This book, inclusive of 39 chapters, provides a detailed discussion on the biotechnological methods and processes, as well as the industrial applications, of various microbial resources. Current use of these microbial resources in the medical (anti-cancer substances from bacteria), agricultural (i.e., mycorrhizal fungi, biofertilizers, insect pest control), food (i.e., probiotics, prebiotics), feed, cosmetic, biofuel, and bioremediation industries are highlighted, giving researchers in these various fields a valuable resource for the latest developments in microbial bioresources.

• The Handbook of Microbial Bioresources
• Copyright
• Contents
• Contributors
• Preface
• Foreword
• 1: Microbial Resources for Improved Crop Productivity
  • Abstract
  • 1.1 Introduction
  • 1.2 Microbes Promote Plant Growth and Nutrient Uptake
  • 1.3 Microbes Produce Plant Growth-regulating Substances
  • 1.4 Microbes Reinforce Plant Immunity
  • 1.5 Microbes Provide Protection from Abiotic Stress
  • 1.6 Current Challenges for Agricultural Applications of Microbes
  • Acknowledgements
  • References
• 2: The Contributions of Mycorrhizal Fungi
  • Abstract
  • 2.1 Introduction
  • 2.2 Soil Amendments
  • 2.3 Morphology and Composition of Historical Black-C
  • 2.4 Mycorrhizal Plants and Biochar
  • 2.5 Mycorrhizal Plants and Compost
  • 2.6 Conclusion
  • Acknowledgements
  • Note
  • References
• 3: Trichoderma: Utilization for Agriculture Management and Biotechnology
  • Abstract
  • 3.1 Introduction
  • 3.2 Biology of Genus Trichoderma
  • 3.2.1 Morphological characters of Trichoderma spp.
  • 3.3 Trichoderma as Biocontrol Agents
    • 3.3.1 Type of biocontrol mechanism
      • Antibiosis
      • Mycoparasitism
      • Competition
      • Fungistasis
  • 3.4 Trichoderma as a Source Organism for Useful Genes
    • 3.4.1 Progress in identification of Trichoderma genes
  • 3.5 Commercial Utilization
    • 3.5.1 Trichoderma in the textile industry
    • 3.5.2 Trichoderma in the pulp and paper industry
    • 3.5.3 Trichoderma in the food and livestock feed industries
    • 3.5.4 Use of Trichoderma in agriculture and impacts on plants
      • Colonization of the plant root
      • Trichoderma as a biofertilizer
      • Trichoderma advances plant development
      • Trichoderma induces plant resistance to pathogens
  • References
• 4: The Role of Bacillus Bacterium in Formation of Plant Defence: Mechanism and Reaction
  • Abstract
  • 4.1 Bacilli Preparations in Plant Growing and Defence
    • 4.1.1 Biofungicides: a short classification and general biological activity
    • 4.1.2 Bacilli biofungicides and their activity
  • 4.2 Mechanisms of Plant Disease Resistance, Invoked by PGPR of Bacillus spp.
    • 4.2.1 Synthesis by Bacillus PGPR antibiotic compounds
    • 4.2.2 Improvement of phosphoric and nitrogenous nutrition in plants
    • 4.2.3 Synthesis of siderophores
    • 4.2.4 Hydrolases as active components of Bacilli bacteria
    • 4.2.5 Synthesis of hormone-like compounds and signalling molecules
    • 4.2.6 Activation of the plant defence system
    • 4.2.7 Destruction of mycotoxins and increasing plant resistance against them
  • 4.3 Conclusion
  • Acknowledgements
  • References
• 5: Biofilm Formation on Plant Surfaces by Rhizobacteria: Impact on Plant Growth and Ecological Significance
  • Abstract
  • 5.1 Introduction
  • 5.2 Processes in Biofilm Formation
    • 5.2.1 Initial attachment
    • 5.2.2 Irreversible attachment
    • 5.2.3 Microcolony formation
    • 5.2.4 Maturation
    • 5.2.5 Dispersion
  • 5.3 Ecological Significance of Biofilm Formation
    • 5.3.1 Defence
    • 5.3.2 Availability of nutrients to microbes
    • 5.3.3 Colonization
    • 5.3.4 Acquisition of new genetic traits
  • 5.4 Biofilms in the Rhizosphere
    • 5.4.1 Biofilm formation by PGPR
    • 5.4.2 Biofilm formation by phytopathogens
  • 5.5 Multi-species Biofilms in the Rhizosphere
    • 5.5.1 Role of bacterial signals in biofilm formation
  • 5.6 Role of Plant Root Exudates on Biofilms
  • 5.7 Biofilms in Relation to Plant Growth and Health Protection
