1
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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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2
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Li J, Wang J, He X, Gu H, Xu X, Liang C, Wang Y, Xu X, Jia L, Chen J, Jiang M, Chen J. The ciliate Euplotes balteatus is resistant to Paralytic Shellfish Toxins from Alexandrium minutum (Dinophyceae). WATER RESEARCH X 2024; 23:100229. [PMID: 39099803 PMCID: PMC11294722 DOI: 10.1016/j.wroa.2024.100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 08/06/2024]
Abstract
Research on interactions between grazers and toxigenic algae is fundamental for understanding toxin dynamics within aquatic ecosystems and developing biotic approaches to mitigate harmful algal blooms. The dinoflagellate Alexandrium minutum is a well-known microalga responsible for paralytic shellfish toxins (PSTs) contamination in many coastal regions worldwide. This study investigated the impact of the ciliate Euplotes balteatus on cell density and PSTs transfer in simulated A. minutum blooms under controlled conditions. E. balteatus exhibited resistance to the PSTs produced by A. minutum with a density of up to 10,000 cells/mL, sustaining growth and reproduction while eliminating algal cells within a few days. The cellular PSTs content of A. minutum increased in response to the grazing pressure from E. balteatus. However, due to the substantial reduction in density, the overall toxicity of the algal population decreased to a negligible level. Most PSTs contained within algal cells were temporarily accumulated in E. balteatus before being released into the water column, suggesting unclear mechanisms for PSTs excretion in unicellular grazers. In principle, the grazing of E. balteatus on A. minutum promotes the transfer of the majority of intracellular PSTs into extracellular portions, thereby mitigating the risk of their accumulation and contamination through marine trophic pathways. However, this process also introduces an increase in the potential environmental hazards posed by extracellular PSTs to some extent.
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Affiliation(s)
- Jing Li
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Jinrong Wang
- The Second Geological Institute, China Metallurgical Geology Bureau, Fuzhou, 350108, China
| | - Xiuping He
- Key Laboratory for Marine Bioactive Substances and Modern Analytical Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266071, China
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xin Xu
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Chen Liang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350001, China
| | - Yongchao Wang
- The Second Geological Institute, China Metallurgical Geology Bureau, Fuzhou, 350108, China
| | - Xiao Xu
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Linxuan Jia
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Junhui Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Miaohua Jiang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
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3
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Zhao W, Xiong J, Li M, Bu X, Jiang C, Wang G, Zhang J, Li W, Zou H, Miao W, Chen K, Wang G. Genome assembly of a symbiotic balantidia (Balantidium ctenopharyngodoni) in fish hindgut. Sci Data 2024; 11:323. [PMID: 38548755 PMCID: PMC10978948 DOI: 10.1038/s41597-024-03142-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Balantidium ctenopharyngodoni is identified as the sole ciliate species that exclusively resides within the hindgut of grass carp with high prevalence and intensity. In this study, the successful cultivation of B. ctenopharyngodoni enabled us to collect enough cells for genome sequencing. Consequently, we acquired a high-quality genome assembly spanning 68.66 Mb, encompassing a total of 22,334 nanochromosomes. Furthermore, we predicted 29,348 protein-coding genes, and 95.5% of them was supported by the RNA-seq data. The trend of GC content in the subtelomeric regions of single-gene chromosomes was similar to other ciliates containing nanochromosomes. A large number of genes encoding carbohydrate-binding modules with affinities for starch and peptidoglycans was identified. The identification of mitochondrion-related organelles (MROs) within genome indicates its well-suited adaptation to the anaerobic conditions in the hindgut environment. In summary, our results will offer resources for understanding the genetic basis and molecular adaptations of balantidia to hindgut of herbivorous fish.
