Foundations in Microbiology 10th Edition

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Foundations in Microbiology is an allied health microbiology text with a taxonomic approach to the disease chapters. It offers an engaging and accessible writing style through the use of case studies and analogies to thoroughly explain difficult microbiology concepts

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CHESS TALARO Kathleen Park Barry MICROBIOLOGY FOUNDATIONS IN

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MICROBIOLOGY FOUNDATIONS IN

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Tenth Edition CHESS TALARO Kathleen Park Barry MICROBIOLOGY FOUNDATIONS IN

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FOUNDATIONS IN MICROBIOLOGY TENTH EDITION Published by McGraw-Hill Education 2 Penn Plaza New York NY 10121. Copyright © 2018 by McGraw-Hill Education. All rights reserved. Printed in the United States of America. Previous editions © 2015 2012 and 2009. No part of this publication may be reproduced or distributed in any form or by any means or stored in a database or retrieval system without the prior written consent of McGraw-Hill Education including but not limited to in any network or other electronic storage or transmission or broadcast for distance learning. Some ancillaries including electronic and print components may not be available to customers outside the United States. This book is printed on acid-free paper. 1 2 3 4 5 6 7 8 9 0 LWI 21 20 19 18 17  ISBN 978–1–259–70521-2 MHID 1–259–70521–8 Chief Product Officer SVP Products Markets: G. Scott Virkler Vice President General Manager Products Markets: Marty Lange Vice President Content Production Technology Services: Betsy Whalen Managing Director: Lynn Breithaupt Brand Manager: Marija Magner Director of Development: Rose M. Koos Product Developer: Mandy Clark Digital Product Analyst: John J. Theobald Marketing Manager: Jessica Cannavo Director Content Production: Linda Avenarius Program Manager: Angie FitzPatrick Content Project Managers: core: Jayne Klein assessment: Brent dela Cruz Senior Buyer: Laura Fuller Designer: Tara McDermott Cover Image: © National Institute of Allergy and Infectious Diseases Content Licensing Specialists: Image: Carrie K. Burger Text: Lorraine Buczek Compositor: Aptara ® Inc. Typeface: STIX Mathjax Printer: LSC Communications All credits appearing on page are considered to be an extension of the copyright page. Design elements: Fungi: CDC/Janice Haney Carr Magnifying Glass: © Comstock/PunchStock RF iPad Head/Brain USA Map:  © McGraw-Hill Education Blood Cell/MRSA Neutrophil/MRSA Bacteria: National Institute of Allergy and Infectious Diseases. Photo of Kathy Park Talaro p. vi: Courtesy of Dave Bedrosian Photo of Barry Chess p. vi: Courtesy of Josh Chess Library of Congress Cataloging-in-Publication Data Names: Talaro Kathleen P. author. | Chess Barry author. Title: Foundations in microbiology / Kathleen Park Talaro Pasadena City College Barry Chess Pasadena City College. Description: Tenth edition. | New York NY : McGraw-Hill Education 2018 Identifiers: LCCN 2016040028| ISBN 9781259705212 alk. paper | ISBN 1259705218 alk. paper Subjects: LCSH: Microbiology. | Medical microbiology. Classification: LCC QR41.2 .T35 2018 | DDC 616.9/041—dc23 LC record available at https://lccn.loc.gov/2016040028 2013041001 The Internet addresses listed in the text were accurate at the time of publication. The inclusion of a website does not indicate an endorsement by the authors or McGraw-Hill Education and McGraw-Hill Education does not guarantee the accuracy of the information presented at these sites. www.mhhe.com

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v CHAPTER 1 The Main Themes of Microbiology 1 CHAPTER 2 The Chemistry of Biology 29 CHAPTER 3 Tools of the Laboratory: Methods of Studying Microorganisms 60 CHAPTER 4 A Survey of Prokaryotic Cells and Microorganisms 89 CHAPTER 5 A Survey of Eukaryotic Cells and Microorganisms 124 CHAPTER 6 An Introduction to Viruses 160 CHAPTER 7 Microbial Nutrition Ecology and Growth 188 CHAPTER 8 An Introduction to Microbial Metabolism: The Chemical Crossroads of Life 222 CHAPTER 9 An Introduction to Microbial Genetics 260 CHAPTER 10 Genetic Engineering: A Revolution in Molecular Biology 298 CHAPTER 11 Physical and Chemical Agents for Microbial Control 327 CHAPTER 12 Drugs Microbes Host—The Elements of Chemotherapy 360 CHAPTER 13 Microbe-Human Interactions: Infection Disease and Epidemiology 397 CHAPTER 14 An Introduction to Host Defenses and Innate Immunities 437 CHAPTER 15 Adaptive Specifc Immunity and Immunization 466 CHAPTER 16 Disorders in Immunity 501 CHAPTER 17 Procedures for Identifying Pathogens and Diagnosing Infections 533 CHAPTER 18 The Gram-Positive and Gram-Negative Cocci of Medical Importance 556 CHAPTER 19 The Gram-Positive Bacilli of Medical Importance 587 CHAPTER 20 The Gram-Negative Bacilli of Medical Importance 618 CHAPTER 21 Miscellaneous Bacterial Agents of Disease 648 CHAPTER 22 The Fungi of Medical Importance 681 CHAPTER 23 The Parasites of Medical Importance 710 CHAPTER 24 Introduction to Viruses That Infect Humans: The DNA Viruses 749 CHAPTER 25 The RNA Viruses That Infect Humans 774 CHAPTER 26 Environmental Microbiology 814 CHAPTER 27 Applied and Industrial Microbiology 838 Brief Contents

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vi About the Authors Kathleen Park Talaro is a microbiologist educator au- thor and artist. She has been nurturing her love of microbi - ology since her youth growing up on an Idaho farm where she was frst fascinated by tiny creatures she could just barely see swimming in a pond. This interest in the microbial world led to a biology major at Idaho State University where she worked as a teaching assistant and scientifc illustrator for one of her professors. This was the beginning of an avocation that she continues today—that of lending her artistic hand to interpreta - tion of scientifc concepts. She continued her education at Arizona State University Occidental College California Institute of T echnol - ogy and California State University. She taught microbiology and major’s biology courses at Pasa- dena City College for 30 years during which time she developed new curricula and refned laboratory experiments. She has been an author of and contributor to several publications of the William C. Brown Company and McGraw-Hill Publishers since the early 1980s frst illustrating and writing for laboratory manuals and later developing this textbook. She has also served as a co- author with Kelly Cowan on the frst two editions of Microbiology: A Systems Approach. Kathy continues to make microbiology a major focus of her life and is passionate about conveying the signifcance and practical knowledge of the subject to students colleagues family friends and practically anyone who shows interest. In addition to her writ- ing and illustration she keeps current by attending conferences and participating in the American Society for Microbiology and its undergraduate educational programs. She is gratifed by the many supportive notes and letters she has received over the years from devotees of microbiology and users of her book. She lives in Altadena California with husband Dave Bedrosian and son David. Whenever she can she visits her family in Idaho. In her spare time she enjoys photography reading true crime books music crossword puzzles and playing with her rescued kitties. Barry Chess has been teaching microbiology at Pasadena City College for 20 years. He received his Bachelor’s and Master’s degrees from the California State University and did postgraduate work at the University of California where his research focused on the expression of eukaryotic genes involved in the devel- opment of muscle and bone. At Pasadena City College Barry developed a new course in human genetics and helped to institute a biotechnology pro- gram. He regularly teaches courses in microbiology general biology and genetics and works with students completing inde- pendent research projects in biology and microbiology. Over the past several years Barry’s interests have begun to focus on inno - vative methods of teaching that increase student success. He has written cases for the National Center for Case Study Teaching in Science and given talks at national meetings on the efectiveness of case studies in the classroom. His laboratory manual Labora- tory Applications in Microbiology: A Case Study Approach is cur- rently in its third edition. He feels very fortunate to be collaborating with Kathy Talaro with whom he has worked in the classroom for more than a decade on this tenth edition. Barry is a member of the American Society for Microbiology and the American Association for the Advancement of Science and regularly attends meetings in his felds of interest both to keep current of changes in the disci - pline and to exchange teaching and learning strategies with others in the feld.

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vii A major intent of this textbook has always been to promote an understanding of microbes and their intimate involvement in the lives of humans but our other aim is to stimulate an appreciation that goes far beyond that. We want you to be awed by these tiniest creatures and the tremendous impact they have on all of the earth’s natural activities. We hope you are inspired enough to embrace that knowledge throughout your lives.

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RequiredResults ® McGraw-Hill Connect ® Learn Without Limits Connect is a teaching and learning platform that is proven to deliver better results for students and instructors. Connect empowers students by continually adapting to deliver precisely what they need when they need it and how they need it so your class time is more engaging and efective. Connect Insight ® Connect Insight is Connect’s new one- of-a-kind visual analytics dashboard that provides at-a-glance information regarding student performance which is immediately actionable. By presenting assignment assessment and topical performance results together with a time metric that is easily visible for aggregate or individual results Connect Insight gives the user the ability to take a just-in-time approach to teaching and learning which was never before available. Connect Insight presents data that helps instructors improve class performance in a way that is efcient and efective. 73 of instructors who use Connect require it instructor satisfaction increases by 28 when Connect is required. Analytics ©Getty Images/iStockphoto Using Connect improves retention rates by 19.8 passing rates by 12.7 and exam scores by 9.1.

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SmartBook ® Proven to help students improve grades and study more efciently SmartBook contains the same content within the print book but actively tailors that content to the needs of the individual. SmartBook’s adaptive technology provides precise personalized instruction on what the student should do next guiding the student to master and remember key concepts targeting gaps in knowledge and ofering customized feedback and driving the student toward comprehension and retention of the subject matter. Available on tablets SmartBook puts learning at the student’s fngertips—anywhere anytime. Adaptive Over 8 billion questions have been answered making McGraw-Hill Education products more intelligent reliable and precise. THE ADAPTIVE READING EXPERIENCE DESIGNED TO TRANSFORM THE WAY STUDENTS READ More students earn A’s and B’s when they use McGraw-Hill Education Adaptive products. www.mheducation.com

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x Connecting Instructors to Students— Digital Tools for Your Success Significant faculty demand for content at higher Bloom’s levels led us to examine as- sessment quality and consist- ency of our Connect content to develop a scientific ap- proach to systemically in- crease critical-thinking levels and develop balanced digital assessments that promote student learning. The in- creased challenge at higher Bloom’s levels will help the student grow intellectually and be better prepared to contribute to society. Instructor Resources Customize your lecture with tools such as PowerPoint ® pres- entations animations and editable art from the textbook. An instructor’s manual for the text saves you time in devel- oping your course. Detailed Reports Track individual student performance—by question by assign- ment or in relation to the class overall—with detailed grade reports. Integrate grade reports easily with your Learning Management Systems LMS. Homework and Assessment With Connect for Talaro’s Foundations in Microbiology you can deliver auto-graded assignments quizzes and tests online. Choose from a robust set of interactive questions and activities using high-quality art from the textbook and ani- mations. Assignable content is available for every Learning Outcome in the book and is categorized according to the ASM Curriculum Guidelines. As an instructor you can edit existing questions and author entirely new ones. Lecture Capture McGraw-Hill Tegrity ® records and distributes your class lecture with just a click of a button. Students can view anytime anywhere via computer or mobile device. Indexed as you record students can use keywords to find exactly what they want to study. Save time with auto-graded assessments. Gather powerful performance data. McGraw-Hill Connect for Prescott’s Microbiology provides online presentation assignment and assessment solutions connecting your students with the tools and resources they’ll need to achieve success. Learn more at connect.mheducation.com. ®

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xi Integrated and Adaptive Laboratory Tools LearnSmart Labs® is an adaptive simulated lab experience that brings meaningful scientific exploration to students. Through a series of adaptive questions LearnSmart Labs identifies a student’s knowledge gaps and provides resources to quickly and efficiently close those gaps. Once students have mastered the necessary basic skills and concepts they engage in a highly realistic simulated lab experience that allows for mistakes and the execution of the scientific method. LearnSmart® Prep is an adaptive learning tool that prepares students for college-level work in Microbiology. LearnSmart Prep individually identifies concepts the student does not fully understand and provides learning resources to teach essential concepts so he or she enters the classroom prepared. Data- driven reports highlight areas where students are struggling helping to accurately identify weak areas.

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xii Carefully crafting a textbook to be a truly useful learning tool for students takes time and dedication. Every line of text and every piece of art in this book is scrutinized for instructional usefulness placement and pedagogy and then reexamined with each revision. In this tenth edition the authors have gone through the book page by page with more depth than ever before to make sure it main- tains its instructional quality fantastic art program relevant and current material and engaging user-friendly writing style. Since the first edition the goals of this book have been to explain com- plex topics clearly and vividly and to present the material in a straightforward way that students can understand. The tenth edition continues to meet these goals with the most digitally integrated up-to-date and pedagogically important revision yet. Kathy Talaro introduces new art to a revision by carefully sketching out what she envisions in precise detail with accompanying instructions to the illustrator. The result is accurate beautifully rendered art that helps difcult concepts come to life. 3. The template for the lagging strand runs 5 to 3 opposite to the leading strand so to make the new strand in the 5 to 3 orientation synthesis must proceed backward away from the replication fork. 4. Before synthesis of the lagging strand can start a primase adds an RNA primer to direct the DNA polymerase III. Synthesis produces unlinked segments of RNA primer and new DNA called Okazaki fragments. 5. DNA polymerase I removes the RNA primers and fills in the correct complementary DNA nucleotides at the open sites. 6. Unjoined ends of the nucleotides a nick must be connected by a ligase. 1. The chromosome to be replicated is unwound by a helicase forming a replication fork with two template strands. 2. The template for the leading strand blue is oriented 3 to 5. This allows the DNA polymerase III to add nucleotides in the 5 to 3 direction toward the replication fork so it can be synthesized as a continuous strand. Note that direction of synthesis refers to the order of the new strand red. Template strand New strand RNA primer Helicase Key: Primase DNA polymerase III DNA polymerase I Ligase b a Replication forks 1 2 3 4 5 6 5 3 5 5 3 5 3 5 3 3 LEADING STRAND SYNTHESIS Origin of a replication LAGGING STRAND SYNTHESIS Nick Okazaki fragment The Profile of a Student Success Learning Tool Art and organization of content make this book unique Like a great masterpiece hanging in a museum Foundations in Microbiology is not only beautiful but also tells a story com- posed of many pieces. A great textbook must be carefully con- structed to place art where it makes the most sense in the flow of the narrative create process figures that break down complex processes into their simplest parts provide explanations at the correct level for the student audience and offer pedagogical tools that help all types of learners. Many textbook authors write the narrative of their book and call it a day. It is the rare author team indeed that examines each page and makes changes based on what will help the students the most so that when the pieces come together the result is an expertly crafted learning tool—a story of the microbial world.

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xiii The Structure of a Student Success Learning Tool Chapter-Opening Case Studies Each chapter opens with a Case Study Part 1 which helps the students appreciate and understand how microbiology impacts their lives. Appropriate line art micrographs and quotes have been added to the chapter-opening page to help the students pull together the big picture and grasp the relevance of the material they’re about to learn. The questions that directly follow Parts 1 and 2 of the Case Study challenge students to begin to think critically about relevant text references that will help them answer the questions as they work through the chapter. The Case Study Perspective wraps up the case and can be found on the Connect website. 89 3 I n 2003 a 100 foot sailboat called the Sorcerer II embarked on a highly unusual shing expedition in the Sargasso Sea. What was most strik- ing about this voyage was that it did no involve actually catching sh with hooks or nets. Instead the targets were tiny oating microbes “hooked” by an exceedingly sophisticated and speci c technology. This project was the brainchild of Dr. Craig Ven- ter a prominent genetics researcher and its pri- mary goal was to survey in detail the mircrobial population of ocean water. Scientists aboard the vessel randomly collected surface water about ev- ery 200 miles extracted the tiniest forms of micro- scopic plankton primarily bacteria and sent samples back to Venter’s laboratory. It was here that his scienti c crew engaged in a new and pow- erful way of examining the world. Instead of pains- takingly locating tand identifying the individual microbes in the sample as might have been done in the past they ex tracted the genetic material DNA from the samples and analyzed the DNA using state-of-the-art molecular techniques and computers. Their stunning and somewhat unexpected discovery was that the variety and numbers of microbes liv- ing in the ocean exceeded by far any previous ocean studies. This ambitious undertaking was just the beginning. It was followed by several additional voyages by Dr. Venter’s ship as well as marine microbi- ologists at the Marine Biological Institute in Woods Hole Massachusetts and is continuing today all over the globe. Even though microbiologists had previously described around 5700 di erent types of bacteria the evidence from these studies showed that this number represented only the tiniest “drop in the ocean. ” Some of the data uncovered evidence of more an 20000 di erent kinds of microorganisms in just a single liter of seawater most of them unknown. Realizing that the ocean is a vast space with endless nooks and crannies for organisms to hide by one estimate it could easily contain 5 to 10 million di erent mi- croscopic creatures each of them having unique characteristics and roles in the ocean environment. According to Dr. David Thomassen Chief Scientist Department of Energy “Microbes rule the earth. Sci- entists estimate that there are more microbes on earth than there are stars in the universe—an esti- mated nonillion one followed by thirty zeros. Mi- crobes and their communities make up the foundation of the biosphere and sustain all life on earth. ” Which groups of microorganisms would likey be found in the plankton What elds of microbiology could be involved in the further study of these microbes and in unco eringtheir basic characteristics To continue the case go to page 000. Dr. Venter was one of the main individuals behind the mapping of the human genome in 2001. This technique called metagenomic analysis will be discussed in a later chapter10. An unusual protozoan isolated from a cow’s rumen. Background: Model of the enzyme cullulase Tools of the Laboratory: The Methods for Studying Microorganisms C H A P T E R 3 This is a colorized view of Beribus voluptios magnit o ciis dolum et am id ute cusant. Ferrorest volore voles et lam quam cumquas in reperibusam nullore voluptios magnit. “ Peering through the microscope into a drop of seawater is like looking at stars with a telescope on a clear night.” Dr. Victor Gallardo ocean researcher C A S E F I L E 1 This is an Example of a Longer Case File Title Micro “At least 65 of chronic infections are caused by microbial biofilms.” He began to wonder if the patient had a prior medical history of possible risk factors. From interviewing Mr. Jones he learned that an artifcial valve had been implanted in his heart 10 years before a fact that had been omitted from his medical chart. This fnding im- mediately caused alarm and Mr. Jones was ad- mitted to the intensive care unit and placed on a mixture of intravenous antibiotics. Tests for blood cultures and a white blood cell count were ordered as backup. By that evening Mr. Jones had become confused and lost conscious- ness. He was rushed to the operating room but died during open heart surgery. ■ What appear to be the most important facts in this case ■ Explain why Mr. Jones’s throat culture was negative for infection. To continue the Case Study go to Case Study Part 2 at the end of the chapter. On a summer morning in 2008 Maxwell Jones a 65-year-old man woke up complaining of abnormal fatigue and a scratchy throat. His wife said he felt hot and took his temperature. It was slightly elevated at 100°F. He dismissed his condition saying he was probably tired from working in his garden and sufering one of his regular allergy attacks. Over the next few days his list of symptoms grew. He lost his ap- petite his joints and muscles were sore and he woke up wringing wet from night sweats. He continued to have a fever and his wife was wor- ried over how pale he looked. She insisted he see a physician who performed a physical and took a throat culture. Mr. Jones was sent home with instructions to take oral penicillin and acetaminophen Tylenol and to come back in a week. At the next appointment the patient reported that he still had some of the same symptoms including the fever and that now he had begun to have headaches rapid breathing and coughing. The physician recorded a rapid heart rate and slight heart murmur. When the lab report indicated that the throat culture was negative for bacterial pathogens he had to look for other causes. Heart Valves and Biofilms C A SE S TUD Y Part 1 4 CHAPTER A Survey of Prokaryotic Cells and Microorganisms Looking as harmless as clusters of tiny purple grapes the gram-positive pathogen Staphylococcus aureus is anything but. inset: Source: Janice Carr/CDC Section of a prosthetic heart valve with a patch of MRSA bioflm attached purple. Modifed image reprinted with permission from Medscape Reference http://emedicine.medscape.com/ 2013 available at: http://emedicine. medscape.com/article/216650-overview. taL05218_ch04_089-123.indd 89 10/7/16 11:55 AM 120 Chapter 4 A Survey of Prokaryotic Cells and Microorganisms Figure 4.33 The hottest life forms on earth. A colorized transmission electron micrograph of strain 121. This member of Domain Archaea was isolated from an undersea thermal vent of the coast of Washington State. This organism thrives in habitats above the temperature of boiling water and can even survive being autoclaved. © Derek Lovley/Kazem Kashef/Science Source Check Your Progress SECTION 4.7 36. Discuss several ways in which bacteria are medically and ecologi- cally important. 37. Name two main groups of obligate intracellular parasitic bacteria and explain why these groups can’t live independently. 38. Explain the characteristics of archaea that indicate that they consti- tute a unique domain of living things that is neither bacterial nor eukaryotic. 39. What is meant by the terms extremophile and hyperextremophile 40. Describe the three major archaeal lifestyles and adaptations to extreme habitats. C A SE S TUD Y Part 2 3 I n 2003 a 100 foot sailboat called the Sorcerer II embarked on a highly unusual shing expedition in the Sargasso Sea. What was most strik- ing about this voyage was that it did no involve actually catching sh with hooks or nets. Instead the targets were tiny oating microbes “hooked” by an exceedingly sophisticated and speci c technology. This project was the brainchild of Dr. Craig Ven- ter a prominent genetics researcher and its pri- mary goal was to survey in detail the mircrobial population of ocean water. Scientists aboard the vessel randomly collected surface water about ev- ery 200 miles extracted the tiniest forms of micro- scopic plankton primarily bacteria and sent samples back to Venter’s laboratory. It was here that his scienti c crew engaged in a new and pow- erful way of examining the world. Instead of pains- takingly locating tand identifying the individual microbes in the sample as might have been done in the past they ex tracted the genetic material DNA from the samples and analyzed the DNA using state-of-the-art molecular techniques and computers. Their stunning and somewhat unexpected discovery was that the variety and numbers of microbes liv- ing in the ocean exceeded by far any previous ocean studies. This ambitious undertaking was just the beginning. It was followed by several additional voyages by Dr. Venter’s ship as well as marine microbi- ologists at the Marine Biological Institute in Woods Hole Massachusetts and is continuing today all over the globe. Even though microbiologists had previously described around 5700 di erent types of bacteria the evidence from these studies showed that this number represented only the tiniest “drop in the ocean. ” Some of the data uncovered evidence of more an 20000 di erent kinds of microorganisms in just a single liter of seawater most of them unknown. Realizing that the ocean is a vast space with endless nooks and crannies for organisms to hide by one estimate it could easily contain 5 to 10 million di erent mi- croscopic creatures each of them having unique characteristics and roles in the ocean environment. According to Dr. David Thomassen Chief Scientist Department of Energy “Microbes rule the earth. Sci- entists estimate that there are more microbes on earth than there are stars in the universe—an esti- mated nonillion one followed by thirty zeros. Mi- crobes and their communities make up the foundation of the biosphere and sustain all life on earth. ” Which groups of microorganisms would likey be found in the plankton What elds of microbiology could be involved in the further study of these microbes and in unco eringtheir basic characteristics To continue the case go to page 000. Dr. Venter was one of the main individuals behind the mapping of the human genome in 2001. This technique called metagenomic analysis will be discussed in a later chapter10. An unusual protozoan isolated from a cow’s rumen. Background: Model of the enzyme cullulase Tools of the Laboratory: The Methods for Studying Microorganisms C H A P T E R 3 This is a colorized view of Beribus voluptios magnit o ciis dolum et am id ute cusant. Ferrorest volore voles et lam quam cumquas in reperibusam nullore voluptios magnit. “ Peering through the microscope into a drop of seawater is like looking at stars with a telescope on a clear night.” Dr. Victor Gallardo ocean researcher C A S E F I L E 1 This is an Example of a Longer Case File Title Micro During an autopsy of Mr. Jones’s body the pathologist observed that the prosthetic valve was covered with small patches he called vegetations. The later blood cultures grew a strain of Staphylococcus aureus known as MRSA. Microscopic examination of the valve revealed a thick bioflm coating containing that same bacterium. The pa- thologist concluded that the patient had infective endocarditis and that vegetations on the valve lesions had broken loose and entered the circulation. This event created emboli that blocked arteries in his brain and gave rise to a massive stroke. Upon closer review of Mr. Jones’s case the physician discovered that he had sufered from a skin infection the previous spring that had been treated and cured by a diferent physician. It turned out to be caused by the MRSA type of Staphylococcus aureus. Most bacteria can form structured multicellular communi- ties or bioflms on objects in a moist environment. This is even true of bacterial pathogens in the body. The CDC esti- mates that at least 65 of chronic infections are caused by mi- crobial bioflms. In this case the MRSA bacteria in the patient’s skin infection must have entered the circulation and colonized the artifcial valve over several weeks to months. Most cases of chronic endocarditis are caused by bioflms on valves. When the bioflm grows into larger vegetations portions of it break loose into the circulation. These infect the blood and are spread into organs causing fever and other signs and symptoms including the ones that were fatal. MRSA is an emerging pathogen that started as a problem in the hospital but is now prominent in nonhospital settings as well. ■ What does the acronym MRSA mean and what is its signifcance ■ Why wasn’t penicillin efective in treating the infection For more background on MRSA and endocarditis see chapter 18. To conclude this Case Study go to Connect. Staphylococcus aureus staf′-uh-loh-cok′-us ar-ee-us Gr. staphyle a bunch of grapes kokkus berry and aurum golden. endocarditis en′-doh-car-dye′-tis Gr. endon within kardia heart and itis an inflammation. An inflammation of the lining of the heart and its valves usually caused by infection. 4.1 Basic Characteristics of Cells and Life Forms A. All living things are composed of cells which are complex collections of macromolecules that carry out living processes. All cells must have the minimum structure of an outer cell membrane cytoplasm a chromosome and ribosomes. B. Cells can be divided into two basic types: prokaryotes and eukaryotes. 1. Prokaryotic cells are the basic structural unit of bacteria and archaea. They lack a nucleus or organelles. They are highly successful and adaptable single-cell life forms. 2. Eukaryotic cells contain a membrane-surrounded nucleus and a number of organelles that function in specific ways. A wide variety of organisms from single-celled protozoans to humans are composed of eukaryotic cells. 3. Viruses are not generally considered living or cells and rely on host cells to replicate. C. Cells show the basic essential characteristics of life. Parts of cells and macromolecules do not show these characteristics independently. 1. The primary life indicators are heredity reproduction growth metabolism responsiveness and transport. Chapter Summary with Key Terms taL05218_ch04_089-123.indd 120 11/22/16 8:46 AM

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xiv Truly instructional artwork has always been a hallmark feature of Foundations in Microbiology. Kathy Talaro’s experiences as a teacher microbiologist and illustrator have given her a unique per- spective and the ability to transform abstract concepts into scien- tifically accurate and educational illustrations. Powerful artwork that paints a conceptual picture for students is more important than ever for today’s visual learners. Foundations in Microbiology’s art program combines vivid colors multidimensionality and self- contained narrative to help students study the challenging concepts of microbiology. The Art of a Student Success Learning Tool Author’s experience and talent transforms difcult concepts a Extracellular Transporter protein Extracellular Transport molecule Protein carrier Energy activator ATP ATP ATP-binding site Activated transport molecules Intracellular Section of cell Intracellular Phagocytosis Pinocytosis Oil droplet Liquid enclosed by microvilli Microvilli Pseudopods Vacuoles Vesicle with liquid Solute-binding protein Solute c 1 1 2 2 1 2 3 4 5 Carrier-mediated active transport. 1 Membrane-bound transporter proteins permeases interact with nearby solute binding proteins that carry essential solutes sodium iron sugars. 2 Once a binding protein attaches to a specific site an ATP is activated and generates energy to pump the solute into the cell’s interior through a special channel in the permease. Endocytosis. With phagocytosis solid particles are engulfed by flexible cell extensions or pseudopods 1-4 1000X. 5 With pinocytosis fluids and/or dissoved substances are enclosed in vesicles by very fine protrusions called microvilli 3000X. Oil droplets fuse with the membrane and are released directly into the cell. b In group translocation 1 a specific molecule is actively captured but on its passage through the membrane protein carrier 2 it is chemically altered or activated for use in the cell. By coupling transport with synthesis the cell conserves energy. Process Figure 6.11 General features in the multiplication cycle of an enveloped animal virus. Using an RNA virus rubella virus the major events are outlined although other viruses will vary in exact details of the cycle. New spikes Cell membrane Spikes Receptors New capsomers New RNA Host Cell Cytoplasm 4 5 Synthesis: Replication and Protein Production. Under the control of viral genes the cell synthesizes the basic components of new viruses: RNA molecules capsomers and spikes. 2 Penetration. The virus is engulfed by the cell membrane into a vesicle or endosome and transported internally. 3 Uncoating. Conditions within the endosome cause fusion of the vesicle membrane with the viral envelope followed by release of the viral capsid and RNA into the cytoplasm. Release. Enveloped viruses bud o of the membrane carrying away an envelope with the spikes. This complete virus or virion is ready to infect another cell. Assembly. Viral spike proteins are inserted into the cell membrane for the viral envelope nucleocapsid is formed from RNA and capsomers. Adsorption. The virus attaches to its host cell by specific binding of its spikes to cell receptors. Nucleus 1 1 2 4 3 5 6 6 6.4 Modes of Viral Multiplication 173 taL05218_ch06_160-187.indd 173 17/10/16 3:40 PM Process Figures Many difficult microbiological concepts are best portrayed by breaking them down into stages that students will find easy to follow. These pro- cess figures show each step clearly numbered within a yellow circle and correlated to accompanying narrative to benefit all types of learners. A distinctive process icon precedes the figure number. The accompanying legend provides additional explanation.

