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Zhang B, Xiao L, Lyu L, Zhao F, Miao M. Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists. MICROBIOME 2024; 12:96. [PMID: 38790063 PMCID: PMC11127453 DOI: 10.1186/s40168-024-01809-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates. RESULTS To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range. CONCLUSIONS As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
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Affiliation(s)
- Bing Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Xiao
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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2
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Potekhin A, Plotnikov AO, Gogoleva N, Sonntag B. Editorial: Microbial associations formed and hosted by protists, algae, and fungi. Front Microbiol 2024; 14:1341058. [PMID: 38249461 PMCID: PMC10799554 DOI: 10.3389/fmicb.2023.1341058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Affiliation(s)
- Alexey Potekhin
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Andrey O. Plotnikov
- Institute for Cellular and Intracellular Symbiosis of the UrB RAS, Orenburg Federal Research Center, Orenburg, Russia
| | - Natalia Gogoleva
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Laboratory of Environmental Metagenomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
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3
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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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4
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Manassero V, Vannini C. Protists' microbiome: A fine-scale, snap-shot field study on the ciliate Euplotes. Eur J Protistol 2023; 87:125952. [PMID: 36610375 DOI: 10.1016/j.ejop.2022.125952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023]
Abstract
Host-microbiome relationships play a fundamental role in the evolution and ecology of any living being. As unicellular organisms, protists represent a unique eukaryotic model to investigate selection mechanisms of the prokaryotic microbiome at the cellular level. Field investigations are central to disentangle relative importance of selective drivers in nature. Here we performed an analysis on data from a snap-shot field study reported previously on bacterial microbiomes associated to natural populations of protist ciliates of the genus Euplotes to detect at a fine scale any influence of habitat and/or host identity in microbiome selection. Comparative analyses revealed environment at a relatively large scale (sampling area) as the main driving factor in shaping prokaryotic communities' structures. No evidence of habitat as key-factor emerged when a smaller spatial scale was considered (pond/channel or site). When only microbiomes of ciliates from the same site were compared, a clear assessment on the influence of host identity at the species level was not achieved, probably due to the small and unbalanced number of individuals for the two considered host species. Starting from this point, wider sampling campaigns will contribute in the future to depict a general view of the drivers influencing the prokaryotic microbiomes of natural protist populations.
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Affiliation(s)
| | - Claudia Vannini
- Department of Biology, University of Pisa, 56126 Pisa, Italy.
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5
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Himi E, Miyoshi-Akiyama T, Matsushima Y, Shiono I, Aragane S, Hirano Y, Ikeda G, Kitaura Y, Kobayashi K, Konno D, Morohashi A, Noguchi Y, Ominato Y, Shinbo S, Suzuki N, Takatsuka K, Tashiro H, Yamada Y, Yamashita K, Yoshino N, Kitashima M, Kotani S, Inoue K, Hino A, Hosoya H. Establishment of an unfed strain of Paramecium bursaria and analysis of associated bacterial communities controlling its proliferation. Front Microbiol 2023; 14:1036372. [PMID: 36960277 PMCID: PMC10029143 DOI: 10.3389/fmicb.2023.1036372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/27/2023] [Indexed: 03/09/2023] Open
Abstract
The ciliate Paramecium bursaria harbors several hundred symbiotic algae in its cell and is widely used as an experimental model for studying symbiosis between eukaryotic cells. Currently, various types of bacteria and eukaryotic microorganisms are used as food for culturing P. bursaria; thus, the cultivation conditions are not uniform among researchers. To unify cultivation conditions, we established cloned, unfed strains that can be cultured using only sterile medium without exogenous food. The proliferation of these unfed strains was suppressed in the presence of antibiotics, suggesting that bacteria are required for the proliferation of the unfed strains. Indeed, several kinds of bacteria, such as Burkholderiales, Rhizobiales, Rhodospirillales, and Sphingomonadales, which are able to fix atmospheric nitrogen and/or degrade chemical pollutants, were detected in the unfed strains. The genetic background of the individually cloned, unfed strains were the same, but the proliferation curves of the individual P. bursaria strains were very diverse. Therefore, we selected multiple actively and poorly proliferating individual strains and compared the bacterial composition among the individual strains using 16S rDNA sequencing. The results showed that the bacterial composition among actively proliferating P. bursaria strains was highly homologous but different to poorly proliferating strains. Using unfed strains, the cultivation conditions applied in different laboratories can be unified, and symbiosis research on P. bursaria will make great progress.
