scholarly journals Morphology and phylogenetic analysis of two oxytrichid soil ciliates from China, Oxytricha paragranulifera n. sp. and Oxytricha granulifera Foissner and Adam, 1983 (Protista, Ciliophora, Hypotrichia)

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3016-3027 ◽  
Author(s):  
Chen Shao ◽  
Zhao Lv ◽  
Ying Pan ◽  
Khaled A. S. Al-Rasheid ◽  
Zhenzhen Yi
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
The Body ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Cortical Granules ◽  
Ssu Rrna Gene ◽  
North West ◽  
Significant Difference

The morphology and infraciliature of two hypotrichous ciliates, Oxytricha paragranulifera n. sp. and Oxytricha granulifera Foissner and Adam, 1983, collected respectively from the surface of a sandy soil in the Huguang mangrove forest, Zhanjiang, China, and the surface of soil in a forest beside Ziwu Road, Xian, north-west China, were examined. O. paragranulifera n. sp. is characterized by an elongate body with slightly tapered anterior end, two macronuclear nodules and two micronuclei, paroral and endoral in Stylonychia-pattern, colourless cortical granules distributed in clusters or irregular short rows, adoral zone occupying 37 % of the body length, marginal rows almost confluent posteriorly, six dorsal kineties and three caudal cirri, caudal cirri and dorsal bristles almost indistinguishable when viewed in vivo. The well-known O. granulifera Foissner and Adam, 1983 was also redescribed and can be separated from the novel species by having cortical granules arranged along dorsal kineties and marginal rows on both sides (vs grouped in clusters as well as in short irregular rows), paroral and endoral in Oxytricha-pattern (vs in Stylonychia-pattern), macronuclear nodules obviously detached (vs adjacent) and a non-saline terrestrial habitat (vs saline terrestrial). The separation of these two taxa is also firmly supported by the molecular data, which show a significant difference between the two in their SSU rRNA gene sequences (similarity 97.1 %). Phylogenetic analyses based on SSU rRNA gene sequence data suggest a close relationship within the Oxytrichidae assemblage between O. paragranulifera n. sp. and O. granulifera.

scholarly journals Morphological and phylogenetic studies on three members of the genus Pseudochilodonopsis (Ciliophora, Cyrtophoria) isolated from brackish waters in China, including a novel species, Pseudochilodonopsis quadrivacuolata sp. nov.

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4323-4334 ◽  
Author(s):  
Zhishuai Qu ◽  
Hongbo Pan ◽  
Khaled A. S. Al-Rasheid ◽  
Xiaozhong Hu ◽  
Shan Gao
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Small Subunit ◽  
Dorsal Side ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Ssu Rrna Gene Sequence

Three cyrtophorian ciliates isolated from brackish biotopes in China, Pseudochilodonopsis quadrivacuolata sp. nov., Pseudochilodonopsis fluviatilis Foissner, 1988 and Pseudochilodonopsis mutabilis Foissner, 1981, were investigated using living observation and protargol-staining methods. P. quadrivacuolata sp. nov. can be characterized as follows: cell size 50–70 × 30–40 μm in vivo; body oval with posterior end rounded; four tetragonally positioned contractile vacuoles; 12–15 nematodesmal rods; five right and six left somatic kineties; terminal fragment positioned apically on dorsal side, consisting of 11–14 basal bodies; four or five fragments in preoral kinety. P. fluviatilis and P. mutabilis were generally consistent with previous descriptions. In addition, a brief revision and a key to Pseudochilodonopsis are presented. The small-subunit (SSU) rRNA gene was also sequenced to support the identification of these species. Phylogenetic analyses based on molecular data indicate that the genera Pseudochilodonopsis and Chilodonella are closely related and both are well outlined; that is, all known congeners for which SSU rRNA gene sequence data are available group together, forming the core part of the family Chilodonellidae.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

