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The Prokaryotes

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Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Human Microbiology Fourth Edition With 178 Figures and 41 Tables <0 Springer Reference Table of Contents in Bacteria Human Health and Disease ; 1 1 The Gut Microbiota Petia Kovatcheva-Datchary • Valentino Tremaroli Fredrik Backhed 2 Prebiotics 25 • Gemma E. Walton Jonathan R. Swann • Glenn R. Gibson 3 Probiotics 45 Gregor Reid 4 Identification of Pathogens by Classical Clinical Tests 57 Peter H. Gilligan 5 Identification of Pathogens by Nonculturing Molecular Techniques 91 Natalie N. Whitfield • Donna M. Wolk 6 Bacterial Adhesion 107 Itzhak Ofek • Edward A. Bayer Soman N. Abraham 7 Cholera 125 Aimee L. Richard • Victor J. DiRita 8 Tuberculosis 133 Robindra Basu Roy • Eric Rubin 9 Legionnaires'Disease 147 Nicholas P. Cianciotto • Hubert Hilbi • Carmen Buchrieser 10 Listeria 219 Mobarak Abu Mraheil • Sukhadeo Barbuddhe • Torsten Hain • Trinad Chakraborty 11 Diphtheria 237 Andreas Burkovski 12 Botulism and Tetanus 247 Michel R. Popoff • Christelle Mazuet • B. Poulain 13 Whooping Cough 291 Nathalie Mielcarek • Camille Locht 14 Dysentery 309 Narveen Jandu - Marcia B. Goldberg 15 Urinary Tract Infections 323 Daniel J. Reiss • Michael D. Engstrom • Harry L T. Mobley 16 Burn Infections 353 Deirdre L. Church • Ingrid Slaba • Brent W. Winston • Robert Lindsay xvi Table of Contents 17 Typhoid 375 • Sean-Paul Nuccio Tamding Wangdi • Sebastian E. Winter • Andreas J. Bdumler 18 Meningitis 401 Tone Tenjum • Petter Brandtzceg • Birgitta Henriques-Normark 19 Rickettsiia Diseases 429 Gustavo Valbuena 20 Syphilis 447 Emily L Ho • Sheila A. Lukehart 21 Chlamydial Diseases 469 Raymond M. Johnson 22 Bacterial Toxins 499 Vega Masignani • Mariagrazia Pizza • Rino Rappuoli Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Applied Bacteriology and Biotechnology Fourth Edition With 132 Figures and 63 Tables 4?} Springer Reference Table of Contents Applied Bacteriology and Biotechnology 1 1 Organic Acid and Solvent Production: Acetic, Lactic, Gluconic, Succinic, and Polyhydroxyalkanoic Acids 3 Palmer Rogers • Jianrt-Shin Chen • Mary Jo Zidwick 2 Organic Acid and Solvent Production: Butanol, Acetone, and Isopropanol; 1,3- and 1,2-Propanediol Production; and 2,3-Butanediol Production 77 Jiann-Shin Chen • Mary Jo Zidwick Palmer Rogers 3 Organic Acid and Solvent Production: Propionic and Butyric Acids and Ethanol 135 Mary Jo Zidwick • Jiann-Shin Chen • Palmer Rogers 4 Amino Acid Production 169 Hidehiko Kumagai 5 Microbial Exopolysaccharides 179 Avinash Mishra • Bhavanath Jha 6 Bacterial Enzymes 193 Wim J. Quax 7 Diversity and Biotechnological Applications of Prokaryotic Enzymes 213 Alane Beatriz Vermelho • Eliane Ferreira Noronha • Edivaldo Ximenes Ferreira Filho • Maria Antonieta Ferrara • Elba Pinto S. Bon 8 Bacteria in Food and Beverage Production 241 Michael P. Doyle • Larry R. Steenson • Jianghong Meng 9 Bacterial Pharmaceutical Products 257 Giancarlo Lancini • Arnold L. Demain 10 Biosurfactants 281 Eugene Rosenberg • Eliora