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Fifteenth edition

Global edition

Harlow : Pearson, [2019]

1058 stran : ilustrace (převážně barevné) ; 28 cm

ISBN 978-1-292-23510-3 (brožováno) ISBN !1-292-23510-1 (chyb.)

Na titulní straně uvedena adresa: 330 Hudson Street, NY NY 10030

Terminologické slovníky

Obsahuje rejstřík

001473019

About the Authors 11 // Preface 15 // UNIT 1 The Foundations of Microbiology // 1 The Microbial World 37 // Microorganisms, Our Constant Companions 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 Microorganisms and the Biosphere 41 // 1.4 The Impact of Microorganisms on Human Society 42 // II • Microscopy and the Origins of Microbiology 47 // 1.5 Light Microscopy and the Discovery of Microorgarisms 47 // 1.6 Improving Contrast in Light Microscopy 49 // 1.7 Imaging Cells in Three Dimensions 51 // 1.8 Probing Cel Structure: Electron Microscopy 52 // III • Microbial Cultivation Expands the Horizon of Microbiology 54 // 1.9 Pasteur and Spontaneous Generation 55 // 1.10 Koch, Infectious Diseases, and Pure Cultures 57 // 1.11 Discovery of Microbial Diversity 60 // IV • Molecular Biology and the Unity and Diversity of Life 61 // 1.12 Molecular Basis of Life 61 // 1.13 Woese and the Tree of Life 62 // 1.14 An Introduction to Microbial Life 65 // The Archaellum: Motility for the Archaea 70 // I • Cells of Bacteria and Archaea 71 // 2 Microbial Cell Structure and Function 70 // 2.1 Cell Morphology 71 // 2.2 The Small World 72 // II • The Cell Membrane and Wall 75 // 2.3 The Cytoplasmic Membrane 75 // 2.4 Bacterial Cell Walls: Peptidoglycan 78 // 2.5 LPS: The Outer Membrane 81 // 2.6 Archaeal Cell Walls 83 // III • Cell Surface Structures and Inclusions 84 // 2.7 Cell Surface Structures 84 // 2.8 Cell Inclusions 86 // 2.9 Gas Vesicles 88 // 2.10 Endospores 89 // IV • Cell Locomotion 92 // 2.11 Fagella, Archaella, and Swimming Motility 92 // 2.12 Gliding Motility 96 // 2.13 Chemotaxis and Other Taxes 97 // V • Eukaryotic Microbial Cells 100 // 2.14 The Nucleus and Cell Division 100 // 2.15 Mitochondria, Hydrogenosomes, and Chloroplasts 102 // 2.16 Other Eukaryotic Cell Structures 104 // EXPLORE THE MICROBIAL WORLD Tiny Ceils 74 //

Microbial Metabolism 109 // Sugars and Sweets: Archaea Do It Their Way 109 // I • Microbial Nutrients and Nutrient Uptake 110 // 3.1 Feeding the Microbe: Cell Nutrition 110 // 3.2 Transporting Nutrients into the Cell 111 // II • Energetics, Enzymes, and Redox 113 // 3.3 Energy Classes of Microorganisms 113 // 3.4 Principles of Bioenergetics 114 // 3.5 Catalysis and Enzymes 116 // 3.6 Electron Donors and Acceptors 117 // 3.7 Energy-Rich Compounds 120 // III • Catabolism: Fermentation and Respiration 121 // 3.8 Glycolysis and Fermentation 121 // 3.9 Respiration: Citric Acid and Glyoxylate Cycles 124 // 3.10 Respiration: Electron Carriers 126 // 3.11 Electron Transport and the Proton Motive Force 128 // 3.12 Options for Energy Conservation 130 // IV • Biosyntheses 132 // 3.13 Sugars and Polysaccharides 132 // 3.14 Amino Acids and Nucleotides 133 // 3.15 Fatty Acids and Lipids 134 // 4 Molecular Information Flow and Protein Processing 138 // Synthesis of Jumbo Proteins: Secretion of Halomucin 138 // I • Molecular Biology and Genetic Elements 139 // 4.1 DNA and Genetic Information Flow 139 // 4.2 Genetic Elements: Chromosomes and Plasmids 142 // II • Copying the Genetic Blueprint: DNA Replication 145 // 4.3 Templates, Enzymes, and the Replication Fork 146 // 4.4 Bidirectional Replication, the Replisome, and Proofreading 149 // III • RNA Synthesis: Transcription 151 // 4.5 Transcription in Bacteria 151 // 4.6 Transcription in Archaea and Eukarya 154 // IV • Protein Synthesis: Translation 156 // 4.7 Amino Acids, Polypeptides, and Proteins 156 // 4.8 Transfer RNA 159 // 4.9 Translation and the Genetic Code 160 // 4.10 The Mechanism of Protein Synthesis 162 // V • Protein Processing, Secretion, and Targeting 165 // 4.11 Assisted Protein Folding and Chaperones 165 // 4.12 Protein Secretion: The Sec and Tat Systems 166 // 4.13 Protein Secretion: Gram-Negative Systems 167 // UNIT 2 Microbial Growth and Regulation //

