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Abraham JS, Somasundaram S, Maurya S, Sood U, Lal R, Toteja R, Makhija S. Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. FEMS MICROBES 2024; 5:xtae003. [PMID: 38450097 PMCID: PMC10917447 DOI: 10.1093/femsmc/xtae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.
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Affiliation(s)
- Jeeva Susan Abraham
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Sripoorna Somasundaram
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Ravi Toteja
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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2
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Ivorová S, Kopčaková A, Pristaš P, Kišidayová S. Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus. Life (Basel) 2023; 13:2350. [PMID: 38137951 PMCID: PMC10744686 DOI: 10.3390/life13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E. parvicaudatum prevailed (70%). The DNA of four individual E. parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350-400 bp) were identical to Epidinium sequences in GenBank (E. caudatum, a one-spine morphotype, and E. cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.
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Affiliation(s)
| | | | | | - Svetlana Kišidayová
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Košice, Slovakia; (S.I.); (A.K.); (P.P.)
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3
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Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R, Toteja R. DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 2023; 50:761-775. [PMID: 36308581 DOI: 10.1007/s11033-022-08015-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/07/2022] [Indexed: 02/01/2023]
Abstract
DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
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Affiliation(s)
- Sandeep Antil
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | | | - S Sripoorna
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Jyoti Dagar
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Pooja Bhagat
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, Delhi, 110 021, India
| | - Utkarsh Sood
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Rup Lal
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India.
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4
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Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters. Microorganisms 2022; 10:microorganisms10122512. [PMID: 36557765 PMCID: PMC9787992 DOI: 10.3390/microorganisms10122512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.
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Obert T, Zhang T, Rurik I, Vďačný P. First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora). Front Microbiol 2022; 13:1067315. [PMID: 36569075 PMCID: PMC9772525 DOI: 10.3389/fmicb.2022.1067315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.
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Li Z, Wang X, Zhang Y, Yu Z, Zhang T, Dai X, Pan X, Jing R, Yan Y, Liu Y, Gao S, Li F, Huang Y, Tian J, Yao J, Xing X, Shi T, Ning J, Yao B, Huang H, Jiang Y. Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates. THE ISME JOURNAL 2022; 16:2775-2787. [PMID: 35986094 PMCID: PMC9666518 DOI: 10.1038/s41396-022-01306-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.
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Affiliation(s)
- Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangnan Wang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Tingting Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangyu Pan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruoxi Jing
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- College of Animal Engineering, Yangling Vocational & Technical College, Yangling, 712100, China
| | - Yueyang Yan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangfan Liu
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shan Gao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fei Li
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Youqin Huang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jian Tian
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junhu Yao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - XvPeng Xing
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Tao Shi
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jifeng Ning
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China.
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7
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Chen L, Tanchangya P. Analyzing the role of environmental technologies and environmental policy stringency on green growth in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:55630-55638. [PMID: 35320472 DOI: 10.1007/s11356-022-19673-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
This study aims to investigate the impact of environmental technological innovations and environmental policy stringency on green economic growth in China. The empirical analysis of the study is based on the ARDL model. Findings confirm that environmental technology positively impacts green economic growth in the short and long run. In the robust model, the estimates of all technologies appeared to be significantly positive in the short and long run. Conversely, the estimated coefficients of environmental policy stringency, in the basic and robust model, have only negatively impacted the green economic growth in China in the short run. In the long run, the environmental policy stringency has not shown any significant impact on green economic growth in China in the basic and robust model. China needs to increase environmental technology and environmental policy stringency for achieving green growth and sustainability targets.
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Affiliation(s)
- Li Chen
- Fan Li Business School, Nanyang Institute of Technology, Nanyang, China.
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8
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Li T, Liu M, Warren A, Al-Farraj SA, Yi Z, Sheng Y. Morphology and SSU rRNA gene-based phylogeny of three peniculid ciliates (Ciliophora, Oligohymenophorea) from china, including a new Frontonia species. Eur J Protistol 2022; 85:125910. [DOI: 10.1016/j.ejop.2022.125910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 11/03/2022]
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9
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Li T, Pan X, Lu B, Miao M, Liu M. Taxonomy and molecular phylogeny of a new freshwater ciliate Frontonia apoacuminata sp. nov. (Protista, Ciliophora, Oligohymenophorea) from Qingdao, PR China. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694984 DOI: 10.1099/ijsem.0.005071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The morphology and ciliature of a new freshwater ciliate, Frontonia apoacuminata sp. nov., isolated from an artificial pond in Qingdao, PR China, were investigated using live observation and silver staining methods. The main features separating F. apoacuminata sp. nov. from its congeners are as follows: a broad elliptical body that is slightly pointed at the posterior end, four ophryokineties, one or two spherical micronuclei of a 'compact' type, a dorsally positioned contractile vacuole, and peniculi 1-3 each with five kinetosome rows though the left-most two rows in peniculus 3 are extremely shortened (with only two or three kinetosomes each). Additionally, an improved diagnosis of F. acuminata is provided. Phylogenetic analyses based on the small subunit ribosomal RNA (SSU rRNA) gene show that F. apoacuminata sp. nov. clusters with F. atra, F. minuta, F. acuminata and F. terricola. These five species group with Disematostoma, Marituja and Stokesia rather than with other Frontonia species, causing polyphyly of the genus Frontonia.
