Prescott/Harley/Klein's Microbiology

Visit the link below to download the full version of this book:
https://cheaptodownload.com/product/prescott-harley-kleins-microbiology-7th-edit
ion-full-pdf-download/
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page ii

PRESCOTT, HARLEY, AND KLEIN’S MICROBIOLOGY, SEVENTH EDITION

Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the
Americas, New York, NY 10020. Copyright © 2008 by The McGraw-Hill Companies, Inc. All rights
reserved. No part of this publication may be reproduced or distributed in any form or by any means,
or stored in a database or retrieval system, without the prior written consent of The McGraw-Hill
Companies, Inc., including, but not limited to, in any network or other electronic storage or transmission,
or broadcast for distance learning.

Some ancillaries, including electronic and print components, may not be available to customers outside
the United States.

This book is printed on recycled, acid-free paper containing 10% postconsumer waste.

1 2 3 4 5 6 7 8 9 0 DOW/DOW 0 9 8 7 6

ISBN 978–0–07–299291–5
MHID 0–07–299291–3

Publisher: Colin Wheatley/Janice Roerig-Blong

Senior Developmental Editor: Lisa A. Bruflodt
Senior Marketing Manager: Tami Petsche
Senior Project Manager: Jayne Klein
Lead Production Supervisor: Sandy Ludovissy
Senior Media Project Manager: Jodi K. Banowetz
Senior Media Producer: Eric A. Weber
Designer: John Joran
(USE) Cover Image: Dennis Kunkel Microscopy, Inc.
Lead Photo Research Coordinator: Carrie K. Burger
Photo Research: Mary Reeg
Supplement Producer: Mary Jane Lampe
Compositor: Carlisle Publishing Services
Typeface: 10/12 Times Roman
Printer: R. R. Donnelley Willard, OH

The credits section for this book begins on page C-1 and is considered an extension of the copyright page.

Library of Congress Cataloging-in-Publication Data

Willey, Joanne M.
Prescott, Harley, and Klein’s microbiology / Joanne M. Willey, Linda M. Sherwood, Christopher J.
Woolverton. — 7th ed.
p. cm.
Includes index.
ISBN 978–0–07–299291–5 — ISBN 0–07–299291–3 (hard copy : alk. paper)
1. Microbiology. I. Sherwood, Linda M. II. Woolverton, Christopher J. III. Prescott, Lansing M.
Microbiology. IV. Title.
QR41.2.P74 2008
616.9’041—dc22 2006027152
CIP

www.mhhe.com
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page iii

This text is dedicated to our mentors—John Waterbury, Richard Losick,

Thomas Bott, Hank Heath, Pete Magee, Lou Rigley, Irv Snyder, and
R. Balfour Sartor. And to our students.

—Joanne M. Willey
—Linda M. Sherwood
—Christopher J. Woolverton
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page iv

Brief Contents

Part I Introduction to Microbiology 21 Bacteria: The Deinococci and Nonproteobacteria

1 The History and Scope of Microbiology 1 Gram Negatives 519
2 The Study of Microbial Structure: Microscopy and 22 Bacteria: The Proteobacteria 539
Specimen Preparation 17 23 Bacteria: The Low G  C Gram Positives 571
3 Procaryotic Cell Structure and Function 39 24 Bacteria: The High G  C Gram Positives 589
4 Eucaryotic Cell Structure and Function 79 25 The Protists 605
26 The Fungi (Eumycota) 629
Part II Microbial Nutrition, Growth,
and Control Part VIII Ecology and Symbiosis
5 Microbial Nutrition 101 27 Biogeochemical Cycling and Introductory
6 Microbial Growth 119 Microbial Ecology 643
7 Control of Microorganisms by Physical and Chemical 28 Microorganism in Marine and Freshwater
Agents 149 Environments 667
29 Microorganisms in Terrestrial Environments 687
Part III Microbial Metabolism 30 Microbial Interactions 717
8 Metabolism: Energy, Enzymes, and Regulation 167
9 Metabolism: Energy Release and Conservation 191 Part IX Nonspecific (Innate) Resistance
10 Metabolism: The Use of Energy in Biosynthesis 225 and the Immune Response
31 Nonspecific (Innate) Host Resistance 743
32 Specific (Adaptive) Immunity 773
Part IV Microbial Molecular Biology
and Genetics
11 Microbial Genetics: Gene Structure, Replication, and Part X Microbial Diseases and Their Control
Expression 247 33 Pathogenicity of Microorganisms 815
12 Microbial Genetics: Regulation of Gene Expression 291 34 Antimicrobial Chemotherapy 835
13 Microbial Genetics: Mechanisms of Genetic Variation 317 35 Clinical Microbiology and Immunology 859
36 The Epidemiology of Infectious Disease 885
Part V DNA Technology and Genomics 37 Human Diseases Caused by Viruses and Prions 913
14 Recombinant DNA Technology 357 38 Human Diseases Caused by Bacteria 947
15 Microbial Genomics 383 39 Human Diseases Caused by Fungi and Protists 997

Part VI The Viruses Part XI Food and Industrial Microbiology

16 The Viruses: Introduction and General Characteristics 407 40 Microbiology of Food 1023
17 The Viruses: Viruses of Bacteria and Archaea 427 41 Applied and Industrial Microbiology 1049
18 The Viruses: Eucaryotic Viruses and Other Acellular
Infectious Agents 447 Appendix I A Review of the Chemistry
of Biological Molecules A-1
Part VII The Diversity of the Microbial World
19 Microbial Evolution, Taxonomy, and Diversity 471 Appendix II Common Metabolic
20 The Archaea 503 Pathways A-13

iv
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page v

Contents

About the Authors xi 4.7 Chloroplasts 90

Preface xii ■ Microbial Diversity & Ecology 4.2: The Origin of
the Eucaryotic Cell 91
4.8 The Nucleus and Cell Division 91
Part I Introduction to Microbiology 4.9 External Cell Coverings 94
4.10 Cilia and Flagella 95
1 The History and Scope of Microbiology 1 4.11 Comparison of Procaryotic and Eucaryotic
1.1 Members of the Microbial World 1 Cells 96
1.2 The Discovery of Microorganisms 3
1.3 The Conflict over Spontaneous Generation 6 Part II Microbial Nutrition, Growth,
1.4 The Golden Age of Microbiology 8 and Control
■ Techniques & Applications 1.1: The Scientific
Method 10 5 Microbial Nutrition 101
■ Disease 1.2: Koch’s Molecular Postulates 11 5.1 The Common Nutrient Requirements 101
1.5 The Development of Industrial Microbiology 5.2 Requirements for Carbon, Hydrogen, Oxygen,
and Microbial Ecology 12 and Electrons 102
1.6 The Scope and Relevance of Microbiology 13 5.3 Nutritional Types of Microorganisms 102
1.7 The Future of Microbiology 14 5.4 Requirements for Nitrogen, Phosphorus,
and Sulfur 104
2 The Study of Microbial Structure: Microscopy
5.5 Growth Factors 105
and Specimen Preparation 17
5.6 Uptake of Nutrients by the Cell 105
2.1 Lenses and the Bending of Light 17 5.7 Culture Media 110
2.2 The Light Microscope 18 ■ Historical Highlights 5.1: The Discovery of Agar
2.3 Preparation and Staining of Specimens 25 as a Solidifying Agent and the Isolation of Pure
2.4 Electron Microscopy 28 Cultures 112
2.5 Newer Techniques in Microscopy 31 5.8 Isolation of Pure Cultures 113
■ Techniques & Applications 5.2: The Enrichment
3 Procaryotic Cell Structure and Function 39 and Isolation of Pure Cultures 116
3.1 An Overview of Procaryotic Cell Structure 39
3.2 Procaryotic Cell Membranes 42 6 Microbial Growth 119
■ Microbial Diversity & Ecology 3.1: 6.1 The Procaryotic Cell Cycle 119
Monstrous Microbes 43 6.2 The Growth Curve 123
3.3 The Cytoplasmic Matrix 48 6.3 Measurement of Microbial Growth 128
■ Microbial Diversity & Ecology 3.2: 6.4 The Continuous Culture of Microorganisms 131
Living Magnets 51 6.5 The Influence of Environmental Factors on
3.4 The Nucleoid 52 Growth 132
3.5 Plasmids 53 ■ Microbial Diversity & Ecology 6.1:
3.6 The Bacterial Cell Wall 55 Life Above 100°C 138
3.7 Archaeal Cell Walls 62 6.6 Microbial Growth in Natural Environments 142
3.8 Protein Secretion in Procaryotes 63
3.9 Components External to the Cell Wall 65 7 Control of Microorganisms by Physical
3.10 Chemotaxis 71 and Chemical Agents 149
3.11 The Bacterial Endospore 73 7.1 Definitions of Frequently Used Terms 149
■ Techniques & Applications 7.1: Safety
4 Eucaryotic Cell Structure and Function 79 in the Microbiology Laboratory 150
4.1 An Overview of Eucaryotic Cell Structure 79 7.2 The Pattern of Microbial Death 151
4.2 The Plasma Membrane and Membrane Structure 81 7.3 Conditions Influencing the Effectiveness
4.3 The Cytoplasmic Matrix, Microfilaments, of Antimicrobial Agents 152
Intermediate Filaments, and Microtubules 83 7.4 The Use of Physical Methods in Control 153
■ Disease 4.1: Getting Around 84 7.5 The Use of Chemical Agents in Control 158
4.4 Organelles of the Biosynthetic-Secretory ■ Techniques & Applications 7.2: Universal
and Endocytic Pathways 84 Precautions for Microbiology Laboratories 160
4.5 Eucaryotic Ribosomes 88 7.6 Evaluation of Antimicrobial Agent
4.6 Mitochondria 88 Effectiveness 164

v
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page vi

vi Contents

■ Microbial Tidbits 11.2:

Part III Microbial Metabolism Catalytic RNA (Ribozymes) 268
8 Metabolism: Energy, Enzymes, and Regulation 167 11.7 The Genetic Code 275
11.8 Translation 276
8.1 An Overview of Metabolism 167
8.2 Energy and Work 169
12 Microbial Genetics: Regulation of Gene
8.3 The Laws of Thermodynamics 169
Expression 291
8.4 Free Energy and Reactions 170
8.5 The Role of ATP in Metabolism 171 12.1 Levels of Regulation of Gene Expression 292
8.6 Oxidation-Reduction Reactions, Electron 12.2 Regulation of Transcription Initiation 293
■ Historical Highlights 12.1:
Carriers, and Electron Transport Systems 172
The Discovery of Gene Regulation 294
8.7 Enzymes 174
12.3 Regulation of Transcription Elongation 302
8.8 The Nature and Significance of Metabolic
12.4 Regulation at the Level of Translation 305
Regulation 180
12.5 Global Regulatory Systems 307
8.9 Metabolic Channeling 180
12.6 Regulation of Gene Expression in Eucarya
8.10 Control of Enzyme Activity 181
and Archaea 313
9 Metabolism: Energy Release and Conservation 191 13 Microbial Genetics: Mechanisms
9.1 Chemoorganotrophic Fueling Processes 191 of Genetic Variation 317
9.2 Aerobic Respiration 193
13.1 Mutations and Their Chemical Basis 317
9.3 The Breakdown of Glucose to Pyruvate 194
13.2 Detection and Isolation of Mutants 324
9.4 The Tricarboxylic Acid Cycle 198
13.3 DNA Repair 326
9.5 Electron Transport and Oxidative
13.4 Creating Genetic Variability 329
Phosphorylation 200
13.5 Transposable Elements 332
9.6 Anaerobic Respiration 205
13.6 Bacterial Plasmids 334
9.7 Fermentations 207
13.7 Bacterial Conjugation 337
■ Historical Highlights 9.1:
Microbiology and World War I 210
13.8 DNA Transformation 342
9.8 Catabolism of Carbohydrates and Intracellular 13.9 Transduction 345
Reserve Polymers 210 13.10 Mapping the Genome 349
9.9 Lipid Catabolism 211 13.11 Recombination and Genome Mapping
9.10 Protein and Amino Acid Catabolism 212 in Viruses 350
9.11 Chemolithotrophy 212
9.12 Phototrophy 214 Part V DNA Technology and Genomics
■ Microbial Diversity & Ecology 9.2:
Acid Mine Drainage 215 14 Recombinant DNA Technology 357
14.1 Historical Perspectives 357
10 Metabolism: The Use of Energy in Biosynthesis 225 14.2 Synthetic DNA 361
10.1 Principles Governing Biosynthesis 226 14.3 The Polymerase Chain Reaction 362
10.2 The Precursor Metabolites 227 14.4 Gel Electrophoresis 366
10.3 The Fixation of CO2 by Autotrophs 228 14.5 Cloning Vectors and Creating Recombinant DNA 366
10.4 Synthesis of Sugars and Polysaccharides 230 14.6 Construction of Genomic Libraries 370
10.5 Synthesis of Amino Acids 235 14.7 Inserting Recombinant DNA into Host Cells 371
10.6 Synthesis of Purines, Pyrimidines, 14.8 Expressing Foreign Genes in Host Cells 371
and Nucleotides 241 ■ Techniques & Applications 14.1: Visualizing
10.7 Lipid Synthesis 242 Proteins with Green Fluorescence 374
14.9 Applications of Genetic Engineering 375
■ Techniques & Applications 14.2: Plant Tumors
Part IV Microbial Molecular Biology and Nature’s Genetic Engineer 378
and Genetics 14.10 Social Impact of Recombinant DNA Technology 380
11 Microbial Genetics: Gene Structure, 15 Microbial Genomics 383
Replication, and Expression 247
15.1 Introduction 383
■ Historical Highlights 11.1:
15.2 Determining DNA Sequences 384
The Elucidation of DNA Structure 248
15.3 Whole-Genome Shotgun Sequencing 384
11.1 DNA as Genetic Material 249
15.4 Bioinformatics 388
11.2 The Flow of Genetic Information 251
15.5 Functional Genomics 388
11.3 Nucleic Acid Structure 252
15.6 Comparative Genomics 391
11.4 DNA Replication 253
15.7 Proteomics 393
11.5 Gene Structure 264
15.8 Insights from Microbial Genomes 395
11.6 Transcription 268
15.9 Environmental Genomics 402
wil92913_FM_00i_xx.qxd 11/6/06 11:53 AM Page vii

