This book focuses on successful application of microbial biotechnology in areas such as medicine, agriculture, environment and human health.
Contents
Contributors
Chapter 1: Microbial Applications in Agriculture and the Environment: A Broad Perspective
1.1 Introduction
1.2 Approaches to Studying Soil Microbial Populations
1.2.1 Cultivation-Based Methods
1.2.2 Cultivation-Independent Methods
1.3 Functional Diversity of Microbes
1.4 Application in Agriculture and the Environment
1.4.1 Microbes in Plant Growth Promotion and Health Protection
1.4.1.1 Plant Growth-Promoting Fungi
1.4.2 Microbes in Environmental Problem Management
1.4.2.1 PAH Degradation
1.4.2.2 Microbes in Metal Removal from Water
1.4.2.3 PGPR in Biomanagement of Metal Toxicity
1.5 Microbial Biosensors and Their Applications
1.6 Microbes and Nanoparticles
1.6.1 Fungi in Nanoparticle Synthesis
1.7 Other New Applications
1.7.1 Microbes and Climate Change
1.7.2 Probiotics and Health
1.8 Conclusion
References
Chapter 2: Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment
2.1 Introduction
2.2 Culture Methods in Microbial Ecology: Applications and Limitations
2.3 Molecular Methods of Microbial Community Analyses
2.3.1 Partial Community Analysis Approaches
2.3.1.1 Clone Library Method
2.3.1.2 Genetic Fingerprinting Techniques
Denaturing- or Temperature-Gradient Gel Electrophoresis
Single-Strand Conformation Polymorphism
Random Amplified Polymorphic DNA and DNA Amplification Fingerprinting
Amplified Ribosomal DNA Restriction Analysis
Terminal Restriction Fragment Length Polymorphism
Length Heterogeneity PCR
Ribosomal Intergenic Spacer Analysis
2.3.1.3 DNA Microarrays
16S rRNA gene Microarrays (PhyloChip)
Functional Gene Arrays
2.3.1.4 Quantitative PCR
2.3.1.5 Fluorescence In Situ Hybridization
2.3.1.6 Microbial Lipid Analysis
2.3.2 Whole Community Analysis Approaches
2.3.2.1 DNA–DNA Hybridization Kinetics
2.3.2.2 Guanine-Plus-Cytosine Content Fractionation
2.3.2.3 Whole-Microbial-Genome Sequencing
2.3.2.4 Metagenomics
2.4 Next-Generation DNA Sequencing Techniques Transform Microbial Ecology
2.5 Functional Microbial Ecology: Linking Community Structure and Function
2.5.1 Stable Isotope Probing
2.5.2 Microautoradiography
2.5.3 Isotope Array
2.6 Postgenomic Approaches
2.6.1 Metaproteomics
2.6.2 Proteogenomics
2.6.3 Metatranscriptomics
2.7 Bias in Molecular Community Analysis Methods
2.8 Concluding Remarks and Future Directions
References
Chapter 3: The Biofilm Returns: Microbial Life at the Interface
3.1 Introduction
3.2 Biofilm: A Definition
3.3 Mechanism of Biofilm Formation
3.4 Biofilm Properties: Influence on Biofilm-Based Technologies
3.4.1 Extracellular Polymeric Substances: Role in Biofilm Reactor Performance
3.4.2 Biofilm Architecture: Role in Biofilm Reactor Performance
3.4.3 Quorum Sensing: Role in Bioreactor Cleanup
3.4.4 Antimicrobial Resistance: Role in Bioreactor Cleanup
3.4.5 Gene Transfer Within Biofilms: Role in Bioremediation
3.4.6 External Electron Transfer in Biofilms: Role in MFC Function
3.5 Application of Biofilms
3.5.1 Biofilms as Biocontrol Agents
3.5.1.1 Gram-Positive Bacterial Biofilms as Biocontrol Agents
3.5.2 Biofilms as Corrosion Inhibitors
3.5.2.1 Corrosion Inhibition by Biofilm Through Oxygen Removal
3.5.2.2 Corrosion Inhibition by Biofilms Secreting Antimicrobials
