Prescott's Principles of Microbiology

969 Pages·2008·100.04 MB·English

by  Joanne Willey

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Prescott’s Principles
o f M I C R O B I O L O G Y
Joanne M. Willey
Hofstra University
Linda M. Sherwood
Montana State University
Christopher J. Woolverton
Kent State University
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PRESCOTT’S PRINCIPLES OF MICROBIOLOGY
Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the
Americas, New York, NY 10020. Copyright © 2009 by The McGraw-Hill Companies, Inc. All rights
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This book is printed on acid-free paper.
1 2 3 4 5 6 7 8 9 0 DOW/DOW 0 9 8
ISBN 978–0–07–337523–6
MHID 0–07–337523–3
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The credits section for this book begins on page C-1 and is considered an extension of the copyright page.
Library of Congress Cataloging-in-Publication Data
Willey, Joanne M.
Prescott’s principles of microbiology / Joanne M. Willey, Linda M. Sherwood, Christopher J. Woolverton.—
1st ed.
p. cm.
“In using the seventh edition of PHK’s microbiology as the foundation for the development of
principles, we identifi ed two overarching goals.”
Includes index.
ISBN 978–0–07–337523–6 — ISBN 0–07–337523–3 (hard copy : alk. paper) 1. Microbiology.
I. Sherwood, Linda. II. Woolverton, Christopher J. III. Prescott, Lansing M. Microbiology. IV. Title.
V. Title: Microbiology.
QR41.2.W545 2009
616.9’041—dc22
2007040352
www.mhhe.com
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Brief Table of Contents
INTRODUCTION TO ECOLOGY
Part One Part Six
MICROBIOLOGY AND SYMBIOSIS
1 T he History and Scope of Microbiology 1 25 B iogeochemical Cycling and the Study of
2 M icroscopes and the Study of Microbial Ecology 593
Microbial Structure 13 26 M icroorganisms in Natural Environments 608
3 P rocaryotic Cell Structure and Function 33 27 Microbial Interactions 641
4 E ucaryotic Cell Structure and Function 65
5 Viruses and Other Acellular Agents 87
HOST
Part Seven
DEFENSES
MICROBIAL NUTRITION,
Part Two
GROWTH, AND CONTROL 28 N onspecific (Innate) Host Resistance 661
29 Specific (Adaptive) Immunity 689
6 M icrobial Nutrition 109
7 M icrobial Growth 126
8 Control of Microorganisms 153 MICROBIAL DISEASES
Part Eight
AND THEIR CONTROL
MICROBIAL 30 P athogenicity of Microorganisms 726
Part Three
METABOLISM 31 A ntimicrobial Chemotherapy 746
32 C linical Microbiology and Immunology 768
9 I ntroduction to Metabolism 169 33 The Epidemiology of Infectious Disease 787
10 C atabolism: Energy Release and Conservation 188
11 Anabolism: The Use of Energy in Biosynthesis 219
APPLIED
Part Nine
MICROBIOLOGY
MICROBIAL MOLECULAR
Part Four
BIOLOGY AND GENETICS 34 M icrobiology of Food 809
35 Applied Environmental Microbiology 831
12 G enes: Structure, Replication, and Expression 240
13 R egulation of Gene Expression 277
14 M echanisms of Genetic Variation 300
15 M icrobial Genomics 332 Appendix I A Review of the Chemistry of
16 Biotechnology and Industrial Microbiology 351 Biological Molecules A-1
Appendix II Common Metabolic Pathways A-13
THE DIVERSITY OF THE
Part Five
MICROBIAL WORLD Glossary G-1
17 M icrobial Evolution, Taxonomy, and Diversity 381 Credits C-1
18 T he Archaea 405
19 T he Deinococci and Gram-Negative Index I-1
Nonproteobacteria 420
20 T he Proteobacteria 439
21 T he Low G + C Gram-Positive Bacteria 474
