Microbiology Textbook PDF

Microbiology SENIOR CONTRIBUTING AUTHORS NINA PARKER, SHENANDOAH UNIVERSITY MARK SCHNEEGURT, WICHITA STATE UNIVERSITY ANH-HUE THI TU, GEORGIA SOUTHWESTERN STATE UNIVERSITY PHILIP LISTER, CENTRAL NEW MEXICO COMMUNITY COLLEGE BRIAN M. FORSTER, SAINT JOSEPH’S UNIVERSITY OpenStax Rice University 610...

Microbiology SENIOR CONTRIBUTING AUTHORS NINA PARKER, SHENANDOAH UNIVERSITY MARK SCHNEEGURT, WICHITA STATE UNIVERSITY ANH-HUE THI TU, GEORGIA SOUTHWESTERN STATE UNIVERSITY PHILIP LISTER, CENTRAL NEW MEXICO COMMUNITY COLLEGE BRIAN M. FORSTER, SAINT JOSEPH’S UNIVERSITY OpenStax Rice University 6100 Main Street MS-375 Houston, Texas 77005 To learn more about OpenStax, visit https://openstax.org. Individual print copies and bulk orders can be purchased through our website. ©2016 Rice University. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). 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The future of education. openstax.org Contents Preface 1 CHAPTER 1 An Invisible World 9 Introduction 9 1.1 What Our Ancestors Knew 10 1.2 A Systematic Approach 17 1.3 Types of Microorganisms 22 Summary 31 Review Questions 31 CHAPTER 2 How We See the Invisible World 35 Introduction 35 2.1 The Properties of Light 35 2.2 Peering Into the Invisible World 41 2.3 Instruments of Microscopy 43 2.4 Staining Microscopic Specimens 57 Summary 69 Review Questions 69 CHAPTER 3 The Cell 73 Introduction 73 3.1 Spontaneous Generation 74 3.2 Foundations of Modern Cell Theory 77 3.3 Unique Characteristics of Prokaryotic Cells 85 3.4 Unique Characteristics of Eukaryotic Cells 103 Summary 123 Review Questions 124 CHAPTER 4 Prokaryotic Diversity 129 Introduction 129 4.1 Prokaryote Habitats, Relationships, and Microbiomes 129 4.2 Proteobacteria 136 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria 146 4.4 Gram-Positive Bacteria 153 4.5 Deeply Branching Bacteria 162 4.6 Archaea 164 Summary 167 Review Questions 168 CHAPTER 5 The Eukaryotes of Microbiology 173 Introduction 173 5.1 Unicellular Eukaryotic Parasites 174 5.2 Parasitic Helminths 188 5.3 Fungi 196 5.4 Algae 205 5.5 Lichens 208 Summary 211 Review Questions 211 CHAPTER 6 Acellular Pathogens 215 Introduction 215 6.1 Viruses 216 6.2 The Viral Life Cycle 224 6.3 Isolation, Culture, and Identification of Viruses 235 6.4 Viroids, Virusoids, and Prions 243 Summary 248 Review Questions 248 CHAPTER 7 Microbial Biochemistry 253 Introduction 253 7.1 Organic Molecules 254 7.2 Carbohydrates 259 7.3 Lipids 263 7.4 Proteins 267 7.5 Using Biochemistry to Identify Microorganisms 273 Summary 277 Review Questions 278 CHAPTER 8 Microbial Metabolism 283 Introduction 283 8.1 Energy, Matter, and Enzymes 284 8.2 Catabolism of Carbohydrates 291 8.3 Cellular Respiration 295 8.4 Fermentation 298 8.5 Catabolism of Lipids and Proteins 302 8.6 Photosynthesis 304 8.7 Biogeochemical Cycles 309 Summary 315 Review Questions 317 CHAPTER 9 Microbial Growth 323 Introduction 323 9.1 How Microbes Grow 324 Access for free at openstax.org 9.2 Oxygen Requirements for Microbial Growth 339 9.3 The Effects of pH on Microbial Growth 344 9.4 Temperature and Microbial Growth 346 9.5 Other Environmental Conditions that Affect Growth 350 9.6 Media Used for Bacterial Growth 352 Summary 355 Review Questions 356 CHAPTER 10 Biochemistry of the Genome 361 Introduction 361 10.1 Using Microbiology to Discover the Secrets of Life 362 10.2 Structure and Function of DNA 372 10.3 Structure and Function of RNA 380 10.4 Structure and Function of Cellular Genomes 384 Summary 391 Review Questions 392 CHAPTER 11 Mechanisms of Microbial Genetics 397 Introduction 397 11.1 The Functions of Genetic Material 397 11.2 DNA Replication 400 11.3 RNA Transcription 408 11.4 Protein Synthesis (Translation) 412 11.5 Mutations 418 11.6 How Asexual Prokaryotes Achieve Genetic Diversity 428 11.7 Gene Regulation: Operon Theory 435 Summary 445 Review Questions 448 CHAPTER 12 Modern Applications of Microbial Genetics 453 Introduction 453 12.1 Microbes and the Tools of Genetic Engineering 454 12.2 Visualizing and Characterizing DNA, RNA, and Protein 465 12.3 Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering 480 12.4 Gene Therapy 485 Summary 489 Review Questions 490 CHAPTER 13 Control of Microbial Growth 493 Introduction 493 13.1 Controlling Microbial Growth 494 13.2 Using Physical Methods to Control Microorganisms 501 13.3 Using Chemicals to Control Microorganisms 514 13.4 Testing the Effectiveness of Antiseptics and Disinfectants 530 Summary 536 Review Questions 538 CHAPTER 14 Antimicrobial Drugs 541 Introduction 541 14.1 History of Chemotherapy and Antimicrobial Discovery 542 14.2 Fundamentals of Antimicrobial Chemotherapy 546 14.3 Mechanisms of Antibacterial Drugs 550 14.4 Mechanisms of Other Antimicrobial Drugs 563 14.5 Drug Resistance 574 14.6 Testing the Effectiveness of Antimicrobials 580 14.7 Current Strategies for Antimicrobial Discovery 583 Summary 586 Review Questions 587 CHAPTER 15 Microbial Mechanisms of Pathogenicity 591 Introduction 591 15.1 Characteristics of Infectious Disease 591 15.2 How Pathogens Cause Disease 597 15.3 Virulence Factors of Bacterial and Viral Pathogens 609 15.4 Virulence Factors of Eukaryotic Pathogens 622 Summary 625 Review Questions 626 