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Biotechnology and Biology of Trichoderma - 1st Edition - ISBN: 9780444595768, 9780444595942

Biotechnology and Biology of Trichoderma

1st Edition

Editors: Vijai Gupta Monika Schmoll Alfredo Herrera-Estrella R. Upadhyay Irina Druzhinina Maria Tuohy
Hardcover ISBN: 9780444595768
eBook ISBN: 9780444595942
Imprint: Elsevier
Published Date: 17th February 2014
Page Count: 650
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Biotechnology and Biology of Trichoderma serves as a comprehensive reference on the chemistry and biochemistry of one of the most important microbial agents, Trichoderma, and its use in an increased number of industrial bioprocesses for the synthesis of many biochemicals such as pharmaceuticals and biofuels. This book provides individuals working in the field of Trichoderma, especially biochemical engineers, biochemists and biotechnologists, important information on how these valuable fungi can contribute to the production of a wide range of products of commercial and ecological interest.

Key Features

  • Provides a detailed and comprehensive coverage of the chemistry, biochemistry and biotechnology of Trichoderma, fungi present in soil and plants
  • Includes most important current and potential applications of Trichoderma in bioengineering, bioprocess technology including bioenergy & biofuels, biopharmaceuticals, secondary metabolites and protein engineering
  • Includes the most recent research advancements made on Trichoderma applications in plant biotechnology and ecology and environment


Microbiologists; biotechnologists; professionals, researchers, undergraduates, or post-graduates in bio-chemical engineering and biochemistry/biology; evolution and genetics researchers

Table of Contents



List of Contributors

Seation A Biology and Biodiversity

Chapter 1. Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats


Methodology of Studying Trichoderma Biodiversity

Trichoderma Diversity in Different Habitats


Chapter 2. Ecophysiology of Trichoderma in Genomic Perspective

Trichoderma in Its Ecological Niche

From Diversity to Genomics

Mycotrophy of Trichoderma

Saprotrophy of Trichoderma on Dead Wood

Trichoderma Growth in Soil

Rhizosphere Competence of Trichoderma

Trichoderma versus Mycorrhizae


Facultative Endophytism of Trichoderma

Animal Nourishment of Trichoderma

Most of the Famous Trichoderma Species are Environmental Opportunists

Versatile Carbon Utilization Patterns Reflect Ecological Specialization of Trichoderma spp.

Chapter 3. DNA Barcode for Species Identification in Trichoderma


The Tools

Application of DNA Barcoding in Species-Level Identification of Trichoderma

Taxonomic Studies

Biodiversity Studies

Identification of Industrial Trichoderma Strains

Identification of Biocontrol Trichoderma Strains

Identification of Trichoderma Isolates with Clinical Relevance

Identification of Mushroom Pathogenic Trichoderma Strains


Chapter 4. Understanding the Diversity and Versatility of Trichoderma by Next-Generation Sequencing


Access to Fungal and Trichoderma Diversity—Taxonomic Profiling

Plants Life under Control of Trichoderma—Functional Profiling


Chapter 5. Molecular Evolution of Trichoderma Chitinases


Phylogeny and Evolution of the GH Family 18 Gene Family in Trichoderma

Subgroup A Chitinases

Subgroup B Chitinases

Subgroup C Chitinases


Section B Secretion and Protein Production

Chapter 6. Protein Production—Quality Control and Secretion Stress Responses in Trichoderma reesei

Introduction—Milestones of Trichoderma reesei

Protein Secretome of T. reesei

ER Quality Control and Secretion Stress Responses


Chapter 7. Heterologous Expression of Proteins in Trichoderma


Promoter Options

Fusion Partners

Extracellular Proteases

Secretion Stress in the Frame

Mass Production of Heterologous Protein by Fermentation

N-glycosylation of Heterologous Proteins Produced in T. reesei


Chapter 8. Trichoderma Secretome: An Overview


Proteomic Analysis of Secretory Proteins

Extraction of Extracellular Proteins for Proteomic Analysis

Extracellular Protein Secretion by T. reesei

Polysaccharide Degradation Machinery of T. reesei

New Candidates in Cellulose Degradation

Hemicellulose Hydrolyzing Enzymes

Lignin Degradation by T. reesei

Industrial Applications of T. reesei Cellulolytic Enzymes


Chapter 9. The Secretory Pathway in the Filamentous Fungus Trichoderma



Cotranslational Translocation

Post Translational Translocation

Protein Modifications in the ER

Vesicle Transport from ER to Golgi Complex and Trafficking within the Golgi Cisternae

