Title Details

PART 1 THE MICROBES

1The Microbial World 2

1.1 The Microbes 4

1.2 Microbial Genetics 16

1.3 Microbial Metabolism and Ecology 24

1.4 Microbes and Disease 27

2Bacteria 36

2.1 Morphology of Bacterial Cells 38

2.2 The Cytoplasm 41

2.3 The Bacterial Cytoskeleton 44

2.4 The Cell Envelope 45

2.5 The Bacterial Cell Surface 62

2.6 Bacterial Taxonomy 68

3Eukaryal Microbes 72

3.1 The Morphology of Typical Eukaryal Cells 74

3.2 Diversity of Eukaryal Microbes 87

3.3 Replication of Eukaryal Microbes 92

3.4 The Origin of Eukaryal Cells 95

3.5 Interactions Between Eukaryal Microbes and Animals, Plants, and the Environment 100

4 Archaea 106

4.1 Distinct Properites of Archaea 108

4.2 Archaeal Cell Structure 110

4.3 Diversity of Archaea 119

5Viruses 130

5.1 A Basic Overview of Viruses 132

5.2 Origins of Viruses 140

5.3 Cultivation, Purification, and Quantification of Viruses 142

5.4 Diversity of Viruses 149

5.5 Virus-Like Particles 155

5.6 Virology Today 157

6Cultivating Microorganisms 164

6.1 Nutritional Requirements of Microorganisms 166

6.2 Factors Affecting Microbial Growth 168

6.3 Growing Microorganisms in the Laboratory 173

6.4 Measuring Microbial Population Growth 184

6.5 Eliminating Microbes and Preventing Their Growth 192

PART IIMICROBIAL GENETICS

7DNA Replication and Gene Expression 202

7.1 The Role of DNA 204

7.2 DNA Replication 210

7.3 Transcription 216

7.4 Translation 233

7.5 The Effects of Mutations 229

8Viral Replication Strategies 238

8.1 Recognition of Host Cells 240

8.2 Viral Entry and Uncoating 244

8.3 Viral Replication 248

8.4 Viral Assembly and Egress 256

8.5 Antiviral Drugs 258

9Bacterial Genetic Analysis 266

9.1 Bacteria as Subjects of Genetic Research 268

9.2 Mutations, Mutants, and Strains 271

9.3 Restriction Enzymes, Vectors, and Cloning 278

9.4 Recombination and DNA Transfer 285

10Microbial Genomics 302

10.1 Genome Sequencing 304

10.2 Genomic Analysis of Gene Expression 312

10.3 Comparative Genomics 318

10.4 Metagenomics 323

11Regulation of Gene Expression 328

11.1 Differential Gene Expression 330

11.2 The Operon 332

11.3 Global Gene Regulation 337

11.4 Post-Initiation of Gene Expression 346

11.5 Quorum Sensing 350

11.6 Two-Component Regulatory Systems 352

11.7 Chemotaxis 355

12Microbial Biotechnology 362

12.1 Microbes for Biotechnology 365

12.2 Molecular Genetic Modification 368

12.3 Red Biotechnology 381

12.4 White Biotechnology 382

12.5 Green Biotechnology 391

PART IIIMICROBIAL PHYSIOLOGY AND ECOLOGY

13Metabolism 400

13.1 Energy, Enzymes, and ATP 402

13.2 Central Processes in ATP Synthesis 406

13.3 Carbon Utilization in Microorganisms 412

13.4 Respiration and the Electron Transport System 422

13.5 Metabolism of Non-Glucose Carbon Sources 429

13.6 Phototrophy and Photosynthesis 433

13.7 Nitrogen and Sulfur Metabolism 443

13.8 Biosynthesis of Cellular Components 447

14Biogeochemical Cycles 456

14.1 Nutrient Cycling 459

14.2 Cycling Driven by Carbon Metabolism 463

14.3 Cycling Driven by Nitrogen Metabolism 472

14.4 The Interconnectedness of Cycles 478

15Microbial Ecosystems 484

15.1 Microbes in the Environment 486

15.2 Microbial Community Structure 490

15.3 Aquatic Ecosystems 498

15.4 Terrestrial Ecosystems 406

15.5 Deep Subsurface and Geothermal Ecosystems 512

16The Microbiology of Food and Water 522

16.1 Food Spoilage 524

16.2 Food Preservation 528

16.3 Food Fermentation 534

16.4 Foodborne and Waterborne Illness 541

16.5 Microbiological Aspects of Water Quality 543

17 Microbial Symbionts 560

17.1 Types of Microbe–Host Interactions 563

17.2 Symbionts of Plants 564

17.3 Lichens 569

17.4 Symbionts of Vertebrates 571

17.5 Symbionts of Invertebrates 587

PART IVMICROBES AND DISEASE

18Introduction to Infectious Diseases 600

18.1 Pathogenic Microbes 603

18.2 Virulence Strategies 608

18.3 The Transmission of Infectious Diseases 613

18.4 Proving Cause and Effect in Microbial Infections 621

18.5 The Evolution of Pathogens 625

19Innate Host Defenses Against Microbial Invasion 636

19.1 Immunity 638

19.2 Barriers to Infection 639

19.3 The Inflammatory Response 643

19.4 The Molecules of Innate Immunity 644

19.5 The Cells of Innate Immunity 653

19.6 Invertebrate Defenses 663

20Adaptive Immunity 672

20.1 Features of Adaptive Immunity 674

20.2 T Cells 677

20.3 Antigen Processing 681

20.4 Antigen-Presenting Cells 686

20.5 Humoral and Cell-Mediated

20.6 B Cells and the Production of Antibody 694

21.2 Survival in the Host:

Strategies and Consequences 743

Toolbox 21.2 THE TUBERCULIN TEST FOR TUBERCULOSIS 750

21.3 Evolution of Bacterial Pathogens 751

22Viral Pathogenesis 760

22.1 Recurring Themes in Viral Pathogenesis 762

22.2 Interactions with the Host: Strategies and Consequences 770

22.3 Viral Infections and Cancer 775

22.4 Evolution of Viral Pathogens 785

23Eukaryal Microbe Pathogenesis 792

23.1 Mechanisms of Eukaryal Microbe Pathogenesis 794

23.2 Pathogen Study:

23.3 Macroscopic Eukaryal Pathogens 814

23.4 Evolution of Eukaryal Pathogens 816

24Control of Infectious Diseases 822

24.1 Historical Aspects of Infectious Disease Treatment and Control 824

24.2 Antimicrobial Drugs 825

24.3 Antimicrobial Drug Resistance 836

24.4 Predicting and Controlling Epidemics 850

24.5 Immunization and Vaccines 853

Appendix A Reading and Understanding the Primary Literature A-1

Appendix B Microscopy A-9

Appendix C Classification of Bacteria A-13

Appendix D Classification of Eukarya A-14

Appendix E Classification of Archaea A-15

Appendix F Classification of Viruses A-16

Appendix G Origin of Blood Cells A-17

GLOSSARY G-1

INDEX I-1