Advances in Applied Bioremediation (eBook)

Preface 6
Contents 8
Contributors 10
Chapter 1 15
Biological Remediation of Soil: An Overview of Global Market and Available Technologies 15
1.1 Introduction 15
1.2 Global Remediation Market 16
1.2.1 North America 17
1.2.2 Europe 18
1.2.3 Australia and New Zealand 19
1.2.4 Asia 19
1.2.5 Latin America and Africa 21
1.3 Major Environmental Contaminants of Concern 21
1.4 Biological Remediation of Contaminated Soils 24
1.4.1 In Situ Biological Remediation 25
1.4.2 Ex Situ Biological Remediation 27
1.4.3 Nanotechnology and Site Remediation: An Emerging Field 28
1.4.4 Designing Biological Remediation 29
1.5 Conclusions 30
References 32
Chapter 2 34
Local Gain, Global Loss: The Environmental Cost of Action 34
2.1 Introduction 34
2.2 Better and Worse Treatment Choices 35
2.2.1 Doing Nothing 36
2.2.2 In situ Bioremediation Can be Good or Bad 37
2.2.3 Other In Situ Methods: Manufacture of Materials 37
2.2.4 Excavation or Immobilisation: Surfaces and Transport 38
2.2.5 Landfilling 38
2.3 Case Study: Two Simple Models for a Petrol Filling Station 39
2.3.1 Site Description and Treatment Techniques 39
2.3.2 The Case Models 40
2.3.3 The Case Results 40
2.3.4 Conclusions from the Case Study 42
2.4 Improving Specific Remediations 43
2.4.1 What to Consider 43
2.4.1.1 Energy 43
2.4.1.2 Scarce Natural Resources 43
2.4.1.3 Land Use 44
2.4.1.4 Emissions 44
2.4.1.5 Human Exposure 45
2.4.2 Tools to Use 45
2.6 Conclusion 46
References 47
Chapter 3 48
Bioavailability of Contaminants in Soil 48
3.1 Introduction 48
3.2 Bioavailability Under Thermodynamic Control 52
3.2.1 Structure Activity Relationships 52
3.2.2 Concentration Dependence 55
3.2.3 Competition by Co-Solutes 57
3.2.4 Effect of True Hysteresis 59
3.3 Bioavailability Under Kinetic Control 61
3.3.1 Nature and Geometry of the Diffusing Medium 63
3.3.2 Influence of Molecular Structure 65
3.3.3 Coupled Sorption–Microbial Degradation Models 65
3.3.4 High Desorption Resistance 68
3.3.5 Correlation of Desorption Resistance with Biodegradation Resistance 69
3.3.6 Causes of High Desorption Resistance 71
3.3.7 Facilitated Bioavailability 73
3.4 Conclusions 76
References 77
Chapter 4 85
4.1 Introduction 85
4.2 Natural History of Biosurfactants 86
4.2.1 Biosurfactant Properties and Classes 86
4.2.2 Biosurfactant Chemical Characterization 87
4.2.3 Physiological Roles of Biosurfactants 89
4.3 Biosurfactant Applications in Bioremediation 92
4.3.1 Mass Transfer Effects on Biodegradation 92
4.3.2 Soil Washing 95
4.3.3 Biosurfactant Production 96
4.4 Conclusions 98
References 98
Chapter 5 102
The Diversity of Soluble Di-iron Monooxygenases with Bioremediation Applications 102
5.1 Introduction 102
5.2 Soluble Di-iron Monooxygenases (SDIMOs) 103
5.2.1 Biochemistry 103
5.2.2 Physiological Roles 103
5.2.3 Genetics, Diversity and Classification 104
5.3 Applications of SDIMOs in Bioremediation: Pollutants and Approaches 106
5.3.1 Growth-Linked Metabolism 106
5.3.2 Cometabolism 107
5.3.3 Strategies for Field Application 107
5.4 Monitoring Microbial Communities 108
5.4.1 Culture-Based Sampling for Degradative Organisms 108
