished from its congeners by its obovoidal cell shape and a lack of thigmotactic membranelles. Based on ciliary patterns recognizable in the original slides, Omegastrombidium jankowskii Xu et al. 2009 and O. kahli Xu et al. 2009 should be transferred to the genus Parallelostrombidium Agatha 2004. Phylogenetic analyses based on SSU rRNA gene sequence data demonstrate that all four new sequences cluster with previously described congeners. The genus Parallelostrombidium is separated into two clusters, suggesting its non-monophyly and probably corresponding to the two subgenera proposed by Agatha and Strüder-Kypke (2014), as well as their morphological difference (cell dorsoventrally flattened vs. unflattened)., (© 2018 The Author(s) Journal of Eukaryotic Microbiology © 2018 International Society of Protistologists.)

Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne-like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer somatic kineties, and/or an elongated body shape. Chlamydodon crassidens sp. n. is characterized mainly by an inverted triangular body shape, a posteriorly interrupted cross-striated band (5-6 μm wide), and a large cytostome. Moreover, we provided small-subunit (SSU) rDNA sequences of C. similis sp. n. and C. oligochaetus sp. n. Maximum likelihood (ML) and Bayesian inference (BI) consistently placed C. similis sp. n. as a sister to C. paramnemosyne, but showed different branching position of C. oligochaetus sp. n., which may be due to a low taxon sampling in the Chlamydodontidae and/or an insufficient resolution of the marker gene at species level., (© 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.)

The morphology, including the ciliary pattern, of two cyrtophorid ciliates, namely Aegyria apoliva sp. nov. and Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967, were investigated. They were isolated from coastal water off Qingdao and from an estuarine habitat in south China, respectively. Aegyria apoliva sp. nov. is characterized as following: body size 100-120 × 50-70 μm in vivo with dark pigment spot on anterior left part of cell; 48-69 somatic kineties; one preoral and four or five circumoral kineties; 9-13 transpodial segments; 26-40 nematodesmal rods; 6-10 contractile vacuoles. The Guangzhou population of Trithigmostoma cucullulus corresponds well with previously described populations, therefore only a brief morphological description is presented. Phylogenetic analysis based on small-subunit rRNA gene sequences data supports the establishment of the new species as well as the monophyly of both genera., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

Most species in the anaerobic ciliate family Caenomorphidae Poche, 1913 lack detailed descriptions based on modern morphologic and molecular methods. In this report, two species, Caenomorpha medusula Perty, 1852 and Sulfonecta uniserialis (Levander, 1894) Jankowski, 1978, were isolated from freshwater anaerobic sediments in Qingdao, China. Another population of C. medusula was recorded from Boise, Idaho, USA. We reinvestigated live morphology, ciliature, and the small-subunit (SSU) rRNA gene sequence of both species. The current study supports the opinion of Jankowski that, due to the variation in macronuclear nodule number, this character is of limited taxonomic significance in C. medusula. Scanning electronic micrographs clearly reveal that this species has one posterior spine. The China population of Sulfonecta uniserialis corresponds well with previously described populations in having a single macronucleus, a complex posterior spine, and one bell kinety. Our phylogenetic analyses reveal that the Caenomorphidae is monophyletic. However, the placement of the family is uncertain as it forms a closer relationship with the Litostomatea but with only a medium support value., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

Two oxytrichid ciliates, Stylonychia (Metastylonychia) nodulinucleata Shi and Li, 1993 and Gastrostyla steinii Engelmann, 1862; collected from Huguangyan Maar Lake and Shenzhen Mangrove Nature Protection Area, southern China, respectively, were investigated using standard methods. The uncommon species Stylonychia (Metastylonychia) nodulinucleata can be recognized by its large body size, the conspicuous caudal cirri in vivo, and a moniliform macronucleus. We provide the first record of the small subunit ribosomal RNA (SSU rRNA) gene sequence for the species. The division of Stylonychia into two subgenera based on morphological and morphogenetic data is supported by the phylogenetic analyses, in which Stylonychia (Metastylonychia) nodulinucleata is placed as a sister branch to the clade including all the sequences of Stylonychia (Stylonychia) mytilus complex. The first brackish water population of Gastrostyla steinii is described in detail, with emphasis on its morphogenesis, which corresponds well with previous populations. In the phylogenetic trees, all the available Gastrostyla sequences, except for Gastrostyla sp. Y2 (KT780432) (probably a misidentification), nest together in the big group of the subfamily Stylonychinae with moderate to high support (ML/BI, 91%/0.95), very likely revealing the monophyly of the genus Gastrostyla., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

