Professional Documents
Culture Documents
Full Download PDF of (Ebook PDF) Brock Biology of Microorganisms 16th Edition All Chapter
Full Download PDF of (Ebook PDF) Brock Biology of Microorganisms 16th Edition All Chapter
http://ebooksecure.com/product/ebook-pdf-brock-biology-of-
microorganisms-14th-edition/
http://ebooksecure.com/product/ebook-pdf-brock-biology-of-
microorganisms-15th-edition/
http://ebooksecure.com/product/ebook-pdf-brock-biology-of-
microorganisms-global-edition-15th-edition/
http://ebooksecure.com/product/ebook-pdf-human-biology-16th-
edition-by-sylvia-mader/
Progress in Heterocyclic Chemistry Volume 29 1st
Edition - eBook PDF
https://ebooksecure.com/download/progress-in-heterocyclic-
chemistry-ebook-pdf/
http://ebooksecure.com/product/ebook-pdf-power-and-everyday-
practice-by-deborah-brock/
http://ebooksecure.com/product/ebook-pdf-translational-medicine-
in-cns-drug-development-volume-29/
http://ebooksecure.com/product/foundations-of-financial-
management-16th-edition-ebook-pdf/
https://ebooksecure.com/download/microorganisms-for-sustainable-
environment-and-health-ebook-pdf/
About the Authors
Michael T. Madigan received his B.S. in Biology and Education from Wisconsin State Univer-
sity–Stevens Point (1971) and his M.S. (1974) and Ph.D. (1976) in Bacteriology from the University
of Wisconsin–Madison in the laboratory of Thomas Brock. Following a postdoc at Indiana University
with Howard Gest, Mike moved to Southern Illinois University Carbondale, where he taught courses
in introductory microbiology and bacterial diversity as a professor of microbiology for 33 years. In
1988 Mike was selected as the Outstanding Teacher in the College of Science and in 1993, the Out-
standing Researcher. In 2001 he received the SIUC Outstanding Scholar Award and Distinguished
Professor title. In 2003 Mike received the Carski Award for Distinguished Undergraduate Teaching from
the American Society for Microbiology (ASM), and he is an elected Fellow of the American Academy
of Microbiology (ASM) and the American Association for the Advancement of Science (AAAS). He has
also been recognized by the American Red Cross as a major volunteer blood donor for the 24 gallons
of blood he has donated since 1967. Mike’s research is focused on phototrophic bacteria that inhabit
extreme environments, and for the past 20 years his emphasis has been Antarctic microbiology. Mike
has co-edited a major treatise on phototrophic bacteria and served for 10 years as chief editor of the
journal Archives of Microbiology. He currently serves on the editorial board of the journals Environmen-
tal Microbiology and Antonie van Leeuwenhoek. Mike’s other interests include forestry, swimming, reading,
and caring for his dogs and horses. He lives on a small farm near a quiet lake with his wife, Nancy,
three dogs (Kato, Nut, and Merlyn), and three horses (Eddie, Georgie, and Roscoe).
Kelly S. Bender received her B.S. in Biology from Southeast Missouri State University (1999)
and her Ph.D. (2003) in Molecular Biology, Microbiology, and Biochemistry from Southern Illinois
University Carbondale. Her dissertation research focused on the genetics of perchlorate-reducing bac-
teria. During her postdoctoral fellowship, Kelly worked on the genetic regulation of sulfate-reducing
bacteria in the laboratory of Judy Wall at the University of Missouri–Columbia. She also completed a
transatlantic biotechnology fellowship at Uppsala University in Sweden researching regulatory small
RNAs in bacteria. In 2006, Kelly returned to her alma mater, Southern Illinois University Carbondale,
as an Assistant Professor in the Department of Microbiology and in 2012 was tenured and promoted
to Associate Professor. She has served as Chair of the SIUC Department of Microbiology since 2018.
Her lab studies a range of topics including regulation in sulfate-reducing bacteria, the microbial com-
munity dynamics of sites impacted by acid mine drainage, and diversity of phototrophic heliobacteria.
Kelly teaches courses in introductory microbiology and microbial diversity, has served on numerous
federal grant review panels, and is an active member of the American Society for Microbiology (ASM).
Her other interests include spending time with her daughter, Violet, and husband, Dick.
Daniel H. Buckley is a Professor at Cornell University in the School of Integrative Plant Science
and the Department of Microbiology. He earned his B.S. in Microbiology (1994) at the University of
Rochester and his Ph.D. in Microbiology (2000) at Michigan State University. His graduate research in
the laboratory of Thomas M. Schmidt explored environmental factors that influence microbial diversity
in soils. Dan then received a National Science Foundation Postdoctoral Fellowship to work with Pieter
T. Visscher, University of Connecticut, investigating linkages between microbial diversity and biogeo-
chemistry within microbial mats and stromatolites. Dan moved to Cornell in 2003 where he investi-
gates the ecology and evolution of the diverse microorganisms that live in soils. He has taught both
introductory and advanced courses in microbiology, microbial diversity, and microbial genomics. He
received a National Science Foundation Faculty Early Career Development (CAREER) award in 2005
for excellence in integrating research and education, and served as Co-Director of the MBL Microbial
Diversity summer course in Woods Hole, Massachusetts (2009–2013). He currently serves on the edi-
torial boards of Applied and Environmental Microbiology and Environmental Microbiology. Dan lives in
Ithaca, New York, with his wife, Merry, and sons, Finn and Colin.
