Brock biology of microorganismsPDF电子书下载

About the Authors 3

Preface 5

Acknowledgments 15

UNIT 1 Basic Principles of Microbiology 29

Chapter 1 Microorganisms and Microbiology 29

Ⅰ Introduction to Microbiology 30

1.1 The Science of Microbiology 30

1.2 Microbial Cells 31

1.3 Microorganisms and Their Environments 32

1.4 Evolution and the Extent of Microbial Life 33

1.5 The Impact of Microorganisms on Humans 35

Ⅱ Pathways of Discovery in Microbiology 38

1.6 The Historical Roots of Microbiology：Hooke，van Leeuwenhoek，and Cohn 39

1.7 Pasteur and the Defeat of Spontaneous Generation 40

1.8 Koch，Infectious Disease，and Pure Culture Microbiology 43

1.9 The Rise of Microbial Diversity 46

1.10 The Modern Era of Microbiology 48

Microbial Sidebar 45

Solid Media，Pure Cultures，and the Birth of Microbial Systematics 45

Chapter 2 A Brief Journey to the Microbial World 52

Ⅰ Seeing the Very Small 53

2.1 Some Principles of Light Microscopy 53

2.2 Improving Contrast in Light Microscopy 54

2.3 Imaging Cells in Three Dimensions 57

2.4 Electron Microscopy 58

Ⅱ Cell Structure and Evolutionary History 59

2.5 Elements of Microbial Structure 59

2.6 Arrangement of DNA in Microbial Cells 61

2.7 The Evolutionary Tree of Life 62

Ⅲ Microbial Diversity 64

2.8 Metabolic Diversity 64

2.9 Bacteria 66

2.10 Archaea 69

2.11 Phylogenetic Analyses of Natural Microbial Communities 71

2.12 Microbial Eukarya 71

Chapter 3 Cell Structure and Function in Bacteria and Archaea 75

Ⅰ Cell Shape and Size 76

3.1 Cell Morphology 76

3.2 Cell Size and the Significance of Smallness 77

Ⅱ The Cytoplasmic Membrane and Transport 79

3.3 The Cytoplasmic Membrane 79

3.4 Functions of the Cytoplasmic Membrane 82

3.5 Transport and Transport Systems 83

Ⅲ Cell Walls of Prokaryotes 86

3.6 The Cell Wall of Bacteria：Peptidoglycan 86

3.7 The Outer Membrane 88

3.8 Cell Walls of Archaea 91

Ⅳ Other Cell Surface Structures and Inclusions 92

3.9 Cell Surface Structures 92

3.10 Cell Inclusions 94

3.11 Gas Vesicles 96

3.12 Endospores 97

Ⅴ Microbial Locomotion 101

3.13 Flagella and Motility 101

3.14 Gliding Motility 105

3.15 Microbial Taxes 106

Microbial Sidebar 99

The Mycobacterium tuberculosis Cell Wall：A Complex Architecture of Lipids and Carbohydrates 99

