Chapters 1 to 28
Chapter 1: Microbial Life: Origin and Discovery
1.1 From Germ to Genome: What Is a Microbe? 路 1.2 Microbes Shape Human History 路 1.3 Medical Microbiology 路 1.4 Environment and Ecology 路 1.5 The Microbial Family Tree 路 1.6 Cell Biology and the DNA Revolution
Chapter 2: Observing the Microbial Cell
2.1 Observing Microbes 路 2.2 Optics and Properties of Light 路 2.3 Bright-Field Microscopy and Phase-Contrast Microscopy 路 2.4 Fixation and Staining for Bright-Field Microscopy 路 2.5 Fluorescence Microscopy, FISH, and Chemical Imaging Microscopy 路 2.6 Electron Microscopy, Scanning Probe Microscopy, and X-Ray Crystallography
Chapter 3: Cell Structure and Function
3.1 The Bacterial Cell: An Overview 路 3.2 Membrane Molecules and Transport 路 3.3 The Envelope and Cytoskeleton 路 3.4 Bacterial Cell Division 路 3.5 Cell Asymmetry, Membrane Vesicles, and Extensions 路 3.6 Specialized Structures
Chapter 4: Bacterial Culture, Growth, and Development
4.1 Microbial Nutrition 路 4.2 Nutrient Uptake 路 4.3 Culturing and Counting Bacteria 路 4.4 The Growth Cycle 路 4.5 Biofilms 路 4.6 Cell Differentiation
Chapter 5: Environmental Influences and Control of Microbial Growth
5.1 Extremophiles and the Constraints of Temperature and Pressure 路 5.2 Osmolarity and Halophiles 路 5.3 Hydronium (pH) and Hydroxide Ion Concentrations 路 5.4 Oxygen 路 5.5 Starvation and Eutrophication 路 5.6 Physical, Chemical, and Biological Control of Microbes
Chapter 6: Viruses
6.1 Viruses in Ecosystems 路 6.2 Virus Structure 路 6.3 Viral Genomes and Classification 路 6.4 Bacteriophages: The Gut Virome 路 6.5 Coronavirus SARS-CoV-2 and Other Viral Pathogens 路 6.6 Culturing Viruses
Chapter 7: Genomes and Chromosomes
7.1 DNA: The Genetic Material 路 7.2 Genome Organization 路 7.3 DNA Replication 路 7.4 Plasmids and Secondary Chromosomes 路 7.5 Eukaryotic and Archaeal Chromosomes 路 7.6 Microbiomes and Metagenomes
Chapter 8: Transcription, Translation, and Protein Processing
8.1 From DNA to RNA to Protein 路 8.2 Transcription of DNA to RNA 路 8.3 Translation of RNA to Protein 路 8.4 Protein Modification, Folding, and Degradation 路 8.5 Secretion: Protein Traffic Control
Chapter 9: Genetic Change and Genome Evolution
9.1 Mutations 路 9.2 DNA Repair 路 9.3 Gene Transfer Mechanisms 路 9.4 Mobile Genetic Elements 路 9.5 Genome Evolution
Chapter 10: Molecular Regulation
10.1 Transcription Repressors and Activators 路 10.2 Alternative Sigma Factors and Anti-Sigma Factors 路 10.3 Regulation by RNA 路 10.4 Second Messengers 路 10.5 Clocks, Thermometers, and Switches
Chapter 11: Viral Molecular Biology
11.1 Phage Lambda: Enteric Bacteriophage 路 11.2 Influenza Virus: (negative) strand RNA Virus 路 11.3 Human Immunodeficiency Virus (HIV): Retrovirus 路 11.4 Endogenous Retroviruses and Lentiviral Gene Therapy 路 11.5 Herpes Simplex Virus: DNA Virus
Chapter 12: Molecular Complexity and Synthetic Biology
12.1 Chemotaxis: Movement with a Destination 路 12.2 Biofilm Formation by Pseudomonas aeruginosa 路 12.3 CRISPR and Other Antiphage Defenses 路 12.4 Synthetic Biology: Biology by Design
Chapter 13: Energetics and Catabolism
13.1 Energy for Life 路 13.2 Energy Carriers and Electron Transfer 路 13.3 Catabolism: The Microbial Buffet 路 13.4 Glucose Fermentation and Respiration 路 13.5 Our Gut Microbiome: Friends with Benefits 路 13.6 Aromatic Catabolism and Syntrophy
Chapter 14: Electron Flow in Organotrophy, Lithotrophy, and Phototrophy
14.1 Electron Transport Systems and the Proton Motive Force 路 14.2 The Respiratory ETS and ATP Synthase 路 14.3 Anaerobic Respiration 路 14.4 Nanowires, Electron Shuttles, and Fuel Cells 路 14.5 Lithotrophy and Methanogenesis 路 14.6 Phototrophy
Chapter 15: Biosynthesis
15.1 Overview of Biosynthesis 路 15.2 CO 2 Fixation: The Calvin Cycle and Other Pathways 路 15.3 Fatty Acids and Antibiotics 路 15.4 Nitrogen Fixation and Regulation 路 15.5 Amino Acids and Nucleobases
Chapter 16: Food and Industrial Microbiology
16.1 Microbial Foods 路 16.2 Acid-Fermented and Alkali-Fermented Foods 路 16.3 Ethanolic Fermentation: Bread and Wine 路 16.4 Food Spoilage and Preservation 路 16.5 Industrial Microbiology 路 16.6 Vaccines and Gene Therapy Vectors
