1
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Suzuki-Tellier S, Kiørboe T, Simpson AGB. The function of the feeding groove of 'typical excavate' flagellates. J Eukaryot Microbiol 2024; 71:e13016. [PMID: 38108228 DOI: 10.1111/jeu.13016] [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: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Phagotrophic flagellates are the main consumers of bacteria and picophytoplankton. Despite their ecological significance in the 'microbial loop', many of their predation mechanisms remain unclear. 'Typical excavates' bear a ventral groove, where prey is captured for ingestion. The consequences of feeding through a 'semi-rigid' furrow on the prey size range have not been explored. An unidentified moving element called 'the wave' that sweeps along the bottom of the groove toward the site of phagocytosis has been observed in a few species; its function is unclear. We investigated the presence, behavior, and function of the wave in four species from the three excavate clades (Discoba, Metamonada, and Malawimonadida) and found it present in all studied cases, suggesting the potential homology of this feature across all three groups. The wave displayed a species-specific behavior and was crucial for phagocytosis. The morphology of the feeding groove had an upper-prey size limit for successful prey captures, but smaller particles were not constrained. Additionally, the ingestion efficiencies were species dependent. By jointly studying these feeding traits, we speculate on adaptations to differences in food availability to better understand their ecological functions.
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Affiliation(s)
- Sei Suzuki-Tellier
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Eglit Y, Shiratori T, Jerlström-Hultqvist J, Williamson K, Roger AJ, Ishida KI, Simpson AGB. Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora. Curr Biol 2024; 34:451-459.e6. [PMID: 38262350 DOI: 10.1016/j.cub.2023.12.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024]
Abstract
"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.
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Affiliation(s)
- Yana Eglit
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Takashi Shiratori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Jon Jerlström-Hultqvist
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kelsey Williamson
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ken-Ichiro Ishida
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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3
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Weston EJ, Eglit Y, Simpson AGB. Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles. J Eukaryot Microbiol 2024; 71:e13003. [PMID: 37803921 DOI: 10.1111/jeu.13003] [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: 01/13/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator-prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free-swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di-eukaryotic (predator-prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single-cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 105 ± 4.0 × 104 cells ml-1 . Small-subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well-defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage.
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Affiliation(s)
- Elizabeth J Weston
- Institute for Comparative Genomics, and Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yana Eglit
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics, and Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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4
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Ebenezer TE, Low RS, O'Neill EC, Huang I, DeSimone A, Farrow SC, Field RA, Ginger ML, Guerrero SA, Hammond M, Hampl V, Horst G, Ishikawa T, Karnkowska A, Linton EW, Myler P, Nakazawa M, Cardol P, Sánchez-Thomas R, Saville BJ, Shah MR, Simpson AGB, Sur A, Suzuki K, Tyler KM, Zimba PV, Hall N, Field MC. Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Biol Open 2022; 11:bio059561. [PMID: 36412269 PMCID: PMC9836076 DOI: 10.1242/bio.059561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.
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Affiliation(s)
- ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross S. Low
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ishuo Huang
- Office of Regulatory Science, United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Antonio DeSimone
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Scott C. Farrow
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Robert A. Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Sergio Adrián Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral. CCT CONICET Santa Fe, Santa Fe 3000, Argentina
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 25250, Czech Republic
| | - Geoff Horst
- Kemin Industries, Research and Development, Plymouth, MI 48170, USA
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue 690-8504, Japan
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Warsaw 02-089, Poland
| | - Eric W. Linton
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Masami Nakazawa
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, 599-8531, Japan
| | - Pierre Cardol
- Department of Life Sciences, Institut de Botanique, Université de Liège, Liège 4000, Belgium
| | | | - Barry J. Saville
- Forensic Science, Environmental and Life Sciences Graduate Program, Trent University, Peterborough K9L 0G2, Canada
| | - Mahfuzur R. Shah
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Aakash Sur
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Kengo Suzuki
- R&D Company, Euglena Co., Ltd., 2F Yokohama Bio Industry Center (YBIC), 1-6 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kevin M. Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Center of Excellence for Bionanoscience Research, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Paul V. Zimba
- PVZimba, LLC, 12241 Percival St, Chester, VA 23831, USA
- Rice Rivers Center, VA Commonwealth University, Richmond, VA 23284, USA
| | - Neil Hall
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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5
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Gerbracht JV, Harding T, Simpson AGB, Roger AJ, Hess S. Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation. Curr Biol 2022; 32:3374-3384.e5. [PMID: 35700733 DOI: 10.1016/j.cub.2022.05.049] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/11/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Microbial eukaryotes display a stunning diversity of feeding strategies, ranging from generalist predators to highly specialized parasites. The unicellular "protoplast feeders" represent a fascinating mechanistic intermediate, as they penetrate other eukaryotic cells (algae and fungi) like some parasites but then devour their cell contents by phagocytosis.1 Besides prey recognition and attachment, this complex behavior involves the local, pre-phagocytotic dissolution of the prey cell wall, which results in well-defined perforations of species-specific size and structure.2 Yet the molecular processes that enable protoplast feeders to overcome cell walls of diverse biochemical composition remain unknown. We used the flagellate Orciraptor agilis (Viridiraptoridae, Rhizaria) as a model protoplast feeder and applied differential gene expression analysis to examine its penetration of green algal cell walls. Besides distinct expression changes that reflect major cellular processes (e.g., locomotion and cell division), we found lytic carbohydrate-active enzymes that are highly expressed and upregulated during the attack on the alga. A putative endocellulase (family GH5_5) with a secretion signal is most prominent, and a potential key factor for cell wall dissolution. Other candidate enzymes (e.g., lytic polysaccharide monooxygenases) belong to families that are largely uncharacterized, emphasizing the potential of non-fungal microeukaryotes for enzyme exploration. Unexpectedly, we discovered various chitin-related factors that point to an unknown chitin metabolism in Orciraptor agilis, potentially also involved in the feeding process. Our findings provide first molecular insights into an important microbial feeding behavior and new directions for cell biology research on non-model eukaryotes.
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Affiliation(s)
- Jennifer V Gerbracht
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Tommy Harding
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada
| | - Sebastian Hess
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada; Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada.
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6
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Author Correction: Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:7350. [PMID: 34916502 PMCID: PMC8677737 DOI: 10.1038/s41467-021-27605-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Dayana E Salas-Leiva
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
| | - Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Bruce A Curtis
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jon Jerlström-Hultqvist
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Joan S Salas-Leiva
- CONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136, Chihuahua, Chihuahua, México
| | - Lucie Gallot-Lavallée
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Shelby K Williams
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute - KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M Archibald
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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7
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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8
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More K, Simpson AGB, Hess S. Description of the marine predator Sericomyxa perlucida gen. et sp. nov., a cultivated representative of the deepest branching lineage of vampyrellid amoebae (Vampyrellida, Rhizaria). J Eukaryot Microbiol 2021; 68:e12864. [PMID: 34152052 DOI: 10.1111/jeu.12864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vampyrellids (Vampyrellida, Rhizaria) are naked amoebae of considerable genetic diversity. Three families have been well-defined (Vampyrellidae, Leptophryidae, and Placopodidae), but most vampyrellid lineages detected by environmental sequencing are poorly known or completely uncharacterized. In the brackish sediment of Lake Bras D'Or, Nova Scotia, Canada, we discovered an amoeba with a vampyrellid-like life history that was morphologically dissimilar from previously known vampyrellid taxa. We established a culture of this amoeba, studied its feeding behavior and prey range specificity, and characterized it with molecular phylogenetic methods and light and electron microscopy. The amoeba was a generalist predator (i.e. eukaryotroph), devouring a range of marine microalgae, with a strong affinity for some benthic diatoms and Chroomonas. Interestingly, the amoeba varied its feeding strategy depending on the prey species. Small diatoms were engulfed whole, while larger species were fed on through extraction with an invading pseudopodium. The SSU rRNA gene phylogenies robustly placed the amoeba in the most basal, poorly described lineage ("clade C") of the Vampyrellida. Based on the phylogenetic position and the distinct morphology of the studied amoeba, we here describe it as Sericomyxa perlucida gen. et sp. nov., and establish the new vampyrellid family Sericomyxidae for "clade C."
