Organohalide respiring bacteria

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Lorenz Adrian · Frank E. Löffler Editors OrganohalideRespiring Bacteria Organohalide-Respiring Bacteria Lorenz Adrian · Frank E Löffler Editors Organohalide-Respiring Bacteria 13 Editors Lorenz Adrian Department of Isotope Biogeochemistry Helmholtz Centre for Environmental Research—UFZ Leipzig Germany Frank E Löffler Department of Microbiology, Department of Civil and Environmental Engineering, Center for Environmental Biotechnology University of Tennessee Knoxville, TN USA and Biosciences Division Oak Ridge National Laboratory Oak Ridge TN, USA ISBN 978-3-662-49873-6 ISBN 978-3-662-49875-0  (eBook) DOI 10.1007/978-3-662-49875-0 Library of Congress Control Number: 2016938398 © Springer-Verlag Berlin Heidelberg 2016 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 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 The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer-Verlag GmbH Berlin Heidelberg Contents Part I  Introduction Organohalide-Respiring Bacteria—An Introduction Lorenz Adrian and Frank E Löffler Natural Production of Organohalide Compounds in the Environment James A Field Energetic Considerations in Organohalide Respiration 31 Jan Dolfing Part II  Diversity of Organohalide-Respiring Bacteria Discovery of Organohalide-Respiring Processes and the Bacteria Involved 51 Perry L McCarty Overview of Known Organohalide-Respiring Bacteria— Phylogenetic Diversity and Environmental Distribution 63 Siavash Atashgahi, Yue Lu and Hauke Smidt The Genus Dehalococcoides 107 Stephen H Zinder The Genus Dehalogenimonas 137 William M Moe, Fred A Rainey and Jun Yan The Genus Dehalobacter 153 Julien Maillard and Christof Holliger The Genus Desulfitobacterium 173 Taiki Futagami and Kensuke Furukawa 10 The Genus Sulfurospirillum 209 Tobias Goris and Gabriele Diekert v vi Contents 11Organohalide-Respiring Deltaproteobacteria 235 Robert A Sanford, Janamejaya Chowdhary and Frank E Löffler 12 Comparative Physiology of Organohalide-Respiring Bacteria 259 Koshlan Mayer-Blackwell, Holly Sewell, Maeva Fincker and Alfred M Spormann Part III  Ecology of Organohalide-Respiring Bacteria 13 Electron Acceptor Interactions Between Organohalide-Respiring Bacteria: Cross-Feeding, Competition, and Inhibition 283 Kai Wei, Ariel Grostern, Winnie W.M Chan, Ruth E Richardson and Elizabeth A Edwards 14 Organohalide-Respiring Bacteria as Members of Microbial Communities: Catabolic Food Webs and Biochemical Interactions 309 Ruth E Richardson Part IV Genomics and Regulation of Organohalide-Respiring Bacteria 15 Comparative Genomics and Transcriptomics of OrganohalideRespiring Bacteria and Regulation of rdh Gene Transcription 345 Thomas Kruse, Hauke Smidt and Ute Lechner 16 Diversity, Evolution, and Environmental Distribution of Reductive Dehalogenase Genes 377 Laura A Hug Part V  Biochemistry of Organohalide-Respiring Bacteria 17 Comparative Biochemistry of Organohalide Respiration 397 Torsten Schubert and Gabriele Diekert 18 Evaluation of the Microbial Reductive Dehalogenation Reaction Using Compound-Specific Stable Isotope Analysis (CSIA) 429 Julian Renpenning and Ivonne Nijenhuis 19 Corrinoid Metabolism in Dehalogenating Pure Cultures and Microbial Communities 455 Theodore C Moore and Jorge C Escalante-Semerena 20 Insights into Reductive Dehalogenase Function Obtained from Crystal Structures 485 Holger Dobbek and David Leys Contents vii Part VI  Applications 21 Redox Interactions of Organohalide-Respiring Bacteria (OHRB) with Solid-State Electrodes: Principles and Perspectives of Microbial Electrochemical Remediation 499 Federico Aulenta, Simona Rossetti, Bruna Matturro, Valter Tandoi, Roberta Verdini and Mauro Majone 22 Current and Future Bioremediation Applications: Bioremediation from a Practical and Regulatory Perspective 517 Robert J Steffan and Charles E Schaefer 23 The Microbiology of Anaerobic PCB Dechlorination 541 Jianzhong He and Donna L Bedard 24“Dehalobium chlorocoercia” DF-1—from Discovery to Application 563 Harold D May and Kevin R Sowers 25 Use of Compound-Specific Isotope Analysis (CSIA) to Assess the Origin and Fate of Chlorinated Hydrocarbons 587 Daniel Hunkeler Part VII  Outlook 26 Outlook—The Next Frontiers for Research on OrganohalideRespiring Bacteria 621 Lorenz Adrian and Frank E Löffler Index 629 Part I Introduction Chapter 1 Organohalide-Respiring Bacteria—An Introduction Lorenz Adrian and Frank E Löffler Abstract  Organohalide-respiring bacteria (OHRB) “breath” halogenated compounds for energy conservation This fascinating process has received increasing attention over the last two decades revealing the physiological, biochemical, genomic, and ecological features of this taxonomically diverse bacterial group The discovery of OHRB enabled successful bioremediation at sites impacted with toxic chlorinated compounds, and has drawn researchers with diverse science and engineering backgrounds to study this process Chapters discussing fundamental and applied aspects of OHRB demonstrate a vibrant research field that will continue to spur scientific discovery and innovate practice The realization in the 1970s of potentially