CHAPTER 16 Disease and Epidemiology 629 Introduction 629 16.1 The Language of Epidemiologists 630 16.2 Tracking Infectious Diseases 634 16.3 Modes of Disease Transmission 640 16.4 Global Public Health 649 Summary 654 Review Questions 654 CHAPTER 17 Innate Nonspecific Host Defenses 659 Introduction 659 17.1 Physical Defenses 660 17.2 Chemical Defenses 666 17.3 Cellular Defenses 675 17.4 Pathogen Recognition and Phagocytosis 683 17.5 Inflammation and Fever 688 Summary 693 Review Questions 694 Access for free at openstax.org CHAPTER 18 Adaptive Specific Host Defenses 699 Introduction 699 18.1 Overview of Specific Adaptive Immunity 700 18.2 Major Histocompatibility Complexes and Antigen-Presenting Cells 708 18.3 T Lymphocytes and Cellular Immunity 711 18.4 B Lymphocytes and Humoral Immunity 720 18.5 Vaccines 724 Summary 733 Review Questions 734 CHAPTER 19 Diseases of the Immune System 739 Introduction 739 19.1 Hypersensitivities 740 19.2 Autoimmune Disorders 756 19.3 Organ Transplantation and Rejection 763 19.4 Immunodeficiency 766 19.5 Cancer Immunobiology and Immunotherapy 769 Summary 772 Review Questions 773 CHAPTER 20 Laboratory Analysis of the Immune Response 777 Introduction 777 20.1 Polyclonal and Monoclonal Antibody Production 778 20.2 Detecting Antigen-Antibody Complexes 784 20.3 Agglutination Assays 795 20.4 EIAs and ELISAs 804 20.5 Fluorescent Antibody Techniques 813 Summary 820 Review Questions 821 CHAPTER 21 Skin and Eye Infections 825 Introduction 825 21.1 Anatomy and Normal Microbiota of the Skin and Eyes 826 21.2 Bacterial Infections of the Skin and Eyes 833 21.3 Viral Infections of the Skin and Eyes 848 21.4 Mycoses of the Skin 852 21.5 Protozoan and Helminthic Infections of the Skin and Eyes 857 Summary 862 Review Questions 863 CHAPTER 22 Respiratory System Infections 867 Introduction 867 22.1 Anatomy and Normal Microbiota of the Respiratory Tract 868 22.2 Bacterial Infections of the Respiratory Tract 873 22.3 Viral Infections of the Respiratory Tract 889 22.4 Respiratory Mycoses 901 Summary 908 Review Questions 909 CHAPTER 23 Urogenital System Infections 913 Introduction 913 23.1 Anatomy and Normal Microbiota of the Urogenital Tract 914 23.2 Bacterial Infections of the Urinary System 918 23.3 Bacterial Infections of the Reproductive System 924 23.4 Viral Infections of the Reproductive System 932 23.5 Fungal Infections of the Reproductive System 938 23.6 Protozoan Infections of the Urogenital System 940 Summary 944 Review Questions 945 CHAPTER 24 Digestive System Infections 949 Introduction 949 24.1 Anatomy and Normal Microbiota of the Digestive System 950 24.2 Microbial Diseases of the Mouth and Oral Cavity 956 24.3 Bacterial Infections of the Gastrointestinal Tract 963 24.4 Viral Infections of the Gastrointestinal Tract 979 24.5 Protozoan Infections of the Gastrointestinal Tract 985 24.6 Helminthic Infections of the Gastrointestinal Tract 989 Summary 1001 Review Questions 1002 CHAPTER 25 Circulatory and Lymphatic System Infections 1005 Introduction 1005 25.1 Anatomy of the Circulatory and Lymphatic Systems 1006 25.2 Bacterial Infections of the Circulatory and Lymphatic Systems 1010 25.3 Viral Infections of the Circulatory and Lymphatic Systems 1030 25.4 Parasitic Infections of the Circulatory and Lymphatic Systems 1041 Summary 1052 Review Questions 1053 CHAPTER 26 Nervous System Infections 1057 Introduction 1057 26.1 Anatomy of the Nervous System 1058 26.2 Bacterial Diseases of the Nervous System 1063 26.3 Acellular Diseases of the Nervous System 1074 26.4 Fungal and Parasitic Diseases of the Nervous System 1085 Summary 1092 Review Questions 1093 Access for free at openstax.org Appendix A Fundamentals of Physics and Chemistry Important to Microbiology 1097 Appendix B Mathematical Basics 1107 Appendix C Metabolic Pathways 1113 Appendix D Taxonomy of Clinically Relevant Microorganisms 1121 Appendix E Glossary 1133 Answer Key 1171 Index 1175 Access for free at openstax.org  Preface 1 PREFACE Welcome to Microbiology, an OpenStax resource. This to remaining transparent about all updates, so you will textbook was written to increase student access to also find a list of past errata changes on your book high-quality learning materials, maintaining highest page on openstax.org. standards of academic rigor at little to no cost. Format About OpenStax You can access this textbook for free in web view or PDF through openstax.org, and for a low cost in print. OpenStax is part of Rice University, which is a 501(c)(3) nonprofit charitable corporation. As an educational About Microbiology initiative, it's our mission to improve educational Microbiology is designed to cover the scope and access and learning for everyone. Through our sequence requirements for the single-semester partnerships with philanthropic organizations and our Microbiology course for non-majors. The book presents alliance with other educational resource companies, the core concepts of microbiology with a focus on we're breaking down the most common barriers to applications for careers in allied health. The learning. Because we believe that everyone should and pedagogical features of Microbiology make the can have access to knowledge. material interesting and accessible to students while