Development of a PNA Probe for Fluorescence in Situ Hybridization Detection of Prorocentrum Donghaiense
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Role of Metopus Es in the Anaerobic Degradation of Organic Matter and Biomethanation Process
Role of Metopus es in the anaerobic degradation of organic matter and biomethanation process Thesis submitted to the University of Kerala for award of the degree of Doctor of Philosophy in Microbiology By Nimi Narayanan Under the Supervision of Dr. V. B. Manilal Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), CSIR, Thiruvananthapuram, Kerala, INDIA - 695019 2011 To my Family DECLARATION I hereby declare that the work presented in this thesis is based on the original work done by me under the guidance of Dr. V. B. Manilal, Principal Scientist, Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology, and that no part of this has been included in any other thesis submitted previously for the award of any degree. Nimi Narayanan Acknowledgement It is a great pleasure to express my sincere gratitude and sense of appreciation to my research guide, Dr. V.B. Manilal, Principal Scientist, Environmental Technology, NIIST, Trivandrum, for his constant encouragement, enthusiastic support and valuable guidance throughout the period of study. I am indebted to him for giving me the ample freedom to do the work and express my ideas during this period. I am grateful to Dr. Ajit Haridas, Scientist-in-charge, Environmental Technology, NIIST for his valuable suggestions and constructive criticism during my tenure. It is an honor for me to thank the present Director, Dr. Suresh Das and the former directors of NIIST, Trivandrum for providing the necessary infrastructural facilities for the successful completion of work. I would like to thank Council of Scientific and Industrial Research, New Delhi, for the research fellowship. -
Morphology and Phylogeny of the Soil Ciliate Metopus Yantaiensis N. Sp
Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria Atef Omara,b, Qianqian Zhanga, Songbao Zoua,c & Jun Gonga,c a Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China b Department of Zoology, Al-Azhar University, Assiut 71524, Egypt c University of Chinese Academy of Sciences, Beijing 100049, China Keywords ABSTRACT Anaerobic ciliates; Armophorea; digestion- resistant bacteria; Metopus contortus; The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., Metopus hasei. discovered in coastal soil of northern China, were investigated. It is distin- guished from its congeners by a combination of the following features: nuclear Correspondence apparatus situated in the preoral dome; 18–21 somatic ciliary rows, of which J. Gong, Yantai Institute of Coastal Zone three extend onto the preoral dome (dome kineties); three to five distinctly Research, Chinese Academy of Sciences, elongated caudal cilia, and 21–29 adoral polykinetids. The 18S rRNA genes of Yantai 264003, China this new species and two congeners, Metopus contortus and Metopus hasei, Telephone number: +86-535-2109123; were sequenced and phylogenetically analyzed. The new species is more clo- FAX number: +86-535-2109000; sely related to M. hasei and the clevelandellids than to other congeners; both e-mail: [email protected] the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identi- Received: 13 January 2017; revised 2 March fied, using a 16S rRNA gene clone library, sequencing, and fluorescence 2017; accepted March 8, 2017. -
Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the Mcmurdo Dry Valleys, Antarctica
Reference: Biol. Bull. 227: 175–190. (October 2014) © 2014 Marine Biological Laboratory Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica YUAN XU1,*†, TRISTA VICK-MAJORS2, RACHAEL MORGAN-KISS3, JOHN C. PRISCU2, AND LINDA AMARAL-ZETTLER4,5,* 1Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; 2Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, Bozeman, Montana 59717; 3Department of Microbiology, Miami University, Oxford, Ohio 45056; 4The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543; and 5Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island 02912 Abstract. We report an in-depth survey of next-genera- trends in dissolved oxygen concentration and salinity may tion DNA sequencing of ciliate diversity and community play a critical role in structuring ciliate communities. A structure in two permanently ice-covered McMurdo Dry PCR-based strategy capitalizing on divergent eukaryotic V9 Valley lakes during the austral summer and autumn (No- hypervariable region ribosomal RNA gene targets unveiled vember 2007 and March 2008). We tested hypotheses on the two new genera in these lakes. A novel taxon belonging to relationship between species richness and environmental an unknown class most closely related to Cryptocaryon conditions -
