Table of Contents

Cover

Title Page

Preface

List of Contributors

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
2.4 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
5.4 Metabolites Affecting Biofilm Formation
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
6.3 Conclusions
References

Chapter 7: Biofilm Formation and Quorum Sensing in Rhizosphere

7.1 Introduction
7.2 Importance of Rhizosphere
7.3 Constituents of Rhizosphere
7.4 Communication in Rhizosphere
7.5 Quorum Sensing in Rhizobia
7.6 Quorum Sensing in Pseudomonads
7.7 Biofilm Formation in Rhizosphere
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
8.7 Examples of Fungal Biofilms in Soils and the Rhizosphere
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
9.3 Properties of Matrices
9.4 Functions of the Extracellular Polymer Matrix: The Role of Matrix in Biofilm Biology
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
10.5 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
11.5 Conclusion
References

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

12.1 Introduction
12.3 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
12.7 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
13.3 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
14.5 Static Reactors
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
15.3 Factor Influencing Biofilm Formation
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
16.4 Quorum Sensing as a Way of Interaction between Bacteria and Host Plant
16.5 Biofilms
16.6 Effects of Stress on Plants
16.7 Stress Tolerance in Plants
16.8 Conclusion
16.9 Future Perspectives
Acknowledgments
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
17.7 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
18.5 Bioremediation of Contaminants in Rhizospheric Soils
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
19.2 Polycyclic Aromatic Hydrocarbons
19.3 Chlorinated Ethanes, Ethenes, and Aromatics
19.4 Chlorinated Aromatics
19.5 Polychlorinated Biphenyls (PCBs)
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
20.3 Quorum Sensing Mechanism
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
21.3 Plant Physiological Alteration by Plant Pathogens
21.4 Virulence Strategies of Plant Pathogenic Bacteria
21.5 Biofilm Formations
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
21.9 Chemical Methods
21.10 Biological Methods
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

End User License Agreement

List of Illustrations

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

Figure 1.1 Key steps involved in biofilm formation and the role of regulatory factors.
Figure 1.2 Biofilm interactions with plant and soil, and their significance.

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

Figure 2.1 Schematic diagram showing various plant growth–promoting Attributes. (A) Phosphate solubilization; (B) Siderophore Production; (C) Indole acetic production; (D) HCN Production; (E) Control (M. phaseolina); (F) Inhibition of M. phaseolina; (G) Control (F. solani); (H) Inhibition of F. solani; (I) Biofilm formation. (See color plate section for the color representation of this figure.)

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

Figure 3.1 Biofilm in a community of mixed species.

Chapter 4: Bacillus Biofilms and Their Role in Plant Health

Figure 4.1 Schematic diagram showing the life cycle of Bacillus biofilm formation on the root surface of wheat (Triticum aestivum) plant. (a–b) Attachment of microorganism to sterile surface and suppression of motility. (c) Production of extracellular matrix, irreversible attachment and aggregation of planktonic cells. (d) Maturation and development of biofilm architecture. (e) Dispersion of planktonic cells from biofilm.
Figure 4.2 Representative images of Bacillus cereus biofilm. (a) Side view of biofilm formed on air-liquid interface on 96 well polystyrene microtiter plates using crystal violet assay. (b) Biofilm on glass coverslips as viewed by light microscopy (Magnification 100x).
Figure 4.4 Scanning electron micrograph of Bacillus subtilis colonization and biofilm formation on root of Cicer arietinum (chickpea).

Chapter 6: Quorum Sensing Mechanisms in Rhizosphere Biofilms

Figure 6.1 Confocal laser scanning micrograph of bacterium Serratia liquefaciens MG44 labeled with red probe Eub-338-I-Cy3, forming biofilm on the roots of Arabidopsis thaliana. (See color plate section for the color representation of this figure.)
Figure 6.2 Representation of bacteria cells secreting a QSM in the rhizosphere.
Figure 6.3 Tobacco transgenic plant leaf transformed with the AHL-synthase LuxI from Burkholderia graminis. Production of violacein (purple color) in the agar plate is due to the detection of the QSM by the strain CV026 of Chromobacterium violaceum. (See color plate section for the color representation of this figure.)

