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Song W, Jiao H, Yang J, Tang D, Ye T, Li L, Yang L, Li L, Song W, Al-Farraj SA, Hines HN, Liu W, Chen X. New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora). Mol Phylogenet Evol 2023; 188:107911. [PMID: 37648182 DOI: 10.1016/j.ympev.2023.107911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
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.
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Affiliation(s)
- Wen Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Huixin Jiao
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Juan Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Danxu Tang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Tingting Ye
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lu Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lei Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hunter N Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China.
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Suzhou Research Institute of Shandong University, Suzhou 215123, China.
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He J, Jiang J, Agatha S, Pan H. Taxonomy and phylogeny of the freshwater tintinnid Tintinnopsis tubuformis Chiang, 1956 (Ciliophora, Oligotrichea) and a proposed synonymization of T. longa nom. corr. Chiang, 1956. J Eukaryot Microbiol 2022; 69:e12918. [PMID: 35466480 DOI: 10.1111/jeu.12918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022]
Abstract
Tintinnid ciliates are traditionally identified by their loricae; however, increasing evidence indicates that some lorica features (e.g., its length, spiralled structures) are not reliable. The vast majority of tintinnids inhabit the marine pelagial; merely, about thirty species live in freshwater. In the present study, two morphotypes with similar lorica shapes and opening diameters but deviating lorica lengths were isolated from freshwater samples collected at different water temperatures near Chongming Island in the Yangtze Estuary, China. The specimens were studied in vivo and after protargol staining, and their phylogenetic placement was inferred from three ribosomal RNA markers; further, cell division was investigated in the short morphotype. Based on the original descriptions, the longer morphotype is identified as Tintinnopsis longa nom. corr. Chiang, 1956 and the shorter one as Tintinnopsis tubuformis Chiang, 1956. Despite distinct differences in the lorica lengths, the identity of the three molecular markers in both morphotypes suggests conspecificity, which is supported by overlapping ranges in the lorica opening diameters and the length-independent features of the somatic ciliary pattern (e.g., number of kineties). Hence, we synonymised T. longa nom. corr. with T. tubuformis and neotypified the later species.
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Affiliation(s)
- Jialian He
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Sabine Agatha
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, 5020, Salzburg, Austria
| | - Hongbo Pan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.,Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University
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3
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Agatha S, Bartel H. A comparative ultrastructural study of tintinnid loricae (Alveolata, Ciliophora, Spirotricha) and a hypothesis on their evolution. J Eukaryot Microbiol 2022; 69:e12877. [PMID: 34850491 DOI: 10.1111/jeu.12877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tintinnid ciliates build loricae, whose structure, shape, and size still largely represent the basis for taxonomy and classification, although genetic analyses demonstrated their limited utility for inferring evolutionary relationships. The textures of the lorica walls, however, result from the chemical and physical properties of the forming material, which is supposed to be rather conserved in closely related taxa, viz., congeners and confamilial genera. Within a particular texture, small deviations in the chemical composition might affect the wall's stickiness and accordingly its capability to adhere foreign particles, explaining the intertwining of tintinnids with hyaline and agglutinated loricae in phylogenetic inferences. In a comprehensive comparative study, the lorica textures were electron microscopically and morphometrically analyzed in 21 species from 17 genera and more than nine families together with literature data. Most species were investigated for the first time, and the taxa cover a substantial portion of the molecular genealogy. The phylogeny-aware analysis of the lorica-related features provides a preliminary hypothesis on lorica evolution. Eventually, this conspectus suggests the dominance of hard lorica walls with an alveolar texture and proposes different modes of lorica formation.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Heidi Bartel
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
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4
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Tsai SF, Lee ML, Chiang KP. Morphological, Molecular, and Growth Characteristics of a Cryptic Species, Strombidium parasulcatum n. sp. (Alveolata: Ciliophora: Oligotrichida). Front Microbiol 2022; 12:770768. [PMID: 35222293 PMCID: PMC8866572 DOI: 10.3389/fmicb.2021.770768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
A new marine planktonic ciliate from Taiwan, Strombidium parasulcatum sp. n., is described based on live observations, protargol staining, and molecular data. Its morphological characters are similar to those of Strombidium sulcatum Claparède and Lachmann, 1859 sensu Song et al., 2000 but differ from S. sulcatum sensu Fauré-Fremiet, 1912 and sensu Fauré-Fremiet and Ganier, 1970 by several morphological characters. The 18S rRNA gene sequences of the two forms display 76 base pair differences (about 5%), indicating that they should be considered separate species. The highest observed specific growth rates of S. parasulcatum in culture were 1.79 day–1 over 1 day and 1.52 day–1 over 2 days, both starting at day 5. Bacteria appear to be an important food resource for the cultivation of this medium-sized oligotrich ciliate. This and other recent studies suggest that cryptic species may be common in the genus Strombidium, and an integrative approach including morphological, ecological, and molecular data should be used to address this question.
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Affiliation(s)
- Sheng-Fang Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Meng-Lun Lee
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- *Correspondence: Kuo-Ping Chiang,
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Molecular signature characters complement taxonomic diagnoses: a bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2022; 170:107433. [DOI: 10.1016/j.ympev.2022.107433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
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Agatha S, Ganser MH, Santoferrara LF. The importance of type species and their correct identification: A key example from tintinnid ciliates (Alveolata, Ciliophora, Spirotricha). J Eukaryot Microbiol 2021; 68:e12865. [PMID: 34243218 DOI: 10.1111/jeu.12865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
Types and the corresponding rules in the International Code of Zoological Nomenclature are crucial for taxonomy and are meant to provide nomenclatural stability. In the case of neotypification, especially diligent taxonomic work is required to retain continuity. In the present communication, we first outline the main principles of typification and neotypification. We then discuss a critical case, using a current example from the marine planktonic tintinnid genus Tintinnopsis Stein, 1867 (Alveolata, Ciliophora). This diverse and ubiquitous genus is nonmonophyletic, but its revision and the erection of new related genera is currently prevented by the uncertain affiliation of its type species.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Luciana F Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut at Stamford, Stamford, CT, USA.,Department of Marine Sciences, University of Connecticut at Stamford, Stamford, CT, USA
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Bai Y, Wang R, Song W, Li L, Santoferrara LF, Hu X. Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes. BMC Microbiol 2020; 20:374. [PMID: 33317450 PMCID: PMC7737391 DOI: 10.1186/s12866-020-02057-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/02/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. RESULTS Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. CONCLUSION The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.