UNIT 2 Metabolism and Growth 113

Chapter 4 Nutrition，Culture，and Metabolism of Microorganisms 113

Ⅰ Nutrition and Culture of Microorganisms 114

4.1 Nutrition and Cell Chemistry 114

4.2 Culture Media 116

4.3 Laboratory Culture 118

Ⅱ Energetics and Enzymes 120

4.4 Bioenergetics 120

4.5 Catalysis and Enzymes 121

Ⅲ Oxidation-Reduction and Energy-Rich Compounds 122

4.6 Electron Donors and Electron Acceptors 122

4.7 Energy-Rich Compounds and Energy Storage 125

Ⅳ Essentials of Catabolism 126

4.8 Glycolysis 126

4.9 Respiration and Electron Carriers 129

4.10 The Proton Motive Force 131

4.11 The Citric Acid Cycle 133

4.12 Catabolic Diversity 134

Ⅴ Essentials of Anabolism 136

4.13 Biosynthesis of Sugars and Polysaccharides 136

4.14 Biosynthesis of Amino Acids and Nucleotides 137

4.15 Biosynthesis of Fatty Acids and Lipids 138

4.16 Regulating the Activity of Biosynthetic Enzymes 139

Microbial Sidebar 127

Yeast Fermentation，the Pasteur Effect，and the Home Brewer 127

Chapter 5 Microbial Growth 145

Ⅰ Bacterial Cell Division 146

5.1 Cell Growth and Binary Fission 146

5.2 Fts Proteins and Cell Division 146

5.3 MreB and Determinants of Cell Morphology 148

5.4 Peptidoglycan Synthesis and Cell Division 149

Ⅱ Population Growth 151

5.5 The Concept of Exponential Growth 151

5.6 The Mathematics of Exponential Growth 152

5.7 The Microbial Growth Cycle 153

5.8 Continuous Culture：The Chemostat 154

Ⅲ Measuring Microbial Growth 156

5.9 Microscopic Counts 156

5.10 Viable Counts 157

5.11 Turbidimetric Methods 159

Ⅳ Temperature and Microbial Growth 160

5.12 Effect of Temperature on Growth 162

5.13 Microbial Life in the Cold 162

5.14 Microbial Life at High Temperatures 166

Ⅴ Other Environmental Factors Affecting Growth 168

5.15 Acidity and Alkalinity 168

5.16 Osmotic Effects 169

5.17 Oxygen and Microorganisms 171

5.18 Toxic Forms of Oxygen 174

Microbial Sidebar 161

Microbial Growth in Aquatic Systems：Cyanobacterial Blooms 161

UNIT 3 Molecular Biology and Gene Expression 178

Chapter 6 Molecular Biology of Bacteria 178

Ⅰ DNA Structure and Genetic Information 179

6.1 Macromolecules and Genes 179

6.2 The Double Helix 181

6.3 Supercoiling 183

6.4 Chromosomes and Other Genetic Elements 184

Ⅱ Chromosomes and Plasmids 185

6.5 The Escherichia coli Chromosome 185

6.6 Plasmids：General Principles 187

6.7 The Biology of Plasmids 189

Ⅲ DNA Replication 190

6.8 Templates and Enzymes 190

6.9 The Replication Fork 191

6.10 Bidirectional Replication and the Replisome 193

6.11 The Polymerase Chain Reaction （PCR） 197

Ⅳ RNA Synthesis：Transcription 198

6.12 Overview of Transcription 198

6.13 Sigma Factors and Consensus Sequences 200

6.14 Termination of Transcription 201

6.15 The Unit of Transcription 201

Ⅴ Protein Structure and Synthesis 202

6.16 Polypeptides，Amino Acids，and the Peptide Bond 202

6.17 Translation and the Genetic Code 203

6.18 Transfer RNA 206

6.19 Steps in Protein Synthesis 208

6.20 The Incorporation of Selenocysteine and Pyrrolysine 211

6.21 Folding and Secreting Proteins 211

Chapter 7 Archaeal and Eukaryotic Molecular Biology 219

Ⅰ Molecular Biology of Archaea 220

7.1 Chromosomes and DNA Replication in Archaea 220

7.2 Transcription and RNA Processing in Archaea 221

7.3 Protein Synthesis in Archaea 223

7.4 Shared Features of Bacteria and Archaea 224

Ⅱ Eukaryotic Molecular Biology 225

7.5 Genes and Chromosomes in Eukarya 225

7.6 Overview of Eukaryotic Cell Division 226

7.7 Replication of Linear DNA 227

7.8 RNA Processing 228

7.9 Transcription and Translation in Eukarya 231

7.10 RNA Interference （RNAi） 233

7.11 Regulation by MicroRNA 234

Microbial Sidebar 231

Inteins and Protein Splicing 231

Chapter 8 Regulation of Gene Expression 237

Ⅰ Overview of Regulation 238