About OpenStax Resources maintaining the career-application focus and scientific rigor inherent in the subject matter. Customization Microbiology is licensed under a Creative Commons Coverage and Scope Attribution 4.0 International (CC BY) license, which The scope and sequence of Microbiology has been means that you can distribute, remix, and build upon developed and vetted with input from numerous the content, as long as you provide attribution to instructors at institutions across the US. It is designed OpenStax and its content contributors. to meet the needs of most microbiology courses for non-majors and allied health students. In addition, we Because our books are openly licensed, you are free to have also considered the needs of institutions that use the entire book or pick and choose the sections offer microbiology to a mixed audience of science that are most relevant to the needs of your course. Feel majors and non-majors by frequently integrating topics free to remix the content by assigning your students that may not have obvious clinical relevance, such as certain chapters and sections in your syllabus, in the environmental and applied microbiology and the order that you prefer. You can even provide a direct link history of science. in your syllabus to the sections in the web view of your book. With these objectives in mind, the content of this textbook has been arranged in a logical progression Instructors also have the option of creating a from fundamental to more advanced concepts. The customized version of their OpenStax book. The opening chapters present an overview of the discipline, custom version can be made available to students in with individual chapters focusing on microscopy and low-cost print or digital form through their campus cellular biology as well as each of the classifications of bookstore. Visit your book page on openstax.org for microorganisms. Students then explore the more information. foundations of microbial biochemistry, metabolism, Errata and genetics, topics that provide a basis for All OpenStax textbooks undergo a rigorous review understanding the various means by which we can process. However, like any professional-grade control and combat microbial growth. Beginning with textbook, errors sometimes occur. Since our books are Chapter 15, the focus turns to microbial pathogenicity, web-based, we can make updates periodically when emphasizing how interactions between microbes and deemed pedagogically necessary. If you have a the human immune system contribute to human health correction to suggest, submit it through the link on your and disease. The last several chapters of the text book page on openstax.org. Subject matter experts provide a survey of medical microbiology, presenting review all errata suggestions. OpenStax is committed the characteristics of microbial diseases organized by 2 Preface body system. About ASM The American Society for Microbiology is the largest A brief Table of Contents follows. While we have made single life science society, composed of over 47,000 every effort to align the Table of Contents with the scientists and health professionals. ASM's mission is to needs of our audience, we recognize that some promote and advance the microbial sciences. instructors may prefer to teach topics in a different order. A particular strength of Microbiology is that ASM advances the microbial sciences through instructors can customize the book, adapting it to the conferences, publications, certifications, and approach that works best in their classroom. educational opportunities. It enhances laboratory capacity around the globe through training and Chapter 1: An Invisible World resources and provides a network for scientists in Chapter 2: How We See the Invisible World academia, industry, and clinical settings. Additionally, Chapter 3: The Cell ASM promotes a deeper understanding of the microbial Chapter 4: Prokaryotic Diversity sciences to diverse audiences and is committed to Chapter 5: The Eukaryotes of Microbiology offering open-access materials through their new Chapter 6: Acellular Pathogens journals, American Academy of Microbiology reports, Chapter 7: Microbial Biochemistry and textbooks. Chapter 8: Microbial Metabolism Chapter 9: Microbial Growth ASM Recommended Curriculum Guidelines for Chapter 10: Biochemistry of the Genome Undergraduate Microbiology Education Chapter 11: Mechanisms of Microbial Genetics PART 1: Concepts and Statements Chapter 12: Modern Applications of Microbial Genetics Evolution Chapter 13: Control of Microbial Growth 1. Cells, organelles (e.g., mitochondria and Chapter 14: Antimicrobial Drugs chloroplasts) and all major metabolic pathways Chapter 15: Microbial Mechanisms of evolved from early prokaryotic cells. Pathogenicity 2. Mutations and horizontal gene transfer, with the Chapter 16: Disease and Epidemiology immense variety of microenvironments, have Chapter 17: Innate Nonspecific Host Defenses selected for a huge diversity of microorganisms. Chapter 18: Adaptive Specific Host Defenses 3. Human impact on the environment influences Chapter 19: Diseases of the Immune System the evolution of microorganisms (e.g., emerging Chapter 20: Laboratory Analysis of the Immune