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Cavalier-Smith T. Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi. PROTOPLASMA 2022; 259:487-593. [PMID: 34940909 PMCID: PMC9010356 DOI: 10.1007/s00709-021-01665-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/03/2021] [Indexed: 05/19/2023]
Abstract
I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
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Xu Z, Gu S, Sun Z, Zhang D, Zhou Y, Gao Y, Qi R, Chen W. Synthesis of char-based adsorbents from cotton textile waste assisted by iron salts at low pyrolysis temperature for Cr(VI) removal. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11012-11025. [PMID: 31953756 DOI: 10.1007/s11356-019-07588-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
Char-based adsorbents (char-FeCl3, char-FeCl2, and char-FeCit) derived from cotton textile waste (CTW) were synthesized by one-step low-temperature pyrolysis approach with different iron salts. The properties of the samples were conducted by BET, SEM, EDS, XRD, XPS, TEM, and FTIR. The results suggested that the surface areas of char-FeCl3 and char-FeCl2 were higher than those of char-FeCit. The presence of Fe2O3 as well as pyrolysis gas (HCl (g) and H2O (g)) could catalyze the formation of porosity. Meanwhile, FeCl3 showed the strongest catalysis effect to decompose cellulose to produce char. The pyrolysis process analysis was investigated by means of thermogravimetry-DSC. FeCl3 and FeCl2 could accelerate the breakage of cellulose structure whereas FeC6H5O7 was not beneficial to form char at low temperature as the incomplete decomposition of citrate. The adsorption property of Cr(VI) for the chars was evaluated. Adsorption processes were fitted well with the Freundlich model, and char-FeCl3 presented the best adsorptive capacity (70.39 mg/g). Thus, this low-temperature pyrolysis method was economical and technologically simplified as well as efficient adsorption capacity of Cr(VI) removal. Graphical abstract.
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Affiliation(s)
- Zhihua Xu
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Siyi Gu
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Zhenhua Sun
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Daofang Zhang
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China.
| | - Yuwei Zhou
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Yuquan Gao
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Renzhi Qi
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China
| | - Weifang Chen
- School of Environment and Architecture, University of Shanghai for Science and Technology, 516 Jungong Rd., Shanghai, 200093, People's Republic of China.
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Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade. Protist 2018; 169:853-874. [DOI: 10.1016/j.protis.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
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Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature 2018; 564:410-414. [PMID: 30429611 DOI: 10.1038/s41586-018-0708-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/21/2018] [Indexed: 12/11/2022]
Abstract
Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics1-4. The 'phylum' Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture5-7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here we report phylogenomic analyses based on high-coverage, cultivation-independent transcriptomics that place Hemimastigophora outside of all established eukaryote supergroups. They instead comprise an independent supra-kingdom-level lineage that most likely forms a sister clade to the 'Diaphoretickes' half of eukaryote diversity (that is, the 'stramenopiles, alveolates and Rhizaria' supergroup (Sar), Archaeplastida and Cryptista, as well as other major groups). The previous ranking of Hemimastigophora as a phylum understates the evolutionary distinctiveness of this group, which has considerable importance for investigations into the deep-level evolutionary history of eukaryotic life-ranging from understanding the origins of fundamental cell systems to placing the root of the tree. We have also established the first culture of a hemimastigote (Hemimastix kukwesjijk sp. nov.), which will facilitate future genomic and cell-biological investigations into eukaryote evolution and the last eukaryotic common ancestor.
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Cavalier-Smith T, Chao EE, Lewis R. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. PROTOPLASMA 2018; 255:1517-1574. [PMID: 29666938 PMCID: PMC6133090 DOI: 10.1007/s00709-018-1241-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/12/2018] [Indexed: 05/18/2023]
Abstract
Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade 'eSarcomonad', not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.
