Applied Microbial Systematics

480 Pages·2000·17.34 MB·English

by  Michael Goodfellow (auth.), Fergus G. Priest, Michael Goodfellow (eds.)

APPLIED MICROBIAL SYSTEMATICS
Applied Microbial
Systematics
Edited by
Fergus G. Priest
Heriot-Watt University,
Edinburgh
and
Michael Goodfellow
University of NewcastIe,
Newcastle upon Tyne
SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.
Library of Congress Cataloging-in-Publication Data
ISBN 978-0-7923-6518-1 ISBN 978-94-011-4020-1 (eBook)
DOI 10.1007/978-94-011-4020-1
Printed on acid-free paper
AlI Rights Reserved
© 2000 Springer Science+Business Media Dordrecht
OrigIDally published by Kluwer Academic Publishers in 2000
Softcover reprint ofthe hardcover 18t edition 2000
No part of the material protected by this copyright notice may be reproduced or
utilized in any form or by any means, electronic or mechanical,
including photocopying, recording or by any information storage and
retrieval system, without written permission from the copyright owner.
TABLE OF CONTENTS
Addresses of the Contributors vii
Preface xi
I INTRODUCTION 1
1 Microbial Systematics: Background and Uses 1
MICHAEL GOODFELLOW
II PHYLOGENY 19
2 Universal Trees: Discovering the Archaeal and Bacterial Legacies 19
JAMES R BROWN and KRISTIN K. KORETKE
3 Phylogenetic Relationships among Fungi Inferred from
Small Subunit Ribosomal RNA Gene Sequences 57
MAKIKO HAMAMOTO and TAKASm NAKASE
III SOIL, PLANTS AND INSECTS 73
4 Molecular Ecology of Mycorrhizal Fungi 73
PETER JEFFRIES and JOHN C. DODD
5 Systematics of Legume Nodule Nitrogen Fixing Bacteria:
Agronomic and Ecological Applications 107
REITOR L.C. COUTINHO, VALERIA M. DE OLIVEIRA
and FATIMA M.S. MOREIRA
6 Recent Systematic Developments in Systematics and
their Implications for Plant Pathogenic Bacteria 135
JOHN M. YOUNG
vi M Goodfellow
7 Bacteria and Insects 165
FERGUS G. PRIEST and SUSAN J. DEWAR
8 Fungal Pathogens and Parasites of Insects 203
RICHARD A. HUMBER
IV ENVIRONMENT AND ITS EXPLOITATION 231
9 Taxonomy of Extremophiles 231
JAKOB 1. KRISTIJANSSON, GUDMUNDUR O. HREGGVIDSSON
and WILLIAM D. GRANT
10 Acidophiles in Biomining 293
BRETT M. GOEBEL, PAUL R. NORRIS
and NICOLAS P. BURTON
11 Microbial Communities in Oil Fields 315
GERRIT VOORDOUW
12 Systematics of Sphingomonas Species
that Degrade Xenobiotic Pollutants 333
MARTINA M. EDERER and RONALD L. CRAWFORD
V FOOD AND MEDICINE 367
13 Lactic Acid Bacteria 367
LARS AXELSSON and SlY AHRNE
14 A Slow Ramble in the Acid-Fast Lane:
The Coming of Age of Mycobacterial Taxonomy 389
LAWRENCE G. WAYNE
VI REGULATORY ASPECTS 421
15 Microbial Resource Centres and Ex-situ Conservation 421
VANDERLEI P. CANHOS and GILSON P. MANFIO
16 Systematics and Legislation 447
DAGMAR FRITZE and VERA WEIHS
Organism Index 471
Subject Index
ADDRESSES OF THE CONTRIBUTORS
Siv Ahrne Department of Food Technology, University of Lund, PO Box 124,
S-221 00 Lund, Sweden. (e-mail: [email protected])
Lars Axelsson MATFORSK, Norwegian Food Research Institute, Oslovein 1,
N-1430 AS, Norway. (e-mail: [email protected])
