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Choi JH, Omar A, Jung JH. Morphology, morphogenesis, and molecular phylogeny of Aspidisca koreana n. sp. (Ciliophora, Euplotida) from South Korea. Eur J Protistol 2024; 92:126037. [PMID: 38100886 DOI: 10.1016/j.ejop.2023.126037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The morphology, morphogenesis, and molecular phylogeny of a new ciliate, Aspidisca koreana n. sp., discovered in the eastern coast of South Korea, were investigated. The morphological description is based on the observation of living cells, 4'-6-diamidino-2-phenylindole (DAPI) and silver-stained specimens (e.g., protargol, silver nitrate), and scanning electron micrographs. The new species is characterized by having a small body size (17-25 × 15-18 μm in vivo), a distinct peristomial spur on the posterior portion of left margin, seven frontoventral cirri in "polystyla-arrangement", and the arrangement of the anterior portion of adoral zone of membranelles, i.e., anteriormost membranelle is distinctly separated from the other three membranelles. The morphogenesis follows the typical pattern of this genus. Phylogenetic analyses, using the 18S rDNA sequence, also support the establishment of a new species.
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Affiliation(s)
- Ji Hye Choi
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Atef Omar
- Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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2
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Dirren-Pitsch G, Bühler D, Salcher MM, Bassin B, Le Moigne A, Schuler M, Pernthaler J, Posch T. FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Front Microbiol 2022; 13:1070232. [PMID: 36578568 PMCID: PMC9790926 DOI: 10.3389/fmicb.2022.1070232] [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: 10/14/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.
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Affiliation(s)
- Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland,*Correspondence: Gianna Dirren-Pitsch,
| | - Dominique Bühler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M. Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budĕjovice, Czechia
| | - Barbara Bassin
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Alizée Le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Martina Schuler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
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Melekhin M, Yakovleva Y, Lebedeva N, Nekrasova I, Nikitashina L, Castelli M, Mayén-Estrada R, Romanovich AE, Petroni G, Potekhin A. Cryptic Diversity in Paramecium multimicronucleatum Revealed with a Polyphasic Approach. Microorganisms 2022; 10:microorganisms10050974. [PMID: 35630417 PMCID: PMC9143557 DOI: 10.3390/microorganisms10050974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/01/2022] [Accepted: 05/03/2022] [Indexed: 02/06/2023] Open
Abstract
Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.
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Affiliation(s)
- Maksim Melekhin
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
| | - Yulia Yakovleva
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Natalia Lebedeva
- Centre for Culture Collection of Microorganisms, Saint Petersburg State University, 198504 Saint Petersburg, Russia
| | - Irina Nekrasova
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Liubov Nikitashina
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Michele Castelli
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, 27100 Pavia, Italy
| | - Rosaura Mayén-Estrada
- Laboratorio de Protozoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Ext. s/núm. Ciudad Universitaria, Av. Universidad 3000, Coyoacán, Ciudad de Mexico 04510, Mexico
| | - Anna E Romanovich
- Center for Molecular and Cell Technologies, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126 Pisa, Italy
| | - Alexey Potekhin
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
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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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Isolation and identification of herbivorous ciliates from contaminated microalgal cultures. Eur J Protistol 2020; 76:125743. [PMID: 33166874 DOI: 10.1016/j.ejop.2020.125743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 11/23/2022]
Abstract
Ciliates are a common but understudied group of grazers that can invade microalgal cultures. To estimate the potential impact of ciliates on microalgal culture productivity, the identification of species that can invade these cultures is essential. Furthermore, isolation of these herbivorous ciliates allows to use them in experiments that investigate the impact of ciliate grazing on the productivity of microalgal cultures. The main aims of this study were to isolate and identify ciliates that invade cultures of the freshwater microalgae Chlorella and Chlamydomonas, and to establish a live collection of these ciliates for usage in future experiments. To this end, we optimized a method for isolating ciliates from contaminated microalgal cultures and we developed a new PCR primer set for amplifying the partial 18S rDNA of ciliates belonging to the classes Spirotrichea, Oligohymenophorea and Colpodea. As a result, we isolated 11 ciliates from microalgal enrichment cultures inoculated with non-sterile dust and various freshwater sources. Of these 11 species, 7 were found to be feeding on Chlamydomonas. Ciliate species that fed on Chlorella could not be isolated in this study. Ciliate species feeding on Chlamydomonas were identified based on a combination of morphological observations and molecular analyses of partial 18S rDNA sequences.
