Biofilms in Plant and Soil Health

Biofilms are predominant mode of life for microbes under natural conditions. The three-dimensional structure of the biofilm provides enhanced protection from physical, chemical and biological stress conditions to associated microbial communities. These complex and highly structured microbial communities play a vital role in maintaining the health of plants, soils and waters. Biofilm associated with plants may be pathogenic or beneficial based on the nature of their interactions. Pathogenic or undesirable biofilm requires control in many situations, including soil, plants, food and water.

Written by leading experts from around the world, Biofilms in Plant and Soil Health provides an up-to-date review on various aspects of microbial biofilms, and suggests future and emerging trends in biofilms in plant and soil health.

Issues are addressed in four sub areas:

I) The fundamentals and significance of biofilm in plant and soil health, and the concept of mono and mixed biofilms by PGPR and fungal biofilms.

II) Biochemical and molecular mechanisms in biofilm studies in plant associated bacteria, and techniques in studying biofilms and their characterization, gene expression and enhanced antimicrobial resistance in biofilms, as well as biotic and biotic factors affecting biofilm in vitro.

III) The ecological significance of soil associated biofilms and stress management and bioremediation of contaminated soils and degraded ecosystems.

IV) Pathogenic biofilm associated with plant and food and its control measures.

This book is recommended for students and researchers working in agricultural and environmental microbiology, biotechnology, soil sciences, soil and plant health and plant protection. Researchers working in the area of quorum sensing, biofilm applications, and understanding microbiome of soil and plants will also find it useful.

Preface xviii

List of Contributors xx

1 Biofilms: An Overview of Their Significance in Plant and Soil Health 1
Iqbal Ahmad, Mohammad Shavez Khan, Mohd Musheer Altaf, Faizan Abul Qais, Firoz Ahmad Ansari and Kendra P. Rumbaugh

1.1 Introduction 1

1.2 Biofilm Associated with Plants 3

1.3 Biofilm Formation Mechanisms: Recent Update on Key Factors 4

1.4 Biofilm in Soil and Rhizospheres 7

1.5 Genetic Exchange in Biofilms 7

1.6 Diversity and Function of Soil Biofilms 8

1.7 The Role of Biofilms in Competitive Colonization by PGPR 8

1.8 Biofilm Synergy in Soil and Environmental Microbes 9

1.9 Biofilms in Drought Stress Management 10

1.10 Plant Health and Biofilm 10

1.11 How Microbial Biofilms Influence Plant Health? 10

1.12 Soil Health and Biofilms 12

1.13 How to Assess Soil Health? 13

1.14 Impact of Biofilms on Soil Health 14

1.15 Biofilm EPS in Soil Health 14

1.16 Conclusions and Future Directions 15

References 15

2 Role of PGPR in Biofilm Formations and Its Importance in Plant Health 27
Govind Gupta, Sunil Kumar Snehi and Vinod Singh

2.1 Introduction 27

2.2 Rhizosphere: A Unique Source of Microorganisms for Plant Growth Promotion 27

2.3 Plant Growth–Promoting Rhizobacteria 28

2.4 Biofilm Producing Plant Growth–Promoting Rhizobacteria 34

2.5 Role of PGPR in Biofilm Formations 35

2.6 Future Research and Development Strategies for Biofilm Producing Sustainable Technology 35

2.7 Conclusions 36

Acknowledgments 36

References 36

3 Concept of Mono and Mixed Biofilms and Their Role in Soil and in Plant Association 43
Janaína J. de V. Cavalcante, Alexander M. Cardoso and Vânia L. Muniz de Pádua

3.1 Introduction 43

3.2 Soil- and Plant-Associated Biofilms 45

3.3 Microbial Signaling, Regulation, and Quorum Sensing 46

3.4 Biotechnology 48

3.5 Outlook 49

Acknowledgments 49

References 49

4 Bacillus Biofilms and Their Role in Plant Health 55
Mohd Musheer Altaf, Iqbal Ahmad, Mohd Sajjad Ahmad Khan and Elisabeth Grohmann

4.1 Introduction 55

4.2 Interaction of Bacillus within Plant Rhizosphere and Biofilm Development 57

4.3 Multispecies Biofilms and Their Significance 59

4.4 Biofilm Detection and Characterization 60

4.5 Bacillus Biofilm and Plant Health Promotion 60

4.6 Conclusion and Future Prospects 62

References 63

5 Biofilm Formation by Pseudomonas spp. and Their Significance as a Biocontrol Agent 69
Zaki A. Siddiqui and Masudulla Khan