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Affiliation(s)
- Yang Bai
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Rui Wang
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wen Song
- Marine College, Shandong University, Weihai, 264209, China
| | - Lifang Li
- Marine College, Shandong University, Weihai, 264209, China
| | - Luciana F Santoferrara
- Department of Ecology and Evolutionary Biology and Department of Marine Sciences, University of Connecticut, One University Place, Stamford, CT, 06901, USA
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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8
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Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12100388] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step.
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Gruber MS, Weißenbacher B, Agatha S. Ultrastructural Studies on a Model Tintinnid - Schmidingerella meunieri (Kofoid & Campbell, 1929) Agatha & Strüder-Kypke, 2012 (Ciliophora). II. The Oral Apparatus. J Eukaryot Microbiol 2020; 67:463-479. [PMID: 32259364 PMCID: PMC7384128 DOI: 10.1111/jeu.12795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/06/2020] [Accepted: 03/21/2020] [Indexed: 12/01/2022]
Abstract
The ultrastructure of the oral apparatus is supposed to be significant for elucidating more recent common ancestry and might thus provide support for particular groupings of oligotrichean ciliates. The transmission electron microscopical study on mainly cryofixed Schmidingerella meunieri specimens provides the first detailed data for tintinnids and Oligotrichea in general. Ten new characters are included into the cladistic analysis. These features together with the very limited body of literature suggest that substantial changes in the oral ultrastructure correlate only with the formation of a circular adoral zone in choreotrichids. Despite homoplasious morphological and ontogenetic adaptations to the planktonic lifestyle in halteriid hypotrichs and oligotrichids, their oral apparatuses generally retain the plesiomorphic ultrastructure of the Perilemmaphora. The highly complex ultrastructure of the adoral zone is thus able to accomplish an extension in the zone's functionality without obvious changes; only the position of the adoral zone at the apical cell portion together with a globular to obconical cell shape are apparently crucial. Merely, minute apomorphies characterise the Oligotrichea and tintinnids, respectively. Tintinnids with derived somatic ciliary patterns possess distinct microtubular bundles connecting the oral apparatus with the myoneme in the peduncle.
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Affiliation(s)
- Michael S Gruber
- Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
| | | | - Sabine Agatha
- Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
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10
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Agatha S, Utz LRP, Zufall RA, Warren A. Symposium on Ciliates in Memory of Denis Lynn. Eur J Protistol 2020; 78:125694. [PMID: 33500175 DOI: 10.1016/j.ejop.2020.125694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Denis Lynn (1947-2018) was an outstanding protistologist, applying multiple techniques and data sources and thus pioneering an integrative approach in order to investigate ciliate biology. For example, he recognized the importance of the ultrastructure for inferring ciliate phylogeny, based on which he developed his widely accepted classification scheme for the phylum Ciliophora. In this paper, recent findings regarding the evolution and systematics of both peritrichs and the mainly marine planktonic oligotrichean spirotrichs are discussed and compared with the concepts and hypotheses formulated by Denis Lynn. Additionally, the state of knowledge concerning the diversity of ciliates in bromeliad phytotelmata and amitosis in ciliates is reviewed.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Laura R P Utz
- School of Health and Life Sciences, PUCRS, Porto Alegre, Brazil
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK.
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Wang R, Song W, Bai Y, Warren A, Li L, Hu X. Morphological redescriptions and neotypification of two poorly known tintinnine ciliates (Alveolata, Ciliophora, Tintinnina), with a phylogenetic investigation based on SSU rRNA gene sequences. Int J Syst Evol Microbiol 2020; 70:2515-2530. [PMID: 32118526 DOI: 10.1099/ijsem.0.004065] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Rui Wang
- Institute of Evolution and Marine Biodiversity; Key Laboratory of Mariculture, Ministry of Education, Ocean University of China (OUC), Qingdao 266003, PR China
| | - Wen Song
- Marine College, Shandong University, Weihai 264209, PR China
| | - Yang Bai
- Institute of Evolution and Marine Biodiversity; Key Laboratory of Mariculture, Ministry of Education, Ocean University of China (OUC), Qingdao 266003, PR China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Lifang Li
- Marine College, Shandong University, Weihai 264209, PR China
| | - Xiaozhong Hu
- Institute of Evolution and Marine Biodiversity; Key Laboratory of Mariculture, Ministry of Education, Ocean University of China (OUC), Qingdao 266003, PR China
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12
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Dong J, Li L, Fan X, Ma H, Warren A. Two Urosoma species (Ciliophora, Hypotrichia): A multidisciplinary approach provides new insights into their ultrastructure and systematics. Eur J Protistol 2019; 72:125661. [PMID: 31841799 DOI: 10.1016/j.ejop.2019.125661] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/18/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Jingyi Dong
- Institute of Evolution and Marine Biodiversity and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lifang Li
- Marine College, Shandong University, Weihai 264209, China
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Honggang Ma
- Institute of Evolution and Marine Biodiversity and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
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13
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Bai Y, Wang R, Liu W, Warren A, Zhao Y, Hu X. Redescriptions of three tintinnine ciliates (Ciliophora: Tintinnina) from coastal waters in China based on lorica features, cell morphology, and rDNA sequence data. Eur J Protistol 2019; 72:125659. [PMID: 31825791 DOI: 10.1016/j.ejop.2019.125659] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
Three species of tintinnines, namely Tintinnopsis tentaculata Nie and Cheng, 1947, Tintinnopsis orientalis Kofoid and Campbell, 1929, and Eutintinnus lususundae (Entz, 1885) Kofoid and Campbell, 1939, were isolated from coastal waters of China. The morphology of each was investigated based on observations of live and protargol-stained specimens, and their SSU rDNA- and LSU rDNA-based phylogenetic relationships were analyzed. The ciliary patterns of these species are revealed for the first time. Based on the original descriptions and data from the present study, an improved diagnosis is given for each species. Unlike its congeners, the second dorsal kinety of Eutintinnus lususundae is displaced below the left ciliary field, which may suggest that the second dorsal kinety is evolving into a posterior kinety by a migration process. The ventral kinety in Eutintinnus is redefined. A neotype is fixed for T. tentaculata to stabilize the species name objectively, mainly because of the unavailability of type material.