    • 5.7.1 Role of biofilms in biocontrol of plant diseases
    • 5.7.2 Role of biofilms in mitigating stress in the rhizosphere
  • 5.8 Conclusion
  • Acknowledgement
  • References
• 6: Biofilmed Biofertilizers: Application in Agroecosystems
  • Abstract
  • 6.1 Introduction
  • 6.2 Biofertilizers and theCommunity Approach of Microbes
  • 6.3 Role of BFBFs in Agroecosystems
  • 6.4 Fertilizing Potential of BFBFs
  • 6.5 Conclusion
  • Acknowledgements
  • References
• 7: Microbial Nanoformulation: Exploring Potential for Coherent Nano-farming
  • Abstract
  • 7.1 Introduction
  • 7.2 Applications of Nanotechnology in Agriculture: Bridging the Gap
  • 7.3 Role of Various Microbes in the Synthesis of NPs
    • 7.3.1 Metallic NPs
    • 7.3.2 Oxide NPs
    • 7.3.3 Sulfide NPs
    • 7.3.4 Other NPs
  • 7.4 Possible Mechanisms for Antimicrobial Action of NPs Against Plant Pathogens
  • 7.5 Issues Related to Environmental Biosafety of Metal NPs
    • Forecasting severe threats
  • 7.6 Regulations for Nanotechnology
    • 7.6.1 European Union’s approach to regulating nanotechnology
    • 7.6.2 International standards for nanotechnology-based research
    • 7.6.3 International scenario on biosafety of nanoproducts
  • 7.7 Conclusions and Recommendations
  • Acknowledgements
  • References
• 8: Bacillus thuringiensis: a Natural Tool in Insect Pest Control
  • Abstract
  • 8.1 Short Story of Bacillus thuringiensis
  • 8.2 Biodiversity of Toxin Proteins
  • 8.3 Mode of Action of Bacillus thuringiensis Cry Proteins
  • 8.4 B. thuringiensis Cry toxins as Bioinsecticide Products
  • 8.5 Development of Transgenic B. thuringiensis Crops
  • 8.6 Protein Engineering in B. thuringiensis Toxins
  • 8.7 Conclusion and Future Prospects
  • References
• 9: Pleurotus as an Exclusive Eco-Friendly Modular Biotool
  • Abstract
  • 9.1 Introduction
  • 9.2 Historic Details of Pleurotus
  • 9.3 Biological Species of Pleurotus
  • 9.4 Pleurotus as a Modular Biotool
    • 9.4.1 Biotool for degradation and bioremediation
      • Degradation of lignocelluloses
      • Decolorization of textile dyes
      • Bioremediation of heavy metals
      • Degradation of pesticides
      • Degradation of herbicides
      • Degradation of explosives
      • Degradation of polycyclic aromatic hydrocarbons(PAH)
    • 9.4.2 Biotool for productionof multipurpose enzymes
      • Production of protease
      • Production of cellulase
      • Production of xylanase
      • Production of peroxidases
      • Production of laccase
    • 9.4.3 Biotool for production of food and food derivatives
      • Biotool producing single cell protein (SCP)
      • Biotool producing mushrooms
      • Biotool producing multivitamins
      • Biotool producing minerals
      • Biotool producing dietary fibres
    • 9.4.4 Biotool for production of medicinal products
      • Biotool producing antioxidants
      • Biotool producing polysaccharides
    • 9.4.5 Biotool for production of animal feed and fodder
    • 9.4.6 Biotool for production of compost
    • 9.4.7 Biotool for biobleaching
      • Biotool of pulp bleaching
      • Biotool of skin bleaching
  • 9.5 Conclusion
  • References
• 10: Use of Biotechnology in Promoting Novel Food and Agriculturally Important Microorganisms
  • Abstract
  • 10.1 Introduction
  • 10.2 Role of Microbes in Agriculture and the Food Industry
    • 10.2.1 Biofertilizers and plant growth promoters
    • 10.2.2 Microbes as biotic stress managers
    • 10.2.3 Microbes as abiotic stress alleviators
    • 10.2.4 Microbes in food processing
      • Degradation of natural toxins
      • Biotransformation of mycotoxins
      • Novel microbial enzymes with wider adoptability and utility
  • 10.3 Biotechnology for Characterization of Agricultural Microbes
    • 10.3.1 Identification of microbes using 16S rRNA analysis
    • 10.3.2 Characterization of microbial genes useful in agriculture
    • 10.3.3 Targeted gene sequence
    • 10.3.4 Differential expression studies
    • 10.3.5 Genome sequencing
    • 10.3.6 Metagenomics for new beneficial inoculants
  • 10.4 Biotechnology to Enhance the Activity of Microorganisms Useful to Agriculture
