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About the Authors3

Preface5

Acknowledgments15

UNIT 1 Basic Principles of Microbiology29

Chapter 1 Microorganisms and Microbiology29

Ⅰ Introduction to Microbiology30

1.1 The Science of Microbiology30

1.2 Microbial Cells31

1.3 Microorganisms and Their Environments32

1.4 Evolution and the Extent of Microbial Life33

1.5 The Impact of Microorganisms on Humans35

Ⅱ Pathways of Discovery in Microbiology38

1.6 The Historical Roots of Microbiology：Hooke，van Leeuwenhoek，and Cohn39

1.7 Pasteur and the Defeat of Spontaneous Generation40

1.8 Koch，Infectious Disease，and Pure Culture Microbiology43

1.9 The Rise of Microbial Diversity46

1.10 The Modern Era of Microbiology48

Microbial Sidebar45

Solid Media，Pure Cultures，and the Birth of Microbial Systematics45

Chapter 2 A Brief Journey to the Microbial World52

Ⅰ Seeing the Very Small53

2.1 Some Principles of Light Microscopy53

2.2 Improving Contrast in Light Microscopy54

2.3 Imaging Cells in Three Dimensions57

2.4 Electron Microscopy58

Ⅱ Cell Structure and Evolutionary History59

2.5 Elements of Microbial Structure59

2.6 Arrangement of DNA in Microbial Cells61

2.7 The Evolutionary Tree of Life62

Ⅲ Microbial Diversity64

2.8 Metabolic Diversity64

2.9 Bacteria66

2.10 Archaea69

2.11 Phylogenetic Analyses of Natural Microbial Communities71

2.12 Microbial Eukarya71

Chapter 3 Cell Structure and Function in Bacteria and Archaea75

Ⅰ Cell Shape and Size76

3.1 Cell Morphology76

3.2 Cell Size and the Significance of Smallness77

Ⅱ The Cytoplasmic Membrane and Transport79

3.3 The Cytoplasmic Membrane79

3.4 Functions of the Cytoplasmic Membrane82

3.5 Transport and Transport Systems83

Ⅲ Cell Walls of Prokaryotes86

3.6 The Cell Wall of Bacteria：Peptidoglycan86

3.7 The Outer Membrane88

3.8 Cell Walls of Archaea91

Ⅳ Other Cell Surface Structures and Inclusions92

3.9 Cell Surface Structures92

3.10 Cell Inclusions94

3.11 Gas Vesicles96

3.12 Endospores97

Ⅴ Microbial Locomotion101

3.13 Flagella and Motility101

3.14 Gliding Motility105

3.15 Microbial Taxes106

Microbial Sidebar99

The Mycobacterium tuberculosis Cell Wall：A Complex Architecture of Lipids and Carbohydrates99

