Professional Documents
Culture Documents
ebook download (eBook PDF) Microbiology: An Evolving Science (Fifth Edition) 5th Edition by Joan L. Slonczewski all chapter
ebook download (eBook PDF) Microbiology: An Evolving Science (Fifth Edition) 5th Edition by Joan L. Slonczewski all chapter
ebook download (eBook PDF) Microbiology: An Evolving Science (Fifth Edition) 5th Edition by Joan L. Slonczewski all chapter
http://ebooksecure.com/product/microbiology-an-evolving-
science-4th-edition-ebook-pdf/
http://ebooksecure.com/product/ebook-pdf-microbiology-an-
evolving-science-4th-edition/
http://ebooksecure.com/product/ebook-pdf-microbiology-an-
evolving-science-3rd-edition/
https://ebooksecure.com/download/progress-in-heterocyclic-
chemistry-ebook-pdf/
(eBook PDF) Translational Medicine in CNS Drug
Development, Volume 29
http://ebooksecure.com/product/ebook-pdf-translational-medicine-
in-cns-drug-development-volume-29/
https://ebooksecure.com/download/cardiology-an-integrated-
approach-human-organ-systems-dec-29-2017_007179154x_mcgraw-hill-
ebook-pdf/
https://ebooksecure.com/download/netter-atlas-of-human-anatomy-
classic-regional-approach-8e-mar-29-2022_0323793738_elsevier-not-
true-pdf-ebook-pdf/
http://ebooksecure.com/product/original-pdf-horizons-canadian-
edition-by-joan-manley/
http://ebooksecure.com/product/ebook-pdf-microbiology-with-
diseases-by-taxonomy-5th-edition/
FI F TH ED ITI O N
Microbiology
An Evolving Science
CHAPTER 3
Cell Structure and Function .....................................................................................75
3.1 The Bacterial Cell: An Overview 77
3.2 The Cell Membrane and Transport 82
3.3 The Envelope and Cytoskeleton 87
3.4 Bacterial Cell Division 97
3.5 Cell Polarity, Membrane Vesicles, and Nanotubes 103
Special Topic 3.1: Turrets and Horseshoes: What Are They For? 108
3.6 Specialized Structures 108
CHAPTER 4
Bacterial Culture, Growth, and Development ................................................. 119
4.1 Microbial Nutrition 120
4.2 Nutrient Uptake 124
4.3 Culturing and Counting Bacteria 130
Special Topic 4.1: Antibiotic Hunters Culture the “Unculturable” 136
4.4 The Growth Cycle 140
4.5 Biofilms 147
4.6 Cell Differentiation 151
CHAPTER 5
Environmental Influences and Control of Microbial Growth ..................... 159
5.1 Environmental Limits on Growth: Temperature and Pressure 160
5.2 Osmolarity 167
5.3 Hydronium (pH) and Hydroxide Ion Concentrations 168
5.4 Oxygen 173
5.5 Nutrient Deprivation and Starvation 176
5.6 Physical, Chemical, and Biological Control of Microbes 180
Special Topic 5.1: Phage “Smart Bombs” Target Biofilms 190
CHAPTER 6
Viruses ........................................................................................................................... 195
6.1 Viruses in Ecosystems 196
6.2 Virus Structure 202
6.3 Viral Genomes and Classification 208
6.4 Bacteriophages: The Gut Virome 215
Special Topic 6.1: Phages Go Everywhere 222
6.5 Animal and Plant Viruses 222
6.6 Culturing Viruses 233
PART 2
Genes and Genomes
5 µm
CHAPTER 7
Genomes and Chromosomes ................................................................................239
7.1 DNA: The Genetic Material 240
7.2 Genome Organization 241
Special Topic 7.1: DNA as Digital Storage 246
7.3 DNA Replication 251
7.4 Plasmids and Secondary Chromosomes 261
7.5 Eukaryotic and Archaeal Chromosomes 266
7.6 Microbiomes and Metagenomes 268
CHAPTER 8
Transcription, Translation, and Protein Processing ...................................... 277
8.1 RNA Polymerases and Sigma Factors 278
8.2 Transcription of DNA to RNA 281
8.3 Translation of RNA to Protein 288
Special Topic 8.1: Translocation: EF-G Gets Physical 298
8.4 Protein Modification, Folding, and Degradation 302
8.5 Secretion: Protein Traffic Control 306
CHAPTER 9
Genetic Change and Genome Evolution ........................................................... 315
9.1 Mutations 316
9.2 DNA Repair 322
Special Topic 9.1: DNA as a Live Wire: Using Electrons to Find DNA Damage 324
9.3 Gene Transfer: Mechanisms and Barriers 329
9.4 Mobile Genetic Elements 343
9.5 Genome Evolution 348
CHAPTER 10
Molecular Regulation ............................................................................................... 357