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Affiliation(s)
- Tao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,College of Fisheries and Key Laboratory of Mariculture of the Education Ministry of China, Ocean University of China, Qingdao, PR China
| | - Xuming Pan
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, PR China
| | - Borong Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,College of Fisheries and Key Laboratory of Mariculture of the Education Ministry of China, Ocean University of China, Qingdao, PR China
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingjian Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,College of Fisheries and Key Laboratory of Mariculture of the Education Ministry of China, Ocean University of China, Qingdao, PR China
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Wang C, Hu Y, Warren A, Hu X. Genetic Diversity and Phylogeny of the Genus Euplotes (Protozoa, Ciliophora) Revealed by the Mitochondrial CO1 and Nuclear Ribosomal Genes. Microorganisms 2021; 9:microorganisms9112204. [PMID: 34835330 PMCID: PMC8624429 DOI: 10.3390/microorganisms9112204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/03/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Nuclear ribosomal and mitochondrial genes have been utilized individually or in combination to identify known species and discriminate closely related species. However, compared with metazoans, genetic diversity within the ciliate order Euplotida is poorly known. The aim of this study is to investigate how much nucleotide sequence divergence occurs within Euplotes. A total of 14 new gene sequences, comprising four SSU rDNA and 10 CO1 (including three species for the first time) were obtained. Phylogenetic analyses were carried out based on sequences of two DNA fragments from the same 27 isolates. We found that CO1 revealed a larger interspecific divergence than the SSU rRNA gene, thus demonstrating a higher resolution for separating congeners. Genetic distances differ significantly at the species level. Euplotes balteatus was revealed to have a large intraspecific variation at two loci, while E. vannus showed different levels of haplotype variability, which appeared as a polyphyletic cluster on the CO1 tree. These high genetic divergences suggest the presence of more cryptic species. By contrast, the CO1 gene showed low variability within E. raikovi, appearing as monophyletic clusters, which indicates that this species could be identified based on this gene. Conclusively, CO1 is a suitable marker for the study of genetic diversity within Euplotes, and increased taxon sampling gives an opportunity to screen relationships among members of this genus. Additionally, current data present no clear biogeographical pattern for Euplotes.
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Affiliation(s)
- Congcong Wang
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China;
| | - Yue Hu
- Oxford Sixth Form College, Oxford OX1 4HT, UK;
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK;
| | - Xiaozhong Hu
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China;
- Correspondence: ; Tel.: +86-532-8203-1610
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Shchepin O, Novozhilov Y, Woyzichovski J, Bog M, Prikhodko I, Fedorova N, Gmoshinskiy V, Borg Dahl M, Dagamac NHA, Yajima Y, Schnittler M. Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing. Mol Ecol 2021; 31:372-390. [PMID: 34676941 DOI: 10.1111/mec.16239] [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: 06/14/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.
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Affiliation(s)
- Oleg Shchepin
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Jan Woyzichovski
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Ilya Prikhodko
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda Fedorova
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir Gmoshinskiy
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Polistovsky National Nature Reserve, Pskov Region, Russia
| | - Mathilde Borg Dahl
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nikki H A Dagamac
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Yuka Yajima
- Muroran Institute of Technology, Muroran, Japan
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
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12
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Pecina L, Vďačný P. DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Phylogenetically distinct lineages may be hidden behind identical or highly similar morphologies. The phenomenon of morphological crypticity has been recently detected in symbiotic ciliates of the family Clevelandellidae, as multivariate and Fourier shape analyses failed to distinguish genetically distinct taxa. To address the question of species boundaries, the phylogenetic information contained in the rDNA cistron of clevelandellid ciliates, which had been isolated from the digestive tract of blaberid cockroaches, was studied using a multifaceted statistical approach. Multigene phylogenies revealed that the genus Clevelandella is paraphyletic containing members of the genus Paraclevelandia. To resolve the paraphyly of Clevelandella, two new genera, Anteclevelandella gen. nov. and Rhynchoclevelandella gen. nov., are proposed based on morphological synapomorphies and shared molecular characters. Multigene analyses and Bayesian species delimitation supported the existence of 13 distinct species within the family Clevelandellidae, eight of which represent new taxa. Moreover, two new Nyctotherus species were recognized within the clade that is sister to the Clevelandellidae. According to the present distance and network analyses, the first two domains of the 28S rRNA gene showed much higher power for species discrimination than the 18S rRNA gene and ITS region. Therefore, the former molecular marker was proposed to be a suitable group-specific barcode for the family Clevelandellidae.
