Ebook Alcamo’s fundamentals of microbiology (9/E): Part 1

Pronouncing Organism Names
Some of the scientific names for microorganisms, which have Latin or Greek roots, can be hard to pronounce. As an aid
in pronouncing these names, the primary microorganisms used in this textbook are listed alphabetically below, followed by the pronunciation. The following pronunciation key will aid you in saying these names. The accented syllable
(') is placed directly after the syllable being stressed.
Pronunciation Key
a add
–a ace

ch check

g go

ã care

e end
–e even

i it
–ı ice

ä father

e˙ term

ng ring

Acanthamoeba castellani a-kan-thä-me–'bä kas-tel-än'e–
Acetobacter aceti a-se–'to–-bak-te˙r a-set'e–
–-bak-te˙r
Acinetobacter baumannii a-si-ne'to

bou-mä'ne–-e–
Actinobacillus muris
–-bä'cil-lus mu
–'ris
ak-tin-o
–r'us
Agaricus bisporis ä-gãr'i-kus bı–-spo
Agrobacterium tumefaciens ag'ro–-bak-ti're–-urn
tü'me-fa–sh-enz
–-mı–'se–s
Ajellomyces dermatitidis ä-jel-lo
de˙r-mä-tit'i-dis
Alcaligenes viscolactis al'kä-li-gen-e–s vis-co-lak'tis
Amanita muscaria am-an-ı–'tä mus-kãr'e-ä
A. phalloides fal-loi'dez
Amoeba proteus ä-me–'bä pro–'te–-us
–Anaplasma phagocytophilum an'ä-plaz-mä fäg'-o-sı–-to
fil-um
–'sto–-mä du
–-o–-de'näl-e–
Ancylostoma duodenale an-sil-o
–
Aquifex ä'kwe -feks
Armillaria är-mil-lãr'e–-ä
Arthrobacter är-thro–-bak'te˙r
Arthroderma är-thro–-de˙r'mä
Ascaris lumbricoides as'kar-is lum-bri-koi'de–z
Aspergillus favus a-spe˙r-jil'lus fla–'vus
A. fumigatus fü-mi-gä'tus
A. niger nı–'je˙r

A. oryzae ô'ri-zı–
A. parasiticus pãr-ä-si-ti-kus
Azotobacter ä-zo'to-bak-te˙r
Babesia bigemina ba-be–'se–-ä big-em-e–'na
B. microti mı–-kro–'te–
Bacillus amyloliquefaciens bä-sil'lus
–-li-kwä-fäs'e–-enz
am-i-lo
B. anthracis an-thra–'sis

62582_CH30_CVRS_p002-005.pdf 2

o odd
– open
o

ou out

u put

sh rush

ô order

th thin

ü rule
– use
u

oi oil

u up

B. cereus se're–-us
B. sphaericus sfe'ri-kus
B. subtilis su'til-us
B. thuringiensis thur-in-je–-en'sis
Bacteroides fragilis bak-te˙-roi'de–z fra'gil-is
B. thetaiotaomicron tha–-tä-ı–-o–-täw-mi'kron
Bartonella henselae bär-to–-nel'lä hen'sel-ı–
Beggiatoa bej'je–-ä-to–-ä
Blastomyces dermatitidis blas-to–-mı–'se–z
de˙r-mä-tit'i-dis
Bordetella bronchiseptica bor-de-tel'lä
bron-ke–-sep'ti-kä
B. parapertussis pãr'ä-pe˙r-tus-sis
B. pertussis pe˙r-tus'sis
Borrelia burgdorferi bôr-rel'e–-ä burg-dôr'fe˙r-e–
B. hermsii he˙rm-se–'-e–
B. recurrentis re–-cür-ren'tis
B. turicatae te˙r-i-kät'-ı–
Botrytis cinerea bo-trı–'tis cin-e˙r-e–'ä
Brevibacterium bre-vi-bak-ti're–-um
Brucella abortus brü’sel-lä ä-bôr'tus
B. canis can'is
B. melitensis me-li-ten'sis
B. suis sü'is
Brugia malayi brü'-ge–-ä mä-la–'e–
–ld-e˙r-e–-ä se-pa–'se–-ä

Burkholderia cepacia berk'ho
–-bak-te˙r ko–'lı– (or ko–'le–)
Campylobacter coli kam'pi-lo
–
–
–
C. jejuni je -ju'ne
Candida albicans kan'did-ä al'bi-kanz
–-lo–-bak'te˙r kre-sen'tus
Caulobacter crescentus ko
Cellulomonas sel-u-lo-mo–'näs
Cephalosporium acremonium sef-ä-lo–-spô're–-um
ac-re-mo–'ne–-um
Chlamydia trachomatis kla-mi'de–-a trä-ko–'mä-tis

2/4/10 3:16 PM


Pronouncing Organism Names (continued)
–-mo
–'näs
Chlamydomonas klam-i-do
–'ne–-ı–
Chlamydophila pneumoniae kla-mi'dof-i-la nü-mo
–
C. psittaci sit'a-se
–-bak'-te˙r
Chromobacter violaceum kro–-mo
–
–

–
–
vı -o-la 'se -um
Claviceps purpurea kla'vi-seps pür-pü-re–'ä
Clostridium acetobutylicum klôs-tri’de–-um –a -se–-to––-til'i-kum
bu
–-lı–'num
C. botulinum bot-u
C. difficile dif'fi-sil-e–
C. perfringens pe˙r-frin'jens
C. tetani te'tän-e–
Coccidioides immitis kok-sid-e–-oi'de–z im'mi-tis
–-sä-da'se–-e–
C. posadasii po
Corynebacterium diphtheriae kôr'e–-ne–-bak-ti-re–-um
dif-thi're–-ı–
Coxiella burnetii käks'e–-el-lä be˙r-ne'te–-e–
–-kok-kus
Cryptococcus neoformans krip'to
–
–
ne -o-fôr'manz
–-spô-ri-de–-um
Cryptosporidium coccidi krip'to
–
kok'sid-e
C. hominis ho–'mi-nis
C. parvum pär'vum
Cyclospora cayetanensis sı–'klo–-spô-rä kı–'e–-tan-en-sis
Deinococcus radiodurans dı–'no–-kok-kus ra–-de–-o–dür'anz

–-vib-re–-o
–
Desulfovibrio de–'sul-fo
–
–
–-näs
Desulfuromonas de 'sul-für-o-mo
–-kok'kus
Echinococcus granulosus –e -kı–n-o
–-1o
–'sis
gra-nu
Ehrlichia chaffeensis e˙r'lik-e–-ä chäf-fen'sis
–-cı–-to'fı–-lä
E. phagocytophila fa–-go
Emmonsiella capsulata em'mon-se–-el-lä cap-sül-ä'tä
–-li'ti-kä
Entamoeba histolytica en-tä-me–'bä his-to
–
Enterobacter aerogenes en-te-ro-bak'te˙r ã-rä'jen-e–z
E. cloacae klo–-a–'ki
–'be–-us ver-mi-ku
–-lar'is
Enterobius vermicularis en-te-ro
–-kok'kus fe–-ka–'lis
Enterococcus faecalis en-te˙-ro
–
–
E. faecium fe 'se -um
–-fı–'ton

Epidermophyton ep-e–-der-mo
Erysipelothrix rhusiopathiae –a r-e–-sip'e-lo–-thriks
rü'sı–-o–-pa-the–
–’le–)
Escherichia coli esh-e˙r-e–'ke–-ä ko–'lı– (or ko
–-gle–'nä
Euglena u

