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Tables of Contents for Microbiology
Chapter/Section Title
Page #
Page Count
Preface
x
Visual Preview
xv
About the Authors
xxii
Part I Introduction to Microbiology
The History and Scope of Microbiology
1
16
The Discovery of Microorganisms
2
1
The Conflict over Spontaneous Generation
2
5
The Role of Microorganisms in Disease
7
4
Techniques & Applications 1.1: The Scientific Method
9
1
Disease 1.2: Molecular Koch's Postulates
10
1
Industrial Microbiology and Microbial Ecology
11
1
Members of the Microbial World
11
1
The Scope and Relevance of Microbiology
12
2
The Future of Microbiology
14
3
The Study of Microbial Structure: Microscopy and Specimen Preparation
17
22
Lenses and the Bending of Light
18
1
The Light Microscope
18
8
Preparation and Staining of Specimens
26
4
Electron Microscopy
30
5
Newer Techniques in Microscopy
35
4
Procaryotic Cell Structure and Function
39
34
An Overview of Procaryotic Cell Structure
40
4
Microbial Diversity & Ecology 3.1: Monstrous Microbes
43
1
Procaryotic Cell Membranes
44
3
The Cytoplasmic Matrix
47
3
The Nucleoid
50
2
Microbial Diversity & Ecology 3.2: Living Magnets
51
1
The Procaryotic Cell Wall
52
7
Protein Secretion in Procaryotes
59
2
Components External to the Cell Wall
61
6
Chemotaxis
67
1
The Bacterial Endospore
68
5
Eucaryotic Cell Structure and Function
73
20
An Overview of Eucaryotic Cell Structure
75
1
The Cytoplasmic Matrix, Microfilaments, Intermediate Filaments, and Microtubules
76
2
The Endoplasmic Reticulum
78
1
The Golgi Apparatus
78
1
Lysosomes and Endocytosis
79
3
Eucaryotic Ribosomes
82
1
Mitochondria
82
2
Chloroplasts
84
1
Microbial Diversity & Ecology 4.1: The Origin of the Eucaryotic Cell
84
1
The Nucleus and Cell Division
85
3
External Cell Coverings
88
1
Cilia and Flagella
88
2
Comparison of Procaryotic and Eucaryotic Cells
90
3
Part II Microbial Nutrition, Growth, and Control
Microbial Nutrition
93
16
The Common Nutrient Requirements
94
1
Requirements for Carbon, Hydrogen, and Oxygen
94
1
Nutritional Types of Microorganisms
95
1
Requirements for Nitrogen, Phosphorus, and Sulfur
96
1
Growth Factors
96
2
Uptake of Nutrients by the Cell
98
4
Culture Media
102
2
Historical Highlights 5.1: The Discovery of Agar as a Solidifying Agent and the Isolation of Pure Cultures
103
1
Isolation of Pure Cultures
104
5
Techniques & Applications 5.2: The Enrichment and Isolation of Pure Cultures
105
4
Microbial Growth
109
24
The Growth Curve
110
4
Measurement of Microbial Growth
114
3
The Continuous Culture of Microorganisms
117
1
The Influence of Environmental Factors on Growth
118
10
Microbial Diversity & Ecology 6.1: Life above 100°C
124
4
Microbial Growth in Natural Environments
128
5
Control of Microorganisms by Physical and Chemical Agents
133
16
Definition of Frequently Used Terms
134
1
Techniques & Applications 7.1: Safety in the Microbiology Laboratory
134
1
The Pattern of Microbial Death
135
1
Conditions Influencing the Effectiveness of Antimicrobial Agent Activity
136
1
The Use of Physical Methods in Control
136
6
Techniques & Applications 7.2: Universal Precautions for Microbiology Laboratories
142
1
The Use of Chemical Agents in Control
142
4
Evaluation of Antimicrobial Agent Effectiveness
146
3
Part III Microbial Metabolism
Metabolism: Energy, Enzymes, and Regulation
149
18
Energy and Work
150
1
The Laws of Thermodynamics
151
1
Free Energy and Reactions
152
1
The Role of ATP in Metabolism
153
1
Oxidation-Reduction Reactions and Electron Carriers
153
3
Enzymes
156
4
The Nature and Significance of Metabolic Regulation
160
1
Metabolic Channeling
160
1
Control of Enzyme Activity
161
6
Metabolism: Energy Release and Conservation
167
32
An Overview of Metabolism
168
3
The Breakdown of Glucose to Pyruvate
171
3
Fermentations
174
4
