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Pomahač O, Méndez-Sánchez D, Čepička I. Bit by bit toward the diversity of metopids: Description of the genus Pidimetopus n. gen. (Ciliophora: Armophorea). J Eukaryot Microbiol 2024; 71:e13034. [PMID: 38822648 DOI: 10.1111/jeu.13034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/23/2024] [Accepted: 05/03/2024] [Indexed: 06/03/2024]
Abstract
While metopids (Armophorea: Metopida) represent the most species-rich group of free-living anaerobic ciliates thriving in hypoxic environments, our understanding of their true diversity remains incomplete. Most metopid species are still characterized only morphologically. Particularly, the so-called IAC clade (named in the past after some of the taxa included, Idiometopus, Atopospira, and Clevelandellida), comprising free-living members as well as the endosymbiotic ones (order Clevelandellida), is in serious need of revision. In our study, we establish a new free-living genus in the IAC clade, Pidimetopus n. gen., with descriptions of two new species, P. nanus n. sp., and P. permonicus n. sp., using up-to-date molecular and morphologic methods. The genus is characterized by small cells (up to 75 μm long), not more than 10 adoral membranelles and eight somatic kineties, and usually, four long caudal cilia that can stiffen. In addition to morphologic and molecular characterizations, we also conducted a statistical morphotype analysis of the polymorphic species P. nanus n. sp. We discuss the relevance of the earlier morphologically described species Metopus minor as a putative collective taxon for several small metopids less than 50 μm long.
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Affiliation(s)
- Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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2
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Feng X, Méndez-Sánchez D, Zhuang W, Li R, Pomahač O, Čepička I, Rotterová J, Hu X. Morphology, morphogenesis, and molecular characterization of Castula specialis sp. nov. (Ciliophora, Armophorea, Metopida). J Eukaryot Microbiol 2024; 71:e13014. [PMID: 38018748 DOI: 10.1111/jeu.13014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
The morphology, morphogenesis, and molecular phylogeny of a new metopid ciliate, Castula specialis sp. nov., comprising three strains from geographically distant (China, Mexico, Czech Republic) anoxic freshwater habitats, were studied based on microscopic observation of live and protargol-stained specimens as well as SSU rRNA gene sequence data. The new species is characterized as follows: size in vivo 105-220 × 25-70 μm, body oblong to elongated ellipsoidal and asymmetrical; preoral dome distinctly projecting beyond the body; 32-46 adoral membranelles; 31-52 somatic kineties; and 4-7 setae. This study brings the first morphogenetic investigation of a member of the genus Castula. The morphogenesis of the type population (China) of the new species proceeds as in Metopus spp. comprising drastic changes in body shape and a pleurotelokinetal stomatogenesis; however, the main difference is the origin of the opisthe's paroral membrane that derives from all perizonal rows and some adjacent dome kineties. Phylogenetically, the genus Castula is paraphyletic.
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Affiliation(s)
- Xiaochen Feng
- College of Fisheries, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Wenbao Zhuang
- College of Fisheries, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Ran Li
- College of Fisheries, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Xiaozhong Hu
- College of Fisheries, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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3
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Rotterová J, Pánek T, Salomaki ED, Kotyk M, Táborský P, Kolísko M, Čepička I. Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade. Mol Phylogenet Evol 2024; 191:107991. [PMID: 38092322 DOI: 10.1016/j.ympev.2023.107991] [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: 09/09/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates - Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic; Department of Marine Sciences, University of Puerto Rico Mayagüez, Mayagüez, PR, USA.
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Michael Kotyk
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic.