Filobasidiella neoformans fı–-lo-ba-si-de–-el'lä
ne–-o-fôr'mäns
Francisella tularensis fran'sis-el-lä tü'lä-ren-sis
–-so–-bak-ti're–-um
Fusobacterium fu
Gambierdiscus toxicus gam'be–-e˙r-dis-kus toks'i-kus
Gardnerella intestinalis gärd-ne˙-rel'lä in-tes-ti-nal'is
G. vaginalis va-jin-al'is
Geobacillus stearothermophilus je–-o–-bä-sil'lus
ste-är-o–-the˙r-mä'fil-us
Giardia lamblia je–-är'de–-ä lam'le–-ä
–-bak-te˙r
Gluconobacter glü'kon-o
Gonyaulax catanella gon-e–-o–'laks kat-ä-nel'lä
–-din'e–-um
Gymnodinium jim-no
Haemophilus ducrcyi he–-mä'fil-us dü-krä'e–
H. influenzae in-flü-en'zı–
–-bak-ti're–-um
Halobacterium salinarum ha-lo
sal-i-när'um
Hartmannella vermiformis hart-mä-nel'lä

vêr-mi-fôr'mis
–-bak-te˙r pı–'lo–-re–
Helicobacter pylori he–'lik-o
–-plaz'mä kap-su-lä'tum
Histoplasma capsulatum his-to
Klebsiella pneumoniae kleb-se–-el'lä nü-mo–'ne-ı–
Lactobacillus acidophilus lak-to–-bä-sil'lus a-sid-o'fil-us
L. bulgaricus bul-gã'ri-kus
L. caseii ka–'se–-e–
L. plantarum plan-tär'um
L. sanfranciscensis san-fran-si-sen'-sis
–-kok'kus lak'tis
Lactococcus lactis lak-to
Lagenidium giganteum la-je-ni'de–-um jı–-gan'te–-üm
Legionella pneumophila le–-jä-nel'lä nü-mo–'fi-lä
Leishmania donovani lish'mä-ne–-ä don'o–-vän-e–
L. tropica trop'i-kä
–-ganz
Leptospira interrogans lep-to–-spı–'rä in-te˙r'ro
–
–
Leuconostoc citrovorum lü-ku-nos'tok sit-ro-vôr'um
L. mesenteroides mes-en-ter-oi'de–z
Listeria monocytogenes lis-te're–-ä mo-no–-sı–-tô'je-ne–z
Methanobacterium meth-a-no–-bak-te˙r'e–-um
Methanococcus jannaschii meth-a-no–-kok'kus
jan-nä'she–-e–
–'te–-us
Micrococcus luteus mı–-kro–-kok'kus lu
–

–
–
–
Micromonospora mı -kro-mo-nos'por-ä

(continued on inside back cover)

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Alcamo’s FUNDAMENTALS OF

Microbiology

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Encounters in Microbiology, Volume 1, Second Edition

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Essential Genetics: A Genomics Perspective, Fifth Edition

Precancer: The Beginning and the End of Cancer

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Evolution: Principles and Processes

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Exploring Bioinformatics: A Project-Based Approach

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Genetics: Analysis of Genes and Genomes, Seventh Edition

Ruby Programming for Medicine and Biology

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Genetics of Populations, Fourth Edition

Strickberger’s Evolution, Fourth Edition

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Guide to Infectious Diseases by Body System

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Jeffrey C. Pommerville

M. Sriram Iyengar

Human Biology, Sixth Edition

Tropical Forests

Daniel D. Chiras

Bernard A. Marcus

Human Biology Laboratory Manual

20th Century Microbe Hunters

Charles Welsh

Robert I. Krasner

Introduction to the Biology of Marine Life, Ninth Edition

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John F. Morrissey & James L. Sumich

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About the cover: A false-color transmission electron microscope image of the bacterium Escherichia coli. These rod-shaped cells are a common inhabitant in the human large intestine where they use the short whisker-like appendages to attach to the intestinal lining.

Library of Congress Cataloging-in-Publication Data
Pommerville, Jeffrey C.
Alcamo’s fundamentals of microbiology / Jeffrey C. Pommerville. — 9th ed.
p. ; cm.
Other title: Fundamentals of microbiology
Includes bibliographical references and index.
ISBN 978-0-7637-6258-2 (alk. paper)
1. Microbiology. 2. Medical microbiology. I. Alcamo, I. Edward. II. Title. III. Title: Fundamentals of microbiology.
[DNLM: 1. Microbiology. QW 4 P787a 2011]
QR41.2.A43 2011
616.9’041—dc22
6048
2010002117
Printed in the United States of America
14 13 12 11 10 10 9 8 7 6 5 4 3 2 1

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Brief Contents
PART 1 FOUNDATIONS OF
MICROBIOLOGY

Chapter 1
Now 3

1

Microbiology: Then and

PART 4 VIRUSES AND EUKARYOTIC
MICROORGANISMS
438
Chapter 14 The Viruses and Virus-Like
Agents 440

Chapter 2 The Chemical Building
Blocks of Life 35

Chapter 15 Viral Infections of the
Respiratory Tract and Skin 474

Chapter 3 Concepts and Tools for
Studying Microorganisms 64

Chapter 16 Viral Infections of the
Blood, Lymphatic, Gastrointestinal,
and Nervous Systems 508

Chapter 4 Cell Structure and Function
in the Bacteria and Archaea 97
Chapter 5 Microbial Growth and
Nutrition 131

Chapter 18 Eukaryotic
Microorganisms: The
Parasites 567

Chapter 6 Metabolism of
Microorganisms 158
Chapter 7 Control of Microorganisms:
Physical and Chemical Methods 189

PART 2 THE GENETICS OF
MICROORGANISMS
Chapter 8

222

Microbial Genetics 224

Chapter 9 Gene Transfer, Genetic
Engineering, and Genomics 260

PART 3 BACTERIAL DISEASES
OF HUMANS

Chapter 17 Eukaryotic
Microorganisms: The Fungi 535

298

Chapter 10 Airborne Bacterial

Diseases 300
Chapter 11 Foodborne and
Waterborne Bacterial Diseases 334
Chapter 12 Soilborne and
Arthropodborne Bacterial
Diseases 371
Chapter 13 Sexually Transmitted
and Contact Transmitted Bacterial
Diseases 396

PART 5 DISEASE AND
RESISTANCE

607

Chapter 19 Infection and
Disease 609
Chapter 20 Resistance and
the Immune System: Innate
Immunity 646
Chapter 21 Resistance and the
Immune System: Acquired
Immunity 669
Chapter 22 Immunity and
Serology 698
Chapter 23 Immune Disorders and
AIDS 729
Chapter 24 Antimicrobial Drugs 767
Appendix A Metric Measurement A-1
Appendix B Temperature Conversion

Chart A-1
Glossary
Index

G-1

I-1

Photograph Acknowledgments

P-1

v

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Contents
Preface
Acknowledgments
About the Author
To the Student—Study Smart
A Tribute to I. Edward Alcamo

PART 1 FOUNDATIONS OF
MICROBIOLOGY
Chapter 1
Now 3

xvii
xxi
xxii
xxiv
xxx

1

Microbiology: Then and

1.1 The Beginnings of Microbiology 6
Microscopy—Discovery of the Very Small 6
Experimentation—Can Life Generate Itself
Spontaneously? 8
1.2 Microorganisms and Disease
Transmission 9
Epidemiology—Understanding Disease
Transmission 9
Variolation and Vaccination—Prevention of
Infectious Disease 14
The Stage Is Set 15
1.3 The Classical Golden Age of
Microbiology (1854–1914) 15
Louis Pasteur Proposes That Germs Cause
Infectious Disease 15
Pasteur’s Work Stimulates Disease Control
and Reinforces Disease Causation 16
Robert Koch Formalizes Standards to
Identify Germs with Infectious Disease 17

