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TH I R D ED ITI O N

Microbiology
An Evolving Science

Joan L. Slonczewski
Kenyon College

John W. Foster
University of South Alabama

Appendices 1 and 2 by
Kathy M. Gillen
Kenyon College

W. W. NORTON & COMPANY

NEW YORK LONDON
W. W. Norton & Company has been independent since its founding in 1923, when William Warder
Norton and Mary D. Herter Norton first published lectures delivered at the People’s Institute, the
adult education division of New York City’s Cooper Union. The firm soon expanded its program
beyond the Institute, publishing books by celebrated academics from America and abroad. By mid-
century, the two major pillars of Norton’s publishing program—trade books and college texts—
were firmly established. In the 1950s, the Norton family transferred control of the company to its
employees, and today—with a staff of four hundred and a comparable number of trade, college, and
professional titles published each year—W. W. Norton & Company stands as the largest and oldest
publishing house owned wholly by its employees.

Copyright © 2014, 2011, 2009 by W. W. Norton & Company, Inc.

All rights reserved.
Printed in the United States of America.
Third Edition

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123456789
 Dedication
We dedicate this Third Edition to the memory of Lynn Margulis
(1938–2011) and Carl Woese (1928–2012), who forever
changed our understanding of evolutionary biology. Margulis
hypothesized that modern-day eukaryotic cells evolved from
symbiotic relationships with bacteria; and Woese used the
evidence of gene sequences to propose the now accepted
paradigm of three, continually evolving, domains of life: Bacteria,
Archaea, and Eukarya. The world will long miss the deep intellect
and larger-than-life personalities of these two scientists. We, the
authors, were profoundly influenced by their thinking and deeply
moved by their passing.
BRIEF CONTENTS

eTopic Contents!xix PART 4

Preface!xxi
Microbial Diversity
About the Authors!xxxiii
and Ecology'662
PART 1 17 Origins and Evolution!665
18 Bacterial Diversity!711
The Microbial Cell'2 19 Archaeal Diversity!757
1 Microbial Life: Origin and Discovery!5
20 Eukaryotic Diversity!797
2 Observing the Microbial Cell!41
21 Microbial Ecology!839
3 Cell Structure and Function!79
22 Microbes in Global Elemental Cycles!889
4 Bacterial Culture, Growth, and
Development!119
5 Environmental Influences and Control PART 5
of Microbial Growth!157 Medicine and Immunology'922
6 Viruses!191
23 Human Microbiota and Innate Immunity!925
24 The Adaptive Immune Response!961
PART 2 25 Microbial Pathogenesis!1003
Genes and Genomes'234 26 Microbial Diseases!1051

7 Genomes and Chromosomes!237 27 Antimicrobial Therapy!1107

8 Transcription, Translation, 28 Clinical Microbiology and Epidemiology!1147

and Bioinformatics!275
9 Gene Transfer, Mutations, and Genome APPENDIX 1: Biological Molecules!A-1
Evolution!321 APPENDIX 2: Introductory Cell Biology:
10 Molecular Regulation!365 Eukaryotic Cells!A-23
11 Viral Molecular Biology!409 APPENDIX 3: Laboratory Methods for
Microbiology!A-43
12 Biotechniques and Synthetic Biology!457
APPENDIX 4: Taxonomy!A-59

PART 3 Answers to Thought Questions!AQ-1

Metabolism and Glossary!G-1

Biochemistry'488 Figure Credits!F-1

Index!I-1
13 Energetics and Catabolism!491
14 Electron Flow in Organotrophy, Lithotrophy,
and Phototrophy!539
15 Biosynthesis!585
16 Food and Industrial Microbiology!623

VI
 CONTENTS

eTopic Contents!xix
Preface!xxi
About the Authors!xxxiii

PART 1
The Microbial Cell 2
AN INTERVIEW WITH RICHARD LENSKI:
Evolution in the Lab

CHAPTER 1
Microbial Life: Origin and Discovery........................................................................ 5
1.1 From Germ to Genome: What Is a Microbe?!7
1.2 Microbes Shape Human History!10
Special Topic 1.1: How Did Life Originate?!18
1.3 Medical Microbiology!20
1.4 Microbial Ecology!26
1.5 The Microbial Family Tree!29
1.6 Cell Biology and the DNA Revolution!32

CHAPTER 2
Observing the Microbial Cell ....................................................................................41
2.1 Observing Microbes!42
2.2 Optics and Properties of Light!46
2.3 Bright-Field Microscopy!51
2.4 Fluorescence Microscopy!58
2.5 Dark-Field and Phase-Contrast Microscopy!63
2.6 Electron Microscopy and Tomography!66
2.7 Visualizing Molecules!73
Special Topic 2.1: Molecular “Snapshots”: Chemical Imaging!74

VII
VIII ! CONTENTS

CHAPTER 3
Cell Structure and Function .....................................................................................79
3.1 The Bacterial Cell: An Overview!81
3.2 The Cell Membrane and Transport!86
3.3 The Cell Wall and Outer Layers!91
3.4 The Nucleoid, RNA, and Protein Synthesis!101
3.5 Cell Division!104
3.6 Cell Polarity and Aging!107
Special Topic 3.1: Senior Cells Make Drug-Resistant Tuberculosis!108
3.7 Specialized Structures!112

CHAPTER 4
Bacterial Culture, Growth, and Development ................................................. 119
4.1 Microbial Nutrition!120
4.2 Nutrient Uptake!127
4.3 Culturing Bacteria!133
4.4 Counting Bacteria!136
4.5 The Growth Cycle!139
4.6 Biofilms!145
Special Topic 4.1: Sharks and Biofilms Don’t Mix!146
4.7 Cell Differentiation!150

CHAPTER 5
Environmental Influences and Control of Microbial Growth ..................... 157
5.1 Environmental Limits on Growth!158
5.2 Adaptation to Temperature!160
Special Topic 5.1: It’s Raining Bacteria!163
5.3 Adaptation to Pressure!164
5.4 Water Activity and Salt!166
5.5 Adaptation to pH!167
5.6 Oxygen and Other Electron Acceptors!172
5.7 Nutrient Deprivation and Starvation!176
5.8 Physical, Chemical, and Biological Control of Microbes!178

CHAPTER 6
Viruses ........................................................................................................................... 191
6.1 What Is a Virus?!192
6.2 Virus Structure!198
6.3 Viral Genomes and Classification!203
6.4 Bacteriophage Replication!208
6.5 Animal and Plant Virus Replication!213
 CONTENTS ! IX

6.6 Culturing Viruses!221

Special Topic 6.1: The Good Viruses!226
6.7 Viral Ecology!226

PART 2
Genes and Genomes 234

AN INTERVIEW WITH CHRISTINE JACOBS-WAGNER:

The Thrill of Discovery in Molecular Microbiology

CHAPTER 7
Genomes and Chromosomes ................................................................................ 237
7.1 DNA: The Genetic Material!238
7.2 Genome Organization!240
7.3 DNA Replication!248
7.4 Plasmids!258
7.5 Eukaryotic Chromosomes!260
7.6 DNA Sequence Analysis!263
Special Topic 7.1: Where Have All the Bees Gone? Metagenomics, Pyrosequencing, and Nature!268

CHAPTER 8
Transcription, Translation, and Bioinformatics .............................................. 275
8.1 RNA Polymerases and Sigma Factors!276
8.2 Transcription of DNA to RNA!280
8.3 Translation of RNA to Protein!286
Special Topic 8.1: Stalking the Lone Ribosome!298
8.4 Protein Modification and Folding!303
8.5 Protein Degradation: Cleaning House!304
8.6 Secretion: Protein Traffic Control!306
8.7 Bioinformatics: Mining the Genomes!312