iii
x P R E FA C E
Chapter 18 Chapter 22
• Along with major updates on eukaryotic phylogeny, a new section • This chapter on the built environment shows how humans create
is devoted to the haptophytes, including the globally and ecologi- new microbial habitats through construction of buildings, sup-
cally important coccolithophore Emiliania huxleyi. Coccolitho- porting infrastructure, and habitat modification, and which
phores play a major role in regulating global climate, illustrating microbes take advantage of these habitats and why.
the power that microbes exert over our biosphere. • Some highlights: The microbial metabolism of biologically pro-
duced and manufactured chlorinated organics has been expanded,
UNIT 5 Microbial Ecology and as has the basis for the bioremediation of major chemical pollut-
ants. How microbes are responding to the mountains of plastics
Environmental Microbiology contaminating the environment and the discovery of novel bacte-
ria capable of degrading plastic bottles are described. New technol-
Chapter 19 ogy that improves the efficiency of wastewater treatment using
• The chapter begins a unit on ecology and environmental microbi- granular sludge technology is presented, and the microbial
ology. The modern tools of the microbial ecologist are described response to the excessive use of common household cleansers is
with examples of how each has helped sculpt the science. considered.
• Some highlights: A new method to visualize protein synthesis in
single cells allows study of microbial activity in the environment. Chapter 23
Metabolomics exploits new methods in mass spectrometry to • A chapter devoted to nonhuman microbial symbioses describes the
unravel the complex metabolic interactions sustaining microbial major microbial partners that live in symbiotic associations with
communities. Nanosensor technologies are revealing how other microbes, with plants, and with animals other than humans.
microbes alter the chemical landscape of three-dimensional sur- • Some highlights: Newly revised section on symbioses between
faces. A new section explores multi-omics, which combines mul- microorganisms addresses the ecological significance of phototroph
tiple state-of-the-art analytical tools to more fully characterize switching in lichens and how certain bacterial species use electri-
microbial communities. cally conductive structures to form intimate symbiotic associations.
Several updates include how insect symbionts are used to combat
Chapter 20 transmission of major viral diseases of humans and how defensive
• The properties and microbial diversity of major microbial ecosys- chemicals produced by symbionts protect insects from predation.
tems including soils and aquatic systems are compared and con- Detailed coverage is given to the elaborate “cross-talk” between
trasted in exciting ways. microbe and animal needed to establish the squid light organ.
• Some highlights: Expansive coverage of surface-attached micro-
bial communities and how those communities are responding
to plastic pollution of the environment. New understanding of UNIT 6 Microbe–Human Interactions
the ecology of iron-oxidizing bacteria revealed by the isolation and the Immune System
of new members of this biogeochemically significant group. The
discovery in deep ocean sediments of novel Archaea that link this Chapter 24
domain with Eukarya. Extensive coverage of marine viruses, their • A chapter on the human microbiome launches the unit on
abundance and diversity, and how they alter the physiology of microbe–human interactions and the immune system by introduc-
organisms they infect. Humans traveling to 10,000-meter depths ing and updating advances in our understanding of the microbes
in the oceans discover the most pressure-tolerant bacterium that inhabit the human body and their relationship to health and
known. disease.
• Some highlights: The discovery of ultrasmall bacteria in the mouth
Chapter 21
parasitizing other bacteria brings a new twist to the microbial ecol-
• Extensive coverage of the major nutrient cycles in nature and the ogy of the oral cavity. A new section on the human virome describes
microbes that catalyze them are presented in a fashion that allows how metagenomics is driving the discovery and isolation of inter-
the cycles to be taught as individual entities or as interrelated met- esting new viruses. Extensive coverage is devoted to the impact of
abolic loops. early-life events on the development of the newborn gut microbi-
• Some highlights: Expanded coverage of the biogeochemistry of ome and of recent successes in probiotic therapy for preventing
sulfur compounds highlights the importance of volatile microbial newborn intestinal diseases.
products such as dimethyl sulfide for cloud formation. Advances
in the biochemistry of extracellular electron transfer add new Chapter 25
understanding to how the ecology and diversity of microorganisms • Beginning with this chapter, the book shifts its focus to pathogenic
drive the biogeochemical cycling of iron and manganese. The mys- microorganisms, the immune system, and disease. Part I of this
tery of how methane is generated (typically a strictly anoxic pro- chapter addresses microbial adherence, colonization and invasion,
cess) in highly oxygenated ocean surface waters is solved by and pathogenicity, including important sections on virulence and
discoveries in the phosphorus cycle described in a new Explore the virulence attenuation. Part II highlights key enzymes and toxins
Microbial World. produced by microbes that contribute to pathogenesis.
