Molecular Phylogeny of Phyllopharyngean Ciliates and their Group I Introns

New contributions to the Cyrtophoria ciliates (Protista, Ciliophora): Establishment of new taxa and phylogenetic analyses using two ribosomal genes

Periphytic ciliates play a vital role in the material cycle and energy flow of microbial food web, however, their taxonomy and biodiversity are inadequately studied given their high species richness. Two new and one little known species, viz. Derouxella lembodes gen. et sp. nov., Cyrtophoron multivacuolatum sp. nov., and Cyrtophoron apsheronica Aliev, 1991, collected from coastal waters of China, were investigated using modern methods. Derouxella gen. nov. can be recognized by having dorsoventrally flattened body, a podite, one fragmented preoral kinety, two parallel circumoral kineties, and somatic kineties progressively shortened from right to left. Morphological classification and phylogenetic analyses based on nuclear small subunit ribosomal RNA (nSSU rRNA) and mitochondrial small subunit ribosomal RNA (mtSSU rRNA) gene sequence data inferred that Derouxella gen. nov. occupies an intermediate position between Hartmannulidae and Dysteriidae. Cyrtophoron multivacuolatum sp. nov. is characterized by large body size, the numbers of somatic kineties and nematodesmal rods, and having numerous contractile vacuoles. The genus Cyrtophoron and the poorly known species C. apsheronica were redefined. Even with the addition of newly obtained nSSU rRNA and mtSSU rRNA gene sequences of Cyrtophoron, the family Chlamydodontidae was still recovered as a monophyletic group, the monophyly of Cyrtophoron was supported too.

Historical Review of Studies on Cyrtophorian Ciliates (Ciliophora, Cyrtophoria) from China

The subclass Cyrtophoria are a group of morphologically specialized ciliates which mainly inhabit soil, freshwater, brackish water, and marine environments. In this study, we revise more than 50 publications on the taxonomy, phylogeny, and ecology of cyrtophorian ciliates in China since the first publication in 1925, most of which were carried out in coastal areas. The research history can be divided into three periods: the early stage, the Tibet stage, and the molecular stage. To date, 103 morpho-species (147 isolates) have been formally recorded in China, with ciliature patterns described for 82 of them. A species checklist and an illustrated identification key to the genera are provided. A total of 100 small subunit rDNA sequences have been obtained for 74 taxonomic hits (lowest taxonomic rank to species or genus). These sequences are used for the study of molecular phylogeny. Based on these morphological data and molecular phylogeny analyses, we synthesize the understanding of the phylogeny of cyrtophorian ciliates. We hypothesize that the key evolutionary event of cyrtophorian ciliates lies in the separation of the stomatogenesis zone (postoral kineties) from the left kineties, namely, the formation of an independent "sexual organelle". We, furthermore, briefly summarize the ecological features of cyrtophorian ciliates and provide a comprehensive bibliography of related research from China. Finally, we give an outlook on the future research directions of these taxa.

New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

Taxonomic studies on Aegyria apoliva sp. nov. and Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967 (Ciliophora, Cyrtophoria) with phylogenetic analyses

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.

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.

Morphology and Phylogeny of Two Novel Ciliates, Arcanisutura chongmingensis n. gen., n. sp. and Naxella paralucida n. sp. from Shanghai, China

The morphologies of two novel ciliates, Arcanisutura chongmingensis n. gen., n. sp. and Naxella paralucida n. sp., collected from Shanghai, China, have been investigated using live observation and silver staining methods. Arcanisutura n. gen. can be easily distinguished from related genera by its inconspicuous, oblique anterior suture. Arcanisutura chongmingensis n. sp. is mainly recognized by its elongated body with a tail-like posterior end, 25-33 somatic kineties, and 4-11 excretory pores. Naxella paralucida n. sp. can be distinguished from its congeners based on its two short nassulid organelles, fusiform trichocysts, 37-49 somatic kineties, and 16 nematodesmal rods. The small-subunit (SSU) rRNA gene sequences of these two species are presented, revealing the phylogenetic positions of Arcanisutura and Naxella. Phylogenetic analyses show that Arcanisutura forms a sister clade to other synhymeniid genera, namely, Chilodontopsis, Orthodonella, and Zosterodasys; Naxella is most closely related to Nassula spp. and is located within the monophyletic clade of the family Nassulidae.

Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon

The morphology of four cyrtophorian ciliates, Dysteria ovalis, D. semilunaris, Phascolodon vorticella, and Chlamydonellopsis calkinsi, were investigated using living observation and protargol-staining. The morphology of D. ovalis is revealed in detail for the first time, and it is characterized by the following combination of features: size 40-50×20-30μm in vivo; oval in outline; four right kineties, including two frontoventral kineties and one shortened leftmost right kinety; three left frontal kineties; two ventrally located contractile vacuoles; marine habitat. New Chinese populations of three other species correspond well with previous descriptions, but a well-developed alveolar layer on the cell surface of P. vorticella is reported for the first time. Phylogenetic analyses based on small subunit rRNA gene sequences clustered Dysteria ovalis with Mirodysteria decora, whereas D. semilunaris is grouped with D. lanceolata. Although Phascolodon appeared as sister to Pseudochilodonopsis in the present work, its accurate phylogenetic position is still uncertain because AU test did not reject the possibility that it clustered with Odontochlamys and Chilodonella.

Molecular phylogeny of the cyrtophorid ciliates (Protozoa, Ciliophora, Phyllopharyngea)

Evolutionary relationships of cyrtophorian ciliates are poorly known because molecular data of most groups within this subclass are lacking. In the present work, the SS rRNA genes belonging to 17 genera, 7 families of Cyrtophoria were sequenced and phylogenetic trees were constructed to assess their inter-generic relationships. The results indicated: (1) the assignment of cyrtophorians into two orders is consistently confirmed in all topologies; (2) the order Dysteriida is an outlined monophyletic assemblage while Chlamydodontida is paraphyletic with three separate monophyletic families; (3) Microxysma, which is currently assigned within the family Hartmannulidae, should be transferred to the family Dysteriidae; (4) the systematic position of Plesiotrichopidae remains unclear, yet the two genera that were placed in this family before, Pithites and Trochochilodon, should be transferred to Chlamydodontida; (5) a new family, Pithitidae n. fam., based on the type genus Pithites was suggested; and (6) the sequence of Isochona sp., the only available data of Chonotrichia so far, is probably from a misidentified species. In addition, three group I introns of SS rRNA gene were discovered in Aegyriana oliva, among which Aol.S516 is the first IE group intron reported in ciliates.

Phylogeny and systematic position of Zosterodasys (Ciliophora, Synhymeniida): a combined analysis of ciliate relationships using morphological and molecular data

The Synhymeniida is characterized both by a band of somatic dikinetids, the synhymenium, extending across the surface of the cell and by a ventral cell mouth lacking specialized feeding cilia but subtended by a well-developed cyrtos. The synhymeniids have been hypothesized to be members of the class Nassophorea but our previous ultrastructural study of the synhymeniid genus Zosterodasys did not show any clear synapomorphies that would permit definitive placement in the Nassophorea or as a sister taxon to any of the other ciliate groups possessing a cyrtos. In the present study, simultaneous analysis of morphological and small subunit rDNA molecular data indicates that the Synhymeniida are sister to the class Phyllopharyngea and that this clade is, in turn, sister to the remaining Nassophorea, although this result is sensitive to dataset inclusion and alignment parameters. While this suggests that taxa with a ventral cyrtos might be united into a named taxon (e.g. resurrecting the Hypostomata), additional data are needed to reach a definitive conclusion.

Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora)

The hypostome ciliates have been generally classified into two classes, Phyllopharyngea and Nassophorea. The status of Nassophorea and its relationship with Phyllopharyngea is one of the most controversial issues in ciliate systematics. Here we focus on the phylogenetic interrelationships of Nassophorea and Phyllopharyngea based on small subunit ribosomal RNA gene sequences. The three nassophorean subgroups, synhymeniids, microthoracids, and nassulids, each emerged as monophyletic, with synhymeniids as a sister group of Phyllopharyngea, and microthoracids as a sister of the synhymeniids+Phyllopharyngea clade in all phylogenies. The exact placement of the nassulids, however, remains uncertain. Following a detailed analysis of phenotypic characters, we hypothesize that: (1) the Phyllopharyngea could have evolved from synhymeniids, with the further development of their subkinetal microtubules as one of the major events; and (2) the development of monokinetid structures, as well as the reduction and specialization of the cyrtos and cortex, might have occurred during the diversifications of the microthoracids, synhymeniids, and Phyllopharyngea from a common ancestor. Expanding the class Phyllopharyngea to include the synhymeniids as a subclass, and designating a new subclass Subkinetalia n. subcl. for the group comprising cyrtophorians, chonotrichians, rhynchodians, and suctorians, are proposed.