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Affiliation(s)
- Lukáš Pecina
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
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13
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De Luca D, Piredda R, Sarno D, Kooistra WHCF. Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets. THE ISME JOURNAL 2021; 15:1931-1942. [PMID: 33589768 PMCID: PMC8245484 DOI: 10.1038/s41396-021-00895-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/23/2020] [Accepted: 01/14/2021] [Indexed: 12/21/2022]
Abstract
Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.
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Affiliation(s)
- Daniele De Luca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biology, Botanical Garden of Naples, University of Naples Federico II, Naples, Italy
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Diana Sarno
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Wiebe H C F Kooistra
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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14
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Rataj M, Vd'ačný P. Cryptic host-driven speciation of mobilid ciliates epibiotic on freshwater planarians. Mol Phylogenet Evol 2021; 161:107174. [PMID: 33831547 DOI: 10.1016/j.ympev.2021.107174] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 01/18/2023]
Abstract
Mobilids are among the most taxonomically diverse but morphologically uniform groups of epibiotic ciliates. They attach to their hosts by means of an adhesive disc as harmless commensals such as Urceolaria, or as parasites causing significant economic loss such as some Trichodina species. We investigated the diversity, species boundaries, and phylogenetic relationships of mobilids associated with freshwater planarians, using 114 new sequences of two mitochondrial (16S rRNA gene and cytochrome c oxidase gene) and five nuclear (18S rRNA gene, ITS1-5.8S-ITS2 region, D1/D2 domains of 28S rRNA gene) markers. Although the morphological disparity of the isolated trichodinids and urceolariids was low, Bayesian coalescent analyses revealed the existence of five distinct evolutionary lineages/species given the seven molecular markers. The occurrence of mobilids perfectly correlated with their planarian hosts: Trichodina steinii and two Urceolaria mitra-like taxa were associated exclusively with the planarian Dugesia gonocephala, Trichodina polycelis sp. n. with the planarian Polycelis felina, and Trichodina schmidtea sp. n. with the planarian Schmidtea polychroa. Host organisms thus very likely constitute sharply isolated niches that might permit speciation of their epibiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different hosts.
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Affiliation(s)
- Matej Rataj
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Peter Vd'ačný
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic.
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15
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Serra V, D’Alessandro A, Nitla V, Gammuto L, Modeo L, Petroni G, Fokin SI. The neotypification of Frontonia vernalis (Ehrenberg, 1833) Ehrenberg, 1838 and the description of Frontonia paravernalis sp. nov. trigger a critical revision of frontoniid systematics. BMC ZOOL 2021; 6:4. [PMID: 37170316 PMCID: PMC10127333 DOI: 10.1186/s40850-021-00067-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Among Oligohymenophorea (Ciliophora, Alveolata) the subclass Peniculia stands as one of the most well-known groups. Frontonia is the largest genus of Peniculia, and its representatives are spread in any type of water bodies as well as in soil. At a first glance, Frontonia species exhibit an overall similar morphology, and form a well-recognizable taxon of ciliates. Despite the general morphological homogeneity, the phylogenetic analysis based on the 18S rDNA sequencing showed that Frontonia is a non-monophyletic group. The systematics of this genus should be deeply reviewed, although additional issues complicate the task solving. First, type species of the genus is not yet clearly established, and no type material is available. In this context, the situation of F. vernalis, one of the first Frontonia ever described, is somehow puzzled: the description of this ciliate made by Ehrenberg (in 1833 and 1838) contains several inaccuracies and subsequent misidentifications by other authors occurred. Moreover, the 18S rDNA sequence of a putative F. vernalis is available on GenBank, but no morphological description of the correspondent specimens is provided; thus, in our opinion, it should be only prudently associated with F. vernalis or at least indicated as “F. vernalis”.
Results
In the present work, we provide the neotypification of F. vernalis newly found in Italy, presenting its multidisciplinary description and its neotype material. Similarly, we describe a novel species bearing Chlorella-like endosymbionts, Frontonia paravernalis sp. nov., retrieved in two far distant locations (Italy, Russia). A critical discussion on the status of Frontonia taxonomy and phylogeny is also presented, based on the 18S rDNA sequencing of both these two newly collected species and other 14 frontoniids isolated in different parts of the world. Finally, in the present study F. leucas was neotypified and proposed as the type species of the genus.
Conclusions
Green frontoniids form a monophyletic clade of freshwater organisms characterized by having a single contractile vacuole and bearing intracytoplasmatic Chlorella-like symbionts. With the neotypification of F. vernalis and F. leucas a fundamental step in Frontonia systematics was taken, and the bases for further taxonomic studies were laid.