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Affiliation(s)
- Yang Bai
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Rui Wang
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Xiaozhong Hu
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
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14
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Ganser MH, Agatha S. Redescription of Antetintinnidium mucicola (Claparède and Lachmann, 1858) nov. gen., nov. comb. (Alveolata, Ciliophora, Tintinnina). J Eukaryot Microbiol 2019; 66:802-820. [PMID: 30861256 PMCID: PMC6736674 DOI: 10.1111/jeu.12728] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 11/30/2022]
Abstract
Tintinnid ciliates have traditionally been described and classified exclusively based on their lorica features. Although information on the cell characters is urgently needed for a natural classification, more molecular than cytological data has been accumulated over recent years. Apparently, the tintinnids developed in the marine environment and entered freshwater several times independently. Typical freshwater tintinnids belong to the genera Tintinnidium and Membranicola. The species are comparatively well-known regarding their morphology and characterised by two unusual de novo originating ciliary rows, the ventral organelles. In contrast, the cell features in the marine/brackish Tintinnidium species, specifically their somatic ciliary patterns, are insufficiently known or not known at all. Therefore, the morphology of a common marine/brackish representative, Tintinnidium mucicola, is redescribed based on live observation and protargol-stained material. Furthermore, biogeographical and autecological data of the species are compiled from literature and own records. The phylogenetic relationships of T. mucicola are inferred and the diversity of the family Tintinnidiidae is assessed from 18S rDNA sequences. The study shows that T. mucicola is not only molecularly distinct, but also characterised by many plesiomorphic features, for instance, it does not possess a verifiable homologue to the ventral organelles. Hence, a new genus, Antetintinnidium nov. gen., is established for T. mucicola. The new insights into the diversity of Tintinnidiidae shed light on the early evolution of tintinnids and might provide clues on their adaptions to freshwater.
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Affiliation(s)
| | - Sabine Agatha
- Department of BiosciencesUniversity of Salzburg5020SalzburgAustria
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15
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Bardele CF, Stockmann N, Agatha S. Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa. ACTA PROTOZOOL 2019; 57:169-193. [PMID: 31168162 PMCID: PMC6546604 DOI: 10.4467/16890027ap.18.014.10090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The first transmission and scanning electron microscopical studies in combination with freeze-fracture technology have disclosed some important morphological and ultrastructural features in the freshwater oligotrichid Limnostrombidium viride. (I) The dikinetids (paired basal bodies) of the girdle kinety have a club-shaped cilium associated only with each left basal body. The electron-dense (paraflagellar) body on one side of its "9×2+2"-axoneme and the regular array of intramembranous particles indicate a sensory, perhaps photoreceptor function of these club-shaped cilia. (II) The stichomonad endoral membrane is proximally covered by a cytoplasmic fold and distally by multiple membranous layers. Thus entirely covered, the endoral is probably no longer involved in food capture; nonetheless, its associated microtubules might stabilise the cytopharynx. (III) Instead of a contractile vacuole, a horizontal ring-canal with supposed osmoregulatory function occurs. (IV) The extrusive nature of the trichites is not only observed in electron micrographs, but the attachment sites of these organelles also display a rosette of "8+1"-particles in the P-face of freeze-fracture replicas typical for ciliate extrusomes. (V) The neoformation organelle, the subsurface tube in which stomatogenesis takes place, shows short basal bodies and normal axonemes about 1 μm long. It is accompanied by numerous membrane vesicles, which might provide membrane material for the outgrowing cilia.
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Affiliation(s)
| | - Nicole Stockmann
- Department of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Sabine Agatha
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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16
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Gruber MS, Mühlthaler A, Agatha S. Ultrastructural Studies on a Model Tintinnid - Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012 (Ciliophora). I. Somatic Kinetids with Unique Ultrastructure. ACTA PROTOZOOL 2019; 57:195-214. [PMID: 31168163 DOI: 10.4467/16890027ap.18.015.10091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Molecular phylogenies of Oligotrichea currently do not contain all genera and families and display topologies which are often incongruent with morphological findings. In ciliates, the somatic kinetids are rather conserved, i.e., their ultrastructures, particularly the fibrillar associates, often characterise the main groups, except for the choreotrichids. Four different kinetid types are found in protargol-stained choreotrichids and used for reconstructing the taxon's evolution (the "Kinetid Transformation Hypothesis"). Proof for this hypothesis requires transmission electron microscopic studies, which are very rare in the choreotrichids and oligotrichids. Such an approach provides insights into the ultrastructural variability of somatic kinetids in spirotrichs and may also detect apomorphies characterising certain choreotrichid families. In the model tintinnid Schmidingerella meunieri, the ultrastructure of the three kinetid types in the somatic ciliature is studied in cryofixed cells. The data support the "Kinetid Transformation Hypothesis" regarding tintinnids with a ventral kinety. This first detailed study on kinetids in tintinnids and choreotrichids in general reveals totally new kinetid types in ciliates: beyond the three common associates, they are characterised by two or three conspicuous microtubular ribbons extending on the kinetids' left sides. These extraordinary ribbons form together with the overlapping postciliary ribbons a unique network in the cortex of the anterior cell portion. The evolutionary constrains which might have fostered the development of such structures are discussed for the Oligotrichea, the choreotrichids, and tintinnids as their first occurrence is currently uncertain. Additionally, the kinetids in tintinnids, aloricate choreotrichids, oligotrichids, hypotrichs, and euplotids are compared.
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Affiliation(s)
- Michael S Gruber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Sabine Agatha
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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17
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Gruber MS, Strüder-Kypke M, Agatha S. Redescription of Tintinnopsis everta Kofoid and Campbell 1929 (Alveolata, Ciliophora, Tintinnina) Based on Taxonomic and Genetic Analyses-Discovery of a New Complex Ciliary Pattern. J Eukaryot Microbiol 2018; 65:484-504. [PMID: 29316045 PMCID: PMC6055699 DOI: 10.1111/jeu.12496] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 11/30/2022]
Abstract
The about 1,000 species of tintinnid ciliates are identified and classified almost exclusively based on their lorica features, although the shortcomings of this structure are well‐known, e.g. causing uncertain species limitations and nonmonophyletic taxa. Hence, the present redescription of Tintinnopsis everta Kofoid and Campbell, 1929 considers not only the lorica characteristics, but focuses on cell and genetic features. The species is redescribed from the North Atlantic and adjacent sea areas, namely the east coast of the USA, using live observation, protargol‐stained material, scanning electron microscopy, and genetic analyses. The main stages of cell division are described, and the species’ phylogenetic relationships are inferred from morphological data and the small subunit ribosomal RNA gene sequence. The estimates of its biogeographical distribution and autecology are based on a literature survey. The species is characterised by a complex somatic ciliary pattern with a unique position of the posterior kinety and a conspicuously large distance between the somatic ciliary fields and the collar membranelles. The phylogenetic relationships of Tintinnopsis everta vary in the molecular trees depending on the algorithms used and are, therefore, regarded as unresolved. Nevertheless, the new kind of complex somatic ciliary pattern distinctly contributes to a better understanding of the tintinnid biodiversity and evolution and provides features for a future split of the nonmonophyletic genus Tintinnopsis.
