Microbial LifeSECOND EDITION

James T. StaleyDepartment of Microbiology,

University of Washington

Robert P. GunsalusDepartment of Microbiology,

University of California, Los Angeles

Stephen LoryDepartment of Microbiology and Molecular Genetics,

Harvard Medical School

Jerome J. PerryRaleigh, North Carolina

SINAUER ASSOCIATES, INC., Publishers • Sunderland, Massachusetts

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PART I

The Scope of Microbiology 1

1 Evolution, Microbial Life, and the Biosphere 3

2 Historical Overview 31

3 Fundamental Chemistry of the Cell 55

4 Structure and Function of Bacteriaand Archaea 75

PART II

Microbial Physiology: Nutrition and Growth 123

5 Nutrition, Cultivation, and Isolation ofMicroorganisms 125

6 Microbial Growth 153

7 Control of Microbial Growth 179

PART III

Microbial Physiology: Metabolism 201

8 Cellular Energy Derived from Chemicals 203

9 Cellular Energy Derived from Light 233

10 Biosynthesis of Monomers 255

11 Assembly of Bacterial Cell Structures 287

12 Roles of Microbes in Biodegradation 317

PART IV

Genetics and Basic Virology 339

13 Basic Genetics 341

14 Viruses 389

15 Genetic Exchange 423

16 Microbial Genomics 451

PART V

Microbial Evolution and Diversity 483

17 Taxonomy of Bacteria and Archaea 485

18 Archaea 515

19 Nonphotosynthetic Proteobacteria 545

20 Gram-Positive Bacteria: Firmicutes andActinobacteria 601

21 Phototrophic Bacteria 633

22 Exploring Bacterial Diversity: Other Phyla, OtherMicrobial Worlds 663

23 Eukaryotic Microorganisms 687

PART VI

Microbial Ecology 737

24 Microbial Ecology 739

25 Beneficial Symbiotic Associations 785

26 Human Host–Microbe Interaction 811

PART VII

Immunology and Medical Microbiology 845

27 Immunology 847

28 Microbial Diseases of Humans 893

29 Viral Diseases of Humans 943

30 Epidemiology and Clinical Microbiology 973

PART VIII

Applied Microbiology 1007

31 Industrial Microbiology 1009

32 Applied Environmental Microbiology 1045

Brief Contents

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1 Evolution, Microbial Life, and the Biosphere 3

1.1 Origin of Earth and Life 3Fossil Evidence of Microorganisms 4Origin of Life on Earth 8

1.2 Tracing Biological Evolution 9Cell Theory: A Definition of Life 9The Tree of Life 10

1.3 Prokaryotic versus Eukaryotic Microorganisms 12

Other Morphological Differences 14Reproductive Differences 15Cell Size: Volume and Surface Area 17Microbial Nutrition 18

1.4 Microbial Evolution and Biogeochemical Cycles 19

Possible Early Metabolic Types 19Cyanobacteria and the Production of Oxygen 20

Impact of Bacteria and Archaea on BiogeochemicalCycles 21

1.5 Evolution of Eukaryotes 21Impact of Oxygen on the Evolution of Plants and

Animals 23Endosymbiotic Evolution 23Origin of the Ozone Layer 24

1.6 Sequence of Major Events during BiologicalEvolution 24

1.7 Astrobiology 25

2 Historical Overview 312.1 Effects of Infectious Diseases on Civilization 312.2 Why Study the History of a Science? 332.3 Status of Microbial Science Prior to 1650 332.4 Microbiology from 1650 to 1850 34

Antony van Leeuwenhoek 34From Leeuwenhoek to Pasteur 36Classification Systems 37

2.5 Medical Microbiology and Immunology 382.6 Microbiology after 1850: The Beginning of

Modern Microbiology 39The Pasteur School 39The Koch School 43Microbes as Agents of Environmental Changes 46Microbes and Plant Disease 49

2.7 Transition to the Modern Era 50

3 Fundamental Chemistry of the Cell 55

3.1 Atoms 553.2 Electronic Configurations of Molecules 583.3 Molecules 59

The Scope of Microbiology 1IPART

Contents

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Contents xiii

5 Nutrition, Cultivation, and Isolation of Microorganisms 125

5.1 Fundamental Aspects of Diversity 126The Evolution of Metabolic Diversity 126Nutritional Types of Microorganisms 126Nutritional Requirements for Cell Growth 127Composition of Microbial Cells 127Carbon 128Oxygen 129Nitrogen 129Hydrogen 130Sulfur 131Phosphorus 131

