Brock Biology of Microorganisms PDF
Preview Brock Biology of Microorganisms
MarineEuryarchaeota MarineCrenarchaeota Euryarchaeota Halobacterium Halococcus Archaeoglobus Extreme Natronococcus halophiles Methanobacterium Methanocaldococcus Crenarchaeota Halophilic methanogen Methanothermus Sulfolobus Pyrodictium Methanosarcina Thermococcus/ Pyrococcus Methanospirillum Nanoarchaeum Thermoproteus Hyperthermophiles Thermoplasma Methanopyrus Desulfurococcus Picrophilus Ferroplasma Root Extreme acidophiles Protists Stramenopiles Oomycetes Brown Cercozoans Chlorarach- Rlaaridainos- Diatoms algae Galogladeen Ciliates Alveolates niophytes Dinoflagellates Foramin- Apicomplexans iferans Parabasalids Red algae Diplomonads Green (Secondary algae endosymbioses) Kinetoplastids Plants Euglenozoa Euglenids Cellular slime molds Plasmodial slime molds Entamoebas Gymnamoebas Amoebozoa Chloroplast ancestor Animals (primary endosymbiosis) Mitochondrial ancestor Fungi (primary endosymbiosis) Fungi Microsporidia Bacteria Brock Biology of Microorganisms Thirteenth Edition Michael T. Madigan Southern Illinois University Carbondale John M. Martinko Southern Illinois University Carbondale David A. Stahl University of Washington Seattle David P. Clark Southern Illinois University Carbondale Executive Editor:Deirdre Espinoza Art Coordinator:Jean Lake Project Editor:Katie Cook Photo Researcher:Maureen Spuhler Associate Project Editor:Shannon Cutt Director, Media Development:Lauren Fogel Development Editor:Elmarie Hutchinson Media Producers:Sarah Young-Dualan, Lucinda Bingham, and Ziki Dekel Art Development Manager:Laura Southworth Art:Imagineering Media Services, Inc. Art Editor:Elisheva Marcus Text Design:Riezebos Holzbaur Design Group Managing Editor:Deborah Cogan SeniorManufacturing Buyer:Stacey Weinberger Production Manager:Michele Mangelli Senior Marketing Manager:Neena Bali Production Supervisor:Karen Gulliver Compositor:Progressive Information Technologies Copyeditor:Anita Wagner Cover Design:Riezebos Holzbaur Design Group Cover Image:(front cover) Peter Siver/Visuals Unlimited/Corbis; (back cover) J.-H. Becking, Wageningen Agricultural University, Wageningen, Netherlands Credits for selected images can be found on page P-1. Copyright © 2012, 2009, 2006 Pearson Education, Inc., publishing as Benjamin Cummings, 1301 Sansome Street, San Francisco, CA 94111. All rights reserved. Manufactured in the United States of America. This publication is protected by copyright and permission should be obtained from the publisher prior to any prohibited reproduction, storage in a retrieval system, or transmission in any form or by any means, electronic, mechanical, photocopying, recording, or likewise. To obtain permission(s) to use material from this work, please submit a written request to Pearson Education, Inc., Permissions Department, 1900 E. Lake Ave., Glenview, IL 60025. For information regarding permissions, call (847) 486-2635. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and the publisher was aware of a trademark claim, the designations have been printed in initial caps or all caps. Library of Congress Cataloging-in-Publication Data Brock biology of microorganisms / Michael T. Madigan . . . [et al.].—13th ed. p. cm. Includes index. ISBN-13: 978-0-321-64963-8 (hardcover : alk. paper) ISBN-10: 0-321-64963-X (hardcover : alk. paper) 1. Microbiology. I. Madigan, Michael T., 1949– II. Title: Biology of microorganisms. QR41.2.B77 2011 579—dc22 2010044962 ISBN 10: 0-321-64963-X (student edition) ISBN 13: 978-0-321-64963-8 (student edition) ISBN 10: 0-321-72675-8 (professional copy) ISBN 13: 978-0-321-72675-9(professional copy) 1 2 3 4 5 6 7 8 9 10—CRK—14 13 12 11 10 About the Authors Michael T. Madigan John M. Martinko re- received ceived his B.S. in Biology and his B.S. in Biology from Cleveland Education from Wisconsin State State University. He then worked at University–Stevens Point (1971) and Case Western Reserve University, his M.S. (1974) and Ph.D. (1976) in conducting research on the serology Bacteriology from the University of and epidemiology of Streptococcus Wisconsin–Madison. His graduate pyogenes. His doctoral work at the research was on the hot spring bac- State University of New York–Buffalo terium Chloroflexus in the labora- investigated antibody specificity and tory of Thomas Brock. Following a antibody idiotypes. As a postdoc- three-year postdoctoral in the Department of Microbiology, toral fellow, he worked at Albert Einstein College of Medicine Indiana University, Mike moved to Southern Illinois University– in New York on the structure of major histocompatibility com- Carbondale, where he has been a professor of microbiology for plex proteins. Since 1981, he has been in the Department of 