microbiology - gbv · energy and metabolism 139 concepts of energy 140 thermodynamics is the study...

Microbiologysecond e d i t i o n ^ ^ ^*

Daniel LimUniversity of South Florida

Technische Universitat DarmstadtFACHBEREICH 10 — BIOLOGIE

— B i b l i o t h e k —SchnittspahnstraBe 10

D-6 4 2 8 7 D a r m s t a d t

[[•McGraw-HillBoston, Massachusetts Burr Ridge, Illinois Dubuque, Iowa

Madison, Wisconsin New York, New York San Francisco, California St. Louis, Missouri

v

BRIEF CONTENTS

part oneIntroduction to Microbiology

[ 1 ] Foundations of Modern Microbiology 1

[ 2 ] Cell Morphology and Microscopy 17

[ 3 ] Composition and Structure of Procaryotic andEucaryotic Cells 41

part twoMicrobial Growth and Metabolism

[4] Nutrition and Environmental Influence 79

[5] Growth and Control of Growth 105

[6] Energy and Metabolism 139

[7] Photosynthesis and Other Metabolic Pathways 177

o

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part threeMicrobial Genetics

[ 8 ] Molecular Genetics 211

[ 9 ] > Microbial Genetics 245

[ 1 0 ] Recombinant DNA Technology 271

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part fourSurvey of Microorganisms

[ 1 1 ] Procaryotes: The Bacteria and the Archaea 305

[ 1 2 ] The Eucaryotic Microorganisms 349

[ 1 3 ] The Viruses 383

part fiveMicrobial Interactionswith Other Organisms

[14] Symbiosis 417

[15] Host-Parasite Relationships 439

[16] Immunology 467

[17J Infectious Diseases 497

[18] Public Health and Epidemiology 549

part sixEnvironmental and EconomicImpact of Microorganisms

[ 1 9 ] Microbial Ecology 569

[ 2 0 ] Food and Industrial Microbiology 607

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VI

Preface xixLearning Aids xx i

part oneIntroduction to Microbiology

[ chapter 1 ]FOUNDATIONS OF MODERNMICROBIOLOGY 1

Historical Perspectives 2Microorganisms Were Once Thought to AriseSpontaneously 2 *

The Germ Theory of Disease States That InfectiousDiseases Are Caused by Microorganisms 5

Immunology Is the Study of Resistance of Organisms toInfection 7

Viruses Are Submicroscopic Filterable Agents Consistingof Nucleic Acid Surrounded by a Protein Coat 8 .

Modern Microbiology 9Recombinant DNA Technology Involves the Manipulationof Genes in Organisms 9

Microbes in Space 10

The Polymerase Chain Reaction Permits RapidAmplification of Genes Outside the Cell 11

Microorganisms Have Important Roles in Medicine, theEnvironment, Agriculture, and Industry 11

Perspective 13

Summary 14

Evolution and Biodiversity 14

[ chapter 2 ]CELL MORPHOLOGY ANDMICROSCOPY 17

Size, Shape, and Arrangement of Procaryotic Cells 18

Size and Scale: Procaryotes Are Small 18

Procaryotes Have Different Shapes 19

Procaryotes Have Different Cell Arrangements 19

Microscopy 20The Compound (Bright-Field) Light MicroscopeMagnifies Objects Tpo Small to Be Seen by theHuman Eye 21

Stains Increase the Contrast between a Specimenand Its Background 25" ...

: ; .The Gram Stain 26 . ' '

The Dark-Field Microscope Provides Contrast inSpecimens That Normally Lack Sufficient Contrastto Be'Seen with the Bright-Field Microscope 28

The Phase-Contrast Microscope Amplifies SmallDifferences in Refractive Indices to EnhanceSpecimen Contrast 28

The Fluorescence Microscope Detects FluorescentObjectsThat Are Illuminated by Ultraviolet or Near-Ultraviolet Light 31

The Electron Microscope Magnifies Objects Too Smallto Be Seen by Light Microscopy 31

\, Seeing Atoms Through a New Generation of\)k. Microscopes 34

Perspective 36 *

Summary 38


COMPOSITION AND STRUCTUREOF PROCARYOTIC ANDEUCARYOTIC CELLS 41

Macromolecules: Building Blocks of the Cell 42ProteinsAre Composed 'of. Amino Acids 42

Nucleic Acids Are Composed of Nucleotides 44•' ' • " . " * " ~ ' - v * • • " • ' * " j ' . ' • •" , " . ' * /

r . Carbohydrates and Lipids.Are Organic".,-. Macromolecules 46 ;

TheProcaryoticCei 48 ^The Cell Envelope Is the Outer Covering of a Procaryote

, Consisting of the.Plasmg Membrane, the Cell Wall, and,;, in Gram-Negative Procaryotes, ah Outer Membrane 48

' The Plasma Membrane Is a. Selectively Permeable,"- '•,-: - B a r r i e r ' - 4 ' 9 - " ; , , \ ' r '• '::: :~~.'^;:-;:- ' ' '••' '" .'• "