CHAPTER 9
Gene Transfer, Mutations, and Genome Evolution ....................................... 321
9.1 The Mosaic Nature of Genomes!322
9.2 Gene Transfer!322
Special Topic 9.1: There’s a Bacterial Genome Hidden in My Fruit Fly!330
X ! CONTENTS

9.3 Recombination!338
9.4 Mutations!341
9.5 DNA Repair!348
9.6 Mobile Genetic Elements!355
9.7 Genome Evolution!358

CHAPTER 10
Molecular Regulation ............................................................................................... 365
10.1 Regulating Gene Expression!366
10.2 Paradigm of the Lactose Operon!369
10.3 Other Systems of Operon Control!376
10.4 Sigma Factor Regulation!382
10.5 Regulatory RNAs!385
10.6 DNA Rearrangements: Phase Variation by Shifty Pathogens!389
10.7 Integrated Control Circuits!391
10.8 Quorum Sensing: Chemical Conversations!397
10.9 Transcriptomics and Proteomics!401
Special Topic 10.1: Networking with Nanotubes!402

CHAPTER 11
Viral Molecular Biology ...........................................................................................409
11.1 Phage T4: The Classic Molecular Model!410
11.2 Hepatitis C: (+) Strand RNA Virus!417
11.3 Influenza Virus: (–) Strand RNA Virus!424
11.4 Human Immunodeficiency Virus (HIV): Retrovirus!432
11.5 Herpes Simplex Virus: DNA Virus!443
Special Topic 11.1: Cytomegalovirus!448
11.6 Gene Therapy with Viruses!450

CHAPTER 12
Biotechniques and Synthetic Biology ................................................................ 457
12.1 Basic Tools of Biotech: A Research Case Study!458
12.2 Genetic Analyses!458
12.3 Classic Molecular Techniques!463
12.4 Viewing the Interactions and Movements of Proteins!471
12.5 Applied Biotechnology!474
12.6 Synthetic Biology: Biology by Design!477
Special Topic 12.1: Bacteria “Learn” to Keep Time and Signal Danger!478
 CONTENTS ! XI

PART 3
Metabolism and Biochemistry 488

AN INTERVIEW WITH DAN WOZNIAK:

Polymer Biosynthesis Makes a Pathogenic Biofilm

CHAPTER 13
Energetics and Catabolism .................................................................................... 491
13.1 Energy and Entropy for Life!494
13.2 Energy in Biochemical Reactions!498
13.3 Energy Carriers and Electron Transfer!501
Special Topic 13.1: Microbial Syntrophy Cleans Up Oil!502
13.4 Catabolism: The Microbial Buffet!510
13.5 Glucose Breakdown and Fermentation!516
13.6 The Tricarboxylic Acid (TCA) Cycle!527
13.7 Aromatic Pollutants!532

CHAPTER 14
Electron Flow in Organotrophy, Lithotrophy, and Phototrophy .............. 539
14.1 Electron Transport Systems!541
14.2 The Proton Motive Force!546
Special Topic 14.1: Testing the Chemiosmotic Theory!548
14.3 The Respiratory ETS and ATP Synthase!551
14.4 Anaerobic Respiration in Organotrophs!559
Special Topic 14.2: Bacterial Electric Power!562
14.5 Lithotrophy and Methanogenesis!563
14.6 Phototrophy!571

CHAPTER 15
Biosynthesis ................................................................................................................585
15.1 Overview of Biosynthesis!586
15.2 CO2 Fixation: The Calvin Cycle!589
15.3 CO2 Fixation: Diverse Pathways!597
15.4 Biosynthesis of Fatty Acids and Polyketides!601
15.5 Nitrogen Fixation!605
Special Topic 15.1: Mining a Bacterial Genome for Peptide Antibiotics!606
15.6 Biosynthesis of Amino Acids and Nitrogenous Bases!612
15.7 Biosynthesis of Tetrapyrroles!618
XII ! CONTENTS

CHAPTER 16
Food and Industrial Microbiology ........................................................................623
16.1 Microbes as Food!625
16.2 Fermented Foods: An Overview!627
16.3 Acid- and Alkali-Fermented Foods!629
16.4 Ethanolic Fermentation: Bread and Wine!637
16.5 Food Spoilage and Preservation!641
16.6 Industrial Microbiology!650
Special Topic 16.1: Companies Take On Tuberculosis!652
Special Topic 16.2: Microbial Enzymes Make Money!654

PART 4
Microbial Diversity and Ecology 662

AN INTERVIEW WITH NICOLE DUBILIER:

Marine Animals with Bacterial Symbionts

CHAPTER 17
Origins and Evolution............................................................................................... 665
17.1 Origins of Life!667
17.2 Early Metabolism!676
17.3 Microbial Phylogeny and Gene Transfer!681
Special Topic 17.1: Phylogeny of a Shower Curtain Biofilm!686
17.4 Adaptive Evolution!692
17.5 Microbial Species and Taxonomy!696
Special Topic 17.2: Jump-Starting Evolution of a Hyperthermophilic Enzyme!698
17.6 Symbiosis and the Origin of Mitochondria and Chloroplasts!703

CHAPTER 18
Bacterial Diversity ..................................................................................................... 711
18.1 Bacterial Diversity at a Glance!712
18.2 Cyanobacteria: Oxygenic Phototrophs!718
18.3 Firmicutes and Actinobacteria (Gram-Positive)!723
18.4 Proteobacteria (Gram-Negative)!734
Special Topic 18.1: Carbon Monoxide: Food for Bacteria?!738
18.5 Deep-Branching Gram-Negative Phyla!748
18.6 Spirochetes: Sheathed Spiral Cells with Internalized Flagella!750
18.7 Chlamydiae, Planctomycetes, and Verrucomicrobia: Irregular Cells!752
 CONTENTS ! XIII

CHAPTER 19
Archaeal Diversity ..................................................................................................... 757
19.1 Archaeal Traits!758
19.2 Crenarchaeota across the Temperature Range!766
19.3 Thaumarchaeota: Symbionts and Ammonia Oxidizers!773
19.4 Methanogens!775
Special Topic 19.1: Eating Ammonia: Thaumarchaeotes!776
19.5 Haloarchaea!784
Special Topic 19.2: Haloarchaea in the Classroom!786
19.6 Thermophilic and Acidophilic Euryarchaeota!790
19.7 Deeply Branching Divisions!793

CHAPTER 20
Eukaryotic Diversity ................................................................................................. 797
20.1 Phylogeny of Eukaryotes!798
20.2 Fungi!806
Special Topic 20.1: Yeast: A Single-Celled Human Brain?!810
20.3 Algae!818
20.4 Amebas and Slime Molds!824
20.5 Alveolates: Ciliates, Dinoflagellates, and Apicomplexans!827
20.6 Trypanosomes and Metamonads!833
Special Topic 20.2: The Trypanosome: A Shape-Shifting Killer!834

CHAPTER 21
Microbial Ecology ...................................................................................................... 839
21.1 Metagenomes—and Beyond!841
21.2 Functional Ecology!849
21.3 Symbiosis!852
21.4 Marine and Aquatic Microbes!857
Special Topic 21.1: Cleaning Up the Deepwater Oil Spill!858
21.5 Soil and Subsurface Microbes!869
21.6 Plant Microbial Communities!876
21.7 Animal Microbial Communities!882

CHAPTER 22
Microbes in Global Elemental Cycles .................................................................889
22.1 Biogeochemical Cycles!890
22.2 The Carbon Cycle and Bioremediation!894
22.3 The Hydrologic Cycle and Wastewater Treatment!896
Special Topic 22.1: Bioremediation of Weapons Waste!902
22.4 The Nitrogen Cycle!903
22.5 Sulfur, Phosphorus, and Metals!908
22.6 Astrobiology!916
XIV ! CONTENTS

