Environmental Degradation and Transformation of Organic Chemicals

Environmental Degradation and Transformation of Organic ChemicalsAlasdair H. Neilson and Ann-Sofie Allard

Boca Raton London New York

CRC Press is an imprint of the Taylor & Francis Group, an informa business

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 information 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 organizations 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 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com 2007012219

ContentsPreface ............................................................................................................................................xix Acknowledgments ........................................................................................................................ xxiii Authors ...........................................................................................................................................xxv

SECTION I Degradation and Transformation ProcessesChapter 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 Fentons Reagent .....................................................................................................................9 Polyoxometalates (Heteropolyacids) ..................................................................................... 10 Photolytic Degradation on TiO2 ........................................................................................... 10 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 Sulfides and Disulfides ......................................................................................................... 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

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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 DefinitionsDegradation 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 C1 Compounds: Methanotrophs, Methylotrophs, 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

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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 (, -Unsaturated Ketones) and Related Reductases ............................................. 163 Aerobic Conditions .................................................................................................. 163 Anaerobic Conditions .............................................................................................. 163 Azo Reductase .................................................................................................................... 163

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Aldehyde Oxidoreductases ................................................................................................. 164 F420 -Dependent (Desazatetrahydrofolate) Reductases........................................................ 164 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 Efflux 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

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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 ProceduresChapter 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

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Stable Enrichment Cultures ................................................................................................260 Use of Dense Cell Suspensions........................................................................................... 261 Use of Immobilized Cells ................................................................................................... 261 Application of Continuous Culture Procedures.................................................................. 262 Simultaneous Presence of Two Substrates ......................................................................... 263 Use of Unenriched Cultures: Undefined Natural Consortia ...............................................264 Microcosm Experiments.....................................................................................................264 Experiments in Models of Natural Aquatic Systems .........................................................266 Evaluation of Degradation Using Metabolites.................................................................... 267 Experimental Problems: Water Solubility, Volatility, Sampling, and Association of the Substrate with Microbial Cells ........................................... 268 References ...................................................................................................................................... 269

Chapter 6

Elucidation of Metabolic Pathways .......................................................................... 277

Introduction.................................................................................................................................... 277 Part 1 Application of Natural and Synthetic Isotopes ................................................................... 277 Carbon (14C and 13C)........................................................................................................... 277 Sulfur (35S) and Chlorine (36Cl) .......................................................................................... 278 Hydrogen (2H) and Oxygen (18O) ........................................................................................ 278 Other Isotopes .....................................................................................................................280 Isotope Effects and Stable Isotope Fractionation ...............................................................280 Experimental Procedures......................................................................................... 282 References ........................................................................................................................... 282 Part 2 Nondestructive Methods for Structure Determination .......................................................284 Application of NMR ...........................................................................................................284 Hydrogen 1H ............................................................................................................ 285 Carbon 13C ............................................................................................................... 285 Nitrogen 15N ............................................................................................................. 286 Oxygen 17O ............................................................................................................... 287 Fluorine 19F .............................................................................................................. 287 Phosphorus 31P ......................................................................................................... 288 Silicon 29Si ............................................................................................................... 288 Application of EPR ............................................................................................................. 288 Elucidation of the Unexpected Complexity of an Apparently Straightforward Metabolic Pathway ..................................................................................... 289 Hydroxyl Radicals and Their Role in the Toxicity of H2O2 to Bacteria ......................................................................................... 289 Elucidation of the Mechanism of Pyruvate Formate Lyase........................................................................................................... 289 The Function of Humic Acids in Reactions Catalyzed by Geobacter metallireducens .......................................................................................... 289 The Mechanism of Anaerobic Activation of Toluene .............................................. 289 Dioxygenation with Elimination of Halide .............................................................. 289 The Anaerobic Degradation of Benzoate ................................................................290 Manganese-Containing Enzymes ............................................................................ 290 Turnover of Naphthalene Dioxygenase ....................................................................290 Enzyme Structure ...............................................................................................................290 References ........................................................................................................................... 291

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SECTION III Pathways and Mechanisms of Degradation and TransformationChapter 7 Aliphatic Compounds............................................................................................... 297

