Brock Biology of Microorganisms, 16th Edition PDF by Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, and David A. Stahl

By

Brock Biology of Microorganisms, Sixteenth Edition

By Michael t. Madigan, Kelly s. Bender, Daniel h. Buckley, W. Matthew sattley, and David a. Stahl

Brock Biology of Microorganisms 17th edition

Contents

About the Authors 11

Preface 15

Acknowledgments 21

UNIT 1 The Foundations of Microbiology

1 The Microbial World 37

MICROBIOLOGYNOW Microbiology in Motion 37

I • Exploring the Microbial World 38

1.1 Microorganisms, Tiny Titans

of the Earth 38

1.2 Structure and Activities of

Microbial Cells 39

1.3 Cell Size and Morphology 41

1.4 An Introduction to Microbial Life 46

1.5 Microorganisms and the Biosphere 48

1.6 The Impact of Microorganisms on

Human Society 49

II • Microscopy and the Origins

of Microbiology 54

1.7 Light Microscopy and the Discovery

of Microorganisms 54

1.8 Improving Contrast in Light

Microscopy 56

1.9 Imaging Cells in Three Dimensions 58

1.10 Probing Cell Structure: Electron Microscopy 59

III • Microbial Cultivation Expands the Horizon

of Microbiology 61

1.11 Pasteur and Spontaneous

Generation 61

1.12 Koch, Infectious Diseases,

and Pure Cultures 63

1.13 Discovery of Microbial Diversity 65

IV • Molecular Biology and the Unity

and Diversity of Life 67

1.14 Molecular Basis of Life 67

1.15 Woese and the Tree of Life 68

Explore the Microbial World

Tiny Cells 45

2 Microbial Cell Structure

and Function 74

MICROBIOLOGYNOW Exploring the Microbial Cell 74

v • The Cell Envelope 75

2.1 The Cytoplasmic Membrane 75

2.2 Transporting Nutrients into the Cell 78

2.3 The Cell Wall 80

2.4 LPS: The Outer Membrane 83

2.5 Diversity of Cell Envelope Structure 85

II • Cell Surface Structures and

Inclusions 87

2.6 Cell Surface Structures 87

2.7 Cell Inclusions 89

2.8 Endospores 91

III • Cell Locomotion 94

2.9 Flagella, Archaella, and Swimming Motility 94

2.10 Surface Motility 97

2.11 Chemotaxis 99

2.12 Other Forms of Taxis 101

IV • Eukaryotic Microbial Cells 102

2.13 The Nucleus and Cell Division 102

2.14 Mitochondria and Chloroplasts 104

2.15 Other Eukaryotic Cell Structures 106

3 Microbial Metabolism 111

MICROBIOLOGYNOW Life Begins with Metabolism 111

I • Fundamentals of Metabolism 112

3.1 Defining the Requirements for Life 112

3.2 Electron Transfer Reactions 114

3.3 Calculating Changes in Free Energy 116

3.4 Cellular Energy Conservation 118

3.5 Catalysis and Enzymes 120

II • Catabolism: Chemoorganotrophs 121

3.6 Glycolysis, the Citric Acid Cycle,

and the Glyoxylate Cycle 122

3.7 Principles of Fermentation 124

3.8 Principles of Respiration: Electron Carriers 125

3.9 Principles of Respiration: Generating a Proton

Motive Force 127

III • Catabolism: Electron Transport

and Metabolic Diversity 130

3.10 Anaerobic Respiration and Metabolic Modularity 130

3.11 Chemolithotrophy and Phototrophy 132

IV • Biosynthesis 134

3.12 Autotrophy and Nitrogen Fixation 134

3.13 Sugars and Polysaccharides 137

3.14 Amino Acids and Nucleotides 138

3.15 Fatty Acids and Lipids 139

4 Microbial Growth

and Its Control 144

MICROBIOLOGYNOW Growing Their Own Way 144

I • Culturing Microbes and Measuring Their

Growth 145

4.1 Feeding the Microbe: Cell Nutrition 145

4.2 Growth Media and Laboratory Culture 147

4.3 Microscopic Counts of Microbial Cell Numbers 150

4.4 Viable Counting of Microbial Cell Numbers 151

4.5 Turbidimetric Measures of Microbial Cell

Numbers 153

II • Dynamics of Microbial Growth 154

4.6 Binary Fission and the Microbial Growth Cycle 154

4.7 Quantitative Aspects of Microbial Growth 156

4.8 Continuous Culture 158

4.9 Biofilm Growth 159

4.10 Alternatives to Binary Fission 160

III • Environmental Effects on Growth:

Temperature 162

4.11 Temperature Classes of Microorganisms 162

4.12 Microbial Life in the Cold 163

4.13 Microbial Life at High Temperatures 165

IV • Environmental Effects on Growth: pH, Osmolarity,

and Oxygen 167

4.14 Effects of pH on Microbial Growth 168

4.15 Osmolarity and Microbial Growth 169

4.16 Oxygen and Microbial Growth 171

V • Controlling Microbial Growth 173

4.17 General Principles and Microbial Growth Control by

Heat 174

4.18 Other Physical Control Methods: Radiation and

Filtration 175

4.19 Chemical Control of Microbial Growth 177

5 Viruses and Their

Multiplication 184

MICROBIOLOGYNOW When Antibiotics Fail, Bacteriophage

Therapy to the Rescue 184

I • The Nature of Viruses 185

5.1 What Is a Virus? 185

5.2 Structure of the Virion 187

5.3 Culturing, Detecting, and Counting Viruses 189

II • Overview of the Viral Replication Cycle 191

5.4 Steps in the Replication Cycle 191

5.5 Bacteriophage T4: A Model Lytic Virus 192

5.6 Temperate Bacteriophages and Lysogeny 195

5.7 An Overview of Viruses of Eukaryotes 195

UNIT 2 Molecular Biology

and Genetics

6 Molecular Information Flow

and Protein Processing 201

MICROBIOLOGYNOW Injectisomes: Salmonella’s Mode of Attack 201

I • Molecular Biology and Genetic Elements 202

6.1 DNA and Genetic Information Flow 202

6.2 Genetic Elements: Chromosomes

and Plasmids 205

II • Copying the Genetic Blueprint: DNA

Replication 208

6.3 Templates, Enzymes, and the Replication Fork 208

6.4 Bidirectional Replication, the Replisome, and

Proofreading 211

III • RNA Synthesis: Transcription 213

6.5 Transcription in Bacteria 213

6.6 Transcription in Archaea and Eukarya 217

IV • Protein Synthesis: Translation 219

6.7 Amino Acids, Polypeptides, and Proteins 219

6.8 Transfer RNA 222

6.9 Translation and the Genetic Code 223

6.10 The Mechanism of Protein Synthesis 225

V • Protein Processing, Secretion,

and Targeting 228

6.11 Assisted Protein Folding and Chaperones 228

6.12 Protein Secretion: The Sec and Tat Systems 229

6.13 Protein Secretion: Gram-Negative Systems 230

7 Microbial Regulatory

Systems 236

MICROBIOLOGYNOW As Bacterial Cells Chatter,

Viruses Eavesdrop 236

I • DNA-Binding Proteins and Transcriptional

Regulation 237

7.1 DNA-Binding Proteins 237

7.2 Transcription Factors and Effectors 238

7.3 Repression and Activation 240

7.4 Transcription Controls in Archaea 243

II • Sensing and Signal Transduction 245

7.5 Two-Component Regulatory Systems 245

7.6 Regulation of Chemotaxis 246

7.7 Cell-to-Cell Signaling 249

III • Global Control 251

7.8 The lac Operon 252

7.9 Stringent and General Stress Responses 254

7.10 The Phosphate (Pho) Regulon 256

7.11 The Heat Shock Response 257

IV • RNA-Based Regulation 258

7.12 Regulatory RNAs 259

7.13 Riboswitches 260

7.14 Attenuation 262

V • Regulation of Enzymes and Other Proteins 263

7.15 Feedback Inhibition 264

7.16 Post-Translational Regulation 264

8 Molecular Aspects of Microbial

Growth 270

MICROBIOLOGYNOW Membrane Vesicles: Nano Vehicles

Transporting Important Cargo 270

I • Bacterial Cell Division 271

8.1 Visualizing Molecular Growth 271

8.2 Chromosome Replication and Segregation 272

8.3 Cell Division and Fts Proteins 275

8.4 Determinants of Cell Morphology 277

8.5 Peptidoglycan Biosynthesis 279

II • Regulation of Development

in Model Bacteria 282

8.6 Regulation of Endospore Formation 282

8.7 Regulation of Endospore Germination 283

8.8 Caulobacter Differentiation 284

8.9 Heterocyst Formation in Anabaena 286

8.10 Biofilm Formation 287

III • Antibiotics and Microbial Growth 291

8.11 Antibiotic Targets and Antibiotic Resistance 291

8.12 Persistence and Dormancy 293

9 Genetics of Bacteria

and Archaea 297

MICROBIOLOGYNOW Live Cell Imaging Captures Bacterial

Promiscuity 297

I • Mutation 299

9.1 Mutations and Mutants 299

9.2 Molecular Basis of Mutation 301

9.3 Reversions and Mutation Rates 303

9.4 Mutagenesis 304

II • Gene Transfer in Bacteria 306

9.5 Genetic Recombination 307