Contents vii

Part VI The Viruses 20 The Archaea 503

20.1 Introduction to the Archaea 503
16 The Viruses: Introduction and General 20.2 Phylum Crenarchaeota 507
Characteristics 407 20.3 Phylum Euryarchaeota 508
16.1 Early Development of Virology 407 ■ Microbial Diversity & Ecology 20.1:
■ Historical Highlights 16.1: Disease and the Early Archaeal Phylogeny: More Than Just
Colonization of America 408 the Crenarchaeota and Euryarchaeota? 511
16.2 General Properties of Viruses 409 ■ Microbial Diversity & Ecology 20.2:
16.3 The Structure of Viruses 409 Methanotrophic Archaea 513
16.4 Virus Reproduction 417
16.5 The Cultivation of Viruses 417 21 Bacteria: The Deinococci
16.6 Virus Purification and Assays 419 and Nonproteobacteria Gram Negatives 519
16.7 Principles of Virus Taxonomy 423 21.1 Aquificae and Thermotogae 519
■ Microbial Tidbits 16.2: The Origin of Viruses 423 21.2 Deinococcus-Thermus 520
21.3 Photosynthetic Bacteria 520
17 The Viruses: Viruses of Bacteria and Archaea 427 ■ Microbial Diversity & Ecology 21.1:
17.1 Classification of Bacterial and Archaeal Viruses 428 The Mechanism of Gliding Motility 527
17.2 Virulent Double-Stranded DNA Phages 428 21.4 Phylum Planctomycetes 530
■ Microbial Diversity & Ecology 17.1: 21.5 Phylum Chlamydiae 531
Host-Independent Growth of an Archaeal Virus 429 21.6 Phylum Spirochaetes 532
17.3 Single-Stranded DNA Phages 436 21.7 Phylum Bacteroidetes 534
17.4 RNA Phages 437
17.5 Temperate Bacteriophages and Lysogeny 438 22 Bacteria: The Proteobacteria 539
17.6 Bacteriophage Genomes 444 22.1 Class Alphaproteobacteria 540
22.2 Class Betaproteobacteria 546
18 The Viruses: Eucaryotic Viruses and Other 22.3 Class Gammaproteobacteria 551
Acellular Infectious Agents 447 ■ Microbial Diversity & Ecology 22.1:
18.1 Taxonomy of Eucaryotic Viruses 447 Bacterial Bioluminescence 559
18.2 Reproduction of Vertebrate Viruses 448 22.4 Class Deltaproteobacteria 562
■ Microbial Diversity & Ecology 18.1: 22.5 Class Epsilonproteobacteria 567
SARS: Evolution of a Virus 451
■ Techniques & Applications 18.2: 23 Bacteria: The Low G  C Gram Positives 571
Constructing a Virus 458
23.1 General Introduction 571
18.3 Cytocidal Infections and Cell Damage 459
23.2 Class Mollicutes (The Mycoplasmas) 571
18.4 Persistent, Latent, and Slow Virus Infections 461
23.3 Peptidoglycan and Endospore Structure 572
18.5 Viruses and Cancer 461 ■ Microbial Tidbits 23.1: Spores in Space 576
18.6 Plant Viruses 463 23.4 Class Clostridia 576
18.7 Viruses of Fungi and Protists 466 23.5 Class Bacilli 578
18.8 Insect Viruses 466
18.9 Viroids and Virusoids 467
24 Bacteria: The High G  C Gram Positives 589
18.10 Prions 468
24.1 General Properties of the Actinomycetes 589
24.2 Suborder Actinomycineae 593
Part VII The Diversity of the Microbial World 24.3 Suborder Micrococcineae 593
24.4 Suborder Corynebacterineae 595
19 Microbial Evolution, Taxonomy, and Diversity 471 24.5 Suborder Micromonosporineae 597
19.1 Microbial Evolution 471 24.6 Suborder Propionibacterineae 598
19.2 Introduction to Microbial Classification 24.7 Suborder Streptomycineae 598
and Taxonomy 477 24.8 Suborder Streptosporangineae 601
19.3 Taxonomic Ranks 480 24.9 Suborder Frankineae 601
19.4 Techniques for Determining Microbial 24.10 Order Bifidobacteriales 602
Taxonomy and Phylogeny 481
19.5 Assessing Microbial Phylogeny 488 25 The Protists 605
19.6 The Major Divisions of Life 489 25.1 Distribution 606
19.7 Bergey’s Manual of Systematic Bacteriology 493 25.2 Nutrition 606
■ Microbial Diversity & Ecology 19.1:
25.3 Morphology 607
“Official” Nomenclature Lists—A Letter
25.4 Encystment and Excystment 608
from Bergey’s 494
25.5 Reproduction 608
19.8 A Survey of Procaryotic Phylogeny
25.6 Protist Classification 609
and Diversity 494
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page viii

viii Contents

■ Disease 25.1: Harmful Algal Blooms (HABs) 621 ■ Microbial Diversity & Ecology 30.2: Coevolution
■ Techniques & Applications 25.2: Practical of Animals and Their Gut Microbial Communities 725
Importance of Diatoms 624 30.2 Human-Microbe Interactions 734
30.3 Normal Microbiota of the Human Body 735
26 The Fungi (Eumycota) 629 ■ Techniques & Applications 30.3: Probiotics
26.1 Distribution 630 for Humans and Animals 739
26.2 Importance 630
26.3 Structure 631 Part IX Nonspecific (Innate) Resistance
26.4 Nutrition and Metabolism 632 and the Immune Response
26.5 Reproduction 632
26.6 Characteristics of the Fungal Divisions 635 31 Nonspecific (Innate) Host Resistance 743
31.1 Overview of Host Resistance 743
Part VIII Ecology and Symbiosis 31.2 Cells, Tissues, and Organs of the Immune System 744
31.3 Phagocytosis 752
27 Biogeochemical Cycling and Introductory 31.4 Inflammation 756
Microbial Ecology 643 31.5 Physical Barriers in Nonspecific (Innate)
27.1 Foundations in Microbial Diversity and Ecology 643 Resistance 758
■ Microbial Diversity & Ecology 27.1: Microbial 31.6 Chemical Mediators in Nonspecific (Innate)
Ecology Versus Environmental Microbiology 644 Resistance 762
27.2 Biogeochemical Cycling 644
27.3 The Physical Environment 653 32 Specific (Adaptive) Immunity 773
27.4 Microbial Ecology and Its Methods: 32.1 Overview of Specific (Adaptive) Immunity 774
An Overview 659 32.2 Antigens 774
■ Techniques & Applications 27.2: Thermophilic
32.3 Types of Specific (Adaptive) Immunity 776
Microorganisms and Modern Biotechnology 660
32.4 Recognition of Foreignness 778
■ Techniques & Applications 32.1: Donor Selection
28 Microorganisms in Marine and Freshwater
for Tissue or Organ Transplants 779
Environments 667
32.5 T Cell Biology 781
28.1 Marine and Freshwater Environments 667 32.6 B Cell Biology 786
■ Disease 28.1: New Agents in Medicine—
32.7 Antibodies 789
The Sea as the New Frontier 668
32.8 Action of Antibodies 799
28.2 Microbial Adaptations to Marine and Freshwater
■ Techniques & Applications 32.2: Monoclonal
Environments 671 Antibody Technology 800
28.3 Microorganisms in Marine Environments 673 32.9 Summary: The Role of Antibodies
28.4 Microorganisms in Freshwater Environments 682 and Lymphocytes in Immune Defense 802
32.10 Acquired Immune Tolerance 802
29 Microorganisms in Terrestrial Environments 687
32.11 Immune Disorders 803
29.1 Soils as an Environment for Microorganisms 687
29.2 Soils, Plants, and Nutrients 689
■ Microbial Tidbits 29.1: An Unintended Part X Microbial Diseases
Global-Scale Nitrogen Experiment 691 and Their Control
29.3 Microorganisms in the Soil Environment 692
29.4 Microorganisms and the Formation 33 Pathogenicity of Microorganisms 815
of Different Soils 693 33.1 Host-Parasite Relationships 815
29.5 Microorganism Associations with Vascular 33.2 Pathogenesis of Viral Diseases 818
Plants 696 33.3 Overview of Bacterial Pathogenesis 820
■ Microbial Diversity & Ecology 29.2: Mycorrhizae 33.4 Toxigenicity 824
and the Evolution of Vascular Plants 697 ■ Techniques & Applications 33.1: Detection
29.6 Soil Microorganisms and the Atmosphere 708 and Removal of Endotoxins 830
■ Microbial Diversity & Ecology 29.3: Soils, Termites, 33.5 Host Defense Against Microbial Invasion 830
Intestinal Microbes, and Atmospheric Methane 709
33.6 Microbial Mechanisms for Escaping Host
■ Techniques & Applications 29.4: Keeping Inside
Air Fresh with Soil Microorganisms 710
Defenses 832
29.7 The Subsurface Biosphere 711
29.8 Soil Microorganisms and Human Health 713 34 Antimicrobial Chemotherapy 835
34.1 The Development of Chemotherapy 835
30 Microbial Interactions 717 ■ Techniques & Applications 34.1: The Use
of Antibiotics in Microbiological Research 837
30.1 Microbial Interactions 717
■ Microbial Diversity & Ecology 30.1: Wolbachia 34.2 General Characteristics of Antimicrobial Drugs 837
pipientis: The World’s Most Infectious Microbe? 720 34.3 Determining the Level of Antimicrobial Activity 840
34.4 Antibacterial Drugs 841
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page ix

Contents ix

34.5 Factors Influencing Antimicrobial Drug 38.3 Direct Contact Diseases 964
Effectiveness 849 ■ Disease 38.2: Biofilms 969
34.6 Drug Resistance 849 ■ Disease 38.3: Antibiotic-Resistant Staphylococci 972
■ Disease 34.2: Antibiotic Misuse and Drug ■ Disease 38.4: A Brief History of Syphilis 974
Resistance 850 38.4 Food-Borne and Waterborne Diseases 979
34.7 Antifungal Drugs 854 ■ Techniques & Applications 38.5: Clostridial
34.8 Antiviral Drugs 855 Toxins as Therapeutic Agents—Benefits
34.9 Antiprotozoan Drugs 856 of Nature’s Most Toxic Proteins 983
38.5 Sepsis and Septic Shock 987
35 Clinical Microbiology and Immunology 859 38.6 Zoonotic Diseases 987
38.7 Dental Infections 991
35.1 Specimens 859
■ Techniques & Applications 35.1: Standard
39 Human Diseases Caused by Fungi and Protists 997
Microbial Practices 861
35.2 Identification of Microorganisms from Specimens 864 39.1 Pathogenic Fungi and Protists 997
■ Microbial Tidbits 35.2: Biosensors: 39.2 Airborne Diseases 999
The Future Is Now 871 39.3 Arthropod-Borne Diseases 1001
35.3 Clinical Immunology 875 ■ Disease 39.1: A Brief History of Malaria 1002
■ Techniques & Applications 35.3: History 39.4 Direct Contact Diseases 1008
and Importance of Serotyping 876 39.5 Food-Borne and Waterborne Diseases 1012
35.4 Susceptibility Testing 882 39.6 Opportunistic Diseases 1016
35.5 Computers in Clinical Microbiology 882 ■ Disease 39.2: The Emergence of Candidiasis 1018

