Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
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A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L
JOURNAL OF BACTERIOLOGY, Feb. 1990, p. 756-761 Vol. 172, No. 2 0021-9193/90/020756-06$02.00/0 Copyright © 1990, American Society for Microbiology A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L. HOLMES* AND MICHAEL L. DYALL-SMITH Department of Microbiology, University of Melbourne, Parkville, Victoria 3052, Australia Received 25 May 1989/Accepted 10 November 1989 A mutant resistant to the gyrase inhibitor novobiocin was selected from a halophilic archaebacterium belonging to the genus Haloferax. Chromosomal DNA from this mutant was able to transform wild-type ceils to novobiocin resistance, and these transformants formed visible colonies in 3 to 4 days on selective plates. The resistance gene was isolated on a 6.7-kilobase DNA KpnI fragment, which was inserted into a cryptic multicopy plasmid (pHK2) derived from the same host strain. The recombinant plasmid transformed wild-type cells at a high efficiency (>106/pg), was stably maintained, and could readily be reisolated from transformants. It could also transform Halobacterium volcanii and appears to be a useful system for genetic analysis in halophilic archaebacteria. Archaebacteria are phylogenetically distinct from eubac- cle was the lack of selectable traits, such as antibiotic teria and eucaryotes and can be broadly divided into three resistance. groups: methanogens, sulfur-dependent thermoacidophiles, The aim of this study was to find a selectable marker for and extreme halophiles (for a review, see reference 22). use in constructing plasmid vectors suitable for isolating and Numerous halobacteria have been isolated from hypersaline studying genes in halobacteria. We report the successful environments around the world, but it is only recently that construction of such a vector by using a gene conferring their taxonomy has been analyzed in a rigorous and compre- resistance to novobiocin and a cryptic plasmid from Halo- hensive fashion. -
Microbial Community Responses to Modern Environmental
Originally published as: Genderjahn, S., Alawi, M., Wagner, D., Schüller, I., Wanke, A., Mangelsdorf, K. (2018): Microbial Community Responses to Modern Environmental and Past Climatic Conditions in Omongwa Pan, Western Kalahari: A Paired 16S rRNA Gene Profiling and Lipid Biomarker Approach. - Journal of Geophysical Research, 123, 4, pp. 1333—1351. DOI: http://doi.org/10.1002/2017JG004098 Journal of Geophysical Research: Biogeosciences RESEARCH ARTICLE Microbial Community Responses to Modern Environmental 10.1002/2017JG004098 and Past Climatic Conditions in Omongwa Pan, Western Key Points: Kalahari: A Paired 16S rRNA Gene Profiling • Kalahari pan structures possess high potential to act as geoarchives for and Lipid Biomarker Approach preserved biomolecules in arid to semiarid regions S. Genderjahn1 , M. Alawi1 , D. Wagner1,2 , I. Schüller3, A. Wanke4, and K. Mangelsdorf1 • Past microbial biomarker suggests changing climatic conditions during 1GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany, 2Institute of Earth and the Late Glacial to Holocene transition 3 in the western Kalahari Environmental Science, University of Potsdam, Potsdam, Germany, Marine Research Department, Senckenberg am Meer, 4 • Based on taxonomic investigations, Wilhelmshaven, Germany, Department of Geology, University of Namibia, Windhoek, Namibia the abundance and diversity of the microbial community in the pan is related to near-surface processes Abstract Due to a lack of well-preserved terrestrial climate archives, paleoclimate studies are sparse in southwestern Africa. Because there are no perennial lacustrine systems in this region, this study relies on a Supporting Information: saline pan as an archive for climate information in the western Kalahari (Namibia). Molecular biological and • Supporting Information S1 biogeochemical analyses were combined to examine the response of indigenous microbial communities to modern and past climate-induced environmental conditions. -
Extremozymes of the Hot and Salty Halothermothrix Orenii
Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry. -
Delft University of Technology Halococcoides Cellulosivorans Gen
Delft University of Technology Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose- utilizing haloarchaeon from hypersaline lakes Sorokin, Dimitry Y.; Khijniak, Tatiana V.; Elcheninov, Alexander G.; Toshchakov, Stepan V.; Kostrikina, Nadezhda A.; Bale, Nicole J.; Sinninghe Damsté, Jaap S.; Kublanov, Ilya V. DOI 10.1099/ijsem.0.003312 Publication date 2019 Document Version Accepted author manuscript Published in International Journal of Systematic and Evolutionary Microbiology Citation (APA) Sorokin, D. Y., Khijniak, T. V., Elcheninov, A. G., Toshchakov, S. V., Kostrikina, N. A., Bale, N. J., Sinninghe Damsté, J. S., & Kublanov, I. V. (2019). Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose-utilizing haloarchaeon from hypersaline lakes. International Journal of Systematic and Evolutionary Microbiology, 69(5), 1327-1335. [003312]. https://doi.org/10.1099/ijsem.0.003312 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. International Journal of Systematic and Evolutionary Microbiology Halococcoides cellulosivorans gen. -