Chapter 17: Origins and Evolution
17.1 Origins of Life 路 17.2 Forming the First Cells 路 17.3 Evolution: Phylogeny and Gene Transfer 路 17.4 Natural Selection and Adaptation 路 17.5 Microbial Species and Taxonomy 路 17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts
Chapter 18: Bacterial Diversity
18.1 Bacterial Diversity at a Glance 路 18.2 Cyanobacteria: Oxygenic Phototrophs 路 18.3 Firmicutes, Mycoplasma, and Actinobacteria 路 18.4 Proteobacteria: From Photoheterotrophs to Lithotrophs 路 18.5 Spirochetes, Acidobacteria, Bacteroidetes, and Chlorobi 路 18.6 Planctomycetes, Verrucomicrobia, and Chlamydiae
Chapter 19: Archaeal Diversity
19.1 Archaeal Diversity at a Glance 路 19.2 TACK Hyperthermophiles Eat Sulfur 路 19.3 Thaumarchaeota: Ammonia Oxidizers and Animal Symbionts 路 19.4 Euryarchaeota: Methanogens from Gut to Globe 路 19.5 Haloarchaea and Other Euryarchaeotes: Underground and Under Ocean 路 19.6 DPANN Symbionts, Altiarchaeales, and Asgard: Branch to Eukaryotes
Chapter 20: Eukaryotic Diversity
20.1 Phylogeny of Eukaryotes 路 20.2 Fungi 路 20.3 Amoebozoa: Amebas and Slime Molds 路 20.4 Algae 路 20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans 路 20.6 Parasitic Protozoa and Microscopic Animals
Chapter 21: Microbial Ecology
21.1 Microbial Communities: Omics Analysis 路 21.2 Functional Ecology: Microbial Culture and Abiotic Factors 路 21.3 Symbiosis 路 21.4 Animal Digestive Microbiomes 路 21.5 Marine and Freshwater Microbes 路 21.6 Soil and Plant Microbial Communities
Chapter 22: Element Cycles and Environmental Microbiology
22.1 The Carbon Cycle and Climate Change 路 22.2 The Hydrologic Cycle and Wastewater Treatment 路 22.3 The Nitrogen Cycle 路 22.4 Sulfur, Phosphorus, and Metals 路 22.5 Our Built Environment 路 22.6 Astrobiology
Chapter 23: The Human Microbiome and Innate Immunity
23.1 The Human Microbiome 路 23.2 Benefits and Risks of Microbiota 路 23.3 Overview of the Immune System 路 23.4 Physical and Chemical Defenses against Infection 路 23.5 Innate Immunity: Surveillance, Cytokines, and Inflammation 路 23.6 Complement and Fever
Chapter 24: The Adaptive Immune Response
24.1 Overview of Adaptive Immunity 路 24.2 Antibody Structure, Diversity, and Synthesis 路 24.3 T Cells Link Antibody and Cellular Immune Systems 路 24.4 Complement as Part of Adaptive Immunity 路 24.5 Gut Mucosal Immunity and the Microbiome 路 24.6 Immunization 路 24.7 Hypersensitivity and Autoimmunity
Chapter 25: Pathogenesis
25.1 Host-Pathogen Interactions 路 25.2 Microbial Attachment: First Contact 路 25.3 Toxins Subvert Host Functions 路 25.4 Deploying Toxins and Effectors 路 25.5 Surviving within the Host 路 25.6 Tools Used to Probe Pathogenesis
Chapter 26: Microbial Diseases
26.1 Basics of Diagnosis and Infections of Skin, Soft Tissue, and Bone 路 26.2 Respiratory Tract Infections 路 26.3 Gastrointestinal Tract Infections 路 26.4 Genitourinary Tract Infections 路 26.5 Cardiovascular and Systemic Infections 路 26.6 Central Nervous System Infections
Chapter 27: Antimicrobial Therapy and Discovery
27.1 Fundamentals of Antimicrobial Therapy 路 27.2 Antibiotic Mechanisms of Action 路 27.3 Challenges of Drug Resistance and Discovery 路 27.4 Antiviral Agents 路 27.5 Antifungal Agents
Chapter 28: Clinical Microbiology and Epidemiology
28.1 Clinical Specimen Collection and Handling 路 28.2 Pathogen Identification by Culture and Phenotype 路 28.3 Molecular and Serological Identification of Pathogens 路 28.4 Epidemiology 路 28.5 Detecting Emerging Microbial Diseases 路 28.6 Infectious Disease and Health Disparities
eAppendices, answers and glossary
eAppendix 1: Biological Molecules
Elements and bonding, organic molecules, proteins, carbohydrates, nucleic acids, lipids.
eAppendix 2: Introductory Cell Biology, Eukaryotic Cells
Cell membrane, nucleus and mitosis, endomembrane system, cytoskeleton, mitochondria and chloroplasts.
eAppendix 3: Laboratory Methods for Microbiology
Centrifugation, gels, blots, PCR, DNA sequencing (A3.6), cloning, microarrays, ChIP-seq, microscopy.
eAppendix 4: Molecular Biology of Diverse Viruses
Phage T4, phage M13, poliovirus, hepatitis C.
Answers to Thought Questions
The book's answers to the thought questions in every chapter.