36 The Epidemiology of Infectious Disease 885 Part XI Food and Industrial Microbiology
36.1 Epidemiological Terminology 886
■ Historical Highlights 36.1: John Snow—The First 40 Microbiology of Food 1023
Epidemiologist 886 40.1 Microorganism Growth in Foods 1024
36.2 Measuring Frequency: The Epidemiologist’s Tools 887 40.2 Microbial Growth and Food Spoilage 1026
36.3 Recognition of an Infectious Disease 40.3 Controlling Food Spoilage 1028
in a Population 888 ■ Historical Highlights 40.1: An Army Travels
■ Historical Highlights 36.2:“Typhoid Mary” 889 on Its Stomach 1030
36.4 Recognition of an Epidemic 889 40.4 Food-Borne Diseases 1032
36.5 The Infectious Disease Cycle: Story of a Disease 891 ■ Historical Highlights 40.2: Typhoid Fever
■ Historical Highlights 36.3:The First Indications and Canned Meat 1033
of Person-to-Person Spread of an Infectious Disease 896 40.5 Detection of Food-Borne Pathogens 1035
36.6 Virulence and the Mode of Transmission 897 40.6 Microbiology of Fermented Foods 1036
36.7 Emerging and Reemerging Infectious Diseases ■ Techniques & Applications 40.3: Chocolate:
and Pathogens 897 The Sweet Side of Fermentation 1037
36.8 Control of Epidemics 900 ■ Techniques & Applications 40.4: Starter Cultures,
■ Historical Highlights 36.4:The First Immunizations 902 Bacteriophage Infections, and Plasmids 1039
36.9 Bioterrorism Preparedness 905 40.7 Microorganisms as Foods and Food
■ Historical Highlights 36.5: 1346—The First Amendments 1046
Recorded Biological Warfare Attack 905
36.10 Global Travel and Health Considerations 907 41 Applied and Industrial Microbiology 1049
36.11 Nosocomial Infections 908 41.1 Water Purification and Sanitary Analysis 1050
■ Techniques & Applications 41.1: Waterborne
37 Human Diseases Caused by Viruses and Prions 913 Diseases, Water Supplies, and Slow Sand Filtration 1051
37.1 Airborne Diseases 914 41.2 Wastewater Treatment 1054
■ Disease 37.1: Reye’s and Guillain-Barré Syndromes 918 41.3 Microorganisms Used in Industrial
37.2 Arthropod-Borne Diseases 922 Microbiology 1060
■ Disease 37.2: Viral Hemorrhagic Fevers— ■ Techniques & Applications 41.2: The Potential
A Microbial History Lesson 923 of Thermophilic Archaea in Biotechnology 1061
37.3 Direct Contact Diseases 925 41.4 Microorganism Growth in Controlled
37.4 Food-Borne and Waterborne Diseases 939 Environments 1064
■ Historical Highlights 37.3: A Brief History of Polio 941 41.5 Major Products of Industrial Microbiology 1070
37.5 Zoonotic Diseases 941 41.6 Biodegradation and Bioremediation by Natural
37.6 Prion Diseases 944 Communities 1075
■ Microbial Diversity & Ecology 41.3: Methanogens—
38 Human Diseases Caused by Bacteria 947 A New Role for a Unique Microbial Group 1078
38.1 Airborne Diseases 948 41.7 Bioaugmentation 1080
38.2 Arthropod-Borne Diseases 960 ■ Microbial Diversity & Ecology 41.4: A Fungus
■ Historical Highlights 38.1: The Hazards with a Voracious Appetite 1081
of Microbiological Research 960
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page x

x Contents

41.8 Microbes As Products 1082

■ Techniques & Applications 41.5: Streptavidin-Biotin
Binding and Biotechnology 1084
41.9 Impacts of Microbial Biotechnology 1086

Appendix I A Review of the Chemistry

of Biological Molecules A-1

Appendix II Common Metabolic

Pathways A-13

Glossary G-1

Credits C-1

Index I-1
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xi

About the Authors

years, she has taught courses in general microbiology, genetics, bi-

Joanne M. Willey has been a ology, microbial genetics, and microbial physiology. She has served
professor at Hofstra University on as the editor for ASM’s Focus on Microbiology Education, and has
Long Island, New York since participated in and contributed to numerous ASM Conferences for
1993, and was recently promoted Undergraduate Educators (ASMCUE). She also has worked with
to full professor. Dr. Willey re- K-12 teachers to develop a kit-based unit to introduce microbiology
ceived her B.A. in Biology from into the elementary school curriculum, and has coauthored with
the University of Pennsylvania, Barbara Hudson a general microbiology laboratory manual, Explo-
where her interest in microbiology rations in Microbiology: A Discovery Approach, published by Pren-
began with work on cyanbacterial tice-Hall. Her association with McGraw-Hill began when she
growth in eutrophic streams. She prepared the study guides for the fifth and sixth editions of Micro-
earned her Ph.D. in biological biology. Her non-academic interests focus primarily on her family.
oceanography (specializing in marine microbiology) from the She also enjoys reading, hiking, gardening, and traveling. She can
Massachusetts Institute of Technology-Woods Hole Oceanographic be reached at [email protected].
Institution Joint Program in 1987. She then went to Harvard Uni-
versity where she spent four years as a postdoctoral fellow studying Christopher J. Woolverton
the filamentous soil bacterium Streptomyces coelicolor. Dr. Willey is Professor of Biological Sciences
continues to actively investigate this fascinating microbe and has and a member of the graduate fac-
co-authored a number of publications that focus on its complex de- ulty in Biological Sciences and
velopmental cycle. She is an active member of the American Soci- The School of Biomedical Sci-
ety for Microbiology and has served on the editorial board of the ences at Kent State University in
journal Applied and Environmental Microbiology since 2000. Dr. Kent, Ohio. Dr. Woolverton also
Willey regularly teaches microbiology to biology majors as well as serves as the Director of the KSU
allied health students. She also teaches courses in cell biology, ma- Center for Public Health Prepared-
rine microbiology, and laboratory techniques in molecular genetics. ness, overseeing its BSL-3 Train-
Dr. Willey lives on the north shore of Long Island with her husband ing Facility. He earned his B.S. from Wilkes College,
and two sons. She is an avid runner and enjoys skiing, hiking, sail- Wilkes-Barre, Pennsylvania and a M.S. and a Ph.D. in Medical
ing, and reading. She can be reached at [email protected]. Microbiology from West Virginia University, College of Medi-
cine. He spent two years as a postdoctoral fellow at the Univer-
Linda M. Sherwood is a sity of North Carolina at Chapel Hill studying cellular
member of the Department of Mi- immunology. Dr. Woolverton’s research interests are focused on
crobiology at Montana State Uni- the detection and control of bacterial pathogens. Dr. Woolverton
versity. Her interest in and his colleagues have developed the first liquid crystal biosen-
microbiology was sparked by the sor for the immediate detection and identification of microorgan-
last course she took to complete a isms, and a natural polymer system for controlled antibiotic
B.S. degree in Psychology at delivery. He publishes and frequently lectures on these two tech-
Western Illinois University. She nologies. Dr. Woolverton has taught microbiology to science ma-
went on to complete an M.S. de- jors and allied health students, as well as graduate courses in
gree in Microbiology at the Uni- Immunology and Microbial Physiology. He is an active member
versity of Alabama, where she studied histidine utilization by of ASM, serving on the editorial boards of ASM’s Microbiology
Pseudomonas acidovorans. She subsequently earned a Ph.D. in Ge- Education and Focus on Microbiology Education. He has partic-
netics at Michigan State University where she studied sporulation in ipated in and contributed to numerous ASM conferences for Un-
Saccharomyces cerevisiae. She briefly left the microbial world to dergraduate Educators, serving as co-chair of the 2001
study the molecular biology of dunce fruit flies at Michigan State conference. Dr. Woolverton resides in Kent, Ohio with his wife
University before her move to Montana State University. Dr. Sher- and three daughters. When not in the lab or classroom, he enjoys
wood has always had a keen interest in teaching, and her psychol- hiking, biking, tinkering with technology, and just spending time
ogy training has helped her to understand current models of with his family. His email address is [email protected].
cognition and learning and their implications for teaching. Over the

xi
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xii

Preface

Prescott, Harley, and Klein’s Microbiology has acquired the repu- duced the use of the first person to describe the flow of information
tation of covering the broad discipline of microbiology at a depth (e.g., see chapter openers) and we pose questions within the text,
not found in any other textbook. The seventh edition introduces a prompting students to reflect on the matter at hand. Each chapter is
new author team. As new authors, we were faced with the daunting divided into numbered section headings and organized in an out-
task of making a superior textbook even better. We bring over 40 line format. Some chapters have been significantly reorganized to
years of combined research and teaching experience. Our keen in- present the material in a more logical format (e.g., chapters 12, 28,
terest in teaching has been fostered by our involvement in work- and 39). As in previous editions, key terminology is boldfaced and
shops and conferences designed to explore, implement, and assess clearly defined. In addition, some words are now highlighted in red
various pedagogical approaches. Thus one of our goals for this edi- font: these include names of scientists with whom the students
tion was to make the book more accessible to students. To accom- should be acquainted, as well as names of techniques and microbes.
plish this we focused on three specific areas: readability, artwork, Every term in the extensive glossary, which includes over 200 new
and the integration of several key themes throughout the text. and revised entries, includes a page reference.

OUR STRENGTHS Artwork

To engage today’s students, a textbook must do more than offer text
Readability and images that just adequately describe the topic at hand. Our goal
We have retained the relatively simple and direct writing style used is to make the students want to read the text because they find the
in previous editions of Prescott, Harley, and Klein’s Microbiology. material interesting and appealing. The seventh edition brings a
However, for the seventh edition, we have added style elements de- new art program that features three-dimensional renditions and
signed to further engage students. For example, we have intro- bright, attractive colors. However, not only have existing figures
been updated, over 200 new figures have been added. The updated
From glycolysis

O
art program also includes new pedagogical features such as con-
C O
Pyruvate
cept maps (see figures 8.1, 12.1, and 31.1) and annotation of key
1 Pyruvate is decarboxylated (i.e., it loses a
C O
carbon in the form of CO2). The two
remaining carbons are attached to
pathways and processes (see figures 9.9 and 11.17).
CH3
coenzyme A by a high-energy bond. The
energy in this bond will be used to drive
NAD the next reaction. Acetyl-CoA is a
precursor metabolite.
9 Malate is oxidized, NADH  H β clamp
1 Leading
generating more NADH Core
and regenerating CO2 strand
1 The leading-strand core polymerase synthesizes
oxaloacetate, which is O DNA as the parental DNA strands are unwound by
CoA β clamp
needed to accept the two waiting to be Parental DNA DnaB helicase. The lagging strand core polymerase
carbons from acetyl-CoA C S CoA Acetyl CoA 2 The two remaining carbons of strands is nearing completion of an Okazaki fragment. DNA
loaded DnaB helicase
and continue the cycle. pyruvate are combined with the γ complex primase begins synthesis of the RNA primer for the
CH3 next Okazaki fragment to be synthesized.
Oxaloacetate is also a four carbons of oxaloacetate. This Lagging DNA primase
precursor metabolite. Oxaloacetate creates the 6-carbon molecule strand
Citrate Previously synthesized
citrate.
COO COO Okazaki fragment
NADH  H C O 2
CH2 RNA primer
CH2 HO C COO
NAD 3 Citrate changes the
COO CH2 arrangement of atoms to
9 COO form isocitric acid.
Malate
3
COO
Isocitric acid
HO CH
4-carbon
6-carbon COO 2 Upon completion of the new RNA primer, DNA
stage primase dissociates, and the γ complex (clamp
HC stage
CH2 loader) loads a β clamp onto the template primer.
β clamp being loaded
COO HC COO onto template primer
TCA Cycle HO CH
H 2O 8
8 Fumarate COO
COO NAD
reacts with H2O 4
5-carbon
to form malate. CH stage NADH  H
HC COO
CoA CH2 CO2
COO
Fumarate CH2 4 Another carbon is
7 removed, creating the
3 The lagging-strand core polymerase reaches the
COO C O 5-carbon precursor
previously synthesized Okazaki fragment and
FADH2 metabolite -
COO– Discarded dissociates from the DNA.
CH2 O ketoglutarate. In the
-ketoglutarate β clamp
FAD 5 process, NADH is
CH2 C O formed.
6 NAD  CoA
7 Succinate is oxidized to COO CH2 DNA polymerase I
fumarate. FAD serves as
the electron acceptor.
Succinate NADH  H (not shown) eventually
CH2 removes primer and
fills gap
C CO2
GTP GDP
 O S CoA
Pi 5 The last carbon of glucose is
Succinyl CoA released as carbon dioxide. 4 The lagging-strand core polymerase associates
6 CoA is cleaved from the More NADH is formed for use with the newly loaded β clamp and synthesis of a
high-energy molecule in the ETS, and the 4-carbon new Okazaki fragment begins.
succinyl-CoA. The energy precursor metabolite
released is used to form succinyl-CoA is formed.
GTP, which can be used to
make ATP or used directly
to supply energy to
processes such as
translation.