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xv The Relevance of a Student Success Learning Tool Real clinical photos help students visualize 18.1 General Characteristics of the Staphylococci 559 associate. The microbe is present in most environments frequented by humans and is readily isolated from fomites. Colonization of some infants begins within hours after birth and continues throughout life. Anywhere from 20 to 60 of healthy adults may carry S. aureus and in these instances the pathogen tends to be harbored intermit- tently rather than chronically. Carriage occurs mostly in the anterior nares nostrils and to a lesser extent in the skin nasopharynx and intestine. Usually this colonization is not associated with symptoms nor does it ordinarily lead to disease in carriers or their contacts. Circumstances that predispose an individual to infection include poor hygiene and nutrition tissue injury preexisting primary infections diabetes mellitus and immunodeficiency states. Staphylococcus au- reus is the third most common cause of infections in the newborn nursery and surgical wards. The “hospital strains” can readily spread in an epidemic pattern within and outside the hospital. A serious concern has arisen from the increase in community infections by strains of S. aureus called MRSA methicillin-resistant S. aureus. Several outbreaks have been reported in prison inmates athletes and schoolchildren. The infections are spread by contact with skin lesions and have proved to be very difficult to treat and control. The Scope of Staphylococcal Disease Depending on the degree of invasion or toxin production by S. aureus disease ranges from localized to systemic. A local staphylococcal in- fection often presents as an inflamed fibrous lesion enclosing a core of pus called an abscess figure 18.3a. Toxigenic disease—disease that is due to the presence of toxins rather than the bacterium itself— can present as a toxemia if the toxins are produced in the body or as food intoxication if S. aureus toxins present in food are ingested. Localized Cutaneous Infections Staphylococcus aureus usually invades the skin through wounds follicles or skin glands. The most common infection is a mild su- perficial inflammation of hair follicles termed folliculitis figure 18.3b or glands hidradenitis. Although these lesions are usually resolved with no complications they can lead to infections of sub- cutaneous tissues. A furuncle boil results when the inflamma- tion of a single hair follicle or sebaceous gland progresses into a digests blood clots a nuclease that digests DNA DNase and li- pases that help bacteria colonize oily skin surfaces. Enzymes that inactivate penicillin penicillinase or other drugs are produced by a majority of strains and many isolates show multiple resistance. The toxic products of this species include blood cell toxins hemolysins and leukocidins intestinal toxins and epithelial tox- ins. Hemolysins lyse red blood cells an effect that can be seen in the laboratory figure 18.2. The most important in terms of bio- logical effect is alpha-toxin α-toxin which lyses red blood cells while also causing damage to leukocytes renal tissue and both skeletal and heart muscle. Other hemolysins are designated by the Greek letters β δ and γ. Note that the Greek letters used to de- scribe the hemolysins do not correspond to the Greek letters de- scribing patterns of hemolysis in chapter 13. For example alpha-toxin produces beta-hemolysis. Other staphylococcal exotoxins include leukocidin which dam- ages cell membranes of neutrophils and macrophages causing them to lyse. This toxin probably helps incapacitate the phagocytic line of defense. Some strains produce exotoxins called enterotoxins that act upon the gastrointestinal tract of humans. A few strains produce an exfoliative toxin that separates the epidermal layer from the dermis and causes the skin to peel away. This toxin is responsible for staphy - lococcal scalded skin syndrome in which the skin looks burned see figure 18.5b. The most recent toxin brought to light is toxic shock syndrome toxin TSST. The presence of this toxin in victims of toxic shock syndrome indicates its probable role in the development of this dangerous condition. The contributions of these toxins and enzymes to disease are discussed in the section on pathology. Epidemiology and Pathogenesis of S. aureus It is surprising that a bacterium with such great potential for viru- lence as Staphylococcus aureus is a common intimate human Infiltrating granulocytes phagocytes Staphylococci Core of pus Subcutaneous tissue a Fibrin Sectional view of a boil or furuncle a single pustule that develops in a hair follicle or gland and is the classic lesion of the species. The inflamed infection site becomes abscessed when masses of phagocytes bacteria and fluid are walled o by fibrin. b Appearance of folliculitis caused by S. aureus. Note the clusters of inflamed papules and pustules. c An abscess on the knee caused by methicillin-resistant Staphylococcus aureus MRSA. Figure 18.3 Cutaneous lesions of Staphylococcus aureus. Fundamentally all are skin abscesses that vary in size depth and degree of tissue involvement. b © DermNet New Zealand Trust c: © Gregory Moran exfoliative eks-foh′-lee-ay″-tiv L. exfoliatio falling off in layers. furuncle fur′-unkl L. furunculus little thief. taL05218_ch18_556-586.indd 559 10/11/16 6:26 PM Clinical Photos Color photos of individuals affected by disease provide students with a real-life clinical view of how microorganisms manifest themselves in the human body. Combination Figures Line drawings combined with photos give students two perspectives: the realism of photos and the explanatory clarity of illustrations. The authors chose this method of presentation often to help students comprehend difficult concepts. a Glycoprotein spikes Matrix protein Nucleocapsid b

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xvi Secret World of Microbes The living world abounds with incredible fascinating microbes that have yet to be discovered or completely understood. This feature en- riches our coverage of the latest research discoveries and applications in the field of microbiology. Almost like reading a mystery novel The Secret World of Microbes reveals little-known and surprising facts about this hidden realm. The Purpose of a Student Success Learning Tool 182 Chapter 6 An Introduction to Viruses Would you be alarmed to be told that your cells carry around bits and pieces of fossil viruses Well we now know that they do. A fascinating aspect of the virus–host rela- tionship is the extent to which viral genetic material becomes affixed to host chromo- somes and is passed on possibly even for millions of years. We know this from data obtained by the Human Genome Project which sequenced all of the genetic codes on the 46 human chromosomes. While searching through the genome sequences virologists began to find DNA they identi- fied as viral in origin. So far they have found about 100000 different fragments of viral DNA. In fact over 8 of the DNA in human chromosomes comes from viruses These researchers are doing the work of molecular fossil hunters locating and identifying these ancient viruses. Many of them are retrovi- ruses that converted their RNA codes to DNA codes inserted the DNA into a site in a host chromosome and then became dormant and did not kill the cell. When this happened in an egg or sperm cell the virus could be transmitted basically unchanged for hundreds of generations. One of the most tantalizing questions is what effect if any such retroviruses might have on modern humans. Some virologists contend that these virus genes would not have been maintained for thousands and even millions of years if they did not serve some function. Others argue that they are just genetic “garbage” that has accumulated over a long human history. So far we have only small glimpses of the possible roles of these viruses. One type of endogenous retrovirus has been shown to be inti- mately involved in forming the human pla- centa leading microbiologists to conclude that some viruses have become an essen- tial factor in evolution and development. Other retroviruses may be involved in dis- eases such as prostate cancer and chronic fatigue syndrome. Evidence is mounting that certain vi- ruses may contribute to human obesity. Several studies with animals revealed that chickens and mice infected with a human adenovirus see figure had larger fat de- posits and were heavier than uninfected animals. Studies in humans show a similar association between infection with the strain of virus—called Ad-36—and an in- crease in adipose fat tissue. Although adenoviruses have usually been involved in respiratory and eye infections they can also infect adipose cells. One of the possible explanations for this association suggests that a chronic infection with the virus allows its DNA to regulate cellular dif- ferentiation of stem cells into adipocytes fat cells. This increase in both the number and the size of fat cells adds adipose tissue more fat produc- tion and storage and more body fat. Simultaneously the adipocytes may also store more sugar helping to keep blood sugar levels under control and maintaining insulin sensitivity to glucose. In general such an association does not prove causation but it certainly warrants additional research. Using information you have learned about viruses explain how vi- ruses could become a permanent component of an organism’s genetic material. Answer available on Connect. 6.1 Secret World of Microbes Seeking Your Inner Viruses Does this virus make us look fat Source: CDC prominent viral infections found only in certain regions of the world dengue fever Rift Valley fever and yellow fever the total could easily exceed several billion cases each year. Although most viral infections do not result in death some such as rabies HIV and Ebola have very high mortality rates and others polio hepatitis can lead to long-term debility. Continuing research is focused on the connection of viruses to chronic afflictions of unknown cause such as type 1 diabetes multiple sclerosis various cancers and even con- ditions such as obesity 6.1 Secret World of Microbes. Because some viral diseases can be life threatening it is essen- tial to have a correct diagnosis as soon as possible. Obtaining the overall clinical picture of the disease specific signs is often the first step in diagnosis. This may be followed by identification of the virus in clinical specimens by means of rapid tests that detect the virus or signs of cytopathic changes in cells or tissues see CMV herpesvi- rus figure 6.15. Immunofluorescence techniques or direct exami- nation with an electron microscope are often used for this see figure 6.8. Samples can also be screened for the presence of indicator molecules antigens from the virus itself. A standard procedure for many viruses is the polymerase chain reaction PCR which can detect and amplify minute amounts of viral nucleic acid in a sample. In certain infections definitive diagnosis requires cultivation of the virus using cell culture embryos or animals but this method can be time-consuming and slow to give results. Screening tests can detect specific antibodies that indicate signs of virus infection in a patient’s blood. This is the main test for HIV infection see figure 17.16. Ad- ditional details of viral diagnosis are provided in chapter 17. The nature of viruses has at times been a major impediment to effective therapy. Because viruses are not bacteria antibiotics aimed at bacterial infections do not work for viruses. Although more antiviral drugs are being developed most of them block virus replication by targeting the function of host cells. This can cause severe side effects. Antiviral drugs are designed to target one of the steps in the viral life cycle you learned about earlier in this chapter. Azidothymidine AZT a drug used to treat AIDS targets the nu- cleic acid synthesis stage. A different class of HIV drugs the prote- ase inhibitors disrupts the final assembly phase of the viral life cycle. Another compound that shows some potential for treating and preventing viral infections is a naturally occurring human cell product called interferon see chapters 12 and 14. Vaccines that stimulate immunity are an extremely valuable tool but are available for only a limited number of viral diseases see chapter 15. taL05218_ch06_160-187.indd 182 17/10/16 3:40 PM Learning Outcomes and Check Your Progress Every numbered section in the book opens with Expected Learning Outcomes and closes with assessment questions Check Your Progress. The Learning Outcomes are tightly correlated to digital material. Instructors can easily measure student learning in relation to the specific learning outcomes used in their course. You can also assign Check Your Progress questions to students through McGraw- Hill Connect. 13.2 Major Factors in the Development of an Infection 407 a mixed population similar to that of prepuberty. These transitions are not abrupt but occur over several months to years. Maintenance of the Normal Microbiota There is no question that the normal residents are essential to the health of humans and other animals. When living in balance with their host the flora create an environment that may prevent infec- tions and can enhance certain host defenses. In general the microbes replace themselves naturally on a regular basis to maintain the types and numbers in their zones. However because the exact content of the microbiota is not fixed a number of changes can disrupt this bal- ance. Use of broad-spectrum antibiotics changes in diet and under- lying disease all have the potential to alter the makeup of the microbiota and tilt the system toward disease. A growing trend in therapy is the use of live cultures of known microbes in the form of probiotics discussed in chapter 12. This essentially involves intro- ducing pure cultures of known microbes into the body through in- gestion or inoculation. The microbes chosen for this process are known to be beneficial and are considered nonpathogenic. For a look into laboratory studies that address the effects of microbiota see 13.1 Making Connections. anterior urethra in males figure 13.6. The internal reproductive organs are kept sterile through physical barriers such as the cervical plug and other host defenses. The kidney ureter bladder and upper urethra are presumably kept sterile by urine flow and regular blad- der emptying. The shortness of the urethra in women about 3.5 cm long frequently leads to urinary tract infections. The principal residents of the urethra are nonhemolytic streptococci staphylo- cocci corynebacteria and occasionally coliforms. The vagina presents a notable example of how changes in physiology can greatly influence the composition of the normal microbiota. An important factor influencing these changes in women is the hormone estrogen. Estrogen normally stimulates the vaginal mucosa to secrete glycogen which certain bacteria pri- marily Lactobacillus species ferment thus lowering the pH to about 4.5. Before puberty a girl produces little estrogen and little glycogen and has a vaginal pH of about 7. These conditions favor the establishment of diphtheroids 3 staphylococci streptococci and some coliforms. As hormone levels rise at puberty the vagina be- gins to deposit glycogen and the microbiota shift to the acid- producing lactobacilli. It is thought that the acidic pH of the vagina during this time prevents the establishment and invasion of mi- crobes with potential to harm a developing fetus. The estrogen- glycogen effect continues with minor disruption throughout the childbearing years until menopause when the microbiota return to Uterus Rectum Vagina Anus Rectum Figure 13.6 Microbiota of the reproductive tract. a Female and b male genitourinary residents location indicated by color. Check Your Progress SECTION 13.1 1. Describe the significant relationships that humans have with microbes. 2. Explain what is meant by microbiota and microbiome and sum- marize their importance to humans. 3. Differentiate between contamination colonization infection and disease and explain some possible outcomes in each. 4. How are infectious diseases different from other diseases 5. Outline the general body areas that are sterile and those regions that harbor normal resident microbiota. 6. Differentiate between transient and resident microbes. 7. Explain the factors that cause variations in the microbiota of the newborn intestine and the vaginal tract. 13.2 Major Factors in the Development of an Infection Expected Learning Outcomes 7. Review the main stages in the development of an infection. 8. Categorize the diferent types and degrees of pathogens and diferentiate pathogenicity from virulence. 9. Describe the diferences among the portals of entry and give examples of pathogens that invade by these means. 10. Explain what is meant by the infectious dose using examples. 11. Describe the process of adhesion and various mechanisms by which microbes use it to gain entry. 12. Identify and discuss invasive factors and virulence factors. 13. Compare and contrast the major characteristics of exotoxins and endotoxins. 3. Any nonpathogenic species of Corynebacterium. taL05218_ch13_397-436.indd 407 12/11/16 10:54 AM 6.1 Overview of Viruses 161 SCOPING OUT THE CHAPTER Smaller and simpler than even the most modest prokaryotic cell viruses are responsible for some of the most virulent diseases on Earth Ebola fever as well as some of the most mundane the common cold. In this chapter we survey viruses—so small they cannot be seen without an elec- tron microscope so simple that most scientists don’t consider them to be alive and yet each of us has been infected by them many many times. Composed only of an inner molecule of genetic material surrounded by a protein coat and occasionally an outer envelope viruses are far simpler than cells. Unlike bacterial cells the growth of viruses in the lab requires that a living host be used as the “growth medium.” Cell culture live animals and eggs are all commonly used to cultivate viruses. Even simpler than viruses prions consist exclusively of protein. They cause a number of transmissible spongiform encepahalopathies named for the spongy appearance of brain cells infected with the pathogen. Proteins anchored in the viral envelope guide the attachment of the virus to its host cell. The virus enters the host and redirects the metabolism of the host cell toward the production of hundreds of additional viral particles. After replication the newly created viruses exit the cell and commence the search for a new host. top: right: Source: National Institute of Allergy and Infectious Diseases NIAID/CDC bottom: left: © State Hygenic Laboratory at The University of Iowa bottom: right: Source: Sherif Zaki MD PhD Wun-Ju Shieh MD PhD MPH/CDC 6.1 Overview of Viruses Expected Learning Outcomes 1. Indicate how viruses were discovered and characterized. 2. Describe the unique characteristics of viruses. 3. Discuss the origin and importance of viruses. Early Searches for the Tiniest Microbes The discovery of the light microscope made it possible to see first- hand the agents of many bacterial fungal and protozoan diseases. But the techniques for observing and cultivating these relatively large microorganisms were useless for viruses. For many years the cause of viral infections such as smallpox and polio was unknown even though it was clear that the diseases were transmitted from person to person. The French bacteriologist Louis Pasteur was taL05218_ch06_160-187.indd 161 17/10/16 3:40 PM Pathogen Profles Pathogen Profiles are abbreviated snapshots of the major pathogens in each disease chapter. The pathogen is featured in a micrograph along with a description of the microscopic morphology identification descriptions habitat information and virulence factors. Artwork displays the primary infections/disease as well as the organs and systems primarily impacted. 570 Chapter 18 The Gram-Positive and Gram-Negative Cocci of Medical Importance This bacterial pathogen is the most prevalent cause of neonatal pneumonia sepsis and meningitis in the United States and Europe. Approximately 2200 babies a year acquire infection in the United States alone. A later complication arises in 2 to 6 weeks with symptoms of meningitis—fever vomiting and seizures. About 20 of children have long-term neurological damage. Because most cases occur in the hospital personnel must be aware of the risk of passively transmitting this pathogen especially in the neo- natal and surgical units. Pregnant women should be screened for colonization in the third trimester and immunized with globulin and treated with a course of antibiotics if infection is found. Group D Enterococci and Groups C and G Streptococci Enterococcus faecalis E. faecium and E. durans are collectively re- ferred to as “enterococci” because they are normal colonists of the hu - man large intestine. Two other members of group D Streptococcus bovis and S. equinus are nonenterococci that colonize other animals and oc - casionally humans. Infections caused by E. faecalis arise most often in elderly patients undergoing surgery and affect the urinary tract wounds blood the endocardium the appendix and other intestinal structures. Enterococci are emerging as serious opportunists in the health care set - ting primarily because of the rising incidence of multidrug-resistant strains especially vancomycin-resistant enterococci VRE. Groups C and G are common microbiota of domestic animals but are frequently isolated from the human upper respiratory tract. The possibility of one of these serious or long-term complications is the reason that severe sore throats should be taken seriously. A simple throat swab can distinguish between group A streptococci and other causes so that antibiotics if called for can be administered immediately. Group B: Streptococcus agalactiae Several other species of beta-hemolytic Streptococcus in groups B C and D live among the normal microbiota of humans and other mam - mals and can be isolated in clinical specimens from diseased human tissue. The group B streptococci GBS represented by the species S. agalactiae demonstrate clearly how the distribution of a pathogen can change in a relatively short time. The species has been associated with cattle in which it is a frequent cause of bovine mastitis. 4 It has also become a resident in the human vagina pharynx and large intestine. Since its colonization of humans there has been a dramatic increase in serious infections in newborns and compromised people. The CDC estimates there are approximately 20000 cases per year. Streptococcus agalactiae is primarily implicated in neonatal meningitis wound and skin infections and endocarditis. Elderly peo- ple suffering from diabetes and vascular disease are particularly sus- ceptible to wound infections. Because of its location in the vagina GBS can be transferred to the infant during delivery sometimes with dire consequences. An early-onset infection develops a few days after birth and is accompanied by sepsis pneumonia and high mortality. Microscopic Morphology Gram-positive cocci arranged in chains and pairs very rarely motile non-spore-forming. Identifed by Results of a catalase test are used to distinguish Streptococcus negative from Staphylococcus positive. Beta-hemolysis and sensitivity to bacitracin are hallmarks of S. pyogenes. Rapid methods of identifcation use monoclonal antibodies to detect the C-carbohydrate found on the cell surface of S. pyogenes. Such tests provide accurate identifcation in as little as 10 minutes. Habitat A fairly strict parasite S. pyogenes is found in the throat nasopharynx and oc- casionally the skin of humans. From 5 to 15 of persons are asymptomatic carriers. Virulence Factors S. pyogenes possesses several cell surface antigens that serve as virulence factors. C-carbohydrate helps prevent the bacterium from being dissolved by the lysozyme of the host fmbriae on the outer sur - face of the cell enhance adherence of the bacterium M-protein helps the cell resist phagocytosis while also improving adherence and C5a protease catalyzes the cleavage of the C5a protein of the comple - ment system inhibiting the actions of complement. Most strains of S. pyogenes are covered with a capsule composed of hyaluronic acid HA identical to the HA found in host cells preventing an immune response by the host. Two diferent he- molysins streptolysin O SLO and streptolysin S SLS cause damage to leukocytes and liver and heart muscle whereas erythrogenic toxin produces fever and the bright red rash characteristic of S. pyogenes disease. Invasion of the body is aided by several en- zymes that digest fbrin clots streptokinase connec- tive tissue hyaluronidase or DNA streptodornase. Primary Infections/Disease Local cutaneous infections include pyoderma impetigo or the more invasive erysipelas. Infection of the tonsils or pharyngeal mucous membranes can lead to streptococcal pharyngitis strep throat which if left untreated may lead to scarlet fever. Rarer infections include streptococcal toxic shock syndrome S. pyo- genes pneumonia and necrotizing fasciitis. Long- term complications of S. pyogenes infections include rheumatic fever and acute glomerulonephritis. Control and Treatment Control of S. pyogenes in- fection involves limiting contact between carriers of the bacterium and immunocompromised potential hosts. Patients should be isolated and care must be taken when handling infectious secretions. As the bacterium shows little drug resistance treatment is generally a simple course of penicillin. Pathogen Profle 2 Streptococcus pyogenes Modifed image reprinted with permission from Medscape Reference http://emedicine. medscape.com/ 2013 available at: http://emedicine. medscape.com/ article/228936- overview. 4. Inflammation of the mammary glands. taL05218_ch18_556-586.indd 570 10/11/16 6:26 PM 596 Chapter 19 The Gram-Positive Bacilli of Medical Importance Botulism is an intoxication usually associated with eating improperly canned or poorly preserved foods though it can occur as a result of infection. Until recent times it was relatively prevalent and commonly fatal but modern techniques of food preservation and medical treatment have reduced both its incidence and its fatal- ity rate. However botulism is a common cause of death in livestock that have grazed on contaminated food and in aquatic birds that have eaten decayed vegetation. There is a high correlation between cultural dietary prefer- ences and food-borne botulism. In the United States the disease is often associated with low-acid vegetables green beans corn and occasionally meats fish and dairy products. Most botulism out- breaks occur in home-processed foods including canned vegeta- bles smoked meats and cheese spreads. The demand for prepackaged convenience foods such as vacuum-packed cooked vegetables and meats has created a new risk but commercially canned foods are only rarely a source of botulism. One of the most recent outbreaks of botulism traced to a commer - cial source occurred in 2007 among people who had consumed canned chili sauce. The cans were traced to a food plant that apparently had defects in its sterilization procedures. Due to the potential for additional cases 90 other food products processed by that plant were recalled and millions of cans removed from stores. Most foods contained peppers potatoes or meats. This outbreak was one of the first incidents of com - mercial botulism in more than a decade and it emphasized the reality that preventing botulism must always remain a priority for canneries. The constant presence of C. botulinum spores in the soil and on pro - duce means that there is zero tolerance for errors in quality control. Pathogenesis of Botulism The factors in food processing that lead to botulism depend upon several circumstances. Spores are present on the vegetables or meat at the time of gathering and are difficult to remove by washing alone. When contaminated food is bottled and steamed in a pressure cooker that does not reach reliable pressure and temperature some spores survive botulinum spores are highly heat-resistant. At the same time the pressure is sufficient Mild uncomplicated cases respond to withdrawal of antibiotics and replacement therapy for lost fluids and electrolytes. More severe infections are treated with oral vancomycin or metronidazole and re - placement cultures to restore normal microbiota. Fecal microbiota transplantation a procedure in which feces from a healthy donor are transferred via enema swallowed capsules or colonoscopy directly to the colon of patients suffering C. difficile infection has gained prominence—though not FDA approval—in recent years. Anecdotal evidence suggests that the technique produces a rapid cure in 80 to 90 of patients as the transplanted microbiota quickly establishes it - self throughout the colon. Because of the potential risks and ethical questions involved in purposefully inoculating a patient with another person’s microbiota federal agencies have been hesitant to oversee the process. In 2016 the FDA began to increase oversight of fecal micro - biota transplants tightening the regulations governing the procedure.  In the clinical setting stringent precautions are necessary to pre- vent the spread of the agent from infected persons who shed large numbers of spores in their feces to other patients who may be on antimicrobic therapy. Immediate diagnosis is obtained by a rapid ELISA that detects toxins in fecal samples. Work is progressing on a vaccine containing C. difficile toxoid for use in high-risk populations. Clostridial Food Poisoning Two Clostridium species are involved in food poisoning. Clostrid- ium botulinum produces a severe intoxication usually from home- canned food. Clostridium perfringens type A accounts for a mild intestinal illness that is one of the most common forms of food poisoning worldwide. Epidemiology of Botulinum Food Poisoning Clostridium bot- ulinum is a spore-forming anaerobe that commonly inhabits soil and water and occasionally the intestinal tract of animals. It is distributed worldwide but occurs most often in the Northern Hemi- sphere. The species has eight distinctly different types designated A B C α and C β D E F and G which vary in distribution among animals regions of the world and type of exotoxin produced. Human disease is usually associated with types A B E and F and animal disease with types A B C D and E. Microscopic Morphology Gram-positive bacilli present singly or in short chains. Endospores are subterminal and distend the cell altering its shape. Identifed by Gram reaction and endospore formation. Clostridium is diferentiated from Bacillus as the former is typically a strict anaer- obe and the latter is not. ELISA is often used to detect toxins of C. difcile in fecal samples. Habitat Found in small numbers as part of the normal microbiota of the intestine. Virulence Factors Enterotoxins that cause epithelial necrosis of the colon. Primary Infections/Disease Clostridium difcile infection CDI refers to disease caused by the overgrowth of C. difcile. Symptoms may range from diarrhea to infammation of the colon cecal perforation and rarely death. Although C. difcile is ordinarily present in low numbers treatment with broad-spectrum antibiotics may disrupt the normal microbiota of the colon leading to a C. difcile superinfection. Control and Treatment Mild cases generally re- spond to withdrawal of the antibiotic. Severe cases are treated with oral vancomycin or metronidazole along with probiotics or fecal microbiota trans- plants to restore the normal microbiota. Pathogen Profle 3 Clostridium difcile Source: CDC botulism boch′s-oo-lizm L. botulis sausage. The disease was originally linked to spoiled sausage. taL05218_ch19_587-617.indd 596 12/11/16 1:52 PM

