The Prokaryotes

Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.)

The Prokaryotes

Applied Bacteriology and Biotechnology

Fourth Edition

With 132 Figures and 63 Tables Editor-in-Chief Eugene Rosenberg Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv, Israel

Editors Edward F. DeLong Fabiano Thompson Department of Biological Engineering Laboratory of Microbiology, Institute of Biology, Center for Massachusetts Institute of Technology Health Sciences Cambridge, MA, USA Federal University of Rio de Janeiro (UFRJ) Ilha do Funda˜o, Rio de Janeiro, Brazil Stephen Lory Department of Microbiology and Immunology Harvard Medical School Boston, MA, USA

Erko Stackebrandt Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany

ISBN 978-3-642-31330-1 ISBN 978-3-642-31331-8 (eBook) ISBN 978-3-642-31332-5 (print and electronic bundle) DOI 10.1007/978-3-642-31331-8 Springer Heidelberg New York Dordrecht London

Library of Congress Control Number: 2012955035

3rd edition: © Springer Science+Business Media, LLC 2006 4th edition: © Springer-Verlag Berlin Heidelberg 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

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Springer is part of Springer ScienceþBusiness Media (www.springer.com) Foreword

The purpose of this brief foreword is unchanged from the first edition; it is simply to make you, the reader, hungry for the scientific feast that follows. These 11 volumes (planned) on the prokaryotes offer an expanded scientific menu that displays the biochemical depth and remarkable physiological and morphological diversity of prokaryote life. The size of the volumes might initially discourage the unprepared mind from being attracted to the study of prokaryote life, for this landmark assemblage thoroughly documents the wealth of present knowledge. But in confronting the reader with the state of the art, the Handbook also defines where more work needs to be done on well-studied bacteria as well as on unusual or poorly studied organisms. This edition of The Prokaryotes recognizes the almost unbelievable impact that the work of Carl Woese has had in defining a phylogenetic basis for the microbial world. The concept that the ribosome is a highly conserved structure in all cells and that its nucleic acid components may serve as a convenient reference point for relating all living things is now generally accepted. At last, the phylogeny of prokaryotes has a scientific basis, and this is the first serious attempt to present a comprehensive treatise on prokaryotes along recently defined phylogenetic lines. Although evidence is incomplete for many microbial groups, these volumes make a statement that clearly illuminates the path to follow. There are basically two ways of doing research with microbes. A classical approach is first to define the phenomenon to be studied and then to select the organism accordingly. Another way is to choose a specific organism and go where it leads. The pursuit of an unusual microbe brings out the latent hunter in all of us. The intellectual challenges of the chase frequently test our ingenuity to the limit. Sometimes the quarry repeatedly escapes, but the final capture is indeed a wonderful experience. For many of us, these simple rewards are sufficiently gratifying so that we have chosen to spend our scientific lives studying these unusual creatures. In these endeavors, many of the strategies and tools as well as much of the philosophy may be traced to the Delft School, passed on to us by our teachers, Martinus Beijerinck, A. J. Kluyver, and C. B. van Niel, and in turn passed on by us to our students. In this school, the principles of the selective, enrichment culture technique have been developed and diversified; they have been a major force in designing and applying new principles for the capture and isolation of microbes from nature. For me, the ‘‘organism approach’’ has provided rewarding adventures. The organism continually challenges and literally drags the investigator into new areas where unfamiliar tools may be needed. I believe that organism-oriented research is an important alternative to problem-oriented research, for new concepts of the future very likely lie in a study of the breadth of microbial life. The physiology, biochemistry, and ecology of the microbe remain the most powerful attractions. Studies based on classical methods as well as modern genetic techniques will result in new insights and concepts. To some readers, this edition of The Prokaryotes may indicate that the field is now mature, that from here on it is a matter of filling in details. I suspect that this is not the case. Perhaps we have assumed prematurely that we fully understand microbial life. Van Niel pointed out to his students that—after a lifetime of study—it was a very humbling experience to view in the microscope a sample of microbes from nature and recognize only a few. Recent evidence suggests that microbes have been evolving for nearly 4 billion years. Most certainly, those microbes now domesticated and kept in captivity in culture collections represent only a minor portion of the species that have evolved in this time span. Sometimes we must remind ourselves that evolution is actively taking place at the present moment. That the eukaryote cell evolved as a chimera of certain prokaryote parts is a generally accepted concept today. Higher as well as lower eukaryotes evolved in contact with prokaryotes, and evidence surrounds us of the complex interactions between eukaryotes and prokaryotes as well as among prokaryotes. We have so far only scratched the surface of these biochemical interrelationships. Perhaps the legume nodule is a pertinent example of nature caught in the act of evolving the ‘‘nitrosome,’’ a unique nitrogen-fixing organelle. The study of prokaryotes is proceeding at such a fast pace that major advances are occurring yearly. The increase of this edition to four volumes documents the exciting pace of discoveries. To prepare a treatise such as The Prokaryotes requires dedicated editors and authors; the task has been enormous. I predict that the scientific community of microbiologists will again show its appreciation through use of these volumes—such that the pages will become ‘‘dog-eared’’ and worn as students seek basic information for the hunt. These volumes belong in the laboratory, not in the library. I believe that a most effective way to introduce students to microbiology is for them to isolate microbes from nature, that is, from their habitats in soil, water, clinical specimens, or plants. The Prokaryotes enormously simplifies this process and should encourage the construction of courses that contain a wide spectrum of diverse topics. For the student as well as the advanced investigator, these volumes should generate excitement. Happy hunting!