UNIT 2 Metabolism and Growth113

Chapter 4 Nutrition，Culture，and Metabolism of Microorganisms113

Ⅰ Nutrition and Culture of Microorganisms114

4.1 Nutrition and Cell Chemistry114

4.2 Culture Media116

4.3 Laboratory Culture118

Ⅱ Energetics and Enzymes120

4.4 Bioenergetics120

4.5 Catalysis and Enzymes121

Ⅲ Oxidation-Reduction and Energy-Rich Compounds122

4.6 Electron Donors and Electron Acceptors122

4.7 Energy-Rich Compounds and Energy Storage125

Ⅳ Essentials of Catabolism126

4.8 Glycolysis126

4.9 Respiration and Electron Carriers129

4.10 The Proton Motive Force131

4.11 The Citric Acid Cycle133

4.12 Catabolic Diversity134

Ⅴ Essentials of Anabolism136

4.13 Biosynthesis of Sugars and Polysaccharides136

4.14 Biosynthesis of Amino Acids and Nucleotides137

4.15 Biosynthesis of Fatty Acids and Lipids138

4.16 Regulating the Activity of Biosynthetic Enzymes139

Microbial Sidebar127

Yeast Fermentation，the Pasteur Effect，and the Home Brewer127

Chapter 5 Microbial Growth145

Ⅰ Bacterial Cell Division146

5.1 Cell Growth and Binary Fission146

5.2 Fts Proteins and Cell Division146

5.3 MreB and Determinants of Cell Morphology148

5.4 Peptidoglycan Synthesis and Cell Division149

Ⅱ Population Growth151

5.5 The Concept of Exponential Growth151

5.6 The Mathematics of Exponential Growth152

5.7 The Microbial Growth Cycle153

5.8 Continuous Culture：The Chemostat154

Ⅲ Measuring Microbial Growth156

5.9 Microscopic Counts156

5.10 Viable Counts157

5.11 Turbidimetric Methods159

Ⅳ Temperature and Microbial Growth160

5.12 Effect of Temperature on Growth162

5.13 Microbial Life in the Cold162

5.14 Microbial Life at High Temperatures166

Ⅴ Other Environmental Factors Affecting Growth168

5.15 Acidity and Alkalinity168

5.16 Osmotic Effects169

5.17 Oxygen and Microorganisms171

5.18 Toxic Forms of Oxygen174

Microbial Sidebar161

Microbial Growth in Aquatic Systems：Cyanobacterial Blooms161

UNIT 3 Molecular Biology and Gene Expression178

Chapter 6 Molecular Biology of Bacteria178

Ⅰ DNA Structure and Genetic Information179

6.1 Macromolecules and Genes179

6.2 The Double Helix181

6.3 Supercoiling183

6.4 Chromosomes and Other Genetic Elements184

Ⅱ Chromosomes and Plasmids185

6.5 The Escherichia coli Chromosome185

6.6 Plasmids：General Principles187

6.7 The Biology of Plasmids189

Ⅲ DNA Replication190

6.8 Templates and Enzymes190

6.9 The Replication Fork191

6.10 Bidirectional Replication and the Replisome193

6.11 The Polymerase Chain Reaction （PCR）197

Ⅳ RNA Synthesis：Transcription198

6.12 Overview of Transcription198

6.13 Sigma Factors and Consensus Sequences200

6.14 Termination of Transcription201

6.15 The Unit of Transcription201

Ⅴ Protein Structure and Synthesis202

6.16 Polypeptides，Amino Acids，and the Peptide Bond202

6.17 Translation and the Genetic Code203

6.18 Transfer RNA206

6.19 Steps in Protein Synthesis208

6.20 The Incorporation of Selenocysteine and Pyrrolysine211

6.21 Folding and Secreting Proteins211

Chapter 7 Archaeal and Eukaryotic Molecular Biology219

Ⅰ Molecular Biology of Archaea220

7.1 Chromosomes and DNA Replication in Archaea220

7.2 Transcription and RNA Processing in Archaea221

7.3 Protein Synthesis in Archaea223

7.4 Shared Features of Bacteria and Archaea224

Ⅱ Eukaryotic Molecular Biology225

7.5 Genes and Chromosomes in Eukarya225

7.6 Overview of Eukaryotic Cell Division226

7.7 Replication of Linear DNA227

7.8 RNA Processing228

7.9 Transcription and Translation in Eukarya231

7.10 RNA Interference （RNAi）233

7.11 Regulation by MicroRNA234

Microbial Sidebar231

Inteins and Protein Splicing231

Chapter 8 Regulation of Gene Expression237

Ⅰ Overview of Regulation238