3.5.2.3 Corrosion Inhibition with Biofilms Secreting Corrosion Inhibitors
3.5.2.4 Corrosion Inhibition Through Protective Layers (Biofilm Matrix)
3.6 Biofilm-Based Technologies
3.6.1 Biofilm Reactors
3.6.1.1 Biofilm Reactors in Wastewater and Waste Gas Treatment
3.6.1.2 Biofilm Reactors in Bioremediation Process
Bioremediation of Hydrocarbons
Bioremediation of Heavy Metals
3.6.1.3 Biofilm Reactors in Productive Biocatalysis
3.6.2 Microbial Fuel Cells
3.6.2.1 Marine MFCs
3.6.2.2 Wastewater MFCs
3.6.2.3 Farm Field MFCs
3.6.2.4 Photosynthetic MFCs
3.6.2.5 Applications of MFCs
References
Chapter 4: Future Application of Probiotics: A Boon from Dairy Biology
4.1 Introduction
4.2 Probiotics as Antibiotics or Lactobiotics
4.3 LAB as an Immune Enhancer
4.4 Probiotics and GALT Immunity
4.5 The Demise of the Needle
4.5.1 Malaria
4.5.2 AIDS
4.5.3 Infantile Diarrhea
4.5.4 Trichomoniasis
4.5.5 Ischemic Heart Diseases
4.5.6 Gastritis, Peptic Ulcer, and Gastric Adenocarcinoma
4.6 Conclusion/Future Recommendations
References
Chapter 5: Microbially Synthesized Nanoparticles: Scope and Applications
5.1 Introduction
5.2 Nanoparticle Synthesis by Bacteria
5.2.1 Silver Nanoparticles
5.2.2 Gold Nanoparticles
5.2.3 Magnetic Nanoparticles
5.2.4 Uranium Nanoparticles
5.2.5 Cadmium Nanoparticles
5.2.6 Selenium Nanoparticles
5.2.7 Titanium, Platinum, and Palladium Nanoparticles
5.3 Nanoparticle Biosynthesis by Actinomycetes
5.4 Nanoparticle Biosynthesis by Cyanobacteria
5.5 Nanoparticle Biosynthesis by Yeast
5.6 Nanoparticle Biosynthesis by Fungi
5.7 Scope and Applications of Nanoparticles
5.8 Conclusions
References
Chapter 6: Bacterial Quorum Sensing and Its Interference: Methods and Significance
6.1 Introduction
6.2 Quorum Sensing Pathways in Bacteria
6.2.1 Autoinducer Type 1 Signaling System
6.2.2 Autoinducer Type 2 Signaling System
6.2.3 Autoinducer Type 3 System
6.2.4 Short Peptide Signaling (AIP) System in Gram-Positive Bacteria
6.3 QS Signal Molecules Diversity
6.3.1 Gram-Negative Bacteria
6.4 QS-Regulated Bacterial Traits
6.5 Isolation, Purification, and Characterization of AHL Molecules
6.6 Assays for AHL Detection
6.6.1 Detection Through Bioassays
6.6.2 Chemical Detection
6.6.3 Application of Microbial and Chemical Assays
6.7 Interferences in Bacterial Quorum Sensing
6.7.1 Inhibition of AHL-Mediated QS
6.7.1.1 Inhibition of Signal Molecule Biosynthesis
6.7.1.2 Blocking Signal Transduction
Synthetic Analogues for Quorum Sensing Autoinducers
Modification of the Acyl Side Chain
Modification of the Lactone Ring
Simultaneous Modifications on Both the Lactone Ring and Side Chain
6.7.1.3 Chemical Inactivation and Biodegradation of Signal Molecules
Chemical Inactivation
Biodegradation
6.7.2 Inhibition of Other Quorum-Sensing Systems
6.7.3 Quorum-Sensing Inhibitors Expressed by Higher Organisms
6.7.3.1 Inhibition of QS by Halogenated Furanone Compounds
6.7.3.2 Inhibition of QS by Plant Products
6.7.4 Practical Significance of Bacterial QS Modulation in the Environment/Agriculture
6.7.4.1 Roles of AHL-Degradation Enzymes in Host
6.7.4.2 Biotechnological and Pharmaceutical Implications of AHL Degradation Enzymes
6.7.4.3 Transgenic Plants
6.8 Conclusion
References
Chapter 7: Horizontal Gene Transfer Between Bacteria Under Natural Conditions
7.1 Introduction
7.2 Horizontal Gene Transfer in Soil, Sediments, and Other Solid Surfaces