22 T he High G + C Gram-Positive Bacteria 499
23 E ucaryotic Microbes 517
24 Viral Diversity 554
iii
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Table of Contents
About the Authors ix 4.9 Overview of Protist Structure and
Preface x Function 79
4.10 Overview of Fungal Structure and
Function 82
Part One INTRODUCTION TO 5 V iruses and Other Acellular Agents 87
MICROBIOLOGY 5.1 Introduction to Viruses 88
5.2 Structure of Viruses 88
1 T he History and Scope of Microbiology 1 Microbial Diversity & Ecology 5.1:
1.1 Members of the Microbial World 2 Host-Independent Growth of an
1.2 Scope and Relevance of Microbiology 3 Archaeal Virus 89
1.3 Discovery of Microorganisms 6 5.3 Viral Multiplication 95
1.4 Confl ict over Spontaneous Generation 7 5.4 Types of Viral Infections 99
1.5 Golden Age of Microbiology 8 5.5 Cultivation and Enumeration of Viruses 103
Disease 1.1: 5.6 Viroids and Virusoids 105
A Molecular Approach to Koch’s 5.7 Prions 106
Postulates 10
1.6 Development of Industrial Microbiology and
Microbial Ecology 11
Part Two MICROBIAL NUTRITION,
2 M icroscopes and the Study of Microbial GROWTH, AND CONTROL
Structure 13
6 M icrobial Nutrition 109
2.1 Lenses and the Bending of Light 14
6.1 Elements of Life 110
2.2 L ight Microscopes 14
6.2 Requirements for Carbon, Hydrogen,
2.3 P reparation and Staining of Specimens 21
Oxygen, and Electrons 110
2.4 E lectron Microscopy 24
6.3 Nutritional Types of Microorganisms 111
2.5 Newer Techniques in Microscopy 29
6.4 Requirements for Nitrogen,
3 P rocaryotic Cell Structure and Function 33 Phosphorus, and Sulfur 113
3.1 Overview of Procaryotic Cell Structure 34 6.5 Growth Factors 113
Microbial Diversity & Ecology 3.1: 6.6 Uptake of Nutrients 114
Monstrous Microbes 36 6.7 Culture Media 118
3.2 Procaryotic Cell Membranes 38 Techniques & Applications 6.1:
3.3 Procaryotic Cytoplasm 42 Enrichment Cultures 121
3.4 Bacterial Cell Walls 46 6.8 Isolation of Pure Cultures 121
3.5 Archaeal Cell Walls 53
3.6 Components External to the Cell Wall 53 7 M icrobial Growth 126
3.7 Bacterial Motility and Chemotaxis 57 7.1 B acterial Cell Cycle 127
3.8 Bacterial Endospores 60 7.2 Growth Curve 130
7.3 Measurement of Microbial Growth 134
4 E ucaryotic Cell Structure and Function 65 7.4 Continuous Culture of
4.1 Overview of Eucaryotic Cell Microorganisms 136
Structure 66 7.5 Infl uences of Environmental Factors
4.2 Eucaryotic Membranes 67 on Growth 138
4.3 Eucaryotic Cytoplasm 67 Microbial Diversity & Ecology 7.1:
4.4 Organelles of the Biosynthetic-Secretory Life Above 100 ° C 144
and Endocytic Pathways 70 7.6 Microbial Growth in Natural
4.5 Organelles Involved in Genetic Environments 148
Control of the Cell 73
4.6 Organelles Involved in Energy 8 C ontrol of Microorganisms 153
Conservation 75 8.1 Defi nitions of Frequently Used Terms 154
4.7 Structures External to the Plasma 8.2 The Pattern of Microbial Death 154
Membrane 76 8.3 Conditions Infl uencing the Effectiveness of
4.8 Comparison of Procaryotic and Eucaryotic Antimicrobial Agents 156
Cells 79 8.4 The Use of Physical Methods in Control 157
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Table of Contents v
8.5 The Use of Chemical Agents in Control 160 12.3 DNA Replication 245
T echniques & Applications 8.1: 12.4 Gene Structure 253
S tandard Microbiological Practices 162 12.5 Transcription 255
8.6 Evaluation of Antimicrobial Agent 12.6 The Genetic Code 262
Effectiveness 165 12.7 Translation 263
