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

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