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Chen L, Liu Y, Long Y, Lyu J, Feng C, Ning Y, Yi Z. Morphology and molecular phylogeny of two new soil ciliates, Hemiurosomoida warreni nov. spec. and Hemiurosoma clampi nov. spec. (Ciliophora, Hypotrichia) from Tibet. Eur J Protistol 2020; 77:125746. [PMID: 33276198 DOI: 10.1016/j.ejop.2020.125746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Two novel hypotrichous ciliates, Hemiurosomoida warreni nov. spec. and Hemiurosoma clampi nov. spec., isolated from soil in the Lhalu Wetland and Motuo Virgin Forest in Tibet, respectively, were investigated using live observation and protargol staining. Hemiurosomoida warreni nov. spec. strongly resembles the type species H. longa but can be distinguished by its body size in vivo (110-145 × 30-40 μm vs. 50-100 × 18-40 μm), number of adoral membranelles (25-38 vs. 15-22), and numbers of right (29-39 vs. 14-23) and left (26-35 vs. 13-23) marginal cirri, transverse cirri (3 vs. 4 or 5) and macronuclear nodules (4-8 vs. 2). Hemiurosoma clampi nov. spec. is characterized by its vermiform body shape, colourless cortical granules distributed in irregular rows, two macronuclear nodules, three frontal cirri, one buccal cirrus, four frontoventral cirri ranged in a line, two transverse cirri, lacking postoral ventral and pretransverse ventral cirri, and marginal rows that are not posteriorly confluent. Phylogenetic analyses based on SSU rDNA gene sequences suggest that Hemiurosomoida is not monophyletic. A close relationship is revealed between Hemiurosomoida warreni nov. spec., Parakahilella macrostoma, Hemiurosoma clampi nov. spec., and the type species Hemiurosoma terricola. As expected, all these species are classified within the "non-oxytrichid Dorsomarginalia".
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Affiliation(s)
- Lingyun Chen
- Laboratory of Microbiota, College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Yongqiang Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yongli Long
- Laboratory of Microbiota, College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Jing Lyu
- Laboratory of Microbiota, College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Chunyan Feng
- Laboratory of Microbiota, College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Yingzhi Ning
- Laboratory of Microbiota, College of Life Science, Northwest Normal University, Lanzhou 730070, China.
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou 510631, China.
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Zhang Q, Xu J, Warren A, Yang R, Shen Z, Yi Z. Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora). BMC Evol Biol 2020; 20:86. [PMID: 32677880 PMCID: PMC7364784 DOI: 10.1186/s12862-020-01653-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates. RESULTS A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests. CONCLUSIONS Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.
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Affiliation(s)
- Qi Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.,Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.,Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Zhuo Shen
- Institute of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China. .,Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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Jung JH, Omar A, Kim KS, Kang SC, Kwak DY, Sun JH, Min GS. A study on the non-monophyletic genera Australothrix and Holostichides based on multigene and morphological analyses with a reexamination of type materials (Protozoa: Ciliophora). Mol Phylogenet Evol 2019; 139:106538. [PMID: 31220579 DOI: 10.1016/j.ympev.2019.106538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
Abstract
In a study of ciliate diversity, we collected two new species of the genera Australothrix and Holostichides. Based on nuclear ribosomal genes, our study shows that these two genera are genetically non-monophyletic. To clarify the issues of the non-monophyly, we reexamined type material of H. heterotypicus, H. terrae, and Birojimia soyaensis. Based on multigene and morphometric analyses, Australothrix and Holostichides are clearly non-monophyletic even in mitochondrial CO1 gene trees. The multigene analyses show a clade composed of A. lineae sp. nov., H. terrae, and B. soyaensis, suggesting that a cytopharynx with argyrophilic structures might be their synapomorphy. A list of species with this type of cytopharynx is provided for further studies to either accept or reject this hypothesis. Based on the reexamination, we discriminate the morphologically nearly identical (cryptic/sibling) species H. obliquocirratus sp. nov. from H. heterotypicus and they show significant genetic dissimilarities in the multigene trees. They showed only few morphological (non-quantitative) differences and thus distinguishing them morphologically needs careful investigation.