The Life of Brine: Halophiles in 2001 Comment Mike Dyall-Smith* and Michael Danson
http://genomebiology.com/2001/2/12/reports/4033.1 Meeting report The life of brine: halophiles in 2001 comment Mike Dyall-Smith* and Michael Danson Addresses: *Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia. Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK. Correspondence: Mike Dyall-Smith. E-mail: [email protected] Published: 21 November 2001 reviews Genome Biology 2001, 2(12):reports4033.1–4033.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2001/2/12/reports/4033 © BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) reports haloarchaea found in salt ponds that have 8% salt (or A report on the International conference on Halophilic 2.3-fold concentrated seawater) but are not detectable at the Microorganisms, Sevilla, Spain, 23-27 September 2001. higher salinities usually associated with haloarchaea (20-35% salt). Discovered using 16S rRNA libraries, the new haloar- chaea are distantly related to Haloarcula. None has been cul- The 2001 halophiles meeting covered archaea, bacteria, tured but these results suggest an optimum salt concentration fungi and algae adapted to living hypersaline environments. for growth far lower than that of known haloarchaea. These deposited research Despite the absence of some American colleagues as a result represent an intermediate group of haloarchaea, not previ- of the recent terrorist attack, the meeting was full of exciting ously suspected, and offer insight into the evolution of advances (as well as pictures of salt lakes, salterns, brines extreme halophiles. -
Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies
Protocol Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies Mirko Stauffer 1 , Stephan Hirschi 1 , Zöhre Ucurum 1, Daniel Harder 1 , Ramona Schlesinger 2,* and Dimitrios Fotiadis 1,* 1 Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; mirko.stauff[email protected] (M.S.); [email protected] (S.H.); [email protected] (Z.U.); [email protected] (D.H.) 2 Department of Physics, Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany * Correspondence: [email protected] (R.S.); [email protected] (D.F.) Received: 6 July 2020; Accepted: 19 July 2020; Published: 22 July 2020 Abstract: The light-driven proton pump bacteriorhodopsin (BR) from the extreme halophilic archaeon Halobacterium salinarum is a retinal-binding protein, which forms highly ordered and thermally stable 2D crystals in native membranes (termed purple membranes). BR and purple membranes (PMs) have been and are still being intensively studied by numerous researchers from different scientific disciplines. Furthermore, PMs are being successfully used in new, emerging technologies such as bioelectronics and bionanotechnology. Most published studies used the wild-type form of BR, because of the intrinsic difficulty to produce genetically modified versions in purple membranes homologously. However, modification and engineering is crucial for studies in basic research and, in particular, to tailor BR for specific applications in applied sciences. We present an extensive and detailed protocol ranging from the genetic modification and cultivation of H. -
Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus Dombrowskii and Other Extremely Halophilic Archaebacteria
ASTROBIOLOGY Volume 9, Number 1, 2009 © Mary Ann Liebert, Inc. DOI: 10.1089/ast.2007.0234 Special Paper Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus dombrowskii and Other Extremely Halophilic Archaebacteria Sergiu Fendrihan,1 Attila Bérces,2 Helmut Lammer,3 Maurizio Musso,4 György Rontó,2 Tatjana K. Polacsek,1 Anita Holzinger,1 Christoph Kolb,3,5 and Helga Stan-Lotter1 Abstract The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibil- ity of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloar- chaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522T was ex- posed to UV doses over a wavelength range of 200–400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m2, and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m2. The estimated Ն 2 D37 (dose of 37 % survival) for Hcc. dombrowskii was 400 kJ/m . However, exposure of cells to UV flux while 2 in liquid culture reduced D37 by 2 orders of magnitude (to about 1 kJ/m ); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica. -
Halophilic Microorganisms Springer-Verlag Berlin Heidelberg Gmbh Antonio Ventosa (Ed.)
