Bacterial Diversity and Systematics PDF
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Bacterial Diversity and Systematics FEDERATION OF EUROPEAN MICROBIOLOGICAL SOCIETIES SYMPOSIUM SERIES Recent FEMS Symposium volumes publisbed by Plenum Press 1991 • GENETICS AND PRODUCT FORMATION IN STREPTOMYCES Edited by Simon Baumberg, Hans Kriigel, and Dieter Noack (FEMS Symposium No. 55) 1991 • THE BIOLOGY OF A CINETOBACTER: Taxonomy, Clinical Importance, Molecular Biology, Physiology, Industrial Relevance Edited by K. ]. Towner. E. Bergogne-Berezin, and C. A. Fewson (FEMS Symposium Ko. 57) 1991 • MOLECULAR PATHOGENESIS OF GASTROINTESTINAL INFECTIONS Edited by T. Wadstrom, P. H. Makela, A.-M. Svennerholm, and H. Wolf-Watz (FEMS Symposium No. 58) 1992 • MOLECULAR RECOGNITION IN HOST-PARASITE IKTERACTIONS Edited by Timo K. Korhonen, Tapani Hovi, and P. Helena Makela (FEMS Symposium No. 61) 1992 • THE RELEASE OF GENETICALLY MODIFIED MICROORGANISMS-REGEM 2 Edited by Duncan E. S. Stewart-Tull and Max Sussman (FEMS Symposium No. 63) 1993 • RAPID DIAGNOSIS OF MYCOPLASMAS Edited by Itzhak Kahane and Amiram Adoni (FEMS Symposium No. 62) 1993 • BACTERIAL GROWTH AND LYSIS: Metabolism and Structure of the Bacterial Sacculus Edited by M. A. de Pedro, ].-V. Hoitje, and W. Loffelhardt (FEMS Symposium No. 65) 1994 • THE GENUS ASPERGILLUS: From Taxonomy and Genetics to Industrial Application Edited by Keith A. Powell, Annabel Renwick, and John F. Peberdy (FEMS Symposium No. 69) 1994 • BACTERIAL DIVERSITY AND SYSTEMATICS Edited by Fergus G. Priest, Alberto Ramos-Cormenzana, and B. ]. Tindall (FEMS Symposium 1\0. 75) A Continuation Order Plan is a"ailable for this series. A continuation order will bring de!i\'ery of each new volume immediately upon publication. Volumes are billed only upon actual shipment. For further information please contact the publisher. Bacterial Diversity and Systematics Edited by Fergus G. Priest Heriot Watt University Edinburgh, Scotland, United Kingdom Alberto Ramos-Cormenzana University of Granada Granada, Spain and B.J. Tindall Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany SPRINGER SCIENCE+ BUSINESS MEDIA, LLC Ltbrary of Congress Cataloging-in-Publication Data Bacterlal dlversity and systemat'cs / edited by Fergus G. Priest. Alberto Ramos-Cormenzana. and B.J. T,ndall. p. cm. -- (Federatlon of European Microbiological Socletles sympas 1 um ser 1 es ; 75) Includes blbllographlcal references and lndex. ISBN 978-1-4613-5760-5 ISBN 978-1-4615-1869-3 (eBook) DOI 10.1007/978-1-4615-1869-3 1. Bacterla 1 dlverS1ty. 2. Bacterlo1ogy--ClasSlflcatlon. 1. Pr1est. F. G. II. Ramos-Cormenzana. Alberto. III. Tindall. B.J. IV. Ser'es, FEMS symposiu. , no. 75. QR73 . 8326 1994 589.9' 00 12--dc20 94-43384 CIP Proceedings of a symposium held under the auspices of the Federation of European Microbiological Societies, September 19-22, 1993, in Granada, Spain ISBN 978-1-4613-5760-5 © 1994 Springer Science+Business Media New York Originally published by Plenum Press, New York in 1994 Softcover reprint of the hardcover lst edition 1994 AII rights reserved No part of this book may be reproduced, stored in a retrieval system. or transmitted in any form or by any means, electronic, mechanical. photocopying, microfilming, recording, or otherwise, without written permission from the Publisher Preface Bacterial taxonomy as a specialized discipline is practised by a minority but the applications of taxonomy are important to most, if not all microbiologists. It is the implementation of taxonomic ideas and practises which gives rise to identification and typing systems, procedures for the analysis and characterization of biodiversity, hypotheses about the evolution of micro-organisms, and improved procedures for the isolation and implementation of bacteria in biotechnological processes. Without taxonomic theory providing a sound basis to these many facets of microbiology there would be severe problems faced by many scientists working with micro-organisms. Taxonomy comprises three sequential but independent processes; classification, nomenclature and identification. The first two stages are the prime concern of the specialist taxonomist but the third stage should result in identification