5 Microbial Growth and Its Control 173 // Picking Apart a Microbial Consortium 173 // I • Cell Division and Population Growth 174 // 5.1 Binary Fission, Budding, and Biofilms 174 // 5.2 Quantitative Aspects of Microbial Growth 176 // 5.3 The Microbial Growth Cycle 178 // 5.4 Continuous Culture 179 // II • Culturing Microbes and Measuring Their Growth 180 // 5.5 Growth Media and Laboratory Culture 180 // 5.6 Microscopic Counts of Microbial Cell Numbers 184 // 5.7 Viable Counting of Microbial Cell Numbers 185 // 5.8 Turbidimetric Measures of Microbial Cell Numbers 187 // III • Environmental Effects on Growth: Temperature 188 // 5.9 Temperature Classes of Microorganisms 188 // 5.10 Microbial Life in the Cold 189 // 5.11 Microbial Life at High Temperatures 192 // IV • Environmental Effects on Growth: pH, Osmolarity, and Oxygen 194 // 5.12 Effects of pH on Microbial Growth 194 // 5.13 Osmolarity and Microbial Growth 195 // 5.14 Oxygen and Microbial Growth 196 // V • Controlling Microbial Growth 200 // 5.15 General Principles and Growth Control by Heat 200 // 5.16 Other Physical Control Methods: Radiation and Filtration 202 // 5.17 Chemical Control of Microbial Growth 203 // 6 Microbial Regulatory Systems 209 // Microbial Hunter: Pseudomonas aeruginosa Senses and Scavenges Nutrients from Damaged Tissues 209 // I • DNA-Binding Proteins and Transcriptional Regulation 210 // 6.1 DNA-Binding Proteins 210 // 6.2 Negative Control: Repression and Induction 212 // 6.3 Positive Control: Activation 213 // 6.4 Global Control and the lac Operon 215 // 6.5 Transcription Controls in Archaea 217 // II • Sensing and Signal Transduction 219 // 6.6 Two-Component Regulatory Systems 219 // 6.7 Regulation of Chemotaxis 220 // 6.8 Quorum Sensing 222 // 6.9 Stringent Response 224 // 6.10 Other Global Networks 226 // III • RNA-Based Regulation 228 // 6.11 Regulatory RNAs 228 // 6.12 Riboswitches 230 //

6.13 Attenuation 231 // IV • Regulation of Enzymes and Other Proteins 232 // 6.14 Feedback Inhibition 232 // 6.15 Post-Translational Regulation 233 // 7 Molecular Biology of Microbial Growth 238 // Explosive Cell Death Promotes Biofilm Formation 238 // I • Bacterial Cell Division 239 // 7.1 Visualizing Molecular Growth 239 // 7.2 Chromosome Replication and Segregation 241 // 7.3 Cell Division and Fts Proteins 243 // 7.4 MreB and Cell Morphology 245 // 7.5 Peptidoglycan Biosynthesis 246 // II • Regulation of Development in Model Bacteria 248 // 7.6 Regulation of Endospore Formation 248 // 7.7 Caulobacter Differentiation 249 // 7.8 Heterocyst Formation in Anabaena 250 // 7.9 Biofilm Formation 251 // III • Antibiotics and Microbial Growth 253 // 7.10 Antibiotic largets and Antibiotic Resistance 253 // 7.11 Persistence and Dormancy 255 // 8 Viruses and Their Replication 259 // Virophages: Viruses That Parasitize Other Viruses 259 // I • The Nature of Viruses 260 // 8.1 What Is a Virus? 260 // 8.2 Structure of the Virion 261 // 8.3 Overview of the Virus Life Cycle 263 // 8.4 Culturing, Detecting, and Counting Viruses 264 // II • The Viral Replication Cycle 266 // 8.5 Attachment and Entry of Bacteriophage T4 266 // 8.6 Replication of Bacteriophage T4 267 // 8.7 Temperate Bacteriophages and Lysogeny 270 // 8.8 An Overview of Animal Virus Infection 272 // UNIT 3 Genomics and Genetics // 9 Microbial Systems Biology 277 // Sequencing in the Palm of Your Hand 277 // I • Genomics 278 // 9.1 Introduction to Genomics 278 // 9.2 Sequencing and Annotating Genomes 280 // 9.3 Genome Size and Gene Content in Bacteria and Archaea 283 // 9.4 Organelle and Eukaryotic Microbial Genomes 285 // II • The Evolution of Genomes 288 // 9.5 Gene Families, Duplications, and Deletions 288 // 9.6 Horizontal Gene Transfer and the Mobilome 290 // 9.7 Core Genome Versus Pan Genome 291 // III • Functional Omics 293 // 9.8 Metagenomics 293 //