7.2.1 Environmental Factors Affecting HGT in Nature
7.2.2 Tools to Study Horizontal Gene Transfer in the Environment
7.3 Plasmid-Mediated Gene Mobilization in Soil
7.3.1 Horizontal Gene Transfer in Metal- and Radionuclide-Contaminated Soils and Sediments
7.3.2 Horizontal Gene Transfer in Mixed Waste Sites
7.3.3 Horizontal Gene Transfer in Agricultural Soils
7.4 Horizontal Gene Transfer in Aquatic Environments
7.4.1 Evidence of Plasmid Transfer in Aquatic Environments
7.4.2 Evidence of Plasmid Transfer in Sewage Filter Beds and Activated Sludge Units
7.5 Modeling of Conjugative Plasmid Transfer
7.6 Monitoring Horizontal Gene Transfer and Assessing Transfer Frequencies
7.7 Spread of Biodegradation Traits
7.8 Conclusions
7.9 Future Recommendations
References
Chapter 8: Molecular Strategies: Detection of Foodborne Bacterial Pathogens
8.1 Introduction
8.2 Molecular Typing Methods for the Detection of Bacterial Pathogens
8.2.1 PCR-Based Detection Methods
8.2.1.1 Multiplex PCR and Real-Time PCR
8.2.1.2 Random Amplified Polymorphic DNA
8.2.1.3 Restriction Fragment Length Polymorphism
8.2.1.4 Amplified Fragment Length Polymorphism
8.2.2 Pulsed-Field Gel Electrophoresis
8.2.3 Biosensors
8.2.4 Microarrays
8.2.5 Integrated Systems
8.3 Conclusions and Future Prospectives
References
Chapter 9: Recent Advances in Bioremediation of Contaminated Soil and Water Using Microbial Surfactants
9.1 Introduction
9.2 Microbial Surfactants/Biosurfactants
9.2.1 Sources and Types of Biosurfactants
9.2.2 Important Properties of Biosurfactants
9.2.3 Surface and Interfacial Tension Reduction
9.2.4 Emulsification and De-emulsification Activity
9.2.5 Biodegradability
9.2.6 Low Toxicity
9.3 Remediation of Contaminated Soil and Water Using Different Physical, Chemical, and Biological Techniques
9.3.1 Physical Techniques
9.3.2 Chemical Techniques
9.3.3 Biological Techniques or Bioremediation
9.3.3.1 Ex Situ Bioremediation
9.4 Bioremediation of Contaminated Soil and Water Using Biosurfactants
9.4.1 Hydrocarbons
9.4.2 Polycyclic Aromatic Hydrocarbons
9.4.3 Petroleum Hydrocarbons
9.4.4 Pesticides and Herbicides
9.4.5 Heavy Metals
9.5 Recent Advances in Bioremediation Processes Using Biosurfactants and Future Prospects
9.5.1 Use of Immobilized Microorganisms and Contaminants
9.5.2 Novel Strains for Producing Biosurfactants
9.6 Applications of Biosurfactants in Agriculture
9.7 Conclusion
References
Chapter 10: Bioaugmentation-Assisted Phytoextraction Applied to Metal-Contaminated Soils: State of the Art and Future Prospect
10.1 Introduction
10.2 Mechanisms Driving Metal Extraction in Plant–Microorganism Systems
10.2.1 Metal Bioaccessibility as a Result of Microbial Mechanisms
10.2.2 Mechanisms Controlling Metal Uptake by Plants
10.3 Practical Issues and Recommendations with Phytoextraction-Assisted Bioaugmentation
10.3.1 Mutualistic and Symbiotic Relationships with Plants
10.3.2 Microbial Consortia
10.3.3 Factors Impairing Bioaugmentation Success
10.3.4 Genetically Engineered Microorganisms
10.4 Plants
10.4.1 Hyperaccumulators vs. High-Biomass Species
10.4.2 Mobilization of Metals by Plants: The Role of Siderophores and Phytosiderophores
10.4.3 Plant Development
10.4.4 Genetically Engineered Plants
10.5 Practical Recommendations for Selection of Plant–Microorganism Couples and Implementation of the Bioaugmentation-Phytoextraction Technique
