About the Authors 3
Preface 5
Acknowledgments 15
UNIT 1 Basic Principles of Microbiology 29
Chapter 1 Microorganisms and Microbiology 29
Ⅰ Introduction to Microbiology 30
1.1 The Science of Microbiology 30
1.2 Microbial Cells 31
1.3 Microorganisms and Their Environments 32
1.4 Evolution and the Extent of Microbial Life 33
1.5 The Impact of Microorganisms on Humans 35
Ⅱ Pathways of Discovery in Microbiology 38
1.6 The Historical Roots of Microbiology：Hooke，van Leeuwenhoek，and Cohn 39
1.7 Pasteur and the Defeat of Spontaneous Generation 40
1.8 Koch，Infectious Disease，and Pure Culture Microbiology 43
1.9 The Rise of Microbial Diversity 46
1.10 The Modern Era of Microbiology 48
Microbial Sidebar 45
Solid Media，Pure Cultures，and the Birth of Microbial Systematics 45
Chapter 2 A Brief Journey to the Microbial World 52
Ⅰ Seeing the Very Small 53
2.1 Some Principles of Light Microscopy 53
2.2 Improving Contrast in Light Microscopy 54
2.3 Imaging Cells in Three Dimensions 57
2.4 Electron Microscopy 58
Ⅱ Cell Structure and Evolutionary History 59
2.5 Elements of Microbial Structure 59
2.6 Arrangement of DNA in Microbial Cells 61
2.7 The Evolutionary Tree of Life 62
Ⅲ Microbial Diversity 64
2.8 Metabolic Diversity 64
2.9 Bacteria 66
2.10 Archaea 69
2.11 Phylogenetic Analyses of Natural Microbial Communities 71
2.12 Microbial Eukarya 71
Chapter 3 Cell Structure and Function in Bacteria and Archaea 75
Ⅰ Cell Shape and Size 76
3.1 Cell Morphology 76
3.2 Cell Size and the Significance of Smallness 77
Ⅱ The Cytoplasmic Membrane and Transport 79
3.3 The Cytoplasmic Membrane 79
3.4 Functions of the Cytoplasmic Membrane 82
3.5 Transport and Transport Systems 83
Ⅲ Cell Walls of Prokaryotes 86
3.6 The Cell Wall of Bacteria：Peptidoglycan 86
3.7 The Outer Membrane 88
3.8 Cell Walls of Archaea 91
Ⅳ Other Cell Surface Structures and Inclusions 92
3.9 Cell Surface Structures 92
3.10 Cell Inclusions 94
3.11 Gas Vesicles 96
3.12 Endospores 97
Ⅴ Microbial Locomotion 101
3.13 Flagella and Motility 101
3.14 Gliding Motility 105
3.15 Microbial Taxes 106
Microbial Sidebar 99
The Mycobacterium tuberculosis Cell Wall：A Complex Architecture of Lipids and Carbohydrates 99
UNIT 2 Metabolism and Growth 113
Chapter 4 Nutrition，Culture，and Metabolism of Microorganisms 113
Ⅰ Nutrition and Culture of Microorganisms 114
4.1 Nutrition and Cell Chemistry 114
4.2 Culture Media 116
4.3 Laboratory Culture 118
Ⅱ Energetics and Enzymes 120
4.4 Bioenergetics 120
4.5 Catalysis and Enzymes 121
Ⅲ Oxidation-Reduction and Energy-Rich Compounds 122
4.6 Electron Donors and Electron Acceptors 122
4.7 Energy-Rich Compounds and Energy Storage 125
Ⅳ Essentials of Catabolism 126
4.8 Glycolysis 126
4.9 Respiration and Electron Carriers 129
4.10 The Proton Motive Force 131
4.11 The Citric Acid Cycle 133
4.12 Catabolic Diversity 134
Ⅴ Essentials of Anabolism 136
4.13 Biosynthesis of Sugars and Polysaccharides 136
4.14 Biosynthesis of Amino Acids and Nucleotides 137
4.15 Biosynthesis of Fatty Acids and Lipids 138
4.16 Regulating the Activity of Biosynthetic Enzymes 139
Microbial Sidebar 127
Yeast Fermentation，the Pasteur Effect，and the Home Brewer 127
Chapter 5 Microbial Growth 145
Ⅰ Bacterial Cell Division 146
5.1 Cell Growth and Binary Fission 146
5.2 Fts Proteins and Cell Division 146
5.3 MreB and Determinants of Cell Morphology 148
5.4 Peptidoglycan Synthesis and Cell Division 149
Ⅱ Population Growth 151
5.5 The Concept of Exponential Growth 151
5.6 The Mathematics of Exponential Growth 152