P R E FA C E xi
Chapter 33 Chapter 34
• Pathogens in contaminated water or food are easily transmitted to • Eukaryotic pathogens present a special challenge to medicine
humans, with waterborne diseases being especially common in because, on a cellular level, they are not that different from our
developing countries lacking adequate water treatment facilities. own cells. Thus, it can be difficult to find selective targets for che-
This chapter highlights the most prevalent water- and foodborne motherapeutic drugs. Yet the microbes highlighted in this highly
diseases and emphasizes the importance of clean water and proper visual chapter cause some of the most devastating and prevalent
food preparation and preservation in preventing these physically diseases today.
uncomfortable and occasionally fatal illnesses. • Some highlights: New color photos adorn the chapter, including
• Some highlights: Updated statistics have been incorporated for all two stunning fluorescent micrographs of Entamoeba histolytica, the
major water- and foodborne diseases, including Campylobacter causative agent of amebic dysentery. Broader coverage of distinc-
infections, which have now overtaken salmonellosis as the leading tive features of several diseases, including cyclosporiasis, toxoplas-
cause of bacterial food infection in the United States. New discus- mosis, and malaria, has been seamlessly incorporated. All statistics
sions cover recently elucidated norovirus pathology and new food have been updated with the most recent surveillance data to yield
safety developments, including the use of eBeam technology and a global picture of fungal and parasitic diseases.
bacteriophage sprays. A new overview figure of cholera infection
integrates photos with artwork to emphasize key aspects of this
devastating and all too common disease.
Acknowledgments
xiii
xiv ACKNOWLEDGMENTS
Ankur Dalia, Indiana University Donghyun Park, Yale University School of Medicine
Bertram Daum, University of Exeter (England) Nicolás Pinel, Universidad de Antioquia (Colombia)
Svetlana N. Dedysh, Winogradsky Institute of Microbiology (Russia) Marie Pizzorno, Bucknell University
David J. Des Marais, NASA Ames Joe Pogliano, University of California, San Diego
Adam Deutschbauer, Lawrence Berkeley National Laboratory Martin Polz, Massachusetts Institute of Technology
Omar Din, University of California, San Diego Tessa Quax, University of Freiburg (Germany)
Alice Dohnalkova, Pacific Northwest National Laboratory Katherine Ralston, University of California
(Richland, WA) Ines Rauschenbach, Rutgers University
Steven Dominy, Cortexyme, Inc. Tara Renbarger, Indiana Wesleyan University
Paul Dunlap, University of Michigan Niels Peter Revsbech, Aarhus University (Denmark)
David Emerson, Bigelow Laboratory for Ocean Sciences (Maine) Ned Ruby, University of Hawaii at Manoa
Susanne Erdmann, University of New South Wales (Australia) Bernhard Schink, University of Konstanz (Germany)
Belinda Ferrari, University of New South Wales (Australia) Susan Schlimpert, John Innes Centre (England)
Derek J. Fisher, Southern Illinois University Andrey Shkoporov, University College Cork (Ireland)
Jason Flowers, Murraysmith (Seattle, WA) Simon Silver, University of Illinois Chicago
Bruce Fouke, University of Illinois Urbana–Champaign Janice Speshock, Tarleton State University
Andreas Giesen, Royal HaskoningDHV (The Netherlands) Emily Stowe, Bucknell University
Mariana Gomes de Pinho, Universidade Nova de Lisboa (Portugal) Shunichi Takahashi, National Institute for Basic Biology (Japan)
Hans-Peter Grossart, Leibniz-Institute of Freshwater Ecology and Inland Francisco Tenllado, Centro de Investigaciones Biológicas (Spain)
Fisheries (Germany) Andreas Teske, University of North Carolina
Ricardo Guerrero, University of Barcelona (Spain) David Valentine, University of California, Santa Barbara
Jennifer Hatchel, College of Coastal Georgia Mikel Valle, Asociación Centro de Investigación Cooperativa en
Roland Hatzenpichler, Montana State University Biociencias (Spain)
Jennifer Hess, Aquinas College Nicholas Verola, Verola Studio (Vero Beach, FL)
Donald Hilvert, ETH Zürich (Switzerland) Marilyn B. Vogel, Auburn University
Jay Hodgson, Georgia Southern University Judy Wall, University of Missouri
William Inskeep, Montana State University Dave Ward, Montana State University
Anthony James, University of California, Irvine Bishop Wash, The Richards Group (Dallas TX)
Joshua Jenkins, University of Bristol Dental School (England) Jillian L. Waters, Max Planck Institute for Developmental Biology
Grant Jensen, California Institute of Technology (Germany)
Deborah O. Jung, Southeast Missouri State University Nicki Watson, Massachusetts Institute of Technology
Kathryn Kauffman, Massachusetts Institute of Technology Gunter Wegener, Max Planck Institute of Marine Microbiology
Vjollca Konjufca, Southern Illinois University (Germany)
Klaus Koren, University of Copenhagen (Denmark) Mari Winkler, University of Washington
Michael Kovach, Baldwin Wallace University Gerry Wright, McMaster University
Michael Kühl, University of Copenhagen (Denmark) Vamsi Yadavalli, Virginia Commonwealth University
Philippe Laissue, University of Essex (England) Jeremy R. Young, University College London (England)
Christian Lesterlin, Institut de Biologie et Chimie des Carl Zeiss AG (Jena, Germany)
Protéines (France) Jizhong (Joe) Zhou, University of Oklahoma
Ruth E. Ley, Max-Planck Institute for Developmental Biology (Germany) Steve Zinder, Cornell University
Shee-Mei Lok, Duke-NUS Medical School (Singapore)
E. Erin Mack, Dupont Corporate Remediation Group (Newark, DE) As hard as a publishing team may try, no textbook can ever be com-
Jessica Mark Welch, Marine Biological Laboratory, Woods Hole pletely error-free. Although we are confident the reader will be hard
Francis Martin, Lab of Excellence ARBRE, INRA-Nancy (France) pressed to find errors in BBOM 16e, any errors that do exist, either of
Sean McAllister, University of Delaware commission or omission, are the responsibility of the authors. In past
Margaret McFall-Ngai, University of Hawaii at Manoa editions, users have been kind enough to contact us when they spot an
Jeffrey McLean, University of Washington, Seattle error so we can fix it in a subsequent printing. Users should feel free to
Nancy Moran, University of Texas continue to contact the authors directly about any errors, concerns, ques-
Phillip Nadeau, Massachusetts Institute of Technology tions, or suggestions they have about the book. We are always happy to
National Aeronautics and Space Administration (USA) hear from our readers; through the years, your comments have helped
Jeniel Nett, University of Wisconsin make the book stronger.