Transport after Trafficking within the Golgi Complex

Secreted Proteins in Trichoderma

Concluding Remarks

Section C Secondary Metabolism

Chapter 10. Secondary Metabolism and Antimicrobial Metabolites of Trichoderma



Diketopiperazine-Like Compounds




Concluding Remarks and Future Directions

Chapter 11. Recent Advancements on the Role and Analysis of Volatile Compounds (VOCs) from Trichoderma


Detection Techniques of VOCs

Types of Volatiles Compounds

Application of VOCs in Agriculture


Section D Tools

Chapter 12. Molecular Tools for Strain Improvement of Trichoderma spp.


Genetic Transformation Techniques

Auxotrophic and Dominant Selection Markers

Marker Recycling Strategies and Marker Free Strains

Advanced Methods for Gene Targeting

RNA Mediated Gene Silencing

Promoters for Recombinant Protein Expression and Targeting

Concluding Remarks

Chapter 13. Genetic Transformation and Engineering of Trichoderma reesei for Enhanced Enzyme Production


Engineering Cellulase and Hemicellulase Regulation

Homologous and Heterologous Gene Expression and Gene Disruption

Protein Engineering

Engineering Promoters


Chapter 14. Applications of RNA Interference for Enhanced Cellulase Production in Trichoderma


RNA Interference in Fungus

Transcriptional Regulation of Cellulase Gene Expression

Application of Gene Downregulation Strategy for Enhanced Cellulase Production

Combination of RNAi and Overexpression of the Regulating Genes

Conclusions and Prospects

Chapter 15. RNAi-Mediated Gene Silencing in Trichoderma: Principles and Applications


Molecular Mechanisms

Advantages and Disadvantages of Using RNAi-Mediated Gene Silencing as a Genetic Manipulation Tool in Filamentous Fungi

Strategies of Applying RNAi for Gene Silencing in Trichoderma and Other Filamentous Fungi


Section E Cellulases

Chapter 16. Cellulase Systems in Trichoderma: An Overview


Degradation of Cellulose by Cellulase Systems

History of the Trichoderma Cellulase Research

Structural and Functional Diversity of Trichoderma Cellulases

Cellulase Systems and Complexes

Chapter 17. Use of Cellulases from Trichoderma reesei in the Twenty-First Century—Part I: Current Industrial Uses and Future Applications in the Production of Second Ethanol Generation

Overview of the Global Enzyme Market

Industrial Cellulases

Current Applications


Application of Trichoderma Cellulases in the Bioethanol Industry

Chapter 18. Use of Cellulases from Trichoderma reesei in the Twenty-First Century—Part II: Optimization of Cellulolytic Cocktails for Saccharification of Lignocellulosic Feedstocks

Genetics of Industrial Trichoderma reesei Strains

The T. reesei Enzyme Cocktail

Hydrolysis of Cellulose

Limitations in Lignocellulose Hydrolysis

Improvement of Enzyme Cocktails by Optimization of Enzyme Ratios

Improvement by Supplementation of T. reesei Enzyme Cocktails

Adapting Cellulose Cocktails to Process Conditions

Conclusions and Perspectives

Chapter 19. Beta-Glucosidase from Trichoderma to Improve the Activity of Cellulase Cocktails


