Cover

Title Page

Copyright

Contents

List of Contributors

Preface

Chapter 1 Biofilms: An Overview of Their Significance in Plant and Soil Health

1.1 Introduction

1.2 Biofilm Associated with Plants

1.3 Biofilm Formation Mechanisms: Recent Update on Key Factors

1.4 Biofilm in Soil and Rhizospheres

1.5 Genetic Exchange in Biofilms

1.6 Diversity and Function of Soil Biofilms

1.7 The Role of Biofilms in Competitive Colonization by PGPR

1.8 Biofilm Synergy in Soil and Environmental Microbes

1.9 Biofilms in Drought Stress Management

1.10 Plant Health and Biofilm

1.11 How Microbial Biofilms Influence Plant Health?

1.12 Soil Health and Biofilms

1.13 How to Assess Soil Health?

1.14 Impact of Biofilms on Soil Health

1.15 Biofilm EPS in Soil Health

1.16 Conclusions and Future Directions

References

Chapter 2 Role of PGPR in Biofilm Formations and Its Importance in Plant Health

2.1 Introduction

2.2 Rhizosphere: A Unique Source of Microorganisms for Plant Growth Promotion

2.3 Plant Growth–Promoting Rhizobacteria

2.3.1 Direct Impact of Plant Growth–Promoting Rhizobacteria on Plant Nutrition

2.3.1.1 Nitrogen Fixation

2.3.1.2 Phosphorus Solubilization

2.3.1.3 Potassium Solubilization

2.3.1.4 Siderophore Production

2.3.1.5 Phytohormone Production

2.3.1.6 Indole Acetic Acid (IAA) Production

2.3.1.7 Gibberellins and Cytokinins Production

2.3.2 In Direct Impact of Plant Growth–Promoting Rhizobacteria on Plant Nutrition

2.3.2.1 Antibiotic Production

2.3.2.2 Enzyme Production

2.3.2.3 Induced Systemic Resistance

2.3.2.4 Hydrogen Cyanide Production

2.3.2.5 Exopolysaccharides Production or Biofilm Formation

2.4 Biofilm Producing Plant Growth–Promoting Rhizobacteria

2.5 Role of PGPR in Biofilm Formations

2.6 Future Research and Development Strategies for Biofilm Producing Sustainable Technology

2.7 Conclusions

Acknowledgments

References

Chapter 3 Concept of Mono and Mixed Biofilms and Their Role in Soil and in Plant Association

3.1 Introduction

3.2 Soil- and Plant-Associated Biofilms

3.3 Microbial Signaling, Regulation, and Quorum Sensing

3.4 Biotechnology

3.5 Outlook

Acknowledgments

References

Chapter 4 Bacillus Biofilms and Their Role in Plant Health

4.1 Introduction

4.2 Interaction of Bacillus within Plant Rhizosphere and Biofilm Development

4.3 Multispecies Biofilms and Their Significance

4.4 Biofilm Detection and Characterization

4.5 Bacillus Biofilm and Plant Health Promotion

4.6 Conclusion and Future Prospects

References

Chapter 5 Biofilm Formation by Pseudomonas spp. and Their Significance as a Biocontrol Agent

