DOCSLIB.ORG

Autochthonous Eukaryotic Diversity in Hydrothermal Sediment and Experimental Microcolonizers at the Mid-Atlantic Ridge

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Autochthonous Eukaryotic Diversity in Hydrothermal Sediment and Experimental Microcolonizers at the Mid-Atlantic Ridge Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge Purificacio´ nLo´ pez-Garcı´a†‡, Herve´ Philippe§¶, Franc¸oise Gail†, and David Moreira‡§ʈ †Biologie Marine, Unite´Mixte de Recherche, Centre National de la Recherche Scientifique 7622, Universite´Pierre et Marie Curie, 7 Quai St. Bernard, 75005 Paris, France; and §Phyloge´nie, Bioinformatique et Ge´nome, Unite´Mixte de Recherche, Centre National de la Recherche Scientifique 7622, Universite´Pierre et Marie Curie, 9 Quai St. Bernard, 75005 Paris, France Edited by Rita R. Colwell, National Science Foundation, Arlington, VA, and approved November 27, 2002 (received for review September 24, 2002) The diversity and mode of life of microbial eukaryotes in hydro- having an insight on the in situ microbial colonization process. thermal systems is very poorly known. We carried out a molecular For this, we analyzed the eukaryotic diversity in experimental survey based on 18S ribosomal RNA genes of eukaryotes present microcolonizers containing different substrates that were col- in different hydrothermal niches at the Mid-Atlantic Ridge. These lected after a 15-day exposure at a fluid emission source. These included metal-rich and rare-earth-element-rich hydrothermal sed- data also should provide information about the potential spec- iments of the Rainbow site, fluid–seawater mixing regions, and ificity of microbes for a particular substrate. colonization devices (microcolonizers) containing organic, iron- rich, and porous mineral substrates that were exposed for 15 days Methods to a fluid source. We identified considerable phylogenetic diver- Sampling. Samples were taken with the aid of the remotely sity, both at kingdom level and within kinetoplastids and alveo- operated vehicle (ROV) Victor during the French cruise ATOS lates. None of our sequences affiliates to photosynthesizing 2001 to the Mid-Atlantic Ridge hydrothermal area. A sediment lineages, suggesting that we are targeting only autochthonous core was obtained from Rainbow hydrothermal sediment deep-sea communities. Although sediment harbored most phylo- (36°6ЈN, 33°11ЈW, depth 2,264 m). After removal of the Ϸ1- to genetic diversity, microcolonizers predominantly contained 2-mm uppermost layer in a laminar flux chamber, a fraction of bodonids and ciliates, indicating that these protists pioneer the the sediment corresponding to the Ϸ1-cm upper part was frozen colonization process. Given the large variety of divergent lineages in liquid nitrogen until used. Fluid–seawater mixtures were detected within the alveolates in deep-sea plankton, hydrothermal collected from vents by using 0.75-liter titanium bottles at Lucky sediments, and vents, alveolates seem to dominate the deep ocean Strike (37°17ЈN, 32°16ЈW, depth 1,695 m) and Rainbow chim- in terms of diversity. Compared with data from the Pacific Guaymas neys; they were then filtered sequentially through 5- and 0.2- basin, some protist lineages seem ubiquitous in hydrothermal ␮m-diameter Millipore filters. Filters then were frozen in lysis areas, whereas others, notably kinetoplastid lineages, very abun- buffer (40 mM EDTA͞50 mM Tris⅐HCl͞0.75 M sucrose) and dant and diverse in our samples, so far have been detected only in stored in liquid nitrogen. Sterile microcolonizers were deployed Atlantic systems. Unexpectedly, although alvinellid polychaetes adjacent to a fluid emission at the Tour Eiffel chimney (Lucky are considered endemic of Pacific vents, we detected alvinellid- Strike site) for 15 days (Fig. 2) and collected in a closed sterile related sequences at the fluid–seawater interface and in micro- container by the ROV Victor. Microcolonizers consisted of colonizers. This finding can boost further studies on deep-sea vent different substrates placed into extensively perforated 50-ml animal biology and biogeography. Corning tubes. Two of them consisted of an inert plastic mesh containing, respectively, a meat-based substrate and iron frag- ompared with prokaryotes, microbial eukaryotes thriving in ments, and a third one was made of basalt and pumice fragments. MICROBIOLOGY Cextreme environments have rarely been studied. This fact is The container was opened in a laminar flux chamber on board, partly because of the difficulties imposed by classical cultivation and the microcolonizers were stored at 4°C in 75% ethanol͞2% approaches. Recent eukaryotic diversity surveys based on 18S NaCl. Because of the turbulent mixture of cold deep-sea water rRNA are revealing an unexpected variety of often divergent and hot hydrothermal fluid at the sampling sites, reliable tem- lineages in different biotopes, including some extreme environ- perature