    • 10.4.1 Protoplast fusion
    • 10.4.2 Genetic recombination
    • 10.4.3 Use of regulators for expression of microbial genes
  • 10.5 Concerns About the Use of GMMs
  • 10.6 Future Work
  • References
• 11: Endophytes: an Emerging Microbial Tool for Plant Disease Management
  • Abstract
  • 11.1 Introduction
    • 11.1.1 Advantages of endophytes in plant disease management
    • 11.1.2 Biodiversity of endophytes
  • 11.2 Major Endophytic Microorganisms
    • 11.2.1 Fungal endophytes
    • 11.2.2 Bacterial endophytes
    • 11.2.3 Actinomycetes
      • Antimicrobial activity of endophytic actinomycetes
  • 11.3 Endophyte–Host Relationship
  • 11.4 Bioactivity of Endophytes
  • 11.5 Mechanisms of Action of Endophytes
    • 11.5.1 Direct parasitism
      • Antibiosis
      • Production of lytic enzymes
      • Detoxification and degradation of virulence factors
      • Hyperparasites and predation
    • 11.5.2 Indirect effects
      • Induction of plant resistance
      • Stimulation of plant secondary metabolites
      • Promotion of plant growth and physiology
      • Competition
  • 11.6 Endophytes: an Emerging Tool as Biocontrol Agents
    • 11.6.1 Potential endophytic antagonists
    • 11.6.2 Endophytes’ metabolites active against insects and nematodes
      • Insects
      • Nematodes
    • 11.6.3 Protocol for isolation of endophyticmicroorganisms
  • 11.7 Conclusion
  • References
• 12: Role of Listeria monocytogenes in Human Health: Disadvantages and Advantages
  • Abstract
  • 12.1 Introduction
  • 12.2 Disadvantages and Advantages of the Bacterium
    • 12.2.1 Disadvantages
      • Food poisioning
      • Abortion
      • Meningitis
      • Other infections
    • 12.2.2 Advantages
      • L. monocytogenes as a live bacterial vaccine vector
      • L. monocytogenes in anti-cancer therapies
      • Treatment of infectious diseases
  • 12.3 Conclusion and Future Prospects
  • Acknowledgements
  • References
• 13 Natural Weapons against Cancer from Bacteria
  • Abstract
  • 13.1 Introduction
  • 13.2 Anticancer Compounds from Marine Bacteria
  • 13.3 Anticancer Activities of Lactic Acid Bacteria (LAB)
  • 13.4 Anticancer Activities of Bacteriocins/Antimicrobial Peptides Isolated from Bacteria
  • 13.5 Conclusion
  • References
• 14: Giardia and Giardiasis: an Overview of Recent Developments
  • Abstract
  • 14.1 Introduction
  • 14.2 Historical Background of Giardia
  • 14.3 Systemic Classification of Giardia
  • 14.4 Epidemiology
  • 14.5 Life Cycle
    • 14.5.1 Trophozoite structure
    • 14.5.2 Mitosome
    • 14.5.3 Cyst structure
  • 14.6 Molecular Biology
    • 14.6.1 Transfection
    • 14.6.2 Transcription and translation
  • 14.6.3 Tranposons
  • 14.7 The RNA Interference (RNAi) Pathway in Giardia
  • 14.8 Oxidative Stress
  • 14.9 Mode of Cell Death
  • 14.10 Immunology
    • 14.10.1 Humoral response
    • 14.10.2 Cell-mediated response
  • 14.11 Antigenic Variation
    • 14.11.1 Occurrence of antigenic variation
    • 14.11.2 Molecular mechanism in the control of antigenic variation
  • 14.12 Pathology and Pathogenesis
    • 14.12.1 Clinical features
    • 14.12.2 Diagnosis
      • Microscopic stool examination
      • Examination of intestinal fluid
      • Small bowel biopsy
      • Gastrointestinal radiology
      • Immunodiagnosis
      • DNA probe
      • Molecular diagnosis – nucleic acid detection methods
  • 14.13 Treatment of Giardiasis
    • 14.13.1 G. lamblia susceptibility towards aminoglycosides
    • 14.13.2 Susceptibility to nitroheterocyclic drugs
      • Mode of action of tinidazole
    • 14.13.3 Susceptibility to benzimidazoles
    • 14.13.4 Other agents
    • 14.14 Potential Drug Target Against Giardia
    • 14.15 Prevention of Giardiasis
  • References
• 15: Power of Bifidobacteria in Food Applications for Health Promotion
  • Abstract
  • 15.1 Introduction
  • 15.2 The Bifidobacterium
    • 15.2.1 Taxonomy and general features
    • 15.2.2 Structure of the cell wall
    • 15.2.3 Oxygen tolerance
    • 15.2.4 Temperature and pH
    • 15.2.5 Metabolism of carbohydrates