Z. Ron 11 Bioremediation 295 Ronald L. Crawford • Eugene Rosenberg 12 Biodeterioration 309 Ji-Dong Gu • Ralph Mitchell 13 Microbial Biofilms 343 Dirk De Beer • Paul Stoodley xvi Table of Contents 14 Biofuels * 373 Stefano Freguia • Bernardino Virdis • Korneel Rabaey 15 The Metabolic Pathways of Biodegradation 383 Lawrence P. Wackett Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Prokaryotic Physiology and Biochemistry Fourth Edition With 220 Figures and 62 Tables <£) Springer Reference Table of Contents Physiology and Biochemistry 1 1 Acetogenic Prokaryotes Harold L. Drake • Kirsten Kiisel • Carola Matthies 2 Virulence Strategies of Plant Pathogenic Bacteria 61 Maeli Melotto • Barbara N. Kunkel 3 Oxidation of Inorganic Nitrogen Compounds as an Energy Source 83 Ebcrhard Bock • Michael Wagner 4 H2-Metabolizing Prokaryotes Edward Schwartz • Johannes Fritsch • Barbel Friedrich 5 Hydrocarbon-Oxidizing Bacteria 201 Eugene Rosenberg 6 Lignocellulose-Decomposing Bacteria and Their Enzyme Systems 215 Edward A. Bayer Ynval Shoham • Raphael Lamed 7 Aerobic Methylotrophic Prokaryotes 267 Ludmila Chistoserdova • Mary E. Lidstrom 8 Dissimilatory Fe(III)- and Mn(IV)-Reducing Prokaryotes 287 Derek Lovley 9 Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes 309 RalfRabus • Theo A. Hansen • Friedrich Widdel 10 Denitrifying Prokaryotes 405 James P. Shapleigh 11 Dinitrogen-Fixing Prokaryotes 427 Ernesto Ortneno-Orrillo • Mariangela Hungria • Esperattza Martinez-Romero 12 Magnetotactic Bacteria 453 Dennis A. Bazylittski • Christopher T. Lefevre- Dirk Schiiler 13 Luminous Bacteria 495 Paul V. Dunlap • Henryk Urbanczyk 14 Halophilic and Haioalkaliphilic Sulfur-Oxidizing Bacteria 529 Dimitry Y. Sorokin • Horia Banciu • Lesley A. Robertson • J. Gijs Kuenen • M. S. Muntyan • Gerard Muyzer 15 Colorless Sulfur Bacteria ....555 Gerard Muyzer • /. Gijs Kuenen - Lesley A. Robertson xvi Table of Contents 16 Bacterial Stress Response 589 Eliora Z. Ron 17 Anaerobic Biodegradation of Hydrocarbons Including Methane 605 Johann Heider • Karola Schiihle 18 Physiology and Biochemistry of the Methane-Producing Archaea 635 Reiner Hedderich • William B. Whitman Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Prokaryotic Communities and Ecophysiology Fourth Edition With 179 Figures and 43 Tables Springer Reference Table of Contents Section 1: Prokaryotic Communities 1 1 Structure and Function of Microbial Communities 3 David A. Stahl Jason ]. Flowers • Meredith Hullar • Seana Davidson 2 Quantitative and Theoretical Microbial Population Biology 31 Martin F. Polz • William P. Manage 3 Alpine and Arctic Soil Microbial Communities 43 • M. Rhodes /. Knelman - R. C. Lynch • J. L. Darcy D. R. Nemergut • S. K. Schmidt 4 Plant Rhizosphere Microbial Communities 57 Dror Mitiz • Maya Ofek • Yitzhak Hadar 5 Tropical Soil Microbial Communities 85 Andrew Macrae • Rosalie R. R. Coelho • Raquel Peixoto • Alexandre S. Rosado 6 Freshwater Microbial Communities 97 Jakob Pernthaler 7 Pelagic Oxygen Minimum Zone Microbial Communities 113 Osvaldo Ulloa • Jody J. Wright • Lucy Belmar' Steven J. Hallam 8 Marine Deep Sediment Microbial