Read this alongside your own copy
This is a text rendering, so tables and equation layouts are simplified. Where the exact figure matters, open the same section in your First Day ebook. Worth knowing: eAppendix 3 §A3.6 is assigned in Unit 2 and exists in no print copy — it is here.
Chapter 1 — Microbial Life: Origin and Discovery
Chapter 2 — Observing the Microbial Cell
Chapter 3 — Cell Structure and Function
Chapter 4 — Bacterial Culture, Growth, and Development
Chapter 5 — Environmental Influences and Control of Microbial Growth
Chapter 6 — Viruses
Chapter 7 — Genomes and Chromosomes
Chapter 8 — Transcription, Translation, and Protein Processing
Chapter 9 — Genetic Change and Genome Evolution
Chapter 10 — Molecular Regulation
Chapter 11 — Viral Molecular Biology
Chapter 12 — Molecular Complexity and Synthetic Biology
Chapter 13 — Energetics and Catabolism
Chapter 14 — Electron Flow in Organotrophy, Lithotrophy, and Phototrophy
Chapter 15 — Biosynthesis
Chapter 16 — Food and Industrial Microbiology
Chapter 17 — Origins and Evolution
Chapter 18 — Bacterial Diversity
Chapter 19 — Archaeal Diversity
Chapter 20 — Eukaryotic Diversity
Chapter 21 — Microbial Ecology
Chapter 22 — Element Cycles and Environmental Microbiology
Chapter 23 — The Human Microbiome and Innate Immunity
Chapter 24 — The Adaptive Immune Response
Chapter 25 — Pathogenesis
Chapter 26 — Microbial Diseases
Chapter 27 — Antimicrobial Therapy and Discovery
Chapter 28 — Clinical Microbiology and Epidemiology
eAppendix 1 — Biological Molecules By Kathy Gillen
eAppendix 2 — Introductory Cell Biology: Eukaryotic Cells
eAppendix 3 — Laboratory Methods for Microbiology
eAppendix 4 — Molecular Biology of Diverse Viruses
Answers to Thought Questions — Answers to Thought Questions
Glossary — Glossary
68 sections are assigned across the five units.
Chapter 1Microbial Life: Origin and Discoveryread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 1.1 From Germ to Genome: What Is a Microbe?
- 1.2 Microbes Shape Human History
- 1.3 Medical Microbiology
- 1.4 Environment and Ecology
- 1.5 The Microbial Family Tree
- 1.6 Cell Biology and the DNA Revolution
Chapter 2Observing the Microbial Cellread →
6 assigned sections — Unit 1 · Methods. Exam 1 — Oct 5.
Sections
- 2.1 Observing Microbes U1
- 2.2 Optics and Properties of Light U1
- 2.3 Bright-Field Microscopy and Phase- Contrast Microscopy U1
- 2.4 Fixation and Staining for Bright-Field Microscopy U1
- 2.5 Fluorescence Microscopy, FISH, and Chemical Imaging Microscopy U1
- 2.6 Electron Microscopy, Scanning Probe Microscopy, and X-Ray Crystallography U1
Chapter 3Cell Structure and Functionread →
5 assigned sections — Unit 3 · Structure. Exam 2 — Oct 28.
Sections
- 3.1 The Bacterial Cell: An Overview
- 3.2 Membrane Molecules and Transport U3
- 3.3 The Envelope and Cytoskeleton U3
- 3.4 Bacterial Cell Division U3
- 3.5 Cell Asymmetry, Membrane Vesicles, and Extensions U3
- 3.6 Specialized Structures U3
Chapter 4Bacterial Culture, Growth, and Developmentread →
4 assigned sections — Unit 1 · Methods, Unit 5 · Regulation. Exam 1 — Oct 5.
Sections
- 4.1 Microbial Nutrition
- 4.2 Nutrient Uptake
- 4.3 Culturing and Counting Bacteria U1
- 4.4 The Growth Cycle U1
- 4.5 Biofilms U5
- 4.6 Cell Differentiation U5
Chapter 5Environmental Influences and Control of Microbial Growthread →
6 assigned sections — Unit 5 · Regulation. Exam 4 — Dec 16.
