Prescott’s Microbiology, Twelfth Edition
By Joanne M. Willey, Kathleen M. Sandman and Dorothy H. Wood
Contents:
Part One Introduction to Microbiology
1 The Evolution of Microorganisms and Microbiology 1
Micro Focus:
Microbiology’s Reach 1
1.1 Members of the Microbial World 2
1.2 Microbes Have Evolved and Diversified for Billions of Years 4
Microbial Diversity & Ecology 1.1
Hydrothermal Vents: Did Life Begin Under the Sea? 7
1.3 Microbiology Advanced as New Tools for Studying Microbes Were Developed 14
1.4 Microbiology Encompasses Many Subdisciplines 19
2 Microscopy 23
Micro Focus: Anthrax Bioterrorism Attack 23
2.1 Lenses Create Images by Bending Light 24
2.2 There Are Several Types of Light Microscopes 24
2.3 Staining Helps to Visualize and Identify Microbes 32
2.4 Electron Microscopes Use Beams of Electrons to Create Highly Magnified Images 35
2.5 Scanning Probe Microscopy Can Visualize Molecules and Atoms 40
3 Bacterial Cell Structure 44
Micro Focus:
Bacteria Use Rapid Transport 44
3.1 Use of the Term Prokaryote Is Controversial 45
3.2 Bacteria Are Diverse but Share Some Common Features 45
3.3 Bacterial Plasma Membranes Control
What Enters and Leaves the Cell 48
3.4 Cell Walls Have Many Functions 54
3.5 Extracellular Vesicles Emerge from
3.6 The Cell Envelope Often Includes Layers
Outside the Cell Wall 61
3.7 The Bacterial Cytoplasm Is More Complex than Once Thought 62
Microbial Diversity & Ecology 3.1
Organelles Without Membranes? 65
3.8 External Structures Are Used for
Attachment and Motility 67
3.9 Bacteria Move in Response to
Environmental Conditions 70
3.10 Bacterial Endospores Are a Survival Strategy 74
4 Archaeal Cell Structure 80
Micro Focus:
Methane—The Other Greenhouse Gas 80
4.1 Archaea Are Diverse but Share Some Common Features 81
4.2 Archaeal Cell Envelopes Are Structurally Diverse 83
4.3 Archaeal Cytoplasm Is Similar to Bacterial Cytoplasm 86
4.4 Many Archaea Have External Structures
Used for Attachment and Motility 88
5 Eukaryotic Cell Structure 91
Micro Focus: Red Means Dead 91
5.1 Eukaryotic Cells Are Diverse but Share
Some Common Features 92
5.2 Eukaryotic Cell Envelopes 93
5.3 The Eukaryotic Cytoplasm Contains
a Cytoskeleton and Organelles 94
5.4 Several Organelles Function in the
Secretory and Endocytic Pathways 96
5.5 The Nucleus and Ribosomes Are Involved
in Genetic Control of the Cell 100
5.6 Mitochondria, Related Organelles, and
Chloroplasts Are Involved in Energy Conservation 101
Microbial Diversity & Ecology 5.1
There Was an Old Woman Who Swallowed a Fly 104
5.7 Many Eukaryotic Microbes Have External
Structures Used for Motility 105
6 Viruses and Other Acellular Infectious Agents 109
Micro Focus:
Viruses to the Rescue 109
6.1 Viruses Are Acellular 110
6.2 Virion Structure Is Defined by Capsid
Symmetry and Presence or Absence of an Envelope 110
6.3 Viral Life Cycles Have Five Steps 114
6.4 There Are Several Types of Viral Infections 119
6.5 Virus Cultivation and Enumeration 120
6.6 Viroids and Satellites: Nucleic Acid-Based Subviral Agents 123
6.7 Prions Are Composed Only of Protein 124
Part Two Microbial Nutrition, Growth, and Control
7 Bacterial and Archaeal Growth 127
Micro Focus:
How Low Can You Go? 127
7.1 Most Bacteria and Archaea Reproduce by Binary Fission 128
7.2 Bacterial Cell Cycles Are Divided into Three Phases 129
7.3 Archaeal Cell Cycles Are Unique 133
7.4 Growth Curves Consist of Five Phases 134
7.5 Environmental Factors Affect Microbial Growth 138
