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Brief Contents
Preface
Acknowledgments
About the Author

PART 1 The Microbial World

Chapter 1 The Microbial World: An
Introduction
Chapter 2 Microbes in Perspective:
The Pioneers, Classifiers,
and Observers

Chapter 3 Molecules of the Cell: The

Building Blocks of Life

Chapter 4 Exploring the Prokaryotic

World: The Bacteria and
Archaea Domains

Chapter 5 The Eukaryotic World:

Protists and Fungi
Chapter 6 Viruses: At the Threshold of
Life

Chapter 7 Growth and Metabolism:

Running the Microbial
Machine
 Chapter 8 The DNA Story:
Chromosomes, Genes, and
Genomics

Chapter 9 Microbial Genetics: From

Genes to Genetic
Engineering

Chapter 10 Controlling Microbes: In

Our Surroundings and
Close to Home
Chapter 11 Microbial Crosstalk:
Uncovering the Social Life
of Microbes

PART 2 Microbes and Human Affairs

Chapter 12 Microbes and Food: Food
Preservation and Safety

Chapter 13 Microbes and Food: A Menu

of Microbial Delights
Chapter 14 Biotechnology and
Industry: Putting Microbes
to Work

Chapter 15 Microbes and Agriculture:

No Microbes, No
Hamburgers

Chapter 16 Microbes and the

Environment: No Microbes,
No Life
Chapter 17 Disease and Resistance:
The Wars Within

Chapter 18 Viral Diseases of Humans:

AIDS to Zika

Chapter 19 Bacterial Diseases of

Humans: Slate-Wipers and
Current Concerns

Appendix Pronouncing
Microorganism Names and Taxonomic
Terms
Glossary
Index
 ©NYCstocker/iStock/Thinkstock

Contents
Preface
Acknowledgments
About the Author

PART I The Microbial World

Chapter 1 The Microbial World: An Introduction

Good Morning Microbes!
1.1 Microbiology and Society: A Connected World
1.2 Why Microbes Matter: Protecting the Planet
The Ocean Microbiome
The Soil Microbiome
The Microbiome of the Atmosphere
The Microbiome in Earth’s Crust
1.3 Why Microbes Matter: Helping Maintain Human
Health
1.4 Why Microbes Matter: Causing Infections and
Disease
1.5 Why Microbes Matter: Benefiting Society
With Most Meals
In the Environment
A CLOSER LOOK 1.1: Microbes to the Rescue!
In the Pharmaceutical/Biotechnology Industries
1.6 Microbiology Today: Challenges Remain
 Air Travel
Urbanization and Poverty
Drug-Resistant Pathogens
Climate Change
A Final Thought
Chapter Discussion Questions

Chapter 2 Microbes in Perspective: The Pioneers,

Classifiers, and Observers

What Shall We Call This One?

2.1 The Roots of Microbiology: The Pioneers
Robert Hooke (1635–1703)
Antony van Leeuwenhoek (1632–1723)
Louis Pasteur (1822–1895)
A CLOSER LOOK 2.1: Experimentation and Scientific Inquiry
Robert Koch (1843–1910)
The Golden Age of Microbiology (1857–1917)
2.2 Naming Microbes: What’s in a Name?
Binomial Nomenclature
2.3 The Microbial World: The Observers
Microbial Measurements and Cell Size
A CLOSER LOOK 2.2: “What’s in a Name?”
The Light Microscope
The Electron Microscope
2.4 Microbial Groups: Eukaryotes, Prokaryotes, and
Viruses
Eukaryotic Microorganisms
Prokaryotic Organisms
The Viruses
2.5 Taxonomy: Cataloging Life
 Cataloging and Organizing Life
The Tree of Life
The Tree of Life and Society
A Final Thought
Chapter Discussion Questions