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Affiliation(s)
- Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea.
| | - Atef Omar
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea; Department of Zoology, Al-Azhar University, Assiut 71524, Egypt
| | - Kang-San Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Seung-Chae Kang
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Dong-Yoon Kwak
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Jun-Hyeok Sun
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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Monographic treatment of Paraholosticha muscicola (Ciliophora, Keronopsidae), including morphological and molecular biological characterization of a brackish water population from Korea. Eur J Protistol 2019; 68:48-67. [DOI: 10.1016/j.ejop.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
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Jung JH, Park KM, Min GS. Morphology and Molecular Phylogeny of Pseudocyrtohymena koreana
n. g., n. sp. and Antarctic Neokeronopsis asiatica
Foissner et al., 2010 (Ciliophora, Sporadotrichida), with a Brief Discussion of the Cyrtohymena
Undulating Membranes Pattern. J Eukaryot Microbiol 2014; 62:280-97. [DOI: 10.1111/jeu.12179] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Jae-Ho Jung
- Department of Biological Sciences; Inha University; Incheon 402-751 South Korea
| | - Kyung-Min Park
- Department of Biological Sciences; Inha University; Incheon 402-751 South Korea
| | - Gi-Sik Min
- Department of Biological Sciences; Inha University; Incheon 402-751 South Korea
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11
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The symbiotic intestinal ciliates and the evolution of their hosts. Eur J Protistol 2014; 50:166-73. [DOI: 10.1016/j.ejop.2014.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022]
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12
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Xia Y, Kong YH, Seviour R, Forster RJ, Kisidayova S, McAllister TA. Fluorescence in situ hybridization probing of protozoal Entodinium spp. and their methanogenic colonizers in the rumen of cattle fed alfalfa hay or triticale straw. J Appl Microbiol 2013; 116:14-22. [PMID: 24118832 DOI: 10.1111/jam.12356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/12/2013] [Accepted: 09/23/2013] [Indexed: 11/30/2022]
Abstract
AIMS To develop and test a fluorescence in situ hybridization (FISH) based technique and to identify and quantify simultaneously those methanogenic populations colonizing Entodinium spp. in the rumen of cows fed different forages. METHODS AND RESULTS New FISH probes targeting protozoal Entodinium spp. were designed and used together with FISH probes for methanogens in the cow rumen. The composition and relative abundance of methanogenic populations colonizing Entodinium simplex-, E. caudaum- and Entodinium furca-related populations were similar. Methanogens including Methanobrevibacter thaueri, Methanobrevibacter millerae and Methanobrevibacter smithii, and members of Methanomicrobium and Methanosphaera were generally the predominant colonizers of protozoa, regardless of the forage fed to cattle. Individual animals appeared to differ in which ruminal methanogenic populations colonized each of the individual Entodinium spp. CONCLUSIONS Simultaneous FISH probing is shown here to be a reliable and effective approach to investigate the dynamics of symbiotic relationships between ruminal protozoa and methanogens at a single cell level. Phylogenetically closely related Entodinium spp. were colonized by similar methanogenic populations regardless of the forage fed. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of the methanogenic archaeal populations that specifically colonize Entodinium spp. as identified using simultaneous FISH probing.