10.1 Transcription Repressors and Activators 358
10.2 Alternative Sigma Factors and Anti-Sigma Factors 370
10.3 Regulation by RNA 372
10.4 Second Messengers 380
10.5 Clocks, Thermometers, and Switches 388
Special Topic 10.1: Inteins, Exteins and “Spliced-Up” Regulation 390
10.6 Chemotaxis: Posttranslational Regulation of Cell Behavior 395
CHAPTER 11
Viral Molecular Biology ...........................................................................................401
11.1 Phage Lambda: Enteric Bacteriophage 402
11.2 Influenza Virus: (–) Strand RNA Virus 410
Special Topic 11.1: Designing a Pandemic Flu 418
11.3 Human Immunodeficiency Virus (HIV): Retrovirus 420
11.4 Endogenous Retroviruses and Gene Therapy 431
11.5 Herpes Simplex Virus: DNA Virus 435
CHAPTER 12
Biotechniques and Synthetic Biology ................................................................443
12.1 DNA Amplification and Sequence Analysis 444
12.2 Genetic Manipulation of Microbes 457
Special Topic 12.1: Constructing the Smallest Genome for Cellular Life 462
12.3 Gene Expression Analysis 466
12.4 Applied Biotechnology 472
12.5 Synthetic Biology: Biology by Design 475
PART 3
Metabolism and Biochemistry
CHAPTER 13
Energetics and Catabolism ....................................................................................485
13.1 Energy for Life 487
13.2 Energy Carriers and Electron Transfer 493
13.3 Catabolism: The Microbial Buffet 501
13.4 Glucose Fermentation and Respiration 505
13.5 The Gut Microbiome: Friends with Benefits 520
13.6 Aromatic Catabolism and Syntrophy 523
Special Topic 13.1: Gut Bacteria Rule Host Behavior 524
CHAPTER 14
Electron Flow in Organotrophy, Lithotrophy, and Phototrophy .............. 533
14.1 Electron Transport Systems and the Proton Motive Force 535
14.2 The Respiratory ETS and ATP Synthase 544
14.3 Anaerobic Respiration 551
14.4 Nanowires, Electron Shuttles, and Fuel Cells 553
14.5 Lithotrophy and Methanogenesis 557
Special Topic 14.1: The Ocean Floor Is a Battery 558
14.6 Phototrophy 566
CHAPTER 15
Biosynthesis ................................................................................................................ 581
15.1 Overview of Biosynthesis 582
15.2 CO2 Fixation: The Calvin Cycle and Other Pathways 586
15.3 Fatty Acids and Antibiotics 594
Special Topic 15.1: Mining Bacterial Genomes for Antibiotics 600
15.4 Nitrogen Fixation and Regulation 602
15.5 Amino Acids and Nitrogenous Bases 608
CHAPTER 16
Food and Industrial Microbiology ........................................................................ 617
16.1 Microbial Foods 618
16.2 Acid- and Alkali-Fermented Foods 623
16.3 Ethanolic Fermentation: Bread and Wine 629
16.4 Food Spoilage and Preservation 633
16.5 Industrial Microbiology 643
Special Topic 16.1: Microbial Vitamins for Sale 644
16.6 Microbial Gene Vectors for Plants and Human Gene Therapy 652
PART 4
Microbial Diversity and Ecology
CHAPTER 17
Origins and Evolution............................................................................................... 659
17.1 Origins of Life 660
17.2 Forming the First Cells 669
17.3 Evolution: Phylogeny and Gene Transfer 673
17.4 Natural Selection and Adaptation 681
Special Topic 17.1: A Giant Petri Dish and the Race to Resistance 682
17.5 Microbial Species and Taxonomy 690
17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts 694
CHAPTER 18
Bacterial Diversity ..................................................................................................... 701
18.1 Bacterial Diversity at a Glance 702
18.2 Cyanobacteria: Oxygenic Phototrophs 708
18.3 Firmicutes, Tenericutes, and Actinobacteria (Gram-Positive) 714
Special Topic 18.1: Gut Bacterial Hair Balls 720
18.4 Proteobacteria (Gram-Negative) 726
18.5 Spirochetes, Acidobacteria, Bacteroidetes, and Chlorobi (Deep-Branching Gram-Negative) 738
18.6 Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC Superphylum) 741
CHAPTER 19
Archaeal Diversity ..................................................................................................... 747
19.1 Archaeal Diversity at a Glance 748
19.2 TACK Hyperthermophiles Eat Sulfur 756
19.3 Thaumarchaeota: Ammonia Oxidizers and Animal Symbionts 763
19.4 Euryarchaeota: Methanogens from Gut to Globe 766