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xvii The Framework of a Student Success Learning Tool Pedagogy created to promote active learning 146 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms An Outbreak of Fungal Meningitis Most fungi are not invasive and do not ordinarily cause serious infec- tions unless a patient’s immune system is compromised or the fun- gus is accidentally introduced into sterile tissues. In 2012 we witnessed how a simple medical procedure could turn into a medical nightmare because a common mostly harmless fungus got into the wrong place at the wrong time. It all started when a small compound- ing pharmacy in Massachusetts unknowingly sent out hundreds of mold-contaminated vials of medication to medical facilities for injec- tions to control pain. These vials were sent to 23 states and used to inject the drug into the spinal columns or joints of around 14000 patients. By the time any problems were reported several hundred cases of infection had occurred half of which settled in the menin- ges. The most drastic outcome was the deaths of 39 patients from complications of meningitis. After months of investigation the CDC isolated a black mold Exserohilum rostratum from both the patients and the drug vials. This mold resides in plants and soil from which it spreads into the air and many human habitats. But it is not considered a human patho - gen and infections with it are very rare. Examination of the compound- ing facility uncovered negligence and poor quality controls along with dirty preparation rooms. Mold spores were introduced during flling of the vials and because the medication lacked preservatives they sur- vived and grew. The owner of the compounding pharmacy and the head pharmacist were each charged with 25 counts of second-degree murder their trial is expected to start in late 2016. This case drives home several important facts about fungi: 1 They can grow rapidly even in low nutrient environments 2 just a single spore introduced into a sterile environment whether it is a vial of medicine or the human body can easily multiply into millions of fungal cells and 3 even supposedly “harmless” fungi are often op- portunistic meaning that they will infect tissues “if given an opportu- nity.” This case also emphasizes the need for zero tolerance for microbes of any kind in a drug that is being injected—such a proce- dure demands sterility. When you think of it the patients were actu- ally being inoculated in a way that assured the development of serious mycoses. Explain how a supposedly harmless airborne mold could get all the way into the brain and cause meningitis. Answer available on Connect. CLINICAL CONNECTIONS Check Your Progress SECTIONS 5.4 AND 5.5 15. Review the major differences and similarities between prokaryotic and eukaryotic cells. 16. Compare the structures of yeast and hyphal cells and differentiate between yeasts and molds. 17. Tell how fungi obtain nutrients and in what habitats one would expect to find them. 5.6 Survey of Protists: Algae Expected Learning Outcomes 27. Discuss the major characteristics of algae and explain how they are classifed. 28. Describe several ways that algae are important microorganisms. Even though the terms algae and protozoa do not have taxonomic status they are still scientifically useful. These are terms like protist that provide a shorthand label for certain eukaryotes. Mi- crobiologists use such general terms to reference organisms that possess a collection of predictable characteristics. For example protozoa are considered unicellular eukaryotic protists that lack tissues and share similarities in cell structure nutrition life cy- cles and biochemistry. They are all microorganisms and most of them are motile. Algae are eukaryotic protists usually unicellular or colonial that photosynthesize with chlorophyll a. They lack vascular systems for transport and have simple reproductive structures. The Algae: Photosynthetic Protists The algae are a group of photosynthetic organisms most readily recognized by their larger members such as seaweeds and kelps. In addition to being beautifully colored and diverse in appearance they vary in length from a few micrometers to 100 meters. Algae occur in unicellular colonial and filamentous forms and the larger forms can possess tissues and sim- ple organs. Examples of algal forms are shown in figure 5.23 and table 5.7. An algal cell exhibits most of the organelles figure  5.23a. The most noticeable of these are the chloroplasts which contain in addition to the green pigment chlorophyll a number of other pig- ments that create the yellow red and brown coloration of some groups. Algae are widespread inhabitants of fresh and marine waters. They are one of the main components of the large floating com- munity of microscopic organisms called plankton. In this capacity Quick Search Find the video “Brink: Algae to Oil” on the Science Channel to learn about a new source of “green” products. 18. Describe the two main types of asexual fungal spores and how they are formed. Name several types of conidia. 19. Describe the three main types of sexual spores and construct a simple diagram to show how each is formed. 20. Explain general features of fungal classification give exam - ples  of the four fungal phyla and describe their structure and significance. 21. Define the term mycosis and explain the levels of invasion of the body by fungi. taL05218_ch05_124-159.indd 146 17/10/16 2:49 PM 4.6 Classifcation Systems of Prokaryotic Domains: Archaea and Bacteria 113 TABLE 4.3 continued Volume 3 Phylum Firmicutes This collection of mostly gram-positive bacteria is characterized by having a low G + C content less than 50. The three classes in the phylum display significant diversity and a number of the members are pathogenic. Endospore-forming genera include Bacillus and Clostridium. Other important pathogens are found in genera Staphylococcus and Streptococcus. Although they lack a cell wall entirely mycoplasmas see figure 4.17 have been placed with the Firmicutes because of their genetic relatedness. See figures H and I. K. Mycobacterium tuberculosis—the bacillus that causes tuberculosis. Source: Janice Carr/CDC L. View of an infected host cell revealing a vacuole containing Chlamydia cells in various stages of development. Source: N. Borel et al. “Mixed infections with Chlamydia and porcine epidemic diarrhea virus - a new in vitro model of chlamydial persistence” BMC Microbiology 2010 10:201 Fig. 3a Volume 4 Phylum Actinobacteria This taxonomic category includes the high G + C over 50 gram- positive bacteria. Members of this small group differ considerably in life cycles and morphology. Prominent members include the branching filamentous Actinomycetes the spore-bearing Streptomycetes Corynebacterium see figure 4.24 Mycobacterium and Micrococcus see figure 4.23a. See figures J and K. Volume 5 This represents a mixed assemblage of nine phyla all of which are gram-negative but otherwise widely varied. The following is a selected array of examples. Phylum Chlamydiae Another group of obligate intracellular parasites that reproduce inside host cells. These are among the smallest of bacteria with a unique mode of reproduction. Several species cause diseases of the eyes reproductive tract and lungs. An example is Chlamydia figure L. Phylum Spirochetes These bacteria are distinguished by their shape and mode of locomotion. They move their slender twisted cells by means of periplasmic flagella. Members live in a variety of habitats including the bodies of animals and protozoans fresh and marine water and even muddy swamps. Important genera are Treponema figure M and Borrelia see figure 4.23e. Phylum Planctomycetes This group lives in fresh and marine water habitats and reproduces by budding. Many have a stalk that they use to attach to substrates. A unique feature is having a membrane around their DNA and special compartments enclosed in membranes. This has led to the speculation that they are similar to an ancestral form that gave rise to eukaryotes. An example is Gemmata figure N. Phylum Bacteriodetes These are widely distributed gram-negative anaerobic rods inhabiting soil sediments and water habitats and frequently found as normal residents of the intestinal tracts of animals. They may be grouped with related Phyla Fibrobacteres and Chlorobi. Several members play an important role in the function of the human gut and some are involved in oral and intestinal infections. An example is Bacteroides figure O. H. Bacillus anthracis—SEM micrograph showing the rod-shaped cells next to a red blood cell. Source: Arthur Friedlander I. Streptococcus pneumoniae—image displays the diplococcus arrangement of this species. Source: Janice Carr/CDC I J. Streptomyces species—common soil bacteria often the source of antibiotics. Source: Dr. David Berd/CDC K M. Treponema pallidum— spirochetes that cause syphilis. Source: Joyce Ayers/CDC N. Gemmata—view of a budding cell through a fuorescent microscope note the large blue nucleoid. Source: K-C Lee R Webb JA Fuerst “The cell cycle of the planctomycete Gemmata obscuriglobus with respect to cell compartmentalization” BMC Cell Biol. 2009 10:4 Fig 3i. NCBI O. Bacteroides species—may cause intestinal infections. Source: V.R. Dowell/CDC G + C base composition The overall percentage of guanine and cytosine in DNA is a general indicator of relatedness because it is a trait that does not change rapidly. Bacteria with a significant difference in G + C percentage are less likely to be genetically related. This classification scheme is partly based on this percentage. taL05218_ch04_089-123.indd 113 10/7/16 11:56 AM Quick Search This feature reminds students that videos animation and pictorial displays that provide further information on the topic are just a “click” away using their smart-phone tablet or computer. This integration of learning via technology helps students become more engaged and empowered in their study of the featured topic. 128 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms forward like a fishtail or by pulling it by a lashing or twirling mo- tion figure 5.4c. The placement and number of flagella can be useful in identifying flagellated protozoa and certain algae. Cilia are very similar in overall architecture to flagella but they are shorter and more numerous some cells have several thousand. They are found only in certain protozoa and animal cells. In the ciliated protozoa the cilia occur in rows over the cell surface where they beat back and forth in regular oarlike strokes figure 5.5 and provide rapid motility. The fastest ciliated proto- zoan can swim up to 2500 μm/s—a meter and a half per minute On some cells cilia also function as feeding and filtering structures. Although they share the same name the flagella of eukary- otes are much different from those of prokaryotes. The eukaryotic flagellum is thicker by a factor of 10 has a much different con- struction and is covered by an extension of the cell membrane. A flagellum is a long sheathed cylinder containing regularly spaced hollow tubules—microtubules—that extend along its entire length figure 5.4b. A cross section reveals nine pairs of closely attached microtubules surrounding a single central pair. This scheme called the 9 + 2 arrangement is a typical pattern of flagella and cilia figure 5.4a. The nine pairs are linked together and anchored to the pair in the center. This architecture permits the microtubules to “walk” by sliding past each other whipping the flagellum back and forth. Although details of this process are too complex to discuss here it involves expenditure of energy and a coordinating mecha- nism in the cell membrane. Flagella can move the cell by pushing it Nuclear envelope with pores Nucleolus Nucleus Centrioles Microvilli Glycocalyx Rough endoplasmic reticulum Mitochondrion Cell wall Cell membrane Golgi apparatus Microtubules Chloroplast Structure not present in all cell types Smooth endoplasmic reticulum Lysosome Microfilaments Flagellum or cilium Figure 5.3 Overview of composite eukaryotic cell. This drawing represents all structures associated with eukaryotic cells but no microbial cell possesses all of them. See fgures 5.16 5.23 and 5.25 for examples of individual cell types. Quick Search Find videos using the search words amoebic fagellate and ciliate movement on YouTube. taL05218_ch05_124-159.indd 128 17/10/16 2:48 PM 38 Chapter 2 The Chemistry of Biology these same electrons. Keep in mind that because electrons are being added during reduction the atom that receives them will become more nega- tive and that is the meaning of reduction in this context. It does not imply that an atom is getting smaller. In fact reduction often results in a greater complexity of the molecule. To analyze the phenomenon let us again re - view the production of NaCl but from a different standpoint. When these two atoms called the redox pair react to form sodium chloride a sodium atom gives up an electron to a chlorine atom. During this reaction sodium is oxidized because it loses an electron and chlorine is reduced because it gains an electron figure 2.9. With this system an atom such as sodium that can donate electrons and thereby reduce another atom is a reducing agent. An atom that can receive extra electrons and thereby oxidize another molecule is an oxidizing agent. You may find this concept easier to keep straight if you think of redox agents as partners: The reducing partner gives its electrons away and is oxidized the oxi - dizing partner receives the electrons and is reduced. 5 Redox reactions are essential to many of the biochemical pro- cesses discussed in chapter 8. In cellular metabolism electrons are frequently transferred from one molecule to another as described here. In other reactions oxidation and reduction occur with the transfer of a hydrogen atom a proton and an electron from one compound to another. Formulas Models and Equations The atomic content of molecules can be represented by a few con- venient formulas. We have already been using the molecular for- mula which concisely gives the atomic symbols and the number of the atoms involved in subscripts CO 2 H 2 O. More complex mol- ecules such as glucose C 6 H 12 O 6 can also be symbolized this way but this formula is not unique because fructose and galactose also share it. Molecular formulas are useful but they only summarize the atoms in a compound they do not show the position of bonds between atoms. For this purpose chemists use structural formulas illustrating the relationships of the atoms and the number and types of bonds figure 2.10. Other structural models present the three-dimensional appearance of a molecule illustrating the orien- tation of atoms differentiated by color codes and the molecule’s overall shape figure 2.11. Many complex molecules such as pro- teins are now represented by computer-generated images see figure 2.23 step 4. Molecules including those in cells are constantly involved in chemical reactions leading to changes in the composition of the matter they contain. These changes generally involve the breaking and making of bonds and the rearrangement of atoms. The chemi- cal substances that start a reaction and that are changed by the reac- tion are called the reactants. The substances that result from the reaction are called the products. Keep in mind that all of the matter in any reaction is retained in some form and the same types and numbers of atoms going into the reaction will be present in the products. Chemists and biologists use shorthand to summarize the content of a reaction by means of a chemical equation. In an equa- tion the reactants are on the left of an arrow and the products are on the right. The number of atoms of each element must be bal- anced on either side of the arrow. Note that the numbers of reac- tants and products are indicated by a coefficient in front of the formula no coefficient means 1. We have already reviewed the reaction with sodium and chloride which would be shown with this equation: 2Na + Cl 2 → 2NaCl Most equations do not give the details or even exact order of the reaction but are meant to keep the expression a simple overview of the process being shown. Some of the common reactions in organ- isms are syntheses decompositions and exchanges. Na Reducing agent can donate an electron. Oxidizing agent can accept an electron. Oxidized cation donated an electron and converted to a positively charged ion. Reduced anion accepted the electron and converted to a negatively charged ion. 2 8 1 Na 2 8 Cl 2 8 7 Cl 2 8 8 + − Figure 2.9 Simplifed diagram of the exchange of electrons during an oxidation-reduction reaction. Numbers indicate the total electrons in that shell. 5. A mnemonic device to keep track of this is LEO says GER: Lose Electrons Oxidized Gain Electrons Reduced. Check Your Progress SECTION 2.2 7. Explain how the concepts of molecules and compounds are related. 8. Distinguish between the general reactions in covalent ionic and hydrogen bonds. 9. Which kinds of elements tend to make covalent bonds 10. Distinguish between a single and a double bond. 11. Define polarity and explain what causes it. 12. Which kinds of elements tend to make ionic bonds 13. Differentiate between an anion and a cation using examples. 14. Differentiate between oxidation and reduction and between an oxidizing agent and a reducing agent using examples. 2.3 Chemical Reactions Solutions and pH Expected Learning Outcomes 12. Classify diferent forms of chemical shorthand and types of reactions. 13. Explain solutes solvents and hydration. 14. Diferentiate between hydrophilic and hydrophobic. 15. Describe the pH scale and how it was derived defne acid base and neutral levels. taL05218_ch02_029-059.indd 38 10/7/16 2:35 PM Footnotes Footnotes provide the reader with additional information about the text content. Tables This edition contains numerous illustrated tables. Horizontal contrasting lines set off each entry making them easy to read. 128 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms forward like a fishtail or by pulling it by a lashing or twirling mo- tion figure 5.4c. The placement and number of flagella can be useful in identifying flagellated protozoa and certain algae. Cilia are very similar in overall architecture to flagella but they are shorter and more numerous some cells have several thousand. They are found only in certain protozoa and animal cells. In the ciliated protozoa the cilia occur in rows over the cell surface where they beat back and forth in regular oarlike strokes figure 5.5 and provide rapid motility. The fastest ciliated proto- zoan can swim up to 2500 μm/s—a meter and a half per minute On some cells cilia also function as feeding and filtering structures. Although they share the same name the flagella of eukary- otes are much different from those of prokaryotes. The eukaryotic flagellum is thicker by a factor of 10 has a much different con- struction and is covered by an extension of the cell membrane. A flagellum is a long sheathed cylinder containing regularly spaced hollow tubules—microtubules—that extend along its entire length figure 5.4b. A cross section reveals nine pairs of closely attached microtubules surrounding a single central pair. This scheme called the 9 + 2 arrangement is a typical pattern of flagella and cilia figure 5.4a. The nine pairs are linked together and anchored to the pair in the center. This architecture permits the microtubules to “walk” by sliding past each other whipping the flagellum back and forth. Although details of this process are too complex to discuss here it involves expenditure of energy and a coordinating mecha- nism in the cell membrane. Flagella can move the cell by pushing it Nuclear envelope with pores Nucleolus Nucleus Centrioles Microvilli Glycocalyx Rough endoplasmic reticulum Mitochondrion Cell wall Cell membrane Golgi apparatus Microtubules Chloroplast Structure not present in all cell types Smooth endoplasmic reticulum Lysosome Microfilaments Flagellum or cilium Figure 5.3 Overview of composite eukaryotic cell. This drawing represents all structures associated with eukaryotic cells but no microbial cell possesses all of them. See fgures 5.16 5.23 and 5.25 for examples of individual cell types. Quick Search Find videos using the search words amoebic fagellate and ciliate movement on YouTube. taL05218_ch05_124-159.indd 128 17/10/16 2:48 PM

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xviii This new feature follows the opening case study in Chapters 1-17 and 26-27. Students are provided with a descriptive pictorial guide for the main topics covered within these respective chapters. Scoping Out The Chapter Scoping Out the Chapter 361 Modern antimicrobial drugs have revolutionized medical treatment. Literally billions of lives have been saved since they were frst introduced 80 years ago. Having an efective drug to treat most infectious diseases is now expected whether bacterial viral fungal protozoan or helminth. Though we may take this availability for granted there are numerous factors that complicate their use. In this chapter we will explore “the good the bad and the ugly” elements of antimicrobial drug therapy. Drug Discovery Antimicrobial drugs come from many sources. Most of them called antibiotics are produced by certain bacteria or fungi others are synthesized through chemical reactions alone and some are made by combining the two methods. How Antimicrobial Drugs Stop Infections Drugs are chemicals that can interfere with some specific microbial structure or function such as the cell wall cell membrane proteins DNA RNA ribosomes or metabolic pathways. While in contact with the drug the microbes are either destroyed or severely inhibited and can no longer grow. Toxicity and Other Side Eects The promise of antimicrobial therapy is spoiled by the numerous possibilities of adverse side eects. Drugs can harm body tissues and organs disrupt the normal microbiota that help keep a balance in the bodys organs and induce allergies and hypersensitivities. Choosing an Appropriate Drug Selection of an eective drug is guided by several factors. Among the most important considerations are the nature of the infectious agent knowing which drugs it is sensitive to the possible side eects of the drug and the medical condition of the patient. The Global Race Against Drug Resistance Microbes are very adept at rapidly altering their physiology and genetics to adapt to drugs making them less eective. They may develop enzyme systems that dismantle the drugs block the drugs entrance expel the drugs or use an alternate pathway that bypasses the drug’s eects. Do No Harm: Selective Toxicity Antibiotic literally means “against life” but the actual intention of these drugs is to target only microbial life. This is a very important guiding principle—that drugs do not harm humans while they are getting rid of the infectious agent. Host Microbe Drug 1. Cell wall inhibitors Block synthesis and repair Penicillins Cephalosporins Vancomycin Bacitracin Monobactams/carbapenems Fosfomycin Cycloserine Isoniazid 2. Cell membrane Cause loss of selective permeability Polymyxins 3. DNA/RNA DNA mRNA Inhibit replication and transcription Inhibit gyrase unwinding enzyme Quinolones ciprofloxacin Inhibit RNA polymerase Rifampin 4. Protein synthesis inhibitors acting on ribosomes Site of action 50S subunit Chloramphenicol Erythromycin Clindamycin Streptogramin Synercid Site of action 30S subunit Aminoglycosides Gentamicin Streptomycin Tetracyclines Both 30S and 50S Blocks initiation of protein synthesis Linezolid Zyvox 5. Metabolic pathways and products Substrate Ribosome Product Block pathways and inhibit metabolism Sulfonamides sulfa drugs Trimethoprim Enzyme a b c Circulat- ing drug Intestine Intestine Intestine Superinfection Drug Infection Pathogen overgrows Drug destroys beneficial flora Potential pathogen resistant to drug but held in check by other microbes Normal flora important to maintain intestinal balance Transformation Transduction Conjugation Transfer of free DNA Transfer by viral delivery Plasmid transfer Bacterium receiving resistance genes Resistance gene Virus Resistance gene Plasmid Dead bacterium Transformation Transduction Conjugation Plasmid donor DNA fragment Transfer of free DNA Transfer by viral delivery Plasmid transfer Bacterium receiving resistance genes Gene goes to plasmid or to chromosome Drug Discovery © Kathy Park Talaro Choosing an Appropriate Drug © Copyright AB BIODISK 2008. Re-printed with permission of AB BIODISK SCOPING OUT THE CHAPTER taL05218_ch12_360-396.indd 361 05/11/16 1:06 AM 90 Chapter 4 A Survey of Prokaryotic Cells and Microorganisms SCOPING OUT THE CHAPTER We don’t need to take a course in ornithology to be able to recognize the structure of a bird’s wing and describe how it functions. And even when they’re too far away for us to see them clearly we can instantly know that a group of animals fying in a “V” formation is a fock of birds not butter- fies or bats. And though they are about as diferent as two animals could be we all understand intuitively that a hummingbird and a turkey are related and should be grouped together. In this chapter we will gain the same type of familiarity with bacterial cells by studying their structure function and evolutionary history. left: top: Source: Louisa Howard/Dartmouth Electron Microscope Facility left: bottom: © Kwangshin Kim/Science Source middle: top-left: Source: Janice Carr/CDC middle: top-right: Source: Joyce Ayers/CDC middle: bottom: Source: Jef Hageman M.H.S./Janice Carr/CDC right: top-left: Source: Maryland Astrobiology Consortium NASA and STScI right: top-right: Source: NASA Johnson Space Center/ISS007E8738/ http://eol.jsc.nasa.gov right: bottom: © Heide N. Schulz/Max Planck Institue for Marine Microbiology Cellular Structure The chapter opens with a discussion of what makes up a prokaryotic cell. Beginning with external structures like flagella moving to the fluid- mosaic barrier of the cell membrane and finally to internal structures like inclusion bodies. Understanding the anatomy of a cell is key to understanding its biology. Bacterial Shapes and Arrangements The cell wall and cytoskeleton of a bacterial cell are responsible for its shape and correctly recognizing the shape of a cell is one of the first steps in determining its identity. The grouping of individual cells into more complex arrangements reveals a great deal about the manner in which a cell multiplies. Classification and Unusual Bacteria The chapter continues by explaining the ways in which prokaryotic cells may be organized based on their evolutionary relationships. Finally we introduce several examples of novel bacteria that thrive in boiling water top left extraordinarily high concentrations of salt top right or are so big that they threaten to redefine what it means to be a bacterium bottom. 4.1 Basic Characteristics of Cells and Life Forms Expected Learning Outcomes 1. Describe the fundamental characteristics of cells. 2. Identify the primary properties that defne life and living things. There is a universal biological truth that the basic unit of life is the cell whether the organism is a bacterium whose entire body is just a single cell or an elephant made up of trillions of cells. Regardless of their origins all cells share a few common characteristics. They tend to assume cubical spherical or cylindrical shapes and have a cell membrane that encases an internal matrix called the cytoplasm. All cells have one or more chromosomes containing DNA. They all also possess ribosomes for protein synthesis and exhibit highly complex chemical reactions. As we learned in chapter 1 all cells taL05218_ch04_089-123.indd 90 10/7/16 11:55 AM