5.1 Introduction 69

5.2 Biofilms 79

5.3 Mechanisms of Biofilm Formation 81

5.4 Metabolites Affecting Biofilm Formation 84

5.5 Biofilm Formation and Biological Control of Plant Diseases 84

5.6 Conclusion 85

References 86

6 Quorum Sensing Mechanisms in Rhizosphere Biofilms 99
Jorge Barriuso

6.1 Background 99

6.2 QS in Biofilms Formation 101

6.3 Conclusions 106

References 107

7 Biofilm Formation and Quorum Sensing in Rhizosphere 111
Kusum Harjai and Neha Sabharwal

7.1 Introduction 111

7.2 Importance of Rhizosphere 111

7.3 Constituents of Rhizosphere 112

7.4 Communication in Rhizosphere 113

7.5 Quorum Sensing in Rhizobia 115

7.6 Quorum Sensing in Pseudomonads 118

7.7 Biofilm Formation in Rhizosphere 120

7.8 Conclusions 124

References 124

8 The Significance of Fungal Biofilms in Association with Plants and Soils 131
Michael W. Harding, Lyriam L.R. Marques, Bryon Shore and G.C. Daniels

8.1 Introduction 131

8.2 What Is a Biofilm? 132

8.3 Where Do We Find Filamentous Fungal Biofilms? 132

8.4 Fungal Biofilms: What Have We Learned from the Budding Yeasts? 133

8.5 What Does a Filamentous Fungal Biofilm Look Like? 134

8.6 Examples of Filamentous Fungal Biofilms 136

8.7 Examples of Fungal Biofilms in Soils and the Rhizosphere 139

8.8 The Mycorhizosphere 141

8.9 A Biofilm Approach to Plant Disease Management 141

References 143

9 Chemical Nature of Biofilm Matrix and Its Significance 151
Mohd Sajjad Ahmad Khan, Mohd Musheer Altaf and Iqbal Ahmad

9.1 Introduction 151

9.2 Structural Composition of EPS 154

9.3 Properties of Matrices 160

9.4 Functions of the Extracellular Polymer Matrix: The Role of Matrix in Biofilm Biology 162

9.5 Conclusion 168

Acknowledgments 168

References 169

10 Root Exudates: Composition and Impact on Plant–Microbe Interaction 179
Shamsul Hayat, Ahmad Faraz and Mohammad Faizan

10.1 Introduction 179

10.2 Chemical Composition of Root Exudates and Their Significance 180

10.3 Root Exudates in Mediating Plant–Microbe Interaction in Rhizosphere (Negative and Positive Interactions) 180

10.4 Direct and Indirect Effect of Root Exudates on PGPR, Root Colonization, and in Stress Tolerance 182

10.5 Role of Root Exudates in Biofilm Formation by PGPR 185

10.6 Role of Root Exudates in Protecting Plants Pathogenic Biofilm, Quorum Sensing Inhibition 186

10.7 Isolation of Root Exudates 187

10.8 Conclusion 188

References 189

11 Biochemical and Molecular Mechanisms in Biofilm Formation of PlantAssociated Bacteria 195
Alwar Ramanujam Padmavathi, Dhamodharan Bakkiyaraj and Shunmugiah Karutha Pandian

11.1 Introduction 195

11.2 Plant-Associated Bacteria 196

11.3 Biofilms and Plant Pathogens 196

11.4 Molecular and Biochemical Mechanisms Involved in Biofilm Formation 197

11.5 Conclusion 205

References 205

12 Techniques in Studying Biofilms and Their Characterization: Microscopy to Advanced Imaging System in vitro and in situ 215
Elisabeth Grohmann and Ankita Vaishampayan

12.1 Introduction 215

12.2 Classical Techniques to Study Biofilms 216

12.3 The Gold Standard: Flow-Cell Technology and Confocal Laser Scanning Microscopy (CLSM) 218

12.4 The Biofilm Flow Cell 218

12.5 Advanced Digital Analysis of Confocal Microscopy Images 221

12.6 Biofilm Studies at Different Scales 222

12.7 Conclusions and Perspectives 224

Acknowledgments 225

References 225

13 Gene Expression and Enhanced Antimicrobial Resistance in Biofilms 231
Daniel Padilla-Chacón, Israel Castillo-Juárez, Naybi Muñoz-Cazares and Rodolfo García-Contreras