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Affiliation(s)
- Kira More
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Sebastian Hess
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
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9
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Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol 2021; 159:107088. [PMID: 33545276 DOI: 10.1016/j.ympev.2021.107088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/22/2022]
Abstract
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.
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Affiliation(s)
- G Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - M Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Y Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - W J Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - N Yubuki
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, Orsay, France; Department of Zoology, University of British Columbia, Vancouver, Canada
| | - A Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Poland
| | - B S Leander
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - G Burger
- Robert-Cedergren Centre for Bioinformatics and Genomics, Biochemistry Department, Université de Montréal, Montréal, Canada
| | - P J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - A G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
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10
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Heiss AA, Warring SD, Lukacs K, Favate J, Yang A, Gyaltshen Y, Filardi C, Simpson AGB, Kim E. Description of Imasa heleensis, gen. nov., sp. nov. (Imasidae, fam. nov.), a Deep-Branching Marine Malawimonad and Possible Key Taxon in Understanding Early Eukaryotic Evolution. J Eukaryot Microbiol 2020; 68:e12837. [PMID: 33274482 DOI: 10.1111/jeu.12837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/30/2020] [Revised: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 12/23/2022]
Abstract
Malawimonadida is a deep-level (arguably "kingdom-scale") lineage of eukaryotes whose phylogenetic affinities are uncertain but of great evolutionary interest, as the group is suspected to branch close to the root of the tree of eukaryotes. Part of the difficulty in placing Malawimonadida phylogenetically is its tiny circumscription: at present, it comprises only two described and one cultured but undescribed species, all of them are freshwater suspension-feeding nanoflagellates. In this study, we cultivated and characterised Imasa heleensis gen. nov., sp. nov. (Imasidae fam. nov.), the first marine malawimonad to be described. Light and electron microscopy observations show that Imasa is largely similar to other malawimonads, but more frequently adheres to the substrate, often by means of a pliable posterior extension. Phylogenetic analyses based on two ribosomal RNA genes and four translated protein-coding genes using three different taxon sets place Imasa as sister to the three freshwater malawimonad strains with strong support. Imasa's mitochondrial genome is circular-mapping and shows a similar gene complement to other known malawimonads. We conclude that Imasa represents an important expansion of the range of taxa available for future evolutionary study.
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Affiliation(s)
- Aaron A Heiss
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | - Sally D Warring
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | - Kaleigh Lukacs
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | - John Favate
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | - Ashley Yang
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | - Yangtsho Gyaltshen
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
| | | | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, 1355 Oxford St, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Eunsoo Kim
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York City, New York, 10024, USA
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11
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Ettahi K, Lhee D, Sung JY, Simpson AGB, Park JS, Yoon HS. Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea). Genome Biol Evol 2020; 13:5981115. [PMID: 33185659 PMCID: PMC7900873 DOI: 10.1093/gbe/evaa241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 12/29/2022] Open
Abstract
Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), because this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829-bp-long circular molecule, including 40 coding sequences (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and Naegleria fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).
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Affiliation(s)
- Khaoula Ettahi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Duckhyun Lhee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Ji Yeon Sung
- Department of Oceanography, Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, South Korea
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jong Soo Park
- Department of Oceanography, Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, South Korea.,Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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12
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Yazaki E, Kume K, Shiratori T, Eglit Y, Tanifuji G, Harada R, Simpson AGB, Ishida KI, Hashimoto T, Inagaki Y. Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP. Proc Biol Sci 2020; 287:20201538. [PMID: 32873198 PMCID: PMC7542792 DOI: 10.1098/rspb.2020.1538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected a putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
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Affiliation(s)
- Euki Yazaki
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Saitama, Japan
| | - Keitaro Kume
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takashi Shiratori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Ibaraki, Japan
| | - Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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13
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Lax G, Simpson AGB. The Molecular Diversity of Phagotrophic Euglenids Examined Using Single-cell Methods. Protist 2020; 171:125757. [PMID: 33126020 DOI: 10.1016/j.protis.2020.125757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/16/2023]
Abstract
Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, and phagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose. We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from Urceolus, Jenningsia, Chasmostoma, and Sphenomonas, and expanded coverage for Dinema and Heteronema sensu lato, amongst others. Urceolus monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. Heteronema vittatum and similar cells branch separately from Heteronema (c.f.) globuliferum and Teloprocta/Heteronema scaphurum, while Dinema appears as 2-3 clades. Sphenomonas is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.
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Affiliation(s)
- Gordon Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
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14
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Kolisko M, Flegontova O, Karnkowska A, Lax G, Maritz JM, Pánek T, Táborský P, Carlton JM, Čepička I, Horák A, Lukeš J, Simpson AGB, Tai V. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. Database (Oxford) 2020; 2020:5996027. [PMID: 33216898 PMCID: PMC7678783 DOI: 10.1093/database/baaa080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/04/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists—a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.
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Affiliation(s)
- Martin Kolisko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Olga Flegontova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland.,Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 128 43 Vestec, Czech Republic
| | - Gordon Lax
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julia M Maritz
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Tomáš Pánek
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Petr Táborský
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Jane M Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ivan Čepička
- Department of Zoology, Charles University, 128 00 Prague, Czech Republic
| | - Aleš Horák
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budeějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, 370 05 České Budeějovice (Budweis), Czech Republic
| | - Alastair G B Simpson
- Department of Biology and Centre of Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Vera Tai
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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15
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Abstract
For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - Alastair G B Simpson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada; Department of Biology, Dalhousie University, Halifax, NS, Canada.
