BROC KEleventh Edition

BIOLOGY O FMICROORGANISM S

Michael T. Madigan

John M. Martinko

NIU NIT IPRINCIPLES OF MICROBIOLOG Y

Chapter 1

Microorganisms and Microbiolog yChapter 2

An Overview of Microbial Life

2 1Chapter 3

Macromolecules

38Chapter 4

Cell Structure/ Function

55Chapter 5

Nutrition, Laboratory Culture, and Metabolism of Microorganisms

101Chapter 6

Microbial Growth

135Chapter 7

Essentials of Molecular Biology

166Chapter 8

Metabolic Regulation

205Chapter 9

Essentials of Virology

230Chapter 10 Bacterial Genetics

256

U NIT I IEVOLUTIONARY MICROBIOLOGY AND MICROBIAL DIVERSIT Y

Chapter 11 Microbial Evolution and Systematics

299Chapter 12 Prokaryotic Diversity: The Bacteria

329Chapter 13 Prokaryotic Diversity: The Archaea

419Chapter 14 Eukaryotic Cell Biology and Eukaryotic Microorganisms

447Chapter 15 Microbial Genomics

479Chapter 16 Viral Diversity

502

U N IT IIIMETABOLIC DIVERSITY AND MICROBIAL ECOLOG Y

Chapter 17 Metabolic Diversity

53 1Chapter 18 Methods in Microbial Ecology

593Chapter 19 Microbial Ecology

613

U NIT I V IMMUNOLOGY, PATHOGENICITY, AND HOST RESPONSE S

Chapter 20 Microbial Growth Control

669Chapter 21 Microbial Interactions with Humans

700Chapter 22 Essentials of Immunology

727Chapter 23 Molecular Immunology

761Chapter 24 Diagnostic Microbiology and Immunology

778

NIT VMICROBIAL DISEASE S

Chapter 25 Epidemiology

817Chapter 26 Person-to-Person Microbial Diseases

847Chapter 27 Animal-Transmitted, Arthropod-Transmitted, and Soilborne Microbial Diseases

885Chapter 28 Wastewater Treatment, Water Purification, and Waterborne Microbial Diseases

906Chapter 29 Food Preservation and Foodborne Microbial Diseases

923

E U N IT VIMICROORGANISMS AS TOOLS FOR INDUSTRY AND RESEARC H

Chapter 30 Industrial Microbiology

94 1Chapter 31 Genetic Engineering and Biotechnology

969

PREFACE

XX111

CHAPTER 4CELL STRUCTURE/FUNCTIO N

EU N I T I

I MICROSCOPY AND CELL MORPHOLOGY

5 6

PRINCIPLES OF MICROBIOLOGY

4 .1 Light Microscopy

56

CHAPTER 1

4.2 Three-Dimensional Imaging :

MICROORGANISMS AND MICROBIOLOGY

1

Interference Contrast, Atomic Force ,

I INTRODUCTION TO MICROBIOLOGY

3

and Confocal Scanning LaserMicroscopy

601 .1

Microbiology

3

4 .3

Electron Microscopy

621 .2

Microorganisms as Cells

3

4 .4 Cell Morphology and the Significanc e1 .3

Microorganisms and Their Natural

of Being Small

63Environments

5

II CELL MEMBRANES AND CELL WALLS

661 .4

The Impact of Microorganisms onHumans

6

4.5 Cytoplasmic Membrane: Structure

66

II PATHWAYS OF DISCOVERY IN MICROBIOLOGY

9

4.6 Cytoplasmic Membrane: Function

69

4.7 Membrane Transport Systems

7 11 .5

The Historical Roots of Microbiology :

