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Hideaki Nojiri · Masataka Tsuda Masao Fukuda · Yoichi Kamagata Editors Biodegradative Bacteria How Bacteria Degrade, Survive, Adapt, and Evolve Biodegradative Bacteria Hideaki Nojiri (cid:129) Masataka Tsuda Masao Fukuda (cid:129) Yoichi Kamagata Editors Biodegradative Bacteria How Bacteria Degrade, Survive, Adapt, and Evolve Editors Hideaki Nojiri Masataka Tsuda Biotechnology Research Center Graduate School of Life Sciences The University of Tokyo Tohoku University Tokyo, Japan Sendai, Miyagi, Japan Masao Fukuda Yoichi Kamagata Department of Bioengineering Bioproduction Research Institute Nagaoka University of Technology National Institute of Advanced Industrial Nagaoka, Niigata, Japan Science and Technology Sapporo, Hokkaido, Japan ISBN 978-4-431-54519-4 ISBN 978-4-431-54520-0 (eBook) DOI 10.1007/978-4-431-54520-0 Springer Tokyo Heidelberg New York Dordrecht London Library of Congress Control Number: 2013950987 © Springer Japan 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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 specifi cally 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 specifi c 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. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Pref ace From a macroscopic standpoint, the environment where we live maintains con- stancy to some extent. This means the environment has a buffering capacity for various types of impacts. Bacterial metabolic capacity, which plays an important role in the global material cycle, contributes largely to the buffering capacity for huge and unintended release of various chemicals. Recently, however, the prosperity and glo- balization of material civilization has led not only to severe local contamination by hazardous chemicals, but also to continuous increment of contaminant concentra- tions worldwide. To solve such urgent global issues, bacterial functions that are involved in biodegradation of hazardous chemicals have been analyzed. The term “biodegradative bacteria” refers to the bacteria that have the ability to degrade such xenobiotic (man-made) and/or hazardous chemicals. Since the 1980s, following on the development of microbial genetics, molecular genetic research techniques have been applied to the investigation of the function of biodegradative bacteria. This research has resulted in the cloning of many genes and gene clusters involved in the biodegradation of various types of contaminated chemicals. Similarly, many enzymes involved in unique biodegradative reactions with recalcitrant hazardous chemicals have been analyzed to understand why biodegradative bacteria can decompose corresponding chemicals. These analyses have pro- vided an understanding of the structural bases of such novel reactions for xenobiotic chemicals. As readers may know, the recent development of genome-wide investi- gative techniques has largely promoted the comprehensive interpretation of a whole-cell system of biodegradative bacteria. The degradative capacity of bacteria for xenobiotic compounds may be developed through the adaptive change of native enzymatic function and/or recruitment of genes or gene clusters accounting for the new metabolic capacities. Therefore, analyses of biodegradative bacteria can be said to have partially dealt with the rapid evolution process of bacteria in natural ecosystems. From the application point of view, to remediate actual contaminated sites by the biodegradative capacity of bacteria, it is quite important to know or to control the behavior of biodegradative bacteria in the environment. These are quite v vi Preface diffi cult issues, however, because there are numerous bacterial strains and diverse environmental conditions in actual contaminated sites. Thus, in situ analyses of biodegradative bacterial function should include investigation by recently developed molecular ecological techniques. As mentioned earlier, analyses of biodegradative bacteria include various types of studies, such as genetics, enzymology, genomics, cell physiology, ecology, and evolutional biology. In another words, the targets investigated in research on biodegradative bacteria include single molecules, single cell systems, bacterial consortia (interaction with surrounding microorganisms), and interaction with surrounding biotic and abiotic materials. Such complexity makes the research on biodegradative bacteria diffi cult but quite interesting. Biodegradative Bacteria consists of three parts, each consisting of fi ve to seven chapters: (1) Genetic