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Affiliation(s)
| | - Ema E Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Rhodri Lewis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Yabuki A, Ishida KI. An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa. J Eukaryot Microbiol 2018; 65:729-732. [PMID: 29345018 DOI: 10.1111/jeu.12502] [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: 09/25/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 11/27/2022]
Abstract
Quadricilia rotundata is a heterotrophic flagellate with four flagella. However, because this species has no clear morphological characteristics or molecular data affiliating it with any known group, Q. rotundata has been treated as a protist incertae sedis, for a long time. Here, we established a clonal culture of Q. rotundata and sequenced its 18S rDNA sequence. Molecular phylogenetic analysis successfully placed Q. rotundata in an environmental clade within Cercozoa, which contributes to expand the morphological and species diversity within Cercozoa. We also discuss morphological evolution within Cercozoa based on this finding.
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Affiliation(s)
- Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. PROTOPLASMA 2018; 255:297-357. [PMID: 28875267 PMCID: PMC5756292 DOI: 10.1007/s00709-017-1147-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated 'endocytosis' from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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Shiratori T, Ishida KI. A New Heterotrophic Cryptomonad: Hemiarma marina n. g., n. sp. J Eukaryot Microbiol 2016; 63:804-812. [PMID: 27218475 DOI: 10.1111/jeu.12327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 11/28/2022]
Abstract
We report a new heterotrophic cryptomonad Hemiarma marina n. g., n. sp. that was collected from a seaweed sample from the Republic of Palau. In our molecular phylogenetic analyses using the small subunit ribosomal RNA gene, H. marina formed a clade with two marine environmental sequences, and the clade was placed as a sister lineage of the freshwater cryptomonad environmental clade CRY1. Alternatively, in the concatenated large and small subunit ribosomal RNA gene phylogeny, H. marina was placed as a sister lineage of Goniomonas. Light and electron microscopic observations showed that H. marina shares several ultrastructural features with cryptomonads, such as flattened mitochondrial cristae, a periplast cell covering, and ejectisomes that consist of two coiled ribbon structures. On the other hand, H. marina exhibited unique behaviors, such as attaching to substrates with its posterior flagellum and displaying a jumping motion. H. marina also had unique periplast arrangement and flagellar transitional region. On the basis of both molecular and morphological information, we concluded that H. marina should be treated as new genus and species of cryptomonads.
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Affiliation(s)
- Takashi Shiratori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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Bass D, Silberman JD, Brown MW, Pearce RA, Tice AK, Jousset A, Geisen S, Hartikainen H. Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. Environ Microbiol 2016; 18:1604-19. [PMID: 26914587 DOI: 10.1111/1462-2920.13235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 11/30/2022]
Abstract
A wide diversity of organisms utilize faecal habitats as a rich nutrient source or a mechanism to traverse through animal hosts. We sequenced the 18S rRNA genes of the coprophilic, fruiting body-forming amoeba Guttulinopsis vulgaris and its non-fruiting relatives Rosculus 'ithacus' CCAP 1571/3, R. terrestris n. sp. and R. elongata n. sp. and demonstrate that they are related to the coprophilic flagellate Helkesimastix in a strongly supported, but highly divergent 18S sister clade. PCR primers specific to both clades were used to generate 18S amplicons from a range of environmental and faecal DNA samples. Phylogenetic analysis of the cloned sequences demonstrated a high diversity of uncharacterised sequence types within this clade, likely representing previously described members of the genera Guttulinopsis, Rosculus and Helkesimastix, as well as so-far unobserved organisms. Further, an Illumina MiSeq sequenced set of 18S V4-region amplicons generated from faecal DNAs using universal eukaryote primers showed that core-cercozoan assemblages in faecal samples are as diverse as those found in more conventionally examined habitats. These results reveal many novel lineages, some of which appear to occur preferentially in faecal material, in particular cercomonads and glissomonads. More broadly, we show that faecal habitats are likely untapped reservoirs of microbial eukaryotic diversity.
