| About the Authors |
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iii | |
| Preface |
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vii | |
| Acknowledgments |
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xiii | |
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UNIT 1 The Foundations of Microbiology |
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1 | (37) |
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Microbiologynow Microbiology in Motion |
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1 | (1) |
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I Exploring the Microbial World |
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2 | (1) |
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1.1 Microorganisms, Tiny Titans of the Earth |
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2 | (1) |
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1.2 Structure and Activities of Microbial Cells |
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3 | (2) |
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1.3 Cell Size and Morphology |
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5 | (5) |
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1.4 An Introduction to Microbial Life |
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10 | (2) |
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1.5 Microorganisms and the Biosphere |
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12 | (1) |
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1.6 The Impact of Microorganisms on Human Society |
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13 | (5) |
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II Microscopy and the Origins of Microbiology |
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18 | (1) |
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1.7 Light Microscopy and the Discovery of Microorganisms |
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18 | (2) |
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1.8 Improving Contrast in Light Microscopy |
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20 | (2) |
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1.9 Imaging Cells in Three Dimensions |
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22 | (1) |
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1.10 Probing Cell Structure: Electron Microscopy |
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23 | (2) |
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III Microbial Cultivation Expands the Horizon of Microbiology |
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25 | (1) |
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1.11 Pasteur and Spontaneous Generation |
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25 | (2) |
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1.12 Koch, Infectious Diseases, and Pure Cultures |
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27 | (2) |
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1.13 Discovery of Microbial Diversity |
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29 | (2) |
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IV Molecular Biology and the Unity and Diversity of Life |
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31 | (1) |
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1.14 Molecular Basis of Life |
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31 | (1) |
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1.15 Woese and the Tree of Life |
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32 | |
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Explore the Microbial World Tiny Cells |
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9 | (29) |
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2 Microbial Cell Structure and Function |
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38 | (37) |
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Microbiologynow Exploring the Microbial Cell |
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38 | (1) |
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39 | (1) |
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2.1 The Cytoplasmic Membrane |
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39 | (3) |
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2.2 Transporting Nutrients into the Cell |
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42 | (2) |
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44 | (3) |
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2.4 LPS: The Outer Membrane |
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47 | (2) |
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2.5 Diversity of Cell Envelope Structure |
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49 | (2) |
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II Cell Surface Structures and Inclusions |
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51 | (1) |
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2.6 Cell Surface Structures |
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51 | (2) |
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53 | (2) |
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55 | (3) |
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58 | (1) |
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2.9 Flagella, Archaella, and Swimming Motility |
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58 | (3) |
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61 | (2) |
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63 | (2) |
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2.12 Other Forms of Taxis |
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65 | (1) |
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IV Eukaryotic Microbial Cells |
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66 | (1) |
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2.13 The Nucleus and Cell Division |
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66 | (2) |
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2.14 Mitochondria and Chloroplasts |
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68 | (2) |
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2.15 Other Eukaryotic Cell Structures |
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70 | (5) |
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75 | (33) |
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Microbiologynow Life Begins with Metabolism |
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75 | (1) |
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I Fundamentals of Metabolism |
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76 | (1) |
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3.1 Defining the Requirements for Life |
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76 | (2) |
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3.2 Electron Transfer Reactions |
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78 | (2) |
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3.3 Calculating Changes in Free Energy |
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80 | (2) |
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3.4 Cellular Energy Conservation |
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82 | (2) |
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3.5 Catalysis and Enzymes |
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84 | (1) |
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II Catabolism: Chemoorganotrophs |
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85 | (1) |
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3.6 Glycolysis, the Citric Acid Cycle, and the Glyoxylate Cycle |
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86 | (2) |