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Affiliation(s)
- Weishan Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Xialian Bu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
| | - Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
| | - Guangying Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
| | - Jing Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
| | - Wenxiang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hong Zou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Protist 10,000 Genomics Project (P10K) Consortium, Wuhan, China.
| | - Guitang Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Wang R, Meng Q, Wang X, Xiao Y, Sun R, Zhang Z, Fu Y, Di Giuseppe G, Liang A. Comparative genomic analysis of symbiotic and free-living Fluviibacter phosphoraccumulans strains provides insights into the evolutionary origins of obligate Euplotes-bacterial endosymbioses. Appl Environ Microbiol 2024; 90:e0190023. [PMID: 38334408 PMCID: PMC10952467 DOI: 10.1128/aem.01900-23] [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: 10/25/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Endosymbiosis is a widespread and important phenomenon requiring diverse model systems. Ciliates are a widespread group of protists that often form symbioses with diverse microorganisms. Endosymbioses between the ciliate Euplotes and heritable bacterial symbionts are common in nature, and four essential symbionts were described: Polynucleobacter necessarius, "Candidatus Protistobacter heckmanni," "Ca. Devosia symbiotica," and "Ca. Devosia euplotis." Among them, only the genus Polynucleobacter comprises very close free-living and symbiotic representatives, which makes it an excellent model for investigating symbiont replacements and recent symbioses. In this article, we characterized a novel endosymbiont inhabiting the cytoplasm of Euplotes octocarinatus and found that it is a close relative of the free-living bacterium Fluviibacter phosphoraccumulans (Betaproteobacteria and Rhodocyclales). We present the complete genome sequence and annotation of the symbiotic Fluviibacter. Comparative analyses indicate that the genome of symbiotic Fluviibacter is small in size and rich in pseudogenes when compared with free-living strains, which seems to fit the prediction for recently established endosymbionts undergoing genome erosion. Further comparative analysis revealed reduced metabolic capacities in symbiotic Fluviibacter, which implies that the symbiont relies on the host Euplotes for carbon sources, organic nitrogen and sulfur, and some cofactors. We also estimated substitution rates between symbiotic and free-living Fluviibacter pairs for 233 genes; the results showed that symbiotic Fluviibacter displays higher dN/dS mean value than free-living relatives, which suggested that genetic drift is the main driving force behind molecular evolution in endosymbionts. IMPORTANCE In the long history of symbiosis research, most studies focused mainly on organelles or bacteria within multicellular hosts. The single-celled protists receive little attention despite harboring an immense diversity of symbiotic associations with bacteria and archaea. One subgroup of the ciliate Euplotes species is strictly dependent on essential symbionts for survival and has emerged as a valuable model for understanding symbiont replacements and recent symbioses. However, almost all of our knowledge about the evolution and functions of Euplotes symbioses comes from the Euplotes-Polynucleobacter system. In this article, we report a novel essential symbiont, which also has very close free-living relatives. Genome analysis indicated that it is a recently established endosymbiont undergoing genome erosion and relies on the Euplotes host for many essential molecules. Our results provide support for the notion that essential symbionts of the ciliate Euplotes evolve from free-living progenitors in the natural water environment.
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Affiliation(s)
- Ruanlin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Qingyao Meng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Xue Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Yu Xiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Ruijuan Sun
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Zhiyun Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | | | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
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5
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Song Q, Zhao F, Hou L, Miao M. Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates. THE ISME JOURNAL 2024; 18:wrae117. [PMID: 38916437 PMCID: PMC11253213 DOI: 10.1093/ismejo/wrae117] [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: 02/16/2024] [Revised: 05/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.
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Affiliation(s)
- Qi Song
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Fangqing Zhao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
- Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, No. 1 Xiangshan Road, Hangzhou 310024, China
| | - Lina Hou
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
| | - Miao Miao
- Medical School, University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Huairou District, Beijing 100049, China
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Espada‐Hinojosa S, Karthäuser C, Srivastava A, Schuster L, Winter T, de Oliveira AL, Schulz F, Horn M, Sievert S, Bright M. Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative. Mol Ecol Resour 2024; 24:e13889. [PMID: 38010882 PMCID: PMC10952691 DOI: 10.1111/1755-0998.13889] [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: 01/09/2023] [Revised: 08/31/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.
