Ecological Interplays in Microbial Enzymology

Foreword
Preface
Acknowledgements
Contents
Editors and Contributors
Part I: Microbial Enzymes: Distribution in the Environment
Ecological Interplays in Microbial Enzymology: An Introduction
1 Environmental Occurrence of Microbial Enzymes
1.1 Microbes
1.2 Enzymes
2 Classification of Enzymes
3 Occurrence and the Role of Oxidoreductases and Amylases in the Environment
3.1 Oxidoreductases
3.2 Amylases
3.3 α-Amylases Occur Either as α-Amylase or β-Amylase
3.4 β-Amylases
4 The Role of Microbial Enzymes in Environmental Sustainability
4.1 Application of Enzymes
4.2 Bioremediation
4.3 Application of Enzymes in Medicine
4.4 Application of Enzymes in Environmental Monitoring
4.5 Application of Enzymes in Wastewater Treatment
4.6 Removal of Solid Wastes Using Enzymes
5 Impact of Environmental Pollution on Microbial Enzymes
5.1 Effects of Petroleum Hydrocarbons
5.2 Effects of PAHs
5.3 Effects of Solvents
5.4 Effects of Pesticides
5.5 Effects of Heavy Metals
6 The Purpose of this Book
7 Conclusions
References
Diversity of Microbial Enzymes in a Soil Ecosystem
1 Introduction
2 Microbial Enzymes
2.1 Microbial Oxidoreductases
Oxidases
Laccases
Peroxidases
Oxygenases
2.2 Microbial Hydrolases
2.3 Microbial Isomerases
2.4 Microbial Lyases
3 Microbes and Microbial Enzymes in a Soil Ecosystem
3.1 Decomposition of Organic Matter
Microbial Decomposition of Cellulose
Microbial Decomposition of Hemicellulose
Microbial Decomposition of Lignin
Microbial Decomposition of Lipids
Microbial Decomposition of Proteins
3.2 Nutrient Cycling
Microbial Cycling of Phosphorus
Microbial Cycling of Nitrogen
4 Factors That Enhance the Production of Microbial Enzymes in a Soil Ecosystem
4.1 pH of the Soil
4.2 Temperature of the Soil
4.3 Organic Matter Concentration of a Soil Ecosystem
4.4 Moisture Content of the Soil
4.5 The Presence of Inhibitors
4.6 Soil Inorganic Matter
4.7 Cropping System
References
Microbial Enzymes of Wastewater and Sludge
1 Introduction
2 Microbial Enzymes
3 Microbial Enzyme Activities and Distribution in Activated Sludge
3.1 Microbial Abundance and Enzyme Activities
3.2 Distribution of Enzymes in Extracellular Polymeric Substances: Ectoenzymes and Exoenzymes
3.3 Factors Affecting Enzyme Activities in Wastewater
4 Modeling of Biological Wastewater Treatment Processes
5 Immobilization and Extraction of Microbial Enzymes
5.1 Immobilization of Enzymes
5.2 Extraction of Microbial Enzymes from Wastewater and Sludge
5.3 Methods of Enzyme Extraction
5.4 Applications of Extracted Enzymes in Different Wastewaters
5.5 Industrial Applications of Extracted Enzymes
6 Conclusions
References
Occurrence and Distribution of Microbial Enzymes in Freshwater
1 Introduction
2 Sources of Microbial Enzymes in Freshwater
2.1 Types of Enzymes in Freshwater
3 Distribution and Activity of Microbial Enzymes in Freshwater
4 Factors Influencing the Occurrence and Distribution of Microbial Enzymes in Freshwater
4.1 Temperature
4.2 pH
4.3 Enzyme Concentration
4.4 Abiotic Factors
Surface Interactions as Controls on Enzymatic Activity
5 Synthesis and Secretion of Microbial Enzymes in Freshwater
6 Connecting Bacterial Communities and Enzyme Activity
7 Evaluation of Microbial Enzymes in Water and Its Importance
7.1 Enzyme Assays in Freshwater
7.2 Determination of Microbial Enzyme Activity
8 Functions of Microbial Enzymes in Freshwater and Water Quality
9 Conclusions
References
Marine Microbial Enzymes: An Overview
1 Introduction
2 Classification of Enzymes
3 Marine Microbial Enzymes
4 Properties and Applications of Some Marine Microbial Enzymes
4.1 Starch Hydrolyzing Enzymes
4.2 α-Amylases
4.3 α-Glucosidases
4.4 Pullulanases (Debranching Enzymes)
4.5 Agarases
4.6 Cellulases
4.7 Proteases
4.8 Lipases
5 The Role of Marine Microbial Enzymes
6 Medicinal Use of Marine Microbial Enzymes
6.1 Treatment of Damaged Tissues
6.2 Treatment of Infectious Diseases
6.3 Treatment of Cancer
6.4 General Therapeutic Applications of Enzymes
7 Modern Applications of Enzymes: A Biotechnological Perspective
References
Hydrolytic Enzyme-Producing Bacteria from Algerian Hot Springs: Attractive Industrial Molecules
