Bacterial Genetics in Natural Environments PDF
Preview Bacterial Genetics in Natural Environments
BACTERIAL GENETICS IN NATURAL ENVIRONMENTS BACTERIAL GENETICS IN NATURAL ENVIRONMENTS Edited by John C. Fry and Martin J. Day School of Pure and Applied Biology, University of Wales College of Cardiff, Cardiff, UK. CHAPMAN AND HALL London· New York· Tokyo' Melbourne· Madras UK Chapman and Hall, 11 New Fetter Lane, London EC4P 4EE USA Chapman and Hall, 29 West 35th Street, New York NY10001 JAPAN Chapman and Hall Japan, Thomson Publishing Japan, Hirakawacho Nemoto Building, 7F, 1-7-11 Hirakawa-cho, Chiyoda-ku, Tokyo 102 AUSTRALIA Chapman and Hall Australia, Thomas Nelson Australia, 480 La Trobe Street, PO Box 4725, Melbourne 3000 INDIA Chapman and Hall India, R. Sheshadri, 32 Second Main Road, CIT East, Madras 600 035 First edition 1990 Published in association with Marius Press Box 15, Camforth, Lancashire LA61HW © 1990 Chapman and Hall Softcover reprint of the hardcover 1s t edition 1990 Typeset in 10 on 12 Times by Keytec Typesetting Ltd, Bridport, Dorset Printed in Great Britain at the University Press, Cambridge ISBN-I3: 978-94-010-7318-9 e-ISBN-13: 978-94-009-1834-4 DOl: 10.1007/978-94-009-1834-4 All rights reserved. No part of this publication may be rcproduced or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or othetwise, or stored in any retrieval system of any nature, without the written permission of the copyright holder and the publisher, application for which shall be made to the publisher. British Library Cataloguing in Publication Data Bacterial genetics in natural environments. 1. Bacteria, Genetics 1. Fry, J. C. II. Day, Martin J. (Martin John) 1946- 589.901 ISBN-13: 978-94-010-7318-9 Library of Congress Cataloging-in-Publication Data available Contents Preface vii Contributors ix Section I: General Aspects of Studying Genetics in Nature 1 Genetic approaches to the study of gene transfer in micro- bial communities 3 J. R. Saunders, J. A. W. Morgan, C. Winstanley, F. C. Raitt, J. P. Carter, R. W. Pickup, J. G. Jones and V. A. Saunders 2 Factors influencing the dissemination of DNA by bacterial ~~~ TI B. M. Wilkins 3 Factors limiting gene transfer in bacteria 31 P. R. Hirsch 4 Phage genetics and ecology 41 H. Schmieger Section II: Aquatic Habitats 5 Plasmid transfer in the epilithon 55 J. C. Fry and M. J. Day 6 Laboratory standardised biofilms as a tool to investigate genetic transfers in water systems 81 P. Bauda, P. Menon, J. C. Block, M. C. Lett, B. Roux and J. C. Hubert 7 Survival of laboratory and freshwater bacteria carrying an extrachromosomal xyLE gene in freshwater microcosms 89 R. W. Pickup, B. M. Simon, J. G. Jones, J. R. Saunders, J. P. Carter, J. A. W. Morgan, C. Winstanley and F. C. Raitt 8 Gene transfer in marine environments 100 M. J. Gauthier and V. A. Breittmayer 9 Gene transfer in activated sludge 111 N. C. McClure, J. C. Fry and A. J. Weightman v VI Contents Section III: Terrestial Habitats 10 Plasmid transfer between soil bacteria 133 W. Klingmiiller, A. Dally, C. Fentner and M. Steinlein 11 Gene transfer in polluted soils 152 M. Mergeay, D. Springael and E. Top 12 The potential for gene exchange between rhizosphere bacteria 172 J. M. Lynch 13 The use of a Sesbania rostrata microcosm for studying gene transfer among microorganisms 182 H. Schneidereit and F. R. 1. Schmidt 14 Plasmid transfer to indigenous bacteria in soil and rhizo- sphere: problems and perspectives 188 J. D. van Elsas and J. T. Trevors 15 Use of wide host range promoters to monitor the fate of 200 recombinant DNA in soil R. B. Henschke and F. R. J. Schmidt 16 The role of soil bacteria in risk assessment analysis 207 F. R. J. Schmidt, J. Rosien and A. Brokamp 17 Gene transfer between streptomycetes in soil 216 E. M. H. Wellington, N. Cresswell, P. R. Herron, L. J. Clewlow, V. A. Saunders and A. Wipat 18 The survival of genetically engineered microorganisms and bacteria on inanimate surfaces and in animals 231 M. J. Bale, P. M. Bennett, M. Hinton and J. E. Beringer Section IV: Conclusions 19 Plasmid transfer and the release of genetically engineered bacteria in nature: a discussion and summary 243 1. C. Fry and M. J. Day Index 251 Preface This book has arisen from the Second European Meeting on Bacterial