4.8

The Cell Wall of Prokaryotes :Hooke, van Leeuwenhoek, and Cohn

9

Peptidoglycan and Related Molecules

741 .6 Pasteur, Koch, and Pure Cultures

11

4 .9 The Outer Membrane of Gram-Negativ e1 .7

Microbial Diversity and the Rise of

Bacteria

79General Microbiology

16

lII SURFACE STRUCTURES AND INCLUSIONS O F1 .8 The Modern Era of Microbiology

17

PROKARYOTES

82

CHAPTER 2

4.10 Bacterial Cell Surface Structures

82

AN OVERVIEW OF MICROBIAL LIFE

21

4 .11 Cell Inclusions

83

I CELL STRUCTURE AND EVOLUTIONARY HISTORY 22

4 .12 Gas Vesicles

85

4.13 Endospores

872.1

Elements of Cell and Viral Structure

22

IV MICROBIAL LOCOMOTION

9 12 .2 Arrangement of DNA in Microbial Cells 24

2 .3

The Tree of Life

26

4 .14 Flagella and Motility

92

II MICROBIAL DIVERSITY

28

4 .15 Gliding Motility

95

4.16 Cell Motion as a Behavioral Response :2.4 Physiological Diversity of

Chemotaxis and Phototaxis

9 7Microorganisms

28

2.5

Prokaryotic Diversity

30

2.6 Eukaryotic Microorganisms

35

CHAPTER 5NUTRITION, LABORATORY CULTURE ,AND METABOLISM OF MICROORGANISMS 10 1

CHAPTER 3

MACROMOLECULES

38

I NUTRITION AND CULTURE OF MICROORGANISMS 10 2

I CHEMICAL BONDING AND WATER IN LIVING

5 .1

Microbial Nutrition

10 2

SYSTEMS

39

5 .2 Culture Media

105

3 .1

Strong and Weak Chemical Bonds

39

5 .3 Laboratory Culture of Microorganisms 107

3.2 An Overview of Macromolecules

II ENERGETICS AND ENZYMES

108

and Water as the Solvent of Life

42

5 .4

Bioenergetics

10 8

II NONINFORMATIONAL MACROMOLECULES

43

5 .5 Catalysis and Enzymes

11 0

3.3 Polysaccharides

43

III OXIDATION-REDUCTION AND ENERGY-RIC H

3.4 Lipids

45

COMPOUNDS

11 2

III INFORMATIONAL MACROMOLECULES

46

5 .6 Oxidation-Reduction

11 2

3 .5

Nucleic Acids

46

5 .7 NAD as a Redox Electron Carrier

114

.6 Amino Acids and the Peptide Bond

48

5 .8 Energy-Rich Compounds and Energy3

3.7

Proteins : Primary and Secondary

Storage

11 6

Structure

50

IV MAJOR CATABOLIC PATHWAYS, ELECTRON

3.8 Proteins : Higher Order Structure and

TRANSPORT, AND THE PROTON MOTIVE FORCE 11 7

Denaturation

51

5 .9 Energy Conservation : Options

117

5 .10 Glycolysis as an Example of

II DNA STRUCTURE

16 9Fermentation

118

7 .2

DNA Structure : The Double Helix

16 95 .11 Respiration and Membrane-Associated

7.3

DNA Structure : Supercoiling

17 2Electron Carriers

120

7.4

Chromosomes and Other Geneti c5 .12 Energy Conservation from the Proton

Elements

17 4Motive Force

123

III DNA REPLICATION

17 6V CARBON FLOW IN RESPIRATION AND CATABOLIC

7.5 DNA Replication: Templates an dALTERNATIVES

126

Enzymes

17 65 .13 Carbon Flow in Respiration: The Citric

7.6

DNA Replication: The Replication Fork 17 7Acid Cycle

12 75 .14 Catabolic Alternatives

127

IV TOOLS FOR MANIPULATING DNA

18 2

VI BIOSYNTHESIS

130

7.7

Restriction Enzymes and Hybridization 18 27.8 Sequencing and Synthesizing DNA

1845.15 Biosynthesis of Sugars and

7.9

Amplifying DNA : The PolymerasePolysaccharides

130

Chain Reaction

18 65 .16 Biosynthesis of Amino Acid s

and Nucleotides

131

V RNA SYNTHESIS : TRANSCRIPTION

188

5.17 Biosynthesis of Fatty Acids and Lipids 132

7.10 Overview of Transcription

1887 .11 Diversity of Sigma Factors, Consensus

CHAPTER 6

Sequences, and Other RN A

MICROBIAL GROWTH

135

Polymerases

1907.12 Transcription Terminators

19 1BACTERIAL CELL DIVISION

136

7 .13 The Unit of Transcription

1926 .1

Cell Growth and Binary Fission

136

VI PROTEIN SYNTHESIS

1936 .2

Fts Proteins, the Cell Division Plane,and Cell Morphology

137

7 .14 The Genetic Code

193

6.3 Peptidoglycan Synthesis and Cell

7 .15 Transfer RNA

196

Division

139

7 .16 Translation: The Process of Protei n

GROWTH OF BACTERIAL POPULATIONS

140

Synthesis

1997.17 Folding and Secreting Proteins

2026.4 Growth Terminology and the Concep t

of Exponential Growth

140

CHAPTER 8

6.5 The Mathematics of Bacterial Growth 142

METABOLIC REGULATION

2056.6 The Growth Cycle

142

I OVERVIEW OF REGULATION

206III MEASURING MICROBIAL GROWTH

1448 .1

Major Modes of Regulation

2066.7 Direct Measurements of Microbial

II REGULATION OF ENZYME ACTIVITY

207Growth : Total and Viable Counts

144

6 .8 Indirect Measurements of Microbial

8 .2 Noncovalent Enzyme Inhibition

207

Growth : Turbidity

147

8 .3 Covalent Modification of Enzymes

209

6 .9 Continuous Culture : The Chemostat

148

III DNA-BINDING PROTEINS AND REGULATION

IV ENVIRONMENTAL EFFECTS ON MICROBIAL

OF TRANSCRIPTION BY NEGATIV E

GROWTH: TEMPERATURE

150

AND POSITIVE CONTROL

210

6 .10 Effect of Temperature on Growth

150

8 .4 DNA Binding Proteins

21 1

6 .11 Microbial Growth at Cold Temperatures 152

8 .5

Negative Control of Transcription :