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Zhuang W, Feng X, Li R, Al-Farraj SA, Hu X. Morphogenesis of an anaerobic ciliate Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 (Ciliophora, Armophorea) with notes on its morphological and molecular characterization. Protist 2024; 175:126007. [PMID: 38141417 DOI: 10.1016/j.protis.2023.126007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 12/25/2023]
Abstract
The morphology, morphogenesis, and molecular phylogeny of Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 were studied using microscopical observations on live and protargol-stained specimens as well SSU rRNA gene sequencing. The morphogenetic data for the genus are presented for the first time. Compared to other metopids, the morphogenesis of H. palaeformis is distinct since its (1) perizonal stripe rows 4 and 5 are involved in the formation of the opisthe's adoral polykinetids; (2) perizonal stripe rows 3-5 and two adjacent preoral dome kineties contribute to most of the opisthe's paroral membrane while perizonal stripe rows 1 and 2 contribute very little; (3) four kinety rows are formed to the left of the opisthe's adoral zone of polykinetids. The Chinese population resembles the original and neotype populations well in terms of general morphology - characterized by a life size of 55-120 × 10-20 μm, an elongate ellipsoidal body with a hardly spiralized flat preoral dome, about 18 somatic kineties and 20 adoral polykinetids. The SSU rDNA sequence of the present population exhibits a disparity of 1.33%-2.22% divergence from sequences of other populations. Nevertheless, phylogenetic analysis reveals that populations of H. palaeformis form a separate, stable cluster within the paraphyletic Metopidae clade.
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Affiliation(s)
- Wenbao Zhuang
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaochen Feng
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Ran Li
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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5
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Méndez-Sánchez D, Schrecengost A, Rotterová J, Koštířová K, Beinart RA, Čepička I. Methanogenic symbionts of anaerobic ciliates are host and habitat specific. THE ISME JOURNAL 2024; 18:wrae164. [PMID: 39163261 PMCID: PMC11378729 DOI: 10.1093/ismejo/wrae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/29/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024]
Abstract
The association between anaerobic ciliates and methanogenic archaea has been recognized for over a century. Nevertheless, knowledge of these associations is limited to a few ciliate species, and so the identification of patterns of host-symbiont specificity has been largely speculative. In this study, we integrated microscopy and genetic identification to survey the methanogenic symbionts of 32 free-living anaerobic ciliate species, mainly from the order Metopida. Based on Sanger and Illumina sequencing of the 16S rRNA gene, our results show that a single methanogenic symbiont population, belonging to Methanobacterium, Methanoregula, or Methanocorpusculum, is dominant in each host strain. Moreover, the host's taxonomy (genus and above) and environment (i.e. endobiotic, marine/brackish, or freshwater) are linked with the methanogen identity at the genus level, demonstrating a strong specificity and fidelity in the association. We also established cultures containing artificially co-occurring anaerobic ciliate species harboring different methanogenic symbionts. This revealed that the host-methanogen relationship is stable over short timescales in cultures without evidence of methanogenic symbiont exchanges, although our intraspecific survey indicated that metopids also tend to replace their methanogens over longer evolutionary timescales. Therefore, anaerobic ciliates have adapted a mixed transmission mode to maintain and replace their methanogenic symbionts, allowing them to thrive in oxygen-depleted environments.
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Affiliation(s)
- Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
| | - Anna Schrecengost
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, United States
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, United States
- Department of Marine Sciences, University of Puerto Rico Mayagüez, Mayagüez, PR 00680, United States
| | - Kateřina Koštířová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, United States
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
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Li R, Zhuang W, Feng X, Hines HN, Hu X. First redescription and molecular phylogeny of Trimyema claviforme Kahl, 1933 with the description of a Chinese population of Plagiopyla nasuta Stein, 1860 (Ciliophora, Plagiopylea). Eur J Protistol 2023; 90:126003. [PMID: 37453202 DOI: 10.1016/j.ejop.2023.126003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023]
Abstract
Ciliates belonging to the class Plagiopylea are obligate anaerobes that are often neglected due to their cryptic lifestyles, difficulty of observation, and overall under-sampling. Here, we investigate two species, namely Trimyema claviforme Kahl, 1933 and Plagiopyla nasuta Stein, 1860, collected in China from marine and freshwater anaerobic sediments, respectively. A complete morphological dataset, together with SSU rRNA gene sequence data were obtained and used to diagnose the species. No molecular sequencing had ever been performed on Trimyema claviforme, with its ciliature also previously unknown. Based on these novel data presented here, the ciliate is characterized by a claviform cell shape, with a size of 35-45 × 10-20 μm in vivo, 28-39 longitudinal somatic ciliary rows forming five ciliary girdles (four complete girdles and a shorter one), two dikinetids left to anterior end of oral kinety 1, and an epaulet. A Chinese population of the well-known ciliate P. nasuta was investigated, and morphological comparisons revealed phenotypic stability of the species. The phylogenetic analyses supported previous findings about the monophyly of the families Trimyemidae and Plagiopylidae, with Trimyema claviforme branching off early in the genus Trimyema. The Chinese population of P. nasuta clusters together with two other populations with full support corroborating their conspecificity.
