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Preface x Visual Preview xv About the Authors xxii Part I Introduction to Microbiology 1 The History and Scope of Microbiology 1 1.1 The Discovery of Microorganisms 2 1.2 The Conflict over Spontaneous Generation 2 1.3 The Role of Microorganisms in Disease 7 Techniques & Applications 1.1: The Scientific Method 9 Disease 1.2: Molecular Koch?s Postulates 10 1.4 Industrial Microbiology and Microbial Ecology 11 1.5 Members of the Microbial World 11 1.6 The Scope and Relevance of Microbiology 12 1.7 The Future of Microbiology 14 2 The Study of Microbial Structure: Microscopy and Specimen Preparation 17 2.1 Lenses and the Bending of Light 18 2.2 The Light Microscope 18 2.3 Preparation and Staining of Specimens 26 2.4 Electron Microscopy 30 2.5 Newer Techniques in Microscopy 35 3 Procaryotic Cell Structure and Function 39 3.1 An Overview of Procaryotic Cell Structure 40 Microbial Diversity & Ecology 3.1: Monstrous Microbes 43 3.2 Procaryotic Cell Membranes 44 3.3 The Cytoplasmic Matrix 47 3.4 The Nucleoid 50 Microbial Diversity & Ecology 3.2: Living Magnets 51 3.5 The Procaryotic Cell Wall 52 3.6 Protein Secretion in Procaryotes 59 3.7 Components External to the Cell Wall 61 3.8 Chemotaxis 67 3.9 The Bacterial Endospore 68 4 Eucaryotic Cell Structure and Function 73 4.1 An Overview of Eucaryotic Cell Structure 75 4.2 The Cytoplasmic Matrix, Microfilaments, Intermediate Filaments, and Microtubules 76 4.3 The Endoplasmic Reticulum 78 4.4 The Golgi Apparatus 78 4.5 Lysosomes and Endocytosis 79 4.6 Eucaryotic Ribosomes 82 4.7 Mitochondria 82 4.8 Chloroplasts 84 ? Microbial Diversity & Ecology 4.1: The Origin of the Eucaryotic Cell 84 4.9 The Nucleus and Cell Division 85 4.10 External Cell Coverings 88 4.11 Cilia and Flagella 88 4.12 Comparison of Procaryotic and Eucaryotic Cells 90 Part II Microbial Nutrition, Growth, and Control 5 Microbial Nutrition 93 5.1 The Common Nutrient Requirements 94 5.2 Requirements for Carbon, Hydrogen, and Oxygen 94 5.3 Nutritional Types of Microorganisms 95 5.4 Requirements for Nitrogen, Phosphorus, and Sulfur 96 5.5 Growth Factors 96 5.6 Uptake of Nutrients by the Cell 98 5.7 Culture Media 102 Historical Highlights 5.1: The Discovery of Agar as a Solidifying Agent and the Isolation of Pure Cultures 103 5.8 Isolation of Pure Cultures 104 Techniques & Applications 5.2: The Enrichment and Isolation of Pure Cultures 105 6 Microbial Growth 109 6.1 The Growth Curve 110 6.2 Measurement of Microbial Growth 114 6.3 The Continuous Culture of Microorganisms 117 6.4 The Influence of Environmental Factors on Growth 118 Microbial Diversity & Ecology 6.1: Life above 100?C 124 6.5 Microbial Growth in Natural Environments 128 7 Control of Microorganisms by Physical and Chemical Agents 133 7.1 Definition of Frequently Used Terms 134 Techniques & Applications 7.1: Safety in the Microbiology Laboratory 134 7.2 The Pattern of Microbial Death 135 7.3 Conditions Influencing the Effectiveness of Antimicrobial Agent Activity 136 7.4 The Use of Physical Methods in Control 136 ? Techniques & Applications 7.2: Universal Precautions for Microbiology Laboratories 142 7.5 The Use of Chemical Agents in Control 142 7.6 Evaluation of Antimicrobial Agent Effectiveness 146 Part III