Description
Book SynopsisTable of ContentsPart I The Microbes
1 The Microbial World 1
1.1 The Microbes 3
Mini-Paper: A Focus on the Research the Three Domains of Life 9
Toolbox 1.1 Polymerase Chain Reaction Amplification of rRNA Genes 11
1.2 Microbial Physiology, Genetics, and Cultivation 14
Perspective 1.1 Creating Life in the Laboratory: The Miller–Urey Experiment 17
1.3 Microbial Ecology and Biotechnology 23
1.4 Microbes and Disease 25
2 Bacteria 35
2.1 Morphology of Bacterial Cells 36
Perspective 2.1 Making the Microbiology Laboratory Accessible 39
2.2 The Cytoplasm 40
2.3 The Bacterial Cytoskeleton 43
Mini-Paper: A Focus on the Research Magnetosomes: Uncovering the Structure of Bacterial Organelles 44
2.4 The Cell Envelope 46
Toolbox 2.1 The Gram Stain 55
Perspective 2.2 The Protective Shells of Endospores 56
2.5 The Bacterial Cell Surface 60
2.6 Diversity of Bacteria 67
3 Eukaryal Microorganisms 75
3.1 Morphology of Eukaryal Cells 76
Mini-Paper: A Focus on the Research Lipid Rafts: Organized Clustering of Lipids within a Membrane 82
Toolbox 3.1 Using Microscopy to Examine Cell Structure 85
Perspective 3.1 Hijacking the Cytoskeleton 88
3.2 Diversity of Eukaryal Microorganisms 89
3.3 Replication of Eukaryal Microorganisms 94
3.4 The Origin of Eukaryal Cells 97
Perspective 3.2 Secondary endosymbiosis: The origins of an organelle with four membranes 101
3.5 Interactions Between Eukaryal Microorganisms and Animals, Plants, and the Environment 102
4 Archaea 109
4.1 Evolution of Archaea 111
4.2 Archaeal Cell Structure 113
Toolbox 4.1 Vaccine Delivery Strategies 117
4.3 Diversity of Archaea 121
Mini-Paper: A Focus on the Research The Role of Archaea in Our Digestive System 124
Perspective 4.1 Extremophiles and Biotechnology 129
5 Viruses 136
5.1 A Basic Overview of Viruses 137
Mini-Paper: A Focus on the Research New Findings in the Packaging of DNA by the Model Bacteriophage T4 146
5.2 Origins of Viruses 148
Perspective 5.1 Ribozymes: Evidence for an RNA-Based World 149
5.3 Cultivation, Purification, and Quantification of Viruses 150
Toolbox 5.1 Cell Culture Techniques 151
Perspective 5.2 Measurement of HIV Viral Load 155
5.4 Diversity of Viruses 158
Toolbox 5.2 Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) 162
5.5 Virus-Like Particles 163
5.6 Virology Today 166
6 Metabolism 172
6.1 Acquisition of Carbon, Energy, and Electrons 174
6.2 Energy, Enzymes, and ATP 176
Perspective 6.1 Who Needs Vitamins? 179
6.3 Central Processes in ATP Synthesis 180
6.4 Carbon Utilization in Microorganisms 185
6.5 Respiration and the Electron Transport System 195
Perspective 6.2 Electricigenic Bacteria and Microbial Fuel Cells 198
6.6 Metabolism of Non-glucose Carbon Sources 202
Toolbox 6.1 Metabolism and Rapid Bacterial Identification Systems 204
6.7 Phototrophy and Photosynthesis 206
Mini-Paper: A Focus on the Research Genome Sequence of a Deep Sea Symbiont 216
6.8 Nitrogen and Sulfur Metabolism 217
6.9 Biosynthesis of Cellular Components 222
Part II Microbial Genetics
7 Cultivating Microorganisms 231
7.1 Factors Affecting Microbial Growth 233
Toolbox 7.1 Phenotype Microarrays for Examining Microbial Growth 234
7.2 Growing Microorganisms in the Laboratory 238
Perspective 7.1 The Discovery of Helicobacter pylori 243