6.12 Microbial Growth at High Temperatures 154

Repression and Induction

21 2

V ENVIRONMENTAL EFFECTS ON MICROBIAL

8 .6 Positive Control of Transcription

21 5

GROWTH : PH, OSMOLARITY, AND OXYGEN

157

IV GLOBAL REGULATORY MECHANISMS

216

6 .13 Microbial Growth at Low or High pH

157

8 .7 Global Control and the lac Operon

216

6 .14 Osmotic Effects on Microbial Growth

158

8 .8 The Stringent Response

218

6 .15 Oxygen and Microbial Growth

160

8 .9 Other Global Control Networks

219

6 .16 Toxic Forms of Oxygen

163

8 .10 Quorum Sensing

22 1

V OTHER MECHANISMS OF REGULATION

222CHAPTER 7

ESSENTIALS OF MOLECULAR BIOLOGY

166

8 .11 Attenuation

222

8 .12AND GENE EXPRESSION

167

.12 Signal Transduction andTwo-Component Regulatory Systems 224

7.1

Macromolecules and Genetic

8.13 Regulation of Chemotaxis

226

Information

167

8 .14 RNA Regulation and Riboswitches

228

CHAPTER 9 WO-ESSENTIALS OF VIROLOGY

230

UNIT I IVIRUS AND VIRION

231

EVOLUTIONARY MICROBIOLOGY AN D

9 .1

General Properties of Viruses

231

MICROBIAL DIVERSITY

9.2

Nature of the Virion

232

CHAPTER 1 1

GROWTH AND QUANTIFICATION

236

MICROBIAL EVOLUTION AN D

9.3 The Virus Host

236

SYSTEMATICS

299

9.4 Quantification of Viruses

236

I

EARLY EARTH, THE ORIGIN OF LIFE ,

III VIRAL REPLICATION

238

AND MICROBIAL DIVERSIFICATION

300

9.5

General Features of Virus Replication

238

11 .1 Evolution of Earth and Earliest Life

9.6

Virus Multiplication : Attachment

Forms

300

and Penetration

239

11 .2 Primitive Life : The RNA World an d

9.7

Virus Multiplication : Production of

Molecular Coding

303

Viral Nucleic Acid and Protein

240

11 .3 Primitive Life: Energy and Carbon

IV VIRAL DIVERSITY

242

Metabolism

30411 .4 Eukaryotes and Organelles :

9.8 Overview of Bacterial Viruses

242

Endosymbiosis

3079.9 Virulent Bacteriophages and T4

243

II METHODS FOR DETERMINING EVOLUTIONAR Y9.10 Temperate Bacteriophages

245

RELATIONSHIPS

3099.11 Bacteriophage Lambda

246

9.12 Overview of Animal Viruses

250

11 .5 Evolutionary Chronometers

309

9.13 Retroviruses

251

11 .6 Ribosomal RNA Sequences as a Too l

V SUB-VIRAL PARTICLES

253

of Molecular Evolution

30911 .7 Signature Sequences, Phylogenetic

9.14 Viroids and Prions

253

Probes, and Microbial Community

CHAPTER 10

Analyses

31 2

BACTERIAL GENETICS

256

III MICROBIAL EVOLUTION

314

MUTATION AND RECOMBINATION

257

11 .8 Microbial Phylogeny Derived from

10.1 Mutations and Mutants

257

Ribosomal RNA Sequences

314

10 .2 Molecular Basis of Mutation

259

11 .9 Characteristics of the Domain s

10 .3 Mutation Rates

262

of Life

31 6

10 .4 Mutagenesis

263

IV MICROBIAL TAXONOMY AND ITS RELATIONSHI P

10 .5 Mutagenesis and Carcinogenesis :