Sections
- 5.1 Extremophiles and the Constraints of Temperature and Pressure U5
- 5.2 Osmolarity and Halophiles U5
- 5.3 Hydronium (pH) and Hydroxide Ion Concentrations U5
- 5.4 Oxygen U5
- 5.5 Starvation and Eutrophication U5
- 5.6 Physical, Chemical, and Biological Control of Microbes U5
Chapter 6Virusesread →
6 assigned sections — Unit 2 · Genomes, Unit 3 · Structure. Exam 1 — Oct 5.
Sections
- 6.1 Viruses in Ecosystems U3
- 6.2 Virus Structure U3
- 6.3 Viral Genomes and Classification U2
- 6.4 Bacteriophages: The Gut Virome U3
- 6.5 Coronavirus SARS-CoV-2 and Other Viral Pathogens U3
- 6.6 Culturing Viruses U3
Chapter 7Genomes and Chromosomesread →
6 assigned sections — Unit 2 · Genomes. Exam 1 — Oct 5.
Sections
- 7.1 DNA: The Genetic Material U2
- 7.2 Genome Organization U2
- 7.3 DNA Replication U2
- 7.4 Plasmids and Secondary Chromosomes U2
- 7.5 Eukaryotic and Archaeal Chromosomes U2
- 7.6 Microbiomes and Metagenomes U2
Chapter 8Transcription, Translation, and Protein Processingread →
5 assigned sections — Unit 5 · Regulation. Exam 4 — Dec 16.
Sections
- 8.1 From DNA to RNA to Protein U5
- 8.2 Transcription of DNA to RNA U5
- 8.3 Translation of RNA to Protein U5
- 8.4 Protein Modification, Folding, and Degradation U5
- 8.5 Secretion: Protein Traffic Control U5
Chapter 9Genetic Change and Genome Evolutionread →
5 assigned sections — Unit 2 · Genomes. Exam 1 — Oct 5.
Sections
- 9.1 Mutations U2
- 9.2 DNA Repair U2
- 9.3 Gene Transfer Mechanisms U2
- 9.4 Mobile Genetic Elements U2
- 9.5 Genome Evolution U2
Chapter 10Molecular Regulationread →
5 assigned sections — Unit 5 · Regulation. Exam 4 — Dec 16.
Sections
- 10.1 Transcription Repressors and Activators U5
- 10.2 Alternative Sigma Factors and Anti-Sigma Factors U5
- 10.3 Regulation by RNA U5
- 10.4 Second Messengers U5
- 10.5 Clocks, Thermometers, and Switches U5
Chapter 11Viral Molecular Biologyread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 11.1 Phage Lambda: Enteric Bacteriophage
- 11.2 Influenza Virus: (–) strand RNA Virus
- 11.3 Human Immunodeficiency Virus (HIV): Retrovirus
- 11.4 Endogenous Retroviruses and Lentiviral Gene Therapy
- 11.5 Herpes Simplex Virus: DNA Virus
Chapter 12Molecular Complexity and Synthetic Biologyread →
2 assigned sections — Unit 5 · Regulation. Exam 4 — Dec 16.
Sections
- 12.1 Chemotaxis: Movement with a Destination U5
- 12.2 Biofilm Formation by Pseudomonas aeruginosa U5
- 12.3 CRISPR and Other Antiphage Defenses
- 12.4 Synthetic Biology: Biology by Design
Chapter 13Energetics and Catabolismread →
6 assigned sections — Unit 4 · Metabolism. Exam 3 — Nov 23.
Sections
- 13.1 Energy for Life U4
- 13.2 Energy Carriers and Electron Transfer U4
- 13.3 Catabolism: The Microbial Buffet U4
- 13.4 Glucose Fermentation and Respiration U4
- 13.5 Our Gut Microbiome: Friends with Benefits U4
- 13.6 Aromatic Catabolism and Syntrophy U4
Chapter 14Electron Flow in Organotrophy, Lithotrophy, and Phototrophyread →
6 assigned sections — Unit 4 · Metabolism. Exam 3 — Nov 23.
