Microbiology Thirteen Edition PDF

Brief Contents PART ONE Fundamentals of Microbiology Exploring the Microbiome   1 The Microbial World and You 1   1 How Does Your Microbiome Grow? 3   2 Chemical Principles 24   2 Feed Our...

Brief Contents PART ONE Fundamentals of Microbiology Exploring the Microbiome   1 The Microbial World and You 1   1 How Does Your Microbiome Grow? 3   2 Chemical Principles 24   2 Feed Our Intestinal Bacteria, Feed Ourselves:   3 Observing Microorganisms Through a Microscope 51 A Tale of Two Starches 37   4 Functional Anatomy of Prokaryotic and Eukaryotic Cells 72   3 Obtaining a More Accurate Picture of Our Microbiota 67   5 Microbial Metabolism 107   4 Eukaryotes Are Microbiota, Too 94   6 Microbial Growth 151   5 Do Artificial Sweeteners (and the Intestinal Microbiota   7 The Control of Microbial Growth 178 That Love Them) Promote Diabetes? 132   8 Microbial Genetics 204   6 Circadian Rhythms and Microbiota Growth Cycles 168   9 Biotechnology and DNA Technology 242   7 Antimicrobial Soaps: Doing More Harm Than Good? 191 PART TWO A Survey of the Microbial World 10 Classification of Microorganisms 269   8 Horizontal Gene Transfer and the Unintended 11 The Prokaryotes: Domains Bacteria and Archaea 295 Consequences of Antibiotic Usage 230 12 The Eukaryotes: Fungi, Algae, Protozoa, and   9 Crime Scene Investigation and Your Microbiome 261 Helminths 323 10 Techniques for Identifying Members of Your 13 Viruses, Viroids, and Prions 361 Microbiome 291 PART THREE Interaction between Microbe 11 Microbiome in Space 320 and Host 12 The Mycobiome 335 14 Principles of Disease and Epidemiology 393 15 Microbial Mechanisms of Pathogenicity 423 13 The Human Virome 364 16 Innate Immunity: Nonspecific Defenses of the 14 Connections between Birth, Microbiome, Host 445 and Other Health Conditions 395 17 Adaptive Immunity: Specific Defenses of the Host 475 15 Skin Microbiota Interactions and the Making of MRSA 427 18 Practical Applications of Immunology 499 16 The Microbiome’s Shaping of Innate Immunity 452 19 Disorders Associated with the Immune System 524 20 Antimicrobial Drugs 558 17 The Relationship between Your Immune Cells and Skin Microbiota 491 PART FOUR Microorganisms and Human Disease 21 Microbial Diseases of the Skin and Eyes 590 18 Microbiome May Enhance Response to Oral Vaccines 505 22 Microbial Diseases of the Nervous System 619 19 The Link between Blood Type and Composition 23 Microbial Diseases of the Cardiovascular and of the Intestinal Microbiome 532 Lymphatic Systems 650 20 Looking to the Microbiome for the Next Great 24 Microbial Diseases of the Respiratory System 688 Antibiotic 585 25 Microbial Diseases of the Digestive System 721 21 Normal Skin Microbiota and Our Immune System: 26 Microbial Diseases of the Urinary and Reproductive Allies in “Skin Wars” 594 Systems 760 22 Microbes Impacting the CNS 644 Environmental and Applied PART FIVE Microbiology 23 Is Blood Sterile? 653 27 Environmental Microbiology 786 24 Discovering the Microbiome of the Lungs 691 28 Applied and Industrial Microbiology 809 25 Sorting Out Good Neighbors from Bad in the GI Tract 723 26 Resident Microbes of the Urinary System 763 All chapter content is tagged to 27 Resident Microbes of Earth’s Most Extreme ASM Curriculum Guidelines for Environments 794 Undergraduate Microbiology 28 Using Bacteria to Stop the Spread of Zika Virus 823 Contents PART ONE Fundamentals of Microbiology 3 Observing Microorganisms Through a Microscope 51 1 The Microbial World and You 1 Microbes in Our Lives 2 Units of Measurement 52 Microscopy: The Instruments 52 Light Microscopy Two-Photon Microscopy Super-Resolution The Microbiome Light Microscopy Scanning Acoustic Microscopy Electron Naming and Classifying Microorganisms 4 Microscopy Scanned-Probe Microscopy Nomenclature Types of Microorganisms Classification of Preparation of Specimens for Light Microscopy 61 Microorganisms Preparing Smears for Staining Simple Stains Differential A Brief History of Microbiology 6 Stains Special Stains The First Observations The Debate over Spontaneous Study Outline Study Questions 69 Generation The First Golden Age of Microbiology 4 The Second Golden Age of Microbiology The Third Golden Age of Microbiology F  unctional Anatomy of Prokaryotic Microbes and Human Welfare 14 and Eukaryotic Cells 72 Recycling Vital Elements Sewage Treatment: Using Microbes Comparing Prokaryotic and Eukaryotic Cells: to Recycle Water Bioremediation: Using Microbes to Clean An Overview 73 Up Pollutants Insect Pest Control by Microorganisms Biotechnology and Recombinant DNA Technology THE PROKARYOTIC CELL 73 Microbes and Human Disease 16 The Size, Shape, and Arrangement of Bacterial Cells 73 Biofilms Infectious Diseases Emerging Infectious Diseases Structures External to the Cell Wall 75 Glycocalyx Flagella and Archaella Axial Filaments Fimbriae Study Outline Study Questions 20 and Pili 2 The Cell Wall 80 Composition and Characteristics Cell Walls and the Gram Stain Chemical Principles 24 Mechanism Atypical Cell Walls Damage to the Cell Wall Structures Internal to the Cell Wall 85 The Structure of Atoms 25 The Plasma (Cytoplasmic) Membrane The Movement of Chemical Elements Electronic Configurations Materials across Membranes Cytoplasm The Nucleoid How Atoms Form Molecules: Chemical Bonds 27 Ribosomes Inclusions Endospores Ionic Bonds Covalent Bonds Hydrogen Bonds Molecular THE EUKARYOTIC CELL 94 Mass and Moles Flagella and Cilia 96 Chemical Reactions 30 The Cell Wall and Glycocalyx 96 Energy in Chemical Reactions Synthesis Reactions The Plasma (Cytoplasmic) Membrane 97 Decomposition Reactions Exchange Reactions The Reversibility of Chemical Reactions Cytoplasm 98 IMPORTANT BIOLOGICAL MOLECULES 31 Ribosomes 98 Inorganic Compounds 31 Organelles 98 Water Acids, Bases, and Salts Acid–Base Balance: The Nucleus Endoplasmic Reticulum Golgi Complex The Concept of pH Lysosomes Vacuoles Mitochondria Chloroplasts Peroxisomes Centrosome Organic Compounds 33 The Evolution of Eukaryotes 102 Structure and Chemistry Carbohydrates Lipids Proteins Nucleic Acids Adenosine Triphosphate (ATP) Study Outline Study Questions 103 Study Outline Study Questions 47 ix x CONTENTS 5 Microbial Metabolism 107 7  he Control of Microbial T Growth 178 The Terminology of Microbial Control 179 Catabolic and Anabolic Reactions 110 Enzymes 111 The Rate of Microbial Death 180 Collision Theory Enzymes and Chemical Reactions Actions of Microbial Control Agents 180 Enzyme Specificity and Efficiency Naming Enzymes Alteration of Membrane Permeability Damage to Proteins Enzyme Components Factors Influencing Enzymatic and Nucleic Acids Activity Feedback Inhibition Ribozymes Physical Methods of Microbial Control 182 Energy Production 117 Heat Filtration Low Temperatures High Pressure Oxidation-Reduction Reactions The Generation of ATP Desiccation Osmotic Pressure Radiation Metabolic Pathways of Energy Production Chemical Methods of Microbial Control 187 Carbohydrate Catabolism 119 Principles of Effective Disinfection Evaluating a Disinfectant Glycolysis Additional Pathways to Glycolysis Cellular Types of Disinfectants Respiration Fermentation Microbial Characteristics and Microbial Control 198 Lipid and Protein Catabolism 133 Study Outline Study Questions 200 Biochemical Tests and Bacterial Identification 134 8 Photosynthesis 135 The Light-Dependent Reactions: Photophosphorylation The Light-Independent Reactions: The Calvin-Benson Cycle Microbial Genetics 204 A Summary of Energy Production Mechanisms 138 Structure and Function of the Genetic Material 205 Metabolic Diversity among Organisms 138 Genotype and Phenotype DNA and Chromosomes The Flow Photoautotrophs Photoheterotrophs Chemoautotrophs of Genetic Information DNA Replication RNA and Protein Chemoheterotrophs Synthesis Metabolic