Daniela Nicastro, University of Texas Southwestern
Trent Northen, Lawrence Berkeley National Laboratory Michael T. Madigan (madigan@siu.edu)
Gal Ofir, Weizmann Institute of Science (Israel) Kelly S. Bender (bender@siu.edu)
Catherine Oikonomou, California Institute of Technology Daniel H. Buckley (dbuckley@cornell.edu)
Jörg Overmann, Leibniz Institute DSMZ Braunschweig (Germany) W. Matthew Sattley (matthew.sattley@indwes.edu)
Niki Parenteau, NASA Ames David A. Stahl (dastahl@uw.edu)
Contents
2
About the Authors iii
Preface vii Microbial Cell Structure
Acknowledgments xiii and Function 38
UNIT 1 The Foundations MICROBIOLOGYNOW Exploring the Microbial Cell 38
of Microbiology I
• The Cell Envelope 39
2.1 The Cytoplasmic Membrane 39
3
1.9 Imaging Cells in Three Dimensions 22
1.10 Probing Cell Structure: Electron Microscopy 23 Microbial Metabolism 75
III • Microbial Cultivation Expands the Horizon
of Microbiology 25
MICROBIOLOGYNOW Life Begins with Metabolism 75
1.11 Pasteur and Spontaneous
Generation 25 I
• Fundamentals of Metabolism 76
1.12 Koch, Infectious Diseases,
3.1 Defining the Requirements for Life 76
and Pure Cultures 27
3.2 Electron Transfer Reactions 78
1.13 Discovery of Microbial Diversity 29
3.3 Calculating Changes in Free Energy 80
IV • Molecular Biology and the Unity 3.4 Cellular Energy Conservation 82
and Diversity of Life 31 3.5 Catalysis and Enzymes 84
1.14 Molecular Basis of Life 31 II • Catabolism: Chemoorganotrophs 85
1.15 Woese and the Tree of Life 32
3.6 Glycolysis, the Citric Acid Cycle,
Explore the Microbial World and the Glyoxylate Cycle 86
Tiny Cells 9 3.7 Principles of Fermentation 88
xv
xvi CONTENTS
5
3.8 Principles of Respiration: Electron Carriers 89
3.9 Principles of Respiration: Generating a Proton Viruses and Their
Motive Force 91 Multiplication 148
III • Catabolism: Electron Transport
and Metabolic Diversity 94 MICROBIOLOGYNOW hen Antibiotics Fail, Bacteriophage
W
3.10 Anaerobic Respiration and Metabolic Modularity 94 Therapy to the Rescue 148
3.11 Chemolithotrophy and Phototrophy 96
I
• The Nature of Viruses 149
IV • Biosynthesis 98 5.1 What Is a Virus? 149
3.12 Autotrophy and Nitrogen Fixation 98 5.2 Structure of the Virion 151
3.13 Sugars and Polysaccharides 101 5.3 Culturing, Detecting, and Counting Viruses 153
3.14 Amino Acids and Nucleotides 102
3.15 Fatty Acids and Lipids 103 II • Overview of the Viral Replication Cycle 155
5.4 Steps in the Replication Cycle 155
5.5 Bacteriophage T4: A Model Lytic Virus 156
4
5.6 Temperate Bacteriophages and Lysogeny 159
Microbial Growth 5.7 An Overview of Viruses of Eukaryotes 159
and Its Control 108
4.5 Turbidimetric Measures of Microbial Cell MICROBIOLOGYNOW Injectisomes: Salmonella’s Mode of Attack 165
Numbers 117
I
• Molecular Biology and Genetic Elements 166
II • Dynamics of Microbial Growth 118 6.1 DNA and Genetic Information Flow 166
4.6 Binary Fission and the Microbial Growth Cycle 118 6.2 Genetic Elements: Chromosomes
4.7 Quantitative Aspects of Microbial Growth 120 and Plasmids 169
4.8 Continuous Culture 122
4.9 Biofilm Growth 123 II • Copying the Genetic Blueprint: DNA
4.10 Alternatives to Binary Fission 124 Replication 172
6.3 Templates, Enzymes, and the Replication Fork 172
III • Environmental Effects on Growth: 6.4 Bidirectional Replication, the Replisome, and
Temperature 126 Proofreading 175
4.11 Temperature Classes of Microorganisms 126
4.12 Microbial Life in the Cold 127 III • RNA Synthesis: Transcription 177
4.13 Microbial Life at High Temperatures 129 6.5 Transcription in Bacteria 177
6.6 Transcription in Archaea and Eukarya 181
IV • Environmental Effects on Growth: pH, Osmolarity,
and Oxygen 131 IV • Protein Synthesis: Translation 183
4.14 Effects of pH on Microbial Growth 132 6.7 Amino Acids, Polypeptides, and Proteins 183
4.15 Osmolarity and Microbial Growth 133 6.8 Transfer RNA 186
4.16 Oxygen and Microbial Growth 135 6.9 Translation and the Genetic Code 187
6.10 The Mechanism of Protein Synthesis 189
V • Controlling Microbial Growth 137
4.17 General Principles and Microbial Growth Control by V • Protein Processing, Secretion,
Heat 138 and Targeting 192
