Prescott, Harley, and Klein's Microbiology (7th Ed.) [7th ed.] 0072992913, 9780072992915

Table of contents :
Cover Page......Page 1
Title Page......Page 2
Copyright Page......Page 3
Dedication......Page 4
Brief Contents......Page 5
Contents......Page 6
About the Authors......Page 12
Preface......Page 13
ACKNOWLEGMENTS......Page 21
1.1 Members of the Microbial World......Page 22
1.2 The Discovery of Microorganisms......Page 24
1.3 The Conflict over Spontaneous Generation......Page 27
1.4 The Golden Age of Microbiology......Page 29
■ Techniques & Applications 1.1: The Scientific Method......Page 31
■ Disease 1.2: Koch’s Molecular Postulates......Page 32
1.5 The Development of Industrial Microbiology......Page 33
1.6 The Scope and Relevance of Microbiology......Page 34
1.7 The Future of Microbiology......Page 35
2.1 Lenses and the Bending of Light......Page 38
2.2 The Light Microscope......Page 39
2.3 Preparation and Staining of Specimens......Page 46
2.4 Electron Microscopy......Page 49
2.5 Newer Techniques in Microscopy......Page 52
3.1 An Overview of Procaryotic Cell Structure......Page 60
3.2 Procaryotic Cell Membranes......Page 63
■ Microbial Diversity & Ecology 3.1: Monstrous Microbes......Page 64
3.3 The Cytoplasmic Matrix......Page 69
■ Microbial Diversity & Ecology 3.2: Living Magnets......Page 72
3.4 The Nucleoid......Page 73
3.5 Plasmids......Page 74
3.6 The Bacterial Cell Wall......Page 76
3.7 Archaeal Cell Walls......Page 83
3.8 Protein Secretion in Procaryotes......Page 84
3.9 Components External to the Cell Wall......Page 86
3.10 Chemotaxis......Page 92
3.11 The Bacterial Endospore......Page 94
4.1 An Overview of Eucaryotic Cell Structure......Page 100
4.2 The Plasma Membrane and Membrane Structure......Page 102
4.3 The Cytoplasmic Matrix, Microfilaments, Intermediate Filaments, and Microtubules......Page 104
4.4 Organelles of the Biosynthetic-Secretory and Endocytic Pathways......Page 105
4.6 Mitochondria......Page 109
4.7 Chloroplasts......Page 111
4.8 The Nucleus and Cell Division......Page 112
4.9 External Cell Coverings......Page 115
4.10 Cilia and Flagella......Page 116
4.11 Comparison of Procaryotic and Eucaryotic......Page 117
5.1 The Common Nutrient Requirements......Page 122
5.3 Nutritional Types of Microorganisms......Page 123
5.4 Requirements for Nitrogen, Phosphorus, and Sulfur......Page 125
5.6 Uptake of Nutrients by the Cell......Page 126
5.7 Culture Media......Page 131
■ Historical Highlights 5.1: The Discovery of Agar as a Solidifying Agent and the Isolation of Pure Cultures......Page 133
5.8 Isolation of Pure Cultures......Page 134
■ Techniques & Applications 5.2: The Enrichment and Isolation of Pure Cultures......Page 137
6.1 The Procaryotic Cell Cycle......Page 140
6.2 The Growth Curve......Page 144
6.3 Measurement of Microbial Growth......Page 149
6.4 The Continuous Culture of Microorganisms......Page 152
6.5 The Influence of Environmental Factors on Growth......Page 153
■ Microbial Diversity & Ecology 6.1: Life Above 100°C......Page 159
6.6 Microbial Growth in Natural Environments......Page 163
7.1 Definitions of Frequently Used Terms......Page 170
■ Techniques & Applications 7.1: Safety in the Microbiology Laboratory......Page 171
7.2 The Pattern of Microbial Death......Page 172
7.3 Conditions Influencing the Effectiveness of Antimicrobial Agents......Page 173
7.4 The Use of Physical Methods in Control......Page 174
7.5 The Use of Chemical Agents in Control......Page 179
■ Techniques & Applications 7.2: Universal Precautions for Microbiology Laboratories......Page 181
7.6 Evaluation of Antimicrobial Agent Effectiveness......Page 185
8.1 An Overview of Metabolism......Page 188
8.3 The Laws of Thermodynamics......Page 190
8.4 Free Energy and Reactions......Page 191
8.5 The Role of ATP in Metabolism......Page 192
8.6 Oxidation-Reduction Reactions, Electron Carriers, and Electron Transport Systems......Page 193