Pathways of Energy Use 140 The Regulation of Bacterial Gene Expression 215 Polysaccharide Biosynthesis Lipid Biosynthesis Amino Acid Pre-transcriptional Control Post-transcriptional Control and Protein Biosynthesis Purine and Pyrimidine Biosynthesis Changes in Genetic Material 221 The Integration of Metabolism 143 Mutation Types of Mutations Mutagens The Frequency Study Outline Study Questions 145 of Mutation Identifying Mutants Identifying Chemical Carcinogens 6 Genetic Transfer and Recombination 229 Plasmids and Transposons Transformation in Bacteria Microbial Growth 151 Conjugation in Bacteria Transduction in Bacteria The Requirements for Growth 152 Genes and Evolution 237 Physical Requirements Chemical Requirements Study Outline Study Questions 238 Biofilms 157 Culture Media 159 Chemically Defined Media Complex Media Anaerobic Growth Media and Methods Special Culture Techniques Selective and Differential Media Enrichment Culture 9 Biotechnology and DNA Technology 242 Introduction to Biotechnology 243 Obtaining Pure Cultures 163 Recombinant DNA Technology An Overview of Recombinant DNA Procedures Preserving Bacterial Cultures 164 Tools of Biotechnology 245 The Growth of Bacterial Cultures 165 Selection Mutation Restriction Enzymes Vectors Bacterial Division Generation Time Logarithmic Polymerase Chain Reaction Representation of Bacterial Populations Phases of Growth Direct Measurement of Microbial Growth Estimating Techniques of Genetic Modification 248 Bacterial Numbers by Indirect Methods Inserting Foreign DNA into Cells Obtaining DNA Selecting a Study Outline Study Questions 174 Clone Making a Gene Product  CONTENTS xi Applications of DNA Technology 254 Algae 337 Therapeutic Applications Genome Projects Scientific Characteristics of Algae Selected Phyla of Algae Roles of Algae Applications Agricultural Applications in Nature Safety Issues and the Ethics of Using DNA Technology 262 Protozoa 341 Study Outline Study Questions 265 Characteristics of Protozoa Medically Important Protozoa Slime Molds 346 Helminths 347 PART TWO A Survey of the Microbial World Characteristics of Helminths Platyhelminths Nematodes 10 Classification of Microorganisms 269 The Study of Phylogenetic Relationships 270 Arthropods as Vectors 355 Study Outline Study Questions 357 The Three Domains A Phylogenetic Tree Classification of Organisms 274 Scientific Nomenclature The Taxonomic Hierarchy 13 Viruses, Viroids, and Prions 361 General Characteristics of Viruses 362 Classification of Prokaryotes Classification of Eukaryotes Host Range Viral Size Classification of Viruses Viral Structure 363 Methods of Classifying and Identifying Microorganisms 277 Nucleic Acid Capsid and Envelope General Morphology Morphological Characteristics Differential Staining Biochemical Tests Serology Phage Typing Fatty Acid Taxonomy of Viruses 366 Profiles Flow Cytometry DNA Sequencing DNA Isolation, Cultivation, and Identification of Viruses 370 Fingerprinting Nucleic Acid Hybridization Putting Growing Bacteriophages in the Laboratory Growing Animal Classification Methods Together Viruses in the Laboratory Viral Identification Study Outline Study Questions 291 Viral Multiplication 372 Multiplication of Bacteriophages Multiplication of Animal 11 Viruses The Prokaryotes: Domains Viruses and Cancer 384 Bacteria and Archaea 295 The Transformation of Normal Cells into Tumor Cells DNA Oncogenic Viruses RNA Oncogenic Viruses Viruses The Prokaryotic Groups 296 to Treat Cancer DOMAIN BACTERIA 296 Latent Viral Infections 386 Gram-Negative Bacteria 297 Persistent Viral Infections 386 Proteobacteria The Nonproteobacteria Gram-Negative Bacteria Plant Viruses and Viroids 386 The Gram-Positive Bacteria 312 Prions 388 Firmicutes (Low G + C Gram-Positive Bacteria) Tenericutes Actinobacteria (High G + C Gram-Positive Bacteria) Study Outline Study Questions 389 DOMAIN ARCHAEA 318 Diversity within the Archaea 318 PART THREE Interaction between MICROBIAL DIVERSITY 319 Microbe and Host Discoveries Illustrating the Range of Diversity 319 Study Outline Study Questions 321 14 Principles of Disease and Epidemiology 393 12 Fungi 324 The Eukaryotes: Fungi, Algae, Protozoa, and Helminths 323 Pathology, Infection, and Disease 394 Human Microbiome 394 Relationships between the Normal Microbiota and the Host Opportunistic Microorganisms Cooperation among Characteristics of Fungi Medically Important Fungi Fungal Microorganisms Diseases Economic Effects of Fungi Lichens 335 xii CONTENTS The Etiology of Infectious Diseases 398 Chemical Factors 450 Koch’s Postulates Exceptions to Koch’s Postulates Normal Microbiota and Innate Immunity 451 Classifying Infectious Diseases 400 SECOND LINE OF DEFENSE 453 Occurrence of a Disease Severity or Duration of a Disease Formed Elements in Blood 453 Extent of Host Involvement The Lymphatic System 455 Patterns of Disease 402 Phagocytes 456 Predisposing Factors Development of Disease Actions of Phagocytic Cells The Mechanism of Phagocytosis The Spread of Infection 403 Inflammation 459 Reservoirs of Infection Transmission of Disease Vasodilation and Increased Permeability of Blood Vessels Healthcare-Associated Infections (HAIs) 408 Phagocyte Migration and Phagocytosis Tissue Repair Microorganisms in the Hospital Compromised Host Chain of Fever 462 Transmission Control of Healthcare-Associated Infections Antimicrobial Substances 463 Emerging Infectious Diseases 411 The Complement System Interferons Iron-Binding Proteins Epidemiology 413 Antimicrobial Peptides Other Factors Descriptive Epidemiology Analytical Epidemiology Study Outline Study Questions 472 Experimental Epidemiology Case Reporting The Centers for Disease Control and Prevention (CDC) Study Outline Study Questions 418 17 Adaptive Immunity: Specific Defenses of the Host 475 15 Microbial Mechanisms of Pathogenicity 423 How Microorganisms Enter a Host 424 The Adaptive Immune System 476 Dual Nature of the Adaptive Immune System 476 Overview of Humoral Immunity Overview of Cellular Immunity Portals of Entry The Preferred Portal of Entry Numbers of Cytokines: Chemical Messengers of Immune Cells 477 Invading Microbes Adherence Antigens and Antibodies 478 How Bacterial Pathogens Penetrate Host Defenses 427 Antigens Humoral Immunity: Antibodies Capsules Cell Wall Components Enzymes Antigenic Humoral Immunity Response Process 482 Variation Penetration into the Host Biofilms Activation and Clonal Expansion of Antibody-Producing Cells How Bacterial Pathogens Damage Host Cells 430 The Diversity of Antibodies Using the Host’s Nutrients: Siderophores Direct Damage Results of the Antigen–Antibody Interaction 484 Production of Toxins Plasmids, Lysogeny, and Pathogenicity Cellular Immunity Response Process 486 Pathogenic Properties of Viruses 436 Antigen-Presenting Cells (APCs) Classes of T Cells Viral Mechanisms for Evading Host Defenses Cytopathic Effects of Viruses Nonspecific Cells and Extracellular Killing by the Adaptive Immune System 492 Pathogenic Properties of Fungi, Protozoa, Helminths, and Algae 438 Immunological Memory 493 Fungi Protozoa Helminths Algae Types of Adaptive Immunity 494 Portals of Exit 440 Study Outline Study Questions 496 Study Outline Study Questions 441 16 Innate Immunity: Nonspecific Defenses of the Host 445 18 P  ractical Applications of Immunology 499 Vaccines 500 The Concept of Immunity 448 Principles and Effects of Vaccination Types of Vaccines and Their Characteristics Vaccine Production, Delivery Methods, FIRST LINE OF DEFENSE: SKIN AND MUCOUS and Formulations MEMBRANES 448 Physical Factors 448  CONTENTS xiii Diagnostic Immunology 507 Tests to Guide Chemotherapy 577 Use of Monoclonal Antibodies Precipitation Reactions The Diffusion Methods Broth Dilution Tests Agglutination Reactions Neutralization Reactions Resistance to Antimicrobial Drugs 