Morphogenesis in the soil hypotrich ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011; was investigated using protargol staining. The main events during binary fission are as follows: (1) the proter retains the parental adoral zone of membranelles entirely, whereas the old undulating membranes dedifferentiate into an anlage that gives rise to the leftmost frontal cirrus and the new undulating membranes of the proter; (2) six streaks of frontoventral-transverse cirral anlagen are segmented in the pattern 1:3:3:3:4:4 from left to right, which form three frontal, four frontoventral, one buccal, five ventral and five transverse cirri, respectively; (3) the postoral ventral cirrus V/3 is not involved in primordia formation demonstrating that this species belongs to the stylonychines; (4) marginal anlagen are formed intrakinetally and the right marginal anlagen develop much earlier than the left ones; (5) the generation of the dorsal kineties is of typical Oxytricha-pattern and three caudal cirri are formed, one at the posterior end of each of dorsal kineties 1, 2 and 4. Phylogenetic analyses based on SSU rDNA sequence data indicate that Rigidohymena is polyphyletic and that R. quadrinucleata clusters with R. candens with full support., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

The morphology and ciliary pattern of three brackish pleurostomatid ciliates, Litonotus gracilis spec. nov., L. tropicus spec. nov., and L. duplostriatus, were investigated. Litonotus gracilis differs from its congeners by body size (200-400×15-40μm in vivo), body shape (slenderly spindle-shaped, long neck), the number of somatic kineties (6-7 left and 11-17 right somatic kineties), long bar-shaped extrusomes arranged along oral slit, tiny cortical granules arranged like honeycomb, one subterminally located contractile vacuole and, usually, four macronuclear nodules. Litonotus tropicus is characterized by four contractile vacuoles dorsally located, 8-11 right and four or five left somatic kineties. Litonotus duplostriatus is lanceolate-shaped, with 11-14 right and five or six left somatic kineties, one subterminally located contractile vacuole, fusiform-shaped extrusomes distributed along oral slit. Litonotus dragescoiPan et al., 2013 is not a valid name, it still be named as Litonotus fasciolatus (basionym Loxophyllum fasciolatusDragesco, 1966). Molecular phylogenetic analyses based on SSU rDNA sequence data indicate that neither the family Litonotidae nor the genus Litonotus is monophyletic, and L. gracilis has a closer relationship with the genus Kentrophyllum than with other Litonotus species., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

The morphology and morphogenesis of an oxytrichid ciliate, Rubrioxytricha haematoplasma (Blatterer & Foissner, 1990) Berger, 1999, collected from brackish and marine waters in China, were investigated using live observation and the protargol staining method. The main features of the morphogenetic process are: (i) the parental adoral zone of membranelles is retained completely in the proter and the anlage of undulating membranes originates from dedifferentiation of the old structures; (ii) three frontal, four frontoventral, one buccal, five ventral and five transverse cirri are derived from the anlagen of the undulating membranes and the five streaks of frontal-ventral-transverse anlagen in the pattern of 1:3:3:3:4:4 from left to right; (iii) the morphogenesis of the dorsal kineties is simpler than the Oxytricha pattern, i.e. without fragmentation of the dorsal kinety 3 anlagen; (iv) the single caudal cirrus originates from the dorsal kinety 3 anlage on the right side; (v) the two macronuclear nodules fuse into a single mass during the mid-stage of morphogenesis. These features correspond well with Rubrioxytricha indica, indicating that the morphogenetic pattern of Rubrioxytricha is stable. Phylogenetic analysis based on small-subunit rRNA gene sequence data supports the monophyly of the genus Rubrioxytricha, which is nested within the non-Stylonychinae clade., (© 2015 IUMS.)