harmful impacts of chlorinated o­ rganics on human and environmental health triggered extensive research on degradation mechanisms and pathways At the time, chloroorganic compounds were considered to be predominantly of anthropogenic origin, and it was somewhat surprising that microbes capable of degrading many chlorinated chemicals were found in diverse environments Carbon–chlorine bond breakage is mediated by dehalogenating enzyme ­systems (i.e., dehalogenases), and three main mechanisms were discovered: hydrolytic L Adrian (*)  Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany e-mail: F.E Löffler (*)  Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA e-mail: F.E Löffler  University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Joint Institute for Biological Sciences (JIBS), Oak Ridge, TN 37831, USA F.E Löffler  Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA © Springer-Verlag Berlin Heidelberg 2016 L Adrian and F.E Löffler (eds.), Organohalide-Respiring Bacteria, DOI 10.1007/978-3-662-49875-0_1 L Adrian and F.E Löffler dehalogenases replace the halogen substituent with a hydroxyl group derived from water, oxygenolytic dehalogenases replace the halogen substituent with a hydroxyl group derived from oxygen, and reductive dehalogenases replace the halogen substituent with a hydrogen atom The degree of chlorine substitution has a strong effect on hydrolytic and oxygenolytic dehalogenation, and highly chlorinated compounds such as polychlorinated dibenzodioxins, polychlorinated biphenyls, hexachlorobenzene, lindane, or tetrachloroethene appeared recalcitrant Reductive dechlorination was an interesting alternate mechanism as it acted on polychlorinated pollutants but the process was slow, incomplete, and presumably co-metabolic A scientific breakthrough was the discovery of the bacterium Desulfomonile tiedjei (DeWeerd et al 1990), an organism that derived all its energy required for growth from the reductive dechlorination of 3-chlorobenzoate to benzoate (Suflita et al 1982) Then, this type of metabolism was described in a mixed culture capable of reductive dechlorination of the priority groundwater contaminant tetrachloroethene (Holliger et al 1993), which was the prelude to the discovery of a diversity of bacteria capable of using chloroorganic compounds as electron acceptors Due to pressing environmental problems, practical interests, at least in the United States, mostly drove research on reductive dechlorination, and support from the U.S Department of Defense was crucial for developing this field The observation of complete reductive dechlorination of tetrachloroethene to environmentally benign ethene in a mixed culture was a seminal contribution (Freedman and Gossett 1989) that lead to the discovery of Dehalococcoides (MaymóGatell et al 1997) A growing research community has contributed substantially to our understanding of microbial taxa capable of using halogenated compounds as terminal electron acceptors A key feature of these organisms is their ability to couple reductive dehalogenation to energy conservation and growth In the case of Dehalococcoides, no other electron acceptors support growth, which gives these organisms a selective advantage at sites impacted with chloroorganic contaminants and makes them ideal agents for bioremediation A few years ago, experts in the field coined the term ‘Organohalide Respiration’ to describe the respiratory reductive dehalogenation process This term is analogous to terms describing other respiratory processes such as nitrate respiration, fumarate respiration, or sulfate respiration and has replaced ambiguous expressions such as “halorespiration”, “dehalorespiration” and “chlororespiration” Organohalide respiration accurately describes the process under study, has been widely adopted in the peer-reviewed literature, and is used in this book Organohalide respiration is a mode of energy conservation under anoxic conditions Organohalide-respiring bacteria (OHRB) “breathe” halogenated organic molecules (called organohalides or organohalogens) just like humans breathe oxygen In biochemical terms, OHRB use organohalides as terminal electron acceptors in a respiratory chain, which is coupled to vectorial proton movement across the cell membrane and energy conservation The required electrons stem from external electron donors such as molecular hydrogen or other oxidizable compounds In respiratory processes, none of the participating compounds themselves 25  Use of Compound-Specific Isotope Analysis (CSIA) … 615 Jin B, Haderlein SB, Rolle M (2013) Integrated 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Environ Sci Technol 42(21):7793–7800 Wolfsberg M, Van Hook WA, Paneth P (2010) Isotope effects in chemical, geological and bio sciences Springer, Dortrecht Zhang N, Bashir S, Qin J, Schindelka J, Fischer A, Nijenhuis I, Herrmann H, Wick LY, Richnow HH (2014) Compound specific stable isotope analysis (CSIA) to characterize transformation mechanisms of alpha-hexachlorocyclohexane J Hazard Mater 280:750–757 doi:10.1016/j.jhazmat.2014.08.046 Zwank L, Berg M, Schmidt TC, Haderlein SB (2003) Compound-specific carbon isotope analysis of volatile