Microbes and Microbial Technology - Agricultural and Environmental Applications

Microbes and Microbial Technology - Agricultural and Environmental Applications

von: Iqbal Ahmad, Farah Ahmad, John Pichtel

Springer-Verlag, 2011

ISBN: 9781441979315 , 516 Seiten

Format: PDF, OL

Kopierschutz: Wasserzeichen

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Mehr zum Inhalt

Microbes and Microbial Technology - Agricultural and Environmental Applications


 

Preface

6

About the Editors

10

Contents

12

Contributors

14

Chapter 1: Microbial Applications in Agriculture and the Environment: A Broad Perspective

18

1.1 Introduction

19

1.2 Approaches to Studying Soil Microbial Populations

20

1.2.1 Cultivation-Based Methods

20

1.2.2 Cultivation-Independent Methods

21

1.3 Functional Diversity of Microbes

21

1.4 Application in Agriculture and the Environment

21

1.4.1 Microbes in Plant Growth Promotion and Health Protection

22

1.4.1.1 Plant Growth-Promoting Fungi

24

1.4.2 Microbes in Environmental Problem Management

25

1.4.2.1 PAH Degradation

27

1.4.2.2 Microbes in Metal Removal from Water

28

1.4.2.3 PGPR in Biomanagement of Metal Toxicity

28

1.5 Microbial Biosensors and Their Applications

29

1.6 Microbes and Nanoparticles

30

1.6.1 Fungi in Nanoparticle Synthesis

32

1.7 Other New Applications

33

1.7.1 Microbes and Climate Change

33

1.7.2 Probiotics and Health

34

1.8 Conclusion

36

References

36

Chapter 2: Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment

45

2.1 Introduction

46

2.2 Culture Methods in Microbial Ecology: Applications and Limitations

47

2.3 Molecular Methods of Microbial Community Analyses

48

2.3.1 Partial Community Analysis Approaches

49

2.3.1.1 Clone Library Method

49

2.3.1.2 Genetic Fingerprinting Techniques

50

Denaturing- or Temperature-Gradient Gel Electrophoresis

50

Single-Strand Conformation Polymorphism

51

Random Amplified Polymorphic DNA and DNA Amplification Fingerprinting

51

Amplified Ribosomal DNA Restriction Analysis

52

Terminal Restriction Fragment Length Polymorphism

52

Length Heterogeneity PCR

53

Ribosomal Intergenic Spacer Analysis

54

2.3.1.3 DNA Microarrays

54

16S rRNA gene Microarrays (PhyloChip)