This paper investigates the morphology and infraciliature of three karyorelictean ciliates, Trachelocerca chinensis sp. n., Tracheloraphis dragescoi sp. n. and a rarely known form, Geleia acuta (Dragesco, 1960) Foissner, 1998, which were isolated from the intertidal zone of sandy beaches at Zhanjiang and Qingdao, China. Trachelocerca chinensis sp. n. is distinguished from related forms by having 26-30 somatic kineties, a narrow glabrous stripe and a single nuclear group composed of approximately four to six macronuclei and two micronuclei. Tracheloraphis dragescoi sp. n. can be recognized through its 14-22 somatic kineties, wide glabrous stripe and a single nuclear group composed of about four macronuclei. Phylogenetic analyses based on small-subunit (SSU) rRNA gene sequences indicated that the genera Trachelocerca and Tracheloraphis are closely related but that neither of them appears to be a clearly monophyletic group. Nonetheless, the monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.143, >0.05), although that of Tracheloraphis is rejected (P = 0.011, <0.05). Geleia acuta, meanwhile, branched with Geleia fossata and falls in the Geleia clade., (© 2014 IUMS.)

Three species of Microthoracids, Lopezoterenia paratorpens n. sp., Trochiliopsis australis Foissner et al., 1988 and Discotricha papillifera Tuffrau, 1954, collected from Chinese coastal waters, were investigated using live observation and protargol staining methods. Lopezoterenia paratorpens n. sp. was characterized by its squarely shaped cortical papillae and by dorsal kineties which contained loosely distributed basal bodies. Trochiliopsis australis was revealed to have two oral membranelles, which was not recorded in the original report. Phylogenetic analyses were carried out based on SSU rRNA gene sequence data from each of the three species, and on other available data for microthoracids. The results showed that the order Microthoracida is not monophyletic because the family Discotrichidae, which contains L. paratorpens and D. papillifera, forms a clade separated from the "core" Microthoracids clade. The topologies of the maximum likelihood and Bayesian inference trees, along with the distinct morphological characteristics found previously, suggest that the family Discotrichidae should not be assigned to the order Microthoracida. We propose to designate a new order, Discotrichida n. ord. which diagnosed as: flattened ciliates with conspicuous cortical papillae on both dorsal and ventral faces, rod-shaped mucocysts, and an asymmetric cytopharyngeal basket. Also, the fact that Leptopharynx clusters with the assemblage including T. australis, and Pseudomicrothorax is located distantly from Leptopharynx indicates that the classification of Pseudomicrothoracidae and Microthoracidae by Foissner (1985) is justified., (© 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.)

The morphology and morphogenesis of a new ciliate, Heterokeronopsis pulchra g. n., sp. n., isolated from a mangrove wetland near Shenzhen, southern China, were investigated using live observation and protargol impregnation methods. Heterokeronopsis g. n. is characterized by having a bipartite adoral zone, an extremely shortened paroral membrane, frontal cirri arranged in an indistinct bicorona, a midventral complex composed of midventral pairs and midventral row(s), one left and one right marginal row, bipolar dorsal kineties, and buccal cirri; frontoterminal, transverse, and caudal cirri are absent. The single species H. pulchra sp. n. has a long, slender body that is brownish in colour, two kinds of cortical granules, one posteriorly located contractile vacuole, one buccal cirrus, usually six frontal cirri, three dorsal kineties, and one midventral row. The main morphogenetic features are: (i) the old oral apparatus is completely replaced by new structures derived from the oral primordium of the proter which originates de novo on the dorsal wall of the buccal cavity, (ii) the posteriormost frontal-midventral-transverse cirral anlage generates a midventral row, (iii) no frontoterminal and transverse cirri are formed, (iv) the anlagen for the marginal rows and the dorsal kineties are formed intrakinetally, and (v) the macronuclear nodules fuse into a mass at the middle stage. Phylogenetic analyses based on SSU rRNA gene sequence data reveal that Heterokeronopsis pulchra is a member of the family Pseudokeronopsidae and is most closely related to Nothoholosticha fasciola., (Copyright © 2012 Elsevier GmbH. All rights reserved.)