8.1 Major Modes of Regulation238

Ⅱ DNA-Binding Proteins and Regulation of Transcription238

8.2 DNA-Binding Proteins239

8.3 Negative Control of Transcription：Repression and Induction240

8.4 Positive Control of Transcription242

8.5 Global Control and the lac Operon244

8.6 Control of Transcription in Archaea245

Ⅲ Sensing and Signal Transduction246

8.7 Two-Component Regulatory Systems246

8.8 Regulation of Chemotaxis248

8.9 Quorum Sensing249

8.10 The Stringent Response251

8.11 Other Global Control Networks252

Ⅳ Regulation of Development in Model Bacteria253

8.12 Sporulation in Bacillus254

8.13 Caulobacter Differentiation255

Ⅴ RNA-Based Regulation256

8.14 RNA Regulation and Antisense RNA256

8.15 Riboswitches258

8.16 Attenuation259

Microbial Sidebar257

The CRISPR Antiviral Defense System257

UNIT 4 Virology，Genetics，and Genomics264

Chapter 9 Viruses and Virology264

Ⅰ Virus Structure and Growth265

9.1 General Properties of Viruses265

9.2 Nature of the Virion266

9.3 The Virus Host269

9.4 Quantification of Viruses269

Ⅱ Viral Replication271

9.5 General Features of Virus Replication271

9.6 Viral Attachment and Penetration271

9.7 Production of Viral Nucleic Acid and Protein273

Ⅲ Viral Diversity275

9.8 Overview of Bacterial Viruses275

9.9 Virulent Bacteriophages and T4278

9.10 Temperate Bacteriophages，Lambda and P1279

9.11 Overview of Animal Viruses282

9.12 Retroviruses283

Ⅳ Subviral Entities285

9.13 Defective Viruses285

9.14 Viroids285

9.15 Prions286

Microbial Sidebar276

Did Viruses Invent DNA？276

Chapter 10 Genetics of Bacteria and Archaea291

Ⅰ Mutation292

10.1 Mutations and Mutants292

10.2 Molecular Basis of Mutation294

10.3 Mutation Rates296

10.4 Mutagenesis297

10.5 Mutagenesis and Carcinogenesis：The Ames Test300

Ⅱ Gene Transfer301

10.6 Genetic Recombination301

10.7 Transformation303

10.8 Transduction305

10.9 Conjugation：Essential Features307

10.10 The Formation of Hfr Strains and Chromosome Mobilization309

10.11 Complementation312

10.12 Gene Transfer in Archaea313

10.13 Mobile DNA：Transposable Elements314

Chapter 11 Genetic Engineering319

Ⅰ Methods for Manipulating DNA320

11.1 Restriction and Modification Enzymes320

11.2 Nucleic Acid Hybridization322

11.3 Essentials of Molecular Cloning323

11.4 Molecular Methods for Mutagenesis325

11.5 Gene Fusions and Reporter Genes327

Ⅱ Gene Cloning328

11.6 Plasmids as Cloning Vectors328

11.7 Hosts for Cloning Vectors330

11.8 Shuttle Vectors and Expression Vectors332

11.9 Bacteriophage Lambda as a Cloning Vector335

11.10 Vectors for Genomic Cloning and Sequencing336

Microbial Sidebar329

Combinatorial Fluorescence Labeling329

Chapter 12 Microbial Genomics341

Ⅰ Genomes and Genomics342

12.1 Introduction to Genomics342

12.2 Sequencing and Annotating Genomes342

12.3 Bioinformatic Analyses and Gene Distributions346

12.4 The Genomes of Eukaryotic Organelles351

12.5 The Genomes of Eukaryotic Microorganisms353

12.6 Metagenomics355

Ⅱ Genorne Function and Regulation355

12.7 Microarrays and the Transcriptome355

12.8 Proteomics and the Interactome357

12.9 Metabolomics359

Ⅲ The Evolution of Genomes360

12.10 Gene Families，Duplications，and Deletions360

12.11 Horizontal Gene Transfer and Genome Stability361

12.12 Transposons and Insertion Sequences362

12.13 Evolution of Virulence：Pathogenicity Islands363

Microbial Sidebar348

The Synthetic Cell：Assembly Details348

UNIT 5 Metabolic Diversity and Commercial Biocatalyses368

Chapter 13 Phototrophy，Chemolithotrophy，and Major Biosyntheses368

Ⅰ Phototrophy369

13.1 Photosynthesis369

13.2 Chlorophylls and Bacteriochlorophylls370

13.3 Carotenoids and Phycobilins373