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Affiliation(s)
| | - Clarissa Karthäuser
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Abhishek Srivastava
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Lukas Schuster
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Deakin UniversityBurwoodAustralia
| | - Teresa Winter
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - André Luiz de Oliveira
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Frederik Schulz
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Present address:
DOE Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Matthias Horn
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Stefan Sievert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Monika Bright
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
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7
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Chi Y, Tang D, Lei J, Wei F, Al-Farraj SA, Bourland WA, Chen Z. Highly divergent morphology but a close molecular phylogenetic relationship between two little-known ciliate genera Actinobolina and Papillorhabdos (Protozoa: Ciliophora: Litostomatea) with description of two new species. J Eukaryot Microbiol 2024; 71:e13007. [PMID: 37886908 DOI: 10.1111/jeu.13007] [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: 05/04/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Free-living litostomatean ciliates, prominent microeukaryote predators commonly encountered in freshwater and marine habitats, play vital roles in maintaining energy flow and nutrient cycles. Nevertheless, understanding their biodiversity and phylogenetic relationships remains challenging due to insufficient morphological information and molecular data. As a new contribution to this group, three haptorian ciliates, including two new species (Actinobolina bivacuolata sp. nov. and Papillorhabdos foissneri sp. nov.) and the insufficiently described type species, Actinobolina radians, were isolated from wetlands around Lake Weishan, China and investigated by a combination of living morphology, stained preparations, and 18S rRNA gene sequence data. An illustrated key of the valid species within the two genera is provided. In addition, we reveal the phylogenetic positions of these two genera for the first time. Although they differ in all key morphologic characters such as general appearance (ellipsoidal with numerous tentacles vs. cylindrical), extrusomes (stored in tentacles vs. anchored to pellicle), circumoral kinety (present vs. absent), composition of somatic kineties (kinetosome clusters vs. monokinetids), and number of dorsal brush rows (1 vs. 4), they both cluster in a fully supported clade in the phylogenetic tree, which indicates that the biodiversity and additional molecular markers of this group need further exploration.
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Affiliation(s)
- Yong Chi
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Danxu Tang
- Marine College, Shandong University, Weihai, China
| | - Jingtao Lei
- Weishan Fishery Development Service Center, Jining, China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - William A Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Zigui Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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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: 1.0] [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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9
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Fokin SI, Lebedeva NA, Potekhin A, Gammuto L, Petroni G, Serra V. Holospora-like bacteria "Candidatus Gortzia yakutica" and Preeria caryophila: Ultrastructure, promiscuity, and biogeography of the symbionts. Eur J Protistol 2023; 90:125998. [PMID: 37356197 DOI: 10.1016/j.ejop.2023.125998] [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: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
Two already known representatives of Holospora-like bacteria, "Candidatus Gortzia yakutica" from Paramecium putrinum and Preeria caryophila, originally retrieved from the Paramecium aurelia complex, were found in new hosts: Paramecium nephridiatum and Paramecium polycaryum, respectively. In the present study, these bacteria were investigated using morphological and molecular methods. For "Ca. G. yakutica", the first details of the electron microscopic structure in the main and new hosts were provided. Regarding Pr. caryophila, the ultrastructural description of this species was implemented by several features previously unknown, such as the so called "membrane cluster" dividing periplasm from cytoplasm and fine composition of infectious forms before and during its releasing from the infected macronucleus. The new combinations of these Holospora-like bacteria with ciliate hosts were discussed from biogeographical and ecological points of view. Host specificity of symbionts as a general paradigm was critically reviewed as well.
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Affiliation(s)
| | - Natalia A Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Russia
| | - Alexey Potekhin
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia; Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | | | - Giulio Petroni
- Department of Biology, University of Pisa, Italy; CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy; CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, Italy
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10
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Zhang X, Bi L, Gentekaki E, Zhao J, Shen P, Zhang Q. Culture-Independent Single-Cell PacBio Sequencing Reveals Epibiotic Variovorax and Nucleus Associated Mycoplasma in the Microbiome of the Marine Benthic Protist Geleia sp. YT (Ciliophora, Karyorelictea). Microorganisms 2023; 11:1500. [PMID: 37375002 DOI: 10.3390/microorganisms11061500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Microbes in marine sediments constitute up to five-sixths of the planet's total biomass, but their diversity is little explored, especially for those forming associations with unicellular protists. Heterotrophic ciliates are among the most dominant and diversified marine benthic protists and comprise hotspot niches of bacterial colonization. To date, studies using culture-independent single-cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent, even for the most ubiquitous species. Here, we characterize the major bacterial groups associated with a representative marine benthic ciliate, Geleia sp. YT, collected directly from the coastal zone of Yantai, China. PacBio sequencing of the nearly full-length 16Sr RNA genes was performed on single cells of Geleia. Fluorescence in situ hybridization (FISH) analysis with genus-specific probes was further applied to locate the dominant bacterial groups. We identified a Variovorax-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host. We provide evidence of a nucleus-associated bacterium related to the human pathogen Mycoplasma, which appeared prevalently in the local populations of Geleia sp. YT for 4 months. The most abundant bacterial taxa associated with Geleia sp. YT likely represent its core microbiome, hinting at the important roles of the ciliate-bacteria consortium in the marine benthos. Overall, this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic ciliate and its symbioses.