5.7 The Microbial Growth Cycle 153
5.8 Continuous Culture：The Chemostat 154
Ⅲ Measuring Microbial Growth 156
5.9 Microscopic Counts 156
5.10 Viable Counts 157
5.11 Turbidimetric Methods 159
Ⅳ Temperature and Microbial Growth 160
5.12 Effect of Temperature on Growth 162
5.13 Microbial Life in the Cold 162
5.14 Microbial Life at High Temperatures 166
Ⅴ Other Environmental Factors Affecting Growth 168
5.15 Acidity and Alkalinity 168
5.16 Osmotic Effects 169
5.17 Oxygen and Microorganisms 171
5.18 Toxic Forms of Oxygen 174
Microbial Sidebar 161
Microbial Growth in Aquatic Systems：Cyanobacterial Blooms 161
UNIT 3 Molecular Biology and Gene Expression 178
Chapter 6 Molecular Biology of Bacteria 178
Ⅰ DNA Structure and Genetic Information 179
6.1 Macromolecules and Genes 179
6.2 The Double Helix 181
6.3 Supercoiling 183
6.4 Chromosomes and Other Genetic Elements 184
Ⅱ Chromosomes and Plasmids 185
6.5 The Escherichia coli Chromosome 185
6.6 Plasmids：General Principles 187
6.7 The Biology of Plasmids 189
Ⅲ DNA Replication 190
6.8 Templates and Enzymes 190
6.9 The Replication Fork 191
6.10 Bidirectional Replication and the Replisome 193
6.11 The Polymerase Chain Reaction （PCR） 197
Ⅳ RNA Synthesis：Transcription 198
6.12 Overview of Transcription 198
6.13 Sigma Factors and Consensus Sequences 200
6.14 Termination of Transcription 201
6.15 The Unit of Transcription 201
Ⅴ Protein Structure and Synthesis 202
6.16 Polypeptides，Amino Acids，and the Peptide Bond 202
6.17 Translation and the Genetic Code 203
6.18 Transfer RNA 206
6.19 Steps in Protein Synthesis 208
6.20 The Incorporation of Selenocysteine and Pyrrolysine 211
6.21 Folding and Secreting Proteins 211
Chapter 7 Archaeal and Eukaryotic Molecular Biology 219
Ⅰ Molecular Biology of Archaea 220
7.1 Chromosomes and DNA Replication in Archaea 220
7.2 Transcription and RNA Processing in Archaea 221
7.3 Protein Synthesis in Archaea 223
7.4 Shared Features of Bacteria and Archaea 224
Ⅱ Eukaryotic Molecular Biology 225
7.5 Genes and Chromosomes in Eukarya 225
7.6 Overview of Eukaryotic Cell Division 226
7.7 Replication of Linear DNA 227
7.8 RNA Processing 228
7.9 Transcription and Translation in Eukarya 231
7.10 RNA Interference （RNAi） 233
7.11 Regulation by MicroRNA 234
Microbial Sidebar 231
Inteins and Protein Splicing 231
Chapter 8 Regulation of Gene Expression 237
Ⅰ Overview of Regulation 238
8.1 Major Modes of Regulation 238
Ⅱ DNA-Binding Proteins and Regulation of Transcription 238
8.2 DNA-Binding Proteins 239
8.3 Negative Control of Transcription：Repression and Induction 240
8.4 Positive Control of Transcription 242
8.5 Global Control and the lac Operon 244
8.6 Control of Transcription in Archaea 245
Ⅲ Sensing and Signal Transduction 246
8.7 Two-Component Regulatory Systems 246
8.8 Regulation of Chemotaxis 248
8.9 Quorum Sensing 249
8.10 The Stringent Response 251
8.11 Other Global Control Networks 252
Ⅳ Regulation of Development in Model Bacteria 253
8.12 Sporulation in Bacillus 254
8.13 Caulobacter Differentiation 255
Ⅴ RNA-Based Regulation 256
8.14 RNA Regulation and Antisense RNA 256
8.15 Riboswitches 258
8.16 Attenuation 259
Microbial Sidebar 257
The CRISPR Antiviral Defense System 257
UNIT 4 Virology，Genetics，and Genomics 264
Chapter 9 Viruses and Virology 264
Ⅰ Virus Structure and Growth 265
9.1 General Properties of Viruses 265
9.2 Nature of the Virion 266
9.3 The Virus Host 269
9.4 Quantification of Viruses 269
Ⅱ Viral Replication 271
9.5 General Features of Virus Replication 271