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Affiliation(s)
- Michael S Gruber
- Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
| | - Michaela Strüder-Kypke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Sabine Agatha
- Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
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18
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Smith SA, Song W, Gavrilova NA, Kurilov AV, Liu W, McManus GB, Santoferrara LF. Dartintinnus alderae
n. g., n. sp., a Brackish Water Tintinnid (Ciliophora, Spirotrichea) with Dual‐ended Lorica Collapsibility. J Eukaryot Microbiol 2017; 65:400-411. [DOI: 10.1111/jeu.12485] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Susan A. Smith
- Department of Marine Sciences University of Connecticut Groton Connecticut 06340 USA
| | - Wen Song
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao 266003 China
| | - Nelly A. Gavrilova
- Kovalevsky Institute of Marine Biological Research Russian Academy of Sciences Sevastopol 299011 Russia
| | - Alexander V. Kurilov
- Institute of Marine Biology National Academy of Sciences of Ukraine Odessa 65011 Ukraine
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of Oceanology Chinese Academy of Science Guangzhou 510301 China
| | - George B. McManus
- Department of Marine Sciences University of Connecticut Groton Connecticut 06340 USA
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19
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Chen PC, Chiang KP, Tsai SF. Pelagostrobilidium liui n. sp. (Ciliophora, Choreotrichida) from the Coastal Waters of Northeastern Taiwan and an Improved Description of Pelagostrobilidium minutum Liu et al., 2012. J Eukaryot Microbiol 2017; 64:579-587. [PMID: 28072495 DOI: 10.1111/jeu.12392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/08/2016] [Accepted: 01/02/2017] [Indexed: 11/29/2022]
Abstract
The number of somatic kineties in Pelagostrobilidium ranges from 4 to 6 according to the present state of knowledge. This study investigates Pelagostrobilidium liui n. sp. using live observation, protargol stain, and small subunit rDNA data sequencing. Pelagostrobilidium liui n. sp. is characterized by having a spherical-shaped body, four somatic kineties, with kinety 2 spiraled around the left side of body, about six elongated external membranelles, and invariably no buccal membranelle. It differs from its most similar congener, Pelagostrobilidium minutum Liu et al., , in (i) cell shape; (ii) macronucleus width; (iii) oral apparatus; (iv) anterior orientation of kinety 2; (v) location where kinety 2 commences; (vi) arrangement of kinety 1; (vii) distance between the anterior cell end and the locations where kineties commence; and (viii) the presence of 12 different bases (including two deletions) in the small subunit rDNA sequences. The diagnosis of P. minutum Liu et al., is also improved to include the following new characteristics: invariably four somatic kineties; kineties 2 and 4 alone commence at the same level; kinety 2 originates from right anterior cell half on ventral side, extends sinistrally posteriorly, over kinety 1, around left posterior region, terminates near posterior cell end on dorsal side; kinety 1 commences below anterior third of kinety 2.
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Affiliation(s)
- Po-Cheng Chen
- Institute of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung, 202-24, Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, 202-24, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202-24, Taiwan
| | - Sheng-Fang Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, 202-24, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202-24, Taiwan
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20
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Zhang Q, Agatha S, Zhang W, Dong J, Yu Y, Jiao N, Gong J. Three rDNA Loci-Based Phylogenies of Tintinnid Ciliates (Ciliophora, Spirotrichea, Choreotrichida). J Eukaryot Microbiol 2016; 64:226-241. [PMID: 27509323 DOI: 10.1111/jeu.12354] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/29/2022]
Abstract
To improve understanding of diversity, phylogeny and evolution in tintinnid ciliates, it is essential to link multiple molecular markers with properly identified and documented morphospecies. Accordingly, 54 tintinnid morphospecies/isolates mainly from the Yellow and East China Seas were collected and analysed. Using single-cell approaches, sequences were obtained for three rDNA loci (18S, ITS1-5.8S-ITS2, D1-D5 region of 28S). Twenty-six tintinnid morphospecies (29 isolates) are documented by micrographs, measurements, morphologically described, and compared with the original species description. Three rDNA loci-based phylogenetic analyses were then performed for these identified isolates. Sequences from 25 unidentified species/isolates were also included in the comparison of the three rDNA loci. Ribosomal DNA genes of the genus Leprotintinnus were analysed for the first time, showing that Leprotintinnus was closely related to Tintinnopsis radix and branched distinctly apart from the family Tintinnidiidae. Four novel clades (VI to IX) of the Tintinnopsis complex emerged in the 18S genealogies. Analyses of the relative variability in the ITS and 28S regions vs. the 18S rDNA showed that the ITS1-5.8S-ITS2 and ITS2 regions well co-varied with the 18S rDNA when the variations of the latter were less than 3%, whereas at difference of less than 1%, no correlation was found between the compared loci. These findings highlight the difficulties in using variable locus-based cut-off divergences in circumscribing tintinnid morphospecies.