Cellulase Classification

Trichoderma reesei Cellulases

Trichoderma reesei BGLs

BGLs from Aspergillus oryzae

Synergism between Cellulases

Heterologous Expression of Cellulases

Yarrowia lipolytica Expression Platforms

Pichia pastoris Expression Platforms

β-Glucosidase from Trichoderma to Improve the Activity of Cellulase Cocktails

Chapter 20. Regulation of Glycoside Hydrolase Expression in Trichoderma


Regulation by Environmental Parameters

Regulatory Mechanisms

Physiological Responses

Chapter 21. Trichoderma Proteins with Disruption Activity on Cellulosic Substrates

Structure and Occurrence of Cellulose in Nature

General Aspects of Cellulose Degradation

Cellulose Degradation by T. reesei

Cellulolytic Enzymes in Other Trichoderma Species

Chapter 22. Molecular Mechanism of Cellulase Production Systems in Trichoderma


Cellulase System of T. reesei

Induction Mechanism of Cellulase Production

Promoter Involved in Cellulase Production

Molecular Mechanism of Cellulase Production

Approaches for Refining the Cellulases Production System in T. reesei

Chapter 23. Trichoderma in Bioenergy Research: An Overview


Fungal Enzyme Systems and Trichoderma Technology

Industrial Applications of Trichoderma

Trichoderma Enzyme Systems in Bioenergy Research


Section F Industrial Applications

Chapter 24. Trichoderma Enzymes for Food Industries


Fungus of Industrial Interest

Trichoderma Enzymes for Industries



Other Enzymes

Food Industry

Perspectives for Biotechnological Production of Enzymes by Trichoderma

Chapter 25. Trichoderma: A Dual Function Fungi and Their Use in the Wine and Beer Industries


Application in the Wine and Beer Industries

Chapter 26. Trichoderma Enzymes for Textile Industries



Textile Processes

Trichoderma Enzymes in Textile Finishing Processes

Trichoderma as a Production Host for Textile Enzymes

Future Trends

Chapter 27. Metabolic Diversity of Trichoderma


Global Metabolism

Carbohydrate Metabolism and Glycoside Hydrolases

Energy Metabolism

Secondary Metabolism

Metabolism and Transporters

Chapter 28. Sequence Analysis of Industrially Important Genes from Trichoderma


Gene Sequence Analysis Fundamentals

Genome Analysis of Trichoderma

Industrially Genes from Trichoderma

Sequence Analysis of Industrially Genes from Trichoderma


Chapter 29. Biosynthesis of Silver Nano-Particles by Trichoderma and Its Medical Applications


SNP Biosynthesis


Medical Application

Chapter 30. Role of Trichoderma Species in Bioremediation Process: Biosorption Studies on Hexavalent Chromium


Hexavalent Chromium Bioremediation will be Discussed Here with a Case Study Representing Chromium Biosorption by Trichoderma Species


Section G Biocontrol and Plant Growth Promotion

Chapter 31. Applications of Trichoderma in Plant Growth Promotion


Trichoderma as a Plant Growth Promoter

Consistency of Growth Promotion


Mechanisms of Growth Promotion


Chapter 32. Molecular Mechanisms of Biocontrol in Trichoderma spp. and Their Applications in Agriculture



Morphological Changes

Roll of Cell Wall Degrading Enzymes

Signal Transduction in Mycoparasitism

ROS-Nox-Signal Transduction

Antibiosis (Secondary Metabolites Involved in Biocontrol)



Nonribosomal Peptides

Mycotoxins Produced by Trichoderma spp.

Synergism between Enzymes and Antibiotics

Competition for Nutrients

Plant Growth Promotion by Trichoderma

Plant Root Colonization

Induction of Systemic Resistance to Plants by Trichoderma spp.