13.4 Anoxygenic Photosynthesis374

13.5 Oxygenic Photosynthesis378

Ⅱ Chemolithotrophy381

13.6 The Energetics of Chemolithotrophy381

13.7 Hydrogen Oxidation382

13.8 Oxidation of Reduced Sulfur Compounds382

13.9 Iron Oxidation384

13.10 Nitrification386

13.11 Anammox387

Ⅲ Major Biosyntheses：Autotrophy and Nitrogen Fixation389

13.12 The Calvin Cycle389

13.13 Other Autotrophic Pathways in Phototrophs390

13.14 Nitrogen Fixation and Nitrogenase391

13.15 Genetics and Regulation of Nitrogen Fixation395

Chapter 14 Catabolism of Organic Compounds400

Ⅰ Fermentations401

14.1 Energetic and Redox Considerations401

14.2 Lactic and Mixed-Acid Fermentations402

14.3 Clostridial and Propionic Acid Fermentations405

14.4 Fermentations Lacking Substrate-Level Phosphorylation407

14.5 Syntrophy409

Ⅱ Anaerobic Respiration411

14.6 Anaerobic Respiration：General Principles411

14.7 Nitrate Reduction and Denitrification412

14.8 Sulfate and Sulfur Reduction414

14.9 Acetogenesis416

14.10 Methanogenesis418

14.11 Proton Reduction422

14.12 Other Electron Acceptors423

14.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic Respiration425

Ⅲ Aerobic Chemoorganotrophic Processes428

14.14 Molecular Oxygen as a Reactant and Aerobic Hydrocarbon Oxidation428

14.15 Methylotrophy and Methanotrophy429

14.16 Sugar and Polysaccharide Metabolism431

14.17 Organic Acid Metabolism434

14.18 Lipid Metabolism434

Chapter 15 Commercial Products and Biotechnology439

Ⅰ Putting Microorganisms to Work440

15.1 Industrial Products and the Microorganisms That Make Them440

15.2 Production and Scale440

Ⅱ Drugs，Other Chemicals，and Enzymes443

15.3 Antibiotics：Isolation，Yield，and Purification443

15.4 Industrial Production of Penicillins and Tetracyclines445

15.5 Vitamins and Amino Acids447

15.6 Enzymes as Industrial Products448

Ⅲ Alcoholic Beverages and Biofuels451

15.7 Wine451

15.8 Brewing and Distilling453

15.9 Biofuels455

Ⅳ Products from Genetically Engineered Microorganisms456

15.10 Expressing Mammalian Genes in Bacteria457

15.11 Production of Genetically Engineered Somatotropin459

15.12 Other Mammalian Proteins and Products460

15.13 Genetically Engineered Vaccines461

15.14 Mining Genomes463

15.15 Engineering Metabolic Pathways463

Ⅴ Transgenic Eukaryotes465

15.16 Genetic Engineering of Animals465

15.17 Gene Therapy in Humans467

15.18 Transgenic Plants in Agriculture467

Microbial Sidebar464

Synthetic Biology and Microbial Photography464

UNIT 6 Microbial Evolution and Diversity474

Chapter 16 Microbial Evolution and Systematics474

Ⅰ Early Earth and the Origin and Diversification of Life475

16.1 Formation and Early History of Earth475

16.2 Origin of Cellular Life476

16.3 Microbial Diversification：Consequences for Earth’s Biosphere479

16.4 Endosymbiotic Origins of Eukaryotes480

Ⅱ Microbial Evolution482

16.5 The Evolutionary Process482

16.6 Evolutionary Analyses：Theoretical Aspects483

16.7 Evolutionary Analyses：Analytical Methods485

16.8 Microbial Phylogeny487

16.9 Applications of SSU rRNA Phylogenetic Methods490

Ⅲ Microbial Systematics491

16.10 Phenotypic Analysis：Fatty Acid Methyl Esters （FAME）491

16.11 Genotypic Analysis493

16.12 The Species Concept in Microbiology495

16.13 Classification and Nomenclature498

Chapter 17 Bacteria：The Proteobacteria503

Ⅰ The Phylogeny of Bacteria504

17.1 Phylogenetic Overview of Bacteria504

Ⅱ Phototrophic，Chemolithotrophic，and Methanotrophic Proteobacteria505

17.2 Purple Phototrophic Bacteria506

17.3 The Nitrifying Bacteria509

17.4 Sulfur- and Iron-Oxidizing Bacteria510

17.5 Hydrogen-Oxidizing Bacteria513

17.6 Methanotrophs and Methylotrophs514