9.9 Gene Chips and Transcriptomics 295 // 9.10 Proteomics and the Interactome 298 // 9.11 Metabolomics 299 // IV • The Utility of Systems Biology 302 // 9.12 Single-Cell Genomics 302 // 9.13 Integrating Mycobacterium tuberculosis Omics 303 // 9.14 Systems Biology and Human Health 305 // 10 Viral Genomics, Diversity, and Ecology 310 // Viral Imaging to the Rescue: Structural Blueprint of Zika 310 // I • Viral Genomes and Evolution 311 // 10.1 Size and Structure of Viral Genomes 311 // 10.2 Viral Evolution 313 // II • DNA Viruses 315 // 10.3 Single-Stranded DNA Bacteriophages: fíX174 and M13 315 // 10.4 Double-Stranded DNA Bacteriophages: T7 and Mu 317 // 10.5 Viruses of Archaea 319 // 10.6 Uniquely Replicating DNA Animal Viruses 321 // 10.7 DNA Tumor Viruses 322 // 12.2 Molecular Cloning 372 // 12.3 Expressing Foreign Genes in Bacteria 374 // 12.4 Molecular Methods for Mutagenesis 376 // 12.5 Reporter Genes and Gene Fusions 378 // II • Making Products from Genetically Engineered Microbes: Biotechnology 379 // 12.6 Somatotropin and Other Mammalian Proteins 379 // 12.7 Transgenic Organisms in Agriculture and Aquaculture 381 // 12.8 Engineered Vaccines and Therapeutics 383 // 12.9 Mining Genomes and Engineering Pathways 385 // 12.10 Engineering Biofuels 387 // III • Synthetic Biology and Genome Editing 389 // 12.11 From Synthetic Metabolic Pathways to Synthetic Cells 390 // 12.12 Genome Editing and CRISPRs 392 // 12.13 Biocontainment of Genetically Modified Organisms 394 // UNIT 4 Microbial Evolution and Diversity // 13 Microbial Evolution and Systematics 399 // Lokiarchaeota and the Origin of Eukarya 399 // I • Early Earth and the Origin and Diversification of Life 400 // 13.1 Formation and Early History of Earth 400 // 13.2 Photosynthesis and the Oxidation of Earth 403 // 13.3 Living Fossils: DNA Records the History of Life 405 // 13.4 Endosymbiotic Origin of Eukaryotes 406 //

II • Microbial Evolution 408 // 13.5 The Evolutionary Process 408 // 13.6 The Evolution of Microbial Genomes 411 // III • Microbial Phylogeny and Systematics 412 // 13.7 Molecular Phylogeny: Making Sense of Molecular Sequences 412 // 13.8 The Species Concept in Microbiology 418 // 13.9 Taxonomic Methods in Systematics 420 // 13.10 Classification and Nomenclature 423 // EXPLORE THE MICROBIAL WORLD // The Black Queen Hypothesis 413 // III • Viruses with RNA Genomes 324 // 10.8 Positive-Strand RNA Viruses 324 // 10.9 Negative-Strand RNA Animal Viruses 326 // 10.10 Double-Stranded RNA Viruses 328 // 10.11 Viruses That Use Reverse Transcriptase 329 // IV • Viral Ecology 331 // 10.12 The Bacterial and Archael Virosphere 332 // 10.13 Viral Defense Mechanisms of Bacteria and Archaea 333 // 10.14 The Human Virome 335 // V • Subviral Agents 336 // 10.15 Viroids 336 // 10.16 Prions 337 // 11 Genetics of Bacteria and Archaea 342 // Killing and Stealing: DNA Uptake by the Predator Vibrio cholerae 342 // I • Mutation 343 // 11.1 Mutations and Mutants 343 // 11.2 Molecular Basis of Mutation 344 // 11.3 Reversions and Mutation Rates 346 // 11.4 Mutagenesis 348 // II • Gene Transfer in Bacteria 349 // 11.5 Genetic Recombination 350 // 11.6 Transformation 352 // 11.7 Transduction 353 // 11.8 Conjugation 356 // 11.9 The Formation of Hfr Strains and Chromosome Mobilization 357 // III • Gene Transfer in Archaea and Other Genetic Events 360 // 11.10 Horizontal Gene Transfer in Archaea 360 // 11.11 Mobile DNA: Transposable Elements 361 // 11.12 Preserving Genomic Integrity: CRISPR Interference 364 // 12 Biotechnology and Synthetic Biology 368 // Creation of a New Life Form: Design of a Minimal Cell 368 // I • Tools of the Genetic Engineer 369 // 12.1 Manipulating DNA: PCR and Nucleic Acid Hybridization 369 // 14 Metabolie Diversity of Microorganisms 428 // Microbes That Plug into the Matrix 428 // I • Phototrophy 429 //