3.4 Chemical Bonds 60Ionic Bonds 60Covalent Bonds 61Hydrogen Bonds 61

3.5 van der Waals Forces 633.6 Hydrophobic Forces 643.7 Water 643.8 Acids, Bases, and Buffers 653.9 Chemical Constituents of the Cell 663.10 Major Monomers 66

Carbohydrates 66Lipids 69Amino Acids and Proteins 69Nucleic Acids 69

3.11 Isomeric Compounds 70

4 Structure and Function of Bacteria and Archaea 75

4.1 Microscopy 76Simple Microscope 76Compound Microscope 76Brightfield and Darkfield Microscopes 79Phase Contrast Microscope 79

Fluorescence Microscope 81Confocal Scanning Microscope 83Transmission Electron Microscope (TEM) 83Scanning Electron Microscope (SEM) 86Atomic Force Microscopy (AFM) 88

4.2 Morphology of Bacteria and Archaea 89Unicellular Organisms 89Multicellular Bacteria and Archaea 91Size of Bacteria and Archaea 91

4.3 Structure, Composition, and Cell Function 92Cytoplasm of Bacteria and Archaea 92Internal Structures Produced by Some Bacteria and

Archaea 96

4.4 The Cell Envelope 102Cytoplasmic Membrane 102The Cell Wall 105The Outer Membrane 110Periplasm 111

4.5 Extracellular Layers 113Capsules 113Slime Layers 114Sheaths 116Protein Jackets 116Cell Appendages 116Tactic Responses 119Fimbriae, Pili, and Spinae 119

Microbial Physiology: Nutrition and Growth 123IIPART

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The Abundant Cations 131Iron 131Trace Elements 131Growth Factors 132

5.2 Uptake of Nutrients into Cells 133Diffusion 133Active Transport 134Types of Active Transport 134Iron Uptake 136

5.3 Cultivation of Microorganisms 138A Culture Medium 138Sterilization of Media 138Isolation in Pure Culture 138Incubation Conditions 139Streak Plate Procedure 139Spread Plate Procedures 140Pour Plate Procedure 140Maintenance of Stock Cultures 141

5.4 Isolation of Selected Microbes by EnrichmentCulture 142

Origins of Enrichment Culture Methodology 142Applications of Enrichment Culture 143General Enrichment Methods 143Aerobic Enrichment 144Anaerobic Enrichment 145Enrichment for Specific Metabolic Types 147Chemoheterotrophic Aerobic Bacteria 147Chemoheterotrophic Anaerobic Bacteria 147Chemoautotrophic Bacteria and Archaea 147Phototrophic Bacteria 148

6 Microbial Growth 1536.1 Cell Division of Bacteria and Archaea 154

Binary Transverse Fission 154Budding 155Fragmentation 155

6.2 Population Growth 156Growth Curve Characteristics 157

6.3 Ways to Measure Growth 160Total Weight of Cells 160Chemical Analysis of a Cell Constituent 161Direct Count of Cells 161

Viability Count—Living Cells 162Turbidimetry: Scattered Light and Cell Density 162Synchronous Growth of Cells in Culture 163Growth Yield (yS and yATP) 165Effect of Nutrient Concentration on Growth

Rate 166

6.4 Growth of Cells in Batch versus ContinuousCulture 167

Batch Culture 167Continuous Culture 167

6.5 Effect of Environmental Conditions on CellGrowth 169

Acidity and Alkalinity 169Presence of Oxygen (O2) 170Toxicity of Oxygen 171Toxicity of O2 and Growth of Anaerobes 171Effect of Temperature 172Temperature Limitations 174Carbon Dioxide Availability 174Water Availability 174Pressure 175

7 Control of Microbial Growth 179

7.1 Historical Perspective 1807.2 Physical Methods of Control 180

Heat Sterilization and Pasteurization 180Heat Sterilization 181Sterilization by Radiation 183Sterilization by Filtration 184

7.3 Chemical Methods of Control 186Types of Antimicrobial Agents and their

Properties 186Tests for Measuring Antimicrobial Activity 188

7.4 Biological Methods of Control 190Chemotherapeutic Agents 190Chemically Synthesized Chemotherapeutics 190Antibiotics as Chemotherapeutics 192Modes of Antibiotic Action 192Resistance to Antibiotics 196Probiotics 197