PART 5
Medicine and Immunology 922

AN INTERVIEW WITH FERRIC FANG:

Molecular Microbiology Dissects a Pathogen

CHAPTER 23
Human Microbiota and Innate Immunity........................................................... 925
23.1 Human Microbiota: Location and Shifting Composition!926
23.2 Risks and Benefits of Microbiota!934
23.3 Overview of the Immune System!935
Special Topic 23.1: Are NETs a Cause of Lupus?!940
23.4 Barbarians at the Gate: Innate Host Defenses!943
23.5 The Acute Inflammatory Response!946
23.6 How Phagocytes Detect and Kill Microbes!950
23.7 Interferon, Natural Killer Cells, and Toll-like Receptors!953
23.8 Complement’s Role in Innate Immunity!955
23.9 Fever!958

CHAPTER 24
The Adaptive Immune Response ......................................................................... 961
24.1 Overview of Adaptive Immunity!962
24.2 Immunogenicity!965
24.3 Antibody Structure and Diversity!968
24.4 Primary and Secondary Antibody Responses!974
24.5 Genetics of Antibody Production!977
24.6 T Cells Link Antibody and Cellular Immune Systems!982
24.7 Complement as Part of Adaptive Immunity!992
Special Topic 24.1: An Uneasy Peace: Détente at the Microbiota-Intestine Interface!994
24.8 Hypersensitivity and Autoimmunity!995

CHAPTER 25
Microbial Pathogenesis ........................................................................................ 1003
25.1 Host-Pathogen Interactions!1004
25.2 Virulence Factors and Pathogenicity Islands!1010
25.3 Microbial Attachment: First Contact!1013
25.4 Toxins Subvert Host Function!1018
 CONTENTS ! XV

25.5 Deploying Toxins and Effectors!1028

25.6 Surviving within the Host!1033
Special Topic 25.1: Type VI Secretion: Poison Darts!1034
25.7 Experimental Tools That Define Pathogenesis!1045

CHAPTER 26
Microbial Diseases ................................................................................................. 1051
26.1 Characterizing and Diagnosing Microbial Diseases!1052
26.2 Skin and Soft-Tissue Infections!1054
26.3 Respiratory Tract Infections!1058
26.4 Gastrointestinal Tract Infections!1066
Special Topic 26.1: Sprouts and an Emerging Escherichia coli!1068
26.5 Genitourinary Tract Infections!1075
26.6 Central Nervous System Infections!1083
26.7 Cardiovascular System Infections!1090
26.8 Systemic Infections!1094
26.9 Immunization!1102

CHAPTER 27
Antimicrobial Therapy .......................................................................................... 1107
27.1 The Golden Age of Antibiotic Discovery!1108
27.2 Fundamentals of Antimicrobial Therapy!1111
27.3 Measuring Drug Susceptibility!1112
27.4 Mechanisms of Action!1116
27.5 Challenges of Drug Resistance!1126
27.6 The Future of Drug Discovery!1134
27.7 Antiviral Agents!1135
Special Topic 27.1: Anti-Quorum Sensing Drug Blocks Pathogen “Control and Command”!1136
Special Topic 27.2: Resurrecting the 1918 Pandemic Flu Virus!1139
27.8 Antifungal Agents!1142

CHAPTER 28
Clinical Microbiology and Epidemiology .........................................................1147
28.1 Principles of Clinical Microbiology!1148
28.2 Specimen Collection and Processing!1149
28.3 Conventional Approaches to Pathogen Identification!1152
28.4 Rapid Techniques for Pathogen Identification!1160
28.5 Point-of-Care Rapid Diagnostics!1167
28.6 Biosafety Containment Procedures!1169
28.7 Principles of Epidemiology!1171
Special Topic 28.1: What’s Blowing in the Wind?!1178
28.8 Detecting Emerging Microbial Diseases!1179
XVI ! CONTENTS

APPENDIX 1
Biological Molecules .................................................................................................. A-1
A1.1 Elements, Bonding, and Water!A-2
A1.2 Organic Molecules!A-6
A1.3 Proteins!A-8
A1.4 Carbohydrates!A-11
A1.5 Nucleic Acids!A-13
A1.6 Lipids!A-15
A1.7 Biological Chemistry!A-16
Special Topic A1.1: Calculating the Standard Free Energy Change, ∆G°, of Chemical Reactions!A-19

APPENDIX 2
Introductory Cell Biology: Eukaryotic Cells ................................................... A-23
A2.1 The Cell Membrane!A-24
A2.2 The Nucleus and Mitosis!A-31
A2.3 Problems Faced by Large Cells!A-34
A2.4 The Endomembrane System!A-34
A2.5 The Cytoskeleton!A-38
A2.6 Mitochondria and Chloroplasts!A-40

APPENDIX 3
Laboratory Methods for Microbiology ............................................................A-43
A3.1 Isolating Parts of Cells by Using an Ultracentrifuge!A-44
A3.2 Agarose Gel Electrophoresis!A-45
A3.3 Protein Identification on 2D Gels with Mass Spectrometry!A-47
A3.4 RNA and DNA Identification by Northern and Southern Blots!A-49
A3.5 Sanger Method of DNA Sequencing!A-51
A3.6 Gene Fusions Identify Regulatory Mutants!A-52
A3.7 Primer Extension Identifies Transcriptional Start Sites!A-52
A3.8 DNA Microarray!A-54
A3.9 Multiplex PCR!A-55
A3.10 Fluorescence In Situ Hybridization (FISH) and CARD-FISH!A-55
A3.11 Immunoprecipitation Techniques!A-57

APPENDIX 4
Taxonomy ................................................................................................................... A-59
A4.1 Viruses!A-60
A4.2 Bacteria!A-62
A4.3 Archaea!A-66
A4.4 Eukarya!A-68

Answers to Thought Questions!AQ-1

Glossary!G-1
Figure Credits!F-1
Index!I-1
 eTOPIC CONTENTS
Access to the eTopics is available through both the ebook and the Norton Coursepack.

