Table Of ContentBacterial 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
