| Preface |
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xvii | |
| eTopic Contents |
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xxxiii | |
| About the Authors |
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xxxiv | |
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PART 1 The Microbial Cell |
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2 | (216) |
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The Global Impact of Microbiology |
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Chapter 1 Microbial Life: Origin and Discovery |
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5 | (34) |
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1.1 From Germ to Genome: What is a Microbe? |
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6 | (5) |
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1.2 Microbes Shape Human History |
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11 | (6) |
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17 | (9) |
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Special Topic 1.1 How Did Life Originale? |
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18 | (8) |
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26 | (2) |
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1.5 The Microbial Family Tree |
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28 | (3) |
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1.6 Cell Biology and the DNA Revolution |
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31 | (8) |
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Chapter 2 Observing the Microbial Cell |
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39 | (34) |
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40 | (4) |
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2.2 Optics and Properties of Light |
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44 | (4) |
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2.3 Bright-Field Microscopy |
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48 | (7) |
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2.4 Dark-Field, Phase-Contrast, and Interference Microscopy |
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55 | (3) |
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2.5 Fluorescence Microscopy |
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58 | (4) |
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62 | (6) |
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Special Topic 2.1 Cryo-Electron Tomography Images an Entire Cell in Three Dimensions |
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66 | (2) |
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2.7 Visualizing Molecules |
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68 | (5) |
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Chapter 3 Cell Structure and Function |
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73 | (40) |
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3.1 The Bacterial Cell: An Overview |
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75 | (3) |
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3.2 How We Study Cell Parts |
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78 | (4) |
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3.3 The Cell Membrane and Transport |
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82 | (6) |
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3.4 The Cell Wall and Outer Layers |
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88 | (10) |
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Special Topic 3.1 How Antibiotics Cross the Outer Membrane |
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96 | (2) |
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3.5 The Nucleoid and Gene Expression |
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98 | (3) |
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101 | (5) |
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Special Topic 3.2 Bacteria Have a Cytoskeleton |
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104 | (2) |
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3.7 Specialized Structures |
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106 | (7) |
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Chapter 4 Bacterial Culture, Growth, and Development |
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113 | (36) |
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114 | (6) |
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120 | (6) |
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126 | (3) |
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129 | (3) |
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132 | (7) |
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139 | (3) |
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Special Topic 4.1 Biofilms, Disease, and Garlic |
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141 | (1) |
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142 | (7) |
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Chapter 5 Environmental Influences and Control of Microbial Growth |
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149 | (32) |
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5.1 Environmental Limits on Growth |
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150 | (1) |
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5.2 Adaptation to Temperature |
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151 | (5) |
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Special Topic 5.1 It's Raining Bacteria |
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155 | (1) |
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5.3 Adaptation to Pressure |
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156 | (1) |
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5.4 Water Activity and Salt |
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157 | (2) |
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5.5 Adaptation to pH Changes |
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159 | (5) |
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5.6 Oxygen and Other Electron Acceptors |
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164 | (3) |
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5.7 Nutrient Deprivation and Starvation |
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167 | (3) |
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5.8 Physical, Chemical, and Biological Control of Microbes |
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170 | (11) |
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Chapter 6 Virus Structure and Function |
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181 | (37) |
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182 | (5) |
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187 | (4) |
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6.3 Viral Genomes and Classification |
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191 | (6) |
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6.4 Bacteriophage Life Cycles |
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197 | (4) |
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6.5 Animal and Plant Virus Life Cycles |
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201 | (7) |
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208 | (4) |
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Special Topic 6.1 West Nile Virus, an Emerging Pathogen |
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212 | (1) |
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212 | (6) |
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218 | (236) |
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The Thrill of Discovery in Molecular Microbiology |
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Chapter 7 Genomes and Chromosomes |
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221 | (36) |
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7.1 DNA: The Genetic Material |
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222 | (1) |