. The Cell Wall Maintains Ce|| Shape and: , C o n f o r m a t i o n 5 2 _ , • ,'k ,.'—:••-.•

' Peptidoglycan Synthesis ,56

' The Outer Membrane Is the Exterior Portion of the Cell* Envelope in Gram-Negative Procaryotes 57

c BacteriaWithdut'Walls 59

The Periplasm Separates the Plasma Membrane from theOuter Membrane in Gram-Negative Procaryotes 60

C» A Variety of Specialized Structures Are Located Outside-'_= the Cell Envelope 61 '• y r ';'-'•>_

Chemotaxis Is the.Movement of Procaryotes Toward orAway from Chemical Substances 63

Procaryotes Do Not Have Membrane-EnclosedOrganelles, but Do Have Specialized Internal CellStructures 65 ' * ^

Endospores Enable the Cell to Survive Adverse ,Environmental Conditions 68 , ',

The Eucaryotic Cell 70 1 v

The Eucaryotic Cell Wall and Plasma Membrane AreChemically Different from,_but Function Similarly as,

fc Their Procaryotic Counterparts 70 ?.

Eucaryotic Cells Coritdin Membrane-EnclosedOrganelles 72

Eucaryotic Cells Use Flagelja, Cilia, and CytoplasmicStreaming for Locomotion 73 •

Eucaryotes Reproduce Asexually by Fission,Fragmentation, or Spore or Bud Formation, or Sexuallyby Union of Haploid Gametes 73

Perspective 75 :

Summary 76 i


part twoMicrobial Growth and Metabolism

[ chapter .4 ]•NUTRITION ANDENVIRONMENTALINFLUENCENutritional Requirements 80

All Organisms Require a Source of Carbon and Energyfor Growth and Reproduction 80

Nitrogen Is Required for Proteins, Nucleic Acids,Coenzymes/ Cell Walls, and; Other CellularConstituents 81 ; '

Phosphorus Is Required for Nucleic Acids, MembranePhospholipids, and Coenzymes; Sulfur Is Required forCertain Aminb Acids, tRNA, and Coenzymes 83

Other Chemical Elements Are Also Required byMicroorganisms 83 •

Some Microorganisms Require Certain OrganicNutrients as Growth Factors 84

Nutrient Transport 85Passive Diffusion Is the Movement of Small MoleculesAcross the Membrane down a ConcentrationGradient 86 .-'.. ,

Facilitated Diffusion Is the Carrier-Mediated Movementof Molecules Across the Membrane down aConcentration Gradient 86 ; • '

Active Transport Is the Energy-Requiring, Carrier-Mediated Movement of Molecules Across the Membrane

> Against a Concentration Gradient 86

Siderophores and Iron Transport 88

\Group Transbcation Is the Chemical Modification of a* Molecule During Its Movement Across the Membrane 88

% s • ' . ;

" • ' . * " • . - " ' - c • " " - • • • • . ' ,

Physical and Gaseous Requirements 89Microorgaqisms Have Upper and Lower Ranges ofTemperature for Growth 89

Storaqe of BacWrial Cultures 91' • • • • % • " ' • • • - •

VIII Contents

Micrpprgdnisrns Have,Upper'''and Lower Ranges of'pH', for G r o w t h ',9:1,.-1"'. '.-•'•• • • f - ^ v ' ' 1 ' ^ - * ; :'' . ; •• '. •

Water Is Required for Micrpbial Growth 92 .

Bacteria Are Divided into Four Groups fbn the Basis ofTheir Oxygen[Sensitivityand Requirement 93

Growth Media ~~94 ? I •Growth Media Are of Two Types: Complex and

, Synthetic- • 9*4,": :{:\ • •; ':;. ' ^'r'\, '"'•

Specialized Growth Media Are Used to Isolate andEnrich for Specific, Types of "Microorganisms 95

Pure Culture Techniques 96 ; ^ ' ? !The Streak Plate Technique}Sepdrdtes Bacteria in aMixed Population 96 :~, '."'.-;•'. S

Agar ps a Solidifying Argent 98

Aseptic Technique Is Used to transfer Bacteria Without• Cpntamindtipn 98 i / , :

t

Perspective 100

S u m m a r y ; 1 0 2 •• '•'- "'.'.' '.'•:''' " • ;

Evolution and Biodiversity 102 \ ;

[ c h a p t e r . • • • 5 ' , ] : . . : ; . ; • ; , - • ^ i ' S s : : - - . ' - ' - 1 " • .V ' . - ' •••• •'-••'

GROWTH AND CONTROL OF

Bacterial Growth 1 )̂6i The Typical Bacterium Reproduces by Binary Fission 106

Bacterial Populations Increase in Cell Mass andNumbers oyer Time 107 . *

• Quantitqtiye Relationships of Population Growth Can BeExpressed Mathematically 10.7, -..;-.