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Contents xv

8 Cellular Energy Derived from Chemicals 203

8.1 Basic Principles of Energy Generation 2038.2 Substrate-Level Phosphorylation 206

Glycolysis 206Fermentation 207

8.3 Respiration-Linked Phosphorylation 210Electron Transport Chains in Energy-Transducing

Membranes 210Oxidation–Reduction Reactions 211Components of Electron Transport Chains 214

8.4 Generation of the Proton Motive Force 219Inhibitors of Respiration 220

8.5 ATP Synthase 2218.6 Diversity of Bacterial Electron Transport

Chains 222Diversity of Electron Acceptors and Electron

Donors 223Oxygen Reduction (Aerobic Respiration) 223Nitrate Reduction 224Alternative Electron Acceptors and Donors in

Nature 227Iron Oxidation 227

9 Cellular Energy Derived from Light 233

9.1 Photosynthetic Organisms 234Early Evolution 234Origin of Photosynthetic Organisms 235

9.2 The Photosynthetic Apparatus 235The Light-Gathering Systems 237The Electron Transport Chains 239The ATP-Generating System 239Photosynthetic Strategies—The Light-Independent

Reactions 240

9.3 The Photosynthetic Bacterial Groups 241Photosynthesis in Purple Nonsulfur Bacteria 241Photosynthesis in Purple Sulfur Bacteria 243Photosynthesis in Green Sulfur Bacteria 244Photosynthesis in Heliobacteria 246Photosynthesis in Cyanobacteria 246

9.4 Photosynthesis with Rhodopsin 249

10 Biosynthesis of Monomers 255

10.1 Macromolecular Synthesis from PrecursorSubstrates 256

10.2 Macromolecular Synthesis from 1-CarbonSubstrates 258

CO2 Fixation: The Calvin Cycle 259CO2 Fixation: The Reductive Citric Acid

Pathway 261CO2 Fixation: The Hydroxypropionate Pathway 261CO2 Fixation: The Reductive Acetyl-CoA

Pathway 261C-1 Fixation: The Glycine-Serine and Ribulose

Monophosphate Pathways 261

10.3 Pathways that Generate Biosynthetic Precursorsfrom Sugars 263

Role of Pyruvate in the Synthesis of PrecursorMetabolites 265

The Tricarboxylic Acid Cycle 268The Glyoxylate Shunt 270Biosynthesis of Glucose 270

Microbial Physiology: Metabolism 201IIIPART

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13 Basic Genetics 34113.1 The Nature of the Hereditary Information 342

Structure of DNA 343

13.2 DNA Replication 344Overview of DNA Replication 344Details of the Replication Cycle 345Proofreading During DNA Replication 349

10.4 Biosynthesis of Amino Acids, Purines,Pyrimidines, and Lipids 272

Amino Acid Biosynthesis 272Purine and Pyrimidine Biosynthesis 272Biosynthesis of Lipids 275Fatty Acids 275Branched-Chain Lipids 275

10.5 Nitrogen Assimilation 278Nitrate Reduction 279Nitrogen Fixation 279Utilization of Nitrogenous Compounds 281Incorporation of Ammonia 281

10.6 Sulfur Assimilation 282

11 Assembly of Bacterial Cell Structures 287

11.1 Membrane Synthesis 289Synthesis of Lipids 289

11.2 Peptidoglycan Synthesis 289Forming Gram-Positive Cell Envelopes 292Forming Gram-Negative Cell Envelopes 292

11.3 Protein Assembly, Structure, and Function 293Protein Structure 295Structural Arrangements of Proteins 295

11.4 Export of Proteins 299Signal Sequences 299The Sec-Dependent Protein Secretion Pathway 299The Twin-Arginine (TAT) Protein Secretion

Pathway 302Protein Targeting to the Outer Membrane 302

Extracellular Secretion by Gram-Negative Bacteria 303

Protein Secretion in Lower Eukaryotes 307

11.5 Structure and Function of Cell Appendages 307Bacterial Flagella 307Bacterial Pili 311

12 Roles of Microbes in Biodegradation 317

12.1 Overview of the Carbon Cycle 31912.2 Catabolism of Polymeric Materials 322

Polysaccharides 323Starch 323Glycogen 324Chitin 324Cellulose 325Hemicellulose, Xylans, and Pectins 326Catabolism of Proteins 327Catabolism of Nucleic Acids 327

12.3 Catabolism of Low-Molecular-WeightCompounds 328

Uric Acid 328Organic Acids 328

12.4 Catabolism of Lipids 328Phospholipids 328β-Oxidation of Fatty Acids 329

12.5 Catabolism of Aromatic and AliphaticCompounds 330

Lignin 330Alkanes and Aliphatic Hydrocarbons 332Aromatic Hydrocarbons 334Xenobiotic Compounds 335

Genetics and Basic Virology 339IVPART

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Contents xvii

Alternative DNA Replication Mechanisms 349

13.3 Transcription and its Regulation 351Steps in RNA Synthesis 352Promoters and Sigma Factors 354

13.4 Regulation of Gene Expression 356Negative Regulation 356Positive Regulation 357Regulation by Two-Component Signal Transduction

Pathways 359

13.5 Protein Synthesis 360Components of the Protein Synthesis Machinery 362Mechanism of Protein Synthesis 364When the Ribosomal Machinery Stalls… 366

13.6 Regulation by RNA Secondary Structure 368Regulatory Mechanisms Controlling Transcription

and Translation 370Control of Gene Expression by Regulatory

Noncoding RNAs 372

13.7 Quorum Sensing 37413.8 Mutations 376

Fluctuation Test 377Types of Mutation 378Consequence of Mutations 378

13.9 Mutagens and DNA Repair 380Mutagenesis with Base Analogs 380Mutagenesis with Agents That Modify DNA 380Mutagens That Intercalate with DNA 381Radiation Damage 381DNA Repair 381

14 Viruses 38914.1 Origin of Viruses 390

Coevolution 390Retrograde Evolution 391“Escaped” Gene Theory 391

14.2 Size and Structure of Viruses 392Viral Propagation 394

14.3 Cultivation of Viruses 39514.4 Quantitation of Viruses 39514.5 Purification of Viral Particles 39714.6 Viral Genomes and Reproduction 39714.7 Bacterial Viruses 398

Taxonomy 399Lysogenic and Temperate Viruses 400Lysogenic Conversion 400

Lambda (λ) Phage 400M13 401T4 404

14.8 Viral Restriction and Modification 40614.9 Eukaryotic Viruses 407

Classification, Size, and Structure 407

14.10 Animal Viruses 409DNA Viruses 409Herpesviruses 409Poxviruses 410RNA Viruses 412Poliovirus 412Retroviruses 413

14.11 Insect Viruses 41614.12 Plant Viruses 41614.13 Fungal and Algal Viruses 41714.14 Viroids 41714.15 Prions 418

15 Genetic Exchange 42315.1 Plasmids and Bacteriophage 424

Plasmids 424Plasmids Specifying Resistance to Antibiotics 424Virulence Plasmids 424Plasmids Encoding Genes for Specialized

Metabolism 426Plasmid Replication, Maintenance, and Partitioning

During Cell Division 426Bacteriophages 429

15.2 Recombination 429General (Homologous) Recombination 429Site-Specific Recombination 432

15.3 Genetic Exchange among Bacteria 433Conjugation 434Plasmid-Mediated Exchange of Chromosomal

Genes 436Transformation 439Transduction 441Generalized Transduction 441Specialized Transduction 442

15.4 Mobile Genetic Elements and Transposons 443Classification of Transposons 443Mechanism of Transposition 444Integrons 444Conjugative Transposons 447

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xviii Contents

16 Microbial Genomics451

16.1 Basis of Genetic Engineering 452Restriction and Modification 452Analysis of DNA Treated with Restriction

Endonucleases 452Construction of Recombinant Plasmids 458Identification of Recombinant Clones 459

Cloning of Eukaryotic Genes in Bacteria 462Practical Applications of Recombinant DNA

Technology 462

16.2 Microbial Genomics 467Horizontal Gene Transfer 471Metagenomics 473

16.3 Functional Genomics 474DNA Microarrays and Global Transcriptional

Analysis 475DNA Microarrays as Tools of Comparative

Genomics 478

17 Taxonomy of Bacteriaand Archaea 485

17.1 Nomenclature 48617.2 Classification 487

Artificial versus Phylogenetic Classifications 487Phenotypic Properties and Artificial

Classifications 487Numerical Taxonomy 489Phylogenetic Classification and Molecular

Phylogeny 489Speciation 498

17.3 Taxonomic Units 499The Species 500The Genus 503Higher Taxa 504

17.4 Major Groups of Archaea and Bacteria 504Domain: Archaea 505Domain: Bacteria 507

17.5 Identification 508Phenotypic Tests 509Nucleic Acid Probes and Fluorescent Antisera 509Culture Collections 510

Computer Internet Resources 512

18 Archaea 51518.1 Why Study Archaea? 515

Models of Early Life 516Abundance of Archaea 517Diversity of Archaea 517

18.2 Biochemical Differences and Similarities toOther Organisms 517

Archaeal Membranes 518Archaeal Cell Walls 520Archaeal RNA Polymerase 520DNA Replication 520Antibiotic Sensitivity of Archaea 521Similarities to Other Organisms 521

Microbial Evolution and Diversity 483VPART

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Contents xix

18.3 Major Groups of Archaea 522Methane-Producing Archaea:

The Methanoarchaea 522Biochemistry of Methanogenesis 523Methanogenesis from CO2 Reduction Occurs

Stepwise 526Methanogenesis from Other Substrates 528Bioenergetics of Methanogenesis 528Ecology of Methanogenesis 528Interspecies Hydrogen Transfer 529Methanogenic Habitats 530Anaerobic Methane Oxidation 531Extreme Halophiles 531Bacteriorhodopsin and Archaeal

Photophosphorylation 532Adaptations to High Concentrations of Salt 534Extreme Thermophiles 534Habitats and Physiology 535Viruses 539Perspectives and Applications 539Thermoadaptation 540Industrial Applications 540Early Life 541Uncultured and Nitrifying Archaea 541

19 Nonphotosynthetic Proteobacteria 545

19.1 Class Alphaproteobacteria 546Order Rhizobiales 546Order Rhodospirillales 553Order Rickettsiales 554Order Caulobacterales 554Order Hyphomicrobiales 559Order Sphingomonadales 561

19.2 Class Betaproteobacteria 562Order Neisseriales 562Order Burkholderiales 564Order Nitrosomonadales 566Order Hydrogenophilales 572Order Rhodocyclales 573

19.3 Class Gammaproteobacteria 574Order Enterobacteriales 574Order Vibrionales 580

Order Pseudomonadales 582Order Xanthomonadales 584Order Alteromonadales 585Order Legionellales 585Order Aeromonadales 585Order Oceanospirales 585Order Methylococcales: Methylotrophic

Bacteria 585Other Methylotrophs 588Order Thiotrichales 588

19.4 Class Deltaproteobacteria 591Order Bdellovibrionales 591Order Myxobacteriales: The Fruiting, Gliding

Bacteria 593Orders Desulfovibrionales and Desulfobacteriales:

Sulfate- and Sulfur-Reducing Bacteria 595

19.5 Class Epsilonproteobacteria 597

20 Gram-Positive Bacteria: Firmicutes and Actinobacteria 601

20.1 Phylum: Firmicutes 602Class Bacilli 602Order Lactobacillales: Lactic Acid Bacteria 603Order Bacillales 609Class Clostridia 614Class Mollicutes: Cell Wall–Less Bacteria 619

20.2 Phylum: Actinobacteria 621Unicellular Actinobacteria 621Coryneform Bacteria 624Highly Branched and Mycelial Actinobacteria 627

21 Phototrophic Bacteria 633

21.1 Light and Dark Reactions 63421.2 Phototrophic Phyla 63521.3 Proteobacteria 635

Purple Sulfur Bacteria 638Purple Nonsulfur Bacteria 641

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21.4 Chlorobi 64321.5 Chloroflexi 64721.6 Firmicutes—The Heliobacteria 64921.7 Cyanobacteria 649

Structure and Physiology 650Ecological and Environmental Significance of

Cyanobacteria 651Major Taxa of Cyanobacteria 654The Prochlorophytes: Chlorophyll a– and

Chlorophyll b–containing Cyanobacteria 657The Chloroplast 659

22 Exploring Bacterial Diversity: Other Phyla, Other Microbial Worlds663

22.1 Phyla Containing Thermophilic Bacteria 664Phylum Aquificae 665Phylum Thermodesulfobacteria 665Phylum Thermotogae 665Phylum Nitrospirae 666Phylum Deferribacteres 666Phylum Thermomicrobia 667Phylum Dictyoglomi 667Phylum Deinococcus–Thermus 667