Sections
- 14.1 Electron Transport Systems and the Proton Motive Force U4
- 14.2 The Respiratory ETS and ATP Synthase U4
- 14.3 Anaerobic Respiration U4
- 14.4 Nanowires, Electron Shuttles, and Fuel Cells U4
- 14.5 Lithotrophy and Methanogenesis U4
- 14.6 Phototrophy U4
Chapter 15Biosynthesisread →
2 assigned sections — Unit 4 · Metabolism. Exam 3 — Nov 23.
Sections
- 15.1 Overview of Biosynthesis U4
- 15.2 CO 2 Fixation: The Calvin Cycle and Other Pathways U4
- 15.3 Fatty Acids and Antibiotics
- 15.4 Nitrogen Fixation and Regulation
- 15.5 Amino Acids and Nucleobases
Chapter 16Food and Industrial Microbiologyread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 16.1 Microbial Foods
- 16.2 Acid-Fermented and Alkali- Fermented Foods
- 16.3 Ethanolic Fermentation: Bread and Wine
- 16.4 Food Spoilage and Preservation
- 16.5 Industrial Microbiology
- 16.6 Vaccines and Gene Therapy Vectors
Chapter 17Origins and Evolutionread →
2 assigned sections — Unit 2 · Genomes. Exam 1 — Oct 5.
Sections
- 17.1 Origins of Life
- 17.2 Forming the First Cells
- 17.3 Evolution: Phylogeny and Gene Transfer U2
- 17.4 Natural Selection and Adaptation
- 17.5 Microbial Species and Taxonomy U2
- 17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts
Chapter 18Bacterial Diversityread →
1 assigned section — Unit 2 · Genomes. Exam 1 — Oct 5.
Sections
- 18.1 Bacterial Diversity at a Glance U2
- 18.2 Cyanobacteria: Oxygenic Phototrophs
- 18.3 Firmicutes, Mycoplasma, and Actinobacteria
- 18.4 Proteobacteria: From Photoheterotrophs to Lithotrophs
- 18.5 Spirochetes, Acidobacteria, Bacteroidetes, and Chlorobi
- 18.6 Planctomycetes, Verrucomicrobia, and Chlamydiae
Chapter 19Archaeal Diversityread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 19.1 Archaeal Diversity at a Glance
- 19.2 TACK Hyperthermophiles Eat Sulfur
- 19.3 Thaumarchaeota: Ammonia Oxidizers and Animal Symbionts
- 19.4 Euryarchaeota: Methanogens from Gut to Globe
- 19.5 Haloarchaea and Other Euryarchaeotes: Underground and Under Ocean
- 19.6 DPANN Symbionts, Altiarchaeales, and Asgard: Branch to Eukaryotes
Chapter 20Eukaryotic Diversityread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 20.1 Phylogeny of Eukaryotes
- 20.2 Fungi
- 20.3 Amoebozoa: Amebas and Slime Molds
- 20.4 Algae
- 20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans
- 20.6 Parasitic Protozoa and Microscopic Animals
Chapter 21Microbial Ecologyread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 21.1 Microbial Communities: Omics Analysis
- 21.2 Functional Ecology: Microbial Culture and Abiotic Factors
- 21.3 Symbiosis
- 21.4 Animal Digestive Microbiomes
- 21.5 Marine and Freshwater Microbes
- 21.6 Soil and Plant Microbial Communities
Chapter 22Element Cycles and Environmental Microbiologyread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 22.1 The Carbon Cycle and Climate Change
- 22.2 The Hydrologic Cycle and Wastewater Treatment
- 22.3 The Nitrogen Cycle
- 22.4 Sulfur, Phosphorus, and Metals
- 22.5 Our Built Environment
- 22.6 Astrobiology
Chapter 23The Human Microbiome and Innate Immunityread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 23.1 The Human Microbiome
- 23.2 Benefits and Risks of Microbiota
- 23.3 Overview of the Immune System
- 23.4 Physical and Chemical Defenses against Infection
- 23.5 Innate Immunity: Surveillance, Cytokines, and Inflammation
- 23.6 Complement and Fever
Chapter 24The Adaptive Immune Responseread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 24.1 Overview of Adaptive Immunity