Chapter 7: Biofilm Formation and Quorum Sensing in Rhizosphere

Figure 7.1 Model of the P. aeruginosa QS circuitry. LasR and RhlR are symbolized by circles. Plus (+) symbols indicate transcriptional activation of the gene. As culture density increases, lasR is activated by Vfr and PAI-1, reaches a threshold concentration and binds to LasR. Once RhlR associates with PAI-2, autoinduction of rhlI occurs and the remainder of the RhlR–PAI-2-controlled genes are activated. Las system also positively controls the expression of PQS, another system known to be in between the hierarchical level of Las and Rhl [61].

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

Figure 8.1 Stages of filamentous fungal biofilm formation. The upper panel shows a diagrammatic representation of six stages of fungal biofilm development. From left to right, the Adsorption stage involves propagules making contact with a suitable substrate or host. The deposition is reversible until the Attachment stage where secretion of adhesive substances from spores and germlings makes the attachment irreversible. This is followed by the Microcolony I stage, where initial formation of a microcolony occurs via apical elongation and branching of hyphae. Extracellular matrix is produced. The Microcolony II stage includes maturation of the colony where compacted hyphal networks and pervasive hyphal–hyphal adhesion resulting in hyphal bundles and cords. In submerged biofilms, fluid channels appear during this stage, via hydrophobic repulsion between hyphae. The Mature biofilm stage often has aerial growth and three-dimensional colony layering with near-complete encasement within the extracellular matrix. The final stage involves Spore dispersal via formation of fruiting bodies or sporogenous cells often formed apically on aerial hyphae. These structures produce spores or propagules for survival or dispersal and would include spores, sporangia, infective hyphal fragments or other structures. These detached cells can be translocated to new substrates or hosts and reinitiate the cycle. Scanning electron micrographs in the lower panel show Didymella bryoniae biofilms representing Microcolony I (A), Microcolony II (B), Mature biofilm (C) and Spore Dispersal (D). Images A-C were collected from D. bryoniae biofilms produced on wood surfaces in a static multiwall plate biofilm reactor (BEST™ Assay). The aerial hyphae and sporegenous cells shown in (D) were observed as part of a D. bryoniae biofilm on symptomatic cucumber fruit. Scale bars = 20 µm.
Figure 8.2 Didymella bryoniae in vivo biofilms on cucumber fruit (upper panels) and in vitro biofilms on wood surfaces (lower panels). The morphology of the biofilms cultivated on wood surfaces using the BEST™ Assay are quite similar to those on the host tissues. The main exception is that the biofilms on cucumber (upper panels) have a more aerial habit and less matrix material. This likely resulted due to their formation on cucumber fruit at the air interface with no fluid shear. Conversely, the biofilms formed using the BEST™ Assay (lower panels) were submerged in growth media and had a significant fluid shear applied throughout development. These biofilms have a more flattened morphology, lacking aerial hyphae and ample extracellular matrix with clear evidence of fluid channels for fluid movement through the biofilm.

Chapter 9: Chemical Nature of Biofilm Matrix and Its Significance

Figure 9.1 The extracellular polymeric substances matrix at different levels of resolution. (a) A model of a bacterial biofilm attached to a solid surface. Biofilm formation starts with the attachment of a cell to a surface. A microcolony forms through division of the bacterium, and production of the biofilm matrix is initiated. Other bacteria can then be recruited as the biofilm expands owing to cell division and the further production of matrix components. (b) The major matrix components—polysaccharides, proteins, and DNA—are distributed between the cells in a nonhomogeneous pattern, setting up differences between regions of the matrix. (c) The classes of weak physicochemical interactions and the entanglement of biopolymers that dominate the stability of the EPS matrix. (d) Amolecular modeling simulation of the interaction between the exo-polysaccharide alginate (right) and the extracellular enzyme lipase (left) of Pseudomonas aeruginosain aqueous solution. The starting structure for the simulation of the lipase proteinwasobtained from the Protein Data Bank. The coloured spheres represent 1,2-dioctylcarbamoylglycero-3-O-octylphosphonate in the lipase active site (which was present as a part of the crystal structure), except for the green sphere, which represents a Ca2+ ion. The aggregate is stabilized by the interaction of the positively charged amino acids arginine and histidine (indicated in blue) with the polyanionic alginate. Water molecules are not shown.