9.6 Viral Attachment and Penetration 271
9.7 Production of Viral Nucleic Acid and Protein 273
Ⅲ Viral Diversity 275
9.8 Overview of Bacterial Viruses 275
9.9 Virulent Bacteriophages and T4 278
9.10 Temperate Bacteriophages，Lambda and P1 279
9.11 Overview of Animal Viruses 282
9.12 Retroviruses 283
Ⅳ Subviral Entities 285
9.13 Defective Viruses 285
9.14 Viroids 285
9.15 Prions 286
Microbial Sidebar 276
Did Viruses Invent DNA？ 276
Chapter 10 Genetics of Bacteria and Archaea 291
Ⅰ Mutation 292
10.1 Mutations and Mutants 292
10.2 Molecular Basis of Mutation 294
10.3 Mutation Rates 296
10.4 Mutagenesis 297
10.5 Mutagenesis and Carcinogenesis：The Ames Test 300
Ⅱ Gene Transfer 301
10.6 Genetic Recombination 301
10.7 Transformation 303
10.8 Transduction 305
10.9 Conjugation：Essential Features 307
10.10 The Formation of Hfr Strains and Chromosome Mobilization 309
10.11 Complementation 312
10.12 Gene Transfer in Archaea 313
10.13 Mobile DNA：Transposable Elements 314
Chapter 11 Genetic Engineering 319
Ⅰ Methods for Manipulating DNA 320
11.1 Restriction and Modification Enzymes 320
11.2 Nucleic Acid Hybridization 322
11.3 Essentials of Molecular Cloning 323
11.4 Molecular Methods for Mutagenesis 325
11.5 Gene Fusions and Reporter Genes 327
Ⅱ Gene Cloning 328
11.6 Plasmids as Cloning Vectors 328
11.7 Hosts for Cloning Vectors 330
11.8 Shuttle Vectors and Expression Vectors 332
11.9 Bacteriophage Lambda as a Cloning Vector 335
11.10 Vectors for Genomic Cloning and Sequencing 336
Microbial Sidebar 329
Combinatorial Fluorescence Labeling 329
Chapter 12 Microbial Genomics 341
Ⅰ Genomes and Genomics 342
12.1 Introduction to Genomics 342
12.2 Sequencing and Annotating Genomes 342
12.3 Bioinformatic Analyses and Gene Distributions 346
12.4 The Genomes of Eukaryotic Organelles 351
12.5 The Genomes of Eukaryotic Microorganisms 353
12.6 Metagenomics 355
Ⅱ Genorne Function and Regulation 355
12.7 Microarrays and the Transcriptome 355
12.8 Proteomics and the Interactome 357
12.9 Metabolomics 359
Ⅲ The Evolution of Genomes 360
12.10 Gene Families，Duplications，and Deletions 360
12.11 Horizontal Gene Transfer and Genome Stability 361
12.12 Transposons and Insertion Sequences 362
12.13 Evolution of Virulence：Pathogenicity Islands 363
Microbial Sidebar 348
The Synthetic Cell：Assembly Details 348
UNIT 5 Metabolic Diversity and Commercial Biocatalyses 368
Chapter 13 Phototrophy，Chemolithotrophy，and Major Biosyntheses 368
Ⅰ Phototrophy 369
13.1 Photosynthesis 369
13.2 Chlorophylls and Bacteriochlorophylls 370
13.3 Carotenoids and Phycobilins 373
13.4 Anoxygenic Photosynthesis 374
13.5 Oxygenic Photosynthesis 378
Ⅱ Chemolithotrophy 381
13.6 The Energetics of Chemolithotrophy 381
13.7 Hydrogen Oxidation 382
13.8 Oxidation of Reduced Sulfur Compounds 382
13.9 Iron Oxidation 384
13.10 Nitrification 386
13.11 Anammox 387
Ⅲ Major Biosyntheses：Autotrophy and Nitrogen Fixation 389
13.12 The Calvin Cycle 389
13.13 Other Autotrophic Pathways in Phototrophs 390
13.14 Nitrogen Fixation and Nitrogenase 391
13.15 Genetics and Regulation of Nitrogen Fixation 395
Chapter 14 Catabolism of Organic Compounds 400
Ⅰ Fermentations 401
14.1 Energetic and Redox Considerations 401
14.2 Lactic and Mixed-Acid Fermentations 402
14.3 Clostridial and Propionic Acid Fermentations 405
14.4 Fermentations Lacking Substrate-Level Phosphorylation 407
14.5 Syntrophy 409
Ⅱ Anaerobic Respiration 411
14.6 Anaerobic Respiration：General Principles 411
14.7 Nitrate Reduction and Denitrification 412