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3.7 Principles of Fermentation |
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88 | (1) |
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3.8 Principles of Respiration: Electron Carriers |
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89 | (2) |
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3.9 Principles of Respiration: Generating a Proton Motive Force |
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91 | (3) |
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III Catabolism: Electron Transport and Metabolic Diversity |
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94 | (1) |
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3.10 Anaerobic Respiration and Metabolic Modularity |
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94 | (2) |
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3.11 Chemolithotrophy and Phototrophy |
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96 | (2) |
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98 | (1) |
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3.12 Autotrophy and Nitrogen Fixation |
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98 | (3) |
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3.13 Sugars and Polysaccharides |
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101 | (1) |
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3.14 Amino Acids and Nucleotides |
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102 | (1) |
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3.15 Fatty Acids and Lipids |
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103 | (5) |
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4 Microbial Growth and Its Control |
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108 | (40) |
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Microbiologynow Growing Their Own Way |
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108 | (1) |
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I Culturing Microbes and Measuring Their Growth |
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109 | (1) |
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4.1 Feeding the Microbe: Cell Nutrition |
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109 | (2) |
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4.2 Growth Media and Laboratory Culture |
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111 | (3) |
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4.3 Microscopic Counts of Microbial Cell Numbers |
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114 | (1) |
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4.4 Viable Counting of Microbial Cell Numbers |
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115 | (2) |
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4.5 Turbidimetric Measures of Microbial Cell Numbers |
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117 | (1) |
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II Dynamics of Microbial Growth |
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118 | (1) |
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4.6 Binary Fission and the Microbial Growth Cycle |
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118 | (2) |
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4.7 Quantitative Aspects of Microbial Growth |
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120 | (2) |
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122 | (1) |
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123 | (1) |
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4.10 Alternatives to Binary Fission |
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124 | (2) |
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III Environmental Effects on Growth: Temperature |
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126 | (1) |
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4.11 Temperature Classes of Microorganisms |
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126 | (1) |
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4.12 Microbial Life in the Cold |
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127 | (2) |
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4.13 Microbial Life at High Temperatures |
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129 | (2) |
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IV Environmental Effects on Growth: pH, Osmolarity, and Oxygen |
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131 | (1) |
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4.14 Effects of pH on Microbial Growth |
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132 | (1) |
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4.15 Osmolarity and Microbial Growth |
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133 | (2) |
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4.16 Oxygen and Microbial Growth |
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135 | (2) |
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V Controlling Microbial Growth |
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137 | (1) |
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4.17 General Principles and Microbial Growth Control by Heat |
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138 | (1) |
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4.18 Other Physical Control Methods: Radiation and Filtration |
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139 | (2) |
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4.19 Chemical Control of Microbial Growth |
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141 | (7) |
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5 Viruses and Their Multiplication |
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148 | (17) |
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Microbiologynow When Antibiotics Fail, Bacteriophage Therapy to the Rescue |
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148 | (1) |
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149 | (1) |
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149 | (2) |
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5.2 Structure of the Virion |
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151 | (2) |
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5.3 Culturing, Detecting, and Counting Viruses |
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153 | (2) |
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II Overview of the Viral Replication Cycle |
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155 | (1) |
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5.4 Steps in the Replication Cycle |
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155 | (1) |
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5.5 Bacteriophage T4: A Model Lytic Virus |
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156 | (3) |
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5.6 Temperate Bacteriophages and Lysogeny |
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159 | (1) |
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5.7 An Overview of Viruses of Eukaryotes |
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159 | (6) |
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UNIT 2 Molecular Biology and Genetics |
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6 Molecular Information Flow and Protein Processing |
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165 | (35) |
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Microbiologynow Injectisomes: Salmonella's Mode of Attack |
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165 | (1) |
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I Molecular Biology and Genetic Elements |
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166 | (1) |