1.1 An Interview with Rita Colwell: The Global Impact 10.5 The Phage Lambda Lysis/Lysogeny “Decision”
of Microbiology Is to Kill or Not to Kill
1.2 Discovering the Genetic Code 11.1 Poliovirus: (+) Strand RNA
1.3 Clifford W. Houston: From Aquatic Pathogens 11.2 The Filamentous Phage M13: Vaccines
to Outer Space—An Interview and Nanowires
2.1 Confocal Microscopy 11.3 Genetic Resistance to HIV
3.1 Isolation and Analysis of the Ribosome 12.1 Mapping the E. coli Interactome
3.2 How Antibiotics Cross the Outer Membrane 12.2 GFP Proteins Track Cell Movements in Biofilms
3.3 Outer Membrane Proteins: Isolation for Vaccine 12.3 DNA Vaccines
3.4 Experiments That Reveal the Bacterial Cytoskeleton 12.4 Gene Therapy and Gene Delivery Systems
4.1 Transport by Group Translocation: 12.5 Directed Evolution through Phage Display
The Phosphotransferase System Technology
4.2 Eukaryotes Transport Nutrients by Endocytosis 12.6 DNA Shuffling Enables In Vitro Evolution
4.3 Biofilms, Antibiotics, Garlic, and Disease 12.7 Site-Directed Mutagenesis Helps Us Probe Protein
5.1 The Arrhenius Equation Function
5.2 Some Alkaliphilic Enzymes Produce Useful Drug 13.1 Observing Energy Carriers in Living Cells
Delivery Systems 13.2 Swiss Cheese: A Product of Bacterial Catabolism
5.3 Signaling Virulence 13.3 Genomic Analysis of Metabolism
5.4 Oligotrophs 13.4 Pyruvate Dehydrogenase Connects Sugar
6.1 How Did Viruses Originate? Catabolism to the TCA Cycle
6.2 West Nile Virus, an Emerging Pathogen 13.5 Genetic Analysis of Aromatic Catabolism
7.1 Genes and Proteins Involved in DNA Replication 14.1 Caroline Harwood: A Career in Bacterial
Photosynthesis and Biodegradation: An Interview
7.2 Trapping a Sliding Clamp
14.2 Measuring Dy and DpH in Microbes by the Uptake
7.3 Replication Mechanisms of Bacteriophages
of Molecules
7.4 Plasmid Partitioning and Addiction
14.3 Environmental Regulation of the ETS
7.5 Equilibrium Density Gradient Centrifugation
14.4 ATP Synthesis at High pH
8.1 Building the Ribosome Machine
15.1 The Discovery of 14C
8.2 Discovering the mRNA Ribosome-Binding Site
15.2 Metagenomic Screening for Polyketide Drugs
8.3 Ubiquitination: A Ticket to the Proteasome
15.3 Antibiotic Factories: Modular Biosynthesis
8.4 What Is the Minimal Genome? of Vancomycin
9.1 F Pili and Biofilm Formation 15.4 Riboswitch Regulation
9.2 Mapping Bacterial Chromosome Gene Position 16.1 From Barley and Hops to Beer
by Conjugation
16.2 Caterpillar Viruses Produce Commercial Products
9.3 Deinococcus Uses RecA to Repair Fragmented
17.1 The RNA World: Clues for Modern Medicine
Chromosomes
17.2 Horizontal Gene Transfer in E. coli O157:H7
9.4 Mutation Rate
17.3 Leaf-cutter Ants with Partner Fungi and Bacteria
9.5 The Transposase for a Bacterial Transposon
Resembles the Integrase for HIV-1 18.1 Karl Stetter: Adventures in Microbial Diversity Lead
to Products in Industry
9.6 Integrons and Gene Capture
20.1 Oomycetes: Lethal Parasites That Resemble Fungi
10.1 CRP Interactions with RNA Polymerase
and CRP-Dependent Promoters 20.2 A Ciliate Model for Human Aging
10.2 Glucose Transport Alters cAMP Levels 21.1 Mapping Bermuda Phytoplankton
10.3 Slipped-Strand Mispairing 21.2 Cold-Seep Ecosystems
10.4 Toxin-Antitoxin Modules: Mechanisms 22.1 Wetlands: Disappearing Microbial Ecosystems
for Self-preservation or Altruism? 22.2 Metal Contamination and Bioremediation

XVII
XVIII ! ETOPIC CONTENTS

23.1 Microbes as Vaccine Delivery Systems 26.1 Sequenced Genomes of Pathogens

23.2 Do Defensins Help Determine Species Specificity 26.2 Human Papillomavirus
for Infection? 26.3 The Respiratory Tract Pathogen Bordetella Binds
23.3 Cathelicidins to Lung Cilia
24.1 Factors That Influence Immunogenicity 26.4 The Common Cold versus Influenza
24.2 ABO Blood Groups: Antigens, Antibodies, 26.5 Intracellular Biofilm Pods Are Reservoirs of Infection
and Karl Landsteiner 26.6 Human Immunodeficiency Virus: Pathogenesis
24.3 Organ Donation and Transplant Rejection 26.7 Spongiform Encephalopathies
24.4 Case Studies in Hypersensitivity 26.8 Atherosclerosis and Coronary Artery Disease
25.1 Finding Virulence Genes: Signature-Tagged 27.1 Antibiotic Spectrum of Activity
Mutagenesis
27.2 Antibiotic Biosynthesis Pathways
25.2 Finding Virulence Genes: In Vivo Expression
27.3 Poking Holes with Nanotubes: A New Antibiotic
Technologies
Therapy
25.3 Caught in the Act: Streptococcus agalactiae Evolved
27.4 Critical Virulence Factors Found in the 1918 Strain
through Conjugation
of Influenza Virus
25.4 Pili Tip Proteins Tighten Their Grip
28.1 API Reactions and Generating a Seven-Digit Microbe
25.5 Normal G-Factor Control of Adenylate Cyclase Identification Code
25.6 Diphtheria Toxin 28.2 DNA-Based Detection Tests
25.7 Identifying New Microbial Toxins 28.3 Microbial Pathogen Detection Gets Wired Up
25.8 Bacterial Covert Operations: Secreted Shigella
Effector Proteins Jam Communications between
Target Cells and Innate Immunity
 PREFACE

I
n the first two editions of Microbiology: An Evolving Science, we worked to write
the defining core text of our generation—the book that would inspire under-
graduate science majors to embrace the microbial world. Our emphasis on genet-
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In many chapters, we relate topics to current events, to keep students interested
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ple is the use of of viral replication cycles to develop lentiviral treatments for cancer
and inherited disorders, including the first possible “cure” for pediatric leukemia
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Our Third Edition continues as a community project, drawing on our experi-
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We are grateful to you all.

XIX
XX ! PREFACE

While we have expanded and developed new topics, we also recognized the need
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rial they taught from the Second Edition, but now they also have new topics on Myco-
bacterium tuberculosis cell aging and drug resistance (Chapter 3) and on bacteria that
convert phage genes into toxin secretion systems (Chapter 25), and many more.

Major Features
Our book targets the science major in biology, microbiology, or biochemistry. Sev-
eral important features make our book the best text available for undergraduates
today:
! New research on contemporary themes such as evolution, genomics, meta-
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Ample Thought Questions throughout every chapter challenge students to think
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ple, Chapter 1 introduces historical figures such as Koch and Pasteur alongside
genome sequencer Claire Fraser-Liggett and young microbial ecologist Kazem
Kashefi growing a hyperthermophile in an autoclave, and undergraduate students
conducting transcriptomics in E. coli. Medical microbiology is presented using the
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and microbial diseases.
! An innovative media package provides powerful tools for instructors and stu-
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Another Random Scribd Document
with Unrelated Content
 and to the end of his life, notwithstanding his increasing
weakness, they were able to enjoy together peaceful visits to
relatives in Switzerland and Italy. It was on their way home from
one of these visits, that George Butler died in London on March
14th, 1890. Two years later Josephine Butler published her
Recollections of George Butler, from which we have already
quoted so much, and from which we must now make one more
quotation.