Toolbox 7.2 FISHING for Uncultivated Microorganisms 246
Mini-Paper: A Focus on the Research Bringing to Life the Previously Unculturable Using the Soil Substrate Membrane System (SSMS) 247
7.3 Measuring Microbial Population Growth 249
Perspective 7.2 Mycobacterium leprae, An Extraordinarily Slow-growing Pathogen 255
Perspective 7.3 The Human Intestine: A Continuous Culture 257
7.4 Eliminating Microbes and Preventing their Growth 257
8 DNA Replication and Gene Expression 267
8.1 The Role of DNA 269
8.2 DNA Replication 276
Mini-Paper: A Focus on the Research Telomeres with Promoter Activity 283
8.3 Transcription 284
Toolbox 8.1 Using a Gel Shift Assay to Identify DNA-binding Proteins 287
8.4 Translation 291
8.5 The Effects of Mutations 297
Perspective 8.1 Using Mutations to Control Viral Infections 301
9 Viral Replication Strategies 306
9.1 Recognition of Host Cells 308
Perspective 9.1 Identifying Emerging Viral Pathogens 310
Toolbox 9.1 The Western Blot 312
9.2 Viral Entry and Uncoating 315
9.3 Viral Replication 319
Mini-Paper: A Focus on the Research The Discovery of Reverse Transcriptase 326
Perspective 9.2 Phage Therapy: Biocontrol for Infections 328
9.4 Viral Assembly and Egress 330
10 Bacterial Genetic Analysis and Manipulation 335
10.1 Bacteria as Subjects of Genetic Research 336
10.2 Mutations, Mutants, and Strains 340
Toolbox 10.1 Isolating Nutritional Mutants 342
10.3 Restriction Enzymes, Vectors, and Cloning 347
10.4 Recombination and DNA Transfer 354
Perspective 10.1 Plasmids That Produce Pathogens 359
Mini-Paper: A Focus on the Research The Discovery of Transduction 367
11 Microbial Genomics 372
11.1 Genome Sequencing 373
Perspective 11.1 Rate of DNA Sequencing 377
Toolbox 11.1 Genome databases 383
11.2 Genomic Analysis of Gene Expression 385
11.3 Comparative Genomics 391
Mini-Paper: A Focus on the Research Genome Sequence of a Killer Bug 391
Perspective 11.2 The Minimal Genome 393
11.4 Metagenomics and Related Analyses 396
12 Regulation of Gene Expression 402
12.1 Differential Gene Expression 404
12.2 The Operon 405
Mini-Paper: A Focus on the Research Tuning Promoters for Use in Synthetic Biology 412
12.3 Global Gene Regulation 413
Perspective 12.1 The Use of Lactose Analogs in Gene Expression Studies 415
12.4 Post-Initiation Control of Gene Expression 419
Toolbox 12.1 Using RNA molecules to decrease gene expression 421
12.5 Quorum Sensing 423
12.6 Two-Component Regulatory Systems 425
12.7 Chemotaxis 428
13 Biogeochemical Cycles 435
13.1 Nutrient Cycling 437
Toolbox 13.1 Using Microarrays to Examine Microbial Communities: The GeoChip 439
13.2 Cycling Driven by Carbon Metabolism 440
Perspective 13.1 CO2 as a Greenhouse Gas and Its Influence on Climate Change 440
13.3 Cycling Driven by Nitrogen Metabolism 451
Mini-Paper: A Focus on the Research The First Isolation and Cultivation of a Marine Archaeon 454
13.4 Other Cycles and their Connections 456
Perspective 13.2 Life in a World without Microbes 457
Perspective 13.3 The Microbiology of Environmentally Toxic Acid Mine Drainage 458
Toolbox 13.2 Biogeochemistry in a Bottle: The Winogradsky Column 461
Part III Microbial Physiology and Ecology
14 Microbial Ecosystems 465
14.1 Microbes in the Environment 467