32 years. He has coauthored Biology of Microorganisms since Microbiology at Southern Illinois University–Carbondale where the fourth edition (1984) and teaches courses in introductory he was Associate Professor and Chair, and Director of the Molec- microbiology, bacterial diversity, and diagnostic and applied ular Biology, Microbiology, and Biochemistry Graduate Program. microbiology. In 1988 Mike was selected as the Outstanding He retired in 2009, but remains active in the department as a Teacher in the College of Science and in 1993, the Outstanding researcher and teacher. His research investigates structural Researcher. In 2001 he received the SIUC Outstanding Scholar changes in major histocompatibility proteins. He teaches an Award. In 2003 he received the Carski Award for Distinguished advanced course in immunology and presents immunology and Undergraduate Teaching from the American Society for Micro- host defense lectures to medical students. He also chairs the biology (ASM), and he is an elected Fellow of the American Institutional Animal Care and Use Committee at SIUC. He has Academy of Microbiology. Mike’s research is focused on bacteria been active in educational outreach programs for pre-university that inhabit extreme environments, and for the past 12 years he students and teachers. For his educational efforts, he won the has studied the microbiology of permanently ice-covered lakes in 2007 SIUC Outstanding Teaching Award. He is also an avid the McMurdo Dry Valleys, Antarctica. In addition to his research golfer and cyclist. John lives in Carbondale with his wife Judy, a papers, he has edited a major treatise on phototrophic bacteria high school science teacher. and served for over a decade as chief editor of the journal Archives of Microbiology. He currently serves on the editorial board of the journals Environmental Microbiology and Antonie van Leeuwenhoek. Mike’s nonscientific interests include forestry, reading, and caring for his dogs and horses. He lives beside a peaceful and quiet lake with his wife, Nancy, five shelter dogs (Gaino, Snuffy, Pepto, Peanut, and Merry), and four horses (Springer, Feivel, Gwen, and Festus). iii iv About the Authors David A. Stahl David P. Clark received his grew up in B.S. degree in Microbiology from the Croydon, a London suburb. He won University of Washington–Seattle, a scholarship to Christ’s College, later completing graduate studies in Cambridge, where he received his microbial phylogeny and evolution B.A. degree in Natural Sciences in with Carl Woese in the Department 1973. In 1977 he received his Ph.D. of Microbiology at the University of from Bristol University, Department Illinois–Champaign-Urbana. Subse- of Bacteriology, for work on the quent work as a postdoctoral fellow effect of cell envelope composition with Norman Pace, then at the on the entry of antibiotics into National Jewish Hospital in Colorado, focused on early applica- Escherichia coli. He then left England on a postdoctoral studying tions of 16S rRNA-based sequence analysis to the study of natu- the genetics of lipid metabolism in the laboratory of John Cronan ral microbial communities. In 1984 Dave joined the faculty at the at Yale University. A year later he moved with the same labora- University of Illinois–Champaign-Urbana, holding appointments tory to the University of Illinois at Urbana-Champaign. David in Veterinary Medicine, Microbiology, and Civil Engineering. In joined the Department of Microbiology at Southern Illinois 1994 he moved to the Department of Civil Engineering at North- University–Carbondale in 1981. His research has focused on the western University, and in 2000 returned to his alma mater, the growth of bacteria by fermentation under anaerobic conditions. University of Washington–Seattle, as a professor in the Depart- He has published numerous research papers and graduated over ments of Civil and Environmental Engineering and Microbiol- 20 Masters and Doctoral students. In 1989 he won the SIUC ogy. Dave is known for his work in microbial evolution, ecology, College of Science Outstanding Researcher Award. In 1991 he and systematics, and received the 1999 Bergey Award and the was the Royal Society Guest Research Fellow at the Department 2006 Procter & Gamble Award in Applied and Environmental of Molecular Biology and Biotechnology, Sheffield University, Microbiology from the ASM; he is also an elected Fellow of the England. In addition to Brock Biology of Microorganisms, David is American Academy of Microbiology. His main research interests the author of four other science books: Molecular Biology Made are the biogeochemistry of nitrogen and sulfur compounds and Simple and Fun, now in its fourth edition; Molecular Biology: the microbial