Subject Index

Active uptake 47 Agrobacterium radiobacter 160 Alkane-degrading sulfate reducers 71-72 Anaerobic biodegradation 57

alkane 71 benzene 61 methylnaphthalene 70 naphthalene 69 PAHs 68

Anaerobic organisms 58 Anaerobic reduction route 8 Anaerobic-aerobic treatment 140, 143 Aquifer 140 Arthrobacter protophormiae RKJ100

155, 158 Atrazine 162 Azoarcus tolulyticus Tol4 60

Bacterial biosensors 293 community 30

Benzene dioxygenase 182-183 Benzo[a]pyrene 91 Benzoate dioxygenase 181 Benzylsuccinate synthase 61 Bioadsorbents 236-237 Bioaugmentation 106 Bioavailability 34, 42

PAHs 89,91 Biocatalytic strategy 12

system 13 Bioctalysts designing for bioremediation

12 Biodegradation

estimation methods 280 potential 2, 13 systems 4, 9

Biogeochemical cycle 3 BIOLOG 289

Biomarkers 296 Bioremediation of

Nitroaromatic compounds 149-151 PAHs 1 P AHs polluted soil 2 PCBs 1 TCE 1 xenobiotic compounds 2, 12

Bioremediation process assessment 279 monitoring 279

Biosurfactants 44, 46 Biphenyl dioxygenase 129, 180-181,

183,187-188,244 Brown-rot fungi 266-271 BTEX 58-59 Burkholderia cepacia PB4 156

Capacity for hydrocarbon removal 31 Carbazole dioxygenase 183 Carbon metabolism 198,203-204 Carbon source

supplementation 107 utilization proftle 22

Carboxylation 63 Carcinogenic P AHs 86, 92

potency 86 Catabolic enzymes 10

genes 3 Cell-surface expression 237-238 Cellulomonas fimi 241 Cellulose-binding domain 241 Chemotaxis 43, 48 Chimeric enzymes 244 Chlorine pre-treatment 255 Chlorobenzoate dioxygenase 183

reductive dehalogenases 217 Ciprofloaxcnic 269-271

306

Clostridium thermoaceticum 157 Comamonas acidovorans NBA-10 156 Combined remediation technologies

256-261 Co-metabolic processes 203

Cometabolism 9, 127 Community assessment 23

dynamics 26 response to hydrocarbon exposure 26

Community-level physiology profiling 28 Complexity of P AH transformation 92 Composting 139 Contaminant bioavailability 3 Conventional plating 283 Conversion of alkanes

dioxygenase-mediated 6-8 monooxygenase-mediated 6-7

Co-oxidation 127, 130, 142 Creosote-contaminated soil 91 Cytochrome P-450 244

Dealkylation 8, 185 Dechloromonas sp. 62 Dehalobacter restrictus 224 Dehalococcoides ethenogenes 195,

225-226 Dehalogenation mechanism 206-207 Dehalorespiration 134 Dehalospirillum multivorans 223,

225-226 Dehydrogenase activity 288 Dehydrogenation 64 Deinococcus radiodurans 41,240,242 Denaturing gradient gel

electrophoresis 24 Denitration 8 Dense non-aqueous phase liquid

(DNAPL) 87 Desaturation 185, 186 Designer biocatalysts 236 Desulfitobacterium chlororespirans 221 Desulfitobacterium dehalogenans

218-220,226 Desulfitobacterium frappieri TCEl

222-223 Desulfitobacterium hafniense 219-220 Desulfitobacterium PCE1 220,222-223 Desulfitobacterium PCE-S 222 Desulfitobacterium sp. strain Y51 223,

225-226

Subject Index

Desulfobacterium cetonicum 66 Desulfobacula tolulica 61 Desulfococcus multivorans 66 Desulfomonile tiedjei 215-217 DGGE 291 Dichloromethane reductive

dehalogenases 213 Dihydrodiol 177, 184 Dinitrotoluene dioxygenase 183 Dioxygenation of nitroaromatic

ring 152 Diversity of P AH metabolism 102 DNA

adduct formation 213 microarray 292 shuffling 241

DNT degradation 157

Efflux 47 Engineered bacteria 143, 235 Enroflxacin 269-271 Enterobacter cloacae 163 Enzymatic hydrolysis

of organophosphates 241 Enzymatic transformation of metals

239 Enzyme engineering 185, 187 Enzymes for bioremediation 236 Ether lipids 25 Ethylbenzene biodegradation 62

Fenton's reagent 252 Fenton-like system 256-261,269-271 Ferrate

Pre-treatment 254 treatment systems 261-262

Ferredoxin 178, 180-181 FMN-dependent reductases 161 Fumarate addition 63-64

Gene expression 26 Gene probe 293 Genetic diversity of P AH metabolism

104 Geobacter metallireducens GS-15 59 Geotrichum candidum 159-160 Gleophillum sp. 266-271 Glutathione 236

transferase 204, 209 Glycerol trinitrate 159

Subject Index

Green fusion protein 47 Growth on P AHs 94

Haloalkane dehalogenases 243 Heavy metal removal 236 Hexachlorocyclohexane 133 High molecular weight P AHs 92, 105 Highly volatile substances 58 Homology modeling 214 Hydrocarbon