8.1 Major Modes of Regulation 238

Ⅱ DNA-Binding Proteins and Regulation of Transcription 238

8.2 DNA-Binding Proteins 239

8.3 Negative Control of Transcription：Repression and Induction 240

8.4 Positive Control of Transcription 242

8.5 Global Control and the lac Operon 244

8.6 Control of Transcription in Archaea 245

Ⅲ Sensing and Signal Transduction 246

8.7 Two-Component Regulatory Systems 246

8.8 Regulation of Chemotaxis 248

8.9 Quorum Sensing 249

8.10 The Stringent Response 251

8.11 Other Global Control Networks 252

Ⅳ Regulation of Development in Model Bacteria 253

8.12 Sporulation in Bacillus 254

8.13 Caulobacter Differentiation 255

Ⅴ RNA-Based Regulation 256

8.14 RNA Regulation and Antisense RNA 256

8.15 Riboswitches 258

8.16 Attenuation 259

Microbial Sidebar 257

The CRISPR Antiviral Defense System 257

UNIT 4 Virology，Genetics，and Genomics 264

Chapter 9 Viruses and Virology 264

Ⅰ Virus Structure and Growth 265

9.1 General Properties of Viruses 265

9.2 Nature of the Virion 266

9.3 The Virus Host 269

9.4 Quantification of Viruses 269

Ⅱ Viral Replication 271

9.5 General Features of Virus Replication 271

9.6 Viral Attachment and Penetration 271

9.7 Production of Viral Nucleic Acid and Protein 273

Ⅲ Viral Diversity 275

9.8 Overview of Bacterial Viruses 275

9.9 Virulent Bacteriophages and T4 278

9.10 Temperate Bacteriophages，Lambda and P1 279

9.11 Overview of Animal Viruses 282

9.12 Retroviruses 283

Ⅳ Subviral Entities 285

9.13 Defective Viruses 285

9.14 Viroids 285

9.15 Prions 286

Microbial Sidebar 276

Did Viruses Invent DNA？ 276

Chapter 10 Genetics of Bacteria and Archaea 291

Ⅰ Mutation 292

10.1 Mutations and Mutants 292

10.2 Molecular Basis of Mutation 294

10.3 Mutation Rates 296

10.4 Mutagenesis 297

10.5 Mutagenesis and Carcinogenesis：The Ames Test 300

Ⅱ Gene Transfer 301

10.6 Genetic Recombination 301

10.7 Transformation 303

10.8 Transduction 305

10.9 Conjugation：Essential Features 307

10.10 The Formation of Hfr Strains and Chromosome Mobilization 309

10.11 Complementation 312

10.12 Gene Transfer in Archaea 313

10.13 Mobile DNA：Transposable Elements 314

Chapter 11 Genetic Engineering 319

Ⅰ Methods for Manipulating DNA 320

11.1 Restriction and Modification Enzymes 320

11.2 Nucleic Acid Hybridization 322

11.3 Essentials of Molecular Cloning 323

11.4 Molecular Methods for Mutagenesis 325

11.5 Gene Fusions and Reporter Genes 327

Ⅱ Gene Cloning 328

11.6 Plasmids as Cloning Vectors 328

11.7 Hosts for Cloning Vectors 330

11.8 Shuttle Vectors and Expression Vectors 332

11.9 Bacteriophage Lambda as a Cloning Vector 335

11.10 Vectors for Genomic Cloning and Sequencing 336

Microbial Sidebar 329

Combinatorial Fluorescence Labeling 329

Chapter 12 Microbial Genomics 341

Ⅰ Genomes and Genomics 342

12.1 Introduction to Genomics 342

12.2 Sequencing and Annotating Genomes 342

12.3 Bioinformatic Analyses and Gene Distributions 346

12.4 The Genomes of Eukaryotic Organelles 351

12.5 The Genomes of Eukaryotic Microorganisms 353

12.6 Metagenomics 355

Ⅱ Genorne Function and Regulation 355

12.7 Microarrays and the Transcriptome 355

12.8 Proteomics and the Interactome 357

12.9 Metabolomics 359

Ⅲ The Evolution of Genomes 360

12.10 Gene Families，Duplications，and Deletions 360

12.11 Horizontal Gene Transfer and Genome Stability 361

12.12 Transposons and Insertion Sequences 362

12.13 Evolution of Virulence：Pathogenicity Islands 363

Microbial Sidebar 348

The Synthetic Cell：Assembly Details 348

UNIT 5 Metabolic Diversity and Commercial Biocatalyses 368

Chapter 13 Phototrophy，Chemolithotrophy，and Major Biosyntheses 368

Ⅰ Phototrophy 369

13.1 Photosynthesis 369

13.2 Chlorophylls and Bacteriochlorophylls 370

13.3 Carotenoids and Phycobilins 373