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6.1 DNA and Genetic Information Flow |
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166 | (3) |
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6.2 Genetic Elements: Chromosomes and Plasmids |
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169 | (3) |
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II Copying the Genetic Blueprint: DNA Replication |
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172 | (1) |
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6.3 Templates, Enzymes, and the Replication Fork |
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172 | (3) |
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6.4 Bidirectional Replication, the Replisome, and Proofreading |
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175 | (2) |
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III RNA Synthesis: Transcription |
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177 | (1) |
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6.5 Transcription in Bacteria |
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177 | (4) |
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6.6 Transcription in Archaea and Eukarya |
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181 | (2) |
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IV Protein Synthesis: Translation |
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183 | (1) |
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6.7 Amino Acids, Polypeptides, and Proteins |
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183 | (3) |
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186 | (1) |
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6.9 Translation and the Genetic Code |
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187 | (2) |
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6.10 The Mechanism of Protein Synthesis |
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189 | (3) |
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V Protein Processing, Secretion, and Targeting |
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192 | (1) |
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6.11 Assisted Protein Folding and Chaperones |
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192 | (1) |
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6.12 Protein Secretion: The Sec and Tat Systems |
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193 | (1) |
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6.13 Protein Secretion: Gram-Negative Systems |
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194 | (6) |
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7 Microbial Regulatory Systems |
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200 | (34) |
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Microbiologynow As Bacterial Cells Chatter, Viruses Eavesdrop |
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200 | (1) |
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I DNA-Binding Proteins and Transcriptional Regulation |
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201 | (1) |
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201 | (1) |
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7.2 Transcription Factors and Effectors |
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202 | (2) |
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7.3 Repression and Activation |
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204 | (3) |
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7.4 Transcription Controls in Archaea |
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207 | (2) |
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II Sensing and Signal Transduction |
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209 | (1) |
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7.5 Two-Component Regulatory Systems |
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209 | (1) |
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7.6 Regulation of Chemotaxis |
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210 | (3) |
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7.7 Cell-to-Cell Signaling |
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213 | (2) |
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215 | (1) |
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216 | (2) |
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7.9 Stringent and General Stress Responses |
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218 | (2) |
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7.10 The Phosphate (Pho) Regulon |
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220 | (1) |
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7.11 The Heat Shock Response |
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221 | (1) |
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222 | (1) |
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223 | (1) |
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224 | (2) |
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226 | (1) |
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V Regulation of Enzymes and Other Proteins |
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227 | (1) |
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228 | (1) |
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7.16 Post-Translational Regulation |
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228 | (6) |
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8 Molecular Aspects of Microbial Growth |
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234 | (27) |
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Microbiologynow Membrane Vesicles: Nano Vehicles Transporting Important Cargo |
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234 | (1) |
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I Bacterial Cell Division |
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235 | (1) |
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8.1 Visualizing Molecular Growth |
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235 | (1) |
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8.2 Chromosome Replication and Segregation |
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236 | (3) |
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8.3 Cell Division and Fts Proteins |
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239 | (2) |
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8.4 Determinants of Cell Morphology |
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241 | (2) |
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8.5 Peptidoglycan Biosynthesis |
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243 | (3) |
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II Regulation of Development in Model Bacteria |
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246 | (1) |
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8.6 Regulation of Endospore Formation |
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246 | (1) |
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8.7 Regulation of Endospore Germination |
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247 | (1) |
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8.8 Caulobacter Differentiation |
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248 | (2) |
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8.9 Heterocyst Formation in Anabaena |
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250 | (1) |
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251 | (4) |
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III Antibiotics and Microbial Growth |
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255 | (1) |
