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). Under this license, any user of this textbook or the textbook contents herein must provide proper attribution as follows: - If you redistribute this textbook in a digital format (including but not limited to PDF and HTML), then you must retain on every page the following attribution: “Access for free at openstax.org.” - If you redistribute this textbook in a print format, then you must include on every physical page the following attribution: “Access for free at openstax.org.” - If you redistribute part of this textbook, then you must retain in every digital format page view (including but not limited to PDF and HTML) and on every physical printed page the following attribution: “Access for free at openstax.org.” - If you use this textbook as a bibliographic reference, please include https://openstax.org/details/books/microbiology in your citation. For questions regarding this licensing, please contact [email protected]. Trademarks The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, OpenStax CNX logo, OpenStax Tutor name, Openstax Tutor logo, Connexions name, Connexions logo, Rice University name, and Rice University logo are not subject to the license and may not be reproduced without the prior and express written consent of Rice University. HARDCOVER BOOK ISBN-13 978-1-938168-14-7 PAPERBACK BOOK ISBN-13 978-1-50669-811-3 DIGITAL VERSION ISBN-13 978-1-947172-23-4 ENHANCED TEXTBOOK ISBN-13 978-0-9986257-0-6 ORIGINAL PUBLICATION YEAR 2016 4 5 6 7 8 9 10 CJP 24 21 18 16 OPENSTAX OpenStax provides free, peer-reviewed, openly licensed textbooks for introductory college and Advanced Placement® courses and low-cost, personalized courseware that helps students learn. A nonprofit ed tech initiative based at Rice University, we’re committed to helping students access the tools they need to complete their courses and meet their educational goals. RICE UNIVERSITY OpenStax is an initiative of Rice University. As a leading research university with a distinctive commitment to undergraduate education, Rice University aspires to path-breaking research, unsurpassed teaching, and contributions to the betterment of our world. It seeks to fulfill this mission by cultivating a diverse community of learning and discovery that produces leaders across the spectrum of human endeavor. PHILANTHROPIC SUPPORT OpenStax is grateful for the generous philanthropic partners who advance our mission to improve educational access and learning for everyone. To see the impact of our supporter community and our most updated list of partners, please visit openstax.org/foundation. Arnold Ventures Burt and Deedee McMurtry Chan Zuckerberg Initiative Michelson 20MM Foundation Chegg, Inc. National Science Foundation Arthur and Carlyse Ciocca Charitable Foundation The Open Society Foundations Digital Promise Jumee Yhu and David E. Park III Ann and John Doerr Brian D. Patterson USA-International Foundation Bill & Melinda Gates Foundation The Bill and Stephanie Sick Fund Girard Foundation Steven L. Smith & Diana T. Go Google Inc. Stand Together The William and Flora Hewlett Foundation Robin and Sandy Stuart Foundation The Hewlett-Packard Company The Stuart Family Foundation Intel Inc. Tammy and Guillermo Treviño Rusty and John Jaggers Valhalla Charitable Foundation The Calvin K. Kazanjian Economics Foundation White Star Education Foundation Charles Koch Foundation Schmidt Futures Leon Lowenstein Foundation, Inc. William Marsh Rice University The Maxfield Foundation  Study where you want, what you want, when you want. When you access your book in our web view, you can use our new online highlighting and note-taking features to create your own study guides. Our books are free and flexible, forever. Get started at openstax.org/details/books/microbiology Access. 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. 12 1 An Invisible World FIGURE 1.3 A microscopic view of Saccharomyces cerevisiae, the yeast responsible for making bread rise (left). Yeast is a microorganism. Its cells metabolize the carbohydrates in flour (middle) and produce carbon dioxide, which causes the bread to rise (right). (credit middle: modification of work by Janus Sandsgaard; credit right: modification of work by “MDreibelbis”/Flickr) The Iceman and Evidence of Early Treatments Prehistoric humans had a very limited understanding of the causes of disease, and various cultures developed different beliefs and explanations. While many believed that illness was punishment for angering the gods or was simply the result of fate, archaeological evidence suggests that prehistoric people attempted to treat illnesses and infections. One example of this is Ötzi the Iceman, a 5300-year-old mummy found frozen in the ice of the Ötzal Alps on the Austrian-Italian border in 1991. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite Trichuris trichiura, which may have caused him to have abdominal pain 4 and anemia. Researchers also found evidence of Borrelia burgdorferi, a bacterium that causes Lyme disease. Some researchers think Ötzi may have been trying to treat his infections with the woody fruit of the Fomitopsis betulinus 5 fungus, which was discovered tied to his belongings. This fungus has both laxative and antibiotic properties. Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then 6 burning the herbs. There is speculation that this may have been another attempt to treat his health ailments. Early Notions of Disease, Contagion, and Containment Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. This is especially evident in historical attempts to contain the spread of disease. For example, the Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. Ironically, while leprosy is communicable, it is also a disease that progresses slowly. This means that people were likely quarantined after they had already spread the disease to others. Clean water and sanitation are among the most important elements of healthy societies. The earliest examples of urban sanitation systems are from the ancient Indus Valley Civilization cities of Mohenjo-daro and Harappa, located in current-day Pakistan. Constructed in 2500 BCE (about 4,500 years ago), the cities had complex networks of wells, baths, and drainage systems that stored fresh water and carried waste away. About two thousand years later, people in the ancient Greek civilization attributed disease to bad air, mal’aria, which they called “miasmatic odors.” They developed hygiene practices that built on this idea. In Rome, they built aqueducts, which brought fresh water into the city, and a giant sewer, the Cloaca Maxima, which carried waste away and into the river Tiber (Figure 1.4). Some researchers believe that this infrastructure helped protect the Romans from epidemics of waterborne illnesses. 4 A. Keller et al. “New Insights into the Tyrolean Iceman's Origin and Phenotype as Inferred by Whole-Genome Sequencing.” Nature Communications, 3 (2012): 698. doi:10.1038/ncomms1701. 5 L. Capasso. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” The Lancet, 352 (1998) 9143: 1864. doi: 10.1016/ s0140-6736(05)79939-6. 6 L. Capasso, L. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” The Lancet, 352 no. 9143 (1998): 1864. doi: 10.1016/s0140-6736(05)79939-6. Access for free at openstax.org  1.1 What Our Ancestors Knew 13 FIGURE 1.4 (a) The Cloaca Maxima, or “Greatest Sewer” (shown in red), ran through ancient Rome. It was an engineering marvel that carried waste away from the city and into the river Tiber. (b) These ancient latrines emptied into the Cloaca Maxima. Even before the invention of the microscope, some doctors, philosophers, and scientists made great strides in understanding the invisible forces—what we now know as microbes—that can cause infection, disease, and death. The Greek physician Hippocrates (460–370 BC) is considered the “father of Western medicine” (Figure 1.5). Unlike many of his ancestors and contemporaries, he dismissed the idea that disease was caused by supernatural forces. Instead, he posited that diseases had natural causes from within patients or their environments. Hippocrates and his heirs are believed to have written the Hippocratic Corpus, a collection of texts that make up some of the oldest 7 surviving medical books. Hippocrates is also often credited as the author of the Hippocratic Oath, taken by new physicians to pledge their dedication to diagnosing and treating patients without causing harm. 7 G. Pappas et al. “Insights Into Infectious Disease in the Era of Hippocrates.” International Journal of Infectious Diseases 12 (2008) 4:347–350. doi: http://dx.doi.org/10.1016/j.ijid.2007.11.003. 14 1 An Invisible World While Hippocrates is considered the father of Western medicine, the Greek philosopher and historian Thucydides (460–395 BC) is considered the father of scientific history because he advocated for evidence-based analysis of cause-and-effect reasoning (Figure 1.5). Among his most important contributions are his observations regarding the Athenian plague that killed one-third of the population of Athens between 430 and 410 BC. Having survived the epidemic himself, Thucydides made the important observation that survivors did not get re-infected with the 8 disease, even when taking care of actively sick people. This observation shows an early understanding of the concept of immunity. Marcus Terentius Varro (116–27 BC) was a prolific Roman writer who was one of the first people to propose the concept that things we cannot see (what we now call microorganisms) can cause disease (Figure 1.5). In Res Rusticae (On Farming), published in 36 BC, he said that “precautions must also be taken in neighborhood swamps... because certain minute creatures [animalia minuta] grow there which cannot be seen by the eye, which float in 9 the air and enter the body through the mouth and nose and there cause serious diseases.” Centuries later, Islamic scholars, mainly in Persia, built on the knowledge from Hippocrates as well as from Chinese and Indian medicine. Foremost among them was Abū Bakr al-Rāzī, usually refered to as al-Razi or by his Latinized name, Rhazes. He developed a range of experimental methods to test various aspects of medicine. For example, to select a location for a hospital, al-Razi hung raw meat around the city, and located the facility in the place where the meat took the longest to rot. He also was