Measurement of Growth 107 ; v :^Bacterial Growth Can Be Followed, by Increases in CellNumbers 108 : : v /

TurbidimetricMeasyrernents DetectBacteria in a Solutionby ..Light Scattering 113 • , <

Cell Mass Can Be, Determined by. Weighing Cells 114

Cell Growth Can Be Measured by Changes in CellActivity *'l 14 \ V v ' . ' v "^':'::: '.' ' • . ''" ' • ''

Growth Curve 115 v ^^There Is No Increase in CeH Numbers During the Lag/''Phase of Growth 115 / =^ ; .

The Population Grows^at a Constant Rate During the- Exponential Phase ofGrowth 116>. ".»•-'

Growth Slows and, a Steady State in Cell Numbers Is ,! Reached in the Stationary Phase of Growth 116

There Is a Net Decrease in Viable Cell Numbers in the •''.'Death Phase of Growth 117 - ;: : ; v- ' ^

Special Techniques for Culture 1 1 7 ••.,.,/,.Exponential Growth Can Be Prolonged ThroughContinuous Culture 118 ' : ;

Synchronous Cultures Are Cell Populations That Are Allin the Same Stage of Growth 118 ,

Control of Microbial Growth 119High Temperature Can Be Used to Remove All or MostMicroorganisms 119 \

Other Methods Are Effective in Killing or RemoyingMicroorganisms, 120 . ? , . ;

Measurement of Heat-Killing Efficiency 121 . ;,

Antimicrobial Agents 122 *Disinfectants Are Used on. Inanimate Objects, WhereasAntiseptics Are Used on External Body Surfaces 122

Antibiotics and Synthetic Drugs^Are Usedjn.:-.;•".••}".'•.'•'. -Chemotherapy to Selectively Inhibit or Kill , ; :

Microorganisms Without Harming HostvTissue 125

The War Against Antibiotic-Resistant Microbes 130

Antimicrobial Susceptibility Tests Are Used to Determinethe Type and Quantity of Antimicrobial Agents Used inChemotherapy 132 " , " -:-.'.., * 4

Automated Methods for Antimicrobial Susceptibility• T e s t i n g 1 3 4 . ::.^': " •^•^•'.'•'•••: *•-"•'."'; .'-.'•••; --

Perspective 135 - ;

Summary 136 v. - ^


[ c h a p t e r . 6 ] .. ..".•: : •••;..':-. •. .• .•;•.•';. .;

ENERGY AND METABOLISM 139

Concepts of Energy 140Thermodynamics Is the Study of EnergyTransformation ! 140

' Energy Can Be Neither Created nor Destroyed 141

".All Natural Processes Proceed in Such a Manner Thatfliere Is an Increase in Entropy 141

Reversible Chemical Reactions Proceed to an EquilibriumPoinK 142

' Contents IX

Enzymes Accelerate Reaction Rates Without ThemselvesBeing Changed 142 •

Coupled Rections 145Cells Obtain Energy by the Oxidation ofMolecules 145

Substances Differ in Their Oxidation-ReductionPotentials 145

Electron Carriers Transfer Electrons from Electron Donorsto Electron Acceptors 146

High Energy Compounds 148

Concepts of Metabolism 149

Mechanisms of ATP Synthesis 149

Pathways Involving Substrate-Level Phosphorylation 150Chemoheterotrophic Microorganisms Obtain Energy byFermentation and/or Respiration 150

Glucose Is Oxidized to Pyruvate in the Embden-Meyerhof Pathway. 150

Microorganisms Have Other Glycolytic Pathways for theOxidation of Glucose 152 -

Pyruvate Can Be Further Degraded to a Variety ofProducts 154

Homofermentative and HeterofermentativeMicroorganisms 1,58

X

Oxidative Phosphorylation 161The Tricarboxylic Acid Cycle Generates Intermediates forOther Pathways and Cellular Activities and Is Central toCell Metabolism 162

Energy That Is Liberated While Electrons AreTransported in an Electron Transport Chain Can BeCoupled to the Formation of ATP 162

Chemiosmosis Explains How Electron Transport Is Usedto Generate ATP 165

Oxidase Test 166

Aerobic Respiration Is More Efficient Than Fermentationin Coupling Liberated Energy to ATP Formation 168

Anaerobic Respiration. Is a Process Unique toProcaryotes 168

Oxidative Phosphorylation in Eucaryotes 169

ATP Yield from Glucose Oxidation Is Not the Same ini All Microorganisms 171

Chemolithotrophs 171Hydrogen Sulfide Is Oxidized to Elemental Sulfur andEventually to Sulfate 171

Ferrous Iron Is Oxidized to Ferric Iron 172

Ammonia Is Oxidized to Nitrite, Which Then Can BeFurther Oxidized to Nitrate 172

Oxygen Is Reduced to Water During the Oxidation ofHydrogen Gas 172

Perspective 173

Summary 174


[ chapter 1~}PHOTOSYNTHESIS AND OTHERMETABOLIC PATHWAYS I 77

Photosynthesis 1/8Chlorophylls Are the Principal Photosynthetic Pigments inPhototrophic Eucaryotes and Cyanobacteria 178

Bacteripchiorbphylls Are the Principal PhotosyntheticPigments in Bacteria 179 .