10.5.1 Strategy for Choosing the Most Relevant Plant–Microorganism Couples
10.5.2 Preculture Conditions of Microbial Inoculants
10.5.3 Selection and Bioaugmentation with Consortia: More Efficient than Pure Culture?
10.5.4 Microbial Inoculant Formulations and Management
10.5.5 Culture Duration and Planting Density
10.5.6 Experiments on Field Scale
10.5.7 Economic Aspects of the Technique
10.6 Methods for a Better Understanding of the Mechanisms Involved in Bioaugmentation-Phytoextraction Processes
10.6.1 Methods for Inoculant Monitoring, Microbial Biodiversity, and Microbial Activity
10.6.2 Physicochemical and Biological Methods to Estimate Metal Bioavailability
10.7 Efficiency of Phytoextraction-Assisted Bioaugmentation
10.7.1 Evaluation of Phytoextraction Efficiency Must Incorporate Several Parameters
10.7.1.1 Plant Parameters
10.7.1.2 Microbial Parameters
10.7.1.3 Efficiency of Phytoextraction-Assisted Bioaugmentation
10.8 Environmental Aspects
10.9 Future Prospects
References
Chapter 11: Biosorption of Uranium for Environmental Applications Using Bacteria Isolated from the Uranium Deposits
11.1 Introduction
11.2 Screening of Microorganisms Isolated from U Deposits for Their U Accumulating Ability
11.2.1 Factors Affecting U Accumulation by Bacteria
11.2.2 Effect of pH on U Accumulation
11.2.3 Effect of U Concentration on U Absorption
11.2.4 Time Course of U Accumulation
11.2.5 Release of U from Cells by Washing with EDTA
11.2.6 Distribution of U in Microbial Cells
11.2.7 Selective Accumulation of U Using Arthrobacter, US-10 Cells
11.3 Accumulation of Th and Selective Accumulation of Th and U by Bacteria
11.3.1 Recovery of U by Immobilized Bacteria
11.3.2 Removal of U from U Refining Wastewater by Bacteria
11.3.3 Removal of U from Seawater by Bacteria
11.4 Conclusion
References
Chapter 12: Bacterial Biosorption: A Technique for Remediation of Heavy Metals
12.1 Introduction
12.2 Bacterial Biosorbents
12.2.1 Bacterial Structure
12.3 Mechanisms of Biosorption
12.4 Techniques Used in Metal Biosorption Studies
12.5 Factors Affecting Heavy Metal Biosorption
12.5.1 pH
12.5.2 Temperature
12.5.3 Initial Metal Ion Concentration
12.5.4 Initial Concentration of Biosorbent
12.5.5 Presence of Competing Ions
12.6 Development of Bacterial Biosorbents
12.7 Biosorption and Equilibrium Studies of Heavy Metals
12.7.1 Freundlich Isotherm
12.7.2 Langmuir Isotherm
12.7.3 Temkin Isotherm
12.7.4 Dubinin–Radushkevich Equation
12.7.5 Brunauer–Emmer–Teller (BET) Model
12.7.6 Redlich–Paterson Isotherm
12.7.7 Multicomponent Heavy Metals Biosorption
12.8 Kinetics of Heavy Metal Biosorption
12.8.1 Pseudo-First-Order Kinetics
12.8.2 Pseudo-Second-Order Kinetics
12.8.3 The Weber and Morris Sorption Kinetic Model
12.8.4 First-Order Reversible Reaction Model
12.9 Immobilization of Bacteria
12.10 Desorption of Heavy Metals
12.11 Biosorption and Its Column Performance
12.11.1 Column Regeneration
12.11.2 Sorption Column Model
12.12 Conclusion
12.13 Future Prospects
References
Chapter 13: Metal Tolerance and Biosorption Potential of Soil Fungi: Applications for a Green and Clean Water Treatment Technology
13.1 Introduction
13.2 Soil Fungi and Their Diversity
13.3 Heavy Metal Pollution in Water and Soil
13.4 Metal–Fungi Interactions and Development of Metal Resistance/Tolerance
13.5 Mechanisms of Metal Resistance and Tolerance
13.5.1 Metal Solubilization
13.5.2 Metal Immobilization
13.5.3 Metal Transformations
13.6 Biosorption
13.6.1 Biosorbents
13.6.2 Metal Binding to Cell Walls
13.6.2.1 Skeletal Elements
13.6.2.2 Matrix Components
13.6.2.3 Miscellaneous Components
13.6.3 Transport of Toxic Metal Cations
13.6.4 Metal Uptake by Living Cells
13.6.5 Intracellular Fate of Toxic Metals
13.6.6 Metal Transformations Within Fungi
13.6.7 Metal Sorption by Dead Cells
13.6.8 Mechanism of Biosorption
13.6.8.1 Extracellular Accumulation/Precipitation
13.6.8.2 Cell Surface Sorption/Precipitation
