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Thecochaos is not a myth: study of the genus Thecochaos (Amoebozoa, Discosea) – a rediscovered group of lobose amoeba, with short SSU gene. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00581-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Lotonin K, Bondarenko N, Nassonova E, Rayko M, Smirnov A. Balamuthia spinosa n. sp. (Amoebozoa, Discosea) from the brackish-water sediments of Nivå Bay (Baltic Sea, The Sound) - a novel potential vector of Legionella pneumophila in the environment. Parasitol Res 2022; 121:713-724. [PMID: 35022888 DOI: 10.1007/s00436-022-07425-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/02/2022] [Indexed: 11/24/2022]
Abstract
We have found a new free-living amoeba species named Balamuthia spinosa n. sp. (Amoebozoa, Discosea) in the bottom sediments of the brackish-water Nivå Bay (Baltic Sea, The Sound). This species resembles members of the genus Stygamoeba morphologically and was (mis)identified as belonging to this genus during the initial investigation. However, SSU rRNA gene data show that it robustly groups with Balamuthia mandrillaris sequence among Acanthopodida and represents a new species of the genus Balamuthia. Fragments of Legionella pneumophila genome were found among the NGS contigs obtained from B. spinosa n. sp., suggesting that this species may be a vector of Legionella in the environment. We discuss a remarkable morphological and ultrastructural similarity between the genus Balamuthia and the genus Stygamoeba. In addition, our phylogenetic analysis based on the SSU rRNA gene sequences revealed a close relationship between the genera Stygamoeba and Vermistella. It is one more confirmation of the order Stygamoebida, which was formed basing on the morphological evidence. The position of these branches close to Thecamoebida clade is congruent with current phylogenomic data.
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Affiliation(s)
- K Lotonin
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia.
| | - N Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia
| | - E Nassonova
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, Tikhoretsky ave. 4, 194064, St. Petersburg, Russia
| | - M Rayko
- Center for Algorithmic Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia
| | - A Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia
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3
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Kudryavtsev A, Völcker E, Clauß S, Pawlowski J. Ovalopodium rosalinum sp. nov., Planopodium haveli gen. nov, sp. nov., Planopodium desertum comb. nov. and new insights into phylogeny of the deeply branching members of the order Himatismenida (Amoebozoa). Int J Syst Evol Microbiol 2021; 71. [PMID: 33709902 DOI: 10.1099/ijsem.0.004737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The order Himatismenida (Amoebozoa, Discosea) comprises naked amoebae with an organic coat that is located on the dorsal surface of the cell. The phylogenetic relationships among deeply branching genera of the Himatismenida are unclear, as data on the species diversity of the himatismenid genera is largely restricted to the derived genus Cochliopodium. Here, we describe two new amoeba species that branch at the base of the order Himatismenida, evidenced by SSU rRNA gene and multigene analyses. Among them, a freshwater species Planopodium haveli gen. nov., sp. nov. has a dorsal cell coat consisting of flat, oval scales. This species forms a clade at the base of the Himatismenida, and the previously described Ovalopodium desertum, its closest relative, is transferred into the new genus as Planopodium desertum comb. nov. Although the two species are barely distinguishable by their sequence data, they are clearly distinct in morphology. Using this data, we can report the first evidence of a dorsal cell coat consisting of scales outside of the genus Cochliopodium. The other species has a marine origin and branches deeply, close to the root of the phylogenetic tree of Himatismenida. Based on the morphology of this amoeba, it should be described as Ovalopodium rosalinum sp. nov., a new species of the genus Ovalopodium. Analyses of the phylogenetic relationships and the ultrastructure of the deeply branching himatismenids, together with several of the newly obtained gene sequences of Parvamoeba and Cochliopodium, suggest that some elements of the dorsal cell coat of Ovalopodium may be ancestral for Himatismenida and have been partly retained in various more derived species of this clade, in particular, Cochliopodium gallicum. Although actin and Cox1 gene data do not resolve the higher-level relationships in Himatismenida, they correspond to the grouping of species within most genera.