Accessory Pigments Harvest Light frpm Other Portions ofthe Spectrum for Photosynthesis 179

Chlorophylls.Are Contained Within Chloroplasts inEucaryotes 180 ^ .•'/-•• ;••---r",-; .'„?"-".:•'

The Photosynthetic Apparatus of Procaryotes IsContained Within Specialized "Membranes orGhlorobium Vesicles;j 182; - : ' ;'.,*• .

The Nature of Photosynthesis: Photophosphorylation 182Photophosphorylation Occurs in Assemblages ofElectron Carriers Called Photpsysterns 184

The Mechanism of Photpphosphbrylatioh Is Similar inPlants, Algae;: and CyanobaGtend . 184

Procaryptic (Other Than; Cyanbbacterial)Photophosphbrylatipri Is Cyclic 186

Chemjosmosis Explains the Mechanism ofPhotophosphorylation 187 X:^];

The Nature of Photosynthesis: Carbon Dioxide Fixation 188Carbon Dioxide Fixation-Is Catalyzed by RibuloseDiphosphate Carboxylase 188

Carbohydrate Metabolism 189, > /Polysaccharides Are Degraded into Smaller Molecules

^ Before they Enter the Cell 1 9 0 • ; :

> Carbohydrates Are Synthesized by Anabolic ReactionsVUsing Readily Available Substrates ,192

Protein Metabolism 194Profeios Can Be Used as Sources of Carbon and

* ^ 9 4 ^ 7 •.. ;•.. * . : ; ' ; ; K l - 1 '-. ; •

Sticklahd Reqctioh 196^ ' ' ' "V

Contents

Amino Acids Are Synthesized from Intermediates inCentral Metabolic Pathways 197

Lipid Metabolism 197Decarboxylases 1.98

Microorganisms Degrade Fatty Acids byp-Oxidation 200

The Glyoxylate Cycle 201

Fatty Acids Are Synthesized by the Stepwise Addition ofAcetyl Groups to a Growing Chain 202

Purine and Pyrimidine Metabolism 202Nucleases Hydrolyze Nucleic Acids into IndividualMononucleotides, Which Can Then BeCatabolized 202

Purines and Pyrimidines Are Synthesized from a Varietyof Molecules 202

Perspective 204

Summary 206


part threeMicrobial Genetics

[ chapter 8 ]MOLECULAR GENETICS 211

The Genetic Code 213

Deoxyribonudeic Acid 215DNA Is the Genetic Material of the Cell 215

DNA Consists of Two Complementary Polynucleotide•Chains Held Together by Hydrogen Bonds 216

Nucleotide Base Ratios 217

DNA Is Replicated Semiconservatively 219

Some Circular DNAs Are Copied via a Rolling CircleMechanism of Replication 223

DNA Replication in Procaryotes and Eucaryotes IsBasically Similar 223

Ribonucleic Acid 224^ is Divided into Three Classes 224

RNA is Synthesized from DNA 226

• Eucaryotes Have Several Different RNAPolymerases 228

Protein 229Protein Synthesis Begins with the Formation of anInitiation Complex 229

The Wobble Hypothesis 230

Amino Acids Are Added to the Growing Peptide DuringElongation 232

Protein Synthesis Terminates When the RibosomeReaches a Nonsense Codon on the Messenger RNA232

Protein Synthesis Is More Complex in Eucaryotes Than inProcaryotes 233

Regulation 233An Enzyme Is Synthesized in the Presence of an ExternalSubstance (Inducer) in Induction 233

Enzyme Synthesis Is Inhibited in the Presence of anExternal Substance (Corepressor) in Repression 235

Gene Expression Is Controlled by the Termination ofTranscription in Attenuation 236

Catabolites Can Repress Transcription of Genes 236

Eucaryotes Have Mechanisms for Control of GeneExpression Not Found in Procaryotes 238

Perspective 240

Summary 240


[ chapter 9 ]MICROBIAL GENETICS 245

Mutation 246

Bases Can Be Substituted by Other Bases 246

Bases Can Be Deleted or Inserted 246

The Effects of Some Mutations Are Reversible 246

The Rate of Mutations Can Be Increased by MutagenicAgents 246

Bacteria Have Different DNA Repair Mechanisms 248

Replica Plating Differentiates Mutants from Wild Typesby Their Growth Differences 249

Transfer of Genetic Material 250

; The Ames Test for Carcinogenesis 251

DNA Is the Transforming Principle 252

The^Discovery of Transduction 254

Contents X I

: DNA Is Transferred by a Bacteriophage from OneBacterium to'Another During Transduction 255