Chapter 3 Molecules of the Cell: The Building Blocks

of Life

The Spark
3.1 Chemistry Basics: Atoms, Bonds, and Molecules
Atoms and Bonding
Water
A CLOSER LOOK 3.1: Water and Life
The Molecules of Microbes
3.2 Carbohydrates: Simple Sugars and Polysaccharides
Simple Sugars
Oligosaccharides and Polysaccharides
A CLOSER LOOK 3.2: How Sweet It Is
3.3 Lipids: Fats, Phospholipids, and Sterols
Fats and Oils
Phospholipids
Sterols
3.4 Proteins: Amino Acids and Polypeptides
Amino Acids
Polypeptides and Protein Shape
3.5 Nucleic Acids: DNA and RNA
A Final Thought
Chapter Discussion Questions

Chapter 4 Exploring the Prokaryotic World: The

Bacteria and Archaea Domains
Hail Caesar!
A CLOSER LOOK 4.1: Bacteria in Eight Easy Lessons1
4.1 Cell Structure: Shapes and Arrangements
Prokaryotic Cell Shape and Arrangement
Staining Techniques
4.2 Cell Structure: Anatomy of a Cell
Surface Structures
Surface Projections
A CLOSER LOOK 4.2: Diarrhea Doozies
Cytoplasmic Structures
4.3 Prokaryotic Reproduction and Survival: Binary
Fission and Endospores
Prokaryotic Reproduction
Measuring Prokaryotic Growth
Endospores
4.4 Prokaryotic Growth: Culturing Bacteria
Growth Methods
4.5 Meet the Prokaryotes: The Domains Bacteria and
Archaea
Domain Bacteria
A CLOSER LOOK 4.3: The Blood of History
Domain Archaea
A Final Thought
Chapter Discussion Questions

Chapter 5 The Eukaryotic World: Protists and Fungi

The Big Ditch
5.1 Eukaryotic Cells: Their Structure
Endomembrane and Cytoskeletal Systems
Cell Motility
 Energy Organelles
Cell Walls
5.2 Eukaryotic Cells: Their Origin
The Evolution of the Eukaryotic Cell
The Endosymbiont Theory
5.3 The Protists: A Microbial Grab Bag
Protist Characteristics
Meeting the Protists
A CLOSER LOOK 5.1: Tuna Sandwiches
A CLOSER LOOK 5.2: “Black ’47”
5.4 Fungi: Yeasts and Molds
Characteristics of the Fungi
Meeting the Fungi
A CLOSER LOOK 5.3: The Day the Frogs Died
A CLOSER LOOK 5.4: “The Work of the Devil”
Symbiotic Relationships
A Final Thought
Chapter Discussion Questions

Chapter 6 Viruses: At the Threshold of Life

The Tulip Bubble Bursts
6.1 Viruses: Their First Sightings
A Contagious Living Fluid
A CLOSER LOOK 6.1: Into the Virosphere
6.2 Virus Structure: Geometric Perfection
The Component Parts of Viruses
A CLOSER LOOK 6.2: The Amazing Bacteriophages
6.3 Virus Replication: A Massive Production Factory
When Viruses Replicate Without Delay
When Viruses Lay Dormant
 Fighting Back Against Viruses
6.4 New Viral Diseases: Where Are They Coming From?
Emerging Viruses
Jumping Viruses
6.5 Tumors and Cancer: A Role for Some Viruses
The Uncontrolled Growth and Spread of Abnormal Cells
The Involvement of Viruses
How Viruses Transform Cells
A CLOSER LOOK 6.3: The Power of the Virus
6.6 Virus-Like Agents: Viroids and Prions
Viroids and Prions Are Infectious Particles
A Final Thought
Chapter Discussion Questions

Chapter 7 Growth and Metabolism: Running the

Microbial Machine

The Red Planet

7.1 Microbial Growth: Physical Factors
Water
Temperature
Oxygen
pH
Other Physical Factors
7.2 Microbial Metabolism: Enzymes and Energy
The Forms of Cellular Metabolism
Enzymes
Energy and ATP
7.3 Cellular Respiration: The Production of ATP
Aerobic Respiration
A CLOSER LOOK 7.1: “It’s Not Toxic to Us!”
 Anaerobic Respiration
7.4 Fermentation: A Metabolic “Safety Net”
Fermentation
A CLOSER LOOK 7.2: Microbes “Raise a Stink”
Fermentation End Products
7.5 Photosynthesis: An Anabolic Process
Energy-Trapping Reactions
Carbon-Trapping Reactions
A Final Thought
Chapter Discussion Questions