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xix The Planning of a Student Success Learning Tool Pedagogy designed for varied learning styles The end-of-chapter material for the tenth edition has been carefully planned and updated to promote active learning and provide review for different learning styles and levels of Bloom’s Taxonomy. Questions are  divided into two levels: Level I. Knowledge and Comprehension Level II. Application Analysis Evaluation and Synthesis The consistent layout of each chapter allows students to develop a learning strat- egy and gain confidence in their ability to master the concepts leading to success in the class Chapter Summary with Key Terms A brief outline of the chapter’s main concepts is provided for students with important terms highlighted. Key terms are also included in the glossary at the end of the book. Case Study Review These questions provide a quick check of concepts covered by the Case Study and allow instructors to assess students on the case study material. Writing Challenge Writing Challenge questions are suggested as a writing experience. Students are asked to compose a one- or two-paragraph response us- ing the factual information learned in the chapter. Multiple-Choice Questions Students can assess their knowledge of basic concepts by answering these questions and looking up the cor- rect answers in appendix D. In addition SmartBook allows for students to quiz themselves interactively us- ing these questions. Multiple-Choice Questions 157 E. Importance: Ecologically important in food webs and decomposing organic matter. Medical significance: hundreds of millions of people are afflicted with one of the many protozoan infections malaria trypanosomiasis amoebiasis. Can be spread from host to host by insect vectors. 5.8 The Parasitic Helminths Includes three categories: roundworms tapeworms and flukes. A. Overall Morphology: Animal cells multicellular individual organs specialized for reproduction digestion movement protection though some of these are reduced. B. Reproductive Mode: Includes embryo larval and adult stages. Majority reproduce sexually. Sexes may be hermaphroditic. C. Epidemiology: Developing countries in the tropics are hardest hit by helminth infections transmitted via ingestion vectors and direct contact with infectious stages. They afflict billions of humans. 5.7 Survey of Protists: Protozoa Include large single-celled organisms a few are pathogens. A. Overall Morphology: Most are unicellular lack a cell wall. The cytoplasm is divided into ectoplasm and endoplasm. Active feeding stage is the trophozoite many convert to a resistant dormant stage called a cyst. All but one group has some form of organelle for motility. B. Nutritional Mode/Distribution: All are heterotrophic. Most are free-living in a moist habitat water soil feed by engulfing other microorganisms and organic matter. C. Reproduction: Asexual by binary fission and mitosis budding sexual by fusion of free-swimming gametes conjugation. D. Major Groups: Protozoa are subdivided into four groups based upon mode of locomotion and type of reproduction: Mastigophora the flagellates motile by flagella Sarcodina the amoebas motile by pseudopods Ciliophora the ciliates motile by cilia Apicomplexa motility not well developed produce unique reproductive structures. Level I. Knowledge and Comprehension These questions require a working knowledge of the concepts in the chapter and the ability to recall and understand the information you have studied. Select the correct answer from the answers provided. For questions with blanks choose the combination of answers that most accurately completes the statement. 8. Algae generally contain some type of a. spore b. chlorophyll c. locomotor organelle d. toxin 9. Which algal group is most closely related to plants a. diatoms b. Chlorophyta c. Euglenophyta d. dinoflagellates 10. Which characteristics is/are not typical of protozoan cells a. locomotor organelle c. spore b. cyst d. trophozoite 11. The protozoan trophozoite is the a. active feeding stage b. inactive dormant stage c. infective stage d. spore-forming stage 12. All mature sporozoa are a. parasitic b. nonmotile c. carried by an arthropod vector d. both a and b 13. Parasitic helminths reproduce with a. spores d. cysts b. eggs and sperm e. all of these c. mitosis 1. Both flagella and cilia are found primarily in a. algae c. fungi b. protozoa d. both b and c 2. Features of the nuclear envelope include a. ribosomes b. a double membrane structure c. pores that allow communication with the cytoplasm d. b and c e. all of these 3. The cell wall is usually found in which eukaryotes a. fungi c. protozoa b. algae d. a and b 4. What is embedded in rough endoplasmic reticulum a. ribosomes c. chromatin b. Golgi apparatus d. vesicles 5. Yeasts are fungi and molds are fungi. a. macroscopic microscopic b. unicellular filamentous c. motile nonmotile d. water terrestrial 6. In general fungi derive nutrients through a. photosynthesis b. engulfing bacteria c. digesting organic substrates d. parasitism 7. A hypha divided into compartments by cross walls is called a. nonseptate c. septate b. imperfect d. perfect Multiple-Choice Questions taL05218_ch05_124-159.indd 157 17/10/16 2:49 PM Visual Challenge 159 On Connect you can find an Introduction to Concept Mapping that provides guidance for working with concept maps along with concept-mapping activities for this chapter. Concept Mapping These problems go beyond just restating facts and require higher levels of understanding and an ability to interpret problem solve transfer knowledge to new situations create models and predict outcomes. Level II. Application Analysis Evaluation and Synthesis Critical thinking is the ability to reason and solve problems using facts and concepts. These questions can be approached from a number of angles and in most cases they do not have a single correct answer. 6. Explain what factors could cause opportunistic mycoses to be a growing medical problem. 7. a. How are bacterial endospores and cysts of protozoa alike b. How do they differ 8. For what reasons would a eukaryotic cell evolve an endoplasmic reticulum and a Golgi apparatus 9. Can you think of a simple test to determine if a child is suffering from pinworms Hint: Clear adhesive tape is involved. 1. Explain the ways that mitochondria resemble rickettsias and chloroplasts resemble cyanobacteria. 2. Give the common name of a eukaryotic microbe that is unicellular walled nonphotosynthetic nonmotile and bud-forming. 3. How are the eukaryotic ribosomes and cell membranes different from those of prokaryotes 4. What general type of multicellular parasite is composed primarily of thin sacs of reproductive organs 5. a. Name two parasites that are transmitted in the cyst form. b. How must a non-cyst-forming pathogenic protozoan be transmitted Why Critical Thinking 1. What term is used to describe a single species exhibiting both cell types shown below and which types of organisms would most likely have this trait 2. Label the major structures you can observe in the images in figure 5.17a table 5.5A B and D and table 5.8C. Visual Challenge STUDY TIP: Quickly create a customized practice quiz for this chapter by going to your Connect SmartBook “My Reports” section. Don’t have SmartBook and want to learn more Go to whysmartbook.com. taL05218_ch05_124-159.indd 159 17/10/16 2:49 PM End-of-Chapter Questions Questions are divided into two levels. 156 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms C A SE S TUD Y Part 2 3 I n 2003 a 100 foot sailboat called the Sorcerer II embarked on a highly unusual shing expedition in the Sargasso Sea. What was most strik- ing about this voyage was that it did no involve actually catching sh with hooks or nets. Instead the targets were tiny oating microbes “hooked” by an exceedingly sophisticated and speci c technology. This project was the brainchild of Dr. Craig Ven- ter a prominent genetics researcher and its pri- mary goal was to survey in detail the mircrobial population of ocean water. Scientists aboard the vessel randomly collected surface water about ev- ery 200 miles extracted the tiniest forms of micro- scopic plankton primarily bacteria and sent samples back to Venter’s laboratory. It was here that his scienti c crew engaged in a new and pow- erful way of examining the world. Instead of pains- takingly locating tand identifying the individual microbes in the sample as might have been done in the past they ex tracted the genetic material DNA from the samples and analyzed the DNA using state-of-the-art molecular techniques and computers. Their stunning and somewhat unexpected discovery was that the variety and numbers of microbes liv- ing in the ocean exceeded by far any previous ocean studies. This ambitious undertaking was just the beginning. It was followed by several additional voyages by Dr. Venter’s ship as well as marine microbi- ologists at the Marine Biological Institute in Woods Hole Massachusetts and is continuing today all over the globe. Even though microbiologists had previously described around 5700 di erent types of bacteria the evidence from these studies showed that this number represented only the tiniest more an seawater most with endless nooks cr charac According Department entists estimate earth than there mated nonillion one crobes and their communities foundation of the biosphere earth. ” Which groups of microorganisms would likey be found in the plankton What elds of microbiology could be involved in the further study of these microbes and in unco eringtheir basic characteristics To continue the case go to page 000. Dr. Venter was one of the main individuals behind the mapping of the human genome in 2001. This technique called metagenomic analysis will be discussed in a later chapter10. An unusual protozoan isolated from a cow’s rumen. Background: Model of the enzyme cullulase “ Peering through the microscope into a drop of seawater is like looking at stars with a telescope on a clear night.” Dr. Victor Gallardo ocean researcher C A S E F I L E 1 This is an Example of a L Micro There is much more to the story of neglected dis- eases of poverty. Most victims frst become infected as children and continue to harbor the parasite for years even for a lifetime. The chronic nature of the infection adds enormously to the accumulated damage that occurs. Infected people may become involved in an ongoing cycle that contin- ues to produce more parasites and increase their survival and transmission. Many protozoans produce resistant survival cells called cysts and worms go through complex reproductive phases with eggs and larvae. Some parasites are spread by direct contact with an infected person some burrow into the skin and others are ingested in contaminated soil or water. A signifcant factor in transmission of several parasites is the involvement of arthropod vectors such as mosquitoes and fies. For most of these diseases there is efective drug therapy but getting the drugs to the poorest of the poor has been dif- fcult. Many of the countries are not only deeply impoverished but are involved in civil wars and other conficts creating up- heaval in an already overburdened system. One billion of the world’s poorest live on less than 1 per day and 2.7 billion live on less than 2 per day. Most of these people are “out of sight and out of mind”—living in remote rural areas far removed from medical facilities. NTDs are not given much priority for funding because they are not high-profle diseases with noticeable acute symptoms requiring immediate medical care. Any progress in controlling these NTDs will require a global partnership that brings together resources from many countries. ■ What is the defnition of a vector and how are vectors involved in these diseases ■ What are some possible solutions to the problem of neglected diseases For information on NTDs and their current status search for NTDs on the World Health Organization website. To conclude this Case Study go to Connect. 5.1 The History of Eukaryotes 5.2 Form and Function of the Eukaryotic Cell: External Structures A. The exterior configuration of eukaryotic cells is complex and displays numerous structures not found in prokaryotic cells. Biologists have accumulated much evidence that eukaryotic cells evolved through endosymbiosis between early prokaryotic cells. B. Major external structural features include: appendages cilia flagella glycocalyx cell wall and cytoplasmic or cell membrane. 5.3 Form and Function of the Eukaryotic Cell: Internal Structures A. The internal structure of eukaryotic cells is compartmentalized into individual organelles. B. Major organelles and internal structural features include: nucleus nucleolus endoplasmic reticulum Golgi complex mitochondria chloroplasts ribosomes cytoskeleton microfilaments microtubules. 5.4 Eukaryotic-Prokaryotic Comparisons and Taxonomy of Eukaryotes A. Comparisons between eukaryotic cells and prokaryotic cells show major differences in structure size metabolism motility and body form. B. Taxonomic groups of the Domain Eukarya are based on level of organization body plan cell structure nutrition metabolism and certain genetic characteristics. 5.5 The Kingdom of the Fungi Common names of the macroscopic fungi are mushrooms bracket fungi and puffballs. Microscopic fungi are known as yeasts and molds. A. Overall Morphology: At the cellular microscopic level fungi are typical eukaryotic cells with thick cell walls. Yeasts are single cells that form buds and pseudohyphae. Hyphae are long tubular filaments that can be septate or nonseptate and grow in a network called a mycelium hyphae are characteristic of the filamentous fungi called molds. B. Nutritional Mode/Distribution: All are heterotrophic. The majority are harmless saprobes living off organic substrates such as dead animal and plant tissues. A few are parasites living on the tissues of other organisms but none is obligate. Distribution is extremely widespread in many habitats. C. Reproduction: Primarily through spores formed on special reproductive hyphae. In asexual reproduction spores are formed through budding partitioning of a hypha or in special sporogenous structures examples are conidia and sporangiospores. In sexual reproduction spores are formed following fusion of male and female strains and the formation of a sexual structure sexual spores are one basis for classification. D. Major Groups: The four main phyla among the terrestrial fungi given with sexual spore type are Zygomycota zygospores Ascomycota ascospores Basidiomycota basidiospores and Chytridiomycota motile zoospores. E. Importance: Fungi are essential decomposers of plant and animal detritis in the environment. Economically beneficial as sources of antibiotics used in making foods and in genetic studies. Adverse impacts include decomposition of fruits and vegetables and human infections or mycoses some produce substances that are toxic if eaten or inhaled. 5.6 Survey of Protists: Algae General group that traditionally includes single-celled and colonial eukaryotic microbes that lack organization into tissues. A. Overall Morphology: Are unicellular colonial filamentous or larger forms such as seaweeds. B. Nutritional Mode/Distribution: Photosynthetic freshwater and marine water habitats main component of plankton. C. Importance: Provide the basis of the food web in most aquatic habitats and are major producers of oxygen. Certain algae produce neurotoxins that are harmful to humans and animals. Chapter Summary with Key Terms taL05218_ch05_124-159.indd 156 11/18/16 11:18 PM 158 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms Multiple Matching. Select the description that best fits the word in the left column. 17. diatom 18. Rhizopus 19. Histoplasma 20. Cryptococcus 21. euglenid 22. dinoflagellate 23. Trichomonas 24. Entamoeba 25. Plasmodium 26. Enterobius a. the cause of malaria b. single-celled alga with silica in its cell wall c. fungal cause of Ohio Valley fever d. the cause of amebic dysentery e. genus of black bread mold f. helminth worm involved in pinworm infection g. motile flagellated alga with an eyespot h. a yeast that infects the lungs i. flagellated protozoan genus that causes an STD j. alga that causes red tides 14. Mitochondria likely originated from a. archaea b. invaginations of the cell membrane c. rickettsias d. cyanobacteria 15. Human fungal infections involve and affect what areas of the human body a. skin b. mucous membranes c. lungs d. all of these 16. Most helminth infections a. are localized to one site in the body b. spread through major systems of the body c. develop within the spleen d. develop within the liver 1. Which of these is/are an examples of neglected tropical protozoan diseases a. hookworm d. a and b b. Chagas disease e. b and c c. leishmaniasis f. all of these 2. Which is a possible vector of a tropical eukaryotic parasite a. contaminated drinking water c. biting fly b. spoiled food d. person with a cough 3. Provide some explanations for why the eukaryotic parasites are so widespread and successful. Case Study Review For each question compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. Check Your Progress questions can also be used for writing-challenge exercises. 1. Describe the anatomy and functions of each of the major eukaryotic organelles. 2. Trace the synthesis of cell products their processing and their packaging through the organelle network. 3. a. What is the reproductive potential of molds in terms of spore production b. How do mold spores differ from bacterial endospores 4. a. Fill in the following summary table for defining comparing and contrasting eukaryotic cells. b. Briefly describe the manner of nutrition and body plan unicellular colonial filamentous or multicellular for each group. c. Explain some ways that helminths differ from the protozoa and algae in structure and behavior. Commonly Present In Check Organelle/ Briefy Describe Structure Functions in Cell Fungi Algae Protozoa Flagella Cilia Glycocalyx Cell wall Cell membrane Nucleus Mitochondria Chloroplasts Endoplasmic reticulum Ribosomes Cytoskeleton Lysosomes Microvilli Centrioles Writing Challenge taL05218_ch05_124-159.indd 158 17/10/16 2:49 PM Multiple-Choice Questions 157 E. Importance: Ecologically important in food webs and decomposing organic matter. Medical significance: hundreds of millions of people are afflicted with one of the many protozoan infections malaria trypanosomiasis amoebiasis. Can be spread from host to host by insect vectors. 5.8 The Parasitic Helminths Includes three categories: roundworms tapeworms and flukes. A. Overall Morphology: Animal cells multicellular individual organs specialized for reproduction digestion movement protection though some of these are reduced. B. Reproductive Mode: Includes embryo larval and adult stages. Majority reproduce sexually. Sexes may be hermaphroditic. C. Epidemiology: Developing countries in the tropics are hardest hit by helminth infections transmitted via ingestion vectors and direct contact with infectious stages. They afflict billions of humans. 5.7 Survey of Protists: Protozoa Include large single-celled organisms a few are pathogens. A. Overall Morphology: Most are unicellular lack a cell wall. The cytoplasm is divided into ectoplasm and endoplasm. Active feeding stage is the trophozoite many convert to a resistant dormant stage called a cyst. All but one group has some form of organelle for motility. B. Nutritional Mode/Distribution: All are heterotrophic. Most are free-living in a moist habitat water soil feed by engulfing other microorganisms and organic matter. C. Reproduction: Asexual by binary fission and mitosis budding sexual by fusion of free-swimming gametes conjugation. D. Major Groups: Protozoa are subdivided into four groups based upon mode of locomotion and type of reproduction: Mastigophora the flagellates motile by flagella Sarcodina the amoebas motile by pseudopods Ciliophora the ciliates motile by cilia Apicomplexa motility not well developed produce unique reproductive structures. Level I. Knowledge and Comprehension These questions require a working knowledge of the concepts in the chapter and the ability to recall and understand the information you have studied. Select the correct answer from the answers provided. For questions with blanks choose the combination of answers that most accurately completes the statement. 8. Algae generally contain some type of a. spore b. chlorophyll c. locomotor organelle d. toxin 9. Which algal group is most closely related to plants a. diatoms b. Chlorophyta c. Euglenophyta d. dinoflagellates 10. Which characteristics is/are not typical of protozoan cells a. locomotor organelle c. spore b. cyst d. trophozoite 11. The protozoan trophozoite is the a. active feeding stage b. inactive dormant stage c. infective stage d. spore-forming stage 12. All mature sporozoa are a. parasitic b. nonmotile c. carried by an arthropod vector d. both a and b 13. Parasitic helminths reproduce with a. spores d. cysts b. eggs and sperm e. all of these c. mitosis 1. Both flagella and cilia are found primarily in a. algae c. fungi b. protozoa d. both b and c 2. Features of the nuclear envelope include a. ribosomes b. a double membrane structure c. pores that allow communication with the cytoplasm d. b and c e. all of these 3. The cell wall is usually found in which eukaryotes a. fungi c. protozoa b. algae d. a and b 4. What is embedded in rough endoplasmic reticulum a. ribosomes c. chromatin b. Golgi apparatus d. vesicles 5. Yeasts are fungi and molds are fungi. a. macroscopic microscopic b. unicellular filamentous c. motile nonmotile d. water terrestrial 6. In general fungi derive nutrients through a. photosynthesis b. engulfing bacteria c. digesting organic substrates d. parasitism 7. A hypha divided into compartments by cross walls is called a. nonseptate c. septate b. imperfect d. perfect Multiple-Choice Questions taL05218_ch05_124-159.indd 157 17/10/16 2:49 PM

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xx Concept Mapping An Introduction to Concept Mapping can be found on Connect. Concept Mapping 27 On Connect you can find an Introduction to Concept Mapping that provides guidance for working with concept maps along with concept-mapping activities for this chapter. Concept Mapping For each question compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. Check Your Progress questions can also be used for writing-challenge exercises. 5. Explain how microbes are classified into groups according to evolutionary relationships provided with standard scientific names and identified by specific characteristics. 6. a. What are some of the sources for “new” infectious diseases b. Comment on the sensational ways in which some tabloid media portray the dangers of infectious diseases. 1. What does it mean to say microbes are ubiquitous 2. What is meant by diversity with respect to organisms 3. What events discoveries or inventions were probably the most significant in the development of microbiology and why 4. Explain how microbiologists use the scientific method to develop theories and explanations for microbial phenomena. Writing Challenge 1. Many of the bacteria in Lake Whillans derive energy from the oxidation of chemical compounds. What might have made this necessary a. exceedingly low temperatures b. a lack of sunlight c. the size of the bacterial populations they found d. a lack of fresh water 2. How was the number of different species in Lake Whillans determined a. counting individual cells b. analyzing the DNA recovered from the samples c. growing the cells and then classifying them according to their structural characteristics d. measuring the concentration of cells in each milliliter of lake water 3. Do you think scientists working at Pitch Lake were at a great risk of infection from the organisms growing in the lake Explain. Case Study Review rickettsia protein worm coccus-shaped bacterium spirochete atom 15. Which of the following is not an emerging infectious disease a. avian influenza b. Lyme disease c. common cold d. West Nile fever 16. How would you categorize a virus a. as prokaryotic b. as eukaryotic c. as an archaeon d. none of these choices Explain your choice for question 16. 11. Which is the correct order of the taxonomic categories going from most specific to most general a. domain kingdom phylum class order family genus species b. division domain kingdom class family genus species c. species genus family order class phylum kingdom domain d. species family class order phylum kingdom 12. By definition organisms in the same are more closely related than are those in the same . a. order family b. class phylum c. family genus d. phylum division 13. Which of the following are prokaryotic a. bacteria b. archaea c. protists d. both a and b 14. Order the following items by size using numbers: 1 smallest and 8 largest. human immunodeficiency virus HIV protozoan taL05218_ch01_001-028.indd 27 10/7/16 2:26 PM Critical Thinking Using the facts and concepts they just studied students must reason and problem solve to answer these specially developed questions. Questions do not have a single correct answer and thus open doors to discussion and application. The Innovation of a Student Success Learning Tool 156 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms An Introduction to Concept Mapping found at http://www.mhhe.com/talaro9 provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. Golgi apparatus ribosomes chloroplasts f agella cytoplasm nucleolus endoplasmic reticulum cell membrane Concept Mapping 1. What term is used to describe a single species exhibiting both cell types shown below and which types of organisms would most likely have this trait 2. Label the major structures you can observe in the images in f gure 5.16a table 5.3A B and D and table 5.6C. Critical thinking is the ability to reason and solve problems using facts and concepts. These questions can be approached from a number of angles and in most cases they do not have a single correct answer. 6. Explain what factors could cause opportunistic mycoses to be a growing medical problem. 7. a. How are bacterial endospores and cysts of protozoa alike b. How do they differ 8. For what reasons would a eukaryotic cell evolve an endoplasmic reticulum and a Golgi apparatus 9. Can you think of a simple test to determine if a child is suffering from pinworms Hint: Clear adhesive tape is involved. 1. Explain the ways that mitochondria resemble rickettsias and chloroplasts resemble cyanobacteria. 2. Give the common name of a eukaryotic microbe that is unicellular walled nonphotosynthetic nonmotile and bud-forming. 3. How are the eukaryotic ribosomes and cell membranes different from those of prokaryotes 4. What general type of multicellular parasite is composed primarily of thin sacs of reproductive organs 5. a. Name two parasites that are transmitted in the cyst form. b. How must a non-cyst-forming pathogenic protozoan be transmitted Why Critical Thinking Visual Challenge These problems go beyond just restating facts and require higher levels of understanding and an ability to interpret problem solve transfer knowledge to new situations create models and predict outcomes. Level II. Application Analysis Evaluation and Synthesis www.mcgrawhillconnect.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus including the media-rich eBook interactive learning tools and animations. taL22600_ch05_122-156.indd Page 156 10/9/13 9:21 PM f-w-166 /202/MH02004/taL22600_disk1of1/0073522600/taL22600_pagefiles Visual Challenge Visual Challenge questions take images and concepts learned in other chapters and ask students to apply that knowledge to concepts covered in the current chapter. 156 Chapter 5 A Survey of Eukaryotic Cells and Microorganisms An Introduction to Concept Mapping found at http://www.mhhe.com/talaro9 provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. Golgi apparatus ribosomes chloroplasts f agella cytoplasm nucleolus endoplasmic reticulum cell membrane Concept Mapping 1. What term is used to describe a single species exhibiting both cell types shown below and which types of organisms would most likely have this trait 2. Label the major structures you can observe in the images in f gure 5.16a table 5.3A B and D and table 5.6C. Critical thinking is the ability to reason and solve problems using facts and concepts. These questions can be approached from a number of angles and in most cases they do not have a single correct answer. 6. Explain what factors could cause opportunistic mycoses to be a growing medical problem. 7. a. How are bacterial endospores and cysts of protozoa alike b. How do they differ 8. For what reasons would a eukaryotic cell evolve an endoplasmic reticulum and a Golgi apparatus 9. Can you think of a simple test to determine if a child is suffering from pinworms Hint: Clear adhesive tape is involved. 1. Explain the ways that mitochondria resemble rickettsias and chloroplasts resemble cyanobacteria. 2. Give the common name of a eukaryotic microbe that is unicellular walled nonphotosynthetic nonmotile and bud-forming. 3. How are the eukaryotic ribosomes and cell membranes different from those of prokaryotes 4. What general type of multicellular parasite is composed primarily of thin sacs of reproductive organs 5. a. Name two parasites that are transmitted in the cyst form. b. How must a non-cyst-forming pathogenic protozoan be transmitted Why Critical Thinking Visual Challenge These problems go beyond just restating facts and require higher levels of understanding and an ability to interpret problem solve transfer knowledge to new situations create models and predict outcomes. Level II. Application Analysis Evaluation and Synthesis www.mcgrawhillconnect.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus including the media-rich eBook interactive learning tools and animations. taL22600_ch05_122-156.indd Page 156 10/9/13 9:21 PM f-w-166 /202/MH02004/taL22600_disk1of1/0073522600/taL22600_pagefiles

