Industrial Applications (eBook)

Series Preface 8
Addendum to the Series Preface 12
Volume Preface to the Second Edition 14
Volume Preface to the First Edition 16
Contents 18
List of Contributors 20
Traditional Food and Beverage Fermentation 25
1: Production of Bread, Cheese and Meat 26
I. Introduction 26
II. Bread 27
A. Baker´s Yeast 27
B. Technological Properties of Baker´s Yeast 28
C. Manufacture of Baker´s Yeast 29
III. Cheese 30
A. Yeasts 30
1. Debaryomyces hansenii 30
2. Yarrowia lipolytica 33
3. Geotrichum candidum (perfect: Galactomyces candidus) 34
4. Saccharomyces cerevisiae 34
B. Filamentous Fungi 35
1. Blue Mould Cheeses 35
a) Penicillium roqueforti 35
b) Technological Characteristics of Penicillium roqueforti 35
2. White Mould Cheeses 38
a) Penicillium camemberti 38
b) Technological Characteristics of Penicillium camemberti 38
C. Microbial Interactions in Cheeses Involving Yeast and Filamentous Fungi 39
IV. Meat 41
V. Conclusions 42
References 43
2: Asian Fungal Fermented Food 51
I. Introduction 51
A. Food Fermentation 51
B. Useful Fungi 52
C. Fungal Fermented Foods World-Wide 52
D. Categories of Asian Fungal Fermented Foods 53
II. Tempe 53
A. The Product 53
B. Traditional Manufacturing Process 53
C. Fungi Involved and Their Relevant Properties 56
D. Biochemical Modifications and Implications for Health 57
E. Industrial Aspects 58
III. Red Kojic Rice (Angkak) 59
A. The Product 59
B. Traditional Manufacturing Process 59
C. Fungi Involved and Their Relevant Properties 59
D. Industrial Aspects 61
IV. Amylolytic Starters 61
A. The Product 61
B. Traditional Manufacturing Process 62
C. Fungi Involved, Their Relevant Properties and Implications for Health 62
D. Industrial Aspects 63
V. Furu (Sufu) 64
A. The Product 64
B. Traditional Manufacturing Process 64
C. Fungi Involved and Their Relevant Properties 65
D. Industrial Aspects 66
VI. Soy Sauce 66
A. The Product 66
B. Traditional Manufacturing Process 67
C. Fungi Involved, Their Relevant Properties and Implications for Health 68
D. Industrial Aspects 69
VII. Wines 70
A. The Products 70
B. Traditional Manufacturing Process 71
C. Fungi Involved and Their Relevant Properties 71
D. Industrial Aspects 72
VIII. Chinese Liquor 72
A. The Product 72
B. Traditional Manufacturing Process 73
C. Fungi Involved and Their Relevant Properties 73
D. Industrial Aspects 74
IX. Conclusions 74
References 43
3: Production of Beer and Wine 81
I. Introduction 81
II. Beer Brewing 82
A. Raw Materials 83
B. Malt Production 84
C. Steps in the Brew House 85
1. Malt Grinding and Mashing 85
2. Lautering 86
3. Wort Cooking 86
4. Cooling and Wort Treatment 86
D. Fermentation 87
E. Maturation 87
F. Filtration, Stabilisation and Packaging 88
G. Final Beer 88
H. Beer-Like Beverages 89
III. Wine Making 90
A. Grape Varieties and Composition 90
B. Wine Types 91
C. Wine Production 91
1. Grape Harvest 91
2. Crushing 91
3. Pressing Process 92
4. Fermentation 93
5. Clarification 93
6. Stabilisation and Fining 93
7. Storage and Bottling 94
D. Production of Sparkling Wine 94
E. Production of Fortified Wines 94
IV. Conclusions 95
References 96
4: Production of Edible Mushrooms 100
I. Introduction 100
II. Present Scenario of Mushroom Production 101