James R. Brown Department of Bioinformatics, SmithKline Beecham Pharmaceuticals,
1250 S. Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA.
(e-mail: [email protected])
Nicolas P. Burton Department of Biological Sciences, University of Warwick,
Coventry, CV4 7AL,UK. (e-mail: [email protected])
Vanderlei P. Canhos Faculdade de Engenharia de Alimentos (FEA) -Universidade Estadual
de Campinas; Rua Professor Zeferino Vaz, sin; Cidade Universitaria, Barno Geraldo;
CEP 13081-970; Campinas (SP), Brazil. (e-mail: [email protected])
Heitor L. C. Coutinho Embrapa Solos, Rua Jardim Botanico 1024, Rio de Janeiro,
RI, 22460-000, Brazil. (e-mail: [email protected])
Ronald L. Crawford Environmental Biotechnology Institute, University of Idaho,
Moscow, 1D#83844-1052, USA. (e-mail: [email protected])
Susan J. Dewar Department of Biological Sciences, Heriot-Watt University, Edinburgh
EH14 4AS, Scotland UK. (e-mail: [email protected])
John C. Dodd International Institute of Biotechnology, Biotechnology MIRCEN,
Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
(e-mail: [email protected])
Martina M. Ederer Environmental Biotechnology Institute, University of Idaho,
Moscow, ID 83844-1052, USA. (e"mail: [email protected])
Dagmar Fritze DSMZ, Mascheroder Weg 1b, D-38124 Braunschweig, Germany.
(e-mail: [email protected])
Brett M. Goebel Australian Magnesium Corporation, Demonstration Plant, PO Box 488,
Gladstone, Queensland 4680, Australia. (e-mail: [email protected])
viii M Goodfellow
Michael Goodfellow Department of Agricultural and Environmental Science,
University of Newcastle, Newcastle upon Tyne, NEi 7RU, UK. (e-mail:
[email protected])
William D. Grant Department of Microbiology, University of Leicester, PO Box 138,
Leicester, LEi 9HN, UK. (e-mail: [email protected])
Makiko Hamamoto Japan Collection of Microorganisms, RIKEN, Wako-shi, Saitama,
351-0198, Japan. (e-mail: [email protected])
Gudmundur O. Hreggvidsson Institute, Biology University of Iceland, Liftaeknihus,
KeldnahoIt, IS-ll2 Reykjavic, Iceland. (e-mail: [email protected])
Richard A. Humber USDA-ARS Plant Protection Research Unit, US Plant, Soil and
Nutrition Laboratory, Tower Road, Ithaca, Ny 14853-2901, USA. (e-mail:
[email protected])
Peter Jeffries Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ,
UK. (e-mail: [email protected])
Kri"tine K. Koretke Department of Bioinformatics, SmithKline Beecham Pharmaceuticals,
l250 S. Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA.
(e-mail: [email protected])
Jakob K. Kristjansson Institute, Biology University of Iceland, Liftaeknihus,
Keldnaholt, IS-il2 Reykjavic, Iceland. (e-mail: [email protected])
Gilson P. Manfio Colec;iio de Culturas Tropical (CCT) - Fundac;iio Andre Tosello;
Rua Latino Coelho, 1301; Parque Taquaral; CEP 13087-010; Campinas (SP), Brazil.