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Affiliation(s)
- Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Sabine Agatha
- Department of Ecology and Evolution, University of Salzburg, Salzburg, 5020, Austria
| | - Wuchang Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jun Dong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Ying Yu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
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21
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Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists. Mol Phylogenet Evol 2016; 94:718-729. [DOI: 10.1016/j.ympev.2015.10.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/08/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
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22
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Santoferrara LF, Tian M, Alder VA, McManus GB. Discrimination of Closely Related Species in Tintinnid Ciliates: New Insights on Crypticity and Polymorphism in the Genus Helicostomella. Protist 2015; 166:78-92. [DOI: 10.1016/j.protis.2014.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/20/2014] [Accepted: 11/29/2014] [Indexed: 11/15/2022]
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23
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Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Stock A, Kauff F, Stoeck T. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol 2014; 31:993-1009. [PMID: 24473288 DOI: 10.1093/molbev/msu055] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
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Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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24
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Kim SY, Choi JK, Dolan JR, Shin HC, Lee S, Yang EJ. Morphological and Ribosomal DNA-based Characterization of Six Antarctic Ciliate Morphospecies from the Amundsen Sea with Phylogenetic Analyses. J Eukaryot Microbiol 2013; 60:497-513. [DOI: 10.1111/jeu.12057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 03/17/2013] [Accepted: 03/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sun Young Kim
- Department of Oceanography; Inha University; Incheon 402-751 Korea
- Korea Polar Research Institute; KIOST; 213-3 Sondo-dong Yeonsu-gu Incheon 405-840 Korea
| | - Joong Ki Choi
- Department of Oceanography; Inha University; Incheon 402-751 Korea
| | - John R. Dolan
- UMR 7093; Laboratoire d'Océanographie de Villefranche; Marine Microbial Ecology; Université Pierre et Marie Curie and Centre National de la Recherche Scientifique (CNRS); Station Zoologique, B.P. 28 06230 Villefranche-sur-Mer France
| | - Hyoung Chul Shin
- Korea Polar Research Institute; KIOST; 213-3 Sondo-dong Yeonsu-gu Incheon 405-840 Korea
| | - SangHoon Lee
- Korea Polar Research Institute; KIOST; 213-3 Sondo-dong Yeonsu-gu Incheon 405-840 Korea
| | - Eun Jin Yang
- Korea Polar Research Institute; KIOST; 213-3 Sondo-dong Yeonsu-gu Incheon 405-840 Korea
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25
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Xu D, Sun P, Warren A, Noh JH, Choi DL, Shin MK, Kim YO. Phylogenetic investigations on ten genera of tintinnid ciliates (Ciliophora: Spirotrichea: Tintinnida), based on small subunit ribosomal RNA gene sequences. J Eukaryot Microbiol 2013; 60:192-202. [PMID: 23346918 DOI: 10.1111/jeu.12023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 12/01/2022]
Abstract
Tintinnida is a diverse taxon that accommodates over 1,500 morphospecies, which is an important component of marine planktonic food webs. However, evolutionary relationships of tintinnids are poorly known because molecular data of most groups within this order are lacking. In our study, the small subunit (SSU) rRNA genes representing 10 genera, 5 families of Tintinnida were sequenced, including the first SSU rRNA gene sequences for Coxliella, Dadayiella, Epiplocyloides, and Protorhabdonella, and phylogenetic trees were constructed to assess their intergeneric relationships. Phylogenies inferred from different methods showed that (1) Three newly sequenced Eutintinnus species fell into Eutintinnus clade forming a sister group to the clade containing Amphorides, Steenstrupiella, Amphorellopsis, and Salpingella; (2) Surprisingly, the genetic distances between Amphorides amphora and Amphorellopsis acuta population 1 was even smaller than that between the two populations of Amphorellopsis acuta, casting doubt on the validity of Amphorides and Amphorellopsis as presently defined; (3) The SSU rRNA sequences of Dadayiella ganymedes and Parundella aculeata were almost identical. Therefore, Parundella ganymedes novel combination is proposed; (4) Coxliella, which is currently assigned within Metacylididae, branched instead with some Tintinnopsis species. Furthermore, the validation of Coxliella, which was considered to be a "questionable" genus, was confirmed based on evidences from morphology, ecology, and molecular data; (5) Protorhabdonella and Rhabdonella showed rather low intergeneric distance and grouped together with strong support suggesting that Rhabdonellidae is a well-defined taxon; and (6) Epiplocyloides branched with species in Cyttarocylididae indicating their close relationship.
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Affiliation(s)
- Dapeng Xu
- South Sea Institute, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 656-834, Korea
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26
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Multigene-based analyses of the phylogenetic evolution of oligotrich ciliates, with consideration of the internal transcribed spacer 2 secondary structure of three systematically ambiguous genera. EUKARYOTIC CELL 2013; 12:430-7. [PMID: 23314963 DOI: 10.1128/ec.00270-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Oligotrichs are ciliates of great abundance, but their molecular systematics are rarely studied. In this study, nine species representing three genera (Strombidium, Novistrombidium, and Omegastrombidium) of marine oligotrich ciliates were collected from coastal waters of China. The small subunit (SSU) rRNA gene of two species and the internal transcribed spacers and 5.8S region (ITS1-5.8S-ITS2) for all nine species were sequenced for the first time. Phylogenetic trees using both the SSU rRNA gene and ITS1-5.8S-ITS2 region sequences were generated. In addition, the secondary structures of ITS2 RNA transcripts of 11 taxa representing four genera (Novistrombidium, Strombidium, Omegastrombidium, and Laboea) were investigated. The phylogenetic analyses show that (i) the family Strombidiidae is polyphyletic, (ii) the genus Novistrombidium is probably paraphyletic, containing at least two subclades, which is consistent with recent cladistic analyses based on morphological data, and (iii) the tail-less genus Laboea is separate from other genera of Strombidiidae, clustering instead with the tontoniids. Comparisons of the secondary structure of ITS2 regions also show that Laboea is clearly different from other strombidiids. These findings cast doubt on the monophyly of the family Strombidiidae.
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27
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Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist 2013; 164:24-36. [DOI: 10.1016/j.protis.2011.12.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/20/2011] [Accepted: 12/20/2011] [Indexed: 11/17/2022]
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28
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Bachy C, Gómez F, López-García P, Dolan JR, Moreira D. Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora). Protist 2012; 163:873-87. [DOI: 10.1016/j.protis.2012.01.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/21/2011] [Accepted: 01/04/2012] [Indexed: 11/29/2022]
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29
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Bachy C, Dolan JR, López-García P, Deschamps P, Moreira D. Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study. ISME JOURNAL 2012; 7:244-55. [PMID: 23038176 DOI: 10.1038/ismej.2012.106] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Deep-sequencing technologies are becoming nearly routine to describe microbial community composition in environmental samples. The 18S ribosomal DNA (rDNA) pyrosequencing has revealed a vast diversity of infrequent sequences, leading to the proposition of the existence of an extremely diverse microbial 'rare biosphere'. Although rare microbes no doubt exist, critical views suggest that many rare sequences may actually be artifacts. However, information about how diversity revealed by molecular methods relates to that revealed by classical morphology approaches is practically nonexistent. To address this issue, we used different approaches to assess the diversity of tintinnid ciliates, a species-rich group in which species can be easily distinguished morphologically. We studied two Mediterranean marine samples with different patterns of tintinnid diversity. We estimated tintinnid diversity in these samples employing morphological observations and both classical cloning and sequencing and pyrosequencing of two different markers, the 18S rDNA and the internal transcribed spacer (ITS) regions, applying a variety of computational approaches currently used to analyze pyrosequence reads. We found that both molecular approaches were efficient in detecting the tintinnid species observed by microscopy and revealed similar phylogenetic structures of the tintinnid community at the species level. However, depending on the method used to analyze the pyrosequencing results, we observed discrepancies with the morphology-based assessments up to several orders of magnitude. In several cases, the inferred number of operational taxonomic units (OTUs) largely exceeded the total number of tintinnid cells in the samples. Such inflation of the OTU numbers corresponded to 'rare biosphere' taxa, composed largely of artifacts. Our results suggest that a careful and rigorous analysis of pyrosequencing data sets, including data denoising and sequence clustering with well-adjusted parameters, is necessary to accurately describe microbial biodiversity using this molecular approach.