Protistology an International Journal Vol
Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb. -
Diversity of Free-Living Ciliates in the Sandy Sediment of a Spanish Stream in Winter
Journal of General Microbiology (1993), 139, 2855-2863. Printed in Great Britain 2855 Diversity of free-living ciliates in the sandy sediment of a Spanish stream in winter B. J. FINLAY,'*C. TELLEZ~and G. ESTEBAN'~~ 'Institute of Freshwater Ecology, Windermere Laboratory, The Ferry House, Ambleside, Cumbria LA22 ULP, UK 'Departamen to de Microbiologi'a III, Facultad de Biologia, Universidad Complutense, 28040 Madrid, Spain 3Consejo Superior de Investigaciones Cient@cas, Madrid, Spain (Received 24 April 1993; revised 7 June 1993; accepted 17 June 1993) This study had two objectives: to determine the number of (phenotypic) ciliate species co-existing in 1m2 of sandy river sediment at a maximum temperature of 4 "C;and to determine the ecological mechanism(s) facilitating their co-existence. The ciliate community was diverse (65 species [8 of which are new], belonging to 50 genera, from 17 orders). The sediment supported a superficial mat of diatoms (> 30 species). These served as food for at least 16 ciliate species. The size frequency distribution of ingested diatoms was almost identical to that for the diatoms in the sediment: thus the probability of a diatom being ingested appears to be a simple function of its relative abundance. Two factors were probably important for the co-existence of ciliate species :wide variation in cell size and shape enabled them to occupy most habitats; and they deployed a variety of feeding mechanisms to consume the variety of microbial food types. Taken as a whole, the ciliate community was capable of feeding on all microbes, including other protozoa, up to a size of about 80 pm. -
Biologia Celular – Cell Biology
Biologia Celular – Cell Biology BC001 - Structural Basis of the Interaction of a Trypanosoma cruzi Surface Molecule Implicated in Oral Infection with Host Cells and Gastric Mucin CORTEZ, C.*1; YOSHIDA, N.1; BAHIA, D.1; SOBREIRA, T.2 1.UNIFESP, SÃO PAULO, SP, BRASIL; 2.SINCROTRON, CAMPINAS, SP, BRASIL. e-mail:[email protected] Host cell invasion and dissemination within the host are hallmarks of virulence for many pathogenic microorganisms. As concerns Trypanosoma cruzi that causes Chagas disease, the insect vector-derived metacyclic trypomastigotes (MT) initiate infection by invading host cells, and later blood trypomastigotes disseminate to diverse organs and tissues. Studies with MT generated in vitro and tissue culture-derived trypomastigotes (TCT), as counterparts of insect- borne and bloodstream parasites, have implicated members of the gp85/trans-sialidase superfamily, MT gp82 and TCT Tc85-11, in cell invasion and interaction with host factors. Here we analyzed the gp82 structure/function characteristics and compared them with those previously reported for Tc85-11. One of the gp82 sequences identified as a cell binding site consisted of an alpha-helix, which connects the N-terminal beta-propeller domain to the C- terminal beta-sandwich domain where the second binding site is nested. In the gp82 structure model, both sites were exposed at the surface. Unlike gp82, the Tc85-11 cell adhesion sites are located in the N-terminal beta-propeller region. The gp82 sequence corresponding to the epitope for a monoclonal antibody that inhibits MT entry into target cells was exposed on the surface, upstream and contiguous to the alpha-helix. Located downstream and close to the alpha-helix was the gp82 gastric mucin binding site, which plays a central role in oral T. -
Genetic Diversity and Habitats of Two Enigmatic Marine Alveolate Lineages