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Affiliation(s)
- Ran Li
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wenbao Zhuang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaochen Feng
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hunter N Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida 34946, USA
| | - Xiaozhong Hu
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Li J, Li S, Su H, Yu M, Xu J, Yi Z. Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora). Mol Phylogenet Evol 2023; 182:107737. [PMID: 36841269 DOI: 10.1016/j.ympev.2023.107737] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.
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Affiliation(s)
- Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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8
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Méndez-Sánchez D, Pomahač O, Rotterová J, Bourland WA, Čepička I. Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora). J Eukaryot Microbiol 2023; 70:e12965. [PMID: 36727275 DOI: 10.1111/jeu.12965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/17/2022] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
The diversity of the classes Odontostomatea and Muranotrichea, which contain solely obligate anaerobes, is poorly understood. We studied two populations of Mylestoma sp., one of Saprodinium dentatum (Odontostomatea), two of Muranothrix felix sp. nov., and one of Muranothrix sp. (Muranotrichea) employing live observation, protargol impregnation, scanning electron microscopy, and 18S rRNA gene sequencing. Conspecificity of Mylestoma sp., described here, with a previously described species of this genus cannot be excluded since no species have been studied with modern methods. Phylogenetically, the genus Mylestoma is closely related to the odontostomatid Discomorphella pedroeneasi, although the phylogenetic position of class Odontostomatea itself remains unresolved. The newly described muranotrichean species, Muranothrix felix sp. nov., is morphologically similar to M. gubernata but can be distinguished by its fewer macronuclear nodules and fewer adoral membranelles; moreover, it is clearly distinguished from M. gubernata by its 18S rRNA gene sequence. Another population, designated here as Muranothrix sp., most likely represents a separate species.
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Affiliation(s)
- Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - William A Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Méndez-Sánchez D, Pomahač O, Rotterová J, Bourland W, Čepička I. Diversity and Phylogenetic Position of Bothrostoma Stokes, 1887 (Ciliophora: Metopida), with Description of Four New Species. Protist 2022; 173:125887. [PMID: 35714562 DOI: 10.1016/j.protis.2022.125887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/30/2022] [Accepted: 05/13/2022] [Indexed: 10/18/2022]
Abstract
Bothrostoma is a genus of anaerobic ciliates in family Metopidae comprising four species, all described based solely on the morphology of living and fixed cells. Unlike other metopids, cells of Bothrostoma are not twisted anteriorly, have a flattened preoral dome, a very prominent sail-like paroral membrane, and an adoral zone of distinctive, very narrow, curved membranelles confined to a wide, non-spiraling peristome on the ventral side. We examined 20 populations of Bothrostoma from hypoxic freshwater sediments. We provide morphological characterization and 18S rRNA gene sequences of four new species, namely B. bimicronucleatum sp. nov., B. boreale sp. nov., B. kovalyovi sp. nov., and B. robustum sp. nov., as well as B. undulans (type species), B. nasutum, and B. ovale comb. nov. (original combination Metopus undulans var. ovalis Kahl, 1932). Except for B. nasutum, Bothrostoma species show low genetic variability among geographically distant populations. Intraspecific phenotypic variability might be driven by environmental conditions. In phylogenetic analyses, Bothrostoma is not closely related to Metopus sensu stricto and forms a moderately supported clade with Planometopus, here referred to as BoPl clade. The anterior axial torsion of the body, typical of other Metopidae, appears to have been lost in the last common ancestor of the BoPl clade.