Microbial Metabolism 8 Metabolism: Energy, Enzymes, and Regulation 149 8.1 Energy and Work 150 8.2 The Laws of Thermodynamics 151 8.3 Free Energy and Reactions 152 8.4 The Role of ATP in Metabolism 153 8.5 Oxidation-Reduction Reactions and Electron Carriers 153 8.6 Enzymes 156 8.7 The Nature and Significance of Metabolic Regulation 160 8.8 Metabolic Channeling 160 8.9 Control of Enzyme Activity 161 9 Metabolism: Energy Release and Conservation 167 9.1 An Overview of Metabolism 168 9.2 The Breakdown of Glucose to Pyruvate 171 9.3 Fermentations 174 Historical Highlights 9.1: Microbiology and World War I 177 9.4 The Tricarboxylic Acid Cycle 178 9.5 Electron Transport and Oxidative Phosphorylation 179 9.6 Anaerobic Respiration 185 9.7 Catabolism of Carbohydrates and Intracellular Reserve Polymers 186 9.8 Lipid Catabolism 187 9.9 Protein and Amino Acid Catabolism 188 9.10 Oxidation of Inorganic Molecules 188 Microbial Diversity & Ecology 9.2: Acid Mine Drainage 190 9.11 Photosynthesis 190 10 Metabolism: The Use of Energy in Biosynthesis 199 10.1 Principles Governing Biosynthesis 200 Techniques & Applications 10.1: The Identification of Anabolic Pathways 202 10.2 The Photosynthetic Fixation of CO2 202 10.3 Synthesis of Sugars and Polysaccharides 203 10.4 The Assimilation of Inorganic Phosphorus, Sulfur, and Nitrogen 205 10.5 The Synthesis of Amino Acids 209 10.6 Anaplerotic Reactions 209 10.7 The Synthesis of Purines, Pyrimidines, and Nucleotides 211 10.8 Lipid Synthesis 214 10.9 Peptidoglycan Synthesis 216 10.10 Patterns of Cell Wall Formation 217 Part IV Microbial Molecular Biology and Genetics 11 Genes: Structure, Replication, and Mutation 221 11.1 DNA as Genetic Material 222 11.2 Nucleic Acid Structure 224 Historical Highlights 11.1: The Elucidation of DNA Structure 227 11.3 DNA Replication 229 11.4 The Genetic Code 234 11.5 Gene Structure 235 11.6 Mutations and Their Chemical Basis 239 11.7 Detection and Isolation of Mutants 245 11.8 DNA Repair 248 12 Genes: Expression and Regulation 253 12.1 DNATranscription or RNA Synthesis 254 Microbial Tidbits 12.1: Catalytic RNA (Ribozymes) 259 12.2 Protein Synthesis 260 12.3 Regulation of mRNA Synthesis 270 Historical Highlights 12.2: The Discovery of Gene Regulation 272 12.4 Attenuation 274 12.5 Global Regulatory Systems 276 12.6 Small RNAs and Regulation 278 12.7 Two-Component Phosphorelay Systems 279 12.8 Control of the Cell Cycle 280 13 Microbial Recombination and Plasmids 285 13.1 Bacterial Recombination: General Principles 286 13.2 Bacterial Plasmids 288 Disease 13.1: Virulence Plasmids 291 13.3 Transposable Elements 291 13.4 Bacterial Conjugation 296 13.5 DNATransformation 299 13.6 Transduction 301 13.7 Mapping the Genome 306 13.8 Recombination and Genome Mapping in Viruses 307 Part V DNA Technology and Genomics 14 Recombinant DNA Technology 311 14.1 Historical Perspectives 312 14.2 Synthetic DNA 315 14.3 The Polymerase Chain Reaction 316 14.4 Preparation of Recombinant DNA 319 14.5 Cloning Vectors 322 14.6 Inserting Genes into Eucaryotic Cells 326 14.7 Expression of Foreign Genes in Bacteria 327 Techniques & Applications 14.1: Gene Expression and Kittyboo Colors 329 14.8 Applications of Genetic Engineering 329 Techniques & Applications 14.2: Plant Tumors and Nature?s Genetic