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8.11 Antibiotic Targets and Antibiotic Resistance |
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255 | (2) |
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8.12 Persistence and Dormancy |
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257 | (4) |
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9 Genetics of Bacteria and Archaea |
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261 | (31) |
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Microbiologynow Live Cell Imaging Captures Bacterial Promiscuity |
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261 | (2) |
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263 | (1) |
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9.1 Mutations and Mutants |
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263 | (2) |
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9.2 Molecular Basis of Mutation |
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265 | (2) |
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9.3 Reversions and Mutation Rates |
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267 | (1) |
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268 | (2) |
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II Gene Transfer in Bacteria |
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270 | (1) |
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9.5 Genetic Recombination |
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271 | (2) |
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273 | (2) |
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275 | (3) |
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278 | (1) |
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9.9 The Formation of Hfr Strains and Chromosome Mobilization |
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279 | (3) |
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III Gene Transfer in Archaea and Other Genetic Events |
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282 | (1) |
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9.10 Horizontal Gene Transfer in Archaea |
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282 | (2) |
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9.11 Mobile DNA: Transposable Elements |
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284 | (2) |
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9.12 Preserving Genomic Integrity and CRISPR |
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286 | (6) |
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UNIT 3 Genomics, Synthetic Biology, and Evolution |
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10 Microbial Genomics and Other Omics |
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292 | (33) |
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Microbiologynow Omics Tools Unravel Mysteries of "Fettuccine" Rocks |
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292 | (1) |
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293 | (1) |
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10.1 Introduction to Genomics |
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293 | (2) |
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10.2 Sequencing and Annotating Genomes |
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295 | (3) |
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10.3 Genome Size and Gene Content in Bacteria and Archaea |
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298 | (4) |
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10.4 Organelle and Eukaryotic Microbial Genomes |
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302 | (3) |
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305 | (1) |
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305 | (3) |
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10.6 High-Throughput Functional Gene Analysis: Tn-Seq |
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308 | (1) |
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308 | (3) |
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10.8 Gene Chips and Transcriptomics |
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311 | (3) |
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10.9 Proteomics and the Interactome |
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314 | (2) |
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316 | (1) |
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317 | (1) |
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10.11 Single-Cell Genomics |
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318 | (1) |
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10.12 Integrating Mycobacterium tuberculosis Omics |
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319 | (2) |
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10.13 Systems Biology and Human Health |
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321 | |
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Explore the Microbial World DNA Sequencing in the Palm of Your Hand |
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300 | (25) |
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11 Viral Genomics and Diversity |
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325 | (29) |
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Microbiologynow Bacteriophages Mimicking Eukaryotes---Discovery of a Phage-Encoded Nucleus and Spindle |
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325 | (1) |
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I Viral Genomes and Classification |
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326 | (1) |
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11.1 Size and Structure of Viral Genomes |
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326 | (2) |
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11.2 Viral Taxonomy and Phylogeny |
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328 | (2) |
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330 | (1) |
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11.3 Single-Stranded DNA Bacteriophages: ΦX174 and M13 |
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330 | (2) |
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11.4 Double-Stranded DNA Bacteriophages: T4, T7, and Lambda |
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332 | (3) |
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335 | (3) |
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11.6 Uniquely Replicating DNA Animal Viruses |
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338 | (1) |
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339 | (2) |
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341 | (1) |
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11.8 Positive-Strand RNA Viruses |
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341 | (2) |
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11.9 Negative-Strand RNA Animal Viruses |
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343 | (2) |
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11.10 Double-Stranded RNA Viruses |
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345 | (1) |
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11.11 Viruses That Use Reverse Transcriptase |
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346 | (3) |
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349 | (1) |
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349 | (1) |
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350 | (4) |
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12 Biotechnology and Synthetic Biology |
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354 | (38) |
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Microbiologynow An Ingestible Biosensor: Using Bacteria to Monitor Gastrointestinal Health |