We read in the Gospels that the disciples of Christ found themselves

one dark evening separated from the Master, “in the midst of the
sea”; that He saw them from the shore “toiling in rowing, for the
wind was contrary.” Such is sometimes the position, spiritually and
morally, of one who has up to a certain point “fought a good fight
and kept the faith,” but against whom arise contrary winds and
buffeting waves; one for whom “fightings without and fears within”
have proved too severe, and who is now “toiling in rowing,” with
faint heart and gloomy outlook—the presence of the Master no
longer realised to reassure and guide. “Old Satan is too strong for
young Melancthon,” said one of the reformers of the sixteenth
century, and the same enemy has proved many a time since then
too strong for much humbler workers. The problems of life at times
appear so perplexing as to be incapable of any solution. The lines of
good and evil, of right and wrong, light and darkness, appear
blurred; and the weak and burdened spirit loses the hold it had
retained hitherto of the highest standard, fidelity to which alone can
bring us again out of darkness and trouble into light and hope.
Moses for the hardness of the people’s hearts allowed a relaxation of
the severity of the original law given from on high, and so suffered
the moral standard to be lowered in some of the most important
relations of life. There was a time when it seemed to me that hearts
are harder now than even in the old days, and when the stern ethics
of Christ—the divine standard—seemed to become impossible as a
matter of practical enforcement. Horribly perplexed, I was tempted
to give up the perfect ideal. It is in this way, I think, through lack of
faith, that compromises creep in among us—compromises with error,
with sin, with wrong-doing, unbelief taking root first in the individual
soul, and then gradually spreading until a lower standard is accepted
in family life, in society, in legislation, and in Government. And at
last, as even in our own land, we may see publicly endorsed and
signed what the Hebrew prophet calls “a covenant with death” and
an “agreement with hell.” Such an acceptance and public
endorsement of a compromise with evil proclaims the failure of faith
of a whole nation, and the beginning of a “downgrade,” in which
virtue is regarded as no longer possible for man.
To speak of clouded moments of one’s own life involves no small
effort. But in justice both to my husband and to the movement I
have tried to serve I am impelled to do so. There are some people
who, if they remember at all that moral uprising against national
unrighteousness in which we took part, still regard it as an illusion,
and its advocacy as a “fad,” or even as a blot on an otherwise
inoffensive career—something which must always require
explanation or apology. But there are others who understood from
the first its true meaning and far-reaching issues, and who have
perhaps imagined that an unbroken consistency of action, based on
an immovable strength of conviction, must at all times have
characterised any man or woman destined to take a representative
part in it. A sense of justice forces me to confess that the fact (in
regard to myself) was not always as they imagined; for there was a
time when I resembled the faint-hearted though loyal disciple, who,
when venturing to walk on the waters, in an evil moment looked
away from Christ and around upon the weltering, unstable floor on
which he stood, and immediately began to sink. When moreover the
sense of justice of which I speak regards one who was and is dear
to me as my own soul, then I am doubly forced to speak, and to
give “honour to whom honour is due” by telling of the wisdom which
God gave him in encouraging and supporting through a few troubled
years the tried and wavering advocate of a cause in which both faith
and courage were put to a severe test.
A deeply-rooted faith—a personal, and not merely a traditional faith
—in the central truths of Christ, and moral strength, the fruit of that
faith, were in him united with other qualities which were needful for
the task he so well fulfilled. Others whom I have known—teachers
and fathers in God—have had this moral and spiritual faith in a high
degree, together with an eloquence and power in argument to which
he had no pretension. But few—it seemed to me at least—possessed
such patience as he had, such long-suffering, such a power of silent
waiting, such a dignified reserve, and such a strong respect for
individuality as to forbid all probing of inner wounds, or questioning
of motive or action, even in the case of one so near to him as
myself. He had great delicacy and refinement in dealing with the
bitterness or petulance of a soul in trouble. He had great faith in his
fellow-creatures. And these, together with his unfailing love, like the
sun in the heavens surmounting the hours of cold and darkness,
gradually overcame the mists which had wrapped themselves round
the heart and obscured the spiritual vision of her for whom he never
ceased to pray.
At this time his voice, when simply reading the words of Christ at
family prayers, used to sound in my ears with a strange and
wonderful pathos, which pierced the depths of rebellious or
despairing thought. At times his attitude—probably unconsciously to
himself—assumed in my eyes an unaccustomed and almost awful
sternness. Sometimes my unrest of mind found vent in words of
bitterness (which however only skimmed the surface of the inward
trouble), and I waited for him to speak. Then he seemed to rise
before me to a stature far above my level, above that of other men,
and even above his own at other times, while he gently led me back
to great first principles and to the Source of all Truth, presenting to
me, in a way which I could sometimes hardly bear, the perfection
and severity of the law of God, and our own duty in patient
obedience and perseverance, even when the ascent is steepest, and
the road darkest and longest. He very seldom gave me direct
personal advice or warning. He simply stood there before me in the
light of God, truthful, upright, single-minded; and all that had been
distorted or wrong in me was rebuked by that attitude alone; and a
kind of prophetic sense of returning peace, rather than actual peace,
entered my soul, and my heart replied, “Where you stand now,
beloved, I shall also stand again one day, perhaps soon, on firm
ground, and in the light of God.” And my soul bowed in reverence
before him, although never could he bear any outward expression of
that reverence. It seemed to hurt him. He would gently turn away
from it. He spoke firmly when he differed from any doubtful
sentiment expressed or argument used. His simple “no,” or “I think
you are wrong,” were at times more powerful to me, than the most
awful pulpit denunciation or argumentative demonstration of my
error could have been; and then, even if he condemned, his love
and reverence never failed.
He knew the Psalms almost by heart, and the inspired words which
he always had so ready were more potent for me, when spoken by
him, than any other thing. His religion, and his method of consoling,
were not of a subtle or philosophical kind; and he was all the better
a comforter to me because he did not—perhaps could not—easily
enter into and follow all the windings of my confused thinkings and
doubtings and revolted feelings. Strong swimmer as he was, I felt in
my half-drowned state his firm grasp, and his powerful stroke upon
the waters as we neared the land; and when by his aid my feet
stood once more upon the solid rock, I understood the full force of
the grateful acknowledgment of the Psalmist, “Thou hast kept my
feet from falling, and mine eyes from tears.”
I have not up till now dwelt upon the wrongs and sorrows which we
were forced deliberately to look upon and measure, nor shall I do
so. Could I do so, my readers would not wonder at any suffering or
distress of brain caused by such a subject of contemplation. Dante
tells us that when, in his dream, he entered the Inferno and met its
sights and sounds, he fell prone “as one dead.” I once replied to a
friend, who complained of my using strong expressions and asked
the meaning of them, as follows: “Hell hath opened her mouth. I
stand in the near presence of the powers of evil. What I see and
hear are the smoke of the pit, the violence of the torture inflicted by
man on his fellows, the cries of lost spirits, the wail of the murdered
innocents, and the laughter of demons.” But these, it will be said,
are mere figures of speech. So they are, used purposely to cover—
for no words can adequately express—the reality which they
symbolise. But the reality is there, not in any dream or poetic vision
of woe, but present on this earth; hidden away, for the most part,
from the virtuous and the happy, but not from the eyes of God.
Turning from the contemplation of such unspeakable woes and
depths of moral turpitude, it was a strength and comfort beyond
description, through the years of strife, to look upon the calm face of
my best earthly friend. It was a peace-imparting influence. And now
that I walk alone and look only at his portrait, even that seems to
take me into the presence of God, where he now dwells among the
“spirits of just men made perfect,” and to whisper hope of the
approaching solution of the great mystery of sin and pain.
I often recall an incident, which occurred at Winchester in the
cathedral, a trifle in itself, but which dwells in my memory as an
illustration of the help he gave to me spiritually in time of need. It
was during the service on Sunday. I suddenly felt faint, the effect of
a week of unusual effort and hard work. Wishing not to disturb
anyone or make a scene, I took the opportunity, when all heads
were bowed in prayer, to creep down from the stalls as silently as
possible, past the tomb of William Rufus, and down the choir,
holding on when possible by the carved woodwork of the seats. A
moment more, and I should have dropped. I could scarcely steady
my steps, and my sight failed, when suddenly there passed a flash
of light, as it seemed, before my eyes, something as white as snow
and as soft as an angel’s wing; it enveloped me, and I felt myself
held up by a strong, loving arm, and supported through the nave to
the west door, where the cool summer breeze restored me. It was
my husband. He was in his own seat near the entrance to the nave,
and his quick ear had caught the sound of my footstep. Quite
noiselessly he left his seat and took me in his arms, unobserved by
anyone. The flash of light (the angel’s wing) was the quick
movement of the wide sleeve of his fine linen surplice, upon which
the sun shone as he drew me towards him.
 CHAPTER XIV.
INDIA.