4.18 Other Physical Control Methods: Radiation and 6.11 Assisted Protein Folding and Chaperones 192
Filtration 139 6.12 Protein Secretion: The Sec and Tat Systems 193
4.19 Chemical Control of Microbial Growth 141 6.13 Protein Secretion: Gram-Negative Systems 194
CONTENTS xvii
7 Microbial Regulatory
Systems 200
8.11
8.12
Antibiotic Targets and Antibiotic Resistance 255
Persistence and Dormancy 257
9
MICROBIOLOGYNOW s Bacterial Cells Chatter,
A
Viruses Eavesdrop 200 Genetics of Bacteria
I
• DNA-Binding Proteins and Transcriptional
and Archaea 261
Regulation 201
7.1 DNA-Binding Proteins 201 MICROBIOLOGYNOW L ive Cell Imaging Captures Bacterial
7.2 Transcription Factors and Effectors 202 Promiscuity 261
7.3 Repression and Activation 204 I
• Mutation 263
7.4 Transcription Controls in Archaea 207
9.1 Mutations and Mutants 263
II • Sensing and Signal Transduction 209 9.2 Molecular Basis of Mutation 265
7.5 Two-Component Regulatory Systems 209 9.3 Reversions and Mutation Rates 267
7.6 Regulation of Chemotaxis 210 9.4 Mutagenesis 268
7.7 Cell-to-Cell Signaling 213 II • Gene Transfer in Bacteria 270
III • Global Control 215 9.5 Genetic Recombination 271
7.8 The lac Operon 216 9.6 Transformation 273
7.9 Stringent and General Stress Responses 218 9.7 Transduction 275
7.10 The Phosphate (Pho) Regulon 220 9.8 Conjugation 278
7.11 The Heat Shock Response 221 9.9 The Formation of Hfr Strains and Chromosome
Mobilization 279
IV • RNA-Based Regulation 222
III • Gene Transfer in Archaea and Other
7.12 Regulatory RNAs 223
7.13 Riboswitches 224
Genetic Events 282
7.14 Attenuation 226 9.10 Horizontal Gene Transfer in Archaea 282
9.11 Mobile DNA: Transposable Elements 284
V • Regulation of Enzymes and Other Proteins 227 9.12 Preserving Genomic Integrity and CRISPR 286
7.15 Feedback Inhibition 228
and Evolution
8 Molecular Aspects of Microbial
Growth 234
11 Viral Genomics
and Diversity 325
12.9 Mining Genomes and
Engineering Pathways 375
12.10 Engineering Biofuels 377
13 Microbial Evolution
11.3 Single-Stranded DNA Bacteriophages: fX174 and
M13 330
11.4 Double-Stranded DNA Bacteriophages: T4, T7, and and Genome Dynamics 392
Lambda 332
11.5 Viruses of Archaea 335
MICROBIOLOGYNOW Exploring Viral Genesis 392
11.6 Uniquely Replicating DNA Animal Viruses 338
11.7 DNA Tumor Viruses 339 I
• Early Earth and the Origin
and Diversification of Life 393
III • RNA Viruses 341
13.1 Formation and Early History of Earth 393
11.8 Positive-Strand RNA Viruses 341
13.2 Photosynthesis and the Oxidation
11.9 Negative-Strand RNA Animal Viruses 343
of Earth 396
11.10 Double-Stranded RNA Viruses 345
13.3 Living Fossils: DNA Records the History
11.11 Viruses That Use Reverse Transcriptase 346 of Life 398
IV • Subviral Agents 349 13.4 Endosymbiotic Origin of Eukaryotes 399
13.5 Viral Evolution 402
11.12 Viroids 349
11.13 Prions 350 II • Mechanisms of Microbial
Evolution 403
13.6 The Evolutionary Process 403
14 Metabolic Diversity
of Microorganisms 424 MICROBIOLOGYNOW Cyanobacterial Diversity
and Environmental Change 478
16 Phylogenetic Diversity of
Considerations 460
14.18 Lactic and Mixed-Acid
Fermentations 462 Bacteria 519
14.19 Fermentations of Obligate
Anaerobes 464 MICROBIOLOGYNOW Bacterial Diversity and Human Health 519
14.20 Secondary Fermentations 466
14.21 Fermentations That Lack Substrate-Level I
• Proteobacteria 520
Phosphorylation 467 16.1 Alphaproteobacteria 521
14.22 Syntrophy 469 16.2 Betaproteobacteria 524
VII • Hydrocarbon Metabolism 471 16.3 Gammaproteobacteria: Enterobacteriales 526
16.4 Gammaproteobacteria: Pseudomonadales
14.23 Aerobic Hydrocarbon
and Vibrionales 528
Metabolism 471
16.5 Deltaproteobacteria and
14.24 Anaerobic Hydrocarbon
Epsilonproteobacteria 529
Metabolism 472
xx CONTENTS
II • Firmicutes, Tenericutes, and Actinobacteria 531 IV • Evolution and Life at High Temperature 578
16.6 Firmicutes: Lactobacillales 531 17.12 An Upper Temperature Limit for Microbial Life 578
16.7 Firmicutes: Nonsporulating Bacillales and 17.13 Molecular Adaptations to Life at High
Clostridiales 533 Temperature 580
16.8 Firmicutes: Sporulating Bacillales and 17.14 Hyperthermophilic Archaea, H2, and Microbial
Clostridiales 534 Evolution 581