III. Main Genera of Cultivated Mushrooms 101
IV. Cultivation of Calocybe indica P. and C. (Milky Mushroom) 102
A. Substrate and Substrate Preparation 102
B. Spawn Preparation 103
C. Spawning 103
D. Casing 104
E. Cropping 104
F. Precautions during Cropping 104
G. Harvesting 105
V. Cultivation of Pleurotus spp. (Oyster Mushrooms) 105
A. Advantages of Growing Oyster Mushrooms 105
B. History of Oyster Mushroom Cultivation 106
C. Biology of the Oyster Mushroom 106
D. Varieties of Oyster Mushrooms 106
E. Cultivation 107
1. Preparation or Procurement of Spawn 107
2. Substrate Preparation and Nutrition Quality 107
3. Spawning of Substrates 108
4. Crop Management and Incubation 108
F. Harvesting and Post-Harvest Practice 109
G. Medicinal and Nutritional Value of Oyster Mushrooms 109
H. Precautions While Growing Oyster Mushrooms 109
VI. Cultivation of Auricularia spp. (Black Ear Mushroom) 109
A. Biology of Black Ear Mushrooms 110
B. Cultivation Techniques 110
1. Wood Log Cultivation 110
2. Composted Sawdust Method (``Synthetic Log´´ Cultivation) 110
3. Composting of Saw Dust, Spawning and Culture Conditions 110
4. Harvesting 111
C. Nutritional Value of Auricularia spp 111
VII. Cultivation of Lentinula edodes (Shiitake) 111
A. Cultivation Technique on Wood Logs 111
1. Log Preparation 111
2. Spawn Preparation and Spawning the Logs 112
3. Crop Management 112
B. ``Synthetic Log´´ Cultivation 112
1. Substrate Preparation 112
2. Spawning and Spawn Run 112
3. Fruiting and Harvesting 113
4. Special Features of the Plastic Bag (``Synthetic Log´´) Method 113
VIII. Cultivation of Stropharia rugoso-annulata (Wine-Cap Stropharia) 113
IX. Cultivation of Volvariella spp. (Paddy Straw Mushrooms) 114
X. Cultivation of Flammulina velutipes (Enokitake) 115
A. Future Prospects 116
XI. Conclusions 116
References 116
Metabolites and Enzymes 119
5: The beta-Lactam Antibiotics: Current Situation and Future Prospects in Manufacture and Therapy 120
I. Introduction 120
II. Manufacturing Aspects 121
A. Strain Improvement 121
1. Characterization of Biosynthetic Pathways 121
a) Cephalosporin C Synthesis in Acremonium chrysogenum 121
b) Penicillin Formation by Penicillium chrysogenum 123
2. Genetic Engineering 123
a) Acremonium chrysogenum 123
b) Penicillium chrysogenum 123
3. Approaches and Goals for Further Strain Improvement 124
B. Fermentation 125
1. Cultivation Media 125
a) Complex Ingredients 125
b) Synthetic Components 125
c) Amino Acids 126
d) Productivity-Enhancing Substrates 126
e) Concentration of Carbon, Nitrogen and Phosphor Sources 126
2. Physical Process Parameters 127
a) Influence of pH 127
b) Oxygen Supply 127
3. Scale-Up 128
C. Downstream Processing 128
1. Recovery and Purification 128
2. Side Chain Cleavage 129
a) 7-Aminocephalosporanic Acid 129
b) 6-Aminopenicillanic Acid 130
3. Economization of the Cleavage Process 131
D. Options for Future Production Processes 131
1. One-Enzyme Cleavage of Cephalosporin C 131
2. Production of Adipyl-Cephalosporins in Penicillium chrysogenum 131
3. Production of 7-ADOCA 131
4. Direct Expression of 7-ACA in A. chrysogenum 132
III. Therapeutic Aspects 133
A. Multidrug Resistance 133
B. beta-Lactamase Resistance 133