. Plasmids Are Extrachromosomal Circular Pieces of, DNA 258 : ' - V - 1 .;

Transposdble Genetic Elements 260

Cell-to-Cell Contact Is Required for DNA Transfer DuringConjugation 263

P e r s p e c t i v e 2 6 6

S u m m a r y 2 6 8 '.. V ; v . ; ' : ' . - • • . • ; . / , ; • : . » • ! : . . * ; - - - i ] ' ; ' ; - '

Evo lu t ion ar id B i o d i v e r s i t y 2 6 8 : V

part fourSurvey of Microorganisms

[ chapter I f fRECOMBINANT DNA ;

•*; T E C H N O L O G Y -'"Zi.A...••-•):, •.•...• •/' ' •

Historical Perspectives 2 W

Gene Cloning 274The TargetGene Can Be Obtained in Different ,W a y s ' : - 2 7 4 - ' < i ' ^ ; V . : ' - : . ' ' ; ; V v ' . : ; : .: .• • V • '••;:_. .'.- ',--.

Southern Blotting 276 ; " '

The Target Gene'Is Incorpbrated into a Cloning: ' . V e c t o r 2 7 9 ; '••'-•' \ : ' J - - / , . ' ' . ' • ' ; ' ' , - ' " •"•' • ' • ' " • .

The Cloning" Vector Is Inserted into a,Host Where theTarget Gene Is Amplified -285 ,

, Various Methods Are Available to Detect Host Cells withthe Cloned Gene 287 / , . • . " ;

— ; The Polymerase Chain Reaction 288

Applications of Recombinant DNA Technology 291' " Applications of Recombinant DNA Technolpgy in

x Medicine Have Important Ramifications for HumanHealthCare/, 291 . - '.• - :^ .'•- „

DNA fingerprinting 292

Recombinant. D N A Technology Has Improved- ; •• Agricul ture-1*^297 '••;.•.'• : • . : ;' ,; .

Public and Scientific Concerns About the Regulation of Recombinant DNATechnology 297 - ^

; Perspective 300 ' . I :

Summary 302' : » * • - • ' • • " • • • • ; . - • " • • - • ' " • ' • • • • • ' • • ' . ' • • , . ' • .

Evolution and Biodiversity 302 ? ,

•r,

PROCARYOTES: THE BACTERIAAND THE ARCHAEA 3O5

Classification of Microorganisms 306Classification Schemes,for Microorganisms HaveEvolved over the Years 306

Three Major Approaches Have Been Used to Identifyand Place Microorganisms in ClassificationSystems 307 • » , *,

Ribosomal RNA and Phylogeny 311Sequencing of Ribosomal RNA is RelativelySimple 311 / ' .

Phylogenetic Trees Can Be Developed from RibosomalRNA Sequences 311

Classification of Procaryotes 314

Gram-Negative Bacteria of General, Medical, or IndustrialImportance 316 "

The Spirochetes 316

Aerobic/Microaerophilic, Motile, Helical/VibrioidGram-Negative Bacteria 318 "•'-

Nonmotile (or Rarely Motile), Gram-Negative, Curved: Bacteria 319 J' . :' l \

Gram-Negative Aerobic Rods and Cocci 319

Facultatively Anaerobic Gram-Negative Rods 322

Using Flowcharts to identify Bacteria 324

Anaerobic, Grdm-Negdtive Straight, Curved, andHelical Rods 325 . "

Dissimilatory Sulfdte- or Sulfur-Reducing Bacteria 326

Anaerobic, Gram-Negative Cocci•',, 326

. The Rickettsias and Chlahnydids 326

Mycoplasmas 327 ,

•% Endbsymbionts 328

Gram-Positive Bacteria Other Than the Actinomycetes 328

v.Gram-Positive Cocci. 328.

Endpspore-Forming Gram-Positive Rods and Cocci 328

Revival of 25:Million^Year-Old Procaryotes? 330

Regular,: Nonspbring Gram-Positive Rods 331

X I I , Contents;

Irregular, Nonsporing Gram-Positive Rods . 331

The Mycobqcteria• 331 :. ''",,-••".•

The Archaea, Cyanobacteria, and RemainingGram-Negative Bacteria 332 "

Anoxygehic Phototrophic Bacteria 332

Oxygenic Photosynthetic Bacteria 333 • "

Aerobic Chemolithbtrophic Bacteria and AssociatedOrganisms 336 * . •:••'.

Budding and/or Appendaged Bacteria ^ 3 7

Sheathed Bacteria 337

Nonphotosynthetic, Nonfruiting Gliding Bacteria 338

Fruiting Gliding Bacteria: The Myxobacteria 338

Archaea 339 'i- ."

