1st Edition
Industrial and Environmental Microbiology
I. Scope of Microorganisms and Microbial Research
1. Scope of Microorganisms in Industries
2. Scope of Microorganisms in the Environment
3. Microbial Research and Industrial Biotechnology
3.1. Academic Disciplines
3.2. Research Activities
3.3. Professional Societies
3.4. Microbiome Projects
3.5. Outsourced Facilities
3.6. Resources
3.7. Industrial Biotechnology
II. Fermentation Technology
4. The Basics of Fermentation
4.1. Fermentation: a Multifaceted Term
4.2. Respiration vs. Fermentation
4.3. Historical Background
4.4. Microorganisms for Fermentation
4.5. Fermentation Enzymes
4.6. Biochemistry of Fermentation
4.7. Industrial Fermentation
4.8. Process of Industrial Fermentation
5. Upstream Processing
5.1. Upstream Process: A Preparatory Stage
5.2. Sterilisation
5.3. Isolation and Characterisation of Microorganisms
5.4. Microbial Genetic Manipulation
5.5. Microbial Stock Preservation
5.6. Raw Materials and their Processing
5.7. Optimisation
5.8. Preparation of Industrial Fermentation Media
5.9. Inoculum Development
6. Different Types of Fermentation Processes
6.1. Fermentation Based on the Nature of Substrates
6.2. Operational Mode of Industrial Fermentation
6.3. Fermentation in Different Aerated Conditions
7. Fermenters and their Basic Components
7.1. Fermenters and Their Characteristics
7.2. Fermenter Scale-Up
7.3. Aspect Ratio
7.4. Mechanical Constituents
7.5. Foam Control
7.6. Monitoring Components
7.7. Accessory Components
7.8. Containment Components
8. Different Types of Fermenters
8.1. Fermenter Configurations
8.2. Fermenters for Solid-State Fermentation (SSF)
8.3. Bed Reactors
8.4. Fermenters for Submerged Fermentation (SmF)
8.5. Fermenters for Anaerobic Fermentation
8.6. Special Types of Fermenters
III. Microbial Production of Industrial Products
9. Microorganisms in the Fermentation Industry
9.1. Natural Microorganisms
9.2. Genetically Modified Organisms (GMOs)
9.3. Genetic Modification in Industrial Microbiology
9.4. Strain Improvement Strategies
9.5. Mutagenesis
9.6. Genetic Engineering
9.7. Containments for Safe Biotechnology
9.8. Generally Recognised as Safe (GRAS) Microorganisms
10. Fermentation Conditions
10.1. Microbial Growth Phases
10.2. Stages of Microbial Metabolite Production
10.3. Physical Parameters
10.4. Chemical Parameters
10.5. Inoculum Size
10.6. Fermenter Designs and Operation
10.7. Mixed Culture Fermentation (MCF)
11. Downstream Processing
11.1. An Introduction to Downstream Processing
11.2. Liquid-Solid Separation
11.3. Extraction
11.4. Concentration and Purification
11.5. Formulation
12. Important Techniques in Downstream Processing
12.1. Filtration
12.2. Cell Disruption
12.3. Centrifugation
12.4. Flocculation
12.5. Flotation
12.6. Solvent Extraction
12.7. Precipitation
12.8. Ultrafiltration and Reverse Osmosis
12.9. Chromatography
12.10. Lyophilisation
12.11. Spray Drying
12.12. Crystallisation
13. Production of Industrially Important Products
13.1. Production of Microbial Enzymes
13.2. Production of Organic Acids
13.3. Production of Ethanol
13.4. Production of Antibiotics
13.5. Production of Vitamins
IV. Microbial Enzymes and their Immobilisation
14. Microbial Enzymes of Industrial Interest
14.1. Enzymes and their Characteristics
14.2. Classification of Enzymes
14.3. Enzyme Catalysis
14.4. Kinetic Parameters
14.5. Historical Account of Enzyme Technology
14.6. Advantages of Enzyme Technology
14.7. State-of-the-Art Strategies of Enzyme Production
14.8. Applications of Microbial Enzymes in Industries
14.9. Kinetic Parameters
14.10. Advantages of Enzyme Technology
14.11. State-of-the-Art Strategies of Enzyme Production
14.12. Application of Microbial Enzymes in Industries
15. Enzyme Immobilisation
15.1. Immobilisation
15.2. A Brief Historical Account
15.3. Immobilisation Principles
