Table Of Content

Environmental Degradation and Transformation of Organic Chemicals CCRRCC__77224411__FFmm..iinndddd ii 66//2211//22000077 11::1122::3311 PPMM CCRRCC__77224411__FFmm..iinndddd iiii 66//2211//22000077 11::1122::3322 PPMM Environmental Degradation and Transformation of Organic Chemicals Alasdair H. Neilson Ann-Sofie Allard and Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business CCRRCC__77224411__FFmm..iinndddd iiiiii 66//2211//22000077 11::1122::3322 PPMM CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2008 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number-10: 0-8493-7241-0 (Hardcover) International Standard Book Number-13: 978-0-8493-7241-4 (Hardcover) This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any informa- tion storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http:// www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For orga- nizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice:Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Neilson, Alasdair H. Environmental degradation and transformation of organic chemicals / Alasdair H. Neilson and Ann-Sofie Allard. p. cm. Rev. ed. of: Organic chemicals. c2000. Includes bibliographical references and index. ISBN 978-0-8493-7241-4 (alk. paper) 1. Aquatic organisms--Effect of water pollution on. 2. Organic water pollutants--Environmental aspects. I. Allard, Ann-Sofie. II. Neilson, Alasdair H. Organic chemicals. III. Title. QH545.W3N45 2008 577’.14--dc22 2007012219 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com CCRRCC__77224411__FFmm..iinndddd iivv 66//2211//22000077 11::1122::3322 PPMM Contents Preface ............................................................................................................................................xix Acknowledgments ........................................................................................................................xxiii Authors ...........................................................................................................................................xxv SECTION I Degradation and Transformation Processes Chapter 1 Abiotic Reactions .........................................................................................................3 Introduction ........................................................................................................................................3 Photochemical Reactions in Aqueous and Terrestrial Environments ...............................................3 The Diversity of Photochemical Transformations .............................................................................4 The Role of Hydroxyl Radicals ..............................................................................................4 Illustrative Examples of Photochemical Transformations in Aqueous Solutions ..................5 Hydroxyl Radicals in the Destruction of Contaminants ....................................................................9 Fenton’s Reagent .....................................................................................................................9 Polyoxometalates (Heteropolyacids) .....................................................................................10 Photolytic Degradation on TiO ...........................................................................................10 2 Other Photochemically Induced Reactions......................................................................................11 The Role of Humic Matter: Singlet Dioxygen .................................................................................12 Interactions between Photochemical and Other Reactions .............................................................13 Reactions in the Troposphere...........................................................................................................14 Survey of Reactions ..............................................................................................................15 Survey of Reactants ..............................................................................................................17 Aliphatic Hydrocarbons .............................................................................................17 Aromatic Hydrocarbons.............................................................................................17 Biogenic Terpenes ......................................................................................................17 Reentry of Tropospheric Transformation Products .........................................................................18 Halogenated Alkanes and Alkenes .......................................................................................18 Arenes and Nitroarenes ........................................................................................................20 Alkylated Arenes ..................................................................................................................21 Sulfi des and Disulfi des .........................................................................................................21 Chemically Mediated Transformations ...........................................................................................22 Hydrolysis .............................................................................................................................22 Reductive Displacement: Dehalogenation and Desulfurization ...........................................25 Reductive Dehalogenation ...............................................................................................................25 Zero-Valent Metals ...............................................................................................................25 Chromous Chloride ..............................................................................................................26 Porphyrins and Corrins ........................................................................................................26 Thiol Reductants ..............................................................................................................................27 Reductive Desulfurization ...............................................................................................................28 Reductions Other than Dehalogenation ................................................................................28 Nucleophilic Reactions .........................................................................................................29 v CCRRCC__77224411__FFmm..iinndddd vv 66//2211//22000077 11::1122::3322 PPMM vi Contents Oxidations .............................................................................................................................30 Anodic Oxidation .......................................................................................................30 Ozone ......................................................................................................................30 Hydrogen Peroxide .....................................................................................................32 Manganese Dioxide ...................................................................................................32 Sulfate Radicals .........................................................................................................32 Halogenation .........................................................................................................................32 Thermal Reactions ................................................................................................................34 Gas Phase ...................................................................................................................34 In Water ......................................................................................................................36 Electrocatalytic Reactions ....................................................................................................37 References ........................................................................................................................................38 Chapter 2 Biotic Reactions..........................................................................................................51 Part 1 Microbial Reactions ..............................................................................................................51 Introduction ..........................................................................................................................51 Defi nitions—Degradation and Transformation ....................................................................51 Biodegradation of Enantiomers ............................................................................................54 Sequential Microbial and Chemical Reactions ....................................................................55 The Spectrum of Organisms .................................................................................................57 Bacteria in Their Natural Habitats .............................................................................57 Marine and Oligotrophic Bacteria .............................................................................58 Lithotrophic Bacteria .................................................................................................60 Phototrophic Organisms ............................................................................................61 Aerobic and Facultatively Anaerobic Bacteria ..........................................................62 Bacterial Metabolism of C Compounds: Methanotrophs, Methylotrophs, 1 and Related Organisms ..............................................................................................69 Methane Monooxygenase and Related Systems ........................................................69 Anaerobic Bacteria ...............................................................................................................72 Clostridia ....................................................................................................................73 Anaerobic Sulfate-Reducing Bacteria .......................................................................73 Other Anaerobic Bacteria ..........................................................................................73 