communities that sustain these nutrient cycles. His Understanding the Genetic Revolution; Biotechnology: Applying laboratory was first to culture ammonia-oxidizing Archaea, a the Genetic Revolution; and Germs, Genes, & Civilization: How group now believed to be the main mediators of this key process Epidemics Shaped Who We Are Today. David is unmarried and in the nitrogen cycle. He has taught several courses in environ- lives with two cats, Little George, who is orange and very nosey, mental microbiology, is one of the co-founding editors of the and Mr. Ralph, who is mostly black and eats cardboard. journal Environmental Microbiology, and has served on many advisory committees. Outside teaching and the lab, Dave enjoys hiking, bicycling, spending time with family, reading a good sci- ence fiction book, and, with his wife Lin, renovating an old farm- house on Bainbridge Island, Washington. Dedications Michael T. Madigandedicates this book to the memory of his children who rest on Boot Hill: Andy, Marcy, Willie, Plum, Teal, and Sugar. Whether in good times or bad, they always greeted him with tails a waggin’. John M. Martinkodedicates this book to his daughters Sarah, Helen, and Martha, and to his wife Judy. Thanks for all of your support! David A. Stahldedicates this book to his wife, Lin. My love, and one that helps me keep the important things in perspective. David P. Clarkdedicates this book to his father, Leslie, who set him the example of reading as many books as possible. Preface The authors and Benjamin Cummings Publishers proudly key concepts from each numbered section in a wrap-up style that present the 13th edition of Brock Biology of Microorganisms is certain to be a big hit with students, especially the night before (BBOM 13/e). This book is truly a milestone in the annals of examinations! Our end-of-chapter key terms list, two detailed microbiology textbooks. Brock Biology of Microorganisms, and its appendices, a comprehensive glossary, and a thorough index predecessor, Biology of Microorganisms, has introduced the field complete the hard copy learning package. Many additional learn- of microbiology to students for 41 years, more than any other ing resources are available online (see below). textbook of microbiology. Nevertheless, although this book goes In terms of presentation, BBOM 13/e will easily draw in and back over four decades, its two main objectives have remained engage the reader. The book has been designed in a beautiful yet firm since the first edition was published in 1970: (1) to present simple fashion that gives the art and pedagogical elements the the principles of microbiology in a clear and engaging fashion, breathing room they need to be effective and the authors the and (2) to provide the classroom tools necessary for delivering freedom to present concepts in a more visually appealing way. outstanding microbiology courses. The 13th edition of BBOM Supporting the narrative are spectacular illustrations, with every fulfills these objectives in new and exciting ways. piece of art rendered in a refreshing new style. Moreover, the art Veteran textbook authors Madigan, Martinko, and Clark wel- complements, and in many cases integrates, the hundreds of come our new coauthor, Dave Stahl, to this edition of BBOM. Dave photos in BBOM, many of which are new to the 13th edition. is one of the world’s foremost experts in microbial ecology and has And, as users of BBOMhave come to expect, our distinctive illus- masterfully crafted an exciting new view of the ecology material in trations remain the most accurate and consistent of those in any BBOM, including a new chapter devoted entirely to microbial microbiology textbook today. symbioses, a first for any textbook of microbiology. Users will find The authors are keenly aware that it is easy to keep piling on that the themes of ecology and evolution that have permeated this new material and fattening up a textbook. In response to this book since its inception reach new heights in the 13th edition. trend, BBOM13/e went on a diet. With careful attention to con- These fundamental themes also underlie the remaining content tent and presentation, BBOM13/e is actually a shorter book than of the book—the basic principles of microbiology, the molecular BBOM12/e. The authors have carefully considered every topic to biology and genetics that support microbiology today, the huge ensure that content at any point in the book is a reflection of both diversity of metabolisms and organisms, and the medical and what the student already knows and what the student needs to immunological facets of microbiology. It is our belief that out- know in a world where microbiology has become the most excit- standing content coupled with