Special Topic 19.1: Methanogens for Dinner 772
19.5 Haloarchaea and Other Euryarchaeotes: Underground and Under Ocean 774
19.6 DPANN Symbionts, Altiarchaeales, and Asgard: Branch to Eukaryotes? 780
CHAPTER 20
Eukaryotic Diversity ................................................................................................. 785
20.1 Phylogeny of Eukaryotes 786
20.2 Fungi 793
Special Topic 20.1: Yeast: A Single-Celled Human Brain 796
20.3 Amebas and Slime Molds 805
20.4 Algae 808
20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans 815
20.6 Parasitic Protozoa 821
CHAPTER 21
Microbial Ecology ...................................................................................................... 827
21.1 Microbial Communities: Metagenomes and Single-Cell Sequencing 829
21.2 Functional Ecology 838
21.3 Symbiosis 845
Special Topic 21.1: Antarctic Lake Mats: Have Ecosystem, Will Travel 846
21.4 Animal Digestive Microbiomes 851
21.5 Marine and Freshwater Microbes 857
21.6 Soil and Plant Microbial Communities 867
CHAPTER 22
Element Cycles and Environmental Microbiology .........................................883
22.1 The Carbon Cycle and Climate Change 885
22.2 The Hydrologic Cycle and Wastewater Treatment 893
22.3 The Nitrogen Cycle 899
22.4 Sulfur, Phosphorus, and Metals 905
22.5 Our Built Environment 911
Special Topic 22.1: A Microbial Jungle: The Kitchen Sponge 914
22.6 Astrobiology 914
PART 5
Medicine and Immunology
5 mm
CHAPTER 23
The Human Microbiome and Innate Immunity ............................................... 921
23.1 The Human Microbiome 922
23.2 Benefits and Risks of Microbiota 931
23.3 Overview of the Immune System 936
Special Topic 23.1: Why Do Tattoos Last Forever? 940
23.4 Physical and Chemical Defenses against Infection 945
23.5 Innate Immunity: Surveillance, Cytokines, and Inflammation 949
23.6 Complement and Fever 957
CHAPTER 24
The Adaptive Immune Response .........................................................................963
24.1 Overview of Adaptive Immunity 964
24.2 Antibody Structure, Diversity, and Synthesis 970
24.3 T Cells Link Antibody and Cellular Immune Systems 982
24.4 Complement as Part of Adaptive Immunity 993
24.5 Gut Mucosal Immunity and the Microbiome 994
24.6 Immunization 997
24.7 Hypersensitivity and Autoimmunity 1001
Special Topic 24.1: A Monoclonal Magic Bullet for Ebola? 1002
CHAPTER 25
Pathogenesis ............................................................................................................ 1011
25.1 Host-pathogen Interactions 1012
25.2 Microbial Attachment: First Contact 1020
25.3 Toxins Subvert Host Functions 1025
Special Topic 25.1: Chronic Staph Infections Work with a NET 1028
25.4 Deploying Toxins and Effectors 1036
25.5 Surviving within the Host 1040
25.6 Tools Used to Probe Pathogenesis 1051
CHAPTER 26
Microbial Diseases ................................................................................................. 1057
26.1 Skin, Soft-Tissue, and Bone Infections 1059
26.2 Respiratory Tract Infections 1064
26.3 Gastrointestinal Tract Infections 1072
26.4 Genitourinary Tract Infections 1083
26.5 Cardiovascular and Systemic Infections 1092
Special Topic 26.1: How Neutrophils Ambush Staphylococcus aureus in a Lymph Node 1094
26.6 Central Nervous System Infections 1104
CHAPTER 27
Antimicrobial Therapy and Discovery ............................................................. 1115
27.1 Fundamentals of Antimicrobial Therapy 1116
27.2 Antibiotic Mechanisms of Action 1123
27.3 Challenges of Drug Resistance and Discovery 1135
Special Topic 27.1: Are Designer Antibodies the Next Antibiotics? 1146
27.4 Antiviral Agents 1147
27.5 Antifungal Agents 1153
CHAPTER 28
Clinical Microbiology and Epidemiology ........................................................ 1159
28.1 Clinical Specimen Collection and Handling 1160
28.2 Pathogen Identification by Culture and Phenotype 1166
28.3 Molecular and Serological Identification of Pathogens 1174
Special Topic 28.1: Next-Generation Diagnostics: CRISPR Launches a “Flare” 1180
28.4 Epidemiology 1187
28.5 Detecting Emerging Microbial Diseases 1193
APPENDIX
Reference and Review .............................................................................................. A-1
