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Microbiology Microbiology SENIOR CONTRIBUTING AUTHORS NINA PARKER, SHENANDOAH UNIVERSITY MARK SCHNEEGURT, WICHITA STATE UNIVERSITY ANH-HUE THI TU, GEORGIA SOUTHWESTERN STATE UNIVERSITY BRIAN M. FORSTER, SAINT JOSEPH'S UNIVERSITY PHILIP LISTER, CENTRAL NEW MEXICO COMMUNITY COLLEGE 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. ©2018 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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We’ll send you an OpenStax sticker to thank you for your support! Access. The future of education. OpenStax.org Table of Contents Preface . 1 Chapter 1: An Invisible World . 15 1.1 What Our Ancestors Knew . 16 1.2 A Systematic Approach . 23 1.3 Types of Microorganisms . 29 Chapter 2: How We See the Invisible World . 43 2.1 The Properties of Light . 44 2.2 Peering Into the Invisible World . 50 2.3 Instruments of Microscopy . 53 2.4 Staining Microscopic Specimens . 71 Chapter 3: The Cell . 89 3.1 Spontaneous Generation . 90 3.2 Foundations of Modern Cell Theory . 94 3.3 Unique Characteristics of Prokaryotic Cells . 102 3.4 Unique Characteristics of Eukaryotic Cells . 122 Chapter 4: Prokaryotic Diversity . 149 4.1 Prokaryote Habitats, Relationships, and Microbiomes . 150 4.2 Proteobacteria . 157 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria . 168 4.4 Gram-Positive Bacteria . 174 4.5 Deeply Branching Bacteria . 184 4.6 Archaea . 185 Chapter 5: The Eukaryotes of Microbiology . 197 5.1 Unicellular Eukaryotic Parasites . 198 5.2 Parasitic Helminths . 213 5.3 Fungi . 221 5.4 Algae . 231 5.5 Lichens . 235 Chapter 6: Acellular Pathogens . 243 6.1 Viruses . 244 6.2 The Viral Life Cycle . 253 6.3 Isolation, Culture, and Identification of Viruses . 264 6.4 Viroids, Virusoids, and Prions . 275 Chapter 7: Microbial Biochemistry . 285 7.1 Organic Molecules . 286 7.2 Carbohydrates . 292 7.3 Lipids . 296 7.4 Proteins . 300 7.5 Using Biochemistry to Identify Microorganisms . 307 Chapter 8: Microbial Metabolism . 317 8.1 Energy, Matter, and Enzymes . 318 8.2 Catabolism of Carbohydrates . 326 8.3 Cellular Respiration . 331 8.4 Fermentation . 334 8.5 Catabolism of Lipids and Proteins . 338 8.6 Photosynthesis . 340 8.7 Biogeochemical Cycles . 346 Chapter 9: Microbial Growth . 361 9.1 How Microbes Grow . 362 9.2 Oxygen Requirements for Microbial Growth . 379 9.3 The Effects of pH on Microbial Growth . 385 9.4 Temperature and Microbial Growth . 388 9.5 Other Environmental Conditions that Affect Growth . 392 9.6 Media Used for Bacterial Growth . 394 Chapter 10: Biochemistry of the Genome . 405 10.1 Using Microbiology to Discover the Secrets of Life . 406 10.2 Structure and Function of DNA . 418 10.3 Structure and Function of RNA . 427 10.4 Structure and Function of Cellular Genomes . 431 Chapter 11: Mechanisms of Microbial Genetics . 445 11.1 The Functions of Genetic Material . 446 11.2 DNA Replication . 448 11.3 RNA Transcription . 458 11.4 Protein Synthesis (Translation) . 462 11.5 Mutations . 469 11.6 How Asexual Prokaryotes Achieve Genetic Diversity . 480 11.7 Gene Regulation: Operon Theory . 488 Chapter 12: Modern Applications of Microbial Genetics . 509 12.1 Microbes and the Tools of Genetic Engineering . 510 12.2 Visualizing and Characterizing DNA, RNA, and Protein . 521 12.3 Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering . 538 12.4 Gene Therapy . 543 Chapter 13: Control of Microbial Growth . 553 13.1 Controlling Microbial Growth . 554 13.2 Using.
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