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THE PROKARYOTES 3RD EDITION
THE PROKARYOTES 3RD EDITION
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,The ProkaryotesThird Edition
,The Prokaryotes
A Handbook on the Biology of Bacteria
Third Edition
Volume 3: Archaea. Bacteria: Firmicutes, Actinomycetes
Martin Dworkin (Editor-in-Chief), Stanley Falkow, Eugene Rosenberg,
Karl-Heinz Schleifer, Erko Stackebrandt (Editors)
,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
URLs in The Prokaryotes: Uncommon Web sites have been listed in the text. However, the following Web sites
have been referred to numerous times and have been suppressed for aesthetic purposes: www.bergeys.org;
www.tigr.org; dx.doi.org; www.fp.mcs.anl.gov; www.ncbi.nlm.nih.gov; www.genome.ad.jp; www.cme.msu.edu;
umbbd.ahc.umn.edu; www.dmsz.de; and www.arb-home.de. The entirety of all these Web links have been main-
tained in the electronic version.
Library of Congress Control Number: 91017256
Volume 3
ISBN-10: 0-387-25493-5
ISBN-13: 978-0387-25493-7
e-ISBN: 0-387-30743-5
Print + e-ISBN: 0-387-33489-0
DOI: 10.1007/0-387-30743-5
Volumes 1–7 (Set)
ISBN-10: 0-387-25499-4
ISBN-13: 978-0387-25499-9
e-ISBN: 0-387-30740-0
Print + e-ISBN: 0-387-33488-2
Printed on acid-free paper.
© 2006 Springer Science+Business Media, LLC
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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.
,Foreword
The purpose of this brief foreword is unchanged well as much of the philosophy may be traced to
from the first edition; it is simply to make you, the Delft School, passed on to us by our teach-
the reader, hungry for the scientific feast that ers, Martinus Beijerinck, A. J. Kluyver, and C. B.
follows. These four volumes on the prokaryotes van Niel, and in turn passed on by us to our
offer an expanded scientific menu that displays students.
the biochemical depth and remarkable physio- In this school, the principles of the selective,
logical and morphological diversity of prokary- enrichment culture technique have been devel-
ote life. The size of the volumes might initially oped and diversified; they have been a major
discourage the unprepared mind from being force in designing and applying new principles
attracted to the study of prokaryote life, for this for the capture and isolation of microbes from
landmark assemblage thoroughly documents the nature. For me, the “organism approach” has
wealth of present knowledge. But in confronting provided rewarding adventures. The organism
the reader with the state of the art, the Hand- continually challenges and literally drags the
book also defines where more work needs to be investigator into new areas where unfamiliar
done on well-studied bacteria as well as on tools may be needed. I believe that organism-
unusual or poorly studied organisms. oriented research is an important alternative to
This edition of The Prokaryotes recognizes problem-oriented research, for new concepts of
the almost unbelievable impact that the work of the future very likely lie in a study of the breadth
Carl Woese has had in defining a phylogenetic of microbial life. The physiology, biochemistry,
basis for the microbial world. The concept that and ecology of the microbe remain the most
the ribosome is a highly conserved structure in powerful attractions. Studies based on classical
all cells and that its nucleic acid components methods as well as modern genetic techniques
may serve as a convenient reference point for will result in new insights and concepts.
relating all living things is now generally To some readers, this edition of the The
accepted. At last, the phylogeny of prokaryotes Prokaryotes may indicate that the field is now
has a scientific basis, and this is the first serious mature, that from here on it is a matter of filling
attempt to present a comprehensive treatise on in details. I suspect that this is not the case.
prokaryotes along recently defined phylogenetic Perhaps we have assumed prematurely that we
lines. Although evidence is incomplete for many fully understand microbial life. Van Niel pointed
microbial groups, these volumes make a state- out to his students that—after a lifetime of
ment that clearly illuminates the path to follow. study—it was a very humbling experience to
There are basically two ways of doing research view in the microscope a sample of microbes
with microbes. A classical approach is first to from nature and recognize only a few. Recent
define the phenomenon to be studied and then evidence suggests that microbes have been
to select the organism accordingly. Another way evolving for nearly 4 billion years. Most certainly
is to choose a specific organism and go where it those microbes now domesticated and kept in
leads. The pursuit of an unusual microbe brings captivity in culture collections represent only a
out the latent hunter in all of us. The intellectual minor portion of the species that have evolved in
challenges of the chase frequently test our inge- this time span. Sometimes we must remind our-
nuity to the limit. Sometimes the quarry repeat- selves that evolution is actively taking place at
edly escapes, but the final capture is indeed a the present moment. That the eukaryote cell
wonderful experience. For many of us, these evolved as a chimera of certain prokaryote parts
simple rewards are sufficiently gratifying so that is a generally accepted concept today. Higher as
we have chosen to spend our scientific lives well as lower eukaryotes evolved in contact with
studying these unusual creatures. In these prokaryotes, and evidence surrounds us of the
endeavors many of the strategies and tools as complex interactions between eukaryotes and
,viii Foreword
prokaryotes as well as among prokaryotes. We hunt.These volumes belong in the laboratory, not
have so far only scratched the surface of these in the library. I believe that a most effective way
biochemical interrelationships. Perhaps the to introduce students to microbiology is for them
legume nodule is a pertinent example of nature to isolate microbes from nature, i.e., from their
caught in the act of evolving the “nitrosome,” habitats in soil, water, clinical specimens, or
a unique nitrogen-fixing organelle. Study of plants. The Prokaryotes enormously simplifies
prokaryotes is proceeding at such a fast pace that this process and should encourage the construc-
major advances are occurring yearly. The tion of courses that contain a wide spectrum of
increase of this edition to four volumes docu- diverse topics. For the student as well as the
ments the exciting pace of discoveries. advanced investigator these volumes should
To prepare a treatise such as The Prokaryotes generate excitement.
requires dedicated editors and authors; the task Happy hunting!
has been enormous. I predict that the scientific
community of microbiologists will again show its
appreciation through use of these volumes— Ralph S. Wolfe
such that the pages will become “dog-eared” and Department of Microbiology
worn as students seek basic information for the University of Illinois at Urbana-Champaign
,Contents
Preface v
Foreword by Ralph S. Wolfe vii
Contributors xxix
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
,x Contents
1.11 Origin of Life: RNA World versus Autocatalytic Anabolism 275
günter wächtershäuser
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 475
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 511
palmer rogers, jiann-shin chen and mary jo zidwick
3.2 Amino Acid Production 756
hidehiko kumagai
3.3 Microbial Exopolysaccharides 766
timothy harrah, bruce panilaitis and david kaplan
3.4 Bacterial Enzymes 777
wim j. quax
3.5 Bacteria in Food and Beverage Production 797
michael p. doyle and jianghong meng
3.6 Bacterial Pharmaceutical Products 812
arnold l. demain and giancarlo lancini
3.7 Biosurfactants 834
eugene rosenberg
3.8 Bioremediation 850
ronald l. crawford
, Contents xi
3.9 Biodeterioration 864
ji-dong gu and ralph mitchell
3.10 Microbial Biofilms 904
dirk de beer and paul stoodley
Index 939
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 ferran 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
harold l. drake, kirsten küsel and carola matthies
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