Part 1 Alkanes and Related Compounds ....................................................................................... 297 Alkanes ............................................................................................................................... 297 Aerobic Conditions .................................................................................................. 297 Anaerobic Conditions ..............................................................................................304 Alkenes ............................................................................................................................... 305 Aerobic Conditions .................................................................................................. 305 Anaerobic Conditions ..............................................................................................308 Alkynes ...............................................................................................................................308 Alkanols ..............................................................................................................................309 Aerobic Conditions ..................................................................................................309 Anaerobic Conditions .............................................................................................. 310 Alkanones ........................................................................................................................... 310 Alkylamines and Amino Acids .......................................................................................... 311 Aerobic Conditions .................................................................................................. 311 Anaerobic Conditions .............................................................................................. 316 Alkanoic Acids ................................................................................................................... 317 Aerobic Conditions .................................................................................................. 317 Anaerobic Conditions .............................................................................................. 318 Anaerobic Conditions .............................................................................................. 318 Amides and Related Compounds ....................................................................................... 321 Amides .................................................................................................................... 321 Nitriles ................................................................................................................................ 322 Isonitriles ............................................................................................................................ 322 Sulfonylureas and Thiocarbamates .................................................................................... 322 Carbon Monoxide ............................................................................................................... 323 Cyanide ............................................................................................................................... 323 Thiocyanate ........................................................................................................................ 324 References ........................................................................................................................... 324 Part 2 Cycloalkanes ....................................................................................................................... 336 Monoterpenes ..................................................................................................................... 339 Steroids ............................................................................................................................... 341 Hydroxylation........................................................................................................... 341 Other Aerobic Transformations and Degradation ................................................... 341 Anaerobic Transformation ....................................................................................... 343 Diterpenoids........................................................................................................................344 Polycyclic Substrates ..........................................................................................................344 References ...........................................................................................................................346 Part 3 Alkanes, Cycloalkanes and Related Compounds with Chlorine, Bromine, or Iodine Substituents ......................................................................................................................... 349 Chlorinated, Brominated, and Iodinated Alkanes, Alkenes, and Alkanoates ................... 349 Elimination Reactions.............................................................................................. 350 Corrinoid Pathways .................................................................................................. 355 Nucleophilic Substitution: Hydrolytic Reactions of Halogenated Alkanes and Alkanoates ....................................................... 358

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Glutathione-Mediated and Other Reactions Involving Nucleophilic Sulfur .................................................................................... 363 Monooxygenation..................................................................................................... 363 Reductive Reactions: Dehalogenation Including Dehalorespiration ....................... 366 References ........................................................................................................................... 370 Part 4 Fluorinated Aliphatic Compounds ...................................................................................... 378 Alkanes and Alkenes .......................................................................................................... 378 Fluorohydrocarbons ................................................................................................. 378 Chlorofluorocarbons and Hydrochlorofluorocarbons .............................................. 379 Carboxylic Acids...................................................................................................... 380 Perfluoroalkyl Carboxylates and Sulfonates ............................................................ 382 References ........................................................................................................................... 382

Chapter 8

Carbocyclic Aromatic Compounds without Halogen Substituents .......................... 385

Part 1 Monocyclic Aromatic Hydrocarbons .................................................................................. 385 Introduction ........................................................................................................................ 385 Monocyclic Arenes ............................................................................................................. 385 Aerobic Conditions .................................................................................................. 385 Anaerobic Conditions .............................................................................................. 389 Synthetic Applications ............................................................................................. 392 References ........................................................................................................................... 394 Part 2 Polycyclic Aromatic Hydrocarbons (PAHs)........................................................................ 398 Introduction ........................................................................................................................ 398 Aerobic Reactions Carried Out by Bacteria ............................................................ 399 PAHs with Three or More Rings .............................................................................402 Anaerobic Reactions Carried Out by Bacteria ........................................................408 Fungal Transformations ...........................................................................................409 White-Rot Fungi ...................................................................................................... 413 References ........................................................................................................................... 417 Part 3 Aromatic Carboxylates, Carboxaldehydes, and Related Compounds ................................ 424 Introduction ........................................................................................................................ 424 Benzoates ............................................................................................................................ 424 Aerobic Conditions .................................................................................................. 424 Hydroxybenzoates and Related Compounds ...................................................................... 425 Mechanisms for Fission of Oxygenated Rings ........................................................ 428 Alternative Pathways for the Degradation of Benzoates and Related Compounds............................................................................. 432 Aerobic Reduction of Arene Carboxylates ......................................................................... 433 Arenes with an Oxygenated C2 or C3 Side Chain ............................................................... 433 Anaerobic Metabolism ............................................................................................. 435 Aldehydes ........................................................................................................................... 439 References ........................................................................................................................... 439 Part 4 Nonhalogenated Phenols and Anilines ...............................................................................446 Phenols ................................................................................................................................446 Aerobic Degradation ................................................................................................446 Anaerobic Degradation ............................................................................................449 Anilines.................................................................................................................... 452 References ........................................................................................................................... 452