A.1 A Periodic Table of the Elements A-2
A.2 Chemical Functional Groups A-2
A.3 Amino Acids A-4
A.4 The Genetic Code A-5
A.5 Calculating the Standard Free Energy Change, ΔG⁰, of Chemical Reactions A-5
A.6 Generalized Cells A-6
A.7 Semipermeable Membranes A-6
A.8 The Eukaryotic Cell Cycle and Cell Division A-8
1.1 Rita Colwell: The Global Impact of Microbiology—An 9.7 There’s a Bacterial Genome Hidden in My Fruit Fly
Interview 10.1 Glucose Transport Alters cAMP Levels
1.2 Clifford W. Houston: From Aquatic Pathogens to 10.2 In Sporulation, Different Sigma Factors Are
Outer Space—An Interview Activated in the Mother Cell and Forespore
2.1 Confocal Microscopy 10.3 Virulence Gene Control by sRNA in Staphylococcus
2.2 Differential Interference Contrast Microscopy aureus
3.1 Isolation and Analysis of the Ribosome 10.4 Slipped-Strand Mispairing
3.2 Christine Jacobs-Wagner: The Thrill of Discovery in 11.1 Phage T4: The Classic Molecular Model
Molecular Microbiology—An Interview 11.2 The Filamentous Phage M13: Vaccines and
3.3 Senior Cells Make Drug-Resistant Tuberculosis Nanowires
4.1 Transport by Group Translocation: The 11.3 Poliovirus: (+) Strand RNA Virus: A Research Model
Phosphotransferase System for Non-Polio Enterovirus That May Cause Acute
4.2 Eukaryotes Transport Nutrients by Endocytosis Flaccid Myelitis
4.3 Sharks and Biofilms Don’t Mix 11.4 Hepatitis C: (+) Strand RNA Virus
4.4 Biofilm Quorum Sensing Triggers Antibiotic 12.1 Acid Survival: A Research Case Study
Resistance 12.2 Equilibrium Density Gradient Centrifugation
5.1 The Arrhenius Equation 12.3 Error Correction for Single-Molecule, Real-Time
5.2 It’s Raining Bacteria Sequencing
5.3 Membrane-Permeant Organic Acids Alter Cell pH 12.4 Site-Directed Mutagenesis Helps Us Probe Protein
Function
5.4 Signaling Virulence
12.5 Mapping Transcriptional Start Sites with RNAseq
5.5 Evolution in Aging Colonies
12.6 Green Fluorescent Proteins Track Cell Movements
5.6 Oligotrophs
in Biofilms
5.7 The Phenol Coefficient
12.7 Mapping the E. coli Interactome
6.1 How Did Viruses Originate?
12.8 DNA Vaccines
6.2 Virus to the Rescue
12.9 Gene Therapy and Gene Delivery Systems
6.3 West Nile Virus, an Emerging Pathogen
12.10 Directed Evolution through Phage Display
7.1 Trapping a Sliding Clamp Technology
7.2 Nucleoid Occlusion Factors and the Septal 12.11 DNA Shuffling Enables In Vitro Evolution
“Guillotine”
12.12 Bacteria “Learn” to Keep Time and Signal Danger
8.1 Building the Ribosome Machine
13.1 Genomic Analysis of Metabolism
8.2 Discovering the mRNA Ribosome-Binding Site
13.2 Pyruvate Dehydrogenase Connects Sugar
8.3 Stalking the Lone Ribosome Catabolism to the TCA Cycle
8.4 Unsticking Stuck Ribosomes: tmRNA and Protein 14.1 Environmental Regulation of the ETS
Tagging
14.2 Caroline Harwood: A Career in Bacterial
8.5 The Shifty Chaperone: GroEL-GroES Photosynthesis and Biodegradation—An Interview
8.6 Ubiquitination: A Ticket to the Proteasome 15.1 Dan Wozniak: Polymer Biosynthesis Makes a
9.1 Repair of UV Damage by Nucleotide Excision Repair Pathogenic Biofilm—An Interview
and Homologous Recombination 15.2 The Discovery of 14C
9.2 Homologous Recombination and RecA 15.3 Calvin Cycle Intermediates
9.3 Mapping Bacterial Chromosome Gene Position by 15.4 The 3-Hydroxypropionate Cycle
Conjugation
16.1 From Barley and Hops to Beer
9.4 F-Prime
16.2 Microbial Enzymes Make Money
9.5 How Nonreplicative and Replicative Transposons
16.3 Caterpillar Viruses Produce Commercial Products
Hop into New Locations
17.1 The RNA World: Clues for Modern Medicine
9.6 Integrons and Gene Capture
xvi
17.2 Phylogeny of a Shower Curtain Biofilm 25.1 Finding Virulence Genes: Signature-Tagged
17.3 Jump-Starting Evolution of a Hyperthermophilic Mutagenesis
Enzyme 25.2 Finding Virulence Genes: In Vivo Expression
17.4 Richard Lenski: Evolution in the Lab—An Interview Technologies
17.5 The Dichotomous Key 25.3 Caught in the Act: Streptococcus agalactiae Evolved
through Conjugation
17.6 Leaf-cutter Ants with Partner Fungi and Bacteria
25.4 Pilus Tip Proteins Tighten Their Grip
18.1 Karl Stetter: Adventures in Microbial Diversity Lead
to Products in Industry—An Interview 25.5 Normal G-Factor Control of Adenylate Cyclase
18.2 Carbon Monoxide: Food for Bacteria? 25.6 Diphtheria Toxin
19.1 Haloarchaea in the Classroom 25.7 Identifying New Microbial Toxins
19.2 Archaeoglobus Partly Reverses Methanogenesis 25.8 Type VI Secretion: Poison Darts
20.1 Oomycetes: Lethal Parasites That Resemble Fungi 26.1 Human Papillomavirus
20.2 A Ciliate Model for Human Aging 26.2 The Respiratory Tract Pathogen Bordetella Binds to
Lung Cilia
20.3 The Trypanosome: A Shape-Shifting Killer
26.3 Case History: Blastomycosis
21.1 Mapping Bermuda Phytoplankton
26.4 The Common Cold versus Influenza
21.2 Cold-Seep Ecosystems
26.5 Sprouts and Emerging Escherichia coli
22.1 Bioremediation of Weapons Waste
26.6 Intracellular Biofilm Pods Are Reservoirs of Infection
22.2 Metal Contamination and Bioremediation
26.7 Human Immunodeficiency Virus: Pathogenesis
22.3 Subterranean Arsenic Bioremoval
26.8 Atherosclerosis and Coronary Artery Disease
23.1 Are NETs a Cause of Lupus?
26.9 Spongiform Encephalopathies
23.2 Do Defensins Help Determine Species Specificity
for Infection? 27.1 Antibiotic Spectrum of Activity
23.3 Cathelicidins 27.2 Antibiotic Biosynthesis Pathways
24.1 The “Bubble Boy” 27.3 Anti-Quorum Sensing Drug Blocks Pathogen
“Control and Command”
24.2 Factors That Influence Immunogenicity
27.4 Resurrection, Analysis and Treatment of the 1918
24.3 ABO Blood Groups: Antigens, Antibodies, and Karl
Pandemic Flu Virus
Landsteiner
28.1 API Reactions and Generating a Microbe ID Code
24.4 How T Cells Meet B Cells in Lymph Nodes
28.2 DNA-Based Detection Tests
24.5 MHC Restriction, Organ Donation, and Transplant
Rejection 28.3 Microbial Pathogen Detection Gets Wired Up
24.6 Microbiota Minimize Inflammation 28.4 Whipple’s Disease
24.7 Do Vaccines Stimulate Cell-Mediated Immunity? 28.5 What’s Blowing in the Wind?
24.8 Case Studies in Hypersensitivity 28.6 SARS: An Epidemiological Success Story
xvii
M
icrobiology: An Evolving Science is the defining core text of our generation—
the book that inspires undergraduate science majors to embrace the
microbial world. This Fifth Edition expands our focus on the intestinal
microbiome—including remarkable new discoveries of the gut-brain axis,
how our microbial communities may modulate brain function. We also present a new
breathtaking view of marine microbiology. We highlight marine discoveries, from the
molecular basis of the tiniest phototrophs to the global expanse of our ocean ecosys-
tem, including the crucial roles of marine microbes in climate change.