9.6 Transformation 309

9.7 Transduction 311

9.8 Conjugation 314

9.9 The Formation of Hfr Strains and Chromosome

Mobilization 315

III • Gene Transfer in Archaea and Other

Genetic Events 318

9.10 Horizontal Gene Transfer in Archaea 318

9.11 Mobile DNA: Transposable Elements 320

9.12 Preserving Genomic Integrity and CRISPR 322

UNIT 3 Genomics, Synthetic Biology,

and Evolution

10 Microbial Genomics and Other

Omics 328

MICROBIOLOGYNOW Omics Tools Unravel Mysteries

of “Fettuccine” Rocks 328

I • Genomics 329

10.1 Introduction to Genomics 329

10.2 Sequencing and Annotating Genomes 331

10.3 Genome Size and Gene Content in Bacteria and

Archaea 334

10.4 Organelle and Eukaryotic Microbial Genomes 338

II • Functional Omics 341

10.5 Functional Genomics 341

10.6 High-Throughput Functional Gene

Analysis: Tn-Seq 344

10.7 Metagenomics 344

10.8 Gene Chips and Transcriptomics 347

10.9 Proteomics and the Interactome 350

10.10 Metabolomics 352

III • Systems Biology 353

10.11 Single-Cell Genomics 354

10.12 Integrating Mycobacterium tuberculosis Omics 355

10.13 Systems Biology and Human Health 357

Explore the Microbial World

DNA Sequencing in the Palm of Your Hand 336

11 Viral Genomics

and Diversity 361

MICROBIOLOGYNOW Bacteriophages Mimicking Eukaryotes—

Discovery of a Phage-Encoded Nucleus

and Spindle 361

I • Viral Genomes and Classification 362

11.1 Size and Structure of Viral Genomes 362

11.2 Viral Taxonomy and Phylogeny 364

II • DNA Viruses 366

11.3 Single-Stranded DNA Bacteriophages: fX174 and

M13 366

11.4 Double-Stranded DNA Bacteriophages: T4, T7, and

Lambda 368

11.5 Viruses of Archaea 371

11.6 Uniquely Replicating DNA Animal Viruses 374

11.7 DNA Tumor Viruses 375

III • RNA Viruses 377

11.8 Positive-Strand RNA Viruses 377

11.9 Negative-Strand RNA Animal Viruses 379

11.10 Double-Stranded RNA Viruses 381

11.11 Viruses That Use Reverse Transcriptase 382

IV • Subviral Agents 385

11.12 Viroids 385

11.13 Prions 386

12 Biotechnology and Synthetic

Biology 390

MICROBIOLOGYNOW An Ingestible Biosensor: Using Bacteria to

Monitor Gastrointestinal Health 390

I • Tools of the Genetic Engineer 391

12.1 Manipulating DNA: PCR and Nucleic Acid

Hybridization 391

12.2 Molecular Cloning 394

12.3 Expressing Foreign Genes

in Bacteria 398

12.4 Molecular Methods for

Mutagenesis 400

12.5 Reporter Genes and Gene Fusions 401

II • Making Products from Genetically Engineered

Microbes: Biotechnology 403

12.6 Somatotropin and Other

Mammalian Proteins 403

12.7 Transgenic Organisms in Agriculture and

Aquaculture 405

12.8 Engineered Vaccines and

Therapeutic Agents 407

12.9 Mining Genomes and

Engineering Pathways 411

12.10 Engineering Biofuels 413

III • Synthetic Biology and Genome Editing 415

12.11 Synthetic Metabolic Pathways, Biosensors,

and Genetic Circuits 416

12.12 Synthetic Cells 419

12.13 Genome Editing and CRISPRs 420

12.14 Biocontainment of Genetically Modified

Organisms 424

13 Microbial Evolution

and Genome Dynamics 428

MICROBIOLOGYNOW Exploring Viral Genesis 428

I • Early Earth and the Origin

and Diversification of Life 429

13.1 Formation and Early History of Earth 429

13.2 Photosynthesis and the Oxidation

of Earth 432

13.3 Living Fossils: DNA Records the History

of Life 434

13.4 Endosymbiotic Origin of Eukaryotes 435

13.5 Viral Evolution 438

II • Mechanisms of Microbial

Evolution 439

13.6 The Evolutionary Process 439

13.7 Experimental Evolution 441

13.8 Gene Families, Duplications,

and Deletions 443

13.9 Horizontal Gene Transfer 445

13.10 The Evolution of Microbial Genomes 446

III • Microbial Phylogeny and

Systematics 448

13.11 Molecular Phylogeny: Making Sense

of Molecular Sequences 448

13.12 Microbial Systematics 452

UNIT 4 Microbial Diversity

14 Metabolic Diversity

of Microorganisms 460

MICROBIOLOGYNOW Ferreting Out the Peculiar Life

of Iron Bacteria 460

I • Introduction to Metabolic Diversity 461

14.1 Foundational Principles of Metabolic