xii
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xiii

Preface xiii

Thematic Integration CHANGES TO THE SEVENTH EDITION

With the advent of genomics and the increased reach of cell biol-
The seventh edition of Prescott, Harley, and Klein’s Microbiol-
ogy, the divisions among microbiology subdisciplines have be-
ogy is the result of extensive review and analysis of previous edi-
come blurred; for instance, the microbial ecologist must also be
tions, the input from reviewers, and casual discussions with our
well-versed in microbial physiology, evolution, and the principles
colleagues. As a new author team, we were committed to keeping
and practices of molecular biology. In addition, the microbiologist
the in-depth coverage that Microbiology is known for, while at
must be acquainted with all major groups of microorganisms:
the same time bringing a fresh perspective not only to specific
viruses, bacteria, archaea, protists, and fungi. Students new to mi-
topics but to the overall presentation as well.
crobiology are asked to assimilate vocabulary, facts, and most im-
portantly, concepts, from a seemingly vast array of subjects. The
challenge to the professor of microbiology is to integrate essential Up-to-Date Coverage
concepts throughout the presentation of material while conveying Each year exciting advances are made in microbiology. While we
the beauty of microbes and excitement of this dynamic field. understand that not all of these are appropriate for discussion in
While previous editions of Microbiology excelled in incorpo- an introductory textbook, we have incorporated the most up-to-
rating genetics and metabolism throughout the text, in this edition date information and exciting, recent discoveries to maintain ac-
we have attempted to bring the diversity of the microbial world curate descriptions of structures and processes and to illustrate
into each chapter. Of course this was most easily done in those essential points. A few specific examples include a current de-
chapters devoted to microbial evolution, diversity, and ecology scription of the structure and function of DNA polymerase III, the
(chapters 19 to 30), but we challenged ourselves to bring micro- role of viruses in marine ecosystems, the ubiquitous nature of
bial diversity into chapters that are traditionally E. coli-based. So, type III secretion systems, an updated coverage of the inflamma-
although the chapters on genetics (chapters 11 to 13) principally tory response, and the current understanding of HIV origins and
review processes as they are revealed in E. coli, we also explore avian influenza epidemiology.
other systems as well, such as the regulation of sporulation in
Bacillus subtilis and quorum sensing in V. fischerii (see figures
12.19 through 12.21). Increased Emphasis on Microbial Evolution
We also thought it was important to weave the thread of evo- and Diversity
lution throughout the text. We start in the first chapter with a dis- Microbial evolution, diversity, and ecology are no longer subdis-
cussion of the universal tree of life (see figure 1.1), with various ciplines to be ignored by those interested in microbial genetics,
renditions of “the big tree” appearing in later chapters. Impor- physiology, or pathogenesis. For example, within the last 10
tantly, we remind students that structures and processes evolved years, polymicrobial diseases, intercellular communication, and
to their current state; that natural selection is always at work (e.g., biofilms have been recognized as important microbial processes
the title and the tone of chapter 13—now called Microbial Ge- that closely tie evolution to genetics, ecology to physiology, and
netics: Mechanisms of Genetic Variations—have been changed). ecology to pathogenesis. The seventh edition strives to integrate
Finally, the seventh edition of Microbiology explores theories re- these themes throughout the text. We begin chapter 1 with a dis-
garding the origin of life at a depth not seen in other microbiol- cussion of the universal tree of life and whenever possible, bring
ogy texts (chapter 19). diverse microbial species into discussions so that students can
Indeed, depth of coverage has been one of the mainstays of begin to appreciate the tremendous variation in the microbial
Prescott, Harley, and Klein’s Microbiology. The text was founded world. Chapter 19 now covers microbial evolution in greater
on two fundamental principles: (1) students need an introduction depth than other texts. It has been retitled Microbial Evolution,
to the whole of microbiology before concentrating on specialized Taxonomy, and Diversity and the content significantly revised so
areas, and (2) this introduction should provide the level of under- that microbial evolution is presented as a key component of mi-
standing required for students to grasp the conceptual underpin- crobiology. We also introduce and frequently remind students of
ning of facts. We remain committed to this approach. Thus the the enormity of microbial diversity. Like previous editions, the
seventh edition continues to provide a balanced and thorough in- seventh edition features specific chapters that review the mem-
troduction to all major areas of microbiology. This book is suitable bers of the microbial world. The chapters that are specifically de-
for courses with orientations ranging from basic microbiology to voted to ecology (chapters 27 through 29) have undergone
medical and applied microbiology. Students preparing for careers significant revisions. We continue to use the classification
in medicine, dentistry, nursing, and allied health professions will scheme set forth in the second edition of Bergey’s Manual of Sys-
find the text as useful as will those aiming for careers in research, tematic Bacteriology; in addition, we have introduced the Balti-
teaching, and industry. While two courses each of biology and more System of virus classification and the International Society
chemistry are assumed, we provide a strong overview of the rele- of Protistologists’ new classification scheme for eucaryotes in
vant chemistry in appendix I. chapters 18 and 25, respectively.
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xiv

xiv Preface

tions of Microbiology may notice that in addition to questions that

Mitochond

ces
Bacteria quiz the retention of key facts, new questions designed to be more

my
Rhodocyclus
Escherichovibrio
Syn

Chlo

ac ncto
m thought provoking have been added.

xib Pla m
Desu st riu
ec

cte

eriu
rion
roplaccus ter
hoc ob

ba

r
C

te
o
hl

act
Gl ydia

lf
Ch lav
o
a

oe

ia
m

lor F
rob
o
Lep bium
Fle

Methanoba
ac

Ag
ton

p
Thermococcus
e

m
Clo ma
CONTENT CHANGES BY PART

s
ccu

te
strid
Me

w
ium

lo
oco
Bacillus tha

ine
s
ma lobu
M

than
no

cterium s

ar
Heliobacterium las
et

M
the
op eog Each chapter has been thoroughly reviewed and almost all have
ha

Arthrobacter erm cha

Me
no

rm

pOPS19 Th Ar
py

u
ax
Halofer
ru

flexus undergone significant revision. In some chapters, there are

s

Chloro hermus
T a Methanospirillu
otog 6 Marine G m
Therm PS6
pO ifex Ro
pS pS GpGp. 1 lo
L 2 L 1 . 2 lo w te
p. 1 low
temp changes in both organization and content (e.g., chapters 11 to 13),
u Gp 2 2
Aq ot w mp
while many other chapters retain the same order of presentation
17

. tem
Su 3 lo p
Py Th ofilum
EM

lfo w t
The L 50
ro erm

lob em
pS

di o

us p
but the content has been updated. A summary of important new
pJP 27
pJP

ct pr
rm

iu ote
Co ushr

m
(m

78

Archaea
pri oo

material by parts includes:

nu m)

Ho
s

mo
s

Zea (corn)
Cryptomonas 0.1 changes per site
Achlyaia
r
sta a
Co phyr Part I
Babe m

r
Po
sia
iu
ec
m

Gi
Chapter 1—Expanded introduction to the three domains of life
ra

ar
m

dia
Pa

osteliu

and the microbes found in each domain.

Entamoeba

Phy
Dicty

Tr
Naegleria

ic
sar

Chapter 3—Increased coverage of the difference between ar-

ho
Euglena
Tryp

um

m
Ence

on

chaeal and bacterial cellular structure.

as
ano

Va
phali

inm
som

Eucarya
Chapter 4—Reorganized and updated discussion of the
tozo

orp
a

ha
on

biosynthetic-secretory pathway and endocytosis.

Writing for Student Understanding

Our goal as a new author team was to retain the straightforward
writing style of previous editions while at the same time making
the text more readable for the average college student. We have
thus added style elements designed to help the reader understand
the larger context of the topic at hand. For example, the opening
text in several chapters is accompanied by a concept map, en-
abling the student to visualize the relationships among component
topics found within a chapter. Parts of the text are now written in
first person; we want students to appreciate that we, as authors, un-
derstand that learning is a process that needs to be guided.

Significantly Enhanced Art Program

Today’s student must be visually engaged. The artwork in each
chapter of the seventh edition has been revised and updated to
include realistic, three-dimensional images designed to spark
student interest and curiosity. This new program uses bright
and appealing colors that give the text an attractive look. We Part II
have taken the opportunity to both update and annotate a num- Chapter 6—Updated discussion of the procaryotic cell cycle, in-
ber of images so that students can picture a complex process cluding current models of chromosome partitioning and septation;
step-by-step. New pedagogical features such as concept maps updated and expanded coverage of biofilms and quorum sensing.
and annotation of key pathways have been added. The three-
dimensional renderings help the student appreciate the beauty
Part III
and elegance of the cell, while at the same time making the ma-
terial more comprehendible. Chapter 8—A new section providing an overview of metabolism
and a framework for the more detailed discussions of metabo-
lism that follow; chemotaxis is introduced as an example of
Questions for Review and Reflection regulation of a behavioral response by covalent modification
Our belief that concepts are just as important as facts, if not more, of enzymes.
is also reflected in the questions for review and reflection that ap- Chapter 9—Reorganized discussion of chemoorganotrophic me-
pear throughout each chapter. Those who have used previous edi- tabolism to illustrate the connections among the pathways used
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xv

Preface xv

and how these pathways supply the materials needed for an- Part VIII
abolism; addition of a discussion of rhodopsin-based phototrophy. Chapter 27—Rewritten and re-titled Biogeochemical Cycling
Chapter 10—Reorganized to more clearly correlate N-, P-, and and Introductory to Microbial Ecology. Expanded coverage of
S-assimilation mechanisms with the synthesis of amino acids biogeochemical cycling now includes the phosphorus cycle.
and nucleotides; discussion of peptidoglycan synthesis is in- Discussion on microbial ecology emphasizes the importance
cluded in the discussion of polysaccharide biosynthesis. and application of culture-independent approaches. Discus-
sion of water purification and wastewater treatment has been
Part IV moved to chapter 41, Applied and Industrial Microbiology.
Chapter 28—Expanded and reorganized to cover the microbial
Chapter 11—Reorganized to focus solely on genome structure
communities found in the major biomes within marine and
and replication, gene structure, and gene expression.
freshwater environments. The role of the oceans in regulating
Chapter 12—Focuses exclusively on the regulation of gene ex-
global warming is introduced.
pression; reorganized according to level at which regulation
Chapter 29—Reorganized to first introduce soils as an environ-
occurs; updated and expanded discussion of riboswitches and
ment, is followed by more in-depth and updated treatment of
regulation by small RNA molecules.
mycorrhizae, the rhizobia, and plant pathogens. Approaches to
Chapter 13—Covers mutation, repair, and recombination in the
studying the subsurface environment and new discoveries in
context of processes that introduce genetic variation into pop-
this growing field are now included.
ulations.
Chapter 30—Microbial interactions previously introduced in
chapter 27 have been moved to this chapter, where they are
Part V presented along with human-microbe interactions (previously
Chapter 14—Begins with, and then builds upon, a concept map presented with innate immunity), helping to convey the con-
describing the principal steps involved in the construction of cept that the human body is an ecosystem.
recombinant DNA molecules with emphasis that recombinant
DNA technology is not confined to a few model and industrial Part IX
microorganisms.
Chapter 15—Rewritten to explore the many ways in which ge- Chapter 31—Reorganized and updated “nonspecific host resist-
nomics has changed microbiology. Expanded sections on ance” as its own chapter (normal microflora is now in chapter
bioinformatics and functional genomics, and a new section in- 30); enhanced sections on natural antimicrobial substances.
troduces environmental genomics (metagenomics). Chapter 32—Reorganized and updated to enhance linkages be-
tween innate and acquired immune activities; integrated med-
ical immunology concepts.
Part VI Chapter 33—Most virulence mechanisms have been either up-
Chapter 16—A new section describing virus reproduction in dated and/or expanded; added section on host defenses to mi-
general terms, so that this chapter can now stand alone as an crobial invasion to link infectious disease processes with host
introduction to viruses. immunity.