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

Figure 10.1 Flow chart shows type of plants root interaction with microbe due the secretion of root exudates.
Figure 10.2 Possible interactions of microorganism due to the secretion of root exudates.

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

Figure 12.1 The biofilm flow-cell system allows the cultivation and analysis of biofilm cells under continuous hydrodynamic conditions. The system consists of five major components: a medium reservoir, a multichannel peristaltic pump, bubble traps, flow-cells, and an effluent reservoir. All parts are consecutively connected via silicone tubes, splitters and connectors (A). Working drawing of the flow-cell base (design copyright DTU-Biosys). Reproduced from Curr. Protoc. Microbiol. 1B.2.1—1B.2.15 with permission from John Wiley & Sons, Inc. (B). Working drawing of the advanced bubble trap base (design copyright DTU-Biosys). Reproduced from Curr. Protoc. Microbiol. 1B.2.1—1B.2.15 with permission from John Wiley & Sons, Inc. (C). The whole Figure is reproduced from Pamp et al., Cytometry Part A, 75A, 90–103 (2009) with permission from John Wiley & Sons, Inc.
Figure 12.2 Maximum intensity projection of a multichannel dataset showing a complex river biofilm landscape. The sample was stained for nucleic acids, lectin-specific glycoconjugates, and β-D-glucans (with a 1→3 or 1→4 linkage). For multichannel imaging of reflection, autofluorescence and fluorescence staining, the data were recorded in five separate detector channels in combination with colocalization. Color allocation: green, nucleic acids; red, glycoconjugates; blue, algae; pink, cyanobacteria; yellow, β-D-glucans; white, reflection. Reproduced from Neu and Lawrence, Trends in Microbiol., 23, 233–242 (2015) with permission from Elsevier.

Chapter 13: Gene Expression and Enhanced Antimicrobial Resistance in Biofilms

Figure 13.1 Molecules that inhibit quorum sensing and/or biofilm formation in plant pathogenic bacteria: (A–D) 4 different N,N'-bisalkylated imidazolium; (E) D-leucine; (F) 3-indolylacetonitrile; (G) casbane; (H) vainillin; (I) (−)-epicatechin; (J) analogous 18; (K) N-acetylcysteine.

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

Figure 14.1 The flow-cell reactor is an example of a continuous plug flow reactor. In this system, a flow-cell biofilm reactor is continuously fed broth culture. Biofilms form within the flow cell and/or on the surface of the glass or plastic covering slip. This system is often used to visualize biofilms formed under continuous flow.
Figure 14.2 The drip-flow reactor is an example of a continuous plug flow reactor. In this system, a biofilm reactor is continuously fed broth culture drop wise onto the upper end of an inclined reaction chamber. Gravitational forces pull the culture down the reaction chamber surface and a biofilm forms along the chamber surface. This reactor can be used to produce biofilms in a low fluid shear environment.
Figure 14.3 CDC biofilm reactor is an example of a continuous plug flow reactor with constant stirring. In this system, a biofilm reactor is continuously fed broth culture. Polypropylene rods each containing three removable coupons are suspended in the reaction chamber. The contents of the reaction vessel are constantly stirred using a magnetic stir bar. Biofilms form on the surface of the removable coupons.
Figure 14.4 The rotating disk reactor is an example of a continuous plug flow reactor with constant stirring. In this system, a biofilm reactor is continuously fed broth culture. Inside the reactor, coupons are flush-mounted within a Teflon disk and spun via a magnetic stir bar attached to the bottom of the disk. Biofilms form on the surfaces of the flush-mounted coupon.
Figure 14.5 A 96-well microtiter plate with flat-bottom wells can be used as a closed, static biofilm reactor.
Figure 14.6 Examples of static biofilm reactors with peg lids. The MBEC™ Assay with polystyrene pegs (top left) and the BEST™ Assay with concrete pegs (top right), stainless steel pegs (bottom left) and wood pegs (bottom right).
Figure 14.7 Colony biofilm reactor utilizes a standard Petri dish with semi-solid agar medium as a platform. A polycarbonate filter is placed on the agar surface and inoculated. A second filter is placed on the bacterial biofilm and capped with a paper disc impregnated with a test material. This type of reactor can be used to produce biofilms in the absence of fluid shear, and can evaluate antimicrobial susceptibility without the requirement of tenacious surface attachment.