14.8 Sulfate and Sulfur Reduction 414
14.9 Acetogenesis 416
14.10 Methanogenesis 418
14.11 Proton Reduction 422
14.12 Other Electron Acceptors 423
14.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic Respiration 425
Ⅲ Aerobic Chemoorganotrophic Processes 428
14.14 Molecular Oxygen as a Reactant and Aerobic Hydrocarbon Oxidation 428
14.15 Methylotrophy and Methanotrophy 429
14.16 Sugar and Polysaccharide Metabolism 431
14.17 Organic Acid Metabolism 434
14.18 Lipid Metabolism 434
Chapter 15 Commercial Products and Biotechnology 439
Ⅰ Putting Microorganisms to Work 440
15.1 Industrial Products and the Microorganisms That Make Them 440
15.2 Production and Scale 440
Ⅱ Drugs，Other Chemicals，and Enzymes 443
15.3 Antibiotics：Isolation，Yield，and Purification 443
15.4 Industrial Production of Penicillins and Tetracyclines 445
15.5 Vitamins and Amino Acids 447
15.6 Enzymes as Industrial Products 448
Ⅲ Alcoholic Beverages and Biofuels 451
15.7 Wine 451
15.8 Brewing and Distilling 453
15.9 Biofuels 455
Ⅳ Products from Genetically Engineered Microorganisms 456
15.10 Expressing Mammalian Genes in Bacteria 457
15.11 Production of Genetically Engineered Somatotropin 459
15.12 Other Mammalian Proteins and Products 460
15.13 Genetically Engineered Vaccines 461
15.14 Mining Genomes 463
15.15 Engineering Metabolic Pathways 463
Ⅴ Transgenic Eukaryotes 465
15.16 Genetic Engineering of Animals 465
15.17 Gene Therapy in Humans 467
15.18 Transgenic Plants in Agriculture 467
Microbial Sidebar 464
Synthetic Biology and Microbial Photography 464
UNIT 6 Microbial Evolution and Diversity 474
Chapter 16 Microbial Evolution and Systematics 474
Ⅰ Early Earth and the Origin and Diversification of Life 475
16.1 Formation and Early History of Earth 475
16.2 Origin of Cellular Life 476
16.3 Microbial Diversification：Consequences for Earth’s Biosphere 479
16.4 Endosymbiotic Origins of Eukaryotes 480
Ⅱ Microbial Evolution 482
16.5 The Evolutionary Process 482
16.6 Evolutionary Analyses：Theoretical Aspects 483
16.7 Evolutionary Analyses：Analytical Methods 485
16.8 Microbial Phylogeny 487
16.9 Applications of SSU rRNA Phylogenetic Methods 490
Ⅲ Microbial Systematics 491
16.10 Phenotypic Analysis：Fatty Acid Methyl Esters （FAME） 491
16.11 Genotypic Analysis 493
16.12 The Species Concept in Microbiology 495
16.13 Classification and Nomenclature 498
Chapter 17 Bacteria：The Proteobacteria 503
Ⅰ The Phylogeny of Bacteria 504
17.1 Phylogenetic Overview of Bacteria 504
Ⅱ Phototrophic，Chemolithotrophic，and Methanotrophic Proteobacteria 505
17.2 Purple Phototrophic Bacteria 506
17.3 The Nitrifying Bacteria 509
17.4 Sulfur- and Iron-Oxidizing Bacteria 510
17.5 Hydrogen-Oxidizing Bacteria 513
17.6 Methanotrophs and Methylotrophs 514
Ⅲ Aerobic and Facultatively Aerobic Chemoorganotrophic Proteobacteria 516
17.7 Pseudomonas and the Pseudomonads 517
17.8 Acetic Acid Bacteria 519
17.9 Free-Living Aerobic Nitrogen-Fixing Bacteria 519
17.10 Neisseria，Chromobacterium，and Relatives 521
17.11 Enteric Bacteria 522
17.12 Vibrio，Aliivibrio，and Photobacterium 524
17.13 Rickettsias 526
Ⅳ Morphologically Unusual Proteobacteria 527
17.14 Spirilla 528
17.15 Sheathed Proteobacteria：Sphaerotilus and Leptothrix 530
17.16 Budding and Prosthecate/Stalked Bacteria 531
Ⅴ Delta- and Epsilonproteobacteria 535
17.17 Myxobacteria 535
17.18 Sulfate- and Sulfur-Reducing Proteobacteria 538
17.19 The Epsilonproteobacteria 540
Chapter 18 Other Bacteria 545
Ⅰ Firmicutes，Mollicutes，and Actinobacteria 546