Historical Highlights 9.1: Microbiology and World War I
177
1
The Tricarboxylic Acid Cycle
178
1
Electron Transport and Oxidative Phosphorylation
179
6
Anaerobic Respiration
185
1
Catabolism of Carbohydrates and Intracellular Reserve Polymers
186
1
Lipid Catabolism
187
1
Protein and Amino Acid Catabolism
188
1
Oxidation of Inorganic Molecules
188
2
Microbial Diversity & Ecology 9.2: Acid Mine Drainage
190
1
Photosynthesis
190
9
Metabolism: The Use of Energy in Biosynthesis
199
22
Principles Governing Biosynthesis
200
2
Techniques & Applications 10.1: The Identification of Anabolic Pathways
202
1
The Photosynthetic Fixation of CO2
202
1
Synthesis of Sugars and Polysaccharides
203
2
The Assimilation of Inorganic Phosphorus, Sulfur, and Nitrogen
205
4
The Synthesis of Amino Acids
209
1
Anaplerotic Reactions
209
2
The Synthesis of Purines, Pyrimidines, and Nucleotides
211
3
Lipid Synthesis
214
2
Peptidoglycan Synthesis
216
1
Patterns of Cell Wall Formation
217
4
Part IV Microbial Molecular Biology and Genetics
Genes: Structure, Replication, and Mutation
221
32
DNA as Genetic Material
222
2
Nucleic Acid Structure
224
5
Historical Highlights 11.1: The Elucidation of DNA Structure
227
2
DNA Replication
229
5
The Genetic Code
234
1
Gene Structure
235
4
Mutations and Their Chemical Basis
239
6
Detection and Isolation of Mutants
245
3
DNA Repair
248
5
Genes: Expression and Regulation
253
32
DNA Transcription or RNA Synthesis
254
6
Microbial Tidbits 12.1: Catalytic RNA (Ribozymes)
259
1
Protein Synthesis
260
10
Regulation of mRNA Synthesis
270
4
Historical Highlights 12.2: The Discovery of Gene Regulation
272
2
Attenuation
274
2
Global Regulatory Systems
276
2
Small RNAs and Regulation
278
1
Two-Component Phosphorelay Systems
279
1
Control of the Cell Cycle
280
5
Microbial Recombination and Plasmids
285
26
Bacterial Recombination: General Principles
286
2
Bacterial Plasmids
288
3
Disease 13.1: Virulence Plasmids
291
1
Transposable Elements
291
5
Bacterial Conjugation
296
3
DNA Transformation
299
2
Transduction
301
5
Mapping the Genome
306
1
Recombination and Genome Mapping in Viruses
307
4
Part V DNA Technology and Genomics
Recombinant DNA Technology
311
24
Historical Perspectives
312
3
Synthetic DNA
315
1
The Polymerase Chain Reaction
316
3
Preparation of Recombinant DNA
319
3
Cloning Vectors
322
4
Inserting Genes into Eucaryotic Cells
326
1
Expression of Foreign Genes in Bacteria
327
2
Techniques & Applications 14.1: Gene Expression and Kittyboo Colors
329
1
Applications of Genetic Engineering
329
3
Techniques & Applications 14.2: Plant Tumors and Nature's Genetic Engineer
331
1
Social Impact of Recombinant DNA Technology
332
3
Microbial Genomics
335
16
Introduction
336
1
Determining DNA Sequences
336
1
Whole-Genome Shotgun Sequencing
336
3
Bioinformatics
339
1
General Characteristics of Microbial Genomes
339
6
Functional Genomics
345
4
The Future of Genomics
349
2
Part VI The Viruses
The Viruses: Introduction and General Characteristics
351
20
Early Development of Virology
352
1
Historical Highlights 16.1: Disease and the Early Colonization of America
353
1
General Properties of Viruses
353
1
The Cultivation of Viruses
353
2
Virus Purification and Assays
355
3
The Structure of Viruses
358
9
Principles of Virus Taxonomy
367
4
Microbial Tidbits 16.2: The Origin of Viruses
369
2
The Viruses: Bacteriophages
371
16
Classification of Bacteriophages
372
1
Microbial Diversity & Ecology 17.1: An Ocean of Viruses
372
1
Reproduction of Double-Stranded DNA Phages: The Lytic Cycle
373
5
Reproduction of Single-Stranded DNA Phages
378
1
Reproduction of RNA Phages
379
1
Temperate Bacteriophages and Lysogeny
380
7
The Viruses: Viruses of Eucaryotes
387
22
Classification of Animal Viruses
388
1
Reproduction of Animal Viruses
388
10