Part VII Part X

Chapter 19—Rewritten and re-titled Microbial Evolution, Tax- Chapter 34—Content focuses on mechanism of action of each
onomy, and Diversity; the chapter now opens with an in-depth antimicrobial agent; added section on anti-protozoan drugs.
discussion of the origin of life. Discussion of molecular tech- Chapter 35—Now includes both clinical microbiology and im-
niques and their importance in microbial taxonomy has also munology; reorganized and updated to reflect current clinical
been expanded. laboratory practices.
Chapter 20—In keeping with recent discoveries describing the Chapter 36—New focus on the important role of epidemiology
ubiquity of archaea, the seventh edition presents the differ- in preventative medicine, thus vaccines are now covered in
ences between microbes in the bacterial and archaeal domains this chapter (formerly found in chapter 32); new section on
in chapter 3. Thus chapter 20 now presents a more in-depth bioterorrism preparedness added.
look at some of the specifics of archaeal physiology, genetics, Chapter 37—Reorganized and updated to reflect viral pathogene-
taxonomy, and diversity. sis; select (potential bioterrorism) agents highlighted; influenza
Chapter 25—The protist chapter has been completely rewritten in section augmented to include the most current information re-
accordance with the 2005 reclassification of the Eucarya by the garding avian influenza; HIV etiology, pathogenesis and treat-
International Society of Protistologists. Emphasis is placed on ment sections updated; new section on viral zoonoses.
medically and environmentally important protists. Thus the chap- Chapter 38—Expanded coverage of bacterial pathogenesis; se-
ter entitled The Algae found in previous editions has been elimi- lect (potential bioterrorism) agents highlighted; new sections
nated and photosynthetic protists are now covered in chapter 25. on group B streptococcal disease and bacterial zoonoses.
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xvi

xvi Preface

Chapter 39—Reorganized and updated to reflect disease trans- Cross-Referenced Notes

mission routes (similar to chapters 37 and 38); new sections on • In-text notes in blue type refer students to other parts of the
cyclospora and microsporidia. book to review.

Part XI Review and Reflection Questions within Narrative

Chapter 40—Expanded discussion of lactic acid bacteria, probi- • Review questions throughout each chapter assist students in
otics: chocolate fermentation now featured in a Techniques & mastering section concepts before moving on to other topics.
Applications box.
Chapter 41—Revised to include water purification and waste-
water treatment. New section on nanotechnology; expanded the color they fluoresce after treatment with a special mixture of 2.3 PREPARATION AND STAINING OF SPECIMENS
stains (figure 2.13a). Thus the microorganisms can be viewed
section on the biochemistry of bioremediation. and directly counted in a relatively undisturbed ecological niche. Although living microorganisms can be directly examined with
Identification of microorganisms from specimens: Immunologic techniques the light microscope, they often must be fixed and stained to in-
(section 35.2) crease visibility, accentuate specific morphological features, and
preserve them for future study.
1. List the parts of a light microscope and describe their functions.
2. Define resolution,numerical aperture,working distance,and fluorochrome. Fixation
TOOLS FOR LEARNING 3. If a specimen is viewed using a 5X objective in a microscope with a 15X eye-
piece,how many times has the image been magnified?
The stained cells seen in a microscope should resemble living cells
as closely as possible. Fixation is the process by which the internal
4. How does resolution depend on the wavelength of light,refractive index,
and external structures of cells and microorganisms are preserved
and numerical aperture? How are resolution and magnification related?
Chapter Preview 5. What is the function of immersion oil?
and fixed in position. It inactivates enzymes that might disrupt cell
morphology and toughens cell structures so that they do not change
6. Why don’t most light microscopes use 30X ocular lenses for greater magnifi-
during staining and observation. A microorganism usually is killed
cation?
• Each chapter begins with a preview—a list of important con- 7. Briefly describe how dark-field, phase-contrast, differential interference
and attached firmly to the microscope slide during fixation.
There are two fundamentally different types of fixation.
contrast, and epifluorescence microscopes work and the kind of image
cepts discussed in the chapter. provided by each. Give a specific use for each type.
Heat fixation is routinely used to observe procaryotes. Typi-
cally, a film of cells (a smear) is gently heated as a slide is passed

1 The History and Scope

of Microbiology

Louis Pasteur, one of the greatest scientists of the nineteenth century, Energy Source
maintained that “Science knows no country, because knowledge belongs to Chemoorganotroph—organic molecules
humanity, and is a torch which illuminates the world.”
Chemolithotroph—inorganic molecules

Phototroph—light
PREVIEW ATP

• Microbiology is defined not only by the size of its subjects but the they are necessary for the production of bread, cheese, beer, an- Carbon Source
techniques it uses to study them. tibiotics, vaccines, vitamins, enzymes, and many other important Autotroph—CO2 Precursor Monomers
products. Indeed, modern biotechnology rests upon a microbio- metabolites and other Macromolecules
• Microorganisms include acellular entities (e.g., viruses), procarytic Heterotroph—organic molecules building blocks
cells, and eucaryotic cells. Cellular microorganisms are found in all logical foundation.
three domains of life: Bacteria, Archaea, Eucarya. Although the majority of microorganisms play beneficial or
• The development of microbiology as a scientific discipline has de- benign roles, some harm humans and have disrupted society over Electron Source
pended on the availability of the microscope and the ability to iso- the millennia. Microbial diseases undoubtedly played a major Organotroph—organic molecules
Reducing power (electrons)
late and grow pure cultures of microorganisms. The development role in historical events such as the decline of the Roman Empire Lithotroph—inorganic molecules
of these techniques in large part grew out of studies disproving the and the conquest of the New World. In 1347, plague or black
Theory of Spontaneous Generation and others establishing that death, an arthropod-borne disease, struck Europe with brutal
microorganisms can cause disease. force, killing 1/3 of the population (about 25 million people) Figure 8.1 Overview of Metabolism. The cell structures of organisms are assembled from various macromolecules (e.g., nucleic acids
• Microbiology is a large discipline; it has had and will continue to within four years. Over the next 80 years, the disease struck again and proteins). Macromolecules are synthesized from monomers and other building blocks (e.g., nucleotides and amino acids), which are the
have a great impact on other areas of biology and general human and again, eventually wiping out 75% of the European popula- products of biochemical pathways that begin with precursor metabolites (e.g., pyruvate and -ketoglutarate). In autotrophs, the precursor
welfare. tion. The plague’s effect was so great that some historians believe metabolites arise from CO2-fixation pathways and related pathways; in heterotrophs, they arise from reactions of the central metabolic
it changed European culture and prepared the way for the Re- pathways. Reducing power and ATP are consumed in many metabolic pathways. All organisms can be defined metabolically in terms of
naissance. Today the struggle by microbiologists and others their energy source, carbon source, and electron source. In the case of chemoorganotrophs, the energy source is an organic molecule that is

T
he importance of microorganisms can’t be overempha- against killers like AIDS and malaria continues. also the source of carbon and electrons. For chemolithotrophs, the energy source is an inorganic molecule that is also the electron source;
sized. In terms of sheer number and mass—it is estimated In this introductory chapter, we introduce the microbial the carbon source can be either CO2 (autotrophs) or an organic molecule (heterotrophs). For phototrophs, the energy source is light, the car-
that microbes contain 50% of the biological carbon and world to provide a general idea of the organisms and agents that bon source can be CO2 or organic molecules, and the electron source can be water (oxygenic phototrophs) or another reduced molecule
90% of the biological nitrogen on Earth—they greatly exceed microbiologists study. Then we describe the historical develop- such as hydrogen sulfide (anoxygenic phototrophs).
every other group of organisms on the planet. Furthermore, they ment of the science of microbiology and its relationship to medi-
are found everywhere: from geothermal vents in the ocean depths cine and other areas of biology. Finally, we discuss the scope,
to the coldest arctic ice, to every person’s skin. They are major relevance, and future of modern microbiology.
1 Isolate DNA to
contributors to the functioning of the biosphere, being indispens- be cloned.
able for the cycling of the elements essential for life. They also
are a source of nutrients at the base of all ecological food chains
and webs. Most importantly, certain microorganisms carry out
photosynthesis, rivaling plants in their role of capturing carbon
1.1 MEMBERS OF THE MICROBIAL WORLD BACTERIA ARCHAEA

dioxide and releasing oxygen into the atmosphere. Those mi- Microbiology often has been defined as the study of organisms 2 Use a restriction
enzyme or PCR to
crobes that inhabit humans also play important roles, including and agents too small to be seen clearly by the unaided eye—that generate fragments
helping the body digest food and producing vitamins B and K. In is, the study of microorganisms. Because objects less than about of DNA.
addition, society in general benefits from microorganisms, as one millimeter in diameter cannot be seen clearly and must be
Gene
Genetic regulatory proteins can bind Gene
Transcription
to the DNA and control whether or not
transcription begins. Transcription Genetic regulatory proteins can
bind to the DNA and control
Dans les champs de l’observation, le hasard ne favorise que les esprits préparés. Attenuation: Transcription can terminate
whether or not transcription begins.
3 Generate a recombinant
very early after it has begun due to the Linear vector molecule by inserting
(In the field of observation, chance favors only prepared minds.) formation of a transcriptional terminator. The compaction level of chromatin DNA fragments into a
may influence transcription. Vector cloning vector.
—Louis Pasteur Binding of a metabolite to a riboswitch in
mRNA can cause premature termination
of transcription.
mRNA mRNA
Translation Translational repressor proteins 4 Introduce recombinant
can bind to the mRNA and prevent Translation Antisense RNA can bind to mRNA molecule into new host.
translation from starting. and control whether or not translation New host
Antisense RNA can bind to mRNA and begins.
control whether or not translation begins.
Binding of a metabolite to a riboswitch in Protein
mRNA can block translation.
Protein Posttranslation Feedback inhibition and covalent
Posttranslation Small molecules can bind modifications (reversible and
(noncovalently) to a protein and affect irreversible) may regulate Figure 14.1 Steps in Cloning a Gene. Each step shown in
its function. An example is feedback protein function. this overview is discussed in more detail in Chapter 14.
inhibition, in which the product of a
metabolic pathway inhibits the first
enzyme in the pathway. Functional protein
The structure and function of a
protein can be altered by covalent

Concept Maps changes to the protein. These can be

reversible (e.g., phosphorylation/
dephosphorylation) or irreversible
(e.g., removal of amino acid residues).
These are called posttranslational
• Many chapters include a concept map, new to modifications.
Functional protein (b)

this edition, that outlines critical themes.

Figure 12.1 Gene Expression and Common Regulatory
(a) Mechanisms in the Three Domains of Life.
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xvii

Preface xvii

Special Interest Essays

• Interesting essays on relevant topics are included
35.2 Biosensors: The Future Is Now
in each chapter. Readings are organized into these
The 120-plus-year-old pathogen detection systems based on culture “communicate” detection through some type of transducing system.
topics: Historical Highlights, Techniques & Appli- and biochemical phenotyping are being challenged. Fueled by the Biosensors that detect specific DNA sequences, expressed proteins,
release of anthrax spores in the U.S. postal system, government and metabolic products have been developed that use optical
cations, Microbial Diversity & Ecology, Disease, agencies have been calling for newer technologies for the near-
immediate detection and identification of microbes. In the past, de-
(mostly fluorescence), electrochemical, or even mass displacement,
to report detection. The high degree of recognition required to re-
and Microbial Tidbits. tection technologies have traded speed for cost and complexity. The
agar plate technique, refined by Robert Koch and his contempo-
duce false-positive results has demanded the uniquely specific,
receptor-like capture that is associated with nucleic acid hybridiza-
raries in the 1880s, is a trusted and highly efficient method for the tion and antibody binding. Several microbial biosensors employ
isolation of bacteria into pure cultures. Subsequent phenotyping single-stranded DNA or RNA sequences, or antibody, for the detec-
biochemical methods, often using differential media in a manner tion component. The transducing or sensing component of biosen-
similar to that used in the isolation step, then identifies common sors may be markedly different, however. For example,
bacterial pathogens. Unfortunately, reliable results from this microcantilever systems detect the increased mass of the receptor-
process often take several days. More rapid versions of the pheno- bound ligand; the surface acoustic wave device detects change in
typing systems can be very efficient, yet still require pure culture specific gravity; the bulk quartz resonator monitors fluid density
inoculations. The rapid immunological tests offer faster detection and viscosity; the quartz crystal microbalance measures frequency
responses but may sacrifice sensitivity. Even DNA sequence com- change in proportion to the mass of material deposited on the crys-
18.1 SARS: Evolution of a Virus parisons, which are extremely accurate, may require significant tal; the micromirror sensor uses an optical fiber waveguide that
time for DNA amplification and significant cost for reagents and changes reflectivity; and the liquid crystal-based system reports the
sensitive readers. As usual, necessity has begat invention. reorientation of polarized light. Thus the specific capture of a lig-
In November 2002, a mysterious pneumonia was seen in the Receptor Activity The more recent microbial detection systems, many of which and is reflected in the net change measured by each system and re-
Guangdong Province of China, but the first case of this new type of are still untested in the clinical arena, sound like science fiction giz- sults in a signal that announces the initial capture event. Microchip
pneumonia was not reported until February 2003. Thanks to the mos, yet promise a new age for near-immediate detection and iden- control of the primary and subsequent secondary signals has re-
Human SARS Human SARS Human SARS
ease of global travel, it took only a couple of months for the pneu- tification of pathogens. These technologies are collectively referred sulted in automation of the detection process. The reliable detection
receptor ACE2 receptor ACE2 receptor ACE2
monia to spread to more than 25 countries in Asia, Europe, and to as “biosensors,” and if the biosensor is integrated with a com- of pathogens in complex specimens will be the real test as each of
North and South America. This newly emergent pneumonia was la- puter microchip for information management, it is then called a these technologies continues to compete for a place in the clinical
beled Severe Acute Respiratory Syndrome (SARS) and its “biochip.” Biosensors should ideally be capable of highly specific laboratory.
causative agent was identified as a previously unrecognized mem- recognition so as to discriminate between nearest relatives, and
ber of the coronavirus family, the SARS-CoV. Almost 10% of the N479K L472P T487S