8.7 Biological Control of Microorganisms 167 12.8 Protein Maturation and Secretion 270
13 R egulation of Gene Expression 277
1 3.1 Levels of Regulation of Gene
MICROBIAL
Part Three Expression 278
METABOLISM
13.2 Regulation of Transcription Initiation 279
13.3 Regulation of Transcription Elongation 287
9 I ntroduction to Metabolism 169
13.4 Regulation at the Level of Translation 289
9.1 Energy and Work 170
13.5 Global Regulatory Systems 290
9.2 Laws of Thermodynamics 170
13.6 Regulation of Gene Expression in
9.3 Free Energy and Reactions 170
Eucarya and Archaea 296
9.4 ATP 171
9.5 Oxidation-Reduction Reactions 173
14 M echanisms of Genetic Variation 300
9.6 Electron Transport Chains 174
14.1 Mutations and Their Chemical Basis 301
9.7 Enzymes 176
14.2 Detection and Isolation of Mutants 306
9.8 Ribozymes 180
14.3 DNA Repair 308
9.9 Regulation of Metabolism 181
14.4 Creating Genetic Variability 311
9.10 Posttranslational Regulation of Enzyme
14.5 Transposable Elements 312
Activity 182
14.6 Bacterial Plasmids 316
14.7 Bacterial Conjugation 317
10 C atabolism: Energy Release and Conservation 188
14.8 Bacterial Transformation 322
10.1 Chemoorganotrophic Fueling Processes 189
14.9 Transduction 324
10.2 Aerobic Respiration 190
14.10 Mapping the Genome 326
10.3 Breakdown of Glucose to Pyruvate 192
10.4 Tricarboxylic Acid Cycle 195 15 M icrobial Genomics 332
10.5 Electron Transport and Oxidative 15.1 Introduction 333
Phosphorylation 197 15.2 Determining DNA Sequences 333
10.6 Anaerobic Respiration 200 15.3 Whole-Genome Shotgun Sequencing 335
10.7 Fermentation 202 15.4 Bioinformatics 337
10.8 Catabolism of Carbohydrates and Intracellular 15.5 Functional Genomics 337
Reserve Polymers 206 15.6 Proteomics 344
10.9 Lipid Catabolism 207 15.7 Comparative Genomics 346
10.10 Protein and Amino Acid Catabolism 207 15.8 Environmental Genomics 348
10.11 Chemolithotrophy 208
Microbial Diversity & Ecology 10.1: 16 B iotechnology and Industrial Microbiology 351
Acid Mine Drainage 210 16.1 Key Developments in Recombinant DNA
10.12 Phototrophy 211 Technology 352
16.2 Polymerase Chain Reaction 357
11 A nabolism: The Use of Energy in Biosynthesis 219 16.3 Gel Electrophoresis 357
11.1 Principles Governing Biosynthesis 220 16.4 Cloning Vectors and Creating Recombinant
11.2 Precursor Metabolites 221 DNA 359
11.3 CO2 Fixation 222 16.5 Construction of Genomic Libraries 363
11.4 Synthesis of Sugars and 16.6 Introducing Recombinant DNA into Host
Polysaccharides 224 Cells 365
11.5 Synthesis of Amino Acids 228 16.7 Expressing Foreign Genes in Host Cells 365
11.6 Synthesis of Purines, Pyrimidines, and 16.8 Microorganisms Used in Industrial
Nucleotides 233 Microbiology 366
11.7 Lipid Synthesis 236 Techniques & Applications 16.1 :
Visualizing Proteins with Green
Fluorescence 367
MICROBIAL MOLECULAR 16.9 Microorganism Growth in Controlled
Part Four
BIOLOGY AND GENETICS Environments 370
16.10 Major Products of Industrial
12 G enes: Structure, Replication, and Expression 240 Micro biology 371
12.1 Flow of Genetic Information 241 16.11 Recombinant DNA Technology in
12.2 Nucleic Acid Structure 242 Agriculture 374
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vi Table of Contents
16.12 Microbes as Products 376 22 T he High G + C Gram-Positive Bacteria 499
T echniques & Applications 16.2: 22.1 General Properties of the
S treptavidin-Biotin Binding and Actinomycetes 500
Biotechnology 378 22.2 Suborder Actinomycineae 503