Our new coauthor, Erik Zinser, presents a fresh take on microbial genetics
(Chapters 7–10 and 12). For example, we show how certain bacteria expanded their
genetic code to include new amino acids. Our discussion of posttranslational protein
modifications has been expanded to include protein glycosylation in gut microbes
and the use of mass spectrometry to identify posttranslational protein modifications.
A new section (Section 7.6) presents advances in analyzing genomes, transcriptomes,
and proteomes through current research on human gut microbiomes and marine
microbiomes.
This Fifth Edition maintains our signature balance between cutting-edge ecology
and medicine, including the use of case histories in the medical section (Part 5). Our
balanced depiction of women and minority scientists, including young researchers,
continues to draw enthusiastic responses from our adopters. Our focus on evolution,
along with our modern organization of topics, has set the standard that other text-
books follow. Unlike other texts, we maintain our consistent chapter organization to
facilitate year-to-year course transitions for instructors.
In many chapters we relate topics to current events, to keep students interested
in and informed on the role of microbiology in the world today. One example is the
invention of microbial fuel cells that use environmental microbes to generate elec-
tricity (Chapter 14, Electron Flow in Organotrophy, Lithotrophy, and Phototrophy).
Another example is the development of lentiviral treatments for cancer and inherited
disorders, including the landmark FDA approval of CAR-T therapy for pediatric leu-
kemia (presented in Chapter 11, Viral Molecular Biology; and in Chapter 16, Food
and Industrial Microbiology).
The Fifth Edition continues our vision of this text as a community project, draw-
ing not only on the authors’ experience as researchers and educators, but also on the
input of hundreds of colleagues from around the world to create a comprehensive
microbiology book for the twenty-first century. We present the full story of molecu-
lar microbiology and microbial ecology from its classical history of Koch, Pasteur,
and Winogradsky right up to the research of twenty-first-century researchers Stanley
Falkow and Ariane Briegel. We have included countless contributions recommended
by colleagues from around the globe, at institutions such as Washington University;
University of California, Davis; University of Wisconsin–Madison; Cornell Univer-
sity; Florida State University; University of Toronto; University of Edinburgh; Uni-
versity of Antwerp; Seoul National University; Chinese University of Hong Kong;
and many more. We are grateful to you all.
Major Features
Our book targets the science major in biology, microbiology, or biochemistry. Several
important features make it the best text available for undergraduates today:
Updated and restructured coverage of microbial genetics and genomics. New
author Erik Zinser brings his experience as an active teacher and researcher to capture
how these central topics are being studied by microbiologists today. Chapters 7–10
and 12 have been comprehensively updated to reflect the current state of the field
and thoughtfully restructured to improve pedagogy and the flow of topics.
Themes of discovery: marine microbiology and our intestinal microbiome. The
Fifth Edition features new content on two exciting and relevant themes. One is the
new theme of marine microbiology, an exciting area of research that features cutting-
edge approaches such as metagenomics and single-cell whole-genome sequencing to
investigate how microbes contribute to the vast ocean ecosystem. And for the popu-
lar theme of the gut microbiome, new examples have been added throughout the
Fifth Edition, connecting engaging examples to important concepts in medical and
ecological microbiology. Icons in the margin make it easy to locate examples of each
theme, such as:
■ In Chapter 21, research by Olivia Mason (Pacific Northwest National Laboratory,
U.S. Department of Energy) that assessed marine microbes following the 2010
Deepwater Horizon oil well blowout in the Gulf of Mexico. Mason’s research
analyzed metagenomes to reveal which marine microbes had the ability to
degrade petroleum. These findings suggest the potential for bioremediation of
oil spills.
■ In Chapter 13, research by James Versalovic (Baylor University) and colleagues
that explored whether gut bacteria might regulate function in the brain. Their
research showed that certain gut bacteria had a probiotic effect to suppress the
activity of pain sensory neurons in rats.
A new mini-interview at the start of each chapter, offering a total of twenty-eight
new perspectives from cutting-edge researchers. Examples include:
Organization
The topics in this book are arranged so that students can progressively develop an
understanding of microbiology from key concepts and research tools. The chapters
of Part 1 present key foundational topics: history, visualization, the bacterial cell,
microbial growth and control, and virology.
The six chapters in Part 1 present many topics that are then developed in further
detail throughout Parts 2 through 5. Part 2 presents modern genetics and genom-
ics. Part 3 presents cell metabolism and biochemistry, although the chapters in Part 3
are written in such a way that they can be presented before the genetics material if
so desired. Part 4 explores microbial ecology and diversity and discusses the roles of
microbial communities in local ecosystems and global cycling. And then the chap-
ters of Part 5 (Chapters 23–28) present medical and disease microbiology from an
investigative perspective, founded on the principles of genetics, metabolism, and
microbial ecology.