5.1 Introduction

5.2 Biofilms

5.3 Mechanisms of Biofilm Formation

5.3.1 Quorum Sensing

5.3.2 Regulation in Response to Phosphorus Starvation

5.3.3 Phase Variation

5.3.4 Motility and Chemotaxis

5.3.5 Surface Adhesins

5.3.6 Biofilm Matrix Components

5.4 Metabolites Affecting Biofilm Formation

5.4.1 Plant Defense Compounds

5.4.2 Phenazine

5.4.3 Surfactants

5.5 Biofilm Formation and Biological Control of Plant Diseases

5.6 Conclusion

References

Chapter 6 Quorum Sensing Mechanisms in Rhizosphere Biofilms

6.1 Background

6.2 QS in Biofilms Formation

6.2.1 Positive Interactions

6.2.1.1 Plant Growth–Promoting Rhizobacteria (PGPR)

6.2.1.2 Rhizobia

6.2.2 Negative Interactions

6.2.3 Cross‐Communication

6.3 Conclusions

References

Chapter 7 Biofilm Formation and Quorum Sensing in Rhizosphere

7.1 Introduction

7.2 Importance of Rhizosphere

7.3 Constituents of Rhizosphere

7.3.1 Physical/Chemical

7.3.2 Rhizosphere—A Hot Niche of Microbial Activity

7.3.2.1 Bacteria

7.3.2.2 Fungi

7.3.2.3 Actinomycetes and Protozoa

7.4 Communication in Rhizosphere

7.5 Quorum Sensing in Rhizobia

7.5.1 Quorum Sensing in Rhizobium

7.5.1.1 cinI and cinR

7.5.1.2 raiI and raiR

7.5.1.3 rhiI and rhiR

7.5.1.4 traI and traR

7.5.2 Quorum Sensing in Sinorhizobium

7.5.2.1 sinI and sinR

7.5.2.2 expR

7.5.2.3 traI, traR and melI

7.5.3 Quorum Sensing in Mesorhizobium

7.6 Quorum Sensing in Pseudomonads

7.6.1 Quorum Sensing in Pseudomonas aeruginosa

7.6.1.1 Las System

7.6.1.2 Rhl System

7.6.1.3 PQS System

7.6.2 Quorum Sensing in Other Pseudomonads

7.7 Biofilm Formation in Rhizosphere

7.7.1 Beneficial Root Biofilm

7.7.2 Pathogenic Root Biofilm

7.7.3 Mixed-Species Biofilm

7.8 Conclusions

References

Chapter 8 The Significance of Fungal Biofilms in Association with Plants and Soils

8.1 Introduction

8.2 What Is a Biofilm?

8.3 Where Do We Find Filamentous Fungal Biofilms?

8.4 Fungal Biofilms: What Have We Learned from the Budding Yeasts?

8.5 What Does a Filamentous Fungal Biofilm Look Like?

8.6 Examples of Filamentous Fungal Biofilms

8.6.1 Ascomycete Biofilms

8.6.2 Zygomycete Biofilms

8.6.3 Basidiomycete Biofilms

8.6.4 Oomycete Biofilms

8.7 Examples of Fungal Biofilms in Soils and the Rhizosphere

8.7.1 Mycorrhizae

8.7.2 Ectomycorrhizae as a Biofilm

8.7.3 A Brief Look at Endomycorrhiza as a Biofilm

8.8 The Mycorhizosphere

8.9 A Biofilm Approach to Plant Disease Management

References

Chapter 9 Chemical Nature of Biofilm Matrix and Its Significance

9.1 Introduction

9.2 Structural Composition of EPS

9.2.1 Exopolysaccharides of the Biofilm Matrix

9.2.1.1 Carbohydrate Content of Exopolysaccharides

9.2.1.2 Polysaccharides of Gram-Negative Bacteria

9.2.1.3 Polysaccharides and Related Compounds in Gram-Positive Bacteria

9.2.2 Proteins

9.2.3 eDNA

9.2.4 Surfactants and Lipids

9.2.5 Water

9.3 Properties of Matrices

9.4 Functions of the Extracellular Polymer Matrix: The Role of Matrix in Biofilm Biology

9.4.1 Role of EPS in Biofilm Architecture

9.4.2 Role of EPS in Mechanisms of Antimicrobial Resistance/Tolerance to Other Toxic Substances

9.5 Conclusion

Acknowledgments

References

Chapter 10 Root Exudates: Composition and Impact on Plant–Microbe Interaction

10.1 Introduction

10.2 Chemical Composition of Root Exudates and Their Significance

10.3 Root Exudates in Mediating Plant–Microbe Interaction in Rhizosphere (Negative and Positive Interactions)

10.4 Direct and Indirect Effect of Root Exudates on PGPR, Root Colonization, and in Stress Tolerance

10.4.1 Root Colonization

10.4.2 Root Exudates and Stress Tolerance

10.5 Role of Root Exudates in Biofilm Formation by PGPR

10.6 Role of Root Exudates in Protecting Plants Pathogenic Biofilm, Quorum Sensing Inhibition

10.7 Isolation of Root Exudates

10.8 Conclusion

References

Chapter 11 Biochemical and Molecular Mechanisms in Biofilm Formation of Plant-Associated Bacteria