    • 15.2.6 Sensitivity to antibiotics
  • 15.3 Microbial Ecosystem and Health Effects
    • 15.3.1 Gut microbiota
    • 15.3.2 Diarrhoea
    • 15.3.3 Inflammatory bowel diseases
    • 15.3.4 Allergenic diseases
    • 15.3.5 Cancer prevention
    • 15.3.6 Helicobacter pylori infection
    • 15.3.7 Lactose intolerance
  • 15.4 Bifidobacteria in Food Products
    • 15.4.1 Dairy-based matrices
      • Milk
      • Yoghurt
      • Cheese
      • Ice cream
    • 15.4.2 Non-dairy based matrices
      • Fruits and vegetables
      • Cereals
  • 15.5 Concluding Remarks
  • Acknowledgements
  • References
• 16: Probiotics and Dental Caries: a Recent Outlook on Conventional Therapy
  • Abstract
  • 16.1 Introduction
  • 16.2 Dental Caries
  • 16.3 Potential of Probiotics for Prevention or Treatment of Dental Caries
  • 16.3.1 Using probiotics to replace the pathogenic flora
  • 16.4 Direct and Indirect Mechanisms of Probiotic Action
    • 16.4.1 Modulation of systemic immune system
    • 16.4.2 Effect on local immunity
    • 16.4.3 Effect on non-immunologic/non-specific defence mechanisms
    • 16.4.5 Prevention of plaque formation by neutralizing free electrons and production of antioxidants
    • 16.4.6 Probiotics change the environment
  • 16.5 Concluding Remarks and Future Directions
  • References
• 17: Human Microbiota for Human Health
  • Abstract
  • 17.1 Introduction
  • 17.2 Distribution of Microbes in the Human Body
  • 17.3 Microbial Flora Acquired During Development
  • 17.4 Human Microbiota and Health
  • 17.5 Variation in the Human Microbiota
  • 17.6 Gut Microflora and Human Metabolism
  • 17.7 Horizontal Gene Transfer (HGT) Favours Bacterial Efficiency
  • 17.8 Microbiota and Disease
  • 17.9 Biotherapeutic Agents from Human Milk
  • 17.10 Microbiota and its Future in Wealth Generation
  • References
• 18: Biotechnological Production of Polyunsaturated Fatty Acids
  • Abstract
  • 18.1 Introduction
  • 18.2 Microbial Metabolism for PUFA Production
  • 18.3 Oleaginous Microorganisms
  • 18.4 Production, Extraction and Chemical Characterization of Microbial Oil
    • 18.4.1 Production of Microbial Oil
    • 18.4.2 Extraction of Microbial Oil
    • 18.4.3 Chemical Characterization of Microbial Oil
  • 18.5 Microbial Oil’s Applications
  • 18.6 Future Trends
  • 18.7 Concluding Remarks
  • Acknowledgements
  • References
• 19: Functional Enzymes for Animal Feed Applications
  • Abstract
  • 19.1 Introduction
  • 19.2 Application of Functional Enzymes in Animal Feeding
  • 19.3 Phytases (Chemical Abstracts Service (CAS) # 37288-11-2)
    • 19.3.1 Characterization and production of phytase
    • 19.3.2 Enzymatic hydrolysis of phytic acid
    • 19.3.3 Application of phytases in animal feed
  • 19.4 Xylanases (CAS # 9025-57-4)
    • 19.4.1 Classification and production
    • 19.4.2 Application in animal feed
  • 19.5 Future Trends
  • References
• 20: Microbial Xylanases: Production, Applications and Challenges
  • Abstract
  • 20.1 Introduction
  • 20.2 Xylan: Composition and Structure
  • 20.3 Xylanases: Classification and Characteristics
    • 20.3.1 Endo-1,4-β-xylanases
    • 20.3.2 β-Xylosidases
    • 20.3.3 α-Arabinofuranosidases
    • 20.3.4 Acetylxylan esterase
    • 20.3.5 α-Glucuronidases
  • 20.4 Production of Xylanases
    • 20.4.1 Fungi
    • 20.4.2 Bacteria
  • 20.5 Production of Xylanases Under Solid State Fermentation (SSF) and Submerged Fermentation (SmF)
    • 20.5.1 Xylanase production by SmF
    • 20.5.2 Production of xylanase by SSF
  • 20.6 Biotechnological Applications
    • 20.6.1 Bioethanol production
    • 20.6.2 Animal feedstocks
    • 20.6.3 Xylanases in the pulp and paper industry
      • Pulp fibre morphology
      • Biobleaching of pulp
    • 20.6.4 Xylanases in the baking industry
    • 20.6.5 Fruit juice and beer clarification
    • 20.6.6 Improving silage
    • 20.6.7 Lignocellulosic bioconversions
    • 20.6.8 Xylanases in textile processing
    • 20.6.9 Bioenergy
  • 20.7 Xylanases: Challenges
  • 20.8 Conclusion and Future Prospects
  • References
• 21: Microbial Chitinase: Production and Potential Applications
