Table of Contents
PART I The Microbes
1 The Microbial World
1.1The Microbes
Mini-Paper: A Focus on the Research The Three Domains of Life
Toolbox 1.1 Polymerase Chain Reaction Amplification of rRNA Genes
1.2Microbial Physiology, Genetics, and Cultivation
Outlook 1.1 Creating Life in the Laboratory: The Miller-Urey Experiment
1.3Microbial Ecology and Biotechnology
1.4 Microbes Associated with Diseases
2 Bacteria and Archaea
2.1Morphology of Bacterial Cells
Outlook 2.1 Making the Microbiology Laboratory Accessible
2.2The Cytoplasm
2.3The Cytoskeleton
Mini-Paper: A Focus on the Research Magnetosomes: Uncovering the Structure of Bacterial Organelles
2.4The Cell Envelope
Toolbox 2.1 The Gram Stain
Outlook 2.2 The Protective Shells of Endospores
2.5The Cell Surface
2.6 Evolution of Archaea
2.7 Morphology of Archaeal Cells
2.8Diversity of Bacteria and Archaea
Mini-Paper: A Focus on the Research The Role of Archaea in Our Digestive System
Outlook 2.3 Extremophiles and Biotechnology
3 Eukaryotic Microorganisms
3.1Structure of Eukaryotic Cells
Mini-Paper: A Focus on the Research Lipid Rafts: Organized Clustering of Lipids within a Membrane
Toolbox 3.1 Using Microscopy to Examine Cell Structure
Outlook 3.1 Hijacking the Cytoskeleton
3.2Diversity of Eukaryotic Microorganisms
3.3Replication of Eukaryotic Microorganisms
3.4The Origin of Eukaryotic Cells
Outlook 3.2 Secondary endosymbiosis: The origins of an organelle with four membranes
3.5Interactions Between Eukaryotic Microorganisms and Animals, Plants, and the Environment
4 Virology
4.1A Basic Overview of Viruses
Mini-Paper: A Focus on the Research New Findings in the Packaging of DNA by the Model Bacteriophage T4
4.2Origins of Viruses
Outlook 4.1 Ribozymes: Evidence for an RNA-Based World
4.3Cultivation, Purification, and Quantification of Viruses
Toolbox 4.1 Cell Culture Techniques
Outlook 4.2 Measurement of HIV Viral Load
4.4Diversity of Viruses
Toolbox 4.2 Reverse Transcriptase Polymerase Chain Reaction (RT-PCR)
4.5Virus-Like Agents
4.6Present Prospective in Virology
5 Microbial Metabolism
5.1Acquisition of Carbon, Energy, and Electrons
5.2Energy, Enzymes, and ATP
Outlook 5.1 Who Needs Vitamins?
5.3ATP Synthesis
5.4Metabolism of Glucose Carbon Sources
5.5Respiration and the Electron Transport System
Outlook 5.2 Electricigenic Bacteria and Microbial Fuel Cells
5.6Metabolism of Non-glucose Carbon Sources
Toolbox 5.1 Metabolism and Rapid Bacterial Identification Systems
5.7Phototrophy and Photosynthesis
Mini-Paper: A Focus on the Research Genome Sequence of a Deep Sea Symbiont
5.8Metabolism of Nitrogen and Sulfur
5.9Biosynthesis of Cellular Components
PART II Microbial Genetics
6 Cultivating Microorganisms
6.1Factors Affecting Microbial Growth
Toolbox 6.1 Phenotype Microarrays for Examining Microbial Growth
6.2Growing Microorganisms in the Laboratory
Outlook 6.1 The Discovery of Helicobacter pylori
Toolbox 6.2 FISHING for Uncultivated Microorganisms
Mini-Paper: A Focus on the Research Bringing to Life the Previously Unculturable Using the Soil Substrate Membrane System (SSMS)
6.3Measuring Microbial Growth
Outlook 6.2 Mycobacterium leprae, An Extraordinarily Slow-growing Pathogen
Outlook 6.3 The Human Intestine: A Continuous Culture
6.4Preventing Microbial Growth
7 DNA Replication and Gene Expression
7.1The Role of DNA
7.2Replication of DNA
Mini-Paper: A Focus on the Research Telomeres with Promoter Activity
7.3Transcription
Toolbox 7.1 Using a Gel Shift Assay to Identify DNA-binding Proteins
7.4Translation
7.5The Effects of Mutations
Outlook 7.1 Using Mutations to Control Viral Infections
8 Viral and their Replication
8.1Recognition of Host Cells
Outlook 8.1 Identifying Emerging Viral Pathogens
Toolbox 8.1 The Western Blot
8.2Viral Penetration and Uncoating
8.3Viral Replication
Mini-Paper: A Focus on the Research The Discovery of Reverse Transcriptase
Outlook 8.2 Phage Therapy: Biocontrol for Infections
8.4Viral Assembly and Release
9 Bacterial Genetic Analysis and Manipulation
9.1Bacteria as Subjects of Genetic Research
9.2Mutations, Mutants, and Strains
Toolbox 9.1 Isolating Nutritional Mutants
9.3Restriction Enzymes, Vectors, and Cloning