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354 | (1) |
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I Tools of the Genetic Engineer |
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355 | (1) |
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12.1 Manipulating DNA: PCR and Nucleic Acid Hybridization |
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355 | (3) |
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358 | (4) |
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12.3 Expressing Foreign Genes in Bacteria |
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362 | (2) |
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12.4 Molecular Methods for Mutagenesis |
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364 | (1) |
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12.5 Reporter Genes and Gene Fusions |
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365 | (2) |
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II Making Products from Genetically Engineered Microbes: Biotechnology |
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367 | (1) |
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12.6 Somatotropin and Other Mammalian Proteins |
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367 | (2) |
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12.7 Transgenic Organisms in Agriculture and Aquaculture |
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369 | (2) |
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12.8 Engineered Vaccines and Therapeutic Agents |
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371 | (4) |
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12.9 Mining Genomes and Engineering Pathways |
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375 | (2) |
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12.10 Engineering Biofuels |
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377 | (2) |
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III Synthetic Biology and Genome Editing |
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379 | (1) |
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12.11 Synthetic Metabolic Pathways, Biosensors, and Genetic Circuits |
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380 | (3) |
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383 | (1) |
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12.13 Genome Editing and CRISPRs |
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384 | (4) |
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12.14 Biocontainment of Genetically Modified Organisms |
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388 | (4) |
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13 Microbial Evolution and Genome Dynamics |
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392 | (32) |
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Microbiologynow Exploring Viral Genesis |
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392 | (1) |
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I Early Earth and the Origin and Diversification of Life |
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393 | (1) |
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13.1 Formation and Early History of Earth |
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393 | (3) |
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13.2 Photosynthesis and the Oxidation of Earth |
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396 | (2) |
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13.3 Living Fossils: DNA Records the History of Life |
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398 | (1) |
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13.4 Endosymbiotic Origin of Eukaryotes |
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399 | (3) |
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402 | (1) |
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II Mechanisms of Microbial Evolution |
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403 | (1) |
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13.6 The Evolutionary Process |
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403 | (2) |
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13.7 Experimental Evolution |
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405 | (2) |
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13.8 Gene Families, Duplications, and Deletions |
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407 | (2) |
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13.9 Horizontal GeneTransfer |
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409 | (1) |
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13.10 The Evolution of Microbial Genomes |
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410 | (2) |
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III Microbial Phylogeny and Systematics |
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412 | (1) |
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13.11 Molecular Phylogeny: Making Sense of Molecular Sequences |
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412 | (4) |
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13.12 Microbial Systematics |
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416 | (8) |
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UNIT 4 Microbial Diversity |
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14 Metabolic Diversity of Microorganisms |
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424 | (54) |
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Microbiologynow Ferreting Out the Peculiar Life of Iron Bacteria |
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424 | (1) |
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I Introduction to Metabolic Diversity |
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425 | (1) |
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14.1 Foundational Principles of Metabolic Diversity: Energy and Redox |
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425 | (3) |
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14.2 Autotrophic Pathways |
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428 | (2) |
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430 | (1) |
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14.3 Photosynthesis and Chlorophylls |
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430 | (4) |
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14.4 Carotenoids and Phycobilins |
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434 | (1) |
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14.5 Anoxygenic Photosynthesis |
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435 | (3) |
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14.6 Oxygenic Photosynthesis |
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438 | (2) |
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III Respiratory Processes Defined by lectron Donor |
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440 | (1) |
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14.7 Oxidation of Sulfur Compounds |
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440 | (2) |
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14.8 Iron (Fe2+) Oxidation |
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442 | (1) |
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443 | (2) |
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14.10 Anaerobic Ammonia Oxidation (Anammox) |
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445 | (1) |
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IV Respiratory Processes Defined by Electron Acceptor |
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446 | (1) |
