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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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2
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Baños H, Susko E, Roger AJ. Is Over-parameterization a Problem for Profile Mixture Models? Syst Biol 2024; 73:53-75. [PMID: 37843172 PMCID: PMC11129589 DOI: 10.1093/sysbio/syad063] [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: 02/18/2022] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023] Open
Abstract
Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency vectors can adversely affect tree topology estimates because of over-parameterization. Here, we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies, and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore the performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency vectors. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency vectors does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional "F-class" representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.
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Affiliation(s)
- Hector Baños
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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3
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Zakharova A, Tashyreva D, Butenko A, Morales J, Saura A, Svobodová M, Poschmann G, Nandipati S, Zakharova A, Noyvert D, Gahura O, Týč J, Stühler K, Kostygov AY, Nowack ECM, Lukeš J, Yurchenko V. A neo-functionalized homolog of host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr Biol 2023:S0960-9822(23)00542-0. [PMID: 37201521 DOI: 10.1016/j.cub.2023.04.060] [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: 01/17/2023] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]
Abstract
The stability of endosymbiotic associations between eukaryotes and bacteria depends on a reliable mechanism ensuring vertical inheritance of the latter. Here, we demonstrate that a host-encoded protein, located at the interface between the endoplasmic reticulum of the trypanosomatid Novymonas esmeraldas and its endosymbiotic bacterium Ca. Pandoraea novymonadis, regulates such a process. This protein, named TMP18e, is a product of duplication and neo-functionalization of the ubiquitous transmembrane protein 18 (TMEM18). Its expression level is increased at the proliferative stage of the host life cycle correlating with the confinement of bacteria to the nuclear vicinity. This is important for the proper segregation of bacteria into the daughter host cells as evidenced from the TMP18e ablation, which disrupts the nucleus-endosymbiont association and leads to greater variability of bacterial cell numbers, including an elevated proportion of aposymbiotic cells. Thus, we conclude that TMP18e is necessary for the reliable vertical inheritance of endosymbionts.
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Affiliation(s)
- Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Jorge Morales
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Gereon Poschmann
- Institute of Molecular Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Satish Nandipati
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Alena Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - David Noyvert
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Kai Stühler
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany; Institute of Molecular Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Eva C M Nowack
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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Muñoz-Gómez SA, Hess S. Purple photosymbioses. Curr Biol 2023; 33:R167-R170. [PMID: 36917934 DOI: 10.1016/j.cub.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Muñoz-Gómez and Hess introduce purple photosymbioses, which involve a heterotrophic protist host and anoxygenic photosymbionts from the phylum Proteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biological Sciences, Lilly Hall of Life Sciences, Purdue University, 915 W State Street, West Lafayette, IN 47907, USA.
| | - Sebastian Hess
- Institute for Zoology, Cologne Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
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6
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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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7
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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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8
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Oren A. Candidatus List No. 4: Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748458 DOI: 10.1099/ijsem.0.005545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
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9
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Symbiont-Induced Phagosome Changes Rather than Extracellular Discrimination Contribute to the Formation of Social Amoeba Farming Symbiosis. Microbiol Spectr 2022; 10:e0172721. [PMID: 35442071 PMCID: PMC9241765 DOI: 10.1128/spectrum.01727-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Symbiont recognition is essential in many symbiotic relationships, especially for horizontally transferred symbionts. Therefore, how to find the right partner is a crucial challenge in these symbiotic relationships. Previous studies have demonstrated that both animals and plants have evolved various mechanisms to recognize their symbionts. However, studies about the mechanistic basis of establishing protist-bacterium symbioses are scarce. This study investigated this question using a social amoeba Dictyostelium discoideum and their Burkholderia symbionts. We found no evidence that D. discoideum hosts could distinguish different Burkholderia extracellularly in chemotaxis assays. Instead, symbiont-induced phagosome biogenesis contributed to the formation of social amoeba symbiosis, and D. discoideum hosts have a higher phagosome pH when carrying symbiotic Burkholderia than nonsymbiotic Burkholderia. In conclusion, the establishment of social amoeba symbiosis is not linked with extracellular discrimination but related to symbiont-induced phagosome biogenesis, which provides new insights into the mechanisms of endosymbiosis formation between protists and their symbionts. IMPORTANCE Protists are single-celled, extremely diverse eukaryotic microbes. Like animals and plants, they live with bacterial symbionts and have complex relationships. In protist-bacterium symbiosis, while some symbionts are strictly vertically transmitted, others need to reestablish and acquire symbionts from the environment frequently. However, the mechanistic basis of establishing protist-bacterium symbioses is mostly unclear. This study uses a novel amoeba-symbiont system to show that the establishment of this symbiosis is not linked with extracellular discrimination. Instead, symbiont-induced phagosome biogenesis contributes to the formation of social amoeba-bacterium symbiosis. This study increases our understanding of the mechanistic basis of establishing protist-bacterium symbioses.
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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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11
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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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12
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Fokin SI, Serra V. Bacterial Symbiosis in Ciliates (Alveolata, Ciliophora): Roads Traveled and Those Still to be Taken. J Eukaryot Microbiol 2022; 69:e12886. [PMID: 35006645 PMCID: PMC9539572 DOI: 10.1111/jeu.12886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
The diversity of prokaryotic symbionts in Ciliophora and other protists is fascinatingly rich; they may even include some potentially pathogenic bacteria. In this review, we summarize currently available data on biodiversity and some morphological and biological peculiarities of prokaryotic symbionts mainly within the genera Paramecium and Euplotes. Another direction of ciliate symbiology, neglected for a long time and now re‐discovered, is the study of epibionts of ciliates. This promises a variety of interesting outcomes. Last, but not least, we stress the new technologies, such as next generation sequencing and the use of genomics data, which all can clarify many new aspects of relevance. For this reason, a brief overview of achievements in genomic studies on ciliate's symbionts is provided. Summing up the results of numerous scientific contributions, we systematically update current knowledge and outline the prospects as to how symbiology of Ciliophora may develop in the near future.
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Affiliation(s)
- Sergei I Fokin
- University of Pisa, Pisa, Italy.,St. Petersburg State University, St. Petersburg, Russia
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Karlicki M, Antonowicz S, Karnkowska A. Tiara: deep learning-based classification system for eukaryotic sequences. Bioinformatics 2021; 38:344-350. [PMID: 34570171 PMCID: PMC8722755 DOI: 10.1093/bioinformatics/btab672] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity. RESULTS We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data. AVAILABILITY AND IMPLEMENTATION Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland
| | - Stanisław Antonowicz
- Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland
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