Josephine Butler’s constant advocacy of Women’s Suffrage is

illustrated by the following short speech given at a conference in
the City Temple on July 20th, 1891.

I told your chairman that I would come forward just to tell you that I
cannot say anything. Still perhaps I may be able to put one little
thought before you. I am sorry that fear and timidity are growing up
again, and that a fresh conspiracy of silence threatens us.
God gives us a phraseology, a pure and chaste and holy indignation,
which makes it possible for us to go to the bottom of these things
without offending the chastest ear. For twenty-one years I have
worked with my dear fellow-workers in a public manner against
these hateful laws, which one of the resolutions pronounced and
which I pronounce as accursed. During these twenty-one years there
was one thing which made our battle harder than it would have
been. We have had to fight outside the Constitution. We have been
knocking at the door of the Constitution all these years, and there
are men who even now tell me that they would give us anything in
the way of justice except the parliamentary vote. We have been
talking about certain Members of Parliament who are not fit to
occupy that position. Give the women a vote, and see what will be
the result. In all my work my one strength has been the strength of
the Almighty, sought and won by constant prayer; and the prayer
which I now offer in my secret chamber is that the veil may be taken
away, and the selfishness—the perhaps unconscious selfishness—
may be removed from the hearts of men who deny women equality,
and keep them outside the Constitution. Think what we could do in
the cause of morality, think of the pain and trouble and martyrdom
that we might be saved in the future, if we had that little piece of
justice.

The same question is dealt with in a letter written in the

following year to a meeting in London of the World’s Women’s
Christian Temperance Union.

We may pray and we may preach about these things, and we may
raise our voices to some little extent during the excitement of a
contested election; but that is not enough. My friends, we must have
the suffrage. It is our right, and it is cruel, and a continued injustice,
to withhold it from us. It has lately been said that the women
generally of the country have not shown any desire for the suffrage.
Some years ago I can assert that the women of the country showed
a very great desire for it. Men do not know that at the bottom of
that desire, underneath many other good motives, there lies a
bitterness of woe which is the most powerful stimulus towards the
desire for representation in the Legislature. I am sometimes afraid
that one of these days some other terrible injustice may be enacted
in Parliament through which women will again suffer as they did
under those laws I have alluded to. Perhaps it might not be an
altogether bad thing, if it caused women to utter once more the
bitter cry to which none of our legislators could pretend to be deaf.
But have we not, as it is, sufficient trouble, and misery, and
degradation among our own sex to make us utter even now the
bitter cry—a cry however at the same time of hope, courage and
confidence?

In June, 1893, Josephine Butler published The Present Aspect of

the Abolitionist Cause in relation to British India: a letter “giving
a recital illustrative of the truth that a golden thread of Divine
guidance runs throughout the lives and work of those who give
themselves to the cause of truth, leading them out of every
labyrinth of difficulty towards the goal at which they aim.” She
tells how information having been received from various sources
that the Regulation System had been continued in several of the
 Indian Cantonments, notwithstanding the repeal of the
Contagious Diseases Act in 1888, and official denial having been
made of the allegations to this effect, the British Branch of the
Federation decided to make a thorough investigation of the
actual state of affairs, which was carried out in the early part of
1892 by two American ladies, members of the World’s Women’s
Christian Temperance Union, Mrs. Andrew and Dr. Kate Bushnell.

The wonderful manner in which Providence answered our wish and

prayer to find suitable instruments for so serious an investigation I
shall now relate. In the year 1878 I was staying with my sister,
Madame Meuricoffre at her country home on the borders of the Lake
of Geneva. One exquisite summer evening we sat together, with
another friend, on the shore of the lake. The water and the snow-
capped mountains were lighted up with gorgeous tints of rose and
amber from the setting sun. In such an hour of calm repose it is
sometimes granted to us to see with greater clearness the past, the
present and the future of God’s dealings with us, and of any work to
which we have been called. My mind had long been troubled by the
thought of the growing and gigantic nature of the Abolitionist work
in the various countries of the world, and of the need and lack of
women workers. I knew that women must always continue to be at
the heart and in the forefront of the work in order to ensure success.
I saw around me hundreds of true and faithful women whose hearts
were deeply stirred on the question. But where were those, I asked,
who would form the powerful phalanx needed for the one object of
continued attack on and resistance to that masterpiece of Satan,
official or State recognised and regulated prostitution?
These thoughts I expressed to my sister and my friend. It was one
of those moments in which, whether in sadness or perplexity, or
passive waiting for light, it is sometimes given to us to realise, as
with the disciples at Emmaus, that “Jesus Himself drew nigh.” We
were asking ourselves: “Whence shall this army of women come?
Where shall we find them? What will be the sign of their fitness for
this work?” We sat some time in silence; and then I recollect there
came to me one of those moments of re-assurance and hope, which
are sometimes granted during such silence of the soul. I somewhat
dimly recall now that there came before my mind’s eye a host of
women presenting themselves from different quarters of the globe,
speaking different languages, and possessing various gifts, but all
having the special call and the necessary qualifications for this great
conflict. It reminded me of the incident recorded in Swiss history,
during one of Switzerland’s brave struggles in defence of her
freedom; that occasion, I mean, when a great white mist covering
the mountains in the early morning rolled upwards, and disclosed to
the astonished gaze of the invading army entrenched in the valley a
long procession of angels, clad in white, descending the mountain
side; an apparition which so alarmed the enemy that it is said they
lost nerve, turned, and were defeated. This was but a stratagem
devised by a number of shrewd peasant women, inhabitants of the
mountain villages, who dressed themselves in white and slowly
descended the mountain, thus working upon the superstitious fears
of the enemy. So the white-robed army appeared to my mental
vision on this occasion. The mists cleared away, and the hosts were
descending to the plains to engage in this great spiritual conflict. It
was one of those mental pictures which do not fade, a prophetic
thought, the fulfilment of which I have been led to remark year by
year as noble women of different lands have from time to time
appeared just as they were wanted in this cause. Since then I have
not doubted as to the advent of the women workers who would be
needed in great crises, and especially when the physical forces of
the pioneers become exhausted and they must contemplate passing
on and leaving the work to other hands. I shall give in the unstudied
language in which Dr. Kate Bushnell and Mrs. Elizabeth Andrew
recounted it to me, their own narrative of their call to this work. Dr.
Kate Bushnell writes:—
“One hot summer day, while searching my Bible for light, I turned
first as by accident to Joseph’s dream. As it did not interest me, and
seemed inapplicable to my need, I turned the pages quickly, and my
attention was next arrested by the account of Belshazzar’s dream,
and Daniel’s interpretation. This seemed to me as foreign to my
expectations of help as the other, and turning the leaves over to the
Gospel of St. Matthew, I read there that ‘when Herod was dead,
behold an angel of the Lord appeared in a dream to Joseph in
Egypt.’ My feeling was that I had been baffled in my search for
consolation and help in the sacred pages. Being very weary, I threw
myself on my couch, thinking of the darkness of Egypt in my own
plans. I said to the Lord that I was so stupid in understanding His
guidance, that I thought He might have to send me the instructions
I needed through a dream, and to guide me at times as He did His
simple children of old. I fell asleep almost instantly, and dreamed
that I felt myself tossed on the billows of the Atlantic on my way to
England to see Josephine Butler.” [At this time we had never met nor
corresponded.—J.E.B.] “It became plain to me that she had
something for me to do. It was one of those brief, refreshing periods
of unconsciousness, from which I awoke almost instantly, but with a
strong impression that I must write to Mrs. Butler. This I did, telling
her that I came to her much under such an impulse as urged Peter
to go to Cornelius, and that I was deeply impressed that she could
counsel me as to my future course. She replied, giving me a brief
account of the situation in India, telling me that she and some of her
friends had been earnestly praying that God would raise up an
English-speaking woman to go to that country, and make careful
enquiry into the condition of things there, with a view to ridding that
conquered people of the oppressive tyranny and shame imposed
upon them by the Army authorities, who she had reason to fear had
never carried out the will of Parliament in abolishing the system of
regulation. This letter I showed to Mrs. Andrew, and we took counsel
together. Mrs. Butler had asked me to come over to England, if
possible, that we might talk face to face on this matter. Mrs. Andrew
was then on the eve of starting for England, and very soon after my
decision was taken to join her and to begin our world’s tour together,
taking in the special Indian work, if after full consultation with Mrs.
Butler this should seem advisable.”
 Similarly Mrs. Andrew told how she had received inspiration for
this special work from reading Mr. Stead’s Life of Josephine
Butler—when “the Spirit’s voice whispered to me, ‘You have not
worked, you have not loved as she has worked and loved.’” The
pamphlet proceeds to tell the story of these ladies’
investigations, and the wonderful way in which they touched the
hearts and won the confidence of the poor Indian women. They
found that all these women, “whether of high or of low caste,
Hindoo or Mohammedan, and of whatever nationality, whether
brought up in virtue and afterwards betrayed, or brought up
from infancy in vicious surroundings,” felt a deep sense of the
degradation of their position; and that “the fire of their hatred
and indignation all centred upon the heart of the regulations,
the examinations, and the violation of womanhood which these
examinations were felt to be.” Mrs. Andrew and Dr. Kate
Bushnell gave evidence before a Departmental Committee as to
the action of the Cantonment officials, and the truth of their
reports was amply substantiated by the further evidence which
the Committee obtained in India. The Report of this Committee
led to the passing, in 1895, of an Act which prohibited all
examination or registration of women in the Indian
Cantonments.

