BiologyofMicroorganismsFifth Edition

Thomas D. BrockI'niversitv of Wisconsin

Michael T. MadiganSouthern Illinois University

PRENTICE HALL INTERNATIONAL, INC

ContentsPreface iIX

1 Introduction: An Overviewof Microbiology and CellBiology 1

1.1 Microorganisms as Cells 21.2 Cell Structure 81.3 The Procaryotic Cell 101.4 The Eucaryotic Cell 131.5 Algae 141.6 Fungi 151.7 Lichens 181.8 Protozoa 191.9 The Slime Molds 191.10 Classification of Living Organisms

211.11 Populations, Communities, and

Ecosystems 221.12 The Laboratory Study of

Microorganisms 241.13 Microscopy 241.14 The Culture of Microorganisms 281.15 Sterilization and Aseptic Technique

301.16 Procedures for Isolating

Microorganisms from Nature 321.17 The Impact of Microorganisms on

» Human Affairs 331.18 A Brief History of Microbiology 35

Study Questions 40Supplementary Readings 41

Z Cell Chemistry 42

2.1 Atoms, Molecules, and ChemicalBonding 42

2.2 Chemical Bonds 432.3 Small Molecules: Monomers 46

2.4 From Carbohydrate toPolysaccharide 46

2.5 From Fatty Acids to Lipids 492.6 From Nucleotides to Nucleic Acids

502.7 From Amino Acids to Proteins 522.8 Stereoisomerism 58

Study Questions 59Supplementary Readings 59

Cell Biology 60

3.3.

60

6367

81

3 • 1 The Importance of Being Small3-2 Comparative Structure

and Function of Procaryoticand Eucaryotic Cells 61

3.3 Cell Membrane: Structure3.4 Cell Membrane: Function3.5 Cell Wall: Eubacteria 723.6 Cell Wall: Archaebacteria3.7 Cell Wall: Eucaryotes 823.8 Flagella and Motility 843-9 Chemotaxis in Bacteria 893 10 Procaryotic Cell Surface Structures

and Cell Inclusions 933.11 Gas Vesicles 943.12 Bacterial Endospores 95

.13 Eucaryotic Organelles 100

. 14 Relationships of Chloroplasts andMitochondria to Bacteria 103

3 15 Arrangement of DNA in Procaryotes104

3.16 The Eucaryotic Nucleus 1053.17 Cell Division and Sexual

Reproduction 1073 18 Comparisons of the Procaryotic and

Eucaryotic Cell 1Q9Study Questions 111Supplementary Readings 112

i i i

i v Contents

Nutrition, Metabolism,and Biosynthesis 1134.1 Nutrition and Biosynthesis 1154.2 Energy 1174.3 Activation Energy, Catalysis, and

Enzymes 1184.4 Oxidation-Reduction 1204.5 Electron Carriers 1224.6 High Energy Phosphate Compounds

and ATP 1244.7 Energy Release in Biological Systems

1254.8 Fermentation 1254.9 Respiration 128 -4.10 The Tricarboxylic Acid Cycle 1284.11 Electron Transport Systems 1284.12 Energy Conservation in the Electron

Transport System 1314.13 The Balance Sheet of Aerobic

Respiration 1344.14 Turnover of ATP and the Role of

Energy-Storage Compounds 1354.15 Alternate Modes of Energy

-Generation 1364.16 Biosynthetic Pathways: Anabolism

1374.17 Sugar Metabolism 1384.18 Amino Acid Biosynthesis 1394.19 Purine and Pyrimidine Biosynthesis

1414.20 Regulation of Enzyme Activity 1424.21 Laboratory Culture of

Microorganisms 144Study Questions 148Supplementary Readings 149

Macromoleculesand Molecular Genetics 150

5 .ol Overview 1515".2 DNA Structure 1535.3 Restriction Enzymes and Their

Action on DNA 1665.4 DNA Replication 1685.5 Genetic Elements 1715.6 Rearrangement of Genes 1735.7 Synthetic DNA 1745 8 RNA Structure and Function 1755.9 Transfer RNA 180510 Translation: The Process of Protein

Synthesis 181511 Regulation of Protein Synthesis 184

5 12 Positive Control of Protein Synthesis186

5 13 Attenuation 1885.14 Contrasts Between Gene Expression

in Procaryotes and Eucaryotes 189515 The Genetic Code 190516 Mutants and Their Isolation 1925 17 The Molecular Basis of Mutation