16.9 Tenericutes: The Mycoplasmas 535
16.10 Actinobacteria: Coryneform and Propionic Acid
18 Diversity of Microbial
Bacteria 536
16.11 Actinobacteria: Mycobacterium 538
16.12 Filamentous Actinobacteria: Streptomyces and Eukarya 585
Relatives 539
17
18.12 Mucoromycota and Glomeromycota 603
Diversity of Archaea 556 18.13 Ascomycota 604
18.14 Basidiomycota 605
19
II • Thaumarchaeota and Cryptic Archaeal Phyla 567
17.5 Thaumarchaeota and Nitrification in Archaea 568 Taking the Measure
17.6 Nanoarchaeota and the “Hospitable Fireball” 569 of Microbial Systems 612
17.7 Korarchaeota, the “Secret Filament” 570
17.8 Other Cryptic Archaeal Phyla 571
MICROBIOLOGYNOW T ouring Microbial Biogeography Using
III • Crenarchaeota 572 Combinatorial Imaging 612
17.9 Habitats and Energy Metabolism of I
• Culture-Dependent Analyses of Microbial
Crenarchaeota 572
Communities 613
17.10 Crenarchaeota from Terrestrial Volcanic Habitats 574
19.1 Enrichment Culture Microbiology 613
17.11 Crenarchaeota from Submarine Volcanic Habitats 576
CONTENTS xxi
19.2 Classical Procedures for Isolating Microbes 617 20.14 The Deep Sea 682
19.3 Selective Single-Cell Isolation: Laser Tweezers, Flow 20.15 Deep-Sea Sediments 685
Cytometry, Microfluidics, and High-Throughput 20.16 Hydrothermal Vents 687
Methods 618
21
II • Culture-Independent Microscopic Analyses
of Microbial Communities 620 Nutrient Cycles 693
19.4 General Staining Methods 620
19.5 Microscopic Specificity: Fluorescence In Situ
Hybridization (FISH) 622
MICROBIOLOGYNOW n Uncertain Future for Coral Reef
A
III • Culture-Independent Molecular Analyses Ecosystems 693
of Microbial Communities 625 I
• Carbon, Nitrogen, and Sulfur Cycles 694
19.6 PCR Methods of Microbial Community
21.1 The Carbon Cycle 694
Analysis 626
21.2 Syntrophy and Methanogenesis 697
19.7 Microarrays for Analysis of Microbial Phylogenetic
21.3 The Nitrogen Cycle 699
and Functional Diversity 630
21.4 The Sulfur Cycle 701
19.8 Environmental Multi-omics: Integration of Genomics,
Transcriptomics, Proteomics, and II • Other Nutrient Cycles 702
Metabolomics 631
21.5 The Iron and Manganese Cycles: Reductive
IV • Measuring Microbial Activities in Nature 637 Activities 702
19.9 Chemical Assays, Radioisotopic Methods, 21.6 The Iron and Manganese Cycles: Oxidative
Microsensors, and Nanosensors 638 Activities 706
19.10 Stable Isotopes and Stable Isotope Probing 641 21.7 The Phosphorus, Calcium, and Silicon Cycles 708
19.11 Linking Functions to Specific Organisms 643 III • Humans and Nutrient Cycling 710
19.12 Linking Genes and Cellular Properties to
21.8 Mercury Transformations 711
Individual Cells 646
21.9 Human Impacts on the Carbon and Nitrogen
Cycles 713
MICROBIOLOGYNOW
I
Living on Fumes 651
24
IV • Indoor Microbiology and Microbially
Influenced Corrosion 737
Microbial Symbioses with
22.11 The Microbiology of Homes and Humans 783
Public Spaces 737
22.12 Microbially Influenced Corrosion MICROBIOLOGYNOW ne of the Most Abundant Viruses on
O
of Metals 739 Earth Discovered First in the Human
22.13 Biodeterioration of Stone and Concrete 740 Viral Microbiome 783
I
• Structure and Function of the Healthy Adult
IV • Other Invertebrates as Microbial Habitats 765 V • Modulation of the Human Microbiome 809
24.11 Antibiotics and the Human Microbiome 809
23.10 Bioluminescent Symbionts and the Squid
Symbiosis 765 24.12 Probiotics, Prebiotics, and Synbiotics 810
23.11 Marine Invertebrates at Hydrothermal Vents Explore the Microbial World
and Cold Seeps 769 The Gut–Brain Axis 790
23.12 Entomopathogenic Nematodes 770
23.13 Reef-Building Corals 771
26
IV • T Cells and Their Receptors 873
Innate Immunity: Broadly
27.7 T Cell Receptors: Proteins, Genes,
Specific Host Defenses 832 and Diversity 874
27.8 T Cell Subsets and Their Functions 877
MICROBIOLOGYNOW eriodontal Disease and Alzheimer’s:
P
Evidence for Causation? 832
I
• Fundamentals of Host Defense 833
26.1
26.2
Basic Properties of the Immune System 833
Barriers to Pathogen Invasion 834
28 Immune Disorders and
Antimicrobial Therapy 883
II • Isolating and Characterizing Infectious II • Airborne Viral Diseases 959
Microorganisms 910 31.6 MMR and Varicella-Zoster Infections 959