13.4 Anoxygenic Photosynthesis 374

13.5 Oxygenic Photosynthesis 378

Ⅱ Chemolithotrophy 381

13.6 The Energetics of Chemolithotrophy 381

13.7 Hydrogen Oxidation 382

13.8 Oxidation of Reduced Sulfur Compounds 382

13.9 Iron Oxidation 384

13.10 Nitrification 386

13.11 Anammox 387

Ⅲ Major Biosyntheses：Autotrophy and Nitrogen Fixation 389

13.12 The Calvin Cycle 389

13.13 Other Autotrophic Pathways in Phototrophs 390

13.14 Nitrogen Fixation and Nitrogenase 391

13.15 Genetics and Regulation of Nitrogen Fixation 395

Chapter 14 Catabolism of Organic Compounds 400

Ⅰ Fermentations 401

14.1 Energetic and Redox Considerations 401

14.2 Lactic and Mixed-Acid Fermentations 402

14.3 Clostridial and Propionic Acid Fermentations 405

14.4 Fermentations Lacking Substrate-Level Phosphorylation 407

14.5 Syntrophy 409

Ⅱ Anaerobic Respiration 411

14.6 Anaerobic Respiration：General Principles 411

14.7 Nitrate Reduction and Denitrification 412

14.8 Sulfate and Sulfur Reduction 414

14.9 Acetogenesis 416

14.10 Methanogenesis 418

14.11 Proton Reduction 422

14.12 Other Electron Acceptors 423

14.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic Respiration 425

Ⅲ Aerobic Chemoorganotrophic Processes 428

14.14 Molecular Oxygen as a Reactant and Aerobic Hydrocarbon Oxidation 428

14.15 Methylotrophy and Methanotrophy 429

14.16 Sugar and Polysaccharide Metabolism 431

14.17 Organic Acid Metabolism 434

14.18 Lipid Metabolism 434

Chapter 15 Commercial Products and Biotechnology 439

Ⅰ Putting Microorganisms to Work 440

15.1 Industrial Products and the Microorganisms That Make Them 440

15.2 Production and Scale 440

Ⅱ Drugs，Other Chemicals，and Enzymes 443

15.3 Antibiotics：Isolation，Yield，and Purification 443

15.4 Industrial Production of Penicillins and Tetracyclines 445

15.5 Vitamins and Amino Acids 447

15.6 Enzymes as Industrial Products 448

Ⅲ Alcoholic Beverages and Biofuels 451

15.7 Wine 451

15.8 Brewing and Distilling 453

15.9 Biofuels 455

Ⅳ Products from Genetically Engineered Microorganisms 456

15.10 Expressing Mammalian Genes in Bacteria 457

15.11 Production of Genetically Engineered Somatotropin 459

15.12 Other Mammalian Proteins and Products 460

15.13 Genetically Engineered Vaccines 461

15.14 Mining Genomes 463

15.15 Engineering Metabolic Pathways 463

Ⅴ Transgenic Eukaryotes 465

15.16 Genetic Engineering of Animals 465

15.17 Gene Therapy in Humans 467

15.18 Transgenic Plants in Agriculture 467

Microbial Sidebar 464

Synthetic Biology and Microbial Photography 464

UNIT 6 Microbial Evolution and Diversity 474

Chapter 16 Microbial Evolution and Systematics 474

Ⅰ Early Earth and the Origin and Diversification of Life 475

16.1 Formation and Early History of Earth 475

16.2 Origin of Cellular Life 476

16.3 Microbial Diversification：Consequences for Earth’s Biosphere 479

16.4 Endosymbiotic Origins of Eukaryotes 480

Ⅱ Microbial Evolution 482

16.5 The Evolutionary Process 482

16.6 Evolutionary Analyses：Theoretical Aspects 483

16.7 Evolutionary Analyses：Analytical Methods 485

16.8 Microbial Phylogeny 487

16.9 Applications of SSU rRNA Phylogenetic Methods 490

Ⅲ Microbial Systematics 491

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

16.11 Genotypic Analysis 493

16.12 The Species Concept in Microbiology 495

16.13 Classification and Nomenclature 498

Chapter 17 Bacteria：The Proteobacteria 503

Ⅰ The Phylogeny of Bacteria 504

17.1 Phylogenetic Overview of Bacteria 504

Ⅱ Phototrophic，Chemolithotrophic，and Methanotrophic Proteobacteria 505

17.2 Purple Phototrophic Bacteria 506

17.3 The Nitrifying Bacteria 509

17.4 Sulfur- and Iron-Oxidizing Bacteria 510

17.5 Hydrogen-Oxidizing Bacteria 513

17.6 Methanotrophs and Methylotrophs 514

