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Cover Title Copyright Brief Contents About the Authors Contents Part One: Introduction to Microbiology 1 The Evolution of Microorganisms and Microbiology Micro Focus: Microbiology's Reach 1.1 Members of the Microbial World 1.2 Microbes Have Evolved and Diversified for Billions of Years Microbial Diversity & Ecology 1.1 Hydrothermal Vents: Did Life Begin Under the Sea? 1.3 Microbiology Advanced as New Tools for Studying Microbes Were Developed 1.4 Microbiology Encompasses Many Subdisciplines 2 Microscopy Micro Focus: Anthrax Bioterrorism Attack 2.1 Lenses Create Images by Bending Light 2.2 There Are Several Types of Light Microscopes 2.3 Staining Helps to Visualize and Identify Microbes 2.4 Electron Microscopes Use Beams of Electrons to Create Highly Magnified Images 2.5 Scanning Probe Microscopy Can Visualize Molecules and Atoms 3 Bacterial Cell Structure Micro Focus: Bacteria Use Rapid Transport 3.1 Use of the Term Prokaryote Is Controversial 3.2 Bacteria Are Diverse but Share Some Common Features 3.3 Bacterial Plasma Membranes Control What Enters and Leaves the Cell 3.4 Cell Walls Have Many Functions 3.5 Extracellular Vesicles Emerge from Bacterial Membranes 3.6 The Cell Envelope Often Includes Layers Outside the Cell Wall 3.7 The Bacterial Cytoplasm Is More Complex than Once Thought Microbial Diversity & Ecology 3.1 Organelles Without Membranes? 3.8 External Structures Are Used for Attachment and Motility 3.9 Bacteria Move in Response to Environmental Conditions 3.10 Bacterial Endospores Are a Survival Strategy 4 Archaeal Cell Structure Micro Focus: Methane—The Other Greenhouse Gas 4.1 Archaea Are Diverse but Share Some Common Features 4.2 Archaeal Cell Envelopes Are Structurally Diverse 4.3 Archaeal Cytoplasm Is Similar to Bacterial Cytoplasm 4.4 Many Archaea Have External Structures Used for Attachment and Motility 5 Eukaryotic Cell Structure Micro Focus: Red Means Dead 5.1 Eukaryotic Cells Are Diverse but Share Some Common Features 5.2 Eukaryotic Cell Envelopes 5.3 The Eukaryotic Cytoplasm Contains a Cytoskeleton and Organelles 5.4 Several Organelles Function in the Secretory and Endocytic Pathways 5.5 The Nucleus and Ribosomes Are Involved in Genetic Control of the Cell 5.6 Mitochondria, Related Organelles, and Chloroplasts Are Involved in Energy Conservation Microbial Diversity & Ecology 5.1 There Was an Old Woman Who Swallowed a Fly 5.7 Many Eukaryotic Microbes Have External Structures Used for Motility 6 Viruses and Other A cellular Infectious Agents Micro Focus: Viruses to the Rescue 6.1 Viruses Are A cellular 6.2 Virion Structure Is Defined by Capsid Symmetry and Presence or Absence of an Envelope 6.3 Viral Life Cycles Have Five Steps 6.4 There Are Several Types of Viral Infections 6.5 Virus Cultivation and Enumeration 6.6 Viroids and Satellites: Nucleic Acid-Based Subviral Agents 6.7 Prions Are Composed Only of Protein Part Two: Microbial Nutrition, Growth, and Control 7 Bacterial and Archaeal Growth Micro Focus: How Low Can You Go? 7.1 Most Bacteria and Archaea Reproduce by Binary Fission 7.2 Bacterial Cell Cycles Are Divided into Three Phases 7.3 Archaeal Cell Cycles Are Unique 7.4 Growth Curves Consist of Five Phases 7.5 Environmental Factors Affect Microbial Growth Microbial Diversity & Ecology 7.1 Microbial Sculptors 7.6 Microbial Growth in Natural Environments 7.7 Laboratory Culture of Microbes Requires Conditions that Mimic Their Normal Habitats 7.8 Microbial Population Size Can Be Measured Directly or Indirectly 7.9 Chemostats and Turbidostats Are Used for Continuous Culture of Microorganisms 8 Control of Microorganisms in the Environment Micro Focus: To Wipe or Not to Wipe? That Is the Question. 