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16
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Fan X, Yao S, Luo X, Dong T, Xu Y, Chen L, Bourland W, Zhao Y, Huang J. Some morphologically distinguishable hypotrich ciliates share identical 18S rRNA gene sequences – taxonomic insights from a case study on Oxytricha species (Protista, Ciliophora). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Modern taxonomic studies of ciliated protozoa require both morphological and molecular data. One dilemma is how to distinguish morphologically similar species with few nucleotide differences in the widely used marker, the 18S rRNA gene. In the present study, two Oxytricha species were morphologically documented using light and electron microscopy. The mitochondrial cytochrome c oxidase subunit I (COI) gene and a fragment of the rRNA gene covering the 18S-ITS1-5.8S-ITS2-28S rRNA gene regions were sequenced. Phylogenetic analyses of all available Oxytricha granulifera-related populations were performed to reveal the internal relationships of this group. We described a new species, Oxytricha atypica sp. nov., distinguished from its congeners by having seven postoral ventral cirri resulting from the additional fragmentation of anlage V during ontogenesis. Although their 18S rRNA genes differ by only one nucleotide, divergence of the COI gene is as high as 11.8% between O. atypica and the closely related species, O. granulifera. All but one of the COI nucleotide substitutions were synonymous. We documented the highly conserved nature of the 18S rRNA gene in the morphospecies of Oxytricha. Based on these findings, we speculate that O. granulifera contains cryptic species or morphospecies needing further characterization, and new insights for the taxonomy of hypotrich ciliates are also discussed.
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Affiliation(s)
- Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Shunli Yao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiaotian Luo
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tianyao Dong
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Lingyun Chen
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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17
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Serra V, Fokin SI, Gammuto L, Nitla V, Castelli M, Basuri CK, Satyaveni A, Sandeep BV, Modeo L, Petroni G. Phylogeny of
Neobursaridium
reshapes the systematics of
Paramecium
(Oligohymenophorea, Ciliophora). ZOOL SCR 2020. [DOI: 10.1111/zsc.12464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Sergei I. Fokin
- Department of Biology University of Pisa Pisa Italy
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology Russian Academy of Sciences St. Petersburg Russia
| | | | | | - Michele Castelli
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’ Pavia University Pavia Italy
| | - Charan Kumar Basuri
- National Centre for Coastal Research Ministry of Earth Sciences Government of IndiaNIOT Campus Pallikaranai, Chennai India
- Department of Zoology Andhra University Visakhapatnam India
| | | | | | - Letizia Modeo
- Department of Biology University of Pisa Pisa Italy
- CIME Centro Interdipartimentale di Microscopia Elettronica Università di Pisa Pisa Italy
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa Pisa Italy
| | - Giulio Petroni
- Department of Biology University of Pisa Pisa Italy
- CIME Centro Interdipartimentale di Microscopia Elettronica Università di Pisa Pisa Italy
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa Pisa Italy
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18
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Xu J, Wilkinson M, Chen M, Zhang Q, Yang R, Yi Z. Concatenated data and dense taxon sampling clarify phylogeny and ecological transitions within Hypotricha. ZOOL SCR 2020. [DOI: 10.1111/zsc.12459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Mark Wilkinson
- Department of Life Sciences Natural History Museum London UK
| | - Miaoying Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Qi Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
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19
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Further insights into the phylogeny of peniculid ciliates (Ciliophora, Oligohymenophorea) based on multigene data. Mol Phylogenet Evol 2020; 154:107003. [PMID: 33137410 DOI: 10.1016/j.ympev.2020.107003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
Peniculids comprise a large order of ciliated protists in Class Oligohymenophorea having many unresolved evolutionary relationships. Herein, we report 27 new sequences, including 18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA and the mitochondrial cox1 genes of eight peniculids. We conducted phylogenetic analyses based on each these markers and on a four-gene concatenated data set (18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA, and cox1 gene). The main findings are: 1) subclass Peniculia and family Parameciidae are monophyletic, with genus Frontonia remaining non-monophyletic; 2) Urocentrids have traditionally been regarded as a family, multi-gene analyses support the rank of Urocentrida and consistently recovers this order as sister to Peniculida, and Urocentrida and Peniculida comprise subclass Peniculia in agreement with Lynn's (2008) classification; 3) discrepancies between multiple-gene phylogenies, and conflicts with morphologic data regarding genus Frontonia necessitate expansion and revision of species diagnoses and we propose consideration of Group III of Frontonia (including F. didieri, F. ocularis, F. anatolica, F. pusilla and F. elegans) as incertae sedis in Peniculida; 4) multi-gene analyses of Parameciidae support five previously established subgenera. Paramecium buetschlii is placed in subgenus Chloroparamecium, and P. chlorelligerum into subgenus Viridoparamecium.
