Diversity and geographic distribution of ciliates (Protista: Ciliophora)

About 4,500 free-living ciliate morphospecies have been described, applying an average synonymy rate of 20%. We estimate that 83–89% of the ciliate diversity is still undescribed, using the following probabilities: detailed habitat studies suggest that the described number of morphospecies must be doubled: 4,500 → 9,000; this figure has to be increased by about 50% due to species with similar interphase morphology but different resting cysts: 9,000 → 13,500; the genetic and molecular data suggest that this value must be doubled or trebled: 13,500 → 27,000 to 40,000 free-living, biological ciliate species. The knowledge on geographic distribution of ciliates heavily depends on flagship species and statistical analyses because reliable faunistic studies are rare and molecular data are still in its infancy. We present a list of 52 ciliate flagship species as a testable hypothesis, i.e., the hypothesis of restricted distribution of certain ciliate species must be refused when a considerable number of them is found in all or most biogeographic regions. Flagship species and statistical analyses consistently show Gondwanan and Laurasian ciliate communities, suggesting that the split of Pangaea deeply influenced ciliate distribution and rare species play a key role in geographic differentiation. However, there is also substantial evidence for continental, regional, and local endemism of free-living ciliates. The molecular studies usually show a high level of genetic diversity underlying ciliate morphospecies, suggesting that morphologic and molecular evolution may be decoupled in many ciliate species. Molecular studies on ciliate biogeography are at variance, possibly because most are still focusing on single molecular markers. In sum, the data indicate that ciliate biogeography is similar to that of plants and animals, but with an increased proportion of cosmopolites, favouring the moderate endemicity model. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Large-scale phylogenetic analysis provides insights into the diversification and evolution of sessilid peritrich ciliates (Protista: Ciliophora)

The Peritrichia is a speciose and morphologically distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades, the phylogenetic relationships of this group have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions, mainly owing to limited sampling. In the present study, we performed expanded phylogenetic analyses of 152 sessilid peritrichs collected from 14 different provinces of China and 141 SSU rDNA peritrich sequences from GenBank. The results of the analyses revealed new divergent relationships between and within major clades that challenge the morphological classification of this group including, (1) the recovery of four major phylogenetically divergent clades in the monophyletic order Sessilida, (2) aboral structures such as the stalk and spasmoneme were evolutionary labile, (3) the stalk or/and spasmoneme was lost in each divergent clade indicating that parallel evolution occurred in sessilid peritrichs and (4) the life cycle and habit drive the diversity of aboral structures as well as diversification and evolution in peritrichs.     

Molecular characterization and revised systematics of Microdiaphanosoma arcuatum (Ciliophora, Colpodea)

Microdiaphanosoma arcuatum Wenzel, 1953 is a world-wide distributed ciliate, recorded mainly in soil samples, which we have also identified in ground water samples from South Africa. This ciliate has been frequently overlooked or not determined due to its small size, ～12 μm. The genus Microdiaphanosoma is nowadays included in the class Colpodea, order Bryometopida, family Kreyellidae. The first complete small subunit (SSU) rDNA gene sequence of this ciliate was obtained from a South African isolate. Phylogenetic analysis including available SSU rDNA sequences from another Colpodea species in the GenBank strongly supported the position of M. arcuatum within the order Cyrtolophosidida instead of the order Bryometopida. The analysis also suggested a sister relationship between this species and species from the family Cyrtolophosididae.     