8.1 Microbial Growth and Replication: Targets for Control 8.2 Microbes Can Be Controlled by Physical Means Techniques & Applications 8.1 Come Fly with Me? 8.3 Microorganisms Are Controlled with Chemical Agents 8.4 Antimicrobial Agents Must Be Evaluated for Effectiveness 8.5 Microorganisms Can Be Controlled by Biological Methods 9 Antimicrobial Chemotherapy Micro Focus: A Gift from Traditional Chinese Medicine 9.1 Antimicrobial Chemotherapy Evolved from Antisepsis Efforts 9.2 Antimicrobial Drugs Have Selective Toxicity 9.3 Antimicrobial Activity Can Be Measured by Specific Tests 9.4 Antibacterial Drugs 9.5 Antiviral Drugs 9.6 Antifungal Drugs 9.7 Antiprotozoan Drugs Disease 9.1 Chloroquine and COVID-19: A Cautionary Tale 9.8 Antimicrobial Drug Resistance Is a Public Health Threat Part Three: Microbial Metabolism 10 Introduction to Metabolism Micro Focus: Flushed Away 10.1 Metabolism: Important Principles and Concepts 10.2 ATP: The Major Energy Currency of Cells 10.3 Redox Reactions: Reactions of Central Importance in Metabolism 10.4 Electron Transport Chains: Sets 10.5 Biochemical Pathways: Sets of Linked Chemical Reactions 10.6 Enzymes and Ribozymes Speed Up Cellular Chemical Reactions 10.7 Metabolism Must Be Regulated to Maintain Homeostasis 11 Catabolism: Energy Release and Conservation Micro Focus: The Richest Hill on Earth 11.1 Metabolic Diversity and Nutritional Types 11.2 There Are Two Chemoorganotrophic Fueling Processes 11.3 Aerobic Respiration Starts with Glucose Oxidation 11.4 Electron Transport and Oxidative Phosphorylation Generate the Most ATP 11.5 Anaerobic Respiration Uses the Same Steps as Aerobic Respiration 11.6 Fermentation Does Not Involve an Electron Transport Chain 11.7 Catabolism of Organic Molecules Other than Glucose 11.8 Chemolithotrophy: "Eating Rocks" 11.9 Flavin-Based Electron Bifurcation 11.10 Phototrophy 12 Anabolism: The Use of Energy in Biosynthesis Micro Focus: Building Penicillin 12.1 Principles Governing Biosynthesis 12.2 Precursor Metabolites: Starting Molecules for Biosynthesis 12.3 CO[sub(2)] Fixation: Reduction and Assimilation of CO[sub(2)] Carbon 12.4 Synthesis of Carbohydrates 12.5 Synthesis of Amino Acids Consumes Many Precursor Metabolites 12.6 Synthesis of Purines, Pyrimidines, and Nucleotides 12.7 Lipid Synthesis Part Four: Microbial Molecular Biology and Genetics 13 Bacterial Genome Replication and Expression Micro Focus: Making Code 13.1 Experiments Using Bacteria and Viruses Demonstrated that DNA Is the Genetic Material 13.2 Nucleic Acid and Protein Structure 13.3 DNA Replication in Bacteria 13.4 Bacterial Genes Consist of Coding Regions and Other Sequences Important for Gene Function 13.5 Transcription in Bacteria 13.6 The Genetic Code Consists of Three-Letter "Words" 13.7 Translation in Bacteria 13.8 Coordination of Gene Expression Processes 13.9 Protein Maturation and Secretion 14 Regulation of Cellular Processes Micro Focus: Promoting Expression 14.1 Bacteria Use Many Regulatory Strategies 14.2 Regulation of Transcription Initiation Saves Considerable Energy and Materials 14.3 Attenuation and Riboswitches Stop Transcription Prematurely 14.4 RNA Secondary Structures Control Translation 14.5 Mechanisms Used for Global Regulation 14.6 Bacteria Combine Several Regulatory Mechanisms to Control Complex Cellular Processes 15 Eukaryotic and Archaeal Genome Replication and Expression Micro Focus: Pharming 15.1 Genetic Processes in the Three Domains 15.2 DNA Replication: Similar Overall, but with Different Replisome Proteins 15.3 Transcription 15.4 Translation and Protein Maturation and Localization 15.5 Regulation of Cellular Processes 16 Mechanisms of Genetic Variation Micro Focus: Manure Happens 16.1 Mutations: Heritable Changes in a Genome 16.2 Detection and Isolation of Mutants 16.3 DNA Repair Maintains Genome Stability 16.4 Microbes Use Mechanisms Other than Mutation to Create Genetic Variability 16.5 Mobile Genetic Elements Move