measurements are unavailable. ments (1–6). The only available molecular survey of microbial eukaryotes from deep-sea vents was recently carried out in Electron Microscopy and Sediment Chemical Analysis. Samples were hydrothermal sediments from the Pacific Guaymas basin and dehydrated in increasing ethanol concentrations (50%, 70%, revealed an important diversity of hitherto unknown lineages 90%, and 100%), critical-point-dried, and gold-coated. Obser- (5). Surprisingly, many of these sequences affiliated to typical vation was carried out with a JEOL (JSM-840A) scanning photosynthesizing groups (such as green algae or diatoms), leading to the conclusion that autochthonous eukaryotes cannot be distinguished from those deposited from the water column This paper was submitted directly (Track II) to the PNAS office. (5). There were two objectives in this study. First, we aimed at Abbreviations: MP, maximum parsimony; ML, maximum likelihood. characterizing the diversity of autochthonous microbial eu- Data deposition: The sequences reported in this paper have been deposited in the GenBank karyotes from Mid-Atlantic Ridge hydrothermal systems. Thus, database (accession nos. AF530516–AF530552). we have carried out a molecular survey of hydrothermal sedi- ‡Present address: Unite´d’Ecologie, Syste´matique et Evolution, Unite´Mixte de Recherche ment and seawater–fluid interface. These results should consti- Centre National de la Recherche Scientifique 8079, Universite´ Paris-Sud, Baˆtiment 360, tute a first base for comparison with data from the Pacific 91405 Orsay Cedex, France. systems. To date, whereas prokaryotes seem ubiquitous in ¶Present address: De´partement de Biochimie, Universite´de Montre´al, C.P. 6128 Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7. different oceanic regions (7), possibly including vent areas, ʈTo whom correspondence should be addressed at: Unite´ d’Ecologie, Syste´matique et metazoans are subject to a defined biogeographical distribution Evolution, Unite´Mixte de Recherche Centre National de la Recherche Scientifique 8079, (8). At present, molecular data on the oceanic distribution of Universite´ Paris-Sud, Baˆtiment 360, 91405 Orsay Cedex, France. E-mail: david.moreira@ microbial eukaryotes are still negligible. Second, we aimed at ese.u-psud.fr. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0235779100 PNAS ͉ January 21, 2003 ͉ vol. 100 ͉ no. 2 ͉ 697–702 Downloaded by guest on October 1, 2021 identification of identical or nearly identical sequences and the selection of clones for complete sequencing. Representative clones (n ϭ 37) were completely sequenced, and their sequences were automatically aligned, by using the program BABA (H.P., unpublished work), with 4,575 eukaryotic 18S rDNA sequences retrieved from GenBank (http://ncbi.nlm.nih.gov/). The multiple alignment was then manually edited by using the program ED from the MUST package (11). NJ trees were constructed for the different eukaryotic taxa to choose a representative subset of sequences, avoiding partial, redundant, and fast-evolving ones, for further phylogenetic analyses. Three different subsets of 18S rDNA sequences were selected: one included alveolate se- quences (55 sequences), another included representatives of most major eukaryotic groups (55 sequences), and a third included metazoan sequences (46 sequences). Gaps and ambig- uously aligned positions were excluded from our analyses, re- sulting in alignments of 883, 877, and 1,256 positions, respec- tively. The smaller number of positions used for the first two Fig. 1. Scanning electron microscopy photographs of Rainbow sediment analyses was because of the inclusion of environmental partial showing coccoliths and foraminifer shells. [Bars ϭ 1 ␮m(A and B), 10 ␮m(C), and 100 ␮m(D).] sequences from a molecular survey of eukaryotic diversity in the Guaymas basin (5), which were Ϸ550 nucleotides shorter than our sequences (the average length was Ϸ1,200 nucleotides vs. Ϸ electron microscope operated at 17 kV at the Service de 1,750 nucleotides, respectively). The three data sets were Microscopie Electronique de l’Institut Federatif de Recherche subjected to maximum parsimony (MP) and maximum likeli- de Biologie Inte´grative (Paris). Major elements in sediment were hood (ML) analysis by using PAUP* 4b8 (12). By using an MP analyzed by inductively coupled plasma (ICP)–atomic emission tree, the parameter values for a general time-reversible model of spectrometry; trace elements and rare-earth composition were nucleotide substitution were estimated, with a six-category dis- crete approximation of a ⌫ distribution plus invariable sites analyzed by ICP–mass spectrometry by the Service d’Analyze ϩ⌫ϩ des Roches et Mine´raux du Centre National de la Recherche (GTR I model). The ML trees were constructed by using Scientifique (Nancy, France). 20 random additions
Load more

Recommended publications
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
    [Show full text]
  • Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms
    Review Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms John W. Stiller Department of Biology, East Carolina University, Greenville, NC 27858, USA. Sequence-based molecular phylogenies have provided new models of early eu- karyotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alter- native tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomor- phic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution. Key words: genomics, proteomics, evolution, animals, plants, fungi Introduction The results of sequence-based, molecular phylogenetic two di®erent and conflicting phylogenetic signals; analyses have reshaped current thinking about an- most available sequences supported an animals + cient evolutionary relationships, and have begun to es- fungi relationship, but a smaller subset of genes in- tablish a new framework for systematizing broad-scale dicated a closer relationship between animals and eukaryotic diversity. Among the most widely accepted plants. Curiously, there was little or no support of the new evolutionary hypotheses is a proposed for the third possible relationship (plants + fungi). sister relationship between animals (+ choanoflagel- This suggested that a persistent phylogenetic artifact, lates) and fungi (see ref.
    [Show full text]
  • Protist Phylogeny and the High-Level Classification of Protozoa
    Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane).
    [Show full text]
  • Barthelonids Represent a Deep-Branching Metamonad Clade with Mitochondrion-Related Organelles Generating No
    bioRxiv preprint doi: https://doi.org/10.1101/805762; this version posted October 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 3 Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related 4 organelles generating no ATP. 5 6 Euki Yazaki1*, Keitaro Kume2, Takashi Shiratori3, Yana Eglit 4,5,, Goro Tanifuji6, Ryo 7 Harada7, Alastair G.B. Simpson4,5, Ken-ichiro Ishida7,8, Tetsuo Hashimoto7,8 and Yuji 8 Inagaki7,9* 9 10 1Department of Biochemistry and Molecular Biology, Graduate School and Faculty of 11 Medicine, The University of Tokyo, Tokyo, Japan 12 2Faculty of Medicine, University of Tsukuba, Ibaraki, Japan 13 3Department of Marine Diversity, Japan Agency for Marine-Earth Science and Technology, 14 Yokosuka, Japan 15 4Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada 16 5Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, 17 Halifax, Nova Scotia, Canada 18 6Department of Zoology, National Museum of Nature and Science, Ibaraki, Japan 19 7Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 20 Ibaraki, Japan 21 8Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan 22 9Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 23 24 Running head: Phylogeny and putative MRO functions in a new metamonad clade. 25 26 *Correspondence addressed to Euki Yazaki, [email protected] and Yuji Inagaki, 27 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/805762; this version posted October 29, 2019.
    [Show full text]
  • Final Copy 2021 05 11 Scam
    This electronic thesis or dissertation has been downloaded from Explore Bristol Research, http://research-information.bristol.ac.uk Author: Scambler, Ross D Title: Exploring the evolutionary relationships amongst eukaryote groups using comparative genomics, with a particular focus on the excavate taxa General rights Access to the thesis is subject to the Creative Commons Attribution - NonCommercial-No Derivatives 4.0 International Public License. A copy of this may be found at https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode This license sets out your rights and the restrictions that apply to your access to the thesis so it is important you read this before proceeding. Take down policy Some pages of this thesis may have been removed for copyright restrictions prior to having it been deposited in Explore Bristol Research. However, if you have discovered material within the thesis that you consider to be unlawful e.g. breaches of copyright (either yours or that of a third party) or any other law, including but not limited to those relating to patent, trademark, confidentiality, data protection, obscenity, defamation, libel, then please contact [email protected] and include the following information in your message: •Your contact details •Bibliographic details for the item, including a URL •An outline nature of the complaint Your claim will be investigated and, where appropriate, the item in question will be removed from public view as soon as possible. Exploring the evolutionary relationships amongst eukaryote groups using comparative genomics, with a particular focus on the excavate taxa Ross Daniel Scambler Supervisor: Dr. Tom A. Williams A dissertation submitted to the University of Bristol in accordance with the requirements for award of the degree of Master of Science (by research) in the Faculty of Life Sciences, Novem- ber 2020.