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Affiliation(s)
- David Bass
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK.,Cefas, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, MS State, 39762, MS, USA
| | - Rebecca A Pearce
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, MS State, 39762, MS, USA
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584, Utrecht, The Netherlands
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708, PB, Wageningen, The Netherlands
| | - Hanna Hartikainen
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
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Ultrastructure of the Algivorous Amoeboflagellate Viridiraptor invadens (Glissomonadida, Cercozoa). Protist 2014; 165:605-35. [PMID: 25150610 DOI: 10.1016/j.protis.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/15/2014] [Accepted: 07/05/2014] [Indexed: 11/22/2022]
Abstract
The family Viridiraptoridae represents a morphologically and ecologically distinct lineage of glissomonad flagellates (Cercozoa, Rhizaria). It currently comprises two highly specialised, algivorous genera inhabiting freshwater ecosystems, Orciraptor and Viridiraptor, for which ultrastructural data were lacking. In this study, the ultrastructure of Viridiraptor invadensHess et Melkonian, the sole described species of the viridiraptorid type genus, has been studied by transmission and scanning electron microscopy. In particular the flagellar transitional region and basal apparatus, both reconstructed from serial sections, revealed ultrastructural traits, that agree with the phylogenetic placement of the viridiraptorids within Glissomonadida: The transitional region contains a distal plate/collar complex and the basal apparatus comprises two ventral posterior roots and an anterior root, all known from other glissomonads. However, two additional small microtubular roots, two conspicuous rhizoplasts and probasal bodies present during interphase represent novel characteristics. Furthermore, an acorn/V-shaped filament system was discovered at the proximal end of the flagellar transitional region and used to establish a basal body triplet numbering system for flagellate cells of the Rhizaria. Finally, ultrastructural data on perforated algal cell walls suggest that the previously described reticulocyst of Viridiraptor represents an extrusome-derived, mesh-like coat supporting the invasion/feeding process.
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Hoef-Emden K. Osmotolerance in the Cryptophyceae: jacks-of-all-trades in the Chroomonas Clade. Protist 2014; 165:123-43. [PMID: 24568876 DOI: 10.1016/j.protis.2014.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 12/23/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022]
Abstract
No detailed studies have been performed to date on osmotolerance in cryptophytes, although one species, Chroomonas africana, had previously been reported to grow in freshwater as well as seawater. This study focused on osmotolerance in Chroomonas. Growth at different osmolalities and parameters of contractile vacuole function were examined and compared across a high-resolution phylogeny. Two evolutionary lineages in the Chroomonas clade proved to be euryhaline. Ranges of osmotolerance depended not only on osmolality, but also on culture medium. All cryptophytes contained contractile vacuoles. In the euryhaline strain CCAP 978/08 contractile vacuoles could be observed even at an osmolality beyond that of seawater. In addition the cells accumulated floridoside, an osmoprotectant likely originating from the red algal carbohydrate metabolism of the complex rhodoplast. Further evidence for functional contractile vacuoles also in marine cryptophytes was provided by identification of contractile vacuole-specific genes in the genome of Guillardia theta.
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Affiliation(s)
- Kerstin Hoef-Emden
- Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Str. 47B, 50674 Köln, Germany.
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Bass D, Yabuki A, Santini S, Romac S, Berney C. Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases. PLoS One 2012; 7:e49090. [PMID: 23226495 PMCID: PMC3514243 DOI: 10.1371/journal.pone.0049090] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/08/2012] [Indexed: 11/27/2022] Open
Abstract
We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.
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Affiliation(s)
- David Bass
- Department of Life Sciences, The Natural History Museum, London, United Kingdom.