roughly 8,000 people with SARS died. However, once the epidemic T487S
was contained, the virus appeared to “die out,” and with the excep- Human SARS Civet SARS Human SARS
tion of a few mild, sporadic cases in 2004, no additional cases have spike 2002-2003 spike spike 2003-2004
been identified. From where does a newly emergent virus come?
What does it mean when a virus “dies out”? (a) Good (b) Poor (c) Poor
We can answer these questions thanks to the availability of the
complete SARS-CoV genome sequence and the power of molecular
modeling. Coronaviruses are large, enveloped viruses with positive- Host Range of SARS-CoV Is Determined by Several
strand RNA genomes. They are known to infect a variety of mammals Amino Acid Residues in the Spike Protien. (a) The spike
and birds. Researchers suspected that SARS-CoV had “jumped” protien of the SARS-CoV that caused the SARS epidemic in
from its animal host to humans, so samples of animals at open mar- 2002–2003 fits tightly to the human host cell receptor ACE2. (b)
kets in Guangdong were taken for nucleotide sequencing. These stud- The civit SARS-CoV has two different amino acids at positions 479
ies revealed that cat-like animals called masked palm civits (Paguma and 487.This spike protein binds very poorly to human ACE2,
larvata) harbored variants of the SARS-CoV. Although thousands of thus the receptor is only weakly activated. (c) The spike protein
civits were then slaughtered, further studies failed to find widespread on the human SARS-CoV that was isolated from patients in 2003
infection of domestic or wild civits. In addition, experimental infec- 40.3 Chocolate: The Sweet Side of Fermentation
and 2004 also differs from that seen in the epidemic-causing
tion of civits with human SARS-CoV strains made these animals ill,
SARS-CoV by two amino acids.This SARS-CoV variant caused only
making the civit an unlikely candidate for the reservoir species. Such Chocolate could be characterized as the “world’s favorite food,” Like most fermentations, this process involves a succession of
mild, sporadic cases. and yet few people realize that fermentation is an essential part of
a species would be expected to harbor SARS-CoV without symptoms microbes. First, a community of yeasts, including Candida rugosa
so that it could efficiently spread the virus. chocolate production. The Aztecs were the first to develop choco- and Kluyveromyces marxianus, hydrolyze the pectin that covers the
Bats are reservoir hosts of several zoonotic viruses (viruses within the RBD, only four differ between civit and human. Two of late fermentation, serving a chocolate drink made from the seeds of seeds and ferment the sugars to release ethyl alcohol and Co2. As
spread from animals to people) including the emerging Hendra and these amino acids appear to be critical. As shown in the Box figure, the chocolate tree, Theobroma cocao [Greek theos, god and broma, the temperature and the alcohol concentration increase, the yeasts
Nipah viruses that have been found in Australia and East Asia, re- compared to the spike RBD in the SARS-CoV that caused the food, or “food of the gods”]. Chocolate trees now grow in West are inhibited and lactic acid bacteria increase in number. The mix-
spectively. Thus it was perhaps not too surprising when in 2005, two 2002–2003 epidemic, the civit spike has a serine (S) substituted for Africa as well as South America. ture is stirred to aerate the microbes and ensure an even temperature
groups of international scientists independently demonstrated that a threonine (T) at position 487 (T487S) and a lysine (K) at position The process of chocolate fermentation has changed very little distribution. Lactic acid production drives the pH down; this en-
Chinese horseshoe bats (genus Rhinolophus) are the natural reservoir 479 instead of asparagine (N), N479K. This causes a 1,000-fold de- over the past 500 years. Each tree produces a large pod that contains courages the growth of bacteria that produce acetic acid as a fer-
of a SARS-like coronavirus. When the genomes of the human and bat crease in the capacity of the virus to bind to human ACE2. Further- 30 to 40 seeds in a sticky pulp (see Box Figure). Ripe pods are har- mentation end product. Acetic acid is critical to the production of
SARS-CoV are aligned, 92% of the nucleotides are identical. More more, the spike found in SARS-CoV isolated from patients in 2003 vested and slashed open to release the pulp and seeds. The sooner the fine chocolate because it kills the sprout inside the seed and releases
revealing is alignment of the translated amino acid sequences of the and 2004 also has a serine at position 487 as well as a proline (P) for fermentation begins, the better the product, so fermentation occurs on enzymes that cause further degradation of proteins and carbohy-
proteins encoded by each virus. The amino acid sequences are 96 to leucine (L) substitution at position 472 (L472P). These amino acid the farm where the trees are grown. The seeds and pulp are placed in drates, contributing to the overall taste of the chocolate. In addition,
100% identical for all proteins except the receptor-binding spike pro- substitutions could be responsible for the reduced virulence of the “sweat boxes” or in heaps in the ground and covered, usually with ba- acetate esters, derived from acetic acid, are important for the devel-
teins, which are only 64% identical. The SARS-CoV spike protein virus found in these more recent infections. In other words, these nana leaves. opment of good flavor. Fermentation takes five to seven days. An
mediates both host cell surface attachment and membrane fusion. mutations could be the reason the SARS virus “died out.” experienced chocolate grower will know when the fermentation is
Thus a mutation of the spike protein allowed the virus to “jump” from Meanwhile a SARS vaccine based on the virulent 2002–2003 complete—if it is stopped too soon the chocolate will be bitter and
bat host cells to those of another species. It is not clear if the SARS- strain is being tested. This raises additional questions. Does the astringent. On the other hand, if fermentation lasts too long, mi-
CoV was transmitted directly to humans (bats are eaten as a delicacy original virulent SARS CoV strain still exist? Will the most re crobes start growing on the seeds instead of in the pulp. “Off-tastes”
arise when the gram-positive bacterium Bacillus and the filamen-
tous fungi Aspergillis, Penicillium, and Mucor hydrolyze lipids in
the seeds to release short-chain fatty acids. As the pH begins to rise,
the bacteria of the genera Pseudomonas, Enterobacter, and Es-
cherichia also contribute to bad tastes and odor.
After fermentation, the seeds, now called beans, are spread out to
dry. Ideally this is done in the sun, although drying ovens are also
used. The oven-drying method is considered inferior because the
beans can acquire a smoky taste. The dried beans are brown and lack
the pulp. They are bagged and sold to chocolate manufacturers, who
first roast the beans to further reduce the bitter taste and kill most of
the microbes (some Bacillus spores may remain). The beans are then
ground and the nibs—the inner part of each bean—are removed. The
5.1 The Discovery of Agar as a Solidifying Agent and the Isolation of Pure Cultures
(a)
nibs are crushed into a thick paste called a chocolate liquor, which
contains cocoa solids and cocoa butter, but no alcohol. Cocoa solids
The earliest culture media were liquid, which made the isolation of pathogenic bacteria. Koch decided to try solidifying this medium. are brown and have a rich flavor and cocoa butter has a high fat con-
bacteria to prepare pure cultures extremely difficult. In practice, a Koch was an amateur photographer—he was the first to take pho-
mixture of bacteria was diluted successively until only one organ- tomicrographs of bacteria—and was experienced in preparing his
ism, as an average, was present in a culture vessel. If everything own photographic plates from silver salts and gelatin. Precisely the
went well, the individual bacterium thus isolated would reproduce same approach was employed for preparing solid media. He spread
to give a pure culture. This approach was tedious, gave variable re- a mixture of Loeffler’s medium and gelatin over a glass plate, al-
sults, and was plagued by contamination problems. Progress in iso- lowed it to harden, and inoculated the surface in the same way he
lating pathogenic bacteria understandably was slow. had inoculated his sliced potatoes. The new solid medium worked
The development of techniques for growing microorganisms on well, but it could not be incubated at 37°C (the best temperature for
solid media and efficiently obtaining pure cultures was due to the most human bacterial pathogens) because the gelatin would melt.
efforts of the German bacteriologist Robert Koch and his associ- Furthermore, some bacteria digested the gelatin.
ates. In 1881 Koch published an article describing the use of boiled About a year later, in 1882, agar was first used as a solidifying
potatoes, sliced with a flame-sterilized knife, in culturing bacteria. agent. It had been discovered by a Japanese innkeeper, Minora
The surface of a sterile slice of potato was inoculated with bacteria Tarazaemon. The story goes that he threw out extra seaweed soup 1.2 Koch’s Molecular Postulates
from a needle tip, and then the bacteria were streaked out over the and discovered the next day that it had jelled during the cold winter
surface so that a few individual cells would be separated from the night. Agar had been used by the East Indies Dutch to make jellies
Although the criteria that Koch developed for proving a causal rela- 2. Inactivation of the gene or genes associated with the suspected
remainder. The slices were incubated beneath bell jars to prevent and jams. Fannie Eilshemius Hesse (see figure 1.7), the New Jersey-
tionship between a microorganism and a specific disease have been virulence trait should substantially decrease pathogenicity.
airborne contamination, and the isolated cells developed into pure born wife of Walther Hesse, one of Koch’s assistants, had learned
of great importance in medical microbiology, it is not always possi- 3. Replacement of the mutated gene with the normal wild-type gene
colonies. Unfortunately many bacteria would not grow well on po- of agar from a Dutch acquaintance and suggested its use when she
ble to apply them in studying human diseases. For example, some should fully restore pathogenicity.
tato slices. heard of the difficulties with gelatin. Agar-solidified medium was
pathogens cannot be grown in pure culture outside the host; because 4. The gene should be expressed at some point during the infection
At about the same time, Frederick Loeffler, an associate of an instant success and continues to be essential in all areas of
other pathogens grow only in humans, their study would require ex- and disease process.
Koch, developed a meat extract peptone medium for cultivating microbiology.
perimentation on people. The identification, isolation, and cloning of 5. Antibodies or immune system cells directed against the gene
genes responsible for pathogen virulence have made possible a new products should protect the host.
molecular form of Koch’s postulates that resolves some of these dif-
ficulties. The emphasis is on the virulence genes present in the infec- The molecular approach cannot always be applied because of prob-
tious agent rather than on the agent itself. The molecular postulates lems such as the lack of an appropriate animal system. It also is dif-
can be briefly summarized as follows: ficult to employ the molecular postulates when the pathogen is not
well characterized genetically.
1. The virulence trait under study should be associated much more
with pathogenic strains of the species than with nonpathogenic
strains.
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xviii

xviii Preface

Chapter Summaries
Summary 37
• End-of-chapter summaries are organized by num-
bered headings and provide a snapshot of impor-
has been used to study the interactions between the E. coli GroES
and GroEL chaperone proteins, to map plasmids by locating re-
1. How does a confocal microscope operate? Why does it provide better im- tant chapter concepts.
ages of thick specimens than does the standard compound microscope?
striction enzymes bound to specific sites, to follow the behavior of
2. Briefly describe the scanning probe microscope and compare and con-
living bacteria and other cells, and to visualize membrane proteins
trast its most popular versions—the scanning tunneling microscope and
(figure 2.29).
the atomic force microscope.What are these microscopes used for?

Summary
2.1 Lenses and the Bending of Light b. Most dyes are either positively charged basic dyes or negative acidic dyes and
a. A light ray moving from air to glass, or vice versa, is bent in a process known bind to ionized parts of cells.
as refraction. c. In simple staining a single dye is used to stain microorganisms.
b. Lenses focus light rays at a focal point and magnify images (figure 2.2). d. Differential staining procedures like the Gram stain and acid-fast stain distin-
guish between microbial groups by staining them differently (figure 2.15).
2.2 The Light Microscope e. Some staining techniques are specific for particular structures like bacterial
capsules, flagella, and endospores (figure 2.14).
a. In a compound microscope like the bright-field microscope, the primary im-
age is formed by an objective lens and enlarged by the eyepiece or ocular lens
to yield the final image (figure 2.3). 2.4 Electron Microscopy
b. A substage condenser focuses a cone of light on the specimen. a. The transmission electron microscope uses magnetic lenses to form an im-
c. Microscope resolution increases as the wavelength of radiation used to illu- age from electrons that have passed through a very thin section of a speci-
minate the specimen decreases. The maximum resolution of a light micro- men (figure 2.19). Resolution is high because the wavelength of electrons
scope is about 0.2 m. is very short.
d. The dark-field microscope uses only refracted light to form an image (fig- b. Thin section contrast can be increased by treatment with solutions of heavy
ure 2.7), and objects glow against a black background. metals like osmium tetroxide, uranium, and lead.
e. The phase-contrast microscope converts variations in the refractive index and c. Specimens are also prepared for the TEM by negative staining, shadowing
density of cells into changes in light intensity and thus makes colorless, un- with metal, or freeze-etching.
stained cells visible (figure 2.9). d. The scanning electron microscope (figure 2.23) is used to study external sur-
f. The differential interference contrast microscope uses two beams of light to face features of microorganisms.
create high-contrast, three-dimensional images of live specimens.
g. The fluorescence microscope illuminates a fluorochrome-labeled specimen 2.5 Newer Techniques in Microscopy
and forms an image from its fluorescence (figure 2.12). a. The confocal scanning laser microscope (figure 2.25) is used to study thick,
complex specimens.
2.3 Preparation and Staining of Specimens b. Scanning probe microscopes reach very high magnifications that allow scien-
a. Specimens usually must be fixed and stained before viewing them in the tists to observe biological molecules (figures 2.27 and 2.29).
bright-field microscope.