Taxonomy and molecular systematics of three oligotrich (s.l.) ciliates including descriptions of two new species,Strombidium guangdongense sp. nov. and Strombidinopsis sinicum sp. nov. (Protozoa,Ciliophora)

In this study we investigated the morphology of three oligotrich (s.l.) ciliates, Strombidium guangdongense sp. nov., Cyrtostrombidium paralongisomum Tsai et al., 2015 and Strombidinopsis sinicum sp. nov. Strombidium guangdongense sp. nov. is characterized by its elongate obconical to obovoidal body shape and widely spaced dikinetids in the girdle and ventral kineties. Another new species, Strombidinopsis sinicum sp. nov. is diagnosed by its small size and semi-globular body shape without mineral envelopes. Some additional morphological data of the recently described species Cyrtostrombidium paralongisomum Tsai et al., 2015, such as the endoral membrane, are supplied based on our population. We also analysed the molecular phylogeny of each species based on small subunit rRNA (SSU rRNA) gene sequence data. The monophyly of Cyrtostrombidium is supported by our phylogenetic analyses, but the monophyly of Strombidinopsis and of the family Strombidinopsidae are both rejected by AU tests. In addition, Strombidium species have a tail branch separately from one another in phylogenetic trees, whereas strombidiids with a pigment spot group together, suggesting the latter character is a synapomorphy for this group of strombidiids.

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Redefinition of the hypotrichous ciliate Uncinata,with descriptions of the morphology and phylogeny of three urostylids (Protista,Ciliophora)

We investigated the morphology, morphogenesis and small subunit rRNA gene-based phylogeny of three marine urostylids, Uncinata gigantea Bullington, 1940 Bullington, W. E. (1940). Some ciliates from Tortugas. Papers from the Tortugas Laboratory, 32, 179–221. [Google Scholar], Holosticha heterofoissneri Hu & Song, 2001 Hu, X., & Song, W. (2001). Morphology and morphogenesis of Holosticha heterofoissneri n. sp. from the Yellow Sea, China (Ciliophora, Hypotrichida). Hydrobiologia, 448, 171–179. doi:10.1023/A:1017553406031.[Crossref], [Web of Science ®] , [Google Scholar], and Holosticha cf. heterofoissneri. The dorsal morphogenesis of Uncinata gigantea shows de novo formation of two groups of anlagen near the marginal rows. Holosticha cf. heterofoissneri demonstrates fragmentation of the first dorsal kinety anlage as in Holosticha heterofoissneri. Our population of H. heterofoissneri corresponds well with previously described populations in terms of its general morphology and ciliary pattern. Uncinata gigantea can be recognized by its large and highly contractile body, yellowish to brownish cell colour, two types of cortical granules, and 20–30 transversely oriented and densely arranged cirri in the left marginal row, which often overlie the buccal vertex. Based on the new data, especially infraciliature, the genus Uncinata is here redefined. Both the morphology and phylogenetic analyses suggest that the genus Uncinata should be classified within the family Urostylidae. In addition, both morphological and morphogenetic data suggest that Holosticha bradburyae Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar] should be transferred to Uncinata as U. bradburyae (Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar]) comb. nov., due to its possession of a characteristically prominent beak-like, leftwards curved projection and the developmental mode of the dorsal kineties. This assignment is supported by the phylogenetic analyses, which placed Uncinata gigantea in a clade with U. bradburyae (Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar]) comb. nov., and revealed only 1.13% (19 bp) difference in their SSU-rDNA gene sequence.     

Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small- and large-subunit rRNA genes

Concatenated sequences of small- and large-subunit rRNA genes were used to infer the phylogeny of 29 species in six genera of Tintinnida. We confirmed previous results on the positions of major clusters and the grouping of various genera, including Stenosemella, the paraphyletic Tintinnopsis, the newly investigated Helicostomella, and some species of the polyphyletic Favella. Tintinnidium and Eutintinnus were found to be monophyletic. This study contributes to tintinnid phylogenetic reconstruction by increasing both the number of species and the range of genetic markers analyzed.     

