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Zhang Y, Dou H, Fu Y, Liang F, Wang Z, Warren A, Li L. Comparative genomics provides insights into the phylogeny and environmental adaptations of Peritrichia (Protista, Ciliophora) - a potential resource for environmental pollution control and bioremediation. Mol Phylogenet Evol 2023:107835. [PMID: 37263457 DOI: 10.1016/j.ympev.2023.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation.
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Affiliation(s)
- Ying Zhang
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Huan Dou
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Yu Fu
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Zhe Wang
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Asadzadeh SS, Nielsen LT, Andersen A, Dölger J, Kiørboe T, Larsen PS, Walther JH. Hydrodynamic functionality of the lorica in choanoflagellates. J R Soc Interface 2019; 16:20180478. [PMID: 30958164 PMCID: PMC6364640 DOI: 10.1098/rsif.2018.0478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/22/2018] [Indexed: 11/12/2022] Open
Abstract
Choanoflagellates are unicellular eukaryotes that are ubiquitous in aquatic habitats. They have a single flagellum that creates a flow toward a collar filter composed of filter strands that extend from the cell. In one common group, the loricate choanoflagellates, the cell is suspended in an elaborate basket-like structure, the lorica, the function of which remains unknown. Here, we use Computational Fluid Dynamics to explore the possible hydrodynamic function of the lorica. We use the choanoflagellate Diaphaoneca grandis as a model organism. It has been hypothesized that the function of the lorica is to prevent refiltration (flow recirculation) and to increase the drag and, hence, increase the feeding rate and reduce the swimming speed. We find no support for these hypotheses. On the contrary, motile prey are encountered at a much lower rate by the loricate organism. The presence of the lorica does not affect the average swimming speed, but it suppresses the lateral motion and rotation of the cell. Without the lorica, the cell jiggles from side to side while swimming. The unsteady flow generated by the beating flagellum causes reversed flow through the collar filter that may wash away captured prey while it is being transported to the cell body for engulfment. The lorica substantially decreases such flow, hence it potentially increases the capture efficiency. This may be the main adaptive value of the lorica.
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Affiliation(s)
- Seyed Saeed Asadzadeh
- Department of Mechanical Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Lasse Tor Nielsen
- National Institute of Aquatic Resources and Centre for Ocean Life, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Anders Andersen
- Department of Physics and Centre for Ocean Life, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Julia Dölger
- Department of Physics and Centre for Ocean Life, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Thomas Kiørboe
- National Institute of Aquatic Resources and Centre for Ocean Life, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Poul S. Larsen
- Department of Mechanical Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jens H. Walther
- Department of Mechanical Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Computational Science and Engineering Laboratory, ETH, Zürich, Switzerland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Agatha S, Simon P. On the Nature of Tintinnid Loricae (Ciliophora: Spirotricha: Tintinnina): a Histochemical, Enzymatic, EDX, and High-resolution TEM Study. ACTA PROTOZOOL 2012; 51:1-19. [PMID: 22988335 PMCID: PMC3442249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Tintinnids (Ciliophora: Spirotricha: Tintinnina) are occasionally the dominant ciliates in the marine plankton. The tintinnid loricae are minute artworks fascinating scientists for more than 230 years, but their chemical composition remained unclear, viz., chitinous or proteinaceous substances were discussed. Since sedimenting loricae contribute to the flux of elements and organic compounds in the oceans, knowledge about their nature is necessary in assessing their ecological role. Previous techniques and new methods, e.g. enzymatic digestion and high-resolution transmission electron microscopy, are applied in the present study. A chitinous nature of the loricae is rejected by the Van-Wisselingh test and failure of chitinase digestion. Only proteins might show a resistance against strong hot bases (KOH at 160°C for ~ 40 min. in tintinnid loricae) similar to that of chitin. Actually, the presence of nitrogen in the EDX analyses and the digestion of at least some loricae by proteinase K strongly indicate a proteinaceous nature. Furthermore, the crystal lattice revealed by high-resolution TEM in Eutintinnus loricae is similar to the proteinaceous surface layer (S-layer) of archaea, and the striation recognizable in transverse sections of Eutintinnus loricae has a periodicity resembling that of the crystalline proteins in the extruded trichocysts of Paramecium and Frontonia. The proteolytic resistance of some loricae does not reject the idea of a proteinaceous nature, as proteins in S-layers of some archaea and in most naturally occurring prions show comparable reactions. The data from the present study and the literature indicate proteins in the loricae of thirteen genera. Differences in the proteolytic resistance and staining properties between genera and congeners are probably due to deviations in the protein composition and the additional substances, e.g. lipids, carbohydrates. At the present state of knowledge, correlations between lorica structure, wall texture, ultrastructure of the lorica forming granules, and the histochemical and enzymatic findings are not evident. Therefore, further studies are required to estimate the taxonomic significance of these features and the ecological role of sedimenting loricae.
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Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology, University of Salzburg, Salzburg, Austria
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