TO PHYLOGENY

31 8

The Ames Test

266

11 .10 Classical Taxonomy

31 810 .6 Genetic Recombination

267

11 .11 Molecular Taxonomy

320

GENETIC EXCHANGE IN PROKARYOTES

268

11 .12 The Species Concept in Microbiology 324

10 .7 Transformation

2 68

11 .13 Nomenclature and Bergey 's Manual

326

10 .8 Transduction

27 1

10 .9 Plasmids : General Principles

274

CHAPTER 1 2

10 .10 Types of Plasmids and Their Biological

PROKARYOTIC DIVERSITY : THE BACTERIA 329

Significance

276

I THE PHYLOGENY OF BACTERIA

33 110 .11 Conjugation : Essential Features

278

12 .1 Phylogenetic Overview of Bacteria

33 110 .12 The Formation of Hfr Strains an d

Chromosome Mobilization

279

II PHYLUM I : PROTEOBACTERIA

332

10 .13 Complementation

282

12 .2 Purple Phototrophic Bacteria

332

10 .14 Transposons and Insertion Sequences

284

12 .3 The Nitrifying Bacteria

335

III BACTERIAL GENETICS AND GENE CLONING

287

12 .4 Sulfur- and Iron-Oxidizing Bacteria

33 7

10 .15 Essentials of Molecular Cloning

287

12 .5 Hydrogen-Oxidizing Bacteria

340

10.16 Plasmids as Cloning Vectors

288

12 .6 Methanotrophs and Methylotrophs

342

10 .17 Bacteriophage Lambda as a Cloning

12 .7 Pseudomonas and the Pseudomonads

345

Vector

290

12 .8 Acetic Acid Bacteria

348

10 .18 In Vitro and Site-Directed Mutagenesis 292

12 .9 Free-Living Aerobic Nitrogen-FixingBacteria

348IV THE BACTERIAL CHROMOSOME

294

12 .10 Neisseria, Chromobacterium, and Relatives 350

10 .19 Genetic Map of the Escherichia coli

12 .11 Enteric Bacteria

35 1

Chromosome

294

12 .12 Vibrio and Photobacterium

355

12 .13 Rickettsias

357

12 .37 Aquifex, Thermocrinis, and Relatives

41512 .14 Spirilla

359

XV PHYLUM 17 AND 18 : NITROSPIRA AN D12 .15 Sheathed Proteobacteria : Sphaerotilus

DEFERRIBACTER

416and Leptothrix

362

12 .38 Nitrospira, Deferribacter, and Relatives

41612 .16 Budding and Prosthecate/Stalke dBacteria

36312 .17 Gliding Myxobacteria

367

CHAPTER 1 3

12 .18 Sulfate- and Sulfur-Reducing

PROKARYOTIC DIVERSITY : THE ARCHAEA 419

Proteobacteria

371

I PHYLOGENY AND GENERAL METABOLISM

420

III PHYLUM 2 AND 3 : GRAM-POSITIVE BACTERIA

13 .1 Phylogenetic Overview of theAND ACTINOBACTERIA

374

Archaea

420

12 .19 Nonsporulating, Low GC, Gram-Positive

13 .2 Energy Conservation and Autotrophy

Bacteria : Lactic Acid Bacteria

in Archaea

42 1

and Relatives

374

II PHYLUM EURYARCHAEOTA

42212 .20 Endospore-Forming, Low GC,

13 .3 Extremely Halophilic Archaea

422Gram-Positive Bacteria : Bacillus,

13 .4 Methane-Producing Archaea:Clostridium, and Relatives

379

Methanogens

42612 .21 Cell Wall-Less, Low GC, Gram-Positive

13 .5 Thermoplasmatales : Thermoplasma ,Bacteria : The Mycoplasmas

383

Ferroplasma, and Picrophilus

43012 .22 High GC, Gram-Positive Bacteria

13 .6 Hyperthermophilic Euryarchaeota :(Actinobacteria) : Coryneform

Thermococcales and Methanopyrus

432and Propionic Acid Bacteria

386

13 .7 Hyperthermophilic Euryarchaeota :12 .23 Actinobacteria : Mycobacterium

388

The Archaeoglobales

43312 .24 Filamentous Actinobacteria :