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14.11 Nitrate Reduction and Denitrification |
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446 | (2) |
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14.12 Sulfate and Sulfur Reduction |
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448 | (2) |
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14.13 Other Electron Acceptors |
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450 | (2) |
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V One-Carbon (C1) Metabolism |
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452 | (1) |
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452 | (2) |
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454 | (4) |
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458 | (2) |
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460 | (1) |
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14.17 Energetic and Redox Considerations |
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460 | (2) |
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14.18 Lactic and Mixed-Acid Fermentations |
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462 | (2) |
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14.19 Fermentations of Obligate Anaerobes |
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464 | (2) |
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14.20 Secondary Fermentations |
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466 | (1) |
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14.21 Fermentations That Lack Substrate-Level Phosphorylation |
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467 | (2) |
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469 | (2) |
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VII Hydrocarbon Metabolism |
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471 | (1) |
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14.23 Aerobic Hydrocarbon Metabolism |
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471 | (1) |
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14.24 Anaerobic Hydrocarbon Metabolism |
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472 | (6) |
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15 Ecological Diversity of Bacteria |
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478 | (41) |
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Microbiologynow Cyanobacterial Diversity and Environmental Change |
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478 | (1) |
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I Ecological Diversity Among Microorganisms |
|
|
479 | (1) |
|
15.1 Making Sense of Microbial Diversity |
|
|
479 | (1) |
|
II Ecological Diversity of Phototrophic Bacteria |
|
|
480 | (1) |
|
15.2 Overview of Phototrophic Bacteria |
|
|
480 | (1) |
|
|
|
481 | (4) |
|
15.4 Purple Sulfur Bacteria |
|
|
485 | (2) |
|
15.5 Purple Nonsulfur Bacteria and Aerobic Anoxygenic Phototrophs |
|
|
487 | (1) |
|
15.6 Green Sulfur Bacteria |
|
|
488 | (2) |
|
15.7 Green Nonsulfur Bacteria |
|
|
490 | (1) |
|
15.8 Other Phototrophic Bacteria |
|
|
491 | (1) |
|
III Diversity of Bacteria Defined by Metabolic Traits |
|
|
492 | (1) |
|
15.9 Diversity of Nitrogen Fixers |
|
|
492 | (2) |
|
15.10 Diversity of Nitrifiers and Denitrifiers |
|
|
494 | (2) |
|
15.11 Dissimilative Sulfur-and Sulfate-Reducers |
|
|
496 | (2) |
|
15.12 Dissimilative Sulfur-Oxidizers |
|
|
498 | (4) |
|
15.13 Dissimilative Iron-Reducers |
|
|
502 | (1) |
|
15.14 Dissimilative Iron-Oxidizers |
|
|
503 | (1) |
|
15.15 Methanotrophs and Methylotrophs |
|
|
504 | (2) |
|
IV Morphologically and Ecologically Distinctive Bacteria |
|
|
506 | (1) |
|
15.16 Microbial Predators |
|
|
506 | (2) |
|
|
|
508 | (3) |
|
15.18 Budding and Prosthecate/Stalked Bacteria |
|
|
511 | (3) |
|
|
|
514 | (1) |
|
|
|
515 | (4) |
|
16 Phylogenetic Diversity of Bacteria |
|
|
519 | (66) |
|
Microbiologynow Bacterial Diversity and Human Health |
|
|
519 | (1) |
|
|
|
520 | (1) |
|
|
|
521 | (3) |
|
|
|
524 | (2) |
|
16.3 Gammaproteobacteria: Enterobacteriales |
|
|
526 | (2) |
|
16.4 Gammaproteobacteria: Pseudomonadales and Vibrionales |
|
|
528 | (1) |
|
16.5 Deltaproteobacteria and Epsilonproteobacteria |
|
|
529 | (2) |
|
II Firmicutes, Tenericutes, and Actinobacteria |
|
|
531 | (1) |
|
16.6 Firmicutes: Lactobacillales |
|
|
531 | (2) |
|
16.7 Firmicutes: Nonsporulating Bacillales and Clostridiales |
|
|
533 | (1) |
|
16.8 Firmicutes: Sporulating Bacillales and Clostridiales |
|
|
534 | (1) |
|
16.9 Tenericutes: The Mycoplasmas |
|
|
535 | (1) |
|
16.10 Actinobacteria: Coryneform and Propionic Acid Bacteria |
|
|
536 | (2) |
|
16.11 Actinobacteria: Mycobacterium |
|
|
538 | (1) |
|
16.12 Filamentous Actinobacteria: Streptomyces and Relatives |
|
|
539 | (3) |
|
|
|
542 | (1) |
|
|
|
542 | (1) |
|
16.14 Cytophagales, Flavobacteriales, and Sphingobacteriales |
|
|
543 | (1) |
|
IV Chlamydiae, Planctomycetes, and Verrucomicrobia |
|
|
544 | (1) |
|
|
|
544 | (2) |
|
|
|
546 | (1) |
|
|
|
547 | (1) |
|
V Hyperthermophilic Bacteria |
|
|
548 | (1) |
|
16.18 Thermotogae and Thermodesulfobacteria |
|
|
548 | (1) |
|
|
|
549 | (1) |
|
|
|
550 | (1) |
|
16.20 Deinococcus-Thermus |
|
|
550 | (1) |
|
16.21 Acidobacteria and Nitrospirae |
|
|
551 | (1) |
|
16.22 Other Notable Phyla of Bacteria |
|
|
552 | (4) |
|
|
|
556 | (1) |
|
Microbiologynow Methanogens and Global Climate Change |
|
|
556 | (2) |
|
|
|
558 | (1) |
|
17.1 Extremely Halophilic Archaea |
|
|
558 | (3) |
|
17.2 Methanogenic Archaea |
|
|
561 | (4) |
|
|
|
565 | (1) |
|
17.4 Thermococcales and Archaeoglobales |
|
|
566 | (1) |
|
II Thaumarchaeota and Cryptic Archaeal Phyla |
|
|
567 | (1) |
|
17.5 Thaumarchaeota and Nitrification in Archaea |
|
|
568 | (1) |
|
17.6 Nanoarchaeota and the "Hospitable Fireball" |
|
|
569 | (1) |
|
17.7 Korarchaeota, the "Secret Filament" |
|
|
570 | (1) |
|
17.8 Other Cryptic Archaeal Phyla |
|
|
571 | (1) |
|
|
|
572 | (1) |
|
17.9 Habitats and Energy Metabolism of Crenarchaeota |
|
|
572 | (2) |
|
17.10 Crenarchaeota from Terrestrial Volcanic Habitats |
|
|
574 | (2) |
|
17.11 Crenarchaeota from Submarine Volcanic Habitats |
|
|
576 | (2) |
|
IV Evolution and Life at High Temperature |
|
|
578 | (1) |
|
17.12 An UpperTemperature Limit for Microbial Life |
|
|
578 | (2) |
|
17.13 Molecular Adaptations to Life at High Temperature |
|
|
580 | (1) |
|
17.14 Hyperthermophilic Archaea, H2, and Microbial Evolution |
|
|
581 | (4) |
|
18 Diversity of Microbial Eukarya |
|
|
585 | (27) |
|
Microbiologynow Coccolithophores, Engineers of Global Climate |
|
|
585 | (1) |
|
I Organelles and Phylogeny of Microbial Eukarya |
|
|
586 | (1) |
|
18.1 Endosymbioses and the Eukaryotic Cell |
|
|
586 | (2) |
|
18.2 Phylogenetic Lineages of Eukarya |
|
|
588 | (1) |
|
|
|
589 | (1) |
|
|
|
589 | (2) |
|
|
|
591 | (2) |
|
|
|
593 | (2) |
|
|
|
595 | (1) |
|
|
|
596 | (1) |
|
|
|
597 | (2) |
|
|
|
599 | (1) |
|
18.9 Fungal Physiology, Structure, and Symbioses |
|
|
599 | (2) |
|
18.10 Fungal Reproduction and Phylogeny |
|
|
601 | (1) |
|
18.11 Microsporidia and Chytridiomycota |
|
|
602 | (1) |
|
18.12 Mucoromycota and Glomeromycota |
|
|
603 | (1) |
|
|
|
604 | (1) |
|
|
|
605 | (1) |
|
|
|
606 | (1) |
|
|
|
606 | (1) |
|
|
|
607 | (5) |
|
UNIT 5 Microbial Ecology and Environmental Microbiology |
|
|
|
19 Taking the Measure of Microbial Systems |
|
|
612 | (39) |
|
Microbiologynow Touring Microbial Biogeography Using Combinatorial Imaging |
|
|
612 | (1) |
|
I Culture-Dependent Analyses of Microbial Communities |
|
|
613 | (1) |
|
19.1 Enrichment Culture Microbiology |
|
|
613 | (4) |
|
19.2 Classical Procedures for Isolating Microbes |
|
|
617 | (1) |
|
19.3 Selective Single-Cell Isolation: Laser Tweezers, Flow Cytometry, Microfluidics, and High-Throughput Methods |
|
|
618 | (2) |
