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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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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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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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Wu T, Cheng T, Cao X, Jiang Y, Al-Rasheid KAS, Warren A, Wang Z, Lu B. On four epibiotic peritrichous ciliates (Protozoa, Ciliophora) found in Lake Weishan Wetland: morphological and molecular data support the establishment of a new genus, Parapiosoma gen. nov., and two new species. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:337-358. [PMID: 37637257 PMCID: PMC10449748 DOI: 10.1007/s42995-023-00184-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/21/2023] [Indexed: 08/29/2023]
Abstract
During a study on the diversity of ciliated protists in Lake Weishan Wetland, the largest wetland in northern China, four epibiotic sessilid peritrichs were isolated from aquatic host animals. Two of them, i.e., Epistylis cambari Kellicott, 1885 and Epistylis lwoffi Fauré-Fremiet, 1943, were known species whereas the other two, i.e., Parapiosoma typicum gen. nov., sp. nov. and Orborhabdostyla gracilis sp. nov., are new to science. The new genus Parapiosoma gen. nov. is characterized by its branched non-contractile stalk, everted peristomial lip, obconical macronucleus and transverse silverlines. Two species are assigned to the new genus, namely Parapiosoma typicum sp. nov. and Parapiosoma gasterostei (Fauré-Fremiet, 1905) comb. nov. Morphologically, P. typicum sp. nov. is recognized by its goblet-shaped zooids, single-layered peristomial lip, dichotomously branched stalk, and infundibular polykinety 3 (P3) containing three equal-length rows. Orborhabdostyla gracilis sp. nov. is characterized by its slender zooid, curved macronucleus, and three equal-length rows in infundibular P3. Improved diagnoses and redescriptions of E. cambari and E. lwoffi are provided including, for the first time, data on the ciliature of E. cambari. Phylogenetic analyses based on SSU rDNA, ITS1-5.8S rDNA -ITS2, and LSU rDNA sequence data strongly support the assertion that the family Epistylididae comprises morphospecies with different evolutionary lineages and indicate that Parapiosoma gen. nov. may represent a new taxon at family level.
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Affiliation(s)
- Tong Wu
- Marine College, Shandong University, Weihai, 264209 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Ting Cheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao Cao
- Weishan Fishery Development Service Center, Jining, 277600 China
| | - Yaohan Jiang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | | | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Zhe Wang
- Marine College, Shandong University, Weihai, 264209 China
| | - Borong Lu
- 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: 8.0] [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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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: 1.0] [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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