Techniques & Applications 18.1: Constructing a Virus
396
2
Cytocidal Infections and Cell Damage
398
1
Persistent, Latent, and Slow Virus Infections
399
1
Viruses and Cancer
400
1
Plant Viruses
401
3
Viruses of Fungi, Algae, and Protozoa
404
1
Insect Viruses
404
1
Viroids and Prions
405
4
Part VII The Diversity of the Microbial World
Microbial Taxonomy and Phylogeny
409
28
General Introduction and Overview
410
1
Microbial Evolution and Diversity
410
2
Taxonomic Ranks
412
2
Classification Systems
414
2
Major Characteristics Used in Taxonomy
416
4
Assessing Microbial Phylogeny
420
3
The Major Divisions of Life
423
5
Microbial Diversity & Ecology 18.1: ``Official'' Nomenclature Lists---A Letter from Bergey's
428
1
Bergey's Manual of Systematic Bacteriology
428
3
A Survey of Procaryotic Phylogeny and Diversity
431
6
The Archaea
437
16
Introduction to the Archaea
438
4
Phylum Crenarchaeota
442
2
Phylum Euryarchaeota
444
9
Microbial Diversity & Ecology 20.1: Methanotrophic Archaea
447
3
Microbial Tidbits 20.2: Photosynthesis in Halobacterium salinarium
450
3
Bacteria: The Deinococci and Nonproteobacteria Gram Negatives
453
20
Aquificae and Thermotogae
454
1
Deinococcus-Thermus
455
1
Photosynthetic Bacteria
456
8
Microbial Diversity & Ecology 21.1: The Mechanism of Gliding Motility
461
3
Phylum Planctomycetes
464
1
Phylum Chlamydiae
464
2
Phylum Spirochaetes
466
3
Phylum Bacteroidetes
469
4
Bacteria: The Proteobacteria
473
30
Class Alphaproteobacteria
474
8
Class Betaproteobacteria
482
3
Class Gammaproteobacteria
485
10
Microbial Diversity & Ecology 22.1: Bacterial Bioluminescence
492
3
Class Deltaproteobacteria
495
5
Class Epsilonproteobacteria
500
3
Bacteria: The Low G + C Gram Positives
503
18
General Introduction
504
1
Class Mollicutes (the Mycoplasmas)
504
3
Low G + C Gram-Positive Bacteria in Bergey's Manual
507
1
Class Clostridia
508
3
Microbial Tidbits 23.1: Spores in Space
509
2
Class Bacilli
511
10
Bacteria: The High G + C Gram Positives
521
16
General Properties of the Actinomycetes
522
2
High G + C Gram-Positive Bacteria in Bergey's Manual
524
2
Suborder Actinomycineae
526
1
Suborder Micrococcineae
527
1
Suborder Corynebacterineae
528
1
Suborder Micromonosporineae
529
2
Suborder Propionibacterineae
531
1
Suborder Streptomycineae
531
2
Suborder Streptosporangineae
533
1
Suborder Frankineae
533
1
Order Bifidobacteriales
534
3
The Fungi (Eumycota), Slime Molds, and Water Molds
537
16
Distribution
538
1
Importance
539
1
Structure
539
2
Nutrition and Metabolism
541
1
Reproduction
542
1
Characteristics of the Fungal Divisions
543
5
Slime Molds and Water Molds
548
5
The Algae
553
12
Distribution of Algae
555
1
Classification of Algae
555
1
Ultrastructure of the Algal Cell
556
1
Algal Nutrition
556
1
Structure of the Algal Thallus (Vegetative Form)
556
1
Algal Reproduction
556
1
Characteristics of the Algal Divisions
557
8
Techniques & Applications 26.1: Practical Importance of Diatoms
560
2
Disease 26.2: Toxic Algal Blooms
562
3
The Protozoa
565
12
Distribution
566
1
Importance
566
1
Morphology
566
1
Nutrition
567
1
Encystment and Excystment
568
1
Locomotory Organelles
568
1
Reproduction
568
1
Classification
568
1
Representative Types
569
8
Microbial Diversity & Ecology 27.1: The Importance of Foraminiferans
572
5
Part VIII Ecology and Symbiosis
Microorganism Interactions and Microbial Ecology
577
38
Foundations of Microbial Ecology
578
1
Microbial Interactions
578
15
Microbial Diversity & Ecology 28.1: Microbial Ecology Versus Environmental Microbiology
579
5
Microbial Diversity & Ecology 28.2: Coevolution of Animals and Their Gut Microbial Communities
584
9
Nutrient Cycling Interactions
593
9
The Physical Environment
602
5
Techniques & Applications 28.3: Thermophilic Microorganisms and Modern Biotechnology
607
1
Microbial Ecology and Its Methods: An Overview
