1 Introduction ................................................. 1
1.1 Fungal Biodegradation and Biodeterioration .............. 2
1.2 How a Fungus Escapes Water to Grow in Air ............... 3
1.3 Fungal Morphology, Analysis, and Growth Measurement ..... 3
1.3.1 Fungal Morphology ................................ 3
1.3.2 Analysis of Fungal Morphology .................... 4
1.3.3 Pellet Formation and Structure ................... 5
1.3.4 Growth Measurement ............................... 6
1.4 Mass Transfer, Growth Kinetics, and Bioreactors ......... 7
1.5 Methods for Detection of Degradative Fungi ............. 10
1.5.1 Immunological Assays ............................ 10
1.5.2 Molecular Assays ................................ 11
1.6 Fungi as Environmental Indicators ...................... 13
1.7 Fungal Attack on Coal .................................. 14
1.8 Thermophilic, Alpine, and Lichen-Forming Fungi ......... 15
1.9 Mycoremediation: Fungal Bioremediation ................. 16
1.9.1 White-Rot Fungi in Bioremediation ............... 16
1.10 Ecology of Mycoremediation ............................. 18
1.11 Genetic Engineering of Mycoremediation ................. 19
References .................................................. 20
2 Fungal Treatment of Industrial Wastewaters .................. 29
2.1 Introduction ........................................... 29
2.2 Alternative Industrial Wastewater Bioreactors .......... 30
2.3 Fungal Treatment of Industrial Wastewaters ............. 31
2.3.1 Starch-Processing Wastewater .................... 32
2.3.1.1 Background ............................. 32
2.3.1.2 Composition and Characteristics ........ 33
2.3.1.3 Bioreactors and Fermentation ........... 33
2.3.1.4 Enzyme Treatment ....................... 34
2.3.1.5 Production of Fungal Protein ........... 35
2.3.2 Dairy Industry Wastewater ....................... 36
2.3.2.1 Background ............................. 36
2.3.2.2 Bioreactors and Modeling ............... 37
2.3.2.3 Production of Fungal Biomass ........... 39
2.3.2.4 Lactases ............................... 40
2.3.2.5 Genetics of Lactose Utilization ........ 40
2.3.3 Pharmaceutical Industry Wastewater .............. 41
2.3.3.1 Background ............................. 41
2.3.3.2 Process Development .................... 42
2.3.3.3 Conclusions ............................ 42
2.3.4 Protein-Containing Wastewater ................... 42
2.3.4.1 Background ............................. 42
2.3.4.2 Bioreactors ............................ 43
2.3.5 Oil Manufacturing Plant Wastewater .............. 44
2.3.5.1 Background ............................. 44
2.3.5.2 Assay of Oil-Decomposing Ability ....... 45
2.3.5.3 Bioreactors ............................ 45
2.3.6 Silage Wastewater ............................... 47
2.3.6.1 Background ............................. 47
2.3.6.2 Legislation ............................ 48
2.3.6.3 Growth of Fungi ........................ 48
2.3.6.4 On-Farm Treatment ...................... 50
2.3.6.5 Production of Fungal Biomass ........... 50
2.3.7 Acidogenic Wastewater ........................... 50
2.3.7.1 Background ............................. 50
2.3.7.2 Bioreactors and Modeling ............... 51
2.3.8 Olive Mill Wastewater ........................... 53
2.3.8.1 Background ............................. 53
2.3.8.2 Composition and Characteristics ........ 54
2.3.8.3 Fermentation ........................... 54
2.3.8.4 Modeling ............................... 57
2.3.8.5 Immobilization ......................... 57
2.3.8.6 Enzyme Treatment ....................... 59
2.3.8.7 Toxicity Testing ....................... 60
2.3.8.8 Economic Importance .................... 61
2.4 Biotechnology .......................................... 62
2.5 Conclusions and Future Perspectives .................... 63
References .................................................. 63
3 Fungal Treatment of Distillery and Brewery Wastes ........... 76
3.1 Introduction ........................................... 76
3.2 Composition and Characteristics of Stillage ............ 77
3.3 Alternative Industrial Stillage Treatment Reactors ..... 78
3.4 Fungal Treatment of Distillery and Brewery Wastes ...... 80
3.5 Fungal Fermentation and Decolorization ................. 80