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Affiliation(s)
- Y Xia
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada; Department of Biological Science and Technology, Kunming University, Kunming, China
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Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium. Mol Phylogenet Evol 2012; 65:1004-13. [DOI: 10.1016/j.ympev.2012.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/12/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022]
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14
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Agatha S, Strüder-Kypke MC. Reconciling Cladistic and Genetic Analyses in Choreotrichid Ciliates (Ciliophora, Spirotricha, Oligotrichea). J Eukaryot Microbiol 2012; 59:325-50. [DOI: 10.1111/j.1550-7408.2012.00623.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/23/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology; University of Salzburg; Hellbrunnerstraße 34; A-5020; Salzburg; Austria
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15
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Intraspecific variability in several isolates of Philasterides dicentrarchi (syn. Miamiensis avidus), a scuticociliate parasite of farmed turbot. Vet Parasitol 2011; 175:260-72. [DOI: 10.1016/j.vetpar.2010.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 09/28/2010] [Accepted: 10/08/2010] [Indexed: 11/23/2022]
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16
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Bochdansky AB, Huang L. Re-evaluation of the EUK516 probe for the domain eukarya results in a suitable probe for the detection of kinetoplastids, an important group of parasitic and free-living flagellates. J Eukaryot Microbiol 2010; 57:229-35. [PMID: 20236188 DOI: 10.1111/j.1550-7408.2010.00470.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two frequently used universal eukaryote probes, EUK1209 and EUK516, are not consistent with one branch of the eukaryotic phylogenetic tree, the Kinetoplastida, which has undergone rapid evolution of their small subunit rRNA gene. Kinetoplastids include medically important parasitic organisms (e.g. Trypanosoma, Leishmania) and free-living flagellates that occur in all aquatic environments and in soils (e.g. Bodo, Neobodo, Rhynchomonas). A modified probe presented here as KIN516, now based on the kinetoplastid sequence, provides a strong signal with Neobodo designis, Leishmania donovani, and Trypanosoma cruzi using the catalyzed reporter deposition protocol. EUK516 and KIN516 function as competitor probes, thereby greatly increasing discriminatory power when used in combination. The probe pair was tested in field samples collected in a freshwater pond in Norfolk, the mesohaline Elizabeth River, Norfolk, Virginia, and a tropical lagoon in Belize. The combined probes bound to 58-84% of organisms identified as eukaryotic based on having large DAPI-stained nuclei. The contribution of kinetoplastids to total eukaryotes (positive signal of EUK516+KIN516) was much higher in marine samples (ca. 17%) than in either the freshwater or brackish water sites (<0.2%).
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Affiliation(s)
- Alexander B Bochdansky
- Department of Ocean Earth and Atmospheric Sciences, Old Dominion University, 4600 Elkhorn Avenue, Norfolk, Virginia 23529, USA.
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17
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Lynn DH, Pinheiro M. A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR. J Eukaryot Microbiol 2009; 56:406-12. [PMID: 19737192 DOI: 10.1111/j.1550-7408.2009.00439.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We surveyed a variety of studies that have used single-cell polymerase chain reaction (SC-PCR) to examine the gene sequences of a diversity of unicellular protists. Representatives of all the Super-Groups of eukaryotes have been subjected to SC-PCR with ciliates and dinoflagellates being most commonly examined. The SC-PCR was carried out either by directly amplifying a single lysed cell or by first extracting DNA and following this with amplification of the DNA extract. Cell lysis methods included heating, freezing, mechanical rupture, and enzyme digestion. Cells fixed or preserved with ethanol, methanol, and Lugol's have also been used successfully. Heminested or seminested PCR might follow the initial PCR, whose products were then directly sequenced or cloned and then sequenced. The methods are not complicated. This should encourage protistologists to use SC-PCR in the description of new or revised taxa, especially rare and unculturable forms, and it should also enable the probing of gene expression in relation to life history stages.
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Affiliation(s)
- Denis H Lynn
- Department of Integrative Biology, University of Guelph, Ontario, Canada.
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18
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Ammermann D. Cell size and dorsal cilia: Are they useful features for the identification of Stylonychia mytilus (Ciliophora, Spirotrichea) and its subpopulations? Eur J Protistol 2008; 44:263-8. [DOI: 10.1016/j.ejop.2008.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/19/2008] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
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19
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Schmidt SL, Foissner W, Schlegel M, Bernhard D. Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences. J Eukaryot Microbiol 2008; 54:358-63. [PMID: 17669161 DOI: 10.1111/j.1550-7408.2007.00269.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive molecular analysis of the phylogenetic relationships within the Heterotrichea including all described families is still lacking. For this reason, the complete nuclear small subunit (SSU) rDNA was sequenced from further representatives of the Blepharismidae and the Stentoridae. In addition, the SSU rDNA of a new, undescribed species of the genus Condylostomides (Condylostomatidae) was sequenced. The detailed phylogenetic analyses revealed a consistent branching pattern: while the terminal branches are generally well resolved, the basal relationships remain unsolved. Moreover, the data allow some conclusions about the macronuclear evolution within the genera Blepharisma, Stentor, and Spirostomum suggesting that a single, compact macronucleus represents the ancestral state.