|
II Culture-Independent Microscopic Analyses of Microbial Communities |
|
|
620 | (1) |
|
19.4 General Staining Methods |
|
|
620 | (2) |
|
19.5 Microscopic Specificity: Fluorescence In Situ Hybridization (FISH) |
|
|
622 | (3) |
|
III Culture-Independent Molecular Analyses of Microbial Communities |
|
|
625 | (1) |
|
19.6 PCR Methods of Microbial Community Analysis |
|
|
626 | (4) |
|
19.7 Microarrays for Analysis of Microbial Phylogenetic and Functional Diversity |
|
|
630 | (1) |
|
19.8 Environmental Multi-omics: Integration of Genomics, Transcriptomics, Proteomics, and Metabolomics |
|
|
631 | (6) |
|
IV Measuring Microbial Activities in Nature |
|
|
637 | (1) |
|
19.9 Chemical Assays, Radioisotopic Methods, Microsensors, and Nanosensors |
|
|
638 | (3) |
|
19.10 Stable Isotopes and Stable Isotope Probing |
|
|
641 | (2) |
|
19.11 Linking Functions to Specific Organisms |
|
|
643 | (3) |
|
19.12 Linking Genes and Cellular Properties to Individual Cells |
|
|
646 | (5) |
|
|
|
651 | (42) |
|
Microbiologynow Living on Fumes |
|
|
651 | (1) |
|
|
|
652 | (1) |
|
20.1 General Ecological Concepts |
|
|
652 | (1) |
|
20.2 Ecosystem Service: Biogeochemistry and Nutrient Cycles |
|
|
653 | (1) |
|
II The Microbial Environment |
|
|
654 | (1) |
|
20.3 Environments and Microenvironments |
|
|
654 | (2) |
|
20.4 Surfaces and Biofilms |
|
|
656 | (3) |
|
|
|
659 | (2) |
|
III Terrestrial Environments |
|
|
661 | (1) |
|
20.6 Soils: General Properties |
|
|
661 | (3) |
|
20.7 Prokaryotic Diversity in Soils |
|
|
664 | (2) |
|
20.8 The Terrestrial Subsurface |
|
|
666 | (3) |
|
|
|
669 | (1) |
|
|
|
669 | (2) |
|
20.10 Oxygen Relationships in the Marine Environment |
|
|
671 | (3) |
|
20.11 Major Marine Phototrophs |
|
|
674 | (3) |
|
20.12 Pelagic Bacteria and Archaea |
|
|
677 | (3) |
|
20.13 Pelagic Marine Viruses |
|
|
680 | (2) |
|
|
|
682 | (3) |
|
|
|
685 | (2) |
|
|
|
687 | (6) |
|
|
|
693 | (25) |
|
Microbiologynow An Uncertain Future for Coral Reef Ecosystems |
|
|
693 | (1) |
|
I Carbon, Nitrogen, and Sulfur Cycles |
|
|
694 | (1) |
|
|
|
694 | (3) |
|
21.2 Syntrophy and Methanogenesis |
|
|
697 | (2) |
|
|
|
699 | (2) |
|
|
|
701 | (1) |
|
|
|
702 | (1) |
|
21.5 The Iron and Manganese Cycles: Reductive Activities |
|
|
702 | (4) |
|
21.6 The Iron and Manganese Cycles: Oxidative Activities |
|
|
706 | (2) |
|
21.7 The Phosphorus, Calcium, and Silicon Cycles |
|
|
708 | (2) |
|
III Humans and Nutrient Cycling |
|
|
710 | (1) |
|
21.8 Mercury Transformations |
|
|
711 | (2) |
|
21.9 Human Impacts on the Carbon and Nitrogen Cycles |
|
|
713 | |
|
Explore the Microbial World Solving the Marine Methane Paradox |
|
|
710 | (8) |
|
22 Microbiology of the Built Environment |
|
|
718 | (26) |
|
Microbiologynow Sending Microbes to Clean Up after Polluters |
|
|
718 | (1) |
|
I Mineral Recovery and Acid Mine Drainage |
|
|
719 | (1) |
|
22.1 Mining with Microorganisms |
|
|
719 | (2) |
|
|
|
721 | (1) |
|
|
|
722 | (1) |
|
22.3 Bioremediation of Uranium-Contaminated Environments |
|
|
722 | (1) |
|
22.4 Bioremediation of Organic Pollutants: Hydrocarbons |
|
|
723 | (1) |
|
22.5 Bioremediation and Microbial Degradation of Major Chemical Pollutants: Chlorinated Organics and Plastics |
|
|
724 | (3) |
|
III Wastewater and Drinking Water Treatment |
|
|
727 | (1) |
|
22.6 Primary and Secondary Wastewater Treatment |
|
|
728 | (2) |
|
22.7 Tertiary Wastewater Treatment: Further Removal of Phosphorus and Nitrogen |
|
|
730 | (2) |
|
22.8 Sludge Processing and Contaminants of Emerging Concern |
|
|
732 | (3) |
|
22.9 Drinking Water Purification and Stabilization |
|
|
735 | (1) |
|
22.10 Water Distribution Systems |
|
|
736 | (1) |
|
IV Indoor Microbiology and Microbially Influenced Corrosion |
|
|
737 | (1) |
|
22.11 The Microbiology of Homes and Public Spaces |
|
|
737 | (2) |
|
22.12 Microbially Influenced Corrosion of Metals |
|
|
739 | (1) |
|
22.13 Biodeterioration of Stone and Concrete |
|
|
740 | (4) |
|
23 Microbial Symbioses with Microbes, Plants, and Animals |
|
|
744 | (39) |
|
Microbiologynow Coral Fluorescence Provides the Guiding Light for Their Symbiotic Algae |
|
|
744 | (1) |
|
I Symbioses Between Microorganisms |
|
|
745 | (1) |
|
|
|
745 | (1) |
|
23.2 "Chlorochromatium aggregatum" |
|
|
746 | (2) |
|
23.3 Methanotrophic Consortia: Direct Interspecies Electron Transfer |
|
|
748 | (1) |
|
II Plants as Microbial Habitats |
|
|
749 | (1) |
|
23.4 The Legume--Root Nodule Symbiosis |
|
|
749 | (6) |
|
|
|
755 | (2) |
|
23.6 Agrobacterium and Crown Gall Disease |
|
|
757 | (2) |
|
III Insects as Microbial Habitats |
|
|
759 | (1) |
|
23.7 Heritable Symbionts of Insects |
|
|
759 | (3) |
|
|
|
762 | (1) |
|
|
|
763 | (2) |
|
IV Other Invertebrates as Microbial Habitats |
|
|
765 | (1) |
|
23.10 Bioluminescent Symbionts and the Squid Symbiosis |
|
|
765 | (4) |
|
23.11 Marine Invertebrates at Hydrothermal Vents and Cold Seeps |
|
|
769 | (1) |
|
23.12 Entomopathogenic Nematodes |
|
|
770 | (1) |
|
23.13 Reef-Building Corals |
|
|
771 | (3) |
|
V Mammalian Gut Systems as Microbial Habitats |
|
|
774 | (1) |
|
23.14 Alternative Mammalian Gut Systems |
|
|
774 | (2) |
|
23.15 The Rumen and Rumen Activities |
|
|
776 | (1) |
|
23.16 Rumen Microbes and Their Dynamic Relationships |
|
|
777 | |
|
Explore the Microbial World Combating Mosquito-Borne Viral Diseases with an Insect Symbiont |
|
|
761 | (22) |
|
UNIT 6 Microbe-Human Interactions and the Immune System |
|
|
|
24 Microbial Symbioses with Humans |
|
|
783 | (31) |
|
Microbiologynow One of the Most Abundant Viruses on Earth Discovered First in the Human Viral Microbiome |
|
|
783 | (1) |
|
I Structure and Function of the Healthy Adult Gastrointestinal and Oral Microbiomes |
|
|
784 | (1) |
|
24.1 Overview of the Human Microbiome |
|
|
784 | (1) |
|
24.2 Gastrointestinal Microbiota |
|
|
785 | (6) |
|
24.3 Oral Cavity and Airways |
|
|
791 | (3) |
|
II Urogenital Tract and Skin Microbiomes and the Human Viral Microbiome |
|
|
794 | (1) |
|
24.4 Urogenital Tracts and Their Microbes |
|
|
794 | (1) |
|
24.5 The Skin and Its Microbes |
|
|
795 | (2) |
|
|
|
797 | (3) |
|
III From Birth to Death: Development of the Human Microbiome |
|
|
800 | (1) |
|
24.7 Human Study Groups and Animal Models |
|
|
800 | (1) |
|
24.8 Colonization, Succession, and Stability of the Gut Microbiota |
|
|
801 | (2) |
|
IV Disorders Attributed to the Human Microbiome |
|
|
803 | (1) |
|
24.9 Syndromes Linked to the Gut Microbiota |
|
|
804 | (3) |
|
24.10 Syndromes Linked to the Oral, Skin, and Vaginal Microbiota |
|
|
807 | (2) |
|
V Modulation of the Human Microbiome |
|
|
809 | (1) |
|
24.11 Antibiotics and the Human Microbiome |
|
|
809 | (1) |
|
24.12 Probiotics, Prebiotics, and Synbiotics |
|
|
810 | |
|
Explore the Microbial World The Gut-Brain Axis |
|
|
790 | (24) |
|
25 Microbial Infection and Pathogenesis |
|
|
814 | (18) |
|
Microbiologynow Killing Pathogens on Contact |
|
|
814 | (1) |
|
I Human--Pathogen Interactions |
|
|
815 | (1) |
|
|
|
815 | (2) |
|
25.2 Colonization and Invasion |
|
|
817 | (2) |
|
25.3 Pathogenicity, Virulence, and Virulence Attenuation |
|
|
819 | (1) |
|
25.4 Genetics of Virulence and the Compromised Host |
|
|
820 | (2) |
|
II Enzymes and Toxins of Pathogenesis |
|
|
822 | (1) |
|
25.5 Enzymes as Virulence Factors |
|
|
822 | (2) |
|
|
|
824 | (3) |
|
25.7 Cytolytic and Superantigen Exotoxins |
|
|
827 | (1) |
|
|
|
828 | (4) |
|
26 Innate Immunity: Broadly Specific Host Defenses |
|
|
832 | (24) |
|
Microbiologynow Periodontal Disease and Alzheimer's: Evidence for Causation? |
|
|
832 | (1) |
|
I Fundamentals of Host Defense |
|
|
833 | (1) |
|
26.1 Basic Properties of the Immune System |
|
|
833 | (1) |
|
26.2 Barriers to Pathogen Invasion |
|
|
834 | (2) |
|
II Cells and Organs of the Immune System |
|
|
836 | (1) |
|
26.3 The Blood and Lymphatic Systems |
|
|
836 | (2) |
|