9.4Recombination and DNA Transfer
Outlook 9.1 Plasmids That Produce Pathogens
Mini-Paper: A Focus on the Research The Discovery of Transduction
10 Microbial Genomics
10.1Genome Sequencing
Outlook 10.1 Rate of DNA Sequencing
Toolbox 10.1 Genome databases
10.2Genomic Analysis of Gene Expression
10.3Comparative Genomics
Mini-Paper: A Focus on the Research Genome Sequence of a Killer Bug
Outlook 10.2 The Minimal Genome
10.4Functional Genomics and Related Analyses
11 Regulation of Gene Expression
11.1Differential Gene Expression
11.2The Operon
Mini-Paper: A Focus on the Research Tuning Promoters for Use in Synthetic Biology
11.3Global Gene Regulation
Outlook 11.1 The Use of Lactose Analogs in Gene Expression Studies
11.4Post-Initiation Control of Gene Expression
Toolbox 11.1 Using RNA molecules to decrease gene expression
11.5Quorum Sensing and Biofilm formation
11.6Two-Component Regulatory Systems
11.7Chemotaxis
PART III Microbial Physiology and Ecology
12 Microbial Ecosystems
12.1Microbes in the Environment
12.2Microbial Community Analysis
Toolbox 12.1 Flow Cytometry
Outlook 12.1 Naming the Uncultured and Uncharacterized
Mini-Paper: A Focus on the Research Insights into the Phylogeny and Coding Potential of Microbial Dark Matter
12.3Aquatic Ecosystems
Outlook 12.2 Dead Zones
12.4Terrestrial Ecosystems
12.5Deep Subsurface and Geothermal Ecosystems
13 Symbiotic Microbiome
13.1Types of Microbe-Host Interactions
13.2Plant Microbiome
Outlook 13.1 The Possible Impossible Vegan Patty
13.3Human Microbiome
Toolbox 13.1 Germ-free and Gnotobiotic Animals
Outlook 13.2 Food Probiotics - Do They Work?
Mini-Paper: A Focus on the Research Fecal Bacteriotherapy: “Repoopulation” of the Gut
13.4Herbivore’s Microbiome
Outlook 13.3 Midichlorians - Not Just for Jedi
Outlook 13.4 Death of Coral Reefs
14 Biogeochemical Cycles
14.1Nutrient Cycling
Toolbox 14.1 Using Microarrays to Examine Microbial Communities: The GeoChip
14.2Cycling Driven by Carbon Metabolism
Outlook 14.1 CO2 as a Greenhouse Gas and Its Influence on Climate Change
14.3Cycling Driven by Nitrogen Metabolism
Mini-Paper: A Focus on the Research The First Isolation and Cultivation of a Marine Archaeon
14.4Other Cycles and their Connections
Outlook 14.2 Life in a World without Microbes
Outlook 14.3 The Microbiology of Environmentally Toxic Acid Mine Drainage
Toolbox 14.2 Biogeochemistry in a Bottle: The Winogradsky Column
15 Microbial Biotechnology
15.1Microorganisms for Biotechnology
Outlook 15.1 Bioprospecting: Who Owns the Microbes?
15.2Genetic Engineering
Toolbox 15.1 Site-Directed Mutagenesis
Toolbox 15.2 Fusion Protein Purification
Mini-Paper: A Focus on the Research Making a Synthetic Genome
Outlook 15.2 The International Genetically Engineered Machine (iGEM) Competition, Standard Biological Parts, and Synthetic Biology
15.3Red Biotechnology
15.4White Biotechnology
Outlook 15.3 Biofuels: Biodiesel and Algae
15.5Green Biotechnology
Toolbox 15.3 Plant Transformation Using Bacteria
PART IV Microbes and Disease
16 Introduction to Infectious Diseases
16.1Microbes and their pathogenesis
Toolbox 16.1 Measuring the Virulence of Pathogens
16.2Microbial Virulence Strategies
Outlook 16.1 Genome Editing: A powerful and Controversial New Technique
16.3The Transmission of Infectious Diseases
Mini-Paper: A Focus on the Research Epidemiology of an Infectious Disease
16.4Proving Cause and Effect in Microbial Infections
Outlook 16.2 Animal models to Study Infectious diseases (Ex: Mice, Guinea Pigs, C. elegans etc.,)
16.5The Evolution of Pathogens
17 Clinical Microbiology and Immunology
17.1Immunity
17.2Barriers to Infection
Outlook 17.1 Messy Mucus
17.3The Inflammatory Response
17.4The Molecules of the Innate System
Mini-Paper: A Focus on the Research Mammalian Cells Can Recognize Bacterial DNA
Toolbox 17.1 The Complement Fixation Test
17.5The Cells of Innate Immunity
17.6Invertebrate Defenses
Toolbox 17.2 The Limulus Amoebocyte Assay for LPS
18 Adaptive Immunity
18.1Features of Adaptive Immunity
18.2T Cells
18.3Antigen Processing
18.4Antigen-Presenting Cells
18.5Humoral and Cell-Mediated Immune Responses
Outlook 18.1 Too Much of a Good Thing?