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Affiliation(s)
- Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic.
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
| | - William Bourland
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Vinična 7, 128 00 Prague, Czech Republic
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10
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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11
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Bourland W, Pomahač O, Čepička I. Morphology and phylogeny of two anaerobic freshwater ciliates: Brachonella comma sp. nov. and the widely-distributed but little-known caenomorphid, Ludio parvulus Penard, 1922. J Eukaryot Microbiol 2022; 69:e12892. [PMID: 35113477 DOI: 10.1111/jeu.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/16/2021] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
Abstract
Hypoxic, sulfidic freshwater sediments typically support a diffuse consortium of distinctive ciliated protists, including caenomorphids, metopids, and odontostomatids among others. A recent resurgence of interest in these important members of sapropelic food webs has resulted in the description of many new species and an effort, still in its infancy, to characterize them from a morphologic, molecular, and metabolic standpoint and to determine their phylogenetic relationships. Their seemingly invariable association with prokaryotic endosymbionts and, less commonly, ectosymbionts, has become a focus for many researchers. In this report, based on morphologic and molecular data we describe a Brachonella species (Ciliophora, Metopida) new to science and analyze its phylogeny. We also provide a morphologic and molecular characterization of the smallest representative of the Caenomorphidae Poche, 1913, Ludio parvulus Penard, 1922. The phylogenetic analysis confirms the inclusion of this species in the Caenomorphidae.
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Affiliation(s)
- William Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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12
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Zhuang W, Li S, Bai Y, Zhang T, Al-Rasheid KAS, Hu X. Morphology and molecular phylogeny of the anaerobic freshwater ciliate Urostomides spinosus nov. spec. (Ciliophora, Armophorea, Metopida) from China. Eur J Protistol 2021; 81:125823. [PMID: 34340055 DOI: 10.1016/j.ejop.2021.125823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 06/07/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
The morphology and molecular phylogeny of a new metopid ciliate, Urostomides spinosus nov. spec., discovered in a freshwater ditch in Qingdao, China, were investigated using live observation, morphometry and protargol staining as well as molecular phylogenetic methods. Diagnostic features of the new species include a broadly obpyriform body carrying three posterior spines, eight somatic kineties, five preoral dome kineties with specialized row 3, adoral zone composed of about 28 membranelles, making a 270° turn around body axis. Phylogenetic analyses of the SSU rDNA sequence revealed that the genus Urostomides is monophyletic, but its interspecific relationships remained unresolved. Moreover, a closer relationship of the new species with the morphologically similar Urostomides campanula was not supported by the molecular data.
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Affiliation(s)
- Wenbao Zhuang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Song Li
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yang Bai
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tengteng Zhang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Xiaozhong Hu
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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13
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Li S, Zhuang W, Pérez-Uz B, Zhang Q, Hu X. Two Anaerobic Ciliates (Ciliophora, Armophorea) from China: Morphology and SSU rDNA Sequence, with Report of a New Species, Metopus paravestitus nov. spec. J Eukaryot Microbiol 2020; 68:e12822. [PMID: 32770809 DOI: 10.1111/jeu.12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/19/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
Abstract
The morphology and phylogeny of two metopid ciliates, collected from anaerobic habitats in China, were investigated using live observation, protargol staining method, and SSU rDNA sequencing. The new species Metopus paravestitus nov. spec. can be distinguished by a combination of the following features: oblong cell with densely arranged ectobiotic prokaryotes perpendicular to cell surface, filiform intracytoplasmic structures packed in the anterior portion of the cell. Our work also demonstrates the wide geographical distribution of Metopus es (Müller, 1776) Lauterborn, 1916. The order Metopida is consistently depicted as a paraphylum in SSU rDNA phylogeny. Metopus paravestitus nov. spec. is closely related to its marine congeners than to freshwater forms. The present study confirms once again the non-monophyly of the genus Metopus and genus Metopidae.