and genomic systems, (2) Degradative enzyme systems, and (3) Bacterial behavior in natural environmental systems. The reader will fi nd that the scope of the various chapters is not uniform. In our opinion, they all are fascinat- ing, however. We hope this book will contribute to readers’ knowledge of how far biodegradative bacteria research has progressed and how various recent technical innovations have led to such progress. To all the authors who in spite of their numerous other duties found time to review the novel work in their fi eld, we express our gratitude. We are also grateful to Springer Japan and especially to Kaoru Hashimoto and Yoshiko Shikano of the editorial staff for their support and counsel. Tokyo , Japan Hideaki Nojiri Sendai , Japan Masataka Tsuda Sapporo , Japan Yoichi Kamagata Nagaoka , Japan Masao Fukuda Contents Part I Genetic and Genomic Systems 1 Rhodococcus Multiple-Enzyme and Parallel- Degradation System for Aromatic Compounds ........................................................ 3 Masao Fukuda 2 Appearance and Evolution of γ-Hexachlorocyclohexane- Degrading Bacteria ................................................................................ 19 Yuji Nagata, Michiro Tabata, Satoshi Ohhata, and Masataka Tsuda 3 Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D)- Degradative Genes and Degrading Bacteria ....................................... 43 Wataru Kitagawa and Yoichi Kamagata 4 Genetic System of Organohalide-Respiring Bacteria ......................... 59 Taiki Futagami, Masatoshi Goto, and Kensuke Furukawa 5 Mobile Catabolic Genetic Elements in Pseudomonads ...................... 83 Masataka Tsuda, Yoshiyuki Ohtsubo, and Hirokazu Yano 6 Adaptation to Xenobiotics and Toxic Compounds by Cupriavidus and Ralstonia with Special Reference to Cupriavidus metallidurans CH34 and Mobile Genetic Elements .................................................................................... 105 Max Mergeay and Rob Van Houdt 7 Conjugative Elements: Host Chromosome Function Modifi ers ................................................................................. 129 Masaki Shintani, Yurika Takahashi, and Hideaki Nojiri vii viii Contents Part II Enzyme Systems 8 Online Monitoring of Biodegradation Processes Using Enzymatic Biosensors ................................................................. 155 Sarka Bidmanova, Eva Hrdlickova, Tana Koudelakova, Jiri Damborsky, and Zbynek Prokop 9 Structure and Function of Aromatic-Ring Hydroxylating Dioxygenase System ............................................................................... 181 Kengo Inoue and Hideaki Nojiri 10 The Protocatechuate 4,5-Cleavage Pathway: Overview and New Findings ................................................................. 207 Naofumi Kamimura and Eiji Masai 11 Toluene Tolerance Systems in Pseudomonas ....................................... 227 Ana Segura and Juan Luis Ramos 12 Diversity and Evolution of Aromatic Degradation Pathway Enzymes in an Activated Sludge ........................................................... 249 Kentaro Miyazaki Part III Bacterial Behavior in Natural Environmental Systems 13 Syntrophic Interactions in Biodegradative Consortia ........................ 267 Kazuya Watanabe and Atsushi Kouzuma 14 Strategies to Reveal Genomic Function in Natural Soil Systems ............................................................................................ 279 Yoshiyuki Ohtsubo, Eri Nishiyama, Yoko Ishibashi, Yuji Nagata, and Masataka Tsuda 15 Monitoring Microbial Community Dynamics to Evaluate Bioremediation ................................................................... 293 Brett R. Baldwin, Dora Ogles, and Cindy H. Nakatsu 16 Selective Stimulation of Aromatic Compound Degradation by the Indigenous Marine Bacterium Cycloclasticus for Bioremediation of Oil Spills in the Marine Environment ................................................................... 313 Noriyuki Iwabuchi 17 Biofi lm as a Multicellular Bacterial System ........................................ 335 Masanori Toyofuku and Nobuhiko Nomura Index ................................................................................................................ 353 Part I Genetic and Genomic Systems

Description:

Biodegradative Bacteria highlights the novel nature of bacterial cell functions in the field of biodegradation by putting them into three parts: (1) Genetic and genomic systems, (2) Degradative enzyme systems, and (3) Bacterial behavior in natural environmental systems. The first part of the book in