organic compounds in the low-microgram per liter range Anal Chem 20:5575–5583 Zwank L, Elsner M, Aeberhard A, Schwarzenbach RP, Haderlein SB (2005) Carbon isotope fractionation in the reductive dehalogenation of carbon tetrachloride at iron (hydr)oxide and iron sulfide minerals Environ Sci Technol 39(15):5634–5641 Part VII Outlook Chapter 26 Outlook—The Next Frontiers for Research on Organohalide-Respiring Bacteria Lorenz Adrian and Frank E Löff ler Abstract  Research efforts over the last two decades have substantially advanced the understanding of organohalide-respiring bacteria (OHRB), and this progress has enabled successful bioremediation applications at chlorinated solventcontaminated sites Yet, major knowledge gaps remain, and detailed biochemical, genetic, regulatory, evolutionary, taxonomic, and ecological questions should be explored to reveal the underlying principles of organohalide respiration, to better define the roles of OHRB in natural microbial communities, and to fully exploit their activities for contaminated site cleanup The chapters in this book summarize the various advances that have been achieved following the discovery, physiological description, and practical application of OHRB But where will the field go next? Which major topics will be targeted in the coming decade? What are the major unresolved questions? What new discoveries will be made overcoming insufficient concepts and leading to new questions and hypotheses? What new techniques will drive research in the near- and midterm future? Will scientists be able to convince funding agencies to invest in this field to enable further transformative discoveries? Will environmental scientists and L Adrian (*)  Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany e-mail: F.E Löff ler  Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA F.E Löff ler  Joint Institute for Biological Sciences (JIBS), University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Oak Ridge, TN 37831, USA F.E Löff ler (*)  Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA e-mail: © Springer-Verlag Berlin Heidelberg 2016 L Adrian and F.E Löffler (eds.), Organohalide-Respiring Bacteria, DOI 10.1007/978-3-662-49875-0_26 621 622 L Adrian and F.E Löffler engineers be successful in demonstrating that the current achievements are just the beginning, and that support for developing precision bioremediation treatment can substantially improve the current practice and realize considerable benefits to society, including safe drinking water, a cleaner environment and financial benefits to the taxpayer? We expect major progress in the biological understanding as well as more sophisticated engineering applications of organohalide respiration in the coming years 26.1 Microbiology As outlined in several book chapters, bacteria from diverse taxa conserve energy associated with reductive dechlorination reactions There is little doubt that a larger diversity of microbes sharing this metabolic capability awaits discovery As an example, enrichment and isolation efforts for Dehalococcoidia strains always included the addition of cell wall antibiotics to the growth medium While this approach is productive for members of the Dehalococcoidia, this approach selects against OHRB with a peptidoglycan cell wall Not surprisingly, diverse reductive dehalogenation reactions observed in initial microcosms by many researchers were lost during further enrichment Isolation work is tedious and short-term rewards are unlikely; however, isolates are very important and will remain the cornerstone of microbiology Different and innovative enrichment and isolation techniques should be pursued to increase the chances to find yet-unknown organisms The value of these efforts cannot be overemphasized, especially in the current situation where more and more research is done exclusively on a computer As observed in many other biological fields, a huge amount of data is now available describing dehalogenating microbial populations, including (meta) genomes, (meta) transcriptomes, and (meta) proteomes, allowing the construction of detailed metabolic models It is important to keep in mind that these models must be used with caution and that all hypotheses need to be experimentally verified, ideally with pure or defined cultures As described in various chapters in this book, we can distinguish two groups of OHRB Opportunistic OHRB (i.e., generalists) that can grow by other means but take advantage of chlorinated compounds as electron acceptors when they are available, and obligate OHRB (i.e., specialists) that strictly depend on chlorinated compounds and cannot derive energy for growth by any other means The environmental constraints and evolution of OHRB specialists and OHRB generalists are poorly understood Is the occurrence of OHRB recent and a consequence of the introduction of organohalogens from anthropogenic sources? Is organohalide respiration an evolutionary old process driven by naturally occurring organohalogens? And what are the reasons for the specialization of Dehalobacter compared to the related opportunistic Desulfitobacterium strains? Recently, single-cell genome analyses have