Ⅲ Aerobic and Facultatively Aerobic Chemoorganotrophic Proteobacteria516

17.7 Pseudomonas and the Pseudomonads517

17.8 Acetic Acid Bacteria519

17.9 Free-Living Aerobic Nitrogen-Fixing Bacteria519

17.10 Neisseria，Chromobacterium，and Relatives521

17.11 Enteric Bacteria522

17.12 Vibrio，Aliivibrio，and Photobacterium524

17.13 Rickettsias526

Ⅳ Morphologically Unusual Proteobacteria527

17.14 Spirilla528

17.15 Sheathed Proteobacteria：Sphaerotilus and Leptothrix530

17.16 Budding and Prosthecate/Stalked Bacteria531

Ⅴ Delta- and Epsilonproteobacteria535

17.17 Myxobacteria535

17.18 Sulfate- and Sulfur-Reducing Proteobacteria538

17.19 The Epsilonproteobacteria540

Chapter 18 Other Bacteria545

Ⅰ Firmicutes，Mollicutes，and Actinobacteria546

18.1 Nonsporulating Firmicutes546

18.2 Endospore-Forming Firmicutes549

18.3 Mollicutes：The Mycoplasmas553

18.4 Actinobacteria：Coryneform and Propionic Acid Bacteria554

18.5 Actinobacteria：Mycobacterium556

18.6 Filamentous Actinobacteria：Streptomyces and Relatives557

Ⅱ Cyanobacteria and Prochlorophytes560

18.7 Cyanobacteria560

18.8 Prochlorophytes564

Ⅲ Chlamydia565

18.9 The Chlamydia565

Ⅳ The Planctomycetes567

18.10 Planctomyces：A Phylogenetically Unique Stalked Bacterium567

Ⅴ The Verrucomicrobia568

18.11 Verrucomicrobium and Prosthecobacter568

Ⅵ The Flavobacteria and Acidobacteria569

18.12 Bacteroides and Flavobacterium569

18.13 Acidobacteria569

Ⅶ The Cytophaga Group570

18.14 Cytophaga and Relatives570

Ⅷ Green Sulfur Bacteria571

18.15 Chlorobium and Other Green Sulfur Bacteria571

Ⅸ The Spirochetes573

18.16 Spirochetes573

Ⅹ The Deinococci576

18.17 Deinococcus and Thermus576

Ⅺ The Green Nonsulfur Bacteria：Chloroflexi577

18.18 Chloroflexus and Relatives577

Ⅻ Hyperthermophilic Bacteria578

18.19 Thermotoga and Thermodesulfobacterium578

18.20 Aquifex，Thermocrinis，and Relatives579

ⅩⅢ Nitrospira and Deferribacter580

18.21 Nitrospira and Deferribacter580

Chapter 19 Archaea584

Ⅰ Diversity585

19.1 Phylogenetic and Metabolic Diversity of Archaea585

Ⅱ Euryarchaeota586

19.2 Extremely Halophilic Archaea586

19.3 Methanogenic Archaea590

19.4 Thermoplasmatales593

19.5 Thermococcales and Methanopyrus595

19.6 Archaeoglobales596

19.7 Nanoarchaeum and Aciduliprofundum597

Ⅲ Crenarchaeota598

19.8 Habitats and Energy Metabolism598

19.9 Crenarchaeota from Terrestrial Volcanic Habitats599

19.10 Crenarchaeota from Submarine Volcanic Habitats602

19.11 Crenarchaeota from Nonthermal Habitats and Nitrification in Archaea604

Ⅳ Evolution and Life at High Temperatures605

19.12 An Upper Temperature Limit for Microbial Life605

19.13 Molecular Adaptations to Life at High Temperature606

19.14 Hyperthermophilic Archaea，H2，and Microbial Evolution608

Chapter 20 Eukaryotic Cell Biology and Eukaryotic Microorganisms612

Ⅰ Eukaryotic Cell Structure and Function613

20.1 Eukaryotic Cell Structure and the Nucleus613

20.2 The Mitochondrion and the Hydrogenosome614

20.3 The Chloroplast615

20.4 Endosymbiosis：Relationships of Mitochondria and Chloroplasts to Bacteria616

20.5 Other Organelles and Eukaryotic Cell Structures617

Ⅱ Eukaryotic Microbial Diversity619

20.6 Phylogeny of the Eukarya619

Ⅲ Protists621

20.7 Diplomonads and Parabasalids621

20.8 Euglenozoans622

20.9 Alveolates622

20.10 Stramenopiles624

20.11 Cercozoans and Radiolarians626

20.12 Amoebozoa626

Ⅳ Fungi629

20.13 Fungal Physiology，Structure，and Symbioses629

20.14 Fungal Reproduction and Phylogeny631

20.15 Chytridiomycetes632

20.16 Zygomycetes and Glomeromycetes632

20.17 Ascomycetes633

20.18 Basidiomycetes and the Mushroom Life Cycle635

Ⅴ Red and Green Algae635

20.19 Red Algae636

20.20 Green Algae636