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16
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Wideman JG, Lax G, Leonard G, Milner DS, Rodríguez-Martínez R, Simpson AGB, Richards TA. A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190100. [PMID: 31587636 PMCID: PMC6792441 DOI: 10.1098/rstb.2019.0100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Affiliation(s)
- Jeremy G Wideman
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Gordon Lax
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Guy Leonard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Raquel Rodríguez-Martínez
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Thomas A Richards
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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17
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Galindo LJ, Torruella G, Moreira D, Eglit Y, Simpson AGB, Völcker E, Clauß S, López-García P. Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190094. [PMID: 31587649 DOI: 10.1098/rstb.2019.0094] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nucleariid amoebae (Opisthokonta) have been known since the nineteenth century but their diversity and evolutionary history remain poorly understood. To overcome this limitation, we have obtained genomic and transcriptomic data from three Nuclearia, two Pompholyxophrys and one Lithocolla species using traditional culturing and single-cell genome (SCG) and single-cell transcriptome amplification methods. The phylogeny of the complete 18S rRNA sequences of Pompholyxophrys and Lithocolla confirmed their suggested evolutionary relatedness to nucleariid amoebae, although with moderate support for internal splits. SCG amplification techniques also led to the identification of probable bacterial endosymbionts belonging to Chlamydiales and Rickettsiales in Pompholyxophrys. To improve the phylogenetic framework of nucleariids, we carried out phylogenomic analyses based on two datasets of, respectively, 264 conserved proteins and 74 single-copy protein domains. We obtained full support for the monophyly of the nucleariid amoebae, which comprise two major clades: (i) Parvularia-Fonticula and (ii) Nuclearia with the scaled genera Pompholyxophrys and Lithocolla. Based on these findings, the evolution of some traits of the earliest-diverging lineage of Holomycota can be inferred. Our results suggest that the last common ancestor of nucleariids was a freshwater, bacterivorous, non-flagellated filose and mucilaginous amoeba. From the ancestor, two groups evolved to reach smaller (Parvularia-Fonticula) and larger (Nuclearia and related scaled genera) cell sizes, leading to different ecological specialization. The Lithocolla + Pompholyxophrys clade developed exogenous or endogenous cell coverings from a Nuclearia-like ancestor. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Guifré Torruella
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Yana Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
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Tikhonenkov DV, Jhin SH, Eglit Y, Miller K, Plotnikov A, Simpson AGB, Park JS. Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats. PLoS One 2019; 14:e0216188. [PMID: 31465455 PMCID: PMC6715209 DOI: 10.1371/journal.pone.0216188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/14/2019] [Indexed: 12/26/2022] Open
Abstract
The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide, from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rRNA gene phylogenies, unlike most previous analyses based on two sequences.
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Affiliation(s)
- Denis V. Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Soo Hwan Jhin
- Department of Oceanography, Research Institute for Dok-do and Ulleung-do Island and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kai Miller
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrey Plotnikov
- Center of Shared Scientific Equipment “Persistence of Microorganisms”, Institute for Cellular and Intracellular Symbiosis UB RAS, Orenburg, Russia
| | - Alastair G. B. Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Diversity, Toronto, Ontario, Canada
| | - Jong Soo Park
- Department of Oceanography, Research Institute for Dok-do and Ulleung-do Island and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea
- * E-mail:
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19
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Hess S, Eme L, Roger AJ, Simpson AGB. A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nat Microbiol 2019; 4:1620-1626. [DOI: 10.1038/s41564-019-0478-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 05/01/2019] [Indexed: 01/08/2023]
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20
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More K, Simpson AGB, Hess S. Two New Marine Species of Placopus (Vampyrellida, Rhizaria) That Perforate the Theca of Tetraselmis (Chlorodendrales, Viridiplantae). J Eukaryot Microbiol 2018; 66:560-573. [PMID: 30372564 DOI: 10.1111/jeu.12698] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 04/25/2018] [Revised: 09/18/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Vampyrellids (Vampyrellida, Rhizaria) are a major group of predatory amoebae known primarily from freshwater and soil. Environmental sequence data indicate that there is also a considerable diversity of vampyrellids inhabiting marine ecosystems, but their phenotypic traits and ecology remain largely unexplored. We discovered algivorous vampyrellids of the filoflabellate morphotype in coastal habitats in Atlantic Canada, established cultures by single-cell isolation, and characterised three strains using light microscopy, SSU rRNA gene sequencing, feeding experiments and growth experiments at various salinities. These strains exhibit orange, discoid trophozoites with ventral filopodia, moving granules ("membranosomes"), and rolling locomotion, similar to freshwater species previously assigned to Hyalodiscus Hertwig & Lesser, but here moved to Placopus Schulze (due to homonymy with Hyalodiscus Ehrenberg). SSU rRNA gene phylogenies place our strains in two distinct positions within "lineage B3" (here referred to as Placopodidae). Based on these morphological, habitat and molecular data, we describe two new species, Placopus melkoniani sp. nov. and Placopus pusillus sp. nov., both of which feed on chlorophyte flagellates (Tetraselmis, Pyramimonas) and the cryptophyte Chroomonas. They perforate the theca of Tetraselmis to extract the protoplast, and thereby represent the first vampyrellids known to degrade the biochemically exotic cell wall of the Chlorodendrales (Chlorophyta, Viridiplantae).
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Affiliation(s)
- Kira More
- Department of Biology, Dalhousie University, Halifax, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Sebastian Hess
- Department of Biology, Dalhousie University, Halifax, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
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21
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Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AGB, Roger AJ. Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group. Genome Biol Evol 2018; 10:427-433. [PMID: 29360967 PMCID: PMC5793813 DOI: 10.1093/gbe/evy014] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 01/13/2023] Open
Abstract
Recent phylogenetic analyses position certain “orphan” protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas, and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel super-group-level clade that includes collodictyonids, rigifilids, and Mantamonas, which we name “CRuMs”. Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.
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Affiliation(s)
- Matthew W Brown
- Department of Biological Sciences, Mississippi State University, USA.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA
| | - Aaron A Heiss
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, USA.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA
| | - Takashi Shiratori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Ken-Ichiro Ishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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22
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Goodwin JD, Lee TF, Kugrens P, Simpson AGB. Allobodo chlorophagus n. gen. n. sp., a Kinetoplastid that Infiltrates and Feeds on the Invasive Alga Codium fragile. Protist 2018; 169:911-925. [PMID: 30445354 DOI: 10.1016/j.protis.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 04/08/2018] [Revised: 07/21/2018] [Accepted: 07/24/2018] [Indexed: 11/24/2022]
Abstract
A novel biflagellate protist that consumed chloroplasts inside material of the invasive marine green alga Codium fragile was reported from the U.S. east coast in 2003. We observed a similar association in C. fragile from five sites in Nova Scotia, Canada during 2013 and 2014. After incubating Codium fragments for 2-3 days, some utricles and filaments contained numerous chloroplast-consuming cells. Transmission electron microscopy (TEM) confirmed that these were kinetoplastids with a pankinetoplast, large electron-dense droplets in the cytoplasm and a connective between the paraxonemal rod bases, but no conspicuous para-cytopharyngeal rod, all consistent with U.S. material observed in 2003. The ITS1-5.8S rRNA-ITS2 sequences from 13 Nova Scotia isolates were identical. SSU rRNA gene phylogenies placed the Codium-associated kinetoplastid in neobodonid clade '1E'. Clade 1E likely contains no previously described species, and branches outside all other major neobodonid groups, either as their sister or as a separate lineage, depending on rooting. These results indicate that the kinetoplastid represents a single species that merits a new genus (and family), and we describe it as Allobodo chlorophagus n. gen., n. sp. The lack of evidence for food sources other than Codium is consistent with a parasitic association, but other possibilities exist (e.g. necrotrophy).
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Affiliation(s)
- Joshua D Goodwin
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax B3H 4R2, Canada
| | | | | | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax B3H 4R2, Canada.