The ciliate genus Protocruzia belongs to one of the most ambiguous taxa considering its systematic position, possible as a member of the classes Heterotrichea, Spirotrichea or Karyorelictea, which is tentatively placed into Spirotrichea in Lynn's 2008 system. To test these hypotheses, multigene trees (Bayesian inference, evolutionary distance, maximum parsimony, and maximum likelihood) were constructed using the small subunit rRNA (SSU rRNA) gene, internal transcribed spacer 2 (ITS2) and a protein coding gene (histone H4). All analyses agree that: (1) four morphotypes of Protocruzia from different geographical origins group together and form a monophyletic clade, which cannot be assigned to any of the eleven described ciliate classes; (2) it is invariably positioned on an isolated branch separated from the class Spirotrichea suggesting that this clade should be clearly removed from Spirotrichea; (3) this leads us to hypothesize that this taxon may indeed represent a lineage on a class rank. Based on the fact that it is, both morphologically and in molecular features, closely related to heterotrichs, Colpodea and Oligohymenophorea, Protocruziida might be an ancestral form for the subphylum Intramacronucleata in the evolutionary line from the class Heterotrichea (subphylum Postciliodesmatophora) to higher taxa.

In order to re-evaluate the systematics of sessilid peritrich ciliates, small subunit (SSU) rRNA gene sequences were determined for 12 species belonging to five genera: Vorticella, Pseudovorticella, Epicarchesium, Zoothamnium, and Zoothamnopsis. Phylogenetic trees were deduced using Bayesian inference, maximum parsimony, and maximum likelihood methods. The phylogenetic analyses suggest that (1) sessilids which have stalks with continuous myonemes that contract in a zig-zag fashion form a separate clade from those which have stalks that contract independently and in a spiral fashion, supporting the separation of the family Zoothamniidae from the family Vorticellidae and (2) Epicarchesium and Pseudovorticella, both of which have reticulate silverline systems, are more closely related to each other than to other vorticellids, suggesting that differences in the silverline system (i.e. transverse vs. reticulate) may be the result of genuine evolutionary divergence among sessilid peritrichs. However, the newly sequenced Zoothamnopsis sinica, which has a reticulate silverline pattern, nests within the unresolved Zoothamnium species that have transverse silverline patterns. Thus, there were at least two evolutions of the reticulate silverline pattern character state from a plesiomorphic transverse state in the peritrichid ciliates. The molecular work demonstrates the genus Zoothamnium to be paraphyletic in relation to morphological studies, and suggests that Astylozoon, Opisthonecta, and Vorticella microstoma possibly share a SSU rRNA secondary structure in the helix E10-1 region.

The small subunit rRNA (SSrRNA) gene was sequenced for Cardiostomatella vermiforme, a large marine ciliate the systematic position of which is uncertain but which has been regarded as a scuticociliate for about forty years. The present work indicates that this organism, together with a closely related species, Dexiotrichides pangi, always form a separate assemblage as a sister group to the scuticociliates sensu stricto. The fact that the clade comprising Cardiostomatella and Dexiotrichides branches between the typical scuticociliates and Hymenostomatia, and shares a series of morphological and morphogenetical characters with both, supports the conclusion that it belongs to an intermediate group between the two. We suggest that this group represents a new order, Loxocephalida n. ord. within the subclass Scuticociliatia, which possibly contains all taxa within the families Loxocephalidae and Cinetochilidae and with Loxocephalidae as the type family.