607
8
Microorganisms in Aquatic Environments
615
30
Aquatic Environments and Microorganisms
616
5
Disease 29.1: New Agents in Medicine--The Sea as the New Frontier
617
4
The Microbial Community
621
3
Marine Environments
624
4
Freshwater Environments
628
2
Waters and Disease Transmission
630
6
Techniques & Applications 29.2: Waterborne Diseases, Water Supplies, and Slow Sand Filtration
632
4
Wastewater Treatment
636
6
Disease 29.3: Sewage Sludge: Long-Term Concerns with Land and Water Disposal
641
1
Groundwater Quality and Home Treatment Systems
642
3
Microorganisms in Terrestrial Environments
645
28
Soils as an Environment for Microorganisms
646
1
Microorganisms in the Soil Environment
647
1
Microorganisms and the Formation of Different Soils
648
3
Soil Microorganism Associations with Vascular Plants
651
11
Microbial Diversity & Ecology 30.1: Mycorrhizae and the Evolution of Vascular Plants
656
6
Soils, Plants, and Nutrients
662
2
Microbial Tidbits 30.2: An Unintended Global-Scale Nitrogen Experiment
664
1
Soils, Plants, and the Atmosphere
664
2
Techniques & Applications 30.3: Keeping Inside Air Fresh with Soil Microorganisms
665
1
Microbial Diversity & Ecology 30.4: Soils, Termites, Intestinal Microbes, and Atmospheric Methane
666
1
Microorganisms and Plant Decomposition
666
1
The Subsurface Biosphere
667
2
Soil Microorganisms and Human Health
669
1
Understanding Microbial Diversity in the Soil
670
3
Part IX Nonspecific (Innate) Resistance and the Immune Response
Normal Microbiota and Nonspecific (Innate) Host Resistance
673
32
Gnotobiotic Animals
674
1
Normal Microbiota of the Human Body
675
5
Techniques & Applications 31.1: Probiotics for Humans and Animals
679
1
Overview of Host Resistance
680
1
Cells, Tissues, and Organs of the Immune System
681
4
Physical and Chemical Barriers in Nonspecific (Innate) Resistance
685
3
Inflammation
688
3
The Complement System
691
2
Phagocytosis
693
4
Cytokines
697
3
Natural Killer Cells
700
5
Specific (Adaptive) Immunity
705
34
Overview of Specific (Adaptive) Immunity
706
2
Antigens
708
2
Antibodies
710
11
Techniques & Applications 32.1: Immunotoxins
721
1
T-Cell Biology
721
7
Techniques & Applications 32.2: Donor Selection for Tissue or Organ Transplants
724
4
B-Cell Biology
728
3
Action of Antibodies
731
3
The Classical Complement Pathway
734
1
Acquired Immune Tolerance
734
1
Summary: The Role of Antibodies and Lymphocytes in Resistance
734
5
Medical Immunology
739
22
Vaccines and Immunizations
740
4
Historical Highlights 33.1: The First Immunizations
740
4
Immune Disorders
744
7
Antigen-Antibody Interactions In Vitro
751
10
Techniques & Applications 33.2: History and Importance of Serotyping
757
4
Part X Microbial Diseases and Their Control
Pathogenicity of Microorganisms
761
18
Host-Parasite Relationships
762
2
Pathogenesis of Viral Diseases
764
1
Pathogenesis of Bacterial Diseases
765
10
Techniques & Applications 34.1: Detection and Removal of Endotoxins
774
1
Microbial Mechanisms for Escaping Host Defenses
775
4
Antimicrobial Chemotherapy
779
20
The Development of Chemotherapy
780
1
Techniques & Applications 35.1: The Use of Antibiotics in Microbiological Research
781
1
General Characteristics of Antimicrobial Drugs
781
2
Determining the Level of Antimicrobial Activity
783
1
Mechanisms of Action of Antimicrobial Agents
784
2
Factors Influencing the Effectiveness of Antimicrobial Drugs
786
1
Antibacterial Drugs
787
5
Drug Resistance
792
3
Disease 35.2: Antibiotic Misuse and Drug Resistance
793
2
Antifungal Drugs
795
1
Antiviral Drugs
796
3
Clinical Microbiology
799
22
Specimens
800
4
Techniques & Applications 36.1: Universal Precautions for Health-Care Professionals
802
2
Identification of Microorganisms from Specimens
804
13
Techniques & Applications 36.2: Monoclonal Antibodies in Clinical Microbiology