13.6.8.3 Intracellular Accumulation/Precipitation
13.6.9 Factors Affecting Heavy Metal Biosorption
13.6.9.1 Biomass Pretreatment Effect on Biosorption
13.7 Biosorption Potential of Fungal Biomass
13.8 Conclusions
References
Chapter 14: Rhizosphere and Root Colonization by Bacterial Inoculants and Their Monitoring Methods: A Critical Area in PGPR Research
14.1 Introduction
14.2 The Rhizosphere and Rhizospheric Effect
14.2.1 Rhizosphere Colonization
14.2.2 Competition for Root Niches and Bacterial Determinants Directly Involves Root Colonization
14.2.3 Biofilms in the Rhizosphere
14.2.4 Factors Affecting Root Colonization and Efficacy of Rhizobacteria
14.3 Monitoring of Microbial Inoculants (Biocontrol Agents/PGPR)
14.3.1 Microbiological Monitoring Methods
14.3.2 Direct Monitoring Methods
14.3.3 Molecular Monitoring Methods
14.3.4 Use of Reporter Genes
14.3.5 Green Fluorescent Protein
14.3.6 Lac Z and Lux Gene-Based Reporting Methods
14.3.7 Luciferase Gene
14.4 Conclusions and Future Prospects
References
Chapter 15: Pesticide Interactions with Soil Microflora: Importance in Bioremediation
15.1 Introduction
15.2 Toxicity of Pesticides to Soil Microorganisms and Plants
15.2.1 Insecticidal Impact on Rhizobacteria and Crops
15.3 Bioremediation
15.3.1 Bioremediation of Insecticides
15.3.1.1 Lindane and Its Isomers
Anaerobic Biodegradation Pathway
Aerobic Biodegradation Pathway
15.3.1.2 Biodegradation of Chlorpyrifos
15.3.1.3 Monocrotophos
15.4 Conclusion
References
Chapter 16: Baculovirus Pesticides: Present State and Future Perspectives
16.1 Introduction
16.2 State of Taxonomy and Biology of Baculoviruses
16.2.1 Taxonomy
16.2.2 Viral Life Cycle
16.2.3 Molecular Biology of Baculoviruses
16.3 Baculovirus Production Technology
16.3.1 In Vivo Production
16.3.2 In Vitro Production
16.4 Use of Baculoviruses for Pest Control
16.4.1 Use of the Alphabaculovirus of Anticarsia gemmatalis (AgMNPV) in Brazil and Latin America: A Case Study
16.4.1.1 Historical Perspective
16.4.1.2 AgMNPV Field Production
16.4.1.3 AgMNPV Commercial Laboratory Production: A Breakthrough
16.4.1.4 Why Did the AgMNPV Program Experience a Setback in Brazil?
16.5 Factors Limiting Baculovirus Use
16.6 Genetically Modified Baculoviruses to Control Insects
16.7 Final Considerations and Further Prospects on Use of Baculoviruses as Biopesticides
References
Chapter 17: Fungal Bioinoculants for Plant Disease Management
17.1 Introduction
17.1.1 Management of Plant Diseases
17.1.1.1 Biological Control
Bioinoculant Fungi and Mechanisms of Action
Fungistatic
Competition for Nutrients
Antibiosis
Mycoparasitism
Stimulation of Host Defense Response
Fungal Diseases and Their Management by Bioinoculants
In Vitro
Pot Culture
Field Conditions
Bioinoculants in IPM
Bacterial Diseases and Their Management
Nematode Diseases and Their Management
In Vitro Studies
Pot Conditions
Field Conditions
17.1.2 Production Technology of Bioinoculants
17.1.2.1 Pellet Formulations
17.1.2.2 Powder Formulations
17.1.2.3 Liquid Formulations
17.2 Conclusion
17.2.1 Future Recommendations
References
Chapter 18: Mycorrhizal Inoculants: Progress in Inoculant Production Technology
18.1 Introduction
18.2 Inocula Production of AM Fungi
18.2.1 Soil-Based Systems
18.2.2 Soil-Less Techniques
18.2.2.1 Aeroponic Culture
18.2.2.2 Monoxenic Culture
18.2.2.3 Nutrient Film Technique
18.2.2.4 Polymer-Based Inoculum
18.2.2.5 Integrated Method
18.3 Storage of AM Inocula
18.4 Inocula Production of Ectomycorrhizal Fungi
18.4.1 Formulation of ECM
18.4.2 Storage of ECM
18.5 Discussion
References
Index
downloadingf
megaupload.com [ندعوك للتسجيل في المنتدى أو التعريف بنفسك لمعاينة هذا الرابط]fileserve.com [ندعوك للتسجيل في المنتدى أو التعريف بنفسك لمعاينة هذا الرابط]mediafire.com [ندعوك للتسجيل في المنتدى أو التعريف بنفسك لمعاينة هذا الرابط]
موضوع: Microbes and Microbial Technology: Agricultural and Environmental Applications 
السبت مارس 12, 2011 8:33 am