diseases and the selection of antibiotic Response resistance). Chapter 21: Skin and Eye Infections 4. The traditional concept of species is not readily Chapter 22: Respiratory System Infections applicable to microbes due to asexual Chapter 23: Urogenital System Infections reproduction and the frequent occurrence of Chapter 24: Digestive System Infections horizontal gene transfer. Chapter 25: Circulatory and Lymphatic System 5. The evolutionary relatedness of organisms is Infections best reflected in phylogenetic trees. Chapter 26: Nervous System Infections Appendix A: Fundamentals of Physics and Cell Structure and Function Chemistry Important to Microbiology 6. The structure and function of microorganisms Appendix B: Mathematical Basics have been revealed by the use of microscopy Appendix C: Metabolic Pathways (including bright field, phase contrast, Appendix D: Taxonomy of Clinically Relevant fluorescent, and electron). Microorganisms 7. Bacteria have unique cell structures that can be Appendix E: Glossary targets for antibiotics, immunity and phage American Society of Microbiology (ASM) Partnership infection. Microbiology is produced through a collaborative 8. Bacteria and Archaea have specialized structures publishing agreement between OpenStax and the (e.g., flagella, endospores, and pili) that often American Society for Microbiology Press. The book has confer critical capabilities. been developed to align to the curriculum guidelines of 9. While microscopic eukaryotes (for example, the American Society for Microbiology. fungi, protozoa and algae) carry out some of the same processes as bacteria, many of the cellular Access for free at openstax.org  Preface 3 properties are fundamentally different. biogeochemical cycles and plant and/or animal 10. The replication cycles of viruses (lytic and microbiota). lysogenic) differ among viruses and are 25. Microorganisms provide essential models that determined by their unique structures and give us fundamental knowledge about life genomes. processes. 26. Humans utilize and harness microorganisms and Metabolic Pathways their products. 11. Bacteria and Archaea exhibit extensive, and often 27. Because the true diversity of microbial life is unique, metabolic diversity (e.g., nitrogen largely unknown, its effects and potential fixation, methane production, anoxygenic benefits have not been fully explored. photosynthesis). PART 2: Competencies and Skills 12. The interactions of microorganisms among themselves and with their environment are Scientific Thinking determined by their metabolic abilities (e.g., 28. Ability to apply the process of science quorum sensing, oxygen consumption, nitrogen a. Demonstrate an ability to formulate transformations). hypotheses and design experiments based on 13. The survival and growth of any microorganism in the scientific method. a given environment depends on its metabolic b. Analyze and interpret results from a variety of characteristics. microbiological methods and apply these 14. The growth of microorganisms can be controlled methods to analogous situations. by physical, chemical, mechanical, or biological 29. Ability to use quantitative reasoning means. a. Use mathematical reasoning and graphing Information Flow and Genetics skills to solve problems in microbiology. 30. Ability to communicate and collaborate with 15. Genetic variations can impact microbial functions other disciplines (e.g., in biofilm formation, pathogenicity and drug a. Effectively communicate fundamental resistance). concepts of microbiology in written and oral 16. Although the central dogma is universal in all format. cells, the processes of replication, transcription, b. Identify credible scientific sources and and translation differ in Bacteria, Archaea, and interpret and evaluate the information therein. Eukaryotes. 31. Ability to understand the relationship between 17. The regulation of gene expression is influenced science and society by external and internal molecular cues and/or a. Identify and discuss ethical issues in signals. microbiology. 18. The synthesis of viral genetic material and proteins is dependent on host cells. Microbiology Laboratory Skills 19. Cell genomes can be manipulated to alter cell 32. Properly prepare and view specimens for function. examination using microscopy (bright field and, if Microbial Systems possible, phase contrast). 33. Use pure culture and selective techniques to 20. Microorganisms are ubiquitous and live in diverse enrich for and isolate microorganisms. and dynamic ecosystems. 34. Use appropriate methods to identify 21. Most bacteria in nature live in biofilm microorganisms (media-based, molecular and communities. serological). 22. Microorganisms and their environment interact 35. Estimate the number of microorganisms in a with and modify each other. sample (using, for example, direct count, viable 23. Microorganisms, cellular and viral, can interact plate count, and spectrophotometric methods). with both human and nonhuman hosts in 36. Use appropriate microbiological and molecular beneficial, neutral or detrimental ways. lab equipment and methods. Impact of Microorganisms 37. Practice safe microbiology, using appropriate protective and emergency procedures. 