Engineer 331 14.9 Social Impact of Recombinant DNA Technology 332 15 Microbial Genomics 335 15.1 Introduction 336 15.2 Determining DNA Sequences 336 15.3 Whole-Genome Shotgun Sequencing 336 15.4 Bioinformatics 339 15.5 General Characteristics of Microbial Genomes 339 15.6 Functional Genomics 345 15.7 The Future of Genomics 349 Part VI The Viruses 16 The Viruses: Introduction and General Characteristics 351 16.1 Early Development of Virology 352 Historical Highlights 16.1: Disease and the Early Colonization of America 353 16.2 General Properties of Viruses 353 16.3 The Cultivation of Viruses 353 16.4 Virus Purification and Assays 355 16.5 The Structure of Viruses 358 16.6 Principles of Virus Taxonomy 367 Microbial Tidbits 16.2: The Origin of Viruses 369 17 The Viruses: Bacteriophages 371 17.1 Classification of Bacteriophages 372 Microbial Diversity & Ecology 17.1: An Ocean of Viruses 372 17.2 Reproduction of Double-Stranded DNA Phages: The Lytic Cycle 373 17.3 Reproduction of Single-Stranded DNA Phages 378 17.4 Reproduction of RNA Phages 379 17.5 Temperate Bacteriophages and Lysogeny 380 18 The Viruses: Viruses of Eucaryotes 387 18.1 Classification of Animal Viruses 388 18.2 Reproduction of Animal Viruses 388 Techniques & Applications 18.1: Constructing a Virus 396 18.3 Cytocidal Infections and Cell Damage 398 18.4 Persistent, Latent, and Slow Virus Infections 399 18.5 Viruses and Cancer 400 18.6 Plant Viruses 401 18.7 Viruses of Fungi, Algae, and Protozoa 404 18.8 Insect Viruses 404 18.9 Viroids and Prions 405 Part VII The Diversity of the Microbial World 19 Microbial Taxonomy and Phylogeny 409 19.1 General Introduction and Overview 410 19.2 Microbial Evolution and Diversity 410 19.3 Taxonomic Ranks 412 19.4 Classification Systems 414 19.5 Major Characteristics Used in Taxonomy 416 19.6 Assessing Microbial Phylogeny 420 19.7 The Major Divisions of Life 423 Microbial Diversity & Ecology 19.1: Official Nomenclature Lists?A Letter from Bergey?s 428 19.8 Bergey?s Manual of Systematic Bacteriology 428 19.9 A Survey of Procaryotic Phylogeny and Diversity 431 20 The Archaea 437 20.1 Introduction to the Archaea 438 20.2 Phylum Crenarchaeota 442 20.3 Phylum Euryarchaeota 444 Microbial Diversity & Ecology 20.1: Methanotrophic Archaea 447 Microbial Tidbits 20.2: Photosynthesis in Halobacterium salinarium 450 21 Bacteria: The Deinococci and Nonproteobacteria Gram Negatives 453 21.1 Aquificae and Thermotogae 454 21.2 Deinococcus-Thermus 455 21.3 Photosynthetic Bacteria 456 Microbial Diversity & Ecology 21.1: The Mechanism of Gliding Motility 461 21.4 Phylum Planctomycetes 464 21.5 Phylum Chlamydiae 464 21.6 Phylum Spirochaetes 466 21.7 Phylum Bacteroidetes 469 22 Bacteria: The Proteobacteria 473 22.1 Class Alphaproteobacteria 474 22.2 Class Betaproteobacteria 482 22.3 Class Gammaproteobacteria 485 Microbial Diversity & Ecology 22.1: Bacterial Bioluminescence 492 22.4 Class Deltaproteobacteria 495 22.5 Class Epsilonproteobacteria 500 23 Bacteria: The Low G _ C Gram Positives 503 23.1 General Introduction 504 23.2 Class Mollicutes (the Mycoplasmas) 504 23.3 Low G _ C Gram-Positive Bacteria in Bergey?s Manual 507 23.4 Class Clostridia 508 Microbial Tidbits 23.1: Spores in Space 509 23.5 Class Bacilli 511 24 Bacteria: The High G _ C