Koch Develops Pure Culture Techniques 18

Competition Fuels the Study of Infectious
Disease 18
Other Global Pioneers Contribute to New
Disciplines in Microbiology 20
1.4 Studying Microorganisms 22
The Spectrum of Microorganisms and
Viruses Is Diverse 22
1.5 The Second Golden Age of
Microbiology (1943–1970) 25
Molecular Biology Relies on
Microorganisms 25
Two Types of Cellular Organization Are
Realized 25
Antibiotics Are Used to Cure Infectious
Disease 26
1.6 The Third Golden Age of
Microbiology—Now 28
Microbiology Continues to Face Many
Challenges 28
Microbial Ecology and Evolution Are
Helping to Drive the New Golden Age 30
Chapter Review 31

Chapter 2 The Chemical Building
Blocks of Life 35
2.1 The Elements of Life 37
Matter Is Composed of Atoms 37
Atoms Can Vary in the Number of Neutrons

or Electrons 38
Electron Placement Determines Chemical
Reactivity 38
2.2 Chemical Bonding 39
Ionic Bonds Form between Oppositely
Charged Ions 40
Covalent Bonds Share Electrons 40
Hydrogen Bonds Form between Polar
Groups or Molecules 42
Chemical Reactions Change Bonding
Partners 43
2.3 Water, pH, and Buffers 44
Water Has Several Unique Properties 44
Acids and Bases Affect a Solution’s pH 44
Cell Chemistry Is Sensitive to pH
Changes 46

vi

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Contents

2.4 Major Organic Compounds of Living
Organisms 47
Functional Groups Define Molecular
Behavior 47

Carbohydrates Consist of Sugars and Sugar
Polymers 48
Lipids Are Water-Insoluble Compounds 48
Nucleic Acids Are Large, InformationContaining Polymers 50
Proteins Are the Workhorse Polymers in
Cells 54
Chapter Review 60

Chapter 3 Concepts and Tools for
Studying Microorganisms 64
3.1 The Bacteria/Eukaryote
Paradigm 66
Bacterial Complexity: Homeostasis and
Biofilm Development 66
Bacteria and Eukaryotes: The Similarities in
Organizational Patterns 70
Bacteria and Eukaryotes: The Structural
Distinctions 71

62582_FMXX_i_xxx.pdf vii

vii

3.2 Classifying Microorganisms 73
Classification Attempts to Catalog
Organisms 73
Kingdoms and Domains: Trying to Make
Sense of Taxonomic Relationships 73
Nomenclature Gives Scientific Names to
Organisms 78

Classification Uses a Hierarchical System 78
Many Methods Are Available to Identify and
Classify Microorganisms 79
3.3 Microscopy 83
Many Microbial Agents Are In the
Micrometer Size Range 83
Light Microscopy Is Used to Observe Most
Microorganisms 84
Staining Techniques Provide Contrast 84
Light Microscopy Has Other Optical
Configurations 89
Electron Microscopy Provides Detailed
Images of Cells, Cell Parts, and Viruses 91
Chapter Review 93

2/10/10 10:38 AM


viii

Contents

Other Subcompartments Exist in the Cell
Cytoplasm 121
Many Bacterial/Archaeal Cells Have a
“Cytoskeleton” 122
4.7 The Bacteria/Eukaryote
Paradigm—Revisited 124
What Is a Prokaryote? 124
Chapter Review 127

Chapter 5 Microbial Growth and
Nutrition 131
5.1 Microbial Reproduction 133
Most Bacteria Reproduce by Binary
Fission 133
Bacterial and Archaeal Cells Reproduce
Asexually 134

Chapter 4 Cell Structure and Function
in the Bacteria and Archaea 97
4.1 Diversity among the Bacteria and
Archaea 98
The Domain Bacteria Contains Some of the
Most Studied Microbial Organisms 99
The Domain Archaea Contains Many
Extremophiles 102
4.2 Cell Shapes and
Arrangements 104
Variations in Cell Shape and Cell
Arrangement Exist 104
4.3 An Overview to Bacterial and
Archaeal Cell Structure 106
Cell Structure Organizes Cell Function 106
4.4 External Cell Structures 108
Pili Are Protein Fibers Extending from the
Cell Surface 108
Flagella Are Long Appendages Extending
from the Cell Surface 108
The Glycocalyx Is an Outer Layer External

to the Cell Wall 110
4.5 The Cell Envelope 113
The Bacterial Cell Wall Is a Tough and
Protective External Shell 113
The Archaeal Cell Wall Also Provides
Mechanical Strength 117
The Cell Membrane Represents the Interface
between the Cell Environment and the
Cell Cytoplasm 117
The Archaeal Cell Membrane Differs from
Bacterial and Eukaryal Membranes 119
4.6 The Cell Cytoplasm and Internal
Structures 120
The Nucleoid Represents a Subcompartment
Containing the Chromosome 120
Plasmids Are Found in Many Bacterial and
Archaeal Cells 120

62582_FMXX_i_xxx.pdf viii

5.2 Microbial Growth 136
A Bacterial Growth Curve Illustrates the
Dynamics of Growth 136
Endospores Are a Response to Nutrient
Limitation 137
Optimal Microbial Growth Is Dependent on
Several Physical Factors 141
5.3 Culture Media and Growth
Measurements 146
Culture Media Are of Two Basic Types 146

Culture Media Can Be Devised to Select
for or Differentiate between Microbial
Species 148
Population Measurements Are Made Using
Pure Cultures 152
Population Growth Can Be Measured in
Several Ways 153
Chapter Review 155

Chapter 6 Metabolism of
Microorganisms 158
6.1 Enzymes and Energy in
Metabolism 159
Enzymes Catalyze All Chemical Reactions
in Cells 160
Enzymes Act through Enzyme-Substrate
Complexes 161
Enzymes Often Team Up in Metabolic
Pathways 162
Enzyme Activity Can Be Inhibited 162
Energy in the Form of ATP Is Required for
Metabolism 164
6.2 The Catabolism of Glucose 166
Glucose Contains Stored Energy That Can
Be Extracted 166
Glycolysis Is the First Stage of Energy
Extraction 167
The Citric Acid Cycle Extracts More Energy
from Pyruvate 167
Oxidative Phosphorylation Is the Process by

Which Most ATP Molecules Form 169

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Contents

6.3 Other Aspects of Catabolism 173
Other Nutrients Represent Potential Energy
Sources 173
Anaerobic Respiration Produces ATP Using
Other Final Electron Acceptors 177
Fermentation Produces ATP Using an
Organic Final Electron Acceptor 177
6.4 The Anabolism of
Carbohydrates 180
Photosynthesis Is a Process to Acquire
Chemical Energy 180
6.5 Patterns of Metabolism 183
Autotrophs and Heterotrophs Get Their
Energy and Carbon in Different Ways 183
Chapter Review 186

Chapter 7 Control of Microorganisms:
Physical and Chemical Methods 189
7.1 General Principles of Microbial
Control 191
Sterilization and Sanitization Are Key to
Good Public Health 191
7.2 Physical Methods of Control 192

Heat Is One of the Most Common Physical
Control Methods 192
Dry Heat Has Useful Applications 192
Moist Heat Is More Versatile Than Dry
Heat 194
Filtration Traps Microorganisms 198
Ultraviolet Light Can Be Used to Control
Microbial Growth 200
Other Types of Radiation Also Can Sterilize
Materials 200
Preservation Methods Retard Spoilage by
Microorganisms in Foods 202

PART 2 THE GENETICS OF
MICROORGANISMS
Chapter 8

ix

222

Microbial Genetics 224

8.1 DNA and Chromosomes 226
Bacterial and Archaeal DNA Is Organized
within the Nucleoid 227
DNA within a Chromosome Is Highly
Compacted 228
Many Microbial Cells also Contain
Plasmids 228

8.2 DNA Replication 229
DNA Replication Occurs in “Replication
Factories” 229
DNA Polymerase Only Reads in the 3Ј to 5Ј
Direction 231
8.3 Protein Synthesis 232
Transcription Copies Genetic Information
into Complementary RNA 232
The Genetic Code Consists of Three-Letter
Words 234
Translation Is the Process of Making
the Polypeptide 236
Antibiotics Interfere with Protein
Synthesis 240
Protein Synthesis Can Be Controlled
in Several Ways 240
Transcription and Translation
Are Compartmentalized 240