Diversity: Energy and Redox 461

14.2 Autotrophic Pathways 464

II • Phototrophy 466

14.3 Photosynthesis and Chlorophylls 466

14.4 Carotenoids and Phycobilins 470

14.5 Anoxygenic Photosynthesis 471

14.6 Oxygenic Photosynthesis 474

III • Respiratory Processes Defined by

Electron Donor 476

14.7 Oxidation of Sulfur Compounds 476

14.8 Iron (Fe2+) Oxidation 478

14.9 Nitrification 479

14.10 Anaerobic Ammonia Oxidation

(Anammox) 481

IV • Respiratory Processes Defined by

Electron Acceptor 482

14.11 Nitrate Reduction and Denitrification 482

14.12 Sulfate and Sulfur Reduction 484

14.13 Other Electron Acceptors 486

V • One-Carbon (C1) Metabolism 488

14.14 Acetogenesis 488

14.15 Methanogenesis 490

14.16 Methanotrophy 494

VI • Fermentation 496

14.17 Energetic and Redox

Considerations 496

14.18 Lactic and Mixed-Acid

Fermentations 498

14.19 Fermentations of Obligate

Anaerobes 500

14.20 Secondary Fermentations 502

14.21 Fermentations That Lack Substrate-Level

Phosphorylation 503

14.22 Syntrophy 505

VII • Hydrocarbon Metabolism 507

14.23 Aerobic Hydrocarbon

Metabolism 507

14.24 Anaerobic Hydrocarbon

Metabolism 508

15 Ecological Diversity of

Bacteria 514

MICROBIOLOGYNOW Cyanobacterial Diversity

and Environmental Change 514

I • Ecological Diversity Among

Microorganisms 515

15.1 Making Sense of Microbial Diversity 515

II • Ecological Diversity of

Phototrophic Bacteria 516

15.2 Overview of Phototrophic Bacteria 516

15.3 Cyanobacteria 517

15.4 Purple Sulfur Bacteria 521

15.5 Purple Nonsulfur Bacteria and Aerobic

Anoxygenic Phototrophs 523

15.6 Green Sulfur Bacteria 524

15.7 Green Nonsulfur Bacteria 526

15.8 Other Phototrophic Bacteria 527

III • Diversity of Bacteria Defined by

Metabolic Traits 528

15.9 Diversity of Nitrogen Fixers 528

15.10 Diversity of Nitrifiers and Denitrifiers 530

15.11 Dissimilative Sulfur- and Sulfate-Reducers 532

15.12 Dissimilative Sulfur-Oxidizers 534

15.13 Dissimilative Iron-Reducers 538

15.14 Dissimilative Iron-Oxidizers 539

15.15 Methanotrophs and Methylotrophs 540

IV • Morphologically and Ecologically

Distinctive Bacteria 542

15.16 Microbial Predators 542

15.17 Spirochetes 544

15.18 Budding and Prosthecate/Stalked Bacteria 547

15.19 Sheathed Bacteria 550

15.20 Magnetic Microbes 551

16 Phylogenetic Diversity of

Bacteria 555

MICROBIOLOGYNOW Bacterial Diversity and Human Health 555

I • Proteobacteria 556

16.1 Alphaproteobacteria 557

16.2 Betaproteobacteria 560

16.3 Gammaproteobacteria: Enterobacteriales 562

16.4 Gammaproteobacteria: Pseudomonadales

and Vibrionales 564

16.5 Deltaproteobacteria and

Epsilonproteobacteria 565

II • Firmicutes, Tenericutes, and Actinobacteria 567

16.6 Firmicutes: Lactobacillales 567

16.7 Firmicutes: Nonsporulating Bacillales and

Clostridiales 569

16.8 Firmicutes: Sporulating Bacillales and

Clostridiales 570

16.9 Tenericutes: The Mycoplasmas 571

16.10 Actinobacteria: Coryneform and Propionic Acid

Bacteria 572

16.11 Actinobacteria: Mycobacterium 574

16.12 Filamentous Actinobacteria: Streptomyces and

Relatives 575

III • Bacteroidetes 578

16.13 Bacteroidales 578

16.14 Cytophagales, Flavobacteriales, and

Sphingobacteriales 579

IV • Chlamydiae, Planctomycetes, and

Verrucomicrobia 580

16.15 Chlamydiae 580

16.16 Planctomycetes 582

16.17 Verrucomicrobia 583

V • Hyperthermophilic Bacteria 584

16.18 Thermotogae and Thermodesulfobacteria 584

16.19 Aquificae 585

VI • Other Bacteria 586

16.20 Deinococcus–Thermus 586

16.21 Acidobacteria and Nitrospirae 587

16.22 Other Notable Phyla of Bacteria 588

17 Diversity of Archaea 592

MICROBIOLOGYNOW Methanogens and Global Climate Change 592

I • Euryarchaeota 594

17.1 Extremely Halophilic Archaea 594

17.2 Methanogenic Archaea 597

17.3 Thermoplasmatales 601

17.4 Thermococcales and Archaeoglobales 602

II • Thaumarchaeota and Cryptic Archaeal Phyla 603

17.5 Thaumarchaeota and Nitrification in Archaea 604

17.6 Nanoarchaeota and the “Hospitable Fireball” 605