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Shiratori T, Yabuki A, Ishida KI. Esquamula lacrimiformis n. g., n. sp., a new member of thaumatomonads that lacks siliceous scales. J Eukaryot Microbiol 2012; 59:527-36. [PMID: 22742560 DOI: 10.1111/j.1550-7408.2012.00635.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/07/2012] [Indexed: 11/29/2022]
Abstract
We report a new naked cercozoan flagellate, Esquamula lacrimiformis n. g., n. sp., collected from a sandy beach in Japan. Its cells were 4.5-11.3 μm in length and 3.9-8.8 μm in width and possess two unequal flagella. Cells move in a smooth gliding motion and have a trailing long posterior flagellum. Phylogenetic analyses with small and large subunit ribosomal RNA genes revealed that E. lacrimiformis forms a novel lineage within the Thaumatomonadida, the members of which are flagellates with siliceous scales. However, our light and electron microscopic observations indicated that E. lacrimiformis cells do not possess any siliceous structures. Furthermore, other morphological characteristics, such as the shape of the extrusomes and the structural arrangement of the microbody, were clearly different from those of previously described thaumatomonads. On the basis of a combination of these morphological observations and our phylogenetic analyses, we conclude that E. lacrimiformis should be treated as a new species of a new genus and placed into a new family, Esquamulidae n. fam., under Thaumatomonadida.
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Affiliation(s)
- Takashi Shiratori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
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Yabuki A, Ishida KI, Cavalier-Smith T. Rigifila ramosa n. gen., n. sp., a filose apusozoan with a distinctive pellicle, is related to Micronuclearia. Protist 2012; 164:75-88. [PMID: 22682062 DOI: 10.1016/j.protis.2012.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 04/18/2012] [Accepted: 04/21/2012] [Indexed: 12/17/2022]
Abstract
We report the ultrastructure, 18S and 28S rDNA sequences, and phylogenetic position of a distinctive free-living heterotrophic filose protist, Rigifila ramosa n. gen., n. sp., from a freshwater paddyfield. Rigifila lacks cilia and has a semi-rigid, radially symmetric, well-rounded, partially microtubule-supported, dorsal pellicle, and flat mitochodrial cristae. From a central aperture in a ventral depression emerges a protoplasmic stem that branches into several branching filopodia that draw bacteria to it. Electron microscopy reveals a general cell structure similar to Micronuclearia, the only non-flagellate previously known in Apusozoa; the large basal vacuole is probably an unusual giant contractile vacuole. Phylogenetic analysis of concatenated rDNA sequences groups Rigifila and Micronuclearia as sisters with maximal statistical support. However, novel morphological differences unique to Rigifila, notably a double (not single) proteinaceous layer beneath the cell membrane, and cortical microtubules, lead us to place it in a new family Rigifilidae. Our morphological and molecular analyses show that Rigifila is the closest known relative of Micronuclearia. Therefore we group Micronucleariidae and Rigifilidae as a new order Rigifilida within the existing class Hilomonadea, which now excludes planomonads. Rigifilida groups weakly with Collodictyon (Diphyllatea). We discuss the possible relationships of Rigifilida to other Apusozoa and Diphyllatea.
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Affiliation(s)
- Akinori Yabuki
- Japan Agency for Marine-Earth and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
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Brown MW, Kolisko M, Silberman JD, Roger AJ. Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr Biol 2012; 22:1123-7. [PMID: 22608512 DOI: 10.1016/j.cub.2012.04.021] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/23/2012] [Accepted: 04/12/2012] [Indexed: 11/19/2022]
Abstract
Multicellular forms of life have evolved many times, independently giving rise to a diversity of organisms such as animals, plants, and fungi that together comprise the visible biosphere. Yet multicellular life is far more widespread among eukaryotes than just these three lineages. A particularly common form of multicellularity is a social aggregative fruiting lifestyle whereby individual cells associate to form a "fungus-like" sorocarp. This complex developmental process that requires the interaction of thousands of cells working in concert was made famous by the "cellular slime mold"Dictyostelium discoideum, which became an important model organism. Although sorocarpic protistan lineages have been identified in five of the major eukaryote groups, the ubiquitous and globally distributed species Guttulinopsis vulgaris has eluded proper classification. Here we demonstrate, by phylogenomic analyses of a 159-protein data set, that G. vulgaris is a member of Rhizaria and is thus the first member of this eukaryote supergroup known to be capable of aggregative multicellularity.