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Chapter 9

Substituted Carbocyclic Aromatic Compounds ....................................................... 455

Part 1 Halogenated Arenes and Carboxylates with Chlorine, Bromine, or Iodine Substituents.......................................................................................................... 455 Introduction ........................................................................................................................ 455 Halogenated Arene Hydrocarbons ..................................................................................... 455 Aerobic Conditions .................................................................................................. 455 Monocyclic Chlorinated Arenes ......................................................................................... 456 Anaerobic Conditions .............................................................................................. 458 Polychlorinated Biphenyls .................................................................................................. 458 Aerobic Degradation ................................................................................................ 458 Degradation Is Initiated by Dioxygenation .............................................................. 459 Ring Fission by 2,3-Dihydroxybiphenyl Dioxygenase ............................................ 461 Metabolites............................................................................................................... 463 Fungal Dehalogenation .......................................................................................................465 Reductive Dehalogenation ..................................................................................................465 The Role of Temperature .........................................................................................466 Polyhalogenated Dioxins and Diphenyl Ethers........................................................468 Halogenated Benzoates.......................................................................................................468 Dioxygenation ..........................................................................................................469 Hydrolytic Reactions................................................................................................ 472 Mechanisms for the Ring Fission of Substituted Catechols ............................................... 472 Reductive Loss of Halogen ...................................................................................... 474 Halogenated Phenylacetates ............................................................................................... 475 Fungal Reactions...................................................................................................... 476 References ........................................................................................................................... 476 Part 2 Halogenated (Chlorine, Bromine, and Iodine) Phenols and Anilines ........................................................................................................................ 482 Phenols ................................................................................................................................ 482 Aerobic Conditions .................................................................................................. 482 Fungi and Yeasts ...................................................................................................... 486 Anaerobic Conditions .............................................................................................. 487 Anilines .............................................................................................................................. 489 Aerobic Conditions .................................................................................................. 489 Anaerobic Conditions .............................................................................................. 490 References ........................................................................................................................... 491 Part 3 Fluorinated Hydrocarbons, Carboxylates, Phenols, and Anilines ...................................... 494 Fluorinated Aromatic Hydrocarbons.................................................................................. 494 Aerobic Conditions .................................................................................................. 494 Metabolism by Yeasts and Fungi ............................................................................. 495 Anaerobic Denitrifying Conditions ......................................................................... 495 Fluorobenzoates .................................................................................................................. 496 Aerobic Conditions .................................................................................................. 496 Difluorobenzoates .................................................................................................... 498 Degradation under Denitrifying Conditions ............................................................ 499 Fluorinated Phenols ............................................................................................................500 Aerobic Conditions ..................................................................................................500 Anaerobic Conditions .............................................................................................. 501 Aromatic Trifluoromethyl Compounds ..............................................................................502 References ........................................................................................................................... 503

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Part 4 Arene Sulfonates .................................................................................................................506 References ...........................................................................................................................508 Part 5 Aromatic Compounds with Nitro Substituents ...................................................................508 Nitroarenes..........................................................................................................................508 Reduction of Nitro Groups.......................................................................................509 Reduction of the Ring .............................................................................................. 512 Dioxygenation .......................................................................................................... 512 Side-Chain Oxidation .............................................................................................. 513 Peroxidase Oxidation ............................................................................................... 513 Nitrobenzoates .................................................................................................................... 514 Nitrophenols........................................................................................................................ 514 References ........................................................................................................................... 517 Part 6 Azoarenes ............................................................................................................................ 520 References ........................................................................................................................... 521 Chapter 10 Heterocyclic Aromatic Compounds ....................................................................... 523