17.7 Korarchaeota, the “Secret Filament” 606

17.8 Other Cryptic Archaeal Phyla 607

III • Crenarchaeota 608

17.9 Habitats and Energy Metabolism of

Crenarchaeota 608

17.10 Crenarchaeota from Terrestrial Volcanic Habitats 610

17.11 Crenarchaeota from Submarine Volcanic Habitats 612

IV • Evolution and Life at High Temperature 614

17.12 An Upper Temperature Limit for Microbial Life 614

17.13 Molecular Adaptations to Life at High

Temperature 616

17.14 Hyperthermophilic Archaea, H2, and Microbial

Evolution 617

18 Diversity of Microbial

Eukarya 621

MICROBIOLOGYNOW Coccolithophores, Engineers

of Global Climate 621

I • Organelles and Phylogeny

of Microbial Eukarya 622

18.1 Endosymbioses and the Eukaryotic Cell 622

18.2 Phylogenetic Lineages of Eukarya 624

II • Protists 625

18.3 Excavates 625

18.4 Alveolata 627

18.5 Stramenopiles 629

18.6 Rhizaria 631

18.7 Haptophytes 632

18.8 Amoebozoa 633

III • Fungi 635

18.9 Fungal Physiology, Structure,

and Symbioses 635

18.10 Fungal Reproduction and Phylogeny 637

18.11 Microsporidia and Chytridiomycota 638

18.12 Mucoromycota and Glomeromycota 639

18.13 Ascomycota 640

18.14 Basidiomycota 641

IV • Archaeplastida 642

18.15 Red Algae 642

18.16 Green Algae 643

UNIT 5 Microbial Ecology and

Environmental Microbiology

19 Taking the Measure

of Microbial Systems 648

MICROBIOLOGYNOW Touring Microbial Biogeography Using

Combinatorial Imaging 648

I • Culture-Dependent Analyses of Microbial

Communities 649

19.1 Enrichment Culture Microbiology 649

19.2 Classical Procedures for Isolating Microbes 653

19.3 Selective Single-Cell Isolation: Laser Tweezers, Flow

Cytometry, Microfluidics, and High-Throughput

Methods 654

II • Culture-Independent Microscopic Analyses

of Microbial Communities 656

19.4 General Staining Methods 656

19.5 Microscopic Specificity: Fluorescence In Situ

Hybridization (FISH) 658

III • Culture-Independent Molecular Analyses

of Microbial Communities 661

19.6 PCR Methods of Microbial Community

Analysis 662

19.7 Microarrays for Analysis of Microbial Phylogenetic

and Functional Diversity 666

19.8 Environmental Multi-omics: Integration of Genomics,

Transcriptomics, Proteomics, and

Metabolomics 667

IV • Measuring Microbial Activities in Nature 673

19.9 Chemical Assays, Radioisotopic Methods,

Microsensors, and Nanosensors 674

19.10 Stable Isotopes and Stable Isotope Probing 677

19.11 Linking Functions to Specific Organisms 679

19.12 Linking Genes and Cellular Properties to

Individual Cells 682

20 Microbial Ecosystems 687

MICROBIOLOGYNOW Living on Fumes 687

I • Microbial Ecology 688

20.1 General Ecological Concepts 688

20.2 Ecosystem Service: Biogeochemistry

and Nutrient Cycles 689

II • The Microbial Environment 690

20.3 Environments and Microenvironments 690

20.4 Surfaces and Biofilms 692

20.5 Microbial Mats 695

III • Terrestrial Environments 697

20.6 Soils: General Properties 697

20.7 Prokaryotic Diversity in Soils 700

20.8 The Terrestrial Subsurface 702

IV • Aquatic Environments 705

20.9 Freshwaters 705

20.10 Oxygen Relationships in the Marine

Environment 707

20.11 Major Marine Phototrophs 710

20.12 Pelagic Bacteria and Archaea 713

20.13 Pelagic Marine Viruses 716

20.14 The Deep Sea 718

20.15 Deep-Sea Sediments 721

20.16 Hydrothermal Vents 723

21 Nutrient Cycles 729

MICROBIOLOGYNOW An Uncertain Future for Coral Reef

Ecosystems 729

I • Carbon, Nitrogen, and Sulfur Cycles 730

21.1 The Carbon Cycle 730

21.2 Syntrophy and Methanogenesis 733

21.3 The Nitrogen Cycle 735

21.4 The Sulfur Cycle 737

II • Other Nutrient Cycles 738

21.5 The Iron and Manganese Cycles: Reductive

Activities 738

21.6 The Iron and Manganese Cycles: Oxidative

Activities 742

21.7 The Phosphorus, Calcium, and Silicon Cycles 744

III • Humans and Nutrient Cycling 746

21.8 Mercury Transformations 747

21.9 Human Impacts on the Carbon and Nitrogen

Cycles 749

Explore the Microbial World

Solving the Marine Methane Paradox 746

22 Microbiology of the Built