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Affiliation(s)
- Matthew W Brown
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
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Microheliella maris (Microhelida ord. n.), an Ultrastructurally Highly Distinctive New Axopodial Protist Species and Genus, and the Unity of Phylum Heliozoa. Protist 2012; 163:356-88. [DOI: 10.1016/j.protis.2011.10.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 10/09/2011] [Indexed: 11/30/2022]
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Paracercomonas Kinetid Ultrastructure, Origins of the Body Plan of Cercomonadida, and Cytoskeleton Evolution in Cercozoa. Protist 2012; 163:47-75. [DOI: 10.1016/j.protis.2011.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 06/04/2011] [Indexed: 11/20/2022]
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Ultrastructure of Allapsa vibrans and the body plan of Glissomonadida (Cercozoa). Protist 2011; 163:165-87. [PMID: 22209009 DOI: 10.1016/j.protis.2011.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Accepted: 10/15/2011] [Indexed: 11/23/2022]
Abstract
Biciliate, gliding zooflagellate Cercozoa are globally the most abundant and genetically diverse predators in soil (glissomonads and cercomonads). We present the first detailed ultrastructural study of a phylogenetically well-characterized glissomonad, Allapsa vibrans. There are two ventral posterior centriolar roots as in Cercomonadida, but fewer other microtubular roots. Allapsa's centriolar roots and rhizoplast basically resemble those of the less well studied glissomonads Bodomorpha and Neoheteromita. The posterior centriole of Allapsa attaches laterally to the base of the anterior centriole and to the nucleus by striated fibrillar connectors and nests in a shallow cup-like ventrolateral depression; two broad fans of single microtubules line the cup's posterior and inner side. The anterior centriole has a dorsal two-microtubule root and probably also a singlet root. Its medium-length ciliary transition zones have a proximal hub-lattice and a prominent dense distal transverse plate/collar complex. Golgi bodies are anterior/paranuclear; isodiametric extrusomes are anterior mid-ventral. Tubulicristate mitochondria attach to the nucleus, as do prominent microbodies. We characterize the body plan of glissomonads, comparing it with other Sarcomonadea: their sister group (Pansomonadida) and the phylogenetically more distant Cercomonadida. We discuss glissomonad radiation into families Sandonidae, Proleptomonadidae, Dujardinidae, Bodomorphidae and Allapsidae, establishing Aurigamonadidae fam. n. for the amoeboflagellate pansomonad Aurigamonas.
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Ota S, Eikrem W, Edvardsen B. Ultrastructure and molecular phylogeny of thaumatomonads (Cercozoa) with emphasis on Thaumatomastix salina from Oslofjorden, Norway. Protist 2011; 163:560-73. [PMID: 22177453 DOI: 10.1016/j.protis.2011.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/16/2011] [Accepted: 10/24/2011] [Indexed: 10/14/2022]
Abstract
A culture of Thaumatomastix was isolated from a sediment sample collected in Oslofjorden and established as a monospecific strain (UIO286). Based on this culture, light and transmission electron microscopy and phylogenetic analyses were carried out. Thaumatomastix species are confined within the order Thaumatomonadida of the class Imbricatea and phylum Cercozoa. They are heterotrophic and their cell bodies are covered with silica scales. Observations of thin sections as well as whole mounts indicate that the morphology and ultrastructure of UIO286 is identical to T. salina, which was initially described from salt pools in Denmark. Detailed examination revealed some new features such as the presence of pseudopodia and silica deposition vesicles producing spine scales. The phylogeny presented here includes ribosomal DNA sequences from both imbricatean cultures and environmental samples. The 18S rDNA phylogenetic tree suggests that (i) Thaumatomastix is paraphyletic within the Thaumatomonadida clade, (ii) there is no close affinity between T. salina and other cultured and sequenced strains, but it is closely related to a sequence obtained from environmental DNA; we propose the present strain to serve as a reference culture of Thaumatomastix species and T. salina. Further, we discuss the distribution, habitats, and evolution of scale formation among euglyphids and thaumatomonads.