Organisms from Extreme Environments ..............................................................................74 Psychrophiles .............................................................................................................74 Thermophiles .............................................................................................................75 Alkaliphiles ................................................................................................................75 Halophiles ..................................................................................................................75 Eukaryotic Microorganisms: Fungi and Yeasts ...................................................................75 Metabolism by Fungi .................................................................................................75 Metabolism by Yeasts ................................................................................................77 References .............................................................................................................................78 Part 2 Reactions Mediated by Higher Organisms ...........................................................................91 Introduction ..........................................................................................................................91 Metabolism by Fish ..............................................................................................................93 Metabolism by Other Organisms..........................................................................................95 Mussels ......................................................................................................................95 Insects ...................................................................................................................................96 Invertebrates .........................................................................................................................96 Isopods ......................................................................................................................97 Oligochaetes ...............................................................................................................97 Polychaetes .................................................................................................................97 CCRRCC__77224411__FFmm..iinndddd vvii 66//2211//22000077 11::1122::3322 PPMM Contents vii Higher Plants ........................................................................................................................97 Other Organisms ...................................................................................................................99 References ...........................................................................................................................100 Chapter 3 Mechanistic Aspects ................................................................................................103 Part 1 Introduction of Oxygen .......................................................................................................103 Monooxygenation ...............................................................................................................103 Hydroxylation of Alkanes ........................................................................................103 Epoxidation of Alkenes ...........................................................................................104 Cycloalkanone Monooxygenases .............................................................................105 Monooxygenation of Aromatic Compounds ............................................................106 Reactions of Aromatic Hydrocarbons .....................................................................107 Reactions of Hydroxybenzoates and Related Compounds ......................................108 Monooxygenation of Phenols ...................................................................................110 Cytochrome P450 Systems .................................................................................................113 Prokaryotic Organisms ............................................................................................114 Eukaryotic Organisms .............................................................................................116 Dioxygenation .....................................................................................................................118 Dioxygenases Involved in Dihydroxylation of Arenes ............................................118 Ring-Fission Dioxygenases ......................................................................................123 Incorporation of Oxygen from Water: Oxidoreductases and Hydratases ...........................129 Oxidoreductases .......................................................................................................129 Hydratases ................................................................................................................130 Oxidases, Peroxidases, and Haloperoxidases .....................................................................131 Oxidases ...................................................................................................................131 Peroxidases ..............................................................................................................133 Haloperoxidases .......................................................................................................134 References ...........................................................................................................................135 Part 2 Electron Acceptors Other than Oxygen ..............................................................................147 Introduction ........................................................................................................................147 Oxyanions: Nitrate, Sulfate, Chlorate, Selenate, and Arsenate ..........................................148 Nitrate and Related Compounds ..............................................................................148 Sulfate and Related Compounds ..............................................................................150 Chlorate and Perchlorate ..........................................................................................150 Selenate and Arsenate ..............................................................................................151 Metal Cations and Oxyanions ............................................................................................152 V(V), Mn(IV), Fe(III), Tc(VII), and U(VI) .............................................................152 Humic Acid and Anthraquinone-2,6-Disulfonate in Redox Systems .....................................................................................................154 Dehalorespiration................................................................................................................156 Alkane Sulfonates as Terminal Electron Acceptors ...........................................................156 Nitroalkanes as Electron Acceptor .....................................................................................156 References ...........................................................................................................................157 Part 3 Reductases and Related Enzymes .......................................................................................162 Reduction of Nitroarenes ....................................................................................................162 Nitrate Ester Reductase ......................................................................................................162 Enones (α, β-Unsaturated Ketones) and Related Reductases .............................................163 Aerobic Conditions ..................................................................................................163 Anaerobic Conditions ..............................................................................................163 Azo Reductase ....................................................................................................................163 CCRRCC__77224411__FFmm..iinndddd vviiii 66//2211//22000077 11::1122::3333 PPMM viii Contents Aldehyde Oxidoreductases .................................................................................................164 F -Dependent (Desazatetrahydrofolate) Reductases ........................................................164 420 Other Carbocyclic Aromatic Compounds ..........................................................................164 Reduction of Carbocyclic Rings ..............................................................................164 Dehydroxylation .......................................................................................................165 Reduction of Azaarene Rings ..................................................................................165 Metal Cations and Oxyanions ............................................................................................165 References ...........................................................................................................................166 Part 4 Microbial Reactions to Chemical Stress .............................................................................168 Introduction ........................................................................................................................168 Hydrocarbon Tolerance ............................................................................................168 Antibiotic Resistance ...............................................................................................170 Resistance to Metals and Metalloids ..................................................................................172 Reduction .................................................................................................................172 Methylation ..............................................................................................................173 Effl ux Systems .........................................................................................................175 Chlorophenol Tolerance ...........................................................................................176 Resistance to High Acidity ......................................................................................176 References ...........................................................................................................................177 Part 5 Enzymes Containing Manganese, Iron, Nickel, Copper, Molybdenum, Tungsten, and Vanadium .....................................................................................................181 Manganese ..........................................................................................................................181 Iron ..................................................................................................................................181 Nickel ..................................................................................................................................182 Copper.................................................................................................................................184 Molybdenum .......................................................................................................................185 Molybdopterin Oxidoreductases ..............................................................................185 Tungsten ..............................................................................................................................187 Vanadium ............................................................................................................................188 References ...........................................................................................................................188 Chapter 4 Determinants and Interactions .................................................................................193 Single Substrates: Several Organisms ...........................................................................................193 Cometabolism and Related Phenomena.........................................................................................195 Induction of Catabolic Enzymes ....................................................................................................195 Pre-Exposure to an Analog Substrate ................................................................................195 Enzyme Induction by Growth on Structurally Unrelated Compounds ..............................197 Role of Readily Degraded Substrates ............................................................................................198 Physical Parameters .......................................................................................................................200 Temperature ........................................................................................................................200 Oxygen Concentration ........................................................................................................201 Anaerobic Bacteria ..................................................................................................202 Aerobic and Facultatively Anaerobic Organisms ....................................................202 Redox Potential ...................................................................................................................205 Association of Bacteria with Particulate Material: “Free” and “Bound” Substrates .............................................................................................................205 Biological Mechanisms for Association with Organic Components of Soil and Sediment ...........................................................................................................206 Aging ..................................................................................................................................208 CCRRCC__77224411__FFmm..iinndddd vviiiiii 66//2211//22000077 11::1122::3333 PPMM Contents ix Substrate Concentration, Transport into Cells, and Toxicity .........................................................210 Utilization of Low Substrate Concentrations .....................................................................211 Existence of Threshold Concentrations ..............................................................................212 Strategies Used by Cells for Substrates with Low or Negligible Water Solubility ............213 Transport Mechanisms .......................................................................................................214 Pre-Exposure: Pristine and Contaminated Environments .............................................................215 Rates of Metabolic Reaction ..........................................................................................................218 Kinetic Aspects ...................................................................................................................218 Metabolic Aspects: Nutrients.........................................................................................................219 Regulation and Toxic Metabolites .................................................................................................220 Regulation ...........................................................................................................................220 Toxic or Inhibitory Metabolites ..........................................................................................222 Catabolic Plasmids .........................................................................................................................224 References ......................................................................................................................................227 SECTION II Experimental Procedures Chapter 5 General Experimental Procedures ...........................................................................245 Introduction ....................................................................................................................................245 Abiotic Reactions ................................................................................................................245 Microbial Reactions ............................................................................................................246 Storage of Samples .............................................................................................................247 Determination of Ready Biodegradability .........................................................................247 The Inoculum ...........................................................................................................248 Concentration of the Substrate .................................................................................248 Endpoints .................................................................................................................248 Design of Experiments on Inherent Biodegradability ........................................................248 Metabolic Limitations ..............................................................................................248 Application to Marine Systems................................................................................249 Isolation and Elective Enrichment ...........................................................................249 General Procedures ..................................................................................................250 Basal Media .............................................................................................................252 Mineral Media .........................................................................................................252 Trace Elements .........................................................................................................253 Control of pH ...........................................................................................................254 Vitamins ...................................................................................................................254 Sterilization ..............................................................................................................254 Metal Concentration in Metabolism ........................................................................254 Redox Potential of Media ........................................................................................256 Organic Substrates ..............................................................................................................256 Toxic Compounds ....................................................................................................256 Volatile Compounds .................................................................................................257 Solid Media .........................................................................................................................257 Growth at the Expense of Alternative Substrates ...............................................................258 Techniques for Anaerobic Bacteria ....................................................................................258 Design of Experiments on Biodegradation and Biotransformation ...................................259 Pure Cultures and Stable Consortia ....................................................................................259 Cell Growth at the Expense of the Xenobiotic ...................................................................260 CCRRCC__77224411__FFmm..iinndddd iixx 66//2211//22000077 11::1122::3344 PPMM

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Addressing the persistent environmental threat of organic chemicals with a fresh approach to degradation and tranformation processes, this book examines a wide range of compounds as well as both abiotic and microbiological reactions mediated by microorganisms. It emphasizes the pathways used and the
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Addressing the persistent environmental threat of organic chemicals with a fresh approach to degradation and tranformation processes, this book examines a wide range of compounds as well as both abiotic and microbiological reactions mediated by microorganisms. It emphasizes the pathways used and the

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