22.2 Phyla that May Contain Thermophiles 669Phylum Bacteroidetes 669Phylum Fibrobacteres 672Phylum Spirochaetes 672Phylum Planctomycetes 675Phylum Chlamydiae 680Phylum Verrucomicrobia 680Phylum Chrysiogenetes 681Phylum Acidobacteria 681Phylum Fusobacteria 682

23 Eukaryotic Microorganisms 687

23.1 Eukaryotic Organelles 688The Cell Membrane and Cortex 688The Endomembrane Network 689The Cytoskeleton 691The Nucleus 694The Mitochondrion 695Plastids 696Other Organelles 696Diversity of Feeding Mechanisms 697Sex 697

23.2 Diversity of Protists 69823.3 Opisthokonta 698

Choanoflagellata 699Fungi 699Chytridiomycetes 700Zygomycota 701Glomeromycota 702Ascomycota 702Basidiomycota 706Urediniomycetes 708Ustilaginomycetes 710Microsporidia 711

23.4 Excavata 713Diplomonadida 713Parabasala 713Heterolobosea 714Euglenozoa 714

23.5 Rhizaria 717Foraminifera 717Radiolaria 718

23.6 Archaeplastida 719Rhodophyta 719Chloroplastida 721

23.7 Chromalveolates 723Cryptophyta 723Haptophyta 724Stramenopiles 724Alveolata 727

23.8 Amoebozoa 732Lobose Amoebas 732Eumycetozoa 732

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24 Microbial Ecology 73924.1 The Concept of an Ecosystem 74024.2 The Microenvironment 74124.3 Autecology: Ecology of the Species 742

Identification of Species in the Environment 743Enumeration of Microorganisms in the

Environment 743The Bacterial Enumeration Anomaly 745Sampling Environments and Assessing the Habitat

of a Species 747Evaluation of the Role of a Species 749

24.4 Microbial Communities 751Microbial Mat Communities and Biofilms 751Biomass and Biomarkers 753Is It a Microbial or Chemical Process? 753Rate Measurements 756

24.5 Major Environments 761Freshwater Habitats 761Marine Environments 764Terrestrial Environments 767Extreme Environments 768

24.6 Biogeochemical Cycles 772Atmospheric Effects of Nutrient Cycles 772Carbon Cycle 773Nitrogen Cycle 775Sulfur Cycle 776Other Cycles 778

24.7 Dispersal, Colonization, and Succession 77824.8 Biodiversity of Microbial Life 779

Assessing Microbial Diversity 780

24.9 Biogeography of Bacteria 781

25 Beneficial Symbiotic Associations 785

25.1 Functions of Symbiotic Relationships 786Protection 786Access to New Habitats 786Recognition Aids 787Nutrition 787

25.2 Establishment of Symbioses 78725.3 Types of Symbioses 78725.4 Microbe–Microbe Symbioses 788

“Chlorochromatium aggregatum” 788Bacteria–Archaea 788Archaea–Protist 788Lichens 788

25.5 Microbe–Plant Symbioses 789Rhizosphere 790Mycorrhizae 790Ectomycorrhizae 791Endomycorrhizae 792Frankia–Plant 792Rhizobium–Legume 792Azorhizobium–Legume 796Cyanobacteria–Plant 797Bacteria–Plant Leaf 797

25.6 Microbe–Animal Symbioses 798Symbiotic Invertebrates 798Termites–Microbes 800Aphid–Microbe 801Microbe–Mealybug 801Wolbachia–Animals 802Bioluminescent Bacteria–Fish 802Bacteria–Bird 803Ruminant Symbioses 806

Microbial Ecology 737VIPART

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27 Immunology 84727.1 Cells and General Organization of the Immune

System 84827.2 Inflammation and Innate Immunity 851

Early Events in Inflammation 852Activating Complement 854Recruiting Phagocytes to Sites of Infection 854Molecular Tags Facilitate Phagocytosis 857Phagocytosis and Killing of Infectious Agents 857Tissue Macrophages Originate from Monocytes 858Macrophage Pattern Receptors and Nonphagocytic

Defenses 858Surviving Phagocytosis—Intracellular Microbes 859Wasting, Fever, and the Acute Phase Response 860