Balanion masanensis n. sp. (ciliophora: prostomatea) from the coastal waters of Korea: morphology and small subunit ribosomal RNA gene sequence

The planktonic ciliate Balanion masanensis n. sp. is described from living cells, from cells prepared by quantitative protargol staining (QPS), scanning electron microscopy (SEM), and transmitted electron microscopy (TEM) preparations, and the sequence of its nuclear small subunit rDNA (SSU rDNA) is reported. This species is almost ovoid with a flattened anterior oral region when the cells are alive and stained. The flattened anterior region of a living cell often forms a dome with the perimeter receded in a groove, and this region is easily inflated or depressed. In SEM photos, a brosse of six to nine monokinetids (or possibly three to five dikinetids) was observed inside the circumoral dikinetids. In TEM photos, circumoral microtubular ribbons were observed below the oral cilia, which along with the oral flaps were 8-16 microm in length. The cytostome is a slight funnel-like central depression on the flattened anterior end. The morphological characteristics of this ciliate are identical to those of the genus Balanion (Order Prorodontida). The ranges (and mean+/-standard deviation) of cell length, cell width, and oral diameter of living cells (n=23-26) were 27-43 microm (35.2+/-4.6), 25-32 microm (28.6+/-2.3), and 25-30 microm (27.6+/-1.3), respectively, while those of the QPS-stained specimens (n=70) were 23-37 microm (30.6+/-3.5), 26-35 microm (30.7+/-2.2), and 26-33 microm (29.5+/-1.5), respectively. Forty-six to 55 somatic kineties (SKs) were equally spaced around the cell body and extended from the oral to near the posterior regions with 24-50 monokinetids per kinety. Each kinetid bore a cilium 2.8-7.2 microm long. A caudal cilium (ca 14 microm long) arose on the posterior end. The single ellipsoid macronucleus is 6.8-13.4 x 6.8-10.5 microm, accompanied by a single micronucleus (2.0-2.8 x 1.5-2.5 microm) visible only in QPS specimens. Because, the cell size, the number of SKs, and the number of kinetosomes per SK of this ciliate were much greater than those of Balanion comatum and Balanion planctonicum, the only two Balanion species so far reported, we have established B. masanensis n. sp. When properly aligned, the sequence of the SSU rDNA of B. masanensis n. sp. (GenBank Accession No. AM412525) was approximately 9% different from that of Coleps hirtus (Colepidae, Prorodontida) and 12% different from that of Prorodon teres (Prorodontidae, Prorodontida).

Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil

Using cultivation-independent methods the ciliate communities of a clay-rich soil with a 90-year record of pollution by polycyclic aromatic hydrocarbons (PAH) (4.5 g kg(-1) PAH) were compared with that of a nonpolluted soil collected in its vicinity and with similar properties. A ciliate-specific set of 18S rRNA gene targeting primers was designed and used to amplify DNA extracted from both soils (surface and 20 cm depth). Four clone libraries were generated with PCR products that covered an 18S rRNA gene fragment of up to 670 bp. Comparative sequence analysis of representative clones proved that the primer set was highly specific for ciliates. Calculation of similarity indices based on operational taxonomic units after amplified ribosomal DNA restriction analysis of the clones showed that the community from the nonpolluted surface soil was highly dissimilar to the other communities. The presence of several taxa, namely sequences affiliated to the orders Phyllopharyngia, Haptoria, Nassophorea, Peniculida and Scuticociliatia in samples from nonpolluted soil, points to the existence of various trophic functional groups. In contrast, the 18S rRNA gene diversity was much lower in the clone libraries from the polluted soil. More than 90% of these sequences belonged to the class Colpodea, a well-known clade of mainly bacterivorous and r-selected species, thus potentially also indicating a lower functional diversity.

Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling

The ciliate class Colpodea provides a powerful case in which a molecular genealogy can be compared to a detailed morphological taxonomy of a microbial group. Previous analyses of the class using the small-subunit rDNA are based on sparse taxon sampling, and are therefore of limited use in comparisons with morphologically-based classifications. Taxon sampling is increased here to include all orders within the class, and more species within previously sampled orders and in the species rich genus Colpoda. Results indicate that the Colpodea may be paraphyletic, although there is no support for deep nodes. The orders Bursariomorphida, Grossglockneriida, and Sorogenida are monophyletic. The orders Bryometopida, Colpodida, and Cyrtolophosidida, and the genus Colpoda, are not monophyletic. Although congruent in many aspects, the conflict between some nodes on this single gene genealogy and morphology-based taxonomy suggests the need for additional markers as well as a reassessment of the Colpodea taxonomy.