Biofilms in Plant and Soil Health

About the EditorsIqbal 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.

• Preface xviiiList of Contributors xx1 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. Rumbaugh1.1 Introduction 11.2 Biofilm Associated with Plants 31.3 Biofilm Formation Mechanisms: Recent Update on Key Factors 41.4 Biofilm in Soil and Rhizospheres 71.5 Genetic Exchange in Biofilms 71.6 Diversity and Function of Soil Biofilms 81.7 The Role of Biofilms in Competitive Colonization by PGPR 81.8 Biofilm Synergy in Soil and Environmental Microbes 91.9 Biofilms in Drought Stress Management 101.10 Plant Health and Biofilm 101.11 How Microbial Biofilms Influence Plant Health? 101.12 Soil Health and Biofilms 121.13 How to Assess Soil Health? 131.14 Impact of Biofilms on Soil Health 141.15 Biofilm EPS in Soil Health 141.16 Conclusions and Future Directions 15References 152 Role of PGPR in Biofilm Formations and Its Importance in Plant Health 27Govind Gupta, Sunil Kumar Snehi and Vinod Singh2.1 Introduction 272.2 Rhizosphere: A Unique Source of Microorganisms for Plant Growth Promotion 272.3 Plant Growth–Promoting Rhizobacteria 282.4 Biofilm Producing Plant Growth–Promoting Rhizobacteria 342.5 Role of PGPR in Biofilm Formations 352.6 Future Research and Development Strategies for Biofilm Producing Sustainable Technology 352.7 Conclusions 36Acknowledgments 36References 363 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 Pádua3.1 Introduction 433.2 Soil- and Plant-Associated Biofilms 453.3 Microbial Signaling, Regulation, and Quorum Sensing 463.4 Biotechnology 483.5 Outlook 49Acknowledgments 49References 494 Bacillus Biofilms and Their Role in Plant Health 55Mohd Musheer Altaf, Iqbal Ahmad, Mohd Sajjad Ahmad Khan and Elisabeth Grohmann4.1 Introduction 554.2 Interaction of Bacillus within Plant Rhizosphere and Biofilm Development 574.3 Multispecies Biofilms and Their Significance 594.4 Biofilm Detection and Characterization 604.5 Bacillus Biofilm and Plant Health Promotion 604.6 Conclusion and Future Prospects 62References 635 Biofilm Formation by Pseudomonas spp. and Their Significance as a Biocontrol Agent 69Zaki A. Siddiqui and Masudulla Khan5.1 Introduction 695.2 Biofilms 795.3 Mechanisms of Biofilm Formation 815.4 Metabolites Affecting Biofilm Formation 845.5 Biofilm Formation and Biological Control of Plant Diseases 845.6 Conclusion 85References 866 Quorum Sensing Mechanisms in Rhizosphere Biofilms 99Jorge Barriuso6.1 Background 996.2 QS in Biofilms Formation 1016.3 Conclusions 106References 1077 Biofilm Formation and Quorum Sensing in Rhizosphere 111Kusum Harjai and Neha Sabharwal7.1 Introduction 1117.2 Importance of Rhizosphere 1117.3 Constituents of Rhizosphere 1127.4 Communication in Rhizosphere 1137.6 Quorum Sensing in Pseudomonads 1187.7 Biofilm Formation in Rhizosphere 1207.8 Conclusions 124References 1248 The Significance of Fungal Biofilms in Association with Plants and Soils 131Michael W. Harding, Lyriam L.R. Marques, Bryon Shore and G.C. Daniels8.1 Introduction 1318.2 What Is a Biofilm? 1328.3 Where Do We Find Filamentous Fungal Biofilms? 1328.4 Fungal Biofilms: What Have We Learned from the Budding Yeasts? 1338.5 What Does a Filamentous Fungal Biofilm Look Like? 1348.6 Examples of Filamentous Fungal Biofilms 1368.7 Examples of Fungal Biofilms in Soils and the Rhizosphere 1398.8 The Mycorhizosphere 1418.9 A Biofilm Approach to Plant Disease Management 141References 1439 Chemical Nature of Biofilm Matrix and Its Significance 151Mohd Sajjad Ahmad Khan, Mohd Musheer Altaf and Iqbal Ahmad9.1 Introduction 1519.2 Structural Composition of EPS 1549.3 Properties of Matrices 1609.4 Functions of the Extracellular Polymer Matrix: The Role of Matrix in Biofilm Biology 1629.5 Conclusion 168Acknowledgments 168References 16910 Root Exudates: Composition and Impact on Plant–Microbe Interaction 179Shamsul Hayat, Ahmad Faraz and Mohammad Faizan10.1 Introduction 17910.2 Chemical