Halophilic Microorganisms Springer-Verlag Berlin Heidelberg GmbH Antonio Ventosa (Ed.) Halophilic Microorganisms With 58 Figures Springer Dr.ANTONIO VENTOSA Department of Microbiology and Parasitology Faculty of Pharmacy University of Sevilla 41012 Sevilla Spain e-mail: [email protected] ISBN 978-3-642-05664-2 ISBN 978-3-662-07656-9 (eBook) DOI 10.1007/978-3-662-07656-9 Library of Congress Cataloging-in-Publication Data applied for A catalog record for this book is available from the Library of Congress. Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publicati an in the Deutsche Nationalbibliographie; detailed bibliographic data is available in the Internet at http://dnb.ddb.de This work is subject ta copyright. AII rights are reservod, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of iIIustrations, recitation, broadcasting, reproduction an microfilm ar in any other way, and storage in data banks. Duplication of this publication ar parts thereofis permit ted only under the provisions of the German Copyright Law of September 9, 1965, in ils current version, and per missions for use must always be obtained from Springcr-Vcrlag Berlin Heiddhcrg GmbH. Violations are liable for prosecution under the German Copyright Law. http://www.springer.de © Springer-Verlag Berlin Heidelberg 2004 Originally published by Springer-Vcrlag lkrlin Hcidclbcrg New York in 2004 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. -
Susceptibility of Archaea to Antimicrobial Agents: Applications to Clinical Microbiology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector REVIEW 10.1111/j.1469-0691.2012.03913.x Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology S. Khelaifia and M. Drancourt Unite´ de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, Me´diterrane´e Infection, Faculte´ de Me´decine, Aix-marseille-Universite´, Marseille, France Abstract We herein review the state of knowledge regarding the in vitro and in vivo susceptibility of archaea to antimicrobial agents, including some new molecules. Indeed, some archaea colonizing the human microbiota have been implicated in diseases such as periodontopathy. Archaea are characterized by their broad-spectrum resistance to antimicrobial agents. In particular, their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents interfering with peptidoglycan biosynthesis. Archaea are, however, susceptible to the pro- tein synthesis inhibitor fusidic acid and imidazole derivatives. Also, squalamine, an antimicrobial agent acting on the cell wall, proved effective against human methanogenic archaea. In vitro susceptibility data could be used to design protocols for the decontamination of complex microbiota and the selective isolation of archaea in anaerobic culture. Keywords: Antimicrobial agent, archaea, methanogenic archaea, microbiota, susceptibility testing Article published online: 23 May 2012 Clin Microbiol Infect 2012; 18: 841–848 Corresponding author: M. Drancourt, Unite´ des Rickettsies, Fa- culte´ de Me´decine, 27, Boulevard Jean Moulin-Cedex 5, France E-mail: [email protected] Methanogenic archaea (herein referred to as methano- Introduction gens) are the sole organisms producing methane from H2 +CO2 [6]. -
Life at Low Water Activity
Published online 12 July 2004 Life at low water activity W. D. Grant Department of Infection, Immunity and Inflammation, University of Leicester, Maurice Shock Building, University Road, Leicester LE1 9HN, UK ([email protected]) Two major types of environment provide habitats for the most xerophilic organisms known: foods pre- served by some form of dehydration or enhanced sugar levels, and hypersaline sites where water availability is limited by a high concentration of salts (usually NaCl). These environments are essentially microbial habitats, with high-sugar foods being dominated by xerophilic (sometimes called osmophilic) filamentous fungi and yeasts, some of which are capable of growth at a water activity (aw) of 0.61, the lowest aw value for growth recorded to date. By contrast, high-salt environments are almost exclusively populated by prokaryotes, notably the haloarchaea, capable of growing in saturated NaCl (aw 0.75). Different strategies are employed for combating the osmotic stress imposed by high levels of solutes in the environment. Eukaryotes and most prokaryotes synthesize or accumulate organic so-called ‘compatible solutes’ (osmolytes) that have counterbalancing osmotic potential. A restricted range of bacteria and the haloar- chaea counterbalance osmotic stress imposed by NaCl by accumulating equivalent amounts of KCl. Haloarchaea become entrapped and survive for long periods inside halite (NaCl) crystals. They are also found in ancient subterranean halite (NaCl) deposits, leading to speculation about survival over geological time periods. Keywords: xerophiles; halophiles; haloarchaea; hypersaline lakes; osmoadaptation; microbial longevity 1. INTRODUCTION aw = P/P0 = n1/n1 ϩ n2, There are two major types of environment in which water where n is moles of solvent (water); n is moles of solute; availability can become limiting for an organism. -
Genome Sequence and Description of Haloferax Massiliense Sp. Nov., a New Halophilic Archaeon Isolated from the Human Gut
Extremophiles (2018) 22:485–498 https://doi.org/10.1007/s00792-018-1011-1 ORIGINAL PAPER Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut Saber Khelaifa1 · Aurelia Caputo1 · Claudia Andrieu1 · Frederique Cadoret1 · Nicholas Armstrong1 · Caroline Michelle1 · Jean‑Christophe Lagier1 · Felix Djossou2 · Pierre‑Edouard Fournier1 · Didier Raoult1,3 Received: 14 November 2017 / Accepted: 5 February 2018 / Published online: 12 February 2018 © The Author(s) 2018. This article is an open access publication Abstract By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the frst known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characteriza- tion as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplifed 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. -
Characterization of the First Cultured Representative of Verrucomicrobia Subdivision 5 Indicates the Proposal of a Novel Phylum
The ISME Journal (2016) 10, 2801–2816 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum Stefan Spring1, Boyke Bunk2, Cathrin Spröer3, Peter Schumann3, Manfred Rohde4, Brian J Tindall1 and Hans-Peter Klenk1,5 1Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 2Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 3Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and 4Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate.