Contents

About the Authors iii 2.6 Arrangement of DNA in Microbial Cells 33

Preface v 2.7 The Evolutionary Tree of Life 34
Acknowledgments xv
III Microbial Diversity 36
UNIT 1 Basic Principles 2.8
2.9
Metabolic Diversity 36
Bacteria 38
of Microbiology 2.10 Archaea 41
2.11 Phylogenetic Analyses of Natural Microbial
Chapter 1 Microorganisms and Communities 43
Microbiology 1 2.12 Microbial Eukarya 43

I Introduction to Microbiology 2 Chapter 3 Cell Structure and Function

1.1 The Science of Microbiology 2 in Bacteria and Archaea 47
1.2 Microbial Cells 3
1.3 Microorganisms and Their Environments 5 I Cell Shape and Size 48
1.4 Evolution and the Extent of Microbial Life 5 3.1 Cell Morphology 48
1.5 The Impact of Microorganisms on Humans 7 3.2 Cell Size and the Significance of Smallness 49

II Pathways of Discovery in II The Cytoplasmic Membrane and

Microbiology 10 Transport 51
1.6 The Historical Roots of Microbiology: Hooke, 3.3 The Cytoplasmic Membrane 51
van Leeuwenhoek, and Cohn 11 3.4 Functions of the Cytoplasmic Membrane 54
1.7 Pasteur and the Defeat of Spontaneous 3.5 Transport and Transport Systems 56
Generation 12
1.8 Koch, Infectious Disease, and Pure Culture III Cell Walls of Prokaryotes 58
Microbiology 15 3.6 The Cell Wall of Bacteria: Peptidoglycan 58
1.9 The Rise of Microbial Diversity 18 3.7 The Outer Membrane 60
1.10 The Modern Era of Microbiology 20 3.8 Cell Walls of Archaea 63
Microbial Sidebar
Solid Media, Pure Cultures, and the Birth of IV Other Cell Surface Structures
Microbial Systematics 17 and Inclusions 64
3.9 Cell Surface Structures 64
Chapter 2 A Brief Journey to the Microbial 3.10 Cell Inclusions 66
World 24 3.11 Gas Vesicles 68
3.12 Endospores 69
I Seeing the Very Small 25
2.1 Some Principles of Light Microscopy 25 V Microbial Locomotion 73
2.2 Improving Contrast in Light Microscopy 26 3.13 Flagella and Motility 73
2.3 Imaging Cells in Three Dimensions 29 3.14 Gliding Motility 77
2.4 Electron Microscopy 30 3.15 Microbial Taxes 78
Microbial Sidebar
II Cell Structure and Evolutionary History 31 Can an Endospore Live Forever? 71
2.5 Elements of Microbial Structure 31

xix
xx Contents

IV Temperature and Microbial Growth 132

UNIT 2 Metabolism and Growth
Chapter 4 Nutrition, Culture, and Metabolism
of Microorganisms 85
I Nutrition and Culture of
Microorganisms 86
4.1 Nutrition and Cell Chemistry
4.2 Culture Media 88
4.3 Laboratory Culture 90
II Energetics and Enzymes 92
4.4 Bioenergetics 92
4.5 Catalysis and Enzymes 93
5.12 Effect of Temperature on Growth 134
5.13 Microbial Life in the Cold 134
5.14 Microbial Life at High Temperatures 138
V Other Environmental Factors
Affecting Growth 140
5.15 Acidity and Alkalinity 140
86
5.16 Osmotic Effects 141
5.17 Oxygen and Microorganisms 143
5.18 Toxic Forms of Oxygen 146
Microbial Sidebar
Microbial Growth in the Real World: Biofilms 133

III Oxidation–Reduction and Energy-Rich

UNIT 3 Molecular Biology
Compounds 94 and Gene Expression
4.6 Electron Donors and Electron Acceptors 94
4.7 Energy-Rich Compounds and Energy Storage 97 Chapter 6 Molecular Biology of Bacteria 150

IV Essentials of Catabolism 98 I DNA Structure and Genetic

4.8 Glycolysis 98 Information 151
4.9 Respiration and Electron Carriers 101 6.1 Macromolecules and Genes 151
4.10 The Proton Motive Force 103 6.2 The Double Helix 153
4.11 The Citric Acid Cycle 105 6.3 Supercoiling 155
4.12 Catabolic Diversity 106 6.4 Chromosomes and Other Genetic Elements 156

V Essentials of Anabolism 108 II Chromosomes and Plasmids 157

4.13 Biosynthesis of Sugars and Polysaccharides 108 6.5 The Escherichia coli Chromosome 157
4.14 Biosynthesis of Amino Acids and Nucleotides 109 6.6 Plasmids: General Principles 159
4.15 Biosynthesis of Fatty Acids and Lipids 110 6.7 The Biology of Plasmids 161
4.16 Regulating the Activity of Biosynthetic Enzymes 111
III DNA Replication 162
Microbial Sidebar
6.8 Templates and Enzymes 162
Yeast Fermentation, the Pasteur Effect, and the
Home Brewer 99 6.9 The Replication Fork 163
6.10 Bidirectional Replication and the Replisome 165
6.11 The Polymerase Chain Reaction (PCR) 169
Chapter 5 Microbial Growth 117
IV RNA Synthesis: Transcription 170
I Bacterial Cell Division 118
6.12 Overview of Transcription 170
5.1 Cell Growth and Binary Fission 118
6.13 Sigma Factors and Consensus Sequences 172
5.2 Fts Proteins and Cell Division 118
6.14 Termination of Transcription 173
5.3 MreB and Determinants of Cell Morphology 120
6.15 The Unit of Transcription 173
5.4 Peptidoglycan Synthesis and Cell Division 121
V Protein Structure and Synthesis 174
II Population Growth 123
6.16 Polypeptides, Amino Acids, and the Peptide
5.5 The Concept of Exponential Growth 123
Bond 174
5.6 The Mathematics of Exponential Growth 124
6.17 Translation and the Genetic Code 175
5.7 The Microbial Growth Cycle 125
6.18 Transfer RNA 178
5.8 Continuous Culture: The Chemostat 126
6.19 Steps in Protein Synthesis 180
6.20 The Incorporation of Selenocysteine
III Measuring Microbial Growth 128
and Pyrrolysine 183
5.9 Microscopic Counts 128 6.21 Folding and Secreting Proteins 183
5.10 Viable Counts 129
5.11 Turbidimetric Methods 131
 Contents xxi

Chapter 7 Archaeal and Eukaryotic UNIT 4 Virology, Genetics,

Molecular Biology 191
and Genomics
I Molecular Biology of Archaea 192
7.1 Chromosomes and DNA Replication in Archaea 192 Chapter 9 Viruses and Virology 236
7.2 Transcription and RNA Processing in Archaea 193
7.3 Protein Synthesis in Archaea 195 I Virus Structure and Growth 237
7.4 Shared Features of Bacteria and Archaea 196 9.1 General Properties of Viruses 237
9.2 Nature of the Virion 238
II Eukaryotic Molecular Biology 197 9.3 The Virus Host 241
7.5 Genes and Chromosomes in Eukarya 197 9.4 Quantification of Viruses 241
7.6 Overview of Eukaryotic Cell Division 198
7.7 Replication of Linear DNA 199 II Viral Replication 243
7.8 RNA Processing 200 9.5 General Features of Virus Replication 243
7.9 Transcription and Translation in Eukarya 203 9.6 Viral Attachment and Penetration 244
7.10 RNA Interference (RNAi) 205 9.7 Production of Viral Nucleic Acid and Protein 245
7.11 Regulation by MicroRNA 205
III Viral Diversity 247
Microbial Sidebar
9.8 Overview of Bacterial Viruses 247
Inteins and Protein Splicing 203
9.9 Virulent Bacteriophages and T4 250
9.10 Temperate Bacteriophages, Lambda and P1 251
Chapter 8 Regulation of Gene Expression 209 9.11 Overview of Animal Viruses 254
9.12 Retroviruses 255
I Overview of Regulation 210
8.1 Major Modes of Regulation 210 IV Subviral Entities 257
9.13 Defective Viruses 257
II DNA-Binding Proteins and
9.14 Viroids 257
Regulation of Transcription 210
9.15 Prions 258
8.2 DNA-Binding Proteins 211
8.3 Negative Control of Transcription: Microbial Sidebar
Repression and Induction 212 Did Viruses Invent DNA? 248
8.4 Positive Control of Transcription 214
8.5 Global Control and the lac Operon 216 Chapter 10 Genetics of Bacteria
8.6 Control of Transcription in Archaea 217 and Archaea 263
III Sensing and Signal Transduction 218 I Mutation 264
8.7 Two-Component Regulatory Systems 218 10.1 Mutations and Mutants 264
8.8 Regulation of Chemotaxis 220 10.2 Molecular Basis of Mutation 266
8.9 Quorum Sensing 221 10.3 Mutation Rates 268
8.10 The Stringent Response 223 10.4 Mutagenesis 269
8.11 Other Global Control Networks 224 10.5 Mutagenesis and Carcinogenesis: The Ames Test 272

IV Regulation of Development II Gene Transfer 273

in Model Bacteria 225 10.6 Genetic Recombination 273
8.12 Sporulation in Bacillus 226 10.7 Transformation 275
8.13 Caulobacter Differentiation 227 10.8 Transduction 277
10.9 Conjugation: Essential Features 279
V RNA-Based Regulation 228 10.10 The Formation of Hfr Strains and
8.14 RNA Regulation and Antisense RNA 228 Chromosome Mobilization 281
8.15 Riboswitches 230 10.11 Complementation 284
8.16 Attenuation 231 10.12 Gene Transfer in Archaea 285
10.13 Mobile DNA: Transposable Elements 286
Microbial Sidebar
The CRISPR Antiviral Defense System 229
xxii Contents

Chapter 11 Genetic Engineering 291 II Chemolithotrophy 353

13.6 The Energetics of Chemolithotrophy 353
I Methods for Manipulating DNA 292 13.7 Hydrogen Oxidation 354
11.1 Restriction and Modification Enzymes 292 13.8 Oxidation of Reduced Sulfur Compounds 354
11.2 Nucleic Acid Hybridization 294 13.9 Iron Oxidation 356
11.3 Essentials of Molecular Cloning 295 13.10 Nitrification 358
11.4 Molecular Methods for Mutagenesis 297 13.11 Anammox 359
11.5 Gene Fusions and Reporter Genes 299
III Major Biosyntheses: Autotrophy
II Gene Cloning 300 and Nitrogen Fixation 361
11.6 Plasmids as Cloning Vectors 300 13.12 The Calvin Cycle 361
11.7 Hosts for Cloning Vectors 302 13.13 Other Autotrophic Pathways in Phototrophs 362
11.8 Shuttle Vectors and Expression Vectors 304 13.14 Nitrogen Fixation and Nitrogenase 363
11.9 Bacteriophage Lambda as a Cloning Vector 307 13.15 Genetics and Regulation of N2 Fixation 367
11.10 Vectors for Genomic Cloning and Sequencing 308
Microbial Sidebar Chapter 14 Catabolism of Organic
Combinatorial Fluorescence Labeling 301 Compounds 372

Chapter 12 Microbial Genomics 313 I Fermentations 373

14.1 Energetic and Redox Considerations 373
I Genomes and Genomics 314 14.2 Lactic and Mixed-Acid Fermentations 374
12.1 Introduction to Genomics 314 14.3 Clostridial and Propionic Acid Fermentations 377
12.2 Sequencing and Annotating Genomes 314 14.4 Fermentations Lacking Substrate-Level
12.3 Bioinformatic Analyses and Gene Distributions 318 Phosphorylation 379
12.4 The Genomes of Eukaryotic Organelles 323 14.5 Syntrophy 381
12.5 The Genomes of Eukaryotic Microorganisms 325
12.6 Metagenomics 327 II Anaerobic Respiration 383
14.6 Anaerobic Respiration: General Principles 383
II Genome Function and Regulation 327 14.7 Nitrate Reduction and Denitrification 384
12.7 Microarrays and the Transcriptome 327 14.8 Sulfate and Sulfur Reduction 386
12.8 Proteomics and the Interactome 329 14.9 Acetogenesis 388
12.9 Metabolomics 331 14.10 Methanogenesis 390
14.11 Proton Reduction 394
III The Evolution of Genomes 332 14.12 Other Electron Acceptors 395
12.10 Gene Families, Duplications, and Deletions 332 14.13 Anoxic Hydrocarbon Oxidation Linked
12.11 Horizontal Gene Transfer and Genome Stability 333 to Anaerobic Respiration 397
12.12 Transposons and Insertion Sequences 334
12.13 Evolution of Virulence: Pathogenicity Islands 335 III Aerobic Chemoorganotrophic
Processes 400
Microbial Sidebar
14.14 Molecular Oxygen as a Reactant and Aerobic
Record-Holding Bacterial Genomes 320
Hydrocarbon Oxidation 400
14.15 Methylotrophy and Methanotrophy 401
UNIT 5 Metabolic Diversity and 14.16 Sugar and Polysaccharide Metabolism 403
14.17 Organic Acid Metabolism 406
Commercial Biocatalyses 14.18 Lipid Metabolism 406

Chapter 13 Phototrophy, Chemolithotrophy, Chapter 15 Commercial Products

and Major Biosyntheses 340 and Biotechnology 411
I Phototrophy 341 I Putting Microorganisms to Work 412
13.1 Photosynthesis 341
15.1 Industrial Products and the Microorganisms
13.2 Chlorophylls and Bacteriochlorophylls 342 That Make Them 412
13.3 Carotenoids and Phycobilins 345 15.2 Production and Scale 412
13.4 Anoxygenic Photosynthesis 346
13.5 Oxygenic Photosynthesis 350
 Contents xxiii

II Drugs, Other Chemicals, and III Microbial Systematics 463

Enzymes 415 16.10 Phenotypic Analysis: Fatty Acid
15.3 Antibiotics: Isolation, Yield, and Purification 415 Methyl Esters (FAME) 463
15.4 Industrial Production of Penicillins 16.11 Genotypic Analysis 465
and Tetracyclines 417 16.12 The Species Concept in Microbiology 467
15.5 Vitamins and Amino Acids 419 16.13 Classification and Nomenclature 470
15.6 Enzymes as Industrial Products 420
Chapter 17 Bacteria: The Proteobacteria 475
III Alcoholic Beverages and Biofuels 423
15.7 Wine 423 I The Phylogeny of Bacteria 476
15.8 Brewing and Distilling 425 17.1 Phylogenetic Overview of Bacteria 476
15.9 Biofuels 427
II Phototrophic, Chemolithotrophic, and
IV Products from Genetically Engineered Methanotrophic Proteobacteria 477
Microorganisms 428 17.2 Purple Phototrophic Bacteria 478
15.10 Expressing Mammalian Genes in Bacteria 429 17.3 The Nitrifying Bacteria 481
15.11 Production of Genetically Engineered 17.4 Sulfur- and Iron-Oxidizing Bacteria 482
Somatotropin 431 17.5 Hydrogen-Oxidizing Bacteria 485
15.12 Other Mammalian Proteins and Products 432 17.6 Methanotrophs and Methylotrophs 486
15.13 Genetically Engineered Vaccines 433
15.14 Mining Genomes 435 III Aerobic and Facultatively Aerobic
15.15 Engineering Metabolic Pathways 435 Chemoorganotrophic Proteobacteria 488
17.7 Pseudomonas and the Pseudomonads 489
V Transgenic Eukaryotes 437 17.8 Acetic Acid Bacteria 491
15.16 Genetic Engineering of Animals 437 17.9 Free-Living Aerobic Nitrogen-Fixing Bacteria 491
15.17 Gene Therapy in Humans 439 17.10 Neisseria, Chromobacterium, and Relatives 493
15.18 Transgenic Plants in Agriculture 439 17.11 Enteric Bacteria 494
Microbial Sidebar 17.12 Vibrio, Aliivibrio, and Photobacterium 496
Synthetic Biology and Microbial 17.13 Rickettsias 498
Photography 436
IV Morphologically Unusual Proteobacteria 499
17.14 Spirilla 500
UNIT 6 Microbial Evolution 17.15 Sheathed Proteobacteria: Sphaerotilus and
and Diversity Leptothrix 502
17.16 Budding and Prosthecate/Stalked Bacteria 503
Chapter 16 Microbial Evolution and
V Delta- and Epsilonproteobacteria 507
Systematics 446
17.17 Myxobacteria 507
I Early Earth and the Origin and 17.18 Sulfate- and Sulfur-Reducing Proteobacteria 510
17.19 The Epsilonproteobacteria 512
Diversification of Life 447
16.1 Formation and Early History of Earth 447
16.2 Origin of Cellular Life 448 Chapter 18 Other Bacteria 517
16.3 Microbial Diversification: Consequences
I Firmicutes, Mollicutes,
for Earth’s Biosphere 451
16.4 Endosymbiotic Origins of Eukaryotes 452
and Actinobacteria 518
18.1 Nonsporulating Firmicutes 518
II Microbial Evolution 454 18.2 Endospore-Forming Firmicutes 521
16.5 The Evolutionary Process 454 18.3 Mollicutes: The Mycoplasmas 525
16.6 Evolutionary Analyses: Theoretical Aspects 455 18.4 Actinobacteria: Coryneform and
16.7 Evolutionary Analyses: Analytical Methods 457 Propionic Acid Bacteria 526
16.8 Microbial Phylogeny 459 18.5 Actinobacteria: Mycobacterium 528
16.9 Applications of SSU rRNA Phylogenetic 18.6 Filamentous Actinomycetes: Streptomyces
Methods 462 and Relatives 529
xxiv Contents

II Cyanobacteria and Prochlorophytes 532 III Crenarchaeota 570

18.7 Cyanobacteria 532 19.8 Habitats and Energy Metabolism 570
18.8 Prochlorophytes 536 19.9 Crenarchaeota from Terrestrial Volcanic Habitats 571
19.10 Crenarchaeota from Submarine Volcanic Habitats 574
III Chlamydia 537 19.11 Crenarchaeota from Nonthermal Habitats and
18.9 The Chlamydia 537 Nitrification in Archaea 576

IV The Planctomycetes 539 IV Evolution and Life at High

18.10 Planctomyces: A Phylogenetically
Unique Stalked Bacterium 539
V The Verrucomicrobia 540
18.11 Verrucomicrobium and Prosthecobacter
Temperatures 577
19.12 An Upper Temperature Limit for Microbial Life 577
19.13 Molecular Adaptations to Life at High Temperature 578
19.14 Hyperthermophilic Archaea, H2, and Microbial
540 Evolution 580

VI The Flavobacteria and Acidobacteria 541 Chapter 20 Eukaryotic Cell Biology and
18.12 Bacteroides and Flavobacterium 541 Eukaryotic Microorganisms 584
18.13 Acidobacteria 541
I Eukaryotic Cell Structure and
VII The Cytophaga Group 542 Function 585
18.14 Cytophaga and Relatives 542 20.1 Eukaryotic Cell Structure and the Nucleus 585
20.2 The Mitochondrion and the Hydrogenosome 586
VIII Green Sulfur Bacteria 543 20.3 The Chloroplast 587
18.15 Chlorobium and Other Green Sulfur Bacteria 543 20.4 Endosymbiosis: Relationships of Mitochondria and
Chloroplasts to Bacteria 588
IX The Spirochetes 545 20.5 Other Organelles and Eukaryotic Cell Structures 589
18.16 Spirochetes 545
II Eukaryotic Microbial Diversity 591
X The Deinococci 548 20.6 Phylogeny of the Eukarya 591
18.17 Deinococcus and Thermus 548
III Protists 593
XI The Green Nonsulfur Bacteria: 20.7 Diplomonads and Parabasalids 593
Chloroflexi 549 20.8 Euglenozoans 594
18.18 Chloroflexus and Relatives 549 20.9 Alveolates 594
20.10 Stramenopiles 596
XII Hyperthermophilic Bacteria 550 20.11 Cercozoans and Radiolarians 598
18.19 Thermotoga and Thermodesulfobacterium 550 20.12 Amoebozoa 598
18.20 Aquifex, Thermocrinis, and Relatives 551
IV Fungi 601
XIII Nitrospira and Deferribacter 552 20.13 Fungal Physiology, Structure, and Symbioses 601
18.21 Nitrospira and Deferribacter 552 20.14 Fungal Reproduction and Phylogeny 603
20.15 Chytridiomycetes 604
Chapter 19 Archaea 556 20.16 Zygomycetes and Glomeromycetes 604
20.17 Ascomycetes 605
I Diversity 557 20.18 Basidiomycetes and the Mushroom Life Cycle 607
19.1 Phylogenetic and Metabolic Diversity of Archaea 557
V Red and Green Algae 607
II Euryarchaeota 558 20.19 Red Algae 608
19.2 Extremely Halophilic Archaea 558 20.20 Green Algae 608
19.3 Methanogenic Archaea 562
19.4 Thermoplasmatales 565 Chapter 21 Viral Diversity 613
19.5 Thermococcales and Methanopyrus 567
19.6 Archaeoglobales 568 I Viruses of Bacteria and Archaea 614
19.7 Nanoarchaeum and Aciduliprofundum 569 21.1 RNA Bacteriophages 614
21.2 Single-Stranded DNA Bacteriophages 615
 Contents xxv

21.3 Double-Stranded DNA Bacteriophages 618 II The Microbial Environment 672

21.4 The Transposable Phage Mu 620 23.3 Environments and Microenvironments 672
21.5 Viruses of Archaea 622 23.4 Surfaces and Biofilms 674
21.6 Viral Genomes in Nature 623 23.5 Microbial Mats 677

II RNA Viruses of Eukaryotes 623 III Terrestrial Environments 678

21.7 Plant RNA Viruses 624 23.6 Soils 678
21.8 Positive-Strand RNA Animal Viruses 624 23.7 The Subsurface 681
21.9 Negative-Strand RNA Animal Viruses 627
21.10 Double-Stranded RNA Viruses: Reoviruses 629 IV Aquatic Environments 683
21.11 Retroviruses and Hepadnaviruses 630 23.8 Freshwaters 683
23.9 Coastal and Ocean Waters: Phototrophic
III DNA Viruses of Eukaryotes 633 Microorganisms 685
21.12 Plant DNA Viruses 633 23.10 Pelagic Bacteria, Archaea, and Viruses 687
21.13 Polyomaviruses: SV40 635 23.11 The Deep Sea and Deep-Sea Sediments 690
21.14 Herpesviruses 636 23.12 Hydrothermal Vents 693
21.15 Pox Viruses 637
21.16 Adenoviruses 638 Chapter 24 Nutrient Cycles, Biodegradation,
Microbial Sidebar and Bioremediation 698
Mimivirus and Viral Evolution 634
I Nutrient Cycles 699
UNIT 7 Microbial Ecology 24.1
24.2
The Carbon Cycle 699
Syntrophy and Methanogenesis 701
24.3 The Nitrogen Cycle 703
Chapter 22 Methods in Microbial Ecology 642 24.4 The Sulfur Cycle 705
24.5 The Iron Cycle 706
I Culture-Dependent Analyses
24.6 The Phosphorus, Calcium, and Silica Cycles 709
of Microbial Communities 643
22.1 Enrichment 643 II Biodegradation and Bioremediation 711
22.2 Isolation 647
24.7 Microbial Leaching 711
24.8 Mercury Transformations 713
II Culture-Independent Analyses
24.9 Petroleum Biodegradation and Bioremediation 714
of Microbial Communities 649
24.10 Xenobiotics Biodegradation and Bioremediation 715
22.3 General Staining Methods 649
22.4 Fluorescence In Situ Hybridization (FISH) 651 Microbial Sidebar
22.5 PCR Methods of Microbial Community Analysis 652 Microbially Wired 707
22.6 Microarrays and Microbial Diversity: Phylochips 655
22.7 Environmental Genomics and Related Methods 656 Chapter 25 Microbial Symbioses 720

III Measuring Microbial Activities I Symbioses between Microorganisms 721

in Nature 658 25.1 Lichens 721
22.8 Chemical Assays, Radioisotopic Methods, 25.2 “Chlorochromatium aggregatum” 722
and Microelectrodes 658
22.9 Stable Isotopes 660 II Plants as Microbial Habitats 723
22.10 Linking Specific Genes and Functions 25.3 The Legume–Root Nodule Symbiosis 723
to Specific Organisms 662 25.4 Agrobacterium and Crown Gall Disease 729
25.5 Mycorrhizae 730
Chapter 23 Major Microbial Habitats
III Mammals as Microbial Habitats 732
and Diversity 669
25.6 The Mammalian Gut 732
I Microbial Ecology 670 25.7 The Rumen and Ruminant Animals 734
23.1 General Ecological Concepts 670 25.8 The Human Microbiome 738
23.2 Ecosystem Service: Biogeochemistry
and Nutrient Cycles 671
xxvi Contents

IV Insects as Microbial Habitats 741 27.1 Overview of Human–Microbial Interactions 788

25.9 Heritable Symbionts of Insects 741 27.2 Normal Microflora of the Skin 790
25.10 Termites 744 27.3 Normal Microflora of the Oral Cavity 791
27.4 Normal Microflora of the Gastrointestinal Tract 793
V Aquatic Invertebrates 27.5 Normal Microflora of Other Body Regions 797
as Microbial Habitats 745
25.11 Hawaiian Bobtail Squid 746
II Microbial Virulence and Pathogenesis 798
25.12 Marine Invertebrates at Hydrothermal 27.6 Measuring Virulence 798
Vents and Gas Seeps 747 27.7 Entry of the Pathogen into the Host—Adherence 799
25.13 Leeches 749 27.8 Colonization and Infection 801
25.14 Reef-Building Corals 750 27.9 Invasion 802
27.10 Exotoxins 804
Microbial Sidebar
27.11 Endotoxins 807
The Multiple Microbial Symbionts
of Fungus-Cultivating Ants 743 III Host Factors in Infection 808
27.12 Host Risk Factors for Infection 809
UNIT 8 Antimicrobial Agents 27.13 Innate Resistance to Infection 811