Streptomyces and other Actinomycetes 390

III PHYLUM CRENARCHAEOTA

434

IV PHYLUM 4 : CYANOBACTERIA AND

13 .8 Habitats and Energy Metabolism of

PROCHLOROPHYTES

394

Crenarchaeotes

434

394

13 .9 Hyperthermophiles from Terrestria l12 .25 Cyanobacteria

Volcanic Habitats : Sulfolobales and12 .26 Prochlorophytes and Chloroplasts

397

Thermoproteales

436

V PHYLUM 5: CHLAMYDIA

399

13 .10 Hyperthermophiles from Submarine

12 .27 The Chlamydia

399

Volcanic Habitats : Desulfurococcales

439

VI PHYLUM 6: PLANCTOMYCES/PIRELLULA

401

IV PHYLUM NANOARCHAEOTA

441

12 .28 Planctomyces : A Phylogenetically

13 .11 Nanoarchaeum

44 1

Unique Stalked Bacterium

401

V EVOLUTION AND LIFE AT HIG H

VII PHYLUM 7 : THE VERRUCOMICROBIA

402

TEMPERATURES

442

12 .29 Verrucomicrobium and Prosthecobacter

402

13 .12 Heat Stability of Biomolecules

442

VIII PHYLUM 8 : THE FLAVOBACTERIA

403

13 .13 Hyperthermophilic Archaea, H2 ,and Microbial Evolution

44412 .30 Bacteroides and Flavobacterium

403

IX PHYLUM 9 : THE CYTOPHAGA GROUP

404

CHAPTER 1 4

12 .31 Cytophaga and Relatives

404

EUKARYOTIC CELL BIOLOGY AN D

X PHYLUM 10 : GREEN SULFUR BACTERIA

405

EUKARYOTIC MICROORGANISMS

447

12 .32 Chlorobium and Other Green Sulfur

I

EUKARYOTIC CELL STRUCTURE/FUNCTION

448

Bacteria

405

14 .1 Eukaryotic Cell Structure and

XI PHYLUM 11 : THE SPIROCHETES

407

the Nucleus

448

12 .33 Spirochetes

407

14 .2 Respiratory and FermentativeOrganelles: The Mitochondrion an d

XII PHYLUM 12 : DEINOCOCCI

411

the Hydrogenosome

449

12 .34 Deinococcus/Thermus

411

14 .3 Photosynthetic Organelle : The

XIII PHYLUM 13 : THE GREEN NONSULFUR BACTERIA 412

Chloroplast

45 1

12 .35 Chloroflexus and Relatives

412

14 .4 Endosymbiosis : Relationships ofMitochondria and Chloroplasts to

XIV PHYLUM 14-16 : DEEPLY BRANCHING

Bacteria

452HYPERTHERMOPHILIC BACTERIA

414

14 .5 Other Organelles and Eukaryotic Cell

12 .36 Thermotoga and Thermodesulfobacterium 414

Structures

453

ESSENTIALS OF EUKARYOTIC GENETICS AND

16 .10 Double-Stranded RNA Viruses :MOLECULAR BIOLOGY

455

Reoviruses

520

14 .6 Replication of Linear DNA

455

16 .11 Replication of Double-Stranded DNA

14 .7 Overview of Eukaryotic Genetics

456

Viruses of Animals

52 1

14.8 RNA Processing and Ribozymes

458

16 .12 Double-Stranded DNA Viruses:

III EUKARYOTIC MICROBIAL DIVERSITY

460

Herpesviruses

52 316 .13 Double-Stranded DNA Viruses :

14 .9 Phylogeny of the Eukarya

460

Pox Viruses

52414 .10 Protozoa

463

16 .14 Double-Stranded DNA Viruses :14 .11 Slime Molds

467

Adenoviruses

52 514.12 Fungi

469

16 .15 Viruses Using Reverse Transcriptase :14 .13 Algae

472

Retroviruses and Hepadnavirus

526

CHAPTER 15

W. UNIT II IMICROBIAL GENOMICS

479

GENOMIC CLONING TECHNIQUES

480

METABOLIC DIVERSITY AND MICROBIA LECOLOGY

15 .1 Vectors for Genomic Cloning an dSequencing

480

CHAPTER 1 7

15 .2 Sequencing the Genome

483

METABOLIC DIVERSITY

53 1

15 .3 Annotating the Genome

484

I THE PHOTOTROPHIC WAY OF LIFE

533

MICROBIAL GENOMES

485

17.1 Photosynthesis

533

15.4 Prokaryotic Genomes : Sizes and ORF

17.2 Photosynthetic Pigments and Thei r

Contents

485

Location Within the Cell

534

15 .5 Prokaryotic Genomes: Bioinformatic

17.3 Carotenoids and Phycobilins

53 7

Analyses and Gene Distributions

486

17.4 Anoxygenic Photosynthesis

538

15.6 Eukaryotic Microbial Genomes

490

17 .5 Oxygenic Photosynthesis

543

III OTHER GENOMES AND THE EVOLUTION OF

17 .6 Autotrophic CO 2 Fixation : The

GENOMES

492

Calvin Cycle

54517 .7 Autotrophic CO 2 Fixation : Revers e

15 .7 Genomes of Organelles

492

Citric Acid Cycle and the15 .8 Evolution and Gene Families

495

Hydroxypropionate Cycle

54715 .9 Genomic Mining

496

II CHEMOLITHOTROPHY : ENERGY FROM THEIV GENE FUNCTION AND REGULATION

497

OXIDATION OF INORGANIC ELECTRON DONORS 54 8

15 .10 Proteomics

497

17 .8 Inorganic Electron Donors an d15 .11 Microarrays and the Transcriptome

498

Energetics

54817.9 Hydrogen Oxidation

549

CHAPTER 16

17 .10 Oxidation of Reduced Sulfu rVIRAL DIVERSITY

S02

Compounds

550

VIRUSES OF PROKARYOTES

503

17 .11 Iron Oxidation

553

16 .1 RNA Bacteriophages

503

17.12 Nitrification and Anammox

555

16 .2 Icosahedral Single-Stranded DNA

III THE ANAEROBIC WAY OF LIFE : ANAEROBI C

Bacteriophages

505

RESPIRATIONS

55 7

16 .3 Filamentous Single-Stranded DNA

17.13 Anaerobic Respiration

55 7

Bacteriophages

507

17.14 Nitrate Reduction and the

16 .4 Double-Stranded DNA Bacteriophages :

