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The Prokaryotes
Third Edition
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Prokaryotes
The
A Handbook on the Biology of Bacteria
Third Edition
Volume 1: Symbiotic Associations, Biotechnology,
Applied Microbiology
Martin Dworkin (Editor-in-Chief), Stanley Falkow, Eugene Rosenberg,
Karl-Heinz Schleifer, Erko Stackebrandt (Editors)
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Editor-in-Chief
Professor Dr.Martin Dworkin
Department of Microbiology
University of Minnesota
Box 196
University of Minnesota
Minneapolis,MN 55455-0312
USA
Editors
Professor Dr.Stanley Falkow Professor Dr.Karl-Heinz Schleifer
Department of Microbiology Department of Microbiology
and Immunology Technical University Munich
Stanford University Medical School 80290 Munich
299 Campus Drive,Fairchild D039 Germany
Stanford,CA 94305-5124
USA Professor Dr.Erko Stackebrandt
DSMZ- German Collection of Microorganisms
Professor Dr.Eugene Rosenberg and Cell Cultures GmbH
Department of Molecular Microbiology Mascheroder Weg 1b
and Biotechnology 38124 Braunschweig
Tel Aviv University Germany
Ramat-Aviv 69978
Israel
Library of Congress Control Number:2005928710
ISBN-10:0-387-25476-5 e-ISBN 0-387-•••••-• Printed on acid-free paper.
ISBN-13:978-0387-25476-0
© 2006 Springer Science+Business Media,Inc.
All rights reserved.This work may not be translated or copied in whole or in part without the written permission of the
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Preface
Each of the first two editions of The Prokaryotes Moselio Schaechter has referred to the present
took a bold step.The first edition, published in era of microbiology as its third golden age—the
1981, set out to be an encyclopedic, synoptic era of “integrative microbiology.”Essentially all
account of the world of the prokaryotes—a col- microbiologists now speak a common language.
lection of monographic descriptions of the So that the boundaries that previously separated
genera of bacteria.The Archaea had not yet been subdisciplines from each other have faded:phys-
formalized as a group.For the second edition in iology has become indistinguishable from patho-
1992,the editors made the decision to organize genesis; ecologists and molecular geneticists
the chapters on the basis of the molecular phy- speak to each other; biochemistry is spoken by
logeny championed by Carl Woese, which all; and—mirabile dictu!—molecular biologists
increasingly provided a rational, evolutionary are collaborating with taxonomists.
basis for the taxonomy of the prokaryotes. In But before these molecular dissections of
addition, the archaea had by then been recog- complex processes can be effective there must be
nized as a phylogenetically separate and distin- a clear view of the organism being studied.And
guishable group of the prokaryotes. The two it is our goal that these chapters in The Prokary-
volumes of the first edition had by then otes provide that opportunity.
expanded to four.The third edition was arguably There is also yet a larger issue. Microbiology
the boldest step of all.We decided that the mate- is now confronted with the need to understand
rial would only be presented electronically.The increasingly complex processes.And the modus
advantages were obvious and persuasive.There operandi that has served us so successfully for
would be essentially unlimited space. There 150 years—that of the pure culture studied under
would be no restrictions on the use of color illus- standard laboratory conditions—is inadequate.
trations.Film and animated descriptions could be We are now challenged to solve problems of
made available.The text would be hyperlinked multimembered populations interacting with
to external sources. Publication of chapters each other and with their environment under
would be seriati—the edition would no longer constantly variable conditions. Carl Woese has
have to delay publication until the last tardy pointed out a useful and important distinction
author had submitted his or her chapter.Updates between empirical,methodological reductionism
and modifications could be made continuously. and fundamentalist reductionism. The former
And, most attractively, a library could place its has served us well;the latter stands in the way of
subscribed copy on its server and make it avail- our further understanding of complex, interact-
able easily and cheaply to all in its community. ing systems.But no matter what kind of synop-
One hundred and seventy chapters have thus far tic systems analysis emerges as our way of
been presented in 16 releases over a six-year understanding host–parasite relations, ecology,
period.The virtues and advantages of the online or multicellular behavior, the understanding of
edition have been borne out. But we failed to the organism as such is sine qua non.And in that
predict the affection that many have for holding context, we are pleased to present to you the
a bound,print version of a book in their hands. third edition of The Prokaryotes.