55

Functional Gene Arrays

55

2.3.1.4 Quantitative PCR

55

2.3.1.5 Fluorescence In Situ Hybridization

56

2.3.1.6 Microbial Lipid Analysis

57

2.3.2 Whole Community Analysis Approaches

57

2.3.2.1 DNA–DNA Hybridization Kinetics

58

2.3.2.2 Guanine-Plus-Cytosine Content Fractionation

58

2.3.2.3 Whole-Microbial-Genome Sequencing

59

2.3.2.4 Metagenomics

60

2.4 Next-Generation DNA Sequencing Techniques Transform Microbial Ecology

61

2.5 Functional Microbial Ecology: Linking Community Structure and Function

63

2.5.1 Stable Isotope Probing

63

2.5.2 Microautoradiography

64

2.5.3 Isotope Array

65

2.6 Postgenomic Approaches

65

2.6.1 Metaproteomics

66

2.6.2 Proteogenomics

67

2.6.3 Metatranscriptomics

67

2.7 Bias in Molecular Community Analysis Methods

68

2.8 Concluding Remarks and Future Directions

69

References

70

Chapter 3: The Biofilm Returns: Microbial Life at the Interface

74

3.1 Introduction

75

3.2 Biofilm: A Definition

76

3.3 Mechanism of Biofilm Formation

76

3.4 Biofilm Properties: Influence on Biofilm-Based Technologies

77

3.4.1 Extracellular Polymeric Substances: Role in Biofilm Reactor Performance

77

3.4.2 Biofilm Architecture: Role in Biofilm Reactor Performance

78

3.4.3 Quorum Sensing: Role in Bioreactor Cleanup

78

3.4.4 Antimicrobial Resistance: Role in Bioreactor Cleanup

78

3.4.5 Gene Transfer Within Biofilms: Role in Bioremediation

79

3.4.6 External Electron Transfer in Biofilms: Role in MFC Function

79

3.5 Application of Biofilms

79

3.5.1 Biofilms as Biocontrol Agents

79

3.5.1.1 Gram-Positive Bacterial Biofilms as Biocontrol Agents

80

3.5.2 Biofilms as Corrosion Inhibitors

80

3.5.2.1 Corrosion Inhibition by Biofilm Through Oxygen Removal

81

3.5.2.2 Corrosion Inhibition by Biofilms Secreting Antimicrobials

81

3.5.2.3 Corrosion Inhibition with Biofilms Secreting Corrosion Inhibitors

81

3.5.2.4 Corrosion Inhibition Through Protective Layers (Biofilm Matrix)

81

3.6 Biofilm-Based Technologies

82

3.6.1 Biofilm Reactors

82

3.6.1.1 Biofilm Reactors in Wastewater and Waste Gas Treatment

84

3.6.1.2 Biofilm Reactors in Bioremediation Process

84

Bioremediation of Hydrocarbons

87

Bioremediation of Heavy Metals

87

3.6.1.3 Biofilm Reactors in Productive Biocatalysis

89

3.6.2 Microbial Fuel Cells

91

3.6.2.1 Marine MFCs

92

3.6.2.2 Wastewater MFCs

92

3.6.2.3 Farm Field MFCs

92

3.6.2.4 Photosynthetic MFCs

92

3.6.2.5 Applications of MFCs

93

References

94

Chapter 4: Future Application of Probiotics: A Boon from Dairy Biology

101

4.1 Introduction

101

4.2 Probiotics as Antibiotics or Lactobiotics

102

4.3 LAB as an Immune Enhancer

103

4.4 Probiotics and GALT Immunity

104

4.5 The Demise of the Needle

107

4.5.1 Malaria

107

4.5.2 AIDS

108

4.5.3 Infantile Diarrhea

108

4.5.4 Trichomoniasis

109

4.5.5 Ischemic Heart Diseases

109

4.5.6 Gastritis, Peptic Ulcer, and Gastric Adenocarcinoma

110

4.6 Conclusion/Future Recommendations

110

References

111

Chapter 5: Microbially Synthesized Nanoparticles: Scope and Applications

115

5.1 Introduction

116

5.2 Nanoparticle Synthesis by Bacteria

118

5.2.1 Silver Nanoparticles

118

5.2.2 Gold Nanoparticles

120

5.2.3 Magnetic Nanoparticles

123

5.2.4 Uranium Nanoparticles

124

5.2.5 Cadmium Nanoparticles

125

5.2.6 Selenium Nanoparticles

126

5.2.7 Titanium, Platinum, and Palladium Nanoparticles

127

5.3 Nanoparticle Biosynthesis by Actinomycetes

128

5.4 Nanoparticle Biosynthesis by Cyanobacteria

128

5.5 Nanoparticle Biosynthesis by Yeast

128

5.6 Nanoparticle Biosynthesis by Fungi

129

5.7 Scope and Applications of Nanoparticles

131

5.8 Conclusions

133

References

133

Chapter 6: Bacterial Quorum Sensing and Its Interference: Methods and Significance