Ralph S. Wolfe Department of Microbiology University of Illinois at Urbana-Champaign

Preface

During most of the twentieth century, microbiologists studied pure cultures under defined laboratory conditions in order to uncover the causative agents of disease and subsequently as ideal model systems to discover the fundamental principles of genetics and biochemistry. Microbiology as a discipline onto itself, e.g., microbial ecology, diversity, and evolution-based taxonomy, has only recently been the subject of general interest, partly because of the realization that microorganisms play a key role in the environment. The development and application of powerful culture-independent molecular techniques and bioinformatics tools has made this development possible. The fourth edition of the Handbook of the Prokaryotes has been updated and expanded in order to reflect this new era of microbiology. The first five volumes of the fourth edition contain 34 updated and 43 entirely new chapters. Most of the new chapters are in the two new sections: Prokaryotic Communities and Bacteria in Human Health and Disease. A collection of microorganisms occupying the same physical habitat is called a ‘‘community,’’ and several examples of bacterial communities are presented in the Prokaryotic Communities section, organized by Edward F. DeLong. Over the last decade, important advances in molecular biology and bioinformatics have led to the development of innovative culture-independent approaches for describing microbial communities. These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of microorganisms, which are known for their selectivity leading to a nonrepresentative view of prokaryotic diversity. Describing bacterial communities is the first step in understanding the complex, interacting microbial systems in the natural world. The section on Bacteria in Human Health and Disease, organized by Stephen Lory, contains chapters on most of the important bacterial diseases, each written by an expert in the field. In addition, there are separate general chapters on identification of pathogens by classical and non-culturing molecular techniques and virulence mechanisms, such as adhesion and bacterial toxins. In recognition of the recent important research on beneficial bacteria in human health, the section also includes chapters on gut microbiota, prebiotics, and probiotics. Together with the updated and expanded chapter on Bacterial Pharmaceutical Products, this section is a valuable resource to graduate students, teachers, and researchers interested in medical microbiology. Volumes 6–11, organized by Erko Stackebrandt and Fabiano Thompson, contain chapters on each of the ca. 300 known prokaryotic families. Each chapter presents both the historical and current taxonomy of higher taxa, mostly above the genus level; molecular analyses (e.g., DDH, MLSA, riboprinting, and MALDI-TOF); genomic and phenetic properties of the taxa covered; genome analyses including nonchromosomal genetic elements; phenotypic analyses; methods for the enrichment, isolation, and maintenance of members of the family; ecological studies; clinical relevance; and applications. As in the third edition, the volumes in the fourth edition are available both as hard copies and e-books, and as eReferences. The advantages of the online version include no restriction of color illustrations, the possibility of updating chapters continuously and, most importantly, libraries can place their subscribed copies on their servers, making it available to their community in offices and laboratories. The editors thank all the chapter authors and the editorial staff of Springer, especially Hanna Hensler-Fritton, Isabel Ullmann, Daniel Quin˜ones, Alejandra Kudo, and Audrey Wong, for making this contribution possible.