1945.18 Mutagens 197519 Mutagenesis and Carcinogenesis

199Study Questions 201Supplementary Readings 202

Viruses 203

6.1

6.26.36.46.5

6.6

6.76.8

6.96.10

6.11

6.12

6.13

6.14

6.15

6.16

6.176.186.19

6.20

6.216.226.236.24

The Nature of the Virus Particle204The Classification of Viruses 209The Virus Host 210Quantification of Viruses 210General Features of VirusReproduction 214Early Events of Virus Multiplication215Viral Genetics 218General Overview of BacterialViruses 220RNA Bacteriophages 220Single-Stranded Icosahedral DNABacteriophages 222Single-Stranded Filamentous DNABacteriophages 225Double-Stranded DNABacteriophages 226Large Double-Stranded DNABacteriophages 228Temperate Bacterial Viruses:Lysogeny 231A Transposable Phage: BacteriophageMu 236General Overview of Animal Viruses238Small RNA Animal Viruses 243Negative-Strand RNA Viruses 244Double-Stranded RNA Viruses—Reoviruses 248Replication of DNA Viruses ofAnimals 249Herpesviruses 251Pox Viruses 254Adenoviruses 254Retroviruses 256

Contents V

6.25 Therapy for Virus Infections 260Study Questions 261Supplementary Readings 262

/ Microbial Genetics 2637 1 Kinds of Genetic Recombination

2637.2 Genetic Transformation 2667.3 Transduction 2687.4 Plasmids 2707.5 Conjugation and Plasmid:

Chromosome Interactions 2727.6 Kinds of Plasmids and Their

Biological Significance 2787.7 Transposons and Insertion Sequences

2817.8 An Overview of the Bacterial

Genetic Map 2847.9 Genetics in Eucaryotic

Microorganisms 2857.10 Cytoplasmic Inheritance 2897.11 Yeast Genetics 290

Study Questions 294Supplementary Readings 294

O Gene Manipulation andGenetic Engineering 2958.1 Gene Cloning Systems 2968.2 Plasmids as Cloning Vectors 2968.3 Bacteriophages as Cloning Vectors

2988.4 Other Vectors 2998.5 Hosts for Cloning Vectors 3008.6 Finding the Right Clone 3018.7 Expression Vectors 3048.8 The Cloning and Expression of

Mammalian Genes in Bacteria 3068.9 In Vitro and Site-Directed

Mutagenesis 3098.10 Practical Results 3108.11 Genetic Engineering as a Microbial

^Research Tool 3138.12 Principles at the Basis of Genetic

Engineering 313Study Questions 314Supplementary Readings 314

y Growth and Its Control 315

9.4 The Growth Cycle of Populations320

9.5 Effect of Nutrient Concentration onGrowth 322

9.6 Continuous Culture 3229.7 Growth and Macromolecular

Synthesis 3239.8 The Energetics of Growth 3269.9 Cellular Differentiation and

Morphogenesis 3289.10 Effect of Environmental Factors on

Growth 3309.11 Temperature 3309.12 Acidity and Alkalinity (pH) 3359.13 Water Availability 3369.14 Oxygen 3379.15 Control of Microbial Growth: Heat

Sterilization 3409.16 Control of Microbial Growth:

Radiation 3449.17 Filter Sterilization 3469.18 Chemical Control of Microbial

Growth 3489.19 Germicides, Disinfectants, and

Antiseptics 3499.20 Chemotherapeutic Agents 3519.21 Some Aspects of Food Microbiology

353Study Questions 356Supplementary Readings 356

1 U MicrobialBiotechnology 357

9.1 Cell Growth 3159.2 Population Growth 3169.3 Measurement of Growth 317

10.1 Industrial Microorganisms 35810.2 Kinds of Industrial Products 35910.3 Growth and Product Formation in

Industrial Processes 36010.4 The Characteristics of Large-Scale

Fermentations 36310.5 Scale-Up of the Fermentation Process

36510.6 Antibiotics 36610.7 Vitamins and Amino Acids 37510.8 Microbial Bioconversion 37710.9 Enzyme Production by

Microorganisms 37710.10 Vinegar 37910.13 Citric Acid and Other Organic

Compounds 38010.12 Yeasts in Industry 38110.13 Alcohol and Alcoholic Beverages

383

v i Contents

10.14 Food From Microorganisms 38710.15 Production of Mammalian Products

by Engineered Microorganisms 389Study Questions 390Supplementary Readings 390

1 1 Host-ParasiteRelationships 391

11.1 Microbial Interactions with HigherOrganisms 392

11.2 Normal Flora of the Skin 39211.3 Normal Flora of the Oral Cavity

39311.4 Normal Flora of the Gastrointestinal

Tract 39611.5 Normal Flora of Other Body Regions

39911.6 Germ-Free Animals 40011.7 Nonspecific Host Defenses 40111.8 Entry of the Pathogen Into the Host

40411.9 Colonization and Growth 40511.10 Exotoxins 40711.11 Enterotoxins 41011.12 Endotoxins 41211.13 Virulence and Attenuation 41311.14 Interaction of Pathogens with