14.1 Photosynthesis and Chlorophylls 429 // 14.2 Carotenoids and Phycobilins 432 // 14.3 Anoxygenic Photosynthesis 434 // 14.4 Oxygenic Photosynthesis 437 // II • Autotrophy and N2 Fixation 440 // 14.5 Autotrophic Pathways 441 // 14.6 Nitrogen Fixation 443 // III • Respiratory Processes Defined by Electron Donor 446 // 14.7 Principles of Respiration 446 // 14.8 Hydrogen (H2) Oxidation 448 // 14.9 Oxidation of Sulfur Compounds 449 // 14.10 Iron (Fe2+) Oxidation 451 // 14.11 Nitrification 452 // 14.12 Anaerobic Ammonia Oxidation (Anammox) 454 // IV • Respiratory Processes Defined by Electron // Acceptor 455 // 14.13 Nitrate Reduction and Denitrification 455 // 14.14 Sulfate and Sulfur Reduction 457 // 14.15 Other Electron Acceptors 459 // V • One-Carbon (C,) Metabolism 461 // 14.16 Acetogenesis 461 // 14.17 Methanogenesis 463 // 14.18 Methanotrophy 467 // VI • Fermentation 470 // 14.19 Energetic and Redox Considerations 470 // 14.20 Lactic and Mixed-Acid Fermentations 471 // 14.21 Clostridial and Propionate Fermentations 474 // 14.22 Fermentations That Lack Substrate-Level Phosphorylation 476 // 14.23 Syntrophy 477 // VII • Hydrocarbon Metabolism 479 // 14.24 Aerobic Hydrocarbon Metabolism 480 // 14.25 Anaerobic Hydrocarbon Metabolism 481 // 15 Functional Diversity of Microorganisms 487 // New Discoveries Have Redefined the Global Nitrogen Cycle 487 // I • Functional Diversity as a Concept 488 // 15.1 Making Sense of Microbial Diversity 488 // II • Diversity of Phototrophic Bacteria 489 // 15.2 Overview of Phototrophic Bacteria 489 // 15.3 Cyanobacteria 489 // 15.4 Purple Sulfur Bacteria 494 // 15.5 Purple Nonsulfur Bacteria and Aerobic Anoxygenic Phototrophs 495 // 15.6 Green Sulfur Bacteria 496 // 15.7 Green Nonsulfur Bacteria 498 // 15.8 Other Phototrophic Bacteria 499 // III • Microbial Diversity in the Sulfur Cycle 500 // 15.9 Dissimilative Sulfate-Reducers 501 // 15.10 Dissimilative Sulfur-Reducers 502 //

15.11 Dissimilative Sulfur-Oxidizers 503 // IV • Microbial Diversity in the Nitrogen Cycle 506 // 15.12 Diversity of Nitrogen-Fixers 506 // 15.13 Diversity of Nitrifiers and Denitrifiers 508 // V • Other Distinctive Functional Groupings of Microorganisms 510 // 15.14 Dissimilative Iron-Reducers 510 // 15.15 Dissimilative Iron-Oxidizers 511 // 15.16 Methanotrophs and Methylotrophs 512 // 15.17 Microbial Predators 514 // 15.18 Microbial Bioluminescence 517 // VI • Morphologically Diverse Bacteria 519 // 15.19 Spirochetes 519 // 15.20 Budding and Prosthecate/Stalked Microorganisms 521 // 15.21 Sheathed Microorganisms 524 // 15.22 Magnetic Microbes 525 // 16 Diversity of Bacteria 530 // Mystery of the Missing Peptidoglycan 530 // I • Proteobacteria 531 // 16.1 Alphaproteobacteria 532 // 16.2 Betaproteobacteria 535 // 16.3 Gammaproteobacteria: Enterobacteriales 537 // 16.4 Gammaproteobacteria: Pseudomonadales and Vibrionates 539 // 16.5 Deltaproteobacteria and Epsilonproteobacteria 540 // II • Firmiertes, Teneri cutes, and Actinobacteria 542 // 16.6 Firmicutes: Lactobacillales 543 // 16.7 Firmicutes: Nonsporulating Bacillales and Clostridiales 544 // 16.8 Firmicutes: Sporulating Bacillales and Clostridiales 545 // 16.9 Tenericutes: The Mycoplasmas 547 // 16.10 Actinobacteria: Coryneform and Propionic Acid Bacteria 548 // 16.11 Actinobacteria: Mycobacterium 550 // 16.12 Filamentous Actinobacteria: Streptomyces and Relatives 551 // III • Bacteroidetes 553 // 16.13 Bacteroidales 553 // 16.14 Cytophagales, Flavobacteriales, and Sphingobacteriales 554 // IV • Chlamydiae, Planctomycetes, and Verrucomicrobia 556 // 16.15 Chlamydiae 556 // 16.16 Planctomycetes 558 // 16.17 Verrucomicrobia 559 // V • Hyperthermophilic Bacteria 559 // 16.18 Thermotogae and Thermodesulfobacteria 559 // 16.19 Aquificae 560 // VI • Other Bacteria 561 // 16.20 Deinococcus-Thermus 561 // 16.21 Other Notable Phyla of Bacteria 562 // 17 Diversity of Archaea 566 //