3.5.1 Yeasts .......................................... 81
3.5.2 Filamentous Fungi ............................... 84
3.5.3 White-Rot Fungi ................................. 85
3.5.4 Mixed Cultures .................................. 86
3.6 Molasses Toxicity to Fungi ............................. 87
3.7 Factors Affecting Fungal Fermentation and
Decolorization ......................................... 87
3.7.1 Carbon Source ................................... 89
3.7.2 Nitrogen and Phosphorus Sources ................. 89
3.7.3 Temperature ..................................... 90
3.7.4 pH .............................................. 90
3.7.5 Agitation and Aeration .......................... 90
3.7.6 Inoculum Size ................................... 91
3.7.7 Effluent Dilution Rate .......................... 91
3.8 Mechanisms of Melanoidin Degradation ................... 92
3.9 Fungal Bioreactors for Distillery and Brewery Wastes ... 93
3.9.1 Fed-Batch Bioreactors ........................... 95
3.9.2 Bubble Column Bioreactors ....................... 95
3.9.3 Fluidized-Bed Bioreactors ....................... 95
3.9.4 Immobilized Bioreactors ......................... 96
3.10 Modeling ............................................... 97
3.11 Economic Importance .................................... 98
3.11.1 Single-Cell Protein Production .................. 98
3.11.2 Ethanol Production .............................. 99
3.11.3 Bioproducts .................................... 101
3.11.4 Algal Production ............................... 103
3.12 Biotechnology ......................................... 103
3.13 Conclusions and Future Perspectives ................... 104
References ................................................. 106
4 Fungal Metabolism of Petroleum Hydrocarbons ................ 115
4.1 Introduction .......................................... 115
4.2 Fate of Oil in the Environment ........................ 116
4.3 Composition of Petroleum Hydrocarbons ................. 117
4.4 Methods of Analysis of Petroleum Hydrocarbons ......... 117
4.5 Alternative Treatment Technologies .................... 119
4.6 Hydrocarbon-Utilizing Yeasts and Fungi ................ 119
4.7 Fungal Methods of Assessment .......................... 121
4.7.1 Fungal Enumeration ............................. 122
4.7.2 Respirometric Tests ............................ 123
4.7.3 Soil Microcosm Tests ........................... 123
4.7.4 Miscellaneous Tests ............................ 124
4.8 Hydrocarbon Metabolism by Yeasts and Fungi ............ 124
4.9 Taxonomic Relationship of Hydrocarbon-Utilizing
Yeasts and Fungi ...................................... 129
4.10 Factors Affecting Metabolism of Petroleum
Hydrocarbons .......................................... 130
4.10.1 Physical Nature ................................ 130
4.10.2 Temperature .................................... 130
4.10.3 pH ............................................. 131
4.10.4 Oxygen ......................................... 131
4.10.5 Nutrients, Dispersants, and Biosurfactants ..... 131
4.11 Fungal Mechanisms of Metabolism of Petroleum
Hydrocarbons .......................................... 132
4.11.1 Aliphatic Hydrocarbons ......................... 133
4.11.2 Aromatic Hydrocarbons .......................... 134
4.11.3 Cooxidation of Hydrocarbons .................... 134
4.11.4 Uptake of Hydrocarbons ......................... 134
4.12 Oxidation of Petroleum Hydrocarbons by Fungal
Enzymes ............................................... 135
4.13 Cytochrome P450 Enzyme Systems ........................ 136
4.14 Economic Importance ................................... 137
4.14.1 Single-Cell Protein ............................ 137
4.14.2 Surfactant Production .......................... 137
4.14.3 Metabolite Overproduction ...................... 138
4.15 Biotechnology and Bioengineering ...................... 139
4.16 Conclusions and Future Perspectives ................... 140
References ................................................. 140
5 Fungal Degradation of Polychlorinated Biphenyls and
Dioxins .................................................... 149
5.1 Introduction .......................................... 149
5.2 Nomenclature .......................................... 150