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Affiliation(s)
- Shuhei Ota
- Marine Biology, Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway.
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Howe AT, Bass D, Chao EE, Cavalier-Smith T. New Genera, Species, and Improved Phylogeny of Glissomonadida (Cercozoa). Protist 2011; 162:710-22. [DOI: 10.1016/j.protis.2011.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 05/14/2011] [Indexed: 10/18/2022]
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Stern RF, Horak A, Andrew RL, Coffroth MA, Andersen RA, Küpper FC, Jameson I, Hoppenrath M, Véron B, Kasai F, Brand J, James ER, Keeling PJ. Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS One 2010; 5:e13991. [PMID: 21085582 PMCID: PMC2981561 DOI: 10.1371/journal.pone.0013991] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 10/12/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments. METHODOLOGY/PRINCIPAL FINDINGS In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. CONCLUSIONS/SIGNIFICANCE COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.
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Affiliation(s)
- Rowena F Stern
- The Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
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Chantangsi C, Hoppenrath M, Leander BS. Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions. Mol Phylogenet Evol 2010; 57:518-27. [DOI: 10.1016/j.ympev.2010.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 07/15/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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Howe AT, Bass D, Vickerman K, Chao EE, Cavalier-Smith T. Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa). Protist 2009; 160:159-89. [DOI: 10.1016/j.protis.2008.11.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 11/09/2008] [Indexed: 11/30/2022]
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Bass D, Chao EEY, Nikolaev S, Yabuki A, Ishida KI, Berney C, Pakzad U, Wylezich C, Cavalier-Smith T. Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised. Protist 2009; 160:75-109. [DOI: 10.1016/j.protis.2008.07.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 07/30/2008] [Indexed: 11/26/2022]
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Cavalier-Smith T. Predation and eukaryote cell origins: a coevolutionary perspective. Int J Biochem Cell Biol 2008; 41:307-22. [PMID: 18935970 DOI: 10.1016/j.biocel.2008.10.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 12/23/2022]
Abstract
Cells are of only two kinds: bacteria, with DNA segregated by surface membrane motors, dating back approximately 3.5Gy; and eukaryotes, which evolved from bacteria, possibly as recently as 800-850My ago. The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia. Conversion of bacteria (=prokaryotes) into a eukaryote involved approximately 60 major innovations. Numerous contradictory ideas about eukaryogenesis fail to explain fundamental features of eukaryotic cell biology or conflict with phylogeny. Data are best explained by the intracellular coevolutionary theory, with three basic tenets: (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy; (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle; (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns. Eukaryotes plus their archaebacterial sisters form the clade neomura, which evolved from a radically modified derivative of an actinobacterial posibacterium that had replaced the ancestral eubacterial murein peptidoglycan by N-linked glycoproteins, radically modified its DNA-handling enzymes, and evolved cotranslational protein secretion, but not the isoprenoid-ether lipids of archaebacteria. I focus on this phylogenetic background and on explaining how in response to novel phagotrophic selective pressures and ensuing genome internalisation this prekaryote evolved efficient digestion of prey proteins by retrotranslocation and 26S proteasomes, then internal digestion by phagocytosis, lysosomes, and peroxisomes, and eukaryotic vesicle trafficking and intracellular compartmentation.
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Affiliation(s)
- T Cavalier-Smith
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Cavalier-Smith T, Chao EE, Stechmann A, Oates B, Nikolaev S. Planomonadida ord. nov. (Apusozoa): Ultrastructural Affinity with Micronuclearia podoventralis and Deep Divergences within Planomonas gen. nov. Protist 2008; 159:535-62. [DOI: 10.1016/j.protis.2008.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
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