  • Abstract
  • 21.1 Introduction
  • 21.2 General Structure and Properties of Chitin
    • 21.2.1 α-Chitin
    • 21.2.2 β-Chitin
    • 21.2.3 γ-Chitin
  • 21.3 General Structure, Properties and Classification of Chitinase
  • 21.4 Source of Microbial Chitinase
    • 21.4.1 Bacterial chitinase
    • 21.4.2 Fungal chitinase
  • 21.5 Production of Chitinase
    • 21.5.1 Submerged fermentation (SmF) system
      • Carbon sources
      • Nitrogen sources
      • Metal ions
    • 21.5.2 Solid state fermentation (SSF) system
    • 21.5.3 Statistical optimization of chitinase production
    • 21.5.4 Purification of chitinase and its characterization
      • pH
      • Temperature
      • Metal ions and inhibitors
      • Molecular mass
  • 21.6 Applications of Chitinase
    • 21.6.1 Antifungal properties of chitinase
    • 21.6.2 Chitinases and transgenic plants
    • 21.6.3 Chitinases as a biopesticide
    • 21.6.4 Isolation of protoplasts
    • 21.6.5 Medical applications of chitinase
    • 21.6.6 Production of chito-oligosaccharides
    • 21.6.7 Chitinase as a mosquitocidal agent
    • 21.6.8 Chitinase as a nematicidal agent
    • 21.6.9 Treatment of chitinous waste
  • 21.7 Recent Patents and their Significance
  • References
• 22: Characteristics of Microbial Inulinases: Physical and Chemical Bases of their Activity Regulation
  • Abstract
  • 22.1 Introduction
  • 22.2 Physical and Chemical Properties of Inulinases
  • 22.3 Correlation Between Amino Acid Sequences of Inulinases and their Physical and Chemical Properties
  • 22.4 Immobilization – One of the Ways of Regulating Inulinase Activity
  • 22.5 Mechanisms of Interaction between Inulinase and the Matrices of Ion Exchange Materials
  • 22.6 Conclusion
  • Acknowledgements
  • References
• 23: Microbial Resources for Biopolymer Production
  • Abstract
  • 23.1 Introduction
  • 23.2 Biopolymer Production by Bacteria: Biosynthesis and Applications
    • 23.2.1 Bacterial cellulose (BC)
    • 23.2.2 Xanthan
    • 23.2.3 Polyhydroxyalkanoate (PHA)
    • 23.2.4 Summary of bacterial polymers
  • 23.3 Biopolymer Production by Fungi and Yeasts: Biosynthesis and Applications
    • 23.3.1 Chitin and chitosan
    • 23.3.2 Pullulan
    • 23.3.3 Glucan and the chitin–glucan complex (CGC)
    • 23.3.4 Summary of fungal polymers
  • 23.4 Final Remarks and Future Prospects
  • Acknowledgements
  • References
• 24: Microbial Metabolites in the Cosmetics Industry
  • Abstract
  • 24.1 Introduction
  • 24.2 Microbially Produced CompatibleSolutes in Cosmetic Applications
    • 24.2.1 Ectoines
    • 24.2.2 Ectoines in the cosmetics industry
  • 24.3 Kojic Acid (CAS# 501-30-4)
    • 24.3.1 Characterization, preparation and application of kojic acid
  • 24.4 Botulinum Toxin (CAS# 93384-43-1)
  • 24.5 Microbial Polysaccharides
    • 24.5.1 Hyaluronic acid (HA) (CAS# 9004-61-9)
    • 24.5.2 Xanthan (CAS# 11138-66-2)
    • 24.5.3 Pullulan (CAS# 9057-02-7)
    • 24.5.4 Kefiran (CAS# 86753-15-3)
    • 24.5.5 Alginic acid (CAS# 9005-32-7)
  • 24.6 Medicinal Compounds from Mushrooms Used for Cosmetic Applications
    • 24.6.1 Mushroom cosmeceutical products
    • 24.6.2 Mushroom tyrosinase inhibitors
    • 24.6.3 Chitin–glucan
  • 24.7 Microbial Derivatives as FunctionalCosmetics
    • 24.7.1 Depigmenting material from microbialderivatives
    • 24.7.2 Functional cosmetics and photoageing caused by UVB irradiation
  • 24.8 Conclusion and Future Prospects
  • References
• 25: Fungi of the Genus Pleurotus: Importance and Applications
  • Abstract
  • 25.1 Introduction
  • 25.2 Lignocellulosic Biomass
    • 25.2.1 Pleurotus production usingligno cellulosic biomass as a substrate
  • 25.3 Pleurotus Species
    • 25.3.1 Pleurotus ostreatus (Jacq.:Fr) Kummer
    • 25.3.2 Pleurotus florida Eger
    • 25.3.3 Pleurotus eryngii (DC.:Fr) Quel
    • 25.3.4 Pleurotus sajor-caju Fr.:Fr.
    • 25.3.5 Pleurotus cystidiosus O.K. Mill (P. abalonus Han, Chen & Cheng)
    • 25.3.6 Pleurotus cornucopiae (Paulet) Rolland
    • 25.3.7 Pleurotus djamor (Rumph. ex Fr.)
    • 25.3.8 Pleurotus pulmonarius (Fr.) Quél.