Species boundaries in tintinnid ciliates: a case study--morphometric variability, molecular characterization, and temporal distribution of Helicostomella species (Ciliophora, Tintinnina)

Tintinnids are a large group of planktonic ciliates with diverse morphologies. The range of variability in lorica shapes and sizes can be very high even within a single species depending on life stages and environmental conditions, which makes the delimitation of different species based on morphological criteria alone very difficult. Accordingly, comparisons of morphological and molecular variability in tintinnids are necessary to provide a pragmatic approach for establishing species boundaries within this diverse and poorly understood group. We investigated the temporal distribution of species of the hyaline tintinnid Helicostomella (Ciliophora, Tintinnina), which were collected daily from September 2008 to August 2009 in Jangmok Bay of Geoje Island on the south coast of Korea. Two forms - a long form and a short form, were discovered. The long form was found in cold waters in February and March whereas the short form occurred in warm waters from June to October. Thus, these two forms were seasonally isolated. However, all the morphological characteristics for these two forms overlap to some degree. A comparison of the small subunit (SSU) rDNA, ITS1-5.8S-ITS2, and ITS2 sequences from two forms revealed 0.5%, 3.8%, and 5.6% divergences, respectively. Morever, one compensatory base change (CBC) and three hemi-CBCs were identified from ITS2 secondary structures of these two forms. All these data suggest that these two forms represent two distinct species despite their highly similar lorica morphology. The phylogenetic position of the genus Helicostomella was also examined using SSU rDNA sequences.     

Taxonomy and molecular phylogeny of three freshwater scuticociliates,with descriptions of one new genus and two new species (Protista,Ciliophora, Oligohymenophorea)

Three freshwater scuticociliates, Apouronema harbinensis gen. nov. spec. nov., Cyclidium vorax spec. nov., and C. glaucoma Müller, 1773, collected from rivers in Hulan District, Harbin, northeastern China, were investigated using morphological and phylogenetic criteria. Apouronema gen. nov., assigned to the family Uronematidae, is mainly distinguished from the other genera of the family by its paroral membrane extending anteriorly to the middle of membranelle 1. Apouronema harbinensis spec. nov. is defined by body size in vivo about 45–55 × 20–25 μm, buccal field about 70–80% of cell length; 12 or 13 somatic kineties; membranelle 1 having two rows, with 16–18 basal bodies in each kinety; membranelle 2 and membranelle 3 both having two rows each; scutica X-shaped with five pairs of basal bodies. Cyclidium vorax spec. nov. is characterized by the following features: body size 35–40 × 18–20 μm in vivo; 9 or 10 somatic kineties; membranelle 1 having two longitudinal rows, much shorter than M2; M2 triangle-shaped. The phylogenetic analyses show that: (1) Apouronema clustered in the Uronematidae clade, and grouped with genera Uronemita and Uronema; (2) Cyclidium vorax spec. nov. grouped with C. glaucoma and C. sinicum, which supports the assignment of the new species to the genus Cyclidium; (3) Cyclidium remains non-monophyletic with the addition of the new sequence.     

Three New Loxophyllum Species (Ciliophora: Pleurostomatida) from China with a Brief Review of the Marine and Brackish Loxophyllum Species

Recent studies indicate that there is a high diversity of pleurostomatid ciliates in the coastal waters of China. Here, three new congeners of Loxophyllum, L. caudatum sp. n., L. rugosum sp. n., and L. chinense sp. n., are described following observations of live cells and protargol‐impregnated specimens. All three species usually have two macronuclear nodules and prominent warts along the dorsal margin formed by clustered extrusomes. In addition, L. caudatum sp. n. is characterized by its long conspicuous tail, dot‐like cortical granules, 4 or 5 left and 9 or 10 right kineties, and a single subterminal contractile vacuole. Loxophyllum rugosum sp. n. is distinguished by possessing three prominent ridges on the left side, 7–11 right and 5–7 left kineties. Loxophyllum chinense sp. n. is characterized by having several contractile vacuoles distributed along the ventral margin, 13–18 right and 6–8 left kineties. The small subunit ribosomal DNA (SSU rDNA) sequence similarities among six congeners range from 96.46% to 99.94%. Phylogenetic trees based on the SSU rDNA sequences indicate that all Loxophyllum spp. form a well‐supported monophyletic group. A brief review of the marine and brackish Loxophyllum species is supplied and one new combination, Litonotus multiplicatus (Kahl 1931) comb. n. (basionym Loxophyllum multiplicatum Kahl 1931), and one new name, Litonotus dragescoi nom. n. (basionym L. fasciolatus Dragesco 1966), are suggested.     