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223 | (9) |
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232 | (10) |
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242 | (2) |
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7.5 Eukaryotic Chromosomes |
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244 | (2) |
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7.6 DNA Sequence Analysis |
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246 | (11) |
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Special Topic 7.1 Where Have All the Bees Gone? Metagenomics, Pyrosequencing, and Nature |
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252 | (5) |
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Chapter 8 Transcription, Translation, and Bioinformatics |
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257 | (44) |
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8.1 RNA Polymerases and sigma Factors |
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258 | (3) |
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8.2 Transcription of DNA to RNA |
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261 | (7) |
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8.3 Translation of RNA to Protein |
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268 | (16) |
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Special Topic 8.1 Stalking the Lone Ribosome |
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279 | (5) |
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8.4 Protein Modification and Folding |
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284 | (1) |
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8.5 Secretion: Protein Traffic Control |
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285 | (5) |
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8.6 Protein Degradation: Cleaning House |
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290 | (2) |
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8.7 Bioinformatics: Mining the Genomes |
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292 | (9) |
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Chapter 9 Gene Transfer, Mutations, and Genome Evolution |
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301 | (40) |
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9.1 The Mosaic Nature of Genomes |
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302 | (1) |
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302 | (13) |
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Special Topic 9.1 There's a Bacterial Genome Hidden in My Fruit Fly |
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310 | (5) |
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315 | (4) |
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319 | (6) |
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325 | (6) |
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9.6 Mobile Genetic Elements |
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331 | (4) |
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335 | (6) |
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Chapter 10 Molecular Regulation |
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341 | (44) |
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10.1 Regulating Gene Expression |
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342 | (3) |
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10.2 Paradigm of the Lactose Operon |
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345 | (6) |
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10.3 Other Systems of Operon Control |
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351 | (7) |
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10.4 Sigma Factor Regulation |
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358 | (3) |
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10.5 Small Regulatory RNAs |
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361 | (3) |
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10.6 DNA Rearrangements: Phase Variation by Shifty Pathogens |
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364 | (3) |
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10.7 Integrated Control Circuits |
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367 | (7) |
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Special Topic 10.1 Toxin-Antitoxin Modules: Mechanisms for Self-preservation or Altruism? |
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372 | (2) |
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10.8 Quorum Sensing: Chemical Conversations |
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374 | (3) |
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Special Topic 10.2 The Role of Quorum Sensing in Pathogenesis and in Interspecies Communications |
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376 | (1) |
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10.9 Genomics and Proteomics: Tools of the Future |
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377 | (8) |
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Chapter 11 Viral Molecular Biology |
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385 | (42) |
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11.1 Phage T4: The Classic Molecular Model |
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387 | (6) |
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11.2 Poliovirus:(+) Strand RNA |
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393 | (6) |
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11.3 Influenza Virus: (-) Strand RNA |
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399 | (6) |
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11.4 Human Immunodeficiency Virus (HIV): Retrovirus |
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405 | (10) |
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11.5 Herpes Simplex Virus: DNA |
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415 | (7) |
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Special Topic 11.1 How Did Viruses Originate? |
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416 | (6) |
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11.6 Gene Therapy with Viruses |
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422 | (5) |
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Chapter 12 Molecular Techniques and Biotechnology |
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427 | (27) |
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12.1 Basic Tools of Biotech: A Research Case Study |
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428 | (1) |
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428 | (4) |
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432 | (9) |
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12.4 "Global" Questions of Cell Physiology |
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441 | (4) |
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12.5 Applied Biotechnology |
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445 | (9) |
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Special Topic 12.1 DNA Vaccines |
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446 | (8) |
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PART 3 Metabolism and Biochemistry |
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454 | (166) |
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Polymer Biosynthesis Makes a Pathogenic Biofilm |
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Chapter 13 Energetics and Catabolism |
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457 | (44) |
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13.1 Energy and Entropy for Life |
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458 | (4) |
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13.2 Energy and Entropy in Biochemical Reactions |
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462 | (3) |
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13.3 Energy Carriers and Electron Transfer |
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465 | (6) |