shown that organohalide respiration is not ubiquitous in the Dehalococcoidia and that other modes of energy conservation exist in this 26  Outlook—The Next Frontiers for Research… 623 bacterial class What is the reason for the specialization of the obligate organohalide-respiring Dehalococcoides mccartyi strains? Reductive dehalogenase genes appear to be enriched among the Deltaproteobacteria but are these organisms growing by organohalide respiration? Only detailed physiological characterization of existing and new isolates can answer these questions The systematic identification and categorization of naturally occurring halogenated electron acceptors would enable approaches to match the full complement of reductive dehalogenase genes with different classes of electron acceptors Such an effort could also provide significant information for the fate prediction of halogenated contaminants, which so far have not been sufficiently investigated as electron acceptors for OHRB, including many organohalogen pesticides, pharmaceuticals, and the large group of (per)fluorinated compounds Also, alkanes with single halogen substituents seem to resist transformation by OHRB, whereas vicinally halogenated alkanes can be transformed by dihaloelimination reactions Finally, organohalogens with complicated or those with very simple structures (e.g., chlorinated methanes) are insufficiently investigated In essence, many needs and opportunities exist for extending research that would greatly expand our knowledge of OHRB biology and the roles these organisms play to maintain ecosystem services, foremost the recycling of organohalogens from anthropogenic and natural sources In ecological terms, what is the overall contribution of OHRB to the halogen cycle on Earth? Can the masses of halogenated materials turned over by OHRB be estimated? Although several cross-feeding partners in complex communities have been identified, general guidelines on the specifications and importance of accompanying bacteria have been unsatisfactorily described How other bacteria contribute to make suitable carbon source available, which growth factors they provide, how they influence the redox potential and pH in the microenvironment? It has often been described that mixed cultures more efficiently dehalogenate organohalogens than pure cultures What are the biomolecular underpinnings for this observation? Do syntrophic interactions play relevant roles and what type of syntrophy is occurring? Do we observe higher resistance against stress or higher resilience after stress on the single cell or on the population level? Finally, the basis for toxicity of single organohalogens or mixtures of organohalogens on OHRB as well as essential members of the community, should be investigated to establish causal effects for recalcitrance 26.2 Biochemistry and Genes Encoding Reductive Dehalogenases Large steps forward have recently been achieved in the description of the respiratory machinery involved in organohalide respiration Such progress is important as in-depth information about the reductive dehalogenase enzyme systems may lead to biotechnological applications, both in controlled systems and in the environment 624 L Adrian and F.E Löffler The possibility to heterologously express active reductive dehalogenases opens up a wide field for new research With more than 2000 putative reductive dehalogenase sequences identified, the majority without functional assignment, heterologous expression is an important tool to characterize substrate specificity, substrate affinity, cofactor requirement, and to provide structural information A high-throughput expression pipeline is desirable to analyze the hundreds, or possibly thousands of distinct reductive dehalogenases Likely, the traditional approach to induce, enrich, and purify reductive dehalogenases by chromatographic or electrophoretic techniques will still have value Conventional biochemical approaches will also be needed for the investigation of a recently identified larger respiratory complex in Dehalococcoides mccartyi (Kublik et al 2016), for which heterologous expression and reconstitution may not be feasible With more structural information of reductive dehalogenases, comparative analyses can reveal structure-function relationships, relevant binding motifs, and contribute to predictive understanding of substrate range and reaction specificity Among the reductive dehalogenases, a system of orthologous clusters has been established (Hug et al 2013), and it will be a crucial task to refine this system as new information becomes available Also, the role of accessory proteins involved in dehalogenase maturation should be studied (e.g., cofactor incorporation, folding, transport across the cytoplasmic membrane, assembly of larger complexes) Most promising are integrated approaches, and cross-disciplinary team research is most likely to produce transformative discoveries that advance and broaden the field Although some progress has been made elucidating the controls of reductive dehalogenase gene expression (Wagner et al 2013; Kemp et al 2013), the regulatory cascade is poorly understood Regulatory genes are located