Josephine Butler in 1894 published The Lady of Shunem, a

series of Biblical studies, “addressed to fathers and mothers,
more especially to mothers.” We give three extracts from this
volume.

Is it not a thought, a fact which should wake up the whole Christian

world to a truer and clearer view of life as it is around us, that the
first record of a direct communication from Jehovah to a woman is
this of His meeting with the rejected Hagar, alone in the wilderness?
It was not with Sarah, the princess, or any other woman, but with
Hagar, the ill-used slave, that the God of Heaven stooped to
converse, and to whom He brought His supreme comfort and
guidance. This fact has been to me a strength and consolation in
confronting the most awful problem of earth, i.e. the setting apart
for destruction, age after age, of a vast multitude of women—of
those whom we dare to call lost—beyond all others lost—hopelessly
lost. We ourselves, by our utmost efforts, have only so far been able
to save a few, a mere handful among the multitude; and of the
others, unreached by any divinely-inspired human help, we are apt
to think with dark and dismal foreboding. We forget that though
they may be quite beyond the reach of our helping hands, they are
never beyond the reach of His hand—His, who “being put to death in
the flesh” was “quickened by the Spirit, by which also He went and
preached to the spirits in prison.”
Into the vilest prison-houses of earth (I believe) He descends alone
many a time, to save those souls buried out of the sight and ken of
His servants and ministers, even as He—He alone, unaccompanied
by any chosen ministers—descended into Hades and “preached the
Gospel also to those that are dead,” that they who have been
“judged according to men in the flesh” may “live according to God in
the Spirit.”

That God should permit evil seems to some minds as immoral as

that He should Himself create and dispense it. This portion of the
subject is surrounded with difficulty and mystery. It leads us back to
the great unanswered question concerning the origin of evil.
Nowhere would a dogmatic utterance of any kind be more out of
place and presumptuous than here.
The glimpses of truth, the broken lights which we possess
concerning the divine government of the world, come to us often as
a succession of paradoxes, among which however the humble seeker
finds at last the truth which satisfies the heart and fortifies the spirit,
if it does not seem exactly to fit in with our poor logic. God certainly
suffers His children, even His highest saints, to fall now and again
under the power of some of those evil things which we recognise as
having been introduced into the world as the attendants of sin and
death. He allows sickness to visit them. In the prolonging of such
visitations however He is, I believe, sometimes only patiently waiting
for the sufferer to claim deliverance; and it is frequently a long time
before His child recognises the fact that he may glorify God by giving
Him the opportunity of rebuking his disease as much as he is doing
by an unquestioning submission. “Wilt thou be made whole?” is
often His question to a sufferer, as to the cripple at the Pool of
Siloam, as if He would say, “I am ready to rebuke the oppressor and
to heal thee, when thou art ready to take this blessing.”
Those who are tempted to be angry with God for allowing
misfortunes and evils to fall upon us, or who meet these in a spirit
only of a sullen acquiescence, have not yet fully realised that it is
only through conflict and through trial of our integrity that we can
become in the highest sense sons and daughters of God. Christ
Himself was “made perfect through suffering.” There are persons
who seem to think that God could, if He pleased, by a single act of
His will, by a wave of His hand, cause all evil to cease out of the
universe this very day, this very hour. Whether He can do so or not is
beyond our power or province to know or to enquire. But it is
evident to one who studies humbly His Word and His Providence in
the light of His Spirit, that God has been pleased to submit Himself
for a season to a certain limitation of His power; and we may be
sure that this is for an end that will be much more excellent and
glorious than we can now conceive of, when the work of grace in the
salvation of the world is fully accomplished.
“He could not there do many mighty works, because of their
unbelief.” Here we have a clearly confessed limitation of His power,
while at the same time the words point to that blessed truth and
marvel of the appointed working together of God’s will and man’s
will, the union of the divine and the human for the fulfilment of His
loving purposes, and the final triumph of good over evil. If the above
words be true that “He could not,” is not the converse true also, that
He could, and that He can, do many mighty works because of the
faith He finds in man? It would seem that God needs the faith of
man as an allied spiritual agency, for the constant generating of the
force by which He will finally “subdue all things unto Himself,” when
the rebel power, the opposing will, will exist no more.
It is a wonderful and solemn thought that we, who believe in Him,
we fathers and mothers, who have the strongest of all human
motives to exercise the faith which He loves and approves, can
supply to our God the conditions which He has told us He needs,
and which He claims of us, in order to save not only our own
children, but whole generations to come, who shall be fellow-
workers with Him in bringing in the reign of righteousness on the
earth.

I thank God that I long ago got far beyond being taunted with
youth, and suspected of an enthusiasm which is a mere ardour of
the blood, untried by experience of life. The sweet visions of my
early youth, when I used to sit under the shade of the trees in my
father’s home, and read of the holy martyrs and dream of a golden
age, are nothing compared with the hope and enthusiasm which
God gives me now, and which He has continued to give me while
health failed, and some present hopes were blighted, and my way
began to be strewn with the graves of those I loved, and I trod the
lonely path of widowhood, and the world’s worst evils continued to
glare in my eyes. I have had sharp, deep wounds, and long conflict
of soul; but now ought not I, if anyone ought, to tell out the hopes
which God gives me, and to speak of the ever-widening horizon
which I see illumined by His redeeming love?
Return unto thy rest, O my soul;
For the Lord hath dealt bountifully with thee.
 The following paragraph is part of an interview given in Wings,
the official organ of the Women’s Total Abstinence Union,
January, 1895.