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Affiliation(s)
- Stephanie L Schmidt
- Molekulare Evolution und Systematik der Tiere, Universität Leipzig, Leipzig 04103, Germany.
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20
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Barth D, Tischer K, Berger H, Schlegel M, Berendonk TU. High mitochondrial haplotype diversity of Coleps sp. (Ciliophora: Prostomatida). Environ Microbiol 2008; 10:626-34. [PMID: 18190514 DOI: 10.1111/j.1462-2920.2007.01486.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To date the awareness of the temporal population structure in eukaryotic microbes is very limited. This is exemplified in the scarce knowledge about the intraspecific genetic variation in ciliates. To elucidate the genetic variation of Coleps (Ciliophora: Prostomatida), we employed the analysis of the mitochondrial apocytochrome b gene of the Coleps community in a young lake in Germany. The analysis of 111 isolates, sampled from April 2005 to September 2006, revealed a high genetic variation for the two dominant Coleps species (11 mitochondrial haplotypes in Coleps spetai, nine in Coleps hirtus hirtus). The study represents one of the largest datasets of intraspecific diversity in a microbial eukaryote and demonstrates for the first time the suitability of a mitochondrial gene for the detection of genetic variation within populations of eukaryotic microbes. However, the results of our study warrant caution in the application of such an approach, as we amplified some non-orthologous cob-like sequences, whose uncritical acceptance would have led to the erroneous discovery of cryptic species.
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Affiliation(s)
- Dana Barth
- Molecular Evolution and Animal Systematics, Institute of Biology II, University of Leipzig, 04103 Leipzig, Germany.
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21
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Stoeck T, Bruemmer F, Foissner W. Evidence for local ciliate endemism in an alpine anoxic lake. MICROBIAL ECOLOGY 2007; 54:478-86. [PMID: 17323118 DOI: 10.1007/s00248-007-9213-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 12/05/2006] [Accepted: 01/17/2007] [Indexed: 05/14/2023]
Abstract
Despite its long history, biogeography has received relatively little attention within the field of microbial ecology. Consequently, a fierce debate rages whether protists inhabit restricted geographic areas (endemism hypothesis) or are globally dispersed (ubiquitous dispersal hypothesis). The data presented in this article support the endemism hypothesis. We succeeded in isolating an oligohymenophorean ciliate from a microbial mat in a meromictic anoxic alpine lake (Alatsee) in Germany. The ciliary pattern and the morphometry of this isolate are remarkably similar to Urocentrum turbo (Mueller, 1786) Nitzsch, 1827. However, the organism does not possess trichocysts, a conspicuous and characteristic feature of U. turbo. Instead, the U. turbo-like isolate from lake Alatsee displays merely trichocyst anlagen ("ghosts") in the cytoplasm that are only visible after protargol impregnation and which become never attached to the cell's cortex. Despite the distinctness of this difference, such a morphospecies has not been described from any other environment. Thus, we suggest that the U. turbo-like isolate from lake Alatsee is a local endemic ecotype, although the sequences of the 18S rRNA, ITS1, 5.8S rRNA, and ITS2 genes are nearly identical to those of U. turbo (Mueller, 1786) Nitzsch, 1827. This indicates that neither 18S rDNA nor ITS1, ITS2, and 5.8S rDNA sequences are reliable means to conclusively resolve different morphospecies or ecotypes of ciliates. As a consequence, we argue that protist species richness can only be reliably accounted for by considering both molecular and morphological data.
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MESH Headings
- Animals
- Ciliophora/genetics
- Ciliophora/growth & development
- Ciliophora/ultrastructure
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal Spacer/genetics
- Fresh Water/parasitology
- Germany
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Thorsten Stoeck
- Universität Kaiserslautern, FB Biologie, Erwin Schroedinger Str. 14, 67633, Kaiserslautern, Germany.