1 Introduction
2 Thermozymes
3 The Genus Bacillus: Generalities
4 Diversity of the Bacillus Species in Algerian Hot Springs
5 Hydrolytic Enzymes Produced by Thermophilic Bacillus sp.
6 Some Applications of Bacillus Thermozymes
7 Conclusions
References
Enzymology of Microbial Biofilms
1 Introduction
2 Biofilm Enzymes
3 Amylases and Glycosyltransferases
4 Cellulases
5 Lipases
6 Nucleases
7 Proteases
8 Industrial Biofilm Enzymes
9 Medical Biofilm Enzymes
10 Conclusions
References
Changes in the Attributes of the Oxisol ``Arenito Caiu´´ After the Use of the Crop-Livestock Integration System
1 Introduction
2 Materials and Methods
2.1 Description of the Location and Experimental Areas
2.2 Soil Sampling and Density
2.3 Chemical Analyses
2.4 Microbiological Analyses
2.5 Statistical Approaches
3 Results and Discussion
3.1 Soil Density and Chemical Properties
3.2 Microbial Biomass and Activity
4 Conclusions
References
Part II: Microbial Enzymes: Role in the Environmental Sustainability
Microbial Enzymes: Role in Soil Fertility
1 Introduction
2 The Role of Microbial Enzymes in Improving Soil Fertility
2.1 Glucosidases
2.2 Cellulases
2.3 Amylases
2.4 Phosphatases
2.5 Dehydrogenases
2.6 Peroxidases
2.7 Chitinases
2.8 Proteases
2.9 Ureases
2.10 Arylsulfatases
3 Mechanisms of Action of Microbial Enzymes in Soil
4 Factors that Influence the Activities of Soil Microbial Enzymes
4.1 Soil Factors
4.2 Climatic Factors
4.3 Contaminants
4.4 Cropping System
4.5 Soil and/or Crop Management Practices
4.6 Ecological Factors
5 Conclusions
References
Microbial Enzymes in the Recycling of Wastes
1 Introduction
2 Wastes
2.1 Classification of Wastes
2.2 Sources of Wastes
Municipal Wastes
Industrial Wastes
Biomedical Wastes
Agricultural Wastes
Electronic Wastes (E-Wastes)
3 Mechanisms of Enzyme Degradation of Wastes
3.1 Oxidoreductases
3.2 Transferases
3.3 Hydrolases
3.4 Lyases
3.5 Isomerases
3.6 Ligases (Synthetases)
4 Microbial Enzymes in Waste Degradation/Recycling
4.1 Microbial Oxidoreductases
Microbial Oxygenases
Microbial Monooxygenases
Microbial Dioxygenases
Microbial Dehalogenases
Microbial Laccases
Microbial Peroxidases
Microbial Versatile Peroxidases
Microbial Manganese Peroxidases
Microbial Lignin Peroxidases
Microbial Dehydrogenases
4.2 Microbial Hydrolytic Enzymes
Microbial Cellulases
Microbial Lipases
Microbial Proteases
Microbial Amylases
4.3 Other Enzymes
5 Significance of Microbial Enzymes in Waste Recycling
6 Limitations of Microbial Enzymes in Waste Recycling
7 Future Prospects
References
Soil Microbial Enzymes and Mitigation of Heavy Metal Uptake by Plants
1 Introduction
1.1 Enzymes with Special Characteristics in Biotechnology
Proteases
Keratinases
Amylases
Xylanases
Laccases/Ligninases
Cellulases
1.2 Miscellaneous Enzymes in Biotechnology
2 Quantification of Microbial Enzymes in Soil
2.1 Enzyme Factors/Enzyme Sensitivity
2.2 Structural Inhibition of Enzymes
2.3 Seasonal Effects of Enzymes
2.4 Soil Factors
Soil pH
Soil Organic Matter
Clay Minerals
3 Heavy Metals
3.1 Sources of Heavy Metals in Soil
4 Effects of Heavy Metals on Plants and Microbial Enzymes
4.1 Metal Accumulator Plants
Plant Community Effect
4.2 Effects of Heavy Metals on Microbial Enzymes
Special Inhibition Parameters
Ecological Dose
Understanding the Inhibition of Soil Enzymes by Heavy Metals
Combined Effects
Combined Effects of Two Metals
Combined Effects of Three Metals
Combined Effects of pH, Organic Matter (OM), Clay, and Four Metals
Combined Effects of pH, OM, Clay, Cation Exchange Capacity (CEC), and Chemical Form of Metal
Combined Effects of Metal, Metal Oxidation State, and Organic Matter
5 Mitigation of Heavy Metal Uptake by Plants
5.1 Degradation by Genetically Engineered Microorganisms
5.2 Microbial Remediation of Heavy Metals
6 Conclusions
References