Eugene Rosenberg Editor-in-Chief

About the Editors

Eugene Rosenberg (Editor-in-Chief) Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv Israel

Eugene Rosenberg holds a Ph.D. in biochemistry from Columbia University (1961) where he described the chemical structures of the capsules of Hemophilus influenzae, types B, E, and F. His postdoctoral research was performed in organic chemistry under the guidance of Lord Todd in Cambridge University. He was an assistant and associate professor of microbiology at the University of California at Los Angeles from 1962 to 1970, where he worked on the biochemistry of Myxococcus xanthus. Since 1970, he has been in the Department of Molecular Microbiology and Biotechnology, Tel Aviv University, as an associate professor (1970–1974), full professor (1975–2005), and professor emeritus (2006–present). He has held the Gol Chair in Applied and Environmental Micro- biology since 1989. He is a member of the American Academy of Microbiology and European Academy of Microbiology. He has been awarded a Guggenheim Fellowship, a Fogarty International Scholar of the NIH, the Pan Lab Prize of the Society of Industrial Microbiology, the Proctor & Gamble Prize of the ASM, the Sakov Prize, the Landau Prize, and the Israel Prize for a ‘‘Beautiful Israel.’’ His research has focused on myxobacteriology; hydrocarbon microbiology; surface-active polymers from Acinetobacter; biore- mediation; coral microbiology; and the role of symbiotic microorganisms in the adaptation, development, behavior, and evolution of animals and plants. He is the author of about 250 research papers and reviews, 9 books, and 16 patents. x About the Editors

Edward F. DeLong Department of Biological Engineering Massachusetts Institute of Technology Cambridge, MA USA

Edward DeLong received his bachelor of science in bacteriology at the University of California, Davis, and his Ph.D. in marine biology at Scripps Institute of Oceanography at the University of California, San Diego. He was a professor at the University of California, Santa Barbara, in the Department of Ecology for 7 years, before moving to the Monterey Bay Aquarium Research Institute where he was a senior scientist and chair of the science department, also for 7 years. He now serves as a professor at the Massachusetts Institute of Technology in the Department of Biological Engineering, where he holds the Morton and Claire Goulder Family Professorship in Environmental Systems. DeLong’s scientific interests focus primarily on central questions in marine microbial genomics, biogeochemistry, ecology, and evolution. A large part of DeLong’s efforts have been devoted to the study of microbes and microbial processes in the ocean, combining laboratory and field-based approaches. Development and application of genomic, biochemical, and metabolic approaches to study and exploit microbial communities and processes is his another area of interest. DeLong is a fellow in the American Academy of Arts and Science, the U.S. National Academy of Science, and the American Association for the Advancement of Science. About the Editors xi

Stephen Lory Department of Microbiology and Immunology Harvard Medical School Boston, MA USA

Stephen Lory received his Ph.D. degree in Microbiology from the University of California in Los Angeles in 1980. The topic of his doctoral thesis was the structure-activity relationships of bacterial exotoxins. He carried out his postdoctoral research on the basic mechanism of protein secretion by Gram-negative bacteria in the Bacterial Physiology Unit at Harvard Medical School. In 1984, he was appointed assistant professor in the Department of Microbiology at the University of Washington in Seattle, becoming full professor in 1995. While at the University of Washington, he developed an active research program in host-pathogen interactions including the role of bacterial adhesion to mammalian cells in virulence and regulation of gene expression by bacterial pathogens. In 2000, he returned to Harvard Medical School where he is currently a professor of microbiology and immunobiology. He is a regular reviewer of research projects on various scientific panels of governmental and private funding agencies and served for four years on the Scientific Council of Institute Pasteur in Paris. His current research interests include evolution of bacterial virulence, studies on post-translational regulation of gene expression in Pseudomonas, and the development of novel antibiotics targeting multi-drug- resistant opportunistic pathogens. xii About the Editors

