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Tashyreva D, Týč J, Horák A, Lukeš J. Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle. mBio 2023; 14:e0192123. [PMID: 37737610 PMCID: PMC10653844 DOI: 10.1128/mbio.01921-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE The knowledge of cell biology of a eukaryotic group is essential for correct interpretation of ecological and molecular data. Although diplonemid protists are one of the most species-rich lineages of marine eukaryotes, only very fragmentary information is available about the cellular architecture of this taxonomically diverse group. Here, a large serial block-face scanning electron microscopy data set complemented with light and fluorescence microscopy allowed the first detailed three-dimensional reconstruction of a diplonemid species. We describe numerous previously unknown peculiarities of the cellular architecture and cell division characteristic for diplonemid flagellates, and illustrate the obtained results with multiple three-dimensional models, comprehensible for non-specialists in protist ultrastructure.
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Affiliation(s)
- Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
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Yabuki A, Kawato M, Nagano Y, Tsuchida S, Yoshida T, Fujiwara Y. Structural Comparison of Diplonemid Communities around the Izu Peninsula, Japan. Microbes Environ 2021; 36:ME21012. [PMID: 34121037 PMCID: PMC8209450 DOI: 10.1264/jsme2.me21012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022] Open
Abstract
Diplonemea (diplonemids) is one of the most abundant and species-rich protist groups in marine environments; however, their community structures among local and seasonal samples have not yet been compared. In the present study, we analyzed four diplonemid community structures around the Izu Peninsula, Japan using barcode sequences amplified from environmental DNA. These sequences and the results of statistical analyses indicated that communities at the same site were more similar to each other than those in the same season. Environmental variables were also measured, and their influence on diplonemid community structures was examined. Salinity, electrical conductivity, and temperature, and their correlated variables, appeared to influence the structures of diplonemid communities, which was consistent with previous findings; however, since the results obtained did not reach statistical significance, further studies are required. A comparison of each diplonemid community indicated that some lineages were unique to specific samples, while others were consistently detected in all samples. Members of the latter type are cosmopolitan candidates and may be better adapted to the environments of the studied area. Future studies that focus on the more adaptive members will provide a more detailed understanding of the mechanisms by which diplonemids are widely distributed in marine environments and will facilitate their utilization as indicator organisms to monitor environmental changes.
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Affiliation(s)
- Akinori Yabuki
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Masaru Kawato
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Shinji Tsuchida
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Takao Yoshida
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
| | - Yoshihiro Fujiwara
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 2370061, Japan
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George EE, Husnik F, Tashyreva D, Prokopchuk G, Horák A, Kwong WK, Lukeš J, Keeling PJ. Highly Reduced Genomes of Protist Endosymbionts Show Evolutionary Convergence. Curr Biol 2020; 30:925-933.e3. [PMID: 31978335 DOI: 10.1016/j.cub.2019.12.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/24/2019] [Accepted: 12/23/2019] [Indexed: 10/25/2022]
Abstract
Genome evolution in bacterial endosymbionts is notoriously extreme: the combined effects of strong genetic drift and unique selective pressures result in highly reduced genomes with distinctive adaptations to hosts [1-4]. These processes are mostly known from animal endosymbionts, where nutritional endosymbioses represent the best-studied systems. However, eukaryotic microbes, or protists, also harbor diverse bacterial endosymbionts, but their genome reduction and functional relationships with their hosts are largely unexplored [5-7]. We sequenced the genomes of four bacterial endosymbionts from three species of diplonemids, poorly studied but abundant and diverse heterotrophic protists [8-12]. The endosymbionts come from two bacterial families, Rickettsiaceae and Holosporaceae, that have invaded two families of diplonemids, and their genomes have converged on an extremely small size (605-632 kilobase pairs [kbp]), similar gene content (e.g., metabolite transporters and secretion systems), and reduced metabolic potential (e.g., loss of energy metabolism). These characteristics are generally found in both families, but the diplonemid endosymbionts have evolved greater extremes in parallel. They possess modified type VI secretion systems that could function in manipulating host metabolism or other intracellular interactions. Finally, modified cellular machinery like the ATP synthase without oxidative phosphorylation, and the reduced flagellar apparatus present in some diplonemid endosymbionts and nutritional animal endosymbionts, indicates that intracellular mechanisms have converged in bacterial endosymbionts with various functions and from different eukaryotic hosts across the tree of life.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, BC V6T 1Z4, Canada.
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, BC V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, BC V6T 1Z4, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, BC V6T 1Z4, Canada
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Tashyreva D, Prokopchuk G, Votýpka J, Yabuki A, Horák A, Lukeš J. Life Cycle, Ultrastructure, and Phylogeny of New Diplonemids and Their Endosymbiotic Bacteria. mBio 2018; 9:e02447-17. [PMID: 29511084 PMCID: PMC5845003 DOI: 10.1128/mbio.02447-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
Diplonemids represent a hyperdiverse and abundant yet poorly studied group of marine protists. Here we describe two new members of the genus Diplonema (Diplonemea, Euglenozoa), Diplonema japonicum sp. nov. and Diplonema aggregatum sp. nov., based on life cycle, morphology, and 18S rRNA gene sequences. Along with euglenozoan apomorphies, they contain several unique features. Their life cycle is complex, consisting of a trophic stage that is, following the depletion of nutrients, transformed into a sessile stage and subsequently into a swimming stage. The latter two stages are characterized by the presence of tubular extrusomes and the emergence of a paraflagellar rod, the supportive structure of the flagellum, which is prominently lacking in the trophic stage. These two stages also differ dramatically in motility and flagellar size. Both diplonemid species host endosymbiotic bacteria that are closely related to each other and constitute a novel branch within Holosporales, for which a new genus, "Candidatus Cytomitobacter" gen. nov., has been established. Remarkably, the number of endosymbionts in the cytoplasm varies significantly, as does their localization within the cell, where they seem to penetrate the mitochondrion, a rare occurrence.IMPORTANCE We describe the morphology, behavior, and life cycle of two new Diplonema species that established a relationship with two Holospora-like bacteria in the first report of an endosymbiosis in diplonemids. Both endosymbionts reside in the cytoplasm and the mitochondrion, which establishes an extremely rare case. Within their life cycle, the diplonemids undergo transformation from a trophic to a sessile and eventually a highly motile swimming stage. These stages differ in several features, such as the presence or absence of tubular extrusomes and a paraflagellar rod, along with the length of the flagella. These morphological and behavioral interstage differences possibly reflect distinct functions in dispersion and invasion of the host and/or prey and may provide novel insight into the virtually unknown function of diplonemids in the oceanic ecosystem.
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Affiliation(s)
- Daria Tashyreva
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Galina Prokopchuk
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Jan Votýpka
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Akinori Yabuki
- Department of Marine Diversity, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Aleš Horák
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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