26.4 Leukocyte Production and Diversity |
|
|
838 | (2) |
|
III Phagocyte Response Mechanisms |
|
|
840 | (1) |
|
26.5 Pathogen Challenge and Phagocyte Recruitment |
|
|
840 | (1) |
|
26.6 Pathogen Recognition and Phagocyte Signal Transduction |
|
|
841 | (3) |
|
26.7 Phagocytosis and Phagocyte Inhibition |
|
|
844 | (2) |
|
IV Other Innate Host Defenses |
|
|
846 | (1) |
|
26.8 Inflammation and Fever |
|
|
846 | (2) |
|
26.9 The Complement System |
|
|
848 | (3) |
|
26.10 Innate Defenses Against Viruses |
|
|
851 | |
|
Explore the Microbial World Pattern Recognition Receptors of Hydrothermal Vent Tube Worms Facilitate Endosymbiosis |
|
|
843 | (13) |
|
27 Adaptive Immunity: Highly Specific Host Defenses |
|
|
856 | (27) |
|
Microbiologynow Controlling HIV through "Public" T Cell Receptors on CD4T Cells |
|
|
856 | (1) |
|
I Principles of Adaptive Immunity |
|
|
857 | (1) |
|
27.1 Specificity, Memory, Selection Processes, and Tolerance |
|
|
857 | (3) |
|
27.2 Immunogens and Classes of Immunity |
|
|
860 | (2) |
|
|
|
862 | (1) |
|
27.3 Antibody Production and Structural Diversity |
|
|
862 | (4) |
|
27.4 Antigen Binding and the Genetics of Antibody Diversity |
|
|
866 | (3) |
|
III The Major Histocompatibility Complex (MHC) |
|
|
869 | (1) |
|
27.5 MHC Proteins and Their Functions |
|
|
869 | (2) |
|
27.6 MHC Polymorphism, Polygeny, and Peptide Binding |
|
|
871 | (2) |
|
IV T Cells and Their Receptors |
|
|
873 | (1) |
|
27.7 T Cell Receptors: Proteins, Genes, and Diversity |
|
|
874 | (3) |
|
27.8 T Cell Subsets and Their Functions |
|
|
877 | (6) |
|
28 Immune Disorders and Antimicrobial Therapy |
|
|
883 | (24) |
|
Microbiologynow Preventing Autoimmunity with ... Parasitic Worms? |
|
|
883 | (1) |
|
I Disorders and Deficiencies of the Immune System |
|
|
884 | (1) |
|
28.1 Allergy, Hypersensitivity, and Autoimmunity |
|
|
884 | (3) |
|
28.2 Superantigens and Immunodeficiency |
|
|
887 | (2) |
|
II Vaccines and Immunotherapy |
|
|
889 | (1) |
|
28.3 Vaccination Against Infectious Diseases |
|
|
889 | (3) |
|
|
|
892 | (2) |
|
III Drug Treatments for Infectious Diseases |
|
|
894 | (1) |
|
|
|
894 | (6) |
|
28.6 Antimicrobial Drugs That Target Nonbacterial Pathogens |
|
|
900 | (2) |
|
28.7 Antimicrobial Drug Resistance and New Treatment Strategies |
|
|
902 | (5) |
|
UNIT 7 Infectious Diseases Diagnosing Infectious |
|
|
|
|
|
907 | (22) |
|
Microbiologynow Shedding New Light on Diagnosing Tuberculosis |
|
|
907 | (1) |
|
I Microbiology and the Healthcare Environment |
|
|
908 | (1) |
|
29.1 The Clinical Microbiology Laboratory |
|
|
908 | (1) |
|
29.2 Healthcare-Associated Infections |
|
|
909 | (1) |
|
II Isolating and Characterizing Infectious Microorganisms |
|
|
910 | (1) |
|
29.3 Workflow in the Clinical Laboratory |
|
|
910 | (6) |
|
29.4 Choosing the Right Treatment |
|
|
916 | (2) |
|
III Immunological and Molecular Tools for Disease Diagnosis |
|
|
918 | (1) |
|
29.5 Immunoassays and Disease |
|
|
918 | (2) |
|
29.6 Precipitation, Agglutination, and Immunofluorescence |
|
|
920 | (2) |
|
29.7 Enzyme Immunoassays, Rapid Tests, and Immunoblots |
|
|
922 | (3) |
|
29.8 Nucleic Acid-Based Clinical Assays |
|
|
925 | |
|
Explore the Microbial World MRSA---A Formidable Clinical Challenge |
|
|
912 | (17) |
|
30 Epidemiology and Public Health |
|
|
929 | (21) |
|
Microbiologynow A New Urgent Threat is Emerging in Public Health Microbiology |
|
|
929 | (1) |
|
I Principles of Epidemiology |
|
|
930 | (1) |
|
30.1 The Language of Epidemiology |
|
|
930 | (2) |
|
|
|
932 | (1) |
|
30.3 Infectious Disease Transmission and Reservoirs |
|
|
933 | (2) |
|
30.4 Characteristics of Disease Epidemics |
|
|
935 | (2) |
|
II Public and Global Health |
|
|
937 | (1) |
|
30.5 Public Health and Infectious Disease |
|
|
937 | (2) |
|
30.6 Global Health Comparisons |
|
|
939 | (1) |
|
III Emerging Infectious Diseases, Pandemics, and Other Threats |
|
|
940 | (1) |
|
30.7 Emerging and Reemerging Infectious Diseases |
|
|
940 | (3) |
|
30.8 Examples of Pandemics: HIV/AIDS, Cholera, and Influenza |
|
|
943 | (2) |
|
30.9 Public Health Threats from Microbial Weapons |
|
|
945 | (5) |
|
31 Person-to-Person Bacterial and Viral Diseases |
|
|
950 | (33) |
|
Microbiologynow Reversing Antibiotic Resistance in a Recalcitrant Pathogen |
|
|
950 | (1) |
|
I Airborne Bacterial Diseases |
|
|
951 | (1) |
|
|
|
951 | (1) |
|
31.2 Streptococcal Syndromes |
|
|
952 | (3) |
|
31.3 Diphtheria and Pertussis |
|
|
955 | (1) |
|
31.4 Tuberculosis and Leprosy |
|
|
956 | (2) |
|
31.5 Meningitis and Meningococcemia |
|
|
958 | (1) |
|
II Airborne Viral Diseases |
|
|
959 | (1) |
|
31.6 MMR and Varicella-Zoster Infections |
|
|
959 | (2) |
|
|
|
961 | (1) |
|
|
|
962 | (2) |
|
III Direct-Contact Bacterial and Viral Diseases |
|
|
964 | (1) |
|
31.9 Staphylococcus aureus Infections |
|
|
965 | (1) |
|
31.10 Helicobacter pylori and Gastric Diseases |
|
|
966 | (1) |
|
|
|
967 | (2) |
|
31.12 Ebola: A Deadly Threat |
|
|
969 | (1) |
|
IV Sexually Transmitted Infections |
|
|
970 | (1) |
|
31.13 Gonorrhea, Syphilis, and Chlamydia |
|
|
971 | (4) |
|
31.14 Herpes Simplex Viruses (HSV) and Human Papillomavirus (HPV) |
|
|
975 | (1) |
|
31.15 Human Immunodeficiency Virus (HIV) and AIDS |
|
|
976 | (7) |
|
32 Vectorborne and Soilborne Bacterial and Viral Diseases |
|
|
983 | (18) |
|
Microbiologynow The Historical Emergence of an Ancient and Deadly Pathogen |
|
|
983 | (1) |
|
I Animal-Transmitted Viral Diseases |
|
|
984 | (1) |
|
32.1 Rabies Virus and Rabies |
|
|
984 | (2) |
|
32.2 Hantavirus and Hantavirus Syndromes |
|
|
986 | (1) |
|
II Arthropod-Transmitted Bacterial and Viral Diseases |
|
|
987 | (1) |
|
32.3 Rickettsial Diseases |
|
|
987 | (2) |
|
32.4 Lyme Disease and Borrelia |
|
|
989 | (2) |
|
32.5 Yellow Fever, Dengue Fever, Chikungunya, and Zika |
|
|
991 | (2) |
|
|
|
993 | (1) |
|
|
|
994 | (2) |
|
III Soilborne Bacterial Diseases |
|
|
996 | (1) |
|
|
|
996 | (1) |
|
32.9 Tetanus and Gas Gangrene |
|
|
997 | (4) |
|
33 Waterborne and Foodborne Bacterial and Viral Diseases |
|
|
1001 | (22) |
|
Microbiologynow Reverse Zoonosis in the Southern Ocean |
|
|
1001 | (1) |
|
I Water as a Disease Vehicle |
|
|
1002 | (1) |
|
33.1 Agents and Sources of Waterborne Diseases |
|
|
1002 | (1) |
|
33.2 Public Health and Water Quality |
|
|
1003 | (1) |
|
|
|
1004 | (1) |
|
33.3 Vibrio cholerae and Cholera |
|
|
1004 | (2) |
|
|
|
1006 | (1) |
|
33.5 Typhoid Fever and Norovirus Illness |
|
|
1007 | (1) |
|
III Food as a Disease Vehicle |
|
|
1008 | (1) |
|
33.6 Food Spoilage and Food Preservation |
|
|
1008 | (2) |
|
33.7 Foodborne Diseases and Food Epidemiology |
|
|
1010 | (2) |
|
|
|
1012 | (1) |
|
33.8 Staphylococcal Food Poisoning |
|
|
1012 | (1) |
|
33.9 Clostridial Food Poisoning |
|
|
1013 | (1) |
|
|
|
1014 | (1) |
|
|
|
1014 | (1) |
|
33.11 Pathogenic Escherichia coli |
|
|
1015 | (1) |
|
|
|
1016 | (1) |
|
|
|
1017 | (1) |
|
33.14 Other Foodborne Infectious Diseases |
|
|
1018 | (5) |
|
34 Eukaryotic Pathogens: Fungi, Protozoa, and Helminths |
|
|
1023 | (16) |
|
Microbiologynow A Silver Bullet to Kill Brain-Eating Amoebae? |
|
|
1023 | (1) |
|
|
|
1024 | (1) |
|
34.1 Pathogenic Fungi and Classes of Infection |
|
|
1024 | (2) |
|
34.2 Fungal Diseases: Mycoses |
|
|
1026 | (2) |
|
II Visceral Parasitic Infections |
|
|
1028 | (1) |
|
34.3 Amoebae and Ciliates: Entamoeba, Naegleria, and Balantidium |
|
|
1028 | (1) |
|
34.4 Other Visceral Parasites: Giardia, Trichomonas, Cryptosporidium, Toxoplasma, and Cyclospora |
|
|
1029 | (2) |
|
III Blood and Tissue Parasitic Infections |
|
|
1031 | (1) |
|
34.5 Plasmodium and Malaria |
|
|
1031 | (2) |
|
34.6 Leishmaniasis, Trypanosomiasis, and Chagas Disease |
|
|
1033 | (1) |
|
34.7 Parasitic Helminths: Schistosomiasis and Filariases |
|
|
1034 | (5) |
| Photo Credits |
|
1039 | (4) |
| Glossary Terms |
|
1043 | (4) |
| Index |
|
1047 | |
