Front Cover 1
BIOTECHNOLOGY AND BIOLOGY OF 
 
4 
Copyright 
5 
Contents 6
Preface 12
Foreword 14
List of Contributors 16
Section A - BIOLOGY AND BIODIVERSITY 20
Chapter 1 - Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats 22
INTRODUCTION 22
METHODOLOGY OF STUDYING TRICHODERMA BIODIVERSITY 22
TRICHODERMA DIVERSITY IN DIFFERENT HABITATS 24
CONCLUSIONS 37
Acknowledgments 37
References 37
Chapter 2 - Ecophysiology of Trichoderma in Genomic Perspective 44
TRICHODERMA IN ITS ECOLOGICAL NICHE 44
FROM DIVERSITY TO GENOMICS 46
MYCOTROPHY OF TRICHODERMA 47
SAPROTROPHY OF TRICHODERMA ON DEAD WOOD 49
TRICHODERMA GROWTH IN SOIL 50
RHIZOSPHERE COMPETENCE OF TRICHODERMA 51
TRICHODERMA VERSUS MYCORRHIZAE 51
TRICHODERMA+BACTERIA=? 52
FACULTATIVE ENDOPHYTISM OF TRICHODERMA 52
ANIMAL NOURISHMENT OF TRICHODERMA 53
MOST OF THE FAMOUS TRICHODERMA SPECIES ARE ENVIRONMENTAL OPPORTUNISTS 53
VERSATILE CARBON UTILIZATION PATTERNS REFLECT ECOLOGICAL SPECIALIZATION OF TRICHODERMA SPP 54
Acknowledgments 56
References 56
Chapter 3 - DNA Barcode for Species Identification in Trichoderma 60
INTRODUCTION 60
THE TOOLS 61
APPLICATION OF DNA BARCODING IN SPECIES-LEVEL IDENTIFICATION OF TRICHODERMA 62
TAXONOMIC STUDIES 62
BIODIVERSITY STUDIES 64
IDENTIFICATION OF INDUSTRIAL TRICHODERMA STRAINS 66
IDENTIFICATION OF BIOCONTROL TRICHODERMA STRAINS 67
IDENTIFICATION OF TRICHODERMA ISOLATES WITH CLINICAL RELEVANCE 69
IDENTIFICATION OF MUSHROOM PATHOGENIC TRICHODERMA STRAINS 70
CONCLUSIONS 70
Acknowledgments 71
References 71
Chapter 4 - Understanding the Diversity and Versatility of Trichoderma by Next-Generation Sequencing 76
INTRODUCTION 76
ACCESS TO FUNGAL AND TRICHODERMA DIVERSITY—TAXONOMIC PROFILING 77
PLANTS LIFE UNDER CONTROL OF TRICHODERMA—FUNCTIONAL PROFILING 81
CONCLUSION 82
Acknowledgments 82
References 82
Chapter 5 - Molecular Evolution of Trichoderma Chitinases 86
INTRODUCTION 86
PHYLOGENY AND EVOLUTION OF THE GH FAMILY 18 GENE FAMILY IN TRICHODERMA 87
SUBGROUP A CHITINASES 88
SUBGROUP B CHITINASES 90
SUBGROUP C CHITINASES 93
CONCLUSIONS 96
Acknowledgments 96
References 96
Section B - SECRETION AND PROTEIN PRODUCTION 98
Chapter 
100 
INTRODUCTION—MILESTONES OF TRICHODERMA REESEI 100
PROTEIN SECRETOME OF T. REESEI 101
ER QUALITY CONTROL AND SECRETION STRESS RESPONSES 103
CONCLUSION 105
References 105
Chapter 7 - Heterologous Expression of Proteins in Trichoderma 
108 
INTRODUCTION 108
PROMOTER OPTIONS 111
FUSION PARTNERS 112
EXTRACELLULAR PROTEASES 113
SECRETION STRESS IN THE FRAME 114
MASS PRODUCTION OF HETEROLOGOUS PROTEIN BY FERMENTATION 116