C. Future Developments 134
1. beta-Lactams 134
2. Novel Therapeutic Approaches 135
IV. Conclusions 135
References 136
6: Non-beta-Lactam Antibiotics 141
I. Introduction 141
II. Antifungal Drugs 142
A. Griseofulvin 142
B. Inhibitors of Fungal Cell Wall Assembly, (1,3)-beta-d-Glucan Synthase Inhibitors 143
1. Echinocandins and Pneumocandins 143
2. Papulacandins 146
3. Acidic Triterpenes 146
C. Sphingolipid Synthesis Inhibitors 147
1. Inhibitors of Serine Palmitoyltransferase 148
2. Inhibitors of Ceramide Synthase 149
3. Inhibitors of Inositol Phosphorylceramid Synthase 150
D. Inhibitors of Protein Biosynthesis 151
E. Emerging Antifungal Therapies 154
F. The Strobilurins and Oudemansins, Inhibitors of Fungal Respiration 155
III. Antibacterial Antibiotics 157
A. Fusidic Acid 157
B. Pleuromutilins 158
IV. Conclusions 158
References 159
7: Insecticidal and Nematicidal Metabolites from Fungi 168
I. Introduction 168
II. Novel Compounds and Their Producers 168
A. Peptides, Cyclic Peptides, and Cyclic Depsipeptides 168
B. Novel Metabolites and New Derivatives of Insecticidal or Nematicidal Metabolites 169
III. Biological Activities and Mode of Action 175
IV. Ecological Significance 176
V. Conclusions 177
References 177
8: Immunomodulators 181
I. Introduction 181
II. Immunosuppressants 182
A. Cyclosporins 182
1. Chemistry 184
2. Biosynthesis 184
3. Production 186
4. New Generations 187
B. Mycophenolic Acid 187
1. Chemistry 189
2. Biosynthesis 190
3. Production 190
C. Mizoribine 191
D. Other Immunosuppressants 192
1. Ovalicins and Fumagillins 192
2. Gliotoxin 192
3. Trichopolyns 194
4. Myriocin 195
5. Flavidulols 195
6. Kobiins 195
7. Mycestericins 196
8. Terprenins 196
9. FR901483 196
10. Colutellin A 196
III. Mushroom Immunomodulators 196
A. Lectins 197
B. Terpenoids 197
C. Polysaccharides 197
D. Fungal Immunomodulator Proteins 200
E. Industrial Production of Mushroom Immunomodulators 200
IV. Conclusions 201
References 201
9: Ergot Alkaloids 211
I. Introduction 211
II. Ergot Alkaloid-Producing Fungi 212
A. Ergot Alkaloid Producers in the Clavicipitaceae 212
1. Claviceps Species 212
2. Neotyphodium Species 213
3. Other Clavicipitaceous Fungi 213
B. Ergot Alkaloid Producers in the Trichocomaceae 214
1. Aspergillus fumigatus 214
2. Other Trichocomaceous Fungi 214
III. Ergot Alkaloid Profiles and Pathways in Different Fungi 214
A. Early Pathway Steps Shared Among Producers 215
B. Ergot Alkaloid Profile Diversification Through Pathway Divergence 218
1. Terminal Branch in Trichocomaceous Ergot Alkaloid Producers 218
2. Typical Terminal Branch in Clavicipitaceous Ergot Alkaloid Producers 219
3. Dihydroergot Alkaloid Branch in Clavicipitaceous Fungi 221
C. Regulation of Clustered Ergot Pathway Genes 222
IV. Pathway Inefficiency as a Means to Diversify Alkaloid Profiles 222
A. Inefficiency in the Ergot Pathway Provides Diversified Alkaloid Profiles 222
B. Other Pathways that Appear to have Preset, Step-Specific Reductions in Flux 223
V. Activities of Ergot Alkaloids 224
A. Effects on Humans 224
B. Ecological Roles 225
VI. Conclusions 226
References 227
10: Production of Organic Acids by Filamentous Fungi 231
I. Introduction 231
II. Citric Acid 232
