Brock Biology of Microorganisms, Sixteenth Edition
By Michael t. Madigan, Kelly s. Bender, Daniel h. Buckley, W. Matthew sattley, and David a. Stahl
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