Microbes and Microbial Technology - Agricultural and Environmental Applications

Preface

About the Editors

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 Potentialof Soil Fungi: Applications for a Greenand 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 BacterialInoculants 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