schemes of value to all microbiologists. As the classification and identification of micro-organisms improves, largely due to the introduction of new technologies, so does its contribution to the subject as a whole. It therefore seemed timely to hold a conference in the autumn of 1993 devoted to microbial identification. Such a topic could not be addressed without some reference to the enabling discipline of classification, but the principal aims were to assess improvements in identification and typing and how these were benefiting microbiological topics ranging from ecological and biotechnological studies of extremophilic bacteria to the use of pyrolysis mass spectrometry in epidemiology. The meeting, which was held in Granada, Spain, was supported by FEMS (FEMS Symposium No. 75) and the British (SGM), German and Spanish Microbiology Societies. The financial support of Novo Nordisk was also greatly appreciated by the organizers and all who attended, as was the extensive hospitality provided by the state of Andalucia. This book is derived from the Granada Conference. It is not intended as a proceedings of that conference, but each chapter has been drawn from the speakers and topics covered at the meeting. Inevitably, there has been some rearrangement and modification of material and with minor changes in emphasis it was considered that a name change was appropriate to reflect better the contents of the book. Thus 'Microbial Diversity and Systematics' was chosen, but the emphasis remains on identification of bacterial diversity. The Editors are grateful to all the authors who have contributed to this book. The Granada Conference was considered a great success by those who attended, we hope that this book will similarly be found to be timely and useful. Fergus G. Priest; Edinburgh Alberto Ramos-Cormenzana; Granada Brian Tindall; Braunschweig v CONTENTS Molecular Taxonomy: Classification and Identification ........................................... . KH. Schleifer and W Ludwig DNA Sequence Analysis of the Genetic Structure of Populations of Salmonella enterica and Escherichia coli.................................................... 17 RK Selander, J Li, E.F. Boyd, F.-S. Wang, and K Nelson Identification and Typing of Bacteria by Protein Electrophoresis ............................. 51 K Kersters, B. Pot, D. Dewettinck, U Torck, M. Vancanneyt, L. Vauterin, and P. Vandamme Characterisation and Identification of Micro-organisms by FT-IR Spectroscopy and J<'T-IR Microscopy. .................................................. 67 D. Naumann, D. Helm, and C. Schultz Curie Point Pyrolysis Spectrometry and Its Application to Bacterial Systematics ........................................................................................ 87 M. Goodfellow, 1 Chun, E. Atalan, and 1.-J. Sanglier New Methods for Diagnosis and Epidemiological Studies of Tuberculosis Based on PCR and RFLP ............................................................. I05 C. Martin, S. Samper, 1. Otal, P Asensio, R. Gomez-Lus, G. Torrea, and B. Gicquel Typing in situ with Pobes.......................................................................................... 115 R. Amann and W. Ludwig The Use of Molecular Markers for the Detection and Typing of Bacteria in SoiI.............................................................................................. 137 E.M.H. Wellington, AS. Huddleston, and P Marsh vii Phylogenetic Diversity of Methanogen Endosymbionts of Anaerobic Ciliates.......................................................................................... 153 T.M. Embley and B.J. Finlay Diversity, Dynamics and Topographic Arrangement of Microorganisms are Essential Parameters That Identify a Microbial Consortium................................................................................. 161 E. Conway de Macario and AJ.L. Macario Chemotaxonomy and the Identification of Thermophilic Bacteria......................... 173 M.S. da Costa and M.F. Nobre Alkaliphiles : Diversity and Identification................................................................ 195 B.E. Jones, W.D. Grant, N.C. Collins, and W.E. Mwatha Taxonomy and Phylogeny of Moderately Halphilic Bacteria........................................................................................................... 