Genes Within and Between DNA Molecules 16.6 Conjugation Requires Cell-Cell Contact 16.7 Transformation Is the Uptake of Free DNA 16.8 Transduction Is Virus-Mediated DNA Transfer 16.9 Evolution in Action: The Development of Antibiotic Resistance in Bacteria 17 Microbial DNA Technologies Micro Focus: Spinning Stronger Silk 17.1 Key Discoveries Led to the Development of DNA Cloning Technology Techniques & Applications 17.1 Gel Electrophoresis 17.2 Polymerase Chain Reaction Amplifies Targeted DNA 17.3 Genomic and Metagenomic Libraries: Cloning Genomes in Pieces 17.4 Expressing Foreign Genes in Host Cells 17.5 Cas9 Nuclease Is a Programmable Tool for Genome Editing 17.6 Biotechnology Develops Custom Microbes for Industrial Use Techniques & Applications 17.2 How to Build a Microorganism 18 Microbial Genomics Micro Focus: What's in a Genome? 18.1 DNA Sequencing Methods 18.2 Genome Sequencing 18.3 Metagenomics Provides Access to Uncultured Microbes 18.4 Bioinformatics: What Does the Sequence Mean? 18.5 Functional Genomics Links Genes to Phenotype 18.6 Systems Biology: Making and Testing Complex Predictions 18.7 Comparative Genomics Part Five: The Diversity of the Microbial World 19 Archaea Micro Focus: Methanogens Fuel Domestic Energy Debate 19.1 Overview of Archaea 19.2 Phyla Asgardarchaeota and Nanoarchaeota Are Known Primarily from Metagenomics 19.3 Phylum Thermoproteota: Sulfur-Dependent Thermophiles 19.4 Phylum Nitrosphaeria: Mesophilic Ammonia Oxidizers 19.5 Phyla Methanobacteriota, Halobacteriota, and Thermoplasmatota: Methanogens, Haloarchaea, and Others 20 Nonproteobacterial Gram-Negative Bacteria Micro Focus: From Food Waste to Fuel 20.1 Diderm Cell Envelopes Are Not Uniform 20.2 Aquificota and Thermotogota Are Hyperthermophiles 20.3 Deinococcota Includes Radiation-Resistant Bacteria 20.4 Photosynthetic Bacteria Are Diverse 20.5 PVC Superphylum (Planctomycetotaand Verrucomicrobiota): Atypical Cell Division 20.6 Phylum Spirochaetota: Bacteria with a Corkscrew Morphology 20.7 Phylum Bacteroidota Includes Important Gut Microbiota 20.8 Phylum Fusobacteriota: Commensal Anaerobes 20.9 Phylum Desulfobacterota: Anaerobic Sulfate/Sulfur Reducers 20.10 Phyla Bdellovibrionota and Myxococcota: Bacterial Predators 20.11 Phylum Campylobacterota: Human and Animal Commensals 21 Proteobacteria Micro Focus: Bison and Brucellosis Spark Controversy 21.1 Class Alphaproteobacteria Includes Many Oligotrophs 21.2 Gammaproteobacteria Is the Largest Bacterial Class Microbial Diversity & Ecology 21.1 Acid Mine Drainage 22 Gram-Positive Bacteria Micro Focus:Antibiotic Production: Is It Actually Bacterial Chitchat? 22.1 Phylum Actinobacteriota 22.2 Phylum Firmicutes, Class Bacilli: Aerobic Endospore-Forming Bacteria 22.3 Phylum Firmicutes, Class Clostridia: Anaerobic Endospore-Forming Bacteria 22.4 Phylum Firmicutes, Classes Negativicutesand Halanaerobiia: Gram-Positive Bacteria with Outer Membranes 23 Protists Micro Focus: Setting the Record Straight 23.1 Protist Diversity Reflects Broad Phylogeny 23.2 Discoba-Metamonada Clade 23.3 Amoebozoa Clade Includes Protists with Pseudopodia 23.4 TSAR Clade: Protists of Global Importance 23.5 Haptista Clade 23.6 Archaeplastida Clade Includes Green and Red Algae 24 Fungi Micro Focus: The Complex Story of Caterpillar Fungus 24.1 Fungal Biology Reflects Vast Diversity 24.2 Zoosporic Fungi Produce Motile Spores 24.3 Zygomycetous Fungi Have Coenocytic Hyphae 24.4 Dikarya Is the Most Diverse Fungal Group Disease 24.1 White-Nose Syndrome Is Decimating North American Bat Populations 25 Viruses Micro Focus: Disrupting the Viral Life Cycle 25.1 Virus Phylogeny Relies on Genomics 25.2 Double-Stranded DNA Viruses Infect All Cell Types 25.3 Single-Stranded DNA Viruses Use a Double-Stranded Intermediate in Their Life Cycles 25.4 Double-Stranded RNA Viruses: RNA-Dependent RNA