5.3 Bioaccumulation and Toxicity .......................... 150
5.4 Alternative PCB Remediation Technologies .............. 151
5.5 Analysis of Polychlorinated Biphenyls ................. 151
5.6 Bioavailability of Polychlorinated Biphenyls .......... 153
5.7 Fungal Degradation of Polychlorinated Biphenyls ....... 154
5.7.1 Filamentous Fungi .............................. 154
5.7.2 Yeasts ......................................... 156
5.7.3 White-Rot Fungi ................................ 158
5.7.3.1 White-Rot Fungal Bioreactors .......... 158
5.7.3.2 Degradation and Mineralization ........ 159
5.7.3.3 Effects of Chlorination Grades and
Patterns .............................. 162
5.7.3.4 Metabolic Products and Pathways ....... 163
5.7.3.5 Role of Manganese in PCB
Biodegradation ........................ 167
5.7.3.6 PCB Bioremediation in Soils ........... 167
5.7.3.7 Biotransformation of PCBs by
Laccases .............................. 169
5.7.3.8 Comparison with Bacterial Systems ..... 171
5.8 Fungal Degradation of Dioxins ......................... 172
5.9 Genetic Manipulation .................................. 173
5.10 Conclusions and Future Perspectives ................... 173
References ................................................. 174
6 Fungal Degradation of Pesticides ........................... 181
6.1 Introduction .......................................... 181
6.2 Classification ........................................ 182
6.3 Biosensors for Detection of Pesticides ................ 182
6.4 Fungal Degradation of Insecticides .................... 184
6.4.1 Chlorinated Compounds .......................... 184
6.4.2 Organophosphorus Compounds ..................... 189
6.4.3 Miscellaneous Compounds ........................ 190
6.5 Fungal Degradation of Herbicides ...................... 190
6.5.1 Phenoxyalkanoate Compounds ..................... 190
6.5.2 Phenylamide Compounds .......................... 194
6.5.2.1 Acylanilides .......................... 194
6.5.2.2 Phenylureas ........................... 195
6.5.2.3 Phenylcarbamates ...................... 197
6.5.3 s-Triazine Compounds ........................... 198
6.5.4 Miscellaneous Compounds ........................ 199
6.6 Fungal Degradation of Fungicides ...................... 199
6.6.1 Organomercurial Compounds ...................... 200
6.6.2 Organosulfur Compounds ......................... 200
6.6.3 Organophosphorus Compounds ..................... 203
6.6.4 Aromatic and Heterocyclic Compounds ............ 203
6.7 Biotransformation of Pesticides by Fungal Enzymes ..... 203
6.8 Genetic Manipulation .................................. 205
6.9 Conclusions and Future Perspectives ................... 207
References ................................................. 208
7 Fungal Metabolism of Phenols, Chlorophenols, and
Pentachlorophenol .......................................... 215
7.1 Introduction .......................................... 215
7.2 Alternative Treatment Technologies .................... 216
7.2.1 Physicochemical Methods ........................ 216
7.2.2 Biological Methods ............................. 217
7.2.2.1 Metabolism by Bacteria ................ 217
7.2.2.2 Metabolism by Actinomycetes ........... 218
7.2.2.3 Metabolism by Algae and Higher
Plants ................................ 218
7.3 Fungal Biosensors for Determination of Various Types
of Phenols ............................................ 219
7.3.1 Enzyme-Based Systems ........................... 219
7.3.2 Biological Affinity Assays (Immunoassays) ...... 221
7.4 Methods of Analysis of Various Types of Phenols ....... 221
7.5 Fungal Bioreactors for Removal of Various Types of
Phenols ............................................... 221
7.5.1 Rotating Tube Bioreactors ...................... 222
7.5.2 Membrane Bioreactors ........................... 222
7.5.3 Packed-Bed/Immobilized Bioreactors ............. 222
7.5.4 Upflow Column Bioreactors ...................... 225
7.5.5 Miscellaneous Bioreactors ...................... 226
7.6 Fungal Metabolism of Phenols, Chlorophenols, and
Pentachlorophenol ..................................... 226
7.6.1 Fungal Metabolism of Phenols ................... 226
7.6.2 Fungal Metabolism of Chlorophenols ............. 230