in the vicinity of reductive dehalogenase genes but virtually nothing is known about the inducing molecules, how they interact with the transcription regulator(s), and how they trigger physiological responses Also, it is unclear why different types of regulators are involved in the transcriptional regulation of different reductive dehalogenase genes Understanding the regulation of reductive dehalogenation expression will likely reveal a new conceptual understanding of regulatory circuits in prokaryotes Recently, it has been shown that reductive dehalogenases can display strong substrate promiscuity and that relative reductive dechlorination rates follow electron density properties in the electron acceptor (Cooper et al 2015) Apparently, the traditional lock-and-key or induced-fit models for enzymes might not be appropriate for reductive dehalogenases, and a more dynamic substrate binding concept is needed Further investigations are required using structural, kinetic, and quantum chemistry information to analyze enzyme–substrate interplay and electron transfer This will also provide more detailed mechanistic insights into reductive dehalogenation reactions, but more widely, will also contribute to better understanding of coenzyme B12 dependent reactions Another research area of interest will be the elucidation of the components and/or complexes involved in proton translocation across the membrane, and if mechanistic differences distinguish phylogenetically distinct OHRB taxa Especially the electron transfer between the primary oxidizing protein complex 26  Outlook—The Next Frontiers for Research… 625 (e.g., a hydrogenase) and the reductive dehalogenase will need further attention to identify electron carriers and their biochemical characteristics These studies will reveal if obligate OHRB (e.g., members of the Dehalococcoidia) and facultative OHRB (e.g., members of the Deltaproteobacteria) share electron transport components or have distinct machineries to capture energy released in reductive dechlorination reactions Reductive dehalogenases of OHRB share characteristic features including a Tat leader peptide and require the so-called B protein with a putative membraneanchoring function Genome analyses revealed that diverse taxa possess reductive dehalogenase genes not encoding these characteristic features Experiments with Comamonas sp 7D-2 (Chen et al 2013) and Nitratireductor pacificus strain pht-3B (Payne et al 2015) showed that such enzymes have reductive dehalogenase function albeit they are not directly involved in respiration Similar reductive dehalogenase genes were found in marine sediments Possibly, these nonrespiratory reductive dehalogenases are part of degradation pathways that enable the host to oxidize the chloroorganic compound and utilize an alternate electron acceptor such as oxygen Have organisms with nonrespiratory reductive dehalogenase lost the ability to grow via organohalide respiration, or are they possibly the ancestors that gave rise to the evolution of (obligate) OHRB? 26.3 Bioremediation Applications Without extensive contamination of the environment with chlorinated chemicals and ensuing public awareness and pressure, OHRB may not have been studied The reductive dechlorination process is a good example how practical needs enable fundamental scientific discoveries while at the same time delivering solutions for pressing environmental problems It is hoped that funding resources for multidisciplinary team efforts will be available in the future to advance the science, generate economic opportunities, and elevate environmental cleanup from an empirical practice to a science with predictable outcomes Bioaugmentation, the delivery of OHRB consortia into aquifers impacted with chlorinated contaminants, can initiate or accelerate degradation and detoxification, as documented at many chlorinated solvent-contaminated sites (Ellis et al 2000; Lendvay et al 2003; Major et al 2002; Löffler et al 2013) D mccartyi appears to be crucial and only strains of this bacterial species have been demonstrated to detoxify chlorinated ethenes and produce environmentally benign ethene Interestingly, D mccartyi strains are often present in contaminated aquifers but efficient ethene formation does not occur, presumably because the resident Dehalococcoides populations lack the bvcA and/or vcrA reductive dehalogenase genes required for vinyl chloride reductive dechlorination (Krajmalnik-Brown et al 2004; Müller et al 2004) Thus, the complement of reductive dehalogenase genes determines if the resident Dehalococcoides population efficiently degrades the target contaminant(s) An interesting question is if bioaugmentation successes 626 L Adrian and F.E Löffler really rely on the proliferation of the D mccartyi strains introduced with the inoculum, or if the introduction of the genetic material encoding the vinyl chloride reductive dehalogenase(s) is sufficient Mounting evidence suggests that members of the Dehalococcoidia acquire reductive dehalogenase genes via horizontal gene transfer (McMurdie et al 2011; Padilla-Crespo et al 2014), which may offer alternative bioremediation strategies Detailed laboratory