29.3 Workflow in the Clinical Laboratory 910 31.7 The Common Cold 961
29.4 Choosing the Right Treatment 916 31.8 Influenza 962
30
Virus (HIV) and AIDS 976
Epidemiology and Public
Health 929
34 Eukaryotic Pathogens:
Fungi, Protozoa, and
Helminths 1023
I
• Fungal Infections 1024
34.1 Pathogenic Fungi and Classes of Infection 1024
34.2 Fungal Diseases: Mycoses 1026
ASM Recommended Curriculum Guidelines
for Undergraduate Microbiology
xxvi
Making Connections Across
‘My dear Sir,—I do not wonder that you smiled at the affected
secrecy of Macpherson concerning the Censomento. The book
to which he alludes cannot be the “Bilancio dello stato,” &c.,
which was written to please Count Firmian. I knew well the
gentleman who wrote it and gave it to me, as I often met him at
dinner at the count’s.
‘Sometimes he was too decisive. One day he said at the
count’s table that the Bresciano contained 800,000 inhabitants
now. As Count F. knew that I had just come from Brescia, and
had not lost my time there, he asked me what number there was;
on which I told him that there were 376,000 according to a
census taken a few years before. The count smiled, and looked
very attentively on Carpani (for that was the author’s name), who
never liked me so well after that day, nor had Count Firmian so
high an opinion of him. You possibly may not know the history of
Sir John Macpherson. He offered the Duke of Grafton, when he
was at the head of the Treasury, a vast collection of jewels, by
order of the Nabob of Arcot, which the duke absolutely refused,
and Bradshaw, his secretary, also. Sir John, thinking that the
nabob would not believe that he had offered the present,
published for his own vindication the answers of the duke and
Bradshaw, for which he was turned out of the company’s service,
as he was pursuing an interest then opposite to its interests.
‘Scotch influence not long after restored him. You will find the
letters in Lind’s appendix to the defence of Lord Pigot. You are
now, of course, so much of a politician as not to be surprised
(shall I say disgusted?) at Macpherson’s conduct. The opinion of
the King of Prussia as to your book I value not a straw; but that
of the Marshal de Castries certainly carries with it great weight.
‘He is one of the few who adhered to Necker from gratitude,
when the latter was turned out of his post about ten years ago;
and I heard a very good character of the maréchal when I was
last in France. St. Paul, as you and the duke are pleased to call
him, is finished, and the preface is on the stocks.[157]
‘Why do you wish Clarke had commented on the Epistle to the
Romans? Locke and Taylor have done it admirably; and easy as
you may think the Gospels are, they have been rendered much
more so by Clarke.
‘What do you mean by saying that the Gospels want no
explanation? St. John is extremely difficult in some parts,
notwithstanding Clarke’s paraphrase; and I think, with Markland,
that he is as yet very far from being perfectly understood. Adieu!
‘I remain,
‘Ever your sincere friend,
‘John Symonds.’
CHAPTER XI
‘Dear Sir,—We came hither from Lynn near three weeks since,
as Mr. Hoole informed you. We are in very warm and comfortable
lodgings, and the woman of the house is very attentive and
obliging. The air of this place is very mild and very moist, but
they tell us the healthiest of any upon the coast. Mr. Hoole has
been on to Exmouth, which, upon the whole, he does not like so
well. We do not find that Devonshire is cheaper the further you
go, but the contrary, at least on the coast.
‘With regard to myself, I do not find I am any better for this
journey, indeed I have had more fever and cough since I came
here than ever I had. I am at present better, but I know that is
owing to a very strict regimen which I have lately taken to. The
weather has been very unfavourable, for though it has not been
cold we have had almost constantly either rain or wind. We have
been absent from home near nine weeks, and Mr. H. must very
soon return to his curacy; he will either take me with him or leave
me here, and we wish very much to know what you advise,
considering all circumstances.