AQUATIC MICROBIAL ECOLOGY Vol. 42: 277–291, 2006 Published March 29 Aquat Microb Ecol Genetic diversity and habitats of two enigmatic marine alveolate lineages Agnès Groisillier1, Ramon Massana2, Klaus Valentin3, Daniel Vaulot1, Laure Guillou1,* 1Station Biologique, UMR 7144, CNRS, and Université Pierre & Marie Curie, BP74, 29682 Roscoff Cedex, France 2Department de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CMIMA, CSIC. Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain 3Alfred Wegener Institute for Polar Research, Am Handelshafen 12, 27570 Bremerhaven, Germany ABSTRACT: Systematic sequencing of environmental SSU rDNA genes amplified from different marine ecosystems has uncovered novel eukaryotic lineages, in particular within the alveolate and stramenopile radiations. The ecological and geographic distribution of 2 novel alveolate lineages (called Group I and II in previous papers) is inferred from the analysis of 62 different environmental clone libraries from freshwater and marine habitats. These 2 lineages have been, up to now, retrieved exclusively from marine ecosystems, including oceanic and coastal waters, sediments, hydrothermal vents, and perma- nent anoxic deep waters and usually represent the most abundant eukaryotic lineages in environmen- tal genetic libraries. While Group I is only composed of environmental sequences (118 clones), Group II contains, besides environmental sequences (158 clones), sequences from described genera (8) (Hema- todinium and Amoebophrya) that belong to the Syndiniales, an atypical order of dinoflagellates exclu- sively composed of marine parasites. This suggests that Group II could correspond to Syndiniales, al- though this should be confirmed in the future by examining the morphology of cells from Group II. Group II appears to be abundant in coastal and oceanic ecosystems, whereas permanent anoxic waters and hy- drothermal ecosystems are usually dominated by Group I. -
Protista (PDF)
1 = Astasiopsis distortum (Dujardin,1841) Bütschli,1885 South Scandinavian Marine Protoctista ? Dingensia Patterson & Zölffel,1992, in Patterson & Larsen (™ Heteromita angusta Dujardin,1841) Provisional Check-list compiled at the Tjärnö Marine Biological * Taxon incertae sedis. Very similar to Cryptaulax Skuja Laboratory by: Dinomonas Kent,1880 TJÄRNÖLAB. / Hans G. Hansson - 1991-07 - 1997-04-02 * Taxon incertae sedis. Species found in South Scandinavia, as well as from neighbouring areas, chiefly the British Isles, have been considered, as some of them may show to have a slightly more northern distribution, than what is known today. However, species with a typical Lusitanian distribution, with their northern Diphylleia Massart,1920 distribution limit around France or Southern British Isles, have as a rule been omitted here, albeit a few species with probable norhern limits around * Marine? Incertae sedis. the British Isles are listed here until distribution patterns are better known. The compiler would be very grateful for every correction of presumptive lapses and omittances an initiated reader could make. Diplocalium Grassé & Deflandre,1952 (™ Bicosoeca inopinatum ??,1???) * Marine? Incertae sedis. Denotations: (™) = Genotype @ = Associated to * = General note Diplomita Fromentel,1874 (™ Diplomita insignis Fromentel,1874) P.S. This list is a very unfinished manuscript. Chiefly flagellated organisms have yet been considered. This * Marine? Incertae sedis. provisional PDF-file is so far only published as an Intranet file within TMBL:s domain. Diplonema Griessmann,1913, non Berendt,1845 (Diptera), nec Greene,1857 (Coel.) = Isonema ??,1???, non Meek & Worthen,1865 (Mollusca), nec Maas,1909 (Coel.) PROTOCTISTA = Flagellamonas Skvortzow,19?? = Lackeymonas Skvortzow,19?? = Lowymonas Skvortzow,19?? = Milaneziamonas Skvortzow,19?? = Spira Skvortzow,19?? = Teixeiromonas Skvortzow,19?? = PROTISTA = Kolbeana Skvortzow,19?? * Genus incertae sedis. -
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. -
Molecular Investigation of the Ciliate Spirostomum Semivirescens