7.6.3 Fungal Metabolism of Pentachlorophenol ......... 230
7.7 Factors Affecting Fungal Metabolism of Various
Types of Phenols ...................................... 231
7.7.1 Effect of Static Versus Agitated Culture
Conditions ..................................... 231
7.7.2 Effect of Culture Age, Type of Inoculum, and
Carbon and Nitrogen Sources .................... 234
7.8 Physiological Alterations of Fungi by Phenols ......... 235
7.9 Taxonomic Relationship of Phenol-Utilizing Yeasts
and Fungi ............................................. 236
7.10 Mechanisms of Metabolism, Metabolic Pathways, and
Metabolites ........................................... 237
7.11 Degradation of Phenols by Fungal Enzymes .............. 245
7.11.1 Peroxidase-Catalyzed Degradation ............... 246
7.11.1.1 Peroxidase Bioreactors ................ 246
7.11.2 Polyphenol Oxidase/Tyrosinase-Catalyzed
Degradation .................................... 250
7.11.2.1 Polyphenol Oxidase/Tyrosinase
Bioreactors ........................... 251
7.11.3 Laccase-Catalyzed Degradation .................. 253
7.11.3.1 Influence of Cosubstrates ............. 257
7.11.3.2 Laccase Bioreactors ................... 258
7.11.4 Miscellaneous Enzymes .......................... 259
7.12 Fungal Transformation of Pentachlorophenol in Soils ... 261
7.12.1 Bound Residue Formation ........................ 261
7.12.2 Degradation and Mineralization ................. 263
7.12.3 Fungal Augmentation ............................ 264
7.13 Cytochrome P450 Systems in Degradation of Phenols ..... 265
7.14 Conclusions and Future Perspectives, 266 References ... 267
8 Fungal Metabolism of Polycyclic Aromatic Hydrocarbons ...... 283
8.1 Introduction .......................................... 283
8.2 Occurrence of PAHs in the Environment ................. 284
8.3 Alternative PAH Metabolism ............................ 285
8.3.1 Bacteria ....................................... 285
8.3.2 Algae, Cyanobacteria, and Higher Plants ........ 287
8.4 Fungal Metabolism of PAHs ............................. 287
8.4.1 Fungal Metabolism of Naphthalene ............... 296
8.4.2 Fungal Metabolism of Acenaphthene .............. 296
8.4.3 Fungal Metabolism of Anthracene ................ 296
8.4.4 Fungal Metabolism of Phenanthrene .............. 297
8.4.5 Fungal Metabolism of Fluorene .................. 298
8.4.6 Fungal Metabolism of Fluoranthene .............. 300
8.4.7 Fungal Metabolism of Chrysene .................. 300
8.4.8 Fungal Metabolism of Pyrene .................... 302
8.4.9 Fungal Metabolism of Benz [α] anthracene ....... 304
8.4.10 Fungal Metabolism of Benzo[α]pyrene ............ 305
8.5 Mutagenicity of Fungal Metabolites of PAHs ............ 306
8.6 Fungal Bioreactors for Removal of PAHs ................ 306
8.6.1 Immobilized Bioreactors ........................ 307
8.6.2 Closed-Batch Feed Bioreactors .................. 307
8.6.3 Compost Bioreactors ............................ 310
8.6.4 Miscellaneous Bioreactors ...................... 311
8.7 PAH Degradation by Fungal Enzymes ..................... 311
8.7.1 Peroxidase-Catalyzed Degradation ............... 312
8.7.1.1 Role of Miscible Solvents ............. 314
8.7.1.2 Influence of Cyclodextrins ............ 315
8.7.2 Laccase-Catalyzed Degradation .................. 316
8.7.2.1 Laccase Bioreactors ................... 319
8.7.2.2 Influence of Mediators ................ 319
8.7.3 Miscellaneous Enzymes .......................... 320
8.8 Cytochrome P450 in Degradation of PAHs ................ 322
8.9 Fungal Degradation of PAHs in Soils ................... 323
8.9.1 Influence of Cosubstrates and Surfactants ...... 324
8.9.2 Fate of PAH Disappearance ...................... 330
8.9.2.1 PAH Degradation and Mineralization .... 330
8.9.2.2 Bound Residue Formation ............... 333
8.9.3 Factors Affecting Biodegradation of PAHs ....... 334
8.10 Fungal Metabolism of Complex PAH Mixtures ............. 335
8.11 PAH Degradation by Fungal-Bacterial Co-cultures ....... 336
8.12 Biotechnology and Bioengineering ...................... 337
8.13 Conclusions and Future Perspectives ................... 339
References ................................................. 340
9 Fungal Lignin Degradation and Decolorization of Pulp and