A. Biosynthesis of Citric Acid 232
B. Fermentation Conditions 237
C. Strain Breeding 239
D. Production Processes for Citric Acid 240
III. Gluconic Acid 242
A. Biochemistry of Gluconic Acid Formation 243
B. Production of Gluconic Acid 243
IV. Itaconic Acid 244
A. Biochemical Pathways of Itaconic Acid Synthesis 244
B. Production of Itaconic Acid 244
V. Other Acids 245
VI. Conclusions 245
References 246
11: Production of Vitamin B2 and a Polyunsaturated Fatty Acid by Fungi 251
I. Introduction 251
II. Vitamin B2 251
A. Ashbya gossypii 252
1. The Riboflavin Biosynthesis Pathway 252
2. Isolation of RIB Genes 254
3. Regulation of Riboflavin Overproduction 254
4. Classical and Molecular Tools for Strain Improvement 255
5. Engineering of Pathways 255
a) Riboflavin Pathway 255
b) Riboflavin Precursor Supply 255
Purine and Glycine Metabolism 255
Isocitrate Lyase and Isocitrate Dehydrogenase 256
6. Riboflavin Excretion and Vacuolar Accumulation 257
7. Production and Downstream Processing 257
B. Candida famata 258
III. Polyunsaturated Fatty Acids 258
A. Mortierella alpina 260
IV. Conclusions 261
References 261
12: Fungal Flavours 264
I. Introduction 264
II. Volatile Flavours Emitted from Fruiting Bodies 265
A. Volatiles from Sporocarps Emitted by Basidiomycetous Fungi 265
1. Agaricus bisporus 265
a) General Remarks 265
b) Enzymatic Pathways of C8 Volatiles in Fungi 266
2. Pleurotus florida 268
3. Pleurotus ostreatus 268
4. Pleurotus eryngii 268
5. Fistulina hepatica 269
6. Boletus edulis 269
7. Calocybe indica 270
8. Hygrophorus spp 270
9. Termitomyces shimperi 270
10. Lentinula edodes 271
11. Volvariella volvacea 271
12. Polyporus sulfureus 271
13. Tricholoma matsutake 272
14. Phallus impudicus 273
15. Marasmius alliaceus 273
16. Lactarius helvus 273
17. Flavour Profiles of Miscellaneous Fungi 273
18. Fungi Emitting Anis-Like or Bitter Almond-Like Odours 273
19. Key Flavour Compounds of Miscellaneous Fungi 274
B. Volatiles Emitted from Ascomycetes 274
1. Tuber spp 274
2. Tuber aestivum and T. melanosporum 274
3. Tuber magnatum Pico 275
4. Tuber borchii 276
III. Flavour Profiles of Fungi Grown in Submerged Cultures 276
A. Basidiomycetous Fungi 276
1. Flavour Profiles of Miscellaneous Fungi 276
2. Pleurotus florida 277
3. Pleurotus ostreatus 277
4. Nidula niveo-tomentosa 277
5. Fistulina hepatica 278
B. Ascomycetous Fungi 278
1. Tuber borchii 278
2. Penicillium vulpinum 279
3. Ceratocystis moniliformis 279
IV. Conclusions 279
References 279
13: Industrial Applications of Fungal Enzymes 284
I. Introduction 284
II. Fungal Enzymes in Industry 284
III. Safety of Fungal Production Organisms 285
IV. Enzyme Classification System 286
V. Enzymes for Detergents and Personal Care 287
VI. Enzymes for Other Non-Food Industries 291
A. Textiles 291
B. Leather 293
C. Forest Products 294
D. Animal Feed 294
E. Fuel Ethanol 295
F. Biocatalysis - Enzymes in Organic Synthesis 296
VII. Enzymes for Food Industries 297
A. Sweetener Production 297
B. Baking 298
C. Dairy 298
D. Protein Hydrolysis 299
E. Brewing 300
F. Distilling 300
G. Fruit Juice and Wine 301
H. Lipid Modification 301
VIII. Conclusions 302
References 304
Biotransformations, Lignocellulose Conversion and Recovery of Metals from Solution 306