579 Complement-Fixation Reactions Fluorescent-Antibody Techniques Enzyme-Linked Immunosorbent Assay (ELISA) Mechanisms of Resistance Antibiotic Misuse Cost and Western Blotting (Immunoblotting) The Future of Diagnostic Prevention of Resistance and Therapeutic Immunology Antibiotic Safety 583 Study Outline Study Questions 520 Effects of Combinations of Drugs 583 Future of Chemotherapeutic Agents 583 19 Study Outline Study Questions 586 Disorders Associated with the Immune System 524 PART FOUR Microorganisms and Hypersensitivity 525 Human Disease Allergies and the Microbiome Type I (Anaphylactic) Reactions 21  Microbial Diseases of Type II (Cytotoxic) Reactions Type III (Immune Complex) Reactions Type IV (Delayed Cell-Mediated) Reactions Autoimmune Diseases 536 the Skin and Eyes 590 Cytotoxic Autoimmune Reactions Immune Complex Structure and Function of the Skin 591 Autoimmune Reactions Cell-Mediated Autoimmune Reactions Mucous Membranes Reactions to Transplantation 538 Normal Microbiota of the Skin 592 Immunosuppression to Prevent Transplant Rejection Microbial Diseases of the Skin 592 The Immune System and Cancer 542 Bacterial Diseases of the Skin Viral Diseases of the Skin Immunotherapy for Cancer Fungal Diseases of the Skin and Nails Parasitic Infestation Immunodeficiencies 543 of the Skin Congenital Immunodeficiencies Acquired Immunodeficiencies Microbial Diseases of the Eye 612 Acquired Immunodeficiency Syndrome (AIDS) 544 Inflammation of the Eye Membranes: Conjunctivitis Bacterial Diseases of the Eye Other Infectious Diseases of the Eye The Origin of AIDS HIV Infection Diagnostic Methods HIV Transmission AIDS Worldwide Preventing and Treating Study Outline Study Questions 616 AIDS 22 Study Outline Study Questions 554 Microbial Diseases of the Nervous System 619 20 Antimicrobial Drugs 558 The History of Chemotherapy 559 Structure and Function of the Nervous System 620 Bacterial Diseases of the Nervous System 621 Bacterial Meningitis Tetanus Botulism Leprosy Antibiotic Use and Discovery Today Viral Diseases of the Nervous System 630 Spectrum of Antimicrobial Activity 560 Poliomyelitis Rabies Arboviral Encephalitis The Action of Antimicrobial Drugs 561 Fungal Disease of the Nervous System 638 Inhibiting Cell Wall Synthesis Inhibiting Protein Synthesis Cryptococcus neoformans Meningitis (Cryptococcosis) Injuring the Plasma Membrane Inhibiting Nucleic Acid Synthesis Inhibiting the Synthesis of Essential Metabolites Protozoan Diseases of the Nervous System 639 Common Antimicrobial Drugs 564 African Trypanosomiasis Amebic Meningoencephalitis Antibacterial Antibiotics: Inhibitors of Cell Wall Synthesis Nervous System Diseases Caused by Prions 642 Inhibitors of Protein Synthesis Injury to Membranes Bovine Spongiform Encephalopathy and Variant Nucleic Acid Synthesis Inhibitors Competitive Inhibition of Creutzfeldt-Jakob Disease Essential Metabolites Antifungal Drugs Antiviral Drugs Diseases Caused by Unidentified Agents 645 Antiprotozoan and Antihelminthic Drugs Study Outline Study Questions 647 xiv CONTENTS 23 Microbial Diseases of the Viral Pneumonia Respiratory Syncytial Virus (RSV) Influenza (Flu) Cardiovascular  and Lymphatic Fungal Diseases of the Lower Respiratory System 711 Systems 650 Histoplasmosis Coccidioidomycosis Pneumocystis Pneumonia Blastomycosis (North American Blastomycosis) Other Fungi Structure and Function of the Cardiovascular and Lymphatic Involved in Respiratory Disease Systems 651 Study Outline Study Questions 717 Bacterial Diseases of the Cardiovascular and Lymphatic Systems 652 25  icrobial Diseases of M Sepsis and Septic Shock Bacterial Infections of the Heart Rheumatic Fever Tularemia Brucellosis (Undulant Fever) Anthrax Gangrene Systemic Diseases Caused by Bites and the Digestive System 721 Scratches Vector-Transmitted Diseases Structure and Function of the Digestive System 722 Viral Diseases of the Cardiovascular and Lymphatic Systems 668 Normal Microbiota of the Digestive System 722 Burkitt’s Lymphoma Infectious Mononucleosis Other Bacterial Diseases of the Mouth 724 Diseases and Epstein-Barr Virus Cytomegalovirus Infections Dental Caries (Tooth Decay) Periodontal Disease Chikungunya Classic Viral Hemorrhagic Fevers Emerging Bacterial Diseases of the Lower Digestive System 727 Viral Hemorrhagic Fevers Staphylococcal Food Poisoning (Staphylococcal Enterotoxicosis) Protozoan Diseases of the Cardiovascular and Lymphatic Shigellosis (Bacillary Dysentery) Salmonellosis (Salmonella Systems 674 Gastroenteritis) Typhoid Fever Cholera Noncholera Chagas Disease (American Trypanosomiasis) Toxoplasmosis Vibrios Escherichia coli Gastroenteritis Campylobacteriosis Malaria Leishmaniasis Babesiosis (Campylobacter Gastroenteritis) Helicobacter Peptic Ulcer Disease Yersinia Gastroenteritis Clostridium perfringens Helminthic Disease of the Cardiovascular and Lymphatic Gastroenteritis Clostridium difficile–Associated Diarrhea Systems 681 Bacillus cereus Gastroenteritis Schistosomiasis Viral Diseases of the Digestive System 739 Disease of Unknown Etiology 683 Mumps Hepatitis Viral Gastroenteritis Kawasaki Syndrome Fungal Diseases of the Digestive System 746 Study Outline Study Questions 683 Protozoan Diseases of the Digestive System 747 Giardiasis Cryptosporidiosis Cyclosporiasis Amebic 24  icrobial Diseases of the M Dysentery (Amebiasis) Respiratory System 688 Helminthic Diseases of the Digestive System 750 Tapeworms Hydatid Disease Nematodes Structure and Function of the Respiratory System 689 Study Outline Study Questions 755 Normal Microbiota of the Respiratory System 690 26 MICROBIAL DISEASES OF THE UPPER RESPIRATORY SYSTEM 690 Microbial Diseases of the Bacterial Diseases of the Upper Respiratory System 691 Urinary  and Reproductive Streptococcal Pharyngitis (Strep Throat) Scarlet Fever Systems 760 Diphtheria Otitis Media Structure and Function of the Urinary System 761 Viral Disease of the Upper Respiratory System 693 Structure and Function of the Reproductive Systems 761 The Common Cold Normal Microbiota of the Urinary and Reproductive MICROBIAL DISEASES OF THE LOWER RESPIRATORY Systems 762 SYSTEM 695 DISEASES OF THE URINARY SYSTEM 763 Bacterial Diseases of the Lower Respiratory System 695 Bacterial Diseases of the Urinary System 763 Pertussis (Whooping Cough) Tuberculosis Bacterial Pneumonias Melioidosis Cystitis Pyelonephritis Leptospirosis Viral Diseases of the Lower Respiratory System 707 DISEASES OF THE REPRODUCTIVE SYSTEMS 766 Bacterial Diseases of the Reproductive Systems 766  CONTENTS xv Gonorrhea Nongonococcal Urethritis (NGU) Pelvic Industrial Microbiology and Biotechnology 817 Inflammatory Disease (PID) Syphilis Lymphogranuloma Fermentation Technology Industrial Products Venereum (LGV) Chancroid (Soft Chancre) Bacterial Vaginosis Alternative Energy Sources Using Microorganisms Biofuels Viral Diseases of the Reproductive Systems 776 Industrial Microbiology and the Future Genital Herpes Genital Warts AIDS Study Outline Study Questions 824 Fungal Disease of the Reproductive Systems 779 Candidiasis Answers to Knowledge and Comprehension Study Protozoan Disease of the Reproductive Systems 780 Questions AN-1 Trichomoniasis Appendix A Metabolic Pathways AP-1 Study Outline Study Questions 782 Appendix B Exponents, Exponential Notation, Logarithms, and Generation Time AP-7 PART FIVE Environmental Appendix C Methods for Taking Clinical Samples AP-8 and Applied Microbiology Appendix D Pronunciation Rules and Word Roots AP-9 27 Environmental Microbiology 786 Microbial Diversity and Habitats 787 Appendix E Classification of Prokaryotes According Glossary G-1 to Bergey’s Manual AP-12 Symbiosis Credits C-1 Soil Microbiology and Biogeochemical Cycles 787 Trademark Attributions T-1 The Carbon Cycle The Nitrogen Cycle The Sulfur Cycle Life without Sunshine The