11.1 Introduction

11.2 Plant-Associated Bacteria

11.3 Biofilms and Plant Pathogens

11.4 Molecular and Biochemical Mechanisms Involved in Biofilm Formation

11.4.1 Pseudomonas

11.4.2 Xanthomonas

11.4.3 Erwinia

11.4.4 Ralstonia

11.4.5 Pectobacterium carotovorum

11.4.6 Xylella fastidiosa

11.4.7 Agrobacterium tumefaciens

11.4.8 Dickeya

11.4.9 Clavibacter michiganensis

11.4.10 Bacillus subtilis

11.5 Conclusion

References

Chapter 12 Techniques in Studying Biofilms and Their Characterization: Microscopy to Advanced Imaging System in vitro and in situ

12.1 Introduction

12.2 Classical Techniques to Study Biofilms

12.2.1 Nucleic Acid Stains and FISH (in Combination with Epifluorescence Microscopy)

12.2.2 FISH and Confocal Laser Scanning Microscopy (CLSM)

12.3 The Gold Standard: Flow-Cell Technology and Confocal Laser Scanning Microscopy (CLSM)

12.4 The Biofilm Flow Cell

12.5 Advanced Digital Analysis of Confocal Microscopy Images

12.6 Biofilm Studies at Different Scales

12.6.1 Microscale: LSM and Structural Fluorescent Sensors

12.6.2 Nanoscale: Structured Illumination Microscopy (SIM) and Stimulated Emission Depletion (STED) Microscopy

12.6.3 Mesoscale: Optical Coherence Tomography (OCT) and Scanning Laser Optical Tomography (SLOTy)

12.7 Conclusions and Perspectives

Acknowledgments

References

Chapter 13 Gene Expression and Enhanced Antimicrobial Resistance in Biofilms

13.1 Introduction

13.2 Biofilms in the Plant–Microbe Relationship

13.2.1 Biofilm Formation in the Vascular System (Xylem)

13.2.2 Biofilm Formation in Rizosphere (Roots)

13.3 Stress Induces Biofilm Formation

13.4 Relevance for Bacterial-Associated Plants

13.5 Enhanced Antimicrobial Resistance in Biofilms Is Mediated by Biofilm Physicochemical Characteristics and Specific Changes in Gene Expression

13.6 Potential for Implementing Antibiofilm Strategies to Protect Crops

13.6 Conclusions

Acknowledgments

References

Chapter 14 In Vitro Assessment of Biofilm Formation by Soil- and Plant-Associated Microorganisms

14.1 Introduction

14.2 How to Make a Biofilm

14.3 What Is the Best Way to Make a Biofilm in Vitro?

14.4 Flow Systems

14.4.1 Continuous Plug Flow Reactors

14.4.1.1 Flow Cells

14.4.1.2 Tube Biofilms

14.4.1.3 Drip-Flow Reactor

14.4.1.4 Perfused Biofilm Fermenters

14.4.2 Continuous Flow Stirred Tank Reactors

14.4.2.1 CDC Biofilm Reactor

14.4.2.2 Rotating Disk, Concentric Cylinder, and Annular Reactors

14.5 Static Reactors

14.5.1 Microtiter Plate Assay

14.5.2 MBEC™ Assay

14.5.3 Colony Biofilm Assay

14.6 Special Considerations for Filamentous Fungal Biofilms

14.7 Biofilm Reactors Used to Characterize Plant-Associated Biofilms

14.8 Value-Added Products from Biofilm Reactors

References

Chapter 15 Factors Affecting Biofilm Formation in in vitro and in the Rhizosphere

15.1 Introduction

15.2 Process of Biofilm Formation

15.2.1 Attachment

15.2.2 Maturation of the Biofilm

15.2.3 Detachment and Return to the Planktonic Growth Mode

15.3 Factor Influencing Biofilm Formation

15.3.1 Surfaces

15.3.2 Temperature and Moisture Content

15.3.3 Salinity

15.3.4 Nutrient Availability

15.3.5 Microbial Products

15.3.5.1 QS Signal Molecules in Biofilm Formation

15.3.5.2 Antimicrobial Peptides

15.3.5.3 Exopolysaccarides

15.3.6 Soil Enzymes

15.4 Conclusions and Future Direction

References

Chapter 16 Ecological Significance of Soil-Associated Plant Growth–Promoting Biofilm-Forming Microbes for Stress Management