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Affiliation(s)
- Song Li
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Wenbao Zhuang
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Blanca Pérez-Uz
- Department of Genetics, Physiology & Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaozhong Hu
- Institute of Evolution and Marine Biodiversity & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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14
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Bourland W, Rotterová J, Čepička I. Description of Three New Genera of Metopidae (Metopida, Ciliophora): Pileometopus gen. nov., Castula gen. nov., and Longitaenia gen. nov., with Notes on the Phylogeny and Cryptic Diversity of Metopid Ciliates. Protist 2020; 171:125740. [PMID: 32544844 DOI: 10.1016/j.protis.2020.125740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/19/2020] [Accepted: 04/29/2020] [Indexed: 01/22/2023]
Abstract
We report the discovery of three new species of freshwater metopid ciliates, Pileometopus lynni gen. et sp. nov., Castula flexibilis gen. et sp. nov., and Longitaenia australis gen. et sp. nov. Based on morphologic features and the 18S rRNA gene phylogeny, we transfer two known species of Metopus to the new genus Castula, as C. fusca (Kahl, 1927) comb. nov. and C. setosa (Kahl, 1927) comb. nov. and another known species is herein transferred to the new genus Longitaenia, as L. gibba (Kahl, 1927) comb. nov. Pileometopus is characterized by a turbinate body shape, a dorsal field of densely spaced dikinetids, a bipartite paroral membrane, and long caudal cilia. A distinctive morphologic feature of Castula species is long setae arising over the posterior third of the body (as opposed to a terminal tuft). Longitaenia spp. are characterized by an equatorial cytostome and long perizonal ciliary stripe relative to the cell length. Based on phylogenetic analyses of 18S rRNA gene sequences, we identify and briefly discuss strongly supported clades and intraspecific genetic polymorphism within the order Metopida.
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Affiliation(s)
- William Bourland
- Boise State University, Department of Biological Sciences, Boise, Idaho 83725-1515, USA.
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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15
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Luo X, Huang JA, Li L, Song W, Bourland WA. Phylogeny of the ciliate family Psilotrichidae (Protista, Ciliophora), a curious and poorly-known taxon, with notes on two algae-bearing psilotrichids from Guam, USA. BMC Evol Biol 2019; 19:125. [PMID: 31215407 PMCID: PMC6582579 DOI: 10.1186/s12862-019-1450-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/30/2019] [Indexed: 11/27/2022] Open
Abstract
Background The classification of the family Psilotrichidae, a curious group of ciliated protists with unique morphological and ontogenetic features, is ambiguous and poorly understood particularly due to the lack of molecular data. Hence, the systematic relationship between this group and other taxa in the subclass Hypotrichia remains unresolved. In this paper the morphology and phylogenetics of species from two genera of Psilotrichida are studied to shed new light on the phylogeny and species diversity of this group of ciliates. Results The 18S rRNA gene sequences of species from two psilotrichid genera were obtained. In the phylogenetic trees, the available psilotrichid sequences are placed in a highly supported clade, justifying the establishment of the family Psilotrichidae. The morphology of two little-known species, packed with green algae, including a new species, Hemiholosticha kahli nov. spec., and Psilotrichides hawaiiensis Heber et al., 2018, is studied based on live observation, protargol impregnation, and scanning electron microscopy. Both species are easily recognized by their green coloration due to the intracellular algae, and a comprehensive discussion as to the possible roles of the intracellular algae is provided. Conclusions The 18S rRNA gene phylogeny supports the morphological argument that Hemiholosticha, Psilotrichides and Urospinula belong to the same family, Psilotrichidae. However, the single-gene analysis, not surprisingly, does not resolve the deeper relationships of Psilotrichidae within the subclass Hypotrichia. Two little-known psilotrichid genera with green algae were collected from the same puddle on the island of Guam, indicating a high species diversity and broader geographic distribution of this group of ciliates than previously supposed. Phylogenetic inferences from transcriptomic and/or genomic data will likely be necessary to better define the systematic position and evolution of the family Psilotrichidae. Further studies are also needed to clarify the role of the intracellular eyespot-bearing algae in these ciliates. Electronic supplementary material The online version of this article (10.1186/s12862-019-1450-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaotian Luo
- 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, ID, 83725, USA
| | - Jie A Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lifang Li
- Marine College, Shandong University, Weihai, 264209, China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - William A Bourland
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA.