- 24.2 Antibody Structure, Diversity, and Synthesis
- 24.3 T Cells Link Antibody and Cellular Immune Systems
- 24.4 Complement as Part of Adaptive Immunity
- 24.5 Gut Mucosal Immunity and the Microbiome
- 24.6 Immunization
- 24.7 Hypersensitivity and Autoimmunity
Chapter 25Pathogenesisread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 25.1 Host-Pathogen Interactions
- 25.2 Microbial Attachment: First Contact
- 25.3 Toxins Subvert Host Functions
- 25.4 Deploying Toxins and Effectors
- 25.5 Surviving within the Host
- 25.6 Tools Used to Probe Pathogenesis
Chapter 26Microbial Diseasesread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 26.1 Basics of Diagnosis and Infections of Skin, Soft Tissue, and Bone
- 26.2 Respiratory Tract Infections
- 26.3 Gastrointestinal Tract Infections
- 26.4 Genitourinary Tract Infections
- 26.5 Cardiovascular and Systemic Infections
- 26.6 Central Nervous System Infections
Chapter 27Antimicrobial Therapy and Discoveryread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 27.1 Fundamentals of Antimicrobial Therapy
- 27.2 Antibiotic Mechanisms of Action
- 27.3 Challenges of Drug Resistance and Discovery
- 27.4 Antiviral Agents
- 27.5 Antifungal Agents
Chapter 28Clinical Microbiology and Epidemiologyread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- 28.1 Clinical Specimen Collection and Handling
- 28.2 Pathogen Identification by Culture and Phenotype
- 28.3 Molecular and Serological Identification of Pathogens
- 28.4 Epidemiology
- 28.5 Detecting Emerging Microbial Diseases
- 28.6 Infectious Disease and Health Disparities
eAppendix 1Biological Molecules By Kathy Gillenread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- A1.1 Elements, Bonding, and Water
- A1.2 Organic Molecules
- A1.3 Proteins
- A1.4 Carbohydrates
- A1.5 Nucleic Acids
- A1.6 Lipids
- A1.7 Biological Chemistry
eAppendix 2Introductory Cell Biology: Eukaryotic Cellsread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- A2.1 The Cell Membrane
- A2.2 The Nucleus and Mitosis
- A2.3 Problems Faced by Large Cells
- A2.4 The Endomembrane System
- A2.5 The Cytoskeleton
- A2.6 Mitochondria and Chloroplasts
eAppendix 3Laboratory Methods for Microbiologyread →
1 assigned section — Unit 2 · Genomes. Exam 1 — Oct 5.
Sections
- A3.1 Ultracentrifugation to Isolate Parts of Cells
- A3.2 Agarose-Gel Electrophoresis
- A3.3 Protein Identification on 2D Gels with Mass Spectrometry
- A3.4 Northern and Southern Blots to Identify RNA and DNA
- A3.5 DNA Isolation and PCR Amplification
- A3.6 DNA Sequencing by Sanger, Illumina, and Nanopore Methods U2
- A3.7 Gene Cloning and Gibson Assembly
- A3.8 Primer Extension to Identify Transcriptional Start Sites
- A3.9 DNA Microarray
- A3.10 Protein Binding to DNA (ChIP- seq) and Protein-Protein Binding (Yeast Two-Hybrid Assay)
- A3.11 Confocal Microscopy
- A3.12 Immunoprecipitation and Western Blot
- A3.13 ICNP Phylum Nomenclature
eAppendix 4Molecular Biology of Diverse Virusesread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
Sections
- A4.1 Phage T4: The Classic Molecular Model
- A4.2 The Filamentous Phage M13: Vaccines and Nanowires
- A4.3 Poliovirus: (+) Strand RNA Virus
- A4.4 Hepatitis C: (+) Strand RNA Virus
Answers to Thought QuestionsAnswers to Thought Questionsread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.
GlossaryGlossaryread →
No sections from this chapter are on Rowen's schedule. Read it for background or a second explanation.