  • 25.4 Improvements to Pleurotus Strains
  • 25.5 Nutritional Importance of the Genus Pleurotus
  • 25.6 Medicinal and Therapeutic Properties of Pleurotus Species
    • 25.6.1 Antioxidants
    • 25.6.2 Hypocholesterolaemic agents
    • 25.6.3 Antitumour agents
    • 25.6.4 Importance of glucans
  • 25.7 Production of Industrial Enzymes by Pleurotus
    • 25.7.1 Oxidase enzymes
      • Manganese peroxidase (MnP)
      • Versatile peroxidase (VP)
      • Laccases
    • 25.7.2 Hydrolase enzymes
      • Cellulases
      • Xylanases
      • Proteases
  • 25.8 Bioremediation of Contaminated Soils and Water Using Pleurotus
  • 25.9 Conclusion
  • References
• 26: Useful Microorganisms for Environmental Sustainability: Application of Heavy Metal Tolerant Consortia for Surface Water Decontamination in Natural and Artificial Wetlands
  • Abstract
  • 26.1 Introduction
  • 26.2 Study Case
  • 26.3 Methodology
    • 26.3.1 Toxicity test
    • 26.3.2 Reactors
    • 26.3.3 Inoculation of reactors 1 and 3
    • 26.3.4 Statistical analysis
  • 26.4 Results and Discussion
    • 26.4.1 Toxicity test
    • 26.4.2 Reactor experiment
    • 26.4.3 Heavy metals removal
      • Mercury removal
      • Lead removal
      • Chromium removal
  • 26.5 Conclusion
  • 26.6 Final Remarks
  • Acknowledgements
  • Note
  • References
• 27: Exopolysaccharide (EPS)-producing Bacteria: an Ideal Source of Biopolymers
  • Abstract
  • 27.1 Introduction
    • 27.1.1 Gelling agent
    • 27.1.2 Medical applications
    • 27.1.3 Source of monosaccharides
    • 27.1.4 Emulsifiers
    • 27.1.5 Heavy metal removal
    • 27.1.6 Enhanced oil recovery
  • 27.2 Sources of EPS-producing Isolates
  • 27.3 Isolation of EPS-producing Bacteria
  • 27.4 EPS Recovery
  • 27.5 Quantification of EPS
  • 27.6 Purification of EPS
  • 27.7 Examples of Some CommerciallyUsed Bacterial EPS
    • 27.7.1 Dextran
    • 27.7.2 Xanthan gum
    • 27.7.3 Curdlan
  • References
• 28: Microbial Process Development for Fermentation-based Biosurfactant Production
  • Abstract
  • 28.1 Introduction
  • 28.2 Biosurfactants
  • 28.3 Characteristics of Biosurfactants
  • 28.4 Fermentation Requirements
  • 28.5 Production of Biosurfactants
  • 28.6 Monitoring of Biosurfactant Production
  • 28.7 Downstream Processing of Biosurfactants
  • 28.8 General Applications of Biosurfactants
    • 28.8.1 Environmental applications
    • 28.8.2 Agricultural applications
    • 28.8.3 Food industry applications
    • 28.8.4 Cosmetic industry applications
    • 28.8.5 Application as antimicrobials
  • 28.9 Conclusion
  • References
• 29: Recent Developments on Algal Biofuel Technology
  • Abstract
  • 29.1 Introduction
  • 29.2 Algal Growth
    • 29.2.1 Open ponds
    • 29.2.2 Photobioreactors (PBRs)
  • 29.3 Separation Techniques
    • 29.3.1 Flocculation
    • 29.3.2 Sedimentation
    • 29.3.3 Centrifugation
    • 29.3.4 Filtration
    • 29.3.5 Ultrasound
    • 29.3.6 Biologically based harvesting methods
  • 29.4 Drying Methods
  • 29.5 Lipid Extraction
    • 29.5.1 Supercritical CO2 extraction
    • 29.5.2 Electrical extraction
    • 29.5.3 Solvents
  • 29.6 Lipid Conversion
  • 29.7 Alternative Products
  • 29.8 Concerns, Limitations and Further Thoughts
  • References
• 30: Microbial Lipases: Emerging Biocatalysts
  • Abstract
  • 30.1 Introduction
  • 30.2 Three-dimensional Structure of Bacterial Lipase Enzyme
  • 30.3 Mechanism of Lipolysis
  • 30.4 Lipase Production
  • 30.5 Secretion of Extracellular Lipase
  • 30.6 Applications of Bacterial Lipase
    • 30.6.1 Hydrolysis of oils and fats
    • 30.6.2 Interesterification of oils and fats
    • 30.6.3 Esterification of fatty acids
    • 30.6.4 Flavour development in dairy products
    • 30.6.5 Applications in the detergen tindustry
    • 30.6.6 Lipases in the food industry
    • 30.6.7 Lipases in biomedical applications
    • 30.6.8 Lipases in the synthesis of pesticides
    • 30.6.9 Lipases in the leather industry
    • 30.6.10 Lipases in environmental management
    • 30.6.11 Lipases in the cosmetics and perfume industry
  • 30.7 Conclusion
  • References
• 31: Bioremediation of Gaseous and Liquid Hydrogen Sulfide Pollutants by Microbial Oxidation
  • Abstract
  • 31.1 Introduction