Chapter 8 The DNA Story: Chromosomes, Genes, and

Genomics

Microbial Zombies?
8.1 DNA: The Hereditary Molecule in All Organisms
The Double Helix
A CLOSER LOOK 8.1: The Tortoise and the Hare
DNA Replication
8.2 Gene Expression: The Flow of Information
Ribonucleic Acid
Making RNA
Making a Protein
Gene Expression: Controlling the Flow of Information
The lac Operon
8.3 Genes and Genomes: Human and Microbial
Many Microbial Genomes of Prokaryotes and Eukaryotes
Have Been Sequenced
Microbe and Human Genomes
Virus and Human Genomes
A CLOSER LOOK 8.2: The Little Microbial Cell That Could
 Microbial Genomics Will Advance Our Understanding of
the Microbial World
Metagenomics Is Identifying a Previously Unseen
Microbial World
A Final Thought
Chapter Discussion Questions

Chapter 9 Microbial Genetics: From Genes to Genetic

Engineering

An Outbreak of Bacterial Dysentery

9.1 Bacterial DNA: Chromosomes and Plasmids
The Bacterial Chromosome
Plasmids
Genetic Diversity
9.2 Gene Mutations: Subject to “Change Without Notice”
Mutations Affect Genes
Causes of Mutations
9.3 Genetic Recombination: Sharing Genes
Bacterial Conjugation
Transduction
Transformation
A CLOSER LOOK 9.1: Gene Swapping in the World’s Oceans
Other Ways of Transferring Genes Horizontally
Antibiotic Resistance in Today’s World
9.4 Genetic Engineering: Intentional Gene
Recombination
Restriction Enzymes and Recombinant DNA
Using Recombinant DNA Molecules
Diabetes
A Final Thought
A CLOSER LOOK 9.2: Bacteria to the Rescue
Chapter Discussion Questions

Chapter 10 Controlling Microbes: In Our

Surroundings and Close to Home

Sanitation, Hygiene, and Antibiotics

10.1 Physical Methods of Control: From Hot to Cold
Heat Disrupts Cellular Protein Structure
A CLOSER LOOK 10.1: Does Milk Stay Fresher Longer If It’s
Organic?
Radiation Damages Genetic Material
Drying Removes Water
Filtration Traps Microbes
Low Temperatures Slow Microbial Growth
10.2 Chemical Methods of Control: Antiseptics and
Disinfectants
General Principles of Chemical Control
A Survey of Some Common Chemical Agents
A CLOSER LOOK 10.2: Antiseptics in Your Pantry?
Phenols
10.3 Antimicrobial Drugs: Antibiotics and Other Agents
Magic Bullets
Penicillin Is a Game Changer
A CLOSER LOOK 10.3: Hiding a Treasure
Antibiotics Work in Different Ways
Other Antibiotics Have Different Modes of Action
Antiviral, Antifungal, and Antiprotistan Drugs
10.4 Antimicrobial Resistance: A Growing Challenge
Antibiotic Resistance and Superbugs
Controlling the Antibiotic Resistance Problem
A Final Thought
Chapter Discussion Questions