24. Microbes are essential for life as we know it and 38. Document and report on experimental protocols, the processes that support life (e.g., in results and conclusions. 4 Preface OpenStax Microbiology Correlation to ASM OpenStax Microbiology Correlation to ASM Recommended Curriculum Guidelines for Curriculum Guidelines Undergraduate Microbiology Education OpenStax Microbiology Correlation to ASM Chapter ASM Curriculum Curriculum Guidelines Guidelines 22—Respiratory System 7, 8, 9, 14, 18, 23, Chapter ASM Curriculum Infections 24, 31 Guidelines 23—Urogenital System 7, 8, 9, 12, 14, 18, 1—An Invisible World 2, 4, 5, 11, 16, 20, Infections 22, 23, 24, 31 23, 26, 27, 31 24—Digestive System 7, 8, 9, 10, 14, 18, 2—How We See the Invisible 6, 31, 32, 33 Infections 23, 24, 31 World 25—Circulatory and 7, 8, 9, 14, 23, 31 3—The Cell 1, 2, 5, 9, 16, 21, Lymphatic System Infections 25, 31 26—Nervous System 7, 8, 9, 14, 18, 23, 4—Prokaryotic Diversity 2, 4, 8, 11, 12, 16, Infections 24, 31 20, 23, 24, 31 Engaging Feature Boxes 5—The Eukaryotes of 2, 4, 5, 9, 12, 20, Throughout Microbiology, you will find features that Microbiology 23, 31 engage students by taking selected topics a step 6—Acellular Pathogens 4, 10, 18, 23, 31 further. Our features include: 7—Microbial Biochemistry 1, 24, 33, 34 Clinical Focus. Each chapter has a multi-part 8—Microbial Metabolism 1, 11, 12, 13, 22, clinical case study that follows the story of a 24 fictional patient. The case unfolds in several 9—Microbial Growth 12, 13, 29, 31, 33, realistic episodes placed strategically throughout 34, 35 the chapter, each episode revealing new 10—Biochemistry of the 1, 16, 25, 31 symptoms and clues about possible causes and Genome diagnoses. The details of the case are directly 11—Mechanisms of 1, 2, 15, 16, 17, related to the topics presented in the chapter, Microbial Genetics 31 encouraging students to apply what they are 12—Modern Applications of 19, 26, 31 learning to real-life scenarios. The final episode Microbial Genetics presents a Resolution that reveals the outcome 13—Control of Microbial 13, 14, 26, 31, 36, of the case and unpacks the broader lessons to Growth 37 be learned. 14—Antimicrobial Drugs 3, 7, 14, 15, 23, Case in Point. In addition to the Clinical Focus, 26, 31 many chapters also have one or more single-part 15—Microbial Mechanisms 8, 9, 10, 15, 18, case studies that serve to highlight the clinical of Pathogenicity 23, 33 relevance of a particular topic. These narratives 16—Disease and 7, 14, 23, 26, 31 are strategically placed directly after the topic of Epidemiology emphasis and generally conclude with a set of questions that challenge the reader to think 17—Innate Nonspecific Host 7, 8, 23 critically about the case. Defenses Micro Connections. All chapters contain several 18—Adaptive Specific Host 7, 23, 26, 31 Micro Connections feature boxes that highlight Defenses real-world applications of microbiology, drawing 19—Diseases of the Immune 7, 8, 24 often-overlooked connections between System microbiology and a wide range of other 20—Laboratory Analysis of 31, 34 disciplines. While many of these connections the Immune Response involve medicine and healthcare, they also 21—Skin and Eye Infections 8, 9, 10, 14, 18, venture into domains such as environmental 23, 24, 31 science, genetic engineering, and emerging technologies. Moreover, many Micro Connections Access for free at openstax.org  Preface 5 boxes are related to current or recent events, further emphasizing the intersections between microbiology and everyday life. Sigma Xi Eye on Ethics. This unique feature, which appears in most chapters, explores an ethical issue related to chapter content. Developed in cooperation with the scientific research society Sigma Xi, each Eye on Ethics box presents students with a challenging ethical dilemma that arises at the intersection of science and healthcare. Often grounded in historical or current events, these short essays discuss multiple sides of an issue, posing questions that challenge the reader to contemplate the ethical principles that govern professionals in healthcare and the sciences. Disease Profile. This feature, which is exclusive to Chapters 21–26, highlights important connections between related diseases. Each box also includes a table cataloguing unique aspects of each disease, such as the causative agent, symptoms, portal of entry, mode of transmission, and treatment. These concise tables serve as a useful reference that students can use as a study aid. Link to Learning. This feature provides a brief introduction and a link to an online resource that students may use to further explore a topic presented in the chapter. Links typically lead to a website, interactive activity, or animation that students can investigate on their own. Comprehensive Art Program Our art program is designed to enhance students’ understanding of concepts through clear and effective illustrations, diagrams, and photographs. Detailed drawings, comprehensive lifecycles, and clear micrographs provide visual reinforcement for concepts. 