Genetics and Ecology (Bageco-2) held at the University of Wales, College of Cardiff which we organised on 11-12 April 1989. The meeting was attended by some 60 participants from eight European countries and was made possible by partial financial support from the Commission of the European Communities (CEC) and Imperial Chem ical Industries (UK) Ltd. The meeting was organised to discuss modern developments in the genetics of bacteria in aquatic and terrestrial habitats. It followed on from, and complemented, the first meeting of this series organised by Jean-Pierre Gratia in Brussels during April 1987 which concentrated more on medical and epidemiological issues.! The next meeting will be organised by Michel J. Gauthier in 1991 at Nice, France. If you have been fired with enthusiasm for ecological bacterial genetics after having read this book, and want to attend the next meeting but did not hear about the one in Cardiff, you should write to Dr Gauthier to be put on the address list. A lot is now known about bacterial genetics at the physiological, biochemical and molecular level, and bacterial ecology has developed rapidly over the last 20 years. However, until very recently, few researchers have crossed the divide and linked these two specialisms. The current interest in the possible use of genetically engineered microorganisms (GEMs) in the environment, and the public's perception of the potential dangers from their widespread use, has lead to an increased interest in ecological bacterial genetics from both research scientists and funding bodies world wide. This interest is exemplified by the Biotechnology Action Programme, currently being funded by the CEC, and the recent international conference on the Release of GEMs2•3 and the large media interest it received. Legislation about the environmental use of GEMs is imminent, but we still know very little about the transfer, spread, establishment, expression or survival of genes, whether engineered or not, in nature. We know almost as little about the survival and persistence of non-engineered bacteria in most environments, and we are particularly ignorant of the biolgical charac teristics that enable a bacterium to survive and compete in situ. vii viii Preface It is against this background that Bageco-2 was organised. This book has taken shape largely due to pressure from some of the participants who saw the need for a volume to summarize our current knowledge of ecological bacterial genetics. The book is mainly about gene transfer and survival of genetically interesting bacteria in water and soil. Of necess ity, most of the book is about Pseudomonas spp., Streptomyces spp. and Escherichia coli, because their genetics has been most studied. Howev er, at least the first two genera are probably important natural bacteria and the latter is released in large numbers daily in sewage effluents! Most of the main speakers at Bageco-2 have written chapters for the book, as have~ the two workshop chairpersons. Many of the other participants also rose to the challenge and produced very useful chap ters. The book has been organised into three main sections. Section one aims to introduce readers to basic genetic principles and both ecological and genetic approaches of importance to the understanding of later chapters. The next two sections form the bulk of the volume and cover aquatic and terrestrial habitats. Whilst the last section contains only one chapter in which we have tried to pull the whole book together with a short summary and disussion of some points raised in the individual chapters. Each chapter in the first three sections finishes with a short set of conclusions. This should enable readers to find out quickly about the main messages in the chapters. These conclusions should also make the book more useful to final year undergraduate students as well as the research scientists at whom it is primarily aimed. We take this opportunity to thank all the authors for responding so well to the deadlines agreed and our editorial changes. Without this support the book could never have been published less than a year after Bageco-2, particularly as we only finally decided to produce the book at lunchtime on the first day of the meeting! John C. Fry September 1989 Martin J. Day REFERENCES 1. Gratia JP (ed.). Genetic flux and horizontal evolution in bacteria. Brussels: Brussels University Press, 1987. 