The morphology and infraciliature of the type species of the ciliate genus Trachelostyla, T. pediculiformis (Cohn, 1866) Borror, 1972, collected from the Bohai Sea near Tianjin, north China, were investigated using live observation and protargol impregnation. The Chinese population corresponds well with the original description, as follows: size about 80-150 x 20-30 microm in vivo; body dorsoventrally flattened and non-spiral; outline elongate, with anterior region conspicuously narrowed while posterior not; on average 14 macronuclear nodules, two micronuclei and 42 adoral membranelles; 16-24 cirri in left and 21-31 in right marginal row. In total 18 frontoventral-transverse cirri: constantly 11 cirri in frontal area and two ventral ones together with five enlarged transverse cirri (TC). Three inconspicuous caudal cirri (CC); six dorsal kineties with prominent cilia. The literature on T. pediculiformis is critically reviewed, showing that the descriptions so far do not agree very well. To clarify the taxonomic status of this species, the population from the Chinese coast of the Bohai Sea is designated as a neotype. The small subunit rRNA gene was sequenced for the neotype and the molecular phylogenetic tree basically supports the establishment of the family Trachelostylidae Small & Lynn, 1985. Based on the data obtained, the genus Trachelostyla Borror, 1972 is redefined thus: dorsoventrally flattened trachelostylids, body non-spirally twisted and elongate, with peristomal region conspicuously narrowed; ciliature generally in 11:2:5:3 pattern, i.e. 11 cirri in frontal region, two ventral cirri located anterior to five TC, three CC present; one left and one right row of marginal cirri not confluent posteriorly. A new genus Spirotrachelostyla nov. gen. is proposed to include the taxa which were previously assigned to Trachelostyla but characterized by spirally twisted, spindle-like body shape and a variable number of cirri in the peristomal area. Three new combinations are suggested: Spirotrachelostyla spiralis (Dragesco & Dragesco-Kernéis, 1986) nov. comb. [basionym: Trachelostyla spiralis Dragesco & Dragesco-Kernéis, 1986], S. tani (Hu & Song, 2002) nov. comb. [basionym: T. tani Hu & Song, 2002] and S. simplex (Kahl, 1932) nov. comb. [basionym: Stichotricha simplex Kahl, 1932].

The complete small subunit rRNA (SSrRNA) gene sequence of the rare marine hypotrich, Certesia quadrinucleata Fabre-Domergue, 1885, was determined, and found to be 1752 nucleotides long. The phylogenetic position of this species was deduced using distance matrix, maximum parsimony and maximum likelihood methods. Certesia was consistently demonstrated to be a member of the Aspidisca-Euplotes group and clearly exhibits a very close relationship to the well-known genus Euplotes (99% Bay, 99% LS, 99% NJ, 99% MP). The phylogenetic trees further suggest that: (1) Uronychia and Diophrys, traditionally placed in the family Uronychiidae, branch earlier and share a closer relationship to each other than to other hypotrichs; (2) taxa in Gastrocirrhidae, represented by Euplotidium arenarium, might be an "ancestral" group among "traditional" hypotrichs.

Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids. [ABSTRACT FROM AUTHOR]

During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, Campanella sinica n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China. Specimen observations of this species were performed both in vivo and using silver staining. C. sinica n. sp. is characterized by the appearance of the mature colony, which is up to 2 cm high and contains more than 1,000 zooids, the asymmetric horn-shaped zooids, strongly everted and multi-layered peristomial lip, the slightly convex peristomial disc, and the well-developed haplokinety and polykinety, which make more than four circuits of the peristome before descending into the infundibulum. The small subunit ribosomal DNA (SSU rDNA), 5.8s rDNA and its flank internal transcribed spacers (ITS1-5.8s rDNA-ITS2), and large subunit ribosomal DNA (LSU rDNA) are sequenced and used for phylogenetic analyses which reveal that the family Epistylididae Kahl, 1933 is non-monophyletic whereas the genus Campanella is monophyletic and nests within the basal clade of the sessilids. The integrative results support the assertion that the genus Campanella represents a separate lineage from other epistylidids, suggesting a further revision of the family Epistylididae is needed. We revise Campanella including the transfer into this genus of a taxon formerly assigned to Epistylis , which we raise to species rank, i.e., Campanella ovata (Nenninger, 1948) n. grad. & n. comb. (original combination Epistylis purneri f. ovata Nenninger, 1948). In addition, we provide a key to the identification of the species of Campanella. [ABSTRACT FROM AUTHOR]