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

Figure 15.1 Effect of various factors on biofilm formation/disruption in vitro and in the rhizosphere.

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

Figure 16.1 Rhizosphere hub of plant-microbe interactions.
Figure 16.2 Rhizosphere colonization and biofilm formation.
Figure 16.3 Bacterial quorum sensing signaling mediated interaction between host plants and bacteria.
Figure 16.4 Composition of biofilm.
Figure 16.5 Stages involved in biofilm development.
Figure 16.6 Dynamics of biofilm.
Figure 16.7 Stress in plants.
Figure 16.8 Major consequences of drought stress.
Figure 16.9 Major consequences of salinity stress.
Figure 16.10 Major consequences of heat stress
Figure 16.11 Reactive oxygen species.
Figure 16.12 Adaptation mechanisms of plants toward abiotic stress.
Figure 16.13 Plant growth promoting rhizobacteria-mediated abiotic and biotic stress amelioration.
Figure 16.14 Nitrogen fixation and conversion.

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

Figure 17.1 Colletotrichum sp. mycelium colonized by Azotobacter sp. forming fungal–bacterial biofilms (FBBs), when developed under in vitro conditions and stained with lactophenol cotton blue. Magnification, x 400.
Figure 17.2 A conceptual model of fungal-bacterial biofilm (FBB) and its processes.

Chapter 18: Plant Root–Associated Biofilms in Bioremediation

Figure 18.1 Plant and microbe mediated bioremediation in plant root associated soil.
Figure 18.2 Intricate correlation between root exudates, biofilm formation, and chemotaxis.

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

Figure 19.1 Structure of selected polycyclic aromatic hydrocarbons.
Figure 19.2 Schematic of a sample bench-top biofilter apparatus.
Figure 19.3 Structures of selected chlorinated ethanes.
Figure 19.4 Structures of selected chlorinated ethenes.
Figure 19.5 Structures of selected chlorinated phenols.
Figure 19.6 Generic structure of a polychlorinated biphenyl molecule.
Figure 19.7 Generic structures of a polychlorinated dibenzodioxin and a polychlorinated dibenzofuran.

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

Figure 20.1 (a) Bacterial interaction with the roots of A. thaliana plant. (b) Biofilm formation and its interaction with plant root. Image source: nature reviews microbiology 2013 [42].

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

Figure 21.1 Secretory systems used by bacteria to introduce pathogenic compounds into plant cell [115].
Figure 21.2 Bacterial biofilm developmental conditions [117]
Figure 21.3 Diagrammatic representation of various components of bacterial biofilms [118]
Figure 21.4 Biofilm formation by Salmonella cells on a leaf [42].
Figure 21.5 AHL degradation mechanism [71]

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

Figure 22.1 Different modes of action of biofilm/quorum-sensing inhibitors.

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

Figure 23.1 Bacterial resistant strategies to evade antibiotics.
Figure 23.2 Biofilm resistance to antimicrobial agents.

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

Figure 24.1 Post and pre-harvest routes of contamination of enteric bacteria in crop and crop products.

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

Figure 25.1 Role of QS in biofilm formation.
Figure 25.2 Potent plant pathogenic bacterial protein targets for QS inhibitors.

List of Tables

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

Table 2.1 Some Known Rhizospheric Bacteria Used as a Biofilm Promoting Plant Growth.

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

Table 5.1 Effects of Pseudomonas spp. on Nematode Diseases of Plants.
Table 5.2 Effects of Pseudomonas spp. on Fungal Diseases of Plants.
Table 5.3 Effects of Pseudomonas spp. on Bacterial Diseases of Plants

Chapter 9: Chemical Nature of Biofilm Matrix and Its Significance

Table 9.1 Functions Attributed to EPS in Bacterial Biofilms [modified from 27]

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

Table 10.1 Chemical composition of root exudates.

Chapter 13: Gene Expression and Enhanced Antimicrobial Resistance in Biofilms

Table 13.1 Biofilm Molecular Determinants in Important Plant-Associated Bacteria.
Table 13.2 Genes Involved in Biofilm Resistance against Antimicrobials.

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

Table 15.1 Factors Influencing Rhizobacterial Biofim Formation and Root Colonization in the Rhizosphere.