studies unravelled the complicated nutritional requirements of D mccartyi strains In addition to hydrogen, Dehalococcoides requires other growth factors, foremost corrinoid, which is needed to assemble functional reductive dehalogenases The recent observation that the type or corrinoid (i.e., cobamides with different lower bases) has distinct effects on the reductive dechlorination performance of D mccartyi strains expressing different vinyl chloride reductive dehalogenases emphasizes the need to understand the roles of the community to support Dehalococcoides activity (Yan et al 2015) Metagenomics and metaproteomics enable a census of the genetic and actual catalytic potential, respectively, of entire microbial communities Such approaches have not been effectively brought to bear at bioremediation sites but may be ideal tools to develop systems understanding, which is needed to assess the complicated interactions that govern activity of OHRB Such detailed knowledge can inform about reductive dechlorination potential, measure actual activity, and reveal interspecies dependencies, nutritional limitations, and possible synergistic effects, and thus offer opportunities to refine bioremediation to efficiently achieve the desired outcomes References Chen K, Huang L, Xu C, Liu X, He J, Zinder SH, Li S, Jiang J (2013) Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide Mol Microbiol 89(6):1121–1139 doi:10.1111/mmi.12332 Cooper M, Wagner A, Wondrousch D, Sonntag F, Sonnabend A, Brehm M, Schüürmann G, Adrian L (2015) Anaerobic microbial transformation of halogenated aromatics and fate prediction using electron density modelling Environ Sci Technol 49(10):6018–6028 doi:10.1021/acs.est.5b00303 Ellis D, Lutz E, Odom J, Buchanan R, Bartlett C, Lee M, Harkness M, Deweerd K (2000) Bioaugmentation for accelerated in situ anaerobic bioremediation Environ Sci Technol 34(11):2254–2260 doi:10.1021/es990638e Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L (2013) Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases Philos Trans R Soc Lond B Biol Sci 368(1616):20120322 doi:10.1098/r stb.2012.0322 Kemp LR, Dunstan MS, Fisher K, Warwicker J, Leys D (2013) The transcriptional regulator CprK detects chlorination by combining direct and indirect readout mechanisms Philos Trans R Soc B 368(1616):20120323 doi:10.1098/rstb.2012.0323 Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE (2004) Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp strain BAV1 Appl Environ Microbiol 70(10):6347–6351 doi:10.1128/AEM.70.10.6347-6351.2004 26  Outlook—The Next Frontiers for Research… 627 Kublik A, Deobald D, Hartwig S, Schiffmann C, Andrades A, von Bergen M, Sawers RG, Adrian L (2016) Identification of a multiprotein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement Environ Microbiol doi:10.1111/1462-2920.13200 Lendvay JM, Löffler FE, Dollhopf M, Aiello MR, Daniels G, Fathepure BZ, Gebhard M, Heine R, Helton R, Shi J, Krajmalnik-Brown R, Major CL, Barcelona MJ, Petrovskis E, Hickey R, Tiedje JM, Adriaens P (2003) Bioreactive barriers: a comparison of bioaugmentation and biostimulation for chlorinated solvent remediation Environ Sci Technol 37(7):1422–1431 doi:10.1021/es025985u Löffler FE, Ritalahti KM, Zinder SH (2013) Dehalococcoides and reductive dechlorination of chlorinated solvents In: Stroo HF, Leeson A, Ward CH (eds) Bioaugmentation for groundwater remediation, vol SERDP ESTCP environmental remediation technology Springer, New York, pp 39–88 doi:10.1007/978-1-4614-4115-1_2 Major DW, McMaster ML, Cox EE, Edwards EA, Dworatzek SM, Hendrickson ER, Starr MG, Payne JA, Buonamici LW (2002) Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene Environ Sci Technol 36:5106–5116 doi:10.1021/es0255711 McMurdie P, Hug L, Edwards E, Holmes S, Spormann A (2011) Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides BMC Genom 12(1):287 doi:10.1186/1471-2164-12-287 Müller JA, Rosner BM, von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM (2004) Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp strain VS and its environmental distribution Appl Environ Microbiol 70(8):4880–4888 doi:10.1128/AEM.70.8.4880-4888.2004 Padilla-Crespo E, Yan J, Swift C, Wagner DD, Chourey K, Hettich RL, Ritalahti KM, Löffler FE (2014) Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring Chloroflexi Appl Environ Microbiol 80(3):808–818 doi:10.1128/ AEM.02927-13 Payne KAP, Quezada CP, Fisher K, Dunstan MS, Collins FA, Sjuts H, Levy C, Hay S, Rigby SEJ, Leys D (2015) Reductive dehalogenase structure suggests a mechanism for B12dependent dehalogenation Nature 517(7535):513–516 doi:10.1038/nature13901 Wagner A, Segler L, Kleinsteuber S, Sawers G, Smidt H, Lechner U (2013) Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi Philos Trans R Soc B 368:20120317 doi:10.1098/rstb.2012.0317 Yan J, Simsir B, Farmer AT, Bi M, Yang Y, Campagna SR, Löffler FE (2015) The corrinoid cofactor of reductive dehalogenases affects dechlorination rates and extents in organohaliderespiring Dehalococcoides mccartyi ISME J doi:10.1038/ismej.2015.197 Index A Allyl chloride, 140 Ampicillin, 140 Anaerobic degradation, 52 Anaerobic wastewater treatment, 50 