    [Show full text]
  • Diversity, Phylogeny and Phylogeography of Free-Living Amoebae
    School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Diversity, phylogeny and phylogeography of free-living amoebae Ph.D. Thesis RNDr. Tomáš Tyml Supervisor: Mgr. Martin Kostka, Ph.D. Department of Parasitology, Faculty of Science, University of South Bohemia in České Budějovice Specialist adviser: Prof. MVDr. Iva Dyková, Dr.Sc. Department of Botany and Zoology, Faculty of Science, Masaryk University České Budějovice 2016 This thesis should be cited as: Tyml, T. 2016. Diversity, phylogeny and phylogeography of free living amoebae. Ph.D. Thesis Series, No. 13. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 135 pp. Annotation This thesis consists of seven published papers on free-living amoebae (FLA), members of Amoebozoa, Excavata: Heterolobosea, and Cercozoa, and covers three main topics: (i) FLA as potential fish pathogens, (ii) diversity and phylogeography of FLA, and (iii) FLA as hosts of prokaryotic organisms. Diverse methodological approaches were used including culture-dependent techniques for isolation and identification of free-living amoebae, molecular phylogenetics, fluorescent in situ hybridization, and transmission electron microscopy. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v úpravě vzniklé vypuštěním vyznačených částí archivovaných Přírodovědeckou fakultou elektronickou cestou ve veřejně přístupné části databáze STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce.
    [Show full text]
  • Systema Naturae. the Classification of Living Organisms
    Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5).
    [Show full text]
  • Supporting Information
    Supporting Information Sebé-Pedrós et al. 10.1073/pnas.1002257107 Daphnia pulex 5 Integrin α Daphnia pulex 2 -/ - Capitella sp. 2 Capitella sp. 1 Daphnia pulex 1 Lottia gigantea 2 Amphimedon queenslandica 1 Geodia cydonium Drosophila melanogaster PS5 Drosophila melanogaster scab Drosophila melanogaster PS4 Podocoryne carnea Acropora millepora Homo sapiens 9 Homo sapiens 4 Daphnia pulex 4 Nematostella vectensis Homo sapiens 10 Homo sapiens 11 Homo sapiens 1 Homo sapiens 2 Amastigomonas sp. Homo sapiens 5 Homo sapiens 8 30/ 0.99 Homo sapiens IIb Homo sapiens V Lottia gigantea 1 Amphimedon queenslandica 4 Amphimedon queenslandica 2 Amphimedon queenslandica 3 Amphimedon queenslandica 5 Drosophila melanogaster inflated Drosophila melanogaster mew Daphnia pulex 3 Homo sapiens 6 Homo sapiens 7 Capsaspora owczarzaki 3 Capsaspora owczarzaki 4 Capsaspora owczarzaki 2 Capsaspora owczarzaki 1 Kordia algicida Monosiga brevicollis XP_001749484 Chloroherpeton thalassium Flavobacteriales bacterium Gloeobacter violaceus 88/ 1.00 Nostoc punctiforme Stigmatella aurantiaca Other FG-GAP containing proteins Homo sapiens GPI-PL Nematostella vectensis GPI-PL Capitella sp. GPI-PL Proterospongia sp. GPI-PL Capsaspora owczarzaki GPI-PL GPI-PLs Fig. S1. Maximum likelihood tree of the integrin α homolog and other proteins containing FG-GAP repeats. Alignment has been done using the only common region between all these proteins, which are three consecutive FG-GAP repeats. The taxon sampling includes all of the integrin α homologs here described and a wide representation of metazoan homologs. The putative integrin α from Monosiga brevicollis and some FG-GAP repeat-containing bacteria proteins ob- tained when blasting the M. brevicollis sequence have also been included, together with several glycosylphosphatidylinositol phospholipases.
    [Show full text]
  • Marine Biological Laboratory) Data Are All from EST Analyses
    TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878.