Key Terms
acidic dyes 26 differential staining 26 Gram stain 26 resolution 18
acid-fast staining 26 endospore staining 26 heat fixation 25 scanning electron microscope
atomic force microscope 36 eyepieces 18 mordant 26 (SEM) 30
basic dyes 26 fixation 25 negative staining 26 scanning probe microscope 35
bright-field microscope 18 flagella staining 28 numerical aperture 19 scanning tunneling microscope 35
capsule staining 26 fluorescence microscope 23 objective lenses 18 shadowing 29
chemical fixation 26 fluorescent light 23 ocular lenses 18 simple staining 26
chromophore groups 26 fluorochromes 24 parfocal 18 substage condenser 18
confocal scanning laser microscope focal length 18 phase-contrast microscope 21 transmission electron microscope
(CSLM) 34 focal point 18 refraction 17 (TEM) 29
dark-field microscope 21 freeze-etching 30 refractive index 17 working distance 20
differential interference contrast (DIC)
microscope 23

End-of-Chapter Material
• Key Terms highlight chapter terminology and 38 Chapter 2 The Study of Microbial Structure

list term location in the chapter.

• Critical Thinking Questions supplement the Critical Thinking Questions
questions for review and reflection found 1. If you prepared a sample of a specimen for light microscopy, stained with the included in the article and why that particular type of microscopy was the
Gram stain, and failed to see anything when you looked through your light mi- method of choice for the research. What other figures would you like to see
throughout each chapter; they are designed to croscope, list the things that you may have done incorrectly. used in this study? Outline the steps that the investigators would take in order
2. In a journal article, find an example of a light micrograph, a scanning or trans- to obtain such photographs or figures.
stimulate analytical problem solving skills. mission electron micrograph, or a confocal image. Discuss why the figure was

• Learn More includes a short list of recent and

relevant papers for the interested student and Learn More
professor. Additional references can be Binning, G., and Rohrer, H. 1985. The scanning tunneling microscope. Sci. Am.
253(2):50–56.
Rochow, T. G. 1994. Introduction to microscopy by means of light, electrons, X-rays,
or acoustics. New York: Plenum.

found at the Prescott website at www.mhhe. Dufrêne, Y. F. 2003. Atomic force microscopy provides a new means for looking at
microbial cells. ASM News 69(9):438–42.
Scherrer, Rene. 1984. Gram’s staining reaction, Gram types and cell walls of bac-
teria. Trends Biochem. Sci. 9:242–45.

com/prescott7. Hörber, J.K.H., and Miles, M. J. 2003. Scanning probe evolution in biology. Science
302:1002–5.
Stephens, D. J., and Allan, V. J. 2003. Light microscopy techniques for live cell im-
aging. Science 300:82–6.
Lillie, R. D. 1969. H. J. Conn’s biological stains, 8th ed. Baltimore: Williams &
Wilkins.

Please visit the Prescott website at www.mhhe.com/prescott7

for additional references.
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xix

Preface xix

STUDENT RESOURCES other media types that can be used to create customized lectures,
visually enhanced tests and quizzes, compelling course websites,
Student Study Guide or attractive printed support materials.
The Student Study Guide is a valuable resource that provides
learning objectives, study outlines, learning activities, and self- Access to your book, access to all books!
testing material to help students master course content. The Presentation Center library includes thousands of assets from
many McGraw-Hill titles. This ever-growing resource gives in-
structors the power to utilize assets specific to an adopted text-
Laboratory Exercises in Microbiology book as well as content from all other books in the library.
The seventh edition of Laboratory Exercises in Microbiology by
John P. Harley has been prepared to accompany the text. Like the Nothing could be easier!
text, the laboratory manual provides a balanced introduction in Accessed from the instructor side of your textbook’s ARIS web-
each area of microbiology. The class-tested exercises are modu- site, Presentation Center’s dynamic search engine allows you to
lar and short so that an instructor can easily choose those exer- explore by discipline, course, textbook chapter, asset type, or
cises that fit his or her course. keyword. Simply browse, select, and download the files you need
to build engaging course materials. All assets are copyright
McGraw-Hill Higher Education but can be used by instructors for
ARIS classroom purposes.
McGraw-Hill’s ARIS—Assessment, Review, and Instruction
• Art Library—Color-enhanced, digital files of all illustra-
System for Prescott, Harley, and Klein’s Microbiology,
tions in the book can be readily incorporated into lecture pre-
www.mhhe.com/prescott7. This online resource provides helpful
sentations, exams, or custom-made classroom materials. The
study materials that support each chapter in the book. Features
large, bolded labels make the images appropriate for use in
include:
large lecture halls.
Self-quizzes • TextEdit Art Library—Every line art piece is placed into a
Animations (with quizzing) PowerPoint presentation that allows the user to revise, move,
Flashcards or delete labels as desired for creation of customized presen-
Clinical case studies tations or for testing purposes.
Additional course content and more! • Photo Library—Like the Art Library, digital files of all the
photographs from the book are available.
• Table Library—Every table that appears in the book is pro-
INSTRUCTOR RESOURCES vided in electronic form.
• Animations Library—Full-color presentations involving
ARIS (www.mhhe.com/prescott7) key process figures in the book have been brought to life via
McGraw-Hill’s ARIS—Assessment, Review, and Instruction animations. These animations offer flexibility for instructors
System for Prescott, Harley, and Klein’s Microbiology is a com- and were designed to be used in lecture or for self-study. In-
plete, online tutorial, electronic homework, and course manage- structors can pause, rewind, fast forward, and turn audio
ment system. Instructors can create and share course materials off/on to create dynamic lecture presentations.
and assignments with colleagues with a few clicks of the mouse. • PowerPoint Lecture Outlines—These ready-made presen-
All PowerPoint lectures, assignments, quizzes, and tutorials are tations combine art and lecture notes for each of the 41 chap-
directly tied to text-specific materials. Instructors can also edit ters of the book. The presentations can be used as they are, or
questions, import their own content, and create announcements they can be customized to reflect your preferred lecture top-
and due dates for assignments. ARIS has automatic grading and ics and organization.
reporting of easy-to-assign homework, quizzing, and testing. All • PowerPoint Outlines—The art, photos, and tables for each
student activity within McGraw-Hill’s ARIS is automatically chapter are inserted into blank PowerPoint presentations to
recorded and available to the instructor through a fully integrated which you can add your own notes.
grade book that can be downloaded to Excel. Contact your local
McGraw-Hill Publisher’s representative for more information on
getting started with ARIS.
Instructor Testing and Resource CD-ROM
This cross-platform CD contains the Instructor’s Manual and Test
Bank, both available in Word and PDF formats. The Instructor’s
ARIS Presentation Center Manual contains chapter overviews, objectives, and answer
Build instructional materials wherever, whenever, and guidelines for Critical Thinking Questions. The Test Bank pro-
however you want! vides questions that can be used for homework assignments or the
ARIS Presentation Center is an online digital library containing preparation of exams. The computerized test bank allows the user
assets such as photos, artwork, animations, PowerPoints, and to quickly create customized exams. This user-friendly program
wil92913_FM_00i_xx.qxd 11/6/06 11:54 AM Page xx

xx Preface

allows instructors to search for questions by topic, format, or diffi- Colin R. Jackson, Southeastern Louisiana University
culty level; edit existing questions or add new ones; and scramble Shubha Kale Ireland, Xavier University of Louisiana
questions and answer keys for multiple versions of the same test. Judith Kandel, California State University–Fullerton
James Kettering, Loma Linda University
Madhukar B. Khetmalas, Texas Tech University
Transparencies
Peter J. King, Stephen F. Austin State University
A set of 250 full-color acetate transparencies is available to sup- Tina M. Knox, University of Illinois–Urbana
plement classroom lectures. These have been enhanced for pro- Duncan Krause, University of Georgia
jection and are available to adopters of the seventh edition. Don Lehman, University of Delaware
Rita B. Moyes, Texas A&M University
Ronald D. Porter, Pennsylvania State University
ACKNOWLEGMENTS Sabine Rech, San Jose State University
Focus Group Participants Pratibha Saxena, University of Texas at Austin
Geoffrey B. Smith, New Mexico State University
Jeffrey Isaacson, Nebraska Wesleyan University Fred Stutzenberger, Clemson University
Janice Knepper, Villanova University Karen Sullivan, Louisiana State University
Donald Lehman, University of Delaware Jennifer R. Walker, University of Georgia
Susan Lovett, Brandeis University William Whalen, Xavier University of Louisiana
Anne Morris Hooke, Miami University of Ohio John M. Zamora, Middle Tennessee State University
Mark Schneegurt, Wichita State University
Daniel Smith, Seattle University
Michael Troyan, Pennsylvania State University International Reviewers
Russell Vreeland, West Chester University Judy Gnarpe, University of Alberta
Stephen Wagner, Stephen F. Austin State University Shaun Heaphy, University of Leicester
Darla Wise, Concord University Edward E. Ishiguro, University of Victoria
Kuo-Kau Lee, National Taiwan Ocean University
Reviewers Jong-Kang Liu, National Sun Yat-sen University
Cheryl L. Patten, University of New Brunswick
Phillip M. Achey, University of Florida Clive Sweet, University of Birmingham
Shivanti Anandan, Drexel University Chris Upton, University of Victoria
Cynthia Anderson, Mt. San Antonio College Fanus Venter, University of Pretonia
Michelle L. Badon, University of Texas Shang-Shyng Yang, National Taiwan University
Larry L. Barton, University of New Mexico Guang-yu Zheng, Beijing Normal University
Mary Burke, Oregon State University
Frank B. Dazzo, Michigan State University As a new group of authors, we encountered a very steep learning
Johnny El-Rady, University of South Florida curve that we could not have overcome without the help of our
Paul G. Engelkirk, Central Texas College editors, Lisa Bruflodt, Jayne Klein, Janice Roerig-Blong, and
Robert H. Findlay, University of Alabama Colin Wheatley. We would also like to thank our photo editor
Steven Foley, University of Central Arkansas Mary Reeg and the tremendous talent and patience displayed by
Bernard Lee Frye, University of Texas at Arlington the artists. We are also very grateful to Professor Norman Pace for
Amy M. Grunden, North Carolina State University his helpful discussions, and the many reviewers who provided
Janet L. Haynes, Long Island University helpful criticism and analysis. Finally, we thank our spouses and
Diane Herson, University of Delaware children who provided support and tolerated our absences (men-
D. Mack Ivey, University of Arkansas tal if not physical) while we completed this demanding project.
wil92913_ch01.qxd 7/12/06 1:59 PM Page 1

1 The History and Scope

of Microbiology

Louis Pasteur, one of the greatest scientists of the nineteenth century,

maintained that “Science knows no country, because knowledge belongs to
humanity, and is a torch which illuminates the world.”