outstanding presentation have ing and relevant of the biological sciences. The result is a more come together to make BBOM13/e the most comprehensive and streamlined and exciting treatment of microbiology that both effective textbook of microbiology available today. students and instructors will appreciate. What’s New in the 13th Edition? Revision Highlights: In terms of content and pedagogy, instructors who have used Chapter 1 BBOM previously will find the 13th edition to be the same old • Find new coverage on the evolution and major habitats of friend they remember; that is, a book loaded with accurate, up- microorganisms—Earth’s most pervasive and extensive biomass. to-the-minute content that is impeccably organized and visually enticing. The 36 chapters in BBOM13/e are organized into mod- • A more visually compelling presentation of the impacts of ules by numbered head, which allows instructors to fine-tune microorganisms on humans better emphasizes the importance course content to the needs of their students. In addition, study of microorganisms for the maintenance of all life on Earth. aids and review tools are an integral part of the text. Our new Chapter 2 MiniQuiz feature, which debuts in the 13th edition, is designed to quiz students’ comprehension as they work their way through • New coverage of cell biology and the nature of the chromo- each chapter. Also new to this edition is the end-of-chapter review some in prokaryotic and eukaryotic cells is complemented by a tool called “Big Ideas.” These capsule summaries pull together the visually engaging overview of the microbial world. v vi Preface Chapter 3 Chapter 10 • The cell chemistry chapter that previously held this position is • The fundamental principles of microbial genetics are updated now available online (www.microbiologyplace.com). The new and supplemented with new coverage that compares and con- Chapter 3explores cell structure and function with strong new trasts bacterial and archaeal genetics. visuals to carry the text and new coverage of the lipids and cell Chapter 11 walls of Bacteriaand Archaea. • Find “one-stop shopping” for coverage of molecular biological Chapter 4 methods, including cloning and genetic manipulations, as a • Find updated coverage of catabolic principles along with an prelude to the genomics discussion in the next chapter. overview of essential anabolic reactions. • Enjoy the colorful new Microbial Sidebar on new fluorescent • Newly rendered and more instructive art makes mastering key labeling methods that can differentiate even very closely metabolic pathways and bioenergetic principles a more visual related bacteria. experience. Chapter 12 Chapter 5 • Extensive updates on microbial genomics and transcriptomics • Updated coverage of the events in cell division and their will be found along with new coverage of the emerging related relation to medical microbiology connects basic science to areas of metabolomics and interactomics. applications. • Readers will marvel at the diversity of prokaryotic genomes in the • Newly rendered art throughout makes the important concepts new Microbial Sidebar “Record-Holding Bacterial Genomes.” of cell division and population growth more vivid, engaging, Chapter 13 and interactive. • The two chapters covering metabolic diversity have been Chapter 6 revised and moved up to Chapters 13and 14to precede rather • The concise primer on molecular biology that every student than follow coverage of microbial diversity, better linking these needs to know is updated and now includes an overview of the two important and often related areas. structures of nucleic acids and proteins and the nature of chro- • This chapter is loaded with reworked art and text that high- mosomes and plasmids. light the unity and diversity of the bioenergetics underlying phototrophic and chemolithotrophic metabolisms. Chapter 7 Chapter 14 • Find new coverage of the latest discoveries in the molecular biology of Archaea and comparisons with related molecular • Restyled and impeccably consistent art showcases the compar- processes in Bacteria. ative biochemistry of the aerobic and anaerobic catabolism of • A new section highlights the emerging area of regulation by carbon compounds. microRNA in eukaryotes. Chapter 15 Chapter 8 • This retooled chapter combines the essentials of industrial • Review major updates on the regulation of gene expression— microbiology and biotechnology, including the production of one of the hottest areas in microbiology today—including biofuels and emerging green microbial technologies. expanded coverage of cell sensing capacities and signal trans- Chapter 16 duction. • Enjoy the new Microbial Sidebar featuring CRISPR, the newly • Find new coverage of the origin