CHAPTER 9: Genetic Change and Genome Evolution. The chapter has been exten-
sively reorganized and revised, as indicated by the revised chapter title. The main
topics are mutations in the genome, DNA repair and recombination, horizontal gene
transfer, and mobile genetic elements. The final section examines genome evolu-
tion. The revised introduction of Section 9.3, on gene transfer, will help students
better understand gene transfer mechanisms as survival tools and in an evolution-
ary context. The discussion on transformation notes that it has now been observed
in archaea. Vibrio cholerae and its type IV pilus is used as a new detailed example of
transformation. The intestinal microbiome is used as a detailed example of multiple
gene transfer mechanisms operating in a complex environment. The discussion of
CRISPR function has been revised to improve pedagogy and includes a new figure
(Figure 9.29). New material is included on conjugative transposons and mobilizable
genetic islands in archaea and bacteria, including an example in V. cholerae. There is
new material on the use of transposable elements in genetic analysis, including exam-
ples of mutagenesis to investigate purple antimicrobial molecules made by the marine
bacterium Phaeobacter and TnSeq high-throughput screening of the gut bacterium
Bacteroides. There are new figures and text on gene duplication. Also included is
an expanded explanation of genome reduction with new figures illustrating gene
loss and a new example in Pelagibacter. The discussion of horizontal gene transfer
has been reorganized so that the process is described first and then the evidence is
explained. A new figure (Figure 9.43) helps clarify how scientists identify genome
islands within chromosomes.
CHAPTER 10: Molecular Regulation. The chapter opener reveals another fascinating
observation about our gut microbiome: Some enteric bacteria have melatonin recep-
tors and exhibit circadian behavior in response to host melatonin levels. The chap-
ter organization is different from that in the previous edition. Traditional repressors
and activators of transcription are covered first, followed by a section on sigma fac-
tors, anti-sigma factors, and anti-anti-sigma factors. Regulation of transcription and
translation by RNA is next. Section 10.5 presents new information and examples of
control by circadian cycles, RNA thermometers, and DNA switches. The chapter
closes with a look at bacterial chemotaxis as an example of posttranslational control
of proteins. The Special Topic box introduces the mobile genetic elements known as
inteins. An intein is a fragment within a protein that inactivates protein function but,
when given the appropriate signal, will excise itself and splice the remaining protein
back together, thus activating the protein’s function.
CHAPTER 11: Viral Molecular Biology. The chapter opener captures the measles
virus as it assembles its genome within a host cell. New imaging reveals the influ-
enza virus replicating in its host cells. Transmission electron microscopy and fluores-
cence microscopy were used to show the replication process. Updated information
is presented on the inhibitory mechanisms of host cell protein APOBEC3G against
HIV. The description of how HIV integrates into the host genome has been updated
to reflect recent discoveries. Section 11.4 expands the presentation of human gene
therapy using viral vectors. The new Special Topic box discusses a controversial set of
experiments that tested which mutations could transform an avian influenza strain
into a “pandemic” strain.
CHAPTER 12: Biotechniques and Synthetic Biology. The chapter opener presents
an image of the Mona Lisa “painted” in E. coli. The image illustrates the ability
of scientists to control the swimming speed, and hence density, of a population of
E. coli with varying amounts of light. This chapter has been greatly revised. Mate-
rial previously in Chapters 7 and 8 has been moved into this chapter, including DNA
isolation and purification, restriction endonucleases, PCR, DNA sequencing, and
annotation of DNA sequences. There is a new example of quantitative PCR used to
early oxidation-reduction reactions has been expanded. The new Special Topic box
describes a vivid demonstration of natural selection in a giant (2 feet × 4 feet) Petri
dish. Section 17.4 has been updated with new data on antibiotic resistance formation
and new results from Richard Lenski’s Long-Term Evolution Experiment.
CHAPTER 18: Bacterial Diversity. The chapter opener introduces ectosymbiotic bac-
teria that live attached to marine nematodes. These very long bacteria include the
longest bacteria known to divide by classic Z-ring constriction. The phylogenetic
tree of bacteria (now Figure 18.1) has been updated to include genomic data from
over 1,000 uncultivated and little-known organisms sequenced by the latest meth-
ods. Section 18.1 and Table 18.1, which summarize bacterial diversity, have been
revised to reflect our latest understanding of bacterial phylogenetic groupings. The
Special Topic box on the human gut microbiome has been updated with recent data
from 2018.
CHAPTER 19: Archaeal Diversity. The chapter opener presents structural evidence
that the hyperthermophilic Ignicoccus hospitalis has an archaeal endomembrane sys-
tem. Archaeal phylogeny has been updated to incorporate the latest discoveries from
metagenomic and single-cell analysis. The chapter is organized to reflect the lat-
est groupings of archaeal organisms, such as the recent TACK and DPANN super-
phyla. New discoveries are included, such as the aerobic Aigarchaeota phylum and
the strictly anaerobic Halanaeroarchaeum. The Special Topic box has been updated
with recent work showing that administering probiotics reduces the abundance of
Methanobrevibacter in the gut microbiome and consequently reduces flatulence. Sec-
tion 19.6 introduces the Altiarchaeum, with its pilus-like grappling hooks, and pres-
ents the Asgard superphylum, which some scientists speculate may be closely related
to the early Eukarya.
CHAPTER 20: Eukaryotic Diversity. The eukaryotic diversity chapter opens with the
disturbing phenomenon known as coral bleaching. Warming temperatures melt the
photosynthetic membranes of Symbiodinium, the dinoflagellate symbiont found in
coral. Without the ability to photosynthesize, the microbes are expelled and the coral
subsequently dies. This topic is taken up again in Section 20.5 (see Figure 20.36).
In Table 20.1, Figure 20.4, and throughout the chapter, names and groupings
of eukaryotic clades reflect our current knowledge based on genome sequencing,
protein phylogeny, and genetic analysis. The Special Topic box on Saccharomyces
cerevisiae has been updated to include some of the final research performed by the
late Susan Lindquist and her colleagues on “humanized” yeast cells as a model of
beta-amyloid metabolism.