Microbial Diversity & Ecology 7.1
Microbial Sculptors 141
7.6 Microbial Growth in Natural Environments 145
7.7 Laboratory Culture of Microbes Requires
Conditions that Mimic Their Normal Habitats 150
7.8 Microbial Population Size Can Be
Measured Directly or Indirectly 155
7.9 Chemostats and Turbidostats Are Used for
Continuous Culture of Microorganisms 157
8 Control of Microorganisms in the Environment 162
Micro Focus:
To Wipe or Not to Wipe? That Is the Question. 162
8.1 Microbial Growth and Replication: Targets for Control 163
8.2 Microbes Can Be Controlled by Physical Means 166
Techniques & Applications 8.1
Come Fly with Me? 167
8.3 Microorganisms Are Controlled with Chemical Agents 170
8.4 Antimicrobial Agents Must Be Evaluated for Effectiveness 174
8.5 Microorganisms Can Be Controlled by Biological Methods 176
9 Antimicrobial Chemotherapy 179
Micro Focus:
A Gift from Traditional Chinese Medicine 179
9.1 Antimicrobial Chemotherapy Evolved from Antisepsis Efforts 180
9.2 Antimicrobial Drugs Have Selective Toxicity 181
9.3 Antimicrobial Activity Can Be Measured by Specific Tests 181
9.4 Antibacterial Drugs 185
9.5 Antiviral Drugs 190
9.6 Antifungal Drugs 193
9.7 Antiprotozoan Drugs 193 Disease 9.1
Chloroquine and COVID-19:
A Cautionary Tale 195
9.8 Antimicrobial Drug Resistance Is a Public Health Threat 196
Part Three Microbial Metabolism
10 Introduction to Metabolism 201
Micro Focus:
Flushed Away 201
10.1 Metabolism: Important Principles and Concepts 202
10.2 ATP: The Major Energy Currency of Cells 204
10.3 Redox Reactions: Reactions of Central
Importance in Metabolism 205
10.4 Electron Transport Chains: Sets
of Sequential Redox Reactions 207
10.5 Biochemical Pathways: Sets of Linked
Chemical Reactions 209
10.6 Enzymes and Ribozymes Speed
Up Cellular Chemical Reactions 210
10.7 Metabolism Must Be Regulated to
Maintain Homeostasis 214
11 Catabolism: Energy Release and Conservation 219
Micro Focus:
The Richest Hill on Earth 219
11.1 Metabolic Diversity and Nutritional Types 220
11.2 There Are Two Chemoorganotrophic Fueling Processes 222
11.3 Aerobic Respiration Starts with Glucose Oxidation 223
11.4 Electron Transport and Oxidative
Phosphorylation Generate the Most ATP 230
11.5 Anaerobic Respiration Uses the Same
Steps as Aerobic Respiration 235
11.6 Fermentation Does Not Involve
an Electron Transport Chain 236
11.7 Catabolism of Organic Molecules Other than Glucose 239
11.8 Chemolithotrophy: “Eating Rocks” 241
11.9 Flavin-Based Electron Bifurcation 244
11.10 Phototrophy 245
12 Anabolism: The Use of Energy in Biosynthesis 255
Micro Focus:
Building Penicillin 255
12.1 Principles Governing Biosynthesis 256
12.2 Precursor Metabolites: Starting Molecules for Biosynthesis 257
12.3 CO2 Fixation: Reduction and Assimilation of CO2 Carbon 257
12.4 Synthesis of Carbohydrates 260
12.5 Synthesis of Amino Acids Consumes Many
Precursor Metabolites 262
12.6 Synthesis of Purines, Pyrimidines, and Nucleotides 268
12.7 Lipid Synthesis 270
Part Four Microbial Molecular Biology and Genetics
13 Bacterial Genome Replication and Expression 277
Micro Focus:
Making Code 277
13.1 Experiments Using Bacteria and Viruses
Demonstrated that DNA Is the Genetic Material 278
13.2 Nucleic Acid and Protein Structure 280
13.3 DNA Replication in Bacteria 283
13.4 Bacterial Genes Consist of Coding
Regions and Other Sequences Important
for Gene Function 289
13.5 Transcription in Bacteria 291