141

6.1 Introduction

141

6.2 Quorum Sensing Pathways in Bacteria

142

6.2.1 Autoinducer Type 1 Signaling System

142

6.2.2 Autoinducer Type 2 Signaling System

143

6.2.3 Autoinducer Type 3 System

144

6.2.4 Short Peptide Signaling (AIP) System in Gram-Positive Bacteria

144

6.3 QS Signal Molecules Diversity

144

6.3.1 Gram-Negative Bacteria

145

6.4 QS-Regulated Bacterial Traits

147

6.5 Isolation, Purification, and Characterization of AHL Molecules

148

6.6 Assays for AHL Detection

148

6.6.1 Detection Through Bioassays

148

6.6.2 Chemical Detection

149

6.6.3 Application of Microbial and Chemical Assays

150

6.7 Interferences in Bacterial Quorum Sensing

153

6.7.1 Inhibition of AHL-Mediated QS

154

6.7.1.1 Inhibition of Signal Molecule Biosynthesis

154

6.7.1.2 Blocking Signal Transduction

155

Synthetic Analogues for Quorum Sensing Autoinducers

155

Modification of the Acyl Side Chain

157

Modification of the Lactone Ring

158

Simultaneous Modifications on Both the Lactone Ring and Side Chain

158

6.7.1.3 Chemical Inactivation and Biodegradation of Signal Molecules

158

Chemical Inactivation

159

Biodegradation

159

6.7.2 Inhibition of Other Quorum-Sensing Systems

160

6.7.3 Quorum-Sensing Inhibitors Expressed by Higher Organisms

160

6.7.3.1 Inhibition of QS by Halogenated Furanone Compounds

161

6.7.3.2 Inhibition of QS by Plant Products

163

6.7.4 Practical Significance of Bacterial QS Modulation in the Environment/Agriculture

164

6.7.4.1 Roles of AHL-Degradation Enzymes in Host

164

6.7.4.2 Biotechnological and Pharmaceutical Implications of AHL Degradation Enzymes

164

6.7.4.3 Transgenic Plants

165

6.8 Conclusion

166

References

167

Chapter 7: Horizontal Gene Transfer Between Bacteria Under Natural Conditions

176

7.1 Introduction

176

7.2 Horizontal Gene Transfer in Soil, Sediments, and Other Solid Surfaces

177

7.2.1 Environmental Factors Affecting HGT in Nature

178

7.2.2 Tools to Study Horizontal Gene Transfer in the Environment

178

7.3 Plasmid-Mediated Gene Mobilization in Soil

179

7.3.1 Horizontal Gene Transfer in Metal- and Radionuclide-Contaminated Soils and Sediments

180

7.3.2 Horizontal Gene Transfer in Mixed Waste Sites

182

7.3.3 Horizontal Gene Transfer in Agricultural Soils

183

7.4 Horizontal Gene Transfer in Aquatic Environments

185

7.4.1 Evidence of Plasmid Transfer in Aquatic Environments

185

7.4.2 Evidence of Plasmid Transfer in Sewage Filter Beds and Activated Sludge Units

186

7.5 Modeling of Conjugative Plasmid Transfer

186

7.6 Monitoring Horizontal Gene Transfer and Assessing Transfer Frequencies

188

7.7 Spread of Biodegradation Traits

189

7.8 Conclusions

191

7.9 Future Recommendations

191

References

192

Chapter 8: Molecular Strategies: Detection of Foodborne Bacterial Pathogens

201

8.1 Introduction

201

8.2 Molecular Typing Methods for the Detection of Bacterial Pathogens

203

8.2.1 PCR-Based Detection Methods

203

8.2.1.1 Multiplex PCR and Real-Time PCR

203

8.2.1.2 Random Amplified Polymorphic DNA

205

8.2.1.3 Restriction Fragment Length Polymorphism

205

8.2.1.4 Amplified Fragment Length Polymorphism

206

8.2.2 Pulsed-Field Gel Electrophoresis

207

8.2.3 Biosensors

208

8.2.4 Microarrays

209

8.2.5 Integrated Systems

210

8.3 Conclusions and Future Prospectives

211

References

213

Chapter 9: Recent Advances in Bioremediation of Contaminated Soil and Water Using Microbial Surfactants