14: Fungal Biotransformations in Pharmaceutical Sciences 307
I. Introduction 307
II. Types and Properties of Biotransformations 308
III. Biotransformation of Pharmaceutically Relevant Small Molecules 310
A. Alkaloids 310
B. Sterols, Taxanes and Other Terpenes 313
C. Small Peptides 320
D. Polyketides 321
IV. Biotransformation of Drugs and Various Synthetic Small Molecules 324
A. Biotransformations for Preparative Purposes 324
B. Fungi as Models for Mammalian Xenobiotic Metabolism 325
V. Conclusions 328
References 328
15: Fungal Biodegradation of Lignocelluloses 332
I. Introduction 332
II. Fungal Degradation of Lignocellulose 333
A. White-Rot Fungi 333
B. Brown-Rot Fungi 334
C. Soft-Rot Fungi 334
III. Fungal Degradation of Wood Polysaccharides 335
IV. Fungal Degradation of Lignin 337
A. White-Rot and Brown-Rot Fungi 337
1. Ligninolytic Peroxidases of White-Rot Fungi 338
2. Peroxidases of Brown-Rot Fungi? 339
3. Laccases 339
4. Role of Small Oxidants in Incipient Decay 341
5. Hydroquinones 342
6. Cellobiose Dehydrogenases 342
7. Redox-Active Glycopeptides 343
B. Soft-Rot Fungi 343
V. Biopulping as an Example of Potential Applications of White-Rot Fungi 344
VI. Overview of Fungal Lignin Degradation and Outlook 346
References 348
16: (Hemi-)Cellulose Degrading Enzymes and Their Encoding Genes from Aspergillus and Trichoderma 354
I. Introduction 354
A. Plant Cell Wall Composition 354
B. Aspergillus and Trichoderma 355
C. CAZy Database 355
II. Galacto- (Gluco)mannan Degrading and Modifying Enzymes 355
A. Endomannanases and beta-Mannosidases 355
B. Accessory Enzymes 356
C. Presence of Mannan-Related Genes in Genomes of Aspergillus 356
III. Xylan Degrading and Modifying Enzymes 356
A. Endoxylanases and beta-Xylosidases 356
B. Accessory Enzymes 357
C. Presence of Xylan-Related Genes in Genomes of Aspergillus 358
IV. Cellulose and Xyloglucan Degrading and Modifying Enzymes 358
A. Description of Cellulose and Xyloglucan Active Enzymes 358
B. Presence of Cellulose and Xyloglucan-Related Genes in Genomes of Aspergillus 358
V. Regulation of (Hemi-)Cellulolytic Gene Expression 359
VI. Applications of (Hemi-)Celluloses 361
VII. Conclusions and Prospects 362
References 363
17: Fungi and Their Enzymes for Pitch Control in the Pulp and Paper Industry 369
I. Introduction 369
II. Pitch Problems in Pulp and Paper Manufacturing 369
A. Resin in Plant Raw Materials 370
B. Resin in Pulp and Paper 371
III. From ``Natural´´ to ``Controlled´´ Seasoning of Wood 372
A. Sapstain Fungi 373
B. White-Rot Fungi 374
IV. Pitch Biocontrol with Fungal Enzymes 375
A. Hydrolytic Enzymes 375
B. Oxidative Enzymes 378
V. Summary and Conclusions 384
References 385
18: Biosorption of Metals 390
I. Introduction 390
A. Metal Resistance 391
B. Practical Reasons for Using Biosorption 391
II. Structures Involved in Heavy Metal Binding 391
A. Cell Wall 391
B. Chemical Nature of the Binding Groups at the Cell Wall 392
C. Uptake of Metals into the Cell 393
D. Dependence on Metabolic Energy 393
III. Technology of Biosorption 393
A. Retention of Biomass and Mixing with the Solution 393
B. Pretreatment of the Biomass to Improve Biosorption 394