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Affiliation(s)
- Charles Bachy
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
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30
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Lee ES, Xu D, Shin MK, Kim YO. First Record of Six Marine Ciliate Species of Genus Strombidium (Ciliophora: Spirotricha: Oligotrichia) from Korea with Ecological Notes. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2012. [DOI: 10.5635/ased.2012.28.3.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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31
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Agatha S, Strüder-Kypke MC. Reconciling Cladistic and Genetic Analyses in Choreotrichid Ciliates (Ciliophora, Spirotricha, Oligotrichea). J Eukaryot Microbiol 2012; 59:325-50. [DOI: 10.1111/j.1550-7408.2012.00623.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/23/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology; University of Salzburg; Hellbrunnerstraße 34; A-5020; Salzburg; Austria
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Santoferrara LF, McManus GB, Alder VA. Phylogeny of the Order Tintinnida (Ciliophora, Spirotrichea) Inferred from Small- and Large-Subunit rRNA Genes. J Eukaryot Microbiol 2012; 59:423-6. [DOI: 10.1111/j.1550-7408.2012.00627.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/12/2012] [Indexed: 12/01/2022]
Affiliation(s)
| | - George B. McManus
- Department of Marine Sciences; University of Connecticut; Groton; Connecticut; 06340; USA
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Xu D, Sun P, Shin MKYOON, Kim YOK. Species Boundaries in Tintinnid Ciliates: A Case Study - Morphometric Variability, Molecular Characterization, and Temporal Distribution of Helicostomella species (Ciliophora, Tintinnina). J Eukaryot Microbiol 2012; 59:351-8. [DOI: 10.1111/j.1550-7408.2012.00625.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 02/24/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Dapeng Xu
- South Sea Institute; Korea Ocean Research and Development Institute; Geoje; 656-834; Korea
| | - Ping Sun
- Department of Biological Science; University of Ulsan; Ulsan; 680-749; Korea
| | - Mann KYOON Shin
- Department of Biological Science; University of Ulsan; Ulsan; 680-749; Korea
| | - Young OK Kim
- South Sea Institute; Korea Ocean Research and Development Institute; Geoje; 656-834; Korea
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34
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Liu W, Yi Z, Lin X, Warren A, Song W. Phylogeny of three choreotrich genera (Protozoa, Ciliophora, Spirotrichea), with morphological, morphogenetic and molecular investigations on three strobilidiid species. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00542.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Saccà A, Strüder-Kypke MC, Lynn DH. Redescription of Rhizodomus tagatzi (Ciliophora: Spirotrichea: Tintinnida), based on morphology and small subunit ribosomal RNA gene sequence. J Eukaryot Microbiol 2012; 59:218-31. [PMID: 22452414 DOI: 10.1111/j.1550-7408.2012.00615.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/26/2022]
Abstract
Herein, we redescribe a tintinnid ciliate that is most commonly known as Tintinnopsis corniger Hada, 1964; but it has been described several times with different names, specifically Tintinnopsis nudicauda Paulmier, 1997 and Rhizodomus tagatzi Strelkow & Wirketis, 1950. Neotype material was collected from the water column of the coastal saline Lake Faro, a meromictic basin connected to the Straits of Messina, Central Mediterranean. The Lake Faro population is characterized by a hyaline or sparsely agglomerated lorica, which made it possible to observe in detail the basal layer structure, usually concealed by abundant incrusting particles. Along with an improved description of the lorica, we provide novel information, such as the general zooid morphology, the ciliary pattern, and the small subunit rRNA (SSU rRNA) gene sequence. Our phylogenetic analysis, based on the SSU rRNA, groups this species with Tintinnopsis radix, while the first taxonomic study designated it as R. tagatzi, introducing a new genus due to peculiarities in lorica morphology. We conclude that the species should be known as R. tagatzi, the senior synonym for the species. However, we do not transfer any other species to this genus, despite strong molecular similarities. Although it is obvious that the genus Tintinnopsis is in need of a thorough revision, current molecular and cytological information for this genus is too sparse, and the type species has not yet been redescribed with modern methods.
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Affiliation(s)
- Alessandro Saccà
- Dipartimento di Biologia Animale ed Ecologia Marina, Università degli Studi di Messina, viale Ferdinando Stagno d'Alcontres 31, Messina, Italy.
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Jiang Y, Yang J, Al-Farraj SA, Warren A, Lin X. Redescriptions of three tintinnid ciliates, Tintinnopsis tocantinensis, T. radix, and T. cylindrica (ciliophora, spirotrichea), from coastal waters off China. Eur J Protistol 2012; 48:314-25. [PMID: 22425547 DOI: 10.1016/j.ejop.2012.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 02/05/2012] [Accepted: 02/13/2012] [Indexed: 11/30/2022]
Abstract
In the present study the morphology and ciliary pattern of three marine tintinnid ciliates, namely Tintinnopsis tocantinensisKofoid and Campbell, 1929, Tintinnopsis radix (Imhof, 1886) Brandt, 1907, and Tintinnopsis cylindricaDaday, 1887, isolated from Chinese coastal waters off Shenzhen and Qingdao, respectively, were investigated using living observation and silver impregnation methods. Detailed ciliary patterns of T. tocantinensis and T. radix are reported here for the first time, comprising a ventral, dorsal, and posterior kinety as well as a right, left, and lateral ciliary field. Furthermore, based on previous and present investigations, redescriptions for all three species and improved diagnoses for T. tocantinensis and T. radix are supplied.