Gram Positives 521 24.1 General Properties of the Actinomycetes 522 24.2 High G _ C Gram-Positive Bacteria in Bergey?s Manual 524 24.3 Suborder Actinomycineae 526 24.4 Suborder Micrococcineae 527 24.5 Suborder Corynebacterineae 528 24.6 Suborder Micromonosporineae 529 24.7 Suborder Propionibacterineae 531 24.8 Suborder Streptomycineae 531 24.9 Suborder Streptosporangineae 533 24.10 Suborder Frankineae 533 24.11 Order Bifidobacteriales 534 25 The Fungi (Eumycota), Slime Molds, and Water Molds 537 25.1 Distribution 538 25.2 Importance 539 25.3 Structure 539 25.4 Nutrition and Metabolism 541 25.5 Reproduction 542 25.6 Characteristics of the Fungal Divisions 543 25.7 Slime Molds and Water Molds 548 26 The Algae 553 26.1 Distribution of Algae 555 26.2 Classification of Algae 555 26.3 Ultrastructure of the Algal Cell 556 26.4 Algal Nutrition 556 26.5 Structure of the Algal Thallus (Vegetative Form) 556 26.6 Algal Reproduction 556 26.7 Characteristics of the Algal Divisions 557 Techniques & Applications 26.1: Practical Importance of Diatoms 560 Disease 26.2: Toxic Algal Blooms 562 27 The Protozoa 565 27.1 Distribution 566 27.2 Importance 566 27.3 Morphology 566 27.4 Nutrition 567 27.5 Encystment and Excystment 568 27.6 Locomotory Organelles 568 27.7 Reproduction 568 27.8 Classification 568 27.9 Representative Types 569 Microbial Diversity & Ecology 27.1: The Importance of Foraminiferans 572 Part VIII Ecology and Symbiosis 28 Microorganism Interactions and Microbial Ecology 577 28.1 Foundations of Microbial Ecology 578 28.2 Microbial Interactions 578 Microbial Diversity & Ecology 28.1: Microbial Ecology Versus Environmental Microbiology 579 Microbial Diversity & Ecology 28.2: Coevolution of Animals and Their Gut Microbial Communities 584 28.3 Nutrient Cycling Interactions 593 28.4 The Physical Environment 602 Techniques & Applications 28.3: Thermophilic Microorganisms and Modern Biotechnology 607 28.5 Microbial Ecology and Its Methods: An Overview 607 29 Microorganisms in Aquatic Environments 615 29.1 Aquatic Environments and Microorganisms 616 ? Disease 29.1: New Agents in Medicine--The Sea as the New Frontier 617 29.2 The Microbial Community 621 29.3 Marine Environments 624 29.4 Freshwater Environments 628 29.5 Waters and Disease Transmission 630 Techniques & Applications 29.2: Waterborne Diseases, Water Supplies, and Slow Sand Filtration 632 29.6 Wastewater Treatment 636 Disease 29.3: Sewage Sludge: Long-Term Concerns with Land and Water Disposal 641 29.7 Groundwater Quality and Home Treatment Systems 642 30 Microorganisms in Terrestrial Environments 645 30.1 Soils as an Environment for Microorganisms 646 30.2 Microorganisms in the Soil Environment 647 30.3 Microorganisms and the Formation of Different Soils 648 30.4 Soil Microorganism Associations with Vascular Plants 651 Microbial Diversity & Ecology 30.1: Mycorrhizae and the Evolution of Vascular Plants 656 30.5 Soils, Plants, and Nutrients 662 Microbial Tidbits 30.2: An Unintended Global-Scale Nitrogen Experiment 664 30.6 Soils, Plants, and the Atmosphere 664 Techniques & Applications 30.3: Keeping Inside Air Fresh with Soil Microorganisms 665 Microbial Diversity & Ecology 30.4: Soils, Termites, Intestinal Microbes, and Atmospheric Methane 666 30.7 Microorganisms and Plant