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Affiliation(s)
- Eiko Himi
- Faculty of Agriculture, Kibi International University, Minamiawaji, Hyogo, Japan
| | - Tohru Miyoshi-Akiyama
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuri Matsushima
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, Kanagawa, Japan
| | - Iru Shiono
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Seiji Aragane
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Yui Hirano
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Gaku Ikeda
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Yuki Kitaura
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Kyohei Kobayashi
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Daichi Konno
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Ayata Morohashi
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Yui Noguchi
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Yuka Ominato
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Soma Shinbo
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Naruya Suzuki
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Kurama Takatsuka
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Hitomi Tashiro
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Yoki Yamada
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Kenya Yamashita
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Natsumi Yoshino
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Masaharu Kitashima
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
| | - Susumu Kotani
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, Kanagawa, Japan
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
- Research Institute for Integrated Science, Kanagawa University, Kanagawa, Japan
| | - Kazuhito Inoue
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, Kanagawa, Japan
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Kanagawa, Japan
- Research Institute for Integrated Science, Kanagawa University, Kanagawa, Japan
| | - Akiya Hino
- Research Institute for Integrated Science, Kanagawa University, Kanagawa, Japan
| | - Hiroshi Hosoya
- Research Institute for Integrated Science, Kanagawa University, Kanagawa, Japan
- *Correspondence: Hiroshi Hosoya, ;
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6
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Boscaro V, Manassero V, Keeling PJ, Vannini C. Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment. MICROBIAL ECOLOGY 2023; 85:307-316. [PMID: 35048168 DOI: 10.1007/s00248-021-01938-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Claudia Vannini
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
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7
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Zhang Y, Feng S, Gao F, Wen H, Zhu L, Li M, Xi Y, Xiang X. The Relationship between Brachionus calyciflorus-Associated Bacterial and Bacterioplankton Communities in a Subtropical Freshwater Lake. Animals (Basel) 2022; 12:ani12223201. [PMID: 36428428 PMCID: PMC9686566 DOI: 10.3390/ani12223201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Zooplankton bodies are organic-rich micro-environments that support fast bacterial growth. Therefore, the abundance of zooplankton-associated bacteria is much higher than that of free-living bacteria, which has profound effects on the nutrient cycling of freshwater ecosystems. However, a detailed analysis of associated bacteria is still less known, especially the relationship between those bacteria and bacterioplankton. In this study, we analyzed the relationships between Brachionus calyciflorus-associated bacterial and bacterioplankton communities in freshwater using high-throughput sequencing. The results indicated that there were significant differences between the two bacterial communities, with only 29.47% sharing OTUs. The alpha diversity of the bacterioplankton community was significantly higher than that of B. calyciflorus-associated bacteria. PCoA analysis showed that the bacterioplankton community gathered deeply, while the B. calyciflorus-associated bacterial community was far away from the whole bacterioplankton community, and the distribution was relatively discrete. CCA analysis suggested that many environmental factors (T, DO, pH, TP, PO43-, NH4+, and NO3-) regulated the community composition of B. calyciflorus-associated bacteria, but the explanatory degree of variability was only 37.80%. High-throughput sequencing revealed that Raoultella and Delftia in Proteobacteria were the dominant genus in the B. calyciflorus-associated bacterial community, and closely related to the biodegradation function. Moreover, several abundant bacterial members participating in carbon and nitrogen cycles were found in the associated bacterial community by network analysis. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the B. calyciflorus-associated bacterial community were plastic degradation, chemoheterotrophy, and aerobic chemoheterotrophy. Overall, our study expands the current understanding of zooplankton-bacteria interaction and promotes the combination of two different research fields.