N-GLYCOSYLATION OF HETEROLOGOUS PROTEINS PRODUCED IN T. REESEI 116
CONCLUSIONS 117
Acknowledgments 118
References 118
Chapter 
122 
INTRODUCTION 122
PROTEOMIC ANALYSIS OF SECRETORY PROTEINS 124
EXTRACTION OF EXTRACELLULAR PROTEINS FOR PROTEOMIC ANALYSIS 125
EXTRACELLULAR PROTEIN SECRETION BY T. REESEI 126
POLYSACCHARIDE DEGRADATION MACHINERY OF T. REESEI 127
NEW CANDIDATES IN CELLULOSE DEGRADATION 128
HEMICELLULOSE HYDROLYZING ENZYMES 129
LIGNIN DEGRADATION BY T. REESEI 130
INDUSTRIAL APPLICATIONS OF T. REESEI CELLULOLYTIC ENZYMES 130
CONCLUSION 131
References 131
Chapter 
134 
INTRODUCTION 134
TRANSLOCATION 134
COTRANSLATIONAL TRANSLOCATION 135
POST TRANSLATIONAL TRANSLOCATION 135
PROTEIN MODIFICATIONS IN THE ER 135
VESICLE TRANSPORT FROM ER TO GOLGI COMPLEX AND TRAFFICKING WITHIN THE GOLGI CISTERNAE 137
TRANSPORT AFTER TRAFFICKING WITHIN THE GOLGI COMPLEX 138
SECRETED PROTEINS IN TRICHODERMA 138
CONCLUDING REMARKS 139
Acknowledgments 139
References 139
Section C - SECONDARY METABOLISM 
142 
Chapter 10 - 
144 
INTRODUCTION 144
PEPTAIBOLS 145
DIKETOPIPERAZINE-LIKE COMPOUNDS 148
POLYKETIDES 148
PYRONES 149
TERPENES 150
CONCLUDING REMARKS AND FUTURE DIRECTIONS 152
Acknowledgments 153
References 153
Chapter 
158 
INTRODUCTION 158
DETECTION TECHNIQUES OF VOCS 159
TYPES OF VOLATILES COMPOUNDS 161
APPLICATION OF VOCS IN AGRICULTURE 184
CONCLUSION 187
References 187
Section D - TOOLS 
196 
Chapter 12 - 
198 
INTRODUCTION 198
GENETIC TRANSFORMATION TECHNIQUES 199
AUXOTROPHIC AND DOMINANT SELECTION MARKERS 200
MARKER RECYCLING STRATEGIES AND MARKER FREE STRAINS 201
ADVANCED METHODS FOR GENE TARGETING 202
RNA MEDIATED GENE SILENCING 203
PROMOTERS FOR RECOMBINANT PROTEIN EXPRESSION AND TARGETING 204
CONCLUDING REMARKS 207
References 207
Chapter 
212 
INTRODUCTION 212
ENGINEERING CELLULASE AND HEMICELLULASE REGULATION 213
HOMOLOGOUS AND HETEROLOGOUS GENE EXPRESSION AND GENE DISRUPTION 214
PROTEIN ENGINEERING 215
ENGINEERING PROMOTERS 216
CONCLUSION 217
References 217
Chapter 
220 
INTRODUCTION 220
RNA INTERFERENCE IN FUNGUS 221
TRANSCRIPTIONAL REGULATION OF CELLULASE GENE EXPRESSION 222
APPLICATION OF GENE DOWNREGULATION STRATEGY FOR ENHANCED CELLULASE PRODUCTION 223
COMBINATION OF RNAI AND OVEREXPRESSION OF THE REGULATING GENES 227
CONCLUSIONS AND PROSPECTS 230
References 230
Chapter 
234 
INTRODUCTION 234
MOLECULAR MECHANISMS 235
ADVANTAGES AND DISADVANTAGES OF USING RNAI-MEDIATED GENE SILENCING AS A GENETIC MANIPULATION TOOL IN FILAMENTOUS FUNGI 237