Communities of Microbial Enzymes and Biodegradation of Persistent Environmental Pollutants
1 Introduction
2 Biodegradation of Persistent Environmental Pollutants
2.1 Principles of Biodegradation
2.2 Limiting Factors of Bioremediation
2.3 Microbial Enzymes in Bioremediation
2.4 Sources of Microbial Enzymes
3 Classes of Microbial Enzymes in Bioremediation
3.1 Microbial Oxidoreductases
Microbial Oxygenases
Microbial Monooxygenases
Microbial Dioxygenases
Microbial Laccases
Properties of Microbial Laccases
Sources of Microbial Laccases
Mechanism of Microbial Laccase Activity
Production of Microbial Laccases
Microbial Peroxidases
Sources of Microbial Peroxidases
Properties of Microbial Peroxidases
Subclasses of Microbial Peroxidases
Microbial Lignin Peroxidases
Microbial Manganese Peroxidases
Microbial Versatile Peroxidases
Applications of Peroxidases in Degradation of Environmental Pollutants
Biodegradation of Synthetic Dyes
Bioremediation of Wastewater
Mechanism of the Horseradish-H2O2-PhOH Reaction
Biodegradation of Polycyclic Aromatic Hydrocarbon (PAH) Pesticides
Biodegradation of Chlorinated Alkanes and Alkenes
Biodegradation of Phenoxyalkanoid Acid and Triazine Herbicides
Biodegradation of Chlorinated Dioxins
Biodegradation of Chlorinated Insecticides
3.2 Microbial Hydrolytic Enzymes
Microbial Lipases
Sources of Microbial Lipases
Filamentous Fungi
Yeasts
Bacteria
Microbial Cellulases
Sources of Microbial Cellulases
Mechanism of Cellulase Activity
Microbial Proteases
Sources of Microbial Proteases
4 Microbial Degradation of Plastics
4.1 Microbial Degradation of Polyurethane
4.2 Microbial Degradation of Polyethylene Terephthalate
5 Conclusions
References
Implication of Enzymes in the Adaptation of Extremophilic Microbes
1 Introduction
2 Enzymes Against Extreme Temperatures
2.1 Enzymes at High Temperatures
2.2 Enzymes at Low Temperatures
3 Enzymes Against High Salt Concentrations
4 Enzymes Against pH Variations
5 Enzymes Against High Pressure
6 Conclusions
References
Applications of Microbial Enzymes in Industries and Medicine
1 Introduction
2 Microbial Production of Enzymes
2.1 Submerged Fermentation
Batch Fermentation
Continuous Fermentation
2.2 Solid-State Fermentation
2.3 Microbial Enzymes, Enzymatic Action, and Types of Producer Microorganisms
Proteases
Xylanases
Laccases
Lipases
Chitinases
Inulinases
Amylases
Tannases
β-Galactosidases
Cellulases
Peroxidases
Pectinases
Catalases
Glucose Isomerases
Invertases
Keratinases
Transglutaminases
3 Microbial Enzyme Applications in Industry
3.1 Food Industry
Fruit Juice Production
Dairy Products
Baking
Beverages
3.2 Textile Industry
3.3 Detergent Industry
3.4 Paper and Pulp Industry
3.5 Leather Industry
3.6 Animal Feed Industry
3.7 Cosmetic Industry
4 Enzymes in Medicine
4.1 Enzymes for the Treatment of Damaged Tissues
4.2 Enzymes for the Treatment of Infectious Diseases
4.3 Enzymes for the Treatment of Cancer
4.4 Treatment of Exocrine Pancreatic Insufficiency
4.5 Treatment of Dupuytren´s Disease
4.6 Treatment of Inflammation and Pain
4.7 Prevention of Blood Clotting
4.8 Genetic Correction of Gaucher Disease
4.9 Enzymes Used as Digestive Aids
5 Conclusions and Future Perspective
References
Microbial Enzymes in the Biosynthesis of Metal Nanoparticles
1 Introduction
2 Microbial Enzyme-Mediated Synthesis of MtNPs
2.1 Bacteria- and Actinomycete-Mediated MtNP Synthesis
2.2 Fungi- and Yeast-Mediated MtNP Synthesis
2.3 Algae-Mediated MtNP Synthesis
3 Mechanisms Involved in the Microbial Enzyme-Mediated Synthesis of MtNPs
3.1 Mechanisms in Gold NP Green Synthesis
3.2 Mechanisms in Silver NP Green Synthesis
Damage to the Cell Wall and Cell Membrane
Damage by Intracellular Penetration
Damage by Oxidative Stress
3.3 Mechanisms in Platinum NP Green Synthesis
4 Applications
5 Large-Scale Production of MtNPS
6 Regulation of NP Morphology