18.1 Nonsporulating Firmicutes 546
18.2 Endospore-Forming Firmicutes 549
18.3 Mollicutes：The Mycoplasmas 553
18.4 Actinobacteria：Coryneform and Propionic Acid Bacteria 554
18.5 Actinobacteria：Mycobacterium 556
18.6 Filamentous Actinobacteria：Streptomyces and Relatives 557
Ⅱ Cyanobacteria and Prochlorophytes 560
18.7 Cyanobacteria 560
18.8 Prochlorophytes 564
Ⅲ Chlamydia 565
18.9 The Chlamydia 565
Ⅳ The Planctomycetes 567
18.10 Planctomyces：A Phylogenetically Unique Stalked Bacterium 567
Ⅴ The Verrucomicrobia 568
18.11 Verrucomicrobium and Prosthecobacter 568
Ⅵ The Flavobacteria and Acidobacteria 569
18.12 Bacteroides and Flavobacterium 569
18.13 Acidobacteria 569
Ⅶ The Cytophaga Group 570
18.14 Cytophaga and Relatives 570
Ⅷ Green Sulfur Bacteria 571
18.15 Chlorobium and Other Green Sulfur Bacteria 571
Ⅸ The Spirochetes 573
18.16 Spirochetes 573
Ⅹ The Deinococci 576
18.17 Deinococcus and Thermus 576
Ⅺ The Green Nonsulfur Bacteria：Chloroflexi 577
18.18 Chloroflexus and Relatives 577
Ⅻ Hyperthermophilic Bacteria 578
18.19 Thermotoga and Thermodesulfobacterium 578
18.20 Aquifex，Thermocrinis，and Relatives 579
ⅩⅢ Nitrospira and Deferribacter 580
18.21 Nitrospira and Deferribacter 580
Chapter 19 Archaea 584
Ⅰ Diversity 585
19.1 Phylogenetic and Metabolic Diversity of Archaea 585
Ⅱ Euryarchaeota 586
19.2 Extremely Halophilic Archaea 586
19.3 Methanogenic Archaea 590
19.4 Thermoplasmatales 593
19.5 Thermococcales and Methanopyrus 595
19.6 Archaeoglobales 596
19.7 Nanoarchaeum and Aciduliprofundum 597
Ⅲ Crenarchaeota 598
19.8 Habitats and Energy Metabolism 598
19.9 Crenarchaeota from Terrestrial Volcanic Habitats 599
19.10 Crenarchaeota from Submarine Volcanic Habitats 602
19.11 Crenarchaeota from Nonthermal Habitats and Nitrification in Archaea 604
Ⅳ Evolution and Life at High Temperatures 605
19.12 An Upper Temperature Limit for Microbial Life 605
19.13 Molecular Adaptations to Life at High Temperature 606
19.14 Hyperthermophilic Archaea，H2，and Microbial Evolution 608
Chapter 20 Eukaryotic Cell Biology and Eukaryotic Microorganisms 612
Ⅰ Eukaryotic Cell Structure and Function 613
20.1 Eukaryotic Cell Structure and the Nucleus 613
20.2 The Mitochondrion and the Hydrogenosome 614
20.3 The Chloroplast 615
20.4 Endosymbiosis：Relationships of Mitochondria and Chloroplasts to Bacteria 616
20.5 Other Organelles and Eukaryotic Cell Structures 617
Ⅱ Eukaryotic Microbial Diversity 619
20.6 Phylogeny of the Eukarya 619
Ⅲ Protists 621
20.7 Diplomonads and Parabasalids 621
20.8 Euglenozoans 622
20.9 Alveolates 622
20.10 Stramenopiles 624
20.11 Cercozoans and Radiolarians 626
20.12 Amoebozoa 626
Ⅳ Fungi 629
20.13 Fungal Physiology，Structure，and Symbioses 629
20.14 Fungal Reproduction and Phylogeny 631
20.15 Chytridiomycetes 632
20.16 Zygomycetes and Glomeromycetes 632
20.17 Ascomycetes 633
20.18 Basidiomycetes and the Mushroom Life Cycle 635
Ⅴ Red and Green Algae 635
20.19 Red Algae 636
20.20 Green Algae 636
Chapter 21 Viral Diversity 641
Ⅰ Viruses of Bacteria and Archaea 642
21.1 RNA Bacteriophages 642
21.2 Single-Stranded DNA Bacteriophages 643
21.3 Double-Stranded DNA Bacteriophages 646
21.4 The Transposable Phage Mu 648
21.5 Viruses of Archaea 650
21.6 Viral Genomes in Nature 651
Ⅱ RNA Viruses of Eukaryotes 651
21.7 Plant RNA Viruses 652
21.8 Positive-Strand RNA Animal Viruses 652
21.9 Negative-Strand RNA Animal Viruses 655
21.10 Double-Stranded RNA Viruses：Reoviruses 657
21.11 Retroviruses and Hepadnaviruses 658
Ⅲ DNA Viruses of Eukaryotes 661
21.12 Plant DNA Viruses 661