Morphological Redescriptions and Molecular Phylogeny of Three Stentor Species (Ciliophora: Heterotrichea: Stentoridae) from Korea

Zootaxa ◽  
2020 ◽  
Vol 4732 (3) ◽  
pp. 435-452
Author(s):  
MD ABU TAHER ◽  
AHMED SALAHUDDIN KABIR ◽  
SHAHED UDDIN AHMED SHAZIB ◽  
MIN SEOK KIM ◽  
MANN KYOON SHIN
Keyword(s):  
Gene Sequence ◽  
Small Subunit ◽  
Rrna Gene ◽  
Sequence Information ◽  
Ssu Rrna ◽  
Rrna Gene Sequence ◽  
Cortical Granules ◽  
Ssu Rrna Gene ◽  
Ssu Rrna Gene Sequence

The morphologies of the three freshwater stentorid ciliates in Korea, Stentor coeruleus (Pallas, 1766); Stentor muelleri Ehrenberg, 1831, and Stentor tartari Murthy & Bai, 1974, were investigated based on live observations and protargol impregnation. The Korean population of S. tartari exhibits the following characteristics: body size 200–355 × 85–135 µm in vivo, 62–106 somatic kineties, 8–13 peristomial kineties, 110–180 adoral membranelles, mostly two macronuclear nodules and 5–18 micronuclei, reddish and colorless cortical granules and the presence of symbiotic algae. We identified S. tartari based on unique characteristics compared to close congeners. Korean populations of S. coeruleus and S. muelleri are congruent with previously described populations in most aspects of their morphologies. Here, for the first time, we report molecular gene sequence information for S. tartari. Small subunit (SSU) rRNA gene sequence-based phylogeny indicates that S. tartari, which has multiple macronuclei, forms a monophyletic group with other Stentor species having a single macronucleus. Our findings based on morphology and SSU rRNA gene sequence information corroborate the hypothesis that the elongated macronucleus evolved from the compact single or multi macronucleus state. 

Morphology and phylogenies of two hypotrichous brackish-water ciliates from China, Neourostylopsis orientalis n. sp. and Protogastrostyla sterkii (Wallengren, 1900) n. comb., with establishment of a new genus Neourostylopsis n. gen. (Protista, Ciliophora, Hypotrichia)

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1197-1209 ◽  
Author(s):  
Xiangrui Chen ◽  
Chen Shao ◽  
Xihan Liu ◽  
Jie Huang ◽  
Khaled A. S. Al-Rasheid
Keyword(s):  
New Genus ◽  
Southern China ◽  
Molecular Data ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Cortical Granules ◽  
Ssu Rrna Gene ◽  
Shape Ratio

This paper investigates the morphology, infraciliature and small-subunit (SSU) rRNA gene sequences of two hypotrichous ciliates, Neourostylopsis orientalis n. sp., and Protogastrostyla sterkii (Wallengren, 1900) n. comb. (basionym Gastrostyla sterkii), collected from coastal waters in southern China. Neourostylopsis orientalis n. sp. is diagnosed mainly by the arrangement of brownish cortical granules, the numbers of adoral membranelles and frontal and transverse cirri and the characteristics of its midventral cirral pairs. The SSU rRNA gene phylogeny strongly supports the establishment of the new genus Neourostylopsis n. gen., which is characterized mainly by the following features: frontal and transverse cirri clearly differentiated, buccal cirri present, two frontoterminal cirri, midventral complex composed of midventral pairs only and not exceeding the halfway point of the cell, more than one row of marginal cirri on each side which derive from individual anlagen within each parental row, caudal cirri lacking. Thus, two new combinations are required: Neourostylopsis songi (Lei et al., 2005) n. comb., and Neourostylopsis flavicana (Wang et al., 2011) n. comb. Additionally, improved diagnoses for both Metaurostylopsis and Apourostylopsis are supplied in this study. Protogastrostyla sterkii (Wallengren, 1900) n. comb. differs from the similar congener Protogastrostyla pulchra mainly in body shape, ratio of buccal field to body length in vivo and molecular data. Based on the present studies, we conclude that the estuarine population of P. pulchra collected by J. Gong and others [Gong et al., J Eukaryot Microbiol (2007) 54, 468–478] is a population of P. sterkii.