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13.4 Catabolism: The Microbial Buffet |
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471 | (7) |
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Special Topic 13.1 Swiss Cheese: A Product of Bacterial Catabolism |
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476 | (2) |
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13.5 Glucose Breakdown and Fermentation |
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478 | (9) |
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13.6 The Tricarboxylic Acid (TCA) Cycle |
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487 | (6) |
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493 | (8) |
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Special Topic 13.2 Genomic Analysis of Metabolism |
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494 | (7) |
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Chapter 14 Respiration, Lithotrophy, and Photolysis |
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501 | (42) |
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14.1 Electron Transport Systems |
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502 | (5) |
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14.2 The Proton Motive Force |
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507 | (5) |
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Special Topic 14.1 Testing the Chemiosmotic Theory |
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510 | (2) |
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14.3 The Respiratory ETS and ATP Synthase |
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512 | (8) |
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14.4 Anaerobic Respiration |
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520 | (4) |
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Special Topic 14.2 Bacterial Electric Power |
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522 | (2) |
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14.5 Lithotrophy and Methanogenesis |
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524 | (5) |
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529 | (14) |
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543 | (40) |
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15.1 Overview of Biosynthesis |
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544 | (1) |
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15.2 CO2 Fixation: The Calvin Cycle |
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545 | (11) |
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Special Topic 15.1 The Discovery of 14C |
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548 | (8) |
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15.3 CO2 Fixation in Anaerobes and Archaea |
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556 | (3) |
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15.4 Biosynthesis of Fatty Acids, Polyesters, and Polyketides |
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559 | (8) |
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Special Topic 15.2 Metagenomic Screening for Polyketide Drugs |
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564 | (3) |
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567 | (5) |
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15.6 Biosynthesis of Amino Acids and Nitrogenous Bases |
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572 | (6) |
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15.7 Biosynthesis of Tetrapyrroles |
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578 | (5) |
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Chapter 16 Food and Industrial Microbiology |
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583 | (37) |
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584 | (2) |
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16.2 Fermented Foods: An Overview |
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586 | (3) |
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16.3 Acid-and Alkali-Fermented Foods |
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589 | (7) |
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Special Topic 16.1 Chocolate: The Mystery Fermentation |
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594 | (2) |
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16.4 Ethanolic Fermentation: Bread and Wine |
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596 | (5) |
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16.5 Food Spoilage and Preservation |
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601 | (8) |
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16.6 Industrial Microbiology |
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609 | (11) |
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Special Topic 16.2 Start-Up Companies Take On Tuberculosis |
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610 | (10) |
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PART 4 Microbial Diversity and Ecology |
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620 | (238) |
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Adventures in Microbial Diversity Lead to Products in Industry |
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Chapter 17 Origins and Evolution |
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623 | (46) |
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625 | (10) |
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17.2 Models for Early Life |
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635 | (3) |
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17.3 Microbial Divergence and Phylogeny |
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638 | (10) |
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Special Topic 17.1 Phylogeny of a Shower Curtain Biofilm |
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644 | (4) |
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17.4 Horizontal Gene Transfer |
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648 | (2) |
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17.5 Microbial Species and Taxonomy |
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650 | (8) |
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Special Topic 17.2 Horizontal Gene Transfer in E. coli 0157:H7 |
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654 | (4) |
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17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts |
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658 | (11) |
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Chapter 18 Bacterial Diversity |
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669 | (46) |
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18.1 Bacterial Diversity at a Glance |
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671 | (7) |
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18.2 Deep-Branching Thermophiles |
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678 | (3) |
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18.3 Cyanobacteria: Oxygenic Phototrophs |
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681 | (3) |
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18.4 Gram-Positive Firmicutes and Actinobacteria |
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684 | (11) |
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18.5 Gram-Negative Proteobacteria and Nitrospirae |
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695 | (13) |
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Special Topic 18.1 Carbon Monoxide: Food for Bacteria? |
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698 | (10) |
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18.6 Bacteroidetes and Chlorobi |
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708 | (1) |
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18.7 Spirochetes: Sheathed Spiral Cells with Internalized Flagella |
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708 | (2) |
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18.8 Chlamydiae, Planctomycetes, and Verrucomicrobia: Irregular Cells |