The ciliate genus Chlamydodon is characterized by a unique cross-striated band (CSB) along the cell perimeter. To date, more than 15 nominal species have been assigned to this genus, all of which are exclusively from marine or brackish water. In the present work, we have revised the genus according to the available data and suggest an illustrated key to aid species diagnosis. In addition, the systematic relationships of chlamydodontid congeners were analysed based on SSU rRNA gene sequences, indicating that all congeners belong to a well-defined clade. Furthermore, we investigated three species from coastal areas of China, including two new species, Chlamydodon wilberti sp. nov. and C. bourlandi sp. nov., using morphological and phylogenetic criteria. Chlamydodon wilberti sp. nov. is characterized by a cell size of 65-105  ×  35-60 µm, a complete CSB, and 38-49 somatic kineties. Chlamydodon bourlandi sp. nov. has a cell size of 150-250  ×  65-150 µm, a complete CSB, a reddish to violet cell colour, 83-97 somatic kineties, and 40-68 contractile vacuoles. As a further contribution, a well-studied species, C. triquetrus (Müller, 1786) Kahl, 1931, is also re-described. www.zoobank.org/urn:lsid:zoobank.org:pub:B83A5466-9D2B-4502-9A23-F16A61D48172. [ABSTRACT FROM AUTHOR]

Abstract: Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne‐like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer somatic kineties, and/or an elongated body shape. Chlamydodon crassidens sp. n. is characterized mainly by an inverted triangular body shape, a posteriorly interrupted cross‐striated band (5–6 μm wide), and a large cytostome. Moreover, we provided small‐subunit (SSU) rDNA sequences of C. similis sp. n. and C. oligochaetus sp. n. Maximum likelihood (ML) and Bayesian inference (BI) consistently placed C. similis sp. n. as a sister to C. paramnemosyne, but showed different branching position of C. oligochaetus sp. n., which may be due to a low taxon sampling in the Chlamydodontidae and/or an insufficient resolution of the marker gene at species level. [ABSTRACT FROM AUTHOR]

The morphology and phylogeny of three heterotrich ciliates, A nigsteinia clarissima ( Anigstein, 1912) Isquith, 1968, B lepharisma penardi sp. nov., and B lepharisma undulans Stein, 1867, were investigated based on living morphology, infraciliature, and small subunit ( SSU) r DNA sequence data. The new species B . penardi sp. nov. is recognized by the following combination of characters: size about 150-180 × 45-55 μm in vivo, cell colour variable from colourless to pale pink to dark brownish; peristome extending to middle of body; 36-63 adoral membranelles; 24-34 somatic kineties; single macronucleus; cortical granules tiny and colourless; freshwater habitat. A nigsteinia clarissima and B . undulans are both reported from China for the first time and are redescribed based on a combination of previous descriptions and new data from the Chinese populations. Phylogenetic analyses based on SSU r DNA sequence data show that B . penardi sp. nov. and B . undulans are both located within a clade comprising only congeners, thus supporting the monophyly of the genus B lepharisma. A nigsteinia clarissima clusters with its only congener forming a clade that is sister to the S pirostomum assemblage. Both the morphological and the molecular data support the placement of A nigsteinia in the family Spirostomidae. © 2015 The Linnean Society of London [ABSTRACT FROM AUTHOR]

In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence, for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless, Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here, we used all available genetic information for the small subunit of ribosomal RNA (SSU rRNA) and internal transcribed spacer region (ITS1-5.8S-ITS2) for this genus to reconstruct phylogenies for four datasets (SSU rRNA, ITS1, ITS2, and ITS1-5.8S-ITS2) and a combined dataset (SSU rRNA+ITS1-5.8SITS2) using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic, and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly, as with some other groups of ciliates, to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies, covering additional Zoothamnium spp. and members of closely related genera (e.g. Zoothamnopsis, Myoschiston, and Epistylis). [ABSTRACT FROM AUTHOR]