21.13 Polyomaviruses：SV40 663
21.14 Herpesviruses 664
21.15 Pox Viruses 665
21.16 Adenoviruses 666
Microbial Sidebar 662
Mimivirus and Viral Evolution 662
UNIT 7 Microbial Ecology 670
Chapter 22 Methods in Microbial Ecology 670
Ⅰ Culture-Dependent Analyses of Microbial Communities 671
22.1 Enrichment 671
22.2 Isolation 675
Ⅱ Culture-Independent Analyses of Microbial Communities 677
22.3 General Staining Methods 677
22.4 Fluorescent In Situ Hybridization （FISH） 679
22.5 PCR Methods of Microbial Community Analysis 680
22.6 Microarrays and Microbial Diversity：Phylochips 683
22.7 Environmental Genomics and Related Methods 684
Ⅲ Measuring Microbial Activities in Nature 686
22.8 Chemical Assays，Radioisotopic Methods，and Microelectrodes 686
22.9 Stable Isotopes 688
22.10 Linking Specific Genes and Functions to Specific Organisms 690
Chapter 23 Major Microbial Habitats and Diversity 697
Ⅰ Microbial Ecology 698
23.1 General Ecological Concepts 698
23.2 Ecosystem Service：Biogeochemistry and Nutrient Cycles 699
Ⅱ The Microbial Environment 700
23.3 Environments and Microenvironments 700
23.4 Surfaces and Biofilms 702
23.5 Microbial Mats 705
Ⅲ Terrestrial Environments 706
23.6 Soils 706
23.7 The Subsurface 709
Ⅳ Aquatic Environments 711
23.8 Freshwaters 711
23.9 Coastal and Ocean Waters：Phototrophic Microorganisms 713
23.10 Pelagic Bacteria，Archaea，and Viruses 715
23.11 The Deep Sea and Deep-Sea Sediments 718
23.12 Hydrothermal Vents 721
Chapter 24 Nutrient Cycles，Biodegradation，and Bioremediation 726
Ⅰ Nutrient Cycles 727
24.1 The Carbon Cycle 727
24.2 Syntrophy and Methanogenesis 729
24.3 The Nitrogen Cycle 731
24.4 The Sulfur Cycle 733
24.5 The Iron Cycle 734
24.6 The Phosphorus，Calcium，and Silica Cycles 737
Ⅱ Biodegradation and Bioremediation 739
24.7 Microbial Leaching 739
24.8 Mercury Transformations 741
24.9 Petroleum Biodegradation and Bioremediation 742
24.10 Xenobiotics Biodegradation and Bioremediation 743
Microbial Sidebar 735
Microbially Wired 735
Chapter 25 Microbial Symbioses 748
Ⅰ Symbioses between Microorganisms 749
25.1 Lichens 749
25.2 “Chlorochromatium aggregatum” 750
Ⅱ Plants as Microbial Habitats 751
25.3 The Legume-Root Nodule Symbiosis 751
25.4 Agrobacterium and Crown Gall Disease 757
25.5 Mycorrhizae 758
Ⅲ Mammals as Microbial Habitats 760
25.6 The Mammalian Gut 760
25.7 The Rumen and Ruminant Animals 762
25.8 The Human Microbiome 766
Ⅳ Insects as Microbial Habitats 769
25.9 Heritable Symbionts of Insects 769
25.10 Termites 772
Ⅴ Aquatic Invertebrates as Microbial Habitats 773
25.11 Hawaiian Bobtail Squid 774
25.12 Marine Invertebrates at Hydrothermal Vents and Gas Seeps 775
25.13 Leeches 777
25.14 Reef-Building Corals 778
Microbial Sidebar 771
The Multiple Microbial Symbionts of Fungus-Cultivating Ants 771
UNIT 8 Antimicrobial Agents and Pathogenicity 783
Chapter 26 Microbial Growth Control 783
Ⅰ Physical Antimicrobial Control 784
26.1 Heat Sterilization 784
26.2 Radiation Sterilization 787
26.3 Filter Sterilization 788
Ⅱ Chemical Antimicrobial Control 790
26.4 Chemical Growth Control 790
26.5 Chemical Antimicrobial Agents for External Use 791
Ⅲ Antimicrobial Agents Used In Vivo 795
26.6 Synthetic Antimicrobial Drugs 795
26.7 Natural Antimicrobial Drugs：Antibiotics 798
26.8 β-Lactam Antibiotics：Penicillins and Cephalosporins 799
26.9 Antibiotics from Prokaryotes 800
Ⅳ Control of Viruses and Eukaryotic Pathogens 802
26.10 Antiviral Drugs 802
26.11 Antifungal Drugs 804
Ⅴ Antimicrobial Drug Resistance and Drug Discovery 806