8.7 Enzymes......Page 195
8.9 Metabolic Channeling......Page 201
8.10 Control of Enzyme Activity......Page 202
9.1 Chemoorganotrophic Fueling Processes......Page 212
9.2 Aerobic Respiration......Page 214
9.3 The Breakdown of Glucose to Pyruvate......Page 215
9.4 The Tricarboxylic Acid Cycle......Page 219
9.5 Electron Transport and Oxidative Phosphorylation......Page 221
9.6 Anaerobic Respiration......Page 226
9.7 Fermentations......Page 228
9.8 Catabolism of Carbohydrates and Intracellular Reserve Polymers......Page 231
9.9 Lipid Catabolism......Page 232
9.11 Chemolithotrophy......Page 233
9.12 Phototrophy......Page 235
■ Microbial Diversity & Ecology 9.2: Acid Mine Drainage......Page 236
10 Metabolism: The Use of Energy in Biosynthesis......Page 246
10.1 Principles Governing Biosynthesis......Page 247
10.2 The Precursor Metabolites......Page 248
10.3 The Fixation of CO2 by Autotrophs......Page 249
10.4 Synthesis of Sugars and Polysaccharides......Page 251
10.5 Synthesis of Amino Acids......Page 256
10.6 Synthesis of Purines, Pyrimidines, and Nucleotides......Page 262
10.7 Lipid Synthesis......Page 263
11 Microbial Genetics: Gene Structure, Replication, and Expression......Page 268
■ Historical Highlights 11.1: The Elucidation of DNA Structure......Page 269
11.1 DNA as Genetic Material......Page 270
11.2 The Flow of Genetic Information......Page 272
11.3 Nucleic Acid Structure......Page 273
11.4 DNA Replication......Page 274
11.5 Gene Structure......Page 285
■ Microbial Tidbits 11.2: Catalytic RNA (Ribozymes)......Page 289
11.7 The Genetic Code......Page 296
11.8 Translation......Page 297
12 Microbial Genetics: Regulation of Gene Expression......Page 312
12.1 Levels of Regulation of Gene Expression......Page 313
12.2 Regulation of Transcription Initiation......Page 314
■ Historical Highlights 12.1: The Discovery of Gene Regulation......Page 315
12.3 Regulation of Transcription Elongation......Page 323
12.4 Regulation at the Level of Translation......Page 326
12.5 Global Regulatory Systems......Page 328
12.6 Regulation of Gene Expression in Eucarya and Archaea......Page 334
13.1 Mutations and Their Chemical Basis......Page 338
13.2 Detection and Isolation of Mutants......Page 345
13.3 DNA Repair......Page 347
13.4 Creating Genetic Variability......Page 350
13.5 Transposable Elements......Page 353
13.6 Bacterial Plasmids......Page 355
13.7 Bacterial Conjugation......Page 358
13.8 DNATransformation......Page 363
13.9 Transduction......Page 366
13.10 Mapping the Genome......Page 370
13.11 Recombination and Genome Mapping in Viruses......Page 371
14.1 Historical Perspectives......Page 378
14.2 Synthetic DNA......Page 382
14.3 The Polymerase Chain Reaction......Page 383
14.5 Cloning Vectors and Creating Recombinant DNA......Page 387
14.6 Construction of Genomic Libraries......Page 391
14.8 Expressing Foreign Genes in Host Cells......Page 392
■ Techniques & Applications 14.1: Visualizing Proteins with Green Fluorescence......Page 395
14.9 Applications of Genetic Engineering......Page 396
■ Techniques & Applications 14.2: Plant Tumors and Nature’s Genetic Engineer......Page 399
14.10 Social Impact of Recombinant DNA Technology......Page 401
15.1 Introduction......Page 404
15.3 Whole-Genome Shotgun Sequencing......Page 405
15.5 Functional Genomics......Page 409
15.6 Comparative Genomics......Page 412
15.7 Proteomics......Page 414
15.8 Insights from Microbial Genomes......Page 416
15.9 Environmental Genomics......Page 423
16.1 Early Development of Virology......Page 428
■ Historical Highlights 16.1: Disease and the Early Colonization of America......Page 429
16.3 The Structure of Viruses......Page 430
16.5 The Cultivation of Viruses......Page 438
16.6 Virus Purification and Assays......Page 440
■ Microbial Tidbits 16.2: The Origin of Viruses......Page 444
17 The Viruses: Viruses of Bacteria and Archaea......Page 448