Signal Transduction Pathways that Mediate Trichoderma-Plant Communication

Trichoderma Elicitor of Systemic Resistance in Plants

Signal Transduction during Plant–Trichoderma Interaction in Trichoderma

Transgenic Plants Expressing Trichoderma Genes

Concluding Remarks

Chapter 33. Genome-Wide Approaches toward Understanding Mycotrophic Trichoderma Species


Lessons from the Genome Sequence

Transcriptome Analyses

The Functional Genomics View of Mycoparasitism

High-Throughput Analysis of the Trichoderma-Plant Interaction

Future Directions

Concluding Remarks

Chapter 34. Insights into Signaling Pathways of Antagonistic Trichoderma Species


G Protein Signaling

Effector Pathways of G Protein Signaling in Fungi

Signaling Pathways and Characterized Components in Trichoderma Species

Signal Transduction Components and Pathways Affecting Vegetative Growth and Conidiation

The Role of Signaling in Trichoderma Mycoparasitism and Biocontrol


Chapter 35. Enhanced Resistance of Plants to Disease Using Trichoderma spp.


Induced Disease Resistance in Plants

Induced Resistance by Trichoderma spp.

Signaling Pathways of Trichoderma-Induced Resistance

Trichoderma spp.-Secreted Elicitors of Plant Resistance

Engineering Plants for Disease Resistance Using Trichoderma Genes

Combination of Trichoderma with Other Beneficial Microorganisms

Other Effects of Trichoderma spp. Inoculation to the Plant


Chapter 36. Enhanced Plant Immunity Using Trichoderma


Mechanisms of Plant Protection by Microbes

Trichoderma-Induced Immunity

Plant Protection Conferred by Trichoderma


Chapter 37. Genes from Trichoderma as a Source for Improving Plant Resistance to Fungal Pathogen


Trichoderma Inducing Resistance in Plants

Transgenic Plants Expressing Trichoderma Genes Develop Increased Resistance to Fungal Pathogens

Trichoderma Genes Involved in Elicitation of ISR



Chapter 38. Trichoderma Species as Abiotic Stress Relievers in Plants


Microbes for the Management of Abiotic Stresses

Alleviation of Abiotic Stress in Plants by Trichoderma

Alleviation of Drought Stress in Plants by Trichoderma

Alleviation of Salinity Stress in Plants by Trichoderma

Alleviation of Heat Stress in Plants by Trichoderma

Trichoderma Genes for Abiotic Stress Tolerance

Mechanism of Abiotic Stress Tolerance Using Trichoderma

Host Gene: Stress Tolerant Varieties


Chapter 39. Advances in Formulation of Trichoderma for Biocontrol


Types of Formulation


Enhancement of Shelf Life and Application Efficiency

Compatibility with Other Biological Systems

Conclusion and Future Prospects

Chapter 40. Trichoderma: A Silent Worker of Plant Rhizosphere


Diverseness Amongst Trichoderma

Trichoderma as Inducer of Plant Defense Response

Trichoderma as a Biofertilizer and Plant Growth Promoter


Trichoderma Genes Responsible for Playing “Big Games”




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© Elsevier 2014
17th February 2014
Hardcover ISBN:
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About the Editors

Vijai Gupta

Vijai Gupta

Dr Vijai G. Gupta is an Assistant Professor of Biotechnology at MITS University of India. Currently he is working as Research Scientist at National University of Ireland in Galway. Dr. Gupta’s present work is focused on the development and optimization of novel Enzyme-based bioconversion systems for biorefining and bioenergy. He has been honored with several awards, including the prestigious Indian ICAR Senior Research Fellowship and Indian Young Scientist Award. He has submitted 33 new fungal nucleotide sequences and deposited 147 fungal strains in International databases. His work with Fusarium spp., Colletotrichum gloeosporioides, Penicillium spp. and Trichoderma spp. is augmented by contributions to biotechnological development, molecular diversity, secondary metabolites and industrial applications Dr. Gupta is the editor-in-chief of the International Journal of Plant Pathology and a regional editorial board member of 8 other respected journals. He is the author of 40 journal articles and 27 book chapters. Gupta has also written and edited books and series from reputed publishers, including CRC Press, Taylor and Francis, USA; Springer, USA; Elsevier, USA; Nova Science Publisher, USA and LAP Lambert Academic Publishing, Germany.