26.12 Antimicrobial Drug Resistance 806
26.13 The Search for New Antimicrobial Drugs 810
Microbial Sidebar 794
Multi-Drug- and Extensively Drug-Resistant Tuberculosis 794
Chapter 27 Microbial Interactions with Humans 815
Ⅰ Beneficial Microbial Interactions with Humans 816
27.1 Overview of Human-Microbial Interactions 816
27.2 Normal Microflora of the Skin 818
27.3 Normal Microflora of the Oral Cavity 819
27.4 Normal Microflora of the Gastrointestinal Tract 821
27.5 Normal Microflora of Other Body Regions 825
Ⅱ Microbial Virulence and Pathogenesis 826
27.6 Measuring Virulence 826
27.7 Entry of the Pathogen into the Host—Adherence 827
27.8 Colonization and Infection 829
27.9 Invasion 830
27.10 Exotoxins 832
27.11 Endotoxins 835
Ⅲ Host Factors in Infection 836
27.12 Host Risk Factors for Infection 837
27.13 Innate Resistance to Infection 839
Microbial Sidebar 824
Bacteriophages and Infectious Diseases 824
Microbial Sidebar 838
Virulence in Salmonella 838
UNIT 9 Immunology 844
Chapter 28 Immunity and Host Defense 844
Ⅰ Immunity 845
28.1 Cells and Organs of the Immune System 845
28.2 Innate Immunity 848
28.3 Adaptive Immunity 849
28.4 Antibodies 850
28.5 Inflammation 852
Ⅱ Prevention of Infectious Diseases 854
28.6 Natural Immunity 854
28.7 Artificial Immunity and Immunization 855
28.8 New Immunization Strategies 857
Ⅲ Immune Diseases 858
28.9 Allergy，Hypersensitivity，and Autoimmunity 858
28.10 Superantigens：Overactivation of T Cells 862
Microbial Sidebar 859
The Promise of New Vaccines 859
Chapter 29 Immune Mechanisms 866
Ⅰ Overview of Immunity 867
29.1 Innate Response Mechanisms 867
29.2 Adaptive Response Mechanisms 870
Ⅱ Antigens and Antigen Presentation 871
29.3 Immunogens and Antigens 871
29.4 Antigen Presentation to T Cells 872
Ⅲ T Lymphocytes and Immunity 875
29.5 T-Cytotoxic Cells and Natural Killer Cells 875
29.6 T-Helper Cells 876
Ⅳ Antibodies and Immunity 877
29.7 Antibodies 878
29.8 Antibody Production 880
29.9 Antibodies，Complement，and Pathogen Destruction 883
Chapter 30 Molecular Immunology 887
Ⅰ Receptors and Immunity 888
30.1 Innate Immunity and Pattern Recognition 888
30.2 Adaptive Immunity and the Immunoglobulin Superfamily 890
Ⅱ The Major Histocompatibility Complex （MHC） 892
30.3 MHC Protein Structure 892
30.4 MHC Polymorphism and Antigen Binding 894
Ⅲ Antibodies 894
30.5 Antibody Proteins and Antigen Binding 894
30.6 Antibody Genes and Diversity 895
Ⅳ T Cell Receptors 897
30.7 T Cell Receptors：Proteins，Genes and Diversity 897
Ⅴ Molecular Switches in Immunity 899
30.8 Clonal Selection and Tolerance 899
30.9 T Cell and B Cell Activation 901
30.10 Cytokines and Chemokines 902
Microbial Sidebar 889
Leucine-Rich Repeats and the Immune Response 889
UNIT 10 Diagnosing and Tracking Microbial Diseases 906
Chapter 31 Diagnostic Microbiology and Immunology 906
Ⅰ Growth-Dependent Diagnostic Methods 907
31.1 Isolation of Pathogens from Clinical Specimens 907
31.2 Growth-Dependent Identification Methods 912
31.3 Antimicrobial Drug Susceptibility Testing 916
31.4 Safety in the Microbiology Laboratory 916
Ⅱ Immunology and Diagnostic Methods 920
31.5 Immunoassays for Infectious Disease 920
31.6 Polyclonal and Monoclonal Antibodies 922
31.7 In Vitro Antigen-Antibody Reactions：Serology 923
31.8 Agglutination 925
31.9 Immunofluorescence 926
31.10 Enzyme Immunoassay and Radioimmunoassay 928
31.11 Immunoblots 933
Ⅲ Nucleic Acid-Based Diagnostic Methods 934
31.12 Nucleic Acid Hybridization 934
31.13 Nucleic Acid Amplification 936