(e-mail: [email protected])
Fatima M. S. Moreira Departamento de Ciencias do Solo, Universidade Federal de Lavras,
Caixa Postal 37, Lavras-MG, 37200-000, Brazil. (e-mail: [email protected])
Takashi Nakase Japan Collection of Microorganisms, RIKEN, Wako-shi, Saitama 351-
0198, Japan. (e-mail: [email protected])
Paul R. Norris Department Biological Sciences, University of Warwick, Coventry,
CV4 7AL, UK. (e-mail: [email protected])
Valeria M. de Oliveira Fundac;ao Andre Tosello, R. Latino Coelho 1301, Campinas -SP,
13087-010, Brazil. (e-mail [email protected])
Fergus G. Priest Department of Biological Sciences, Heriot-Watt University, Edinburgh
EHi4 4AS, Scotland UK. (e-mail: [email protected])
Systematics and Uses ix
Gerrit Voordouw Department of Biological Sciences, University of Calgary, 2500
University Drive NW, Calgary (AB) T2N IN4, Canada. (e-mail:
[email protected])
Lawrence G. Wayne Tuberculosis Research Laboratory, Veterans Administration Medical
Center, 5901 Long Beach, Ca 90822, USA. (e-mail: [email protected])
Vera Weihs DSMZ, Mascheroder Weg lb, D-38l24 Braunschweig, Germany. (e-mail:
[email protected])
John M. Young Landcare Research, 120 Mt Albert Road, Mt Albert, Auckland, New
Zealand. (e-mail: [email protected])
PREFACE
FERGUS G PRIEST and MICHAEL GOODFELLOW
Microbial systematics has enjoyed two major advances in the latter half of this century:
the introductions of numerical phenetics and molecular techniques for direct comparisons
of organismal genomes. Numerical phenetics (taxonomy) was very influential during
the 1960s and 70s in providing the first objective approach to bacterial classification.
Numerical taxonomy gave microbiologists the solid theoretical base for classification and
identification that had been sought for so long. Indeed, the concepts and procedures are
still used for routine identification in the applied microbiology laboratory in the form of kits
and automated identification machines. Although numerical phenetics no longer ranks as
the primary method of microbial classification, the theoretical base and need for phenotypic
descriptions of new taxa will continue to make the approach important for many years.
While numerical phenetics made no claim to have a phylogenetic content, the lack
of an evolutionary backbone to microbial classification was held by many to be a
serious detraction. A related problem was the inability of phenotypic data to provide a
hierarchical taxonomic system, species could generally be defined with accuracy but
phenotypically defined genera have commonly been shown to be unstable and even the most
committed numerical taxonomists realised that higher taxa (families etc.) could not be derived
from phenotypic descriptions. It had been appreciated in the 1960s that nucleic acids and
proteins contained the necessary information for deriving phylogenetic classifications
but accessing that information was so technically difficult that evolutionary studies
were restricted in scope and could only be conducted by the specialist protein chemist.
However, the scene was set for the application of nucleic acid sequence analysis to microbial
systematics once the analytical techniques became available, and by 1990 bacterial
taxonomy was set on a molecular phylogenetic course from which it is unlikely to be moved
in the foreseeable future. Indeed, the completion of more genome sequences will provide
a more robust basis for molecular phylogenetics and the resultant classifications will be
even more influential.
Molecular systematics has penetrated microbial classification at every level from the very
top in placing prokaryotes in two of the three domains of life to the very bottom in resolving
the population structures of bacterial species and recognition of clones. In so doing it has
influenced the practice of microbiology in numerous ways but particularly by providing
classifications which are more stable than those based on phenotypic characters and yet
which are largely congruent with the latter. In general, microbiologists are appreciating the
polyphasic classifications that are emerging. Phylogenetic trees, ideally supported by
phenetic information, abound in the literature and are being used to address and explain
various aspects of microbiology such as ecology, metabolism, pathogenicity and physiology
xii M Goodfellow
as well as the possible evolution of microorganisms. Molecular methods are offering
powerful approaches to recognizing biodiversity and achieving rapid and accurate iden
tification. In these ways, taxonomy is becoming more widely appreciated as providing
the basic working framework for microbiologists, as it does for botanists and zoologists.
The aim of the book is to illustrate the utility and practical applications of modem
systematics. Little mention is made of the methods of systematics; instead the value of
a taxonomic approach to assist understanding of microbiological problems is emphasized.
We wanted to demonstrate how improved systematics is advancing our knowledge
of related disciplines such as microbial diversity, ecology, evolution and certain areas
of biotechnology.
We would like to express our sincere thanks to all the contributors for their stimulating
and comprehensive chapters and in particular to Olivier Sparagano for his eagle-eyed
proofreading and assistance with the indexes.