13.6 The Genetic Code Consists of
Three-Letter “Words” 294
13.7 Translation in Bacteria 297
13.8 Coordination of Gene Expression Processes 302
13.9 Protein Maturation and Secretion 304
14 Regulation of Cellular Processes 310
Micro Focus:
Promoting Expression 310
14.1 Bacteria Use Many Regulatory Strategies 311
14.2 Regulation of Transcription Initiation Saves
Considerable Energy and Materials 311
14.3 Attenuation and Riboswitches Stop Transcription Prematurely 316
14.4 RNA Secondary Structures Control Translation 319
14.5 Mechanisms Used for Global Regulation 320
14.6 Bacteria Combine Several Regulatory
Mechanisms to Control Complex Cellular Processes 327
15 Eukaryotic and Archaeal Genome Replication and Expression 336
Micro Focus:
Pharming 336
15.1 Genetic Processes in the Three Domains 337
15.2 DNA Replication: Similar Overall, but with
Different Replisome Proteins 337
15.3 Transcription 341
15.4 Translation and Protein Maturation and Localization 344
15.5 Regulation of Cellular Processes 349
16 Mechanisms of Genetic Variation 353
Micro Focus:
Manure Happens 353
16.1 Mutations: Heritable Changes in a Genome 354
16.2 Detection and Isolation of Mutants 358
16.3 DNA Repair Maintains Genome Stability 359
16.4 Microbes Use Mechanisms Other than
Mutation to Create Genetic Variability 362
16.5 Mobile Genetic Elements Move Genes
Within and Between DNA Molecules 364
16.6 Conjugation Requires Cell-Cell Contact 365
16.7 Transformation Is the Uptake of Free DNA 368
16.8 Transduction Is Virus-Mediated DNA Transfer 370
16.9 Evolution in Action: The Development of
Antibiotic Resistance in Bacteria 373
17 Microbial DNA Technologies 377
Micro Focus:
Spinning Stronger Silk 377
17.1 Key Discoveries Led to the Development
of DNA Cloning Technology 378
Techniques & Applications 17.1
Gel Electrophoresis 379
17.2 Polymerase Chain Reaction Amplifies Targeted DNA 383
17.3 Genomic and Metagenomic Libraries:
Cloning Genomes in Pieces 386
17.4 Expressing Foreign Genes in Host Cells 387
17.5 Cas9 Nuclease Is a Programmable
Tool for Genome Editing 389
17.6 Biotechnology Develops Custom
Microbes for Industrial Use 391
Techniques & Applications 17.2
How to Build a Microorganism 394
18 Microbial Genomics 397
Micro Focus:
What’s in a Genome? 397
18.1 DNA Sequencing Methods 398
18.2 Genome Sequencing 402
18.3 Metagenomics Provides Access to
Uncultured Microbes 404
18.4 Bioinformatics: What Does the Sequence Mean? 406
18.5 Functional Genomics Links Genes to Phenotype 407
18.6 Systems Biology: Making and Testing Complex Predictions 413
18.7 Comparative Genomics 413
Part Five The Diversity of the Microbial World
19 Archaea 419
Micro Focus:
Methanogens Fuel Domestic Energy Debate 419
19.1 Overview of Archaea 420
19.2 Phyla Asgardarchaeota and Nanoarchaeota
Are Known Primarily from Metagenomics 423
19.3 Phylum Thermoproteota: Sulfur-
Dependent Thermophiles 424
19.4 Phylum Nitrosphaeria: Mesophilic Ammonia Oxidizers 426
19.5 Phyla Methanobacteriota, Halobacteriota,
and Thermoplasmatota: Methanogens,
Haloarchaea, and Others 426
20 Nonproteobacterial Gram-Negative Bacteria 433
Micro Focus:
From Food Waste to Fuel 433
20.1 Diderm Cell Envelopes Are Not Uniform 434
20.2 Aquificota and Thermotogota Are Hyperthermophiles 434
20.3 Deinococcota Includes Radiation- Resistant Bacteria 434
20.4 Photosynthetic Bacteria Are Diverse 435
20.5 PVC Superphylum (Planctomycetota
and Verrucomicrobiota): Atypical Cell Division 442