Affiliations and Expertise

Department of Chemistry and Biotechnology, Tallinn University of Technology, Estonia

Monika Schmoll

Dr. Monika Schmoll received her degree (1999) and Ph. D. (2003) on regulation of cellulase expression and signal transduction in the filamentous fungus Hypocrea jecorina (Trichoderma reesei) at the Vienna University of Technology. Besides gaining postdoctoral experience and building her own group at the Vienna University of Technology, she has been a visiting scientist in the laboratory of Professor N. Louise Glass (Department of Plant and Microbial Biology, University of California, Berkeley, USA), the University of Rome La Sapienza and the University of Szeged, Hungary. She is author of 33 publications and 2 book chapters. Currently, Dr. Schmoll is group leader in the Research Area Molecular Biotechnology at the Vienna University of Technology. The primary research field of Dr. Schmoll is the interconnection between light response, sexual development and cellulase gene expression in Trichoderma reesei. She showed for the first time that cellulase gene expression is modulated by light in T. reesei and could since then elucidate important mechanistic details on the underlying mechanism. Her group discovered the sexual cycle in the biotechnological workhorse Trichoderma, which had previously considered asexual. This work was published in PNAS in 2009 and since then investigation of this phenomenon and its peculiarities in Trichoderma has become an additional focus. Her work with Trichoderma is complemented by contributions to genome annotation of several fungi (Trichoderma spp., Aspergillus nidulans, Postia placenta, Ceriporiopsis subvermispora), especially in the field of signal transduction.

Affiliations and Expertise

Vienna University of Technology, Austria

Alfredo Herrera-Estrella

Prof. Alfredo Herrera-Estrella grew up in Mexico City and graduated from the National School of Biological Sciences in 1985. He did his graduate research (1986-1990) with Prof. Marc Van Montagu at the State University of Ghent, Belgium, studying the T-DNA transfer process from Agrobacterium tumefaciens to plants. He described for the first time Agrobacterium virulence proteins capable of carrying the T-DNA into the plant cell nucleus, and began to study the mycoparasitic process of the biocontrol agent Trichoderma atroviride. Dr. Herrera-Estrella pioneered the development of molecular tools for the study of a biocontrol agent with the establishment of transformation systems, and cloning of the first mycoparasitism related genes. Such developments opened possibilities for strain improvement. He continued those studies while at the Genetic Engineering Department of the Irapuato Unit of Cinvestav (1991-2004), and began studies towards the elucidation of the mechanisms involved in light perception in Trichoderma. In 2000, he was awarded the prize of the Mexican Academy of Sciences. By 2004, he got involved in the establishment of the National Laboratory of Genomics for Biodiversity. Since then he and his group have been involved in Functional Genomics Projects, including the elucidation of the complete maize genome, and the development of advanced techniques to study gene expression by deep sequencing. Dr. Herrera-Estrella has continuing efforts in the elucidation of signaling cascades triggering asexual development in fungi. In particular his group has been using functional genomics approaches for this purpose, and recently has been involved in the study of the role of reactive oxygen species as signal molecules in injury responses in fungi.