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xxi The Revision of a Student Success Learning Tool Changes to Foundations in Microbiology Tenth Edition Overall Changes: ∙ A new feature “Scoping Out The Chapter” has been placed after the opening case studies. This page will give readers a descriptive pictorial guide for the main topics covered in chapters 1–17 and 26–27. ∙ Ten chapters 6 7 13 19 21 22 24 25 26 and 27 contain new case studies chosen for their relevance to major themes in the chapter. ∙ Approximately 175 new and replacement photographs have been included in the r e vision. ∙ Numerous images and figures have been revised and corrected. ∙ Clinical Connections boxes and side notes have a tinted screen added to set them off from the regular text. Several new Clinical Corrections boxes have been added. ∙ Coverage of diseases statistics and graphic data has been updated.  ∙ Most chapters contain new links and quick searches for exploring topics on the internet. ∙ Special effort has been directed towards clarifying terms wording and definitions to improve understanding of more difficult concepts. Chapter-Specifc Changes: Chapter 1 ∙ The chapter opens with a new case study featuring microorganisms living in extreme habitats ∙ Epidemiology statistics have been updated throughout the chapter  ∙ New information on the spread of chikun- gunya virus and Zika virus has been added ∙ Information concerning the ongoing pertussis epidemic has been updated ∙ Information on the link between microorgan- isms and chronic disease has been updated ∙ The topic of microbial evolution and classification has been updated  Chapter 2 ∙ Discussions of the manner in which electron shells are filled and the importance of valence electrons to the formation of covalent bonds have been clarified  ∙ The section on polymeric biomolecules DNA RNA lipids proteins starches has been clarified Chapter 3 ∙ New photos have been added to illustrate differences in resolution between light microscopes and electron microscopes ∙ New photos have been added to the discussions of fluorescence microscopy electron microscopy and selective and dif f er ential media Chapter 4 ∙ A new discussion and figure concerning bac- terial microcompartments has been added. ∙ New photographs for a hyperthermophile and bacterial inclusion bodies Chapter 5 ∙ The case study concerning neglected tropical diseases NTDs has been updated to include the awarding of the 2015 Nobel Prize in Physiology or Medicine to scientists working in this area  ∙ New tables summarize the function of structures within the eukaryotic cell  ∙ New photos of the nucleus and mitochondria emphasize the importance of these or g anelles ∙ Update on Pseudogymnoascus destructans the fungus responsible for white nose syndrome in bats Chapter 6 ∙ The chapter opens with a new case study fo- cused on highly pathogenic avian influenza. ∙ The role of Adenovirus Ad-36 in weight gain and regulation of blood sugar levels has been updated. ∙ New photomicrograph of an Ebola virus budding from an infected cell Chapter 7 ∙ A new case study “A Creature of Habitat” describes the serious problem of cystic fibrosis and its connection with recurring Pseudomonas infections. ∙ New photographs for satellitism and an anaerobic growth chamber ∙ New information on biofilm formation  Chapter 8 ∙ Addition of coenzymes to table on cofactors. ∙ Clarification of how the term fermentation is used under different contexts Chapter 9 ∙ Improved figure showing input by r egulat or y RN A ∙ Revised table on types of mutations. ∙ Updated box on regulatory noncoding RNA and riboswitches ∙ Improved consistency of figures for conjugation and transduction Chapter 10 ∙ Added details of newer DNA sequencing technologies ∙ Updated box on the human genome ∙ Revised tables on genetically-engineered animals ∙ New graph on genetically engineered crops ∙ Revised and updated Clinical Connections covering gene therapy  ∙ The term DNA fingerprinting has been replaced with DNA profiling ∙ Figure on standardized DNA profiling has been revised ∙ Reorganized section on different uses of DNA profiling ∙ A note describing the gene editing technol- ogy of CRSPR has been added. Chapter 11 ∙ Updated case study on an outbreak of hepatitis C in a colonscopy clinic ∙ Integrated historical aspects of microbial control into main text and removed Making Connections box 11.1. ∙ New Clinical Connections box discusses the sterilization of reusable medical devices ∙ Revised the box on use of triclosan including new FDA ruling Chapter 12 ∙ Integrated Making connections 12.2 on discovery of drugs into main chapter ∙ Added a new figure on the chemical synthesis of penicillin drugs ∙ Included new categories of antibacterial and antiviral drugs ∙ Updated drug resistance box and added a new figure showing carbapenem-resistant enterobacteriaceae CRE  Chapter 13 ∙ New case study “Fatal Filaments from Far Away Africa” that covers the Ebola epidemic in Africa and its spread to the United States. ∙ Introduced new information on the impor- tance of the microbiome to general human physiology ∙ Coverage of the relationship of the placen- tal microbiome to infant development and the development of the intestinal microbi- ome in newborns.  ∙ New surveillance figures for HIV infection pertussis and Ebola fever. ∙ Updated figure on healthcare associated infections HAI replacing use of nosocomial infections with the more commonly used HAI

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xxii ∙ New visual challenge figures to differentiate among different epidemiological patterns for diseases Chapter 14 ∙ Added new information on the hygiene h ypo t hesis ∙ Clarified figure on the actions of complement ∙ Removed discussion of fever from Clinical Connections box and integrated it into text Chapter 15 ∙ Reorganized the order of introduction of T cell and B cell actions and functions  T cells now are covered first followed by B cells. ∙ Revised figure 15.1 to align with new order of coverage.  ∙ Added side note to focus on the functions of T regulatory cells with new information on biologic drugs based on this type of T cell ∙ Updated the list of monoclonal antibody- based drugs and currently-approved v accine sc hedules.  ∙ Coverage of the breast microbiome and the role breast milk has in the development of the immune systems of infants. Chapter 16 ∙ Revised allergen count figure ∙ New photographs of atopic and contact dermatitis ∙ New photograph of blood typing ∙ New photograph of rheumatoid arthritis ∙ Illustration of child with velocardiofacial DiGeorge syndrome  Chapter 17 ∙ Updated box on point-of-care testing ∙ New example of the direct fluorescent antibody tes t ∙ Replacement figure for rapid identification testing ∙ New examples of serological test results Chapter 18 ∙ New electron photomicrograph of methicillin-resistant Staphylococcus aureus has been added ∙ New photos of erysipelas and limb necrosis due to meningococcemia ∙ Updated recommendations for treatment of bacterial infections ∙ Updated statistics on the prevalence of sexually transmitted diseases ∙ The discussion of meningococcemia and meningitis has been clarified Chapter 19 ∙ The chapter opens with a new case study concerning Listeria monocytogenes ∙ New photomicrographs of Bacillus ant hr acis Corynebacterium diphtheriae and fluorescently labeled Mycobacterium tuberculosis have been added ∙ New photographs for myonecrosis erysipeloid the Mantoux skin test for tuberculosis paucibacillary leprosy multibacillary leprosy fish tank granuloma and actinomycosis ∙ Expanded and updated discussion of the use of fecal microbiota transplants as a treatment of C-difficile infection ∙ New electron micrograph of Mycobacterium tuberculosis updated worldwide statistics for tuberculosis and updated treatment recommendations for both active and latent tuberculosis ∙ Updated classification of leprosy to match WHO standards Chapter 20 ∙ New photomicrograph of Pseudomonas aeruginosa and new photo of cutaneous Pseudomonas infection ∙ Updated treatment recommendations for Pseudomonas infection Brucellosis and Tularemia ∙ New information on pertactin-deficient strains of Bordetella pertussis ∙ Updated discussion of E. coli pathotypes ∙ New section on Carbepenem-resistant Enter obacter iaceae inf ections  ∙ New section on naming conventions in Salmonella Chapter 21 ∙ Chapter opens with a new case study on Q fever and live cell transplantation ∙ New photographs of Coxiella burnetti Treponema pallidum Borrelia burgdorferi Vibrio cholera Campylobacter jejuni Orienta tsutsugamushi and lxodes scapularis ∙ Updated statistics on syphilis  ∙ New treatment recommendations for cholera ∙ New photos of dental caries and oral bacteria Chapter 22 ∙ Case study has been updated to include the latest facts concerning the fungal meningitis outbreak connected to the New England Compounding Center ∙ Updates on antifungal drugs and epidemio- logical statistics ∙ New photographs of cutaneous blastomycosis Tinea pedis Aspergillus and aspergillosis ∙ Reclassification of zygomycosis as mucormycosis Chapter 23 ∙ Updated drug recommendations for parasitic diseases ∙ New discussion on genetically engineered mosquitoes resistant to Plasmodium sp. ∙ New feature on Carlos Chagas and his importance to the field of parasitology ∙ The latest information about phase 3/4 trials of malaria vaccine RTSS Chapter 24 ∙ The chapter begins with a new case study concerning unusual varicella zoster virus transmission ∙ New photos of herpes simplex type 1 neonatal herpes and lymphocytes infected with Epstein-Barr virus ∙ Updated recommendations for treatment of neonatal herpes ∙ Update on treatment and prevention of HPV Chapter 25 ∙ New case study on measles and subacute sclerosing panencephalitis ∙ Updates include information on the Ebola outbreak of 2014–2016 the ongoing Zika virus outbreak and widespread outbreaks of chikungunya virus ∙ Updated information on influenza vaccines and new chemotherapeutic treatments for influenza ∙ New information on the measles outbreak of 2015 along with discussion and references to online documentaries about vaccine skepticism ∙ Distribution maps for Aedes mosquitoes the vector of dengue chikungunya and Zika viruses ∙ Feature on the Aedes mosquito ∙ Information about the recently approved vaccine to prevent dengue fever ∙ Updates on treatment strategies for HIV including the use of pre-exposure pr oph y laxis PrEP Chapter 26 ∙ New case study on drinking water contamination as a result of harmful alg ae blooms ∙ New photos of Rhizobium root nodules and mycorrhizae ∙ New discussion concerning fracking as a potential contaminant of groundwater Chapter 27 ∙ New case study concerning three separate outbreaks of food poisoning The Effort of a Student Success Learning Tool

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xxiii This edition marks the 24th anniversary of the first publication of Foundations in 1993. Looking back over the previous nine editions the authors are struck by the extensive discoveries and new devel- opments in the science of microbiology that are reflected in the changing content and character of this book. This 10th edition is no exception. The one thing that has remained constant and unchang- ing over these years is the outstanding collaboration we enjoy with the editorial and production staff at McGraw-Hill Education. This time around we have been fortunate to have the able assistance and expertise of product developer Mandy Clark keeping us on track and providing much needed moral support. We also appreciate the insights and contributions of brand manager Marija Magner and marketing manager Jessica Cannavo. Our project manager Jayne Klein has been an experienced and knowledgeable guide through the intricacies of a digital-style revision.  Other valued members of our team who have been instrumental in developing the text’s visual elements are Carrie Burger the content licensing specialist Danny Meldung at Photo Affairs and the de- signer Tara McDermott who has produced another striking book and cover design. Some of the unsung heroes of authors are the readers who must sift through the text with a fine-tooth comb checking for errors grammatical usage and consistency in style. This tedious job fell this time to copy editor Wendy Nelson. After poring over 800 plus pages of text in a few months she may feel like she has taken a crash course in microbiology. It takes about a year and a half to complete a textbook revision—a process that involves editing manuscript writing new text illustra- tion research and much more. During this time the entire text and art program are inspected at least six times by the authors and team members. Even with the keenest eyes and spell checks some typos errors oversights and other mistakes may end up on the printed page. If you find any of these or wish to make other comments feel free to contact the publisher sales representative or authors ktalaroaol.com and bxchessPasadena.edu. We hope that you enjoy your explorations in the microbial world and that this fascinating science will leave a lasting impression on you. —Kathy Talaro and Barry Chess Acknowledgments

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xxiv A Note to the Student How to Maximize Your Learning Curve Most of you are probably taking this course as a prerequisite to nursing dental hygiene medicine pharmacy optometry physician assistant or other health science programs. Because you are prepar- ing for professions that involve interactions with patients you will be concerned with infection control and precautions which in turn requires you to think about microbes and how to manage them. This means you must not only be knowledgeable about the characteris- tics of bacteria viruses and other microbes and their physiology and primary niches in the world but you must also have a grasp of disease transmission the infectious process disinfection proce- dures and drug treatments. You will need to understand how the immune system interacts with microorganisms and the effects of immunization. All of these areas bring their own vocabulary and language—much of it new to you—and mastering it will require time motivation and preparation. A valid question students often ask is: “How can I learn this information to increase my success in the course as well as retain it for the future” Right from the first you need to be guided by how your instructor has organized your course. Because there is more information than could be covered in one semester or quarter your instructor will select what he or she wants to emphasize and will construct reading assignments and a study outline that corresponds to lectures and discussion sessions. Many instructors have a detailed syllabus or study guide that directs the class to specific content areas and vo- cabulary words. Others may have their own website to distribute assignments and even sample exams. Whatever materials are pro- vided this should be your primary guide in preparing to study. The next consideration involves your own learning style and what works best for you. To be successful you must commit essential concepts and terminology to memory. A list of how we retain infor- mation called the “pyramid of learning” has been proposed by Ed- gar Dale: We remember about 10 of what we read 20 of what we hear 50 of what we see and hear 70 of what we discuss with others 80 of what we experience personally and 95 of what we teach to someone else. There are clearly many ways to go about assimilating informa- tion.  Mainly you will want to focus on more than just reading alone to gather the most important points from a chapter. Try to incorporate writing drawing simple diagrams and discussion or study with others. You must attend lecture and laboratory sessions to listen to your instructors or teaching assistants explain the mate- rial. You can rewrite the notes you’ve taken during lecture or out- line them to organize the main points. This begins the process of laying down memory. You should go over concepts with others— perhaps a tutor or study group—and even take on the role of the teacher-presenter part of the time. With these kinds of interactions you will move beyond simple rote memorization of words and will come to understand the ideas and be able to apply them later. A way to assess your understanding and level of learning is to test yourself. You may use the exam questions in the text on the Con- nect website or make up your own. LearnSmart available within the Connect site is an excellent way to map your own individual- ized learning program. It helps to track what you know pinpoint what you don’t know and creates personalized questions based on your progress. Another big factor in learning is the frequency of studying. It is far more effective to spend an hour or so each day for two weeks than a marathon cramming session on one weekend. If you approach the subject in small bites and remain connected with the terminology and topics over time it will become yours and you will find that the pieces begin to fit together. Just remember that repetition and expe- rience are the most effective ways to acquire knowledge. In the final analysis the process of learning comes down to self- motivation and attitude. There is a big difference between forcing yourself to memorize something to get by and really wanting to know and understand it. Therein is the key to most success and achievement no matter what your final goals. And though it is true that mastering the subject matter in this textbook requires time and effort millions of students will affirm how worthwhile such knowl- edge has been in their professions and everyday life.

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xxv CHAPTER 1 The Main Themes of Microbiology 1 1.1 The Scope of Microbiology 2 1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments 3 The Origins and Dominance of Microorganisms 3 The Cellular Organization of Microorganisms 6 Microbial Dimensions: How Small Is Small 7 Microbial Involvement in Energy and Nutrient Flow 9 1.3 Human Use of Microorganisms 10 1.4 Microbial Roles in Infectious Diseases 11 1.5 The Historical Foundations of Microbiology 13 The Development of the Microscope: “Seeing Is Believing” 13 The Scientific Method and the Search for Knowledge 16 The Development of Medical Microbiology 16 1.6 Taxonomy: Organizing Classifying and Naming Microorganisms 19 The Levels of Classification 19 Assigning Scientific Names 21 1.7 The Origin and Evolution of Microorganisms 22 All Life Is Related and Connected Through Evolution 22 Systems for Presenting a Universal Tree of Life 22 CHAPTER 2 The Chemistry of Biology 29 2.1 Atoms: Fundamental Building Blocks of All Matter in the Universe 30 Different Types of Atoms: Elements and Their Properties 31 The Major Elements of Life and Their Primary Characteristics 32 2.2 Bonds and Molecules 34 Covalent Bonds: Molecules with Shared Electrons 35 Ionic Bonds: Electron Transfer Among Atoms 36 Electron Transfer and Oxidation-Reduction Reactions 37 2.3 Chemical Reactions Solutions and pH 38 Formulas Models and Equations 38 Solutions: Homogeneous Mixtures of Molecules 39 Acidity Alkalinity and the pH Scale 40 2.4 The Chemistry of Carbon and Organic Compounds 41 Functional Groups of Organic Compounds 42 Organic Macromolecules: Superstructures of Life 43 2.5 Molecules of Life: Carbohydrates 43 The Nature of Carbohydrate Bonds 45 The Functions of Carbohydrates in Cells 47 2.6 Molecules of Life: Lipids 47 Membrane Lipids 47 Miscellaneous Lipids 48 2.7 Molecules of Life: Proteins 49 Protein Structure and Diversity 50 2.8 Nucleic Acids: A Program for Genetics 52 The Double Helix of DNA 52 Making New DNA: Passing on the Genetic Message 53 RNA: Organizers of Protein Synthesis 54 ATP: The Energy Molecule of Cells 54 CHAPTER 3 Tools of the Laboratory: Methods of Studying Microorganisms 60 3.1 Methods of Microbial Investigation 62 3.2 The Microscope: Window on an Invisible Realm 63 Magnification and Microscope Design 66 Variations on the Optical Microscope 66 Electron Microscopy 68 3.3 Preparing Specimens for Optical Microscopes 70 Fresh Living Preparations 71 Fixed Stained Smears 71 3.4 Additional Features of the Six “I’s” 73 Inoculation Growth and Identification of Cultures 74 Isolation Techniques 75 Identification Techniques 76 3.5 Media: The Foundations of Culturing 78 Types of Media 79 Physical States of Media 79 Chemical Content of Media 80 Media to Suit Every Function 81 CHAPTER 4 A Survey of Prokaryotic Cells and Microorganisms 89 4.1 Basic Characteristics of Cells and Life Forms 90 What Is Life 91 4.2 Prokaryotic Profles: The Bacteria and Archaea 92 The Structure of a Generalized Bacterial Cell 92 Cell Extensions and Surface Structures 92 Contents

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xxvi Contents 5.7 Survey of Protists: Protozoa 148 Protozoan Form and Function 148 Protozoan Identification and Cultivation 148 Important Protozoan Pathogens 152 5.8 The Parasitic Helminths 154 General Worm Morphology 154 Life Cycles and Reproduction 154 A Helminth Cycle: The Pinworm 155 Helminth Classification and Identification 155 Distribution and Importance of Parasitic Worms 155 CHAPTER 6 An Introduction to Viruses 160 6.1 Overview of Viruses 161 Early Searches for the Tiniest Microbes 161 The Position of Viruses in the Biological Spectrum 162 6.2 The General Structure of Viruses 163 Size Range 163 Viral Components: Capsids Nucleic Acids and Envelopes 165 6.3 How Viruses Are Classifed and Named 170 6.4 Modes of Viral Multiplication 172 Multiplication Cycles in Animal Viruses 172 6.5 The Multiplication Cycle in Bacteriophages 177 Lysogeny: The Silent Virus Infection 177 6.6 Techniques in Cultivating and Identifying Animal Viruses 179 Using Cell Tissue Culture Techniques 180 Using Bird Embryos 181 Using Live Animal Inoculation 181 6.7 Viral Infection Detection and Treatment 181 6.8 Prions and Other Nonviral Infectious Particles 183 CHAPTER 7 Microbial Nutrition Ecology and Growth 188 7.1 Microbial Nutrition 190 Chemical Analysis of Cell Contents 190 Forms Sources and Functions of Essential Nutrients 190 7.2 Classifcation of Nutritional Types 193 Autotrophs and Their Energy Sources 193 Heterotrophs and Their Energy Sources 195 7.3 Transport: Movement of Substances Across the Cell Membrane 196 Diffusion and Molecular Motion 196 The Diffusion of Water: Osmosis 197 Adaptations to Osmotic Variations in the Environment 197 The Movement of Solutes Across Membranes 198 Active Transport: Bringing in Molecules Against a Gradient 199 Endocytosis: Eating and Drinking by Cells 201 4.3 The Cell Envelope: The Outer Boundary Layer of Bacteria 99 Basic Types of Cell Envelopes 99 Structure of Cell Walls 100 Mycoplasmas and Other Cell-Wall-Deficient Bacteria 102 Cell Membrane Structure 102 4.4 Bacterial Internal Structure 103 Contents of the Cell Cytoplasm 103 Bacterial Endospores: An Extremely Resistant Life Form 105 4.5 Bacterial Shapes Arrangements and Sizes 107 4.6 Classifcation Systems of Prokaryotic Domains: Archaea and Bacteria 110 Bacterial Taxonomy: A Work in Progress 111 4.7 Survey of Prokaryotic Groups with Unusual Characteristics 115 Free-Living Nonpathogenic Bacteria 115 Unusual Forms of Medically Significant Bacteria 117 Archaea: The Other Prokaryotes 118 CHAPTER 5 A Survey of Eukaryotic Cells and Microorganisms 124 5.1 The History of Eukaryotes 126 5.2 Form and Function of the Eukaryotic Cell: External Structures 127 Locomotor Appendages: Cilia and Flagella 127 The Glycocalyx 129 Form and Function of the Eukaryotic Cell: Boundary Structures 129 5.3 Form and Function of the Eukaryotic Cell: Internal Structures 130 The Nucleus: The Control Center 130 Endoplasmic Reticulum: A Passageway and Production System for Eukaryotes 131 Golgi Apparatus: A Packaging Machine 132 Mitochondria: Energy Generators of the Cell 133 Chloroplasts: Photosynthesis Machines 133 Ribosomes: Protein Synthesizers 134 The Cytoskeleton: A Support Network 135 5.4 Eukaryotic-Prokaryotic Comparisons and Taxonomy of Eukaryotes 136 Overview of Taxonomy 137 5.5 The Kingdom of the Fungi 138 Fungal Nutrition 139 Organization of Microscopic Fungi 140 Reproductive Strategies and Spore Formation 141 Fungal Classification 143 Fungal Identification and Cultivation 145 Fungi in Medicine Nature and Industry 145 5.6 Survey of Protists: Algae 146 The Algae: Photosynthetic Protists 146

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Contents xxvii 9.2 Applications of the DNA Code: Transcription and Translation 269 The Gene-Protein Connection 270 The Major Participants in Transcription and Translation 271 Transcription: The First Stage of Gene Expression 272 Translation: The Second Stage of Gene Expression 273 Eukaryotic Transcription and Translation: Similar yet Different 275 9.3 Genetic Regulation of Protein Synthesis and Metabolism 278 The Lactose Operon: A Model for Inducible Gene Regulation in Bacteria 278 A Repressible Operon 281 Non-Operon Control Mechanisms 282 9.4 Mutations: Changes in the Genetic Code 283 Causes of Mutations 284 Categories of Mutations 284 Repair of Mutations 285 The Ames Test 285 Positive and Negative Effects of Mutations 286 9.5 DNA Recombination Events 287 Transmission of Genetic Material in Bacteria 287 9.6 The Genetics of Animal Viruses 292 Replication Strategies in Animal Viruses 292 CHAPTER 10 Genetic Engineering: A Revolution in Molecular Biology 298 10.1 Basic Elements and Applications of Genetic Engineering 300 Tools and Techniques of DNA Technology 300 10.2 Recombinant DNA Technology: How to Imitate Nature 308 Technical Aspects of Recombinant DNA and Gene Cloning 309 Construction of a Recombinant Insertion into a Cloning Host and Genetic Expression 310 Protein Products of Recombinant DNA Technology 312 10.3 Genetically Modifed Organisms and Other Applications 313 Recombinant Microbes: Modified Bacteria and Viruses 313 Recombination in Multicellular Organisms 315 Medical Treatments Based on DNA Technology 317 10.4 Genome Analysis: DNA Profling and Genetic Testing 319 DNA Profiling: A Unique Picture of a Genome 320 CHAPTER 11 Physical and Chemical Agents for Microbial Control 327 11.1 Controlling Microorganisms 329 General Considerations in Microbial Control 329 Relative Resistance of Microbial Forms 329 7.4 Environmental Factors That Infuence Microbes 201 Adaptations to Temperature 202 Gas Requirements 204 Effects of pH 206 Osmotic Pressure 206 Miscellaneous Environmental Factors 206 7.5 Ecological Associations Among Microorganisms 206 7.6 The Study of Microbial Growth 212 The Basis of Population Growth: Binary Fission and the Bacterial Cell Cycle 212 The Rate of Population Growth 212 Determinants of Population Growth 214 Other Methods of Analyzing Population Growth 216 CHAPTER 8 An Introduction to Microbial Metabolism: The Chemical Crossroads of Life 222 8.1 An Introduction to Metabolism and Enzymes 223 Enzymes: Catalyzing the Chemical Reactions of Life 224 Regulation of Enzymatic Activity and Metabolic Pathways 230 8.2 The Pursuit and Utilization of Energy 233 Cell Energetics 233 8.3 Pathways of Bioenergetics 236 Catabolism: An Overview of Nutrient Breakdown and Energy Release 237 Energy Strategies in Microorganisms 237 Aerobic Respiration 237 Pyruvic Acid—A Central Metabolite 240 The Krebs Cycle—A Carbon and Energy Wheel 242 The Respiratory Chain: Electron Transport and Oxidative Phosphorylation 242 Summary of Aerobic Respiration 245 Anaerobic Respiration 245 8.4 The Importance of Fermentation 246 8.5 Biosynthesis and the Crossing Pathways of Metabolism 249 The Frugality of the Cell—Waste Not Want Not 249 Assembly of the Cell 251 8.6 Photosynthesis: The Earth’s Lifeline 251 Light-Dependent Reactions 252 Light-Independent Reactions 253 Other Mechanisms of Photosynthesis 254 CHAPTER 9 An Introduction to Microbial Genetics 260 9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity 262 The Nature of the Genetic Material 262 The Structure of DNA: A Double Helix with Its Own Language 264 DNA Replication: Preserving the Code and Passing It On 265