The Actinomycetes 341

Perspective 344

Summary 346 i


THE E U C A R Y O T I C ; •:"-:•"':MICROORGANISMS 349

The Algae 350There Is Considerable Variability in the Morphology andStructure of Algae 350

Algae Exhibit a Variety of Reproductive Processes 352

Algae Are Classified into Six Divisions Based onStructural, Chemical, and ReproductiveCharacteristics 352

The Economic Importance of Algae 355

The Fungi 359Fungi Have Two Morphological Growth Forms: Moldsand Yeasts 361 '

Fungi Reproduce Asexually and Sexually 362

Fungi Are Phylogenetically Grouped into Two Kingdomsand Four Additional Phyla 365

Aspergillus and Aflatoxin 368

The Protozoa 373; Protozoa Lack Cell Walls, but Contain Membrane-BoundOrganelles 373

. Protozoa Reproduce Asexually and Sexually 373

Protozoa Are Divided into Seven Phyla 375

AIDS and Eucaryotic Microbe Infections 376

Perspective 378

Summary 380


[chapter 13 •].THE VIRUSES 383Properties of Viruses 384

Viruses Are Extremely Small 384>

Viruses Consist of DNA or RNA Surrounded by. aProtein Coat 384

Viruses Have Three Basic Forms: Polyhedral, Helical,and Binal 386

Classification of Viruses 387Bacteriophages Are Classified'by Their Morphology andNucleic Acid Content 387 :•.•••>'••'] 5

Viroids and Prions—Agents Smaller Than .Viruses 388 ' •

Viruses Infect Other Microorganisms BesidesBacteria 390 , \

Plant Viruses Are Classified into 23 Virus Groups andTwo Families 390 ';,

Animal Viruses Are Classified into 18 Families 393

Propagation and Assay of Viruses 395 >Viruses Require a Host for Propagation , 3?5 :

Viruses Can Be Assayed by Various Methods1 ,397

Replication of Viruses 398 •Virus Replication Begins with Infection of the Host, 398

Evidence That Bacteriophage Nucleic Acid, NotProtein, Enters the Host Cell During Infection 400

DNA Viruses Have Various Methods for Replication of .DNA 402 :

RNA Viruses Have Various Methods for Replicgtiorj ofRNA 403 V : •

CompleteVirions Are Formed During Assembly ,403

,»• One-Step Growth Curve 404 ;; - \

Intact Virions Are Released from the Host After"Assembly 405 : •

VirqMnfections in Animal and Plant Cells Can Result in rCytopgthic Effects 405 * v / r-> ' V -

Are ViratDiseases Treatable? 406 ,,

Contents

• " V

XIII

Other Consequences of Viral Infections 408Viruses Can Be Continuously Released from a HostCell 408

There Can Be a Significant Reduction or Elimination ofVirus Production in the Host 408

Virus Infection Can Lead to Cell Transformation 408

A Bacteriophage Can Be Incorporated into the HostChromosome in Lysogeny 410

Perspective 412

Summary 414


[ chapter 15 ]

part . fiveMicrobial Interactions with OtherOrganisms

[chapter 14 ]SYMBIOSIS 417Mutualism 418

Rhiziobium, Frankia, Anabaena, and Other Bacteria Fix.-. Nitrogen Symbiotically 418

A Lichen Is.a Mutualistic Association Between a Fungusand an Alga-. 423 '

Flashlight Fishes Have a Symbiotic Relationship withLuminescent Bacteria 425

Some Bacteria Are Symbionts of Protozoa 425

Some Bacteria Are Symbionts of Insects 427

Microbial Symbiosis Assists Ruminants inDigestion . 427

Parasitism 429Bdelloyibrio Parasitizes Gram-Negative Bacteria 429

Chlamydiae Are Animal Parasites with UnusualDevelopmental'Cycles 430

• Germ-Free Animals 432

Commensalism 433

Mutualism, Commensalism, Parasitism—Dynamic Relationships 433 .

' Perspective 434

Summary 434


HOST-PARASITERELATIONSHIPS 439

The Normal Human Microflora 440

Microorganisms Can Compete Antagonistically 440

Microorganisms Can Grow Synergistically 441

The Story of Typhoid Mary 442

General Concepts of Host-Parasite Relationships 442Infectious Microorganisms Persist in Reservoirs 442

Diseases Can Be Transmitted Directly or Indirectly 443

Microorganisms Gain Entry to a Host Through aPortal 445

Infectious Disease Follows a Sequence from Infection toDisease Resolution 446

Measurement of Virulence 447

Parasites Must Overcome Host Defenses to InitiateInfection and Disease 448

Microbial Factors of Virulence 448Microorganisms Have Many Mechanisms to Assist inInvasion 448

Microbes Produce Two Types of Toxins: Exotoxins andEndotoxins 450

Detection of Endotoxin 452

Host Resistance and Tuberculosis 453

Innate (Nonspecific) Host Resistance 454The General Health and Physiological Condition of theHost Can Influence the Course of a Disease 454