Thus,this print version of the third edition shall
accompany the online version. Martin Dworkin
We are now four years into the 21st century. Editor-in-Chief
Indulge us then while we comment on the chal-
lenges,problems and opportunities for microbi-
ology that confront us.
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Contents
Preface v
Contributors xxvii
Volume 1
1. Essays in Prokaryotic Biology
1.1 How We Do,Don’t and Should Look at Bacteria and Bacteriology 3
carl r.woese
1.2 Databases 24
wolfgang ludwig,karl heinz schleifer and erko stackebrandt
1.3 Defining Taxonomic Ranks 29
erko stackebrandt
1.4 Prokaryote Characterization and Identification 58
hans g.trüper and karl-heinz schleifer
1.5 Principles of Enrichment,Isolation,Cultivation,and
Preservation of Prokaryotes 80
jörg overmann
1.6 Prokaryotes and Their Habitats 137
hans g.schlegel and holger w.jannasch
1.7 Morphological and Physiological Diversity 185
stephen h.zinder and martin dworkin
1.8 Cell-Cell Interactions 221
dale kaiser
1.9 Prokaryotic Genomics 246
b.w.wren
1.10 Genomics and Metabolism in Escherichia coli 261
margrethe haugge serres and monica riley
1.11 Origin of Life:RNA World versus Autocatalytic Anabolism 275
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günter wächtershäuser
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1.12 Biotechnology and Applied Microbiology 284
eugene rosenberg
1.13 The Structure and Function of Microbial Communities 299
david a.stahl,meredith hullar and seana davidson
2. Symbiotic Associations
2.1 Cyanobacterial-Plant Symbioses 331
david g.adams,birgitta bergman,s.a.nierzwicki-bauer,
a.n.rai and arthur schüßler
2.2 Symbiotic Associations between Ciliates and Prokaryotes 364
hans-dieter görtz
2.3 Bacteriocyte-Associated Endosymbionts of Insects 403
paul baumann,nancy a.moran and linda baumann
2.4 Symbiotic Associations Between Termites and Prokaryotes 439
andreas brune
2.5 Marine Chemosynthetic Symbioses 473
colleen m.cavanaugh,zoe p.mckiness,irene l.g.newton and
frank j.stewart
3. Biotechnology and Applied Microbiology
3.1 Organic Acid and Solvent Production 509
palmer rogers,jiann-shin chen and mary jo zidwick
3.2 Amino Acid Production 754
hidehiko kumagai
3.3 Microbial Exopolysaccharides 764
timothy harrah,bruce panilaitis and david kaplan
3.4 Bacterial Enzymes 775
wim j.quax
3.5 Bacteria in Food and Beverage Production 795
michael p.doyle and jianghong meng
3.6 Bacterial Pharmaceutical Products 810
arnold l.demain and giancarlo lancini
3.7 Biosurfactants 832
eugene rosenberg
3.8 Bioremediation 848
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ronald l.crawford
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Contents ix
3.9 Biodeterioration 862
ji-dong gu and ralph mitchell
3.10 Microbial Biofilms 902
dirk de beer and paul stoodley
Index 937
Volume 2
1. Ecophysiological and Biochemical Aspects
1.1 Planktonic Versus Sessile Life of Prokaryotes 3
kevin c.marshall
1.2 Bacterial Adhesion 16
itzhak ofek,nathan sharon and soman n.abraham
1.3 The Phototrophic Way of Life 32
jörg overmann and ferrau garcia-pichel
1.4 The Anaerobic Way of Life 86
ruth a.schmitz,rolf daniel,uwe deppenmeier and
gerhard gottschalk
1.5 Bacterial Behavior 102
judith armitage
1.6 Prokaryotic Life Cycles 140
martin dworkin