the first to distinguish measles and smallbox, and undertook experiments to determine which available treatments were most effective for each. While al-Razi did not have the technology to understand the role of microbes, his efforts to identify the causes of illnesses, rather than solely focusing on the symptoms, were highly influential. Islamic physicians created one of the most important medical texts in history, the Canon of Medicine (Arabic: al- Qānūn fī al-Ṭibb). Compiled in 1025 by physician and philosopher Ibn Sina (often referred to as Avicenna), the encyclopedia included detailed descriptions of the parts of the body, a detailed account of over 800 medicinal substances, and pathologies of several illnesses organized by body part or health event. In the work, Ibn Sina described mechanisms of contagion, indicated that organisms could be infected by foreign substances, and that illness could be transmitted by breath. He is also credited with advancing the practice of isolating people who are sick, laying the foundation for historical and contemporary quarantine methods. The Canon was translated into many languages, and was a primary resource for teaching medicine around the world, through the Renaissance and beyond. FIGURE 1.5 (a) Hippocrates, the “father of Western medicine,” believed that diseases had natural, not supernatural, causes. (b) The historian Thucydides observed that survivors of the Athenian plague were subsequently immune to the infection. (c) Marcus Terentius Varro proposed that disease could be caused by “certain minute creatures... which cannot be seen by the eye.” (credit c: modification of work by Alessandro Antonelli) 8 Thucydides. The History of the Peloponnesian War. The Second Book. 431 BC. Translated by Richard Crawley. http://classics.mit.edu/ Thucydides/pelopwar.2.second.html. 9 Plinio Prioreschi. A History of Medicine: Roman Medicine. Lewiston, NY: Edwin Mellen Press, 1998: p. 215. Access for free at openstax.org  1.1 What Our Ancestors Knew 15 CHECK YOUR UNDERSTANDING Give two examples of foods that have historically been produced by humans with the aid of microbes. Explain how historical understandings of disease contributed to attempts to treat and contain disease. The Birth of Microbiology While the ancients may have suspected the existence of invisible “minute creatures,” it wasn’t until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as “animalcules” or “wee little beasties,” swimming in a drop of rain water. From his drawings of these little organisms, we now know he was looking at bacteria and protists. (We will explore Leeuwenhoek’s contributions to microscopy further in How We See the Invisible World.) Nearly 200 years after van Leeuwenhoek got his first glimpse of microbes, the “Golden Age of Microbiology” spawned a host of new discoveries between 1857 and 1914. Two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes (Figure 1.6). Pasteur, a French chemist, showed that individual microbial strains had unique properties and demonstrated that fermentation is caused by microorganisms. He also invented pasteurization, a process used to kill microorganisms responsible for spoilage, and developed vaccines for the treatment of diseases, including rabies, in animals and humans. Koch, a German physician, was the first to demonstrate the connection between a single, isolated microbe and a known human disease. For example, he discovered the bacteria that cause anthrax (Bacillus anthracis), cholera (Vibrio 10 cholera), and tuberculosis (Mycobacterium tuberculosis). We will discuss these famous microbiologists, and others, in later chapters. FIGURE 1.6 (a) Louis Pasteur (1822–1895) is credited with numerous innovations that advanced the fields of microbiology and immunology. (b) Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis. As microbiology has developed, it has allowed the broader discipline of biology to grow and flourish in previously unimagined ways. Much of what we know about human cells comes from our understanding of microbes, and many of the tools we use today to study cells and their genetics derive from work with microbes. 10 S.M. Blevins and M.S. Bronze. “Robert Koch and the ‘Golden Age’ of Bacteriology.” International Journal of Infectious Diseases. 14 no. 9 (2010): e744-e751. doi:10.1016/j.ijid.2009.12.003. 16 1 An Invisible World CHECK YOUR UNDERSTANDING How did the discovery of microbes change human understanding of disease? MICRO CONNECTIONS Microbiology Toolbox Because individual microbes are generally too small to be seen with the naked eye, the science of microbiology is dependent on technology that can artificially enhance the capacity of our natural senses of perception. Early microbiologists like Pasteur and Koch had fewer tools at their disposal than are found in modern laboratories, making their discoveries and innovations that much more impressive. Later chapters of this text will explore many applications of technology in depth, but for now, here is a brief overview of some of the fundamental tools of the microbiology lab. Microscopes produce magnified images of microorganisms, human cells and tissues, and many other types of specimens too small to be observed