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23
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Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. R Soc Open Sci 2018; 5:171707. [PMID: 29765641 PMCID: PMC5936906 DOI: 10.1098/rsos.171707] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/06/2018] [Indexed: 05/16/2023]
Abstract
Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of 'typical excavates', including flagellar vanes (as an opposed pair, unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of '-FS/LB' datasets instead suggested a relationship between malawimonads and metamonads. The 'malawimonad+metamonad signal' in morphological and molecular data argues against a strict Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes.
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Affiliation(s)
- Aaron A. Heiss
- Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Martin Kolisko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Fleming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Matthew W. Brown
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Andrew J. Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alastair G. B. Simpson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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24
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Harding T, Simpson AGB. Recent Advances in Halophilic Protozoa Research. J Eukaryot Microbiol 2018; 65:556-570. [PMID: 29266533 DOI: 10.1111/jeu.12495] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 08/21/2017] [Revised: 11/14/2017] [Accepted: 12/08/2017] [Indexed: 11/30/2022]
Abstract
Most research on microorganisms adapted to hypersaline habitats has focused on Archaea and Bacteria, with microbial eukaryotes receiving much less attention. Over the past 15 yr, our knowledge of phagotrophic microbial eukaryotes, i.e. protozoa, from hypersaline habitats has greatly improved through combinations of microscopy, molecular phylogenetics, environmental sequencing, transcriptomics and growth experiments. High salinity waters from salterns, other landlocked water masses and deep hypersaline anoxic basins contain unique and diverse halophilic protozoan assemblages. These have the potential to exert substantial grazing pressure on prokaryotes and other eukaryotes. They represent many separate evolutionary lineages; species of Heterolobosea, Bicosoecida, and Ciliophora have been most intensively characterized, with several proven to be extreme (or borderline extreme) halophiles. Transcriptomic examinations of the bicosoecid Halocafeteria (and the heteroloboseid Pharyngomonas) indicate that high-salt adaptation is associated with a subtle shift in protein amino acid composition, and involves the differential expression of genes participating in ion homeostasis, signal transduction, stress management, and lipid remodeling. Instances of gene duplication and lateral transfer possibly conferring adaptation have been documented. Indirect evidence suggests that these protozoa use "salt-out" osmoadaptive strategies.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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25
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Yang J, Harding T, Kamikawa R, Simpson AGB, Roger AJ. Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids. Genome Biol Evol 2017; 9:1161-1174. [PMID: 28453770 PMCID: PMC5421314 DOI: 10.1093/gbe/evx086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third main group of Discoba. Here, we studied two heteroloboseids—an undescribed amoeba “BB2” and Pharyngomonas kirbyi. Phylogenomic analysis revealed that they form a clade that is a sister group to all other Heterolobosea. We characterized the mitochondrial genomes of BB2 and P. kirbyi, which encoded 44 and 48 putative protein-coding genes respectively. Their gene contents were similar to that of Naegleria. In BB2, mitochondrially encoded RNAs were heavily edited, with ∼500 mononucleotide insertion events, mostly guanosines. These insertions always have the same identity as an adjacent nucleotide. Editing occurs in all ribosomal RNAs and protein-coding transcripts except one, and half of the transfer RNAs. Analysis of Illumina deep-sequencing data suggested that this RNA editing is very accurate and efficient, and most likely co-transcriptional. The dissimilarity of this editing process to other RNA editing phenomena in discobids, as well as its apparent absence in P. kirbyi, suggest that this remarkably extensive system of insertional editing evolved independently in the BB2 lineage, after its divergence from the P. kirbyi lineage.
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Affiliation(s)
- Jiwon Yang
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tommy Harding
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Japan
| | - Alastair G B Simpson
- Centre for Comparative Genomics and Evolutionary Bioinformatics and Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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26
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Harding T, Roger AJ, Simpson AGB. Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers. Front Microbiol 2017; 8:944. [PMID: 28611746 PMCID: PMC5447177 DOI: 10.3389/fmicb.2017.00944] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa. To gather fundamental knowledge about salt adaptation in these organisms, we studied the transcriptome-level response of Halocafeteria seosinensis (Stramenopiles) grown under contrasting salinities. We provided further evolutionary context to our analysis by identifying genes that underwent recent duplications. Genes that were highly responsive to salinity variations were involved in stress response (e.g., chaperones), ion homeostasis (e.g., Na+/H+ transporter), metabolism and transport of lipids (e.g., sterol biosynthetic genes), carbohydrate metabolism (e.g., glycosidases), and signal transduction pathways (e.g., transcription factors). A significantly high proportion (43%) of duplicated genes were also differentially expressed, accentuating the importance of gene expansion in adaptation by H. seosinensis to high salt environments. Furthermore, we found two genes that were lateral acquisitions from bacteria, and were also highly up-regulated and highly expressed at high salt, suggesting that this evolutionary mechanism could also have facilitated adaptation to high salt. We propose that a transition toward high-salt adaptation in the ancestors of H. seosinensis required the acquisition of new genes via duplication, and some lateral gene transfers (LGTs), as well as the alteration of transcriptional programs, leading to increased stress resistance, proper establishment of ion gradients, and modification of cell structure properties like membrane fluidity.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
| | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie UniversityHalifax, NS, Canada
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Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. UniEuk: Time to Speak a Common Language in Protistology! J Eukaryot Microbiol 2017; 64:407-411. [PMID: 28337822 PMCID: PMC5435949 DOI: 10.1111/jeu.12414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
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Affiliation(s)
- Cédric Berney
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Andreea Ciuprina
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany
| | - Sara Bender
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA
| | - Jeena Rajan
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Laura Wegener Parfrey
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada
| | - Stéphane Audic
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Lucas Czech
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Frank Oliver Glöckner
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | | | - Christian Quast
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Jonathan Z Kaye
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.,Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany
| | - Javier Del Campo
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Colomban de Vargas
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
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Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nat Ecol Evol 2017; 1:0092. [PMID: 28474007 PMCID: PMC5411260 DOI: 10.1038/s41559-017-0092] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Michelle M Leger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Keitaro Kume
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, USA
| | - Jan O Andersson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Feifei Xu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, People's Republic of China
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
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Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016; 16:197. [PMID: 27716026 PMCID: PMC5052871 DOI: 10.1186/s12862-016-0771-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
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Affiliation(s)
- Lukáš Novák
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Anna Karnkowska
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Courtney W. Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | | | | | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ivan Čepička
- Department of Zoology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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30
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Xu F, Jerlström-Hultqvist J, Kolisko M, Simpson AGB, Roger AJ, Svärd SG, Andersson JO. Erratum to: On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biol 2016; 14:77. [PMID: 27619515 PMCID: PMC5018941 DOI: 10.1186/s12915-016-0302-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022] Open
Affiliation(s)
- Feifei Xu
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Present address: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Martin Kolisko