scholarly journals Morphological redescriptions and neotypification of two poorly known tintinnine ciliates (Alveolata, Ciliophora, Tintinnina), with a phylogenetic investigation based on SSU rRNA gene sequences

2020 ◽  
Vol 70 (4) ◽  
pp. 2515-2530 ◽  
Author(s):  
Rui Wang ◽  
Wen Song ◽  
Yang Bai ◽  
Alan Warren ◽  
Lifang Li ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Ssu Rrna Gene ◽  
Unbiased Test ◽  
Rrna Gene Sequencing ◽  
Ssu Rrna Gene Sequence

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.

scholarly journals Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

2018 ◽  
Author(s):  
Jeffrey S. McLean ◽  
Batbileg Bor ◽  
Thao T. To ◽  
Quanhui Liu ◽  
Kristopher A. Kerns ◽  
...  
Keyword(s):  
Oral Cavity ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

The morphology and phylogeny of two euplotid ciliates, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965 (Protozoa, Ciliophora, Euplotida)

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2757-2773 ◽  
Author(s):  
Xiaozhong Hu ◽  
Jie Huang ◽  
Alan Warren
Keyword(s):  
Salt Marshes ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Cladistic Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Rrna Gene Sequence ◽  
Ssu Rrna Gene ◽  
Ssu Rrna Gene Sequence

The morphology, infraciliature and molecular phylogeny of two marine ciliated protozoans, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965, isolated from British salt marshes, were investigated using microscopic observations of live and protargol-impregnated specimens, and by small subunit (SSU) rRNA gene sequence analysis. Diophrys blakeneyensis spec. nov. is characterized as follows: cell oval to rectangular in outline; size variable, approximately 60–180 × 30–80 µm in vivo; adoral zone comprising about 45 membranelles; usually five frontal, two ventral, five transverse, two left marginal and three caudal cirri; five dorsal kineties with more than 10 dikinetids each; 7–23 spherical to ellipsoid macronuclear nodules in a ring-like pattern; marine biotope. The population of Diophrys oligothrix described here corresponds well with previous populations in terms of its general morphology and ciliary pattern, in particular the continuous ciliary rows on the dorsal side with loosely arranged cilia. The main differences between the present and previously reported populations are the broader buccal field and greater number of dorsal kineties in the present population, both of which are regarded as population-dependent features. Phylogenetic analyses based on SSU rRNA gene sequence data demonstrate that Diophrys blakeneyensis is most closely related to Diophrys oligothrix, and both organisms cluster with two congeners with high bootstrap support within a larger group that contain the core species of the Diophrys-complex. Cladistic analysis based on morphological and morphogenetic data broadly agree with the SSU rRNA gene sequence phylogeny. Both analyses suggest that the genus Diophrys may be polyphyletic.

Taxonomy, morphology and molecular systematics of three oligotrich ciliates, including a description of Apostrombidium parakielum spec. nov. (Ciliophora, Oligotrichia)

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1179-1191 ◽  
Author(s):  
Wen Song ◽  
Jiamei Li ◽  
Weiwei Liu ◽  
Jiamei Jiang ◽  
Khaled A. S. Al- Rasheid ◽  
...  
Keyword(s):  
Sequence Data ◽  
Novel Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
The Novel ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Single Clade ◽  
Ssu Rrna Gene Sequence