Composition of Root Exudates and Their Significance 18010.3 Root Exudates in Mediating Plant–Microbe Interaction in Rhizosphere (Negative and Positive Interactions) 18010.4 Direct and Indirect Effect of Root Exudates on PGPR, Root Colonization, and in Stress Tolerance 18210.5 Role of Root Exudates in Biofilm Formation by PGPR 18510.6 Role of Root Exudates in Protecting Plants Pathogenic Biofilm, Quorum Sensing Inhibition 18610.7 Isolation of Root Exudates 18710.8 Conclusion 188References 18911 Biochemical and Molecular Mechanisms in Biofilm Formation of Plant- Associated Bacteria 195Alwar Ramanujam Padmavathi, Dhamodharan Bakkiyaraj and Shunmugiah Karutha Pandian11.1 Introduction 19511.2 Plant-Associated Bacteria 19611.3 Biofilms and Plant Pathogens 19611.4 Molecular and Biochemical Mechanisms Involved in Biofilm Formation 19711.5 Conclusion 205References 20512 Techniques in Studying Biofilms and Their Characterization: Microscopy to Advanced Imaging System in vitro and in situ 215Elisabeth Grohmann and Ankita Vaishampayan12.1 Introduction 21512.2 Classical Techniques to Study Biofilms 21612.3 The Gold Standard: Flow-Cell Technology and Confocal Laser Scanning Microscopy (CLSM) 21812.4 The Biofilm Flow Cell 21812.5 Advanced Digital Analysis of Confocal Microscopy Images 22112.6 Biofilm Studies at Different Scales 22212.7 Conclusions and Perspectives 224Acknowledgments 225References 22513 Gene Expression and Enhanced Antimicrobial Resistance in Biofilms 231Daniel Padilla-Chacón, Israel Castillo-Juárez, Naybi Muñoz-Cazares and Rodolfo García-Contreras13.1 Introduction 23113.2 Biofilms in the Plant–Microbe Relationship 23213.3 Stress Induces Biofilm Formation 23613.4 Relevance for Bacterial-Associated Plants 23713.5 Enhanced Antimicrobial Resistance in Biofilms Is Mediated by Biofilm Physicochemical Characteristics and Specific Changes in Gene Expression 23713.6 Potential for Implementing Antibiofilm Strategies to Protect Crops 23913.6 Conclusions 244Acknowledgments 244References 24414 In Vitro Assessment of Biofilm Formation by Soil- and Plant-Associated Microorganisms 253Michael W. Harding and G.C. Daniels14.1 Introduction 25314.2 How to Make a Biofilm 25414.3 What Is the Best Way to Make a Biofilm in Vitro? 25414.4 Flow Systems 25514.5 Static Reactors 26114.6 Special Considerations for Filamentous Fungal Biofilms 26514.7 Biofilm Reactors Used to Characterize Plant-Associated Biofilms 26614.8 Value-Added Products from Biofilm Reactors 266References 26715 Factors Affecting Biofilm Formation in in vitro and in the Rhizosphere 275Firoz Ahmad Ansari, Huma Jafri, Iqbal Ahmad and Hussein H Abulreesh15.1 Introduction 27515.2 Process of Biofilm Formation 27615.3 Factor Influencing Biofilm Formation 27815.4 Conclusions and Future Direction 285References 28616 Ecological Significance of Soil-Associated Plant Growth–Promoting Biofilm- Forming Microbes for Stress Management 291Arpita Singh and Puneet Singh Chauhan16.1 Introduction 29116.2 Rhizosphere Hub of Plant–Microbe Interactions 29216.3 Commencement of Rhizosphere Effect and Bacterial Colonization by Root Exudates 29316.4 Quorum Sensing as a Way of Interaction between Bacteria and Host Plant 29516.5 Biofilms 29616.6 Effects of Stress on Plants 30216.7 Stress Tolerance in Plants 30916.8 Conclusion 31616.9 Future Perspectives 317Acknowledgments 317List of Abbreviations 317References 31817 Developed Biofilm-Based Microbial Ameliorators for Remediating Degraded Agroecosystems and the Environment 327G. Seneviratne, P.C. Wijepala and K.P.N.K. Chandrasiri17.1 Introduction 32717.2 Developed Microbial Communities as a Potential Tool to Regenerate Degraded Agroecosystems 32817.3 Biochemistry of Fungal-Bacterial Biofilms 33017.4 Endophytic Microbial Colonization with the Application of Fungal- Bacterial Biofilms 33017.5 Biofilm Biofertilizers for Restoration of Conventional Agroecosystems 33117.6 Developed Microbial Biofilms for Environmental Bioremediation 33117.7 