Environment 754

MICROBIOLOGYNOW Sending Microbes to Clean Up

after Polluters 754

I • Mineral Recovery and Acid Mine Drainage 755

22.1 Mining with Microorganisms 755

22.2 Acid Mine Drainage 757

II • Bioremediation 758

22.3 Bioremediation of Uranium-Contaminated

Environments 758

22.4 Bioremediation of Organic Pollutants:

Hydrocarbons 759

22.5 Bioremediation and Microbial Degradation

of Major Chemical Pollutants: Chlorinated

Organics and Plastics 760

III • Wastewater and Drinking Water Treatment 763

22.6 Primary and Secondary Wastewater Treatment 764

22.7 Tertiary Wastewater Treatment: Further Removal

of Phosphorus and Nitrogen 766

22.8 Sludge Processing and Contaminants

of Emerging Concern 768

22.9 Drinking Water Purification and Stabilization 771

22.10 Water Distribution Systems 772

IV • Indoor Microbiology and Microbially

Influenced Corrosion 773

22.11 The Microbiology of Homes and

Public Spaces 773

22.12 Microbially Influenced Corrosion

of Metals 775

22.13 Biodeterioration of Stone and Concrete 776

23 Microbial Symbioses with

Microbes, Plants, and

Animals 780

MICROBIOLOGYNOW Coral Fluorescence Provides the Guiding

Light for Their Symbiotic Algae 780

I • Symbioses Between Microorganisms 781

23.1 Lichens 781

23.2 “Chlorochromatium aggregatum” 782

23.3 Methanotrophic Consortia: Direct Interspecies

Electron Transfer 784

II • Plants as Microbial Habitats 785

23.4 The Legume–Root Nodule Symbiosis 785

23.5 Mycorrhizae 791

23.6 Agrobacterium and Crown Gall Disease 793

III • Insects as Microbial Habitats 795

23.7 Heritable Symbionts of Insects 795

23.8 Defensive Symbioses 798

23.9 Termites 799

IV • Other Invertebrates as Microbial Habitats 801

23.10 Bioluminescent Symbionts and the Squid

Symbiosis 801

23.11 Marine Invertebrates at Hydrothermal Vents

and Cold Seeps 805

23.12 Entomopathogenic Nematodes 806

23.13 Reef-Building Corals 807

V • Mammalian Gut Systems as Microbial

Habitats 810

23.14 Alternative Mammalian Gut Systems 810

23.15 The Rumen and Rumen Activities 812

23.16 Rumen Microbes and Their Dynamic

Relationships 813

Explore the Microbial World

Combating Mosquito-Borne Viral Diseases with

an Insect Symbiont 797

UNIT 6 Microbe–Human Interactions

and the Immune System

24 Microbial Symbioses with

Humans 819

MICROBIOLOGYNOW One of the Most Abundant Viruses on

Earth Discovered First in the Human

Viral Microbiome 819

I • Structure and Function of the Healthy Adult

Gastrointestinal and Oral Microbiomes 820

24.1 Overview of the Human Microbiome 820

24.2 Gastrointestinal Microbiota 821

24.3 Oral Cavity and Airways 827

II • Urogenital Tract and Skin Microbiomes

and the Human Viral Microbiome 830

24.4 Urogenital Tracts and Their Microbes 830

24.5 The Skin and Its Microbes 831

24.6 The Human Virome 833

III • From Birth to Death: Development of the

Human Microbiome 836

24.7 Human Study Groups and

Animal Models 836

24.8 Colonization, Succession, and Stability

of the Gut Microbiota 837

IV • Disorders Attributed to the Human

Microbiome 839

24.9 Syndromes Linked to the Gut Microbiota 840

24.10 Syndromes Linked to the Oral, Skin,

and Vaginal Microbiota 843

V • Modulation of the Human Microbiome 845

24.11 Antibiotics and the Human Microbiome 845

24.12 Probiotics, Prebiotics, and Synbiotics 846

Explore the Microbial World

The Gut–Brain Axis 826

25 Microbial Infection and

Pathogenesis 850

MICROBIOLOGYNOW Killing Pathogens on Contact 850

I • Human–Pathogen Interactions 851

25.1 Microbial Adherence 851

25.2 Colonization and Invasion 853

25.3 Pathogenicity, Virulence, and Virulence

Attenuation 855

25.4 Genetics of Virulence and the

Compromised Host 856

II • Enzymes and Toxins of Pathogenesis 858

25.5 Enzymes as Virulence Factors 858

25.6 AB-Type Exotoxins 860

25.7 Cytolytic and Superantigen Exotoxins 863

25.8 Endotoxins 864

26 Innate Immunity: Broadly

Specific Host Defenses 868

MICROBIOLOGYNOW Periodontal Disease and Alzheimer’s:

Evidence for Causation? 868

I • Fundamentals of Host Defense 869

26.1 Basic Properties of the Immune System 869

26.2 Barriers to Pathogen Invasion 870

II • Cells and Organs of the

Immune System 872

26.3 The Blood and Lymphatic Systems 872

26.4 Leukocyte Production and Diversity 874

III • Phagocyte Response Mechanisms 876

26.5 Pathogen Challenge and Phagocyte

Recruitment 876

26.6 Pathogen Recognition and Phagocyte

Signal Transduction 877

26.7 Phagocytosis and Phagocyte

Inhibition 880

IV • Other Innate Host Defenses 882

26.8 Inflammation and Fever 882

26.9 The Complement System 884

26.10 Innate Defenses Against Viruses 887

Explore the Microbial World

Pattern Recognition Receptors of Hydrothermal

Vent Tube Worms Facilitate Endosymbiosis 879

27 Adaptive Immunity: Highly

Specific Host Defenses 892

MICROBIOLOGYNOW Controlling HIV through “Public” T Cell Receptors

on CD4 T Cells 892

I • Principles of Adaptive Immunity 893

27.1 Specificity, Memory, Selection Processes,

and Tolerance 893

27.2 Immunogens and Classes of Immunity 896

II • Antibodies 898

27.3 Antibody Production and Structural

Diversity 898

27.4 Antigen Binding and the Genetics of

Antibody Diversity 902

III • The Major Histocompatibility

Complex (MHC) 905

27.5 MHC Proteins and Their Functions 905

27.6 MHC Polymorphism, Polygeny, and Peptide

Binding 907

IV • T Cells and Their Receptors 909

27.7 T Cell Receptors: Proteins, Genes,

and Diversity 910

27.8 T Cell Subsets and Their Functions 913

28 Immune Disorders and

Antimicrobial Therapy 919

MICROBIOLOGYNOW Preventing Autoimmunity with . . . Parasitic

Worms? 919

I • Disorders and Deficiencies of the Immune

System 920

28.1 Allergy, Hypersensitivity, and Autoimmunity 920

28.2 Superantigens and Immunodeficiency 923

II • Vaccines and Immunotherapy 925

28.3 Vaccination Against Infectious Diseases 925

28.4 Immunotherapy 928

III • Drug Treatments for Infectious Diseases 930

28.5 Antibacterial Drugs 930

28.6 Antimicrobial Drugs That Target Nonbacterial

Pathogens 936

28.7 Antimicrobial Drug Resistance and New Treatment

Strategies 938

UNIT 7 Infectious Diseases

29 Diagnosing Infectious

Diseases 943

MICROBIOLOGYNOW Shedding New Light on Diagnosing

Tuberculosis 943

I • Microbiology and the Healthcare

Environment 944

29.1 The Clinical Microbiology Laboratory 944

29.2 Healthcare-Associated Infections 945

II • Isolating and Characterizing Infectious

Microorganisms 946

29.3 Workflow in the Clinical Laboratory 946

29.4 Choosing the Right Treatment 952

III • Immunological and Molecular Tools

for Disease Diagnosis 954

29.5 Immunoassays and Disease 954

29.6 Precipitation, Agglutination, and

Immunofluorescence 956

29.7 Enzyme Immunoassays, Rapid Tests, and

Immunoblots 958

29.8 Nucleic Acid–Based Clinical Assays 961

Explore the Microbial World

MRSA—A Formidable Clinical Challenge 948

30 Epidemiology and Public

Health 965

MICROBIOLOGYNOW A New Urgent Threat Is Emerging in Public

Health Microbiology 965

I • Principles of Epidemiology 966

30.1 The Language of Epidemiology 966

30.2 The Host Community 968

30.3 Infectious Disease Transmission

and Reservoirs 969

30.4 Characteristics of Disease Epidemics 971

II • Public and Global Health 973

30.5 Public Health and Infectious Disease 973

30.6 Global Health Comparisons 975

