Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve

354 Pages·2014·8.05 MB·English

by  Masao Fukuda (auth.)

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
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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 vari-
ous 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 chem-
icals. Similarly, many enzymes involved in unique biodegradative reactions with
recalcitrant hazardous chemicals have been analyzed to understand why biodegra-
dative 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 devel-
oped 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 bio-
degradative bacteria include single molecules, single cell systems, bacterial consor-
tia (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 numer-
ous 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