Communities 123 Andreas Teske 9 Sea-Ice Microbial Communities 139 John P. Bowman 10 Coral Reef Bacterial Communities 163 David G. Bourne • Nicole S. Webster Section 2: Ecophysiology 189 11 Planktonic Versus Sessile Life of Prokaryotes 191 Kevin C. Marshall 12 The Phototrophic Way of Life 203 Jorg Overmann • Ferran Garcia-Pichel 13 The Anaerobic Way of Life 259 Ruth A. Schmitz • Rolf Daniel • Uwe Deppentneier • Gerhard Gottschalk 14 The Chemolithotrophic Prokaryotes 275 Donovan P. Kelly • Ann P. Wood 15 Bacterial Behavior 289 Judith P. Armitage • Kathryn A. Scott xvi Table of Contents 16 Prokaryotic Life Cycles 317 Lawrence J. Shimkets 17 Life at High Temperatures 337 Rainer Jaenicke • Reinhard Sterner 18 Life at Low Temperatures .375 Thilo M. Fuchs • Klaus Neuhaus • Siegfried Scherer 19 Life at High Salt Concentrations 421 Aharon Oren 20 Alkaliphilic Prokaryotes 441 Terry Ann Krulwich * Masahiro Ito 21 Syntrophism Among Prokaryotes 471 Bernhard Schink * Alfons J. M. Stams 22 Quorum Sensing .495 Bonnie L. Bassler • Melissa B. Miller 23 Cell-Cell Interactions 511 Dale Kaiser Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Prokaryotic Biology and Symbiotic Associations Fourth Edition With 783 Figures and 62 Tables Springer Reference Table of Contents Section 1: Biology of Bacteria and Archaea 1 1 How We Do, Don't/ and Should Look at Bacteria and Bacteriology 3 Carl R. Woese 2 What Is a Prokaryote? 21 W. Ford Doolittle • Olga Zhaxybayeva 3 Prokaryotes and Their Habitats Hans G. Schlegel • Holger W. Jantiasch 4 Origin of Life: RNA World Versus Autocatalytic Anabolist 81 Giinter Wachtershauser 5 Morphological and Physiological Diversity 89 Stephen H. Zindcr • Martin Dworkin 6 Prokaryote Characterization and Identification 123 Peter Kampfer • Stcfanie P. Glaeser 7 Principles of Enrichment, Isolation, Cultivation, and Preservation of Prokaryotes 149 Jorg Overtnann 8 Comparative Genomics 209 Asli Istnihan Ozeti • Tamrni Vesth • David W. Ussery 9 Defining Taxonomic Ranks 229 Konstantinos T. Konstantinidis • Erko Stackebrandt 10 Population Genetics 255 Santiago Castillo-Ramirez • Edward J. Feil 11 Public Service Collections and Biological Resource Centers of Microorganisms 267 David Smith • Dagmar Fritze • Erko Stackebrandt 12 Repositories for Patented and Safeguarded Material 305 Zea D. V L. Mayerhoff • Irene von der Weid • Alessandra B. G. Valladao 13 Biotechnology and Applied Microbiology 315 Eugene Rosenberg 14 Genomes and Post-genome Technology 329 Betania Ferraz Quirino Cristine Chaves Barreto • Georgios J. Pappas • Karsten Zengler • Konstantinos Krampis • Ricardo H. Kriiger Section 2: Symbiotic Associations 345 15 Role of Microorganisms in Adaptation, Development, and Evolution of Animals and Plants: The Hologenome Concept 347 Eugene Rosenberg • liana Zilber-Rosenberg xvi Table of Contents 16 Cyanobacterial-Plant Symbioses 359 • David G. Adams Birgitta Bergman • Sandra A. Nierzwicki-Bauer' Paula S. Duggan • Amar N. Rai Arthur Schiifiler 17 Root and Stem Nodule Bacteria of Legumes . 401 • Michael J. Sadowsky Peter H. Graham
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