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Affiliation(s)
- Alexander Kudryavtsev
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaya nab., 7/9 199034 Saint-Petersburg, Russia.,Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Universitetskaya nab., 1 199034 Saint-Petersburg, Russia
| | | | | | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland.,ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Sciences III, 1211 Geneva, Switzerland
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4
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Schuler GA, Brown MW. Description of Armaparvus languidus n. gen. n. sp. Confirms Ultrastructural Unity of Cutosea (Amoebozoa, Evosea). J Eukaryot Microbiol 2018; 66:158-166. [PMID: 29858563 DOI: 10.1111/jeu.12640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/27/2018] [Indexed: 12/01/2022]
Abstract
The American Type Culture Collection (ATCC) PRA-29 isolate has a publicly available transcriptome, which has led to its inclusion in recent phylogenomic analyses. The ATCC PRA-29 isolate was originally identified and deposited as "Pessonella sp." This taxon branches robustly within the recently discovered clade Cutosea, very distantly related to the clade in which the genus Pessonella is believed to branch based on morphological data. Using detailed light and electron microscopy, we studied the morphology and ultrastructure of ATCC PRA-29 as well as other cutosean amoebae to better elucidate the morphological affinity of ATCC PRA-29 to other amoebozoans. Here, we show that ATCC PRA-29 was misidentified by the original depositor as Pessonella and name it Armaparvus languidus n. gen. n. sp. We show that a cell coat of microscales separated from the cell membrane is a unique trait found in all known cutosean amoebae. As Cutosea represents a clade at the deepest bifurcation in the amoebozoan group Evosea and because this clade is currently taxon-poor, but likely represents a major understudied group it will be important to isolate and describe more cutosean amoebae in the future.
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Affiliation(s)
- Gabriel A Schuler
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi
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5
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Kang S, Tice AK, Spiegel FW, Silberman JD, Pánek T, Cepicka I, Kostka M, Kosakyan A, Alcântara DMC, Roger AJ, Shadwick LL, Smirnov A, Kudryavtsev A, Lahr DJG, Brown MW. Between a Pod and a Hard Test: The Deep Evolution of Amoebae. Mol Biol Evol 2017; 34:2258-2270. [PMID: 28505375 PMCID: PMC5850466 DOI: 10.1093/molbev/msx162] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features.
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Affiliation(s)
- Seungho Kang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
| | | | | | - Tomáš Pánek
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Ivan Cepicka
- Department of Zoology, Charles University, Prague, Czech Republic
| | - Martin Kostka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Českě Budějovice, Czech Republic.,Department of Parasitology, University of South Bohemia, Českě Budějovice, Czech Republic
| | - Anush Kosakyan
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | | | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Lora L Shadwick
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Daniel J G Lahr
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS
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6
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Shadwick JDL, Silberman JD, Spiegel FW. Variation in the SSUrDNA of the Genus Protostelium Leads to a New Phylogenetic Understanding of the Genus and of the Species Concept for Protostelium mycophaga (Protosteliida, Amoebozoa). J Eukaryot Microbiol 2017; 65:331-344. [PMID: 29044743 DOI: 10.1111/jeu.12476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/01/2017] [Accepted: 09/25/2017] [Indexed: 11/30/2022]
Abstract
Members of the genus Protostelium (including P. mycophaga, P. nocturnum, and P. okumukumu) are protosteloid amoebae commonly found in terrestrial habitats on dead plant matter. They, along with the closely allied nominal genus Planoprotostelium, containing the single species Pl. aurantium, all have an amoeboid trophic stage with acutely pointed subpseudopodia and orange lipid droplets in the granuloplasm. These amoebae form stalked fruiting bodies topped with a single, usually deciduous spore. The species are identified based on their fruiting body morphologies except for Pl. aurantium which looks similar to P. mycophaga in fruiting morphology, but has amoebae that can make flagella in liquid medium. We built phylogenetic trees using nuclear small subunit ribosomal DNA sequences of 35 isolates from the genera Protostelium and Planoprotostelium and found that (1) the nonflagellated P. nocturnum and P. okumukumu branch basally in the genus Protostelium, (2) the flagellate, Pl. aurantium falls within the genus Protostelium in a monophyletic clade with the nominal variety, P. mycophaga var. crassipes, (3) the cultures initially identified as Protostelium mycophaga can be divided into at least three morphologically recognizable taxa, P. aurantium n. comb., P. apiculatum n. sp., and P. m. rodmani n. subsp., as well as a paraphyletic assemblage that includes the remainder of the P. mycophaga morphotype. These findings have implications for understanding the ecology, evolution, and diversity of these amoeboid organisms and for using these amoebae as models for other amoeboid groups.