Denitrification Process

558

T7

508

17.15 Sulfate Reduction

560

16 .5 Mu: A Double-Stranded Transposable

17.16 Acetogenesis

563

DNA Bacteriophage

510

17.17 Methanogenesis

564

16 .6 Viruses of Archaea

512

17.18 Ferric Iron, Manganese, Chlorate, an d

VIRUSES OF EUKARYOTES

513

Organic Electron Acceptors

568

16 .7 Plant Viruses

513

W THE ANAEROBIC WAY OF LIFE : FERMENTATION S

16 .8 Positive-Strand RNA Viruses of

AND SYNTROPHY

571

Animals : Poliovirus and Coronaviruses 515

17 .19 Fermentations : Energetic and Redox

16 .9 Negative-Strand RNA Viruses of

Considerations

57 1

Animals : Rabies, Influenza, and

17.20 Fermentative Diversity

573

Related Viruses

517

17 .21 Svntrophy

575

V HYDROCARBON OXIDATION AND THE ROLE OF 0 2

V OTHER KEY NUTRIENT CYCLES

640

IN THE CATABOLISM OF ORGANIC COMPOUNDS 577

19 .12 The Nitrogen Cycle

64 117.22 Molecular Oxygen (02) as a Reactant

19 .13 The Sulfur Cycle

642in Biochemical Processes

577

19 .14 The Iron Cycle

64417.23 Hydrocarbon Oxidation

578

VI MICROBIAL BIOREMEDIATION

64717.24 Methanotrophy and Methylotrophy

579

19 .15 Microbial Leaching of Ores

64717.25 Hexose, Pentose, and Polysaccharide

19 .16 Mercury and Heavy MetalMetabolism

581

Transformations

64917 .26 Organic Acid Metabolism

584

19 .17 Petroleum Biodegradation

65 117 .27 Lipids as Microbial Nutrients

585

19 .18 Biodegradation of Xenobiotics

653VI NITROGEN FIXATION

586

VII MICROBIAL INTERACTIONS WITH PLANTS

65517.28 Nitrogenase and the Process of

19 .19 The Plant Environment

656Nitrogen Fixation

586

19 .20 Lichens and Mycorrhizae

65617.29 Genetics and Regulation of N2

19 .21 Agrobacterium and Crown Gall Disease 659Fixation

590

19 .22 Root Nodule Bacteria and Symbiosiswith Legumes

66 1

CHAPTER 1 8

METHODS IN MICROBIAL ECOLOGY

593

UNIT IVCULTURE-DEPENDENT ANALYSES OF MICROBIAL

IMMUNOLOGY, PATHOGENICITY,

COMMUNITIES

594

AND HOST RESPONSE S

18 .1 Enrichment and Isolation

594

CHAPTER 2018 .2 Isolation in Pure Culture

598

MICROBIAL GROWTH CONTROL

669

MOLECULAR (CULTURE-INDEPENDENT)

I PHYSICAL ANTIMICROBIAL CONTROL

67 1ANALYSES OF MICROBIAL COMMUNITIES

600

20 .1 Heat Sterilization

67 118 .3 Viability and Quantification Using

20 .2 Radiation Sterilization

67 3Staining Techniques

600

20.3 Filter Sterilization

67518 .4 Genetic Stains

602

II CHEMICAL ANTIMICROBIAL CONTROL

67718 .5 Linking Specific Genes to Specific

20 .4 Chemical Growth Control

677Organisms Using PCR

604

20 .5 Chemical Antimicrobial Agents fo r

18 .6 Environmental Genomics (Metagenomics)606

External Use

679

III MEASURING MICROBIAL ACTIVITIES IN NATURE 607

III ANTIMICROBIAL AGENTS USED IN VIVO

68 118 .7 Radioisotopes and Microelectrodes

608

20 .6 Synthetic Antimicrobial Drugs

68 118 .8 Stable Isotopes

610

20 .7 Naturally Occurring Antimicrobia lDrugs : Antibiotics

685

CHAPTER 19

20.8 ß-LactamAntibiotics : Penicillin s

MICROBIAL ECOLOGY

613

and Cephalosporins

686

MICROBIAL ECOSYSTEMS

614

20 .9 Antibiotics from Prokaryotes

687

19 .1 Populations, Guilds, and Communities 614

IV CONTROL OF VIRUSES AND EUKARYOTIC

19 .2 Environments and Microenvironments 615

PATHOGENS

688

19 .3 Microbial Growth on Surfaces and

20 .10 Antiviral Drugs

688

Biofilm

617

20 .11 Antifungal Drugs

69 1

SOIL AND FRESHWATER MICROBIAL HABITATS 619

V ANTIMICROBIAL DRUG RESISTANCE AND DRU G

19 .4 Terrestrial Environments

619

DISCOVERY

692

19 .5 Freshwater Environments

623

20 .12 Antimicrobial Drug Resistance

692

III MARINE MICROBIOLOGY

624

20 .13 The Search for New AntimicrobialDrugs

69719 .6 Marine Habitats and Microbial

Distribution

625

CHAPTER 2 1

19 .7 Deep-Sea Microbiology

627

MICROBIAL INTERACTIONS WIT H

19 .8 Hydrothermal Vents

628

HUMANS

700

IV THE CARBON AND OXYGEN CYCLES

632

I BENEFICIAL MICROBIAL INTERACTION S

19 .9 The Carbon Cycle

632

WITH HUMANS

70 1

19 .10 Syntrophy and Methanogenesis

634

21 .1 Overview of Human-Microbia l

19 .11 Carbon Cycling in Ruminant Animals 637

Interactions

701

21 .2 Normal Microbial Flora of the Skin

703

CHAPTER 23

21 .3 Normal Microbial Flora of the Oral

MOLECULAR IMMUNOLOGY

76 1

Cavity

704

I RECEPTORS AND IMMUNITY

76 2

21 .4 Normal Microbial Flora of the

23 .1 Innate Immunity and PatternGastrointestinal Tract

706

Recognition

76221 .5 Normal Microbial Flora of Other Body

23.2 Adaptive Immunity and theRegions

708

Immunoglobulin Superfamily

763HARMFUL MICROBIAL INTERACTIONS

II THE MAJOR HISTOCOMPATIBILITY COMPLE XWITH HUMANS

710

(MHC)