7.3 General Principles of Chemical
Control 204
Chemical Control Methods Are Dependent
on the Object to Be Treated 205
Chemical Agents Are Important to
Laboratory and Hospital Safety 206
Antiseptics and Disinfectants Can Be
Evaluated for Effectiveness 207
7.4 Chemical Methods of Control 208
Halogens Oxidize Proteins 208
Phenol and Phenolic Compounds Denature

Proteins 210
Heavy Metals Interfere with Microbial
Metabolism 211
Alcohols Denature Proteins and Disrupt
Membranes 211
Soaps and Detergents Act as Surface-Active
Agents 212
Peroxides Damage Cellular
Components 213
Some Chemical Agents Combine with
Nucleic Acids and/or Cell Proteins 213
Chapter Review 218

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Contents

8.4 Mutations 244
Mutations Are the Result of Heritable
Changes in a Genome 244
Point Mutations Can Be Spontaneous
or Induced 245
Repair Mechanisms Attempt
to Correct Mistakes or Damage
in the DNA 247

Transposable Genetic Elements
Can Cause Mutations 251
8.5 Identifying Mutants 252
Plating Techniques Select for Specific
Mutants or Characteristics 252
The Ames Test Can Identify
Potential Mutagens 253
Chapter Review 255

Chapter 9 Gene Transfer, Genetic
Engineering, and Genomics 260
9.1 Genetic Recombination
in Bacteria 262
Genetic Information Can Be Transferred
Vertically and Horizontally 262
Transformation Is the Uptake and
Expression of DNA in a Recipient
Cell 263
Conjugation Involves Cell-to-Cell Contact
for Horizontal Gene Transfer 266
Conjugation Also Can Transfer
Chromosomal DNA 267
Transduction Involves Viruses as Agents for
Horizontal Transfer of DNA 269
9.2 Genetic Engineering and
Biotechnology 274
Genetic Engineering Was Born
from Genetic Recombination 275

Genetic Engineering Has Many Commercial

and Practical Applications 277
DNA Probes Can Identify a Cloned Gene or
DNA Segment 282
9.3 Microbial Genomics 284
Many Microbial Genomes Have Been
Sequenced 284
Segments of the Human Genome May Have
“Microbial Ancestors” 289
Microbial Genomics Will Advance Our
Understanding of the Microbial
World 290
Comparative Genomics Brings a New
Perspective to Defining Infectious Diseases
and Studying Evolution 291
Metagenomics Is Identifying the Previously
Unseen Microbial World 293
Chapter Review 295

PART 3 BACTERIAL DISEASES
OF HUMANS

298

Chapter 10 Airborne Bacterial
Diseases 300
10.1 Structure and Indigenous
Microbiota of the Respiratory
System 302
Upper Respiratory Tract Defenses Limit
Microbe Colonization of the Lower

Respiratory Tract 302
10.2 Bacterial Diseases Affecting the
Upper Respiratory Tract 304
Pharyngitis Is an Inflammation
of the Throat 304
Diphtheria Is a Life-Threatening Illness 305
The Epiglottis Is Subject to Infection,
Especially in Children 307
The Nose Is the Most Commonly Infected
Region of the Upper Respiratory
Tract 307
Ear Infections Are Common Illnesses
in Early Childhood 308
Acute Bacterial Meningitis Is a Rapidly
Developing Inflammation 310
10.3 Bacterial Diseases of the Lower
Respiratory Tract 312
Pertussis (Whooping Cough) Is Highly
Contagious 312
Tuberculosis Is One of the Greatest
Challenges to Global Health 314
Infectious Bronchitis Is an Inflammation
of the Bronchi 320
Pneumonia Can Be Caused by Several
Bacteria 321
Other Pneumonia-Causing Bacterial
Species Are Obligate, Intracellular
Parasites 327
Chapter Review 331

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xi

Chapter 11 Foodborne and
Waterborne Bacterial
Diseases 334
11.1 The Structure and Indigenous
Microbiota of the Digestive
System 336
The Digestive System Is Composed of Two
Separate Categories of Organs 336
The Human Intestinal Microbiome Has
Not Been Well Studied 338
11.2 Bacterial Diseases of the Oral
Cavity 340
Dental Caries Causes Pain and Tooth Loss
in Affected Individuals 340
Periodontal Disease Can Arise from Bacteria
in Dental Plaque 342
11.3 Introduction to Bacterial Diseases
of the GI Tract 344
GI Tract Diseases May Arise from
Intoxications or Infections 344
There Are Several Ways Foods

or Water Become Contaminated 345
11.4 Foodborne Intoxications Caused
by Bacteria 346
Food Poisoning Illnesses Are the
Result of Enterotoxins 346
11.5 Foodborne and Waterborne
Infections 349
Bacterial Gastroenteritis Often Produces
an Inflammatory Condition 349
Several Bacterial Species Can Cause an
Invasive Gastroenteritis 354
Gastric Ulcer Disease Can Be Spread Person
to Person 360
Chapter Review 367

Chapter 12 Soilborne and
Arthropodborne Bacterial
Diseases 371
12.1 Soilborne Bacterial Diseases 373
Anthrax Is an Enzootic Disease 373
Tetanus Causes Hyperactive Muscle
Contractions 375
Gas Gangrene Causes Massive Tissue
Damage 375
Leptospirosis Is a Zoonotic Disease Found
Worldwide 377
12.2 Arthropodborne Bacterial
Diseases 379
Plague Can Be a Highly Fatal Disease 379
Tularemia Has More Than One Disease

Presentation 381
Lyme Disease Can Be Divided into Three
Stages 382
Relapsing Fever Is Carried by Ticks
and Lice 384

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12.3 Rickettsial and Ehrlichial
Arthropodborne Diseases 386
Rickettsial Infections Are Transmitted by
Arthropods 386
Ehrlichia and Anaplasma Infections
Are Emerging Diseases in the
United States 389
Chapter Review 392

Chapter 13 Sexually Transmitted
and Contact Transmitted Bacterial
Diseases 396
13.1 The Structure and Indigenous
Microbiota of the Female and Male
Reproductive Systems 398
The Male and Female Reproductive Systems
Consist of Primary and Accessory Sex
Organs 398
Portions of the Male and Female
Reproductive Systems Have an Indigenous
Microbiota 399
Common Vaginal Infections Come From

Indigenous Microbiota 399
13.2 Sexually Transmitted Diseases
Caused by Bacteria 400
Chlamydial Urethritis Is the Most
Frequently Reported STD 400
Gonorrhea Can Be an Infection in Any
Sexually Active Person 403
Syphilis Is a Chronic, Infectious
Disease 406
Other Sexually Transmitted Diseases Also
Exist 408

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Contents

Many Scientists Contributed to the Early
Understanding of Viruses 442
14.2 What Are Viruses? 444
Viruses Are Tiny Infectious Agents 444
Viruses Are Grouped by Their Shape 446
Viruses Have a Host Range and Tissue
Specificity 447
14.3 The Classification of Viruses 448
Nomenclature and Classification Do Not
Use Conventional Taxonomic Groups 448