Paper Mill Effluents ....................................... 357
9.1 Introduction .......................................... 357
9.2 Distribution and Structure of Lignin .................. 358
9.3 Lignin-Degrading Microorganisms ....................... 360
9.3.1 Bacterial Degradation .......................... 360
9.3.2 Fungal Degradation ............................. 360
9.4 Fungal Lignin-Degrading Enzymes ....................... 362
9.4.1 Lignin Peroxidases ............................. 363
9.4.2 Manganese Peroxidases .......................... 368
9.4.3 Laccases ....................................... 372
9.4.4 Hydrogen Peroxide-Producing Enzymes ............ 375
9.4.5 Reactive Oxygen Species ........................ 378
9.4.6 Miscellaneous Enzymes .......................... 380
9.5 Mechanisms of Fungal Lignin Degradation and
Metabolic Products .................................... 381
9.6 Fungal Decolorization of Pulp and Paper Mill
Effluents ............................................. 382
9.7 Fungal Bioreactors for Decolorization of Pulp and
Paper Mill Effluents .................................. 384
9.7.1 Batch and Continuous Bioreactors ............... 384
9.7.2 Upflow Column Bioreactors ...................... 387
9.7.3 Immobilized Bioreactors ........................ 388
9.7.4 Miscellaneous Bioreactors ...................... 389
9.8 Factors Affecting Decolorization of Pulp and Paper
Mill Effluents ........................................ 391
9.8.1 Carbon Cosubstrate ............................. 391
9.8.2 Nitrogen, Phosphorus, Sulfur, and Chloride
Concentrations ................................. 391
9.8.3 Hydrogen Ion Concentration and Temperature ..... 395
9.8.4 Dilution of Effluent ........................... 395
9.8.5 Inoculum Dose and Nature ....................... 395
9.8.6 Static Versus Agitated Culture Conditions ...... 396
9.9 Effect of Fungal Treatment on Chlorophenols and
Chloroaldehydes in Effluents .......................... 396
9.10 Decolorization of Effluents by Fungal Enzymes ......... 397
9.11 Wetlands Treatment .................................... 399
9.12 Conclusions and Future Perspectives ................... 399
References ................................................. 400
10 Fungal Decolorization and Degradation of Dyes .............. 420
10.1 Introduction .......................................... 420
10.2 Classification, Structure, and Color Measurements ..... 421
10.3 Legislation and Regulations ........................... 422
10.4 Alternative Decolorization Treatment Technologies ..... 423
10.4.1 Physicochemical Methods ........................ 423
10.4.2 Biological Methods ............................. 425
10.4.2.1 Degradation by Bacteria ............... 425
10.4.2.2 Degradation by Actinomycetes .......... 425
10.4.2.3 Degradation by Algae and Higher
Plants ................................ 425
10.5 Fungal Decolorization and Degradation of Dyes ......... 426
10.5.1 Azo Dyes ....................................... 426
10.5.2 Phthalocyanine Dyes ............................ 434
10.5.3 Anthraquinone Dyes ............................. 434
10.5.4 Heterocyclic Dyes .............................. 435
10.5.5 Indigo Dyes .................................... 435
10.5.6 Polymeric Dyes ................................. 435
10.5.7 Triphenylmethane Dyes .......................... 435
10.6 Yeast Decolorization and Degradation of Dyes .......... 436
10.7 White-Rot Fungal Decolorization and Degradation of
Dyes .................................................. 438
10.8 Mechanisms of Fungal Decolorization and Degradation
of Dyes ............................................... 438
10.9 Metabolic Products and Pathways ....................... 440
10.10 Factors Affecting Fungal Decolorization and
Degradation of Dyes ................................... 442
10.10.1 Media Composition ............................. 443
10.10.2 Static Versus Agitated Culture Conditions ..... 447
10.10.3 pH and Temperature ............................ 447
10.10.4 С and N Sources, TOC/N Ratio, and Salts ....... 447
10.10.5 Initial Dye Concentration ..................... 448
10.11 Fungal Dye Decolorization and Degradation
Bioreactors ........................................... 448
10.11.1 Rotating Drum, Stirred-Tank, and Membrane