27.3 Adaptive Immunity 861T-Cell Development 861Receptors of αβ T Cells 863

26 Human Host–Microbe Interaction 811

26.1 Normal Human Microbiota 813Skin 815Respiratory Tract 815Gastrointestinal Tract 816Genitourinary Tract 818

26.2 Host Barrier Defense 818Physical Barriers 818Mechanical Defenses 818Microbial Barriers 818Chemical Defenses 819

26.3 How Infectious Agents Overcome BarrierDefense: Adherence and Penetration byPathogens 820

Vector-Borne Infections 821Colonization by Bacteria 821Colonization by Viruses 823Colonization by Fungi 824Colonization by Protozoa 824

Colonization by Parasitic Worms 826

26.4 Inflammation and Phagocytosis: The SecondLevel of Host Defense 827

Avoiding Destruction by Phagocytes 828

26.5 Virulence and Pathology 828Bacteria 829Viruses 832Fungi 832Parasites 833Avoiding Adaptive Immunity by Antigenic

Variation 833Immunopathology 834

26.6 Life in Host Cells 835How Viruses Live in Host Cells 835How Bacteria and Protozoa Live in Phagocytes 836How Bacteria and Protozoa Live in Nonphagocytic

Host Cells 837Entry of Non-Viral Pathogens into Host Cells 838Avoiding Adaptive Immune Responses inside Cells

839Latent Infections of Host Cells 840

Immunology and Medical Microbiology 845VIIPART

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Antigen Presentation to CD4 T Cells 864CD4 T-Cell Effector Molecules: Cytokines 865Antigen Presentation to CD8 T Cells 866CD8 T-Cell Effector Function: Cytotoxicity and

Cytokines 868Memory Responses by T Cells 868B Cells: Basic Structure of an Immunoglobulin 868B-Cell Development 870B Cells and Antibodies 872B-Cell Activation and Immunoglobulin Heavy Chain

Switching 873B-Cell Maturation, Memory, and Secondary Immune

Responses 874Functions of Antibody Classes: IgG, IgA, IgM,

and IgE 876

27.4 Bridging Immune Responses 880Primitive T Cells: NK Cells 880Lymphoid Cells with Antigen-Specific Receptors: B-1

and Marginal Zone B Cells 882Lymphoid Cells with Antigen-Specific Receptors: γδ

T Cells 883Lymphoid Cells with Antigen-Specific Receptors:

CD1-Reactive T Cells 885

27.5 Vaccines 885Passive and Active Immunity 885

27.6 Dysfunctions of the Immune System 887Allergy 887Toxic Shock Syndrome and Endotoxemia 888Autoimmunity 889Immunodeficiencies 889

28 Microbial Diseases of Humans 893

28.1 Skin Infections 89428.2 Respiratory Infections 897

Diphtheria 899Whooping Cough 901

28.3 Pneumonia 904Pneumonia Caused by Streptococcus

pneumoniae 904Pneumonia Caused by Staphylococcus aureus 905Legionellosis 905Other Types of Pneumonia 906

28.4 Streptococcal Infections 907Infections Caused by Streptococcus pyogenes 907Streptococcus agalactiae 909

Meningitis 909

28.5 Tuberculosis 910Psittacosis (Ornithosis) 912

28.6 Leprosy 91228.7 Anthrax 913

Gas Gangrene 915

28.8 Fungal Diseases 915Histoplasmosis 915Coccidioidomycosis 916Aspergillosis 916Candidiasis 916Cryptococcosis 916

28.9 Bacterial Diseases of the Gastrointestinal Tract 917

Ulcers 917Food Poisoning 918

28.10 Food- and Water-Borne Infections 920Salmonellosis 920Cholera 921Dysentery 921Campylobacteriosis 922Escherichia coli 922Enterocolitis 923Listeriosis 923Clostridium perfringens 923Clostridium difficile 923Vibrio parahaemolyticus 923

28.11 Urinary Tract Infections 92428.12 Sexually Transmitted Diseases 924

Gonorrhea 924Syphilis 926Chlamydiae 927Chancroid 927

28.13 Vector-Borne Diseases 929Plague 929Lyme Disease 932Rocky Mountain Spotted Fever 932Typhus 933Scrub Typhus 934Q Fever 934Ehrlichiosis 934Relapsing Fever 934Tularemia 934Trench Fever 935Cat Scratch Disease 935Polymicrobial Diseases 935

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28.14 Protists as Agents of Disease 935Amebiasis 936Giardiasis 937Malaria 937