13.1 Introduction 231

13.2 Biofilms in the Plant–Microbe Relationship 232

13.3 Stress Induces Biofilm Formation 236

13.4 Relevance for Bacterial-Associated Plants 237

13.5 Enhanced Antimicrobial Resistance in Biofilms Is Mediated by Biofilm Physicochemical Characteristics and Specific Changes in Gene Expression 237

13.6 Potential for Implementing Antibiofilm Strategies to Protect Crops 239

13.6 Conclusions 244

Acknowledgments 244

References 244

14 In Vitro Assessment of Biofilm Formation by Soil- and Plant-Associated Microorganisms 253
Michael W. Harding and G.C. Daniels

14.1 Introduction 253

14.2 How to Make a Biofilm 254

14.3 What Is the Best Way to Make a Biofilm in Vitro? 254

14.4 Flow Systems 255

14.5 Static Reactors 261

14.6 Special Considerations for Filamentous Fungal Biofilms 265

14.7 Biofilm Reactors Used to Characterize Plant-Associated Biofilms 266

14.8 Value-Added Products from Biofilm Reactors 266

References 267

15 Factors Affecting Biofilm Formation in in vitro and in the Rhizosphere 275
Firoz Ahmad Ansari, Huma Jafri, Iqbal Ahmad and Hussein H Abulreesh

15.1 Introduction 275

15.2 Process of Biofilm Formation 276

15.3 Factor Influencing Biofilm Formation 278

15.4 Conclusions and Future Direction 285

References 286

16 Ecological Significance of Soil-Associated Plant Growth–Promoting Biofilm Forming Microbes for Stress Management 291
Arpita Singh and Puneet Singh Chauhan

16.1 Introduction 291

16.2 Rhizosphere Hub of Plant–Microbe Interactions 292

16.3 Commencement of Rhizosphere Effect and Bacterial Colonization by Root Exudates 293

16.4 Quorum Sensing as a Way of Interaction between Bacteria and Host Plant 295

16.5 Biofilms 296

16.6 Effects of Stress on Plants 302

16.7 Stress Tolerance in Plants 309

16.8 Conclusion 316

16.9 Future Perspectives 317

Acknowledgments 317

List of Abbreviations 317

References 318

17 Developed Biofilm-Based Microbial Ameliorators for Remediating Degraded Agroecosystems and the Environment 327
G. Seneviratne, P.C. Wijepala and K.P.N.K. Chandrasiri

17.1 Introduction 327

17.2 Developed Microbial Communities as a Potential Tool to Regenerate Degraded Agroecosystems 328

17.3 Biochemistry of Fungal-Bacterial Biofilms 330

17.4 Endophytic Microbial Colonization with the Application of Fungal Bacterial Biofilms 330

17.5 Biofilm Biofertilizers for Restoration of Conventional Agroecosystems 331

17.6 Developed Microbial Biofilms for Environmental Bioremediation 331

17.7 Conclusion 333

References 333

18 Plant Root–Associated Biofilms in Bioremediation 337
Sadaf Kalam, Anirban Basu and Sravani Ankati

18.1 Introduction 337

18.2 Biofilms: Definition and Biochemical Composition 337

18.3 Bioremediation and Its Significance 338

18.4 Root-Associated Biofilms 340

18.5 Bioremediation of Contaminants in Rhizospheric Soils 344

18.6 Implications of Rhizospheric Biofilm Formation on Bioremediation 347

18.7 Conclusion and Future Prospects 348

Acknowledgments 349

References 349

19 Biofilms for Remediation of Xenobiotic Hydrocarbons—A Technical Review 357
John Pichtel

19.1 Introduction 357

19.2 Polycyclic Aromatic Hydrocarbons 359

19.3 Chlorinated Ethanes, Ethenes, and Aromatics 364

19.4 Chlorinated Aromatics 369

19.5 Polychlorinated Biphenyls (PCBs) 371

19.6 Polychlorinated Dibenzodioxins 374

19.7 Conclusions 375

References 375

20 Plant Pathogenic Bacteria: Role of Quorum Sensing and Biofilm in Disease Development 387
Deepak Dwivedi, Mayuri Khare, Himani Chaturvedi and Vinod Singh