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Vďačný P, Foissner W. A huge diversity of metopids (Ciliophora, Armophorea) in soil from the Murray River floodplain, Australia. III. Morphology, ontogenesis and conjugation of Metopus boletus nov. spec., with implications for the phylogeny of the SAL supercluster. Eur J Protistol 2019; 69:117-137. [DOI: 10.1016/j.ejop.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 02/02/2023]
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17
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Bourland W, Rotterová J, Čepička I. Morphologic and molecular characterization of Brachonella pulchra (Kahl, 1927) comb. nov. (Armophorea, Ciliophora) with comments on cyst structure and formation. Int J Syst Evol Microbiol 2018; 68:3052-3065. [DOI: 10.1099/ijsem.0.002888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- William Bourland
- 1Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
| | - Johana Rotterová
- 2Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- 2Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Molecular phylogeny and comparative morphology indicate that odontostomatids (Alveolata, Ciliophora) form a distinct class-level taxon related to Armophorea. Mol Phylogenet Evol 2018; 126:382-389. [DOI: 10.1016/j.ympev.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022]
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The Little-known Freshwater Metopid Ciliate, Idiometopus turbo (Dragesco and Dragesco-Kernéis, 1986) nov. gen., nov. comb., Originally Discovered in Africa, Found on the Micronesian Island of Guam. Protist 2018; 169:494-506. [DOI: 10.1016/j.protis.2018.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 11/24/2022]
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20
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Vďačný P, Rajter Ľ, Stoeck T, Foissner W. A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids. J Eukaryot Microbiol 2018; 66:167-181. [PMID: 29873141 DOI: 10.1111/jeu.12641] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 11/30/2022]
Abstract
Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology-based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free-living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ľubomír Rajter
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Wilhelm Foissner
- FB Ecology and Evolution, University of Salzburg, Salzburg, Austria
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Tropidoatractidae fam. nov., a Deep Branching Lineage of Metopida (Armophorea, Ciliophora) Found in Diverse Habitats and Possessing Prokaryotic Symbionts. Protist 2018; 169:362-405. [DOI: 10.1016/j.protis.2018.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
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22
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Description of two species of caenomorphid ciliates (Ciliophora, Armophorea): Morphology and molecular phylogeny. Eur J Protistol 2017; 61:29-40. [DOI: 10.1016/j.ejop.2017.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 08/07/2017] [Indexed: 11/18/2022]
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23
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Morphologic and molecular characterization of seven species of the remarkably diverse and widely distributed metopid genus Urostomides Jankowski, 1964 (Armophorea, Ciliophora). Eur J Protistol 2017; 61:194-232. [DOI: 10.1016/j.ejop.2017.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 11/17/2022]
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24
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Omar A, Zhang Q, Zou S, Gong J. Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis
n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria. J Eukaryot Microbiol 2017; 64:792-805. [DOI: 10.1111/jeu.12411] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Atef Omar
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences; Yantai 264003 China
- Department of Zoology; Al-Azhar University; Assiut 71524 Egypt
| | - Qianqian Zhang
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences; Yantai 264003 China
| | - Songbao Zou
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences; Yantai 264003 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jun Gong
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences; Yantai 264003 China
- University of Chinese Academy of Sciences; Beijing 100049 China
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