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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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Choi A, Seong JW, Kim JH, Lee JY, Cho HJ, Kang SA, Park MK, Jeong MJ, Choi SY, Jeong YJ, Yu HS. Presence and diversity of free-living amoebae and their potential application as water quality indicators. PARASITES, HOSTS AND DISEASES 2024; 62:180-192. [PMID: 38835259 DOI: 10.3347/phd.24020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
Free-living amoebae (FLA) are found in diverse environments, such as soils, rivers, and seas. Hence, they can be used as bioindicators to assess the water quality based solely on their presence. In this study, we determined the presence of FLA in river water by filtering water samples collected from various sites and culturing the resulting filtrates. FLA were detected in all the water samples with varying quality grades (Grades Ι-V). The significant increase in the size of the amoebae population with the deterioration in the water quality. Monoxenic cultures of the amoebae were performed, and genomic DNAs were isolated, among which 18S rDNAs were sequenced to identify the amoeba species. Of the 12 species identified, 10 belonged to the Acanthamoeba genus; of the remaining 2 species, one was identified as Vannella croatica and the other as a species of Vermamoeba. Acanthamoeba was detected in samples with Grades Ι to VI quality, whereas the Vermamoeba species was present only in Grade Ι water. V. croatica was found exclusively in water with Grade ΙΙ quality. Following morphological observations, genomic DNA was sequenced using 16S rDNA to determine whether the species of Acanthamoeba harbored endosymbionts. Most of the isolated Acanthamoeba contained endosymbionts, among which 4 species of endogenous bacteria were identified and examined using transmission electron microscopy. This study provides evidence that the distribution of amoebae other than Acanthamoeba may be associated with water quality. However, further confirmation will be required based on accurate water quality ratings and assessments using a more diverse range of FLA.
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Affiliation(s)
- Areum Choi
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Ji Won Seong
- Department of Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Jeong Hyun Kim
- Department of Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Jun Young Lee
- Department of Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Hyun Jae Cho
- Department of Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Shin Ae Kang
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Mi Kyung Park
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Mi Jin Jeong
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Seo Yeong Choi
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Yu Jin Jeong
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Hak Sun Yu
- Department of Parasitology and Tropical Medicine, School of Medicine, Pusan National University, Yangsan 50612, Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Korea
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Giovannini M, Petroni G, Castelli M. Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics. Environ Microbiol 2024; 26:e16562. [PMID: 38173299 DOI: 10.1111/1462-2920.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.
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Affiliation(s)
| | | | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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Dittmer J, Bredon M, Moumen B, Raimond M, Grève P, Bouchon D. The terrestrial isopod symbiont 'Candidatus Hepatincola porcellionum' is a potential nutrient scavenger related to Holosporales symbionts of protists. ISME COMMUNICATIONS 2023; 3:18. [PMID: 36882494 PMCID: PMC9992710 DOI: 10.1038/s43705-023-00224-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of 'Ca. Hepatincola porcellionum', a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protist-associated Holosporales, suggesting different host-symbiont interactions depending on the host organism.
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Affiliation(s)
- Jessica Dittmer
- Dipartimento di Scienze Agrarie e Ambientali (DISAA), Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
- UMR 1345, Université d'Angers, Institut Agro, INRAE, IRHS, SFR Quasav, 42 Rue Georges Morel, 49070, Beaucouzé, France.
| | - Marius Bredon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
- Université Paris-Sorbonne, Centre de Recherche Saint-Antoine, Equipe Microbiote, Intestin et Inflammation, 27 Rue Chaligny, 75012, Paris, France
| | - Bouziane Moumen
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Maryline Raimond
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Pierre Grève
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Didier Bouchon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France.
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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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George EE, Tashyreva D, Kwong WK, Okamoto N, Horák A, Husnik F, Lukeš J, Keeling PJ. Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes. Genome Biol Evol 2022; 14:6615375. [PMID: 35738252 PMCID: PMC9254644 DOI: 10.1093/gbe/evac099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Instituto Gulbenkian de Ciência, 6, 2780-156 Oeiras, Portugal
| | - Noriko Okamoto
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | - Aleš Horák
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
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