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710 | (5) |
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Chapter 19 Archaeal Diversity |
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715 | (36) |
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717 | (7) |
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19.2 Crenarchaeota: Hyperthermophiles |
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724 | (6) |
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Special Topic 19.1 Research on Deep-Sea Hyperthermophiles |
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727 | (3) |
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19.3 Crenarchaeota: Mesophiles and Psychrophiles |
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730 | (3) |
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19.4 Euryarchaeota: Methanogens |
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733 | (6) |
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19.5 Euryarchaeota: Halophiles |
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739 | (6) |
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Special Topic 19.2 Haloarchaea in the High School Classroom |
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741 | (4) |
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19.6 Euryarchaeota: Thermophiles and Acidophiles |
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745 | (3) |
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19.7 Deeply Branching Divisions |
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748 | (3) |
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Chapter 20 Eukaryotic Diversity |
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751 | (38) |
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20.1 Phylogeny of Eukaryotes |
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752 | (9) |
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20.2 Fungi and Microsporidia |
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761 | (8) |
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769 | (6) |
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20.4 Amebas and Slime Molds |
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775 | (3) |
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20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans |
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778 | (5) |
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20.6 Trypanosomes and Metamonads |
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783 | (6) |
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Special Topic 20.1 The Trypanosome: A Shape-Shifting Killer |
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784 | (5) |
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Chapter 21 Microbial Ecology |
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789 | (40) |
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21.1 Microbes in Ecosystems |
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791 | (3) |
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794 | (4) |
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21.3 Marine and Aquatic Microbiology |
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798 | (12) |
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21.4 Soil and Subsurface Microbiology |
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810 | (7) |
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21.5 Microbial Communities within Plants |
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817 | (4) |
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21.6 Microbial Communities within Animals |
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821 | (8) |
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Special Topic 21.1 A Veterinary Experiment: The Fistulated Cow |
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824 | (5) |
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Chapter 22 Microbes and the Global Environment |
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829 | (29) |
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22.1 Biogeochemical Cycles |
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830 | (3) |
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833 | (2) |
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22.3 The Hydrologic Cycle and Wastewater Treatment |
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835 | (6) |
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Special Topic 22.1 Wetlands: Disappearing Microbial Ecosystems |
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836 | (5) |
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841 | (5) |
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22.5 Sulfur, Phosphorus, and Metals |
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846 | (6) |
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852 | (6) |
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PART 5 Medicine and Immunology |
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858 | |
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Molecular Microbiology Dissects a Pathogen |
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Chapter 23 Human Microbiota and Nonspecific Host Defenses |
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861 | (32) |
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23.1 Human Microbiota: Location and Shifting Composition |
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862 | (8) |
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23.2 Risks and Benefits of Harboring Microbial Populations |
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870 | (1) |
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23.3 Overview of the Immune System |
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871 | (4) |
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23.4 Barbarians at the Gate: Innate Host Defenses |
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875 | (5) |
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Special Topic 23.1 Do Defensins Help Determine Species Specificity for Infection? |
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879 | (1) |
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23.5 Innate Immunity: The Acute Inflammatory Response |
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880 | (3) |
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883 | (2) |
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23.7 Innate Defenses: Interferon, Natural Killer Cells, and Toll-Like Receptors |
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885 | (3) |
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23.8 Complement's Role in Innate Immunity |
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888 | (2) |
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890 | (3) |
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Chapter 24 The Adaptive Immune Response |
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893 | (42) |
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894 | (2) |
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896 | (4) |
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24.3 Antibody Structure and Diversity |
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900 | (5) |
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24.4 Primary and Secondary Antibody Responses |
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905 | (3) |
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24.5 Genetics of Antibody Production |
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908 | (5) |
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24.6 T Cells, Histocompatibility, and Antigen Processing |
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913 | (10) |
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24.7 Complement as Part of Adaptive Immunity |
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923 | (2) |
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24.8 Hypersensitivity and Autoimmunity |
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925 | (10) |