16.1 Introduction

16.2 Rhizosphere Hub of Plant–Microbe Interactions

16.3 Commencement of Rhizosphere Effect and Bacterial Colonization by Root Exudates

16.3.1 Rhizosphere Effect

16.3.2 Rhizosphere Competence

16.3.3 Involvement of Genes and Traits in Rhizosphere Colonization

16.4 Quorum Sensing as a Way of Interaction between Bacteria and Host Plant

16.5 Biofilms

16.5.1 Why Microorganisms Form Biofilms

16.5.2 Composition of Biofilms

16.5.2.1 Extrapolymeric Substance

16.5.2.2 Water

16.5.2.3 Biomolecules

16.5.3 Mechanism of Biofilm Formation

16.5.3.1 Surface Attachment of Bacteria

16.5.3.2 Microcolony Formation

16.5.3.3 Matured Biofilm and Dispersion

16.5.4 Dynamics of Biofilms

16.5.4.1 Nutritional Conditions

16.5.4.2 Surface Characteristics

16.5.4.3 Exopolysaccharides

16.5.4.4 Flagella and Motility

16.5.4.5 Quorum Sensing Signals

16.5.4.6 Gene Expression

16.5.4.7 Shear Stress

16.5.4.8 Phenazines

16.6 Effects of Stress on Plants

16.6.1 Abiotic Stress

16.6.1.1 Drought Stress in Plants

16.6.1.2 Salinity Stress in Plants

16.6.1.3 Flooding Stress in Plants

16.6.1.4 Heat Stress in Plants

16.6.1.5 Oxidative Stress in Plants

16.6.2 Biotic Stress in Plants

16.7 Stress Tolerance in Plants

16.7.1 Adaptation Mechanisms of Plants Toward Abiotic Stress

16.7.2 Management of Abiotic and Biotic Stresses in Plants

16.7.2.1 Phytohormone Production

16.7.2.2 Maintenance of Nutrient Content

16.7.2.3 Nitrogen Fixation

16.7.2.4 Phosphorous Solubilization

16.7.2.5 Siderophore Production

16.7.2.6 Exopolysaccharide (EPS) Production

16.7.2.7 ACC Deaminase Activity

16.7.2.8 Volatile Organic Compounds (VOCs)

16.7.2.9 PGPR as Biotic Elicitors

16.7.2.10 Induction of Systemic Disease Resistance

16.7.3 Management of Abiotic and Biotic Stress in Plants via Biofilm‐Forming Rhizobacteria

16.7.3.1 Salt Stress Amelioration

16.7.3.2 Drought Stress Amelioration

16.7.3.3 Temperature

16.7.3.4 Metal Transformation

16.7.3.5 Biocontrol Activity

16.7.4 Stress Management via Quorum Sensing Signals Producing PGPR

16.8 Conclusion

16.9 Future Perspectives

Acknowledgments

List of Abbreviations

References

Chapter 17 Developed Biofilm-Based Microbial Ameliorators for Remediating Degraded Agroecosystems and the Environment