Conclusion 333References 33318 Plant Root–Associated Biofilms in Bioremediation 337Sadaf Kalam, Anirban Basu and Sravani Ankati18.1 Introduction 33718.2 Biofilms: Definition and Biochemical Composition 33718.3 Bioremediation and Its Significance 33818.4 Root-Associated Biofilms 34018.5 Bioremediation of Contaminants in Rhizospheric Soils 34418.6 Implications of Rhizospheric Biofilm Formation on Bioremediation 34718.7 Conclusion and Future Prospects 348Acknowledgments 349References 34919 Biofilms for Remediation of Xenobiotic Hydrocarbons—A Technical Review 357John Pichtel19.1 Introduction 35719.2 Polycyclic Aromatic Hydrocarbons 35919.3 Chlorinated Ethanes, Ethenes, and Aromatics 36419.4 Chlorinated Aromatics 36919.5 Polychlorinated Biphenyls (PCBs) 37119.6 Polychlorinated Dibenzodioxins 37419.7 Conclusions 375References 37520 Plant Pathogenic Bacteria: Role of Quorum Sensing and Biofilm in Disease Development 387Deepak Dwivedi, Mayuri Khare, Himani Chaturvedi and Vinod Singh20.1 Introduction 38720.2 Mechanism of Biofilm Formation 38820.3 Quorum Sensing Mechanism 39120.4 Plant Pathogenic Bacteria Diversity and Plant Diseases 39520.5 Blocking Quorum Sensing and Virulence in Combating Phytopathogen 39520.6 Conclusion 400References 40021 Biofilm Instigation of Plant Pathogenic Bacteria and Its Control Measures 409A. Robert Antony, R. Janani and V. Rajesh Kannan21.1 Introduction 40921.2 Plant Pathogens 40921.3 Plant Physiological Alteration by Plant Pathogens 41221.4 Virulence Strategies of Plant Pathogenic Bacteria 41321.5 Biofilm Formations 41421.6 Biofilm Controlling Strategies in Plant Pathogens 41921.7 Main Targets and Some Potential Tools to Modify Biofilms 42021.8 Physical Tools for Modifying Biofilms 42121.9 Chemical Methods 42521.10 Biological Methods 42621.11 Future Prospects of Antibiofilm 42921.12 Conclusion 430References 43022 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 Ahmad22.1 Introduction 43922.2 Biofilm Formation by Foodborne Pathogens 43922.3 Significance of Biofilms in Food and Food Environments 44022.4 Biofilm Control Strategies in the Food Industry 44122.5 Natural Products as Antibiofilm Agents and Their Potential Applications 44622.6 Role of QS Inhibitors in Biofilm Control 44922.7 Conclusions 451Acknowledgments 451References 45123 Biofilm Inhibition by Natural Products of Marine Origin and Their Environmental Applications 465Alwar Ramanujam Padmavathi, Dhamodharan Bakkiyaraj and Shunmugiah Karutha Pandian23.1 Introduction 46523.2 Unity Is Strength: Benefits of Biofilm Formers 46623.3 Transition of Slimy Film to Persistent Biofilm 46723.4 Biofilm-Related Infections in Plants 46723.5 Need for Antibiofilm Agents 46723.6 Natural Products of Marine Origin as Antibiofilm Agents 46923.7 Semi-synthetic Antibiofilm Agents Inspired by Marine Natural Products 46923.8 Environmental Applications of Antibiofilm Agents 46923.9 Conclusion 472References 47224 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. Althubiani24.1 Introduction 47924.2 Enteric Pathogens in the Plant Environment 48024.3 Colonization and Biofilm Formation by Enteric Bacteria on Plant Surfaces 48324.4 Biofilm Regulation in Enteric Bacteria 48424.5 Influence of Plant Defense on Survival and Biofilm Formation by Enteropathogens 48524.6 Plant-Associated Enteric Bacteria in Food Safety and Human Health 48624.7 Conclusions 487References 48725 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-Shabib25.1 Introduction 49725.2 Biofilm and Its Significance 49825.3 Bioinformatics Approaches in Drug Target Identification and Drug Discovery 50025.4 Target Identification Using in silico Technologies 50025.5 Data Resources for Drug Target Identification 50125.6 Homology Modeling 50125.7 Docking 50225.8 Virtual Screening 50325.9 Application of Bioinformatics in Development of Anti-QS/anti-biofilm Agents 50325.10 Virtual Screening for Identification of QS Inhibitors 50525.11 Conclusion 507References 507Index 513