STRATEGIES OF APPLYING RNAI FOR GENE SILENCING IN TRICHODERMA AND OTHER FILAMENTOUS FUNGI 239
CONCLUSIONS 242
References 243
Section E - CELLULASES 
246 
Chapter 16 - 
248 
INTRODUCTION 248
DEGRADATION OF CELLULOSE BY CELLULASE SYSTEMS 249
HISTORY OF THE TRICHODERMA CELLULASE RESEARCH 251
STRUCTURAL AND FUNCTIONAL DIVERSITY OF TRICHODERMA CELLULASES 251
CELLULASE SYSTEMS AND COMPLEXES 259
Acknowledgments 260
References 260
Chapter 
264 
OVERVIEW OF THE GLOBAL ENZYME MARKET 264
INDUSTRIAL CELLULASES 265
CURRENT APPLICATIONS 268
PERSPECTIVES 272
APPLICATION OF TRICHODERMA CELLULASES IN THE BIOETHANOL INDUSTRY 272
References 277
Chapter 
282 
GENETICS OF INDUSTRIAL TRICHODERMA REESEI STRAINS 282
THE T. REESEI ENZYME COCKTAIL 283
HYDROLYSIS OF CELLULOSE 285
LIMITATIONS IN LIGNOCELLULOSE HYDROLYSIS 286
IMPROVEMENT OF ENZYME COCKTAILS BY OPTIMIZATION OF ENZYME RATIOS 288
IMPROVEMENT BY SUPPLEMENTATION OF T. REESEI ENZYME COCKTAILS 289
ADAPTING CELLULOSE COCKTAILS TO PROCESS CONDITIONS 294
CONCLUSIONS AND PERSPECTIVES 294
References 294
Chapter 
300 
INTRODUCTION 300
CELLULASE CLASSIFICATION 301
TRICHODERMA REESEI CELLULASES 301
TRICHODERMA REESEI BGLS 303
BGLS FROM ASPERGILLUS ORYZAE 303
SYNERGISM BETWEEN CELLULASES 305
HETEROLOGOUS EXPRESSION OF CELLULASES 305
YARROWIA LIPOLYTICA EXPRESSION PLATFORMS 305
PICHIA PASTORIS EXPRESSION PLATFORMS 306
.-GLUCOSIDASE FROM TRICHODERMA TO IMPROVE THE ACTIVITY OF CELLULASE COCKTAILS 306
Acknowledgments 307
References 307
Chapter 
310 
INTRODUCTION 310
REGULATION BY ENVIRONMENTAL PARAMETERS 311
REGULATORY MECHANISMS 316
PHYSIOLOGICAL RESPONSES 321
References 322
Chapter 
328 
STRUCTURE AND OCCURRENCE OF CELLULOSE IN NATURE 328
GENERAL ASPECTS OF CELLULOSE DEGRADATION 329
CELLULOSE DEGRADATION BY T. REESEI 330
CELLULOLYTIC ENZYMES IN OTHER TRICHODERMA SPECIES 333
Acknowledgments 333
References 333
Chapter 
338 
INTRODUCTION 338
CELLULASE SYSTEM OF T. REESEI 338
INDUCTION MECHANISM OF CELLULASE PRODUCTION 339
PROMOTER INVOLVED IN CELLULASE PRODUCTION 339
MOLECULAR MECHANISM OF CELLULASE PRODUCTION 339
APPROACHES FOR REFINING THE CELLULASES PRODUCTION SYSTEM IN T. REESEI 340
References 341
Chapter 
344 
INTRODUCTION 344
FUNGAL ENZYME SYSTEMS AND TRICHODERMA TECHNOLOGY 345
INDUSTRIAL APPLICATIONS OF TRICHODERMA 346
TRICHODERMA ENZYME SYSTEMS IN BIOENERGY RESEARCH 347
CONCLUSION 351
References 351
Section F - 
356 
Chapter 24 - 
358 
INTRODUCTION 358
FUNGUS OF INDUSTRIAL INTEREST 359
TRICHODERMA ENZYMES FOR INDUSTRIES 359
XYLANASES 360
CELLULASES 360
OTHER ENZYMES 361
FOOD INDUSTRY 361