Bioreactors ................................... 452
10.11.2 Packed- and Fluidized-Bed Bioreactors ......... 452
10.11.3 Immobilized Bioreactors ....................... 453
10.12 Decolorization and Degradation of Dyes by Fungal
Enzymes ............................................... 454
10.12.1 Peroxidase-Catalyzed Decolorization and
Degradation of Dyes ............................ 455
10.12.1.1 Peroxidase Bioreactors .............. 461
10.12.2 Laccase-Catalyzed Decolorization and
Degradation of Dyes ............................ 462
10.12.2.1 Laccase Bioreactors ................. 466
10.12.2.2 Influence of Mediators .............. 467
10.13 Decolorization of Artificial Textile Effluent ........ 467
10.14 Sequential Dye Decolorization ........................ 470
10.15 Conclusions and Future Perspectives .................. 470
References ................................................. 472
11 Fungal Biosorption of Heavy Metals ......................... 484
11.1 Introduction .......................................... 484
11.2 Biosorption and Bioaccumulation of Heavy Metals ....... 485
11.3 Evaluation of Sorption Performance .................... 486
11.4 Mechanisms of Fungal Biosorption of Heavy Metals ...... 487
11.5 Fungal Biosorption Reactors for Heavy Metals .......... 491
11.5.1 Types of Reactors .............................. 491
11.5.1.1 Batch Stirred-Tank Reactors ........... 491
11.5.1.2 Continuous-Flow Stirred-Tank
Reactors .............................. 491
11.5.1.3 Fixed Packed-Bed Reactors ............. 491
11.5.1.4 Immobilized Reactors .................. 491
11.5.2 Models of Process Development .................. 496
11.5.3 Desorption and Regeneration .................... 498
11.5.4 Effect of Effluent Composition ................. 499
11.6 Applications of Fungal Biosorption of Heavy Metals .... 499
11.6.1 Biosorption by Filamentous Fungi ............... 499
11.6.2 Biosorption by White-Rot Fungi ................. 504
11.6.3 Biosorption by Yeasts .......................... 505
11.6.4 Biosorption by Aspergillus niger ............... 507
11.6.4.1 Role in Soil Bioremediation ........... 509
11.7 Fungal Biosorption of Herbicides and Phenols .......... 509
11.8 Fungal Biosorption of Dyes ............................ 512
11.9 Fungal Binary and Ternary Biosorption Systems ......... 512
11.9.1 Binary Biosorption Systems ..................... 512
11.9.2 Ternary Biosorption Systems .................... 515
11.9.3 Effect of Co-cations ........................... 516
11.10 Biosorption of Heavy Metal Anions .................... 516
11.11 Metal Ion Resistance ................................. 517
11.12 Conclusions and Future Perspectives .................. 518
References ................................................. 519
12 Mycorrhizal Fungi in Rhizosphere Remediation ............... 533
12.1 Introduction .......................................... 533
12.2 Classification of Mycorrhizal Fungi ................... 534
12.3 Functions of Mycorrhizal Mycelium ..................... 535
12.4 Methods for Studying Mycorrhizal Fungi ................ 536
12.5 Molecular Mechanisms of Mycorrhizal Symbiosis ......... 538
12.6 Metabolism of Mycorrhizal Fungi ....................... 539
12.6.1 General Metabolism ............................. 539
12.6.2 Degradative Metabolism ......................... 539
12.7 Uptake of Toxic Metals ................................ 541
12.7.1 Metal Tolerance in Mycorrhizal Symbiosis ....... 541
12.7.2 Mechanisms of Response to Metals ............... 543
12.7.3 Transport of Radionuclides ..................... 545
12.7.4 Genetics of Metal Tolerance .................... 547
12.8 Petroleum Hydrocarbon Degradation ..................... 547
12.9 Lignin and Phenolic Degradation ....................... 549
12.10 PAH and TNT Degradation .............................. 552
12.11 PCB Degradation ...................................... 555
12.12 Herbicide Degradation ................................ 555
12.13 Comparison of Mycorrhizal and White-Rot Fungi ........ 556
12.14 Conclusions and Future Perspectives .................. 558
References ................................................. 559
Index ......................................................... 573
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