Ⅲ Aerobic and Facultatively Aerobic Chemoorganotrophic Proteobacteria 516

17.7 Pseudomonas and the Pseudomonads 517

17.8 Acetic Acid Bacteria 519

17.9 Free-Living Aerobic Nitrogen-Fixing Bacteria 519

17.10 Neisseria，Chromobacterium，and Relatives 521

17.11 Enteric Bacteria 522

17.12 Vibrio，Aliivibrio，and Photobacterium 524

17.13 Rickettsias 526

Ⅳ Morphologically Unusual Proteobacteria 527

17.14 Spirilla 528

17.15 Sheathed Proteobacteria：Sphaerotilus and Leptothrix 530

17.16 Budding and Prosthecate/Stalked Bacteria 531

Ⅴ Delta- and Epsilonproteobacteria 535

17.17 Myxobacteria 535

17.18 Sulfate- and Sulfur-Reducing Proteobacteria 538

17.19 The Epsilonproteobacteria 540

Chapter 18 Other Bacteria 545

Ⅰ Firmicutes，Mollicutes，and Actinobacteria 546

18.1 Nonsporulating Firmicutes 546

18.2 Endospore-Forming Firmicutes 549

18.3 Mollicutes：The Mycoplasmas 553

18.4 Actinobacteria：Coryneform and Propionic Acid Bacteria 554

18.5 Actinobacteria：Mycobacterium 556

18.6 Filamentous Actinobacteria：Streptomyces and Relatives 557

Ⅱ Cyanobacteria and Prochlorophytes 560

18.7 Cyanobacteria 560

18.8 Prochlorophytes 564

Ⅲ Chlamydia 565

18.9 The Chlamydia 565

Ⅳ The Planctomycetes 567

18.10 Planctomyces：A Phylogenetically Unique Stalked Bacterium 567

Ⅴ The Verrucomicrobia 568

18.11 Verrucomicrobium and Prosthecobacter 568

Ⅵ The Flavobacteria and Acidobacteria 569

18.12 Bacteroides and Flavobacterium 569

18.13 Acidobacteria 569

Ⅶ The Cytophaga Group 570

18.14 Cytophaga and Relatives 570

Ⅷ Green Sulfur Bacteria 571

18.15 Chlorobium and Other Green Sulfur Bacteria 571

Ⅸ The Spirochetes 573

18.16 Spirochetes 573

Ⅹ The Deinococci 576

18.17 Deinococcus and Thermus 576

Ⅺ The Green Nonsulfur Bacteria：Chloroflexi 577

18.18 Chloroflexus and Relatives 577

Ⅻ Hyperthermophilic Bacteria 578

18.19 Thermotoga and Thermodesulfobacterium 578

18.20 Aquifex，Thermocrinis，and Relatives 579

ⅩⅢ Nitrospira and Deferribacter 580

18.21 Nitrospira and Deferribacter 580

Chapter 19 Archaea 584

Ⅰ Diversity 585

19.1 Phylogenetic and Metabolic Diversity of Archaea 585

Ⅱ Euryarchaeota 586

19.2 Extremely Halophilic Archaea 586

19.3 Methanogenic Archaea 590

19.4 Thermoplasmatales 593

19.5 Thermococcales and Methanopyrus 595

19.6 Archaeoglobales 596

19.7 Nanoarchaeum and Aciduliprofundum 597

Ⅲ Crenarchaeota 598

19.8 Habitats and Energy Metabolism 598

19.9 Crenarchaeota from Terrestrial Volcanic Habitats 599

19.10 Crenarchaeota from Submarine Volcanic Habitats 602

19.11 Crenarchaeota from Nonthermal Habitats and Nitrification in Archaea 604

Ⅳ Evolution and Life at High Temperatures 605

19.12 An Upper Temperature Limit for Microbial Life 605

19.13 Molecular Adaptations to Life at High Temperature 606

19.14 Hyperthermophilic Archaea，H2，and Microbial Evolution 608

Chapter 20 Eukaryotic Cell Biology and Eukaryotic Microorganisms 612

Ⅰ Eukaryotic Cell Structure and Function 613

20.1 Eukaryotic Cell Structure and the Nucleus 613

20.2 The Mitochondrion and the Hydrogenosome 614

20.3 The Chloroplast 615

20.4 Endosymbiosis：Relationships of Mitochondria and Chloroplasts to Bacteria 616

20.5 Other Organelles and Eukaryotic Cell Structures 617

Ⅱ Eukaryotic Microbial Diversity 619

20.6 Phylogeny of the Eukarya 619

Ⅲ Protists 621

20.7 Diplomonads and Parabasalids 621

20.8 Euglenozoans 622

20.9 Alveolates 622

20.10 Stramenopiles 624

20.11 Cercozoans and Radiolarians 626

20.12 Amoebozoa 626

Ⅳ Fungi 629

20.13 Fungal Physiology，Structure，and Symbioses 629

20.14 Fungal Reproduction and Phylogeny 631

20.15 Chytridiomycetes 632

20.16 Zygomycetes and Glomeromycetes 632

20.17 Ascomycetes 633

20.18 Basidiomycetes and the Mushroom Life Cycle 635

Ⅴ Red and Green Algae 635

20.19 Red Algae 636

20.20 Green Algae 636