with the naked eye. Stains and dyes are used to add color to microbes so they can be better observed under a microscope. Some dyes can be used on living microbes, whereas others require that the specimens be fixed with chemicals or heat before staining. Some stains only work on certain types of microbes because of differences in their cellular chemical composition. Growth media are used to grow microorganisms in a lab setting. Some media are liquids; others are more solid or gel-like. A growth medium provides nutrients, including water, various salts, a source of carbon (like glucose), and a source of nitrogen and amino acids (like yeast extract) so microorganisms can grow and reproduce. Ingredients in a growth medium can be modified to grow unique types of microorganisms. A Petri dish is a flat-lidded dish that is typically 10–11 centimeters (cm) in diameter and 1–1.5 cm high. Petri dishes made out of either plastic or glass are used to hold growth media (Figure 1.7). Test tubes are cylindrical plastic or glass tubes with rounded bottoms and open tops. They can be used to grow microbes in broth, or semisolid or solid growth media. A Bunsen burner is a metal apparatus that creates a flame that can be used to sterilize pieces of equipment. A rubber tube carries gas (fuel) to the burner. In many labs, Bunsen burners are being phased out in favor of infrared microincinerators, which serve a similar purpose without the safety risks of an open flame. An inoculation loop is a handheld tool that ends in a small wire loop (Figure 1.7). The loop can be used to streak microorganisms on agar in a Petri dish or to transfer them from one test tube to another. Before each use, the inoculation loop must be sterilized so cultures do not become contaminated. FIGURE 1.7 (a) This Petri dish filled with agar has been streaked with Legionella, the bacterium responsible for causing Legionnaire’s disease. (b) An inoculation loop like this one can be used to streak bacteria on agar in a Petri dish. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Jeffrey M. Vinocur) Access for free at openstax.org  1.2 A Systematic Approach 17 1.2 A Systematic Approach LEARNING OBJECTIVES By the end of this section, you will be able to: Describe how microorganisms are classified and distinguished as unique species Compare historical and current systems of taxonomy used to classify microorganisms Once microbes became visible to humans with the help of microscopes, scientists began to realize their enormous diversity. Microorganisms vary in all sorts of ways, including their size, their appearance, and their rates of reproduction. To study this incredibly diverse new array of organisms, researchers needed a way to systematically organize them. The Science of Taxonomy Taxonomy is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published Systema Naturae, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (Figure 1.8). FIGURE 1.8 Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor. In his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus’s original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit. Evolving Trees of Life (Phylogenies) With advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or phylogenies, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the 18 1 An Invisible World number of limbs. Now, the analysis is more complicated. Today, phylogenic analyses include genetic, biochemical, and embryological comparisons, as will be discussed later in this chapter. Linnaeus’s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure 1.9). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria. FIGURE 1.9 Ernst Haeckel’s rendering of the tree of life, from his 1866 book General Morphology of Organisms, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus. Nearly 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed adding another kingdom—Fungi—in his tree of life. Whittaker’s tree also contained a level of categorization above the kingdom level—the empire or superkingdom level—to distinguish between organisms that have membrane-bound nuclei in their cells (eukaryotes) and those that do not (prokaryotes). Empire Prokaryota contained just the Kingdom Monera. The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker’s five-kingdom tree was considered the standard phylogeny for many years. Figure 1.10 shows how the tree of life has changed over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life. Access for free at openstax.org  1.2 A Systematic Approach 19 FIGURE 1.10 This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology. CHECK YOUR UNDERSTANDING Briefly summarize how our evolving understanding of microorganisms has contributed to changes in the way that organisms are classified. CLINICAL FOCUS Part 2 Antibiotic drugs are specifically designed to kill or inhibit the growth of bacteria. But after a couple of days on antibiotics, Cora shows no signs of improvement. Also, her CSF cultures came back from the lab negative. Since bacteria or fungi were not isolated from Cora’s CSF sample, her doctor rules out bacterial and fungal meningitis. Viral meningitis is still a possibility. However, Cora now reports some troubling new symptoms. She is starting to have difficulty walking. Her muscle stiffness has spread from her neck to the rest of her body, and her limbs sometimes jerk involuntarily. In addition, Cora’s cognitive symptoms are worsening. At this point, Cora’s doctor becomes very concerned and orders more tests on the CSF samples. What types of microorganisms could be causing Cora’s symptoms? Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box. The Role of Genetics in Modern Taxonomy Haeckel’s and Whittaker’s trees presented hypotheses about the phylogeny of different organisms based on readily observable characteristics. But the advent of molecular genetics in the late 20th century revealed other ways to organize phylogenetic trees. Genetic methods allow for a standardized way to compare all living organisms without 20 1 An Invisible World relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be. In the 1970s, American microbiologist Carl Woese discovered what appeared to be a “living record” of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the gene sequences coding for small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of their small subunit rRNA gene sequences. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (Figure 1.11). Analysis of small subunit rRNA gene sequences suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria. FIGURE 1.11 Woese and Fox’s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba) Scientists continue to use analysis of RNA, DNA, and proteins to determine how organisms are related. One interesting, and complicating, discovery is that of horizontal gene transfer—when a gene of one species is absorbed into another organism’s genome. Horizontal gene transfer is especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related. Consequently, some scientists now think in terms of “webs of life” rather than “trees of life.” CHECK YOUR UNDERSTANDING In modern taxonomy, how do scientists determine how closely two organisms are related? Explain why the branches on the “tree of life” all originate from a single “trunk.” Naming Microbes In developing his taxonomy, Linnaeus used a system of binomial nomenclature, a two-word naming system for identifying organisms by genus and specific epithet. For example, modern humans are in the genus Homo and have the specific epithet name sapiens, so their scientific name in binomial nomenclature is Homo sapiens. In binomial nomenclature, the genus part of the name is always capitalized; it is followed by the specific epithet name, which is not capitalized. Both names are italicized. When referring to the species of humans, the binomial nomenclature would be Homo sapiens. Taxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common Access for free at openstax.org  1.2 A Systematic Approach 21 language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon Haloquadratum walsbyi is an example of both of these naming schemes. The genus, Haloquadratum, describes the microorganism’s saltwater habitat (halo is derived from the Greek word for “salt”) as well as the arrangement of its square cells, which are arranged in square clusters of four cells (quadratum is Latin for “foursquare”). The species, walsbyi, is named after Anthony Edward Walsby, the microbiologist who discovered Haloquadratum walsbyi in 1980. While it might seem easier to give an organism a common descriptive name—like a red-headed woodpecker—we can imagine how that could become problematic. What happens when another species of woodpecker with red head coloring is discovered? The systematic nomenclature scientists use eliminates this potential problem by assigning each organism a single, unique two-word name that is recognized by scientists all over the world. In this text, we will typically abbreviate an organism’s genus and species after its first mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium Escherichia coli is shortened to E. coli in its abbreviated form. You will encounter this same convention in other scientific texts as well. Bergey’s Manuals Whether in a tree or a web, microbes can be difficult to identify and classify. Without easily observable macroscopic features like feathers, feet, or fur, scientists must capture, grow, and devise ways to study their biochemical properties to differentiate and classify microbes. Despite these hurdles, a group of microbiologists created and updated a set of manuals for identifying and classifying microorganisms. First published in 1923 and since updated many times, Bergey’s Manual of Determinative Bacteriology and Bergey’s Manual of Systematic Bacteriology are the standard references for identifying and classifying different prokaryotes. (Appendix D of this textbook is partly based on Bergey’s manuals; it shows how the organisms that appear in this textbook are classified.) Because so many bacteria look identical, methods based on nonvisual characteristics must be used to identify them. For example, biochemical tests can be used to identify chemicals unique to certain species. Likewise, serological tests can be used to identify specific antibodies that will react against the proteins found in certain species. Ultimately, DNA and rRNA sequencing can be used both for