accession 45 anaerobic biodegradation 57 inclusions 48, 49

Hydrogenophaga paleronii JS863 157 Hydrogeochemistry 28 Hydrophobic

chemicals 88 contaminants 90

Hydrophobicity 3 Hydroxy radicals 252,261,266-267,

269-271 Hydroxylaminobenzene 153 Hydroxylation 63

Immobilization of novel biocatalysts 240

Immunochemical methods 290 Improved biocatalysts in bioremediation

235 Incomplete P AH metabolism 96-98 Incubation conditions 29 Indigo 177 Isomerase activity 206

Klebsiella pneumoniae 162

Ligninase 13 7 Lindane 133 Low molecular weight P AHs 84

Macroarrays 24 Man-made chemical degradation

269-271 Mass transfer limitations 105 Measuring biodegradation 13 Metabolic

biomarkers 14, 72 diversity 11 pathways 4 processes 9

Metal precipitation 239 Metal sequestering peptides 236 Metalloregulatory proteins 23 7 Metals and metalloids 239 Methane monooxygenase 42, 130 Methanotrophs 42 Methods

biochemical 286 molecular 287 physiological 286

307

Methoxybenzoate monooxygenase 184 Methoxylates quinine 267-269 Methylation 63 Methylobacterium dichloromethanicum

DM4 212-214 Methylophilus sp. strain DM 11 212-214 Microarrays 24, 104 Microbial

biomass 284 cell surface 44, 45 communities 3, 30, 50 community profile 291 diversity 29 enumeration 283 populations 31

Microorganisms designing for bioremediation 11

Microtox assay 295 Mineralization 34 Mixed cultures 101 Mobile genetic elements 144 Molecular diagnostics

in bioremediation 295 Monoaromatic compounds 58 Monooxygenation 185, 186 Moraxella sp. 238 MPN 284 Mycobacterium 102

NADH -dependent monooxygenase 158

Naphthalene dioxygenase (NDO) 40,175-176,180-187

Natural attenuation 142 Neurotoxic organophosphates 240 Nitrate esters 150, 159 Nitrate-reducing condition 68 Nitroaromatics 151 Nitrobenzene 150, 153

dioxygenase 155

308

Nitrobenzoates 155 Nitrocellulose 161 Nitrogen-containing xenobiotics

149-151 Nitrogen-ring heterocycles 151 Nitrophenols 158 Nitroreductase 165 Nitrotoluene-2,3-dioxygenase 156, 183 Nitrotoluenes 156 Nocardiodes sp. 163 Nonaqueous compartments 88 Non-heme monooxygenases 245 Nucleic acid hybridization 23

Organic acids 268-169 Organic pollutants 4 Organophosphorus hydrolase OPH

240 Oxalic acid 268-269 Oxygenases 127, 178, 180-181, 183 Ozone pretreatment 252, 253

P AH -degrading bacteria substrate interactions 100 substrate ranges 99

PCR 291 Pentachlorophenol 131, 139 Pentaerythritol tetranitrate 161 Perchloroethene 136 Permanganate pre-treatment 253 Phanerochaete chrysosporium 160, 166 Phospholipid fatty acid analysis, PLF A

286 Phospholipid fatty acids 25 Phthalate dioxygenase 181, 183 Phylogenetic

changes 31 diversity 29

Phytochelatin synthase 237 Phytotoxicity bioassay 297 polA mutant studies 213 Pollutant

metabolism 38 properties and biodegradation 41

Polychlorinated biphenyls 127, 135, 139, 142

Polycyclic aromatic hydrocarbons (PAHs) 67 biodegradation 83, 89 biotransformation 83, 93

Subject Index

bioremediation 83 contaminated systems 87, 100 degrading bacteria 99 dioxygenase 103-104 metabolism 93 mineralization 94, 95 priority pollutants 86 properties 84

Polymerase chain reaction 23 Pretreatment of recalcitrant compounds

252-256 Protein engineering 243 Proteobacteria 61-62, 65 Pseudomonas fluoroscens KU-7 155 Pseudomonas pseudoalcaligenes JS45

153 Pseudomonas putida 2NP8 153, 159 Pseudomonas putida NCIB 9816 103 Pseudomonas saccharophila 107 Psudomonas aeruginosa 242

QSBR 283, 285

Ralstonia metallidurans 238 Ralstonia paucula SB4 156 RDX 165 Reductase 178, 180-181 Reductive dechlorination 134 Reductive dehalogenation reaction

197-198 Replicate samples 30 Reporter gene fusion 294 Respirometry test 281 Reverse sample genome probing, RSGP

25,292 Rhodococccus eryhtropolis 159, 242 Risk-based approach 282 16S rRNA 23, 292

Salicylate addition 108 Seeded microbial strains 26 Sequenced regions 207 Soil

enzyme assay 288 lipase activity 289 microcosm test 281

Solid-phase microextraction 282 Sorptive behaviour of organic

fraction 88 Spectroscopic techniques 283

Subject Index

Sphingobium chlorophenolicum ATCC 39723 205-210

Sphingomonas sp. UG30 210 Stable isotope ratios 22 Stenotrophomonas maltophila 165 Stereochemistry 185 Substrate utilization pattern 290 Sulfoxidation 185, 186 Surface expression of OPH 240 Surfactants 106

TCLP 282 Terminal electron acceptors 22, 59 Tetrachlorobenzene dioxygenase 183 Tetrachlorohydroquinone reductive

dehalogenases 206 Thauera aromatica 60 TNT degradation 157, 257-258 Toluate dioxygenase 183

Toluene biodegradation 59 dioxygenase (TDO) 175, 180-183,

185-189 monooxygenase 242

Toxicity equivalency factors 84 Toxicity 49 Toxicological risk assessments 296 TPH 285 Trichloroethene 130 Trichloroethylene 42, 43

White-rot fungi 266

Xylene biodegradation 65

Zero-valent iron pre-treatment 254-255 systems 264-266

309