14.2 Microbial Community Analysis 472
Toolbox 14.1 Flow Cytometry 477
Perspective 14.1 Naming the Uncultured and Uncharacterized 479
Mini-Paper: A Focus on the Research Insights into the Phylogeny and Coding Potential of Microbial Dark Matter 479
14.3 Aquatic Ecosystems 481
Perspective 14.2 Dead Zones 482
14.4 Terrestrial Ecosystems 489
14.5 Deep Subsurface and Geothermal Ecosystems 495
15 Microbial Symbionts 504
15.1 Types of Microbe-Host Interactions 506
15.2 Symbionts of Plants 508
Perspective 15.1 The Possible Impossible Vegan Patty 510
15.3 Symbionts of Humans 513
Toolbox 15.1 Germ-free and Gnotobiotic Animals 518
Perspective 15.2 Food Probiotics—Do They Work? 519
Mini-Paper: A Focus on the Research Fecal Bacteriotherapy: “Repoopulation” of the Gut 522
15.4 Symbionts of Herbivores 525
Perspective 15.3 Cows Contribute to Climate Change 531
15.5 Symbionts of Invertebrates 531
Perspective 15.4 Midichlorians—Not Just for Jedi 536
Perspective 15.5 Death of Coral Reefs 539
16 Microbial Biotechnology 544
16.1 Microbes for Biotechnology 546
Perspective 16.1 Bioprospecting: Who Owns the Microbes? 548
16.2 Molecular Genetic Modification 550
Toolbox 16.1 Site-Directed Mutagenesis 552
Toolbox 16.2 Fusion Protein Purification 559
Mini-Paper: A Focus on the Research Making a Synthetic Genome 561
Perspective 16.2 The International Genetically Engineered Machine (iGEM) Competition, Standard Biological Parts, and Synthetic Biology 564
16.3 Red Biotechnology 565
16.4 White Biotechnology 566
Perspective 16.3 Biofuels: Biodiesel and Algae 570
16.5 Green Biotechnology 576
Toolbox 16.3 Plant Transformation Using Bacteria 578
17 The Microbiology of Food and Water 586
17.1 Food Spoilage 588
17.2 Food Preservation 591
17.3 Food Fermentation 598
17.4 Foodborne and Waterborne Illness 605
17.5 Microbiological Aspects of Water Quality 607
Perspective 17.1 Implications of Sludge Bulking 613
Toolbox 17.1 Measuring Biochemical Oxygen Demand (BOD) 614
Mini-Paper: A Focus on the Research Enhanced Biological Removal of Phosphorus 616
Toolbox 17.2 Most Probable Number (MPN) Method 619
Part IV Microbes and Disease
18 Introduction to Infectious Diseases 624
18.1 Pathogenic Microbes 627
Toolbox 18.1 Measuring the Virulence of Pathogens 629
18.2 Microbial Virulence Strategies 631
Perspective 18.1 Genome Editing: A powerful and Controversial New Technique 637
18.3 The Transmission of Infectious Diseases 638
Mini-Paper: A Focus on the Research Epidemiology of an Infectious Disease 645
18.4 Proving Cause and Effect in Microbial Infections 648
Perspective 18.2 The Armadillo—An Ideal Animal Model? 651
18.5 The Evolution of Pathogens 652
19 Innate Host Defenses Against Microbial Invasion 661
19.1 Immunity 682
19.2 Barriers to Infection 664
Perspective 19.1 Messy Mucus 666
Perspective 19.2 Alzheimer’s Disease: Aluminium, B-amyloid, Gum Disease: Which Is It? 666
19.3 The Inflammatory Response 669
19.4 The Molecules of the Innate System 671
Mini-Paper: A Focus on the Research Mammalian Cells Can Recognize Bacterial DNA 673
Toolbox 19.1 The Complement Fixation Test 677
19.5 The Cells of Innate Immunity 682
19.6 Invertebrate Defenses 690
Toolbox 19.2 The Limulus Amoebocyte Assay for LPS 692
20 Adaptive Immunity 696
20.1 Features of Adaptive Immunity 698