Polymerase Replicates the Genome and Synthesizes mRNA 25.5 Positive-Strand RNA Viruses: Genomes that Are Translated upon Entry 25.6 Negative-Strand RNA Viruses: RNA-Dependent RNA Polymerase Is Part of the Virion 25.7 Retroviruses: Positive-Strand Viruses that Use Reverse Transcriptase in Their Life Cycles 25.8 Reverse Transcribing DNA Viruses Part Six: Ecology and Symbiosis 26 Exploring Microbes in Ecosystems Micro Focus: Scientists Search for Intraterrestrial Life—and Find It 26.1 Microbial Biology Relies on Cultures Microbial Diversity & Ecology 26.1 Patience, Hard Work, Luck, and the Evolution of Eukaryotes 26.2 Microbial Identification Is Largely Based on Molecular Characterization 26.3 Assessing Microbial Populations 26.4 Assessing Microbial Community Activity 27 Microbial Interactions Micro Focus: Microbes in Community 27.1 Many Types of Microbial Interactions Exist 27.2 Mutualism: Obligatory Positive Interaction 27.3 Cooperation: Nonobligatory Positive Interaction 27.4 Antagonistic Interactions Prompt Microbial Responses Microbial Diversity & Ecology 27.1 Wolbachia: The World's Most Infectious Microbe? 28 Biogeochemical Cycling and Global Climate Change Micro Focus: Global Climate Change; Infectious Disease Change 28.1 Biogeochemical Cycling Sustains Life on Earth 28.2 Microbes Mediate Nutrient Cycling 28.3 Global Climate Change: Infectious Disease Change 29 Microorganisms in Marine and Freshwater Ecosystems Micro Focus: Ocean Death Coming Soon to a Coast Near You 29.1 Water Is the Largest Microbial Habitat 29.2 Microorganisms in Marine Ecosystems 29.3 Microorganisms in Freshwater Ecosystems Microbial Diversity & Ecology 27.1 Attention All Dog Owners! 30 Microorganisms in Terrestrial Ecosystems Micro Focus: Bread for a Hungry World 30.1 Soils Are an Important Microbial Habitat 30.2 Diverse Microorganisms Inhabit Soil 30.3 Microbe-Plant Interactions Can Be Positive, Negative, or Neutral Disease 30.1 Citrus Greening and the Power of "Why?" 30.4 The Subsurface Biosphere Is Vast Part Seven: Pathogenicity and Host Response 31 Innate Host Resistance Micro Focus: The Hygiene Hypothesis 31.1 Immunity Arises from Innate Resistance and Adaptive Defenses 31.2 Innate Resistance Starts with Barriers 31.3 Innate Resistance Relies on Chemical Mediators 31.4 Each Type of Innate Immune Cell Has a Specific Function 31.5 Organs and Tissues of the Immune System Are Sites of Host Defense 31.6 Phagocytosis Destroys Invaders 31.7 Inflammation Unites All Components of Immunity 32 Adaptive Immunity Micro Focus: Killing Cancer, Immunologically 32.1 Adaptive Immunity Relies on Recognition and Memory 32.2 Antigens Elicit Immunity 32.3 Adaptive Immunity Can Be Earned or Borrowed 32.4 Recognition of Foreignness Is Critical for a Strong Defense 32.5 T Cells Are Critical for Immune Function 32.6 B Cells Make Antibodies 32.7 Antibodies Bind Specific 3-D Antigens 32.8 Antibodies Doom Antigens Historical Highlights 32.2 Convalescent Plasma: An Old Treatment for a New Disease 32.9 The Immune System Can Malfunction 33 The Microbe-Human Ecosystem Micro Focus: Embrace Your Gut Flora 33.1 Humans Are Holobionts 33.2 The Microbiome Develops from Birth to Adulthood 33.3 A Functional Core Microbiome Is Required for Host Homeostasis 33.4 Many Diseases Have a Connection with Dysbiosis 33.5 Microbiome Manipulation Can Be Therapeutic 34 Infection and Pathogenicity Micro Focus: The Unlikely Tale of Miasmas, Bras, and Masks 34.1 The Process of Infection 34.2 Transmission and Entry into the Host Historical Highlights 34.1 The First Indications of Person-to-Person Spread of an Infectious Disease 34.3 Surviving the Host Defenses 34.4 Damage to the Host Part Eight: Microbial Diseases, Detection, and Their Control 35 Epidemiology and Public Health Microbiology Micro Focus: Protecting the Herd 35.1 Epidemiology Is an