IV. Binding of Heavy Metals by Mycorrhizal Fungi 394
V. Examples of Heavy Metal Removal by Fungal Biomass 394
A. Overview of Fungal Species in Biosorption Experiments 394
B. Levels of Accumulation Obtained for Selected Metals and Fungi 396
C. Use of Biosorption for Analytical Purposes 396
VI. Conclusions 396
References 397
Recent Developments and New Strategies 404
19: Bioherbicides 405
I. Introduction 405
II. The Paradigm 406
A. Classical Approach 406
B. Bioherbicide Approach 406
C. Genetic Enhancement 408
III. Virulence Enhancement 408
A. Direct Application of Amino Acids as Herbicides 409
B. Amino Acid Excretion 409
C. Molecular Virulence Enhancement 409
IV. Biological Control of Striga and Orobanche 410
V. Alternative Approaches for Enhancement of Virulence and for Improved Control of Parasitic Plants 411
A. Fusarium as a Model System 411
B. Seed Germination 411
C. Innovations in Delivery Systems of Biocontrol Agents 412
D. Striga and Orobanche Resistant Crop Plants 412
VI. Summary and Outlook 412
References 413
20: Genomic Approaches for Identification of the Biopolymer Degrading Enzyme Network of Aspergillus niger 416
I. Introduction 416
A. Fungal Genomes 416
B. Aspergillus niger 417
II. Biopolymer Degradation by Aspergillus niger 417
A. Starch and Glycogen 417
1. General Remarks 417
2. Genomics of Enzymes Acting on Starch 418
B. Pectin 421
1. General Remarks 421
2. Genomics of Enzymes Acting on Pectin 421
3. Strain Differences 423
4. Expression and Regulation of Pectinases 423
C. Inulin and Sucrose 424
1. General Remarks 424
2. Genomics of Enzymes Acting on Inulin and Sucrose 424
III. Post-Genomic Approaches to Identify Transcriptional Regulators Involved in Carbon Source-Dependent Expression of Extracellular Hydrolases 425
A. Carbohydrate-Related Transcription Factors 425
B. Genome Mining for Transcription Factors 426
C. Transcriptional Regulation of Transcription Factors on Their Substrate 426
D. Clustering of Transcription Factors in the Genome with Target Genes 426
E. Phylogenetic Analysis of Zn(II) Transcription Factors 427
F. Novel Directions for Transcription Regulator Research 429
IV. Outlook 429
References 430
21: New Trends in Fungal Biooxidation 434
I. Introduction 434
II. Peroxidases 435
A. Peroxygenases 435
1. Chloroperoxidase 435
2. Mushroom Peroxygenases 437
3. Artificial Peroxygenases (Peroxygenase Mimics) 443
B. Dye-Decolorizing Peroxidases 445
III. Oxidases 446
A. Laccase 447
1. General Aspects 447
2. Biofuel Cells Using Laccase 447
3. Laccase in Organic Synthesis and Polymer Chemistry 448
B. Tyrosinase 450
IV. Conclusions and Outlook 452
References 453
22: Fungal Soil Bioremediation: Developments Towards Large-Scale Applications 459
I. Introduction 459
II. Groups of Fungi Used in Bioremediation 460
III. Soil Contaminants Degraded by Fungi 461
A. Polycyclic Aromatic Hydrocarbons 461
B. Halo- and Nitroaromatic Compounds 461
C. Agrochemicals 462
D. Endocrine Disrupters 462
E. Pharmaceuticals, Personal Care Products and Dyes 462
F. Other Contaminants 462
IV. Methods 463
A. Screening 465
B. Inoculation 466
C. Small-Scale Trials 468
D. Large-Scale Trials 469
V. Conclusions 471
References 471
Biosystematic Index 476
Subject Index 484