22.3 Suborder Micrococcineae 503
22.4 Suborder Corynebacterineae 505
22.5 Suborder Micromonosporineae 511
22.6 Suborder Propionibacterineae 511
THE DIVERSITY OF THE 22.7 Suborder Streptomycineae 512
Part Five
MICROBIAL WORLD 22.8 Suborder Streptosporangineae 514
22.9 Suborder Frankineae 514
17 M icrobial Evolution, Taxonomy, and Diversity 381
22.10 Order Bifi dobacteriales 514
17.1 Microbial Evolution 382
17.2 Introduction to Microbial Classifi cation and 23 E ucaryotic Microbes 517
Taxonomy 389 23.1 Introduction 519
17.3 Taxonomic Ranks 390 23.2 Protist Classifi cation 519
17.4 Techniques for Determining Microbial Disease 23.1 :
Taxonomy and Phylogeny 392 A Brief History of Malaria 534
17.5 Phylogenetic Trees 398 23.3 Characteristics of the Fungal Divisions 540
17.6 The Major Divisions of Life 399
17.7 B ergey’s Manual of Systematic 24 V iral Diversity 554
Bacteriology 400 24.1 Principles of Virus Taxonomy 555
M icrobial Diversity & Ecology 17.1: 24.2 Viruses with Double-Stranded DNA Genomes
“ Offi cial” Nomenclature Lists— (Group I) 555
A Letter from Bergey’s 401 24.3 Viruses with Single-Stranded DNA Genomes
(Group II) 571
18 T he Archaea 405 24.4 Viruses with Double-Stranded RNA Genomes
18.1 Introduction to the Archaea 405 (Group III) 573
18.2 Phylum Crenarchaeota 411 24.5 Viruses with Plus-Strand RNA Genomes
18.3 Phylum Euryarchaeota 413 (Group IV) 574
Microbial Diversity & Ecology 18.1 : Microbial Diversity & Ecology 24.1:
Methanotrophic Archaea 414 SARS: Evolution of a Virus 579
24.6 Viruses with Minus-Strand RNA Genomes
19 T he Deinococci and Gram-Negative (Group V) 580
Nonproteobacteria 420 24.7 Viruses with Single-Stranded RNA Genomes
19.1 Aquifi cae and T hermotogae 421 (Group VI-Retroviruses) 584
19.2 D einococcus-Thermus 421 24.8 Viruses with Gapped DNA Genomes
19.3 Photosynthetic Bacteria 422 (Group VII) 589
19.4 Phylum Planctomycetes 429
19.5 Phylum Chlamydiae 429
19.6 Phylum Spirochaetes 432
19.7 Phylum Bacteroidetes 436
ECOLOGY
Part Six
AND SYMBIOSIS
20 T he Proteobacteria 439
20.1 Class A lphaproteobacteria 440 25 B iogeochemical Cycling and the Study of
20.2 Class Betaproteobacteria 448 Microbial Ecology 593
20.3 Class G ammaproteobacteria 453 Microbial Diversity & Ecology 25.1:
Microbial Diversity & Ecology 20.1 : Microbial Ecology versus Environmen-
Bacterial Bioluminescence 459 tal Microbiology 594
20.4 Class Deltaproteobacteria 467 25.1 Biogeochemical Cycling 594
20.5 Class E psilonproteobacteria 471 25.2 Microbial Ecology and Its Methods: An
Overview 601
21 T he Low G + C Gram-Positive Bacteria 474
21.1 Class Mollicutes (The Mycoplasmas) 475 26 M icroorganisms in Natural Environments 608
21.2 Peptidoglycan and Endospore 26.1 Marine and Freshwater Microbiology 609
Structure 477 26.2 Microorganisms in Terrestrial
Microbial Tidbits 21.1 : Environments 621
Spores in Space 479 Microbial Diversity & Ecology 26.1:
21.3 Class Clostridia 479 Mycorrhizae and the Evolution of
21.4 Class Bacilli 483 Vascular Plants 628
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Table of Contents vii
27 M icrobial Interactions 641 31.5 Factors Infl uencing Antimicrobial Drug
2 7.1 Microbial Interactions 642 Effectiveness 757
M icrobial Diversity & Ecology 27.1 : 31.6 Drug Resistance 758
Wolbachia pipientis: The World’s Most Disease 31.1:
Infectious Microbe? 645 Antibiotic Misuse and Drug
27.2 H uman-Microbe Interactions 653 Resistance 758