Phosphorus Cycle The Index I-1 Degradation of Synthetic Chemicals in Soil and Water Aquatic Microbiology and Sewage Treatment 795 Aquatic Microorganisms The Role of Microorganisms in Water Quality Water Treatment Sewage (Wastewater) Treatment Study Outline Study Questions 805 28 Applied and Industrial Microbiology 809 Food Microbiology 810 Foods and Disease Industrial Food Canning Aseptic Packaging Radiation and Industrial Food Preservation High-Pressure Food Preservation The Role of Microorganisms in Food Production  The Microbial World and You 1 T he overall theme of this textbook is the relationship between microbes—very small organisms that usually require a microscope to be seen—and our lives. We’ve all heard of epidemics of infectious diseases such as plague or smallpox that wiped out populations. However, there are many positive examples of human-microbe interactions. For example, we use microbial fermentation to ensure safe food supplies, and the human microbiome, a group of microbes that lives in and on our bodies, helps keep us healthy. We begin this chapter by discussing how organisms are named and classified and then follow with a short history of microbiology. Next, we discuss the incredible diversity of microorganisms and their ecological importance, noting how they recycle chemical elements such as carbon and nitrogen among the soil, organisms, and the atmosphere. ASM: Microorganisms provide essential models that give us fundamental We also examine how microbes are knowledge about life processes. used to treat sewage, clean pollutants, control pests, and produce foods, chemicals, and drugs. Finally, we will discuss microbes as the cause of diseases such as Zika virus disease, avian (bird) flu, Ebola virus disease, and diarrhea, and we examine the growing public health problem of antibiotic-resistant bacteria. Shown in the photograph are Staphylococcus aureus (STAF-i-lō- kok'kus OR-ē-us) bacteria on human nasal epithelial cells. These bacteria generally live harmlessly on skin or inside the nose. Misuse of antibiotics, however, allows the survival of bacteria with antibiotic-resistance genes, such as methicillin- resistant S. aureus (MRSA). As illustrated in the Clinical Case, an infection caused by these bacteria is resistant to antibiotic treatment. ◀ Staphylococcus aureus bacteria on skin cell culture. In the Clinic As the nurse practitioner in a rural hospital, you are reviewing a microscope slide of a skin scraping from a 12-year-old girl. The slide shows branched, intertwined nucleated hyphae. The girl has dry, scaly, itchy patches on her arms. What is causing her skin problem? Hint: Read about types of microorganisms (pages 4–6). Play In the Clinic Video @ MasteringMicrobiology 1 2 PART ONE Fundamentals of Microbiology Microbes in Our Lives microbiome, or microbiota. Humans and many other animals depend on these microbes to maintain good health. Bacteria LEARNING OBJECTIVES in our intestines, including E. coli, aid digestion (see Exploring 1-1 List several ways in which microbes affect our lives. the Microbiome on page 3) and even synthesize some vitamins 1-2 Define microbiome, normal microbiota, and transient microbiota. that our bodies require, including B vitamins for metabolism and vitamin K for blood clotting. They also prevent growth For many people, the words germ and microbe bring to mind of pathogenic (disease-causing) species that might otherwise a group of tiny creatures that do not quite fit into any of the take up residence, and they seem to have a role in training our categories in that old question, “Is it animal, vegetable, or immune system to know which foreign invaders to attack and ­mineral?” Germ actually comes from the Latin word germen, which to leave alone. (See Chapter 14 for more details on rela- meaning to spout from, or germinate. Think of wheat germ, the tionships between normal microbiota and the host.) plant embryo from which the plant grows. It was first used in Even before birth, our bodies begin to be populated with relation to microbes in the nineteenth century to explain the bacteria. As newborns, we acquire viruses, fungi, and bacteria rapidly growing cells that caused disease. Microbes, also called (Figure 1.1). For example, E. coli and other bacteria acquired microorganisms, are minute living things that individually are from foods take residence in the large intestine. Many fac- usually too small to be seen with the unaided eye. The group tors influence where and whether a microbe can indefinitely includes bacteria, fungi (yeasts and molds), protozoa, and colonize the body as benign normal microbiota or be only microscopic algae. It also includes viruses, those noncellular a fleeting member of its community (known as transient entities sometimes regarded as straddling the border between ­microbiota). Microbes can colonize only those body sites that life and nonlife (Chapters 11, 12, and 13, respectively). can supply the appropriate nutrients. Temperature, pH, and the We tend to associate these small organisms only with infec- presence or absence of chemical compounds are some factors tions and inconveniences such as spoiled food. However, the that influence what types of microbes can flourish. majority of microorganisms actually help maintain the balance To determine the makeup of typical microbiota of various of life in our environment. Marine and freshwater microor- areas of the body, and to understand the relationship between ganisms form the basis of the food chain in oceans, lakes, and changes in the microbiome and human diseases, is the goal of ­r ivers. Soil microbes break down wastes and incorporate nitro- the Human Microbiome Project, which began in 2007. Like- gen gas from the air into organic compounds, thereby recycling wise, the National Microbiome Initiative (NMI) launched in chemical elements among soil, water, living organisms, and air. 2016 to expand our understanding of the role microbes play Certain microbes play important roles in photosynthesis, a food- in different ecosystems, including soil, plants, aquatic environ- and oxygen-generating process that is critical to life on Earth. ments, and the human body. Throughout the book, look for Microorganisms also have many commercial applications. They are used in the synthesis of such chemical products as vita- mins, organic acids, enzymes, alcohols, and many drugs. For example, microbes are used to produce acetone and butanol, and the vitamins B2 (riboflavin) and B12 (cobalamin) are made biochemically. The process by which microbes produce acetone and butanol was discovered in 1914 by Chaim W ­ eizmann, a Russian-born chemist working in England. With the outbreak of World War I in August of that year, the production of acetone became very important for making cordite (a smokeless form of gunpowder used in munitions). W ­ eizmann’s discovery played a significant role in determining the outcome of the war. The food industry also uses microbes in producing, for example, vinegar, sauerkraut, pickles, soy sauce, cheese, yogurt, bread, and alcoholic beverages. In addition, enzymes from microbes can now be manipulated to cause the microbes to produce substances they normally don’t synthesize, including cellulose, human insulin, and proteins for vaccines. SEM 3 mm The Microbiome Figure 1.1 Several types of bacteria found as part of the normal An adult human is composed of about 30 trillion body cells microbiota in an infant’s intestine. and harbors another 40 trillion bacterial cells. Microbes that Q How do we benefit from the production of vitamin K live stably in and on the human body are called the human by microbes? EXPLORING THE MICROBIOME How Does Your Microbiome Grow? T he specific traits of microbes can swap genes with other species—a algae used in