Accessing uncultivated microorganisms : from the environment to organisms and genomes and back PDF
Preview Accessing uncultivated microorganisms : from the environment to organisms and genomes and back
Accessing Uncultivated Microorganisms FROM THE ENVIRONMENT TO ORGANISMS AND GENOMES AND BACK This page intentionally left blank Accessing Uncultivated Microorganisms FROM THE ENVIRONMENT TO ORGANISMS AND GENOMES AND BACK Edited by Karsten Zengler University of California—SanDiego La Jolla, California Washington,DC Cover images:(from left) Grand Prismatic Spring,Yellowstone National Park,USA (courtesy of Debra Naylor);petri plate with bacteria (©iStockphoto.com/Mr_Jamsey); and bacteria (©iStockphoto.com/dra_schwartz). Copyright © 2008 ASM Press American Society for Microbiology 1752 N Street N.W. Washington,DC 20036-2904 Library of Congress Cataloging-in-Publication Data Accessing uncultivated microorganisms:from the environment to organisms and genomes and back / edited by Karsten Zengler. p.;cm. Includes bibliographical references and index. ISBN-13:978-1-55581-406-9 (hardcover:alk.paper) ISBN-10:1-55581-406-9 (hardcover:alk.paper) 1. Microbial diversity. 2. Microbial ecology. 3. Microbiology—Cultures and culture media. I. Zengler,Karsten. [DNLM: 1. Environmental Microbiology. 2. Bacteria—growth & development. 3. Cell Culture Techniques. 4. Fungi—growth & development. 5. Genetics,Microbial. 6. Microbiological Techniques—methods.QW 55 A169 2008] QR73.A245 2008 579′.17—dc22 2007052360 10 9 8 7 6 5 4 3 2 1 All Rights Reserved Printed in the United States of America Address editorial correspondence to ASM Press, 1752 N St.,N.W.,Washington,DC 20036-2904,USA Send orders to ASM Press,P.O.Box 605,Herndon,VA 20172,USA Phone:800-546-2416;703-661-1593 Fax:703-661-1501 E-mail:[email protected] Online:http://estore.asm.org CONTENTS Contributors vii Preface xi I. INTRODUCTION 1 1. Does Cultivation Still Matter? Karsten Zengler 3 2. The Human Intestinal Microbiota and Its Impact on Health Mirjana Rajili´c-Stojanovi´c,Willem M.de Vos,and Erwin G.Zoetendal 11 II. THE STATUS QUO:WHO IS OUT THERE? HOW TO DETERMINE MICROBIAL DIVERSITY 33 3. The Uncountables William T.Sloan,Christopher Quince,and Thomas P.Curtis 35 4. The Missing Fungi:New Insights from Culture-Independent Molecular Studies of Soil S.K.Schmidt,K.L.Wilson,A.F.Meyer,C.W.Schadt, T.M.Porter,and J.M.Moncalvo 55 5. The Diversity of Free-Living Protists Seen and Unseen, Cultured and Uncultured David A.Caron and Rebecca J.Gast 67 v vi ■ CONTENTS 6. Microbial Biogeography:Patterns in Microbial Diversity across Space and Time Noah Fierer 95 7. The Least Common Denominator:Species or Operational Taxonomic Units? Ramon Rosselló-Mora and Arantxa López-López 117 8. Measuring Diversity Jed A.Fuhrman 131 9. Metagenomics as a Tool To Study Biodiversity Karen E.Nelson 153 III. ARE MICROORGANISMS NONCULTURABLE OR NOT YET CULTURABLE? 171 10. New Cultivation Strategies for Terrestrial Microorganisms Peter H.Janssen 173 11. Cultivation of Marine Symbiotic Microorganisms Todd A.Ciche 193 12. Methods To Study Consortia and Mixed Cultures Boran Kartal and Marc Strous 205 IV. DO WE HAVE TO CHANGE GEAR? NEW CULTIVATION APPROACHES AND NEW MOLECULAR APPROACHES COMBINED 221 13. Microbial Cell Individuality Simon V.Avery 223 14. Nanomechanical Methods To Study Single Cells Ramya Desikan,Laurene Tetard,Ali Passian,Ram Datar,and Thomas Thundat 245 15. Single-Cell Genomics Martin Keller,Christopher W.Schadt,and Anthony V.Palumbo 267 16. How Many Genes Does a Cell Need? Hamilton O.Smith,John I.Glass,Clyde A.Hutchison III,and J.Craig Venter 279 Index 301 CONTRIBUTORS Simon V.Avery School of Biology,Institute of Genetics,University of Nottingham, University Park,Nottingham NG7 2RD,United Kingdom David A.Caron