Part 1 Azaarenes ............................................................................................................................ 523 Five-Membered Monocyclic Aza, Oxa, and Thiaarenes .................................................... 523 Aerobic Conditions .................................................................................................. 523 Indole and Carbazole .......................................................................................................... 524 Indole and 3-Alkylindoles ....................................................................................... 524 Carbazole ................................................................................................................. 527 Pyridine .............................................................................................................................. 527 Aerobic Conditions .................................................................................................. 527 Anaerobic Conditions .............................................................................................. 534 Quinoline and Isoquinoline ................................................................................................ 536 Bacterial Metabolism ............................................................................................... 536 Hydroxylation........................................................................................................... 537 Dioxygenation .......................................................................................................... 537 Pyrimidine and Related Compounds Excluding Purines ...................................................540 Aerobic Conditions ..................................................................................................540 Anaerobic Conditions .............................................................................................. 541 Purines ................................................................................................................................ 542 Aerobic Degradation ................................................................................................ 542 Anaerobic Degradation ............................................................................................ 542 Ring-Fission Reactions ............................................................................................544 Triazines ............................................................................................................................. 545 1,3,5-Triazines.......................................................................................................... 545 1,2,4-Triazines..........................................................................................................546 References ...........................................................................................................................546 Part 2 Oxaarenes ............................................................................................................................ 553 Aerobic Conditions ............................................................................................................. 553 Monocyclic Oxaarenes............................................................................................. 553 Polycyclic Oxaarenes ............................................................................................... 553 References ........................................................................................................................... 562 Part 3 Thiaarenes: Benzothiophenes, Dibenzothiophenes, and Benzothiazole ............................ 565 Benzothiazole ..................................................................................................................... 567 References ........................................................................................................................... 568

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Chapter 11 Miscellaneous Compounds ...................................................................................... 569 Part 1 Carboxylate, Sulfate, Phosphate, and Nitrate Esters ........................................................... 569 Carboxylates ....................................................................................................................... 569 Sulfates ............................................................................................................................... 569 Phosphates .......................................................................................................................... 570 Nitrates................................................................................................................................ 571 References ........................................................................................................................... 572 Part 2 Ethers and Sulfides .............................................................................................................. 573 Aliphatic and Benzylic Ethers ............................................................................................ 573 Aryl Ethers.......................................................................................................................... 576 Diaryl Ethers ............................................................................................................ 576 Aryl-Alkyl Ethers .................................................................................................... 576 Sulfides, Disulfides, and Related Compounds .................................................................... 578 References ........................................................................................................................... 581 Part 3 Aliphatic Nitramines and Nitroalkanes .............................................................................. 585 Nitramines .......................................................................................................................... 585 Nitroalkanes........................................................................................................................ 585 References ........................................................................................................................... 586 Part 4 Aliphatic Phosphonates and Sulfonates .............................................................................. 588 Introduction ........................................................................................................................ 588 Phosphonates ...................................................................................................................... 588 Sulfonates ........................................................................................................................... 589 Boronates ............................................................................................................................ 591 References ........................................................................................................................... 591 Part 5 Degradation of Organic Compounds of Metals and Metalloids ......................................... 592 Tin .................................................................................................................................. 593 Lead .................................................................................................................................. 593 Mercury .............................................................................................................................. 594 Arsenic ................................................................................................................................ 594 References ........................................................................................................................... 594

SECTION IV

Bioremediation

Chapter 12 Bioremediation: Overview ....................................................................................... 599 Introduction.................................................................................................................................... 599 Strategies............................................................................................................................. 599 Contaminants ......................................................................................................................600 Sites ..................................................................................................................................602 Chemical Procedures ..........................................................................................................602 Phytoremediation ................................................................................................................602 Primary Role of Plants.............................................................................................603 Secondary Role of Plants .........................................................................................605 Degradative Enzymes ..............................................................................................606 The Role of Plant Exudates in Degradation ............................................................607 Other Functions of Bacteria in the Rhizosphere .....................................................607 The Role of Mycorrhizal Fungi ...............................................................................609