  • 31.2 Biological Conversion of Sulfide into Elemental Sulfur
  • 31.3 Sulfur-oxidizing Bacteria (SOB)
  • 31.4 Factors Affecting Sulfide Oxidation
    • 31.4.1 Effect of oxygen rate
    • 31.4.2 Effect of pH
    • 31.4.3 Effect of temperature
  • 31.5 Conclusion
  • References
• 32: Archaea, a Useful Group for Unconventional Energy Production: Methane Production From Sugarcane Secondary Distillation Effluents Using Thermotolerant Strains
  • Abstract
  • 32.1 Introduction
  • 32.2 Theoretical Considerations
    • 32.2.1 Classification of living organisms
    • 32.2.2 Methanogenic archaea
    • 32.2.3 Main substrates used by methanogenic archaea
    • 32.2.4 Molecular tools and denaturing gradient gel electrophoresis (DGGE)
  • 32.3 Methodology
    • 32.3.1 Assessment of vinasses composition
    • 32.3.2 Upflow anaerobic sludge blanket (UASB) reactors
    • 32.3.3 Isolating, identifying and establishing the growth kinetics of methanogenic organisms
      • Selection of the optimum working dilution
      • General culture media incubation
      • Specific culture media incubation
      • Selective culture media incubation
      • Quantification using the most probable number (MPN) technique
      • Direct plate counting method
      • Growth kinetics for each selective culture medium
      • Confocal microscopy and scanning electron microscopy
    • 32.3.4 Molecular analysis of the methanogenic community composition
      • PCR amplification
      • DGGE
      • Reamplification, sequencing and phylogenetic analysis
  • 32.4 Results and Discussion
    • 32.4.1 Vinasses composition
    • 32.4.2 Identification and growth kinetics of methanogenic organisms
      • Archaea – traditional identification
      • Methanogenic archaea and SRO quantification using the MPN technique: growth kinetics
      • Comparison of data obtained in this study with previous data
    • 32.4.3 Molecular analysis of the methanogeniccommunity composition
      • Phylogenetic reconstructions for methanogenic archaea in the UASB reactors
  • 32.5 Concluding Remarks
  • Acknowledgements
  • Note
  • References
• 33: Industrial Additives Obtained Through Microbial Biotechnology: Biosurfactants and Prebiotic Carbohydrates
  • Abstract
  • 33.1 Biotechnology: Useful Products for the Future of Industry
  • 33.2 Prebiotic Carbohydrates
    • 33.2.1 Chemical structure and types of non-digestibleoligosaccharides (NDOs)
    • 33.2.2 Technologies for the production of NDOs
      • Fructooligosaccharides (FOS)
      • Galactooligosaccharides (GOS)
      • Xylooligosaccharides (XOS)
    • 33.2.3 Main applications: research and industry
  • 33.3 Biosurfactants
    • 33.3.1 Production of biosurfactants from residues and application of statistical methods for process optimization
    • 33.3.2 Promising environmental applications of biosurfactants
  • 33.4 Concluding Remarks
  • Acknowledgements
  • References
• 34: Industrial Additives Obtained Through Microbial Biotechnology: Bioflavours and Biocolourants
  • Abstract
  • 34.1 Biotechnology: Useful Products for the Future of Industry
  • 34.2 Bioflavours and Aroma Compounds Obtained by Microbial Biotechnology
    • 34.2.1 Bioflavours: microbial production and potential
  • 34.3 Biocolourants
    • 34.3.1 Biocolourants: microbial production and potential
  • 34.4 Trends and Prospects for New Industrial Additives
    • 34.4.1 Additives fitting the sensory trend
    • 34.4.2 Prospects for additives for the healthiness and wellness trend
  • 34.5 Advances in Biotechnology for New Industrial Additives
  • 34.6 Use of ‘Omics’ Tools in Searching for New Bioproducts
  • 34.7 Concluding Remarks
  • Acknowledgements
  • References
• 35: Actinomycetes in Biodiscovery: Genomic Advances and New Horizons
  • Abstract
  • 35.1 Introduction
  • 35.2 Contributions of Actinomycetes to Biodiscovery
    • 35.2.1 Antibiotics: early years (1940–1974) to mid-era (1975–2000)
    • 35.2.2 New age (2001 onwards): genomics-inspired discovery of bioactive compounds
  • 35.3 Genome Mining
    • 35.3.1 Cryptic secondary metabolite pathways
    • 35.3.2 Diverse enzymology and biosynthetic pathways
    • 35.3.3 Polyketides and non-ribosomal peptides
    • 35.3.4 Ribosomal natural products