2. Sussman M, Collins CH, Skinner FA, Stewart-Tull DE (eds). The release of genetically-engineered micro~organisms. London: Academic Press 1988. 3. Dixon B. Engineered organisms in the environment. Cardiff: Regem 1988. Contributors M. J. Bale, Department of Microbiology, The Medical School, University Walk, Bristol BS8lTD, UK. P. Bauda, Centre des Sciences de l'Environnement, 1 rue des Recollets, 57000 Metz, France. P. M. Bennett, Department of Microbiology, The Medical School, University Walk, Bristol BS8 lTD, UK. J. E. Beringer, Department of Microbiology, The Medical School, University Walk, Bristol BS8ITD, UK. J. C. Block, Centre des Sciences de I'Environnement, 1 rue des Recollets, 57000 Metz, France. V. A. Breittmayer, National Institute of Health and Medical Research, Unit 303, 1 Avenue Jean Lorrain, F-06300 Nice, France. A. Brokamp, Institute for Soil Biology, Federal Institute for Agri cultural Research, Bundesallee 50, 3300 Brauns chweig, Federal Republic of Germany. J. P. Carter, Department of Genetics and Microbiology, Uni versity of Liverpool, L69 3BX, UK. L. J. Clewlow, Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK. N. Cresswell, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK. A. Dally, Department of Genetics, University of Bayreuth, Universitatsstrasse 30, D 8580 Bayreuth, Federal Republic of Germany. ix x Contributors M. J. Day, School of Pure and Applied Biology, University of Wales College of Cardiff, P.O. Box 915, Cardiff CF13TL, UK. C. Fentner, Department of Genetics,-University of Bayreuth, Universitatsstrasse 30, D 8580 Bayreuth, Federal Republic of Germany. J. C. Fry, School of Pure and Applied Biology, University of Wales College of Cardiff, P.O. Box 915, Cardiff CF13TL, UK. M. J. Gauthier, National Institute of Health and Medical Research, Unit 303, 1 Avenue Jean Lorrain, F-06300 Nice, France. R. B. Henschke, Institute for Soil Biology, Federal Institute for A~ri cultural Research, Bundesallee 50, 3300 Brauns chweig, Federal Republic of Germany. P. R. Herron, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK. M. Hinton, Department of Veterinary Medicine, University of Bristol, Langford House, Langford, Avon BS18 7DU, UK. P. R. Hirsch, AFRC Institute of Arable Crops Research, Rothamsted Experimental Station, Harpenden, Herts AL5 2JO, UK. J. C. Hubert, Universite Louis Pasteur, 67000 Strasbourg, France. J. G. Jones, Institute of Freshwater Ecology, Ambleside, Cum bria LA22 OLP, UK. W. Klingmiiller, Department of Genetics, University of Bayreuth, Universitatsstrasse 30, D 8580 Bayreuth, Federal Republic of Germany. M. C. Lett, Universite Louis Pasteur, 67000 Strasbourg, France. Contributors xi J. M. Lynch, AFRC Institute of Horticultural Research, Little hampton, West Sussex BN17 6LP, UK. N. C. McClure, School of Pure and Applied Biology, University of Wales College of Cardiff, P.O. Box 915, Cardiff CF13TL, UK. P. Menon, Centre des Sciences de l'Environnement, 1 rue des Recollets, 57000 Metz, France. M. Mergeay, Laboratory of Genetics and Biotechnology, Depart ment for Environment and Energy, S.C.K.iC.E.N., B-2400 Mol, Belgium. J. A. W. Morgan, Department of Genetics and Microbiology, Uni versity of Liverpool, L69 3BX, UK. R. W. Pickup, Institute of Freshwater Ecology, Ambleside, Cum bria LA22 OLP, UK. F. C. Raitt, Department of Genetics and Microbiology, Uni versity of Liverpool, L69 3BX, UK. J. Rosien, Institute for Soil Biology, Federal Institute for Agri cultural Research, Bundesallee 50, 3300 Brauns chweig, Federal Republic of Germany. B. Roux, Universite Louis Pasteur, 67000 Strasbourg, France. J. R. Saunders, Department of Genetics and Microbiology, Uni versity of Liverpool, L69 3BX, UK. V. A. Saunders, School of Biological Sciences, Liverpool Poly technic, Liverpool L3 3AF, UK. F. R. J. Schmidt, Institute for Soil Biology, Federal Institute for Agri cultural Research, Bundesallee 50, 3300 Brauns chweig, Federal Republic of Germany. H. Schmieger, Institute for Genetics and Microbiology, University of Munich, Maria-Ward Str. la, D-8000 Munich 19, Federal Republic of Germany.
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