6 Preface Additional Resources Student and Instructor Resources We’ve compiled additional resources for both students and instructors, including Getting Started Guides, a test bank, and an instructor answer guide. Instructor resources require a verified instructor account, which can be requested on your openstax.org log-in. Take advantage of these resources to supplement your OpenStax book. Partner Resources OpenStax Partners are our allies in the mission to make high-quality learning materials affordable and accessible to students and instructors everywhere. Their tools integrate seamlessly with our OpenStax titles at a low cost. To access the partner resources for your text, visit your book page on openstax.org. Materials That Reinforce Key Concepts About the Authors Learning Objectives. Every section begins with a set of clear and concise learning objectives that Senior Contributing Authors are closely aligned to the content and Review Nina Parker (Content Lead), Shenandoah University Questions. Dr. Nina Parker received her BS and MS from the Summary. The Summary distills the information University of Michigan, and her PhD in Immunology in each section into a series of concise bullet from Ohio University. She joined Shenandoah points. Key Terms in the Summary are bold-faced University's Department of Biology in 1995 and serves for emphasis. as Associate Professor, teaching general microbiology, Key Terms. New vocabulary is bold-faced when medical microbiology, immunology, and epidemiology first introduced in the text and followed by a to biology majors and allied health students. Prior to definition in context. Definitions of key terms are her academic career, Dr. Parker was trained as a also listed in the Glossary in (Appendix E). Medical Technologist and received ASCP certification, Check Your Understanding questions. Each experiences that drive her ongoing passion for training subsection of the text is punctuated by one or health professionals and those preparing for clinical more comprehension-level questions. These laboratory work. Her areas of specialization include questions encourage readers to make sure they infectious disease, immunology, microbial understand what they have read before moving pathogenesis, and medical microbiology. Dr. Parker is on to the next topic. also deeply interested in the history of medicine and Review Questions. Each chapter has a robust set science, and pursues information about diseases often of review questions that assesses students’ associated with regional epidemics in Virginia. mastery of the Learning Objectives. Questions Mark Schneegurt (Lead Writer), Wichita State are organized by format: multiple choice, University matching, true/false, fill-in-the-blank, short Dr. Mark A. Schneegurt is a Professor of Biological answer, and critical thinking. Sciences at Wichita State University and maintains joint Answers to Questions in the Book appointments in Curriculum and Instruction and Answers to Check Your Understanding questions are Biomedical Engineering. Dr. Schneegurt holds degrees not provided. Answers to Review Questions: Multiple from Rensselaer Polytechnic Institute and a Ph.D. from Choice, True/False, Fill in the blank, and Matching are Brown University. He was a postdoctoral fellow at Eli provided in the book's Answer Key. Answers to all Lilly and has taught and researched at Purdue Review Question types are provided in the Instructor University and the University of Notre Dame. His Answer Guide via the Instructor Resources page. Due research focuses on applied and environmental to the variability of potential responses, answers are microbiology, resulting in 70+ scientific publications not provided for students for Short Answer and Critical and 150+ presentations. Thinking questions. Anh-Hue Thi Tu (Senior Reviewer), Georgia Access for free at openstax.org  Preface 7 Southwestern State University Ann Auman, Pacific Lutheran University Dr. Anh-Hue Tu (born in Saigon, Vietnam) earned a BS Graciela Brelles-Mariño, Universidad Nacional de la in Chemistry from Baylor University and a PhD in Plata Medical Sciences from Texas A & M Health Science Myriam Alhadeff Feldman, Lake Washington Institute Center. At the University of Alabama–Birmingham, she of Technology completed postdoctoral appointments in the areas of Paul Flowers, University of North Carolina–Pembroke transcriptional regulation in Escherichia coli and Clifton Franklund, Ferris State University characterization of virulence factors in Streptococcus Ann Paterson, Williams Baptist University pneumoniae and then became a research assistant George Pinchuk, Mississippi University for Women professor working in the field of mycoplasmology. In Ben Rowley, University of Central Arkansas 2004, Dr. Tu joined Georgia Southwestern State Mark Sutherland, Hendrix College University where she currently serves as Professor, Reviewers teaching various biology courses and overseeing Michael Angell, Eastern Michigan University undergraduate student research. Her areas of research Roberto Anitori, Clark College interest include gene regulation, bacterial genetics, James Bader, Case Western Reserve University and molecular biology. Dr. Tu's teaching philosophy is Amy Beumer, College of William and Mary to instill in her students the love of science by using Gilles Bolduc, Massasoit Community College critical thinking. As a teacher, she