231 A. Ventosa Chemical Analysis of Archaea and Bacteria: A Critical Evaluation of Its Use in Taxonomy and Identification ................................... 243 BJ. TindaII The Biotechnological Importance of Molecular Biodiversity Studies for Metal Bioleaching........................................................................ 259 B.M. Goebel and E. Stackebrandt Systematics of Insect Pathogenic Bacilli: Uses in Strain Identification and Isolation of Novel Pathogens ............................................ 275 F.G. Priest, M. Aquino de MUrD, and D.A. Kaji Industries Requirements with Regard to Identification of Bacteria....................................................................................................... 297 H. Gurtler and LAnker Present Trends and Future Prospects for Rapid Methods and Automation in the Chemical Laboratory............................................... 309 K.A Feltham and M. Stevens Contributors............................................................................................................... 323 Index ........................................................................................................................... 327 viii MOLECULAR TAXONOMY: CLASSIFICATION AND IDENTIFICATION Karl-Heinz Schleifer and Wolfgang Ludwig Lehrstuhl fur Mikrobiologie, Technische Universi tat, D-80290 Munchen, Germany INTRODUCTION Bacterial taxonomy or systematics may be defined as the scientific study of the diversity of organisms with the ultimate object of characterizing and arranging them in an orderly manner (Truper and Schleifer, 1991). It comprises the three sUbdisciplines classification, nomenclature and identification. Classification deals with the orderly arran gements of taxonomic units (taxa) into groups on the basis of similarities or relationships. Nomenclature is the assignment of names to the taxonomic units according to the Internatio nal Code of Nomenclature of Bacteria (Sneath, 1992). Finally, in identification, members of a distinct taxonomic unit are identified on the basis of common characteristic properties which distinguish them from other organisms. Classification is often confused with identification. However, it is necessary to describe and characterize first the basic taxonomic unit (classification) before an isolate can be identified as belonging to this taxon. An isolate, _pI which cannot be identified as a member of a known taxon, has to be described and classified as a new species or even genus. Therefore, classification precedes identification. There are two main types of classification based on phenetic (non-evolutionary) and phylogenetic (evolutionary) relationships. The aim of the former is to group organisms on the basis of their phenotypic properties. However, phenetic resemblance is often an unreliable guide to genealogy. Adap tive characters are often acquired independently by unrelated taxa (convergence and lateral gene transfer) and in other Bacterial Diversity and Systematics Edited by F.O. Priest et al., Plenum Press, New York, 1994 cases organisms can resemble one another merely by lacking a particular character. Evolutionary or phylogenetic classifi cation, on the other hand, is not based on phenetic resem blances between species but on their genealogical relation ships. PHYLOGENY OF BACTERIA The morphological diversity and fossil records of plants and higher animals allows reconstruction of the evolution of these organisms. The morphological simplicity of bacteria as well as the lack of meaningful developmental stages and fossil records discouraged microbiologists in their attempt to elucidate the phylogenetic relationships of prokaryotes. This is documented by the ready resignation of van Niel, once the leading exponent of a phylogenetic bacterial classifica tion system, who stated " .