Morphological and Molecular Description of Three New Species of the Cyrtophorid Genus Chlamydodon (Ciliophora,Cyrtophoria)

This study investigates the morphology and molecular characteristics of three new cyrtophorid ciliates isolated from China seas: Chlamydodon salinus n. sp., Chlamydodon caudatus n. sp., and Chlamydodon paramnemosyne n. sp. Of these, C. salinus n. sp. differs from its congeners through a combination of body size, a cross‐striated band that is not continuous, the presence of 30–34 somatic kineties, 11–15 nematodesmal rods, and 13 contractile vacuoles. Chlamydodon caudatus n. sp., meanwhile, is characterized by having a conspicuous tail, a continuous cross‐striated band, 34–40 somatic kineties, about 15 contractile vacuoles, and 20–24 nematodesmal rods. Compared with other Chlamydodon species, the third new one, C. paramnemosyne n. sp., could be identified by its continuous cross‐striated band, 16–18 somatic kineties, 5 contractile vacuoles, and 9–12 nematodesmal rods. Based on the sequence of the small subunit (SSU) rRNA gene, the phylogeny of these three new species was analyzed, indicating that they all clustered with other congeners to form a monophyletic assemblage. Based on previous studies and the present work, a brief revision of the genus Chlamydodon is supplied, and a key to aid the identification of Chlamydodon species is given.     

Redescription of two little-known urostyloid ciliates,Anteholosticha randani () and A. antecirrata (Ciliophora,Urostylida)

The morphology of two little-known urostyloid ciliates, Anteholosticha randani (Grolière, 1975) Berger, 2003 and A. antecirrata Berger, 2006, collected from freshwater biotopes in southern China, was studied based on live observations and protargol staining. Anteholosticha randani is characterized by its bipartite adoral zone and short, longitudinally aligned undulating membranes. One early stage of reorganization/morphogenesis, one early-middle stage of reorganization and one middle stage of morphogenesis are also reported. Anteholosticha antecirrata is characterized by its large body size in vivo (200–400 × 40–80 μm), a row of buccal cirri and conspicuous, yellow-green cortical granules. Phylogenetic analyses based on SSU rDNA sequence data reveal that A. antecirrata may share a most recent common ancestor with Urostyla grandis and Bakuella granulifera, whereas A. randani branches independently and is sister to a large clade that includes Pseudourostyla, Pseudokeronopsis, Caudiholosticha and several species of Anteholosticha.     

Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts,including descriptions of two new species (Ciliophora,Peritrichia)

Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalis Möbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.     

Two New Marine Ciliates,Caryotricha rariseta n. sp. and Discocephalus pararotatorius n. sp. (Ciliophora,Spirotrichea), with Phylogenetic Analyses Inferred from the Small Subunit rRNA Gene Sequences

The morphology, infraciliature, and molecular phylogeny of two novel spirotrich ciliates, Caryotricha rariseta n. sp. and Discocephalus pararotatorius n. sp., isolated from coastal waters of China, were investigated. Caryotricha rariseta n. sp. differs from its congeners mainly in possessing seven sparsely ciliated cirral rows that are conspicuously shortened posteriorly and three transverse cirri aligned in a row. Discocephalus pararotatorius n. sp. is characterized by the conspicuous spine‐like dorsal cilia, one extra (endoral?) membrane, and seven frontal, six ventral, and seven posterolateral marginal cirri. The small subunit rRNA gene was sequenced for both species. Complete SSU rRNA gene sequences of two Caryotricha spp. (including C. rariseta n. sp.) and two Discocephalus spp. (including D. pararotatorius n. sp.), along with those of 40 other ciliates, were used to determine their molecular phylogeny using maximum likelihood, neighbor joining and maximum parsimony analyses. The two Caryotricha species cluster with Kiitricha marina in the well‐supported Protohypotrichia clade that is basal to the main spirotrich assemblage. The two discocephalids form a clade that is sister to the Hypotrichia.     

