Organic chemicals in the environment : mechanisms of degradation and transformation (2013)

Degradation and Transformation Processes Abiotic Reactions: An Outline Introduction Photochemical Reactions in Aqueous and Terrestrial Environments The Diversity of Photochemical Transformations Hydroxyl Radicals in the Destruction of Contaminants Other Photochemically Induced Reactions The Role of Humic Matter: Singlet Dioxygen Interactions between Photochemical and Other Reactions Reactions in the Troposphere Reentry of Tropospheric Transformation Products Chemically Mediated Transformations Reductive Dehalogenation Thiol and Sulfide Reductants Sonication References Biotic Reactions: An Outline of Reactions and Organisms Microbial Reactions Introduction Definitions: Degradation and Transformation Biodegradation of Enantiomers: Racemization Sequential Microbial and Chemical Reactions The Spectrum of Organisms Microbial Metabolism of CCompounds Anaerobic Bacteria Organisms from Extreme Environments: Extremophiles Eukaryotic Microorganisms References Reactions Mediated by Other Biota Aquatic and Terrestrial Biota Metabolism by Fish Metabolism by Other Organisms References Plants and Their Microbial Interactions Introduction Primary Roles of Plants Secondary Role of Plants Plant Metabolites as Antagonists Group Group II Phytoalexins Roles of Bacteria Including Biocontrol Agents Plant Endophytes Microorganisms with Activity as Biocontrol Agents Siderophores in Plants: Roles of Iron The Role of Mycorrhizal and Other Fungi Conclusions References Mechanisms Oxidation, Dehydrogenation, and Reduction Introduction Monooxygenation References Dioxygenation References Oxidases, Peroxidases, and Haloperoxidases References Incorporation of Oxygen from Water: Hydrolases, Oxidoreductases, and Hydratases References Electron Acceptors Other than Oxygen References Dehydrogenation References Reductases and Related Enzymes References Non-Redox Reactions Pyridoxal-'-Phosphate (PLP)-Dependent Reactions References Glutathione-Dependent Reactions References Corrinoid-Dependent Reactions References Free-Radical Reactions References Coenzyme A: Ligase, Transferase, Synthetase References Metalloenzymes Enzymes Containing Manganese, Iron, Cobalt, Copper, Zinc, Molybdenum, Tungsten, and Vanadium References Interactions Environmental Stress Adaptation to Stress Physical Stress References Chemical Stress Enzymatic Covalent Modification of Antibiotic: Range of Reactions Efflux Systems References Metabolic Interactions Single Substrates: Several Organisms Cometabolism and Related Phenomena Induction of Catabolic Enzymes Role of Readily Degraded Substrates Association of Bacteria with Particulate Material: Free and Bound Substrates Substrate Concentration, Transport into Cells, and Toxicity Preexposure: Pristine and Contaminated Environments Rates of Metabolic Reaction Metabolic Aspects: Nutrients Regulation and Toxic Metabolites Catabolic Plasmids References Experimental Procedures Experimental Procedures General Introduction Abiotic Reactions Microbial Reactions Storage of Samples Determination of Ready Biodegradability Design of Experiments on Inherent Biodegradability Organic Substrates Techniques for Anaerobic Bacteria Design of Experiments on Biodegradation and Biotransformation Pure Cultures and Stable Consortia Cell Growth at the Expense of the Xenobiotic Stable Enrichment Cultures Use of Dense Cell Suspensions Use of Immobilized Cells Application of Continuous Culture Procedures Simultaneous Presence of Two Substrates Use of Unenriched Cultures: Undefined Natural Consortia Microcosm Experiments Experiments in Models of Natural Aquatic Systems Evaluation of Degradation Using Metabolites Experimental Problems: Water Solubility, Volatility, Sampling, and Association of the Substrate with Microbial Cells References Study of Microbial Populations Introduction Analysis of Degradative Populations Procedures Directed to Populations for the Degradation of Specific Contaminants Application to Populations of Specific Groups