ISE Prescott's Microbiology

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
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