13.3 The Structure, Indigenous
Microbiota, and Illnesses of the
Female and Male Urinary
System 410
Part of the Urinary Tract Harbors an
Indigenous Microbiota 410
Infections of the Urinary Tract Are the
Second Most Common Type of Infection
in the Body 411
13.4 Contact Diseases Caused by
Indigenous Bacterial Species 414
The Skin Protects Underlying Tissues from
Microbial Colonization 414
The Skin Harbors Indigenous Microbes 416
Acne Is the Most Common Skin Disease
Worldwide 417
Indigenous Microbiota of the Skin Can
Form Biofilms 419
13.5 Contact Diseases Caused by
Exogenous Bacterial Species 419
Staphylococcal Contact Diseases
Have Several Manifestations 419
Streptococcal Diseases Can
Be Mild to Severe 421
Other Wounds Also Can Cause Skin
Infections 424
Animal Bites Can Puncture the Skin 425
Leprosy (Hansen Disease) Is a Chronic,
Systemic Infection 426
13.6 Contact Diseases Affecting

the Eye 430
Some Bacterial Eye Infections Can Cause
Blindness 430
Chapter Review 433

PART 4 VIRUSES AND EUKARYOTIC
MICROORGANISMS
438
Chapter 14 The Viruses
and Virus-Like Agents 440
14.1 Foundations of Virology 442

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14.4 Viral Replication and Its
Control 449
The Replication of Bacteriophages
Is a Five-Step Process 449
Animal Virus Replication Often Results
in a Productive Infection 452
Some Animal Viruses Produce a Latent
Infection 455
14.5 The Cultivation and Detection
of Viruses 457
Detection of Viruses Often Is Critical
to Disease Identification 457
Cultivation and Detection of Viruses Most
Often Uses Cells in Culture 458
14.6 Tumors and Viruses 459
Cancer Is an Uncontrolled Growth

and Spread of Cells 459
Viruses Are Associated with About 20%
of Human Tumors 461
Oncogenic Viruses Transform Infected
Cells 462
14.7 Emerging Viruses and Virus
Evolution 466
Emerging Viruses Usually Arise Through
Natural Phenomena 466
There Are Three Hypotheses for the Origin
of Viruses 468
14.8 Virus-Like Agents 468
Viroids Are Infectious RNA Particles 468
Prions Are Infectious Proteins 469
Chapter Review 470

Chapter 15 Viral Infections of the
Respiratory Tract and Skin 474
15.1 Viral Infections of the Upper
Respiratory Tract 476
Rhinovirus Infections Produce
Inflammation in the Upper
Respiratory Tract 476
Adenovirus Infections Also Produce
Symptoms Typical of a Common
Cold 478
15.2 Viral Infections of the Lower
Respiratory Tract 479
Influenza Is a Highly Communicable Acute
Respiratory Infection 479

Paramyxovirus Infections Affect
the Lower Respiratory Tract 483

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xiii

Other Viruses Also Produce
Pneumonia 484
15.3 Diseases of the Skin Caused by
Herpesviruses 486
Human Herpes Simplex Infections Are
Widespread and Often Recurrent 488
Chickenpox Is No Longer a Prevalent
Disease in the United States 490
Human Herpesvirus 6 Infections Primarily
Occur in Infancy 491
A Few Herpesvirus Infections Are
Oncogenic 493
15.4 Other Viral Diseases
of the Skin 493
Paramyxovirus Infections Can Cause
Typical Childhood Diseases 493
Rubella (German Measles) Is an Acute,
Mildly Infectious Disease 496
Fifth Disease (Erythema Infectiosum)
Produces a Mild Rash 497

Some Human Papillomavirus Infections
Cause Warts 498
Poxvirus Infections Have Had Great Medical
Impacts on Populations 500
Chapter Review 505

Chapter 16 Viral Infections of the
Blood, Lymphatic, Gastrointestinal,
and Nervous Systems 508
16.1 Viral Diseases of the Blood and the
Lymphatic Systems 510
Two Herpesviruses Cause Blood
Diseases 510
Several Hepatitis Viruses Are
Bloodborne 512
16.2 Viral Diseases Causing
Hemorrhagic Fevers 514
Flaviviruses Can Cause a Terrifying
and Severe Illness 514
Members of the Filoviridae Produce
Severe Hemorrhagic Lesions of the
Tissues 516
Members of the Arenaviridae Are Associated
with Chronic Infections in Rodents 518
16.3 Viral Infections of the
Gastrointestinal Tract 519
Hepatitis Viruses A and E Are Transmitted
by the Gastrointestinal Tract 519
Viral Gastroenteritis Is Caused
by Several Unrelated Viruses 522

16.4 Viral Diseases of the Nervous
System 524
The Rabies Virus Is of Great Medical
Importance Worldwide 524
The Polio Virus May Be the Next Infectious
Disease Eradicated 526
Arboviral Encephalitis Is a Result of a
Primary Viral Infection 528
Chapter Review 532

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Chapter 17 Eukaryotic
Microorganisms: The Fungi 535
17.1 Characteristics of Fungi 537
Fungi Share a Combination of
Characteristics 537
Fungal Growth Is Influenced by Several
Factors 538
Reproduction in Fungi Involves Spore
Formation 540
17.2 The Classification of Fungi 543
Fungi Can Be Classified into Five Different
Phyla 543
Yeasts Represent a Term for Any
Single-Celled Stage of a Fungus 551
17.3 Fungal Intoxications 552
Some Fungi Can Be Poisonous or Even
Deadly When Consumed 552
Some Mushrooms Produce Mycotoxins 552

17.4 Fungal Diseases of the Skin 554
Dermatophytosis Is an Infection
of the Skin, Hair, and Nails 554
Candidiasis Often Is a Mild,
Superficial Infection 555
Sporotrichosis Is
an Occupational Hazard 556
17.5 Fungal Diseases of the Lower
Respiratory Tract 558
Cryptococcosis Usually Occurs
in Immunocompromised Individuals 558
Histoplasmosis Can Produce
a Systemic Disease 558
Blastomycosis Usually Is Acquired Via the
Respiratory Route 559

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Contents

Coccidioidomycosis Can Become
a Potentially Lethal Infection 560
Pneumocystis Pneumonia Can Cause a Lethal
Pneumonia 560
Other Fungi Also Cause Mycoses 562
Chapter Review 563

Chapter 18 Eukaryotic
Microorganisms: The Parasites 567
18.1 The Classification and
Characteristics of the Protista 569
The Protista Are a Perplexing Group
of Microorganisms 569
The Protozoa Encompass a Variety of
Lifestyles 572
18.2 Protozoal Diseases of the Skin,
and the Digestive and Urinary
Tracts 576
Leishmania Can Cause a Cutaneous
or Visceral Infection 576
Several Protozoal Parasites Cause Diseases
of the Digestive System 578
A Protozoan Parasite Also Infects the
Urinary Tract 581
18.3 Protozoal Diseases of the Blood
and Nervous System 583
The Plasmodium Parasite Infects
the Blood 583
The Trypanosoma Parasites Can Cause LifeThreatening Systemic Diseases 585
Babesia Is an Apicomplexan Parasite 586
Toxoplasma Causes a Relatively Common
Blood Infection 587
Naegleria Can Infect the Central Nervous
System 588
18.4 The Multicellular Helminths
and Helminthic Infections 591
There Are Two Groups of Parasitic

Helminths 591
Several Trematodes Can Cause Human
Illness 592
Tapeworms Survive in the Human
Intestines 594
Humans Are Hosts to at Least 50
Roundworm Species 595
Roundworms Also Infect the Lymphatic
System 599
Chapter Review 602

PART 5 DISEASE AND
RESISTANCE

607

Chapter 19 Infection
and Disease 609
19.1 The Host–Microbe Relationship 611
The Human Body Maintains a Symbiosis
with Microbes 611
Pathogens Differ in Their Ability to Cause
Disease 615

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Several Events Must Occur for Disease
to Develop in the Host 615
19.2 Establishment of Infection
and Diseases 617