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xxviii Contents CHAPTER 13 Microbe-Human Interactions: Infection Disease and Epidemiology 397 13.1 We Are Not Alone 399 Contact Colonization Infection Disease 399 Resident Microbiota: The Human as a Habitat 399 Indigenous Microbiota of Specific Regions 401 Colonizers of the Human Skin 403 Microbial Residents of the Gastrointestinal Tract 405 Inhabitants of the Respiratory Tract 406 Microbiota of the Genitourinary Tract 406 13.2 Major Factors in the Development of an Infection 407 Becoming Established: Phase 1—Portals of Entry 409 The Requirement for an Infectious Dose 412 Attaching to the Host: Phase 412 Invading the Host and Becoming Established: Phase Three 412 13.3 The Outcomes of Infection and Disease 417 The Stages of Clinical Infections 417 Patterns of Infection 417 Signs and Symptoms: Warning Signals of Disease 419 The Portal of Exit: Vacating the Host 420 The Persistence of Microbes and Pathologic Conditions 421 13.4 Epidemiology: The Study of Disease in Populations 421 Origins and Transmission Patterns of Infectious Microbes 421 The Acquisition and Transmission of Infectious Agents 424 13.5 The Work of Epidemiologists: Investigation and Surveillance 426 Epidemiological Statistics: Frequency of Cases 426 Investigative Strategies of the Epidemiologist 428 Hospital Epidemiology and Health-Care-Associated Infections 429 Universal Blood and Body Fluid Precautions 432 CHAPTER 14 An Introduction to Host Defenses and Innate Immunities 437 14.1 Overview of Host Defense Mechanisms 438 Barriers at the Portal of Entry: An Inborn First Line of Defense 439 14.2 Structure and Function of the Organs of Defense and Immunity 441 How Do White Blood Cells Carry Out Recognition and Surveillance 441 Compartments and Connections of the Immune System 442 14.3 Second-Line Defenses: Infammation 451 The Inflammatory Response: A Complex Concert of Reactions to Injury 451 The Stages of Inflammation 451 Terminology and Methods of Microbial Control 331 What Is Microbial Death 332 How Antimicrobial Agents Work: Their Modes of Action 334 11.2 Physical Methods of Control: Heat 335 Effects of Temperature on Microbial Activities 335 The Effects of Cold and Desiccation 338 11.3 Physical Methods of Control: Radiation and Filtration 340 Radiation as a Microbial Control Agent 340 Modes of Action of Ionizing Versus Nonionizing Radiation 340 Ionizing Radiation: Gamma Rays X Rays and Cathode Rays 340 Nonionizing Radiation: Ultraviolet Rays 342 Filtration—A Physical Removal Process 342 11.4 Chemical Agents in Microbial Control 344 Choosing a Microbicidal Chemical 344 Factors That Affect the Germicidal Activities of Chemical Agents 344 Categories of Chemical Agents 345 CHAPTER 12 Drugs Microbes Host—The Elements of Chemotherapy 360 12.1 Principles of Antimicrobial Therapy 361 The Origins of Antimicrobial Drugs 361 Interactions Between Drugs and Microbes 364 12.2 Survey of Major Antimicrobial Drug Groups 370 Antibacterial Drugs That Act on the Cell Wall 371 Antibiotics That Damage Bacterial Cell Membranes 372 Drugs That Act on DNA or RNA 372 Drugs That Interfere with Protein Synthesis 373 Drugs That Block Metabolic Pathways 374 12.3 Drugs to Treat Fungal Parasitic and Viral Infections 375 Antifungal Drugs 375 Antiparasitic Chemotherapy 376 Antiviral Chemotherapeutic Agents 377 12.4 Interactions Between Microbes and Drugs: The Acquisition of Drug Resistance 381 How Does Drug Resistance Develop 381 Specific Mechanisms of Drug Resistance 381 Natural Selection and Drug Resistance 383 12.5 Interactions Between Drugs and Hosts 386 Toxicity to Organs 386 Allergic Responses to Drugs 387 Suppression and Alteration of the Microbiota by Antimicrobials 387 12.6 The Process of Selecting an Antimicrobial Drug 388 Identifying the Agent 388 Testing for the Drug Susceptibility of Microorganisms 389 The MIC and the Therapeutic Index 390 Patient Factors in Choosing an Antimicrobial Drug 391

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Contents xxix 16.3 Type II Hypersensitivities: Reactions That Lyse Foreign Cells 513 The Basis of Human ABO Antigens and Blood Types 513 Antibodies Against A and B Antigens 514 The Rh Factor and Its Clinical Importance 515 16.4 Type III Hypersensitivities: Immune Complex Reactions 517 Mechanisms of Immune Complex Diseases 517 Types of Immune Complex Disease 517 16.5 Immunopathologies Involving T Cells 518 Type IV Delayed-Type Hypersensitivity 518 T Cells and Their Role in Organ Transplantation 518 Practical Examples in Transplantation 521 16.6 Autoimmune Diseases: An Attack on Self 522 Genetic and Gender Correlation in Autoimmune Disease 522 The Origins of Autoimmune Disease 523 Examples of Autoimmune Disease 523 16.7 Immunodefciency Diseases and Cancer: Compromised Immune Responses 524 Primary Immunodeficiency Diseases 525 Secondary Immunodeficiency Diseases 527 The Role of the Immune System 527 CHAPTER 17 Procedures for Identifying Pathogens and Diagnosing Infections 533 17.1 An Overview of Clinical Microbiology 535 Phenotypic Methods 535 Genotypic Methods 535 Immunologic Methods 535 On the Track of the Infectious Agent: Specimen Collection 535 17.2 Phenotypic Methods 539 Immediate Direct Examination of Specimen 539 Cultivation of Specimen 541 17.3 Genotypic Methods 541 DNA Analysis Using Genetic Probes 541 Roles of the Polymerase Chain Reaction and Ribosomal RNA in Identification 542 17.4 Immunologic Methods 543 General Features of Immune Testing 543 Agglutination and Precipitation Reactions 545 The Western Blot for Detecting Proteins 546 Complement Fixation 547 Miscellaneous Serological Tests 547 Fluorescent Antibody and Immunofluorescent Testing 548 17.5 Immunoassays: Tests of Great Sensitivity 549 Radioimmunoassay RIA 549 Enzyme-Linked Immunosorbent Assay ELISA 550 17.6 Viruses as a Special Diagnostic Case 551 14.4 Second-Line Defenses: Phagocytosis Interferon and Complement 456 Phagocytosis: Ingestion and Destruction by White Blood Cells 456 Interferon: Antiviral Cytokines and Immune Stimulants 458 Complement: A Versatile Backup System 459 An Outline of Major Host Defenses 461 CHAPTER 15 Adaptive Specifc Immunity and Immunization 456 15.1 Specifc Immunities: The Adaptive Line of Defense 468 An Overview of Specific Immune Responses 468 Development of the Immune Response System 468 Specific Events in T-Cell Maturation 473 Specific Events in B-Cell Maturation 474 15.2 The Nature of Antigens and Antigenicity 474 Characteristics of Antigens and Immunogens 474 15.3 Immune Reactions to Antigens and the Activities of T Cells 476 The Role of Antigen Processing and Presentation 476 T-Cell Responses and Cell-Mediated Immunity CMI 477 15.4 Immune Activities of B Cells 480 Events in B-Cell Responses 481 Monoclonal Antibodies: Useful Products from Cancer Cells 486 15.5 A Classifcation Scheme for Specifc Acquired Immunities 486 Defining Categories by Mode of Acquisition 486 15.6 Immunization: Providing Immune Protection Through Therapy 489 Artificial Passive Immunization 490 Artificial Active Immunity: Vaccination 490 Development of New Vaccines 491 Routes of Administration and Side Effects of Vaccines 494 To Vaccinate: Why Whom and When 495 CHAPTER 16 Disorders in Immunity 501 16.1 The Immune Response: A Two-Sided Coin 503 Overreactions to Antigens: Allergy/Hypersensitivity 503 16.2 Allergic Reactions: Atopy and Anaphylaxis 504 Modes of Contact with Allergens 504 The Nature of Allergens and Their Portals of Entry 505 Mechanisms of Allergy: Sensitization and Provocation 505 Cytokines Target Organs and Allergic Symptoms 507 Specific Diseases Associated with IgE- and Mast-Cell-Mediated Allergy 509 Anaphylaxis: A Powerful Systemic Reaction to Allergens 510 Diagnosis of Allergy 511 Treatment and Prevention of Allergy 512

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xxx Contents CHAPTER 20 The Gram-Negative Bacilli of Medical Importance 618 20.1 Aerobic Gram-Negative Nonenteric Bacilli 619 Pseudomonas: The Pseudomonads 619 20.2 Related Gram-Negative Aerobic Rods 622 Brucella and Brucellosis 623 Francisella tularensis and Tularemia 624 Bordetella pertussis and Relatives 624 Legionella and Legionellosis 626 20.3 Identifcation and Diferential Characteristics of Family Enterobacteriaceae 627 Antigenic Structures and Virulence Factors 629 20.4 Coliform Organisms and Diseases 631 Escherichia coli: The Most Prevalent Enteric Bacillus 631 Miscellaneous Infections 632 Other Coliforms 632 Carbepenem-Resistant Enterobacteriaceae 634 20.5 Noncoliform Enterics 634 Opportunists: Proteus and Its Relatives 634 True Enteric Pathogens: Salmonella and Shigella ••• Yersinia pestis and Plague 639 Oxidase-Positive Nonenteric Pathogens in Family Pasteurellaceae 641 Haemophilus: The Blood-Loving Bacilli 642 CHAPTER 21 Miscellaneous Bacterial Agents of Disease 648 21.1 The Spirochetes 649 Treponemes: Members of the Genus Treponema 649 Leptospira and Leptospirosis 654 Borrelia: Arthropod-Borne Spirochetes 655 21.2 Curviform Gram-Negative Bacteria and Enteric Diseases 658 The Biology of Vibrio cholerae 659 Vibrio parahaemolyticus and Vibrio vulnificus: Pathogens Carried by Seafood 660 Diseases of the Campylobacter Vibrios 661 Helicobacter pylori: Gastric Pathogen 661 21.3 Medically Important Bacteria of Unique Morphology and Biology 663 Order Rickettsiales 663 Specific Rickettsioses 664 Emerging Rickettsioses 666 Coxiella and Bartonella: Other Vector-Borne Pathogens 667 Other Obligate Parasitic Bacteria: The Chlamydiaceae 668 21.4 Mollicutes and Other Cell-Wall-Defcient Bacteria 671 Biological Characteristics of the Mycoplasmas 671 Bacteria That Have Lost Their Cell Walls 672 CHAPTER 18 The Gram-Positive and Gram-Negative Cocci of Medical Importance 556 18.1 General Characteristics of the Staphylococci 557 Growth and Physiological Characteristics of Staphylococcus aureus 558 The Scope of Staphylococcal Disease 559 Host Defenses Against S. aureus 560 Other Important Staphylococci 561 Identification of Staphylococcus Isolates in Clinical Samples 562 Clinical Concerns in Staphylococcal Infections 563 18.2 General Characteristics of the Streptococci and Related Genera 565 Beta-Hemolytic Streptococci: Streptococcus pyogenes 565 Group B: Streptococcus agalactiae 570 Group D Enterococci and Groups C and G Streptococci 570 Laboratory Identification Techniques 571 Treatment and Prevention of Group A B and D Streptococcal Infections 571 Alpha-Hemolytic Streptococci: The Viridans Group 572 Streptococcus pneumoniae: The Pneumococcus 572 18.3 The Family Neisseriaceae: Gram-Negative Cocci 575 Neisseria gonorrhoeae: The Gonococcus 575 Neisseria meningitidis: The Meningococcus 578 Differentiating Pathogenic from Nonpathogenic Neisseria 581 Other Genera of Gram-Negative Cocci and Coccobacilli 582 CHAPTER 19 The Gram-Positive Bacilli of Medical Importance 587 19.1 Medically Important Gram-Positive Bacilli 588 19.2 Gram-Positive Spore-Forming Bacilli 588 General Characteristics of the Genus Bacillus 588 The Genus Clostridium 592 19.3 Gram-Positive Regular Non-Spore-Forming Bacilli 599 An Emerging Food-Borne Pathogen: Listeria monocytogenes 599 Erysipelothrix rhusiopathiae: A Zoonotic Pathogen 600 19.4 Gram-Positive Irregular Non-Spore-Forming Bacilli 601 Corynebacterium diphtheriae 601 The Genus Propionibacterium 602 19.5 Mycobacteria: Acid-Fast Bacilli 602 Mycobacterium tuberculosis: The Tubercle Bacillus 603 Mycobacterium leprae: The Leprosy Bacillus 608 Infections by Nontuberculous Mycobacteria NTM 610 19.6 Actinomycetes: Filamentous Bacilli 612 Actinomycosis 612 Nocardiosis 612

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Contents xxxi 23.5 A Survey of Helminth Parasites 728 General Life and Transmission Cycles 728 General Epidemiology of Helminth Diseases 729 Pathology of Helminth Infestation 730 Elements of Diagnosis and Control 730 23.6 Nematode Roundworm Infestations 732 Intestinal Nematodes Cycle A 732 Intestinal Nematodes Cycle B 733 Tissue Nematodes 735 23.7 Flatworms: The Trematodes and Cestodes 737 Blood Flukes: Schistosomes Cycle D 738 Liver and Lung Flukes Cycle D 738 Cestode Tapeworm Infections Cycle C 739 23.8 The Arthropod Vectors of Infectious Disease 741 CHAPTER 24 Introduction to Viruses That Infect Humans: The DNA Viruses 749 24.1 Viruses in Human Infections and Diseases 750 Important Medical Considerations in Viral Diseases 751 Overview of DNA Viruses 752 24.2 Enveloped DNA Viruses: Poxviruses 752 Classification and Structure of Poxviruses 752 Other Poxvirus Diseases 754 24.3 Enveloped DNA Viruses: The Herpesviruses 754 General Properties of Herpes Simplex Viruses 755 Epidemiology of Herpes Simplex 755 The Spectrum of Herpes Infection and Disease 755 The Biology of Varicella-Zoster Virus 758 The Cytomegalovirus Group 760 Epstein-Barr Virus 760 Diseases of Herpesviruses 6 7 and 8 762 24.4 The Viral Agents of Hepatitis 763 Hepatitis B Virus and Disease 764 24.5 Nonenveloped DNA Viruses 766 The Adenoviruses 766 Papilloma- and Polyomaviruses 767 Nonenveloped Single-Stranded DNA Viruses: The Parvoviruses 769 CHAPTER 25 The RNA Viruses That Infect Humans 774 25.1 Enveloped Segmented Single-Stranded RNA Viruses 775 The Biology of Orthomyxoviruses: Influenza 775 Other Viruses with a Segmented Genome: Bunyaviruses and Arenaviruses 781 25.2 Enveloped Nonsegmented Single-Stranded RNA Viruses 781 Paramyxoviruses 781 Mumps: Epidemic Parotitis 782 21.5 Bacteria in Dental Disease 672 The Structure of Teeth and Associated Tissues 672 Hard-Tissue Disease: Dental Caries 673 Plaque and Dental Caries Formation 673 Soft-Tissue and Periodontal Disease 675 Factors in Dental Disease 675 CHAPTER 22 The Fungi of Medical Importance 681 22.1 Fungi as Infectious Agents 682 Primary/True Fungal Pathogens 682 Emerging Fungal Pathogens 683 Epidemiology of the Mycoses 684 Pathogenesis of the Fungi 684 Diagnosis of Mycotic Infections 685 Control of Mycotic Infections 687 22.2 Organization of Fungal Diseases 688 Systemic Infections by True Pathogens 688 22.3 Subcutaneous Mycoses 694 The Natural History of Sporotrichosis: Rose-Gardener’s Disease 694 Chromoblastomycosis and Phaeohyphomycosis: Diseases of Pigmented Fungi 694 Mycetoma: A Complex Disfiguring Syndrome 695 22.4 Cutaneous Mycoses 695 Characteristics of Dermatophytes 696 22.5 Superfcial Mycoses 698 22.6 Opportunistic Mycoses 699 Infections by Candida: Candidiasis 699 Cryptococcus neoformans and Cryptococcosis 700 Pneumocystis jirovecii and Pneumocystis Pneumonia 702 Aspergillosis: Diseases of the Genus Aspergillus 702 Mucormycosis 703 Miscellaneous Opportunists 704 22.7 Fungal Allergies and Intoxications 705 CHAPTER 23 The Parasites of Medical Importance 710 23.1 The Parasites of Humans 711 23.2 Major Protozoan Pathogens 711 Infective Amoebas 712 An Intestinal Ciliate: Balantidium coli 715 23.3 The Flagellates Mastigophorans 716 Trichomonads: Trichomonas Species 716 Giardia intestinalis and Giardiasis 717 Hemoflagellates: Vector-Borne Blood Parasites 717 23.4 Apicomplexan P arasites 722 Plasmodium: The Agent of Malaria 722 Coccidian Parasites 726

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xxxii Contents 26.4 Terrestrial Microbiology: The Composition of the Lithosphere 825 Living Activities in Soil 827 26.5 The Microbiology of the Hydrosphere 828 The Hydrologic Cycle 828 The Structure of Aquatic Ecosystems 829 CHAPTER 27 Applied and Industrial Microbiology 838 27.1 Applied Microbiology and Biotechnology 840 Microorganisms in Water and Wastewater Treatment 840 27.2 The Microbiology of Food 842 27.3 Microbial Fermentations in Food Products 843 Bread Making 843 Production of Beer and Other Alcoholic Beverages 843 Microbes in Milk and Dairy Products 846 Microorganisms as Food 847 27.4 Microbial Involvement in Food-Borne Diseases 847 Prevention Measures for Food Poisoning and Spoilage 849 27.5 General Concepts in Industrial Microbiology 852 From Microbial Factories to Industrial Factories 853 Substance Production 855 APPENDIX A Detailed Steps in the Glycolysis Pathway A-1 APPENDIX B Tests and Guidelines B-1 APPENDIX C General Classifcation Techniques and Taxonomy of Bacteria C-1 APPENDIX D Answers to Multiple-Choice Matching and Case Study Questions D-1 ONLINE APPENDICES An Introduction to Concept Mapping Signifcant Events in Microbiology and Exponents Glossary G-1 Index I-1 Measles: Morbillivirus Infection 783 Respiratory Syncytial Virus: RSV Infections 785 Rhabdoviruses 785 25.3 Other Enveloped RNA Viruses: Coronaviruses Togaviruses and Flaviviruses 787 Coronaviruses 787 Rubivirus: The Agent of Rubella 788 Hepatitis C Virus 788 25.4 Arboviruses: Viruses Spread by Arthropod Vectors 789 Epidemiology of Arbovirus Disease 789 General Characteristics of Arbovirus Infections 790 25.5 Retroviruses and Human Diseases 792 HIV Infection and AIDS 792 Human T-Cell Lymphotropic Viruses 801 25.6 Nonenveloped Single-Stranded and Double-Stranded RNA Viruses 801 Picornaviruses and Caliciviruses 802 Poliovirus and Poliomyelitis 802 Nonpolio Enteroviruses 804 Hepatitis A Virus and Infectious Hepatitis 805 Human Rhinovirus HRV 806 Caliciviruses 806 Reoviruses: Segmented Double-Stranded RNA Viruses 806 25.7 Prions and Spongiform Encephalopathies 807 Pathogenesis and Effects of CJD 808 CHAPTER 26 Environmental Microbiology 814 26.1 Ecology: The Interconnecting Web of Life 816 The Organization of the Biosphere 816 26.2 Energy and Nutritional Flow in Ecosystems 817 Ecological Interactions Between Organisms in a Community 819 26.3 The Natural Recycling of Bioelements 820 Atmospheric Cycles 821 Sedimentary Cycles 824

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1 3 sailboat called the Sorcerer II embarked on a highly shing expedition in the Sargasso Sea. What was most strik- voyage was that it did no involve actually catching sh nets. Instead the targets were tiny oating microbes an exceedingly sophisticated and c technology. This project was the brainchild of Dr. Craig Ven- a prominent genetics researcher and its pri- mary goal was to survey in detail the mircrobial population of ocean water. Scientists aboard the vessel randomly collected surface water about ev- ery 200 miles extracted the tiniest forms of micro- scopic plankton primarily bacteria and sent samples back to Venter’s laboratory. It was here that his scienti c crew engaged in a new and pow- erful way of examining the world. Instead of pains- takingly locating tand identifying the individual microbes in the sample as might have been done in the past they ex tracted the genetic material DNA from the samples and analyzed the DNA using state-of-the-art molecular techniques and computers. Their stunning and somewhat unexpected discovery was that the variety and numbers of microbes liv- ing in the ocean exceeded by far any previous ocean studies. This ambitious undertaking was just the beginning. It was followed by several additional voyages by Dr. Venter’s ship as well as marine microbi- ologists at the Marine Biological Institute in Woods Hole Massachusetts and is continuing today all over the globe. Even though microbiologists had previously described around 5700 di erent types of bacteria the evidence from these studies showed that this number represented only the tiniest “drop in the ocean. ” Some of the data uncovered evidence of more an 20000 di erent kinds of microorganisms in just a single liter of seawater most of them unknown. Realizing that the ocean is a vast space with endless nooks and crannies for organisms to hide by one estimate it could easily contain 5 to 10 million di erent mi- croscopic creatures each of them having unique characteristics and roles in the ocean environment. According to Dr. David Thomassen Chief Scientist Department of Energy “Microbes rule the earth. Sci- entists estimate that there are more microbes on earth than there are stars in the universe—an esti- mated nonillion one followed by thirty zeros. Mi- crobes and their communities make up the foundation of the biosphere and sustain all life on earth. ” Which groups of microorganisms would likey be found in the plankton What elds of microbiology could be involved in the further study of these microbes and in unco eringtheir basic characteristics To continue the case go to page 000. Dr. Venter was one of the main individuals behind the mapping of the human genome in 2001. This technique called metagenomic analysis will be discussed in a later chapter10. : The Methods for This is a colorized view of Beribus voluptios magnit o ciis dolum et am id ute cusant. Ferrorest volore voles et lam quam cumquas in reperibusam nullore voluptios magnit. “ Peering through the microscope into a drop of seawater is like looking at stars with a telescope on a clear night.” Dr. Victor Gallardo ocean researcher This is an Example of a Longer Case File Title Micro “ It’s the first time we’ve gotten a real insight into what organisms might live beneath the Antarctic continent.” David Pearce a microbiologist at Northumbria University UK sediment samples from the lake. Study of those samples which con - tinues today reveals that Lake Whillans hosts a vibrant ecosystem. DNA analysis revealed nearly 4000 diferent microbial species and each milliliter of lake water contained more than 130000 cells comparable to what one fnds in the deepest oceans. The biggest diference between life in Lake Whillans and ecosystems found on the sur - face of the planet is the lack of sunlight. In terres - trial lakes photosynthetic microorganisms use the energy in sunlight to convert dissolved carbon dioxide into sugars. Because sunlight can’t pene- trate the half mile of ice covering Lake Whillans many of the microbes in the lake derive energy from the oxidation of iron sulfur or ammonium compounds a strategy used by some deep-sea bacteria. If it turns out as many scientists believe that the microorganisms in Lake Whillans supply minerals and nutrients to the surrounding ocean then this small dark cold invisible lake may have a tremendous efect on the ecosystem surrounding it. Not bad for a frozen wasteland. ■ One of the environmental pressures microorganisms from Lake Whillans had to adapt to was the ability to grow in very cold temperatures. What were several other environmental challenges these microbes faced ■ What felds of microbiology were used to initially study these microbes and what felds could be involved in the further study of the isolated cells T o continue this Case Study go to Case Study Part 2 at the end of the chapter. A frozen white wasteland a toxic soup a lunar landscape. Three fairly common descriptions of an environment so harsh—cold toxic or lack - ing nutrients—that no life can survive. Lake Whillans a small shallow lake trapped beneath half a mile of ice certainly fts that description. Located 640 kilometers from the South Pole Lake Whillans is completely encased in ice and sits at a slant pressed against the side of a hill far below the icy surface. As heat from the core of the Earth melts the bottom of the Antarctic ice sheet a few millili- ters of liquid water are added to the lake each year. Subglacial lakes like Lake Whillans were dis- covered only in the late 1990s when ice- penetrating radar and satellite measurements allowed researchers to see through the dense ice sheets that cover the polar regions of the planet. The next phase of the project was—as has been the case as long as humans have been exploring their environments—to determine what if anything lived in the newly discovered area. Although the immediate instinct would be to drill through the ice and sample the water in the lake microbial ecologists realized that sampling Lake Whillans was not terribly difer- ent from performing surgery on a human patient aseptic techniques would have to be followed so that external microbes were not allowed to contaminate the lake. Drilling equipment was sterilized using a com- bination of ultraviolet light and hydrogen peroxide the same techniques routinely used in hospitals and laboratories and the water used to bore through the ice was fltered to remove even the smallest microorgan- isms. When the drill penetrated the last of the ice it entered the lake which at −0.5°C was several degrees warmer than the Antarctic surface. Over the next few days until the drilling hole froze shut scien - tists and graduate students collected 30 liters of water and several Microbes Find A Way CASE STUDY Part 1 1 CHAPTER The Main Themes of Microbiology Streams of methane bubbles rise from the seafoor the product of micro - scopic organisms adapted to the extreme environment of the deep ocean. Source: NOAA Okeanos Explorer Program 2013 ROV Shakedown and Field Trials in the U.S. Atlantic Canyons A microbial ecologist carries a water sample from subglacial Lake Whillans 640 kilometers from the South Pole. © JT Thomas