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Present address: Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan O Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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31
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Harding T, Brown MW, Simpson AGB, Roger AJ. Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists. Genome Biol Evol 2016; 8:2241-58. [PMID: 27412608 PMCID: PMC4987115 DOI: 10.1093/gbe/evw152] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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] [Accepted: 06/22/2016] [Indexed: 01/17/2023] Open
Abstract
Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These "salt-in" organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, "salt-out" halophiles accumulate large amounts of organic solutes like amino acids, sugars and polyols, and lack a strong signature of halophilicity in the amino acid composition of cytoplasmic proteins. Studies to date have examined halophilic prokaryotes, yeasts, or algae, thus virtually nothing is known about the molecular adaptations of the other eukaryotic microbes, that is, heterotrophic protists (protozoa), that also thrive in hypersaline habitats. We conducted transcriptomic investigations to unravel the molecular adaptations of two obligately halophilic protists, Halocafeteria seosinensis and Pharyngomonas kirbyi Their predicted cytoplasmic proteomes showed increased hydrophilicity compared with marine protists. Furthermore, analysis of reconstructed ancestral sequences suggested that, relative to mesophiles, proteins in halophilic protists have undergone fewer substitutions from hydrophilic to hydrophobic residues since divergence from their closest relatives. These results suggest that these halophilic protists have a higher intracellular salt content than marine protists. However, absence of the acidic signature of salt-in microbes suggests that Haloc. seosinensis and P. kirbyi utilize organic osmolytes to maintain osmotic equilibrium. We detected increased expression of enzymes involved in synthesis and transport of organic osmolytes, namely hydroxyectoine and myo-inositol, at maximal salt concentration for growth in Haloc. seosinensis, suggesting possible candidates for these inferred organic osmolytes.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University
| | - Alastair G B Simpson
- Department of Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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32
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Xu F, Jerlström-Hultqvist J, Kolisko M, Simpson AGB, Roger AJ, Svärd SG, Andersson JO. On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biol 2016; 14:62. [PMID: 27480115 PMCID: PMC4967989 DOI: 10.1186/s12915-016-0284-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/13/2016] [Indexed: 01/08/2023] Open
Abstract
Background It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living. Results We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes. Conclusions Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0284-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feifei Xu
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Present address: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Martin Kolisko
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Present address: Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan O Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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33
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Zhang Q, Táborský P, Silberman JD, Pánek T, Čepička I, Simpson AGB. Marine Isolates of Trimastix marina Form a Plesiomorphic Deep-branching Lineage within Preaxostyla, Separate from Other Known Trimastigids (Paratrimastix n. gen.). Protist 2015; 166:468-91. [PMID: 26312987 DOI: 10.1016/j.protis.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 03/18/2015] [Revised: 06/12/2015] [Accepted: 07/02/2015] [Indexed: 11/17/2022]
Abstract
Trimastigids are free-living, anaerobic protists that are closely related to the symbiotic oxymonads, forming together the taxon Preaxostyla (Excavata: Metamonada). We isolated fourteen new strains morphologically corresponding to two species assigned to Trimastix (until now the only genus of trimastigids), Trimastix marina and Trimastix pyriformis. Unexpectedly, marine strains of Trimastix marina branch separately from freshwater strains of this morphospecies in SSU rRNA gene trees, and instead form the sister group of all other Preaxostyla. This position is confirmed by three-gene phylogenies. Ultrastructural examination of a marine isolate of Trimastix marina demonstrates a combination of trimastigid-like features (e.g. preaxostyle-like I fibre) and ancestral characters (e.g. absence of thickened flagellar vane margins), consistent with inclusion of marine T. marina within Preaxostyla, but also supporting its distinctiveness from 'freshwater T. marina' and its deep-branching position within Preaxostyla. Since these results indicate paraphyly of Trimastix as currently understood, we transfer the other better-studied trimastigids to Paratrimastix n. gen. and Paratrimastigidae n. fam. The freshwater form previously identified as T. marina is described as Paratrimastix eleionoma n. sp., and Trimastix pyriformis becomes Paratrimastix pyriformis n. comb. Because of its phylogenetic position, 'true' Trimastix is potentially important for understanding the evolution of mitochondrion-related organelles in metamonads.
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Affiliation(s)
- Qianqian Zhang
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Canada; Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, China
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague 2, Czech Republic
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34
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Heiss AA, Lee WJ, Ishida KI, Simpson AGB. Cultivation and Characterisation of New Species of Apusomonads (the Sister Group to Opisthokonts), Including Close Relatives of Thecamonas (Chelonemonas n. gen.). J Eukaryot Microbiol 2015; 62:637-49. [PMID: 25912654 DOI: 10.1111/jeu.12220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 10/12/2014] [Revised: 12/15/2014] [Accepted: 12/28/2014] [Indexed: 11/29/2022]
Abstract
Apusomonads comprise an understudied and undersampled group of heterotrophic flagellates that is closely related to opisthokonts, the supergroup containing animals and fungi. We cultured representatives of a new clade of apusomonads, Chelonemonas n. gen., which is sister to marine forms of Thecamonas in SSU rRNA gene phylogenies. Scanning electron microscopy shows that members of Chelonemonas have a hexagonal patterning to their submembranous pellicle, which is not known to exist in other apusomonads. We propose that the subfamily Thecamonadinae refer to the marine Thecamonas/Chelonomonas clade. We also report two new strains of Multimonas, one of which is genetically divergent from previously described strains, and here described as a new species, Multimonas koreensis. Both strains of Multimonas have appendages on their dorsal surface that could be extrusomes, and a frilled appearance to the border of their pellicle. Explorations of taxon sampling in SSU rRNA gene phylogenies confirm the new strains' evolutionary affinities, but do not resolve relationships among the five main apusomonad clades. These phylogenies also separate the freshwater species "Thecamonas" oxoniensis from the marine members of the genus Thecamonas. The new strains described here may provide valuable genetic and morphological data for evaluating the relationships and evolution of apusomonads.
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Affiliation(s)
- Aaron A Heiss
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Won J Lee
- Department of Urban Environmental Engineering, Kyungnam University, Changwon, 631-701, Korea
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Canadian Institute for Advanced Research, Program in Integrated Microbial Diversity
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35
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Kirby WA, Tikhonenkov DV, Mylnikov AP, Janouškovec J, Lax G, Simpson AGB. Characterization of Tulamoeba bucina n. sp., an extremely halotolerant amoeboflagellate heterolobosean belonging to the Tulamoeba-Pleurostomum clade (Tulamoebidae n. fam.). J Eukaryot Microbiol 2014; 62:227-38. [PMID: 25227416 DOI: 10.1111/jeu.12172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 12/26/2013] [Revised: 06/23/2014] [Accepted: 07/30/2014] [Indexed: 12/01/2022]
Abstract
Most protozoans that have been cultivated recently from high salinity waters appear to be obligate halophiles. Phylogenetic analyses indicate that these species mostly represent independent lineages. Here, we report the cultivation, morphological characterization, and phylogenetic analysis of two strains (XLG1 and HLM-8) of a new extremely halotolerant heterolobosean amoeboflagellate. This species is closely related to the obligate halophiles Tulamoeba peronaphora and Pleurostomum flabellatum, and more specifically to the former. Like Tulamoeba, the new species has a monopodial limax amoeba stage, however, its cyst stage lacks an intrusive pore plug. The flagellate stage bears a combination of a planar spiral feeding apparatus and unequal heterodynamic flagella that discriminates it from described Pleurostomum species. Strain XLG1 grows at salinities from 35‰ to 225‰. This degree of halotolerance is uncommon in protozoa, as most species showing growth in seawater are unable to grow at 200‰ salinity. The unrelatedness of most halophilic protozoa suggested that independent colonization of the hypersaline environment is more common than speciation within it. However, this study supports the idea that the Tulamoeba-Pleurostomum clade underwent an adaptive radiation within the hypersaline environment. A new species Tulamoeba bucina n. sp. is described, with Tulamoebidae n. fam. proposed for the Tulamoeba-Pleurostomum clade.