17.2 Virulent Double-Stranded DNA Phages......Page 449
■ Microbial Diversity & Ecology 17.1: Host-Independent Growth of an Archaeal Virus......Page 450
17.3 Single-Stranded DNA Phages......Page 457
17.4 RNA Phages......Page 458
17.5 Temperate Bacteriophages and Lysogeny......Page 459
17.6 Bacteriophage Genomes......Page 465
18.1 Taxonomy of Eucaryotic Viruses......Page 468
18.2 Reproduction of Vertebrate Viruses......Page 469
■ Microbial Diversity & Ecology 18.1: SARS: Evolution of a Virus......Page 472
■ Techniques & Applications 18.2: Constructing a Virus......Page 479
18.3 Cytocidal Infections and Cell Damage......Page 480
18.5 Viruses and Cancer......Page 482
18.6 Plant Viruses......Page 484
18.8 Insect Viruses......Page 487
18.9 Viroids and Virusoids......Page 488
18.10 Prions......Page 489
19.1 Microbial Evolution......Page 492
19.2 Introduction to Microbial Classification and Taxonomy......Page 498
19.3 Taxonomic Ranks......Page 501
19.4 Techniques for Determining Microbial Taxonomy and Phylogeny......Page 502
19.5 Assessing Microbial Phylogeny......Page 509
19.6 The Major Divisions of Life......Page 510
19.7 Bergey’s Manual of Systematic Bacteriology......Page 514
19.8 A Survey of Procaryotic Phylogeny and Diversity......Page 515
20.1 Introduction to the Archaea......Page 524
20.2 Phylum Crenarchaeota......Page 528
20.3 Phylum Euryarchaeota......Page 529
■ Microbial Diversity & Ecology 20.1: Archaeal Phylogeny: More Than Just the Crenarchaeota and Euryarchaeota?......Page 532
■ Microbial Diversity & Ecology 20.2: Methanotrophic Archaea......Page 534
21.1 Aquificae and Thermotogae......Page 540
21.3 Photosynthetic Bacteria......Page 541
■ Microbial Diversity & Ecology 21.1: The Mechanism of Gliding Motility......Page 548
21.4 Phylum Planctomycetes......Page 551
21.5 Phylum Chlamydiae......Page 552
21.6 Phylum Spirochaetes......Page 553
21.7 Phylum Bacteroidetes......Page 555
22 Bacteria: The Proteobacteria......Page 560
22.1 Class Alphaproteobacteria......Page 561
22.2 Class Betaproteobacteria......Page 567
22.3 Class Gammaproteobacteria......Page 572
■ Microbial Diversity & Ecology 22.1: Bacterial Bioluminescence......Page 580
22.4 Class Deltaproteobacteria......Page 583
22.5 Class Epsilonproteobacteria......Page 588
23.2 Class Mollicutes (The Mycoplasmas)......Page 592
23.3 Peptidoglycan and Endospore Structure......Page 593
23.4 Class Clostridia......Page 597
23.5 Class Bacilli......Page 599
24.1 General Properties of the Actinomycetes......Page 610
24.3 Suborder Micrococcineae......Page 614
24.4 Suborder Corynebacterineae......Page 616
24.5 Suborder Micromonosporineae......Page 618
24.7 Suborder Streptomycineae......Page 619
24.9 Suborder Frankineae......Page 622
24.10 Order Bifidobacteriales......Page 623
25 The Protists......Page 626
25.2 Nutrition......Page 627
25.3 Morphology......Page 628
25.5 Reproduction......Page 629
25.6 Protist Classification......Page 630
■ Disease 25.1: Harmful Algal Blooms (HABs)......Page 642
■ Techniques & Applications 25.2: Practical Importance of Diatoms......Page 645
26 The Fungi (Eumycota)......Page 650
26.2 Importance......Page 651
26.3 Structure......Page 652
26.5 Reproduction......Page 653
26.6 Characteristics of the Fungal Divisions......Page 656
27.1 Foundations in Microbial Diversity and Ecology......Page 664
27.2 Biogeochemical Cycling......Page 665
27.3 The Physical Environment......Page 674
27.4 Microbial Ecology and Its Methods: an Overview......Page 680
■ Techniques & Applications 27.2: Thermophilic Microorganisms and Modern Biotechnology......Page 681
28.1 Marine and Freshwater Environments......Page 688
■ Disease 28.1: New Agents in Medicine— The Sea as the New Frontier......Page 689
28.2 Microbial Adaptations to Marine and Freshwater Environments......Page 692
28.3 Microorganisms in Marine Environments......Page 694