CHAPTER 21: Microbial Ecology. This chapter expands on what we are learning by
sequencing metagenomes from a wide variety of microbial communities. The chap-
ter opener describes a recently discovered microbial endosymbiont, Pantoea car-
bekii, found in the gut of a stinkbug. The explanation of performing a metagenome
sequencing project has been extensively updated. Additional methods for analyzing
microbial communities, such as metatranscriptomics, single-cell sequencing, flow
cytometry, and fluorescence-activated cell sorting are discussed. Numerous new soil,
ocean, and gut examples of microbial communities analyzed by these methods are
presented (see examples throughout the chapter). Section 21.2, on functional ecol-
ogy, presents a bacterium that can hydrolyze polyester, Ideonella sakaiensis, isolated
from soil at a bottle-recycling factory. The Special Topic box on cyanobacterial mats
in Antarctic lakes has been updated with recent data.
CHAPTER 22: Element Cycles and Environmental Microbiology. The new chapter
title reveals this chapter’s greater emphasis on the roles of environmental microbiolo-
gists. The chapter includes new information on climate change and on the human
It was after ten o’clock that evening when Margate returned to the
Clayton residence. He entered with a key by the way of the side door. A
glance at the windows while approaching the stately mansion told him that
most of the household were abed.
Margate hung his cap in the side hall and smoothed with his palms his
neatly plastered hair, effectively hiding the scar caused by Chick Carter’s
bullet many months before. He observed that a dim light was burning in the
library. Upon stepping quietly into the main hall, moreover, he discovered
the new butler.
Peterson was nodding sleepily in a chair near the main stairway. He
started slightly upon hearing the other, then quickly arose, rubbing his eyes
and bowing respectfully.
“You need not have waited for me, Peterson,” Margate said pleasantly,
pausing and regarding him intently.
“It’s the doors, sir,” said Peterson, explaining.
“The doors?”
“It has been my custom, Mr. Garside, sir, to be sure they are locked
before going to bed. I do not mind waiting up, sir.”
“I met a friend and remained longer than I intended,” said Margate,
smiling.
“I do not mind, sir,” repeated the butler.
“That’s very good of you. Has Mr. Clayton retired?”
“He has, Mr. Garside, sir.”
“How long did the detective remain here, Peterson?”
“About half an hour, sir, as I remember.”
“Did he bring any good news?”
“I cannot say, sir.”
“I thought that Mr. Clayton might, perhaps, have mentioned something to
you,” Margate observed, in an explanatory way.
“He did not, Mr. Garside, sir,” said Peterson humbly.
“I see there is a light in the library.”
“I left it for you, Mr. Garside, sir,” Peterson explained. “I thought you
might not wish to retire at once, sir, when you came in.”
“That was very thoughtful, Peterson, I’m sure, but I shall presently do so.
By the way, Peterson, I may be busy in my room to-morrow morning, in
case Mr. Clayton gives me any work to be done at that time,” Margate
added, steadily regarding his hearer. “There is something you can do for
me.”
“I will be very glad to do it, Mr. Garside, sir,” said Peterson, bowing
obsequiously.
“Very good. If Mr. Carter calls during the morning, I wish you would
quietly come to my room and inform me. There are a few questions I wish to
ask him about a personal matter—a purely personal matter, Peterson, I
assure you.”
“Yes, Mr. Garside, sir.”
Peterson’s ruddy face appeared incapable of any material change.
“Will you quietly do so?”
“I will, Mr. Garside, sir.”
“Thank you, Peterson. You are a very accommodating fellow. By the way,
here is something for which I have no great use,” Margate added, producing
a bank note and slipping it into the butler’s hand. “Favor me by accepting
it.”
Peterson smiled now, and appeared pleased.
“Thank you, Mr. Garside, sir,” he said, with some feeling. “Thank you
very much, sir.”
“There is more, Peterson, where that came from,” Margate remarked
significantly.
“I hope so, sir,” smiled Peterson. “I am glad to hear it, sir.”
“Any service you can do for me, Peterson, will always be well repaid.”
“No doubt, sir. Really, sir, I have not a doubt of it,” Peterson vouchsafed.
“By the way, what about Madame Clayton this evening?” questioned
Margate, still pausing at the base of the stairs.
“She is just the same, Mr. Garside, sir,” said Peterson, at once serious and
solemn again.
“That’s too bad.”
“Too bad, sir, indeed.”
“The nurse is with her to-night?”
“Yes, Mr. Garside, sir.”
“Favor me, Peterson, by tapping on the door and asking her to step into
the hall. She gave me a prescription to be filled. I have done so and wish to
hand it to her,” said Margate, displaying a vial wrapped in white paper. “I
wish to say a word to her about it, something the druggist mentioned.”
“I will call her, sir,” bowed Peterson.
“One moment.”
“Yes, sir.”
“Are you coming downstairs again?”
“Only to put out the lights, sir, and look after the doors.”
“Do so before you go up, then,” said Margate. “That will save you the
trouble of returning.”
“Very well, sir,” bowed Peterson. “Thank you, sir.”
Margate waited at the base of the stairs. There was a sinister gleam in his
eyes, a cruel smile on his lips. He thought he had rightly sized up the butler.
He felt reasonably sure that he could, if occasion required it, rely upon
Peterson for almost any service for which he was liberally paid.
Peterson returned in about five minutes, and they went upstairs together.
The butler extinguished the hall light, leaving the lower floor of the house
in darkness.
A dim light burned on the second floor.
Peterson tapped lightly on the door of a side chamber. It brought the
nurse into the hall—a slender girl in the twenties, with thin features, reddish
hair, and shifty gray eyes. She nodded and smiled, with a quick glance at the
private secretary.
“Thank you, Peterson,” Margate said quietly. “That’s all, my good fellow.