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Affiliation(s)
- Yong Jiang
- College of Life Science, South China Normal University, China
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37
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Molecular diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis. Appl Environ Microbiol 2011; 78:334-45. [PMID: 22081578 DOI: 10.1128/aem.06678-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Euduboscquella is one of a few described genera within the syndinean dinoflagellates, an enigmatic lineage with abundant diversity in marine environmental clone libraries based on small subunit (SSU) rRNA. The region composed of the SSU through to the partial large subunit (LSU) rRNA was determined from 40 individual tintinnid ciliate loricae infected with Euduboscquella sampled from eight surface water sites in the Northern Hemisphere, producing seven distinct SSU sequences. The corresponding host SSU rRNA region was also amplified from eight host species. The SSU tree of Euduboscquella and syndinean group I sequences from environmental clones had seven well-supported clades and one poorly supported clade across data sets from 57 to 692 total sequences. The genus Euduboscquella consistently formed a supported monophyletic clade within a single subclade of group I sequences. For most parasites with identical SSU sequences, the more variable internal transcribed spacer (ITS) to LSU rRNA regions were polymorphic at 3 to 10 sites. However, in E. cachoni there was variation between ITS to LSU copies at up to 20 sites within an individual, while in a parasite of Tintinnopsis spp., variation between different individuals ranged up to 19 polymorphic sites. However, applying the compensatory base change model to the ITS2 sequences suggested no compensatory changes within or between individuals with the same SSU sequence, while one to four compensatory changes between individuals with similar but not identical SSU sequences were found. Comparisons between host and parasite phylogenies do not suggest a simple pattern of host or parasite specificity.
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38
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Agatha S. Global diversity of aloricate Oligotrichea (Protista, Ciliophora, Spirotricha) in marine and brackish sea water. PLoS One 2011; 6:e22466. [PMID: 21853034 PMCID: PMC3154192 DOI: 10.1371/journal.pone.0022466] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oligotrichids and choreotrichids are ciliate taxa contributing to the multi-step microbial food web and episodically dominating the marine microzooplankton. The global diversity and distribution of aloricate Oligotrichea are unknown. Here, the geographic ranges of the 141 accepted species and their synonyms in marine and brackish sea water are analyzed, using hundreds of taxonomical and ecological studies; the quality of the records is simultaneously evaluated. The aloricate Oligotrichea match the moderate endemicity model, i.e., the majority (94) of morphospecies has a wide, occasionally cosmopolitan distribution, while 47 morphospecies show biogeographic patterns: they are restricted to single geographic regions and probably include 12 endemic morphospecies. These endemics are found in the Antarctic, North Pacific, and Black Sea, whereas the "flagship" species Strombidinopsis cercionis is confined to the Caribbean Sea. Concerning genera, again several geographic patterns are recognizable. The species richness is distinctly lower in the southern hemisphere than in the northern, ranging from nine morphospecies in the South Pacific to 95 in the North Atlantic; however, this pattern is probably caused by undersampling. Since the loss of species might affect higher trophical levels substantially, the aloricate Oligotrichea should not any longer be ignored in conservation issues. The ecophysiological diversity is considerably larger than the morphological, and even tops the richness of SSrRNA and ITS haplotypes, indicating that probably more than 83-89% of the diversity in aloricate Oligotrichea are unknown. The huge challenge to discover all these species can only be managed by combining the expertises of morphological taxonomists, molecular biologists, ecologists, and physiologists.
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Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology, University of Salzburg, Salzburg, Austria.
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39
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Lee ES, Shin MK, Kim YO. Morphological Descriptions of Four Oligotrich Ciliates (Ciliophora: Oligotrichia) from Southern Coast of Korea. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2011. [DOI: 10.5635/kjsz.2011.27.2.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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40
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Terrado R, Medrinal E, Dasilva C, Thaler M, Vincent WF, Lovejoy C. Protist community composition during spring in an Arctic flaw lead polynya. Polar Biol 2011. [DOI: 10.1007/s00300-011-1039-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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41
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LIU WEIWEI, YI ZHENZHEN, LIN XIAOFENG, AL-RASHEID KHALEDAS. Morphologic and Molecular Data Suggest that Lynnella semiglobulosa n. g., n. sp. Represents a New Family within the Subclass Choreotrichia (Ciliophora, Spirotrichea). J Eukaryot Microbiol 2010; 58:43-9. [DOI: 10.1111/j.1550-7408.2010.00519.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Agatha S. Redescription of Tintinnopsis parvula Jörgensen, 1912 (Ciliophora: Spirotrichea: Tintinnina), Including a Novel Lorica Matrix. ACTA PROTOZOOL 2010; 49:213-234. [PMID: 21339889 PMCID: PMC3040568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Tintinnopsis parvulaJörgensen, 1912 has apparently a cosmopolitan distribution in the pelagial of marine and brackish coastal waters. The species is redescribed based on material from the Irish Sea off the Isle of Man, using live observation, protargol impregnation, and scanning electron microscopy. The agglomerated and stiff lorica measures 38-60 × 24-31 μm and is composed of a usually broadly obovate bowl and a slightly narrowed cylindroidal collar with an inner diameter of ~ 20 μm. The somatic ciliary pattern is of the most complex type, viz., it comprises a ventral, dorsal, and posterior kinety as well as a right, left, and lateral ciliary field. The left ciliary field comprises four kineties, the lateral field about ten kineties, and the right field five kineties. The oral primordium develops apparently apokinetally posterior to the lateral ciliary field and generates ~ 15 collar membranelles and one buccal membranelle. Two further populations were studied: one from the North Sea off the Island of Sylt, the other from brackish polder basins at the German North Sea coast; they match the Irish Sea specimens in all main features. The loricae formed in almost particle-free cultures have a thin wall composed of an irregular network of fibres and very few attached or interwoven particles. This matrix type differs from the other three types found in congeners. Hence, the matrix ultrastructure might represent a promising feature for a reliable subdivision of the species-rich genus TintinnopsisStein, 1867 in the future.