of life and how the evolution- discovered form of RNA-based regulation used by Bacteria ary process works in microorganisms. andArchaeato ward off viral attack. • Microbial phylogenies from small subunit ribosomal RNA gene analyses are compared with those from multiple-gene and Chapter 9 full genomic analyses. • Major updates of the principles of virology are complemented with an overview of viral diversity. • New art reinforces the relevance and importance of viruses as agents of genetic exchange. Preface vii Chapters 17–19 Chapter 25 • Coverage of the diversity of Bacteria and Archaea better • This new chapter focuses entirely on microbial symbioses, emphasizes phylogeny with increased focus on phyla of partic- including bacterial–bacterial symbioses and symbioses between ular importance to plants and animals and to the health of our bacteria and their plant, mammal, or invertebrate hosts. Find planet. coverage here of all of the established as well as more recently • Spectacular photomicrographs and electron micrographs carry discovered symbioses, including the human gut and how its the reader through prokaryotic diversity. microbiome may control obesity, the rumen of animals impor- tant to agriculture, the hindgut of termites, the light organ of Chapter 20 the squid, the symbioses between hydrothermal vent animals and chemolithotrophic bacteria, the essential bacterial sym- • A heavily revised treatment of the diversity of microbial bioses of insects, medicinal leeches, reef-building corals, and eukaryotes is supported by many stunning new color photos more, all supported by spectacular new color photos and art. and photomicrographs. • Learn how insects have shaped the genomes of their bacterial • Find an increased emphasis on the phylogenetic relationships of endosymbionts. eukaryotes and the “bacterial nature” of eukaryotic organelles. • Marvel at the new Microbial Sidebar that tells the intriguing Chapter 21 story of the attine ants and their fungal gardens. • Viruses, the most genetically diverse of all microorganisms, Chapter 26 come into sharper focus with major updates on their diversity. • Key updates will be found on microbial drug resistance and are • A new section describes viruses in nature and their abundance supported by new art that reveals the frightening reality that in aquatic habitats. several human pathogens are resistant to all known antimicro- bial drugs. Chapter 22 Chapter 27 • This chapter features a major new treatment of the latest molecular techniques used in microbial ecology, including • Extensively reworked sections on the normal microbial flora of CARD-FISH, ARISA, biosensors, NanoSIMS, flow cytometry, humans include new coverage of the human microbiome and a and multiple displacement DNA amplification. molecular snapshot of the skin microflora. • Find exciting new coverage of methods for functional analyses • Find revised coverage of the principles of virulence and patho- of single cells, including single-cell genomics and single-cell genicity that connect infection and disease. stable isotope analysis, and expanded coverage of methods for analyses of microbial communities, including metagenomics, Chapter 28 metatranscriptomics, and metaproteomics. • Here we present the perfect overview of immunology for instruc- Chapter 23 tors who wish to cover only the fundamental concepts and how the immune system resists the onslaught of infectious disease. • A comparison of the major habitats of Bacteriaand Archaeais • Find late-breaking practical information on the immune supported by spectacular new photos and by art that summa- response, including vaccines and immune allergies. rizes the phylogenetic diversity and functional significance of prokaryotes in each habitat. Chapter 29 • Find broad new coverage of the microbial ecology of microbial mat communities and prokaryotes that inhabit the deep sub- • Built on the shoulders of the previous chapter, here is a more surface. detailed probe of the mechanisms of immunity with emphasis on the molecular and cellular interactions that control innate Chapter 24 and adaptive immunity. • Revised coverage of the classical nutrient cycles is bolstered by Chapter 30 new art, while new coverage highlights the calcium and silica cycles and how these affect CO sequestration and global climate. • This short chapter presents an exclusively molecular picture of 2 immunology, including receptor–ligand interactions (the “trig- • Improved integration of biodegradation and bioremediation gers” of the immune response), along with genetics of the key shows how natural microbial processes can be exploited for the proteins that drive adaptive immunity. benefit of humankind.
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