Chapter 21 Viral Diversity 641

Ⅰ Viruses of Bacteria and Archaea 642

21.1 RNA Bacteriophages 642

21.2 Single-Stranded DNA Bacteriophages 643

21.3 Double-Stranded DNA Bacteriophages 646

21.4 The Transposable Phage Mu 648

21.5 Viruses of Archaea 650

21.6 Viral Genomes in Nature 651

Ⅱ RNA Viruses of Eukaryotes 651

21.7 Plant RNA Viruses 652

21.8 Positive-Strand RNA Animal Viruses 652

21.9 Negative-Strand RNA Animal Viruses 655

21.10 Double-Stranded RNA Viruses：Reoviruses 657

21.11 Retroviruses and Hepadnaviruses 658

Ⅲ DNA Viruses of Eukaryotes 661

21.12 Plant DNA Viruses 661

21.13 Polyomaviruses：SV40 663

21.14 Herpesviruses 664

21.15 Pox Viruses 665

21.16 Adenoviruses 666

Microbial Sidebar 662

Mimivirus and Viral Evolution 662

UNIT 7 Microbial Ecology 670

Chapter 22 Methods in Microbial Ecology 670

Ⅰ Culture-Dependent Analyses of Microbial Communities 671

22.1 Enrichment 671

22.2 Isolation 675

Ⅱ Culture-Independent Analyses of Microbial Communities 677

22.3 General Staining Methods 677

22.4 Fluorescent In Situ Hybridization （FISH） 679

22.5 PCR Methods of Microbial Community Analysis 680

22.6 Microarrays and Microbial Diversity：Phylochips 683

22.7 Environmental Genomics and Related Methods 684

Ⅲ Measuring Microbial Activities in Nature 686

22.8 Chemical Assays，Radioisotopic Methods，and Microelectrodes 686

22.9 Stable Isotopes 688

22.10 Linking Specific Genes and Functions to Specific Organisms 690

Chapter 23 Major Microbial Habitats and Diversity 697

Ⅰ Microbial Ecology 698

23.1 General Ecological Concepts 698

23.2 Ecosystem Service：Biogeochemistry and Nutrient Cycles 699

Ⅱ The Microbial Environment 700

23.3 Environments and Microenvironments 700

23.4 Surfaces and Biofilms 702

23.5 Microbial Mats 705

Ⅲ Terrestrial Environments 706

23.6 Soils 706

23.7 The Subsurface 709

Ⅳ Aquatic Environments 711

23.8 Freshwaters 711

23.9 Coastal and Ocean Waters：Phototrophic Microorganisms 713

23.10 Pelagic Bacteria，Archaea，and Viruses 715

23.11 The Deep Sea and Deep-Sea Sediments 718

23.12 Hydrothermal Vents 721

Chapter 24 Nutrient Cycles，Biodegradation，and Bioremediation 726

Ⅰ Nutrient Cycles 727

24.1 The Carbon Cycle 727

24.2 Syntrophy and Methanogenesis 729

24.3 The Nitrogen Cycle 731

24.4 The Sulfur Cycle 733

24.5 The Iron Cycle 734

24.6 The Phosphorus，Calcium，and Silica Cycles 737

Ⅱ Biodegradation and Bioremediation 739

24.7 Microbial Leaching 739

24.8 Mercury Transformations 741

24.9 Petroleum Biodegradation and Bioremediation 742

24.10 Xenobiotics Biodegradation and Bioremediation 743

Microbial Sidebar 735

Microbially Wired 735

Chapter 25 Microbial Symbioses 748

Ⅰ Symbioses between Microorganisms 749

25.1 Lichens 749

25.2 “Chlorochromatium aggregatum” 750

Ⅱ Plants as Microbial Habitats 751

25.3 The Legume-Root Nodule Symbiosis 751

25.4 Agrobacterium and Crown Gall Disease 757

25.5 Mycorrhizae 758

Ⅲ Mammals as Microbial Habitats 760

25.6 The Mammalian Gut 760

25.7 The Rumen and Ruminant Animals 762

25.8 The Human Microbiome 766

Ⅳ Insects as Microbial Habitats 769

25.9 Heritable Symbionts of Insects 769

25.10 Termites 772

Ⅴ Aquatic Invertebrates as Microbial Habitats 773

25.11 Hawaiian Bobtail Squid 774

25.12 Marine Invertebrates at Hydrothermal Vents and Gas Seeps 775

25.13 Leeches 777

25.14 Reef-Building Corals 778

Microbial Sidebar 771

The Multiple Microbial Symbionts of Fungus-Cultivating Ants 771

UNIT 8 Antimicrobial Agents and Pathogenicity 783

Chapter 26 Microbial Growth Control 783

Ⅰ Physical Antimicrobial Control 784

26.1 Heat Sterilization 784

26.2 Radiation Sterilization 787

26.3 Filter Sterilization 788

Ⅱ Chemical Antimicrobial Control 790

26.4 Chemical Growth Control 790

26.5 Chemical Antimicrobial Agents for External Use 791