20.2 T Cells 701
20.3 Antigen Processing 705
20.4 Antigen-Presenting Cells 708
20.5 Humoral and Cell-Mediated Immune Responses 712
Perspective 20.1 Too Much of a Good Thing? 714
Mini-Paper: A Focus on the Research Attempting to Engineer a Virus to Improve Immunocontraception 715
20.6 B Cells and the Production of Antibody 716
Perspective 20.2 Vaccines Against T-independent Antigens 720
Toolbox 20.1 Monoclonal Antibody (mAb) Production 721
Toolbox 20.2 Enzyme-linked Immunosorbent Assay (ELISA) 727
Perspective 20.3 Turning Antibody Upside Down 729
21 Bacterial Pathogenesis 735
21.1 Bacterial Virulence Factors 737
Mini-Paper: A Focus on the Research Escherichia Coli Injects Its Own Receptor 742
Perspective 21.1 Iron, Vampires, Fashion, and the White Plague 747
21.2 Bacterial Virulence Factors—Toxins 748
Toolbox 21.1 Serotyping 749
Perspective 21.2 The Good, The Bad, and The Ugly Side of Botulinum Toxin 756
Perspective 21.3 Superabsorbent Tampons and Superantigens 762
21.3 Survival in the Host: Strategies and Consequences 764
Toolbox 21.2 The Tuberculin Test for Tuberculosis 772
21.4 Evolution of Bacterial Pathogens 772
Perspective 21.4 Antibiotics Trigger Toxins? 776
22 Viral Pathogenesis 782
22.1 Recurring Themes in Viral Pathogenesis 784
Perspective 22.1 Vertical Transmission of HIV 789
22.2 Interactions with the Host: Strategies and Consequences 791
Perspective 22.2 Viral Induction of Apoptosis 793
22.3 Viral Infections and Cancer 796
Toolbox 22.1 Immunoprecipitation 799
Mini-Paper: A Focus on the Research Viruses that Cause Cancer by Affecting Cellular Proliferation 800
Perspective 22.3 SV40 and Human Cancers 802
22.4 Evolution of Viral Pathogens 806
Perspective 22.4 What is it about Bats? 809
Perspective 22.5 Ethical Concerns about Avian Flu Research 812
23 Eukaryal Pathogenesis 816
23.1 Mechanisms of Eukaryal Pathogenesis 818
Mini-Paper: A Focus on the Research An Experimental System for the Genomic Study of Dutch Elm Disease 821
Perspective 23.1 Pneumocystis Jirovecii or Carinii : The Evolving Field of Taxonomy 824
Perspective 23.2 Magic Mushrooms 830
23.2 Pathogen Study: Plasmodium Falciparum 831
Toolbox 23.1 Testing for Malaria 835
23.3 Macroscopic Eukaryal Pathogens 837
23.4 Evolution of Eukaryal Pathogens 839
Perspective 23.3 Chytrid Fungus: An Emerging Fungal Pathogen 840
Perspective 23.4 What if the Parasites Disappeared? 842
24 Control of Infectious Diseases 846
24.1 Historical Aspects of Infectious Disease Treatment and Control 848
24.2 Antimicrobial Drugs 849
24.3 Antimicrobial Drug Resistance 863
Mini-Paper: A Focus on the Research Tracking Acquisition of Antibiotic Resistance In Real Time 865
Toolbox 24.1 Drug Susceptibility Testing and MIC 869
Perspective 24.1 The Pursuit of New Antibiotics: Why Bother? 874
Perspective 24.2 Health Care-Associated Infections: A Recipe for Resistance 875
24.4 Predicting and Controlling Epidemics 876
24.5 Immunization and Vaccines 879
Perspective 24.3 Variolation: Deliberate Infection with Smallpox Virus 880
Perspective 24.4 The War Against Vaccines 885
Appendix A Scientific Articles A-1
Appendix B Microscopy A-10
Appendix C Taxonomy and Nomenclature of Microbes A-14
Appendix D Origin of Blood Cells A-16
Glossary / Index