foods today is usually roasted that reside in human intestines process called horizontal gene transfer— or dried; these processes kill any bacteria can vary greatly—even within and at some point, Zobellia must have given that may be present on the surface. the same microbial species. Take Bacteroides the genes to produce algae- Bacteroides, a bacterium commonly found digesting enzymes. (For more on horizontal in gastrointestinal tracts of humans gene transfer, see Chapter 8). worldwide. The strain residing in Japanese In an island nation where algae are people has specialized enzymes that break an important diet component, the ability down nori, the red algae used as the wrap to extract more nutrition from algal component of sushi. These enzymes are carbohydrates would give an intestinal absent from Bacteroides found in the microbe a competitive advantage over others gastrointestinal tracts of North Americans. that couldn’t use it as a food source. Over How did the Japanese Bacteroides time, this Bacteroides strain became the acquire the ability to digest algae? It’s dominant one found within the gastrointestinal thought the skill hails from Zobellia tracts of people living in Japan. galactanivorans, a marine bacterium that You may be wondering whether North lives on this alga. Not surprisingly, Zobellia American sushi eaters can expect their readily breaks down the alga’s main own Bacteroides to shift to the algae-eating carbohydrate with enzymes. Since people variety, too. Researchers say this is unlikely. living in Japan consumed algae regularly, Traditional Japanese food included raw Zobellia routinely met up with Bacteroides algae, which allowed for living Zobellia to that lived in the human intestine. Bacteria reach the large intestine. By contrast, the Porphyra, an alga commonly used in sushi. stories related to the human microbiome, highlighted in the Exploring the Microbiome feature boxes. CLINICAL CASE A Simple Spider Bite? Our realization that some microbes are not only harmless to humans, but also are actually essential, represents a large shift from the traditional view that the only good microbe was a dead A ndrea is a normally healthy 22-year-old college student who lives at home with her mother and younger sister, a high school gymnast. She is trying to work on a paper for her one. In fact, only a minority of microorganisms are pathogenic to psychology class but is having a hard time because a red, humans. Although anyone planning to enter a health care profes- swollen sore on her right wrist is making typing difficult. “Why sion needs to know how to prevent the transmission and spread won’t this spider bite heal?” she wonders. “It’s been there of pathogenic microbes, it’s also important to know that patho- for days!” She makes an appointment with her doctor so she gens are just one aspect of our full relationship with microbes. can show him the painful lesion. Although Andrea does not Today we understand that microorganisms are found almost have a fever, she does have an elevated white blood cell count everywhere. Yet not long ago, before the invention of the micro- that indicates a bacterial infection. Andrea’s doctor suspects scope, microbes were unknown to scientists. Next we’ll look that this isn’t a spider bite at all, but a staph infection. He at the major groups of microbes and how they are named and prescribes a b-lactam antibiotic, cephalosporin. Learn more classified. After that, we’ll examine a few historic milestones in about the development of Andrea’s illness on the following pages. microbiology that have changed our lives. What is staph? Read on to find out. CHECK YOUR UNDERSTANDING ✓ 1-1* Describe some of the destructive and beneficial 3 16 18 19 actions of microbes. ✓ 1-2 What percentage of all the cells in the human body are bacterial cells? * The numbers preceding Check Your Understanding questions refer to the corre- sponding Learning Objectives. 3 4 PART ONE Fundamentals of Microbiology Naming and Classifying coli, reminds us that E. coli live in the colon, or large intestine. Table 1.1 contains more examples. Microorganisms CHECK YOUR UNDERSTANDING LEARNING OBJECTIVES ✓ 1-3 Distinguish a genus from a specific epithet. 1-3 Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. 1-4 Differentiate the major characteristics of each group of Types of Microorganisms microorganisms. In health care, it is very important to know the different types 1-5 List the three domains. of microorganisms in order to treat infections. For example, antibiotics can be used to treat bacterial infections but have no Nomenclature effect on viruses or other microbes. Here is an overview of the The system of nomenclature (naming) for organisms in use main types of microorganisms. (The classification and identifi- today was established in 1735 by Carolus Linnaeus. Scientific cation of microorganisms are discussed in Chapter 10.) names are latinized because Latin was the language tradition- ally used by scholars. Scientific nomenclature assigns each Bacteria organism two names—the genus (plural: genera) is the first Bacteria (singular: bacterium) are relatively simple, single- name and is always capitalized; the specific epithet (species celled (unicellular) organisms. Because their genetic mate- name) follows and is not capitalized. The organism is referred rial is not enclosed in a special nuclear membrane, bacterial to by both the genus and the specific epithet, and both names cells are called prokaryotes (prō-KAR-e-ōts), from Greek words are underlined or italicized. By custom, after a scientific name meaning prenucleus. Prokaryotes include both bacteria and has been mentioned once, it can be abbreviated with the initial archaea. of the genus followed by the specific epithet. Bacterial cells generally appear in one of several shapes. Scientific names can, among other things, describe an organ- Bacillus (bah-SIL-lus) (rodlike), illustrated in Figure 1.2a, coccus ism, honor a researcher, or identify the habitat of a species. For (KOK-kus) (spherical or ovoid), and spiral (corkscrew or curved) example, consider Staphylococcus aureus, a bacterium commonly are among the most common shapes, but some bacteria are star- found on human skin. Staphylo- describes the clustered arrange- shaped or square (see Figures 4.1 through 4.5, pages 74–75). ment of the cells; -coccus indicates that they are shaped like Individual bacteria may form pairs, chains, clusters, or other spheres. The specific epithet, aureus, is Latin for golden, the color groupings; such formations are usually characteristic of a par- of many colonies of this bacterium. The genus of the b ­ acterium ticular genus or species of bacteria. Escherichia coli (esh′er-IK-ē-ah KŌ-lĪ, or KŌ-lē) is named for Bacteria are enclosed in cell walls that are largely composed a physician, Theodor Escherich, whereas its specific epithet, of a carbohydrate and protein complex called peptidoglycan. TABLE 1.1 Making Scientific Names Familiar Use the word roots guide to find out what the name means. The name will not seem so strange if you translate it. When you encounter a new name, practice saying it out loud (guidelines for pronunciation are given in Appendix D). The exact pronunciation is not as important as the familiarity you will gain. Following are some examples of microbial names you may encounter in the popular press as well as in the lab. Pronunciation Source of Genus Name Source of Specific Epithet Salmonella enterica (bacterium) sal'mō-NEL-lah en-TER-i-kah Honors public health microbiologist Found in the intestines (entero-) Daniel Salmon Streptococcus pyogenes strep'tō-KOK-kus pī-AH-jen-ēz Appearance of cells in chains (strepto-) Forms pus (pyo-) (bacterium) Saccharomyces cerevisiae sak'kar-ō-MĪ-sēz se-ri-VIS-ē-ī