Diseases Progress through a Series
of Stages 617
Pathogen Entry into the Host Depends
on Cell Adhesion and the Infectious
Dose 621
Breaching the Host Barriers Can Establish
Infection and Disease 622
Successful Invasiveness Requires Pathogens
to Have Virulence Factors 622
Pathogens Must Be Able to Leave the Host
to Spread Disease 627
19.3 Infectious Disease
Epidemiology 627
Epidemiologists Often Have to Identify the
Reservoir of an Infectious Disease 627
Epidemiologists Have Several Terms that
Apply to the Infectious Disease
Process 628
Infectious Diseases Can Be Transmitted in
Several Ways 628
Diseases Also Are Described by How They
Occur Within a Population 630
Nosocomial Infections Are Serious Health
Threats within the Health Care
System 638
Infectious Diseases Continue to Challenge
Public Health Organizations 640
Chapter Review 643

Chapter 20 Resistance and the

Immune System: Innate
Immunity 646
20.1 An Overview to Host Immune
Defenses 648
Blood Cells Form an Important Defense for
Innate and Acquired Immunity 648
The Lymphatic System Is Composed of
Cells and Tissues Essential to Immune
Function 649
Innate and Acquired Immunity Are
Essential Components of a Fully
Functional Human Immune System 650
20.2 The Innate Immune Response 652
Physical, Chemical, and Microbiological
Barriers Limit Entry of Pathogens 652
Phagocytosis Is a Nonspecific Defense
Mechanism to Clear Microbes from
Infected Tissues 653
Inflammation Plays an Important Role in
Fighting Infection 656
Moderate Fever Benefits Host Defenses 659
Natural Killer Cells Recognize and Kill
Abnormal Cells 660
Complement Marks Pathogens for
Destruction 660

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Contents

Innate Immunity Depends on Receptor
Recognition of Common PathogenAssociated Molecules 661
Interferon Puts Cells in an Antiviral
State 663
Chapter Review 666

Chapter 21 Resistance and the
Immune System: Acquired
Immunity 669
21.1 An Overview of the Acquired
Immune Response 671
The Ability to Eliminate Pathogens Requires
a Multifaceted Approach 671
Acquired Immunity Generates Two
Complementary Responses to Most
Pathogens 674
Clonal Selection Activates the Appropriate B
and T Cells 674
The Immune System Originates from
Groups of Stem Cells 677
21.2 Humoral Immunity 678
Humoral Immunity Is a Response Mediated
by Antigen-Specific B Lymphocytes 678
There Are Five Immunoglobulin
Classes 679
Antibody Responses to Pathogens Are
of Two Types 680
Antibody Diversity Is a Result of Gene
Rearrangements 681

Antibody Interactions Mediate the Disposal
of Antigens (Pathogens) 681
21.3 Cell-Mediated Immunity 685
Cellular Immunity Relies on T Lymphocyte
Receptors and Recognition 686
Naive T Cells Mature into Effector
T Cells 687
Cytotoxic T Cells Recognize MHC-I Peptide
Complexes 691
TH2 Cells Initiate the Cellular Response
to Humoral Immunity 691
Chapter Review 695

Chapter 22 Immunity and
Serology 698
22.1 Immunity to Disease 700
Acquired Immunity Can Result by Actively
Producing Antibodies to an Antigen 700
There Are Several “Generations”
of Vaccines 701
Acquired Immunity Also Can Result
by Passively Receiving Antibodies
to an Antigen 706
Herd Immunity Results from Effective
Vaccination Programs 709
Do Vaccines Have Dangerous
Side Effects? 709

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xv

22.2 Serological Reactions 711
Serological Reactions Have Certain
Characteristics 711
Neutralization Involves Antigen-Antibody
Reactions 713
Precipitation Requires the Formation of
a Lattice between Soluble Antigen and
Antibody 713
Agglutination Involves the Clumping
of Antigens 714
Complement Fixation Can Detect
Antibodies to a Variety of Pathogens 717
Labeling Methods Are Used to Detect
Antigen-Antibody Binding 718
22.3 Monoclonal Antibodies 721
Monoclonal Antibodies Are Becoming a
“Magic Bullet” in Biomedicine 721
Chapter Review 725

Chapter 23 Immune Disorders
and AIDS 729
23.1 Type 1 IgE-Mediated
Hypersensitivity 730
Type I Hypersensitivity Is Induced
by Allergens 731
Systemic Anaphylaxis Is the Most
Dangerous Form of a Type I
Hypersensitivity 733

Atopic Disorders Are the Most Common
Form of a Type I Hypersensitivity 734
Allergic Reactions Also Are Responsible for
Triggering Many Cases of Asthma 736
Why Do Only Some People Have
IgE-Mediated Hypersensitivities? 737
Therapies Sometimes Can Control
Type I Hypersensitivities 738
23.2 Other Types of
Hypersensitivity 740
Type II Hypersensitivity Involves AntibodyMediated Cell Destruction 740
Type III Hypersensitivity Is Caused by
Antigen-Antibody Aggregates 743
Type IV Hypersensitivity Is Mediated
by Antigen-Specific T Cells 744
23.3 Autoimmune Disorders
and Transplantation 748
An Autoimmune Disorder Is a Failure
to Distinguish Self from Non-self 748
Transplantation of Tissues or Organs
Is an Important Medical Therapy 750
Immunosuppressive Agents Prevent
Allograft Rejection 753
23.4 Immunodeficiency Disorders 753
Immunodeficiencies Can Involve Any
Aspect of the Immune System 754
The Human Immunodeficiency Virus (HIV)
Is Responsible for HIV Disease and
AIDS 755
Chapter Review 763

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Contents

Chapter 24 Antimicrobial Drugs 767
24.1 The History and Properties of
Antimicrobial Agents 769
The History of Chemotherapy Originated
with Paul Ehrlich 769
Fleming’s Observation of the Penicillin
Effect Ushered in the Era of
Antibiotics 770
Antimicrobial Agents Have a Number
of Important Properties 771
Antibiotics Are Agents of Natural Biological
Warfare 771
24.2 The Synthetic Antibacterial
Agents 772
Sulfanilamide and Other Sulfonamides
Target Specific Metabolic Reactions 772
Other Synthetic Antimicrobials Have
Additional Bacterial Cell Targets 774
24.3 The Beta-Lactam Family of
Antibiotics 775
Penicillin Has Remained the Most Widely
Used Antibiotic 776

Other Beta-Lactam Antibiotics Also Inhibit
Cell Wall Synthesis 777
24.4 Other Bacterially Produced
Antibiotics 778
Vancomycin Also Inhibits Cell Wall
Synthesis 778
Polypeptide Antibiotics Affect the Cell
Membrane 778
Many Antibiotics Affect Protein
Synthesis 779
Some Antibiotics Inhibit Nucleic Acid
Synthesis 782
24.5 Antiviral, Antifungal, and
Antiparasitic Drugs 782
Antiviral Drugs Can Be Used to Treat a
Limited Number of Human Viral
Diseases 784
Several Classes of Antifungal Drugs Cause
Membrane Damage 785
The Goal of Antiprotozoal Agents
Is to Eradicate the Parasite 786

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Antihelminthic Agents Are Targeted
at Nondividing Helminths 788
24.6 Antibiotic Assays and
Resistance 788
There Are Several Antibiotic Susceptibility
Assays 788

There Are Four Major Mechanisms
of Antibiotic Resistance 790
Antibiotic Resistance Is of Grave Concern
in the Medical Community 795
New Approaches to Antibiotic Therapy Are
Needed 797
Chapter Review 802

PART 6 ENVIRONMENTAL AND
APPLIED MICROBIOLOGY
Available online with access code
Chapter 25 Microbiology of Foods
Available online with access code
Chapter 26 Environmental Microbiology
Available online with access code
Chapter 27 Industrial Microbiology
and Biotechnology
Available online with access code
Appendix A Metric Measurement A-1
Appendix B Temperature Conversion
Chart A-1
Appendix C Answers to EvenNumbered End-of-Chapter Questions
Available online
Appendix D Answers to Textbook Case
and MicroInquiry Questions
Available online
Glossary
Index

G-1

I-1

Photograph Acknowledgments

P-1

2/17/10 2:18 PM


Preface
Do We Need to Know...?
As you embark upon your studies of the microbial world—and a fascinating world it will be—
you will wonder how important some topics are
that will be covered. You may ask yourself—or
your instructor—how important is this topic to
my career? If it is nursing, obviously the material on infectious diseases, epidemiology (the
scientific and medical study of the causes, transmission, and control of a disease within a population), and immunology (the study of how our
bodies fight an infection or disease) are critical.
If you are planning on pharmacy school, add
antimicrobial drugs to that list.
But what about some of the other “science”
topics, like microbial metabolism and genetics?
Are these important to a successful career? A
few years ago, the forum section on a Web site
called allnurses.com (“A Nursing Community
for Nurses”) asked nurses “What [microbiology] topics keep resurfacing in your nursing
classes?” Among the top responses were some
obvious ones, such as antibiotics and antibiotic
resistance, infectious diseases, and immunity.