219

9.1 Introduction

219

9.2 Microbial Surfactants/Biosurfactants

220

9.2.1 Sources and Types of Biosurfactants

220

9.2.2 Important Properties of Biosurfactants

223

9.2.3 Surface and Interfacial Tension Reduction

223

9.2.4 Emulsification and De-emulsification Activity

224

9.2.5 Biodegradability

224

9.2.6 Low Toxicity

224

9.3 Remediation of Contaminated Soil and Water Using Different Physical, Chemical, and Biological Techniques

225

9.3.1 Physical Techniques

225

9.3.2 Chemical Techniques

225

9.3.3 Biological Techniques or Bioremediation

226

9.3.3.1 Ex Situ Bioremediation

227

9.4 Bioremediation of Contaminated Soil and Water Using Biosurfactants

228

9.4.1 Hydrocarbons

228

9.4.2 Polycyclic Aromatic Hydrocarbons

228

9.4.3 Petroleum Hydrocarbons

229

9.4.4 Pesticides and Herbicides

231

9.4.5 Heavy Metals

233

9.5 Recent Advances in Bioremediation Processes Using Biosurfactants and Future Prospects

235

9.5.1 Use of Immobilized Microorganisms and Contaminants

235

9.5.2 Novel Strains for Producing Biosurfactants

236

9.6 Applications of Biosurfactants in Agriculture

236

9.7 Conclusion

236

References

237

Chapter 10: Bioaugmentation-Assisted Phytoextraction Applied to Metal-Contaminated Soils: State of the Art and Future Prospect

241

10.1 Introduction

241

10.2 Mechanisms Driving Metal Extraction in Plant–Microorganism Systems

242

10.2.1 Metal Bioaccessibility as a Result of Microbial Mechanisms

243

10.2.2 Mechanisms Controlling Metal Uptake by Plants

244

10.3 Practical Issues and Recommendations with Phytoextraction-Assisted Bioaugmentation

245

10.3.1 Mutualistic and Symbiotic Relationships with Plants

245

10.3.2 Microbial Consortia

247

10.3.3 Factors Impairing Bioaugmentation Success

247

10.3.4 Genetically Engineered Microorganisms

248

10.4 Plants

248

10.4.1 Hyperaccumulators vs. High-Biomass Species

248

10.4.2 Mobilization of Metals by Plants: The Role of Siderophores and Phytosiderophores

249

10.4.3 Plant Development

250

10.4.4 Genetically Engineered Plants

250

10.5 Practical Recommendations for Selection of Plant–Microorganism Couples and Implementation of the Bioaugmentation-Phytoextraction Technique

251

10.5.1 Strategy for Choosing the Most Relevant Plant–Microorganism Couples

251

10.5.2 Preculture Conditions of Microbial Inoculants

255

10.5.3 Selection and Bioaugmentation with Consortia: More Efficient than Pure Culture?

255

10.5.4 Microbial Inoculant Formulations and Management

256

10.5.5 Culture Duration and Planting Density

257

10.5.6 Experiments on Field Scale

258

10.5.7 Economic Aspects of the Technique

258

10.6 Methods for a Better Understanding of the Mechanisms Involved in Bioaugmentation-Phytoextraction Processes

258

10.6.1 Methods for Inoculant Monitoring, Microbial Biodiversity, and Microbial Activity

258

10.6.2 Physicochemical and Biological Methods to Estimate Metal Bioavailability

260

10.7 Efficiency of Phytoextraction-Assisted Bioaugmentation

261

10.7.1 Evaluation of Phytoextraction Efficiency Must Incorporate Several Parameters

261

10.7.1.1 Plant Parameters

261

10.7.1.2 Microbial Parameters

262

10.7.1.3 Efficiency of Phytoextraction-Assisted Bioaugmentation

262

10.8 Environmental Aspects

263

10.9 Future Prospects

263

References

266

Chapter 11: Biosorption of Uranium for Environmental Applications Using Bacteria Isolated from the Uranium Deposits

279

11.1 Introduction

279

11.2 Screening of Microorganisms Isolated from U Deposits for Their U Accumulating Ability

280

11.2.1 Factors Affecting U Accumulation by Bacteria

281

11.2.2 Effect of pH on U Accumulation

281

11.2.3 Effect of U Concentration on U Absorption

283

11.2.4 Time Course of U Accumulation

285

11.2.5 Release of U from Cells by Washing with EDTA

286

11.2.6 Distribution of U in Microbial Cells

286

11.2.7 Selective Accumulation of U Using Arthrobacter, US-10 Cells

288

11.3 Accumulation of Th and Selective Accumulation of Th and U by Bacteria

288

11.3.1 Recovery of U by Immobilized Bacteria

290

11.3.2 Removal of U from U Refining Wastewater by Bacteria

290

11.3.3 Removal of U from Seawater by Bacteria

292

11.4 Conclusion

292

References

293

Chapter 12: Bacterial Biosorption: A Technique for Remediation of Heavy Metals

294

12.1 Introduction

295

12.2 Bacterial Biosorbents

295

12.2.1 Bacterial Structure

296

12.3 Mechanisms of Biosorption

300

12.4 Techniques Used in Metal Biosorption Studies

302

12.5 Factors Affecting Heavy Metal Biosorption

302

12.5.1 pH

302

12.5.2 Temperature

304

12.5.3 Initial Metal Ion Concentration

304

12.5.4 Initial Concentration of Biosorbent

304

12.5.5 Presence of Competing Ions

305

12.6 Development of Bacterial Biosorbents

306

12.7 Biosorption and Equilibrium Studies of Heavy Metals

307

12.7.1 Freundlich Isotherm

307

12.7.2 Langmuir Isotherm

308

12.7.3 Temkin Isotherm

310

12.7.4 Dubinin–Radushkevich Equation

310

12.7.5 Brunauer–Emmer–Teller (BET) Model

311

12.7.6 Redlich–Paterson Isotherm

311

12.7.7 Multicomponent Heavy Metals Biosorption

312

12.8 Kinetics of Heavy Metal Biosorption

312

12.8.1 Pseudo-First-Order Kinetics

313

12.8.2 Pseudo-Second-Order Kinetics

314

12.8.3 The Weber and Morris Sorption Kinetic Model

315

12.8.4 First-Order Reversible Reaction Model

315

12.9 Immobilization of Bacteria

316

12.10 Desorption of Heavy Metals

317

12.11 Biosorption and Its Column Performance

318

12.11.1 Column Regeneration

320

12.11.2 Sorption Column Model

320

12.12 Conclusion

321

12.13 Future Prospects

322

References

322

Chapter 13:Metal Tolerance and Biosorption Potentialof Soil Fungi: Applications for a Greenand Clean Water Treatment Technology

331

13.1 Introduction

331

13.2 Soil Fungi and Their Diversity

333

13.3 Heavy Metal Pollution in Water and Soil

335

13.4 Metal–Fungi Interactions and Development of Metal Resistance/Tolerance

337

13.5 Mechanisms of Metal Resistance and Tolerance

338

13.5.1 Metal Solubilization

339

13.5.2 Metal Immobilization

341

13.5.3 Metal Transformations

341

13.6 Biosorption

341

13.6.1 Biosorbents

342

13.6.2 Metal Binding to Cell Walls

343

13.6.2.1 Skeletal Elements

343

13.6.2.2 Matrix Components

343

13.6.2.3 Miscellaneous Components

343

13.6.3 Transport of Toxic Metal Cations

344

13.6.4 Metal Uptake by Living Cells

344

13.6.5 Intracellular Fate of Toxic Metals

344

13.6.6 Metal Transformations Within Fungi

345

13.6.7 Metal Sorption by Dead Cells

346

13.6.8 Mechanism of Biosorption

346

13.6.8.1 Extracellular Accumulation/Precipitation

346

13.6.8.2 Cell Surface Sorption/Precipitation

347

13.6.8.3 Intracellular Accumulation/Precipitation

348

13.6.9 Factors Affecting Heavy Metal Biosorption

349

13.6.9.1 Biomass Pretreatment Effect on Biosorption

349

13.7 Biosorption Potential of Fungal Biomass

350

13.8 Conclusions

357

References

358

Chapter 14:Rhizosphere and Root Colonization by BacterialInoculants and Their Monitoring Methods:A Critical Area in PGPR Research