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Affiliation(s)
- Yongzhi Zhang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Sen Feng
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Fan Gao
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Hao Wen
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Lingyun Zhu
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Meng Li
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
| | - Yilong Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, Wuhu 241002, China
| | - Xianling Xiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, Wuhu 241002, China
- Correspondence: author:
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8
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Kuśnierz M, Domańska M, Hamal K, Pera A. Application of Integrated Fixed-Film Activated Sludge in a Conventional Wastewater Treatment Plant. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19105985. [PMID: 35627522 PMCID: PMC9141865 DOI: 10.3390/ijerph19105985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
It is often only at the operation stage of a wastewater treatment plant that there is a need to adjust the treatment process in terms of variable hydraulic capacity, increased pollutant load, high/low concentration of suspended biomass, or the unfavorable phenomenon of reduced sedimentation capacity of the activated sludge. One of the ways to improve the treatment process efficiency is to increase the biologically active surface by using bio-carriers in the form of fibers, materials, or bio-balls. This paper presents the results of a wastewater treatment plant operation during the period of six months after the implementation of the integrated fixed-film activated sludge (IFAS) technology. The research showed that microorganisms developed both in the activated sludge and on the fibers, positively influencing the activated sludge condition. During the start-up of the IFAS process, ciliates predominated over the other species. However, as oxygen content was high (2 mg/dm3 and more) and textile beds were used, the protozoan population developed intensively, and small metazoans became increasingly common. Throughout the research period, nitrifying and phosphorus-accumulating bacteria were observed both in the activated sludge and on the fibers. Between the 59th and 184th day of operation, numerous microorganisms were detected on the fibers and in the activated sludge, testifying to low biological oxygen demand, good aerobic conditions for nitrification, and long sludge age. However, the process seemed to break down after day 72, when the occurrence of metazoan led to reduced sludge production; after day 88, chemical oxygen demand and total suspended solids in the outflow increased, and oligochaetes and rotifers dominated the suspended sludge and fibers. Results also showed that the textile bed and low ammonia concentration became an excellent substrate for the development of Stentor sp. With regard to chemical and biological oxygen demand, total nitrogen- and total phosphorus-effluent concentrations were mostly within the legally permissible limits throughout the 184 days of operation.
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9
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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: 11] [Impact Index Per Article: 5.5] [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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10
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Castelli M, Lanzoni O, Giovannini M, Lebedeva N, Gammuto L, Sassera D, Melekhin M, Potekhin A, Fokin S, Petroni G. 'Candidatus Gromoviella agglomerans', a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:34-49. [PMID: 34766443 DOI: 10.1111/1758-2229.13021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum. This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast-evolving clade within the family Holosporaceae. Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium, thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast-evolving Holosporaceae, with some lineage-specific traits. Interestingly, similar convergent features could be observed in other host-associated lineages, in particular Rickettsiales among Alphaproteobacteria.
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Affiliation(s)
- Michele Castelli
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | | | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Maksim Melekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Sergei Fokin
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Invertebrate Zoology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
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11
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Gomaa F, Utter DR, Loo W, Lahr DJ, Cavanaugh CM. Exploring the protist microbiome: The diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa). Eur J Protistol 2022; 82:125861. [DOI: 10.1016/j.ejop.2021.125861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/08/2021] [Accepted: 12/18/2021] [Indexed: 11/15/2022]
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12
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Husnik F, Tashyreva D, Boscaro V, George EE, Lukeš J, Keeling PJ. Bacterial and archaeal symbioses with protists. Curr Biol 2021; 31:R862-R877. [PMID: 34256922 DOI: 10.1016/j.cub.2021.05.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.
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Affiliation(s)
- Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Emma E George
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Kraus A, Buckley KM, Salinas I. Sensing the world and its dangers: An evolutionary perspective in neuroimmunology. eLife 2021; 10:66706. [PMID: 33900197 PMCID: PMC8075586 DOI: 10.7554/elife.66706] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Detecting danger is key to the survival and success of all species. Animal nervous and immune systems cooperate to optimize danger detection. Preceding studies have highlighted the benefits of bringing neurons into the defense game, including regulation of immune responses, wound healing, pathogen control, and survival. Here, we summarize the body of knowledge in neuroimmune communication and assert that neuronal participation in the immune response is deeply beneficial in each step of combating infection, from inception to resolution. Despite the documented tight association between the immune and nervous systems in mammals or invertebrate model organisms, interdependence of these two systems is largely unexplored across metazoans. This review brings a phylogenetic perspective of the nervous and immune systems in the context of danger detection and advocates for the use of non-model organisms to diversify the field of neuroimmunology. We identify key taxa that are ripe for investigation due to the emergence of key evolutionary innovations in their immune and nervous systems. This novel perspective will help define the primordial principles that govern neuroimmune communication across taxa.
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Affiliation(s)
- Aurora Kraus
- Department of Biology, University of New Mexico, Albuquerque, United States
| | | | - Irene Salinas
- Department of Biology, University of New Mexico, Albuquerque, United States
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