PERSPECTIVES FOR BIOTECHNOLOGICAL PRODUCTION OF ENZYMES BY TRICHODERMA 362
References 362
Chapter 
364 
INTRODUCTION 364
APPLICATION IN THE WINE AND BEER INDUSTRIES 366
Acknowledgments 367
References 367
Chapter 
370 
SUBSTRATE 370
ENZYMES 371
TEXTILE PROCESSES 372
TRICHODERMA ENZYMES IN TEXTILE FINISHING PROCESSES 374
TRICHODERMA AS A PRODUCTION HOST FOR TEXTILE ENZYMES 376
FUTURE TRENDS 378
Acknowledgments 378
References 378
Chapter 
382 
INTRODUCTION 382
GLOBAL METABOLISM 383
CARBOHYDRATE METABOLISM AND GLYCOSIDE HYDROLASES 385
ENERGY METABOLISM 387
SECONDARY METABOLISM 388
METABOLISM AND TRANSPORTERS 391
Acknowledgments 393
References 393
Chapter 
396 
INTRODUCTION 396
GENE SEQUENCE ANALYSIS FUNDAMENTALS 397
GENOME ANALYSIS OF TRICHODERMA 402
INDUSTRIALLY GENES FROM TRICHODERMA 403
SEQUENCE ANALYSIS OF INDUSTRIALLY GENES FROM TRICHODERMA 403
CONCLUSION 408
References 409
Chapter 
412 
INTRODUCTION 412
SNP BIOSYNTHESIS 414
MECHANISM 416
MEDICAL APPLICATION 418
References 419
Chapter 
424 
INTRODUCTION 424
HEXAVALENT CHROMIUM BIOREMEDIATION WILL BE DISCUSSED HERE WITH A CASE STUDY REPRESENTING CHROMIUM BIOSORPTION BY TRICHODERMA SPE... 426
CONCLUSION 430
References 431
Section G - BIOCONTROL AND PLANT 
 
432 
Chapter 31 - 
434 
INTRODUCTION 434
TRICHODERMA AS A PLANT GROWTH PROMOTER 435
CONSISTENCY OF GROWTH PROMOTION 437
COMMERCIALIZATION 438
MECHANISMS OF GROWTH PROMOTION 439
CONCLUSIONS 444
References 444
Chapter 
448 
INTRODUCTION 448
MYCOPARASITISM 449
MORPHOLOGICAL CHANGES 449
ROLL OF CELL WALL DEGRADING ENZYMES 450
SIGNAL TRANSDUCTION IN MYCOPARASITISM 451
ROS-NOX-SIGNAL TRANSDUCTION 452
ANTIBIOSIS (SECONDARY METABOLITES INVOLVED IN BIOCONTROL) 454
PYRONES 455
POLYKETIDES 456
NONRIBOSOMAL PEPTIDES 456
MYCOTOXINS PRODUCED BY TRICHODERMA SPP 457
SYNERGISM BETWEEN ENZYMES AND ANTIBIOTICS 458
COMPETITION FOR NUTRIENTS 458
PLANT GROWTH PROMOTION BY TRICHODERMA 459
PLANT ROOT COLONIZATION 461
INDUCTION OF SYSTEMIC RESISTANCE TO PLANTS BY TRICHODERMA SPP 462
SIGNAL TRANSDUCTION PATHWAYS THAT MEDIATE TRICHODERMA-PLANT COMMUNICATION 463
TRICHODERMA ELICITOR OF SYSTEMIC RESISTANCE IN PLANTS 465
SIGNAL TRANSDUCTION DURING PLANT–TRICHODERMA INTERACTION IN TRICHODERMA 467
TRANSGENIC PLANTS EXPRESSING TRICHODERMA GENES 467
CONCLUDING REMARKS 468
Acknowledgments 468
References 468
Chapter 
474 
INTRODUCTION 474
LESSONS FROM THE GENOME SEQUENCE 476
TRANSCRIPTOME ANALYSES 477
THE FUNCTIONAL GENOMICS VIEW OF MYCOPARASITISM 477
HIGH-THROUGHPUT ANALYSIS OF THE TRICHODERMA-PLANT INTERACTION 478
FUTURE DIRECTIONS 480