Chapter 21 Viral Diversity641

Ⅰ Viruses of Bacteria and Archaea642

21.1 RNA Bacteriophages642

21.2 Single-Stranded DNA Bacteriophages643

21.3 Double-Stranded DNA Bacteriophages646

21.4 The Transposable Phage Mu648

21.5 Viruses of Archaea650

21.6 Viral Genomes in Nature651

Ⅱ RNA Viruses of Eukaryotes651

21.7 Plant RNA Viruses652

21.8 Positive-Strand RNA Animal Viruses652

21.9 Negative-Strand RNA Animal Viruses655

21.10 Double-Stranded RNA Viruses：Reoviruses657

21.11 Retroviruses and Hepadnaviruses658

Ⅲ DNA Viruses of Eukaryotes661

21.12 Plant DNA Viruses661

21.13 Polyomaviruses：SV40663

21.14 Herpesviruses664

21.15 Pox Viruses665

21.16 Adenoviruses666

Microbial Sidebar662

Mimivirus and Viral Evolution662

UNIT 7 Microbial Ecology670

Chapter 22 Methods in Microbial Ecology670

Ⅰ Culture-Dependent Analyses of Microbial Communities671

22.1 Enrichment671

22.2 Isolation675

Ⅱ Culture-Independent Analyses of Microbial Communities677

22.3 General Staining Methods677

22.4 Fluorescent In Situ Hybridization （FISH）679

22.5 PCR Methods of Microbial Community Analysis680

22.6 Microarrays and Microbial Diversity：Phylochips683

22.7 Environmental Genomics and Related Methods684

Ⅲ Measuring Microbial Activities in Nature686

22.8 Chemical Assays，Radioisotopic Methods，and Microelectrodes686

22.9 Stable Isotopes688

22.10 Linking Specific Genes and Functions to Specific Organisms690

Chapter 23 Major Microbial Habitats and Diversity697

Ⅰ Microbial Ecology698

23.1 General Ecological Concepts698

23.2 Ecosystem Service：Biogeochemistry and Nutrient Cycles699

Ⅱ The Microbial Environment700

23.3 Environments and Microenvironments700

23.4 Surfaces and Biofilms702

23.5 Microbial Mats705

Ⅲ Terrestrial Environments706

23.6 Soils706

23.7 The Subsurface709

Ⅳ Aquatic Environments711

23.8 Freshwaters711

23.9 Coastal and Ocean Waters：Phototrophic Microorganisms713

23.10 Pelagic Bacteria，Archaea，and Viruses715

23.11 The Deep Sea and Deep-Sea Sediments718

23.12 Hydrothermal Vents721

Chapter 24 Nutrient Cycles，Biodegradation，and Bioremediation726

Ⅰ Nutrient Cycles727

24.1 The Carbon Cycle727

24.2 Syntrophy and Methanogenesis729

24.3 The Nitrogen Cycle731

24.4 The Sulfur Cycle733

24.5 The Iron Cycle734

24.6 The Phosphorus，Calcium，and Silica Cycles737

Ⅱ Biodegradation and Bioremediation739

24.7 Microbial Leaching739

24.8 Mercury Transformations741

24.9 Petroleum Biodegradation and Bioremediation742

24.10 Xenobiotics Biodegradation and Bioremediation743

Microbial Sidebar735

Microbially Wired735

Chapter 25 Microbial Symbioses748

Ⅰ Symbioses between Microorganisms749

25.1 Lichens749

25.2 “Chlorochromatium aggregatum”750

Ⅱ Plants as Microbial Habitats751

25.3 The Legume-Root Nodule Symbiosis751

25.4 Agrobacterium and Crown Gall Disease757

25.5 Mycorrhizae758

Ⅲ Mammals as Microbial Habitats760

25.6 The Mammalian Gut760

25.7 The Rumen and Ruminant Animals762

25.8 The Human Microbiome766

Ⅳ Insects as Microbial Habitats769

25.9 Heritable Symbionts of Insects769

25.10 Termites772

Ⅴ Aquatic Invertebrates as Microbial Habitats773

25.11 Hawaiian Bobtail Squid774

25.12 Marine Invertebrates at Hydrothermal Vents and Gas Seeps775

25.13 Leeches777

25.14 Reef-Building Corals778

Microbial Sidebar771

The Multiple Microbial Symbionts of Fungus-Cultivating Ants771

UNIT 8 Antimicrobial Agents and Pathogenicity783

Chapter 26 Microbial Growth Control783

Ⅰ Physical Antimicrobial Control784

26.1 Heat Sterilization784

26.2 Radiation Sterilization787

26.3 Filter Sterilization788

Ⅱ Chemical Antimicrobial Control790

26.4 Chemical Growth Control790

26.5 Chemical Antimicrobial Agents for External Use791

