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 1Iqbal 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 27Govind 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 43Janaína 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 69Zaki 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 99Jorge 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 111Kusum 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 131Michael 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 151Mohd 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 179Shamsul 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 215Elisabeth 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 253Michael 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 275Firoz 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 291Arpita 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 327G. 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 337Sadaf 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 357John 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 387Deepak 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 409A. 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 439Ashraf 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 465Alwar 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 479Meenu 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 497K. 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.
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: The fundamentals and significance of biofilm in plant and soil health, and the concept of mono and mixed biofilms by PGPR and fungal biofilms. 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. The ecological significance of soil associated biofilms and stress management and bioremediation of contaminated soils and degraded ecosystems. 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.
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