and Pathogenicity Microbial Sidebar

Probiotics 796
Chapter 26 Microbial Growth Control 755 Microbial Sidebar
Virulence in Salmonella 810
I Physical Antimicrobial Control 756
26.1 Heat Sterilization 756
26.2 Radiation Sterilization 759 UNIT 9 Immunology
26.3 Filter Sterilization 760
Chapter 28 Immunity and Host Defense 816
II Chemical Antimicrobial Control 762
I Immunity 817
26.4 Chemical Growth Control 762
26.5 Chemical Antimicrobial Agents for External Use 763 28.1 Cells and Organs of the Immune System 817
28.2 Innate Immunity 820
III Antimicrobial Agents Used In Vivo 767 28.3 Adaptive Immunity 821
26.6 Synthetic Antimicrobial Drugs 767 28.4 Antibodies 822
26.7 Natural Antimicrobial Drugs: Antibiotics 770 28.5 Inflammation 824
26.8 β-Lactam Antibiotics: Penicillins and
Cephalosporins 771
II Prevention of Infectious Disease 826
26.9 Antibiotics from Prokaryotes 772 28.6 Natural Immunity 826
28.7 Artificial Immunity and Immunization 827
IV Control of Viruses and 28.8 New Immunization Strategies 829
Eukaryotic Pathogens 774
III Immune Diseases 830
26.10 Antiviral Drugs 774
26.11 Antifungal Drugs 776 28.9 Allergy, Hypersensitivity, and Autoimmunity 830
28.10 Superantigens: Overactivation of T Cells 834
V Antimicrobial Drug Resistance and Microbial Sidebar
Drug Discovery 778 The Promise of New Vaccines 831
26.12 Antimicrobial Drug Resistance 778
26.13 The Search for New Antimicrobial Drugs 782 Chapter 29 Immune Mechanisms 838
Microbial Sidebar
I Overview of Immunity 839
Preventing Antimicrobial Drug Resistance 766
29.1 Innate Response Mechanisms 839
29.2 Adaptive Response Mechanisms 842
Chapter 27 Microbial Interactions with
Humans 787 II Antigens and Antigen Presentation 843
29.3 Immunogens and Antigens 843
I Beneficial Microbial Interactions with
29.4 Antigen Presentation to T Cells 844
Humans 788
 Contents xxvii

III T Lymphocytes and Immunity 847 31.7 In Vitro Antigen–Antibody Reactions: Serology 895
29.5 T-Cytotoxic Cells and Natural Killer Cells 847 31.8 Agglutination 897
29.6 T-Helper Cells 848 31.9 Immunofluorescence 898
31.10 Enzyme Immunoassay and Radioimmunoassay 900
IV Antibodies and Immunity 849 31.11 Immunoblots 905
29.7 Antibodies 850
29.8 Antibody Production 852 III Nucleic Acid–Based Diagnostic
29.9 Antibodies, Complement, and Pathogen Methods 906
Destruction 855 31.12 Nucleic Acid Hybridization 906
31.13 Nucleic Acid Amplification 908
Chapter 30 Molecular Immunology 859
Chapter 32 Epidemiology 913
I Receptors and Immunity 860
30.1 Innate Immunity and Pattern Recognition 860 I Principles of Epidemiology 914
30.2 Adaptive Immunity and the Immunoglobulin 32.1 The Science of Epidemiology 914
Superfamily 862 32.2 The Vocabulary of Epidemiology 914
32.3 Disease Reservoirs and Epidemics 916
II The Major Histocompatibility 32.4 Infectious Disease Transmission 919
Complex (MHC) 864 32.5 The Host Community 921
30.3 MHC Protein Structure 864
30.4 MHC Polymorphism and Antigen Binding 866 II Current Epidemics 922
32.6 The HIV/AIDS Pandemic 922
III Antibodies 866 32.7 Healthcare-Associated Infections 925
30.5 Antibody Proteins and Antigen Binding 866
30.6 Antibody Genes and Diversity 867 III Epidemiology and Public Health 926
32.8 Public Health Measures for the Control of Disease 926
IV T Cell Receptors 869 32.9 Global Health Considerations 929
30.7 T Cell Receptors: Proteins, Genes and Diversity 869 32.10 Emerging and Reemerging Infectious Diseases 931
32.11 Biological Warfare and Biological Weapons 936
V Molecular Switches in Immunity 871 32.12 Anthrax as a Biological Weapon 939
30.8 Clonal Selection and Tolerance 871 Microbial Sidebar
30.9 T Cell and B Cell Activation 873 Swine Flu—Pandemic (H1N1) 2009 Influenza 923
30.10 Cytokines and Chemokines 874
Microbial Sidebar
Microbial Sidebar SARS as a Model of Epidemiological Success 938
Drosophila Toll Receptors—An Ancient
Response to Infections 861
UNIT 11 Human- and Animal-
UNIT 10 Diagnosing and Tracking Transmitted Infectious
Microbial Diseases Diseases
Chapter 31 Diagnostic Microbiology Chapter 33 Person-to-Person
and Immunology 878 Microbial Diseases 944