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2 Chapter 1 The Main Themes of Microbiology SCOPING OUT THE CHAPTER The Fields of Microbiology Not every microbiologist works in a lab. Making cheese wine and bread all rely on a knowledge of microbiology. The Organisms of Microbiology The vast majority of microorganisms pose no risk to humans. Some however like certain strains of the bacterium Staphylococcus aureus not only cause severe disease but are resistant to almost all the drugs commonly used to fight them. The History of Microbiology The period from 1850 to 1950 is sometimes known as the Golden Age of Microbiology when people like Louis Pasteur invented the very science of microbiology itself. The recent advent of powerful molecular biology techniques has caused many scientists to view the current era as a second Golden Age. The Power of Microbiology The vats here contain algae that are producing oil through photosynthesis a potentially endless source of clean energy. The Evolution of Microorganisms All life on Earth has evolved from simple microbial cells. Evolutionary trees display the relationship between simpler and more complex organisms. Microbiology is sometimes regarded as an esoteric science concerned primarily with keeping the milk fresh and getting everyone to wash their hands. In fact microbiology encompasses a number of interrelated disciplines a rich history and more organisms than any other branch of biology. In this chapter you’ll get a quick tour of the feld. Fields of Microbiology: © Joe Munroe/Science Source Power of Microbiology: Source: Christopher Botnick/NOAA Organisms of Microbiology: Source: Matthew J. Arduino DRPH/Janice Haney Carr/CDC History of Microbiology: © Dea Picture Library/Getty Images ubiquitous yoo-bik′-wih-tis L. ubique everywhere and ous having. Being or seeming to be everywhere at the same time. 1.1 The Scope of Microbiology Expected Learning Outcomes 1. Defne microbiology and microorganisms and identify the major organisms included in the science of microbiology. 2. Name and defne the primary felds included in microbiological studies. As we observe the natural world teeming with life we cannot help but be struck by its beauty and complexity. But for every feature that is visible to the naked eye there are millions of other features that are concealed from our sight by their small size. This alternate microscopic universe is populated by a vast microbial menagerie that is equally beautiful and complex. To sum up the presence of microbes in one word they are ubiquitous. They are found in all

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1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments 3 natural habitats and most of those that have been created by hu- mans. As scientists continue to explore remote and unusual envi- ronments the one kind of entity they always find is microbes. These exist deep beneath the polar ice caps in the ocean to a depth of 7 miles in hot springs and thermal vents in toxic waste dumps and even in the clouds. Microbiology is a specialized area of biology that deals with tiny life forms that are not readily observed without magnification which is to say they are microscopic. These microscopic organ- isms are collectively referred to as microorganisms microbes or several other terms depending upon the purpose. Some people call them “germs” or “bugs” in reference to their role in infection and disease but those terms have other biological meanings and per- haps place undue emphasis on the disagreeable reputation of micro- organisms. The major groups of microorganisms included in this study are bacteria viruses fungi protozoa algae and helminths parasitic worms. As we will see in subsequent chapters each group exhibits a distinct collection of biological characteristics. The nature of microorganisms makes them both easy and difficult to study. Easy because they reproduce so rapidly and can usually be grown in large numbers in the laboratory. Difficult because we can’t observe or analyze them without special techniques espe- cially the use of microscopes see chapter 3. Microbiology is one of the largest and most complex of the biological sciences because it integrates subject matter from many diverse disciplines. Microbiologists study every aspect of microbes—their genetics their physiology characteristics that may be harmful or beneficial the ways they interact with the environ- ment the ways they interact with other organisms and their uses in industry and agriculture. See table 1.1 for an overview of some fields and occupations that involve basic study or applications in microbiology. Each ma- jor discipline in microbiology contains numerous subdivisions or specialties that deal with a specific subject area or field table 1.1. In fact many areas of this science have become so specialized that it is not uncommon for a microbiologist to spend an entire career concentrating on a single group or type of microbe biochemical process or disease. The specialty professions of microbiology include: ∙ geomicrobiologists who focus on the roles of microbes in the development of earth’s crust table 1.1B ∙ marine microbiologists who study the oceans and its smallest inhabitants ∙ medical technologists who do the tests that help diagnose pathogenic microbes and diseases associated with them ∙ nurse epidemiologists who analyze the occurrence of infec- tious diseases in hospitals and ∙ astrobiologists who study the possibilities of organisms in space see the Case Study for chapter 2. Studies in microbiology have led to greater understanding of many general biological principles. For example the study of microorganisms established universal concepts concerning the chemistry of life see chapters 2 and 8 systems of inheritance see chapter 9 and the global cycles of nutrients minerals and gases see chapter 26. 1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments Expected Learning Outcomes 3. Describe the basic characteristics of prokaryotic cells and eukaryotic cells and their evolutionary origins. 4. State several ways that microbes are involved in the earth’s ecosystems. 5. Describe the cellular makeup of microorganisms and their size range and indicate how viruses difer from cellular microbes. The Origins and Dominance of Microorganisms For billions of years microbes have extensively shaped the devel- opment of the earth’s habitats and influenced the evolution of other life forms. It is understandable that scientists searching for life on other planets first look for signs of microorganisms. The fossil record uncovered in ancient rocks and sediments points to bacteria-like cells having existed on earth for at least 3.5 billion years figure 1.1. Early microorganisms of this type domi nated the earth’s life forms for the first 2 billion years. These ancient cells were small and simple and lacked specialized internal structures to carry out their functions. It is apparent that genetic material of these cells was not bound into a separate compartment called a nucleus or “karyon.” The term assigned to cells and mi- crobes of this type is prokaryotic meaning “before the nucleus.” About 1.8 billion years ago there appeared in the fossil record a more complex cell which had developed a nucleus and various specialized internal structures called organelles. These types of cells and organisms are defined as eukaryotic in reference to their “true” nucleus. Figure 1.2 compares the two cell types and in- cludes some examples of viruses for comparison. In chapter 5 we will learn more about the origins of eukaryotic cells—they didn’t arise suddenly out of nowhere they evolved over millennia from prokaryotic cells through an intriguing process called endosymbio- sis. The early eukaryotes probably similar to algae and protozoa started lines of evolution that eventually gave rise to fungi plants and multicellular animals such as worms and insects. You can see from figure 1.1 how long that took The bacteria preceded even the earliest animals by about 3  billion years. This is a good indication that humans are not likely to nor should we try to eliminate microorganisms from our environment. Having existed for eons they are absolutely essential for maintaining the planet’s life-giving characteristics. microscopic my″-kroh-skaw′-pik Gr. mikros small and scopein to see. microbe my′-krohb Gr. mikros small and bios life. prokaryotic proh″-kar-ee-ah′-tik Gr. pro before and karyon nucleus. Sometimes spelled procaryotic. organelles or-gan′-elz Gr. organa tool and ella little. eukaryotic yoo″-kar-ee-ah′-tik Gr. eu true or good and karyon nucleus. Sometimes spelled eucaryotic.

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4 Chapter 1 The Main Themes of Microbiology TABLE 1.1 A Sampling of Fields and Occupations in Microbiology A. Public Health Microbiology and Epidemiology These branches monitor and control the spread of diseases in communities. Some of the institutions charged with this task are the U.S. Public Health Service USPHS and the Centers for Disease Control and Prevention CDC. The CDC collects information and statistics on diseases from around the United States and publishes it in a newsletter The Morbidity and Mortality Weekly Report see chapter 13. B. Environmental Microbiology This field encompasses the study of microorganisms and their ecological relationships in such natural habitats as soil and water. C. Biotechnology and Industrial Microbiology This branch is defined by any process that harnesses the actions of living things to derive a desired product ranging from beer to stem cells. It includes industrial microbiology which uses microbes to produce and harvest large quantities of such substances as vaccines vitamins drugs and enzymes see chapters 10 and 27. D. Immunology This branch studies the complex web of protective substances and reactions caused by invading microbes and other harmful entities. It includes such diverse areas as blood testing vaccination and allergy see chapters 15 16 and 17. A parasite specialist examines leaf litter for the presence of black-legged ticks— the carriers of Lyme disease. Source: Photo by Scott Bauer/USDA A technician tests the efectiveness of microorganisms in the production of new sources of energy. Source: Lawrence Berkeley National Laboratory A geomicrobiologist from NASA collects samples from Mono Lake as part of an environmental study determining survival strategies of extreme bacteria. © Henry Bortman A CDC virologist examines cultures of infuenza virus that are used in producing vaccines. This work requires high-level biohazard containment. Source: James Gathany/CDC

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1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments 5 E. Genetic Engineering and Recombinant DNA Technology These interrelated fields involve deliberate alterations of the genetic makeup of organisms to create novel microbes plants and animals with unique behavior and physiology. This is a rapidly expanding field that often complements biotechnology see chapter 10. F. Agricultural Microbiology This branch is concerned with the relationships between microbes and domesticated plants and animals. Plant specialists focus on plant diseases soil fertility and nutritional interactions. Animal specialists work with infectious diseases and other interactions between animals and microorganisms. H. Branches of Microbiology Branch Chapter Involved in the Study of: Bacteriology 4 The bacteria—small single-celled prokaryotic organisms Mycology 5 22 The fungi a group of eukaryotes that includes both microscopic eukaryotes molds and yeasts and larger organisms mushrooms puffballs Protozoology 5 23 The protozoa—animal-like and mostly single-celled eukaryotes Virology 6 24 25 Viruses—minute noncellular particles that parasitize cells Parasitology 5 23 Parasitism and parasitic organisms—traditionally including pathogenic protozoa helminth worms and certain insects Phycology or Algology 5 Simple photosynthetic eukaryotes the algae ranging from single-celled forms to large seaweeds Morphology 4 5 6 The detailed structure of microorganisms Physiology 7 8 Microbial function metabolism at the cellular and molecular levels Taxonomy 1 4 5 17 Classification naming and identification of microorganisms Microbial Genetics 9 10 The function of genetic material and biochemical reactions that Molecular Biology make up a cell’s metabolism Microbial Ecology 7 26 Interrelationships between microbes and the environment the roles of microorganisms in the nutrient cycles and natural ecosystems A bacteriologist from the U.S. Department of Energy checks cultures of genetically modifed bacteria for growth. Source: Biological and Environmental Research Information System Oak Ridge National Laboratory. Sponsored by the U.S. Department of Energy Biological and Environmental Research Program. Microbiologists from the U.S. Food and Drug Administration collect soil samples to detect animal pathogens. Source: Photo by Black Star/Steve Yeater for FDA G. Food Microbiologists These scientists are concerned with the impact of microbes on the food supply including such areas as food spoilage food-borne diseases and production. A U.S. Department of Agriculture technician observes tests for the presence of Escherichia coli in foods. Source: Photo by Keith Weller/USDA A medical microbiologist tests specimens for evidence of antibodies to the human immunodefciency virus HIV. Source: James Gathany/CDC

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6 Chapter 1 The Main Themes of Microbiology complexes and several others which perform specific functions such as transport feeding energy release and use and synthesis. Prokaryotes perform similar functions but they lack dedicated or- ganelles to carry them out figure 1.2. The body plan of most microorganisms consists of a single cell or clusters of cells figure 1.3. All prokaryotes are microorganisms The Cellular Organization of Microorganisms As a general rule prokaryotic cells are smaller than eukaryotic cells and in addition to lacking a nucleus they lack organelles which are structures in cells bound by one or more membranes. Examples of organelles include the mitochondria and Golgi Earliest eukaryotic cells appeared. Reptiles appeared. Cockroaches termites appeared. Probable origin of universe. Origin of earth. Earliest prokaryotic cells appeared. Mammals appeared. Humans appeared. 4 billion years ago 14 billion years ago 3 billion years ago 2 billion years ago 1 billion years ago Present time Figure 1.1 Evolutionary time line. The frst simple prokaryotes appeared on earth approximately 3.5 billion years ago and the frst eukaryotes arose about 2 billion years ago. Although these appearances seem abrupt hundreds of millions of years of earth’s history passed while they were evolving to these stages. The fossil record for these periods is incomplete because many of the earliest microbes were too delicate to fossilize. Source: NASA Figure 1.2 Basic structure of cells and viruses. a Comparison of a prokaryotic cell and a eukaryotic cell. b Two examples of viruses. These cell types and viruses are discussed in more detail in chapters 4 5 and 6. Cell membrane Nucleus Mitochondria Ribosomes Cell membrane Cell wall Flagellum Flagellum Chromosome Prokaryotic cell Eukaryotic cell showing selected organelles Capsid Envelope An enveloped virus HIV A complex virus bacteriophage Nucleic acid Ribosomes a Basic cell types b Examples of viruses

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1.2 General Characteristics of Microorganisms and Their R oles in the Earth’s Environments 7 Algae: desmids Spirogyra filament and diatoms golden cells 500x. Helminths: Roundworms of Trichinella spiralis coiled in the muscle of a host 250x. This worm causes trichinellosis. Protozoa: A protozoan Oxytricha trifallax bearing tufts of cilia that function like tiny legs 3500x. Virus: Herpes simplex the cause of cold sores 100000x. Fungi: Histoplasma capsulatum with lollipop-like reproductive structures 750x. This agent is the cause of Ohio Valley fever. Bacteria: Mycobacterium tuberculosis a rod-shaped cell 15500x. A single virus particle A single virus particle Reproductive spores A single virus particle A single virus particle Figure 1.3 The six basic types of microorganisms. Organisms are not shown at the same magnifcations approximate magnifcation is provided. To see these microorganisms arrayed more accurately to scale look for them in fgure 1.4. bacteria: Source: Janice Carr/CDC fungi: Source: Dr. Libero Ajello/CDC algae: © Charles Krebs Photography virus: Source: CDC protozoa: Source: National Human Genome Research Institute helminths: Source: CDC composed essentially of a small amount of hereditary material wrapped up in a protein covering. Some biologists refer to viruses as parasitic particles others consider them to be very primitive organisms. Despite this slight disagreement the impact of viruses is undeniable. Not only are they the most com- mon microbes on earth but they invade their hosts’ cells and can infict serious damage and death. Microbial Dimensions: How Small Is Small When we say that microbes are too small to be seen with the un- aided eye what sorts of dimensions are we talking about This concept is best visualized by comparing microbial groups with some organisms of the macroscopic world and also with the mole- cules and atoms of the molecular world figure 1.4. The dimensions and they include the bacteria and archaea see figure 1.14. Only some of the eukaryotes are microorganisms: primarily algae proto- zoa molds and yeasts types of fungi and certain animals such as worms and arthropods. Not all members of these last two groups are microscopic but certain members are still included in the study of microbiology because worms can be involved in infections and may require a microscope to identify them. Some arthropods such as fleas and ticks may also be carriers of infectious diseases. Additional coverage on cell types and microorganisms appears in chapters 4 and 5. Where Do the Viruses Fit Viruses are considered one type of microbe because they are microscopic and can cause infections and disease but they are not cells. They are small particles that exist at a level of complexity somewhere between large molecules and cells see fgure 1.4. Viruses are much simpler than cells they are An adenovirus Algae: desmids Spirogyra filament and diatoms golden cells 500x. Helminths: Roundworms of Trichinella spiralis coiled in the muscle of a host 250x. This worm causes trichinellosis. Protozoa: A protozoan Oxytricha trifallax bearing tufts of cilia that function like tiny legs 3500x. Virus: Herpes simplex the cause of cold sores 100000x. Fungi: Histoplasma capsulatum with lollipop-like reproductive structures 750x. This agent is the cause of Ohio Valley fever. Bacteria: Mycobacterium tuberculosis a rod-shaped cell 15500x. A single virus particle A single virus particle Reproductive spores A single virus particle A single virus particle

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8 Flea Roundworm Fungus sporangium Protozoan Mold spores Algae Spirochete Microscopic Ultramicroscopic Macroscopic Atomic Rods Most bacterial cells fall between 10 m and 1 m in size. Most viruses fall between 200 and 10 nm in size. Also featured in figure 1.3 Cocci Rickettsias Poxvirus Herpesvirus HIV Poliovirus Range of electromicroscope Requires special microscopes Range of light microscope Range of eye DNA molecule Protein molecule Glucose molecule Hydrogren atom 0.1 nm 0.5 nm 1 nm 2 nm 0.1 nm 0.5 nm 1 nm 2 nm 10 nm 10 nm 70 nm 70 nm 100 nm 100 nm 200 nm 200 nm 1 m 1 m 2 m 2 m 5 m 5 m 10 m 10 m 20 m 20 m 50 m 50 m 200 m 200 m 1 mm 2 mm 1 mm 2 mm Metric Chart Length kilometer hectometer dekameter decimeter centimeter millimeter micrometer nanometer Angstrom picometer km hm dam dm cm mm m nm Å pm 1000x 100x 10x 0.1x 0.01x 0.001x 0.000001x 0.000000001x 0.00000000001x 0.000000000001x 10 3 10 2 10 1 10 -1 10 -2 10 -3 10 -6 10 -9 10 -11 10 -12 Symbol Log No. Multiplier Figure 1.4 The sizes of the smallest organisms and objects. Even though they are all very small they still display extensive variations in size. This illustration organizes the common measurements used in microbiology along with examples of organisms or items that fall into these measurement ranges. The scale includes macroscopic microscopic ultramicroscopic and atomic dimensions. Most microbes we study measure somewhere between 100 micrometers μm and 10 nanometers nm overall. The examples are more or less to scale within a size zone but not between size zones. roundworm: Source: CDC fungus: © Dennis Kunkel Microscopy Inc./Phototake protozoan: Source: National Human Genome Research Institute algae: © Charles Krebs Photography mold spores: Dr. Libero Ajello/CDC spirochete: Source: CDC rods cocci: Source: Janice Carr/CDC herpesvirus: Source: CDC range of eye: Source: Berkeley Lab - Roy Kaltschmidt photographer range of light microscope: Source: Rhoda Baer photographer/National Cancer Institute range of electromicroscope: Source: Pacifc Northwest National Laboratory

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1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments 9 1. Ecosystems are communities of living organisms and their surrounding environment. of macroscopic organisms are usually given in centimeters cm and meters m whereas those of most microorganisms fall within the range of micrometers μm and sometimes nanometers nm and millimeters mm. The size range of most microbes extends from the smallest viruses measuring around 10 nm and actually not much bigger than a large molecule to protozoans measuring 3 to 4 mm and visible with the naked eye. Microbial Involvement in Energy and Nutrient Flow The microbes in all natural environments have lived and evolved there for billions of years. We do not yet know all of their roles but it is likely they are vital components of the structure and function of these ecosystems. Microbes are deeply involved in the flow of energy and food through the earth’s ecosystems. 1 Most people are aware that plants carry out photosynthesis which is the light-fueled conversion of carbon dioxide to organic material accompanied by the formation of oxygen. But microorganisms were photosynthesizing long be- fore the first plants appeared. In fact they were responsible for changing the atmosphere of the earth from one without oxygen to one with oxygen. Today photosynthetic microorganisms includ- ing algae account for more than 50 of the earth’s photosynthe- sis contributing the majority of the oxygen to the atmosphere figure 1.5a. Another process that helps keep the earth in balance is the process of biological decomposition and nutrient recycling. Decomposition involves the breakdown of dead matter and wastes into simple compounds that can be directed back into the natural cycles of living things figure 1.5b. If it were not for multitudes of bacteria and fungi many chemical elements would become locked up and unavailable to organisms. In the long- term scheme of things microorganisms are the main forces that drive the structure and content of the soil water and atmos- phere. For example: ∙ Earth’s temperature is regulated by “greenhouse gases” such as carbon dioxide and methane that create an insulation layer in the atmosphere and help retain heat. A significant propor- tion of these gases is produced by microbes living in the envi- ronment and in the digestive tracts of animals. ∙ Recent estimates propose that based on weight and numbers up to 50 of all organisms exist within and beneath the earth’s crust in soil rocks and even the frozen Antarctic figure 1.5c. It is increasingly evident that this enormous underground com- munity of microbes is a major force in weathering mineral extraction and soil formation. ∙ Bacteria and fungi live in complex associations with plants. They assist the plants in obtaining nutrients and water and may protect them against disease. Microbes form similar interrela- tionships with animals notably as residents of numerous bodily sites. Figure 1.5 A microscopic wonderland. a A summer pond is heavily laden with surface scum that reveals several diferent types of green algae called desmids 600×. b A rotting tomato being invaded by a fuzzy forest of mold. The fungus is Botrytis a common decomposer of tomatoes and grapes 250× . c Even a dry lake in Antarctica one of the coldest places on earth −35°C can harbor microbes under its icy sheet. Here we see a red cyanobacterium Nostoc 3000× that has probably been frozen in suspended animation there for 3000 years. Like the example discussed in the chapter-opening case study this environment may serve as a model for what may one day be discovered on other planets. a: Source: Photo by Lynn Betts USDA Natural Resources Conservation Service a inset © Stephen Sharnof/National Geographic Creative b b inset: © Kathy Park Talaro c © Peter Doran/University of Illinois Chicago c inset Image courtesy of the Priscu Research Group Montana State University Bozeman a c b

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10 Chapter 1 The Main Themes of Microbiology Check Your Progress SECTIONS 1.1–1.2 1. Define what is meant by the term microorganism and outline the im- portant contributions microorganisms make to the earth’s ecosystems. 2. Describe five different ways in which humans exploit microorgan- isms for our benefit. 3. Identify the groups of microorganisms included in the scope of microbiology and explain the criteria for including these groups in the field of microbiology. 4. Observe figure 1.3 and place the microbes pictured there in a size ranking going from smallest to largest. Use the magnification as your gauge. 5. Construct a table that displays all microbial groups based on what kind of cells they have or do not have. 6. Explain this statement: Microorganisms—we need to live with them because we can’t live without them. 1.3 Human Use of Microorganisms Expected Learning Outcome 6. Discuss the ways microorganisms can be used to create solutions for environmental problems and industrial products. The incredible diversity and versatility seen in microbes make them excellent candidates for solving human problems. By accident or choice humans have been using microorganisms for thousands of years to improve life and even to further human progress. Yeasts a type of microscopic fungi cause bread to rise and ferment sugar to make alcoholic beverages. Historical records show that households in ancient Egypt kept moldy loaves of bread to apply directly to wounds and lesions which was probably the first use of penicillin The manipulation of microorganisms to make products in an indus- trial setting is called biotechnology. One newer application of this process uses farmed algae to extract a form of oil biodiesel to be used in place of petroleum products figure 1.6a. Genetic engineering is a newer area of biotechnology that ma- nipulates the genetics of microbes plants and animals for the pur- pose of creating new products and genetically modified organisms. One powerful technique for designing new organisms is termed recombinant DNA. This technology makes it possible to deliber- ately alter DNA 2 and to switch genetic material from one organism to another. Bacteria and fungi were some of the first organisms to be genetically engineered because their relatively simple genetic mate- rial is readily manipulated in the laboratory. Recombinant DNA tech- nology has unlimited potential in terms of medical industrial and agricultural uses. Microbes can be engineered to synthesize desirable proteins such as drugs hormones and enzymes see table 1.1C. Among the genetically unique organisms that have been de- signed by bioengineers are bacteria that contain a natural pesticide yeasts that produce human hormones pigs that produce hemoglo- bin and plants that are resistant to disease see table 1.1E. The biotechnology by′-oh-tek-nol″-oh-gee The use of microbes or their products in the commercial or industrial realm. 2. DNA or deoxyribonucleic acid the chemical substance that comprises the genetic material of organisms. bioremediation by′-oh-ree-mee-dee-ay″-shun bios life re again mederi to heal. The use of biological agents to remedy environmental problems. techniques have also paved the way for characterizing human ge- netic material and diseases. Another way of tapping into the unlimited potential of micro- organisms is the relatively new science of bioremediation. This process introduces microbes into the environment to restore stability or to clean up toxic pollutants. Bioremediation is required to control a a b b Figure 1.6 Microbes at work. a A scientist from the National Oceanic and Atmospheric Agency NOAA demonstrates a series of biodiesel reactors that culture single-celled algae inset 750× as a source of oil. This new “green” renewable energy source looks very promising. b Biotechnology meets bioremediation. Scientists at Pacifc Northwest National Laboratories PNNL test the capacity of two newly discovered bacteria—Shewanella green and Synechococcus yellow 1000×—to reduce and detoxify radioactive waste. The process carried out in large bioreactors could speed the cleanup of hazardous nuclear waste deposits. a: Source: Christopher Botnick/NOAA a inset: © Yuuji Tsukii Protist Information Server b b inset: Source: Pacifc Northwest National Laboratory

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1.4 Microbial Roles in Infectious Diseases 11 the massive levels of pollution that result from human activities. Microbes have a surprising capacity to break down chemicals that would be harmful to other organisms. Agencies and companies have developed microbes to handle oil spills and detoxify sites con- taminated with heavy metals pesticides and even radioactive wastes figure 1.6b. The solid waste disposal industry is focusing on methods for degrading the tons of garbage in landfills especially plastics and paper products. One form of bioremediation that has been in use for some time is the treatment of water and sewage. With clean freshwater supplies dwindling worldwide it will be- come even more important to find ways to reclaim polluted water. 1.4 Microbial Roles in Infectious Diseases Expected Learning Outcomes 7. Review the roles of microorganisms as parasites and pathogens that cause infection and disease. 8. Defne what is meant by emerging and reemerging diseases. It is important to remember that the large majority of microorgan- isms are relatively harmless have quantifiable benefits to humans and the environment and in many cases are essential to life as we know it. They are free living and derive everything they need to survive from the surrounding environment. Much of the time they form cohesive communities with other organisms sharing habitat and nutrients. Examples include the natural partnerships that are found in symbioses and biofilms. 3 Some microbes have adapted to a non-free-living lifestyle called parasitism. A parasite lives in or on the body of a larger or- ganism called the host and derives most of its sustenance from that host. A parasite’s actions generally damage the host through infec- tion and disease. Another term that can be used to specify this type of microbe is pathogen. Humanity is plagued by nearly 2000 different pathogens that can cause various types of disease. Infectious diseases still devastate human populations worldwide despite significant strides in under- standing and treating them. The most recent estimates from the World Health Organization WHO point to around 10 billion infections of all types across the world every year. There are more infections than people because many people acquire more than one infection. Infec- tious diseases are also among the most common causes of death in much of humanity and they still kill a significant percentage of the U.S. population. The worldwide death toll from infections is about 13 million people per year and 90 of the deaths are caused by just six infectious agents. Table 1.2 illustrates the toll of some common in- fectious diseases while figure 1.7 compares the death rate among four groups from around the world that differ significantly in socio- economic levels. It is quite evident which world inhabitants suffer the most from infectious diseases. Table 1.3 displays the number of peo- ple affected by what are commonly known as neglected tropical dis- eases NTDs a collection of conditions that thrive among the worlds 3. A biofilm is a complex network of microbes and their secretions that form in most natural environments discussed further in chapter 4. pathogen path′-oh-jen Gr. pathos disease and gennan to produce. Disease- causing agents. Low-income countries Lower-middle- income countries Upper-middle- income countries High-income countries 14000 12000 10000 8000 6000 4000 2000 0 Total Deaths 000 Communicable infectious diseases maternal and perinatal conditions and nutritional deficiencies Chronic diseases Injuries Chronic diseases include cardiovascular diseases cancers chronic respiratory disorders diabetes neuropsychiatric and sense organ disorders musculoskeletal disorders digestive diseases genitourinary diseases congenital abnormalities and skin diseases. Most of them are not associated with a single infectious agent. Figure 1.7 Chart comparing the major causes of death by world socioeconomic levels. The relationship between income and rate of death from infectious diseases is most evident in this comparison. What other correlations can we make from these data Disease Number of Cases Ascariasis 1000000000 Hookworm infection 700000000 Onchocerciasis river blindness 26000000 Lymphatic filariasis 120000000 Schistosomiasis 240000000 Trachoma 41000000 Trichuriasis 800000000 TABLE 1.3 Neglected Tropical Diseases Disease New Cases per Year Deaths per Year Influenza 3−5 million cases of 250000−500000 severe illness Typhoid fever 21000000 200000 Measles 20000000 145700 HIV/AIDS 2300000 1500000 Dengue fever 96000000 22000 Shigellosis 80000000−165000000 600000 Viral hepatitis 380000000 1280000 A and B Malaria 200000000 627000 Tuberculosis 9000000 1500000 Estimates from most recent CDC and World Health Organization statistics. As many as 2000000000 people are believed to carry the tuberculosis bacterium most as long-term carriers. Source: Data from World Health Organization TABLE 1.2 Worldwide Morbidity and Mortality of Common Diseases