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Affiliation(s)
- John D L Shadwick
- Department of Biological Sciences, University of Arkansas, Science and Engineering Building Room 601, Fayetteville, Arkansas, 72701
| | - Jeffery D Silberman
- Department of Biological Sciences, University of Arkansas, Science and Engineering Building Room 601, Fayetteville, Arkansas, 72701
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Science and Engineering Building Room 601, Fayetteville, Arkansas, 72701
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7
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Táborský P, Pánek T, Čepička I. Anaeramoebidae fam. nov., a Novel Lineage of Anaerobic Amoebae and Amoeboflagellates of Uncertain Phylogenetic Position. Protist 2017; 168:495-526. [DOI: 10.1016/j.protis.2017.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022]
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8
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Tekle YI, Wood FC, Katz LA, Cerón-Romero MA, Gorfu LA. Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae. Genome Biol Evol 2017; 9:375-387. [PMID: 28087686 PMCID: PMC5381635 DOI: 10.1093/gbe/evx002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Fiona C Wood
- Department of Biology, Spelman College, Atlanta, Georgia
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst
| | - Lydia A Gorfu
- Department of Biology, Spelman College, Atlanta, Georgia
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9
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Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus. Eur J Protistol 2017; 61:92-106. [PMID: 28992523 DOI: 10.1016/j.ejop.2017.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/22/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022]
Abstract
Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.
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10
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Tekle YI, Wood FC. Longamoebia is not monophyletic: Phylogenomic and cytoskeleton analyses provide novel and well-resolved relationships of amoebozoan subclades. Mol Phylogenet Evol 2017; 114:249-260. [PMID: 28669813 DOI: 10.1016/j.ympev.2017.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/07/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
Abstract
Longamoebia is one of the most morphologically diverse member of Amoebozoa. It includes the human pathogen Acanthamoeba, which causes minor skin and serious eye infections as well as fatal central nervous system complications. The taxonomy and phylogeny of Longamoebia is poorly understood partly due to the growing number of molecular studies that report unsuspected affiliations of lineages with extremely different morphotypes in the group. A recent molecular study questioned the monophyly of Longamoebia. In this study, we conducted a more comprehensive phylogenomic analysis including all of putative members of Longamoebia to assess its monophyly. We conducted extensive analyses to see effects of outgroup choice, missing data, and gene and taxon sampling on resulting phylogenies. We also collected morphological characters derived from the cytoskeleton using immunocytochemistry to assess homologies of pseudopodia at a finer scale. Our phylogenomic analysis yielded a well-resolved tree of Amoebozoa and highly supported novel relationships. Discosea is recovered as a monophyletic group with all of its known taxonomic orders. However, its within-group relationships dramatically differed from those originally proposed. Our study strongly demonstrates that Longamoebia sensu Smirnov et al. (2011) is not monophyletic and an invalid taxon. Thecamoebida forms a strongly supported sister group relationship with clade Flabellinea (Dactylopodida and Vannellida), while Dermamoebida (Mayorella+Dermamoeba) form an independent branch basal to other members of Discosea. The remaining groups including members of Centramoebida form a consistently well-supported clade that was shown to form a sister group relationship with Himatismenida. This robust clade shares the unique cytoskeletal features of coiled cytoplasmic microtubule network and F-actin characters. Our analyses demonstrated that placement of unstable taxa in large-scale analysis with varying levels of missing data might be compromised by some confounding factors such as outgroup choice and gene and taxon sampling.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA.
| | - Fiona C Wood
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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11
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Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida). Protist 2017; 168:220-252. [PMID: 28343121 DOI: 10.1016/j.protis.2016.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/29/2016] [Accepted: 10/15/2016] [Indexed: 11/20/2022]
Abstract
We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other.