Fungus (-myces) that uses sugar Makes beer (cerevisia) (yeast) (saccharo-) Penicillium chrysogenum pen'i-SIL-lē-um krī-SO-jen-um Tuftlike or paintbrush (penicill-) Produces a yellow (chryso-) pigment (fungus) appearance microscopically Trypanosoma cruzi (protozoan) tri'pa-nō-SŌ-mah KROOZ-ē Corkscrew- (trypano-, borer; soma-, body) Honors epidemiologist Oswaldo Cruz  CHAPTER 1   The Microbial World and You 5 Bacteria Sporangia Nerve cell ZikV Food particle Pseudopod (a) SEM (b) SEM (c) SEM (d) LM (e) TEM 3 mm 50 mm 50 mm 300 mm 70 nm Figure 1.2 Types of microorganisms. (filaments) that absorb nutrients. (c) An ameba, electron microscope) and LM (light microscope) (a) The rod-shaped bacterium Haemophilus a type of protozoan, approaching a food particle. are discussed in detail in Chapter 3. influenzae, one of the bacterial causes of (d) The pond alga Volvox. (e) Zika virus (ZikV). pneumonia. (b) Mucor, a common bread NOTE: Throughout the book, a red icon under Q How are bacteria, archaea, fungi, a micrograph indicates that the micrograph protozoa, algae, and viruses mold, is a type of fungus. When released from distinguished on the basis of structure? sporangia, spores that land on a favorable has been artificially colored. SEM (scanning surface germinate into a network of hyphae (By contrast, cellulose is the main substance of plant and algal visible masses called mycelia, which are composed of long cell walls.) Bacteria generally reproduce by dividing into two filaments (hyphae) that branch and intertwine. The cottony equal cells; this process is called binary fission. For nutrition, growths sometimes found on bread and fruit are mold mycelia. most bacteria use organic chemicals, which in nature can be Fungi can reproduce sexually or asexually. They obtain nourish- derived from either dead or living organisms. Some bacteria ment by absorbing organic material from their e­ nvironment— can manufacture their own food by photosynthesis, and some whether soil, seawater, freshwater, or an animal or plant host. can derive nutrition from inorganic substances. Many bacteria Organisms called slime molds are actually ameba-like protozoa can “swim” by using moving appendages called flagella. (For a (see Chapter 12). complete discussion of bacteria, see Chapter 11.) Protozoa Archaea Protozoa (singular: protozoan) are unicellular eukaryotic Like bacteria, archaea (ar-KĒ-ah) consist of prokaryotic cells, microbes (see Chapter 12, page 341). Protozoa move by pseu- but if they have cell walls, the walls lack peptidoglycan. dopods, flagella, or cilia. Amebae (Figure 1.2c) move by using Archaea, often found in extreme environments, are divided extensions of their cytoplasm called pseudopods (false feet). into three main groups. The methanogens produce methane as Other protozoa have long flagella or numerous shorter append- a waste product from respiration. The extreme halophiles (halo = ages for locomotion called cilia. Protozoa have a variety of salt; philic = loving) live in extremely salty environments such shapes and live either as free entities or as parasites (organisms as the Great Salt Lake and the Dead Sea. The extreme thermo- that derive nutrients from living hosts) that absorb or ingest philes (therm = heat) live in hot sulfurous water, such as hot organic compounds from their environment. Some protozoa, springs at Yellowstone National Park. Archaea are not known such as Euglena (ū-GLĒ-nah), are photosynthetic. They use light to cause disease in humans. as a source of energy and carbon dioxide as their chief source of carbon to produce sugars. Protozoa can reproduce sexually Fungi or asexually. Fungi (singular: fungus) are eukaryotes (ū-KAR-ē-ōts), organ- isms whose cells have a distinct nucleus containing the cell’s Algae genetic material (DNA), surrounded by a special envelope Algae (singular: alga) are photosynthetic eukaryotes with called the nuclear membrane. Organisms in the Kingdom Fungi a wide variety of shapes and both sexual and asexual repro- may be unicellular or multicellular (see Chapter 12, page 324). ductive forms (Figure 1.2d). The algae of interest to microbi- Large multicellular fungi, such as mushrooms, may look some- ologists are usually unicellular (see Chapter 12, page 337). The what like plants, but unlike most plants, fungi cannot carry out cell walls of many algae are composed of a carbohydrate called photosynthesis. True fungi have cell walls composed primar- ­cellulose. Algae are abundant in freshwater and saltwater, in soil, ily of a substance called chitin. The unicellular forms of fungi, and in association with plants. As photosynthesizers, algae yeasts, are oval microorganisms that are larger than bacteria. need light, water, and carbon dioxide for food production and The most typical fungi are molds (Figure 1.2b). Molds form growth, but they do not generally require organic compounds 6 PART ONE Fundamentals of Microbiology from the environment. As a result of photosynthesis, algae pro- 2. Archaea (cell walls, if present, lack peptidoglycan) duce oxygen and carbohydrates that are then utilized by other 3. Eukarya, which includes the following: organisms, including animals. Thus, they play an important role in the balance of nature. Protists (slime molds, protozoa, and algae) Fungi (unicellular yeasts, multicellular molds, and Viruses mushrooms) Viruses (Figure 1.2e) are very different from the other micro- Plants (mosses, ferns, conifers, and flowering plants) bial groups mentioned here. They are so small that most can Animals (sponges, worms, insects, and vertebrates) be seen only with an electron microscope, and they are acel- Classification will be discussed in more detail in Chapters 10 lular (that is, they are not cells). Structurally very simple, a through 12. virus particle contains a core made of only one type of nucleic acid, either DNA or RNA. This core is surrounded by a protein CHECK YOUR UNDERSTANDING coat, which is sometimes encased by a lipid membrane called an envelope. All living cells have RNA and DNA, can carry out ✓ 1-5 What are the three domains? chemical reactions, and can reproduce as self-sufficient units. Viruses can reproduce only by using the cellular machinery of other organisms. Thus, on the one hand, viruses are con- A Brief History of Microbiology sidered to be living only when they multiply within host cells they infect. In this sense, viruses are parasites of other forms of LEARNING OBJECTIVES life. On the other hand, viruses are not considered to be living 1-6 Explain the importance of observations made by Hooke and because they are inert outside living hosts. (Viruses will be dis- van Leeuwenhoek. cussed in detail in Chapter 13.) 1-7 Compare spontaneous generation and biogenesis. 1-8 Identify the contributions to microbiology made by Needham, Multicellular Animal Parasites Spallanzani, Virchow, and Pasteur. Although multicellular animal parasites are not strictly micro- 1-9 Explain how Pasteur’s work influenced Lister and Koch. organisms, they are of medical importance and therefore will 1-10 Identify the importance of Koch’s postulates. be discussed in this text. Animal parasites are eukaryotes. The 1-11 Identify the importance of Jenner’s work. two major groups of parasitic worms are the flatworms and the 1-12 Identify the contributions to microbiology made by Ehrlich roundworms, collectively called helminths (see Chapter 12, and Fleming. page 347). During some stages of their life cycle, helminths are microscopic in size. Laboratory identification of these organ- 1-13 Define bacteriology, mycology, parasitology, immunology, and virology. isms includes many of the same techniques used for identify- ing microbes. 