The Archaea Just Under Your Feet 566 // I • Euryarchaeota 567 // 17.1 Extremely Halophilic Archaea 568 // 17.2 Methanogenic Archaea 571 // 17.3 Thermoplasmatales 574 // 17.4 Thermococcales and Archaeoglobales 576 // II • Thaumarchaeota, Nanoarchaeota, and Korarchaeota 577 // 17.5 Thaumarchaeota and Nitrification in Archaea 577 // 17.6 Nanoarchaeota and the "Hospitable Fireball" 578 // 17.7 Korarchaeota and the "Secret Filament" 579 // III • Crenarchaeota 580 // 17.8 Habitats and Energy Metabolism 580 // 17.9 Crenarchaeota from Terrestrial Volcanic Habitats 581 // 17.10 Crenarchaeota from Submarine Volcanic Habitats 583 // IV • Evolution and Life at High Temperature 586 // 17.11 An Upper Temperature Limit for Microbial Life 586 // 17.12 Molecular Adaptations to Life at High Temperature 588 // 17.13 Hyperthermophilic Archaea, HJ( and Microbial Evolution 589 // 18 Diversity of Microbial Eukarya 593 // Arbuscular Mycorrhizal Fungi: Intimate, Unseen, and Powerful 593 // I • Organelles and Phylogeny of Microbial Eukarya 594 // 18.1 Endosymbioses and the Eukaryotic Cell 594 // 18.2 Phylogenetic Lineages of Eukarya 596 // II • Protists 597 // 18.3 Excavata 597 // 18.4 Alveolata 599 // 18.5 Stramenopiles 601 // 18.6 Rhizaria 603 // 18.7 Amoebozoa 604 // III • Fungi 606 // 18.8 Fungal Physiology, Structure, and Symbioses 606 // 18.9 Fungal Reproduction and Phylogeny 608 // 18.10 Microsporidia and Chytridiomycota 609 // 18.11 Zygomycota and Glomeromycota 610 // 18.12 Ascomycota 611 // 18.13 Basidiomycota 612 // IV • Archaeplastida 613 // 18.14 Red Algae 613 // 18.15 Green Algae 614 // UNIT 5 Microbial Ecology and Environmental Microbiology // 19 Taking the Measure of Microbial Systems 619 // The Vineyard Microbiome Revealed by Next-Generation Sequencing Technology 619 // I • Culture-Dependent Analyses of Microbial Communities 620 // 19.1 Enrichment Culture Microbiology 620 //