Ⅲ Antimicrobial Agents Used In Vivo795

26.6 Synthetic Antimicrobial Drugs795

26.7 Natural Antimicrobial Drugs：Antibiotics798

26.8 β-Lactam Antibiotics：Penicillins and Cephalosporins799

26.9 Antibiotics from Prokaryotes800

Ⅳ Control of Viruses and Eukaryotic Pathogens802

26.10 Antiviral Drugs802

26.11 Antifungal Drugs804

Ⅴ Antimicrobial Drug Resistance and Drug Discovery806

26.12 Antimicrobial Drug Resistance806

26.13 The Search for New Antimicrobial Drugs810

Microbial Sidebar794

Multi-Drug- and Extensively Drug-Resistant Tuberculosis794

Chapter 27 Microbial Interactions with Humans815

Ⅰ Beneficial Microbial Interactions with Humans816

27.1 Overview of Human-Microbial Interactions816

27.2 Normal Microflora of the Skin818

27.3 Normal Microflora of the Oral Cavity819

27.4 Normal Microflora of the Gastrointestinal Tract821

27.5 Normal Microflora of Other Body Regions825

Ⅱ Microbial Virulence and Pathogenesis826

27.6 Measuring Virulence826

27.7 Entry of the Pathogen into the Host—Adherence827

27.8 Colonization and Infection829

27.9 Invasion830

27.10 Exotoxins832

27.11 Endotoxins835

Ⅲ Host Factors in Infection836

27.12 Host Risk Factors for Infection837

27.13 Innate Resistance to Infection839

Microbial Sidebar824

Bacteriophages and Infectious Diseases824

Microbial Sidebar838

Virulence in Salmonella838

UNIT 9 Immunology844

Chapter 28 Immunity and Host Defense844

Ⅰ Immunity845

28.1 Cells and Organs of the Immune System845

28.2 Innate Immunity848

28.3 Adaptive Immunity849

28.4 Antibodies850

28.5 Inflammation852

Ⅱ Prevention of Infectious Diseases854

28.6 Natural Immunity854

28.7 Artificial Immunity and Immunization855

28.8 New Immunization Strategies857

Ⅲ Immune Diseases858

28.9 Allergy，Hypersensitivity，and Autoimmunity858

28.10 Superantigens：Overactivation of T Cells862

Microbial Sidebar859

The Promise of New Vaccines859

Chapter 29 Immune Mechanisms866

Ⅰ Overview of Immunity867

29.1 Innate Response Mechanisms867

29.2 Adaptive Response Mechanisms870

Ⅱ Antigens and Antigen Presentation871

29.3 Immunogens and Antigens871

29.4 Antigen Presentation to T Cells872

Ⅲ T Lymphocytes and Immunity875

29.5 T-Cytotoxic Cells and Natural Killer Cells875

29.6 T-Helper Cells876

Ⅳ Antibodies and Immunity877

29.7 Antibodies878

29.8 Antibody Production880

29.9 Antibodies，Complement，and Pathogen Destruction883

Chapter 30 Molecular Immunology887

Ⅰ Receptors and Immunity888

30.1 Innate Immunity and Pattern Recognition888

30.2 Adaptive Immunity and the Immunoglobulin Superfamily890

Ⅱ The Major Histocompatibility Complex （MHC）892

30.3 MHC Protein Structure892

30.4 MHC Polymorphism and Antigen Binding894

Ⅲ Antibodies894

30.5 Antibody Proteins and Antigen Binding894

30.6 Antibody Genes and Diversity895

Ⅳ T Cell Receptors897

30.7 T Cell Receptors：Proteins，Genes and Diversity897

Ⅴ Molecular Switches in Immunity899

30.8 Clonal Selection and Tolerance899

30.9 T Cell and B Cell Activation901

30.10 Cytokines and Chemokines902

Microbial Sidebar889

Leucine-Rich Repeats and the Immune Response889

UNIT 10 Diagnosing and Tracking Microbial Diseases906

Chapter 31 Diagnostic Microbiology and Immunology906

Ⅰ Growth-Dependent Diagnostic Methods907

31.1 Isolation of Pathogens from Clinical Specimens907

31.2 Growth-Dependent Identification Methods912

31.3 Antimicrobial Drug Susceptibility Testing916

31.4 Safety in the Microbiology Laboratory916

Ⅱ Immunology and Diagnostic Methods920

31.5 Immunoassays for Infectious Disease920

31.6 Polyclonal and Monoclonal Antibodies922

31.7 In Vitro Antigen-Antibody Reactions：Serology923

31.8 Agglutination925

31.9 Immunofluorescence926