28.15 Zoonoses 938

29 Viral Diseases of Humans 943

29.1 Viral Infections Transmitted via the RespiratorySystem 944

Chicken Pox 945Rubella 945Measles 946Smallpox 947Mumps 948Influenza 949Cold Viruses 952Severe Acute Respiratory Syndrome (SARS) 953Respiratory Syncytial Virus 954

29.2 Viral Pathogens with Human Reservoirs 955Acute T-Cell Lymphocytic Leukemia 955Acquired Immune Deficiency Syndrome

(AIDS) 956Cold Sores (Fever Blisters) 959Genital Herpes 959Infectious Mononucleosis 960Poliomyelitis 960Hepatitis 962Warts 963Viral Gastroenteritis 963

29.3 Viral Diseases with Nonhuman Reservoirs 964Colorado Tick Fever 964Encephalitis 965Rabies 966Yellow Fever 967Bird Flu 967Ebola and Marburg 967West Nile 968Emerging Viruses 968

30 Epidemiology and Clinical Microbiology 973

30.1 Epidemiology 974Terminology 974Mortality and Morbidity 975

30.2 Carriers and Reservoirs 97630.3 Modes of Transmission of Infectious Diseases 976

Diseases Spread by Human Contact and AirborneTransmission 978

Water-, Food-, and Soil-Borne Infections 980Sexually Transmitted Diseases 980Vector-Borne Infections 982Animal Contact Diseases 982

30.4 Nosocomial (Hospital-Acquired) Infections 982Major Nosocomial Infections 983

30.5 Public Health Measures 98330.6 Control Measures for Communicable

Diseases 985Reservoir Control 985Quarantine 985Food and Water Measures 986Human and Animal Vaccination 986Antibiotic Resistance 987

30.7 World Health 987Problems in Developing Nations 988Problems in Developed Nations 989Problems for Travelers 989

30.8 Clinical and Diagnostic Methods 989Searching for Pathogens 990Obtaining Clinical Specimens 990

30.9 Identifying Pathogens 992Growth-Dependent Identification 995Serologic Identification 995Automated Identification Systems 995Antigen–Antibody Techniques 998Detection by Immunofluorescence 1000Agglutination 1000Plasmid Fingerprinting 1000Phage Typing 1001Nucleic Acid–Based Diagnostics 1001

30.10 Antibiotic Sensitivity 1003

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Contents xxv

31 Industrial Microbiology 1009

31.1 Microbes Involved in Industrial Processes 1010Primary and Secondary Metabolites 1010

31.2 Major Industrial Products 101131.3 Foods, Flavoring Agents and Food

Supplements, and Vitamins 1012Foods 1012Flavoring Agents and Food Supplements 1018Vitamins 1021

31.4 Beverages Containing Alcohol 1022Wine 1023Beer 1025Distilled Beverages 1026

31.5 Ethanol as Fuel 102731.6 Organic Acids 102831.7 Enzymes, Microbial Transformations, and

Inocula 1029Enzymes 1029Microbial Transformations 1030Inocula 1031

31.8 Inhibitors 1032Biocides 1032Antibiotics 1033Vaccines 1038

31.9 Genetically Engineered Microorganisms 1040Human Insulin 1040Human Growth Hormone 1041Other Cloned Genetic Systems 1041

32 Applied Environmental Microbiology 1045

32.1 Sewage (Wastewater) Treatment 1046Ecological Impact of Raw Sewage on Receiving

Water 1046Public Health Impact of Raw Sewage

Discharge 1047Primary Wastewater Treatment 1048Secondary Treatment 1048Microbial Treatment Problems 1049Tertiary Wastewater Treatment 1050

32.2 Drinking Water Treatment 1051Total Coliform Bacteria Analyses 1052Fecal Coliform Bacteria Analyses 1054

32.3 Landfills and Composting 1055Landfills 1055Composting 1056

32.4 Pesticides 1057Alternatives to Use of Persistent Pesticides 1058

32.5 Bioremediation 1058Biodegradative Organisms 1059Advantages of Bioremediation 1059Problems Associated with Bioremediation 1061Methodology of Bioremediation 1062Land Farming 1063The Future of Bioremediation 1063

32.6 Acid Mine Drainage and Acid Rain 1063

Appendix A–1

Glossary G–1

Notes on Part Opener and Chapter Opener Photos N–1

Index I–1

Applied Microbiology 1007VIIIPART

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