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22
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Miao M, Song W, Chen Z, Al-Rasheid KAS, Shao C, Jiang J, Guo W. A Unique Euplotid Ciliate, Gastrocirrhus (Protozoa, Ciliophora): Assessment of Its Phylogenetic Position Inferred from the Small Subunit rRNA Gene Sequence. J Eukaryot Microbiol 2007; 54:371-8. [PMID: 17669163 DOI: 10.1111/j.1550-7408.2007.00271.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The morphologically unique genus Gastrocirrhus has been considered a distinct but systematically uncertain euplotid due to the absence of both morphogenetic and molecular information. Based on the small subunit rRNA gene sequence, the phylogenetic position of Gastrocirrhus monilifer Ozaki & Yagui, 1942 was re-addressed using multiple algorithms (neighbor-joining, maximum parsimony, least-squares, and Bayesian inference methods). Results indicate that: (1) all phylogenetic trees using different methods are nearly identical in topology, placing G. monilifer closest to Euplotidium arenarium; (2) Gastrocirrhus and Euplotidium form a monophyletic group, namely the family Gastrocirrhidae, and appear to be intermediate taxa bridging the evolution of the Diophrys-Uronychia and Euplotes-complexes (i.e. Euplotes, Certesia, and Aspidisca); (3) the order Euplotida is a paraphyletic group composed of three deeply diverged clades (Euplotes-Certesia-Aspidisca-Gastrocirrhus-Euplotidium; Uronychia-Diophrys; and Prodiscocephalus); (4) together with Prodiscocephalus, the Diophrys-Uronychia complex forms a group at the suborder level and is placed at the root of the order Euplotida, and (5) results from molecular analyses conspicuously challenge the conclusions deduced from morphological as well as morphogenetical investigations-the characteristics traditionally used to define the euplotid taxa at the generic level and/or above may not be uniformly reliable.
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Affiliation(s)
- Miao Miao
- Laboratory of Protozoology, KLM, Ocean University of China, Qingdao 266003, China
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23
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Fried J, Foissner W. Differentiation of Two Very Similar Glaucomid Ciliate Morphospecies (Ciliophora, Tetrahymenida) by Fluorescence in Situ Hybridization with 18S rRNA Targeted Oligonucleotide Probes. J Eukaryot Microbiol 2007; 54:381-7. [PMID: 17669165 DOI: 10.1111/j.1550-7408.2007.00277.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conventional, morphological identification of ciliates and other protozoa needs considerable experience and often is difficult as various staining methods must be applied. New molecular techniques, such as fluorescence in situ hybridization (FISH) with gene probes, are powerful means to overcome this problem. As a test case, the morphology of two very similar, and thus difficult to differentiate ciliate morphospecies, Glaucoma scintillans and Glaucomides bromelicola, were compared. They were then distinguished by applying the Ciliate-FISH technique with a set of eight 18S rRNA targeted oligonucleotide probes, four of which have been developed for specific detection of G. scintillans. The remaining four probes were designed to detect G. bromelicola in order to prove probe specificities by binding to the homologous target region of the probes mentioned before. The tests resulted in a clear and easy differentiation of the two species by fluorescence signals of three of the four tested probe pairs. Thus, FISH techniques are very useful for the identification and detection of protozoa and might be of great help studying geographical distributions of known taxa.
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Affiliation(s)
- Johannes Fried
- Technische Universität München, Lehrstuhl für Mikrobiologie, Am Hochanger 4, 85350 Freising, Germany.
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24
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Schmidt SL, Bernhard D, Schlegel M, Foissner W. Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) Reconstructed with Nuclear Small Subunit rRNA Gene Sequences: Discrepancies and Accordances with Morphological Data. J Eukaryot Microbiol 2007; 54:201-9. [PMID: 17403161 DOI: 10.1111/j.1550-7408.2007.00250.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Stichotrichia, known as an especially various and taxonomically difficult group, were intensely studied with morphological, morphogenetic, and molecular methods in the last years. Nevertheless, a consistent classification is lacking and several important questions about the phylogenetic relationships within this group remain unsolved. In order to gain deeper insights into these relationships, the nuclear small subunit rRNA genes of seven species of the Stichotrichia, representatives of the families Oxytrichidae, Amphisiellidae, and Pseudourostylidae, were phylogenetically analysed. Although our analyses resulted in a poor resolution of the phylogenetic relationships, some conclusions can be drawn. Firstly, following the current classification systems the Oxytrichidae as well as their subfamilies seem to be paraphyletic and the basic 18 FVT cirral pattern has been modified several times independently. Secondly, sequence analyses of several Oxytricha species resulted in a high molecular diversity, which does not support monophyly of this genus. Thirdly, several families of the order Urostylida (Urostylidae, Pseudokeronopsidae, and Pseudourostylidae) also do not form monophyletic groups.