III • Emerging Infectious Diseases, Pandemics,

and Other Threats 976

30.7 Emerging and Reemerging Infectious Diseases 976

30.8 Examples of Pandemics: HIV/AIDS, Cholera,

and Influenza 979

30.9 Public Health Threats from Microbial Weapons 981

31 Person-to-Person Bacterial

and Viral Diseases 986

MICROBIOLOGYNOW Reversing Antibiotic Resistance in a

Recalcitrant Pathogen 986

I • Airborne Bacterial Diseases 987

31.1 Airborne Pathogens 987

31.2 Streptococcal Syndromes 988

31.3 Diphtheria and Pertussis 991

31.4 Tuberculosis and Leprosy 992

31.5 Meningitis and Meningococcemia 994

II • Airborne Viral Diseases 995

31.6 MMR and Varicella-Zoster Infections 995

31.7 The Common Cold 997

31.8 Influenza 998

III • Direct-Contact Bacterial

and Viral Diseases 1000

31.9 Staphylococcus aureus Infections 1001

31.10 Helicobacter pylori and Gastric Diseases 1002

31.11 Hepatitis 1003

31.12 Ebola: A Deadly Threat 1005

IV • Sexually Transmitted Infections 1006

31.13 Gonorrhea, Syphilis, and Chlamydia 1007

31.14 Herpes Simplex Viruses (HSV)

and Human Papillomavirus (HPV) 1011

31.15 Human Immunodeficiency

Virus (HIV) and AIDS 1012

32 Vectorborne and

Soilborne Bacterial

and Viral Diseases 1019

MICROBIOLOGY NOW The Historical Emergence of an

Ancient and Deadly Pathogen 1019

I • Animal-Transmitted Viral Diseases 1020

32.1 Rabies Virus and Rabies 1020

32.2 Hantavirus and Hantavirus Syndromes 1022

II • Arthropod-Transmitted Bacterial and Viral

Diseases 1023

32.3 Rickettsial Diseases 1023

32.4 Lyme Disease and Borrelia 1025

32.5 Yellow Fever, Dengue Fever, Chikungunya,

and Zika 1027

32.6 West Nile Fever 1029

32.7 Plague 1030

III • Soilborne Bacterial Diseases 1032

32.8 Anthrax 1032

32.9 Tetanus and Gas Gangrene 1033

33 Waterborne and

Foodborne Bacterial

and Viral Diseases 1037

MICROBIOLOGY NOW Reverse Zoonosis in the Southern Ocean 1037

I • Water as a Disease Vehicle 1038

33.1 Agents and Sources of Waterborne Diseases 1038

33.2 Public Health and Water Quality 1039

II • Waterborne Diseases 1040

33.3 Vibrio cholerae and Cholera 1040

33.4 Legionellosis 1042

33.5 Typhoid Fever and Norovirus Illness 1043

III • Food as a Disease Vehicle 1044

33.6 Food Spoilage and Food Preservation 1044

33.7 Foodborne Diseases and Food Epidemiology 1046

IV • Food Poisoning 1048

33.8 Staphylococcal Food Poisoning 1048

33.9 Clostridial Food Poisoning 1049

V • Food Infection 1050

33.10 Salmonellosis 1050

33.11 Pathogenic Escherichia coli 1051

33.12 Campylobacter 1052

33.13 Listeriosis 1053

33.14 Other Foodborne Infectious Diseases 1054

34 Eukaryotic Pathogens:

Fungi, Protozoa, and

Helminths 1059

MICROBIOLOGYNOW A Silver Bullet to Kill Brain-Eating

Amoebae? 1059

I • Fungal Infections 1060

34.1 Pathogenic Fungi and Classes of Infection 1060

34.2 Fungal Diseases: Mycoses 1062

II • Visceral Parasitic Infections 1064

34.3 Amoebae and Ciliates: Entamoeba,

Naegleria, and Balantidium 1064

34.4 Other Visceral Parasites: Giardia,

Trichomonas, Cryptosporidium,

Toxoplasma, and Cyclospora 1065

III • Blood and Tissue Parasitic

Infections 1067

34.5 Plasmodium and Malaria 1067

34.6 Leishmaniasis, Trypanosomiasis,

and Chagas Disease 1069

34.7 Parasitic Helminths: Schistosomiasis

and Filariases 1070

Photo Credits 1075

Glossary Terms 1079

Index 1083

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