372

14.1 Introduction

373

14.2 The Rhizosphere and Rhizospheric Effect

374

14.2.1 Rhizosphere Colonization

375

14.2.2 Competition for Root Niches and Bacterial Determinants Directly Involves Root Colonization

376

14.2.3 Biofilms in the Rhizosphere

377

14.2.4 Factors Affecting Root Colonization and Efficacy of Rhizobacteria

379

14.3 Monitoring of Microbial Inoculants (Biocontrol Agents/PGPR)

380

14.3.1 Microbiological Monitoring Methods

380

14.3.2 Direct Monitoring Methods

382

14.3.3 Molecular Monitoring Methods

383

14.3.4 Use of Reporter Genes

385

14.3.5 Green Fluorescent Protein

386

14.3.6 Lac Z and Lux Gene-Based Reporting Methods

387

14.3.7 Luciferase Gene

389

14.4 Conclusions and Future Prospects

389

References

391

Chapter 15: Pesticide Interactions with Soil Microflora: Importance in Bioremediation

401

15.1 Introduction

401

15.2 Toxicity of Pesticides to Soil Microorganisms and Plants

402

15.2.1 Insecticidal Impact on Rhizobacteria and Crops

402

15.3 Bioremediation

406

15.3.1 Bioremediation of Insecticides

408

15.3.1.1 Lindane and Its Isomers

409

Anaerobic Biodegradation Pathway

409

Aerobic Biodegradation Pathway

410

15.3.1.2 Biodegradation of Chlorpyrifos

412

15.3.1.3 Monocrotophos

415

15.4 Conclusion

417

References

418

Chapter 16: Baculovirus Pesticides: Present State and Future Perspectives

422

16.1 Introduction

423

16.2 State of Taxonomy and Biology of Baculoviruses

423

16.2.1 Taxonomy

423

16.2.2 Viral Life Cycle

424

16.2.3 Molecular Biology of Baculoviruses

426

16.3 Baculovirus Production Technology

429

16.3.1 In Vivo Production

429

16.3.2 In Vitro Production

429

16.4 Use of Baculoviruses for Pest Control

431

16.4.1 Use of the Alphabaculovirus of Anticarsia gemmatalis (AgMNPV) in Brazil and Latin America: A Case Study

434

16.4.1.1 Historical Perspective

434

16.4.1.2 AgMNPV Field Production

436

16.4.1.3 AgMNPV Commercial Laboratory Production: A Breakthrough

437

16.4.1.4 Why Did the AgMNPV Program Experience a Setback in Brazil?

438

16.5 Factors Limiting Baculovirus Use

438

16.6 Genetically Modified Baculoviruses to Control Insects

439

16.7 Final Considerations and Further Prospects on Use of Baculoviruses as Biopesticides

444

References

445

Chapter 17: Fungal Bioinoculants for Plant Disease Management

453

17.1 Introduction

453

17.1.1 Management of Plant Diseases

455

17.1.1.1 Biological Control

456

Bioinoculant Fungi and Mechanisms of Action

456

Fungistatic

457

Competition for Nutrients

458

Antibiosis

459

Mycoparasitism

460

Stimulation of Host Defense Response

461

Fungal Diseases and Their Management by Bioinoculants

462

In Vitro

463

Pot Culture

464

Field Conditions

465

Bioinoculants in IPM

467

Bacterial Diseases and Their Management

467

Nematode Diseases and Their Management

469

In Vitro Studies

471

Pot Conditions

473

Field Conditions

474

17.1.2 Production Technology of Bioinoculants

475

17.1.2.1 Pellet Formulations

475

17.1.2.2 Powder Formulations

476

17.1.2.3 Liquid Formulations

480

17.2 Conclusion

482

17.2.1 Future Recommendations

483

References

483

Chapter 18: Mycorrhizal Inoculants: Progress in Inoculant Production Technology

495

18.1 Introduction

496

18.2 Inocula Production of AM Fungi

496

18.2.1 Soil-Based Systems

497

18.2.2 Soil-Less Techniques

498

18.2.2.1 Aeroponic Culture

498

18.2.2.2 Monoxenic Culture

498

18.2.2.3 Nutrient Film Technique

499

18.2.2.4 Polymer-Based Inoculum

500

18.2.2.5 Integrated Method

500

18.3 Storage of AM Inocula

501

18.4 Inocula Production of Ectomycorrhizal Fungi

502

18.4.1 Formulation of ECM

505

18.4.2 Storage of ECM

506

18.5 Discussion

507

References

508

Index

513