Department of Biological Sciences,University of Southern California, 3616 Trousdale Parkway,Los Angeles,CA 90089-0371 Todd A.Ciche Department of Microbiology and Molecular Genetics,Michigan State University, 2215 Biomedical Physical Sciences Building,East Lansing,MI 48824-4320 Thomas P.Curtis School of Civil Engineering and Geosciences,University of Newcastle upon Tyne, Newcastle NE1 7RU,United Kingdom Ram H.Datar Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6123 Ramya Desikan Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6123 Willem M.de Vos Laboratory of Microbiology,Wageningen University, Dreijenplein 10,6703 HB Wageningen,The Netherlands Noah Fierer Department of Ecology & Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado,Boulder,CO 80305 vii viii ■ CONTRIBUTORS Jed A.Fuhrman Department of Biological Sciences and Wrigley Institute,University of Southern California,Los Angeles,CA 90089-0371 Rebecca J.Gast Department of Biology,Woods Hole Oceanographic Institution, Woods Hole,MA 02543 John I.Glass The J.Craig Venter Institute,9704 Medical Center Drive, Rockville,MD 20850 Clyde A.Hutchison III The J.Craig Venter Institute,9704 Medical Center Drive, Rockville,MD 20850 Peter H.Janssen AgResearch Limited,Palmerston North 4442,New Zealand Boran Kartal Department of Microbiology,Faculty of Science,Radbound University Nijmegen, Toernooiveld 1,6525 ED Nijmegen,The Netherlands Martin Keller Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-603 Arantxa López-López Marine Microbiology Group,Institut Mediterrani d’Estudis Avancats (IMEDEA,CSIC-UIB),E-07190 Esporles,Illes Balears,Spain A.F.Meyer Department of Ecology and Evolutionary Biology,University of Colorado, Boulder,CO 80309 J.M.Moncalvo Department of Ecology and Evolutionary Biology,University of Toronto, and Department of Natural History,Royal Ontario Museum, Toronto,ON M5S 2C6,Canada Karen E.Nelson The J.Craig Venter Institute,9704 Medical Center Drive, Rockville,MD 20850 Anthony V.Palumbo Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6035 Ali Passian Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6123 T.M.Porter Department of Ecology and Environmental Biology,University of Toronto, Toronto,ON M5S 3B2,Canada CONTRIBUTORS ■ ix Christopher Quince Department of Civil Engineering,University of Glasgow, Glasgow G12 8LT,United Kingdom Mirjana Rajilic´-Stojanovic´ Laboratory of Microbiology,Wageningen University,Dreijenplein 10, 6703 HB Wageningen,The Netherlands Ramon Rosselló-Mora Marine Microbiology Group,Institut Mediterrani d’Estudis Avancats (IMEDEA,CSICUIB),E-07190 Esporles,Illes Balears,Spain Christopher W.Schadt Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6035 S.K.Schmidt Department of Ecology and Evolutionary Biology,University of Colorado, Boulder,CO 80309 William T.Sloan Department of Civil Engineering,University of Glasgow, Glasgow G12 8LT,United Kingdom Hamilton O.Smith The J.Craig Venter Institute,9704 Medical Center Drive, Rockville,MD 20850 Marc Strous Department of Microbiology,Faculty of Science,Radboud University Nijmegen, Toernooiveld 1,6525 ED Nijmegen,The Netherlands Laurene Tetard Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6123 Thomas Thundat Biosciences Division,Oak Ridge National Laboratory, 1 Bethel Valley Road,Oak Ridge,TN 37831-6123 J.Craig Venter The J.Craig Venter Institute,9704 Medical Center Drive, Rockville,MD 20850 K.L.Wilson Department of Ecology and Evolutionary Biology,University of Colorado, Boulder,CO 80309 Karsten Zengler Department of Bioengineering,University of California—San Diego,9500 Gilman Drive, La Jolla,CA 92093–0412 Erwin G.Zoetendal Laboratory of Microbiology,Wageningen University, Dreijenplein 10,6703 HB Wageningen,The Netherlands
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