Three oligotrich ciliates, Apostrombidium parakielum spec. nov., Novistrombidium apsheronicum (Alekperov & Asadullayeva, 1997) Agatha, 2003 and Novistrombidium testaceum (Anigstein, 1914) Song & Bradbury, 1998 were collected from the coastal waters of China and their morphology and small-subunit rRNA (SSU rRNA) gene sequences were studied. The novel species can be recognized by the combination of its obconical body shape, 14–16 anterior and 6–8 ventral membranelles, somatic kinety in three parts and conspicuously long dorsal cilia. Based on the data obtained for this novel species, an improved diagnosis of the genus Apostrombidium is supplied. Descriptions of the population of N. apsheronicum and N. testaceum collected in this study are also provided and compared with the existing descriptions. In addition, the phylogenetic positions of these three species are inferred from their SSU rRNA gene sequence data. The results indicate that the genus Apostrombidium, the systematics of which has not previously been discussed using molecular information, clusters with Varistrombidium kielum and Omegastrombidium elegans, whereas N. testaceum and N. apsheronicum form a single clade.

Redescriptions of three trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with notes on their phylogeny based on small subunit rRNA gene sequences

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3506-3514 ◽  
Author(s):  
Ying Yan ◽  
Yuan Xu ◽  
Zhenzhen Yi ◽  
Alan Warren
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
Ssu Rrna Gene Sequence ◽  
First Time

Three trachelocercid ciliates, Kovalevaia sulcata (Kovaleva, 1966) Foissner, 1997, Trachelocerca sagitta (Müller, 1786) Ehrenberg, 1840 and Trachelocerca ditis (Wright, 1982) Foissner, 1996, isolated from two coastal habitats at Qingdao, China, were investigated using live observation and silver impregnation methods. Data on their infraciliature and morphology are supplied. The small subunit rRNA (SSU rRNA) genes of K. sulcata and Trachelocerca sagitta were sequenced for the first time. Phylogenetic analyses based on SSU rRNA gene sequence data indicate that both organisms, and the previously sequenced Trachelocerca ditis, are located within the trachelocercid assemblage and that K. sulcata is sister to an unidentified taxon forming a clade that is basal to the core trachelocercids.

scholarly journals Morphology, ontogenetic features and SSU rRNA gene-based phylogeny of a soil ciliate, Bistichella cystiformans spec. nov. (Protista, Ciliophora, Stichotrichia)

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4049-4060 ◽  
Author(s):  
Yangbo Fan ◽  
Xiaozhong Hu ◽  
Feng Gao ◽  
Saleh A. Al-Farraj ◽  
Khaled A. S. Al-Rasheid
Keyword(s):  
Novel Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Final Conclusion ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
The Novel ◽  
Ssu Rrna Gene ◽  
To Come ◽  
Mode 3

The morphology, ontogeny and SSU rRNA gene-based phylogeny of Bistichella cystiformans spec. nov., isolated from the slightly saline soil of a mangrove wetland in Zhanjiang, southern China, were investigated. The novel species was characterized by having five to eight buccal cirri arranged in a row, three to five transverse cirri, four macronuclear nodules aligned, and 17–32 and 20–34 cirri in frontoventral rows V and VI, respectively, both extending to the transverse cirri. The main ontogenetic features of the novel species were as follows: (1) the parental adoral zone of the membranelles is completely inherited by the proter; (2) the frontoventral and transverse cirri are formed in a six-anlagen mode; (3) basically, the frontal-ventral-transverse cirral anlagen II–V generate one transverse cirrus each at their posterior ends, while anlage VI provides no transverse cirrus; (4) both marginal rows and dorsal kineties develop intrakinetally, no dorsal kinety fragment is formed; and (5) the macronuclear nodules fuse into a single mass at the middle stage. Phylogenetic analyses based on the SSU rRNA gene showed that the novel species groups with the clade containing Bistichella variabilis, Parabistichella variabilis, Uroleptoides magnigranulosus and two species of the genus Orthoamphisiella. Given present knowledge, it was considered to be still too early to come to a final conclusion regarding the familial classification of the genus Bistichella; further investigations of key taxa with additional molecular markers are required.

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