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20
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Taxonomy and molecular phylogeny of three freshwater scuticociliates, with descriptions of one new genus and two new species (Protista, Ciliophora, Oligohymenophorea). Eur J Protistol 2020; 74:125644. [DOI: 10.1016/j.ejop.2019.125644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022]
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21
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Kaur H, Shashi, Warren A, Negi RK, Kamra K. Taxonomic resolution of Stylonychia notophora (Alveolata, Ciliophora, Hypotricha) sensu Sapra and Dass 1970 using an integrative approach. Int J Syst Evol Microbiol 2020; 70:3939-3952. [PMID: 32441613 DOI: 10.1099/ijsem.0.004207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only minor differences in morphometry, morphogenesis and in 18S rDNA sequences. The 18S rDNA sequences of all six populations had 99% similarity to both T. pustulata and S. notophora. These findings support the contention that S. notophora sensu Sapra and Dass, 1970 was misidentified and is a population of T. pustulata. This study supports the need for adopting an integrative approach based on morphological, morphogenetic and molecular data in order to understand species delimitation in ciliated protists.
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Affiliation(s)
- Harpreet Kaur
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, Delhi 110007, India.,Ciliate Biology Lab, SGTB Khalsa College, University of Delhi, Delhi 110007, India
| | - Shashi
- Ciliate Biology Lab, SGTB Khalsa College, University of Delhi, Delhi 110007, India
| | - Alan Warren
- Department of Life Sciences, Natural History Museum of London, London SW7 5BD, UK
| | - Ram Krishan Negi
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Komal Kamra
- Ciliate Biology Lab, SGTB Khalsa College, University of Delhi, Delhi 110007, India
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22
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Wang Y, Jiang Y, Liu Y, Li Y, Katz LA, Gao F, Yan Y. Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research. Microorganisms 2020; 8:E316. [PMID: 32106521 PMCID: PMC7142639 DOI: 10.3390/microorganisms8030316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/21/2023] Open
Abstract
While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 104 to 8.1 × 105; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yongqiang Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yuan Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA;
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.J.); (Y.L.); (Y.L.); (F.G.)
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA;
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23
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Shazib SUA, Vďačný P, Slovák M, Gentekaki E, Shin MK. Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Sci Rep 2019; 9:16360. [PMID: 31704993 PMCID: PMC6841689 DOI: 10.1038/s41598-019-52722-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
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Affiliation(s)
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, 845 23, Bratislava, Slovakia.,Department of Botany, Charles University, 128 01, Prague, Czech Republic
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, 44610, South Korea.
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24
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Zhan Z, Li J, Xu K. Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora). Microorganisms 2019; 7:microorganisms7110493. [PMID: 31717798 PMCID: PMC6920991 DOI: 10.3390/microorganisms7110493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/03/2022] Open
Abstract
Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.
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Affiliation(s)
- Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ju Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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25
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Fokin SI, Serra V, Ferrantini F, Modeo L, Petroni G. "Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host. MICROBIAL ECOLOGY 2019; 77:1092-1106. [PMID: 30627761 DOI: 10.1007/s00248-018-1311-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/19/2018] [Indexed: 05/09/2023]
Abstract
We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.
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Affiliation(s)
- Sergei I Fokin
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia, 199034.
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia, 199034.
| | - Valentina Serra
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
| | | | - Letizia Modeo
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126, Pisa, Italy
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Abraham JS, Sripoorna S, Maurya S, Makhija S, Gupta R, Toteja R. Techniques and tools for species identification in ciliates: a review. Int J Syst Evol Microbiol 2019; 69:877-894. [DOI: 10.1099/ijsem.0.003176] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
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Affiliation(s)
- Jeeva Susan Abraham
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - S. Sripoorna
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi 110021, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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27
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Wang Y, Wang C, Jiang Y, Katz LA, Gao F, Yan Y. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. SCIENCE CHINA-LIFE SCIENCES 2019; 62:203-214. [PMID: 30671886 DOI: 10.1007/s11427-018-9422-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/06/2018] [Indexed: 11/26/2022]
Abstract
Sequence-based approaches, such as analyses of ribosome DNA (rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities. However, recent studies demonstrate both rDNA copy number variation and intra-individual (intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA (SSU rDNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that: (i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa; (ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template; (iii) compared with the most common version, other variant sequences differ in only 1-3 nucleotides, likely generated during macronuclear (somatic) amplification; (iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses; (v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall, these analyses indicate the need for careful consideration of SSU rDNA variation in analyses of the role of ciliates in ecosystems.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA.
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28
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Zhao Y, Yi Z, Warren A, Song W. Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora). Proc Biol Sci 2019; 285:rspb.2017.2159. [PMID: 29367393 DOI: 10.1098/rspb.2017.2159] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022] Open
Abstract
Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes (sensu lato) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes (sensu stricto), Euplotoides, Euplotopsis and Moneuplotes are not supported; the vannus-type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1-D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes.