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Microbiological Aspects ................................................................................................................ 610 Regulation of Pathways ...................................................................................................... 610 Alternative Electron Acceptors .......................................................................................... 611 Aging .................................................................................................................................. 611 Biofilms............................................................................................................................... 611 Metabolites and Enzymes ................................................................................................... 611 Utilization of Nitrogen, Sulfur, and Phosphorus ................................................................ 612 Substrate Concentration ...................................................................................................... 612 Temperature ........................................................................................................................ 613 References ...................................................................................................................................... 613

Chapter 13 Evaluation of Bioremediation ................................................................................... 621 Introduction.................................................................................................................................... 621 Analysis of Populations ................................................................................................................. 622 Analysis of Degradative Populations.................................................................................. 622 Application to the Degradation of Specific Contaminants................................................. 623 Hydrocarbons ........................................................................................................... 623 Trichloroethene ........................................................................................................ 624 Phenol .................................................................................................................... 624 Chlorophenol............................................................................................................ 625 Chlorobenzoate ........................................................................................................ 625 Phenylurea Herbicides ............................................................................................. 625 Dehalogenation of Chloroalkanoates....................................................................... 626 Dechlorination of PCBs ........................................................................................... 626 Application to Specific Groups of Organisms .................................................................... 626 Nondirected Examination of Natural Populations ............................................................. 627 Application of Stable Isotopes ....................................................................................................... 627 Stable Isotope Probes.......................................................................................................... 627 Application of Stable Isotope Enrichment.......................................................................... 628 Application of 13C .................................................................................................. 629 References ...................................................................................................................................... 633

Chapter 14 Applications of Bioremediation ............................................................................... 639 Introduction.................................................................................................................................... 639 Part 1 Petroleum Hydrocarbons: Refinery Waste and Stranded Oil.............................................. 639 Terrestrial Habitats .............................................................................................................640 Alkanes ....................................................................................................................640 Naphthenates ............................................................................................................ 641 Marine Habitats .................................................................................................................. 641 The Baffin Island Oil Spill Project .......................................................................... 641 Conclusion .......................................................................................................................... 642 References ........................................................................................................................... 642 Part 2 Coal Distillation Products ................................................................................................... 643 Introduction ........................................................................................................................ 643 On-Site or Off-Site Treatment ............................................................................................644 The Physical State of the Contaminant ..............................................................................646

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Environmental Parameters ................................................................................................. 647 Determinants ...................................................................................................................... 647 The Range of Substrates .......................................................................................... 647 The Range of Degradative Bacteria .........................................................................648 Bioavailability and the Use of Surfactants ..............................................................649 Supplementation with Fungi ............................................................................................... 650 Application of Higher Plants .............................................................................................. 652 Anoxic or Anaerobic Environments ................................................................................... 652 Hydrocarbons ........................................................................................................... 652 Phenols .................................................................................................................... 652 Heteroarenes ............................................................................................................ 653 Abiotic Transformations ..................................................................................................... 653 Conclusions ......................................................................................................................... 654 References ........................................................................................................................... 654 Part 3 Wood Preservation Sites: Chlorophenolic Compounds ...................................................... 658 Aerobic Bacteria ................................................................................................................. 659 Degradation by Fungi ......................................................................................................... 659 Anaerobic Dechlorination ..................................................................................................660 Conclusion ..........................................................................................................................660 References ...........................................................................................................................660 Part 4 Chemical Waste................................................................................................................... 661 Chlorinated Alicyclic Hydrocarbons .................................................................................. 662 Chlorinated and Brominated Aromatic Hydrocarbons ...................................................... 662 Chlorobenzenes .................................................................................................................. 662 DDT .................................................................................................................................. 663 Polychlorinated Biphenyls .................................................................................................. 663 Aerobic Conditions ..................................................................................................664 Anaerobic Conditions ..............................................................................................665 Polybrominated Biphenyls and Diphenyl Ethers ................................................................666 Chlorinated Dibenzodioxins...............................................................................................666 Organofluoro Compounds .................................................................................................. 667 Conclusion ..........................................................................................................................668 References ...........................................................................................................................668 Part 5 Agrochemicals .................................................................................................................... 671 Phenoxyalkanoic Acids....................................................................................................... 672 Chlorinated Anilines .......................................................................................................... 672 Triazines ............................................................................................................................. 673 1,3,5-Triazines.......................................................................................................... 673 1,2,4-Triazines.......................................................................................................... 673 2,4-Dintro-6-sec-Butylphenol (Dinoseb)................................................................. 673 References ........................................................................................................................... 674 Part 6 Military Waste..................................................................................................................... 675 Explosives ........................................................................................................................... 675 Nitroarenes.......................................................................................................................... 675 Nitrodiphenylamines .......................................................................................................... 676 Nitrate Esters ...................................................................................................................... 676 Nitramines .......................................................................................................................... 676 Conclusions ......................................................................................................................... 677 Chemical Warfare Agents .................................................................................................. 677 References ........................................................................................................................... 677