believes it is Susan Bornstein-Forst, Marian University important to take technical information and express it Nancy Boury, Iowa State University in a way that is understandable to any student. Jennifer Brigati, Maryville College Brian M. Forster, Saint Joseph's University Harold Bull, University of Saskatchewan Dr. Brian M. Forster received his BS in Biology from Evan Burkala, Oklahoma State University Binghamton University and his PhD in Microbiology Bernadette Connors, Dominican College from Cornell University. In 2011, he joined the faculty Richard J. Cristiano, Houston Community of Saint Joseph’s University. Dr. Forster is the College–Northwest laboratory coordinator for the natural science AnnMarie DelliPizzi, Dominican College laboratory-based classes designed for students who Elisa M. LaBeau DiMenna, Central New Mexico are not science majors. He teaches courses in general Community College biology, heredity and evolution, environmental science, Diane Dixon, Southeastern Oklahoma State University and microbiology for students wishing to enter nursing Randy Durren, Longwood University or allied health programs. He has publications in the Elizabeth A. B. Emmert, Salisbury University Journal of Bacteriology, the Journal of Microbiology & Karen Frederick, Marygrove College Biology Education and Tested Studies for Laboratory Sharon Gusky, Northwestern Connecticut Community Education (ABLE Proceedings). College Deborah V. Harbour, College of Southern Nevada Philip Lister, Central New Mexico Community College Randall Harris, William Carey University Dr. Philip Lister earned his BS in Microbiology (1986) Diane Hartman, Baylor University from Kansas State University and PhD in Medical Angela Hartsock, University of Akron Microbiology (1992) from Creighton University. He was Nazanin Zarabadi Hebel, Houston Community College a Professor of Medical Microbiology and Immunology Heather Klenovich, Community College of Alleghany at Creighton University (1994-2011), with County appointments in the Schools of Medicine and Kathleen Lavoie, Plattsburgh State University Pharmacy. He also served as Associate Director of the Toby Mapes, Blue Ridge Community College Center for Research in Anti-Infectives and Barry Margulies, Towson University Biotechnology. He has published research articles, Kevin M. McCabe, Columbia Gorge Community College reviews, and book chapters related to antimicrobial Karin A. Melkonian, Long Island University resistance and pharmacodynamics, and has served as Jennifer Metzler, Ball State University an Editor for the Journal of Antimicrobial Ellyn R. Mulcahy, Johnson County Community College Chemotherapy. He is currently serving as Chair of Jonas Okeagu, Fayetteville State University Biology and Biotechnology at Central New Mexico Randall Kevin Pegg, Florida State College–Jacksonville Community College. Judy Penn, Shoreline Community College Contributing Authors Lalitha Ramamoorthy, Marian University Summer Allen, Brown University Drew Rholl, North Park University 8 Preface Hilda Rodriguez, Miami Dade College Paula Steiert, Southwest Baptist University Sean Rollins, Fitchburg State University Robert Sullivan, Fairfield University Sameera Sayeed, University of Pittsburgh Suzanne Wakim, Butte Community College Pramila Sen, Houston Community College Anne Weston, Francis Crick Institute Brian Róbert Shmaefsky, Kingwood College Valencia L. Williams, West Coast University Janie Sigmon, York Technical College James Wise, Chowan State University Denise Signorelli, College of Southern Nevada Virginia Young, Mercer University Molly Smith, South Georgia State College–Waycross Access for free at openstax.org CHAPTER 1 An Invisible World FIGURE 1.1 A veterinarian gets ready to clean a sea turtle covered in oil following the Deepwater Horizon oil spill in the Gulf of Mexico in 2010. After the spill, the population of a naturally occurring oil-eating marine bacterium called Alcanivorax borkumensis skyrocketed, helping to get rid of the oil. Scientists are working on ways to genetically engineer this bacterium to be more efficient in cleaning up future spills. (credit: modification of work by NOAA’s National Ocean Service) CHAPTER OUTLINE 1.1 What Our Ancestors Knew 1.2 A Systematic Approach 1.3 Types of Microorganisms INTRODUCTION From boiling thermal hot springs to deep beneath the Antarctic ice, microorganisms can be found almost everywhere on earth in great quantities. Microorganisms (or microbes, as they are also called) are small organisms. Most are so small that they cannot be seen without a microscope. Most microorganisms are harmless to humans and, in fact, many are helpful. They play fundamental roles in ecosystems everywhere on earth, forming the backbone of many food webs. People use them to make biofuels, medicines, and even foods. Without microbes, there would be no bread, cheese, or beer. Our bodies are filled with 1 microbes, and our skin alone is home to trillions of them. Some of them we can’t live without; others cause diseases that can make us sick or even kill us. Although much more is known today about microbial life than ever before, the vast majority of this invisible world remains unexplored. Microbiologists continue to identify new ways that microbes benefit and threaten humans. 