5.4.2 Culture-Independent Sampling for Degradative Organisms 109
5.5 Conclusion 110
References 111
Chapter 6 114
Bioremediation of Polluted Soil 114
6.1 Introduction 114
6.2 Soil Health 118
6.3 Pollution 119
6.4 Plants and Phytoremediation 120
6.5 Biodegradation 121
6.6 Rhizosphere 124
6.6.1 Exudates 124
6.6.2 Microbial Communities 125
6.6.3 Assessment of Species Richness and Diversity 126
6.6.4 Remediation 127
References 128
Chapter 7 133
Soil Bioremediation Strategies Based on the Use of Fungal Enzymes 133
7.1 Introduction 133
7.2 Principles of Soil Bioremediation 134
7.2.1 Definitions 134
7.2.2 Bioremediation Techniques 135
7.2.3 Interest of Bioremediation Vs. Physico-chemical Processes 136
7.2.4 Biotransformation Pathways of Organic Pollutants 137
7.2.5 Bioremediation of Metal-polluted Soils 137
7.3 Relevance of Fungal Enzymes for Soil Bioremediation 138
7.3.1 Filamentous Fungi 138
7.3.2 Fungal Oxidases 139
7.3.2.1 Peroxidases 139
7.3.2.2 Laccases 140
7.3.3 Examples of Xenobiotic Biotransformation Mediated by Fungal Enzymes 142
7.3.3.1 Polycyclic Aromatic Hydrocarbons (PAH) 142
7.3.3.2 Nitro-Aromatic Compounds 143
7.3.3.3 Endocrine-Disrupting Phenolic Compounds 144
7.3.4 Engineering of Fungal Oxidases 145
7.3.5 Advantages of the use of Enzymes for Soil Bioremediation 147
7.3.6 Limitations of the Use of Enzymes for Soil Bioremediation 148
7.3.6.1 Heterogeneity and Availability of Pollutants in the Soil Medium 149
7.3.6.2 Behaviour of Enzymes in the Soil Medium 149
7.3.6.3 Production of Fungal Oxidases 151
7.4 Prospects for Future Research 152
7.4.1 Improving the Ability of Natural Enzymes to Transform Pollutants 152
7.4.2 Discovering Enzymes with New or Increased Potential 152
7.5 Conclusion 153
References 153
Chapter 8 160
Anaerobic Metabolism and Bioremediation of Explosives-Contaminated Soil 160
8.1 Introduction 160
8.2 Anaerobic Biotransformation of Nitroaromatic Compounds 161
8.3 Sulfate-Reducing Bacteria 162
8.3.1 Metabolism of TNT Metabolism of TNT and Other Nitroaromatic Compounds by Sulfate-Reducing Bacteria 163
8.3.2 Bioremediation of TNT Under Sulfate-Reducing Conditions 166
8.4 Bioremediation of Explosives-Contaminated Soil: A Case Study 171
8.4.1 Soil Slurry Reactor and Landfarming Methods 171
8.4.2 Analyses 172
8.4.3 Results 173
References 178
Chapter 9 182
Biological Remediation of Petroleum Contaminants 182
9.1 Introduction 182
9.2 Fate of Hydrocarbons in Soil 183
9.3 Microbial Diversity and Biodegradation 184
9.4 Biological Remediation 187
9.5 Microbial and Nutrient Amendments 188
9.6 Factors Affecting Hydrocarbon Bioremediation 190
9.7 Conclusion 192
References 192
Chapter 10 197
Bioremediation of Benzene-contaminated Underground Aquifers 197
10.1 Introduction 197
10.2 Analyses of a Gasoline-Contaminated Underground Aquifer 198
10.3 Identification and Isolation of Anaerobic Benzene-Degrading Bacteria 201
10.4 Conclusion 205
References 206
Chapter 11 208
Microbial Remediation of Metals in Soils 208
11.1 Introduction 208
11.2 Concern About Metals in Soils 209
11.3 Metal Interactions in Soil 209