Erko Stackebrandt Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig Germany

Erko Stackebrandt holds a Ph.D. in microbiology from the Ludwig-Maximilians University Munich (1974). During his postdoctoral research, he worked at the German Culture Collection in Munich (1972–1977), 1978 with Carl Woese at the University of Illinois, Urbana Champaign, and from 1979 to 1983 he was a member of Karl Schleifer’s research group at the Technical University, Munich. He habilitated in 1983 and was appointed head of the Departments of Microbiology at the University of Kiel (1984–1990), at the University of Queensland, Brisbane, Australia (1990–1993), and at the Technical University Braunschweig, where he also was the director of the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (1993–2009). He is involved in systematics, and molecular phylogeny and ecology of Archaea and Bacteria for more than 40 years. He has been involved in many research projects funded by the German Science Foundation, German Ministry for Science and Technology, and the European Union, working on pure cultures and microbial communities. His projects include work in soil and peat, Mediterranean coastal waters, North Sea and Baltic Sea, Antarctic Lakes, Australian soil and artesian wells, formation of stromatolites, as well as on giant ants, holothurians, rumen of cows, and the digestive tract of koalas. He has been involved in the description and taxonomic revision of more than 650 bacteria taxa of various ranks. He received a Heisenberg stipend (1982–1983) and his work has been awarded by the Academy of Science at Go¨ttingen, Bergey’s Trust (Bergey’s Award and Bergey’s Medal), the Technical University Munich, the Australian Society for Microbiology, and the American Society for Microbiology. He held teaching positions in Kunming, China; Budapest, Hungary; and Florence, Italy. He has published more than 600 papers in refereed journals and has written more than 80 book chapters. He is the editor of two Springer journals and served as an associate editor of several international journals and books as well as on national and international scientific and review panels of the German Research Council, European Science Foundation, European Space Agency, and the Organisation for Economic Co-Operation and Development. About the Editors xiii

Fabiano Thompson Laboratory of Microbiology Institute of Biology Center for Health Sciences Federal University of Rio de Janeiro (UFRJ) Ilha do Funda˜o Rio de Janeiro Brazil

Fabiano Thompson became the director of research at the Institute of Biology, Federal University of Rio de Janeiro (UFRJ), in 2012. He was an oceanographer at the Federal University of Rio Grande (Brazil) in 1997. He received his Ph.D. in biochemistry from Ghent University (Belgium) in 2003, with emphasis on marine microbial taxonomy and biodiversity. Thompson was an associate researcher in the BCCM/LMG Bacteria Collection (Ghent University) in 2004; professor of genetics in 2006 at the Institute of Biology, UFRJ; and professor of marine biology in 2011 at the same university. He has been a representative of UFRJ in the National Institute of Metrology (INMETRO) since 2009. Thompson is the president of the subcommittee on the Systematics of Vibrionaceae–IUMS and an associate editor of BMC Genomics and Microbial Ecology. The Thompson Lab in Rio currently performs research on marine microbiology in the Blue Amazon, the realm in the southwestern Atlantic that encompasses a variety of systems, including deep sea, Cabo Frio upwelling area, Amazonia river-plume continuum, mesophotic reefs, Abrolhos coral reef bank, and Oceanic Islands (Fernando de Noronha, Saint Peter and Saint Paul, and Trindade).

Table of Contents

Applied Bacteriology and Biotechnology ...... 1

1 Organic Acid and Solvent Production: Acetic, Lactic, Gluconic, Succinic, and Polyhydroxyalkanoic Acids ...... 3 Palmer Rogers . Jiann-Shin Chen . Mary Jo Zidwick

2 Organic Acid and Solvent Production: Butanol, Acetone, and Isopropanol; 1,3- and 1,2-Propanediol Production; and 2,3-Butanediol Production ...... 77 Jiann-Shin Chen . Mary Jo Zidwick . Palmer Rogers

3 Organic Acid and Solvent Production: Propionic and Butyric Acids and Ethanol ...... 135 Mary Jo Zidwick . Jiann-Shin Chen . Palmer Rogers

4 Amino Acid Production ...... 169 Hidehiko Kumagai

5 Microbial Exopolysaccharides ...... 179 Avinash Mishra . Bhavanath Jha

6 Bacterial Enzymes ...... 193 Wim J. Quax

7 Diversity and Biotechnological Applications of Prokaryotic Enzymes ...... 213 Alane Beatriz Vermelho . Eliane Ferreira Noronha . Edivaldo Ximenes Ferreira Filho . Maria Antonieta Ferrara . Elba Pinto S. Bon