Mini-Paper: A Focus on the Research Attempting to Engineer a Virus to Improve Immunocontraception
18.6B Cells and the Production of Antibody
Outlook 18.2 Vaccines Against T-independent Antigens
Toolbox 18.1 Monoclonal Antibody (mAb) Production
Toolbox 18.2 Enzyme-linked Immunosorbent Assay (ELISA)
Outlook 18.3 Turning Antibody Upside Down
19 Bacterial Pathogenesis
19.1Bacterial Virulence Factors
Mini-Paper: A Focus on the Research Escherichia Coli Injects Its Own Receptor
Outlook 19.1 Iron, Vampires, Fashion, and the White Plague
19.2Bacterial Virulence Factors - Toxins
Toolbox 19.1 Serotyping
Outlook 19.2 The Good, The Bad, and The Ugly Side of Botulinum Toxin
Outlook 19.3 Superabsorbent Tampons and Superantigens
19.3Survival in the Host: Strategies and Consequences
Toolbox 19.2 The Tuberculin Test for Tuberculosis
19.4Evolution of Bacterial Pathogens
20 Viral Pathogenesis
20.1Recurring Themes in Viral Pathogenesis
Outlook 20.1 Vertical Transmission of HIV
20.2Interactions with the Host: Strategies and Consequences
Outlook 20.2 Viral Induction of Apoptosis
20.3Viral Infections and Cancer
Toolbox 20.1 Immunoprecipitation
Mini-Paper: A Focus on the Research Viruses that Cause Cancer by Affecting Cellular Proliferation
Outlook 20.3 SV40 and Human Cancers
20.4Evolution of Viral Pathogens
Outlook 20.4 SARS-CoV-2 variants and their Impact
21 Eukaryotic Pathogenesis
21.1Mechanisms of Eukaryotic Pathogenesis
Mini-Paper: A Focus on the Research An Experimental System for the Genomic Study of Dutch Elm Disease
Outlook 21.1 Pneumocystis Jirovecii or Carinii : The Evolving Field of Taxonomy
Outlook 21.2 Magic Mushrooms
21.2Pathogen Study: Plasmodium Falciparum
Toolbox 21.1 Testing for Malaria
21.3Macroscopic Eukaryotic Pathogens
21.4Evolution of Eukaryotic Pathogens
22 Control of Infectious Diseases
22.1Historical Aspects of Infectious Disease Treatment and Control
22.2Antimicrobial Drugs
22.3Antimicrobial Drug Resistance
Mini-Paper: A Focus on the Research Tracking Acquisition of Antibiotic Resistance In Real Time
Toolbox 22.1 Drug Susceptibility Testing and MIC
Outlook 22.1 The Pursuit of New Antibiotics: Why Bother?
Outlook 22.2 Health Care-Associated Infections: A Recipe for Resistance
22.4Predicting and Controlling Epidemics
22.5Immunization and Vaccines
Outlook 22.3 Variolation: Deliberate Infection with Smallpox Virus
Outlook 22.4 The War Against Vaccines
23 The Microbiology of Food and Water
23.1Food Spoilage
23.2Food Preservation
23.3Food Fermentation
23.4Foodborne and Waterborne Illness
23.5Microbiological Aspects of Water Quality
Outlook 23.1 Implications of Sludge Bulking
Toolbox 23.1 Measuring Biochemical Oxygen Demand (BOD)
Mini-Paper: A Focus on the Research Enhanced Biological Removal of Phosphorus
Toolbox 23.2 Most Probable Number (MPN) Method
APPENDIX A Scientific Articles
APPENDIX B Microscopy
APPENDIX C Taxonomy and Nomenclature of Microbes
APPENDIX D Origin of Blood Cells
GLOSSARY / INDEX