1.7 Life at High Temperatures 167
rainer jaenicke and reinhard sterner
1.8 Life at Low Temperatures 210
siegfried scherer and klaus neuhaus
1.9 Life at High Salt Concentrations 263
aharon oren
1.10 Alkaliphilic Prokaryotes 283
terry ann krulwich
1.11 Syntrophism Among Prokaryotes 309
bernhard schink and alfons j.m.stams
1.12 Quorum Sensing 336
bonnie l.bassler and melissa b.miller
1.13 Acetogenic Prokaryotes 354
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harold l.drake,kirsten küsel and carola matthies
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1.14 Virulence Strategies of Plant Pathogenic Bacteria 421
barbara n.kunkel and zhongying chen
1.15 The Chemolithotrophic Prokaryotes 441
donovan p.kelly and ann p.wood
1.16 Oxidation of Inorganic Nitrogen Compounds as an Energy Source 457
eberhard bock and michael wagner
1.17 The H -Metabolizing Prokaryotes 496
2
edward schwartz and bärbel friedrich
1.18 Hydrocarbon-Oxidizing Bacteria 564
eugene rosenberg
1.19 Cellulose-Decomposing Bacteria and Their Enzyme Systems 578
edward a.bayer,yuval shoham and raphael lamed
1.20 Aerobic Methylotrophic Prokaryotes 618
mary e.lidstrom
1.21 Dissimilatory Fe(III)- and Mn(IV)-Reducing Prokaryotes 635
derek lovley
1.22 Dissimilatory Sulfate- and Sulfur-Reducing Prokaryotes 659
ralf rabus,theo hansen and friedrich widdel
1.23 The Denitrifying Prokaryotes 769
james p.shapleigh
1.24 Dinitrogen-Fixing Prokaryotes 793
esperanza martinez-romero
1.25 Root and Stem Nodule Bacteria of Legumes 818
michael j.sadowsky and p.h.graham
1.26 Magnetotactic Bacteria 842
stefan spring and dennis a.bazylinski
1.27 Luminous Bacteria 863
paul v.dunlap and kumiko kita-tsukamoto
1.28 Bacterial Toxins 893
vega masignani,mariagrazia pizza and rino rappuoli
1.29 The Metabolic Pathways of Biodegradation 956
lawrence p.wackett
1.30 Haloalkaliphilic Sulfur-Oxidizing Bacteria 969
dimitry yu.sorokin,horia banciu,lesley a.robertson and
j.gijs kuenen
1.31 The Colorless Sulfur Bacteria 985
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lesley a.robertson and j.gijs kuenen
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Contents xi
1.32 Bacterial Stress Response 1012
eliora z.ron
1.33 Anaerobic Biodegradation of Hydrocarbons Including Methane 1028
friedrich widdel,antje boetius and ralf rabus
1.34 Physiology and Biochemistry of the Methane-Producing Archaea 1050
reiner hedderich and william b.whitman
Index 1081
Volume 3
A: Archaea
1. The Archaea:A Personal Overview of the Formative Years 3
ralph s.wolfe
2. Thermoproteales 10
harald huber,robert huber and karl o.stetter
3. Sulfolobales 23
harald huber and david prangishvili
4. Desulfurococcales 52
harald huber and karl o.stetter
5. The Order Thermococcales 69
costanzo bertoldo and garabed antranikian
6. The Genus Archaeoglobus 82
patricia hartzell and david reed
7. Thermoplasmatales 101
harald huber and karl o.stetter
8. The Order Halobacteriales 113
aharon oren
9. The Methanogenic Bacteria 165
william b.whitman,timothy l.bowen and david r.boone
10. The Order Methanomicrobiales 208
jean-louis garcia,bernard ollivier and william b.whitman
11. The Order Methanobacteriales 231
adam s.bonin and david r.boone
12. The Order Methanosarcinales 244
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melissa m.kendall and david r.boone