    • 35.3.5 Evolutionary systems biology
    • 35.3.6 Bioinformatics
    • 35.3.7 Extracellular microbial environment and metabolomics
    • 35.3.8 Microbiomics
    • 35.3.9 Target-directed screening for antibiotic activity
  • 35.4 Actinomycetes in Nature
    • 35.4.1 Natural roles of antibiotics
    • 35.4.2 Metagenomics
    • 35.4.3 Resistome concept in relation to antibiotic discovery
    • 35.4.4 Target-directed search and recovery of bioactive microorganisms
  • 35.5 Future Prospects
  • Acknowledgements
  • References
• 36: Molecular Strategies for the Study of the Expression of Gene Variation by Real-time PCR
  • Abstract
  • 36.1 Introduction
  • 36.2 Theory of Real-time PCR
    • 36.2.1 Chemistry: types of fluorophores
    • 36.2.2 Strategies for RNA quantification by real-time PCR
      • Absolute quantification
      • Relative quantification
    • 36.2.3 Normalization
    • 36.2.4 Optimization of qPCR
    • 36.2.5 Applications
  • 36.3 Conditions for Quantification of Gene Expression of bgl-A, bgl and CspA from Shewanella sp. G5 Cultures
    • 36.3.1 Methods
      • Culture conditions
      • RNA extraction and cDNA synthesis
      • Design of oligonucleotide primers to detect b-glucosidase genes by conventional PCR
      • Real-time PCR assay
      • Standard curves and normalization
      • Relative quantification and data analysis
    • 36.3.2 Results and discussion
      • Analysis of designing primers for genes of interest
      • Primer evaluation by conventional PCR
      • Optimization of real-time PCR
      • Normalization with the reference gene and generation of standard curves
      • Relative quantification analyses applying the 2–ΔΔCt method
  • 36.4 Conclusion
  • References
• 37: Whole Genome Sequence Typing Strategies for Enterohaemorrhagic Escherichia coli of the O157:H7 Serotype
  • Abstract
  • 37.1 Introduction
  • 37.2 Typing Methodologies and Resolution Power
    • 37.2.1 Multi-locus enzymeel ectrophoresis (MLEE) and sequencing typing
    • 37.2.2 Phage susceptibility assay
    • 37.2.3 Pulsed-field gel electrophoresis (PFGE)
    • 37.2.4 Metabolic typing
    • 37.2.5 Octamer-based genome scanning (OBGS) typing assay
    • 37.2.6 Multiple-locus variable-number tandem repeat analysis (MLVA)
    • 37.2.7 Shiga-toxin-producing bacteriophage insertion site typing (SBI)
    • 37.2.8 Lineage-specific polymorphism assay (LSPA)
    • 37.2.9 Whole genome mapping (WGM)
    • 37.2.10 Comparative genome hybridization
    • 37.2.11 Genome-wide association studies (GWAS)
  • 37.3 Historical View of E. coli O157:H7 Genomics
  • 37.4 Whole Genome Sequence Typing
  • 37.5 Impact of NGS Technologies
  • 37.6 Typing Isolates Based on the Virulence Complement
  • 37.7 Conclusions
  • Acknowledgements
  • References
• 38: Microbial Keratinases: Characteristics, Biotechnological Applications and Potential
  • Abstract
  • 38.1 Introduction
  • 38.2 Characteristics and Properties of Keratinases
    • 38.2.1 Optimal pH and temperature
    • 38.2.2 Biochemical properties of keratinases
    • 38.2.3 Chemical properties of keratinases
    • 38.2.4 Keratinous substrates and their specificities
    • 38.2.5 Mechanism of keratinolysis
  • 38.3 Sources of Microbial Keratinases
  • 38.4 Optimization of Keratinase Production
  • 38.5 Established Applications of Keratinases
    • 38.5.1 Waste management
    • 38.5.2 Agroindustry
      • Animal feed and feed supplements
      • Fertilizers
    • 38.5.3 Leather and textile industry
    • 38.5.4 Consumer products
      • Detergent
      • Personal care products
    • 38.5.5 Pharmaceutical industry
    • 38.5.6 Prion decontamination
  • 38.6 Potential Applications of Keratinases
    • 38.6.1 Biological control
    • 38.6.2 Green energy
    • 38.6.3 Silk degumming
    • 38.6.4 Other applications
  • 38.7 Conclusion
  • References
• 39: Philippine Fungal Diversity: Benefits and Threats to Food Security
  • Abstract
  • 39.1 Introduction
  • 39.2 The Genesis and Development of Philippine Mycology
  • 39.3 Case study 1: Biological Control of Plant Pathogens
  • 39.4 Case Study 2: Microbial Gifts for Agriculture
  • 39.5 Case Study 3. Breeding for Resistance Against Cereal Blast
  • 39.6 Case Study 4. Mycotoxins in Maize
  • References
• Index