    [Show full text]
  • Kingdom Chromista)
    J Mol Evol (2006) 62:388–420 DOI: 10.1007/s00239-004-0353-8 Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista) Thomas Cavalier-Smith, Ema E-Y. Chao Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Received: 11 December 2004 / Accepted: 21 September 2005 [Reviewing Editor: Patrick J. Keeling] Abstract. Heterokonts are evolutionarily important gyristea cl. nov. of Ochrophyta as once thought. The as the most nutritionally diverse eukaryote supergroup zooflagellate class Bicoecea (perhaps the ancestral and the most species-rich branch of the eukaryotic phenotype of Bigyra) is unexpectedly diverse and a kingdom Chromista. Ancestrally photosynthetic/ major focus of our study. We describe four new bicil- phagotrophic algae (mixotrophs), they include several iate bicoecean genera and five new species: Nerada ecologically important purely heterotrophic lineages, mexicana, Labromonas fenchelii (=Pseudobodo all grossly understudied phylogenetically and of tremulans sensu Fenchel), Boroka karpovii (=P. uncertain relationships. We sequenced 18S rRNA tremulans sensu Karpov), Anoeca atlantica and Cafe- genes from 14 phagotrophic non-photosynthetic het- teria mylnikovii; several cultures were previously mis- erokonts and a probable Ochromonas, performed ph- identified as Pseudobodo tremulans. Nerada and the ylogenetic analysis of 210–430 Heterokonta, and uniciliate Paramonas are related to Siluania and revised higher classification of Heterokonta and its Adriamonas; this clade (Pseudodendromonadales three phyla: the predominantly photosynthetic Och- emend.) is probably sister to Bicosoeca. Genetically rophyta; the non-photosynthetic Pseudofungi; and diverse Caecitellus is probably related to Anoeca, Bigyra (now comprising subphyla Opalozoa, Bicoecia, Symbiomonas and Cafeteria (collectively Anoecales Sagenista). The deepest heterokont divergence is emend.). Boroka is sister to Pseudodendromonadales/ apparently between Bigyra, as revised here, and Och- Bicoecales/Anoecales.
    [Show full text]
  • A Revised Six-Kingdom System of Life
    Hi ul. R iv. ' 1998,', 73, p p . 203-266 printed in the United Kingdom © Cambridge Philosophical Society 203 A revised six-kingdom system of life T. CAVALIER-SMITH Evolutionary Biology Programme, Canadian Institute for Advanced Research , Department o f Botany , University o f British Columbia, Vancouver, BC, Canada V6T If4 (.Received 27 M arch 1 9 9 6 ; revised 15 December 1 9 9 7 ; accepted 18 December 1997) ABSTRACT A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Interm ediate high level categories (superkingdom, subkingdom, branch, infrakingdom, supcrphylum, subphylum and infraphylum) arc extensively used lo avoid splitting organisms into an excessive num ber of kingdoms and phyla (60 only being recognized). The two ‘zoological ’ kingdoms. Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three ‘botanical’ kingdoms (Plantae, Fungi, Chromista) lo the International Code of Botanical Nomenclature, Circumscrip­ tions of the kingdoms Bacteria and Plantae remain unchanged since Cavalicr-Smith (1981). The kingdom Fungi is expanded by adding M icrosporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi arc subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa arc actually Animalia, not Protozoa, and that mesozoans arc related lo bilaterian animals.
    [Show full text]
  • Molecular Phylogeny of Unikonts: New Insights Into the Position of Apusomonads and Ancyromonads and the Internal Relationships of Opisthokonts
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Digital.CSICEurope PMC Funders Group Author Manuscript Protist. Author manuscript; available in PMC 2015 February 27. Published in final edited form as: Protist. 2013 January ; 164(1): 2–12. doi:10.1016/j.protis.2012.09.002. Europe PMC Funders Author Manuscripts Molecular phylogeny of Unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of opisthokonts Jordi Paps1,2,§, Luis A. Medina-Chacón1, Wyth Marshall3, Hiroshi Suga1,4, and Iñaki Ruiz- Trillo1,4,5,§ 1Departament de Genètica, Universitat de Barcelona. Av. Diagonal, 645, 08028 Barcelona 3B.C. Centre for Aquatic Health, 871A Island Hwy. Campbell River, B.C., V9W 5B1, Canada 4Institut de Biologia Evolutiva (UPF-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain 5Institució Catalana per a la Recerca i Estudis Avançats (ICREA) Abstract The eukaryotic supergroup Opisthokonta includes animals (Metazoa), fungi, and choanoflagellates, as well as the lesser known unicellular lineages Nucleariidae, Fonticula alba, Ichthyosporea, Filasterea and Corallochytrium limacisporum. Whereas the evolutionary positions of the well-known opisthokonts are mostly resolved, the phylogenetic relationships among the more obscure lineages are not. Within the Unikonta (Opisthokonta and Amoebozoa), it has not Europe PMC Funders Author Manuscripts been determined whether the Apusozoa (apusomonads and ancyromonads) or the Amoebozoa form the sister group to opisthokonts, nor to which side of the hypothesized unikont/bikont divide the Apusozoa belong. Aiming at elucidating the evolutionary tree of the unikonts, we have assembled a dataset with a large sampling of both organisms and genes, including representatives from all known opisthokont lineages.
    [Show full text]