11.4 Physical and Chemical Approaches for Metal Remediation 212
11.4.1 Metal Removal 212
11.4.2 Metal Immobilization 213
11.4.3 New Preventative Methods of Metal Contamination 214
11.5 Microbial Interactions with Metals 214
11.6 Microbial Transformations of Metals 215
11.6.1 Complexation/Precipitation Mechanisms 215
11.6.2 Metal Solubilization Mechanisms 217
11.7 Approaches to Microbial-Based Remediation of Metal-Contaminated Soils 219
11.7.1 Indirect Use of Microbial Activities 219
11.7.2 Augmentation with Microorganisms 220
11.7.3 Soil Washing Using Microorganisms or Their By-products 220
11.7.4 Gene Transfer and Genetic Engineering of Metal-Resistance Genes 221
11.7.5 Microbial Influence on Phytoremediation in the Rhizosphere 222
11.8 New Frontiers in Microbial Metal Remediation 222
References 223
Chapter 12 228
Transformations of Toxic Metals and Metalloids by .Pseudomonas stutzeri. Strain KC and its Siderophore Pyridine-2,6-bis(thio 228
12.1 Introduction 228
12.2 Overview of Pdtc Interactions with Metals 230
12.3 Nature of Pdtc Interactions with Heavy Metals and Metalloids 231
12.4 Reduction and Precipitation of Selenium and Tellurium Oxyanions 233
12.5 Chromium(VI) Reduction Mediated by Pdtc 238
12.6 Biotechnology Perspective of Microbial Interactions with Metals 241
12.7 Conclusion 242
References 243
Chapter 13 246
Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation 246
13.1 Introduction 246
13.2 Metal Mobilization and Generation of Acid Mine Drainage (AMD) 247
13.3 Molecular Aspects of Acidophilic Microorganisms-Mineral Interactions 248
13.4 Biomining Microorganisms and Their Industrial Applications 251
13.5 Environmental Bioremediation of AMD and Metals Using Biomining Microorganisms 253
13.5.1 General Methods for AMD Bioremediation 253
13.5.2 Bioshrouding to Prevent AMD Generation 254
13.5.3 Bioremediation of Heavy Metals 254
13.5.4 Bioremediation of Arsenic 257
13.5.5 Biosensors to Monitor Arsenic and other Metals Bioremediation: Use of Biomining Microorganisms-derived Genetic Constru 258
13.5.6 Recycling Waste Metals to Avoid Environmental Pollution 260
13.6 Conclusions 260
References 261
Chapter 14 264
Advances in Phytoremediation and Rhizoremediation 264
14.1 Introduction 264
14.2 Role of the Rhizosphere 267
14.2.1 Exudates and Enzymes Released 268
14.2.2 Methods Used in Phytoremediation 268
14.2.2.1 Artificial Wetlands 269
14.2.2.2 Perspectives of Plants in Detoxification in CWD 269
14.3 Basic Research Aspects 269
14.3.1 Plant in vitro Cultures in Phytoremediation Studies 269
14.3.1.1 Callus and Cell Suspension Cultures 270
14.3.1.2 Hairy Root Cultures 270
14.4 Genetic Engineering Approach 270
14.4.1 Pollution Prevention 271
14.4.2 Genetically Modified Organisms for Phytoremediation 272
14.4.2.1 Methods for Preparation of Transgenic Plants 272
14.4.3 Examples of GM Plants Tailored for Phytoremediation 273
14.4.3.1 Increased Accumulation of Heavy Metals 273
14.4.3.2 Plants with an Enhanced Ability to Detoxify Persistent Organic Compounds 274
14.5 Other Approaches to Improve the Effectiveness of the Phytoremediation Process 275