Ⅲ Antimicrobial Agents Used In Vivo 795

26.6 Synthetic Antimicrobial Drugs 795

26.7 Natural Antimicrobial Drugs：Antibiotics 798

26.8 β-Lactam Antibiotics：Penicillins and Cephalosporins 799

26.9 Antibiotics from Prokaryotes 800

Ⅳ Control of Viruses and Eukaryotic Pathogens 802

26.10 Antiviral Drugs 802

26.11 Antifungal Drugs 804

Ⅴ Antimicrobial Drug Resistance and Drug Discovery 806

26.12 Antimicrobial Drug Resistance 806

26.13 The Search for New Antimicrobial Drugs 810

Microbial Sidebar 794

Multi-Drug- and Extensively Drug-Resistant Tuberculosis 794

Chapter 27 Microbial Interactions with Humans 815

Ⅰ Beneficial Microbial Interactions with Humans 816

27.1 Overview of Human-Microbial Interactions 816

27.2 Normal Microflora of the Skin 818

27.3 Normal Microflora of the Oral Cavity 819

27.4 Normal Microflora of the Gastrointestinal Tract 821

27.5 Normal Microflora of Other Body Regions 825

Ⅱ Microbial Virulence and Pathogenesis 826

27.6 Measuring Virulence 826

27.7 Entry of the Pathogen into the Host—Adherence 827

27.8 Colonization and Infection 829

27.9 Invasion 830

27.10 Exotoxins 832

27.11 Endotoxins 835

Ⅲ Host Factors in Infection 836

27.12 Host Risk Factors for Infection 837

27.13 Innate Resistance to Infection 839

Microbial Sidebar 824

Bacteriophages and Infectious Diseases 824

Microbial Sidebar 838

Virulence in Salmonella 838

UNIT 9 Immunology 844

Chapter 28 Immunity and Host Defense 844

Ⅰ Immunity 845

28.1 Cells and Organs of the Immune System 845

28.2 Innate Immunity 848

28.3 Adaptive Immunity 849

28.4 Antibodies 850

28.5 Inflammation 852

Ⅱ Prevention of Infectious Diseases 854

28.6 Natural Immunity 854

28.7 Artificial Immunity and Immunization 855

28.8 New Immunization Strategies 857

Ⅲ Immune Diseases 858

28.9 Allergy，Hypersensitivity，and Autoimmunity 858

28.10 Superantigens：Overactivation of T Cells 862

Microbial Sidebar 859

The Promise of New Vaccines 859

Chapter 29 Immune Mechanisms 866

Ⅰ Overview of Immunity 867

29.1 Innate Response Mechanisms 867

29.2 Adaptive Response Mechanisms 870

Ⅱ Antigens and Antigen Presentation 871

29.3 Immunogens and Antigens 871

29.4 Antigen Presentation to T Cells 872

Ⅲ T Lymphocytes and Immunity 875

29.5 T-Cytotoxic Cells and Natural Killer Cells 875

29.6 T-Helper Cells 876

Ⅳ Antibodies and Immunity 877

29.7 Antibodies 878

29.8 Antibody Production 880

29.9 Antibodies，Complement，and Pathogen Destruction 883

Chapter 30 Molecular Immunology 887

Ⅰ Receptors and Immunity 888

30.1 Innate Immunity and Pattern Recognition 888

30.2 Adaptive Immunity and the Immunoglobulin Superfamily 890

Ⅱ The Major Histocompatibility Complex （MHC） 892

30.3 MHC Protein Structure 892

30.4 MHC Polymorphism and Antigen Binding 894

Ⅲ Antibodies 894

30.5 Antibody Proteins and Antigen Binding 894

30.6 Antibody Genes and Diversity 895

Ⅳ T Cell Receptors 897

30.7 T Cell Receptors：Proteins，Genes and Diversity 897

Ⅴ Molecular Switches in Immunity 899

30.8 Clonal Selection and Tolerance 899

30.9 T Cell and B Cell Activation 901

30.10 Cytokines and Chemokines 902

Microbial Sidebar 889

Leucine-Rich Repeats and the Immune Response 889

UNIT 10 Diagnosing and Tracking Microbial Diseases 906

Chapter 31 Diagnostic Microbiology and Immunology 906

Ⅰ Growth-Dependent Diagnostic Methods 907

31.1 Isolation of Pathogens from Clinical Specimens 907

31.2 Growth-Dependent Identification Methods 912

31.3 Antimicrobial Drug Susceptibility Testing 916

31.4 Safety in the Microbiology Laboratory 916

Ⅱ Immunology and Diagnostic Methods 920

31.5 Immunoassays for Infectious Disease 920

31.6 Polyclonal and Monoclonal Antibodies 922

31.7 In Vitro Antigen-Antibody Reactions：Serology 923

31.8 Agglutination 925

31.9 Immunofluorescence 926

