Biofilms in plant and soil health / edited by Iqbal Ahmad, Fohad Mabood Husain. -- Hoboken, NJ : John Wiley & Sons Ltd, c2017. – (65.2653/B615)

Contents

Preface  xviii

List of Contributors  xx

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

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

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

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

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

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

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

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

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

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

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 Plant-Associated Bacteria  195

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

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

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

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

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

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

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

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

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

20.1     Introduction  387

20.2     Mechanism of Biofilm Formation  388

20.3     Quorum Sensing Mechanism  391                             s

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

21.1     Introduction  409

21.2     Plant Pathogens  409

21.3     Plant Physiological Alteration by Plant Pathogens  422

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

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

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

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

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