identifying a particular bacterial species and for classifying newly discovered species. CHECK YOUR UNDERSTANDING What is binomial nomenclature and why is it a useful tool for naming organisms? Explain why a resource like one of Bergey’s manuals would be helpful in identifying a microorganism in a sample. MICRO CONNECTIONS Same Name, Different Strain Within one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacterium Escherichia coli is infamous for causing food poisoning and traveler’s diarrhea. However, there are actually many different strains of E. coli, and they vary in their ability to cause disease. One pathogenic (disease-causing) E. coli strain that you may have heard of is E. coli O157:H7. In humans, infection from E. coli O157:H7 can cause abdominal cramps and diarrhea. Infection usually originates from contaminated water or food, particularly raw vegetables and undercooked meat. In the 1990s, there were several large outbreaks of E. coli O157:H7 thought to have originated in undercooked hamburgers. While E. coli O157:H7 and some other strains have given E. coli a bad name, most E. coli strains do not cause disease. In fact, some can be helpful. Different strains of E. coli found naturally in our gut help us digest our food, 22 1 An Invisible World provide us with some needed chemicals, and fight against pathogenic microbes. LINK TO LEARNING Learn more about phylogenetic trees by exploring the Wellcome Trust’s interactive Tree of Life. The website (https://www.openstax.org/l/22wellcome) contains information, photos, and animations about many different organisms. Select two organisms to see how they are evolutionarily related. 1.3 Types of Microorganisms LEARNING OBJECTIVES By the end of this section, you will be able to: List the various types of microorganisms and describe their defining characteristics Give examples of different types of cellular and viral microorganisms and infectious agents Describe the similarities and differences between archaea and bacteria Provide an overview of the field of microbiology Most microbes are unicellular and small enough that they require artificial magnification to be seen. However, there are some unicellular microbes that are visible to the naked eye, and some multicellular organisms that are microscopic. An object must measure about 100 micrometers (µm) to be visible without a microscope, but most microorganisms are many times smaller than that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller than bacteria (Figure 1.12). See Table 1.1 for units of length used in microbiology. FIGURE 1.12 The relative sizes of various microscopic and nonmicroscopic objects. Note that a typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 µm), which is at least 10 times smaller than a typical plant or animal cell (~10–100 µm). An object must measure about 100 µm to be visible without a microscope. Access for free at openstax.org  1.3 Types of Microorganisms 23 Units of Length Commonly Used in Microbiology Metric Unit Meaning of Prefix Metric Equivalent meter (m) — 1 m = 100 m decimeter (dm) 1/10 1 dm = 0.1 m = 10−1 m centimeter (cm) 1/100 1 cm = 0.01 m = 10−2 m millimeter (mm) 1/1000 1 mm = 0.001 m = 10−3 m micrometer (μm) 1/1,000,000 1 μm = 0.000001 m = 10−6 m nanometer (nm) 1/1,000,000,000 1 nm = 0.000000001 m = 10−9 m TABLE 1.1 Microorganisms differ from each other not only in size, but also in structure, habitat, metabolism, and many other characteristics. While we typically think of microorganisms as being unicellular, there are also many multicellular organisms that are too small to be seen without a microscope. Some microbes, such as viruses, are even acellular (not composed of cells). Microorganisms are found in each of the three domains of life: Archaea, Bacteria, and Eukarya. Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as viruses, do not fall within any of the three domains of life. In this section, we will briefly introduce each of the broad groups of microbes. Later chapters will go into greater depth about the diverse species within each group. LINK TO LEARNING How big is a bacterium or a virus compared to other objects? Check out this interactive website (https://www.openstax.org/l/22relsizes) to get a feel for the scale of different microorganisms. Prokaryotic Microorganisms Bacteria are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are pathogens, causing disease in humans and other animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have cell walls that contain peptidoglycan. Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod- shaped (bacillus), or curved (spirillum, spirochete, or vibrio). Figure 1.13 shows examples of these shapes. FIGURE 1.13 Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rod-shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for Disease Control and Prevention) 24 1 An Invisible World They have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. Some bacteria are photosynthetic, such as oxygenic cyanobacteria and anoxygenic green sulfur and green nonsulfur bacteria; these bacteria use energy derived from sunlight, and fix carbon dioxide for growth. Other types of bacteria are nonphotosynthetic, obtaining their energy