1-14 Explain the importance of microbial genetics, molecular biology, and genomics. CHECK YOUR UNDERSTANDING Bacterial ancestors were the first living cells to appear on Earth. ✓ 1-4 Which groups of microbes are prokaryotes? Which are For most of human history, people knew little about the true eukaryotes? causes, transmission, and effective treatment of disease. Let’s look now at some key developments in microbiology that have spurred the field to its current technological state. Classification of Microorganisms Before the existence of microbes was known, all organisms The First Observations were grouped into either the animal kingdom or the plant In 1665, after observing a thin slice of cork through a crude kingdom. When microscopic organisms with characteristics microscope, Englishman Robert Hooke reported that life’s of animals and plants were discovered late in the seventeenth smallest structural units were “little boxes,” or “cells.” Using century, a new system of classification was needed. Still, biol- his improved microscope, Hooke later saw individual cells. ogists couldn’t agree on the criteria for classifying these new Hooke’s discovery marked the beginning of the cell theory— organisms until the late 1970s. the theory that all living things are composed of cells. In 1978, Carl Woese devised a system of classification based Though Hooke’s microscope was capable of showing large on the cellular organization of organisms. It groups all organ- cells, it lacked the resolution that would have allowed him to see isms in three domains as follows: microbes clearly. Dutch merchant and amateur scientist Anton 1. Bacteria (cell walls contain a protein–carbohydrate van Leeuwenhoek was probably the first to observe live micro- complex called peptidoglycan) organisms through the magnifying lenses of the more than  CHAPTER 1   The Microbial World and You 7 400 microscopes he constructed. Between 1673 and 1723, he flies to lay eggs on the meat, which developed into ­larvae. wrote about the “animalcules” he saw through his simple, single- The second jar was sealed, and because the flies could not get lens microscopes. Van Leeuwenhoek made detailed drawings of inside, no maggots appeared. Still, Redi’s antagonists were organisms he found in rainwater, feces, and material scraped from not convinced; they claimed that fresh air was needed for teeth. These drawings have since been identified as representa- spontaneous generation. So Redi set up a second experiment, tions of bacteria and protozoa (Figure 1.3). in which he covered a jar with a fine net instead of sealing it. No larvae appeared in the gauze-covered jar, even though air CHECK YOUR UNDERSTANDING was present. ✓ 1-6 What is the cell theory? Redi’s results were a serious blow to the long-held belief that large forms of life could arise from nonlife. However, many scientists still believed that small organisms, such as van The Debate over Spontaneous Generation Leeuwenhoek’s “animalcules,” were simple enough to generate After van Leeuwenhoek discovered the previously “invisible” from nonliving materials. world of microorganisms, the scientific community became The case for spontaneous generation of microorganisms interested in the origins of these tiny living things. Until the seemed to be strengthened in 1745, when John Needham found second half of the nineteenth century, many scientists and that even after he heated chicken broth and corn broth before philosophers believed that some forms of life could arise pouring them into covered flasks, the cooled solutions were spontaneously from nonliving matter; they called this hypo- soon teeming with microorganisms. Needham claimed that thetical process spontaneous generation. Not much more than microbes developed spontaneously from the fluids. Twenty 100 years ago, people commonly believed that toads, snakes, years later, Lazzaro Spallanzani suggested that microorganisms and mice could be born of moist soil; that flies could emerge from the air probably entered Needham’s solutions after they from manure; and that maggots (which we now know are the were boiled. Spallanzani showed that nutrient fluids heated larvae of flies) could arise from decaying corpses. after being sealed in a flask did not develop microbial growth. Physician Francesco Redi set out in 1668 to demonstrate Needham responded by claiming the “vital force” necessary for that maggots did not arise spontaneously. Redi filled two spontaneous generation had been destroyed by the heat and jars with decaying meat. The first was left unsealed, allowing was kept out of the flasks by the seals. CENTIMETERS 1 Lens 2 Location of specimen on pin 3 Specimen- 4 positioning screw 5 Focusing control 6 Stage- 7 positioning screw 8 9 (a) Van Leeuwenhoek using his microscope (b) Microscope replica (c) Drawings of bacteria Figure 1.3 Anton van Leeuwenhoek’s microscopic observations. (a) By holding his brass microscope toward a source of light, van Leeuwenhoek was able to observe living organisms too small to be seen with the unaided eye. (b) The specimen was placed on the tip of the adjustable point and viewed from the other side through the tiny, nearly spherical lens. The highest magnification possible with his microscopes was about 3003 (times). (c) Some of van Leeuwenhoek’s drawings of bacteria, made in 1683. The letters represent various shapes of bacteria. C–D represents a path of motion he observed. Q Why was van Leeuwenhoek’s discovery so important? F O U NDATI ON F IG U R E 1.4 Disproving Spontaneous Generation According to the hypothesis of spontaneous generation, life can arise spontaneously from nonliving matter, such as dead corpses and soil. Pasteur’s experiment, described below, demonstrated that microbes are present in nonliving matter—air, liquids, and solids. 1 Pasteur first poured beef 2 Next he heated the neck of the flask 3 Microorganisms did not appear in the broth into a long-necked flask. and bent it into an S-shape; then he cooled solution, even after long periods. boiled the broth for several minutes. Bend prevented microbes from entering flask. Microorganisms were present in the broth. Microorganisms were not present in the broth after boiling. Microorganisms were KEY CONCEPTS not present even after long periods. Pasteur demonstrated that microbes are responsible for food spoilage, leading researchers to the connection between microbes and disease. Some of these original vessels are still on His experiments and observations provided the basis of display at the Pasteur Institute in Paris. They aseptic techniques, which are used to prevent microbial have been sealed but show no sign of contamination, as shown in the photo at right. contamination more than 100 years later. Spallanzani’s observations were also criticized on the flasks with beef broth and then boiled their contents. Some grounds that there was not enough oxygen in the sealed flasks were then left open and allowed to cool. In a few days, these to support microbial life. flasks were found to be contaminated with microbes. The other flasks, sealed after boiling, were free of microorganisms. From The Theory of Biogenesis these results, Pasteur reasoned that microbes in the air were the In 1858 Rudolf Virchow challenged the case for spontaneous agents responsible for contaminating nonliving matter. generation with the concept of biogenesis, hypothesizing that Pasteur next placed broth in open-ended, long-necked living cells arise only from preexisting living cells. Because he flasks and bent the necks into S-shaped curves (Figure 1.4). could offer no scientific proof, arguments about spontaneous The contents of these flasks were then boiled and cooled. The generation continued until 1861, when the issue was finally broth in the flasks did not decay and showed no signs of life, resolved by the French scientist Louis Pasteur. even after