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Hess S. The amoebae of Idionectes vortex (Cutosea, Amoebozoa): Motility, cytoskeleton architecture and extracellular scales. J Eukaryot Microbiol 2021; 68:e12869. [PMID: 34435411 DOI: 10.1111/jeu.12869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cutosea represent a deep-branching lineage within the phylum Amoebozoa that is still relatively poorly explored. Currently, there are four cutosean representatives known - the monotypic genera Armaparvus, Idionectes, Sapocribrum, and Squamamoeba - with marked genetic distances. Idionectes vortex is the deepest-branching species and differs markedly from the other Cutosea in ecology, life history, and most importantly, in its ability to form a flagellated swarmer with an exceptional swimming mechanism. As far as we know, the other Cutosea lack flagella and rather represent small, marine amoebae with a characteristic cell coat. The present paper focuses on the amoeboid life history stage of the algivorous amoeboflagellate Idionectes vortex to provide data for a first in-depth comparison with other Cutosea and to document structural specialties. The amoeboid stage of Idionectes is mainly associated with the specific feeding process, that is, the interaction with algal prey cells and phagocytosis of protoplast material. Yet, the present data from time-lapse microscopy, cytochemical stainings, and electron microscopy demonstrate clear similarities with the other cutosean species concerning amoeboid locomotion and cell coat ultrastructure. Furthermore, Idionectes amoebae exhibit a well-developed microtubular cytoskeleton, and an unusual basal apparatus that seems to undergo marked changes during the life history of this exceptional amoebozoan.
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Affiliation(s)
- Sebastian Hess
- Institute for Zoology, University of Cologne, Cologne, Germany
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3
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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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4
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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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Blandenier Q, Seppey CVW, Singer D, Vlimant M, Simon A, Duckert C, Lara E. Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle. J Eukaryot Microbiol 2016; 64:257-265. [PMID: 27543384 DOI: 10.1111/jeu.12357] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/04/2016] [Accepted: 08/08/2016] [Indexed: 11/30/2022]
Abstract
Since the first environmental DNA surveys, entire groups of sequences called "environmental clades" did not have any cultured representative. LKM74 is an amoebozoan clade affiliated to Dermamoebidae, whose presence is pervasively reported in soil and freshwater. We obtained an isolate from soil that we assigned to LKM74 by molecular phylogeny, close related to freshwater clones. We described Mycamoeba gemmipara based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. M. gemmipara displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. To demonstrate that M. gemmipara is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils to follow changes in eukaryotic communities. Mycamoeba gemmipara was present in all samples, although related reads were uncommon underneath the cadaver.
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Affiliation(s)
- Quentin Blandenier
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - Christophe V W Seppey
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - Michèle Vlimant
- Laboratory of Ecology and Evolution of Parasites, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - Anaële Simon
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Emile Argand 11, Neuchâtel, 2000, Switzerland
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Udalov IA. Pseudoparamoeba microlepis n. sp., Korotnevella fousta n. sp. (Amoebozoa, Dactylopodida), with notes on the evolution of scales among dactylopodid amoebae. Eur J Protistol 2016; 54:33-46. [DOI: 10.1016/j.ejop.2016.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/29/2022]
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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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