28.4 Microorganisms in Freshwater Environments......Page 703
29.1 Soils as an Environment for Microorganisms......Page 708
29.2 Soils, Plants, and Nutrients......Page 710
■ Microbial Tidbits 29.1: An Unintended Global-Scale Nitrogen Experiment......Page 712
29.3 Microorganisms in the Soil Environment......Page 713
29.4 Microorganisms and the Formation of Different Soils......Page 714
29.5 Microorganism Associations with Vascular......Page 717
■ Microbial Diversity & Ecology 29.2: Mycorrhizae and the Evolution of Vascular Plants......Page 718
29.6 Soil Microorganisms and the Atmosphere......Page 729
■ Microbial Diversity & Ecology 29.3: Soils,Termites, Intestinal Microbes, and Atmospheric Methane......Page 730
■ Techniques & Applications 29.4: Keeping Inside Air Fresh with Soil Microorganisms......Page 731
29.7 The Subsurface Biosphere......Page 732
29.8 Soil Microorganisms and Human Health......Page 734
30.1 Microbial Interactions......Page 738
■ Microbial Diversity & Ecology 30.1: Wolbachia pipientis: The World’s Most Infectious Microbe?......Page 741
■ Microbial Diversity & Ecology 30.2: Coevolution of Animals and Their Gut Microbial Communities......Page 746
30.2 Human-Microbe Interactions......Page 755
30.3 Normal Microbiota of the Human Body......Page 756
■ Techniques & Applications 30.3: Probiotics for Humans and Animals......Page 760
31.1 Overview of Host Resistance......Page 764
31.2 Cells, Tissues, and Organs of the Immune System......Page 765
31.3 Phagocytosis......Page 773
31.4 Inflammation......Page 777
31.5 Physical Barriers in Nonspecific (Innate) Resistance......Page 779
31.6 Chemical Mediators in Nonspecific (Innate) Resistance......Page 783
32 Specific (Adaptive) Immunity......Page 794
32.2 Antigens......Page 795
32.3 Types of Specific (Adaptive) Immunity......Page 797
32.4 Recognition of Foreignness......Page 799
■ Techniques & Applications 32.1: Donor Selection for Tissue or Organ Transplants......Page 800
32.5 T Cell Biology......Page 802
32.6 B Cell Biology......Page 807
32.7 Antibodies......Page 810
32.8 Action of Antibodies......Page 820
■ Techniques & Applications 32.2: Monoclonal Antibody Technology......Page 821
32.10 Acquired Immune Tolerance......Page 823
32.11 Immune Disorders......Page 824
33.1 Host-Parasite Relationships......Page 836
33.2 Pathogenesis of Viral Diseases......Page 839
33.3 Overview of Bacterial Pathogenesis......Page 841
33.4 Toxigenicity......Page 845
33.5 Host Defense Against Microbial Invasion......Page 851
33.6 Microbial Mechanisms for Escaping Host Defenses......Page 853
34.1 The Development of Chemotherapy......Page 856
34.2 General Characteristics of Antimicrobial Drugs......Page 858
34.3 Determining the Level of Antimicrobial Activity......Page 861
34.4 Antibacterial Drugs......Page 862
34.6 Drug Resistance......Page 870
■ Disease 34.2: Antibiotic Misuse and Drug Resistance......Page 871
34.7 Antifungal Drugs......Page 875
34.8 Antiviral Drugs......Page 876
34.9 Antiprotozoan Drugs......Page 877
35.1 Specimens......Page 880
■ Techniques & Applications 35.1: Standard Microbial Practices......Page 882
35.2 Identification of Microorganisms from Specimens......Page 885
■ Microbial Tidbits 35.2: Biosensors: The Future Is Now......Page 892
35.3 Clinical Immunology......Page 896
■ Techniques & Applications 35.3: History and Importance of Serotyping......Page 897
35.5 Computers in Clinical Microbiology......Page 903
36 The Epidemiology of Infectious Disease......Page 906
■ Historical Highlights 36.1: John Snow—The First Epidemiologist......Page 907
36.2 Measuring Frequency: The Epidemiologist’s Tools......Page 908
36.3 Recognition of an Infectious Disease In a Population......Page 909
36.4 Recognition of an Epidemic......Page 910
36.5 The Infectious Disease Cycle: Story of a Disease......Page 912
■ Historical Highlights 36.3: The First Indications of Person-to-Person Spread of an Infectious Disease......Page 917