1 J. Hulcr et al. “A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable.” PLoS ONE 7 no. 11 (2012): e47712. doi:10.1371/journal.pone.0047712. 10 1 An Invisible World 1.1 What Our Ancestors Knew LEARNING OBJECTIVES By the end of this section, you will be able to: Describe how our ancestors improved food with the use of invisible microbes Describe how the causes of sickness and disease were explained in ancient times, prior to the invention of the microscope Describe key historical events associated with the birth of microbiology CLINICAL FOCUS Part 1 Cora, a 41-year-old lawyer and mother of two, has recently been experiencing severe headaches, a high fever, and a stiff neck. Her husband, who has accompanied Cora to see a doctor, reports that Cora also seems confused at times and unusually drowsy. Based on these symptoms, the doctor suspects that Cora may have meningitis, a potentially life-threatening infection of the tissue that surrounds the brain and spinal cord. Meningitis has several potential causes. It can be brought on by bacteria, fungi, viruses, or even a reaction to medication or exposure to heavy metals. Although people with viral meningitis usually heal on their own, bacterial and fungal meningitis are quite serious and require treatment. Cora’s doctor orders a lumbar puncture (spinal tap) to take three samples of cerebrospinal fluid (CSF) from around the spinal cord (Figure 1.2). The samples will be sent to laboratories in three different departments for testing: clinical chemistry, microbiology, and hematology. The samples will first be visually examined to determine whether the CSF is abnormally colored or cloudy; then the CSF will be examined under a microscope to see if it contains a normal number of red and white blood cells and to check for any abnormal cell types. In the microbiology lab, the specimen will be centrifuged to concentrate any cells in a sediment; this sediment will be smeared on a slide and stained with a Gram stain. Gram staining is a procedure used to differentiate between two different types of bacteria (gram-positive and gram-negative). 2 About 80% of patients with bacterial meningitis will show bacteria in their CSF with a Gram stain. Cora’s Gram stain did not show any bacteria, but her doctor decides to prescribe her antibiotics just in case. Part of the CSF sample will be cultured—put in special dishes to see if bacteria or fungi will grow. It takes some time for most microorganisms to reproduce in sufficient quantities to be detected and analyzed. What types of microorganisms would be killed by antibiotic treatment? 2 Rebecca Buxton. “Examination of Gram Stains of Spinal Fluid—Bacterial Meningitis.” American Society for Microbiology. 2007. http://www.microbelibrary.org/library/gram-stain/3065-examination-of-gram-stains-of-spinal-fluid-bacterial-meningitis Access for free at openstax.org  1.1 What Our Ancestors Knew 11 FIGURE 1.2 (a) A lumbar puncture is used to take a sample of a patient’s cerebrospinal fluid (CSF) for testing. A needle is inserted between two vertebrae of the lower back, called the lumbar region. (b) CSF should be clear, as in this sample. Abnormally cloudy CSF may indicate an infection but must be tested further to confirm the presence of microorganisms. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by James Heilman) Jump to the next Clinical Focus box. Most people today, even those who know very little about microbiology, are familiar with the concept of microbes, or “germs,” and their role in human health. Schoolchildren learn about bacteria, viruses, and other microorganisms, and many even view specimens under a microscope. But a few hundred years ago, before the invention of the microscope, the existence of many types of microbes was impossible to prove. By definition, microorganisms, or microbes, are very small organisms; many types of microbes are too small to see without a microscope, although some parasites and fungi are visible to the naked eye. Humans have been living with—and using—microorganisms for much longer than they have been able to see them. Historical evidence suggests that humans have had some notion of microbial life since prehistoric times and have used that knowledge to develop foods as well as prevent and treat disease. In this section, we will explore some of the historical applications of microbiology as well as the early beginnings of microbiology as a science. Fermented Foods and Beverages People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from 3 rice, honey, and fruit as early as 7000 BC. Production of these foods and beverages requires microbial fermentation, a process that uses bacteria, mold, or yeast to convert sugars (carbohydrates) to alcohol, gases, and organic acids (Figure 1.3). While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had curdled or old grape juice that had fermented—they later learned to harness the power of fermentation to make products like bread, cheese, and wine. 3 P.E. McGovern et al. “Fermented Beverages of Pre- and Proto-Historic China.” Proceedings of the National Academy of Sciences of the United States of America 1 no. 51 (2004):17593–17598. doi:10.1073/pnas.0407921102.