Physical Barriers Protect the Human Body AgainstInfectious Microorganisms 455

Human Blood Contains Protective Factors 456

Inflammation Is the Body's Response to Injury, Irritation,or Infection 458

Phagocytes Digest Bacteria, Viruses, and Other ForeignMaterials 460

Perspective 462

Summary 464


[ chapter 16 ]IMMUNOLOGY

Humoral Immunity 468 •„

467

X I V Contents

Lymphoid Tissue Is Important in the ImmuneResponse 468

Antigens Induce and React with Antibodies 468

Antibodies Are Glycoproteins That Bind Specifically withthe Antigen That Stimulated Their Production 468

Antibody Diversity Is Made Possible by GeneRearrangement 471

Superantigens • 473

Different T-Cell Subpopulations Perform DifferentFunctions, 473

The Major Histocompatibility Complex Plays a Role inthe Immune Response 473

Monoclonal Antibodies 475

, Activated B Lymphocytes Develop into Antibody-Secreting Plasma Cells 475

Humoral Immunity Is an Important Part of Host DefenseAgainst Microbial Invasion 475

Complement Is a Group of Proteins That Augment theAction of Antibodies 481

Cell-Mediated Immunity 482Cytokines Activate Macrophages and Increase TheirPhagocytic Activity in Cell-Mediated Immunity 483

Delayed Hypersensitive Responses Are Caused by theRelease of Cytokines from Sensitized T Cells 483

Cell-Mediated Immunity May Be Manifested in OtherWays 484

Assays to Measure Cell-Mediated Immunity Dependup6n Delayed Hypersensitive Skin Reactions orDetection of Sensitized Lymphocytes 485

In Vitro Antibody-Antigen Reactions 485Soluble Antigens Mixed with Multivalent AntibodiesForm Large, Precipitable Aggregates 485

Antigens Can Be Separated byImmunoelectrophoresis 486

- Insoluble Antigens Mixed with Multivalent AntibodiesForm Aggregates Detectable by Agglutination 486

Neutralization Tests Are Used to Detect Toxins andViruses or Their Antibodies 487

Complement Can Be Used to Detect Antigen-AntibodyReactions 487

•Fluorescent Dyes Are Used in Immunofluorescence toDetect Antigens or Antibodies 489

Radioactivity Is Used in Radioimmunoassay to DetectSmall Amounts of Antigen 490

Enzymes Are Used in Enzyme-Linked ImmunosorbentAssays to Detect Antigens or Antibodies 490

Perspective 492

Summary 494


[ chapter 17 ]INFECTIOUS DISEASES 497

The Respiratory Tract 498Many Different Types of Microorganisms Are' NormallyFound in the Upper Respiratory Tract 498 "

Respiratory Tract Pathogens Are Highly Contagious andTransmissible 498 ' • . . *

Classification of Streptococci 502 • ." . .

Group B Streptococcal Neonatal Disease- 506 ''

Discovery of the Diphtheria Exotoxin 509 -;.' ' .

Respiratory Tract Diseases Can Be Caused by Other.Microorganisms 512 •

The Oral Cavity and Digestive System 514Many Different Types of Microorganisms Are NormallyFound in the Oral Cavity 514

Dental Diseases Are Caused by an Accumulation of . •Microorganisms on the Surface of Teeth 514

Oral Diseases Can Be Caused by OtherMicroorganisms 515

The Digestive System Is Complex and Contains a WideVariety of Microorganisms 515 .

Bacterial Diseases of the Digestive System Arise fromFood Infection or Food Intoxication 516

Poultry and Salmonella Infections 520

Escherichia coli Is Responsible for Many Different-, .Gastrointestinal Diseases 521 •

An Infectious Cause of Ulcers 522 ,.

* Gastrointestinal Diseases Can Be Caused by Other-Microorganisms 523

Diseases of the Skin and the Genitourinary System 524 . >Few Species of Microorganisms Normally Inhabit theSkin-X 525

Contents X V

Microbial Skin Pathogens Must Overcome MicrobialAntagonism and the Physical Barrier of the Skin toCause Infection • 525

The Male and Female Genitourinary Systems Differ inJheir Norma[Microbial Flora, 532\ '

Acquired Immune Deficiency Syndrome (AIDS) Results ina Deficiency of CD4+Cells 536

4 Emerging Infectious Diseases 542

Perspective 544

Summary 544 ; •


[chapter 18 1PUBLIC HEALTH ANDEPIDEMIOLOGY 549

Some General Concepts of Epidemiology 550An Epidemic Is a Markedly Increased Occurrence of aDisease in a Population 552

Morbidity and Mortality Rates Are Used by. Epidemiologists to Determine the Trend of Disease 553

Epidemiological Analysis of Diseases 555 /, •'. Disease Rates May Change with Time 555

• disease Rates May Be Influenced by Geography 556

. . Disease Rates May Be Affected by the Characteristics ofa Population 556

Collection of Epidemiological Data 558Nosocomial Infections 559

There Are Potential Biases in Interview Surveys 560

Screening and Diagnostic Tests Are More Objective\ Than Interview Surveys 560

Observational and Experimental Studies 561Observational Studies Are of Two Types: Retrospectiveand Prospective 561 y