of Organisms Nonspecific Examination of Natural Populations References Procedures for Elucidation of Metabolic Pathways Introduction Application of Natural and Synthetic Isotopes Carbon (C and C) Sulfur (S) and Chlorine (Cl) Hydrogen (H) and Oxygen (O) Other Isotopes Isotope Effects and Stable Isotope Fractionation References Stable Isotope Probes and Stable Isotope Fractionation Experimental Procedures Expression of Results Stable Isotope Probes Application to Processes Application to Biodegradation Stable Isotope Fractionation References Physical Methods of Structure Determination Nuclear Magnetic Resonance References Electron Paramagnetic Resonance References X-Ray Crystallographic Analysis Acetylene Hydratase Triesterase Dehydrogenases Quinoprotein Amine Oxidase Dehalogenases Atypical Dehydratases Arsenite Oxidase Methyl Coenzyme M Reductase Urease Hydrogenase ss-Lactamases Alkylsulfatase Dioxygenases Superoxide Dismutase Formyl-CoA Transferase PLP-Independent Racemases References Pathways and Mechanisms of Degradation and Transformation Aliphatic Compounds Alkanes References Cycloalkanes: Including Terpenoids and Steroids References Alkenes and Alkynes References Alkanols, Alkanones, Alkanoates, Amides References Alkylamines and Amino Acids Amino Acids References Alkanes, Cycloalkanes, and Related Compounds with Chlorine, Bromine, or Iodine Substituents Chlorinated, Brominated, and Iodinated Alkanes, Alkenes, and Alkanoates References Fluorinated Aliphatic Compounds References Carbocyclic Aromatic Compounds without Halogen Substituents Monocyclic Aromatic Hydrocarbons Introduction: Bacteria Monocyclic Arenes Fungi References Polycyclic Aromatic Hydrocarbons Introduction Aerobic Reactions Carried Out by Bacteria PAHs with Three or More Rings Anaerobic Degradations Carried Out by Bacteria Fungal Transformations Yeasts and Algae White-Rot Fungi References Aromatic Carboxylates, Carboxaldehydes, and Related Compounds Introduction Benzoates Hydroxybenzoates and Related Compounds Mechanisms for Fission of Oxygenated Rings Aerobic Reduction of Arene Carboxylates Arenes with an Oxygenated Cor CSide Chain Aldehydes References Nonhalogenated Phenols and Anilines Phenols Alkylated Phenols: Degradation of Methylcatechols Polyhydric Phenols Anaerobic Degradation References Halogenated Arenes and Carboxylates with Chlorine, Bromine, or Iodine Substituents Arenes and Carboxylated Arenes with Halogen, Sulfonate, Nitro, and Azo Substituents Aerobic Degradation Anaerobic Conditions Polychlorinated Biphenyls Polybrominated Biphenyls and Diphenylmethanes Mechanisms for the Ring Fission of Substituted Catechols Halogenated Phenylacetates References Halogenated (Chlorine, Bromine, and Iodine) Phenols and Anilines Phenols O- and S-methylation Fungi and Yeasts Anilines References Fluorinated Hydrocarbons, Carboxylates, Phenols, and Anilines Fluorinated Aromatic Hydrocarbons Fluorobenzoates -Fluorocinnamate Difluorobenzoates Fluorinated Phenols Aromatic Trifluoromethyl Compounds References Arene Sulfonates References Aromatic Compounds with Nitro Substituents Nitroarenes Nitrobenzoates Nitrophenols References Azoarenes References Heterocyclic Aromatic Compounds Azaarenes Five-Membered Monocyclic Aza, Oxa, and Thiaarenes Aerobic Conditions Indole and -Alkylindoles Carbazole Purines Triazines References Oxaarenes Aerobic Conditions Fungal Reactions References Thiaarenes: Benzothiophenes, Dibenzothiophenes, and Benzothiazole Benzothiophene and Dibenzothiophene Benzothiazole References Miscellaneous Compounds Carboxylate, Sulfate, Phosphate, and Nitrate Esters Carboxylates Sulfates Phosphates Nitrates References Ethers and Sulfides Aliphatic and Benzylic Ethers Aryl Ethers References Sulfides, Disulfides, and Related Compounds References Aliphatic Nitramines and Nitroalkanes Nitramines Nitroalkanes References Aliphatic Phosphonates and Sulfonates Introduction Phosphonates Sulfonates Boronates References Degradation of Organic Compounds of Metals and Metalloids Tin Lead Mercury Arsenic References Index