17.1 Introduction

17.2 Developed Microbial Communities as a Potential Tool to Regenerate Degraded Agroecosystems

17.3 Biochemistry of Fungal-Bacterial Biofilms

17.4 Endophytic Microbial Colonization with the Application of Fungal-Bacterial Biofilms

17.5 Biofilm Biofertilizers for Restoration of Conventional Agroecosystems

17.6 Developed Microbial Biofilms for Environmental Bioremediation

17.6.1 Fungal-Bacterial Biofilms for Heavy Metal Bioremediation in Soil–Plant Environment

17.6.2 Fungal-Bacterial Biofilms for Heavy Metal Bioremediation in Wastewater

17.7 Conclusion

References

Chapter 18 Plant Root–Associated Biofilms in Bioremediation

18.1 Introduction

18.2 Biofilms: Definition and Biochemical Composition

18.3 Bioremediation and Its Significance

18.4 Root-Associated Biofilms

18.4.1 Microbial Biofilm Associations on Plant Root Surface

18.4.2 Formation of Rhizospheric Biofilms by PGPR and Their Application

18.4.3 Role of Root Exudates in Triggering Biofilm Formation

18.4.4 Consequences of Root-Associated Biofilms on Plant Growth

18.5 Bioremediation of Contaminants in Rhizospheric Soils

18.5.1 Rhizosphere, Rhizodeposition, and Bioremediation

18.5.2 Bioremediation of Xenobiotics

18.5.3 Bioremediation of Heavy Metal(loid)s

18.5.4 Rhizobacteria Facilitating Bioremediation

18.5.5 Metal Accumulating Rhizobacteria

18.5.6 Role of Root Exudates in Heavy Metal Decontamination and Degradation of Organic Pollutants

18.6 Implications of Rhizospheric Biofilm Formation on Bioremediation

18.7 Conclusion and Future Prospects

Acknowledgments

References

Chapter 19 Biofilms for Remediation of Xenobiotic Hydrocarbons— A Technical Review

19.1 Introduction

19.1.1 Conventional Bioremediation Technologies

19.1.2 Composition and Properties of Biofilms

19.1.3 Unique Properties of Biofilms

19.1.4 Significance of Biofilms to Environmental Remediation

19.1.5 Objectives

19.2 Polycyclic Aromatic Hydrocarbons

19.2.1 Microbiology of PAH Degradation

19.2.2 Biofilm Processes and PAH Degradation

19.2.3 Microbial Production of Surfactant Molecules

19.2.4 Application of Surfactants

19.2.5 Degradation of PAHs in Biofilm Reactors

19.3 Chlorinated Ethanes, Ethenes, and Aromatics

19.3.1 Chlorinated Ethanes

19.3.1.1 Microbiology of Biodegradation of Chlorinated Ethanes

19.3.1.2 Degradation of Chlorinated Ethanes in Biofilm Reactors

19.3.2 Chlorinated Ethenes

19.3.3 Degradation of Chlorinated Ethenes in Biofilm Reactors

19.4 Chlorinated Aromatics

19.4.1 Degradation of Chlorinated Aromatics in Biofilm Reactors

19.4.2 Benefits of Activated Charcoal and Other Organic Matrixes for Biofilm Reactors

19.5 Polychlorinated Biphenyls (PCBs)

19.5.1 Microbiology of PCB Biodegradation

19.5.2 Biofilms and PCB Degradation

19.5.3 Degradation of PCBs in Biofilm Reactors

19.6 Polychlorinated Dibenzodioxins

19.7 Conclusions

References

Chapter 20 Plant Pathogenic Bacteria: Role of Quorum Sensing and Biofilm in Disease Development

20.1 Introduction

20.2 Mechanism of Biofilm Formation

20.2.1 Biofilm Formation in Vitro in Plants

20.2.1.1 Gram‐Negative Bacteria

20.2.1.2 Gram‐Positive Bacteria

20.3 Quorum Sensing Mechanism

20.3.1 Quorum Sensing Regulated Virulence Factors

20.3.1.1 Mechanisms in Gram‐Negative Bacteria

20.3.1.2 Mechanisms in Gram‐Positive Bacteria

20.3.2 Biofilm Formation in Candida

20.4 Plant Pathogenic Bacteria Diversity and Plant Diseases

20.5 Blocking Quorum Sensing and Virulence in Combating Phytopathogen

20.6 Conclusion

References

Chapter 21 Biofilm Instigation of Plant Pathogenic Bacteria and Its Control Measures