You may go up to bed. I will turn out the light in this hall for you.”
“Very well, sir,” bowed Peterson, evidently unsuspicious. “Thank you, sir.
Good night, miss. Good night, sir.”
“Good night, Peterson.”
The butler turned away and vanished up the servants’ stairway.
Margate took the hands of the nurse, slipping the vial into one of them,
and for five minutes he remained in whispered conversation with her, giving
her such instructions as served his purpose. Then he extinguished the hall
light and went to his room.
Half an hour passed.
The silence in the crime-cursed house was unbroken.
Its gloom was relieved only by a faint thread of light under the door of
the chamber in which Madame Clayton was lying.
Then, for the hundredth part of a second, a swift gleam appeared on the
servants’ stairway. It shot downward, danced for an instant over the stairs
and wall, then vanished.
It appeared again in about a minute. It lingered for several seconds. A
figure was vaguely discernible in the gloom back of the swiftly moving ray,
a figure stealing noiselessly down the stairs—that of Peterson, the house
butler.
He crept down as silently as a shadow, as if he was far from being a
novice in such stealthy work.
He stole to the door of Madame Clayton’s chamber, crouching there in
the darkness, and peered through the keyhole.
He could see the form of the unconscious woman lying on the bed.
He saw, too, that of the nurse bending above her, watching her intently,
with an empty hypodermic syringe in her hand.
“Just in time,” thought Peterson. “Too late to prevent it, but not too late to
see what has been done. That may serve as well.”
He stole away as he had come, but not to return to his room. He remained
crouching near the top of the servants’ stairway, waiting patiently in the inky
darkness, minute after minute, until a tall, old-fashioned clock in the lower
hall struck one.
Then a beam of light from another quarter dispelled the gloom.
Margate stole out of his chamber and crept down the front stairs.
The nurse stepped into the hall and waited, holding a bundle of garments
under her arm.
Margate returned in about three minutes in company with two men—
Dunbar and Haley.
Peterson sat watching them from the top of the stairs.
He saw them enter the room, all three men, from which they presently
emerged with a heavy burden—the senseless woman.
Moving noiselessly, they bore her down the stairs and out of the house.
Peterson started up to follow them, then resumed his seat on the top stair.
His way was barred and pursuit precluded by the nurse, still lingering in
the dimly lighted hall.
CHAPTER VIII.
Nick Carter was called early to the Clayton residence the following
morning. He was summoned by a frantic telephone call from Chester
Clayton, informing him what had occurred the previous night, or what he
supposed had occurred, and Nick lost no time in responding, in company
with Danny Maloney.
It was about seven o’clock when his touring car sped up the driveway and
stopped under the porte-cochère.
“Wait here, Danny,” said Nick, springing out.
Peterson admitted him, looking more serious and solemn than ever.
“This way, Mr. Carter, sir,” he said, while Margate also approached
through the hall to greet him. “Mr. Clayton is waiting for you in the library.”
Nick followed him and shook hands with Margate, then posing as boldly
as ever in the assumed character of the private secretary.
“This is terrible business, Carter, terrible,” he said, with subdued
earnestness, while they paused for a few seconds in the hall. “We are literally
overwhelmed, all of us.”
“Clayton told me only that his mother is missing and that the nurse has
fled,” Nick replied. “Is nothing more known, Garside, of the
circumstances?”
“Only what is contained in a note left by the nurse.”
“What does that state?”
“Merely that she fell asleep about two o’clock and did not awaken until
after three,” Margate earnestly reported. “She then found that Madame
Clayton was not in her room, also that some of her clothing was missing.
Terribly alarmed, yet fearing to arouse the house, she at once began a search
for her, hoping to find her and lead her back to her room. She found, instead,
that the side door of the house was open, and she then knew that Madame
Clayton must have gone out-of-doors.”
“The nurse left this information in writing?” Nick put in.
“Yes, in a hurriedly penciled letter,” Margate nodded. “She states that she
made a hurried search in the grounds, but could not find Madame Clayton,
and that she then returned to the house.”
“And then?”
“She then realized, evidently, that she had been very culpable and feared
the censure and punishment she had incurred,” Margate went on. “For she
adds that she did not dare to remain here, but was going to leave with what
clothing she could carry away. That’s all that her letter states, Carter, but it
seems to cover the ground.”
“I agree with you, Garside, as far as it goes,” said Nick, as gravely as if
he really meant it. “Who discovered their absence?”
“Peterson, the butler, when he came down from his room. He saw that the
door of Madame Clayton’s chamber was open, which is very unusual, and he
looked in and found that both women were missing. He then notified me,
Carter, and I aroused Mr. Clayton and his wife. Both are nearly
overwhelmed by the calamity.”
“No wonder. How long ago was this?”
“Less than half an hour. We notified you immediately.”
“I will have just a word with them,” said Nick.
“Command me in any way, Carter, if I can be of service,” Margate
artfully pleaded, briefly checking him.
“Presently,” Nick nodded. “I will see you again in a moment.”
He hastened into the library with the last, where he found both Clayton
and his wife, the latter in tears and both ghastly with consternation and
anxiety.
Nick said what he could to encourage them, at the same time hurriedly
inspecting the letter left by Martha Dryden, and he then observed that
Margate had followed him into the room. This was precisely what he had
anticipated—and wanted.
“What have you done, Clayton, beyond sending for me?” he abruptly
inquired.
“Nothing whatever,” Clayton declared, with a groan. “I’m all upset. I
know not what to do.”
“One thing must be done without delay, then, for a starter,” said Nick.
“We must try to trace the missing woman.”