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Part 7 Groundwater Contamination ............................................................................................... 679 Benzene/Toluene/Ethylbenzene/Xylenes............................................................................ 679 Aerobic Conditions .................................................................................................. 679 Anoxic or Anaerobic Conditions .............................................................................680 Halogenated Alkanes and Alkenes..................................................................................... 682 Tetrachloromethane ................................................................................................. 682 Chloroethenes .......................................................................................................... 682 Aerobic Conditions .................................................................................................. 682 Application of Indigenous Bacteria ......................................................................... 683 Application of Exogenous Bacteria .........................................................................684 Anoxic and Anaerobic Conditions ...........................................................................684 Application of Higher Plants ................................................................................... 685 Conclusion .......................................................................................................................... 686 Methyl tert-Butyl Ether....................................................................................................... 686 References ........................................................................................................................... 687 Finale: A Hierarchical Strategy .....................................................................................................690 I. Laboratory Experiments..................................................................................................690 II. Microcosm Experiments ................................................................................................ 691 III. Large-Scale Operations ................................................................................................ 691 Concluding Comments................................................................................................................... 692 Index .............................................................................................................................................. 693

PrefaceThis volume is an updated and expanded version of a previous edition Organic Chemicals: An Environmental Perspective. This one deals, however, with only degradation and transformation in their widest senses, and the sections in the earlier volumes on analysis, distribution, and ecotoxicology have been omitted since these lie beyond my current competence. In addition, there are specialized volumes that already cover these topics. I have been extremely fortunate in having as coauthor Ann-Sofie Allard, who has been a research collaborator for many years. She has been both guide and illustrator, and without her constant help and encouragement, this volume would neither have begun nor would it have come to fruition. Degradation and transformation occupy a central position in assessing the environmental impact of organic contaminants. We have avoided the term pollutant on account of its negative connotation. Although phase partition is not discussed, this is an important factor in determining biodegradability since a contaminant will seldom remain in the phase to which it is initially discharged. This must be considered as the following examples illustrate: 1. Compounds deposited as solids (including agrochemicals and contaminants) may reach groundwater and watercourses as a result of partition and leaching. 2. Substances with even marginal volatility will enter the atmosphere, and after transformation may then reenter the aquatic and terrestrial environments through precipitation. 3. Aquatic biota may bring about transformation to metabolites that are then disseminated to a considerable distance from their source. 4. Particularly polar contaminants may associate with polymeric humic components of soil, water, and sediment. Their biodegradation then depends on the degree to which these processes are reversible and the contaminants become accessible to microorganisms (bioavailable). This is especially significant after weathering (aging), even for nonpolar compounds. Contaminants seldom consist of single substances. The pathways used for biodegradation of some components may be incompatible with those for others that are present, or the pathway for a single compound. Examples of this are given, though in less detail than they merit. In this volume, emphasis is placed on the pathways by which degradation or transformation has taken place, and the approach is essentially chemical and mechanistic. There are several reasons for this. 1. Biochemical reactions parallel those in organic chemistry and, for both of them, a mechanistic approach has proved valuable. In addition, most of the principles that have emerged apply equally to the aquatic, the atmospheric, and the terrestrial environments. 2. Metabolites may be produced by biochemical transformation of the substrate rather than by degradation, or may result from partial abiotic reactions. These products may be (a) terminal and persistent or (b) toxic to other components of an ecosystemincluding the microorganisms that produce them. Both of these represent important considerations that are illustrated by examples in this book. 3. Pathways can provide a guide to the probable reactions that other contaminants may undergo including those that bear only a partialor even more remote structural resemblance. This is especially important in view of the widening spectrum of contaminants that is the result of the impressive ingenuity of the organic chemist, and particularly for the complexity and novelty of pharmaceutical and agrochemical products.xix