Abstract: The small subunit rRNA (SSU rRNA) gene for six marine stichotrichs, Pseudokeronopsis carnea, P. flava, Holosticha heterofoissneri, H. diademata, H. bradburyae and Anteholosticha manca, was sequenced and characterized. Using this molecular information, the phylogenetic positions of three related genera, Pseudokeronopsis, Holosticha and Anteholosticha were determined. The results indicate that the family Urostylidae is clearly separated from the family Pseudokeronopsidae. The present phylogenetic analyses unambiguously placed Pseudokeronopsis close to Holosticha, and support the conclusion that these genera should be regarded as the members of the order Urostylidae within the stichotrich clade. Furthermore, the results of this study also support the monophyly of the genus Pseudokeronopsis, the redefinition of Holosticha s. str. and the placement of Anteholosticha in a clade separate from Holosticha. [Copyright &y& Elsevier]

Background: The classification of the family Psilotrichidae, a curious group of ciliated protists with unique morphological and ontogenetic features, is ambiguous and poorly understood particularly due to the lack of molecular data. Hence, the systematic relationship between this group and other taxa in the subclass Hypotrichia remains unresolved. In this paper the morphology and phylogenetics of species from two genera of Psilotrichida are studied to shed new light on the phylogeny and species diversity of this group of ciliates. Results: The 18S rRNA gene sequences of species from two psilotrichid genera were obtained. In the phylogenetic trees, the available psilotrichid sequences are placed in a highly supported clade, justifying the establishment of the family Psilotrichidae. The morphology of two little-known species, packed with green algae, including a new species, Hemiholosticha kahli nov. spec., and Psilotrichides hawaiiensis Heber et al., 2018, is studied based on live observation, protargol impregnation, and scanning electron microscopy. Both species are easily recognized by their green coloration due to the intracellular algae, and a comprehensive discussion as to the possible roles of the intracellular algae is provided. Conclusions: The 18S rRNA gene phylogeny supports the morphological argument that Hemiholosticha, Psilotrichides and Urospinula belong to the same family, Psilotrichidae. However, the single-gene analysis, not surprisingly, does not resolve the deeper relationships of Psilotrichidae within the subclass Hypotrichia. Two little-known psilotrichid genera with green algae were collected from the same puddle on the island of Guam, indicating a high species diversity and broader geographic distribution of this group of ciliates than previously supposed. Phylogenetic inferences from transcriptomic and/or genomic data will likely be necessary to better define the systematic position and evolution of the family Psilotrichidae. Further studies are also needed to clarify the role of the intracellular eyespot-bearing algae in these ciliates. [ABSTRACT FROM AUTHOR]

[Display omitted] • 53 new SSU, ITS1-5.8S rDNA-ITS2, and LSU rDNA sequences of spirotrich ciliates. • Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia. • Division of subgenera Novistrombidium and Parallelostrombidium is fully supported. • Cyrtostrombidiidae, Pelagostrombidiidae and Tontoniidae evolved from Strombidiidae. Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci. [ABSTRACT FROM AUTHOR]

[Display omitted] • The origin of the subclass Peritrichia was estimated to be during the late Proterozoic. • The presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. • Some of the morphological characters used for classifying sessilids are taxonomically unreliable. Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation. [ABSTRACT FROM AUTHOR]

The small subunit rRNA (SSrRNA) gene was sequenced for two marine scuticociliates Metanophrys similis and Pseudocohnilembus hargisi. The results show that this gene comprises 1763 and 1753 nucleotides in the two marine ciliates respectively. Metanophrys similis is phylogenetically closely related to the clade containing Mesanophrys carcini and Anophyroides haernophila, which branches basally to other species within the order Philasterida. Pseudocohnilembus hargisi groups with its congener, P. marinus, with strong bootstrap support. Paranophrys magna groups with the clade including Cohnilembus and Uronema, representing a sister clade to that containing the two Pseudocohnilembus species. [ABSTRACT FROM AUTHOR]