Chapter 18: Plant Root–Associated Biofilms in Bioremediation

Table 18.1 Biofilm-Forming Soil Bacteria with Bioremediation Capability.

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

Table 20.1 List of Bacterial Diseases in Various Crops.

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

Table 21.1 Common Bacterial Plant Pathogens and Their Gram Grouping.
Table 21.2 Cross-Kingdom Plant Pathogenic Bacteria [116]
Table 21.3 Examples of Biofilm Forming Plant-Associated Bacteria [119]
Table 21.4 Strategies for Biofilm Control [45]
Table 21.5 Biosurfactants as Antibiofilm Agents.

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

Table 22.1 Strategies Used in Biofilm Control in Foods and the Food Industries.
Table 22.2 Plant-Derived Products with Promising Antibiofilm Activity and Possible Biofilm Control Agents.
Table 22.3 Natural Quorum Sensing Inhibitors as Potential Biofilm Control Agents.

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

Table 23.1 Biofilm Forming Plant Pathogens and Their Detrimental Effects on Plants.
Table 23.2 Antibiofilm Agents of Marine Origin.
Table 23.3 Semi-synthetic Antibiofilm Agents of Marine Origin

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

Table 24.1 Occurrence of Various Enteric Pathogens in Crops and Crop Products.

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

Table 25.1 Some Widely Tools for Virtual Screening.

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Preface

Microbes are well known for their diverse metabolic activity and unique survival strategies under various natural ecological niches. The lifestyles of microbial community in diverse environments are now being increasingly explored. Throughout the biological world, microbes thrive predominantly in surface-attached, matrix-enclosed, multicellular communities or biofilms, as opposed to isolated planktonic mode.

Our understanding of microbial interaction with biotic and abiotic surfaces in biofilm growth has been extensively investigated, and its relevance in microbial survival under continuously fluctuating environments is recognized. The physiology, molecular mechanism of biofilm formation, and its regulation have been observed in many bacteria and yeasts. The role of biofilm in medical settings, the food industry, and the environment has also been studied. Recently, the functions of biofilm under more complex habitats associated with soil and plants have been investigated. The nature of these biofilms may be synergistic, associative or pathogenic.

Bacteria causing plant diseases are relatively well understood with respect to the role of biofilm in pathogenesis. However, complex environments like plant root, rhizosphere, and bulk soil have been less explored. Several researchers across the globe are attempting to understand the biofilm in these niches, explore polymicrobial biofilm in these conditions, and exploit these interactions for sustainable agriculture through maintenance of plant and soil health. Developing methods for sustaining crop production and environmental health are of prime importance in feeding global populations on a sustainable basis. Using improved ultrastructure techniques to research molecular biology and biofilm has revolutionized the study on biofilm in complex ecosystem.

Recently, many books on biofilm have been published—mainly on medical, food, and environmental aspects, including bioremediation. However, this is probably the first book that takes a holistic view on biofilms and their significance in plant and soil health.

This book addresses current literature and issues in four sub areas: (i) fundamental 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 mechanism in biofilm studies in plant associated bacteria, techniques in studying biofilms and their characterization, gene expression and enhanced antimicrobial resistance in biofilms, and biotic and abiotic factors affecting biofilm in vitro; (iii) the ecological significance of soil-associated biofilms and stress management and bioremediation of contaminated soils and degraded ecosystem; and (iv) pathogenic biofilm associated with plants and food and its control measures.

The book is essential for everyone interested in biofilms and their application in agriculture, plant and soil health, and bioremediation, as well as public health concern with environmental pathogenic biofilms. It is recommended to students and researchers of all disciplines of microbiology, biotechnology, and plant and soil sciences and agriculture and environmental biotechnology industry.

With great pleasure, we extend our sincere thanks to all the learned contributors for their timely response, excellent contributions, and consistent support and cooperation.

We would like to sincerely acknowledge the support for scientific evaluation of chapters from learned professors/senior scientists, especially Professor John Pichtel (Ball State University, USA), Dr. Mahipal Singh (Buffalo University USA), Dr. Ashraf A. Khan and Dr. John B. Sutherland (NCTR, USA), Prof. Rumbaugh Kendra (Texas University, USA), and Prof. Elisabeth Grohmann (Germany).