20.6 Phylum Spirochaetota: Bacteria with a
Corkscrew Morphology 444
20.7 Phylum Bacteroidota Includes Important Gut Microbiota 446
20.8 Phylum Fusobacteriota: Commensal Anaerobes 447
20.9 Phylum Desulfobacterota: Anaerobic Sulfate/Sulfur Reducers 447
20.10 Phyla Bdellovibrionota and Myxococcota: Bacterial Predators 449
20.11 Phylum Campylobacterota: Human and Animal Commensals 451
21 Proteobacteria 455
Micro Focus:
Bison and Brucellosis Spark Controversy 455
21.1 Class Alphaproteobacteria Includes Many Oligotrophs 456
21.2 Gammaproteobacteria Is the Largest Bacterial Class 464
Microbial Diversity & Ecology 21.1
Acid Mine Drainage 469
22 Gram-Positive Bacteria 479
Micro Focus:
Antibiotic Production: Is It Actually Bacterial Chitchat? 479
22.1 Phylum Actinobacteriota 480
22.2 Phylum Firmicutes, Class Bacilli: Aerobic
Endospore-Forming Bacteria 487
22.3 Phylum Firmicutes, Class Clostridia:
Anaerobic Endospore-Forming Bacteria 494
22.4 Phylum Firmicutes, Classes Negativicutes
and Halanaerobiia: Gram-Positive Bacteria
with Outer Membranes 495
23 Protists 498
Micro Focus:
Setting the Record Straight 498
23.1 Protist Diversity Reflects Broad Phylogeny 499
23.2 Discoba-Metamonada Clade 501
23.3 Amoebozoa Clade Includes Protists
with Pseudopodia 503
23.4 TSAR Clade: Protists of Global Importance 505
23.5 Haptista Clade 514
23.6 Archaeplastida Clade Includes Green and Red Algae 514
24 Fungi 518
Micro Focus:
The Complex Story of Caterpillar Fungus 518
24.1 Fungal Biology Reflects Vast Diversity 519
24.2 Zoosporic Fungi Produce Motile Spores 522
24.3 Zygomycetous Fungi Have Coenocytic Hyphae 523
24.4 Dikarya Is the Most Diverse Fungal Group 525
Disease 24.1
White-Nose Syndrome Is Decimating
North American Bat Populations 528
25 Viruses 532
Micro Focus:
Disrupting the Viral Life Cycle 532
25.1 Virus Phylogeny Relies on Genomics 533
25.2 Double-Stranded DNA Viruses Infect All Cell Types 534
25.3 Single-Stranded DNA Viruses Use a
Double-Stranded Intermediate in Their Life Cycles 542
25.4 Double-Stranded RNA Viruses: RNADependent
RNA Polymerase Replicates
the Genome and Synthesizes mRNA 543
25.5 Positive-Strand RNA Viruses: Genomes
that Are Translated upon Entry 545
25.6 Negative-Strand RNA Viruses:
RNA-Dependent RNA Polymerase Is Part of the Virion 549
25.7 Retroviruses: Positive-Strand Viruses
that Use Reverse Transcriptase in Their Life Cycles 551
25.8 Reverse Transcribing DNA Viruses 552
Part Six Ecology and Symbiosis
26 Exploring Microbes in Ecosystems 556
Micro Focus:
Scientists Search for Intraterrestrial Life—and Find It 556
26.1 Microbial Biology Relies on Cultures 557
Microbial Diversity & Ecology 26.1
Patience, Hard Work, Luck, and the Evolution of Eukaryotes 559
26.2 Microbial Identification Is Largely Based
on Molecular Characterization 560
26.3 Assessing Microbial Populations 563
26.4 Assessing Microbial Community Activity 566
27 Microbial Interactions 571
Micro Focus:
Microbes in Community 571
27.1 Many Types of Microbial Interactions Exist 572
27.2 Mutualism: Obligatory Positive Interaction 573
27.3 Cooperation: Nonobligatory Positive Interaction 577
27.4 Antagonistic Interactions Prompt Microbial Responses 579
Microbial Diversity & Ecology 27.1
Wolbachia: The World’s Most Infectious Microbe? 581
28 Biogeochemical Cycling and Global Climate Change 584
Micro Focus:
Global Climate Change; Infectious Disease Change 584
28.1 Biogeochemical Cycling Sustains Life on Earth 585