19.2 Classical Procedures for Isolating Microbes 624 // 19.3 Selective Single-Cell Isolation: Laser Tweezers, Flow Cytometry, Microfluidics, and High-Throughput Methods 625 // II • Culture-Independent Microscopic Analyses of Microbial Communities 627 // 19.4 General Staining Methods 627 // 19.5 Fluorescence In Situ Hybridization (FISH) 630 // III • Culture-Independent Genetic Analyses of Microbial Communities 631 // 19.6 PCR Methods of Microbial Community Analysis 631 // 19.7 Microarrays for Analysis of Microbial Phylogenetic and Functional Diversity 635 // 19.8 Environmental Genomics and Related Methods 636 // IV • Measuring Microbial Activities in Nature 640 // 19.9 Chemical Assays, Radioisotopic Methods, and Microsensors 640 // 19.10 Stable Isotopes and Stable Isotope Probing 642 // 19.11 Linking Functions to Specific Organisms 644 // 19.12 Linking Genes and Cellular Properties to Individual Cells 646 // 20 Microbial Ecosystems 651 // Microbes of the Abyss 651 // I • Microbial Ecology 652 // 20.1 General Ecological Concepts 652 // 20.2 Ecosystem Service: Biogeochemistry and Nutrient Cycles 653 // II • The Microbial Environment 654 // 20.3 Environments and Microenvironments 654 // 20.4 Surfaces and Biofilms 656 // 20.5 Microbial Mats 658 // III • Terrestrial Environments 660 // 20.6 Soils 660 // 20.7 The Terrestrial Subsurface 665 // IV • Aquatic Environments 666 // 20.8 Freshwaters 667 // 20.9 The Marine Environment: Phototrophs and Oxygen Relationships 669 // 20.10 Major Marine Phototrophs 672 // 20.11 Pelagic Bacteria, Archaea, and Viruses 674 // 20.12 The Deep Sea 676 // 20.13 Deep-Sea Sediments 678 // 20.14 Hydrothermal Vents 681 // 21 Nutrient Cycles 687 // The Big Thaw and the Microbiology of Climate Change 687 // I • Carbon, Nitrogen, and Sulfur Cycles 688 // 21.1 The Carbon Cycle 688 // 21.2 Syntrophy and Methanogenesis 690 // 21.3 The Nitrogen Cycle 692 // 21.4 The Sulfur Cycle 694 // II • Other Nutrient Cycles 695 //

21.5 The Iron and Manganese Cycles 696 // 21.6 The Phosphorus, Calcium, and Silica Cycles 698 // III • Humans and Nutrient Cycling 702 // 21.7 Mercury Transformations 702 // 21.8 Human Impacts on the Carbon and Nitrogen Cycles 703 // EXPLORE THE MICROBIAL WORLD // Microbially Wired 698 // 22 Microbiology of the Built Environment 708 // After the Toilet Flushes 708 // I • Mineral Recovery and Acid Mine Drainage 709 // 22.1 Mining with Microorganisms 709 // 22.2 Acid Mine Drainage 711 // II • Bioremediation 712 // 22.3 Bioremediation of Uranium-Contaminated Environments 712 // 22.4 Bioremediation of Organic Pollutants: Hydrocarbons 713 // 22.5 Bioremediation of Organic Pollutants: Pesticides and Plastics 714 // III • Wastewater and Drinking Water Treatment 716 // 22.6 Primary and Secondary Wastewater Treatment 716 // 22.7 Advanced Wastewater Treatment 719 // 22.8 Drinking Water Purification and Stabilization 722 // 22.9 Water Distribution Systems 724 // IV • Indoor Microbiology and Microbially Influenced Corrosion 725 // 22.10 The Microbiology of Homes and Public Spaces 725 // 22.11 Microbially Influenced Corrosion of Metals 727 // 22.12 Biodeterioration of Stone and Concrete 728 // 23 Microbial Symbioses with Microbes, Plants, and Animals 732 // The Inner Life of Bees 732 // I • Symbioses between Microorganisms 733 // 23.1 Lichens 733 // 23.2 “Chlorochromatium aggregatum" 734 // II • Plants as Microbial Habitats 736 // 23.3 The Legume-Root Nodule Symbiosis 736 // 23.4 Mycorrhizae 741 // 23.5 Agrobacterium and Crown Gall Disease 744 // III • Insects as Microbial Habitats 745 // 23.6 Heritable Symbionts of Insects 745 // 23.7 Termites 748 // IV • Other Invertebrates as Microbial Habitats 750 // 23.8 Hawaiian Bobtail Squid 750 // 23.9 Marine Invertebrates at Hydrothermal Vents and Cold Seeps 752 // 23.10 Entomopathogenic Nematodes 753 // 23.11 Reef-Building Corals 754 //