Chapter 32 Epidemiology 941
Ⅰ Principles of Epidemiology 942
32.1 The Science of Epidemiology 942
32.2 The Vocabulary of Epidemiology 942
32.3 Disease Reservoirs and Epidemics 944
32.4 Infectious Disease Transmission 947
32.5 The Host Community 949
Ⅱ Current Epidemics 950
32.6 The HIV/AIDS Pandemic 950
32.7 Healthcare-Associated Infections 953
Ⅲ Epidemiology and Public Health 954
32.8 Public Health Measures for the Control of Disease 954
32.9 Global Health Considerations 957
32.10 Emerging and Reemerging Infectious Diseases 959
32.11 Biological Warfare and Biological Weapons 964
32.12 Anthrax as a Biological Weapon 967
Microbial Sidebar 951
Swine Flu—Pandemic （H1N1） 2009 Influenza 951
Microbial Sidebar 966
SARS as a Model of Epidemiological Success 966
UNIT 11 Human- and Animal-Transmitted Infectious Diseases 972
Chapter 33 Person-to-Person Microbial Diseases 972
Ⅰ Airborne Transmission of Diseases 973
33.1 Airborne Pathogens 973
33.2 Streptococcal Diseases 974
33.3 Diphtheria and Pertussis 977
33.4 Mycobacterium，Tuberculosis，and Hansen’s Disease 979
33.5 Neisseria meningitidis，Meningitis，and Meningococcemia 982
33.6 Viruses and Respiratory Infections 982
33.7 Colds 985
33.8 Influenza 986
Ⅱ Direct-Contact Transmission of Diseases 989
33.9 Staphylococcus 989
33.10 Helicobacter pylori and Gastric Ulcers 991
33.11 Hepatitis Viruses 992
Ⅲ Sexually Transmitted Infections 993
33.12 Gonorrhea and Syphilis 994
33.13 Chlamydia，Herpes，Trichomoniasis，and Human Papillomavirus 997
33.14 Acquired Immunodeficiency Syndrome：AIDS and HIV 999
Chapter 34 Vectorborne and Soilborne Microbial Pathogens 1009
Ⅰ Animal-Transmitted Pathogens 1010
34.1 Rabies Virus 1010
34.2 Hantavirus 1012
Ⅱ Arthropod-Transmitted Pathogens 1014
34.3 Rickettsial Pathogens 1014
34.4 Lyme Disease and Borrelia 1017
34.5 Malaria and Plasmodium 1019
34.6 West Nile Virus 1023
34.7 Plague and Yersinia 1024
Ⅲ Soilborne Pathogens 1026
34.8 Fungal Pathogens 1026
34.9 Tetanus and Clostridium tetani 1028
Microbial Sidebar 1013
Special Pathogens and Viral Hemorrhagic Fevers 1013
UNIT 12 Common-Source Infectious Disease 1032
Chapter 35 Wastewater Treatment，Water Purification，and Waterborne Microbial Diseases 1032
Ⅰ Wastewater Microbiology and Water Purification 1033
35.1 Public Health and Water Quality 1033
35.2 Wastewater and Sewage Treatment 1035
35.3 Drinking Water Purification 1038
Ⅱ Waterborne Microbial Diseases 1040
35.4 Sources of Waterborne Infection 1040
35.5 Cholera 1041
35.6 Giardiasis and Cryptosporidiosis 1043
35.7 Legionellosis （Legionnaires’ Disease） 1045
35.8 Typhoid Fever and Other Waterborne Diseases 1046
Chapter 36 Food Preservation and Foodborne Microbial Diseases 1050
Ⅰ Food Preservation and Microbial Growth 1051
36.1 Microbial Growth and Food Spoilage 1051
36.2 Food Preservation 1052
36.3 Fermented Foods and Mushrooms 1055
Ⅱ Foodborne Disease，Microbial Sampling，and Epidemiology 1058
36.4 Foodborne Disease and Microbial Sampling 1059
36.5 Foodborne Disease Epidemiology 1060
Ⅲ Food Poisoning 1061
36.6 Staphylococcal Food Poisoning 1061
36.7 Clostridial Food Poisoning 1062
Ⅳ Food Infection 1064
36.8 Salmonellosis 1064
36.9 Pathogenic Escherichia coli 1065
36.10 Campylobacter 1066
36.11 Listeriosis 1067
36.12 Other Foodborne Infectious Diseases 1068
Appendix 1 Energy Calculations in Microbial Bioenergetics 1073
Appendix 2 Bergey’s Manual of Systematic Bacteriology，Second Edition：List of Genera and Higher-Order Taxa 1077
Glossary 1087
Photo Credits 1105
Index 1109