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Affiliation(s)
- Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China .,Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, People's Republic of China
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29
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Galen SC, Nunes R, Sweet PR, Perkins SL. Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon. BMC Evol Biol 2018; 18:128. [PMID: 30165810 PMCID: PMC6117968 DOI: 10.1186/s12862-018-1242-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/15/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska. RESULTS We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~ 0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization. CONCLUSION Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.
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Affiliation(s)
- Spencer C. Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Renato Nunes
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Paul R. Sweet
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Susan L. Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
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30
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Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T. A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture. J Eukaryot Microbiol 2018; 66:294-308. [DOI: 10.1111/jeu.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dominik Forster
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Sabine Filker
- Molecular Ecology; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Rebecca Kochems
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Hans-Werner Breiner
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
- ID-Gene ecodiagnostics Ltd.; Campus Biotech Innovation Park 1202 Geneva Switzerland
| | - Thorsten Stoeck
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
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31
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Chen X, Shazib SUA, Kim JH, Kim MS, Shin MK. New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae). Eur J Protistol 2018; 65:16-30. [PMID: 29793141 DOI: 10.1016/j.ejop.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length. However, our molecular analyses of four different genetic markers - three nuclear DNA markers (18S rDNA, ITS1-5.8S-ITS2 region, D1D2 of 28S rDNA) and one mitochondrial (mt) marker (CO1 gene) - indicated that all Korean populations examined were the same species. Based on our present findings and historic works, we propose that G. calkinsi, G. aculeata, and G. beninensis are junior synonyms of G. lanceolata.
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Affiliation(s)
- Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | | | - Ji Hye Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Min Seok Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Nakdong River Environment Research Center, Goryeong-gun, Gyeongbuk 40103, South Korea
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea.
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32
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Park MH, Jung JH, Jo E, Park KM, Baek YS, Kim SJ, Min GS. Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:148-155. [PMID: 29701079 DOI: 10.1080/24701394.2018.1464563] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.
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Affiliation(s)
- Mi-Hyun Park
- a Department of Biological Sciences , Inha University , Incheon , The Republic of Korea
| | - Jae-Ho Jung
- b Department of Biology , Gangneung-Wonju National University , Gangneung , The Republic of Korea
| | - Euna Jo
- a Department of Biological Sciences , Inha University , Incheon , The Republic of Korea
| | - Kyung-Min Park
- a Department of Biological Sciences , Inha University , Incheon , The Republic of Korea.,c Korea Polar Research Institute , Incheon , The Republic of Korea
| | - Ye-Seul Baek
- a Department of Biological Sciences , Inha University , Incheon , The Republic of Korea
| | - Se-Joo Kim
- d KRIBB , Daejeon , The Republic of Korea
| | - Gi-Sik Min
- a Department of Biological Sciences , Inha University , Incheon , The Republic of Korea
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Morphology and systematics of two freshwater Frontonia species (Ciliophora, Peniculida) from northeastern China, with comparisons among the freshwater Frontonia spp. Eur J Protistol 2018; 63:105-116. [DOI: 10.1016/j.ejop.2018.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 01/06/2018] [Accepted: 01/08/2018] [Indexed: 11/24/2022]
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34
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Yan Y, Fan Y, Luo X, El-Serehy HA, Bourland W, Chen X. New contribution to the species-rich genus Euplotes: Morphology, ontogeny and systematic position of two species (Ciliophora; Euplotia). Eur J Protistol 2018; 64:20-39. [PMID: 29621653 DOI: 10.1016/j.ejop.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
Abstract
The morphology, ontogeny and phylogeny of two Euplotes species, E. estuarinus sp. nov. and a population of E. platystoma Dragesco and Dragesco-Kernéis, 1986, both collected from tropical brackish waters in south China, were investigated based on living morphology, ciliary pattern and molecular data. Euplotes estuarinus sp. nov. is small (about 60 × 40 μm in vivo), has a dargyrome of the double-eurystomus type, and the transverse cirri are arranged in two groups, with two left and three right ones. The original description of the poorly known species, E. platystoma, is brief, and the species was never investigated using live observation and molecular methods Hence, we provided a detailed redescription. Some stages of their morphogenesis were observed which proceed in the same pattern as in their congeners. The new species E. estuarinus sp. nov. clusters with E. curdsi, differing only by 1 bp in their SSU rRNA gene sequences, which is likely due to the recent speciation event and the limited resolution of the SSU rRNA gene at species level in this group as the two species are clearly morphologically distinct.