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12
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Hess S. Description of Hyalodiscus flabellus sp. nov. (Vampyrellida, Rhizaria) and Identification of its Bacterial Endosymbiont, “Candidatus Megaira polyxenophila” (Rickettsiales, Alphaproteobacteria). Protist 2017; 168:109-133. [DOI: 10.1016/j.protis.2016.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/15/2016] [Accepted: 11/26/2016] [Indexed: 10/20/2022]
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13
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Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. Biol Direct 2016; 11:69. [PMID: 28031045 PMCID: PMC5192571 DOI: 10.1186/s13062-016-0171-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/03/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Acanthamoebidae is a "family" level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. RESULTS Here we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans "Protostelium" arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that "Protostelium" pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic. CONCLUSIONS Our results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa. REVIEWERS This article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.
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14
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Tekle YI, Williams JR. Cytoskeletal architecture and its evolutionary significance in amoeboid eukaryotes and their mode of locomotion. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160283. [PMID: 27703691 PMCID: PMC5043310 DOI: 10.1098/rsos.160283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
The cytoskeleton is the hallmark of eukaryotic evolution. The molecular and architectural aspects of the cytoskeleton have been playing a prominent role in our understanding of the origin and evolution of eukaryotes. In this study, we seek to investigate the cytoskeleton architecture and its evolutionary significance in understudied amoeboid lineages belonging to Amoebozoa. These amoebae primarily use cytoplasmic extensions supported by the cytoskeleton to perform important cellular processes such as movement and feeding. Amoeboid structure has important taxonomic significance, but, owing to techniques used, its potential significance in understanding diversity of the group has been seriously compromised, leading to an under-appreciation of its value. Here, we used immunocytochemistry and confocal microscopy to study the architecture of microtubules (MTs) and F-actin in diverse groups of amoebae. Our results demonstrate that all Amoebozoa examined are characterized by a complex cytoskeletal array, unlike what has been previously thought to exist. Our results not only conclusively demonstrate that all amoebozoans possess complex cytoplasmic MTs, but also provide, for the first time, a potential synapomorphy for the molecularly defined Amoebozoa clade. Based on this evidence, the last common ancestor of amoebozoans is hypothesized to have had a complex interwoven MT architecture limited within the granular cell body. We also generate several cytoskeleton characters related to MT and F-actin, which are found to be robust for defining groups in deep and shallow nodes of Amoebozoa.
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15
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Cavalier-Smith T, Chao EE, Lewis R. 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. Mol Phylogenet Evol 2016; 99:275-296. [DOI: 10.1016/j.ympev.2016.03.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
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Phylogenomics of 'Discosea': A new molecular phylogenetic perspective on Amoebozoa with flat body forms. Mol Phylogenet Evol 2016; 99:144-154. [PMID: 27015898 DOI: 10.1016/j.ympev.2016.03.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 11/20/2022]
Abstract
The majority of amoeboid lineages with flattened body forms are placed under a taxonomic hypothetical class 'Discosea' sensu Smirnov et al. (2011), which encompasses some of the most diverse morphs within Amoebozoa. However, its taxonomy and phylogeny is poorly understood. This is partly due to lack of support in studies that are based on limited gene sampling. In this study we use a phylogenomic approach including newly-generated RNA-Seq data and comprehensive taxon sampling to resolve the phylogeny of 'Discosea'. Our analysis included representatives from all orders of 'Discosea' and up to 550 genes, the largest gene sampling in Amoebozoa to date. We conducted extensive analyses to assess the robustness of our resulting phylogenies to effects of missing data and outgroup choice using probabilistic methods. All of our analyses, which explore the impact of varying amounts of missing data, consistently recover well-resolved and supported groups of Amoebozoa. Our results neither support the monophyly nor dichotomy of 'Discosea' as defined by Smirnov et al. (2011). Rather, we recover a robust well-resolved clade referred to as Eudiscosea encompassing the majority of discosean orders (seven of the nine studied here), while the Dactylopodida, Thecamoebida and Himatismenida, previously included in 'Discosea,' are non-monophyletic. We also recover novel relationships within the Eudiscosea that are largely congruent with morphology. Our analyses enabled us to place some incertae sedis lineages and previously unstable lineages such as Vermistella, Mayorella, Gocevia, and Stereomyxa. We recommend some phylogeny-based taxonomic amendments highlighting the new findings of this study and discuss the evolution of the group based on our current understanding.