36.7 Emerging and Reemerging Infectious Diseases and Pathogens......Page 918
36.8 Control of Epidemics......Page 921
■ Historical Highlights 36.4: The First Immunizations......Page 923
■ Historical Highlights 36.5: 1346—The First Recorded Biological Warfare Attack......Page 926
36.10 Global Travel and Health Considerations......Page 928
36.11 Nosocomial Infections......Page 929
37 Human Diseases Causedby Viruses and Prions......Page 934
37.1 Airborne Diseases......Page 935
■ Disease 37.1: Reye’s and Guillain-Barré Syndromes......Page 939
37.2 Arthropod-Borne Diseases......Page 943
■ Disease 37.2: Viral Hemorrhagic Fevers— A Microbial History Lesson......Page 944
37.3 Direct Contact Diseases......Page 946
37.4 Food-Borne and Waterborne Diseases......Page 960
37.5 Zoonotic Diseases......Page 962
37.6 Prion Diseases......Page 965
38 Human Diseases Caused by Bacteria......Page 968
38.1 Airborne Diseases......Page 969
■ Historical Highlights 38.1:The Hazards of Microbiological Research......Page 981
38.3 Direct Contact Diseases......Page 985
■ Disease 38.2: Biofilms......Page 990
■ Disease 38.3: Antibiotic-Resistant Staphylococci......Page 993
■ Disease 38.4: A Brief History of Syphilis......Page 995
38.4 Food-Borne and Waterborne Diseases......Page 1000
■ Techniques & Applications 38.5: Clostridial Toxins as Therapeutic Agents—Benefits of Nature’s Most Toxic Proteins......Page 1004
38.6 Zoonotic Diseases......Page 1008
38.7 Dental Infections......Page 1012
39.1 Pathogenic Fungi and Protists......Page 1018
39.2 Airborne Diseases......Page 1020
39.3 Arthropod-Borne Diseases......Page 1022
■ Disease 39.1: A Brief History of Malaria......Page 1023
39.4 Direct Contact Diseases......Page 1029
39.5 Food-Borne and Waterborne Diseases......Page 1033
39.6 Opportunistic Diseases......Page 1037
■ Disease 39.2:The Emergence of Candidiasis......Page 1039
40 Microbiology......Page 1044
40.1 Microorganism Growth in Foods......Page 1045
40.2 Microbial Growth and Food Spoilage......Page 1047
40.3 Controlling Food Spoilage......Page 1049
■ Historical Highlights 40.1: An Army Travels on Its Stomach......Page 1051
40.4 Food-Borne Diseases......Page 1053
■ Historical Highlights 40.2: Typhoid Fever and Canned Meat......Page 1054
40.5 Detection of Food-Borne Pathogens......Page 1056
40.6 Microbiology of Fermented Foods......Page 1057
■ Techniques & Applications 40.3: Chocolate: The Sweet Side of Fermentation......Page 1058
■ Techniques & Applications 40.4: Starter Cultures, Bacteriophage Infections, and Plasmids......Page 1060
40.7 Microorganisms as Foods and Food Amendments......Page 1067
41 Applied and Industrial Microbiology......Page 1070
41.1 Water Purification and Sanitary Analysis......Page 1071
■ Techniques & Applications 41.1: Waterborne Diseases,Water Supplies, and Slow Sand Filtration......Page 1072
41.2 Wastewater Treatment......Page 1075
41.3 Microorganisms Used in Industrial Microbiology......Page 1081
■ Techniques & Applications 41.2: The Potential of Thermophilic Archaea in Biotechnology......Page 1082
41.4 Microorganism Growth in Controlled Environments......Page 1085
41.5 Major Products of Industrial Microbiology......Page 1091
41.6 Biodegradation and Bioremediation by Natural Communities......Page 1096
■ Microbial Diversity & Ecology 41.3: Methanogens— A New Role for a Unique Microbial Group......Page 1099
41.7 Bioaugmentation......Page 1101
■ Microbial Diversity & Ecology 41.4: A Fungus with a Voracious Appetite......Page 1102
41.8 Microbes As Products......Page 1103
■ Techniques & Applications 41.5: Streptavidin-Biotin Binding and Biotechnology......Page 1105
41.9 Impacts of Microbial Biotechnology......Page 1107
Appendix I A Review of the Chemistry of Biological Molecules......Page 1110
Appendix II Common Metabolic Pathways......Page 1122
Glossary......Page 1130
Credits......Page 1166
Index......Page 1174