I have often had occasion, in the course of many years of arduous

work, again and again to meet groups of my fellow-workers,
especially on the Continent, who have confessed themselves
subjected to periods of deep depression and disappointment. Having
gone through the same experience myself, and having been driven
back upon God again and again, when everything seemed dark and
hopeless, He has taught me some precious lessons which I have
been called to impart sometimes to others. The central truth to
which I have learned to hold fast is this truth—that death must
precede resurrection; that in every cause which is truly God’s cause
failures and disappointments are not only familiar things, but even
necessary for the final success of the cause. It is the lesson of the
Cross. That scene on Calvary was for the moment, or seemed to be,
the wreck of all the hopes of the followers of Christ. The spirit of the
poor disciples walking on the road to Emmaus who said, “We trusted
that it had been He who should have redeemed Israel,” is a true
picture of the experience probably of every true reformer. But when
God has Himself led us into some of His secrets, and the inner
meaning of His providential guidings, we no longer despond; for we
come to know that it is a law in the Kingdom of Grace that death
must precede resurrection. “Except a corn of wheat fall into the
ground and die, it abideth alone; but if it die, it bringeth forth much
fruit.” For many years past therefore I have been able, by God’s
grace, not only to acquiesce in apparent failure time after time, but
even in a measure to rejoice, knowing that the way is thus being
prepared, both in our own hearts and in the outward circumstances,
for a more complete victory in the end.
 CHAPTER XV.
GENEVA.

A Doomed Iniquity was the title of a pamphlet issued by

Josephine Butler in 1896. It embodied an authoritative
condemnation of State Regulation of Vice from persons of very
different trains of thought, in France, Germany, and Belgium,
who regarded the question from various points of view—
scientific, political and religious—but all agreed in proclaiming
the complete failure and injustice of the system, “of which they
have had a far longer experience than we in England had.” The
first was from Dr. Charles Mauriac, who at one time strongly
defended the system, but had now published a book on the
hygienic aspect of the question, in which he declared that the
old coercive method was “breaking to pieces on all sides like a
worm-eaten building on the point of falling to ruin,” and
advocated a new method “which will emancipate woman from
the last remnants of slavery, and render her free, as men are, to
enter a hospital and to leave it without constraint whenever it
seems good to her.” The second was from Herr Bebel, the leader
of the Socialist party in Germany, who pointed out the failure,
cruelty and injustice of the system—a flagrant injustice which
was “only possible because it is men alone who govern and who
make the laws.” The third opinion was given in a memorial to
the Pope, from the Belgian Society of Public Morality, signed by
all the Catholic bishops of Belgium, and others including the
Prime Minister, praying his “Holiness to condemn, with an
authority which is recognised by the whole world, this system so
fatal to the well-being of souls, and so dangerous to the social
order.”
Herr Bebel’s statement had been written to a Swiss friend, for
use in the struggle at Geneva, referred to in the following
letters, when a blind popular vote endorsed the recognition by
the administration of “tolerated houses.” It is worth noting that
eleven years later the Federal High Court of Switzerland
pronounced the establishment of such houses in Geneva to be
illegal: “comme contraire aux bonnes mœurs,” adding, “le fait
qu’il serait autorisé par l’administration ne saurait lui enlever ce
caractère.”

To various friends.

Geneva, March 25th, 1896.

I have been called to witness a dark page in the history of
human life. It is pain to me to have to record it; but its lessons
are needful and solemn, and I wish I had a voice to reach to the
end of the civilised world, that those lessons might be heard.
How many years we have had the hard task imposed on us of
trying to show people—good people—the horrible principles
embodied in the State regulation of vice, and the results which
must necessarily follow—and they would not, will not believe us.
I must tell you first the dark side, and we must not shrink from
letting it be known far and wide; and then I will go back and
record the events of the last fortnight, among which you will
find many things which will make you glad, as they have made
us glad, in the midst of so much horror. Well you already know
the result of the Popular Vote. We had 4068 as against 8300—a
crushing defeat. But presently I must explain to you how the
people were misled by the Government; so that this cannot be
quite truly said to be the verdict of the people, though to all the
world it seems so. It will be and is a great triumph for our
adversaries everywhere. As M. Ador said (one of our friends in
the Grand Council), it is (he believed) the first time in the
history of the world when a moral question of such import has
been submitted to the verdict of the people, and their verdict is
in favour of continued legalised vice; and it is the first time that
the popular vote has been taken on the basis of the “Droit
d’Initiative,” a recent law in Switzerland from which much good
was expected.
The horrors revealed last week, and especially those of Sunday
night, have however so far exceeded the dismay caused by the
immense majority against us, that I must speak first of those.
And you will not wonder when I say that I am glad, as many
others are, that the gates of this Inferno were thrown open, and
that the results of a hundred years of Government organised
and protected vice have been for once fully revealed. In a
meeting on Monday of our gentlemen (who now number some
hundreds of really convinced and militant abolitionists) they
asked me some questions about our English battle, and in
answering I said, “Gentlemen, you are able to face the truth,
which is that Geneva is governed by the brothel keepers
(tenanciers). They are the masters of the city, the masters of
the situation. It is they, with their following, who have now
given a mandate to the Council of State and the Grand Council,
to strengthen their position, and to plant more firmly than ever
in your midst government by tenanciers.” They all agreed. “It is
true, it is true,” they cried. “It is of no use to disguise it.”
Sunday morning—the voting day—rose brilliantly, a blue sky
without a cloud, and the most brilliant sunshine. Mme. de
Gingins and I went to an early service in a Free Church, where
most of our friends go. They sent me a message to speak a few
words. (All scruples about women speaking in churches
vanished like a slight cloud before the midday sun in the
presence of such a solemn day for the people, when all the faith
and courage and patience of women were as much wanted as
those of men.) There was great life in that morning service, at
the end of which most of us had the Sacrament together, in
almost absolute silence. I should rather have liked that we had
all received it standing, with a drawn sword in one hand, as the
old crusaders did! The spirit of war however was there, as well
as the Master’s benediction: “My peace I give unto you.” On the
way home we elected to take a drive all round the city, Mme. de
Gingins and I in her carriage, which waited for us. The streets
were already (at 10 a.m.) very crowded, but the people were
quiet, it being so early. I looked with sympathy at the faces of
numbers of poor and honest-looking workmen, who seemed to
be anxious.
Oh, I never saw anything like the beauty of the Rhone that day,
rolling its magnificent waves and curling, dancing waters along
(the waters about which Ruskin has half a chapter of eloquent
description). The main colour is a clear sapphire blue, shading
off into sky blues, purples and pale rose colours, and flecked
with streaks of golden sunlight. Geneva is a beautiful city, and
the birds were singing, and the young leaves appearing on the
avenues of trees.
At 5 p.m. we went, by the invitation of M. Favre, to his house,
where he had invited all the leading abolitionists to assemble to
hear the result of the poll, and, if necessary, to stay all night—
sixty or seventy of us!—because it was well known if we had
had a victory the vengeance of the tenanciers’ mob would have
made it perilous for any of us to pass through the streets.
I shall never forget that memorable evening and night. M. Favre
is the most prominent man of Geneva, belonging to the old
nobility. His house is just a little removed from the town, on a
little rising ground whence you see all Geneva lying like a map
before you. It is one of the fortresses of the old nobles, before
the Reformation, and it was there that some hundreds of
Huguenot refugees from France were harboured by an ancestor
of M. Favre in the times of Louis XIV. There is a huge stone
archway by which you enter a great courtyard, whence stairs
ascend in the open air to different parts of the fortress. It is all
of solid rock and stone; no mob would have a chance to enter,
and here the refugees of March 22nd, 1896, were received.
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