15.4. Characteristics of Immobilised Enzymes
15.5. Carrier Materials
15.6. Methods of Enzyme Immobilisation
15.7. Multienzyme Immobilisation
15.8. Whole-Cell Immobilisation
16. Properties of Immobilised Enzyme Systems
16.1. Kinetic Studies of Immobilised Enzymes
16.2. Estimation of the Performance of Immobilised Systems
16.3. Factors Affecting the Performance of Immobilised Enzymes
16.4. Protein Engineering Strategies
16.5. Workflow for Combined Approaches
16.6. Conformational Analysis
16.7. Bioreactor Configurations
16.8. Advantages and Disadvantages of Enzyme Immobilisation
17. Large-Scale Applications of Immobilised Enzymes
17.1. Examples of Immobilised Enzymes
17.2. Glucose Isomerase (GI)
17.3. Penicillin Acylases (PAs)
V. Microorganisms in Environments and Their Analysis
18. Study of Airborne Microorganisms
18.1. Aeromicrobiology
18.2. Bioaerosols
18.3. Airborne Microorganisms
18.4. Indoor and Outdoor Microbiomes
18.5. Factors Influencing Airborne Microorganisms
18.6. Bioaerosol Cycle
18.7. Detection of Airborne Microorganisms
18.8. Ecological Significance of Airborne Microorganisms
18.9. Global Concern
18.10. Bioaerosol Control
19. Study of Microorganisms in Soil
19.1. Soil Environment
19.2. Soil Microbiology
19.3. Microbial Forms of Soil
19.4. Microbial Processes in Soil Formation
19.5. Factors Influencing Microorganisms in Soil
19.6. Soil Enzyme Activities
19.7. Rhizospheric Microbiome
19.8. Mycorrhizae and Soil Health
19.9. Soil-Borne Pathogens
19.10. Ecological and Economical Importance of Soil Microbiota
19.11. Anthropogenic Impact on Soil Microorganisms
20. Study of Microorganisms in Water
20.1. Water in the Environment
20.2. Properties of Water
20.3. Aquatic Habitats
20.4. Aquatic Microbiology
20.5. Factors Affecting Aquatic Microbiota
20.6. Distribution of Aquatic Microorganisms
20.7. Microorganisms in Inland Ecosystems
20.8. Microorganisms in Marine Ecosystems
20.9. Microorganisms in Estuaries
20.10. Ecological Implications
20.11. Impact of Anthropogenic Activities on Aquatic Microbiota
21. Methods for the Characterisation of Microorganisms
21.1. Identification and Characterisation
21.2. Culture-Dependent Methods
21.3. Microscopy
21.4. Flow Cytometry (FCM or FC)
21.5. Microbial Community Analysis
21.6. Analysis of Microbial Activities
22. Microbial Cultivation
22.1. Sampling and Storage
22.2. Culture Media
22.3. Sterilisation
22.4. Serial Dilution
22.5. Inoculation
22.6. Incubation
22.7. Purification
22.8. Preservation
22.9. Characterisation and Identification
22.10. Endophytes and their Cultivation
VI. Microbial Indicators and Treatment of Water Pollution
23. Water Pollution
23.1. Water and Wastewater
23.2. Point Sources vs. Diffuse Sources
23.3. Control Measures
23.4. Wastewater Treatment Processes
23.5. Fermentation Industry Effluent and its Management
24. Water Quality Parameters and Indicators
24.1. Water Quality Parameters
24.2. Physical Indicators
24.3. Chemical Indicators
24.4. Biological Indicators
24.5. Coliforms
24.6. Detection of the Presence of Total Coliforms
25. Wastewater Treatment Systems
25.1. Wastewater Treatment Objectives
25.2. Wastewater Treatment Plant (WWTP)
25.3. Wastewater Treatment Processes
25.4. Pretreatment of Wastewater
25.5. Primary Treatment of Wastewater
25.6. Secondary Treatment of Wastewater
25.7. Tertiary Treatment of Wastewater
25.8. Sludge Treatment
25.9. Microbial Integrity in Wastewater Treatment
25.10. Microorganisms in Wastewater Treatment
25.11. Phage Treatment
25.12. Carbon Neutrality in Wastewater Treatment
VII. Microorganisms in Biogeochemical Cycles and Bioremediation
26. Biogeochemical Cycles and Microorganisms
26.1. Biogeochemical Cycles on Earth
26.2. Biogeochemical Cycle on Geological Scale Time
26.3. Key Characteristics of Biogeochemical Cycles
26.4. Environmental Compartments