20.1 Introduction 387

20.2 Mechanism of Biofilm Formation 388

20.3 Quorum Sensing Mechanism 391

20.4 Plant Pathogenic Bacteria Diversity and Plant Diseases 395

20.5 Blocking Quorum Sensing and Virulence in Combating Phytopathogen 395

20.6 Conclusion 400

References 400

21 Biofilm Instigation of Plant Pathogenic Bacteria and Its Control Measures 409
A. Robert Antony, R. Janani and V. Rajesh Kannan

21.1 Introduction 409

21.2 Plant Pathogens 409

21.3 Plant Physiological Alteration by Plant Pathogens 412

21.4 Virulence Strategies of Plant Pathogenic Bacteria 413

21.5 Biofilm Formations 414

21.6 Biofilm Controlling Strategies in Plant Pathogens 419

21.7 Main Targets and Some Potential Tools to Modify Biofilms 420

21.8 Physical Tools for Modifying Biofilms 421

21.9 Chemical Methods 425

21.10 Biological Methods 426

21.11 Future Prospects of Antibiofilm 429

21.12 Conclusion 430

References 430

22 Applications of Biofilm and Quorum Sensing Inhibitors in Food Protection and Safety 439
Ashraf A. Khan, John B. Sutherland, Mohammad Shavez Khan, Abdullah S. Althubiani and Iqbal Ahmad

22.1 Introduction 439

22.2 Biofilm Formation by Foodborne Pathogens 439

22.3 Significance of Biofilms in Food and Food Environments 440

22.4 Biofilm Control Strategies in the Food Industry 441

22.5 Natural Products as Antibiofilm Agents and Their Potential Applications 446

22.6 Role of QS Inhibitors in Biofilm Control 449

22.7 Conclusions 451

Acknowledgments 451

References 451

23 Biofilm Inhibition by Natural Products of Marine Origin and Their Environmental Applications 465
Alwar Ramanujam Padmavathi, Dhamodharan Bakkiyaraj and Shunmugiah Karutha Pandian

23.1 Introduction 465

23.2 Unity Is Strength: Benefits of Biofilm Formers 466

23.3 Transition of Slimy Film to Persistent Biofilm 467

23.4 Biofilm-Related Infections in Plants 467

23.5 Need for Antibiofilm Agents 467

23.6 Natural Products of Marine Origin as Antibiofilm Agents 469

23.7 Semi-synthetic Antibiofilm Agents Inspired by Marine Natural Products 469

23.8 Environmental Applications of Antibiofilm Agents 469

23.9 Conclusion 472

References 472

24 Plant-Associated Biofilms Formed by Enteric Bacterial Pathogens and Their Significance 479
Meenu Maheshwari, Mohammad Shavez Khan, Iqbal Ahmad, Ashraf A. Khan, John B. Sutherland and Abdullah S. Althubiani

24.1 Introduction 479

24.2 Enteric Pathogens in the Plant Environment 480

24.3 Colonization and Biofilm Formation by Enteric Bacteria on Plant Surfaces 483

24.4 Biofilm Regulation in Enteric Bacteria 484

24.5 Influence of Plant Defense on Survival and Biofilm Formation by Enteropathogens 485

24.6 Plant-Associated Enteric Bacteria in Food Safety and Human Health 486

24.7 Conclusions 487

References 487

25 Anti-QS/Anti-Biofilm Agents in Controlling Bacterial Disease: An in silico Approach 497
K. Ahmad, M.H. Baig, Fohad Mabood Husain, Iqbal Ahmad, M.E. Khan, M. Oves, Inho Choi and Nasser Abdulatif Al-Shabib

25.1 Introduction 497

25.2 Biofilm and Its Significance 498

25.3 Bioinformatics Approaches in Drug Target Identification and Drug Discovery 500

25.4 Target Identification Using in silico Technologies 500

25.5 Data Resources for Drug Target Identification 501

25.6 Homology Modeling 501

25.7 Docking 502

25.8 Virtual Screening 503

25.9 Application of Bioinformatics in Development of Anti-QS/anti-biofilm Agents 503

25.10 Virtual Screening for Identification of QS Inhibitors 505

25.11 Conclusion 507

References 507

Index 513

About the Editors
Iqbal Ahmad is a Professor in the Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India and former visiting Professor, Department of Biology, Umm Al-Qura University, Makkah, Saudia Arabia.

Fohad Mabood Husain is a Post-doctoral Researcher in the Department of Food Science and Nutrition, King Saud University, Saudi Arabia.