Protist, Vol. 169, 875–886, December 2018 http://www.elsevier.de/protis Published online date 20 August 2018 ORIGINAL PAPER Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records a,c,1,2 b,1,2 b a Hunter N. Hines , Henning Onsbring , Thijs J.G. Ettema , and Genoveva F. Esteban a Bournemouth University, Faculty of Science and Technology, Department of Life and Environmental Sciences, Poole, Dorset BH12 5BB, UK b Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden c Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA Submitted May 4, 2018; Accepted August 9, 2018 Monitoring Editor: Eric Meyer The ciliate Spirostomum semivirescens is a large freshwater protist densely packed with endosymbiotic algae and capable of building a protective coating from surrounding particles. The species has been rarely recorded and it lacks any molecular investigations. We obtained such data from S. semivirescens isolated in the UK and Sweden. Using single-cell RNA sequencing of isolates from both countries, the transcriptome of S. semivirescens was generated. A phylogenetic analysis identified S. semivirescens as a close relative to S. minus. Additionally, rRNA sequence analysis of the green algal endosymbiont revealed that it is closely related to Chlorella vulgaris. Along with the molecular species identification, an analysis of the ciliates’ stop codons was carried out, which revealed a relationship where TGA stop codon frequency decreased with increasing gene expression levels. The observed codon bias suggests that S. semivirescens could be in an early stage of reassigning the TGA stop codon. -
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
J. Eukaryot. Microbiol., 52(5), 2005 pp. 399–451 r 2005 by the International Society of Protistologists DOI: 10.1111/j.1550-7408.2005.00053.x The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists SINA M. ADL,a ALASTAIR G. B. SIMPSON,a MARK A. FARMER,b ROBERT A. ANDERSEN,c O. ROGER ANDERSON,d JOHN R. BARTA,e SAMUEL S. BOWSER,f GUY BRUGEROLLE,g ROBERT A. FENSOME,h SUZANNE FREDERICQ,i TIMOTHY Y. JAMES,j SERGEI KARPOV,k PAUL KUGRENS,1 JOHN KRUG,m CHRISTOPHER E. LANE,n LOUISE A. LEWIS,o JEAN LODGE,p DENIS H. LYNN,q DAVID G. MANN,r RICHARD M. MCCOURT,s LEONEL MENDOZA,t ØJVIND MOESTRUP,u SHARON E. MOZLEY-STANDRIDGE,v THOMAS A. NERAD,w CAROL A. SHEARER,x ALEXEY V. SMIRNOV,y FREDERICK W. SPIEGELz and MAX F. J. R. TAYLORaa aDepartment of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada, and bCenter for Ultrastructural Research, Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA, and cBigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575, USA, and dLamont-Dogherty Earth Observatory, Palisades, New York 10964, USA, and eDepartment of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada, and fWadsworth Center, New York State Department of Health, Albany, New York 12201, USA, and gBiologie des Protistes, Universite´ Blaise Pascal de Clermont-Ferrand, F63177 Aubiere cedex, France, and hNatural Resources Canada, Geological Survey of Canada (Atlantic), Bedford Institute of Oceanography, PO Box 1006 Dartmouth, NS B2Y 4A2, Canada, and iDepartment of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, USA, and jDepartment of Biology, Duke University, Durham, North Carolina 27708-0338, USA, and kBiological Faculty, Herzen State Pedagogical University of Russia, St. -
The Revised Classification of Eukaryotes
Published in Journal of Eukaryotic Microbiology 59, issue 5, 429-514, 2012 which should be used for any reference to this work 1 The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. MITCHELL,l SHARON E. MOZLEY-STANRIDGE,p LAURA W. PARFREY,q JAN PAWLOWSKI,r SONJA RUECKERT,s LAURA SHADWICK,t CONRAD L. SCHOCH,u ALEXEY SMIRNOVv and FREDERICK W. SPIEGELt aDepartment of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada, and bDepartment of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and cDepartment of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA, and dBiology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, Cˇeske´ Budeˇjovice, Czech Republic, and eZoology Department, Natural History Museum, London, SW7 5BD, United Kingdom, and fWadsworth Center, New York State Department of Health, Albany, New York, 12201, USA, and gDepartment of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and hDepartment of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and iDepartment of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany, and jDepartment of Parasitology, Charles University, Prague, 128 43, Praha 2, Czech