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Affiliation(s)
- Stephanie L Schmidt
- Molekulare Evolution und Systematik der Tiere, Universität Leipzig, Leipzig 04103, Germany.
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25
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Modeo L, Rosati G, Andreoli I, Gabrielli S, Verni F, Petroni G. Molecular systematics and ultrastructural characterization of a forgotten species: Chattonidium setense (Ciliophora, Heterotrichea). PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2006; 82:359-74. [PMID: 25792797 PMCID: PMC4338841 DOI: 10.2183/pjab.82.359] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 10/26/2006] [Indexed: 06/04/2023]
Abstract
In the present paper we redescribe the ciliate Chattonidium setense Villeneuve 1937 combining morphological observations (live, stained, scanning, and transmission electron microscope) with behavioral notes and molecular data. Ultrastructural analysis revealed remarkable similarities between Chattonidium and representative members of the class Heterotrichea in cortical structure and cytoplasmic organization. The most similar genus for these aspects appears to be Condylostoma. To verify this relatedness, 18S rRNA genes from Chattonidium and from one Condylostoma species were sequenced. Phylogenetic analysis indicates Chattonidium belongs to the class Heterotrichea defined according to the modern taxonomy, and confirms its relatedness with Condylostoma already hypothesized by Villeneuve-Brachon (1940). The presence of the aboral cavity complex, a unique feature never described in other ciliates, and its peculiar organization revealed by ultrastructural analysis fully justify, in our opinion, the maintenance of Chattonidium in the separate family Chattonidiidae, established by Villeneuve-Brachon in 1940.
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Affiliation(s)
- Letizia Modeo
- Unità di Protistologia-Zoologia, Dipartimento di Biologia, Pisa,
Italy
| | - Giovanna Rosati
- Unità di Protistologia-Zoologia, Dipartimento di Biologia, Pisa,
Italy
| | - Ilaria Andreoli
- Unità di Protistologia-Zoologia, Dipartimento di Biologia, Pisa,
Italy
| | - Simone Gabrielli
- Unità di Protistologia-Zoologia, Dipartimento di Biologia, Pisa,
Italy
| | - Franco Verni
- Unità di Protistologia-Zoologia, Dipartimento di Biologia, Pisa,
Italy
| | - Giulio Petroni
- Correspondence to: Giulio Petroni, Unità di Protistologia-Zoologia, Dipartimento di Biologia, Via A. Volta 4–6, 56126 Pisa, Italy (e-mail: )
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26
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Haentzsch M, Schmidt SL, Bernhard D, Ammermann D, Berendonk TU, Schlegel M. A PCR-Based Method to Distinguish the Sibling Species Stylonychia mytilus and Stylonychia lemnae (Ciliophora, Spirotrichea) Using Isocitrate Dehydrogenase Gene Sequences. J Eukaryot Microbiol 2006; 53:343-7. [PMID: 16968451 DOI: 10.1111/j.1550-7408.2006.00111.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.
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Affiliation(s)
- Madlen Haentzsch
- Institute of Biology II, Molecular Evolution and Animal Systematics, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany.
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27
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Schmidt SL, Ammermann D, Schlegel M, Bernhard D. Stylonychia lemnae Strains from a North American Site Differ in a Single Nucleotide within the Small Subunit rDNA from Eurasian Strains. J Eukaryot Microbiol 2006; 53:308-9. [PMID: 16872299 DOI: 10.1111/j.1550-7408.2006.00105.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Stylonychia lemnae (Ciliophora, Spirotrichea), a member of the Stylonychia mytilus complex, shows a global distribution, occurring in many temperate fresh waters. As there are few descriptions of biogeographical patterns of ubiquitously occurring ciliated protozoans, we report a distinct sequence difference within the small subunit ribosomal DNA gene, which occurs only in the clones of S. lemnae isolated from the surroundings of Ithaca (USA) in comparison with clones of the same species from different regions in Europe, Asia, and South Africa.
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Affiliation(s)
- Stephanie L Schmidt
- Department of Molecular Evolution and Animal Systematics, University of Leipzig, Leipzig 04103, Germany.
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