months. Pasteur’s unique design allowed air to pass Pasteur demonstrated that microorganisms are present into the flask, but the curved neck trapped any airborne micro- in the air and can contaminate sterile solutions, but that air organisms that might contaminate the broth. (Some of these itself does not create microbes. He filled several short-necked original vessels are still on display at the ­Pasteur Institute in 8  CHAPTER 1   The Microbial World and You 9 Paris. They have been sealed but, like the flask in ­Figure 1.4, CHECK YOUR UNDERSTANDING show no sign of contamination more than 100 years later.) Pasteur showed that microorganisms can be present in non- ✓ 1-7 What evidence supported spontaneous generation? living matter—on solids, in liquids, and in the air. Furthermore, ✓ 1-8 How was spontaneous generation disproved? he demonstrated conclusively that microbial life can be destroyed by heat and that methods can be devised to block the access of airborne microorganisms to nutrient environments. These dis- The First Golden Age of Microbiology coveries form the basis of aseptic techniques, procedures that The period from 1857 to 1914 has been appropriately named prevent contamination by unwanted microorganisms, which are the First Golden Age of Microbiology. Rapid advances, now the standard practice in laboratory and many medical pro- spearheaded mainly by Pasteur and Robert Koch, led to cedures. Modern aseptic techniques are among the first and most the establishment of microbiology. Discoveries included important concepts that a beginning microbiologist learns. both the agents of many diseases and the role of immunity Pasteur’s work provided evidence that microorganisms can- in p ­ reventing and curing disease. During this productive not originate from mystical forces present in nonliving materials. period, ­ m icrobiologists studied the chemical activities of Rather, any appearance of “spontaneous” life in nonliving solu- microorganisms, improved the techniques for performing tions can be attributed to microorganisms that were already pres- microscopy and culturing microorganisms, and developed ent in the air or in the fluids themselves. Scientists now believe vaccines and surgical techniques. Some of the major events that a form of spontaneous generation probably did occur on that occurred during the First Golden Age of Microbiology the primitive Earth when life first began, but they agree that this are listed in Figure 1.5. does not happen under today’s environmental conditions. 1857 Pasteur—Fermentation 1861 Pasteur—Disproved spontaneous generation 1864 Pasteur—Pasteurization Louis Pasteur (1822–1895) 1867 Demonstrated that life did not arise Lister—Aseptic surgery spontaneously from nonliving matter. 1876 Koch*—Germ theory of disease 1879 Neisser—Neisseria gonorrhoeae 1881 Koch*—Pure cultures Finlay—Yellow fever 1882 Koch*—Mycobacterium tuberculosis Hess—Agar (solid) media First Golden 1883 Joseph Lister (1827–1912) Koch*—Vibrio cholerae Age of Performed surgery under aseptic conditions 1884 Metchnikoff*—Phagocytosis using phenol. Proved that microbes caused MICROBIOLOGY Gram—Gram-staining procedure surgical wound infections. Escherich—Escherichia coli 1887 Petri—Petri dish 1889 Kitasato—Clostridium tetani 1890 von Bering*—Diphtheria antitoxin Ehrlich*—Theory of immunity 1892 Winogradsky—Sulfur cycle Robert Koch (1843–1910) Established experimental steps for 1898 Shiga—Shigella dysenteriae directly linking a specific microbe to 1908 Ehrlich*—Syphilis treatment a specific disease. 1910 Chagas—Trypanosoma cruzi 1911 Rous*—Tumor-causing virus (1966 Nobel Prize) Figure 1.5 Milestones in the First Golden Age of Microbiology. An asterisk (*) indicates a Nobel laureate. Q Why do you think the First Golden Age of Microbiology occurred when it did? 10 PART ONE Fundamentals of Microbiology Fermentation and Pasteurization demonstrated that physicians, who at the time did not disinfect One of the key steps that established the relationship between their hands, routinely transmitted infections (puerperal, or microorganisms and disease occurred when a group of French childbirth, fever) from one obstetrical patient to another. Lister merchants asked Pasteur to find out why wine and beer soured. had also heard of Pasteur’s work connecting microbes to ani- They hoped to develop a method that would prevent spoilage mal diseases. Disinfectants were not used at the time, but Lister when those beverages were shipped long distances. At the time, knew that phenol (carbolic acid) kills bacteria, so he began many scientists believed that air converted the sugars in these treating surgical wounds with a phenol solution. The practice fluids into alcohol. Pasteur found instead that microorganisms so reduced the incidence of infections and deaths that other called yeasts convert the sugars to alcohol in the absence of air. surgeons quickly adopted it. His findings proved that microor- This process, called fermentation (see Chapter 5, page 128), is ganisms cause surgical wound infections. used to make wine and beer. Souring and spoilage are caused The first proof that bacteria actually cause disease came by different microorganisms, called bacteria. In the presence of from Robert Koch (kōk) in 1876. Koch, a German physician, air, bacteria change the alcohol into vinegar (acetic acid). was Pasteur’s rival in the race to discover the cause of anthrax, Pasteur’s solution to the spoilage problem was to heat the a disease that was destroying cattle and sheep in Europe. Koch beer and wine just enough to kill most of the bacteria that discovered rod-shaped bacteria now known as Bacillus ­anthracis caused the spoilage. The process, called pasteurization, is now (bah-SIL-lus an-THRĀ-sis) in the blood of cattle that had died commonly used to reduce spoilage and kill potentially harmful of anthrax. He cultured the bacteria on nutrients and then bacteria in milk and other beverages as well as in some alco- injected samples of the culture into healthy animals. When holic beverages. these animals became sick and died, Koch isolated the bacteria in their blood and compared them with the originally isolated The Germ Theory of Disease bacteria. He found that the two sets of blood cultures con- Before the time of Pasteur, effective treatments for many dis- tained the same bacteria. eases were discovered by trial and error, but the causes of the Koch thus established Koch’s postulates, a sequence of diseases were unknown. The realization that yeasts play a cru- experimental steps for directly relating a specific microbe to cial role in fermentation was the first link between the activ- a specific disease (see Figure 14.3, page 339). During the past ity of a microorganism and physical and chemical changes in 100 years, these same criteria have been invaluable in inves- organic materials. This discovery alerted scientists to the pos- tigations proving that specific microorganisms cause many sibility that microorganisms might have similar relationships diseases. Koch’s postulates, their limitations, and their applica- with plants and animals—specifically, that microorganisms tion to disease will be discussed in greater detail in Chapter 14. might cause disease. This idea was known as the germ theory of disease. Vaccination The germ theory met great resistance at first—for centu- Often a treatment or preventive procedure is developed before ries, disease was believed to be punishment for an individual’s scientists know why it works. The smallpox vaccine is an exam- crimes or misdeeds. When the inhabitants of an entire vil- ple. Almost 70 years before Koch established that a specific lage became ill, people often blamed the disease on demons microorganism causes anthrax, Edward Jenner, a young British appearing as fou