Phagocytic Cells 41411.15 Growth of the Pathogen

Intracellularly 41911.16 Inflammation 42011.17 Chemotherapy 422

Study Questions 427Supplementary Readings 427

Immunologyand Immunity 428

12.11*212.312.4

12.5

12.6

12.712.812.9

Immunogens and Antigens 429Immunoglobulins (Antibodies) 430Cells of the Immune System 434Histocompatability Antigens and T-Cell Receptors 436The Mechanism of AntibodyFormation 439Genetics and Evolution ofImmunoglobulins and T-CellReceptors 441Monoclonal Antibodies 446Antigen-Antibody Reactions 448ELISA and Radioimmunoassay 453

12.10 Cell-Mediated Immunity 45712.11 Allergy, Immune Tolerance, and

Autoimmunity 46012.12 Complement and Complement

Fixation 46312.13 Applied Immunology: Immunization

Against Infectious Diseases 468Study Questions 472Supplementary Readings 473

Clinical and DiagnosticMicrobiology 474

13-1 Isolation of Pathogens from ClinicalSpecimens 474

13-2 Growth-Dependent IdentificationMethods 479

133 Testing Cultures for AntibioticSensitivity 483

13-4 Diagnostic Virology 48413-5 Safety in the Clinical Laboratory

48513-6 Fluorescent Antibodies 4861 .̂7 Monoclonal Antibodies 48713-8 Diagnostic Procedures Using ELISA

Tests 48713-9 Agglutination Tests Used in the

Clinical Laboratory 49113-10 Immunoblot Procedures 49113 11 Diagnostic Techniques Using

Nucleic Acids 494Study Questions 496Supplementary Readings 497

1 4 Epidemiology and PublicHealth Microbiology 498

14.1 The Science of Epidemiology 49814.2 Terminology 49914.3 Disease Reservoirs 49914.4 Epidemiology of AIDS 50014.5 Modes of Infectious Disease

Transmission 50214.6 Nature of the Host Community 50514.7 Hospital-Acquired (Nosocomial)

Infections 50714.8 Public Health Measures for the

Control of Epidemics 50814.9 Global Health Considerations 510

Study Questions 512Supplementary Readings 512

Contents vii

15 MajorMicrobial Diseases 513

15.1 Airborne Transmission of Pathogens513

15.2 Respiratory Infections: Bacterial514

15.3 Mycobacterium and Tuberculosis519

15.4 Respiratory Infections: Viral 52015.5 Why Are Respiratory Infections So

Common? 52415.6 Sexually Transmitted Diseases 52415.7 Acquired Immune Deficiency

Syndrome (AIDS) 5291,5.8 Rabies 534159 Insect-Transmitted Diseases:

Rickettsias 5351510 Insect-Transmitted Diseases: Malaria

and Plague 53815.11 Foodborne Diseases 54115.12 Waterborne Diseases 544

Study Questions 550Supplementary Readings 551

16Metabolic Diversity amongthe Microorganisms 552

16.1 Photosynthesis 55316.2 The Role of Chlorophyll and

Bacteriochlorophyll inPhotosynthesis 554

16.3 Anoxygenic Photosynthesis 557«16.4 Oxygenic Photosynthesis 55916.5 Additional Aspects of Photosynthetic

Light Reactions 56116.6 Autotrophic CO2 Fixation 56416.7 Lithotrophy: Energy from the

Oxidation of Inorganic ElectronDonors 566

16.8 Hydrogen-Oxidizing Bacteria 56716.9 * Sulfur Bacteria 56716.10 Iron-Oxidizing Bacteria 56816.11 Ammonium and Nitrite Oxidizing

Bacteria 57216.12' Autotrophy and ATP Production

Among Lithotrophs 57216.13 Anaerobic Respiration 57316.14 Nitrate Reduction and the