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Affiliation(s)
- William A Kirby
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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36
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Lee WJ, Simpson AGB. Morphological and Molecular Characterisation of Notosolenus urceolatus
Larsen and Patterson 1990, a Member of an Understudied Deep-branching Euglenid Group (Petalomonads). J Eukaryot Microbiol 2014; 61:463-79. [DOI: 10.1111/jeu.12126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/15/2014] [Accepted: 04/24/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Won Je Lee
- Department of Urban Environmental Engineering; Kyungnam University; Changwon 631-701 Korea
| | - Alastair G. B. Simpson
- Department of Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
- Canadian Institute for Advanced Research; Program in Integrated Microbial Biodiversity
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37
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Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AGB, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 2014; 12:e1001889. [PMID: 24959919 PMCID: PMC4068987 DOI: 10.1371/journal.pbio.1001889] [Citation(s) in RCA: 613] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
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Affiliation(s)
- Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- * E-mail: (PJK); (AZW)
| | - Fabien Burki
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heather M. Wilcox
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Linda A. Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Geological Sciences, Brown University, Providence, Rhode Island, United States of America
| | - E. Virginia Armbrust
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - John M. Archibald
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arvind K. Bharti
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Bank Beszteri
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kay D. Bidle
- Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Connor T. Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Lisa Campbell
- Department of Oceanography, Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - David A. Caron
- Department of Biology, University of Southern California, Los Angeles, California, United States of America
| | - Rose Ann Cattolico
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathryn Coyne
- University of Delaware, School of Marine Science and Policy, College of Earth, Ocean, and Environment, Lewes, Delaware, United States of America
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Phillipe Deschamps
- Unité d'Ecologie, Systematique et Evolution, CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | | | - Ruth D. Gates
- Hawaii Institute of Marine Biology, University of Hawaii, Hawaii, United States of America
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Spencer J. Greenwood
- Department of Biomedical Sciences and AVC Lobster Science Centre, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Stephanie M. Guida
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Jennifer L. Jacobi
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | | | - Erick R. James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bethany Jenkins
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Matthew D. Johnson
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Andrew R. Juhl
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, New York, New York, United States of America
| | - Anja Kamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen, Molecular Life Science Research Center, Bremen, Germany
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Ronald Kiene
- University of South Alabama, Dauphin Island Sea Lab, Mobile, Alabama, United States of America
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Brian S. Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, Canada
| | - Denis Lynn
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adrian Marchetti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - George McManus
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Aurora M. Nedelcu
- University of New Brunswick, Department of Biology, Fredericton, New Brusnswick, Canada
| | - Susanne Menden-Deuer
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Shauna Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, Australia
| | - Govind Nadathur
- Department of Marine Sciences, University of Puerto Rico, Mayaguez, Puerto Rico, United States of America
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Kanagawa, Japan
| | - Peter B. Ngam
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Brian Palenik
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Gwenael Piganeau
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, BIOM, Banyuls-sur-Mer, France
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | | | | | - Mary E. Rumpho
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Tatiana Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Kelly B. Schilling
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Declan C. Schroeder
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
| | - Alastair G. B. Simpson
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H. Slamovits
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - G. Jason Smith
- Moss Landing Marine Laboratories, Moss Landing, California, United States of America
| | - Sarah R. Smith
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Heidi M. Sosik
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Peter Stief
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Edward Theriot
- Section of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Scott N. Twary
- Los Alamos National Laboratory, Biosciences, Los Alamos, New Mexico, United States of America
| | - Pooja E. Umale
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Daniel Vaulot
- UMR714, CNRS and UPMC (Paris-06), Station Biologique, Roscoff, France
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Glen L. Wheeler
- The Marine Biological Association of the United Kingdom, Plymouth, United Kingdom
- Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - William H. Wilson
- NCMA, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Yan Xu
- Princeton University, Princeton, New Jersey, United States of America
| | | | - Alexandra Z. Worden
- Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- * E-mail: (PJK); (AZW)
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Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AGB, Roger AJ. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci 2013; 280:20131755. [PMID: 23986111 DOI: 10.1098/rspb.2013.1755] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most eukaryotic lineages belong to one of a few major groups. However, several protistan lineages have not yet been robustly placed in any of these groups. Both the breviates and apusomonads are two such lineages that appear to be related to the Amoebozoa and Opisthokonta (i.e. the 'unikonts' or Amorphea); however, their precise phylogenetic positions remain unclear. Here, we describe a novel microaerophilic breviate, Pygsuia biforma gen. nov. sp. nov., isolated from a hypoxic estuarine sediment. Ultrastructurally, this species resembles the breviate genera Breviata and Subulatomonas but has two cell morphologies, adherent and swimming. Phylogenetic analyses of the small sub-unit rRNA gene show that Pygsuia is the sister to the other breviates. We constructed a 159-protein supermatrix, including orthologues identified in RNA-seq data from Pygsuia. Phylogenomic analyses of this dataset show that breviates, apusomonads and Opisthokonta form a strongly supported major eukaryotic grouping we name the Obazoa. Although some phylogenetic methods disagree, the balance of evidence suggests that the breviate lineage forms the deepest branch within Obazoa. We also found transcripts encoding a nearly complete integrin adhesome from Pygsuia, indicating that this protein complex involved in metazoan multicellularity may have evolved earlier in eukaryote evolution than previously thought.
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Affiliation(s)
- Matthew W Brown
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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39
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Lax G, Simpson AGB. Combining Molecular Data with Classical Morphology for Uncultured Phagotrophic Euglenids (Excavata): A Single-Cell Approach. J Eukaryot Microbiol 2013; 60:615-25. [DOI: 10.1111/jeu.12068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/13/2013] [Accepted: 06/05/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Gordon Lax
- Department of Ecology; University of Kaiserslautern; Erwin-Schrödinger-Straβe 14 67663 Kaiserslautern Germany
| | - Alastair G. B. Simpson
- Canadian Institute for Advanced Research; Program in Integrated Microbial Diversity and Department of Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
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40
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Kamikawa R, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AGB, Roger AJ, Hashimoto T, Inagaki Y. Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol Biol 2013; 13:131. [PMID: 23800323 PMCID: PMC3699394 DOI: 10.1186/1471-2148-13-131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Elongation factor-1α (EF-1α) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a 'differential loss' hypothesis that assumes that EF-1α and EFL were present in the most recent common ancestor of eukaryotes followed by independent differential losses of one of the two factors in the descendant lineages. To date, however, just one diatom and one fungus have been found to have both EF-1α and EFL (dual-EF-containing species). RESULTS In this study, we characterized 35 new EF-1α/EFL sequences from phylogenetically diverse eukaryotes. In so doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groups including the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested vertical inheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1α genes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to the co-occurring EFL genes. CONCLUSIONS According to the known EF-1α/EFL distribution, the differential loss process should have occurred independently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predict that dual-EF-containing species retain the divergent EF-1α homologues only for a sub-set of the original functions. As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1α function took place in multiple branches in the tree of eukaryotes.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan.