27.3 Normal Microbiota of the Human Body 654 31.7 Antifungal Drugs 762
31.8 Antiviral Drugs 763
31.9 Antiprotozoan Drugs 765
HOST
Part Seven
DEFENSES
32 C linical Microbiology and Immunology 768
32.1 Overview of the Clinical Microbiology
28 N onspecifi c (Innate) Host Resistance 661
Laboratory 769
28.1 Overview of Host Resistance 662
32.2 Identifi cation of Microorganisms from
28.2 Cells, Tissues, and Organs of the Immune
Specimens 769
System 663
Techniques & Applications 32.1 :
2 8.3 Phagocytosis 670
Standard Microbiological
28.4 Infl ammation 673
Practices 770
28.5 Physical Barriers in Nonspecifi c (Innate)
32.3 Clinical Immunology 779
Resistance 675
28.6 Chemical Mediators in Nonspecifi c (Innate)
Resistance 679 33 T he Epidemiology of Infectious Disease 787
33.1 Epidemiological Terminology 788
29 S pecifi c (Adaptive) Immunity 689
Historical Highlights 33.1:
29.1 Overview of Specifi c (Adaptive)
John Snow—The First
Immunity 690
Epidemiologist 788
29.2 Antigens 691
33.2 Measuring Frequency 789
29.3 Types of Specifi c (Adaptive) Immunity 694
33.3 Recognition of an Infectious Disease in a
29.4 Recognition of Foreignness 695
Population 789
29.5 T-Cell Biology 697
Historical Highlights 33.2:
29.6 B-Cell Biology 701
“Typhoid Mary” 791
29.7 Antibodies 704
33.4 Recognition of an Epidemic 791
29.8 Action of Antibodies 712
33.5 The Infectious Disease Cycle: Story of a
Techniques & Applications 29.1 :
Disease 793
Monoclonal Antibody Technology 713
33.6 Virulence and the Mode of
29.9 Summary: The Role of Antibodies and
Transmission 797
Lymphocytes in Immune Defense 715
33.7 Emerging and Reemerging Infectious
29.10 Acquired Immune Tolerance 716
Diseases and Pathogens 798
29.11 Immune Disorders 716
33.8 Control of Epidemics 801
Historical Highlights 33.3:
The First Immunizations 802
MICROBIAL DISEASES
Part Eight 33.9 Bioterrorism Preparedness 804
AND THEIR CONTROL 33.10 Nosocomial Infections 806
30 P athogenicity of Microorganisms 726
30.1 Host-Parasite Relationships 727
APPLIED
30.2 Pathogenesis of Viral Diseases 728 Part Nine
MICROBIOLOGY
30.3 Overview of Bacterial Pathogenesis 730
30.4 Toxigenicity 736
34 M icrobiology of Food 809
Techniques & Applications 30.1 :
34.1 Microorganism Growth in Foods 810
Detection and Removal of
34.2 Microbial Growth and Food Spoilage 811
Endotoxins 741
34.3 Controlling Food Spoilage 814
30.5 Polymicrobial Disease 742
34.4 Food-Borne Diseases 816
31 A ntimicrobial Chemotherapy 746 34.5 Detection of Food-Borne Pathogens 820
31.1 The Development of Chemotherapy 747 34.6 Microbiology of Fermented Foods 821
31.2 General Characteristics of Antimicrobial Techniques & Applications 34.1 :
Drugs 748 Chocolate: The Sweet Side of
31.3 Determining the Level of Antimicrobial Fermentation 822
Activity 748 34.7 Microorganisms as Foods and Food
31.4 Antibacterial Drugs 752 Amendments 829
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viii Table of Contents
35 A pplied Environmental Microbiology 831 Appendix I A Review of the Chemistry of Biological
35.1 Water Purifi cation and Sanitary Analysis 832 Molecules A-1
Techniques & Applications 35.1:
Waterborne Diseases, Water Supplies, Appendix II C ommon Metabolic Pathways A-13
and Slow Sand Filtration 833
35.2 Wastewater Treatment 836
35.3 Biodegradation and Bioremediation by Glossary G-1
Natural Communities 842 Credits C-1
35.4 Bioaugmentation 845 Index I-1
Microbial Diversity & Ecology 35.2 :
A Fungus with a Voracious
Appetite 846