Denitrification Process 57516.15 Sulfate Reduction 57616.16 Carbonate (CO2) as an Electron

Acceptor 578

16.17 Other Electron Acceptors forAnaerobic Respiration 579

16.18 Metabolic Diversity Among theHeterotrophs 580

16.19 Sugar Metabolism 58516.20 Organic Acid Metabolism 58716.21 Lipids As Microbial Nutrients 58816.22 Molecular Oxygen (O2) as a

Reactant in Biochemical Processes589

16.23 Hydrocarbon Transformations 590.16.24 Nitrogen Metabolism 592

Study Questions 596Supplementary Readings 597

1 / Microbial Ecology 598

17.1 Microorganisms in Nature 59917.2 Methods in Microbial Ecology 60017.3 Enrichment, Isolation, and Counting

Methods 60117.4 Measurements of Microbial Activity

in Nature 60517.5 Stable Isotopes and Their Use in

Microbial Biogeochemistry 60917.6 Aquatic Habitats 61117.7 Terrestrial Environments 613178 Deep-Sea Microbiology 61417.9 Hydrothermal Vents 6l617.10 Global Biogeochemical Cycles 62017.11 Biogeochemical Cycles: Carbon

62117.12 Methane and Methanogenesis 6221713 The Rumen Microbial Ecosystem

62517.14 Biogeochemical Cycles: Nitrogen

6281715 Biogeochemical Cycles: Sulfur 6301716 Biogeochemical Cycles: Iron 63217.17 Microbial Mining 6341718 Biogeochemical Cycles: Trace Metals

and Mercury 63717.19 Petroleum and Natural Gas

(Methane) Biodegradation 6391720 Biodegradation of Xenobiotics 6401721 Sewage and Wastewater

Microbiology 6411722 Plant-Microbe Interactions 64417.23 Agrobacterium/Plant Interactions

64517.24 Rhizobium: Legume Symbiosis 648

Study Questions 655Supplementary Readings 656

viii Contents

1 0 Molecular Systematics andMicrobial Evolution 657

18.1 Evolution of the Earth and EarliestLife Forms 657Molecular Approaches to BacterialPhylogeny: Nucleic Acid Sequencing663Ribosomal RNAs as EvolutionaryChronometers 664Microbial Phylogeny as Revealed byRibosomal RNA Sequencing 667Eubacteria 670Archaebacteria 673Eucaryotes 674Characteristics of the PrimaryKingdoms 675Taxonomy, Nomenclature, andBergey's Manual 678

18.10 Molecular Taxonomic Approaches:DNA Base Composition and NucleicAcid Hybridization 680Study Questions 682Supplementary Readings 682

18.2

18.3

18.4

18.518.618.718.8

18.9

1 9 The Bacteria 683

19119.219.319419-5

19619719819919-1019-1119-12191319rl419.15191619.1,719-18

683Phototrophic BacteriaCyandbacteria 697Prochlorophytes 700Nitrifying Bacteria 701Sulfur and Iron Oxidizing Bacteria703Hydrogen Bacteria 705Methylotrophs 707Sulfate Reducing Bacteria 711Acetogenic Bacteria 714Budding Bacteria 715Spirilla 719Spirochetes 723Gliding Bacteria 726Sheathed Bacteria 732The Pseudomonads 734Nitrogen-Fixing Bacteria 736Acetic Acid Bacteria 738Zymomonas 739

1919 Vibrio and Related Genera 7391920 Enteric Bacteria 74119-21 Gram-Negative Cocci 7451922 Rickettsias 74619.23 Chlamydias 74719-24 Gram-Positive Cocci 74919 25 Lactic Acid Bacteria 7 5119 26 Endospore-Forming Bacteria 7551927 Mycoplasmas 7591928 Actinomycetes 76119-29 Coryneform Bacteria 76119 30 Propionic Acid Bacteria 7631931 Mycobacterium 76419 32 Filamentous Actinomycetes 76619 33 Halophilic Archaebacteria 76919-34 Methane-Producing Bacteria:

Methanogens 77319.35 Sulfur-Dependent Archaebacteria

7811936 Thermoplasma 78619-37 Archaebacteria: Earliest Life Forms?

787Supplementary Readings 788

Appendix 1: EnergyCalculations 789

Appendix 2: TheMathematics of Growth andChemostat Operation 793

Appendix 3: Bergey'sClassification of Bacteria796

Glossary soo

Credits 807

Index 809