‘This place is certainly warmer than Surrey, but we have heard
here, as at Lynn, that it sometimes proves unfavourable in
consumptive cases. I do not think Abinger at all in fault; I have
been well or better there than anywhere. But I am not unwilling to
be left here, if it should still be thought advisable. Will you have
the goodness to write as soon as you can, as we shall not
determine till we hear? Mr. Hoole has had but one letter from you
about a month ago. This I mention lest you should have sent any
which may have miscarried.
‘Believe me, dear Sir,
‘Your affectionate Daughter,
‘Elizabeth Hoole.
‘Perhaps you may like to know something of the price of
provisions: Meat 4½d. per lb.; poultry is reasonable; chickens
from 2s. to 2s. 6d. a couple; milk 2d. a quart; butter 10d. per lb.’
‘My dear Sir,—I was very sorry to find from your letter that
what I had written had made you uneasy; I am certain you think
me worse than I am; indeed it is very foolish to write my
symptoms to my friends, as they give way perhaps, or some of
them, in a short time, as is my case. I am now quite free from
pain, and can sleep on one side as well as the other; I think the
last blister was of use. I have been twice in the warm bath since
Mr. Hoole went. My cough must have its course.
‘I had a very kind letter from Agnes yesterday; she offers, if
she can get permission, to come and stay with me until Mr.
Hoole returns, and adds, if she cannot, Mrs. Forbes says she is
at liberty, and would willingly come; but I would not bring them
down upon any account, as I am more comfortably settled than
anybody would suppose, and I am sure Mr. Hoole will be back in
a short time.
‘Sidmouth is certainly very mild; we have had no cold winds,
but this clear weather suits me better than that warm moist
weather we had in February. But I cannot walk by the seaside;
there is always wind, and it seems colder than anywhere else.
‘I would not blame Mrs. F. in the least; I might have been the
same or worse anywhere; if anything in the air disagreed with
me, it was the moisture. We have no post from hence, either
Monday or Tuesday. I wrote to Mr. Hoole last Sunday, or would
have answered yours sooner. The quickness, or rather rapidity,
with which our letters arrive from town, seems surprising—a
letter put in one night we have the next. It is not the custom
indeed to deliver them at night, as the post comes in so late as
nine, but if you send they will give you them. At Lynn, which is
about the same distance from town, they deliver them at six in
the evening, but we have here a cross-post to send for them nine
miles.
‘I beg you will not think me worse than I am, and believe me,
‘Your affectionate Daughter,
‘Elizabeth Hoole.’
‘My dear Sir,—I am to thank you for two letters, which should
not have lain unanswered if a retirement like mine would have
furnished me with any materials. However, I must take notice of
your way of arguing. You say “the people in France are starved,
and assignats are destroyed,” with significant dashes. You told
me just the same in 1793 and 1794, and venture it once more.
Assuredly you seem to reason like the old wizard Tiresias in
Horace, “Quicquid dicam aut erit aut non.” Whether your
predictions be verified or not, you assume, like Tiresias, to speak
the truth.
‘I always thought with you, that Mr. Pitt would receive no real
benefit from his new friends; but I have heard the Duke of
Grafton say that he would not have entered on the war if he had
not been able to detach some from the Opposition. If this be so,
there is great reason to lament that he could detach them.
‘We have received here the Bishop of Llandaff’s speech on the
Duke of Bedford’s motion, published by Debrett. It amazed me to
find that the Bishop of Durham ventured to speak after him. A
gentleman who heard them both says that Watson’s was rich,
clouted cream, and Barrington’s thin, meagre, blue skim milk,
frothed up with an egg, but with so weak a froth that it rose only
to fall instantly. We are told that after Æschines was banished, in
consequence of Demosthenes’ speech de coronâ, one of
Æschines’ friends carried to him in his banishment a copy of
Demosthenes’ speech; on which the former said, “But what if you
had heard it?”
‘Two fellows of this college, who heard Watson, bear the same
ample testimony to the excellent manner in which he delivered it.
‘You tell me “that our situation is prosperous beyond all
example;” I should think so too if it were unnecessary to multiply
loans. The complaints of the dearness of the necessaries of life
seem to pervade the whole island, and I fear they must still be
dearer. If we be forced to persist in this war (and how are we to
get out of it, it is difficult to see) the middle class of the people, of
which you and I form a part, must be driven down to the lower.
They hold it is a principle not to tax the lower, but to tax luxuries,
so that the middle class will be forced to abandon everything but
necessaries, and then the upper class must pay all. This, to use
your words, “must render us prosperous beyond all example.” I
rather accede to Charles Coles’ declaration in his last letter to
me: “Alas! our glory is gone to decay.” A day or two ago I was
looking into the famous pamphlet of my old friend, Israel
Mauduit,[163] on the German war, in which I stumbled on the
following sentence, very applicable to our entering into this just
war to save the Dutch: “Is Britain to make itself the general
knight errant of Europe, to rescue oppressed States, and
exhaust itself in order to save men in spite of themselves, who
will not do anything towards their own deliverance?” Adieu!
‘Yours sincerely,
‘J. Symonds.’