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41
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Feehan CJ, Johnson-Mackinnon J, Scheibling RE, Lauzon-Guay JS, Simpson AGB. Validating the identity of Paramoeba invadens, the causative agent of recurrent mass mortality of sea urchins in Nova Scotia, Canada. Dis Aquat Organ 2013; 103:209-227. [PMID: 23574707 DOI: 10.3354/dao02577] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Green sea urchins Strongylocentrotus droebachiensis along the coast of Nova Scotia, Canada, suffer mass mortalities from infection by the pathogenic amoeba Paramoeba invadens Jones, 1985. It has been speculated that P. invadens could be a form of Neoparamoeba pemaquidensis, a species associated with disease in S. droebachiensis and lobsters in the northeast USA. During a disease outbreak in fall 2011, we isolated amoebae from moribund urchins collected from 4 locations along ~200 km of coastline. In laboratory infection trials, we found that timing and rate of morbidity corresponded to that of similar experiments conducted in the early 1980s, when P. invadens was first identified. All isolates had a similar size and morphology to the original description, including an absence of microscales. Sequences of nuclear SSU rDNA show that disease was caused by one 'species' of amoeba across the range sampled. Phylogenetic analyses prove that P. invadens is not conspecific with N. pemaquidensis, but is a distinct species most closely related to N. branchiphila, a suspected pathogen of sea urchins Diadema aff. antillarum in the Canary Islands, Spain. Morphology and closest phylogenetic affinities suggest that P. invadens would be assignable to the genus Neoparamoeba; however, nuclear SSU rDNA trees show that Neoparamoeba and Paramoeba are phylogenetically inseparable. Therefore, we treat Neoparamoeba as a junior synonym of Paramoeba, with P. invadens retaining that name, and N. pemaquidensis and N. aestuarina reverting to their original names (P. pemaquidensis and P. aestuarina), and with new combinations for N. branchiphila Dykova et al., 2005, and N. perurans Young et al., 2007, namely P. branchiphila comb. nov. and P. perurans comb. nov.
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Affiliation(s)
- Colette J Feehan
- Biology Department, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
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42
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Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. The revised classification of eukaryotes. J Eukaryot Microbiol 2013; 59:429-93. [PMID: 23020233 DOI: 10.1111/j.1550-7408.2012.00644.x] [Citation(s) in RCA: 897] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
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Affiliation(s)
- Sina M Adl
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
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Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EAD, Nitsche F, Romeralo M, Saunders GW, Simpson AGB, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, de Vargas C. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol 2012; 10:e1001419. [PMID: 23139639 PMCID: PMC3491025 DOI: 10.1371/journal.pbio.1001419] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- * E-mail: (JP); (CdV)
| | - Stéphane Audic
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144 and Université Pierre et Marie Curie, Paris 6, Station Biologique de Roscoff, France
| | - Sina Adl
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Lassaâd Belbahri
- Laboratory of Soil Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cédric Berney
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Samuel S. Bowser
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Ivan Cepicka
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
| | - Johan Decelle
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144 and Université Pierre et Marie Curie, Paris 6, Station Biologique de Roscoff, France
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anna Maria Fiore-Donno
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Gillian H. Gile
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maria Holzmann
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Regine Jahn
- Botanischer Garten und Botanischer Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Miloslav Jirků
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Patrick J. Keeling
- Canadian Institute for Advanced Research, Botany Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Kostka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Alexander Kudryavtsev
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Invertebrate Zoology, St-Petersburg State University, St-Petersburg, Russia
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - David G. Mann
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | | | - Frank Nitsche
- Allgemeine Ökologie, Universität zu Köln, Köln, Germany
| | - Maria Romeralo
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Gary W. Saunders
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | | | - Alexey V. Smirnov
- Department of Invertebrate Zoology, St-Petersburg State University, St-Petersburg, Russia
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Computational Biology Branch, Bethesda, Maryland, United States of America
| | - Rowena F. Stern
- Sir Alister Hardy Foundation for Ocean Science, Citadel Hill, Plymouth, United Kingdom
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jonas Zimmermann
- Botanischer Garten und Botanischer Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
- Justus-Liebig-University, Giessen, Germany
| | - David Schindel
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144 and Université Pierre et Marie Curie, Paris 6, Station Biologique de Roscoff, France
- * E-mail: (JP); (CdV)
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Harding T, Brown MW, Plotnikov A, Selivanova E, Park JS, Gunderson JH, Baumgartner M, Silberman JD, Roger AJ, Simpson AGB. Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications. Protist 2012; 164:272-86. [PMID: 23021907 DOI: 10.1016/j.protis.2012.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/16/2012] [Accepted: 08/23/2012] [Indexed: 11/30/2022]
Abstract
The taxon Heterolobosea (Excavata) is a major group of protists well known for its diversity of life stages. Most are amoebae capable of transforming into flagellates (amoeboflagellates), while others are known solely as flagellates or solely as amoebae. The deepest-branching heterolobosean taxon confirmed previously, Pharyngomonas, was generally assumed to be a pure flagellate, suggesting that the amoeba form arose later in the evolution of Heterolobosea sensu lato. Here we report that multiple isolates of Pharyngomonas are actually amoeboflagellates that also have cyst stages, with only amoebae transforming into cysts. The amoeba form of Pharyngomonas showed heterolobosean characteristics (e. g. eruptive movement), but also possessed unusual morphological features like slow-flowing crenulated hyaline crescents with conical subpseudopodia, finger-like projections and branching posterior extensions. Furthermore, phylogenetic analyses of 18S ribosomal RNA gene sequences that included two undescribed species of amoebae showed that Pharyngomonas is not the only deep-branching heterolobosean to possess an amoeba stage. These results suggest that possession of an amoeba stage was ancestral for Heterolobosea, unifying this taxon as a group of species with amoeba stages in their lifecycle or derived from organisms with such stages.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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45
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Park JS, De Jonckheere JF, Simpson AGB. Characterization of Selenaion koniopes n. gen., n. sp., an amoeba that represents a new major lineage within heterolobosea, isolated from the Wieliczka salt mine. J Eukaryot Microbiol 2012; 59:601-13. [PMID: 22888835 DOI: 10.1111/j.1550-7408.2012.00641.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 06/15/2012] [Indexed: 11/30/2022]
Abstract
A new heterolobosean amoeba, Selenaion koniopes n. gen., n. sp., was isolated from 73‰ saline water in the Wieliczka salt mine, Poland. The amoeba had eruptive pseudopodia, a prominent uroid, and a nucleus without central nucleolus. Cysts had multiple crater-like pore plugs. No flagellates were observed. Transmission electron microscopy revealed several typical heterolobosean features: flattened mitochondrial cristae, mitochondria associated with endoplasmic reticulum, and an absence of obvious Golgi dictyosomes. Two types of larger and smaller granules were sometimes abundant in the cytoplasm--these may be involved in cyst formation. Mature cysts had a fibrous endocyst that could be thick, plus an ectocyst that was covered with small granules. Pore plugs had a flattened dome shape, were bipartite, and penetrated only the endocyst. Phylogenies based on the 18S rRNA gene and the presence of 18S rRNA helix 17_1 strongly confirmed assignment to Heterolobosea. The organism was not closely related to any described genus, and instead formed the deepest branch within the Heterolobosea clade after Pharyngomonas, with support for this deep-branching position being moderate (i.e. maximum likelihood bootstrap support--67%; posterior probability--0.98). Cells grew at 15-150‰ salinity. Thus, S. koniopes is a halotolerant, probably moderately halophilic heterolobosean, with a potentially pivotal evolutionary position within this large eukaryote group.