Anaeromyxobacter, 239 Anaeromyxobacter dehalogenans, 253 Apparent kinetic isotope effect (AKIE), 437, 598 Aroclor, 541, 542, 544–555, 550, 558–560, 563 Arsenate, 213, 218, 220 ATP generation, 45 B Base-off conformation, 490 β-hexachlorocyclohexane, 155 Bioaugmentation, 5, 523, 528, 550, 557, 560, 563 Biochemistry, 623 Bioelectrochemical systems, 500 Biogeochemical cycling of organohalides, 328 Biokinetic models, 320 Bioremediation applications, 517, 625 Biostimulation, 143, 520, 563 B protein, 249 Bromide, 140 Brominated ethenes, 223 Bromophenols, 241 C Carbon–Halogen bonds, 44 Carbon isotopes, 592 Catabolic transposon, 194 Catalase, 217 CblC, 490 cDCE, 222, 244–246 Cell envelope, 157 Chlordecone, 40 2-chlorophenol, 240, 243 Chlorinated solvent, 52 Chlorinated ethenes, 492, 517 Chlorinated methanes, 223 Chlorine isotopes, 594 Chlorobenzenes, 563 Chlorobenzoate, 236, 241, 243 Chloroethenes, 193 Chloroflexi, 143, 544, 545, 547, 550, 558, 559 3-chloro-4-hydroxyphenylacetic acid, 175 Chlorophenols, 194 Clostridia, 187 Cobalamin–halide complex, 493, 495 Cobalamin riboswitches, 199 Co-contaminants, 284 CO2 fixation, 164, 226 Co-metabolism, 31, 32 Commercial PCB, 541–544, 546, 551, 559 Commercial scale, 524 Commitment to catalysis, 598 Competition, 283, 284, 316 Complex I, 164, 224 Composite transposon, 161 Compound-specific isotope analysis (CSIA), 429, 587 Consumption threshold concentrations, 246 Corrinoid auxotrophy, 167 Corrinoid-binding domain, 489 Corrinoid biosynthesis, 199, 225, 228, 247 Corrinoid cofactor, 160, 248, 249, 345, 351, 352, 356 CprK, 346, 354, 366 CRISPR, 225 © Springer-Verlag Berlin Heidelberg 2016 L Adrian and F.E Löffler (eds.), Organohalide-Respiring Bacteria, DOI 10.1007/978-3-662-49875-0 629 Index 630 Crystal structures, 487 Cytochromes, 217 D Debromination, 196 Dehalobacter, 153, 213, 346, 348, 350–353, 356, 362, 364, 365, 548, 549, 557–559 Dehalobacter restrictus, 55 Dehalobium chlorocoercia, 550, 559, 563 Dehalococcoides, 213, 346, 347, 350, 353, 357, 360 Dehalococcoides mccartyi, 56, 518, 544–549, 551–553, 555–560 strain 195, 56, 549 strain CBDB1, 57, 551 strain FL2, 57 Dehalococcoidia, 143, 622 Dehalogenimonas, 137, 559 Dehalogenimonas alkenigignens, 138 Dehalogenimonas lykanthroporepellens, 137 Dehalospirillum, 210 Deiodination, 197 Deltaproteobacteria, 235, 250 Desulfitobacterium, 173, 213, 346, 348, 350, 352, 353, 356–359, 362, 364, 367 Desulfoluna spongiiphila, 241 Desulfomonile limimaris, 242 Desulfomonile tiedjei, 55, 228, 236, 253 Desulfovibrio dechloroacetivorans, 243 Desulfuromonas chloroethenica, 245 Desulfuromonas michiganensis, 245 Dibromoethane, 140 Dibromoethene, 223 Dibromophenols, 492 Dibromopropane, 140 Dichlorobenzene, 155 Dichloroethane, 137, 156, 244 Dichloromethane, 156 Dichlorophenol, 223 Dichloropropane, 137 Dihaloelimination, 33, 37, 140, 189 Dimethylbenzimidazole, 249 Dimethylsulfoxide, 139 DNAPL, 529 Dual-element isotope approach, 599 E Ecology, 623 Ecophysiology, 248 Electron acceptors, 218, 220 Electron donor, 218, 518, 520 Electron shuttling, 247 Electron transfer, 494 Electrostimulation, 563 Energetics, 32 Enrichment (culture), 544–549, 552–554, 557–559 Environmental distribution of OHRB, 64, 81, 83, 88 Epsilonproteobacteria, 209 Equilibrium isotope effect (EIE), 589 Evolution, 378, 386 Extracellular electron transfer, 502 F Facilitated fermentation, 261 Fatty acid composition, 180 Fermentation, 42, 213, 219 Fermentative growth, 183 Fermenters, 312, 315, 316, 317 Ferredoxin domain, 490 Ferredoxin-reductase, 491 Ferric iron, 237, 244, 246 4Fe-4S clusters, 160 Firmicutes, 187 Fluorobenzoate, 241 Food webs, 313 Fractured bedrock, 529 Fumarate, 237, 244, 245 Functional heterologous expression of RDase, 200 Fungi, 248 G Gene cluster, 161 Genome, 225 Genome analyses, 250 Geobacter lovleyi, 246, 253 Geobacter sulfurreducens, 248 Geobacter thiogenes, 247 Gibbs free energy, 34, 39 Groundwater, 214 Growth factor requirements, 158 Growth yield, 5, 162, 240, 245 H Habitat, 157 Halogen ligation, 493 Heme, 249 Homoacetogens, 314, 315, 317, 321 Horizontal gene transfer, 250 Hydrogen, 139, 213 Hydrogenase genes, 224 Hydrogenases, 163 Index Hydrogen isotopes, 592 Hydrogenolysis, 33, 189 Hydrogen thresholds, 39 Hydrothermal vent, 251 I Inhibition, 283, 284 Interspecies H2 transfer, 89, 309, 315 Intraprotein electron transfer, 492 Intrinsic kinetic isotope effect, 598 In situ bioremediation, 519 Iodophenols, 241 Iron–sulfur cluster, 491 Iscu, 228 Isotope enrichment factor, 435 Isotope fractionation, 589 Isotope ratio, 588 Isotope ratio mass-spectrometers (IRMS), 432, 592 Isotopic fractionation, 567 K Kinetic isotope effect (KIE), 435, 589 Kinetic model, 286 Kinetics, 563 L Low permeability zones, 534 Low pH aquifers, 530 M Manganate, 218, 220 Marine and estuarine environments, 84 MarR regulators, 365, 366 Mathematical models, 534 Maturation, 227 Mechanism, 495 Membrane-bound hydrogenase, 224 Menaquinone, 157, 199, 217 Mesophilic, 139 Methanogens, 312, 314–317 Microaerophilic, 217 Mixotrophy, 160 Mobile element, 194 Myxococcales, 239 N Natural organohalogen compounds, Nitrate, 217, 218, 220, 223, 237, 242 631 Nitrate reductase, 224 Nitrite reductase, 220 Nitrogenase, 224 