31.10 Enzyme Immunoassay and Radioimmunoassay928

31.11 Immunoblots933

Ⅲ Nucleic Acid-Based Diagnostic Methods934

31.12 Nucleic Acid Hybridization934

31.13 Nucleic Acid Amplification936

Chapter 32 Epidemiology941

Ⅰ Principles of Epidemiology942

32.1 The Science of Epidemiology942

32.2 The Vocabulary of Epidemiology942

32.3 Disease Reservoirs and Epidemics944

32.4 Infectious Disease Transmission947

32.5 The Host Community949

Ⅱ Current Epidemics950

32.6 The HIV/AIDS Pandemic950

32.7 Healthcare-Associated Infections953

Ⅲ Epidemiology and Public Health954

32.8 Public Health Measures for the Control of Disease954

32.9 Global Health Considerations957

32.10 Emerging and Reemerging Infectious Diseases959

32.11 Biological Warfare and Biological Weapons964

32.12 Anthrax as a Biological Weapon967

Microbial Sidebar951

Swine Flu—Pandemic （H1N1） 2009 Influenza951

Microbial Sidebar966

SARS as a Model of Epidemiological Success966

UNIT 11 Human- and Animal-Transmitted Infectious Diseases972

Chapter 33 Person-to-Person Microbial Diseases972

Ⅰ Airborne Transmission of Diseases973

33.1 Airborne Pathogens973

33.2 Streptococcal Diseases974

33.3 Diphtheria and Pertussis977

33.4 Mycobacterium，Tuberculosis，and Hansen’s Disease979

33.5 Neisseria meningitidis，Meningitis，and Meningococcemia982

33.6 Viruses and Respiratory Infections982

33.7 Colds985

33.8 Influenza986

Ⅱ Direct-Contact Transmission of Diseases989

33.9 Staphylococcus989

33.10 Helicobacter pylori and Gastric Ulcers991

33.11 Hepatitis Viruses992

Ⅲ Sexually Transmitted Infections993

33.12 Gonorrhea and Syphilis994

33.13 Chlamydia，Herpes，Trichomoniasis，and Human Papillomavirus997

33.14 Acquired Immunodeficiency Syndrome：AIDS and HIV999

Chapter 34 Vectorborne and Soilborne Microbial Pathogens1009

Ⅰ Animal-Transmitted Pathogens1010

34.1 Rabies Virus1010

34.2 Hantavirus1012

Ⅱ Arthropod-Transmitted Pathogens1014

34.3 Rickettsial Pathogens1014

34.4 Lyme Disease and Borrelia1017

34.5 Malaria and Plasmodium1019

34.6 West Nile Virus1023

34.7 Plague and Yersinia1024

Ⅲ Soilborne Pathogens1026

34.8 Fungal Pathogens1026

34.9 Tetanus and Clostridium tetani1028

Microbial Sidebar1013

Special Pathogens and Viral Hemorrhagic Fevers1013

UNIT 12 Common-Source Infectious Disease1032

Chapter 35 Wastewater Treatment，Water Purification，and Waterborne Microbial Diseases1032

Ⅰ Wastewater Microbiology and Water Purification1033

35.1 Public Health and Water Quality1033

35.2 Wastewater and Sewage Treatment1035

35.3 Drinking Water Purification1038

Ⅱ Waterborne Microbial Diseases1040

35.4 Sources of Waterborne Infection1040

35.5 Cholera1041

35.6 Giardiasis and Cryptosporidiosis1043

35.7 Legionellosis （Legionnaires’ Disease）1045

35.8 Typhoid Fever and Other Waterborne Diseases1046

Chapter 36 Food Preservation and Foodborne Microbial Diseases1050

Ⅰ Food Preservation and Microbial Growth1051

36.1 Microbial Growth and Food Spoilage1051

36.2 Food Preservation1052

36.3 Fermented Foods and Mushrooms1055

Ⅱ Foodborne Disease，Microbial Sampling，and Epidemiology1058

36.4 Foodborne Disease and Microbial Sampling1059

36.5 Foodborne Disease Epidemiology1060

Ⅲ Food Poisoning1061

36.6 Staphylococcal Food Poisoning1061

36.7 Clostridial Food Poisoning1062

Ⅳ Food Infection1064

36.8 Salmonellosis1064

36.9 Pathogenic Escherichia coli1065

36.10 Campylobacter1066

36.11 Listeriosis1067

36.12 Other Foodborne Infectious Diseases1068

Appendix 1 Energy Calculations in Microbial Bioenergetics1073

Appendix 2 Bergey’s Manual of Systematic Bacteriology，Second Edition：List of Genera and Higher-Order Taxa1077

Glossary1087

Photo Credits1105

Index1109