V • Mammalian Gut Systems as Microbial Habitats 757 // 23.12 Alternative Mammalian Gut Systems 757 // 23.13 The Rumen and Ruminant Animals 758 // EXPLORE THE MICROBIAL WORLD - The Symbiotic Organ of The Bean Bug 747 // UNIT 6 Microbe-Human Interactions and the Immune System // 24 Microbial Symbioses with Humans 765 // Frozen in Time: The Iceman Microbiome 765 // I • Structure and Function of the Healthy Adult Human Microbiome 766 // 24.1 Overview of the Human Microbiome 766 // 24.2 Gastrointestinal Microbiota 768 // 24.3 Oral Cavity and Airways 772 // 24.4 Urogenital Tracts and Their Microbes 776 // 24.5 The Skin and Its Microbes 777 // II • From Birth to Death: Development of the Human Microbiome 780 // 24.6 Human Study Groups and Animal Models 780 // 24.7 Colonization, Succession, and Stability of the Gut Microbiota 781 // III • Disorders Attributed to the Human Microbiome 783 // 24.8 Disorders Attributed to the Gut Microbiota 783 // 24.9 Disorders Attributed to the Oral, Skin, and Vaginal Microbiota 786 // IV • Modulation of the Human Microbiome 788 // 24.10 Antibiotics and the Human Microbiome 788 // 24.11 Probiotics and Prebiotics 789 // EXPLORE THE MICROBIAL WORLD - The Gut-Brain Axis 773 // 25 Microbial Infection and Pathogenesis 793 // The Microbial Community That Thrives on Your Teeth 793 // I • Human-Microbial Interactions 794 // 25.1 Microbial Adherence 794 // 25.2 Colonization and Invasion 796 // 25.3 Pathogenicity, Virulence, and Attenuation 798 // 25.4 Genetics of Virulence and the Compromised Host 799 // II • Enzymes and Toxins of Pathogenesis 800 // 25.5 Enzymes as Virulence Factors 801 // 25.6 AB-Type Exotoxins 802 // 25.7 Cytolytic and Superantigen Exotoxins 805 // 25.8 Endotoxins 807 // 26 Innate Immunity: Broadly Specific Host Defenses 811 // Rehabilitating a Much-Maligned Peptide: Amyloid-ß 811 // I • Fundamentals of Host Defense 812 // 26.1 Basic Properties of the Immune System 812 //

26.2 Barriers to Pathogen Invasion 813 // II • Cells and Organs of the Immune System 815 // 26.3 The Blood and Lymphatic Systems 815 // 26.4 Leukocyte Production and Diversity 816 // III • Phagocyte Response Mechanisms 818 // 26.5 Pathogen Challenge and Phagocyte Recruitment 818 // 26.6 Pathogen Recognition and Phagocyte Signal Transduction 820 // 26.7 Phagocytosis and Phagocyte Inhibition 823 // IV • Other Innate Host Defenses 824 // 26.8 Inflammation and Fever 825 // 26.9 The Complement System 826 // 26.10 Innate Defenses against Viruses 829 // EXPLORE THE MICROBIAL WORLD - Drosophila Toll Receptors—An Ancient Response to Infections 821 // 27 Adaptive Immunity: Highly Specific Host Defenses 834 // Got (Raw) Milk? The Role of Unprocessed Cow’s Milk in Protecting against Allergy and Asthma 834 // I • Principles of Adaptive Immunity 835 // 27.1 Specificity, Memory, Selection Processes, and Tolerance 835 // 27.2 Immunogens and Classes of Immunity 838 // II • Antibodies 840 // 27.3 Antibody Production and Structural // Diversity 840 // 27.4 Antigen Binding and the Genetics of Antibody Diversity 844 // III • The Major Histocompatibility Complex (MHC) 847 // 27.5 MHC Proteins and Their Functions 847 // 27.6 MHC Polymorphism, Polygeny, and Peptide Binding 850 // IV • T Cells and Their Receptors 851 // 27.7 T Cell Receptors: Proteins, Genes, and Diversity 851 // 27.8 T Cell Diversity 854 // V • Immune Disorders and Deficiencies 857 // 27.9 Allergy, Hypersensitivity, and Autoimmunity 857 // 27.10 Superantigens and Immunodeficiency 860 // 28 Clinical Microbiology and Immunology 866 // Bacteriophages: Tiny Allies in the Fight against Antibiotic-Resistant Bacteria 866 // I • The Clinical Microbiology Setting 867 // 28.1 Safety in the Microbiology Laboratory 867 // 28.2 Healthcare-Associated Infections 868 // II • Isolating and Characterizing Infectious Microorganisms 869 // 28.3 Workflow in the Clinical Laboratory 869 //