31.10 Enzyme Immunoassay and Radioimmunoassay 928

31.11 Immunoblots 933

Ⅲ Nucleic Acid-Based Diagnostic Methods 934

31.12 Nucleic Acid Hybridization 934

31.13 Nucleic Acid Amplification 936

Chapter 32 Epidemiology 941

Ⅰ Principles of Epidemiology 942

32.1 The Science of Epidemiology 942

32.2 The Vocabulary of Epidemiology 942

32.3 Disease Reservoirs and Epidemics 944

32.4 Infectious Disease Transmission 947

32.5 The Host Community 949

Ⅱ Current Epidemics 950

32.6 The HIV/AIDS Pandemic 950

32.7 Healthcare-Associated Infections 953

Ⅲ Epidemiology and Public Health 954

32.8 Public Health Measures for the Control of Disease 954

32.9 Global Health Considerations 957

32.10 Emerging and Reemerging Infectious Diseases 959

32.11 Biological Warfare and Biological Weapons 964

32.12 Anthrax as a Biological Weapon 967

Microbial Sidebar 951

Swine Flu—Pandemic （H1N1） 2009 Influenza 951

Microbial Sidebar 966

SARS as a Model of Epidemiological Success 966

UNIT 11 Human- and Animal-Transmitted Infectious Diseases 972

Chapter 33 Person-to-Person Microbial Diseases 972

Ⅰ Airborne Transmission of Diseases 973

33.1 Airborne Pathogens 973

33.2 Streptococcal Diseases 974

33.3 Diphtheria and Pertussis 977

33.4 Mycobacterium，Tuberculosis，and Hansen’s Disease 979

33.5 Neisseria meningitidis，Meningitis，and Meningococcemia 982

33.6 Viruses and Respiratory Infections 982

33.7 Colds 985

33.8 Influenza 986

Ⅱ Direct-Contact Transmission of Diseases 989

33.9 Staphylococcus 989

33.10 Helicobacter pylori and Gastric Ulcers 991

33.11 Hepatitis Viruses 992

Ⅲ Sexually Transmitted Infections 993

33.12 Gonorrhea and Syphilis 994

33.13 Chlamydia，Herpes，Trichomoniasis，and Human Papillomavirus 997

33.14 Acquired Immunodeficiency Syndrome：AIDS and HIV 999

Chapter 34 Vectorborne and Soilborne Microbial Pathogens 1009

Ⅰ Animal-Transmitted Pathogens 1010

34.1 Rabies Virus 1010

34.2 Hantavirus 1012

Ⅱ Arthropod-Transmitted Pathogens 1014

34.3 Rickettsial Pathogens 1014

34.4 Lyme Disease and Borrelia 1017

34.5 Malaria and Plasmodium 1019

34.6 West Nile Virus 1023

34.7 Plague and Yersinia 1024

Ⅲ Soilborne Pathogens 1026

34.8 Fungal Pathogens 1026

34.9 Tetanus and Clostridium tetani 1028

Microbial Sidebar 1013

Special Pathogens and Viral Hemorrhagic Fevers 1013

UNIT 12 Common-Source Infectious Disease 1032

Chapter 35 Wastewater Treatment，Water Purification，and Waterborne Microbial Diseases 1032

Ⅰ Wastewater Microbiology and Water Purification 1033

35.1 Public Health and Water Quality 1033

35.2 Wastewater and Sewage Treatment 1035

35.3 Drinking Water Purification 1038

Ⅱ Waterborne Microbial Diseases 1040

35.4 Sources of Waterborne Infection 1040

35.5 Cholera 1041

35.6 Giardiasis and Cryptosporidiosis 1043

35.7 Legionellosis （Legionnaires’ Disease） 1045

35.8 Typhoid Fever and Other Waterborne Diseases 1046

Chapter 36 Food Preservation and Foodborne Microbial Diseases 1050

Ⅰ Food Preservation and Microbial Growth 1051

36.1 Microbial Growth and Food Spoilage 1051

36.2 Food Preservation 1052

36.3 Fermented Foods and Mushrooms 1055

Ⅱ Foodborne Disease，Microbial Sampling，and Epidemiology 1058

36.4 Foodborne Disease and Microbial Sampling 1059

36.5 Foodborne Disease Epidemiology 1060

Ⅲ Food Poisoning 1061

36.6 Staphylococcal Food Poisoning 1061

36.7 Clostridial Food Poisoning 1062

Ⅳ Food Infection 1064

36.8 Salmonellosis 1064

36.9 Pathogenic Escherichia coli 1065

36.10 Campylobacter 1066

36.11 Listeriosis 1067

36.12 Other Foodborne Infectious Diseases 1068

Appendix 1 Energy Calculations in Microbial Bioenergetics 1073

Appendix 2 Bergey’s Manual of Systematic Bacteriology，Second Edition：List of Genera and Higher-Order Taxa 1077

Glossary 1087

Photo Credits 1105

Index 1109