But also on that list was microbial genetics.
Perhaps more revealing were the responses
to a second question: “What do you wish that
you had learned better in microbiology that you
thought you would never see again [in your
nursing classes]?” Among the answers submitted was metabolism.
Another survey published in Focus on
Microbiology Education in 2006 (Volume 12
No. 2, p. 7–9) asked nurse educators what they
thought were important topics for their students
to learn in a microbiology class. The top six in
importance were:
1. Bacterial structures and their functions;
2. Viral structures and their functions;
3. Epidemiology and public heath issues;

4. Antibiotics;
5. Immunology;
6. Disinfection and antisepsis.
Rounding out the top 10 were:
7. Bacterial metabolism;
8. Fungal structures and their functions;
9. Microbial genetics;
10. Biotechnology (production of vaccines,
medicines, and diagnostic techniques).
Notice that in both surveys, the topics of
microbial metabolism and microbial genetics are
among the top 10 concepts to master and understand. So, make sure you pay attention to what
your instructor has to say and what “we need to
know” (understand) about these topics. They

are important—and they will show up again in
your nursing courses!
Besides metabolism and genetics, there is
a substantial amount of other information you
will need to learn and understand. To facilitate
this understanding and coordinate it with class
material, I developed a “learning design” format
for the textbook (described below) to make reading easier, studying more efficient, and learning
uncomplicated. Most importantly, the design
allows you to better evaluate your learning and
provides you with the tools needed to probe your
understanding—that is, chapter learning aids
and assessment drills to evaluate your progress.
Realize, a prepared student knows her or his mastery before an exam—not as a result of the exam!
The “learning design” format facilitates this need.
I am excited that you are using and reading
this new, ninth edition of Alcamo’s Fundamentals
of Microbiology. I hope it is very useful in your
studies and also enjoyable to read. Always take
time to read many of the sidebars (MicroFocus
boxes) whether they are assigned or not. They
will help in your overall microbiology experience and the realization that microorganisms
do rule the world!

xvii

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2/17/10 2:18 PM

xviii

Preface

Audience

What’s New and Important

Alcamo’s Fundamentals of Microbiology, Ninth
Edition, is written for introductory microbiology courses having an emphasis on the biology
of human disease. It is geared toward students
in health and allied health science curricula such
as nursing, dental hygiene, medical assistance,
sanitary science, and medical laboratory technology. It also will be an asset to students studying
pharmacy, food science, agriculture, environmental science, and health administration. In
addition, the text provides a firm foundation
for advanced programs in biological sciences,
as well as medicine, dentistry, and other health
professions.

Besides the continued emphasis on a global
perspective on infection, this edition provides
detailed updates to microbial structure and function, disease information and statistics, and the
immune system.

Organization

Marginal Definition

62582_FMXX_i_xxx.pdf xviii

Alcamo’s Fundamentals of Microbiology, Ninth
Edition, is divided into six major areas of concentration. These areas use basic principles as
frameworks to provide the unity and diversity
of microbiology. Among the principles explored
are the variations in structure and growth of
microorganisms, the basis for infectious disease
and resistance, and the beneficial effects microorganisms have on our lives.
Part 1 deals with the foundations of microbiology. It includes chapters on the origins
of microbiology and the universal concepts
of growth and metabolism that underpin the
science. Part 2 then covers important material
on the genetics of microorganisms, including
genetic engineering and biotechnology. The discussions carry over to Part 3, where the spectrum of bacterial diseases is surveyed. Part 4
looks at the significance of other microorganisms, including viruses, fungi, and the protozoal
and multicellular parasites.
In Part 5 of the text, the emphasis turns
to infectious disease and the body’s resistance
through the immune system. Here, we study the
reasons for disease and the means for surviving it. Antibiotics and antibiotic resistance are
also covered. Part 6 closes the text with brief
discussions of how public health measures interrupt epidemics. Some key insights also are given
on the positive effects microorganisms exert
through biotechnology.

Chapter Organization
The chapter sequence and number remain the
same as in the previous edition, with one exception: the material on physical and chemical
control methods has been moved up to Chapter

7, supplying many applications to the more
detailed material in the previous chapters.
The “Learning Design” Concept
The text format includes activities designed to
encourage student interaction and assessment.
These design elements form an integrated study
and learning package (learning tools) for student
understanding and assessment.
• Chapter Introductions provide a stimulating
thought or historical perspective to set the
tone for the chapter.
• Key Concepts present statements identifying
the important concepts in the upcoming section and alert you to the significance of that
written material.
• Boldface Terms highlight important terms
and ideas in the text.
• Marginal Definitions present succinct definitions of notable terms as they enter the
discussion.
• Marginal Drawings provide visual images of
bacterial shapes and cell arrangements and
eukaryotic cells.
• Marginal Chemical Structures present structural formulas for many of the antimicrobial
drugs described in Chapter 24.
• Concept and Reasoning Checks allow you to
pause and either summarize the information
presented in the previous section or critically reason through a question pertaining
to the previous section.
• MicroFocus Boxes explore interesting topics
concerning microbiology or microorganisms.
• MicroInquiry Boxes allow you to investigate

(usually interactively) some important aspect of the chapter being studied.

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Preface

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•

•

•

•

•

•

•

•

•

Textbook Cases are embedded in many
chapters to help you understand pathogens
by presenting contemporary disease outbreaks originally reported by the Centers

for Disease Control and Prevention.
Figure Questions further reinforce your
understanding of microbiology concepts
described in the text.
Summary Tables pull together the similarities and differences of topics discussed in the
chapter.
Pronouncing Microorganism Names (inside
front and back covers) helps you correctly
pronounce those sometimes tongue-twisting
microorganism names.
Summaries of Key Concepts condense the
major ideas discussed in the chapter. The
“learning design” package also includes
many useful and important end-of-chapter
student assessments.
Learning Objectives outline the important
concepts in the chapters through Bloom’s
Taxonomy, a classification of levels of intellectual skills important in learning.
Self-Test questions (Step A) are multiplechoice questions focusing on concrete
“facts” learned in the chapter. Let’s face it:
there is information that needs to be memorized in order to reason critically.
Chapter Review (Step B) contains questions
of a somewhat unconventional type to assist
review of the chapter contents.
Questions for Thought and Discussion
(Step C) encourage students to use the text
to resolve thought-provoking problems with
contemporary relevance.
Applications (Step D) are questions requiring students to reason critically through a
problem of practical significance.

Being Skeptical
One of the seven types of essay boxes new to
this edition is titled “Being Skeptical.” A good
scientist is a skeptic and skepticism is an important part of science. Skepticism, unlike cynicism,
is not unwilling to accept a claim or observation. Skepticism simply says “Prove it!” Science
applies scientific reasoning as the method for
proof. Thus, a scientist, such as a microbiologist,

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MicroFocus Box

must see the evidence and it must be compelling
before the observation or statement is provisionally accepted. The claim is still open to further
examination and experimentation.
The “Being Skeptical” essays scattered
through the textbook present an often-fantastic
statement or claim. The essay then examines the
claim using reasoning skills and the scientific
process, which is sometimes called the scientific
method.