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Fučíková K, Lahr DJG. Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences. J Eukaryot Microbiol 2015. [PMID: 26211788 DOI: 10.1111/jeu.12253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho-species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.
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Affiliation(s)
- Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
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Cavalier-Smith T, Fiore-Donno AM, Chao E, Kudryavtsev A, Berney C, Snell EA, Lewis R. Multigene phylogeny resolves deep branching of Amoebozoa. Mol Phylogenet Evol 2015; 83:293-304. [DOI: 10.1016/j.ympev.2014.08.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/02/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
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Lahr DJG, Grant J, Molestina R, Katz LA, Anderson OR. Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale-bearing Amoebozoan with Flabellinid Affinities. J Eukaryot Microbiol 2015; 62:444-53. [PMID: 25515047 DOI: 10.1111/jeu.12199] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/24/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
Abstract
The isolate American Type Culture Collection (ATCC)® 50979™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 μm), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a layer with embedded scales, giving the cell an armored appearance. Molecular phylogenetic analyses of data (actin, alpha- and beta-tubulin, elongation factor 2, and 14-3-3) from transcriptomes of this and four other isolates reveals that ATCC® 50979(™) is closely related to the recently described Squamamoeba japonica and in a novel, stable clade. Due to the unique nature of the scale covering, as well as other gross morphological characters and the molecular phylogenetic analyses, we formally describe the isolate as Sapocribrum chincoteaguense n. gen. n. sp.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, University of São Paulo, 05508-090, São Paulo, Brazil.,Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Jessica Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Robert Molestina
- Protistology Collection, American Type Culture Collection, Manassas, Virginia, 20110, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - O Roger Anderson
- Department of Biology, Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York, 10964, USA
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20
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Geisen S, Kudryavtsev A, Bonkowski M, Smirnov A. Discrepancy between species borders at morphological and molecular levels in the genus Cochliopodium (Amoebozoa, Himatismenida), with the description of Cochliopodium plurinucleolum n. sp. Protist 2014; 165:364-83. [PMID: 24859009 DOI: 10.1016/j.protis.2014.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/01/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
Amoebae of the genus Cochliopodium are characterized by a tectum that is a layer of scales covering the dorsal surface of the cell. A combination of scale structure, morphological features and, nowadays, molecular information allows species discrimination. Here we describe a soil species Cochliopodium plurinucleolum n. sp. that besides strong genetic divergence from all currently described species of Cochliopodium differs morphologically by the presence of several peripheral nucleoli in the nucleus. Further, we unambiguously show that the Golgi attachment associated with a dictyosome in Cochliopodium is a cytoplasmic microtubule organizing center (MTOC). Last, we provide detailed morphological and molecular information on the sister clade of C. plurinucleolum, containing C. minus, C. minutoidum, C. pentatrifurcatum and C. megatetrastylus. These species share nearly identical sequences of both, small subunit ribosomal RNA and partial Cox1 genes, and nearly identical structure of the scales. Scales of C. pentatrifurcatum differ, however, strongly from scales of the others while sequences of C. pentatrifurcatum and C. minus are nearly identical. These discrepancies urge for future sampling efforts to disentangle species characteristics within Cochliopdium and to investigate morphological and molecular patterns that allow reliable species differentiation.
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Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Zoological Institute, Cologne Biocenter, Zülpicher Str. 47b, University of Cologne, 50674 Cologne Germany
| | - Alexander Kudryavtsev
- Department of Invertebrate Zoology, Faculty of Biology and Soil Sciences, St. Petersburg State University, Universitetskaja nab. 7/9 199034 Saint-Petersburg, Russia
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Zoological Institute, Cologne Biocenter, Zülpicher Str. 47b, University of Cologne, 50674 Cologne Germany
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology and Soil Sciences, St. Petersburg State University, Universitetskaja nab. 7/9 199034 Saint-Petersburg, Russia
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