CONCLUDING REMARKS 481
Acknowledgments 481
References 481
Chapter 34 - Insights into Signaling Pathways of Antagonistic Trichoderma Species 
484 
INTRODUCTION 484
G PROTEIN SIGNALING 484
EFFECTOR PATHWAYS OF G PROTEIN SIGNALING IN FUNGI 485
SIGNALING PATHWAYS AND CHARACTERIZED COMPONENTS IN TRICHODERMA SPECIES 486
SIGNAL TRANSDUCTION COMPONENTS AND PATHWAYS AFFECTING VEGETATIVE GROWTH AND CONIDIATION 488
THE ROLE OF SIGNALING IN TRICHODERMA MYCOPARASITISM AND BIOCONTROL 490
CONCLUSIONS 493
Acknowledgments 493
References 493
Chapter 
496 
INTRODUCTION 496
INDUCED DISEASE RESISTANCE IN PLANTS 497
INDUCED RESISTANCE BY TRICHODERMA SPP 500
SIGNALING PATHWAYS OF TRICHODERMA-INDUCED RESISTANCE 501
TRICHODERMA SPP.-SECRETED ELICITORS OF PLANT RESISTANCE 502
ENGINEERING PLANTS FOR DISEASE RESISTANCE USING TRICHODERMA GENES 504
COMBINATION OF TRICHODERMA WITH OTHER BENEFICIAL MICROORGANISMS 505
OTHER EFFECTS OF TRICHODERMA SPP. INOCULATION TO THE PLANT 506
CONCLUSION 506
References 507
Chapter 
514 
INTRODUCTION 514
MECHANISMS OF PLANT PROTECTION BY MICROBES 514
TRICHODERMA-INDUCED IMMUNITY 517
PLANT PROTECTION CONFERRED BY TRICHODERMA 519
CONCLUSIONS 520
Acknowledgments 520
References 520
Chapter 
524 
INTRODUCTION 524
TRICHODERMA INDUCING RESISTANCE IN PLANTS 525
TRANSGENIC PLANTS EXPRESSING TRICHODERMA GENES DEVELOP INCREASED RESISTANCE TO FUNGAL PATHOGENS 525
TRICHODERMA GENES INVOLVED IN ELICITATION OF ISR 527
CONCLUSION 530
ABBREVIATIONS 530
Acknowledgments 530
References 530
Chapter 
534 
INTRODUCTION 534
MICROBES FOR THE MANAGEMENT OF ABIOTIC STRESSES 535
ALLEVIATION OF ABIOTIC STRESS IN PLANTS BY TRICHODERMA 535
ALLEVIATION OF DROUGHT STRESS IN PLANTS BY TRICHODERMA 536
ALLEVIATION OF SALINITY STRESS IN PLANTS BY TRICHODERMA 537
ALLEVIATION OF HEAT STRESS IN PLANTS BY TRICHODERMA 538
TRICHODERMA GENES FOR ABIOTIC STRESS TOLERANCE 539
MECHANISM OF ABIOTIC STRESS TOLERANCE USING TRICHODERMA 539
HOST GENE: STRESS TOLERANT VARIETIES 540
CONCLUSION 541
References 542
Chapter 
546 
INTRODUCTION 546
TYPES OF FORMULATION 547
MICROENCAPSULATION 547
ENHANCEMENT OF SHELF LIFE AND APPLICATION EFFICIENCY 547
COMPATIBILITY WITH OTHER BIOLOGICAL SYSTEMS 548
CONCLUSION AND FUTURE PROSPECTS 549
References 549
Chapter 
552 
INTRODUCTION 552
DIVERSENESS AMONGST TRICHODERMA 553
TRICHODERMA AS INDUCER OF PLANT DEFENSE RESPONSE 555
TRICHODERMA AS A BIOFERTILIZER AND PLANT GROWTH PROMOTER 557
COMMERCIALIZATION 557
TRICHODERMA GENES RESPONSIBLE FOR PLAYING “BIG GAMES” 558
CONCLUSION 559
Acknowledgments 559
References 559
Index 562