76521 .6 Entry of the Pathogen into the Host

710

23 .3 MHC Protein Structure

76521 .7 Colonization and Growth

712

23 .4 MHC Genes and Polymorphism

76721 .8 Virulence

713

III ANTIBODIES

76 7III VIRULENCE FACTORS AND TOXINS

71623.5 Antibody Proteins and Antige n

21 .9 Virulence Factors

716

Binding

76721 .10 Exotoxins

716

23 .6 Antibody Genes and Diversity

76821 .11 Enterotoxins

719

IV T-CELL RECEPTORS

77 021 .12 Endotoxins

72 1

IV HOST FACTORS IN INFECTION

722

23 .7 TCR Proteins and Antigen Binding

77 023.8 TCR Genes and Diversity

77 121 .13 Host Risk Factors for Infection

72 221 .14 Innate Resistance to Infection

723

V MOLECULAR SIGNALS IN IMMUNITY

77 1

23.9 Clonal Selection and Tolerance

77 223 .10 Second Signals

77 3

CHAPTER 22

23 .11 Cytokines and Chemokines

77 5

ESSENTIALS OF IMMUNOLOGY

727

OVERVIEW OF THE IMMUNE RESPONSE

72 9

22 .1 Cells and Organs of the Immune

CHAPTER 24

System

729

DIAGNOSTIC MICROBIOLOGY AN D

22 .2 The Innate Immune Response

732

IMMUNOLOGY

778

22 .3 Inflammation, Fever, and Septic

I

GROWTH-DEPENDENT DIAGNOSTIC

Shock

735

METHODS

77 9

22 .4 The Adaptive Immune Response

736

24.1 Isolation of Pathogens from Clinica l

ANTIGENS, T CELLS, AND CELLULAR

Specimens

779

IMMUNITY

Y38

24 .2 Growth-Dependent Identificatio n

22.5 Immunogens and Antigens

738

Methods

785

22.6 Presentation of Antigen to

24.3 Antimicrobial Drug Susceptibility

T Lymphocytes

739

Testing

788

22.7 T-Cytotoxic Cells and Natural Killer

24.4 Safety in the Microbiology

Cells

742

Laboratory

789

22.8 T-Helper Cells : Activating the Immune

II IMMUNOLOGY AND DIAGNOSTI C

Response

743

METHODS

792

III ANTIBODIES AND IMMUNITY

743

24 .5 Immunoassays for Infectiou s

22.9 Antibodies (Immunoglobulins)

744

Disease

792

22.10 Antibody Production

747

24 .6 Polyclonal and Monoclona l

22.11 Complement, Antibodies, and

Antibodies

795

Pathogen Destruction

749

24 .7 In Vitro Antigen-Antibody Reactions :Serology

79 7IV IMMUNITY MID PREVENTION OF INFECTIOUS

24.8 Agglutination

799DISEASE

751

24 .9 Fluorescent Antibodies

80 1

22.12 Natural Immunity

751

24 .10 Enzyme-Linked Immunosorben t22.13 Artificial Immunity

752

Assay and Radioimmunoassay

804

22.14 New Immunization Strategies

754

24.11 Immunoblot Procedures

808

V IMMUNE RESPONSE DISEASES

755

III MOLECULAR AND VISUAL CLINICA L

22.15 Allergy, Hypersensitivity, and

DIAGNOSTIC METHODS

81 0

Autoimmunity

755

24 .12 Nucleic Acid Methods

81 0

22.16 Superantigens

758

24 .13 Diagnostic Virology

812

CHAPTER 2 7

UNIT V

ANIMAL-TRANSMITTED, ARTHROPOD -MICROBIAL DISEASES

TRANSMITTED, AND SOILBORN EMICROBIAL DISEASES

885CHAPTER 25

ANIMAL-TRANSMITTED DISEASES

886EPIDEMIOLOGY

81 7

PRINCIPLES OF EPIDEMIOLOGY

818

27 .1 Rabies

88627 .2 Hantavirus Pulmonary Syndrome

88825 .1 The Science of Epidemiology

818

II ARTHROPOD-TRANSMITTED DISEASES

89025.2 The Vocabulary of Epidemiology

81 925 .3 Disease Reservoirs and Epidemics

821

27 .3 Rickettsial Diseases

890

25.4 Infectious Disease Transmission

824

27 .4 Lyme Disease

892

25.5 The Host Community

825

27 .5 Malaria

895

CURRENT EPIDEMICS

827

27 .6 West Nile Virus

89827 .7 Plague

89925.6 The AIDS Pandemic

828

III SOILBORNE DISEASES

90 125.7 Hospital-Acquired (Nosocomial )

