The Prokaryotes Third Edition The Prokaryotes 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) 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 publisher (Springer Science+Business Media, Inc., 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed in Singapore. (BS/KYO) 987654321 springer.com 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. 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 günter wächtershäuser viii Contents 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 ronald l. crawford 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 harold l. drake, kirsten küsel and carola matthies x Contents 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 H2-Metabolizing Prokaryotes 496 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.