28.2 Microbes Mediate Nutrient Cycling 587
28.3 Global Climate Change: Infectious
Disease Change 594
29 Microorganisms in Marine and Freshwater Ecosystems 599
Micro Focus:
Ocean Death Coming Soon to a Coast Near You 599
29.1 Water Is the Largest Microbial Habitat 600
29.2 Microorganisms in Marine Ecosystems 601
29.3 Microorganisms in Freshwater Ecosystems 610
Microbial Diversity & Ecology 29.1
Attention All Dog Owners! 614
30 Microorganisms in Terrestrial Ecosystems 617
Micro Focus:
Bread for a Hungry World 617
30.1 Soils Are an Important Microbial Habitat 618
30.2 Diverse Microorganisms Inhabit Soil 620
30.3 Microbe-Plant Interactions Can Be
Positive, Negative, or Neutral 621
Disease 30.1
Citrus Greening and the Power of “Why?” 633
30.4 The Subsurface Biosphere Is Vast 633
Part Seven Pathogenicity and Host Response
31 Innate Host Resistance 636
Micro Focus:
The Hygiene Hypothesis 636
31.1 Immunity Arises from Innate Resistance
and Adaptive Defenses 637
31.2 Innate Resistance Starts with Barriers 637
31.3 Innate Resistance Relies on Chemical
Mediators 640
31.4 Each Type of Innate Immune Cell Has a
Specific Function 646
31.5 Organs and Tissues of the Immune
System Are Sites of Host Defense 651
31.6 Phagocytosis Destroys Invaders 654
31.7 Inflammation Unites All Components of Immunity 659
32 Adaptive Immunity 663
Micro Focus:
Killing Cancer, Immunologically 663
32.1 Adaptive Immunity Relies on Recognition and Memory 664
32.2 Antigens Elicit Immunity 664
32.3 Adaptive Immunity Can Be Earned or Borrowed 665
32.4 Recognition of Foreignness Is Critical
for a Strong Defense 666
32.5 T Cells Are Critical for Immune Function 669
32.6 B Cells Make Antibodies 673
32.7 Antibodies Bind Specific 3-D Antigens 676
Techniques & Applications 32.1
Monoclonal Antibody Therapy 683
32.8 Antibodies Doom Antigens 684
Historical Highlights 32.2
Convalescent Plasma: An Old Treatment for a New Disease 684
32.9 The Immune System Can Malfunction 686
33 The Microbe-Human Ecosystem 696
Micro Focus:
Embrace Your Gut Flora 696
33.1 Humans Are Holobionts 697
33.2 The Microbiome Develops from Birth to Adulthood 697
33.3 A Functional Core Microbiome Is
Required for Host Homeostasis 702
33.4 Many Diseases Have a Connection with Dysbiosis 708
33.5 Microbiome Manipulation Can Be Therapeutic 711
34 Infection and Pathogenicity 714
Micro Focus:
The Unlikely Tale of Miasmas, Bras, and Masks 714
34.1 The Process of Infection 715
34.2 Transmission and Entry into the Host 716
Historical Highlights 34.1
The First Indications of Person-to-Person
Spread of an Infectious Disease 717
34.3 Surviving the Host Defenses 722
34.4 Damage to the Host 724
Part Eight Microbial Diseases, Detection, and Their Control
35 Epidemiology and Public Health Microbiology 730
Micro Focus:
Protecting the Herd 730
35.1 Epidemiology Is an Evidence-Based Science 731
Historical Highlights 35.1
John Snow, the First Epidemiologist 732
35.2 Epidemiology Is Rooted in Well-Tested Methods 732
35.3 Infectious Disease Is Revealed Through
Patterns Within a Population 735
Historical Highlights 35.2
“Typhoid Mary” 736
35.4 Infectious Diseases and Pathogens
Are Emerging and Reemerging 738
35.5 Healthcare Facilities Harbor Infectious Agents 740
35.6 Coordinated Efforts Are Required to
Prevent and Control Epidemics 741
Historical Highlights 35.3
The First Immunizations 744
35.7 Bioterrorism Readiness Is an Integral
Component of Public Health Microbiology 746