Decomposition 666 30.8 The Subsurface Biosphere 667 30.9 Soil Microorganisms and Human Health 669 30.10 Understanding Microbial Diversity in the Soil 670 Part IX Nonspecific (Innate) Resistance and the Immune Response 31 Normal Microbiota and Nonspecific (Innate) Host Resistance 673 31.1 Gnotobiotic Animals 674 31.2 Normal Microbiota of the Human Body 675 Techniques & Applications 31.1: Probiotics for Humans and Animals 679 31.3 Overview of Host Resistance 680 31.4 Cells, Tissues, and Organs of the Immune System 681 31.5 Physical and Chemical Barriers in Nonspecific (Innate) Resistance 685 31.6 Inflammation 688 31.7 The Complement System 691 31.8 Phagocytosis 693 31.9 Cytokines 697 31.10 Natural Killer Cells 700 32 Specific (Adaptive) Immunity 705 32.1 Overview of Specific (Adaptive) Immunity 706 32.2 Antigens 708 32.3 Antibodies 710 Techniques & Applications 32.1: Immunotoxins 721 32.4 T-Cell Biology 721 Techniques & Applications 32.2: Donor Selection for Tissue or Organ Transplants 724 32.5 B-Cell Biology 728 32.6 Action of Antibodies 731 32.7 The Classical Complement Pathway 734 32.8 Acquired Immune Tolerance 734 32.9 Summary: The Role of Antibodies and Lymphocytes in Resistance 734 33 Medical Immunology 739 33.1 Vaccines and Immunizations 740 Historical Highlights 33.1: The First Immunizations 740 3.2 Immune Disorders 744 33.3 Antigen-Antibody Interactions In Vitro 751 Techniques & Applications 33.2: History and Importance of Serotyping 757 Part X Microbial Diseases and Their Control 34 Pathogenicity of Microorganisms 761 34.1 Host-Parasite Relationships 762 34.2 Pathogenesis of Viral Diseases 764 34.3 Pathogenesis of Bacterial Diseases 765 Techniques & Applications 34.1: Detection and Removal of Endotoxins 774 34.4 Microbial Mechanisms for Escaping Host Defenses 775 35 Antimicrobial Chemotherapy 779 35.1 The Development of Chemotherapy 780 ? Techniques & Applications 35.1: The Use of Antibiotics in Microbiological Research 781 35.2 General Characteristics of Antimicrobial Drugs 781 35.3 Determining the Level of Antimicrobial Activity 783 35.4 Mechanisms of Action of Antimicrobial Agents 784 35.5 Factors Influencing the Effectiveness of Antimicrobial Drugs 786 35.6 Antibacterial Drugs 787 35.7 Drug Resistance 792 Disease 35.2: Antibiotic Misuse and Drug Resistance 793 35.8 Antifungal Drugs 795 35.9 Antiviral Drugs 796 36 Clinical Microbiology 799 36.1 Specimens 800 Techniques & Applications 36.1: Universal Precautions for Health-Care Professionals 802 36.2 Identification of Microorganisms from Specimens 804 Techniques & Applications 36.2: Monoclonal Antibodies in Clinical Microbiology 813 36.3 Susceptibility Testing 817 36.4 Computers in Clinical Microbiology 817 37 The Epidemiology of Infectious Disease 821 37.1 Epidemiological Terminology 822 Historical Highlights 37.1: John Snow--The First Epidemiologist 822 37.2 Measuring Frequency: The Epidemiologist?s Tools 823 37.3 Infectious Disease Epidemiology 823 37.4 Recognition of an Infectious Disease in a Population 824 37.5 Recognition of an Epidemic 824 Historical Highlights 37.2: Typhoid Mary 825 37.6 The Infectious Disease Cycle: Story of a Disease 827 Historical Highlights 37.3: The First Indications of Person-to-Person Spread of an Infectious Disease 831 37.7 