7 Advances in MtNP Microbial Biosynthesis
8 Challenges and Limitations of Biosynthesized MtNPs
9 Conclusions
References
Part III: Impact of Environmental Disturbances on Microbial Enzymes
Effects of Agrochemicals on Soil Microbial Enzymes
1 Introduction to Agrochemicals
2 Types of Agrochemicals
2.1 Pesticides
2.2 Insecticides
2.3 Herbicides
2.4 Fertilizers
2.5 Soil Conditioners
3 Importance of Agrochemicals
4 Environmental Impacts of Agrochemicals
5 Soil Microbial Enzymes
5.1 Soil Faunas
5.2 Soil Enzymes
6 Production of Soil Enzymes
7 Groups of Cellular Enzymes and Their Activities
7.1 Mobile Extracellular Enzymes
7.2 Immobile Extracellular Enzymes
7.3 Competition
7.4 Cells Engulfed by Extracellular Enzymes
8 Significance of Microbial Enzymes in Soil
9 Effects of Herbicides, Fungicides, and Insecticides on Microbial Enzymes
9.1 Effects on Dehydrogenase Activity
9.2 Fluorescein Diacetate Hydrolase
9.3 Cellulase and β-Glucosidase
9.4 Effects on Phosphomonoesterase Enzymes
9.5 Nitrogen Cycle and Enzymatic Activity of Urease
10 Effects of Application of Fertilizers on Enzymatic Activities
11 Relationships Between Pesticide Mechanisms of Action and Enzymatic Responses
11.1 Pesticides
11.2 Fungicides
11.3 Insecticides
11.4 Herbicides
12 Conclusions
References
Effects of Aquatic (Freshwater and Marine) Pollution on Microbial Enzyme Activities
1 Introduction
1.1 Sources of Water Pollution
2 Aquatic Microbial Enzymes
2.1 Protease
2.2 Chitinase and Chitosanase
2.3 Amylases
2.4 Agarase
2.5 Lipase
2.6 Cellulases
3 Importance of Aquatic Microbial Enzymes
3.1 Protease
3.2 Chitinase
3.3 Amylase
3.4 Agarase
3.5 Lipase
3.6 Cellulase
Paper and Pulp Industry
Textile Industry
Bioethanol Industry
Wine and Brewing Industry
Food Processing
Animal Feed
Agriculture
Waste Management
4 Effects of Pollution on Aquatic Microbial Enzymes
5 Types of Remediation
5.1 Engineered/Physical Remediation Techniques
Aeration
Ecological Floating Beds
Addition of Nutrients Activators
Precipitation and Ion Exchange
5.2 Bioremediation Technique
Aquatic Animal Remediation
Phytoremediation Process
Application of Microbial Agents
6 Possible Solutions to the Effect Pollution on Microbial Enzymes Activities
7 Conclusion
References
In Silico Analysis of Biochemical Pathways in Bacterial Enzyme Synthesis
1 Introduction
2 Mathematical Models in Metabolic Engineering
2.1 Kinetic Models
Brief History
The Structure Kinetic Models in Metabolic Engineering
Extracellular Enzymes
Immobilized Enzymes
Limitations of Kinetic Approaches in the Modelling of Enzyme Activity
2.2 Constraint-Based Analysis Methods
Omics Databases for Soil Bacteria
Genomics Databases
Proteomics Databases
Metabolomics Databases
Data Repositories
Experimental Data Repositories
Genome-Scale Model Repositories
Information Management and Curation
Visualization, Analysis and Simulations Systems
Elementary Flux Modes
Carbon 13 Metabolic Flux Analysis
Applications of Constraint-Based Methods
Carbon Use Efficiency and Cycling
Nitrogen Use and Cycling
Remediation and Detoxification of Soils
Identifying Optimum Production Genes and Pathways
Community Analysis
Limitations of Constraint-Based Approaches
2.3 Combined Kinetic and Constraint-Based Modelling Methods
2.4 Methods Based on Graphical Network Analysis
3 Comparative Advantages and Disadvantages of Applied Modelling Approaches
4 Future Trends and Perspectives
5 Concluding Remarks
References
Microbial Enzymes for Sustainable Development: Future Guidelines
1 Introduction
2 Recent Advances in the Environmental Applications of Microbial Enzymes
2.1 Some Microbial Enzymes Used in Bioremediation
Peroxidases
Laccase
Lignin Peroxidase
Manganese Peroxidase
Versatile Peroxidase (VP)
Cytochrome P450
3 Microbial Enzymes for Environmental Sustainability: Challenges and Future Directions
4 Conclusion
References