Chapter 11 Microbial Crosstalk: Uncovering the

Social Life of Microbes

The Case of the Disappearing Squid

11.1 Microorganisms: Their Rich Social Life
11.2 Bacteria Lead Social Lives: Biofilms and Cell
Communication
Biofilms Represent Multicellular, Social Communities
Cells in Biofilms Communicate by Social Networks
A CLOSER LOOK 11.1: Life in a Biofilm
Bacteria Behaviors Within a Biofilm
Bacteria Behaviors Associated with Learning
Microbes Exhibit Altruistic Behaviors
11.3 Biofilms Within the Human Body: The Human
Microbiome
Why a Symbiosis?
The Skin Harbors a Resident Microbiome
The Healthy Respiratory Tract Harbors a Diverse
Resident Microbiome
The Gastrointestinal Tract Harbors the Largest and Most
Diverse Microbiome
A CLOSER LOOK 11.2: Probiotics and Prebiotics to the
Rescue?
11.4 Microbiome and Host: “Talking” Back and Forth
Immune System Function and the Gut Microbiome
Nervous System Function and the Gut Microbiome
Stress and the Gut Microbiome
11.5 Microbes and Society: What Is a Human?
A Final Thought
Chapter Discussion Questions
PART II Microbes and Human Affairs

Chapter 12 Microbes and Food: Food Preservation

and Safety
Marco Polo and the Silk Road
12.1 Food Spoilage: Terms and Conditions
General Principles
Sources of Microbial Contamination
A CLOSER LOOK 12.1: Free Market Economy and Food
Safety
The Conditions for Spoilage
12.2 Microbes Causing Spoilage: Effects on Foods
Fresh and Processed Meat, Poultry, and Seafood
Milk and Dairy Products
Fruits and Vegetables
Grains and Bakery Products
12.3 Food Preservation: Keeping Microbes Out
Physical Preservation Methods
Other Preservation Methods
A CLOSER LOOK 12.2: It Started with “Stomped Potatoes”
12.4 Maintaining Food Safety: The Challenges
A CLOSER LOOK 12.3: Food Safety Quiz

A Final Thought
Chapter Discussion Questions

Chapter 13 Microbes and Food: A Menu of Microbial

Delights

Waiter! There Are Microbes in My Food!

13.1 Microbes in Action: Fermentation
13.2 Beginning Our Meal: To Your Health!
 A Glass of Wine
A CLOSER LOOK 13.1: A Microbial Terroir
13.3 First Course: The Appetizers
Olives
Cheese
A CLOSER LOOK 13.2: The Microbial Ecology of Cheese
13.4 The Salad Course: Of Vinegar and Bread
Vinegar
Bread
13.5 The Main Course: Salmon, Sausages, and Sides
Teriyaki Salmon
Sausages
Sides Dishes
13.6 Washing It Down: A Refreshing Grain Beverage
Beer Making
Sake Making
13.7 The Dessert Course: Coffee and Chocolates
A Final Thought
A CLOSER LOOK 13.3: Artisanal Food Microbiology

Chapter Discussion Questions

Chapter 14 Biotechnology and Industry: Putting

Microbes to Work

The Spider’s Silk Parlor

14.1 Microbes and Biotechnology: Seeing the Promise
Genetically Engineering Bacterial Cells
14.2 The Products of Microbial Biotechnology: Medical
Therapeutics and Vaccines
Therapeutics
Vaccines
14.3 The Products of Microbial Biotechnology: Diagnostic
Tools and Tests
Diagnostic Tools
Diagnostic Tests
A CLOSER LOOK 14.1: “Not Guilty”
14.4 Microbes and Industry: Working Together
The Industrial Microbes
Producing Metabolites and Growing Microbes in Mass
14.5 Microbes and Industry: The Products
Antibiotics
Vitamins and Amino Acids
Industrial Enzymes
A CLOSER LOOK 14.2: Plastic-Eating Microbes: Our
Saviors?
Organic Acids
Biofuels
Engineering New Skills
A Final Thought
Chapter Discussion Questions

Chapter 15 Microbes and Agriculture: No Microbes,

No Hamburgers
The Man from Delft
15.1 Microbes on the Farm: If the Environment Is
Suitable, They Will Perform
Connecting the Nitrogen Dots
Those Remarkable Ruminants
At the Dairy Plant
A CLOSER LOOK 15.1: Toxic Atmospheres
15.2 Biotechnology on the Farm: The Coming of the
Transgenic Plant
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