14.5.1 Secondary Plant Metabolites and their Role in Phytoremediation 275
14.5.2 Effect of Symbiotic Bacteria 276
14.5.2.1 Genetically Modified Symbiotic Bacteria 276
14.5.2.2 Mycorrhizal Symbiosis 276
14.5.2.3 Metagenomics and Molecular Methods 277
14.6 Conclusions 277
References 279
Chapter 15 285
Phytoremediation for Oily Desert Soils 285
15.1 Introduction 285
15.2 Desert Soils and Oil Pollution 285
15.2.1 Normal Desert Microflora 286
15.2.2 Crude Oil 286
15.2.3 Desert Soil Pollution with Oil 287
15.2.4 Oil-Utilizing Microorganisms 288
15.2.5 Cleaning of Oily Desert Soil 290
15.3 Bioremediation 291
15.4 Phytoremediation by Rhizosphere Technology 291
15.4.1 The Rhizosphere Environment 292
15.4.2 The Rhizosphere Microflora 293
15.4.3 Phytoremediation for Xenobiotic Compounds 293
15.5 Phytoremediation Strategies for Oily Desert Soils 294
15.5.1 Oil Plant Interaction 295
15.5.2 Vegetation for Seeding 295
15.5.3 Vegetation for Fertilization 297
15.6 Conclusions 299
References 299
Chapter 16 305
Heavy Metal Phytoremediation: Microbial Indicators of Soil Health for the Assessment of Remediation Efficiency 305
16.1 Microbial Indicators of Soil Health 305
16.2 Heavy Metal Phytoremediation 308
16.2.1 Continuous Metal Phytoextraction 310
16.2.2 Chelate-Induced Phytoextraction 311
16.2.3 Phytostabilization 313
16.3 Conclusions 315
References 316
Chapter 17 320
The Environment and the Tools in Rhizo- and Bioremediation of Contaminated Soil 320
17.1 Techniques for Culture-Independent Assessment of Microbial Communities 320
17.1.1 Microbial Community Analysis 321
17.1.2 Denaturing Gradient Gel Electrophoresis 323
17.1.3 Single-Strand Conformation Polymorphism 323
17.1.4 Amplified Ribosomal DNA Restriction Analysis 324
17.1.5 Reverse Transcription-PCR 324
17.1.6 Base-Specific Fragmentation and Mass Spectrometry 325
17.1.7 Signature Lipid Biomarker Analysis/Environmental Nucleic Acid Probes 325
17.1.8 Terminal Restriction Fragment Length Polymorphism 325
17.1.9 Other Techniques 326
17.1.10 Possible Molecular Pitfalls 327
17.2 DGGE Technique and Application 328
17.2.1 Community Diversity Analysis 331
17.2.2 Community Dynamics Studies 332
17.2.3 Molecular Community Mapping Across Varied Environments 333
17.2.4 Niche Differentiation 333
17.2.5 Determining Species Diversity 333
17.3 Alternatives to PCR-Based Analyses 334
17.3.1 Morphology 334
17.3.2 Catalase Reaction 335
17.3.3 Aerobic and Anaerobic Bacteria 335
17.3.4 Identification Using API and Biolog 335
17.3.5 DNA Reassociation 336
17.4 Use of 16S rDNA Sequences for Parsimony and Distance Analysis 337
17.4.1 Characterisation of 16S Region 338
17.4.2 Characteristic Base-Pairs 339
References 339
Chapter 18 344
Molecular Tools for Monitoring and Validating Bioremediation 344
18.1 Introduction 344
18.2 High-Throughput Techniques for Characterization of Contaminated Sites 345
18.2.1 Fingerprinting Techniques 346
18.2.2 Real-Time PCR 348
18.2.3 DNA Microarrays 348
18.2.4 Metagenomics 350
18.3 Application of Molecular Techniques in Contaminated Sites for Characterization of Microbial Communities and Assessment o 352
18.4 Conclusion 355
References 356
Index 359