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Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology, University of Salzburg, Salzburg, Austria
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43
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Agatha S. Updated hypothesis on the evolution of oligotrichid ciliates (Ciliophora, Spirotricha, Oligotrichida) based on somatic ciliary patterns and ontogenetic data. Eur J Protistol 2010; 47:51-6. [PMID: 20961741 PMCID: PMC3034029 DOI: 10.1016/j.ejop.2010.09.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 08/24/2010] [Accepted: 09/06/2010] [Indexed: 11/27/2022]
Abstract
The two recently established genera ApostrombidiumXu et al., 2009 and VaristrombidiumXu et al., 2009 and the analysis of ontogenetic data in Strombidium constrictum, S. montagnesi, S. wilberti, Omegastrombidium elegans, and Paratontonia gracillima necessitated a revision of the hypothesis about the somatic ciliary pattern evolution in oligotrichid ciliates. As a consequence, the species-rich genus Strombidium was split, establishing two genera for species with a horizontal girdle kinety posterior to the oral primordium: Opisthostrombidium nov. gen. with the extrusome attachment sites along the anterior margin of the girdle kinety and posterior to the oral primordium and Foissneridium nov. gen. with the extrusome attachment sites distinctly apart from the girdle kinety and anterior to the oral primordium. The ontogenetic data revealed that the Ω-shaped girdle kinety pattern evolved convergently from the Pseudotontonia pattern with its horizontal girdle kinety in the tailed genus Paratontonia and from the Novistrombidium pattern with its dextrally spiralled girdle kinety in the tailless genus Omegastrombidium. The somatic ciliary pattern of the latter genus probably gave rise to the patterns of Apostrombidium and Varistrombidium.
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Affiliation(s)
- Sabine Agatha
- University of Salzburg, Department of Organismic Biology, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria.
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44
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KIM SUNYOUNG, YANG EUNJIN, GONG JUN, CHOI JOONGKI. Redescription of Favella ehrenbergii (Claparède and Lachmann, 1858) Jörgensen, 1924 (Ciliophora: Choreotrichia), with Phylogenetic Analyses Based on Small Subunit rRNA Gene Sequences. J Eukaryot Microbiol 2010; 57:460-7. [DOI: 10.1111/j.1550-7408.2010.00500.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Dunthorn M, Foissner W, Katz LA. Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker. Protist 2010; 162:85-99. [PMID: 20708960 DOI: 10.1016/j.protis.2010.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 06/12/2010] [Indexed: 11/28/2022]
Abstract
Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately- to well-supported incongruences between the loci are the placement of the Sorogenida andColpoda aspera.Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach.
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46
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TSAI SHENGFANG, CHEN JUNYU, CHIANG KUOPING. Spirotontonia taiwanica n. sp. (Ciliophora: Oligotrichida) from the Coastal Waters of Northeastern Taiwan: Morphology and Nuclear Small Subunit rDNA Sequence. J Eukaryot Microbiol 2010; 57:429-34. [DOI: 10.1111/j.1550-7408.2010.00494.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Agatha S. A light and scanning electron microscopic study of the closing apparatus in tintinnid ciliates (Ciliophora, Spirotricha, Tintinnina): a forgotten synapomorphy. J Eukaryot Microbiol 2010; 57:297-307. [PMID: 20584102 DOI: 10.1111/j.1550-7408.2010.00490.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A membranous closing apparatus shuts the lorica opening in disturbed tintinnids of six genera belonging to four families. The homology of the apparatuses is investigated, using data from the literature and Mediterranean tintinnids studied in vivo and by scanning electron microscopy. Morphological and functional similarities indicate that the foldable closing apparatus is not only a synapomorphy of the genera Codonella (Codonellidae) and Dictyocysta (Dictyocystidae), as suggested 80 years ago, but also of Codonaria (Codonellidae) and Codonellopsis (Codonellopsidae). In Codonaria, Codonella, and Dictyocysta, the apparatuses merge posteriorly into membranous lorica sacs, which probably represent homologous structures. The diagnoses of these genera are improved according to the new findings. The close relationship of Codonella, Codonellopsis, and Dictyocysta is also inferred from small subunit rRNA phylogenies and the ultrastructure of the capsules. It contradicts the current lorica-based classification of the tintinnids. The assumption that the diaphragm-like apparatus in the genera Salpingacantha and Salpingella is not homologous to the foldable ones in the genera mentioned above is supported by molecular and cytological features.
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Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology, University of Salzburg, Salzburg, Austria.
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48
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Kivimaki KL, Bowditch BM, Riordan GP, Lipscomb DL. Phylogeny and systematic position of Zosterodasys (Ciliophora, Synhymeniida): a combined analysis of ciliate relationships using morphological and molecular data. J Eukaryot Microbiol 2009; 56:323-38. [PMID: 19602078 DOI: 10.1111/j.1550-7408.2009.00403.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
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.
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Affiliation(s)
- K Lindholm Kivimaki
- Department of Biological Sciences, George Washington University, Washington, District of Columbia 20052, USA
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49
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An updated phylogeny of oligotrich and choreotrich ciliates (Protozoa, Ciliophora, Spirotrichea) with representative taxa collected from Chinese coastal waters. SYST BIODIVERS 2009. [DOI: 10.1017/s1477200009002989] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Conjugation in the spirotrich ciliate Halteria grandinella (Müller, 1773) Dujardin, 1841 (Protozoa, Ciliophora) and its phylogenetic implications. Eur J Protistol 2008; 45:51-63. [PMID: 18929469 DOI: 10.1016/j.ejop.2008.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 07/07/2008] [Accepted: 07/10/2008] [Indexed: 11/22/2022]
Abstract
The conjugation of Halteria grandinella was studied in protargol preparations. The isogamontic conjugants fuse partially with their ventral sides to a homopolar pair. The first maturation division generates dramatic transformations: (i) the partners obtain an interlocking arrangement; (ii) the number of bristle kineties decreases from seven to four in each partner; and (iii) the right conjugant loses its buccal membranelles, the left the whole adoral zone. The remaining collar membranelles arrange around the pair's anterior end and are shared by both partners; finally, the couple resembles a vegetative specimen in size and outline. The vegetative macronucleus fragments before pycnosis. The micronucleus performs three maturation divisions, but only one derivative each performs the second and third division. The synkaryon divides twice, producing a micronucleus, a macronucleus anlage, and two disintegrating derivatives. Scattered somatic kinetids occur during conjugation, but disappear without reorganization. An incomplete oral primordium originates in both partners. The conjugation of Halteria grandinella resembles in several respects that of hypotrich spirotrichs; however, the majority of morphological, ontogenetical, and ultrastructural features still indicates an affiliation with the oligotrich and choreotrich spirotrichs. Accordingly, the cladistic analysis still contradicts the genealogy based on the sequences of the small subunit rRNA gene.
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