Plant Microbiology PDF
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Plant Microbiology Plant Microbiology Michael Gillings and Andrew Holmes Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia LONDON AND NEW YORK © Garland Science/BIOS Scientific Publishers, 2004 First published 2004 This edition published in the Taylor & Francis e-Library, 2005. “ To purchase your own copy of this or any of Taylor & Francis or Routledge’s collection of thousands of eBooks please go to http://www.ebookstore.tandf.co.uk/.” All rights reserved. No part of this book may be reprinted or reproduced or utilised in any form or by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying and recording, or in any information storage or retrieval system, without permission in writing from the publishers. A CIP catalogue record for this book is available from the British Library. ISBN 0-203-50660-X Master e-book ISBN ISBN 0-203-62500-5 (Adobe e-Reader Format) ISBN 1 85996 224 6 (Print Edition) Garland Science/BIOS Scientific Publishers 4 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN, UK and 29 West 35th Street, New York, NY 10001–2299, USA World Wide Web home page: http://www.bios.co.uk/ Garland Science/BIOS Scientific Publishers is a member of the Taylor & Francis Group. Distributed in the USA by Fulfilment Center Taylor & Francis 10650 Toebben Drive Independence, KY 41051, USA Toll Free Tel.: +1 800 634 7064; E-mail: [email protected] Distributed in Canada by Taylor & Francis 74 Rolark Drive Scarborough, Ontario M1R 4G2, Canada Toll Free Tel.: +1 877 226 2237; E-mail: [email protected] Distributed in the rest of the world by Thomson Publishing Services Cheriton House North Way Andover, Hampshire SP10 5BE, UK Tel.: +44 (0)1264 332424; E-mail: [email protected] Library of Congress Cataloging-in-Publication Data Plant microbiology/edited by Michael Gillings and Andrew Holmes. p. cm. ISBN 1-85996-224-6 1. Plants—Microbiology. 2. Plant-microbe relationsips. 3. Rhizobium. I. Gillings, Michael.II. Holmes, Andrew J.III. Title. QR351.P58325 2004 577.8′52--dc22 2004003943 Production Editor: Catherine Jones Contents Abbreviations vii Contributors ix Preface xi 1 The diversity, ecology and molecular detection of arbuscular 1 mycorrhizal fungi R.Husband 2 Rhizobial signals convert pathogens to symbionts at the legume interface 20 A.Bartsev, H.Kobayashi and W.J.Broughton 3 The root nodule bacteria of legumes in natural systems 35 E.L.J.Walkin 4 Effects of transgenic plants on soil micro-organisms and nutrient 59 dynamics A.Sessitsch, K.Smalla, E.Kandeler and M.H.Gerzabek 5 Fungal endophytes: hitch-hikers of the green world 81 K.Saikkonen, M.Helander and S.H.Faeth 6 Actinorhizal symbioses: diversity and biogeography 102 D.R.Benson, B.D.Vanden Heuvel and D.Potter 7 Chemical signalling by bacterial plant pathogens 138 C.L.Pemberton, H.Slater and G.P.C.Salmond 8 Quorum quenching—manipulating quorum sensing for disease control 165 L-H.Zhang 9 Plant disease and climate change 175 S.Chakraborty and I.B.Pangga 10 Genetic diversity of bacterial plant pathogens 194 M.Fegan and C.Hayward 11 Genetic diversity and population structure of plant-pathogenic species in 220 the genus Fusarium B.A.Summerell and J.F.Leslie 12 Genome sequence analysis of prokaryotic plant pathogens 238 D.W.Wood, E.W.Nester and J.C.Setubal 13 Analysis of microbial communities in the plant environment 259 A.J.Holmes 14 The importance of microbial culture collections to plant microbiology 286 E.Cother Index 302 Abbreviations ABC ATP-Binding Cassette ACL acyl carrier protein AFLP amplified fragment length polymorphism AHL acyl homoserine lactone AM arbuscular mycorrhizal AOGCM Atmospheric-Ocean General Circulation Model APG Angiosperm Phylogeny Group BLAST Basic Local Alignment Search Tool bp basepair CGA community genome array CLPP community level physiological profiling DF diffusible factor DGGE denaturing gradient gel electrophoresis DSF diffusible extracellular factor EC enzyme commission ENSO El Nino—Southern Oscillation EPS exopolysaccharide FAME fatty acid methyl ester FGA functional gene array GMP genetically modified plant HGT horizontal gene transfer HR hypersensitive response INVAM International Culture Collection of Arbuscular and Vesicular Mycorrhizal Fungi IS insertion sequence ITS internal transcribed spacer LCO lipo-chito-oligosaccharide LPS lipopolysaccharide LRR leucine-rich repeat MGS metabolic group-specific MYA million years ago NAO North Atlantic Oscillation NCBI National Center for Biotechnological Information NU nodulation unit ORF open reading frame OTU operational taxonomic unit PCR polymerase chain reaction PGS phylogenetic group-specific POA phylogenetic oligonucleotide array R resistance RFLP restriction fragment length polymorphism RISA ribosomal intergenic spacer analysis RNB root nodule bacteria ROS reactive oxygen species SAM S-adenosylmethionine SOI Southern Oscillation Index SSCP single-strand conformation polymorphism SSU small subunit TC transport classification Ti tumour-inducing T-RFLP terminal RFLP TTSS type III secretion systems VCG vegetative compatibility group Contributors Bartsev, A. LBMPS, l’Université de Genève, 1 ch de l’Impératrice, 1292 Chambésy/Genéve, Switzerland Benson, D.R. Dept. Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268–3044, USA Broughton, W.J. LBMPS, l’Université de Genève, 1 ch de l’Impératrice, 1292 Chambésy/Genéve, Switzerland Chakraborty, S. CSIRO Tropical Agriculture, CRC for Tropical Plant Pathology, University of Queensland, Qld 4072, Australia Cother, E. NSW Agriculture, Forest Road, Orange NSW 2800, Australia Faeth, S.H. Department of Biology, Arizona State University, Tempe, AZ 85287–1501, USA Fegan, M. CRC for Tropical Plant Protection, The University of Queensland, St. Lucia, Queensland, 4072, Australia Gerzabek, M.H. Institute of Soil Research, University of Agricultural Sciences Vienna, A-1180 Vienna, Austria Gillings, M. Molecular Prospecting Group and Key Centre for Biodiversity, Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia Hayward, C. CRC for Tropical Plant Protection, The University of Queensland, St. Lucia, Queensland, 4072, Australia Helander, M. Section of Ecology, Department of Biology, FIN-20014 University of Turku, Finland Holmes, A.J. School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, New South Wales, 2006, Australia Husband, R. Department of Biology, University of York, PO Box 373, York, YO10 5YW, UK Kandeler, E. Institute of Soil Science, University of Hohenheim, D-70599 Stuttgart, Germany Kobayashi, H. LBMPS, l’Université de Genève, 1 ch de l’Impératrice, 1292 Chambésy/Genéve, Switzerland Leslie, J.F. Department of Plant Pathology, 4002 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506–5502, USA Nester, E.W. Department of Microbiology, Box 357242, University of Washington, Seattle, WA 98195–7242, USA Pangga, I.B. CSIRO Tropical Agriculture, CRC for Tropical Plant Pathology, University of Queensland, Qld 4072, Australia Pemberton, C.L. Department of Biochemistry, University of Cambridge, Tennis Court Road, Building O, Downing Site, Cambridge, CB2 1QW, UK Potter, D. Dept. Pomology, Univ. of California, Davis, One Shields Avenue, Davis, California 95616, USA
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