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Affiliation(s)
- Ying Yan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yangbo Fan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; School of Civil and Environment Engineering, Harbin Institute of Technology, Shenzhen 518000, China
| | - Xiaotian Luo
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Hamed A El-Serehy
- Department of Zoology, King Saud University, Riyadh 11451, Saudi Arabia
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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35
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Chen X, Wang Y, Sheng Y, Warren A, Gao S. GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes. Mol Ecol Resour 2018; 18:700-713. [DOI: 10.1111/1755-0998.12750] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yurui Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- College of Marine Life Sciences; Ocean University of China; Qingdao China
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36
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Lian C, Luo X, Fan X, Huang J, Yu Y, Bourland W, Song W. Morphological and Molecular Redefinition of Euplotes platystoma Dragesco & Dragesco-Kernéis, 1986 and Aspidisca lynceus (Müller,1773) Ehrenberg, 1859, with Reconsideration of a "Well-known" Euplotes Ciliate, Euplotes harpa Stein, 1859 (Ciliophora, Euplotida). J Eukaryot Microbiol 2018; 65:531-543. [PMID: 29315959 DOI: 10.1111/jeu.12499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/29/2017] [Accepted: 12/27/2017] [Indexed: 11/26/2022]
Abstract
We documented the morphology, infraciliature, silverline system, and molecular data of two euplotid species isolated from China, including two populations of the poorly known Euplotes platystoma Dragesco & Dragesco-Kernéis, and the previously well described Aspidisca lynceus (Müller, ) Ehrenberg, 1830. Based on the information available, an improved diagnosis of Euplotes platystoma is given, including: a narrow adoral zone with 44-68 membranelles, 10 frontoventral, 5 transverse, 2 left marginal and 2 caudal cirri, 11-13 dorsal kineties with 17-25 dikinetids in the mid-dorsal row, and dorsal silverline system of the double-eurystomus type. The Chinese population of Aspidisca lynceus closely resembles previously described populations. Phylogenetic analyses inferred from SSU rDNA sequences show that E. platystoma is closely related with E. neapolitanus, and the internal position of A. lynceus within this genus is still not robust. A reconsideration of the "well-known" Euplotes harpa and a comparison of all SSU rDNA sequences of E. harpa in GenBank are provided. We speculate that the sequences available from GenBank under the name of E. harpa are very likely from misidentified materials, that is, the identity of the species currently associated with the SSU rDNA of this "well-known" form in molecular databases requires further confirmation.
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Affiliation(s)
- Chunyu Lian
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaotian Luo
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Department of Biological Sciences, Boise State University, Boise, 83725, ID, USA
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, 200062, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, 83725, ID, USA
| | - Weibo Song
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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37
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A New Molecular Approach Based on the Secondary Structure of Ribosomal RNA for Phylogenetic Analysis of Mobilid Ciliates. Curr Microbiol 2017; 75:296-304. [DOI: 10.1007/s00284-017-1379-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
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Gao F, Huang J, Zhao Y, Li L, Liu W, Miao M, Zhang Q, Li J, Yi Z, El-Serehy HA, Warren A, Song W. Systematic studies on ciliates (Alveolata, Ciliophora) in China: Progress and achievements based on molecular information. Eur J Protistol 2017; 61:409-423. [DOI: 10.1016/j.ejop.2017.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/25/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
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Investigating the biodiversity of ciliates in the ‘Age of Integration’. Eur J Protistol 2017; 61:314-322. [DOI: 10.1016/j.ejop.2017.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 01/10/2023]
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40
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Chen X, Kim JH, Shazib SUA, Kwon CB, Shin MK. Morphology and molecular phylogeny of three heterotrichid species (Ciliophora, Heterotrichea), including a new species of Anigsteinia. Eur J Protistol 2017; 61:278-293. [DOI: 10.1016/j.ejop.2017.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022]
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Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea. Mol Phylogenet Evol 2017; 112:96-106. [DOI: 10.1016/j.ympev.2017.04.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/11/2017] [Accepted: 04/20/2017] [Indexed: 11/17/2022]
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Pan X, Shi Z, Wang C, Bourland WA, Chen Y, Song W. Molecular Phylogeny and Taxonomy of a New Freshwater Hymenostomatid from Northeastern China, with the Establishment of a New Genus Anteglaucoma
gen. n. (Protista, Ciliophora, Oligohymenophorea). J Eukaryot Microbiol 2016; 64:564-572. [DOI: 10.1111/jeu.12382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/28/2016] [Accepted: 10/28/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Xuming Pan
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Zihan Shi
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - William A. Bourland
- Department of Biological Sciences; Boise State University; Boise Idaho 83725-1515
| | - Ying Chen
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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Vecchi M, Vicente F, Guidetti R, Bertolani R, Rebecchi L, Cesari M. Interspecific relationships of tardigrades with bacteria, fungi and protozoans, with a focus on the phylogenetic position ofPyxidium tardigradum(Ciliophora). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Matteo Vecchi