Revision of the genus Thetidos Hedley, 1899 (Gastropoda: Conoidea: Raphitomidae) in the Indo-Pacific with descriptions of three new species

The genus Thetidos was established to accommodate a single species Thetidos morsura, a minute turriform conoidean with an unremarkable paucispiral protoconch, but possessing characteristic globose whorls of the teleoconch and three strong denticles on the inside of outer apertural lip. Subsequently, Thetidos was considered synonymous with Lienardia, and has rarely been mentioned in literature until the recent discovery of a remarkably similar species Thetidos tridentata, though it is different in protoconch morphology. Both molecular data and protoconch morphology unequivocally suggested placement of the new species in Raphitomidae. Examination of shells from the Indo-Pacific identified a number of similar forms, all referable to the genus Thetidos. Six species are now recognized within the genus; of them three, Thetidos puillandrei n. sp., Thetidos minutissima n. sp., Thetidos pallida n. sp., are here described as new. Thetidos species are now known from subtidal depths from the Philippines and Sulawesi to French Polynesia. Thetidos morsura is the only species of the genus that possesses a paucispiral protoconch suggestive of a non-planktotrophic development, although it displays a wide geographic range and a high morphological variability.

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Integrative systematics of northern and Arctic nudibranchs of the genus Dendronotus (Mollusca,Gastropoda), with descriptions of three new species

The taxonomy of common northern nudibranch molluscs of the genus Dendronotus in the vast cold regions of Eurasia remains largely unknown. Abundant material collected in many localities from the Barents Sea, via the Arctic region, to the north‐west Pacific was analysed for the first time. An integrated approach combining morphological and ontogenetic data with molecular four‐gene (COI, 16S, H3, and 28S) analysis reveals seven species, including three previously undescribed. Dendronotus frondosus (Ascanius, 1774) and Dendronotus dalli Bergh, 1879 were commonly considered as amphiboreal species; however, according to this study they are restricted to the North Atlantic and the North Pacific, respectively. In the north‐west Pacific two new species were discovered, D endronotus kamchaticus sp. nov. and D endronotus kalikal sp. nov. , that are externally similar to D. frondosus, but that show significant distance according to molecular analysis and are considerably different in radular morphology. In the North Atlantic a new species D endronotus niveus sp. nov. , sibling to North Pacific D. dalli, is revealed. The separate status of North Atlantic Dendronotus lacteus (Thompson, 1840) is confirmed, including considerable range extension. The essential similarity of early ontogenetic stages of radular development common for species with disparate adult radular morphology (such as D. frondosus and D. dalli) is shown, and its importance for taxonomy is discussed. © 2015 The Linnean Society of London     

Revision of Strombidium paracalkinsi (Ciliophora: Oligotrichea: Oligotrichia), with Comparison of Strombidiids Bearing Thigmotactic Membranelles

This study analyses the morphological characters of Strombidium paracalkinsi, a species bearing thigmotactic membranelles, collected from Jangmok Bay at the southern coast of Korea. The small subunit ribosomal RNA gene of S. paracalkinsi was sequenced for the first time. By a combination of characters, the thigmotactic membranelles of S. paracalkinsi differ from the thigmotactic membranelles of other strombidiids. They are (1) positioned on dorsal side, (2) contiguous with three membranelles of the adoral zone, but separated by nonciliated portions of the polykinetids, and (3) composed of two rows of kinetids. Except for the thigmotactic membranelles, the morphology of S. paracalkinsi conforms to the diagnosis of the genus Strombidium. Our phylogenetic tree confirms the nonmonophyly of the genus Strombidium. The thigmotactic membranelles are a promising feature for a future split of the genus Strombidium, but require further studies, especially on Strombidium calkinsi Fauré‐Fremiet 1932.     

A Contribution to the Morphology and Phylogeny of Chlamydodon,with Three New Species from China (Ciliophora,Cyrtophoria)

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.