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A word of caution is appropriate. The reactions that are used for illustration are very seldom specific for a single taxonor even close relatives, and it is not generally possible to establish the range of organisms that will be able to carry out the reaction. The contents of the chapters are interdependent. In summary they deal with the following: Chapters 1 through 4 provide a broad perspective on abiotic and biotic reactions, including the significance of a range of environmental determinants. Chapters 5 and 6 attempt to provide a brief introduction to experimental procedures with emphasis on procedures for establishing the structure of metabolites using isotopes and physical methods. Chapters 7 through 11 outline details of biochemical reactions involved in the biodegradation of the major groups of aliphatic, carbocyclic aromatic, and heterocyclic compounds. Although emphasis is placed on the pathways, rather general accounts of the enzymes involved and the genetics are provided where they are available. Chapters 12 through 14 deal with bioremediation that has attracted increasing concern with the realization of the hazard presented by the disposal of unwanted chemicals, or byproducts from their manufacture. These chapters should be viewed within the wider context of metabolic details that have been presented in Chapters 7 through 11. There are a number of inevitable omissions and limitations in the material that is covered. 1. Emphasis is placed exclusively on xenobiotics, although some of them are also naturally occurring metabolites. There are substantial groups of compounds that are not discussed. These include the following: a. Naturally occurring polymerscellulose, chitin, lignin, and polyisoprenoids; synthetic polyamides, polyurethanes, and polysiloxanes. b. Natural products including polypyrroles such as hemin and chlorophyll; plant and microbial metabolites. c. Agrochemicals including veterinary chemotherapeutic agents that have come into use in large-scale animal husbandry. d. Pharmaceuticals including hormone disrupters about which there has arisen serious concern. e. Halogenated metabolites produced by marine biota, even though some such as halomethanes, polybrominated phenols, and polybrominated diphenyl ethers are also xenobiotics. It is expected that the pharmaceutical industry that has hitherto been dominated by synthetic productsexcept for antibioticswill come to rely increasingly on metabolites produced by marine biota including microorganisms. 2. The number of references that are cited is necessarily restrictive and, although numerous, they represent merely an eclectic selection from a vast literature. Relevant references have no doubt been omitted, but the writers can assure the authors of these that there is no malice in the selection. They invariably refer to the primary literature that has been subjected to the scrutiny of peer review. It is therefore assured that even when the interpretations of the authors should prove faultyand this is inevitablea solid and reproducible basis of fact is available to the critical reader. Some older work has been cited when this has led to lasting concepts, though other early work may be difficult to evaluate by the standards of today; and no doubt work at the cutting edge of current research will rightly require modification and extension in the future. 3. Although some of the examples used for illustration in Chapter 14 impinge on biological wastewater treatment technology, a systematic account of these lies beyond the scope of this volume and the competence of the authors. It is worth noting, however, that anaerobic reactors that are developed to treat wastewater with the object of producing methane may

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not necessarily degrade recalcitrant xenobiotics for which inoculation with specific microorganisms may be necessary. 4. No discussion of models will be found in this volume, either for the analysis of degradation kinetics or for the prediction of biodegradability. For these, the interested reader should consult monographs by experts. The nomenclature of bacteria has presented serious problems principally for two reasons: (a) the number of new taxa that are being described appears to be increasing exponentially and (b) it is seldom possible to determine the correct taxonomic assignment for important organisms that have been used in the historical literature. Although no consistent attempt has been made to provide the current assignment for all taxa, we have tried to use those that occur most frequently.

AcknowledgmentsIt is a pleasure to thank sten Ekengren, director of Environmental Technology and Toxicology for his generosity in extending access to library facilities. We thank Springer Verlag for kind permission to use a number of figures that were used in chapters that we have contributed to Volume 3J (1998), Volume 3N (2002), and Volume 3R (2003) of The Handbook of Environmental Chemistry of which I was volume editor.

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AuthorsAlasdair H. Neilson was principal scientist until retirement from IVL Swedish Environmental Research Institute