PREVIEW
• Microbiology is defined not only by the size of its subjects but the they are necessary for the production of bread, cheese, beer, an-
techniques it uses to study them. tibiotics, vaccines, vitamins, enzymes, and many other important
• Microorganisms include acellular entities (e.g., viruses), procarytic products. Indeed, modern biotechnology rests upon a microbio-
cells, and eucaryotic cells. Cellular microorganisms are found in all logical foundation.
three domains of life: Bacteria, Archaea, Eucarya. Although the majority of microorganisms play beneficial or
• The development of microbiology as a scientific discipline has de- benign roles, some harm humans and have disrupted society over
pended on the availability of the microscope and the ability to iso- the millennia. Microbial diseases undoubtedly played a major
late and grow pure cultures of microorganisms. The development role in historical events such as the decline of the Roman Empire
of these techniques in large part grew out of studies disproving the and the conquest of the New World. In 1347, plague or black
Theory of Spontaneous Generation and others establishing that death, an arthropod-borne disease, struck Europe with brutal
microorganisms can cause disease. force, killing 1/3 of the population (about 25 million people)
• Microbiology is a large discipline; it has had and will continue to within four years. Over the next 80 years, the disease struck again
have a great impact on other areas of biology and general human and again, eventually wiping out 75% of the European popula-
welfare. tion. The plague’s effect was so great that some historians believe
it changed European culture and prepared the way for the Re-
naissance. Today the struggle by microbiologists and others

T
he importance of microorganisms can’t be overempha- against killers like AIDS and malaria continues.
sized. In terms of sheer number and mass—it is estimated In this introductory chapter, we introduce the microbial
that microbes contain 50% of the biological carbon and world to provide a general idea of the organisms and agents that
90% of the biological nitrogen on Earth—they greatly exceed microbiologists study. Then we describe the historical develop-
every other group of organisms on the planet. Furthermore, they ment of the science of microbiology and its relationship to medi-
are found everywhere: from geothermal vents in the ocean depths cine and other areas of biology. Finally, we discuss the scope,
to the coldest arctic ice, to every person’s skin. They are major relevance, and future of modern microbiology.
contributors to the functioning of the biosphere, being indispens-
able for the cycling of the elements essential for life. They also
are a source of nutrients at the base of all ecological food chains
and webs. Most importantly, certain microorganisms carry out
photosynthesis, rivaling plants in their role of capturing carbon
1.1 MEMBERS OF THE MICROBIAL WORLD
dioxide and releasing oxygen into the atmosphere. Those mi- Microbiology often has been defined as the study of organisms
crobes that inhabit humans also play important roles, including and agents too small to be seen clearly by the unaided eye—that
helping the body digest food and producing vitamins B and K. In is, the study of microorganisms. Because objects less than about
addition, society in general benefits from microorganisms, as one millimeter in diameter cannot be seen clearly and must be

Dans les champs de l’observation, le hasard ne favorise que les esprits préparés.
(In the field of observation, chance favors only prepared minds.)
—Louis Pasteur
wil92913_ch01.qxd 7/25/06 11:56 AM Page 2

2 Chapter 1 The History and Scope of Microbiology

examined with a microscope, microbiology is concerned pri-

Mitoch
marily with organisms and agents this small and smaller.

s
Bacteria

ce
my
However, some microorganisms, particularly some eucaryotic

Rhodocyclus
Syn

Escherichovibrio
Chlo cocc act

on

cto
m

um
microbes, are visible without microscopes. For example, bread riu

dr
e c h o eo a

Desu st

ib Plan
te

ropla us er

eri
io
c

r
ba

te
o
C

n
molds and filamentous algae are studied by microbiologists, yet

act
Gl yd
vo

hl

ac
Ch

lf
Fla

am
lor

ia

rob
o

ex
are visible to the naked eye, as are the two bacteria Thiomargarita Lep bium

Methanoba
b
i

Fl
Ag

p
ton

m
Thermococcus

s
e
and Epulopiscium. Microbial Diversity & Ecology 3.1: Monstrous Microbes Clo ma

ccu

te
stri

w
diu

et

oco

lo
m
The difficulty in setting the boundaries of microbiology has

ha
Bacillu

e
in
s s
ma lobu

n
no

cterium s

ar
Heliobacterium

tha
las

et
led to the suggestion of other criteria for defining the field. For in-

th
op eog

M
ha
Arthrobacter

e
rm rcha

Me
no

rm
e
stance, an important characteristic of microorganisms, even those pOPS1
9 Th A

py
rax

u
Halofe

ru
flexus

s
that are large and multicellular, is that they are relatively simple in Chloro hermus Methanospirillum
T ga
moto 66 Marine
their construction, lacking highly differentiated cells and distinct Ther PS x Gp. 1 lo
O
p ife pS pS GpGp. 1 lo w temp
L .
u Ro Gp 22 L 12 2 low w temp
tissues. Another suggestion, made by Roger Stanier, is that the Aq ot

17
.3 tem
Su l

Py h
p

EM
lfo ow t
field also be defined in terms of its techniques. Microbiologists

The
ro erm um
T
lob em

pSL 50

di op
us p

pJP 27
pJ

ct
rmo
usually first isolate a specific microorganism from a population

P7

iu rote
m
Archaea

fil
8
Co
and then culture it. Thus microbiology employs techniques—such

pr
Ho

us
mo

in
as sterilization and the use of culture media—that are necessary

us
for successful isolation and growth of microorganisms. Zea
Cryptomonas
Achlyaia
Microorganisms are diverse, and their classification has al- r
sta ra
Co phy

Babe um
ways been a challenge for microbial taxonomists. Their early de- r

sia
Po

i
ec
m
scriptions as either plants or animals were too simple. For Gi

ra
ar

um
Pa
di
a
instance, some microbes are motile like animals, but also have

osteli
Entamoeba

Phy
cell walls and are photosynthetic like plants. Such microbes can-

Dicty

Naegleria

Tr
ic
sar

ho
not be placed easily into one kingdom or another. Another im-

Euglena
Try

um

Enc

m
on
pan
portant factor in classifying microorganisms is that some are

as
eph

Va
oso

ir
composed of procaryotic cells and others of eucaryotic cells.

im
alito
Eucarya

ma

or
ph
Procaryotic cells [Greek pro, before, and karyon, nut or kernel;

zoon

a
organisms with a primordial nucleus] have a much simpler mor-
phology than eucaryotic cells and lack a true membrane-delim-
ited nucleus. In contrast, eucaryotic cells [Greek, eu, true, and Figure 1.1 Universal Phylogenetic Tree. These evolutionary
karyon, nut or kernel] have a membrane-enclosed nucleus; they relationships are based on rRNA sequence comparisons. Man
are more complex morphologically and are usually larger than (Homo) is highlighted in red.
procaryotes. These observations eventually led to the develop-
ment of a classification scheme that divided organisms into five
kingdoms: the Monera, Protista, Fungi, Animalia, and Plantae. microbiologists believe that organisms should be divided among
Microorganisms (except for viruses, which are acellular and have three domains: Bacteria (the true bacteria or eubacteria),
their own classification system) were placed in the first three Archaea,1 and Eucarya (all eucaryotic organisms) (figure 1.1).
kingdoms. This system, which we shall use here, and the results leading to it
In the last few decades, great progress has been made in three are discussed in chapter 19. A brief description of the three do-
areas that profoundly affect microbial classification. First, much mains and of the microorganisms placed in them follows.
has been learned about the detailed structure of microbial cells Bacteria2 are procaryotes that are usually single-celled or-
from the use of electron microscopy. Second, microbiologists ganisms. Most have cell walls that contain the structural molecule
have determined the biochemical and physiological characteris- peptidoglycan. They are abundant in soil, water, and air and are
tics of many different microorganisms. Third, the sequences of also major inhabitants of our skin, mouth, and intestines. Some
nucleic acids and proteins from a wide variety of organisms have bacteria live in environments that have extreme temperatures,
been compared. The comparison of ribosomal RNA (rRNA), be-
gun by Carl Woese in the 1970s, was instrumental in demonstrat-
ing that there are two very different groups of procaryotic
organisms: Bacteria and Archaea, which had been classified to- 1
Although this will be discussed further in chapter 19, it should be noted here that
gether as Monera in the five-kingdom system. Later, studies several names have been used for the Archaea. The two most important are ar-
based on rRNA comparisons suggested that Protista was not a co- chaeobacteria and archaebacteria. In this text, we shall use only the name Archaea.
2
hesive taxonomic unit and that it should be divided into three or In this text, the term bacteria (s., bacterium) will be used to refer to procaryotes
that belong to domain Bacteria, and the term archaea (s., archaeon) will be used
more kingdoms. These studies and others have led many taxono- to refer to procaryotes that belong to domain Archaea. It should be noted that in
mists to conclude that the five-kingdom system is too simple. A some publications, the term bacteria is used to refer to all procaryotes. That is not
number of alternatives have been suggested, but currently, most the case in this text.
wil92913_ch01.qxd 7/12/06 1:59 PM Page 3

The Discovery of Microorganisms 3

pH, or salinity. Although some bacteria cause disease, many play

1. Describe the field of microbiology in terms of the size of its subject mate-
more beneficial roles such as cycling elements in the biosphere,
rial and the nature of its techniques.
breaking down dead plant and animal material, and producing vi-
2. Describe and contrast procaryotic and eucaryotic cells.
tamins. Cyanobacteria produce significant amounts of oxygen
3. Describe and contrast the five-kingdom classification system with the
through the process of photosynthesis.
three-domain system.Why do you think viruses are not included in either
Archaea are procaryotes that are distinguished from
system?
Bacteria by many features, most notably their unique ribosomal
RNA sequences. They also lack peptidoglycan in their cell
walls and have unique membrane lipids. Some have unusual
metabolic characteristics, such as the methanogens, which gen- 1.2 THE DISCOVERY OF MICROORGANISMS
erate methane gas. Many archaea are found in extreme envi-
Even before microorganisms were seen, some investigators sus-
ronments. Pathogenic archaea have not yet been identified.
pected their existence and responsibility for disease. Among oth-
Domain Eucarya includes microorganisms classified as pro-
ers, the Roman philosopher Lucretius (about 98–55 B.C.) and the
tists or Fungi. Animals and plants are also placed in this domain.
physician Girolamo Fracastoro (1478–1553) suggested that dis-
Protists are generally larger than procaryotes and include uni-
ease was caused by invisible living creatures. The earliest mi-
cellular algae, protozoa, slime molds, and water molds. Algae
croscopic observations appear to have been made between 1625
are photosynthetic protists that together with the cyanobacteria
and 1630 on bees and weevils by the Italian Francesco Stelluti,
produce about 75% of the planet’s oxygen. They are also the
using a microscope probably supplied by Galileo. In 1665, the
foundation of aquatic food chains. Protozoa are unicellular,
first drawing of a microorganism was published in Robert
animal-like protists that are usually motile. Many free-living
Hooke’s Micrographia. However, the first person to publish ex-
protozoa function as the principal hunters and grazers of the mi-
tensive, accurate observations of microorganisms was the ama-
crobial world. They obtain nutrients by ingesting organic matter
teur microscopist Antony van Leeuwenhoek (1632–1723) of
and other microbes. They can be found in many different envi-
Delft, The Netherlands (figure 1.3a). Leeuwenhoek earned his
ronments and some are normal inhabitants of the intestinal tracts
living as a draper and haberdasher (a dealer in men’s clothing
of animals, where they aid in digestion of complex materials
and accessories), but spent much of his spare time constructing
such as cellulose. A few cause disease in humans and other ani-
simple microscopes composed of double convex glass lenses
mals. Slime molds are protists that are like protozoa in one stage
held between two silver plates (figure 1.3b). His microscopes
of their life cycle, but are like fungi in another. In the protozoan
could magnify around 50 to 300 times, and he may have illu-
phase, they hunt for and engulf food particles, consuming de-
minated his liquid specimens by placing them between two
caying vegetation and other microbes. Water molds, as their
pieces of glass and shining light on them at a 45° angle to the
name implies, are found in the surface water of freshwater
specimen plane. This would have provided a form of dark-field
sources and moist soil. They feed on decaying vegetation such as
illumination in which the organisms appeared as bright objects
logs and mulch. Some water molds have produced devastating
against a dark background and made bacteria clearly visible
plant infections, including the Great Potato Famine of
(figure 1.3c). Beginning in 1673, Leeuwenhoek sent detailed
1846–1847. Fungi are a diverse group of microorganisms that
letters describing his discoveries to the Royal Society of
range from unicellular forms (yeasts) to molds and mushrooms.
London. It is clear from his descriptions that he saw both bac-
Molds and mushrooms are multicellular fungi that form thin,
teria and protozoa.
threadlike structures called hyphae. They absorb nutrients from
As important as Leeuwenhoek’s observations were, the devel-
their environment, including the organic molecules that they use
opment of microbiology essentially languished for the next 200
as a source of carbon and energy. Because of their metabolic ca-
years. Little progress was made primarily because microscopic
pabilities, many fungi play beneficial roles, including making
observations of microorganisms do not provide sufficient infor-
bread rise, producing antibiotics, and decomposing dead organ-
mation to understand their biology. For the discipline to develop,
isms. Other fungi cause plant diseases and diseases in humans
techniques for isolating and culturing microbes in the laboratory
and other animals.
were needed. Many of these techniques began to be developed as
Viruses are acellular entities that must invade a host cell in
scientists grappled with the conflict over the Theory of
order to replicate. They are the smallest of all microbes (the
Spontaneous Generation. This conflict and the subsequent studies
smallest is 10,000 times smaller than a typical bacterium), but
on the role played by microorganisms in causing disease ulti-
their small size belies their power—they cause many animal and
mately led to what is now called the Golden Age of Microbiology.
plant diseases and have caused epidemics that have shaped hu-
man history. The diseases they cause include smallpox, rabies, in-
1. Give some examples of the kind of information you think can be provided
fluenza, AIDS, the common cold, and some cancers.
by microscopic observations of microorganisms.
The development of microbiology as a science is described in
2. Give some examples of the kind of information you think can be provided
sections 1.2 to 1.5. Figure 1.2 presents a summary of some of the
by isolating microorganisms from their natural environment and cultur-
major events in this process and their relationship to other histor-
ing them in the laboratory.
ical landmarks.