813
4
Susceptibility Testing
817
1
Computers in Clinical Microbiology
817
4
The Epidemiology of Infectious Disease
821
24
Epidemiological Terminology
822
1
Historical Highlights 37.1: John Snow---The First Epidemiologist
822
1
Measuring Frequency: The Epidemiologist's Tools
823
1
Infectious Disease Epidemiology
823
1
Recognition of an Infectious Disease in a Population
824
1
Recognition of an Epidemic
824
3
Historical Highlights 37.2: ``Typhoid Mary''
825
2
The Infectious Disease Cycle: Story of a Disease
827
5
Historical Highlights 37.3: The First Indications of Person-to-Person Spread of an Infectious Disease
831
1
Virulence and the Mode of Transmission
832
1
Emerging and Reemerging Infectious Diseases and Pathogens
832
5
Disease 37.4: The SARS Epidemic of 2003
835
2
Control of Epidemics
837
1
The Emerging Threat of Bioterrorism
837
2
Historical Highlights 37.5: 1346---The First Recorded Biological Warfare Attack
838
1
Global Travel and Health Considerations
839
1
Nosocomial Infections
840
5
Human Diseases Caused by Viruses
845
30
Airborne Diseases
846
6
Disease 38.1: Reye's and Guillain-Barre Syndromes
849
3
Arthropod-Borne Diseases
852
3
Disease 38.2: Viral Hemorrhagic Fevers---A Microbial History Lesson
853
2
Direct Contact Diseases
855
13
Food-Borne and Waterborne Diseases
868
2
Historical Highlights 38.3: A Brief History of Polio
870
1
Slow Virus and Prion Diseases
870
1
Other Diseases
871
4
Human Diseases Caused by Bacteria
875
42
Airborne Diseases
876
9
Arthropod-Borne Diseases
885
4
Historical Highlights 39.1: The Hazards of Microbiological Research
885
4
Direct Contact Diseases
889
13
Disease 39.2: Biofilms
897
3
Disease 39.3: Resistant Staphylococci
900
2
Disease 39.4: A Brief History of Syphilis
902
6
Food-Borne and Waterborne Diseases
905
3
Techniques & Applications 39.5: Clostridial Toxins as Therapeutic Agents---Benefits of Nature's Most Toxic Proteins
908
3
Sepsis and Septic Shock
911
1
Dental Infections
911
6
Human Diseases Caused by Fungi and Protozoa
917
20
Fungal Diseases
918
8
Disease 40.1: The Emergence of Candidiasis
925
1
Protozoan Diseases
926
11
Disease 40.2: A Brief History of Malaria
930
7
Part XI Food and Industrial Microbiology
Microbiology of Food
937
26
Microorganism Growth in Foods
938
2
Microbial Growth and Food Spoilage
940
3
Controlling Food Spoilage
943
3
Historical Highlights 41.1: An Army Travels on Its Stomach
944
2
Food-Borne Diseases
946
3
Historical Highlights 41.2: Typhoid Fever and Canned Meat
947
2
Detection of Food-Borne Pathogens
949
2
Microbiology of Fermented Foods
951
7
Techniques & Applications 41.3: Starter Cultures, Bacteriophage Infections, and Plasmids
951
7
Microorganisms as Foods and Food Amendments
958
5
Industrial Microbiology and Biotechnology
963
Choosing Microorganisms for Industrial Microbiology and Biotechnology
964
6
Techniques & Applications 42.1: The Potential of Thermophilic Archaea in Biotechnology
965
5
Microorganism Growth in Controlled Environments
970
4
Major Products of Industrial Microbiology
974
5
Microbial Growth in Complex Natural Environments
979
7
Microbial Diversity & Ecology 42.2: Methanogens---A New Role for a Unique Microbial Group
981
4
Microbial Diversity & Ecology 42.3: A Fungus with a Voracious Appetite
985
1
Biotechnological Applications
986
4
Techniques & Applications 42.4: Streptavidin-Biotin Binding and Biotechnology
987
3
Impacts of Microbial Biotechnology
990
Appendices
Appendix I A Review of the Chemistry of Biological Molecules
A-1
1
Appendix II Common Metabolic Pathways
A-11
1
Appendix III Classification of Procaryotes According to the Second Edition of Bergey's Manual of Systematic Bacteriology
A-19
1
Appendix IV Classification of Viruses
A-28
1
Appendix V Recommended Readings
A-38
1
Glossary
G-1
1
Credits
C-1
1
Index
I-1