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Filipe Vicente
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
- Centre of Environmental Biology and Department of Animal Biology; University of Lisbon; Campo Grande C2 1749-016 Lisbon Portugal
| | - Roberto Guidetti
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Roberto Bertolani
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Lorena Rebecchi
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Michele Cesari
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
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Syberg-Olsen MJ, Irwin NAT, Vannini C, Erra F, Di Giuseppe G, Boscaro V, Keeling PJ. Biogeography and Character Evolution of the Ciliate Genus Euplotes (Spirotrichea, Euplotia), with Description of Euplotes curdsi sp. nov. PLoS One 2016; 11:e0165442. [PMID: 27828996 PMCID: PMC5102374 DOI: 10.1371/journal.pone.0165442] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 10/06/2016] [Indexed: 01/08/2023] Open
Abstract
Ciliates comprise a diverse and ecologically important phylum of unicellular protists. One of the most specious and best-defined genera is Euplotes, which constitutes more than 70 morphospecies, many of which have never been molecularly tested. The increasing number of described Euplotes taxa emphasizes the importance for detailed characterizations of new ones, requiring standardized morphological observations, sequencing of molecular markers and careful comparison with previous literature. Here we describe Euplotes curdsi sp. nov., distinguishable by the combination of the following features: 45–65 μm length, oval or elongated shape with both ends rounded, narrow peristome with 25–34 adoral membranelles, conspicuous paroral membrane, double-eurystomus dorsal argyrome type, 6–7 dorsolateral kineties and 10 frontoventral cirri. Three populations of the novel species have been found in brackish and marine samples in the Mediterranean and the White Sea. We provide the SSU rRNA gene sequences of these populations, and an updated phylogeny of the genus Euplotes. Using the molecular phylogenetic tree, we inferred aspects of the biogeographical history of the genus and the evolution of its most important taxonomic characters in order to provide a frame for future descriptions. Ultimately, these data reveal recurrent trends of freshwater invasion and highlight the dynamic, yet convergent, morphological evolution of Euplotes.
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Affiliation(s)
- Mitchell J. Syberg-Olsen
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas A. T. Irwin
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Fabrizio Erra
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | | | - Vittorio Boscaro
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Patrick J. Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Shen Z, Ji D, Yi Z, Al-Rasheid KAS, Lin X. Morphology and Phylogenetic Placement of Three NewZoothamniumspecies (Ciliophora: Peritrichia) from Coastal Waters of Southern China. J Eukaryot Microbiol 2016; 64:266-277. [DOI: 10.1111/jeu.12358] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/17/2016] [Accepted: 08/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Zhuo Shen
- Institute of Hydrobiology; Jinan University; Key Laboratory of Eutrophication and Red Tide Control; Educational Department of Guangdong Province; Guangzhou 510632 China
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring; School of Life Science; South China Normal University; Guangzhou 510631 China
| | - Daode Ji
- School of Ocean; Yantai University; Yantai 264005 China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring; School of Life Science; South China Normal University; Guangzhou 510631 China
| | | | - Xiaofeng Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring; School of Life Science; South China Normal University; Guangzhou 510631 China
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Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon. Eur J Protistol 2016; 56:134-146. [PMID: 27652510 DOI: 10.1016/j.ejop.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/09/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022]
Abstract
The morphology of four cyrtophorian ciliates, Dysteria ovalis, D. semilunaris, Phascolodon vorticella, and Chlamydonellopsis calkinsi, were investigated using living observation and protargol-staining. The morphology of D. ovalis is revealed in detail for the first time, and it is characterized by the following combination of features: size 40-50×20-30μm in vivo; oval in outline; four right kineties, including two frontoventral kineties and one shortened leftmost right kinety; three left frontal kineties; two ventrally located contractile vacuoles; marine habitat. New Chinese populations of three other species correspond well with previous descriptions, but a well-developed alveolar layer on the cell surface of P. vorticella is reported for the first time. Phylogenetic analyses based on small subunit rRNA gene sequences clustered Dysteria ovalis with Mirodysteria decora, whereas D. semilunaris is grouped with D. lanceolata. Although Phascolodon appeared as sister to Pseudochilodonopsis in the present work, its accurate phylogenetic position is still uncertain because AU test did not reject the possibility that it clustered with Odontochlamys and Chilodonella.
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Liu M, Fan X, Gao F, Gao S, Yu Y, Warren A, Huang J. Tetrahymena australis
(Protozoa, Ciliophora): A Well-Known But “Non-Existing” Taxon - Consideration of Its Identification, Definition and Systematic Position. J Eukaryot Microbiol 2016; 63:760-770. [DOI: 10.1111/jeu.12323] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/01/2016] [Accepted: 04/18/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Mingjian Liu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan 430072 China
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Xinpeng Fan
- School of Life Sciences; East China Normal University; Shanghai 200241 China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan 430072 China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD United Kingdom
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan 430072 China
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