•. that comparable efforts in the realm of the bacteria are doomed to failure because it does not appear likely that criteria of truly phylogenetic signi ficance can be devised for these organisms" (van Niel, 1955). A similar pessimistic view can be found in the 1970 edition of the well known textbook "The Microbial World" by stanier et al .. They wrote " ..... for (most) major biological groups (such as bacteria), the general course of evolution will never be known, and there is simply not enough objective evidence to base their classification on phylogenetic grounds"(stanier et al., 1970). However, the development of techniques that allowed the sequencing of genetic material revolutionized biology including the taxonomy of bacteria. MOLECULAR CHRONOMETERS The sequence of a macromolecule can be changed in a large number of ways without altering its function. This realizati on has led to the concept of the "evolutionary clock" and to the use of molecular sequences as chronometers (Zuckerkandl and Pauling, 1965). The evolution occurs on the level of the genotype and of the phenotype. The changes of the deoxyribo nucleic acid sequences occur more or less continously on an evolutionary time scale. The majority of these changes are either deleterious or selectively neutral, and therefore do not alter the phenotype (Kimura, 1983). Changes at the pheno typic level, on the other hand, are relatively rare and sporadic. The genotypic changes are the basis for inferring phylo genetic relationships. However, not all molecular chronome ters are equally useful for reconstructing phylogenies. A useful chronomter for inferring the phylogeny of all living organisms has to fulfill the following properties: 1. it has to be ubiquitously distributed among organisms 2 20 it should show a high degree of functional constancy 3. it should be sufficiently conserved to span the full evolutionary spectrum 4. it should share a common ancestor Large size ribosomal ribonucleic acids (rRNA) fulfill these properties. Therefore, a breakthrough in the study of the phylogenetic relationships of prokaryotes was achieved by Woese and coworkers who compared first partial, and later total sequences of 16S rRNA (Woese, 1987). For the first time, it was possible to reconstruct the phylogeny of proka ryotes, The majority of information comes from the analysis of one molecule, the 16S rRNA. Currently about 1500 complete or almost complete 16S rRNA sequences from Bacteria are available. The fact that the whole phylogentic superstructure rests almost solely on a single molecule species is disquie ting. Therefore, the question arises whether these data really reflect the organismal phylogeny or merely the history of a single molecule. Therefore, we decided to sequence further conserved macromolecules which fulfill the properties of a useful chronometer. PHYLOGENTIC TREES INFERRED FROM COMPARATIVE SEQUENCE ANALYSIS OF DIFFERENT HOMOLOGOUS MACROMOLECULES Comparative sequence analyses of genes coding for the following molecules were carried out: 23S rRNA, elongation factor Tu (EF-Tu) and B-subunit of ATP-synthase. 23S rRNA is found in the large subunit of the ribosomes, whereas 16S rRNA is present in the small subunit. EF-Tu is one of the most abundant cellular proteins in E. coli. It is highly conserved among all Bacteria and plays, like rRNAs, an important role in protein biosynthesis. The B-subunit of ATP-synthase, on the other hand, is not involved in protein biosynthesis, but is part of a membrane protein complex. It is present in all Bacteria studied so far and shows a high degree of functional constancy. Phylogentic trees derived from comparative sequence analyses of 23S rRNA, EF-Tu and B-subunit of ATP-synthase molecules are in very good agreement with the tree inferred from 168 rRNA sequences ( Schleifer and Ludwig, 1989; Figs. 1 - 3). There are, however, some minor differences in the topology of the phylogenetic trees derived from the different chronometers. The protein molecules seem to contain less phylogenetic information than the rRNAs. One difference between the 16S rRNA based tree, as published by Woese (1987), and the phylogenetic trees derived from 23S rRNA and EF-Tu sequence data is worth considering. In the 16S rRNA tree shown by Woese (1987), the gram-positive bacteria form a monophyletic group consisting of two subgroups: the gram-positive bacteria with a high DNA G+C content and those with a low DNA G+C content. However, the unity of the two 3
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