Nitroreductase fold, 489 Norpseudovitamin-B12, 495 NpRdhA, 489 O O-demethylation, 183 OHRB generalists, 622 OHRB specialists, 622 OHR region, 227 Organohalide-respiring bacteria, 63, 64, 284 Organohalide respiration, 4, 33, 50, 55, 64, 345, 355, 363, 365, 368, 378, 384–386, 389, 549, 550 Oxidase, 217 Oxidation-reduction potential, 138 Oxidative transformations, 54 Oxygen, 217, 319 P PCB dechlorination, 542–545, 547–549, 552, 555, 557–560 PCB reductive dehalogenase, 541, 556, 560, 557–560 PCE, 244–246, 541, 542, 548, 549, 553, 555–558, 560 PceA, 160, 213, 489 (Per)fluorinated compounds, 45 Peptidoglycan type, 157 Peptococcaceae, 187 Peroxidase, 228 Pesticides, 51 Phenol, 241 Phylogenetic diversity, 64, 73 Polychlorinated biphenyl, 563 Primary isotope effect, 595 Pristine environments, 248 Propenes, 223 Proton transfer, 494 Pyruvate, 178, 237, 241–243 Q Quinol dehydrogenase, 228 R Rate limitation, 442 Rayleigh equation, 591 RdhA active site, 492 Index 632 RdhA maturation, 491 RdhC, 228 Rebound, 532 Redox mediator, 503 Reductive acetyl-CoA pathway, 199 Reductive debromination, 244 Reductive dehalogenase (RDase), 249, 250, 287, 345, 346, 350, 353, 355–357, 360–362, 366, 377–383, 383–389, 541, 542, 548, 549, 551, 552, 555–558, 560, 623 Regulation, 227 Regulatory issues, 531 Remediation technologies, 283, 518 Respiratory processes, Respiratory reductive dehalogenation, Riboswitches, 167 S Secondary isotope effect, 595 Sediment, 251 Sediment-free culture, 546, 547, 553, 559 Selenate, 218, 220 Sludge, 252 Solid-state electrodes, 499 Sponge, 251 Stable isotope fractionation, 435 Stable isotope, 429 Structure–function studies, 495 Substrate access channels, 492 Substrate specificity, 381 Sulfate, 237, 242 Sulfide, 138, 218 Sulfite, 220, 243 Sulfur, 217, 220, 247 Sulfurospirillum, 209, 211, 349, 351–353, 356, 357, 365 Sulfurospirillum carboxydovorans, 211, 214, 222 Sulfurospirillum deleyianum, 210 Sulfurospirillum halorespirans, 211, 213–215, 222, 227 Sulfurospirillum multivorans, 210, 213, 214, 222, 249 Sulfurospirillum species SL2, 209, 211, 349, 351–353, 356, 357, 365 Sulfurospirillum tacomaensis, 211, 222 Syntrophic relationship, 160, 213 T TCE, 222, 244, 245 Tetrachloroethane, 137, 154, 244 Tetrachlorophthalide, 156 Tetrathionate, 220 Thermodynamics, 32, 34 Thiosulfate, 242, 243 Threshold concentrations, 246 Titanium-citrate, 138 Toxicity, 253 Transcriptional analysis, 555 Transcriptional regulator, 195 Transposon mutagenesis, 200 Tribromoethene, 223 Tribromophenol, 243 Trichlorobacter thiogenes, 247 Trichloroethane, 137, 155, 244 Trichloropropane, 137, 140 Twin-arginine motif, 160, 228 Two-component regulatory system, 228 Two-phase system, 154 Tyr-Lys/Arg motif, 492 U Up-flow anaerobic-sludge bed reactor, 197 Uranium, 246 V Vancomycin, 140 Vancomycin resistance gene cluster, 178 W Wastewater reclamation, 52 Wood-Ljungdahl pathway, 164 Y Yield, 240 ... Considerations in Organohalide Respiration 31 Jan Dolfing Part II  Diversity of Organohalide- Respiring Bacteria Discovery of Organohalide- Respiring Processes and the Bacteria Involved.. .Organohalide- Respiring Bacteria Lorenz Adrian · Frank E Löffler Editors Organohalide- Respiring Bacteria 13 Editors Lorenz Adrian Department of... Contents 11 Organohalide- Respiring Deltaproteobacteria 235 Robert A Sanford, Janamejaya Chowdhary and Frank E Löffler 12 Comparative Physiology of Organohalide- Respiring Bacteria
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Xem thêm: Organohalide respiring bacteria , Organohalide respiring bacteria , 8 Change in Gibbs Free Energy Under Environmentally Realistic Conditions, 4 Early Work on Reaction Pathways and Organisms Involved, 4 Nutritional Requirements and Growth Conditions of Dehalobacter spp., 8 Functional Diversity of Reductive Dehalogenases in the Dehalobacter Genus, 3 Morphology, Physiology, and Growth Characteristics, 2 Comparative Genomics and Evolution of Obligate Organohalide-Respiring Bacteria, 2 Lessons from Field Observations and Enrichment Cultures, 4 Inhibition of Reductive Dehalogenases (Enzyme Level), 7 Cross-Feeding and Competition in Anaerobic Dehalogenating Microbial Communities, 6 Organohalide Respiration Rates in OHRB Communities and Modeling of Community Food Webs, 4 RDases as Terminal Reductases in Organohalide Respiratory Chains, 4 Application of CSIA for the Evaluation of the Reductive Dehalogenation Reaction, 5 Intracellular Mass Transfer and the Effect on Observed Isotope Fractionation, 2 Bacteria Involved in the Dechlorination of Commercial PCB Mixtures in Mixed Cultures, 4 Pure Cultures of  Exhibit Diverse Complex Patterns of Dechlorination of Commercial PCB Mixtures, 5 Identification and Characterization of Three PCB Reductive Dehalogenases, 2 Isolation and Characterization of “Dehalobium chlorocoercia” Strain DF-1, 5 Kinetics and Threshold Levels of PCB Organohalide Respiration, 6 Dechlorination and Degradation of PCBs in Contaminated Sediments and Soils, 5 Relating Isotope Fractionation to Isotope Effects and Reaction Mechanisms, 7 Application of Isotope Methods in Field Studies, 2 Biochemistry and Genes Encoding Reductive Dehalogenases

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