26.5. Dynamic Processes of Biogeochemical Cycles
26.6. Microbial Sphere
27. Carbon Cycle and Microorganisms
27.1. Carbon in the Environment
27.2. Carbon Sinks and Sources
27.3. Carbon Cycle
27.4. Key Microbial Activities
27.5. Carbon Fixation Pathways
27.6. Association with Other Elemental Cycles
28. Nitrogen Cycle and Microorganisms
28.1. Nitrogen—an Essential Element
28.2. Nitrogen Cycle
28.3. Biological Nitrogen Fixation (BNF)
28.4. Diazotrophs
28.5. Nitrogenase
28.6. Nitrogen-Fixing Biofertilisers
29. Sulphur Cycle and Microorganisms
29.1. Sulphur in the Environment
29.2. Sulphur Cycle
29.3. Sulphur Metabolising Microorganisms and their Activities
29.4. Dimethyl Sulphide (DMS) in the Marine Sulphur Cycle
29.5. Desulphurisation
30. Bioremediation of Contaminated Soil
30.1. Environmental Contamination
30.2. Contamination in Soil
30.3. Removal of Environmental Contaminants
30.4. Bioremediation
30.5. Microbial Activities for Bioremediation
30.6. Principle of Biodegradation
30.7. Factors Influencing Bioremediation
30.8. Different Setups for Bioremediation
30.9. Integrated Approaches of Treatment
31. Industrial Waste Management and Environmental Monitoring
31.1. Wastes and their Various Types
31.2. Industrial Wastes and their Management
31.3. Circular Economy Approach (CEA)
31.4. Microorganisms in Waste Management
31.5. Microbial Routes for Waste Valorisation
31.6. Bioconversion of Waste into Bioenergy
31.7. Bioprocess Engineering and Synthetic Biology
31.8. Microbiological Environmental Monitoring
31.9. Biosensors
Biography
Zeeshan Ur Rahman is working as an Assistant Professor at Zakir Husain Delhi College, University of Delhi. He received his BSc and MSc from the University of Allahabad, India, and MPhil and PhD from the University of Delhi, India. He was awarded Junior Research Fellowship (JRF) and Senior Research Fellowship (SRF) from the Council of Scientific and Industrial Research (CSIR), India, for his PhD research work, and is a recipient of the prestigious Erasmus Mundus Scholarship funded by the European Union. He is also appointed as a Research Fellow at INTI International University, Malaysia. He has been committed to microbial research and training for the last fifteen years, and his areas of specialisation include environmental microbiology, biogeochemistry, bioremediation, and environmental monitoring, resulting in several articles published in international and national journals and chapters in several edited books. He has served key roles in organising various national and international levels of events such as conferences, seminars, and workshops.
Lebin Thomas is currently serving as an Assistant Professor in the Department of Botany, Dr Hari Singh Gour Vishwavidyala, Sagar. He completed his higher education at the University of Delhi. He was awarded Junior Research Fellowship (JRF) and Senior Research Fellowship (SRF) from the Council of Scientific and Industrial Research (CSIR), India, for his PhD research work. His past teaching experiences include services in different colleges at the University of Delhi, India. He is deeply interested in research in industrial microbiology on various topics related to industrial enzyme production, optimisation studies, solid- state fermentation, and biodegradation of agricultural residues. He has published numerous research and review articles in national and international journals, as well as contributing chapters to various edited books with collaborative research. Academic counselling, journal and book reviews, and organising various extracurricular activities (such as faculty development programs, workshops, webinars, seminars, and conferences) are among his notable administrative responsibilities. He is also a Life Member of the International Society of Plant Morphologists (ISPM), Department of Botany, University of Delhi.