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Special Topic 24.1 An Uneasy Peace: Detente at the Microbiota-Intestinal Interface |
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929 | (6) |
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Chapter 25 Microbial Pathogenesis |
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935 | (42) |
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25.1 Host-Pathogen Interactions |
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936 | (4) |
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25.2 Virulence Factors and Pathogenicity Islands: The Tools and Toolkits of Microbial Pathogens |
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940 | (3) |
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25.3 Virulence Factors: Microbial Attachment |
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943 | (5) |
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25.4 Toxins Subvert Host Function |
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948 | (10) |
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25.5 Protein Secretion and Pathogenesis |
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958 | (3) |
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25.6 Finding Virulence Genes |
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961 | (5) |
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Special Topic 25.1 The Bacterial Trojan Horse: Bacteria That Deliver Their Own Receptor |
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962 | (4) |
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25.7 Surviving within the Host |
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966 | (4) |
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Special Topic 25.2 Bacterial Covert Operations: Secreted Shigella Effector Proteins Jam Communications between Target Cells and Innate Immunity |
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968 | (2) |
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970 | (7) |
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Chapter 26 Microbial Diseases |
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977 | (50) |
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26.1 Characterizing and Diagnosing Microbial Diseases |
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978 | (2) |
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26.2 Skin and Soft-Tissue Infections |
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980 | (4) |
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26.3 Respiratory Tract Infections |
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984 | (6) |
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26.4 Gastrointestinal Tract Infections |
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990 | (5) |
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26.5 Genitourinary Tract Infections |
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995 | (10) |
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Special Topic 26.1 Intracellular Biofilm Pods are Reservoirs of Infection |
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998 | (7) |
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26.6 Central Nervous System Infections |
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1005 | (7) |
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26.7 Cardiovascular System Infections |
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1012 | (2) |
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1014 | (8) |
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1022 | (5) |
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Chapter 27 Antimicrobial Chemotherapy |
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|
1027 | (36) |
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27.1 The Golden Age of Antibiotic Discovery |
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1028 | (2) |
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27.2 Basic Concepts of Antimicrobial Therapy |
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1030 | (1) |
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27.3 Measuring Drug Susceptibility |
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1031 | (4) |
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27.4 Mechanisms of Action |
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1035 | (10) |
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27.5 Antibiotic Biosynthesis |
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1045 | (1) |
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27.6 Challenges of Drug Resistance |
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1046 | (5) |
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27.7 The Future of Drug Discovery |
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1051 | (2) |
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1053 | (5) |
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Special Topic 27.1 Disrupting Cell-Cell Communications to Prevent Infection: Good Idea? |
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1054 | (2) |
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Special Topic 27.2 Resurrecting the 1918 Pandemic Flu Virus |
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1056 | (2) |
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1058 | (5) |
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Chapter 28 Clinical Microbiology and Epidemiology |
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|
1063 | |
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28.1 Principles of Clinical Microbiology |
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|
1064 | (1) |
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28.2 Approaches to Pathogen Identification |
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1065 | (14) |
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1079 | (4) |
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28.4 Biosafety Containment Procedures |
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1083 | (2) |
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28.5 Principles of Epidemiology |
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|
1085 | (6) |
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28.6 Detecting Emerging Microbial Diseases |
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|
1091 | |
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Special Topic 28.1 What's Blowing in the Wind? Quick Pathogen Detection Systems Guard against Bioterrorism |
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|
1092 | |
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APPENDIX 1 Biological Molecules |
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1 | (20) |
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A1.1 Elements, Bonding, and Water |
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2 | (3) |
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5 | (1) |
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6 | (4) |
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10 | (2) |
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12 | (2) |
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14 | (2) |
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A1.7 Biological Chemistry |
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16 | (5) |
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APPENDIX 2 Introductory Cell Biology: Eukaryotic Cells |
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21 | |
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22 | (6) |
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A2.2 The Nucleus and Mitosis |
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28 | (3) |
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A2.3 Problems Faced by Large Cells |
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31 | (1) |
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A2.4 The Endomembrane System |
|
|
32 | (3) |
|
|
|
35 | (2) |
|
A2.6 Mitochondria and Chloroplasts |
|
|
37 | |
| Answers to Thought Questions |
|
1 | (1) |
| Figure Credits |
|
1 | (1) |
| Glossary |
|
1 | (1) |
| Index |
|
1 | |