Historical Highlights 35.4
1346—Early Biological Warfare Attack 747
36 Clinical Microbiology and Immunology 750
Micro Focus:
Ebola and Global Health Security 750
36.1 The Clinical Microbiology Laboratory
Detects Infectious Agents and Protects Its Workers 751
36.2 Identification of Microorganisms from Specimens 753
36.3 Immune Responses Can Be Exploited to
Detect Infections 760
37 Human Diseases Caused by Viruses and Prions 769
Micro Focus:
Remembering HIV/AIDS 769
37.1 Viruses Can Be Transmitted by Airborne Routes 770
37.2 Arthropods Can Transmit Viral Diseases 780
37.3 Direct Contact Diseases Can Be Caused by Viruses 782
37.4 Food and Water Are Vehicles for Viral Diseases 792
Historical Highlights 37.1
A Brief History of Polio 795
37.5 Zoonotic Diseases Arise from
Human-Animal Interactions 795
37.6 Prion Proteins Transmit Disease 798
38 Human Diseases Caused by Bacteria 801
Micro Focus:
The Plague Family Tree 801
38.1 Bacteria Can Be Transmitted by Airborne Routes 802
38.2 Arthropods Can Transmit Bacterial Diseases 811
38.3 Direct Contact Diseases Can Be Caused by Bacteria 814
Disease 38.1
Syphilis and the Tuskegee Study 821
Disease 38.2
Biofilms 822
38.4 Food and Water Are Vehicles for Bacterial Diseases 827
Techniques & Applications 38.3
Clostridial Toxins as Therapeutic Agents:
Benefits of Nature’s Most Toxic Proteins 831
38.5 Zoonotic Diseases Arise from
Human-Animal Interactions 835
38.6 Opportunistic Diseases Can Be Caused by Bacteria 837
39 Human Diseases Caused by Fungi and Protists 845
Micro Focus:
Mushrooms of Death 845
39.1 Relatively Few Fungi and Protists
Are Human Pathogens 846
39.2 Fungi Can Be Transmitted by Airborne Routes 847
39.3 Arthropods Can Transmit Protozoal
Disease 849
Disease 39.1
A Brief History of Malaria 850
39.4 Direct Contact Diseases Can Be Caused
by Fungi and Protists 857
39.5 Food and Water Are Vehicles of Protozoal Diseases 860
39.6 Opportunistic Diseases Can Be Caused
by Fungi and Protists 865
Part Nine Applied Microbiology
40 Microbiology of Food 871
Micro Focus:
The Art, Science, and Genetics of Brewing Beer 871
40.1 Microbial Growth Can Cause Food Spoilage 872
40.2 Environmental Factors Control Food Spoilage 873
40.3 Food-Borne Disease Outbreaks 875
40.4 Detection of Food-Borne Pathogens
Requires Government-Industry Cooperation 877
40.5 Microbiology of Fermented Foods:
Beer, Cheese, and Much More 879
Techniques & Applications 40.1
Chocolate: The Sweet Side of Fermentation 880
41 Biotechnology and Industrial Microbiology 887
Micro Focus:
Where Are the New Antibiotics? 887
41.1 Microbes Are the Source of Many
Products of Industrial Importance 888
41.2 Biofuel Production Is a Dynamic Field 890
41.3 Growing Microbes in Industrial Settings Presents Challenges 892
41.4 Agricultural Biotechnology Relies on a Plant Pathogen 893
41.5 Some Microbes Are Products 894
42 Applied Environmental Microbiology 898
Micro Focus:
Deepwater Horizon Oil Consumed by Microbes 898
42.1 Purification and Sanitary Analysis
Ensure Safe Drinking Water 899
42.2 Wastewater Treatment Maintains Human
and Environmental Health 901
42.3 Microbial Fuel Cells: Batteries Powered by Microbes 906
42.4 Biodegradation and Bioremediation
Harness Microbes to Clean the Environment 907
Appendix 1 A Review of the Chemistry of Biological Molecules A-1
Appendix 2 Common Metabolic Pathways A-9
Appendix 3 Microorganism Pronunciation Guide A-17
Glossary G-1
Index I-1