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12 Chapter 1 The Main Themes of Microbiology most active in the evening. Yet even this inexpensive solution is beyond the reach of people in many developing countries who can- not afford the 3 to 5 for nets to protect their family. Fortunately for many countries in the malaria zone several international organ- izations have collaborated to provide special insecticide-treated nets that can help lower the rate of infections. Emerging and Reemerging Diseases Among the more signifi- cant factors in the overall picture of infectious diseases are emerging and reemerging diseases 1.1 Making Connections. Emerging poorest populations and receive far too little attention. Most NTDs are easily treatable with drugs or preventable with vaccines. Those hardest hit are residents in countries where access to adequate medical care is lacking. One-third of the earth’s 7 billion inhabitants live on less than 1 per day are malnourished are not fully immunized and have no access to drugs. Take the case of malaria caused by a microorganism transmitted by mosquitoes which kills 1 to 2 million people every year worldwide. Currently the most effective way for citizens of developing countries to avoid infection is to sleep under a bed net because the mosquitoes are The Changing Spectacle of Infectious Diseases The middle of the last century was a time of great confidence in science and medicine. The introduction of antibiotics in the 1940s and a lengthening list of vaccines for preventing numerous diseases caused many medical experts to declare victory. For a short time there was a sense that infectious diseases were going to be completely manageable. But this optimistic viewpoint was on a collision course with a vast army of very tiny invaders that are every- where—namely microorganisms. Because humans are constantly interact- ing with microbes we serve as a handy incubator for infectious diseases both those newly recognized and older ones previously identified. Altogether government agencies are keeping track of more than 100 emerging and reemerging infectious diseases. The newer or emerging dis- eases usually erupt suddenly with no warning Middle East respiratory syndrome. Older or reemerging diseases demonstrate just how difficult it is to eradicate microbes and the diseases they cause even though we are very aware of them and often have drugs and vaccines to combat them. Only smallpox has been completely eliminated although we are very close to eradicating polio. In fact we continue to experience epidemics of child- hood diseases that are usually preventable with vaccines. Starting in 2010 pertussis whooping cough cases began to increase dramatically over the next 2 years and even though the increase subsided the number of cases remained nearly double their pre-2010 levels. Some communities recorded the highest rates of pertussis in decades even though children were being vaccinated. It now appears that the vaccine’s effectiveness wears off and may require additional inoculations to create adequate protection. What are some of the reasons for this dilemma with our microbial cohabitants A major contributing factor is our increased mobility and travel especially by air—an infected person can travel around the world before showing any symptoms of infection carrying the infectious agent to many far-flung locations and exposing populations along the way who in turn can infect their contacts. A second factor is the spread of diseases by vectors living organisms such as fleas ticks or mosquitoes. Emerg- ing viruses like chikungunya dengue and Zika are all spread by the Aedes mosquito which is so aggressive it routinely follows people in- doors to partake of a blood meal see figure. Other significant effects involve our expanding population and global food-growing practices. As we continue to encroach into new territory and wild habitats there is potential for contact with emerging pathogens as we saw with Ebola fever Lyme disease and hantavirus pulmonary syndrome. Our agricultural practices can unearth microbes that were lying dormant or hidden. A bacterium carried in the intestine of domestic cattle Escherichia coli O157:H7 the agent of a serious kidney disease has been associated with hundreds of thousands of infections from food and water contami- nated with cattle feces. Much mass-produced fresh food can also travel around the world infecting people along the way. Several large outbreaks of salmonellosis shigellosis and listeriosis have been traced to contami- nated dairy and poultry products and vegetables. In some areas of the world farmers knowingly or unknowingly use fecally contaminated water and fertilizer on fresh produce that will be on your table the next week. Then there is the matter of the incredible resistance of microbes. You know about their capacity to live where no other living things could—volcanoes salt lakes radioactive waste pits—so it has not been a surprise to discover how readily they can adapt to drugs we use to treat them. The emergence of drug-resistant “superbugs” has become a mas- sive problem in medicine. Some forms of Staphylococcus aureus MRSA and Mycobacterium tuberculosis are resistant to so many drugs that there are few and sometimes no treatment choices left. As hard as we may try to manage microbes we keep coming up against a potent reality a sentiment summed up by the renowned micro- biologist Louis Pasteur over 130 years ago when he declared: “Microbes will have the last word.” Why is it unlikely that infectious diseases can ever be completely eradicated Answer available on Connect. 1.1 MAKING CONNECTIONS The Aedes aegypticus mosquito is the vector for several emerging viral diseases. In this female mosquito feeding on her photographer blood can clearly be seen within the fascicle feeding apparatus and flling the distended abdomen of the mosquito. Because this species is found throughout the Americas it is thought to be only a matter of time before the Zika dengue and chikungunya viruses are well established in the United States. Source: James Gathany/Prof. Frank Hadley Collins Dir. Cntr. for Global Health and Infectious Diseases Univ. of Notre Dame/CDC

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1.5 The Historical Foundations of Microbiology 13 People are living longer. Sicker people are staying alive much longer than in the past. Older and sicker people have heightened suscepti- bility to what we might call “garden-variety” microbes. Why would chronic infections be more likely to be associated with diseases like cancer Answer available on Connect. diseases are newly identified conditions that are being reported in increasing numbers. Since 1980 at least 87 novel infectious agents have arisen within the human population. Some of them have been associated with a specific location Ebola fever virus whereas oth- ers have become pandemics meaning they spread across continents human immunodeficiency virus—HIV. A number of them cause zoonoses which are infectious diseases native to animals that can be transmitted to humans. One recent example is chikungunya virus spread by mosquitoes to humans and other mammals. This virus trav- eled from the Caribbean to Florida in 2014. It is unclear how fast the virus will spread throughout the United States as conditions become less favorable to the life cycle of mosquitoes as one moves north. Reemerging diseases are older well-known diseases that are increasing in occurrence for reasons outlined in 1.1 Making Con- nections. Among the most common reemerging infectious diseases are tuberculosis TB influenza malaria cholera and hepatitis B. Tuberculosis which has been known since ancient times still causes 8 million new infections and kills 1 million to 2 million people every year. As you will see numerous factors play a part in the tenaciousness of infectious diseases but fundamental to all of them is the formidable capacity of microbes to adapt to alterations in the individual community and environment. zoonoses zoh″-uh-noh′-seez Gr. zoion animal and nosos disease. Any disease indigenous to animals transmissible to humans. Are Microbes a Hidden Cause of Diseases One of the most eye-opening discoveries has been that many dis - eases once considered noninfectious probably do involve microbial infection. Most scientists expect that in time a majority of chronic conditions will be be linked to microbial agents. The most famous of these is gastric ulcers now known to be caused by a bacterium called Helicobacter see chapter 21. But there are more. Diseases as dispa- rate as type 1 diabetes obsessive compulsive disorder and coronary artery disease have been linked to chronic infections with microorgan- isms. Even the microbiome the collection of microorganisms we all carry with us even when healthy has been shown to have a much greater efect on our health than was previously thought. Recent stud- ies have linked changes in the microbiome population to metabolic syndrome a collection of health conditions including high cholesterol hypertension high blood sugar levels and excess fat all of which can raise the risk of heart disease stroke and diabetes. It seems that the golden age of microbiological discovery during which all of the “obvi - ous” diseases were characterized and cures or preventions were de- vised for them should more accurately be referred to as the frst golden age. We’re now discovering the roles of microorganisms in hidden but slowly destructive diseases. These include female infertility caused by Chlamydia infection and malignancies such as liver cancer hepatitis viruses and cervical cancer human papillomavirus. In fact epidemiologists analyzing statistics on world cancer have estimated that one in six cancers can be associated with an infectious agent. Another important development in infectious disease trends is the increasing number of patients with weakened defenses who are kept alive for extended periods. We are becoming more susceptible to infectious disease precisely because of advances in medicine. CLINICAL CONNECTIONS Check Your Progress SECTIONS 1.3–1.4 7. Describe several ways the beneficial qualities of microbes greatly outweigh microbes’ roles as infectious agents. 8. Look up in the index some of the diseases shown in table 1.2 and de- termine which ones could be prevented by vaccines or cured with drugs. Are there other ways besides vaccines to prevent any of these 9. Distinguish between emerging and reemerging infectious diseases and explain what factors contribute to their development. 1.5 The Historical Foundations of Microbiology Expected Learning Outcomes 9. Outline the major events in the history of microbiology including the major contributors to the early development of microscopy medical advances aseptic techniques and the germ theory of disease. 10. Explain the main features of the scientifc method and diferentiate between inductive and deductive reasoning and between hypothesis and theory. If not for the extensive interest curiosity and devotion of thousands of microbiologists over the last 300 years we would know little about the microscopic realm that surrounds us. Many of the discoveries in this science have resulted from the prior work of men and women who toiled long hours in dimly lit laboratories with the crudest of tools. Each additional insight whether large or small has added to our cur- rent knowledge of life forms and processes. This section summarizes the prominent discoveries made in the past 300 years: microscopy the rise of the scientific method and the development of medical micro- biology including the germ theory and the origins of modern micro- biological techniques. The table “Significant Events in Microbiology” found in Online Appendix 2 summarizes some of the pivotal events in microbiology from its earliest beginnings to the present. The Development of the Microscope: “Seeing Is Believing” It is likely that from the very earliest history humans noticed that when certain foods spoiled they became inedible or caused illness and yet other “spoiled” foods did no harm and even had enhanced flavor. Even several centuries ago there was already a sense that diseases such as the black plague and smallpox were caused by some sort of transmissible matter. But the causes of such phenom- ena were obscure because the technology to study them was lack- ing. Consequently they remained cloaked in mystery and regarded with superstition—a trend that led even well-educated scientists to believe in spontaneous generation 1.2 Making Connections.

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14 Chapter 1 The Main Themes of Microbiology The Fall of Superstition and the Rise of Microbiology For thousands of years people believed that certain living things arose from vital forces present in nonliving or decomposing matter. This an- cient idea known as spontaneous generation was continually rein- forced as people observed that meat left out in the open soon “produced” maggots that mushrooms appeared on rotting wood that rats and mice emerged from piles of litter and that other magical phenomena occurred. Though some of these early ideas seem quaint and ridiculous in light of modern knowledge we must remember that at the time mysteries in life were accepted and the scientific method was not widely practiced. Even after single-celled organisms were discovered during the mid- 1600s the idea of spontaneous generation persisted. Some scientists as- sumed that microscopic beings were an early stage in the development of more complex ones. Over the subsequent 200 years scientists waged an experimental battle over the two hypotheses that could explain the origin of simple life forms. Some tenaciously clung to the idea of abiogenesis which em- braced spontaneous generation. On the other side were advocates of biogenesis saying that living things arise only from others of their same kind. There were serious proponents on both sides and each side put forth what appeared on the surface to be plausible explanations of why their evidence was more correct. Gradually the abiogenesis hypothesis was abandoned as convincing evidence for biogenesis continued to mount. The following series of experiments were among the most impor- tant in finally tipping the balance. Some of the important variables to be considered in testing the hy- potheses were the effects of nutrients air and heat and the presence of preexisting life forms in the environment. One of the first people to test the spontaneous generation theory was Francesco Redi of Italy. He con- ducted a simple experiment in which he placed meat in a jar and covered the jar with fine gauze. Flies gathering at the jar were blocked from enter- ing and thus laid their eggs on the outside of the gauze. The maggots subsequently developed without access to the meat indicating that mag- gots were the offspring of flies and did not arise from some “vital force” in the meat. This and related experiments laid to rest the idea that more complex animals such as insects and mice developed through abiogene- sis but it did not convince many scientists of the day that simpler organ- isms could not arise in that way. The Frenchman Louis Jablot reasoned that even microscopic or- ganisms must have parents and his experiments with infusions dried hay steeped in water supported that hypothesis. He divided an infusion that had been boiled to destroy any living things into two containers: a heated container that was closed to the air and a heated container that was freely open to the air. Only the open vessel developed microorganisms which he presumed had entered in air laden with dust. Regrettably the valida- tion of biogenesis was temporarily set back by John Needham an Eng- lishman who did similar experiments using mutton gravy. His results were in conflict with Jablot’s because both his heated and unheated test containers teemed with microbes. Unfortunately his experiments were done before the realization that heat-resistant microbes are not usually killed by mere boiling. Apparently Jablot had been lucky his infusions were sterile. Then in the mid-1800s the acclaimed microbiologist Louis P as t eur entered the arena. He had recently been studying the roles of microorgan- isms in the fermentation of beer and wine and it was clear to him that these processes were brought about by the activities of microbes intro- duced into the beverage from air fruits and grains. The methods he used to discount abiogenesis were simple yet brilliant. 1.2 MAKING CONNECTIONS abiogenesis ah-bee″-oh-jen′-uh-sis L. a without bios life and genesis beginning. biogenesis by-oh-gen′-uh-sis to begin with life. To further clarify that air and dust were the source of microbes Pasteur filled flasks with broth and fashioned their openings into elon- gate swan-neck-shaped tubes. The flasks’ openings were freely open to the air but were curved so that gravity would cause any airborne dust particles to deposit in the lower part of the necks. He heated the flasks to sterilize the broth and then incubated them. As long as the flask remained intact the broth remained sterile but if the neck was broken off so that dust fell directly down into the container microbial growth immediately commenced. Pasteur summed up his findings “For I have kept from them and am still keeping from them that one thing which is above the power of man to make I have kept from them the germs that float in the air I have kept from them life.” What type of microorganisms were likely responsible for the mis- leading results of John Needham’s experiment and were absent in Jablot’s and Pasteur’s experiments Answer available on Connect. Vigorous heat is applied. Microbes being destroyed Two flasks start out free of live cells sterile Neck of second flask remains intact no growth occurs. One flask is snapped o at the top growth appears in broth. Pasteur’s Experiment

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1.5 The Historical Foundations of Microbiology 15 Leeuwenhoek constructed more than 250 small powerful mi- croscopes that could magnify up to 300 times figure 1.9. Consid- ering that he had no formal training in science and that he was the first person ever to faithfully record this strange new world his de- scriptions of bacteria and protozoa which he called “animalcules” were astute and precise. Because of Leeuwenhoek’s extraordinary contributions to microbiology he is sometimes considered the father of bacteriology and protozoology. True awareness of the widespread distribution of microorgan- isms and some of their characteristics was finally made possible by the development of the first microscopes. These devices revealed microbes as discrete entities sharing many of the characteristics of larger visible plants and animals. Several early scientists fashioned magnifying lenses and microscopes but these lacked the optical clarity needed for examining bacteria and other small single-celled organisms. The most careful and exacting observations awaited the simple single-lens microscope hand-fashioned by Antonie van Leeuwenhoek a Dutch linen merchant and self-made microbiol- ogist figure 1.8. During the late 1600s in Holland Leeuwenhoek used his early lenses to ex- amine the thread patterns of the draperies and upholstery he sold in his shop. Be- tween customers he retired to the work- bench in the back of his shop grinding glass lenses to ever-finer specifications. He could see with increasing clarity but after a few years he became interested in things other than thread counts. He took rainwater from a clay pot smeared it on his specimen holder and peered at it through his finest lens. He found “animals appearing to me ten thousand times more than those which may be perceived in the water with the naked eye.” He didn’t stop there. He scraped plaque from his teeth and from the teeth of volunteers who had never cleaned their teeth in their lives and took a close look at that. He recorded: “In the said matter there were many very little living animalcules very prettily a-moving . . . . Moreover the other animalcules were in such enormous numbers that all the water . . . seemed to be alive.” Leeuwenhoek started sending his observations to the Royal Society of London and eventually he was recognized as a scientist of great merit. Figure 1.8 An oil painting of Antonie van Leeuwenhoek 1632–1723 sitting in his laboratory. How astonishing to realize that this curious and original man was the frst human being on earth ever to glimpse the “cavorting wee beasties” his description of the microbial world © Bettmann/Corbis Quick Search Search for “Through van Leeuwenhoek’s Eyes: Microbiology in a Nutshell” on YouTube to watch a video inspired by Leeuwenhoek’s world Lens Specimen holder Focus screw Handle a b Figure 1.9 Leeuwenhoek’s microscope. a A brass replica of a Leeuwenhoek microscope and how it is held inset. b Early illustrations of bacterial cells from a sample of milk magnifed about 300×. These drawings closely resemble those Leeuwenhoek made of his animalcules. a a inset: © Kathy Park Talaro b: Source: Trouessart E.L. Microbes Ferments and Moulds. © 1895 D. Appleton and Company.

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16 Chapter 1 The Main Themes of Microbiology With inductive reasoning one applies specific observations to develop a general explanation. This method is often used in the early phases of evaluation and can formulate a generalization to be tested deductively. In the previous example induction might begin with the observation of a family in which several people have hemophilia and this may lead to the general idea that it is inheritable. A lengthy process of experimentation analysis and testing eventually leads to conclusions that either support or refute the hy- pothesis. If experiments do not uphold the hypothesis—that is if it is found to be flawed—the hypothesis or some part of it is reconsid- ered. This does not mean the results are invalid it means the hy- pothesis may require reworking or additional tests. Eventually it is either discarded or modified to fit the results of the experiment. If the hypothesis is supported by the experiment it is not or should not be immediately accepted as fact. It then must be tested and re- tested. Indeed this is an important guideline in the acceptance of a hypothesis. The results of the experiment must be published and repeated by other investigators. In time as each hypothesis is supported by a growing body of data and survives rigorous scrutiny it moves to the next level of acceptance—the theory. A theory is a collection of statements propositions or concepts that explains or accounts for a natural event. A theory is not the result of a single experiment repeated over and over again but is an entire body of ideas that expresses or interprets many aspects of a phenomenon. When an unsupported idea is dismissed as being “just a theory” this is an incorrect use of the term as far as science is concerned. A theory is far from a weak notion or wild guess. It is a viable explanation that has stood the test of time and has yet to be disproved by serious scientific inquiries. Often theories develop and progress through decades of research and are added to and modified by new findings. At some point evidence of the accuracy and predictability of a theory is so com- pelling that the next level of confidence is reached and the theory becomes a law or principle. For example the germ theory of disease has been so thoroughly tested that it has clearly passed into the realm of law. Science and its hypotheses and theories must progress along with technology. As advances in instrumentation allow new more detailed views of living phenomena old theories may be reexam- ined and altered and new ones proposed. Scientific knowledge is accumulative and it must have built-in flexibility to accommodate new findings. It is for these reasons that scientists do not take a stance that theories or even laws are absolutely proved. Figure 1.10 provides a summary of the scientific method in action using Edward Jenner’s monumental discovery of vaccines. What is remarkable about Jenner’s work is that he was the first to use scientific thought to construct a rigorous experimental model to in- oculate people against disease and he carried it through to its com- pletion. It is also remarkable that he did this knowing nothing about viruses or even microbes. He worked out the concept of safely con- ferring artificial immunity long before there was any understanding of the immune system see 15.2 Making Connections. The Development of Medical Microbiology Early experiments on the sources of microorganisms led to the pro- found realization that microbes are everywhere: Not only are air and From the time of Leeuwenhoek microscopes became more complex and improved with the addition of refined lenses a con- denser finer focusing devices and built-in light sources. The proto- type of the modern compound microscope in use from about the mid-1800s was capable of magnifications of 1000 times or more largely because it had two sets of lenses for magnification. Even our modern laboratory microscopes are not greatly different in basic structure and function from those early microscopes. The technical characteristics of microscopes and microscopy are a major focus of chapter 3. The Scientifc Method and the Search for Knowledge The research that led to acceptance of biogenesis provides us with one example of the early development of science-based thought. Over the next few sections we will glimpse other important milestones in the development of the scientific method such as vaccination germ the- ory asepsis and Koch’s postulates. The impact of science is so perva- sive that you may not realize how much of our everyday life is built upon applications of the scientific method. Vaccines antibiotics space travel computers medical diagnosis and DNA testing exist primarily because of the work of thousands of scientists doing objec- tive observations and collecting evidence that is measurable can be expressed quantitatively and is subject to critical analysis. The information obtained through the scientific method is ex- planatory and predictive. It aims to explain how and why phenom- ena occur and to predict what is expected to happen under known conditions. Two very recent events dramatically contrast the differ- ences between scientific versus nonscientific reasoning. In 2012 NASA sent the Curiosity spacecraft on a 225-million-mile journey to Mars and landed it at a very precise time and place—an incredible achievement that brought to bear vast knowledge of physics engineering and mathematics. That same year rumors started about doomsday predictions supposedly found in interpretations of an ancient Mayan calendar. A surprisingly large number of people all over the world were convinced that the world would come to an end on December 21 2012. The fact that you are reading this text- book absolutely verifies which of these approaches is more reliable and predictive. How do scientists apply the scientific method In the deductive reasoning approach a scientist uses general observations of some phenomenon to develop a set of facts to explain that phenomenon— that is they deduce the facts that can account for what they have observed. This early explanation is considered a hypothesis and however tentative it may start out it is still based on scientific thought rather than subjective beliefs that come from superstition or myth. A valid hypothesis will allow for experimentation and testing and can be shown to be false. An example of a workable hypothesis based on deduction might be the speculation that a dis- ease such as hemophilia is an inheritable condition. This would pave the way for specific experiments that test for the influence of genetics. A nonworkable hypothesis would be that hemophilia is caused by a curse placed on the royal family of England. Because supernatural beliefs offer no basis for experimentation and must be taken on faith they can never be subjected to the rigors of the sci- entific method.

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1.5 The Historical Foundations of Microbiology 17 by inoculating patients with a closely related disease agent. His contributions to medical science so changed the practice of medi- cine that he is considered the “Father of Immunology.” It is often said of Jenner that his discovery saved more lives than any other in history. His work marked the beginning of an era of great scientific achievement—one that produced some of the most far-reaching de- velopments in microbiology and medicine. The Discovery of Spores and Sterilization Following Pasteur’s inventive work with infusions 1.2 Making Connections it was not long before English physicist John  Tyndall dust full of them but the entire surface of the earth its waters and all objects are inhabited by them. This discovery led to immediate ap- plications in medicine. Thus the seeds of medical microbiology were sown in the middle to latter half of the nineteenth century with the introduction of the first practical vaccine the germ theory of disease and the resulting use of sterile aseptic and pure culture techniques. Jenner and the Introduction of Vaccination We saw in figure 1.10 how the English physician and scientist Edward Jenner modeled the scientific method. His experiments ultimately gave rise to the first viable method to control smallpox Observations/ information gathering 1. Dr. Jenner observed that cows had a form of pox similar to smallpox. Jenner also noted that milkmaids acquired cowpox only on the hands and they appeared to be immune to smallpox. Formation of Jenner’s hypothesis 2. Jenner deduced that the cowpox was closely related to smallpox and could possibly be used on patients to provide protection similar to that of the milkmaids he had seen. Testing the hypothesis experiment I 3. Jenner took scrapings from cowpox blisters on the hand of a milkmaid and inoculated them into a boy who had not had smallpox. He developed minor symptoms but remained healthy. Testing the hypothesis experiment II 4. After a few weeks the child was exposed twice to the pus from an active smallpox lesion. He did not acquire smallpox and appeared to have immune protection. Reproducibility of results 5. Jenner went on to inoculate 23 other test subjects with cowpox. For the first time he used lesions from one child to inoculate another. All subjects remained protected from smallpox. Publishing of results other medical testing 6. Jenner wrote a paper detailing his experiment. He called his technique vaccination from the Latin vacca for cow. Other local English physicians began to vaccinate patients with some success. Vaccination theory becomes widespread. 7. Over the next 100 years vaccination was brought to the rest of the world through local programs. Scientists used Jenner’s methods to develop vaccines for other pathogens. The theory of artificial immunity became well established. Smallpox is eradicated from the world. 8. A massive vaccination campaign aimed to reduce cases and to stamp out the disease completely. Billions of doses given over a decade reduced smallpox to zero. The last cases occurred in 1977 and in 1979 the disease was declared eradicated. 0 1970 1960 1980 1950 Vaccine campaign Countries reporting smallpox 1950-1980 Number of Countries Reporting Cases 10 20 30 40 50 60 70 80 90 1965: 1979: Smallpox eradicated Figure 1.10 Edward Jenner and the saga of the smallpox vaccine. Jenner’s work documents the frst attempt based on the scientifc method to control an infectious disease—smallpox. This disease was characterized by raised skin blisters called pox and it often caused severe damage to organs. Throughout its long history this deadly disease decimated many populations worldwide until 1977 when the last case was reported.

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