I Growth-Dependent I Airborne Transmission of Diseases 945

Diagnostic Methods 879 33.1 Airborne Pathogens 945
31.1 Isolation of Pathogens from Clinical Specimens 879 33.2 Streptococcal Diseases 946
31.2 Growth-Dependent Identification Methods 884 33.3 Diphtheria and Pertussis 949
31.3 Antimicrobial Drug Susceptibility Testing 888 33.4 Mycobacterium, Tuberculosis, and Hansen’s
31.4 Safety in the Microbiology Laboratory 888 Disease 951
33.5 Neisseria meningitidis, Meningitis, and
II Immunology and Diagnostic Methods 892 Meningococcemia 954
33.6 Viruses and Respiratory Infections 954
31.5 Immunoassays for Infectious Disease 892
33.7 Colds 957
31.6 Polyclonal and Monoclonal Antibodies 894
33.8 Influenza 958
xxviii Contents

II Direct-Contact Transmission II Waterborne Microbial Diseases 1012

of Diseases 961 35.4 Sources of Waterborne Infection 1012
33.9 Staphylococcus 961 35.5 Cholera 1013
33.10 Helicobacter pylori and Gastric Ulcers 963 35.6 Giardiasis and Cryptosporidiosis 1015
33.11 Hepatitis Viruses 964 35.7 Legionellosis (Legionnaires’ Disease) 1017
35.8 Typhoid Fever and Other Waterborne Diseases 1018
III Sexually Transmitted Infections 965
33.12 Gonorrhea and Syphilis 966 Chapter 36 Food Preservation and Foodborne
33.13 Chlamydia, Herpes, Trichomoniasis, Microbial Diseases 1022
and Human Papillomavirus 969
33.14 Acquired Immunodeficiency Syndrome: I Food Preservation and Microbial
AIDS and HIV 971 Growth 1023
36.1 Microbial Growth and Food Spoilage 1023
Chapter 34 Vectorborne and Soilborne 36.2 Food Preservation 1024
Microbial Pathogens 981 36.3 Fermented Foods and Mushrooms 1027

II Animal-Transmitted Pathogens 982 II Foodborne Disease, Microbial

34.1 Rabies Virus 982 Sampling, and Epidemiology 1030
34.2 Hantavirus 984 36.4 Foodborne Disease and Microbial Sampling 1031
36.5 Foodborne Disease Epidemiology 1032
II Arthropod-Transmitted Pathogens 986
34.3 Rickettsial Pathogens 986 III Food Poisoning 1033
34.4 Lyme Disease and Borrelia 989 36.6 Staphylococcal Food Poisoning 1033
34.5 Malaria and Plasmodium 991 36.7 Clostridial Food Poisoning 1034
34.6 West Nile Virus 995
34.7 Plague and Yersinia 996 IV Food Infection 1036
36.8 Salmonellosis 1036
III Soilborne Pathogens 998 36.9 Pathogenic Escherichia coli 1037
34.8 Fungal Pathogens 998 36.10 Campylobacter 1038
34.9 Tetanus and Clostridium tetani 1000 36.11 Listeriosis 1039
Microbial Sidebar 36.12 Other Foodborne Infectious Diseases 1040
Special Pathogens and
Viral Hemorrhagic Fevers 985 Appendix 1 Energy Calculations in Microbial
Bioenergetics A-1
UNIT 12 Common-Source
Appendix 2 Bergey’s Manual of Systematic
Infectious Disease Bacteriology, Second Edition:
List of Genera and Higher-Order
Chapter 35 Wastewater Treatment, Water
Taxa A-5
Purification, and Waterborne
Microbial Diseases 1004 Glossary G-1
I Wastewater Microbiology
and Water Purification 1005 Photo Credits P-1
35.1 Public Health and Water Quality 1005
35.2 Wastewater and Sewage Treatment 1007 Index I-1
35.3 Drinking Water Purification 1010