21.1 Introduction

21.2 Plant Pathogens

21.2.1 Importance and Impact of Plant Pathogenic Bacteria

21.2.2 Plant Pathology and Plant Bacteriology: Historical Background

21.2.3 Classification of Plant Pathogenic Bacteria

21.2.3.1 Rhizosphere Pathogen

21.3 Plant Physiological Alteration by Plant Pathogens

21.3.1 Photosynthesis

21.3.2 Vascular Function

21.3.3 Root Function

21.3.4 Respiration

21.3.5 Transpiration

21.4 Virulence Strategies of Plant Pathogenic Bacteria

21.5 Biofilm Formations

21.5.1 Mechanism of Biofilm Formation

21.5.2 Molecular Insights on Biofilm Formation

21.5.3 Structural and Functional Components Involved in Biofilm Formation

21.5.3.1 Surface Bacterial Factors

21.5.3.2 Extracellular Factors Involved in Bacterial Autoaggregation

21.5.4 Factors Favoring Biofilm Formation

21.6 Biofilm Controlling Strategies in Plant Pathogens

21.7 Main Targets and Some Potential Tools to Modify Biofilms

21.8 Physical Tools for Modifying Biofilms

21.8.1 Modification of Biofilm Surfaces

21.8.2 Hydrophobicity, Surface Roughness, and Surface Charge

21.8.3 Exopolysaccharides

21.8.4 Applications of Hydrolytic Enzymes

21.8.5 Applications of Surface Active Compounds and Natural Products

21.8.6 Quorum Quenching

21.8.6.1 Compound Interfering Systems of AHLs

21.8.6.2 Compound Interfering with Regulation Molecules

21.8.6.3 Action of 3‐Indolyl Acetyl Nitrile

21.9 Chemical Methods

21.9.1 Inhibitors of Nucleotide Biosynthesis and DNA Replication as Antibiofilm Agents

21.9.2 Effect of Salicylic Acid on Biofilms

21.9.3 N‐acetyl Cysteine Effects on Biofilm

21.10 Biological Methods

21.10.1 Biosurfactants as Antibiofilm Agents

21.10.2 Phage Mediated Biocontrol as Antibiofilm Agents

21.11 Future Prospects of Antibiofilm

21.12 Conclusion

References

Chapter 22 Applications of Biofilm and Quorum Sensing Inhibitors in Food Protection and Safety

22.1 Introduction

22.2 Biofilm Formation by Foodborne Pathogens

22.3 Significance of Biofilms in Food and Food Environments

22.4 Biofilm Control Strategies in the Food Industry

22.5 Natural Products as Antibiofilm Agents and Their Potential Applications

22.6 Role of QS Inhibitors in Biofilm Control

22.7 Conclusions

Acknowledgments

References

Chapter 23 Biofilm Inhibition by Natural Products of Marine Origin and Their Environmental Applications

23.1 Introduction

23.2 Unity Is Strength: Benefits of Biofilm Formers

23.3 Transition of Slimy Film to Persistent Biofilm

23.4 Biofilm-Related Infections in Plants

23.5 Need for Antibiofilm Agents

23.6 Natural Products of Marine Origin as Antibiofilm Agents

23.7 Semi-synthetic Antibiofilm Agents Inspired by Marine Natural Products

23.8 Environmental Applications of Antibiofilm Agents

23.9 Conclusion

References

Chapter 24 Plant-Associated Biofilms Formed by Enteric Bacterial Pathogens and Their Significance

24.1 Introduction

24.2 Enteric Pathogens in the Plant Environment

24.3 Colonization and Biofilm Formation by Enteric Bacteria on Plant Surfaces

24.4 Biofilm Regulation in Enteric Bacteria

24.5 Influence of Plant Defense on Survival and Biofilm Formation by Enteropathogens

24.6 Plant-Associated Enteric Bacteria in Food Safety and Human Health

24.7 Conclusions

References

Chapter 25 Anti-QS/Anti-Biofilm Agents in Controlling Bacterial Disease: An in silico Approach

25.1 Introduction

25.2 Biofilm and Its Significance

25.3 Bioinformatics Approaches in Drug Target Identification and Drug Discovery

25.4 Target Identification Using in silico Technologies

25.5 Data Resources for Drug Target Identification

25.6 Homology Modeling

25.7 Docking

25.8 Virtual Screening

25.9 Application of Bioinformatics in Development of Anti-QS/anti-biofilm Agents

25.10 Virtual Screening for Identification of QS Inhibitors

25.11 Conclusion

References

Index

Supplemental Images

EULA