8 Bacteria in Food and Beverage Production ...... 241 Michael P. Doyle . Larry R. Steenson . Jianghong Meng

9 Bacterial Pharmaceutical Products ...... 257 Giancarlo Lancini . Arnold L. Demain

10 Biosurfactants ...... 281 Eugene Rosenberg . Eliora Z. Ron

11 Bioremediation ...... 295 Ronald L. Crawford . Eugene Rosenberg

12 Biodeterioration ...... 309 Ji-Dong Gu . Ralph Mitchell

13 Microbial Biofilms ...... 343 Dirk De Beer . Paul Stoodley xvi Table of Contents

14 Biofuels ...... 373 Stefano Freguia . Bernardino Virdis . Korneel Rabaey

15 The Metabolic Pathways of Biodegradation ...... 383 Lawrence P. Wackett List of Contributors

Dirk De Beer Stefano Freguia Max-Planck-Institute for Marine Microbiology Advanced Water Management Centre Bremen The University of Queensland Germany Brisbane Australia Elba Pinto S. Bon Laboratory of Enzyme Technology, Biochemistry Department Ji-Dong Gu Chemistry Institute, Federal University of Rio de Janeiro (UFRJ) School of Biological Sciences Rio de Janeiro, RJ Faculty of Science Brazil The University of Hong Kong Hong Kong SAR Jiann-Shin Chen Bhavanath Jha Department of Biochemistry Virginia Polytechnic Institute and State University Discipline of Marine Biotechnology and Ecology (Virginia Tech) CSIR-Central Salt and Marine Chemicals Research Blacksburg, VA Institute (CSIR-CSMCRI) USA Bhavnagar, Gujarat India Ronald L. Crawford Hidehiko Kumagai Environmental Biotechnology Institute Ishikawa Prefectural University University of Idaho Nonoichi-shi, Ishikawa-ken Moscow, ID Japan USA

Giancarlo Lancini Arnold L. Demain Fondazioe Instituto Insubrico Ricerca per la Vita (FIIRV) Research Institute for Scientists Emeriti Milan Drew University Italy Madison, NJ USA Jianghong Meng Department of Nutrition and Food Science Michael P. Doyle University of Maryland Department of Food Science & Technology College Park, MD University of Georgia USA Griffin, GA USA Avinash Mishra Discipline of Marine Biotechnology and Ecology Maria Antonieta Ferrara CSIR-Central Salt and Marine Chemicals Research Medicines and Drugs Technology Institute Institute (CSIR-CSMCRI) Oswaldo Cruz Foundation Bhavnagar, Gujarat Rio de Janeiro, RJ India Brazil Ralph Mitchell Edivaldo Ximenes Ferreira Filho Laboratory of Applied Microbiology Laboratory of Enzymology, Department of Cellular Biology School of Engineering and Applied Sciences Federal University of Brasilia (UNB) Harvard University Brasilia Cambridge, MA Brazil USA xviii List of Contributors

Eliane Ferreira Noronha Paul Stoodley Laboratory of Enzymology, Department of Cellular Biology Imaging Center for Genomic Sciences Federal University of Brasilia (UNB) Allegheny-Singer Research Institute Brasilia West Penn Allegheny Health System Brazil Pittsburgh, PA USA Wim J. Quax University of Groningen Groningen Alane Beatriz Vermelho The Netherlands Laboratory of Microbial Peptidases Institute of Microbiology Paulo de Go´es Korneel Rabaey BIOINOVAR - Biotechonology center, Federal University of Advanced Water Management Centre Rio de Janeiro (UFRJ) The University of Queensland Rio de Janeiro, RJ Brisbane Brazil Australia and Laboratory of Microbial Ecology and Technology (LabMET) Bernardino Virdis Ghent University Advanced Water Management Centre Ghent The University of Queensland Belgium Brisbane Australia Palmer Rogers∗

Eliora Z. Ron Lawrence P. Wackett Department of Molecular Microbiology and Biotechnology Department of Biochemistry, Molecular Biology and Tel Aviv University Biophysics Tel Aviv BioTechnology Institute Israel University of Minnesota St. Paul, MN Eugene Rosenberg USA Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv Mary Jo Zidwick Israel Biotechnology Development Center Cargill, Incorporated Larry R. Steenson Minneapolis, MN Dupont Nutrition and Health USA New Century, KS USA

∗ Deceased