Evidence-Based Science Historical Highlights 35.1 John Snow, the First Epidemiologist 35.2 Epidemiology Is Rooted in Well-Tested Methods 35.3 Infectious Disease Is Revealed Through Patterns Within a Population Historical Highlights 35.2 "Typhoid Mary" 35.4 Infectious Diseases and Pathogens Are Emerging and Reemerging 35.5 Healthcare Facilities Harbor Infectious Agents 35.6 Coordinated Efforts Are Required to Prevent and Control Epidemics Historical Highlights 35.3 The First Immunizations 35.7 Bioterrorism Readiness Is an Integral Component of Public Health Microbiology Historical Highlights 35.4 1346—Early Biological Warfare Attack 36 Clinical Microbiology and Immunology Micro Focus: Ebola and Global Health Security 36.1 The Clinical Microbiology Laboratory Detects Infectious Agents and Protects Its Workers 36.2 Identification of Microorganisms from Specimens 36.3 Immune Responses Can Be Exploited to Detect Infections 37 Human Diseases Caused by Viruses and Prions Micro Focus: Remembering HIV/AIDS 37.1 Viruses Can Be Transmitted by Airborne Routes 37.2 Arthropods Can Transmit Viral Diseases 37.3 Direct Contact Diseases Can Be Caused by Viruses 37.4 Food and Water Are Vehicles for Viral Diseases Historical Highlights 37.1 A Brief History of Polio 37.5 Zoonotic Diseases Arise from Human-Animal Interactions 37.6 Prion Proteins Transmit Disease 38 Human Diseases Caused by Bacteria Micro Focus: The Plague Family Tree 38.1 Bacteria Can Be Transmitted by Airborne Routes 38.2 Arthropods Can Transmit Bacterial Diseases 38.3 Direct Contact Diseases Can Be Caused by Bacteria Disease 38.1 Syphilis and the Tuskegee Study Disease 38.2 Biofilms 38.4 Food and Water Are Vehicles for Bacterial Diseases Techniques & Applications 38.3 Clostridial Toxins as Therapeutic Agents: Benefits of Nature's Most Toxic Proteins 38.5 Zoonotic Diseases Arise from Human-Animal Interactions 38.6 Opportunistic Diseases Can Be Caused by Bacteria 39 Human Diseases Caused by Fungi and Protists Micro Focus: Mushrooms of Death 39.1 Relatively Few Fungi and Protists Are Human Pathogens 39.2 Fungi Can Be Transmitted by Airborne Routes 39.3 Arthropods Can Transmit Protozoal Disease Disease 39.1 A Brief History of Malaria 39.4 Direct Contact Diseases Can Be Caused by Fungi and Protists 39.5 Food and Water Are Vehicles of Protozoal Diseases 39.6 Opportunistic Diseases Can Be Caused by Fungi and Protists Part Nine: Applied Microbiology 40 Microbiology of Food Micro Focus: The Art, Science, and Genetics of Brewing Beer 40.1 Microbial Growth Can Cause Food Spoilage 40.2 Environmental Factors Control Food Spoilage 40.3 Food-Borne Disease Outbreaks 40.4 Detection of Food-Borne Pathogens Requires Government-Industry Cooperation 40.5 Microbiology of Fermented Foods: Beer, Cheese, and Much More Techniques & Applications 40.1 Chocolate: The Sweet Side of Fermentation 41 Biotechnology and Industrial Microbiology Micro Focus: Where Are the New Antibiotics? 41.1 Microbes Are the Source of Many Products of Industrial Importance 41.2 Biofuel Production Is a Dynamic Field 41.3 Growing Microbes in Industrial Settings Presents Challenges 41.4 Agricultural Biotechnology Relies on a Plant Pathogen 41.5 Some Microbes Are Products 42 Applied Environmental Microbiology Micro Focus: Deepwater Horizon Oil Consumed by Microbes 42.1 Purification and Sanitary Analysis Ensure Safe Drinking Water 42.2 Wastewater Treatment Maintains Human and Environmental Health 42.3 Microbial Fuel Cells: Batteries Powered by Microbes 42.4 Biodegradation and Bioremediation Harness Microbes to Clean the Environment Appendix 1 A Review of the Chemistry of Biological Molecules Appendix 2 Common Metabolic Pathways Appendix 3 Microorganism Pronunciation Guide Glossary A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Index A B C D E F G H I J K L M N O P Q R S T U V W X Y Z