* • > The Investigator Specifies or Manipulates Conditions in

Experimental Studies 563

Perspective 564

Summary 566


part sixEnvironmental and Economic Impactof Microorganisms

[ chapter I f ] ; : :~/ • ',

M I C R O B I A L E C O L O G Y 5 6 9

Biogeochemical Cycles 570

The Carbon Cycle 570Primary Producers Fix Atmospheric Carbon Dioxide intoOrganic Compounds 571

The Greenhouse Effect ^572

Herbivores and Carnivores Contribute to the CarbonCycle by Consuming Organic Carbon and Returning Itto the Atmosphere as Carbon Dioxide 575

Microorganisms Contribute to the Carbon Cycle asDecomposers 575

The Nitrogen Cycle 576Only Certain Procaryotes Can Fix Nitrogen 576

Ammonia.Is Formed During Decomposition of OrganicNitrogenous Compounds 577 , ' . ' , '

The Phosphate Cycle 579

The Sulfur Cycle 579

Microbes and Soil 580Soil Varies in Its Composition and PhysicalProperties 581

There Are Considerable Numbers and Varieties ofMicroorganisms in Soil 581

Bacteria Are Important in the Leaching of Metals fromLow-Grade Ores 582

Hydrocarbon-Degrading Microorganisms Are PotentiallyUseful in Oil Spill Cleanups 583

Microorganisms Are Useful as BiologicalPesticides 584

Microbes and Water 5864 A Wide Variety of Microorganisms Are Found in

Marine Habitats 586 ,

% Many Different Types of Microorganisms Are Also•V. Found in Freshwater Habitats 587

Chemical and Biological Contaminants Affect theQuality of Water 588

X V I Contents

Chesapeake BayrExample of a RevitalizedEstuary 590

Cryptosporidiosis 594

Sewage Treatment,Removes Microorganisms andChemicals from Sewage 594

,, Methane Production from Wastes 598

Microbes and the Air 601

Perspective .602

Summary 604


[chapter^],;/ '": ', •. ' •»'.FOOD A N D INDUSTRIALMICROBIOLOGY 6O7 ;Vf; >

Milk and Dairy Products 608 - • ' • • . . .." Raw Milk Contains Microorganisms Introduced from the

Udder and During Human Handling .608

Bacteria Are Used to Produce Fermented Milks and MilkProducts 609 -

Salmonellosis Outbreak from a Dairy Plant 610

Microorganisms Are Important in CheeseProduction 611 *

An Outbreak of Listeriosis Caused by ContaminatedMilk 613

Microorganisms in Meat and Meat Products 614Microorganisms Are Responsible for MeatSpoilage 614

Many Methods Carl Be Used to Preserve Meats andReduce Spoilage 614

Poultry and Seafood 615

Canned Foods 616 ;.,' • • • ' " • " • !

Fermented Foods 616 7 . <-

Alcoholic Beverages 6 1 7Yeasts Are Used in Beer Production to FermentGrains 61.7 ^

Frost-Proof Fruits and Vegetables 618

Yeasts Are Used in Wine Production to Ferment FruitSugars 619< s> ' ;.-Yeasts Are Used in the Production of DistilledBeverages 619

Industrial Processes 619 "A Desirable Culture Medium Is Inexpensive, yet ContainsAll Essential Ingredients 620 ,

Microorganisms for Industrial Fermentation AreCarefully Selected 620 ^ :

Culture Conditions Are Carefully Controlled in IndustrialFermentors 621

Different Methods Are Used to Culture MicroorganismsIndustrially 621

Enzymes 623 -Microbial Amylases Are Used in Bread Making, BeerProduction, Manufacture of Sugar Syrups, and TextileManufacture 623

Microbial Proteases Are Used in the Clothing Industry, inPhotography, and in Stain Removal 623

- Other Microbial Enzymes Are of IndustrialImportance 624

Metabolic Products 625Primary Metabolites Are Metabolic Compounds Involvedin Cell Growth or Function 625 . . .

Secondary Metabolites Are Products of Pathways ThatApparently Are Not Associated with Primary CellularProcesses 629

Recombinant DNA Techniques for the Production ofAntibiotics 630

Single-Cell Protein 631

Perspective 632

Summary 633


Appendix A: Classification of Procaryotes According to Bergey's Manual of

Systematic Bacteriology 6 3 5

Appendix B: The Mathematics of Bacterial Growth 6 4 2

Appendix C: Microbiology Internet Resources 6 4 5

Appendix D: Chemistry fo the Microbiologist 6 4 7

Appendix E: Answers to the End-of-Chapter Questions 6 5 3

Glossary 6 6 8

Credits 6 8 5 . . .

Index 6 8 9

v,

Contents•'X.

XVII

microbiology - gbv · energy and metabolism 139 concepts of energy 140 thermodynamics is the study...

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