Why Pathogens?
Microorganisms perform many useful services
for humans when they produce food products,
manufacture organic materials in industrial
plants, and recycle such elements as carbon and

nitrogen. The emphasis of this book, however, is
on the tiny, but significant percentage of microorganisms causing human disease, the so-called
pathogens. Why do we emphasize pathogens?
Here are several reasons:
• Pathogens have regularly altered the course
of human history.
• Pathogens are familiar to audiences of microbiology.
• Pathogens add drama to an invisible world
of microorganisms.

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xx

Preface

•

Pathogens illustrate ecological relationships
between humans and microorganisms.
• Pathogens point up the diversity of microorganisms.
Moreover, the study of pathogens makes
basic science relevant and shows how microbiology interfaces with other disciplines such as
sociology, economics, history, politics, and geography. Finally, the study of pathogens helps us
to understand contemporary newspaper articles,
magazine headlines, and stories on the news.
And in the end, that makes us better citizens.
Indeed, the famous essayist Thomas Mann once
wrote, “All interest in disease is only another

expression of interest in life.”

Additional Resources
Jones and Bartlett offers an array of ancillaries to
assist instructors and students in teaching and
mastering the concepts in this text. Additional
information and review copies of any of the following items are available through your Jones
and Bartlett sales representative or by going to
www.jbpub.com/biology.
For the Student
Part 6 of this book, “Environmental and Applied
Microbiology,” is available online with the access
code bound into every new copy of this text (in
North America). Additional access codes are
available for purchase separately.
The Web site we developed exclusively for
the ninth edition of this text, offers a variety of resources
to enhance understanding of microbiology. The
site contains eLearning, a free on-line study
guide with chapter outlines, chapter essay questions, key term reviews, and short study quizzes.
The Study Guide to accompany this textbook contains important information to help
you study, take effective class notes, prepare
properly for exams, and even to manage your
time effectively. The latter is the single most
common reason for poor performance in college courses. The Study Guide also contains over
3,000 practice exercises and study questions of
various types to help you learn and retain the
information in the text.
Laboratory Fundamentals of Microbiology,
Ninth Edition, is a series of over 30 multipart

laboratory exercises providing basic training in

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the handling of microorganisms and reinforcing
ideas and concepts described in the textbook.
Guide to Infectious Diseases by Body Systems
is an excellent tool for learning about microbial
diseases. Each of the fifteen body systems units
presents a brief introduction to the anatomical
system and the bacterial, viral, fungal, or parasitic organism infecting the system.
An anthology called Encounters in
Microbiology (Volume I, Second Edition, and
Volume II) brings together “Vital Signs” articles
from Discover magazine in which health professionals use their knowledge of microbiology in
their medical cases.
For the Instructor
Compatible with Windows® and Macintosh®
platforms, the Instructor’s Media CD-ROM provides instructors with the following traditional
ancillaries:
• The PowerPoint® Image Bank provides the
illustrations, photographs, and tables (to
which Jones and Bartlett Publishers holds
the copyright or has permission to reproduce digitally) inserted into PowerPoint
slides. You can quickly and easily copy individual images or tables into your existing
lecture slides.
• The PowerPoint Lecture Outline Slides presentation package, prepared by Jean Revie of
South Mountain Community College, provides lecture notes and images for each chapter of Alcamo’s Fundamentals of Microbiology.
Instructors with the Microsoft PowerPoint
software can customize the outlines, art, and

order of presentation.
The following materials are also available
online, at />9780763762582.
• The Instructor’s Manual, provided as a text
file, includes chapter summaries and complete chapter lecture outlines and answers
to all the end-of-chapter assessments.
• Chapter Assessments Answers provide short
answers to figure questions, Concept and
Reasoning Checks, and all end-of-chapter
materials.
• The Test Bank is available as straight text
files. It has been updated by Cindy Ault
of Jamestown College, Jackie Reynolds of
Richland College, and Sue Katz of Rogers
State University.

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Acknowledgments
It is always my pleasure to thank everyone at Jones
and Bartlett Publishers who helped put together
this new version of the textbook. Cathleen
Sether has been a more-than-able publisher—
just don’t cross international borders with her.
Leah Corrigan, the production editor, has been
a pleasure to work with, and Lou Bruno continues to display his mastery of the production
process; Anne Spencer developed the new design
format; Caroline Perry ably assisted everyone;
Christine Myaskovsky tracked down many of the

great photos that embellish these pages; Deborah
Patton read every page and created the index;
Shellie Newell was again the “eagle-eye” copy
editor; and Elizabeth Morales provided much of
the excellent art in this new edition.
The book benefited from the expertise of
several fellow microbiologists and biologists. I
wish to thank my colleagues Philip Fernandez
and Michael McKinley for their input during the

writing of this edition. I especially want to thank
Brett Miller, a former microbiology student and
a GCC biotech major who read every word of
the eighth edition, making note of typographic
errors, syntax and grammatical errors, and all
unclear statements found in the text.
After more than 25 years of university and
college instruction, I must thank all my former
students who keep me on my toes in the classroom and require me to always be prepared.
Their suggestions and evaluations have encouraged me to continually assess my instruction so
it can be easily understood. I salute you, and I
hope those of you who read this text will let me
know what works and what still needs improvement to make your learning efficient and still
enjoyable.
Jeff Pommerville
Scottsdale, AZ

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About the
Author

Today I am a microbiologist, researcher, and science educator. My plans did not start with that
intent. While in high school in Santa Barbara,
California, I wanted to play professional baseball, study the stars, and own a ‘66 Corvette.
None of these desires would come true—my
batting average was miserable (but I was a good
defensive fielder), I hated the astronomy correspondence course I took, and I never bought
that Corvette.
I found an interest in biology at Santa
Barbara City College. After squeaking through
college calculus, I transferred to the University
of California at Santa Barbara (UCSB) where I
received a B.S. in Biology and stayed on to pursue
a Ph.D. degree in the lab of Ian Ross studying
cell communication and sexual pheromones in
a water mold. After receiving my doctorate in
Cell and Organismal Biology, my graduation was
written up in the local newspaper as a native son
who was a fungal sex biologist—an image that
was not lost on my three older brothers!

While in graduate school at UCSB, I rescued
a secretary in distress from being licked to death
by a German Shepherd. Within a year, we were

married (the secretary and I). When I finished
my doctoral thesis, I spent several years as a postdoctoral fellow at the University of Georgia. I
worried that I was involved in too many research
projects, but a faculty member told me something I will never forget. He said, “Jeff, it’s when
you can’t think of a project or what to do that you
need to worry.” Well, I have never had to worry!
I then moved on to Texas A&M University,
where I spent eight years in teaching and
research—and telling Aggie jokes. Toward the
end of this time, after publishing over 30 peerreviewed papers in national and international
research journals, I realized I had a real interest in teaching and education. Leaving the sex
biologist nomen behind, I headed farther west
to Arizona to join the biology faculty at Glendale
Community College, where I continue to teach
introductory biology and microbiology.
I have been lucky to be part of several educational research projects and have been honored, with two of my colleagues, with a Team
Innovation of the Year Award by the League
of Innovation in the Community Colleges.
In 2000, I became project director and lead
principal investigator for a National Science
Foundation grant to improve student outcomes in science through changes in curriculum and pedagogy. I had a fascinating three
years coordinating more than 60 science faculty
members (who at times were harder to manage
than students) in designing and field testing
18 interdisciplinary science units. This culminated with me being honored in 2003 with
the Gustav Ohaus Award (College Division)
for Innovations in Science Teaching from the
National Science Teachers Association.

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