Affiliations and Expertise

National Laboratory of Genomics for Biodiversity, Mexico

R. Upadhyay

Professor R. S. Upadhyay (b. November 15, 1955) received his M. Sc. (1976) and Ph. D. (1980) degrees from Banaras Hindu University (BHU), Varanasi, India. Since then he has been actively engaged in research. His main focus on research has been on biological control of plant pathogens, programmed plant cell death in response to pathogens, bioremediation of toxic effluents, induced resistance in plants and their immunization, plant growth promoting microbes, chitinase production from actinomycetes, mycorrhizal technology for reclamation of wastelands, role rhizobacteria in detoxifying phytotoxic effects, development of molecular markers in tracking microbes in environment, effect of biotic and abiotic factors on plants, and molecular basis of plant-microbe interaction specially for Trichoderma spp. & Fusarium spp. His work has been well cited internationally. He has been working at Banaras Hindu University in various positions such as Lecturer, (1984-88), Senior Lecturer, (1988-1991), UGC Research Scientist-B, BHU (1988-1991 on lien from BHU), Reader, Banaras Hindu University (1991-1999, appointed in absentia), Professor, (1999 till date), Student Advisor, Faculty of Science, BHU (2010-11), Coordinator, Environmental Science, BHU (2011 till date) and Dy. Coordinator, Centre of Advanced Study in Botany, BHU (2011, for five years). He has been recipient of six prestigious national fellowships of the Government of India. He is recipient of five national awards in the area of science, two conferred by the Prime Minister of India. In addition he worked in prestigious foreign laboratories as visiting Scientist of The Royal Society, London (1988-89), Research Associate of NIH, U.S.A. (1990-91), and INSA- JSPS Fellowship, Japan (1994-95). He has also visited many other courtiers to participate in International conferences or for delivering invited lectures.

Affiliations and Expertise

Banaras Hindu University, India

Irina Druzhinina

Dr. Irina Druzhinina studied biology at the Lomonosov’s State University in Moscow, Russia, and at the University of Vienna, where she graduated (PhD) in 2001. Thereafter she became a University Assistant in the research area of C.P. Kubicek at Vienna University of Technology, and habilitated in 2011 in “Microbiology”. She is now leader of the working group “Microbiology” at the same institute.

The scientific work of Irina Druzhinina started with a focus on mycology and molecular evolution, working on species diversity and population differentiation in Trichoderma, where she established an online tool for species identification based on DNA barcodes that is today one of the main resources for this purpose for researchers worldwide. In addition, she worked on such diverse topics as phenotype profiling of industrial fungi, peptaibol biosynthesis in Trichoderma, biodiesel production by marine algae, Trichoderma endophytes, biofungicide development and molecular ecology of Trichoderma. In the last years, her interest expanded to ecological genomics, i.e. the use of genome wide information to study the evolutionary adaptation of Trichoderma in its habitats. She acts as a member of the editorial board for Applied and Environmental Microbiology, and is the chair of the International Subcommission on Taxonomy of Trichoderma and Hypocrea, a member of ICTF/IUMS. She published > 60 papers in peer reviewed international journals and edited a book

Affiliations and Expertise

Plants Nutrition Department, College of Resources and Environmental Sciences, Nanjing Agricultural University

Maria Tuohy

Dr. Maria G. Tuohy is the Head of the Molecular Glycobiotechnology Research Group, Department of Biochemistry, School of Natural Sciences, NUI Galway which has developed a strong track record in Glycobiotechnology and Enzyme Biotechnology. She has more than 20 years experience in the molecular biochemistry, genetics and biotechnology of fungi, with a special interest in thermophilic ascomycetes and the characterization of these fungi as cell factories for protein production, including novel thermostable enzymes/enzyme systems. Dr. Tuohy and her group have developed patented enzyme-based technologies for key bioenergy and biorefinery applications from terrestrial and marine biomass and wastes, including 3rd generation feedstocks. The group also investigates the use of enzymes for the recovery and selective modification of high-value biochemicals and plant carbohydrate-derived bioactives (‘Glycobioengineering’). Dr. Tuohy is a PI in the Energy Research Centre, NUI, Galway and the recently funded national Bioenergy and Biorefinery Competence Centre, is a member of the EU FP7 Biofuels Platform and a national research PhytoNetwork. Dr. Tuohy has been a visiting researcher in RUGhent, Belgium and BSH Institut fur Holzchemie, Hamburg. Dr. Tuohy is author of ~132 research publications, including refereed publications, book chapters, conference papers poster/short communications. She is also a reviewer for international journals and funding agencies and several books as co-editor- Springer Science Publisher, USA; CRC Press, Taylor and Francis, USA; Germany; Nova Science Publisher, USA and Elsevier Press, USA (under Progress) with Dr. V. K. Gupta

Affiliations and Expertise

Head of the Molecular Glycobiotechnology Research Group, Department of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland

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