Virulence and the Mode of Transmission 832 37.8 Emerging and Reemerging Infectious Diseases and Pathogens 832 Disease 37.4: The SARS Epidemic of 2003 835 37.9 Control of Epidemics 837 37.10 The Emerging Threat of Bioterrorism 837 Historical Highlights 37.5: 1346--The First Recorded Biological Warfare Attack 838 37.11 Global Travel and Health Considerations 839 37.12 Nosocomial Infections 840 38 Human Diseases Caused by Viruses 845 38.1 Airborne Diseases 846 Disease 38.1: Reye?s and Guillain-Barr Syndromes 849 38.2 Arthropod-Borne Diseases 852 Disease 38.2: Viral Hemorrhagic Fevers--A Microbial History Lesson 853 38.3 Direct Contact Diseases 855 38.4 Food-Borne and Waterborne Diseases 868 Historical Highlights 38.3: A Brief History of Polio 870 38.5 Slow Virus and Prion Diseases 870 38.6 Other Diseases 871 39 Human Diseases Caused by Bacteria 875 39.1 Airborne Diseases 876 39.2 Arthropod-Borne Diseases 885 Historical Highlights 39.1: The Hazards of Microbiological Research 885 39.3 Direct Contact Diseases 889 Disease 39.2: Biofilms 897 Disease 39.3: Resistant Staphylococci 900 Disease 39.4: A Brief History of Syphilis 902 39.4 Food-Borne and Waterborne Diseases 905 Techniques & Applications 39.5: Clostridial Toxins as Therapeutic Agents-- Benefits of Nature?s Most Toxic Proteins 908 39.5 Sepsis and Septic Shock 911 39.6 Dental Infections 911 40 Human Diseases Caused by Fungi and Protozoa 917 40.1 Fungal Diseases 918 Disease 40.1: The Emergence of Candidiasis 925 40.2 Protozoan Diseases 926 Disease 40.2: A Brief History of Malaria 930 Part XI Food and Industrial Microbiology 41 Microbiology of Food 937 41.1 Microorganism Growth in Foods 938 41.2 Microbial Growth and Food Spoilage 940 41.3 Controlling Food Spoilage 943 Historical Highlights 41.1: An Army Travels on Its Stomach 944 41.4 Food-Borne Diseases 946 Historical Highlights 41.2: Typhoid Fever and Canned Meat 947 41.5 Detection of Food-Borne Pathogens 949 41.6 Microbiology of Fermented Foods 951 Techniques & Applications 41.3: Starter Cultures, Bacteriophage Infections, and Plasmids 951 41.7 Microorganisms as Foods and Food Amendments 958 42 Industrial Microbiology and Biotechnology 963 42.1 Choosing Microorganisms for Industrial Microbiology and Biotechnology 964 Techniques & Applications 42.1: The Potential of Thermophilic Archaea in Biotechnology 965 42.2 Microorganism Growth in Controlled Environments 970 42.3 Major Products of Industrial Microbiology 974 42.4 Microbial Growth in Complex Natural Environments 979 Microbial Diversity & Ecology 42.2: Methanogens?A New Role for a Unique Microbial Group 981 Microbial Diversity & Ecology 42.3: A Fungus with a Voracious Appetite 985 42.5 Biotechnological Applications 986 Techniques & Applications 42.4: Streptavidin-Biotin Binding and Biotechnology 987 42.6 Impacts of Microbial Biotechnology 990 Appendices Appendix I A Review of the Chemistry of Biological Molecules A-1 Appendix II Common Metabolic Pathways A-11 Appendix III Classification of Procaryotes According to the Second Edition of Bergey?s Manual of Systematic Bacteriology A-19 Appendix IV Classification of Viruses A-28 Appendix V Recommended Readings A-38 Glossary G-1 Credits C-1 Index I-1
Library of Congress Subject Headings for this publication:
Microbiology.