Infections

829

27 .8 The Pathogenic Fungi

90 1

25.8 Severe Acute Respiratory

27.9 Tetanus

903

Syndrome

830

III EPIDEMIOLOGY AND PUBLIC HEALTH

831

CHAPTER 28

WASTEWATER TREATMENT, WATE R25.9 Public Health Measures for the

PURIFICATION, AND WATERBORN EControl of Disease

831

MICROBIAL DISEASES

90625.10 Global Health Considerations

835

I WASTEWATER MICROBIOLOGY AND WATE R25.11 Emerging and Reemerging Infectious

PURIFICATION

907Diseases

83625.12 Biological Warfare and Biological

28 .1 Public Health and Water Quality

907

Weapons

842

28 .2 Wastewater and Sewage Treatment

909

25.13 Anthrax as a Biological Weapon

844

28 .3 Drinking Water Purification

91 3

II WATERBORNE MICROBIAL DISEASES

914

CHAPTER 26

28.4 Sources of Waterborne Infection

91 5PERSON-TO-PERSON MICROBIAL

28.5 Cholera

916DISEASES

847

28.6 Giardiasis and Cryptosporidiosis

91 7

AIRBORNE TRANSMISSION OF DISEASES

848

28 .7 Legionellosis (Legionnaires' Disease)

919

26 .1 Airborne Pathogens

849

28 .8 Typhoid Fever and Other Waterborn e

26.2 Streptococcal Diseases

850

Diseases

920

26.3 Corynebacterium and Diphtheria

852

26.4 Bordetella and Whooping Cough

853

CHAPTER 29

26.5 Mycobacterium, Tuberculosis, and

FOOD PRESERVATION AND FOODBORN E

Leprosy

854

MICROBIAL DISEASES

923

26 .6 Neisseria meningitides, Meningitis, and

I

FOOD PRESERVATION AND MICROBIAL

Meningococcemia

857

GROWTH

924

26.7 Viruses and Respiratory Infections

858

29 .1 Microbial Growth and Food Spoilage

92426.8 Colds and Influenza

861

29 .2 Food Preservation

925

DIRECT CONTACT TRANSMISSION OF

29 .3 Fermented Foods

928

DISEASES

864

II MICROBIAL SAMPLING AND FOOD POISONING

930

26.9 Staphylococcus

864

29 .4 Foodborne Diseases and Microbia l

26.10 Helicobacter pylori and Gastric

Sampling

930Ulcers

866

29 .5 Staphylococcal Food Poisoning

93 126 .11 Hepatitis Viruses

867

29 .6 Clostridial Food Poisoning

932

III SEXUALLY TRANSMITTED INFECTIONS

869

III FOOD INFECTION

934

26.12 Gonorrhea and Syphilis

870

29 .7 Salmonellosis

934

26.13 Chlamydia, Herpes, and

29 .8 Pathogenic Escherichia coli

935

Trichomoniasis

873

29 .9 Campylobacter

93726 .14 Acquired Immunodeficiency

29 .10 Listeriosis

937Syndrome: AIDS and HIV

875

29 .11 Other Foodborne Infectious Diseases

938

CHAPTER 3 1'UNIT VI

GENETIC ENGINEERING AND

MICROORGANISMS AS TOOLS FOR

BIOTECHNOLOGY

969INDUSTRY AND RESEARCH

I THE TECHNIQUES OF GENETIC ENGINEERING 97 0

CHAPTER 30

31 .1 Review of Principles Underlying

INDUSTRIAL MICROBIOLOGY

941

Genetic Engineering

970

INDUSTRIAL MICROOGANISMS AND PRODUCT

31 .2 Hosts for Cloning Vectors

972

FORMATION

942

31 .3 Finding the Right Clone

97331 .4 Specialized Vectors

97530 .1 Microorganisms and Their Products

942

31 .5 Expression of Mammalian Genes in30.2 Primary and Secondary Metabolites

943

Bacteria

97830.3 Characteristics of Large-Scale

II PRACTICAL APPLICATIONS OF GENETI CFermentations

94530.4 Fermentation Scale-Up

946

ENGINEERING

98 1

II MAJOR INDUSTRIAL PRODUCTS FOR

31 .6 Production of Insulin : The Beginnings

THE HEALTH INDUSTRY

944

of Commercial Biotechnology

98 131 .7 Other Mammalian Proteins an d

30.5 Antibiotics : Isolation and

Products

984Characterization

947

31 .8 Genetically Engineered Vaccines

98430.6 Industrial Production of Penicillins

31 .9 Genetic Engineering in Animal andand Tetracyclines

951

Human Genetics

98630.7 Vitamins and Amino Acids

953

31 .10 Genetic Engineering in Plant30.8 Steroids and the Biotransformation

Agriculture : Transgenic Plants

989Process

95530.9 Enzymes as Industrial Products

955

III MAJOR INDUSTRIAL PRODUCTS FOR TH EFOOD AND BEVERAGE INDUSTRIES

958

APPENDIX 130.10 Alcohol and Alcoholic Beverages

958

ENERGY CALCULATIONS IN MICROBIAL30.11 Vinegar Production

963

BIOENERGETICS

A- 1

30.12 Citric Acid and Other Organic

APPENDIX 2

Compounds

964

BERGEY'S MANUAL OF SYSTEMATIC BACTERIOLOGY,30.13 Yeast as a Food and Food

SECOND EDITION

A- 5Supplement

965

GLOSSARY

G- 130.14 Mushrooms as a Food Source

966

INDEX

I-1