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Affiliation(s)
- Xiaoxin Zhang
- School of Ocean, Yantai University, Yantai 264003, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Luping Bi
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Gut Microbiome Research Group, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Pingping Shen
- School of Ocean, Yantai University, Yantai 264003, China
| | - Qianqian Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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11
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A 63-kDa Periplasmic Protein of the Endonuclear Symbiotic Bacterium Holospora obtusa Secreted to the Outside of the Bacterium during the Early Infection Process Binds Weakly to the Macronuclear DNA of the Host Paramecium caudatum. Microorganisms 2023; 11:microorganisms11010155. [PMID: 36677447 PMCID: PMC9866348 DOI: 10.3390/microorganisms11010155] [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: 11/29/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and high salt resistances. In addition, an infectious form of H. obtusa-specific 63-kDa periplasmic protein with a DNA-binding domain in its amino acid sequence is secreted into the host macronucleus after invasion into the macronucleus and remain within the nucleus. These facts suggest that binding of the 63-kDa protein to the host macronuclear DNA causes changes in the host gene expressions and enhances an environmental adaptability of the host cells. This 63-kDa protein was renamed as periplasmic region protein 1 (PRP1) to distinguish it from other proteins with similar molecular weights. To confirm whether PRP1 indeed binds to the host DNA, SDS-DNA PAGE and DNA affinity chromatography with calf thymus DNA and P. caudatum DNA were conducted and confirmed that PRP1 binds weakly to the P. caudatum DNA with a monoclonal antibody raised for the 63-kDa protein.
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12
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Giannotti D, Boscaro V, Husnik F, Vannini C, Keeling PJ. At the threshold of symbiosis: the genome of obligately endosymbiotic ' Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb Genom 2022; 8:mgen000909. [PMID: 36748607 PMCID: PMC9837558 DOI: 10.1099/mgen.0.000909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.
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Affiliation(s)
- Daniele Giannotti
- Department of Biology, University of Pisa, Pisa, Italy,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada,*Correspondence: Vittorio Boscaro,
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, Canada,Okinawa Institute of Science and Technology, Okinawa, Japan
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Together forever: Inseparable partners of the symbiotic system Paramecium multimicronucleatum/Ca. Trichorickettsia mobilis. Symbiosis 2022. [DOI: 10.1007/s13199-022-00854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Fujishima M, Kodama Y. Mechanisms for Establishing Primary and Secondary Endosymbiosis in Paramecium. J Eukaryot Microbiol 2022; 69:e12901. [PMID: 35243727 DOI: 10.1111/jeu.12901] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Primary (eukaryote and procaryote) and secondary (eukaryote and eukaryote) endosymbiosis are driving forces in eukaryotic cell evolution. These phenomena are still contributing to acquire new cell structures and functions. To understand mechanisms for establishment of each endosymbiosis, experiments that can induce endosymbiosis synchronously by mixing symbionts isolated from symbiont-bearing host cells and symbiont-free host cells are indispensable. Recent progress on endosymbiosis using Paramecium and their endonuclear symbiotic bacteria Holospora or symbiotic green alga Chlorella has been remarkable, and providing excellent opportunities for elucidating host-symbiont interactions. These organisms are now becoming model organisms to know the mechanisms for establishing primary and secondary endosymbiosis. Based on experiments of many researchers, we introduce, how these endosymbionts escape from the host lysosomal fusion, how they migrate in the host cytoplasm to localize specific locations within the host, how their species specificity and strain specificity of the host cells are controlled, how their life cycles are controlled, how they escape from the host cell to infect more young host cell, how they affect to the host viability and to gene expression, what kind of substances are needed in these phenomena, and what changes had been induced in the symbiont and the host genomes.
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Affiliation(s)
- Masahiro Fujishima
- Joint Faculty of Veterinary Medicine, Yamaguchi University, Yoshida 1677-1, Yamaguchi, 753-8515, Japan
| | - Yuuki Kodama
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Nishikawatsu-cho 1060, Matsue, 690-8504, Japan
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