28.4 Choosing the Right Treatment 875 // III • Immunological and Molecular Tools for Disease Diagnosis 876 // 28.5 Immunoassays and Disease 876 // 28.6 Precipitation, Agglutination, and Immunofluorescence 878 // 28.7 Enzyme Immunoassays, Rapid Tests, and Immunoblots 880 // 28.8 Nucleic Acid-Based Clinical Assays 883 // IV • Prevention and Treatment of Infectious Diseases 886 // 28.9 Vaccination 886 // 28.10 Antibacterial Drugs 888 // 28.11 Antimicrobial Drugs That Target Nonbacterial Pathogens 894 // 28.12 Antimicrobial Drug Resistance and New Treatment Strategies 896 // EXPLORE THE MICROBIAL WORLD - MRSA—A Formidable Clinical Challenge 872 // UNIT 7 Infectious Diseases and Their Transmission Epidemiology 902 // A Mysterious New Disease Outbreak 902 // I • Principles of Epidemiology 903 // 29.1 The Language of Epidemiology 903 // 29.2 The Host Community 905 // 29.3 Infectious Disease Transmission and Reservoirs 906 // 29.4 Characteristics of Disease Epidemics 908 // II • Epidemiology and Public Health 910 // 29.5 Public Health and Infectious Disease 910 // 29.6 Global Health Comparisons 913 // III • Emerging Infectious Diseases, Pandemics, and Other Threats 914 // 29.7 Emerging and Reemerging Infectious Diseases 914 // 29.8 Examples of Pandemics: HIV/AIDS, Cholera, and Influenza 916 // 29.9 Public Health Threats from Microbial Weapons 919 // EXPLORE THE MICROBIAL WORLD - Textbook Epidemiology: The SARS Epidemic 909 // 30 Person-to-Person Bacterial and Viral Diseases 923 // A New Weapon against AIDS? 923 // I • Airborne Bacterial Diseases 924 // 30.1 Airborne Pathogens 924 // 30.2 Streptococcal Syndromes 925 // 30.3 Diphtheria and Pertussis 928 // 30.4 Tuberculosis and Leprosy 929 // 30.5 Meningitis and Meningococcemia 931 // II • Airborne Viral Diseases 932 // 30.6 MMR and Varicella-Zoster Infections 932 // 30.7 The Common Cold 934 // 30.8 Influenza 935 // III • Direct-Contact Bacterial and Viral Diseases 937 //

30.9 Staphylococcus aureus Infections 937 // 30.10 Helicobacter pylori and Gastric Diseases 939 // 30.11 Hepatitis 940 // 30.12 Ebola- A Deadly Threat 942 // IV • Sexually Transmitted Infections 943 // 30.13 Gonorrhea and Syphilis 944 // 30.14 Chlamydia, Herpes, and Human Papillomavirus 946 // 30.15 HIV/AIDS 948 // 31 Vectorborne and Soilborne Bacterial and Viral Diseases 955 // A New Look at Rabies Vaccines 955 // I • Animal-Transmitted Viral Diseases 956 // 31.1 Rabies Virus and Rabies 956 // 31.2 Hantavirus and Hantavirus Syndromes 957 // II • Arthropod-Transmitted Bacterial and Viral Diseases 958 // 31.3 Rickettsial Diseases 958 // 31.4 Lyme Disease and Borrelia 961 // 31.5 Yellow Fever, Dengue Fever, Chikungunya, and Zika 962 // 31.6 West Nile Fever 965 // 31.7 Plague 966 // III • Soilborne Bacterial Diseases 968 // 31.8 Anthrax 968 // 31.9 Tetanus and Gas Gangrene 969 // 32 Waterborne and Foodborne Bacterial and Viral Diseases 973 // Classic Botulism Scenario 973 // I • Water as a Disease Vehicle 974 // 32.1 Agents and Sources of Waterborne Diseases 974 // 32.2 Public Health and Water Quality 975 // II • Waterborne Diseases 976 // 32.3 Vibrio cholerae and Cholera 976 // 32.4 Legionellosis 978 // 32.5 Typhoid Fever and Norovirus Illness 978 // III • Food as a Disease Vehicle 979 // 32.6 Food Spoilage and Food Preservation 980 // 32.7 Foodborne Disease and Food Epidemiology 981 // IV • Food Poisoning 983 // 32.8 Staphylococcal Food Poisoning 983 // 32.9 Clostridial Food Poisoning 984 // V • Food Infection 985 // 32.10 Salmonellosis 985 // 32.11 Pathogenic Escherichia coli 986 // 32.12 Campylobacter 987 // 32.13 Listeriosis 988 // 32.14 Other Foodborne Infectious Diseases 989 // 33 Eukaryotic Pathogens: Fungi, Protozoa, and Helminths 994 // Environmental Change and Parasitic Diseases in the Amazon 994 // I • Fungal Infections 995 // 33.1 Pathogenic Fungi and Classes of Infection 995 // 33.2 Fungal Diseases: Mycoses 997 //

II • Visceral Parasitic Infections 998 // 33.3 Amoebae and Ciliates: Entamoeba, Naegleria, and Balantidium 999 // 33.4 Other Visceral Parasites: Giardia, Trichomonas, Cryptosporidium, Toxoplasma, and Cyclospora 1000 // III • Blood and Tissue Parasitic Infections 1002 // 33.5 Plasmodium and Malaria 1002 // 33.6 Leishmaniasis, Trypanosomiasis, and Chagas Disease 1003 // 33.7 Parasitic Helminths: Schistosomiasis and Filariases 1004 // Photo Credits 1009 // Glossary Terms 1013 // Index 1017