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Affiliation(s)
- Jong Soo Park
- Department of Oceanography and Institute for Phylogenomics and Evolution, Kyungpook National University, Sangju, 742-711, Korea
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46
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Takishita K, Kolisko M, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, Smejkalová P, Silberman JD, Hashimoto T, Roger AJ, Simpson AGB. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads. Protist 2012; 163:344-55. [PMID: 22364773 DOI: 10.1016/j.protis.2011.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 12/14/2011] [Indexed: 11/28/2022]
Abstract
Diplomonads, retortamonads, and "Carpediemonas-like" organisms (CLOs) are a monophyletic group of protists that are microaerophilic/anaerobic and lack typical mitochondria. Most diplomonads and retortamonads are parasites, and the pathogen Giardia intestinalis is known to possess reduced mitochondrion-related organelles (mitosomes) that do not synthesize ATP. By contrast, free-living CLOs have larger organelles that superficially resemble some hydrogenosomes, organelles that in other protists are known to synthesize ATP anaerobically. This group represents an excellent system for studying the evolution of parasitism and anaerobic, mitochondrion-related organelles. Understanding these evolutionary transitions requires a well-resolved phylogeny of diplomonads, retortamonads and CLOs. Unfortunately, until now the deep relationships amongst these taxa were unresolved due to limited data for almost all of the CLO lineages. To address this, we assembled a dataset of up to six protein-coding genes that includes representatives from all six CLO lineages, and complements existing rRNA datasets. Multigene phylogenetic analyses place CLOs as well as the retortamonad Chilomastix as a paraphyletic basal assemblage to the lineage comprising diplomonads and the retortamonad Retortamonas. In particular, the CLO Dysnectes was shown to be the closest relative of the diplomonads + Retortamonas clade, with strong support. This phylogeny is consistent with a drastic degeneration of mitochondrion-related organelles during the evolution from a free-living organism resembling extant CLOs to a probable parasite/commensal common ancestor of diplomonads and Retortamonas.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
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Abstract
The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science. Yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. Here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. This approach was validated against well-known taxa, and when applied to all domains of life, it predicts ~8.7 million (± 1.3 million SE) eukaryotic species globally, of which ~2.2 million (± 0.18 million SE) are marine. In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86% of existing species on Earth and 91% of species in the ocean still await description. Renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on Earth is to be closed.
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Affiliation(s)
- Camilo Mora
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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48
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Park JS, Simpson AGB. Characterization of Pharyngomonas kirbyi (= "Macropharyngomonas halophila" nomen nudum), a very deep-branching, obligately halophilic heterolobosean flagellate. Protist 2011; 162:691-709. [PMID: 21723194 DOI: 10.1016/j.protis.2011.05.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 02/14/2011] [Indexed: 11/15/2022]
Abstract
The tetraflagellate Pharyngomonas is among the most commonly reported morphotypes of halophilic protozoa. We have established two cultures of Pharyngomonas kirbyi, SD1A and AS12B, from 300‰ and 210‰ salinity waters from the USA and Australia, respectively. 18S rRNA gene phylogenies confirm that Pharyngomonas is the same entity as 'Macropharyngomonas' (nomen nudum), and represents the deepest branch in the heterolobosean lineage. Pharyngomonas kirbyi (Strain SD1A) has flattened/discoidal cristae, and lacks conspicuous Golgi dictyosomes. It also has a heterolobosean 'double bikont' flagellar apparatus, with two right roots, each associated with an 'I' fibre and part of a rhizoplast-like complex. One right root splits shortly after its origin, and supplies most of the microtubules that support both the ventral groove, and the sub-anterior cytopharynx. Interestingly, Pharyngomonas has some potentially ancestral features not found in typical Heterolobosea, including elongated left roots associated with multilayered 'C' fibres, orthogonal basal bodies, and a spur structure that might represent a 'B' fibre homolog. Both isolates are obligate halophiles that grow best at 100-200‰ salinity and do not grow below 75‰ salinity. Pharyngomonas is therefore of considerable evolutionary importance, both as a deep-branching, plesiomorphic heterolobosean, and a borderline extreme halophile.
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Affiliation(s)
- Jong Soo Park
- School of Life Science, Kyungpook National University, Daegu, 702-701, Republic of Korea
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49
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Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, Yabuki A, Leander BS, Inouye I, Inagaki Y, Roger AJ, Simpson AGB. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environ Microbiol 2011; 12:2700-10. [PMID: 20482740 DOI: 10.1111/j.1462-2920.2010.02239.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last 15 years classical culturing and environmental PCR techniques have revealed a modest number of genuinely new major lineages of protists; however, some new groups have greatly influenced our understanding of eukaryote evolution. We used culturing techniques to examine the diversity of free-living protists that are relatives of diplomonads and retortamonads, a group of evolutionary and parasitological importance. Until recently, a single organism, Carpediemonas membranifera, was the only representative of this region of the tree. We report 18 new isolates of Carpediemonas-like organisms (CLOs) from anoxic marine sediments. Only one is a previously cultured species. Eleven isolates are conspecific and were classified within a new genus, Kipferlia n. gen. The remaining isolates include representatives of three other lineages that likely represent additional undescribed genera (at least). Small-subunit ribosomal RNA gene phylogenies show that CLOs form a cloud of six major clades basal to the diplomonad-retortamonad grouping (i.e. each of the six CLO clades is potentially as phylogenetically distinct as diplomonads and retortamonads). CLOs will be valuable for tracing the evolution of diplomonad cellular features, for example, their extremely reduced mitochondrial organelles. It is striking that the majority of CLO diversity was undetected by previous light microscopy surveys and environmental PCR studies, even though they inhabit a commonly sampled environment. There is no reason to assume this is a unique situation - it is likely that undersampling at the level of major lineages is still widespread for protists.
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Affiliation(s)
- Martin Kolisko
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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50
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Tong J, Dolezal P, Selkrig J, Crawford S, Simpson AGB, Noinaj N, Buchanan SK, Gabriel K, Lithgow T. Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana. Mol Biol Evol 2010; 28:1581-91. [PMID: 21081480 DOI: 10.1093/molbev/msq305] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway. Reclinomonas americana is a unicellular eukaryote with the most gene-rich mitochondrial genome known, and the large collection of membrane proteins encoded on the mitochondrial genome of R. americana includes a bacterial-type SecY protein transporter. Analysis of expressed sequence tags shows R. americana also has components of a mitochondrial protein translocase or "translocase in the inner mitochondrial membrane complex." Along with several other membrane proteins encoded on the mitochondrial genome Cox11, an assembly factor for cytochrome c oxidase retains sequence features suggesting that it is assembled by the SecY complex in R. americana. Despite this, protein import studies show that the RaCox11 protein is suited for import into mitochondria and functional complementation if the gene is transferred into the nucleus of yeast. Reclinomonas americana provides direct evidence that bacterial protein transport pathways were retained, alongside the evolving mitochondrial protein import machinery, shedding new light on the process of mitochondrial evolution.
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Affiliation(s)
- Janette Tong
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
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