We are grateful to Lt. Gen. (retd.) Zameer Uddin Shah (Vice-Chancellor, AMU), Dr. Bakri bin Matouk Bakri Assas (Rector, UQU, Makkah), Prof. Mohammad Iqbal A. Khan, Dr. Waleed Jameel Altaf, Dr. H. H. Abulreesh, and Dr. Abdullah Safar Althubiani (UQU, Makkah, KSA), Prof. Shamim Ahmad (JNMC, AMU, Aligarh), and Dr. Gurbachan Singh (Director, ASRB, ICAR, New Delhi, India), and Dr. S. Farooq, Director, Himalaya Drug Co., for their encouragement and moral support.

We express our deep sense of gratitude to all our respected teachers, scientific collaborators, biofilm scientific community, and friends for their guidance, support, and healthy criticism. The cooperation received from doctoral research students in the preparation of this book is gratefully acknowledged. The names of a few require special mention: Mohd Musheer Altaf, Mohd Shavez Khan, Menu Maheshwari, and Faizan Abul Qais.

The technical assistance and support rendered from the dynamic Wiley book publishing team is most appreciated and acknowledged.

Many thanks to the members of our families for all the support they have provided. Finally, we acknowledge Almighty God, who provided all the inspirations, insights, positive thoughts, and channels to complete this book project.

We hope that the readers will find the book interesting and informative. We have strived to provide current research trends on this rapidly increasing field, both for instruction and as a motivation for further investigation.

We welcome suggestions and comments by readers for future improvement.

Iqbal Ahmad,
Aligarh, India
Fohad Mabood Husain,
Reyadh, KSA

List of Contributors

Hussein H. Abulreesh
Department of Biology
Faculty of Applied Science
Umm Al-Qura University
Makkah, Saudi Arabia

Iqbal Ahmad
Department of Agricultural Microbiology
Faculty of Agricultural Sciences
Aligarh Muslim University
Aligarh, India

K. Ahmad
Department of Biosciences
Integral University
Lucknow, India

Nasser Abdulatif Al-Shabib
Department of Food Science and Nutrition
College of Food and Agriculture
King Saud University
Riyadh, Saudi Arabia

Mohd Musheer Altaf
Plant Biofilm Research Group
Department of Agricultural Microbiology
Aligarh Muslim University
Aligarh, India

Abdullah Safar Althubiani
Department of Biology
Faculty of Applied Science
Umm Al-Qura University
Makkah, Saudi Arabia

Sravani Ankati
Molecular Plant-Microbe Interaction Lab
Department of Plant Sciences
School of Life Sciences
University of Hyderabad
Hyderabad, India

Firoz Ahmad Ansari
Department of Agricultural Microbiology
Aligarh Muslim University
Aligarh, India

A. Robert Antony
Rhizosphere Biology Laboratory
Department of Microbiology
Bharathidasan University
Tiruchirappalli, India

M. H. Baig
Department of Medical Biotechnology
Yeungnam University
Republic of Korea

Dhamodharan Bakkiyaraj
Department of Biotechnology
Alagappa University
Karaikudi, India

Department of Microbiology
Faculty of Science
Prince of Songkla University
Hat Yai, Songkhla, Thailand

Jorge Barriuso
Department of Environmental Biology (Lab 245)
Centro de Investigaciones Biológicas (CIB-CSIC)
Consejo Superior de Investigaciones Científicas
Madrid, Spain

Anirban Basu
Molecular Plant-Microbe Interaction Lab
Department of Plant Sciences
School of Life Sciences
University of Hyderabad
Hyderabad, India

Israel Castillo-Juárez
Colegio de Postgraduados
Campus Montecillo
Posgrado de Botánica
Montecillo, Mexico City, Mexico

Janaina Japiassu de Vasconcelos Cavalcante
Environmental Biotechnology Laboratory
West Zone State University – Uezo
RJ, Brazil

Naybi Muñoz-Cazares
Colegio de Postgraduados
Campus Montecillo
Posgrado de Botánica
Montecillo, Mexico City, Mexico

K.P.N.K. Chandrasiri
Microbial Biotechnology Unit
National Institute of Fundamental Studies (NIFS)
Kandy, Sri Lanka

Himani Chaturvedi
Department of Microbiology
Barkatullah University
Bhopal, India

Inho Choi
Department of Medical Biotechnology
Yeungnam University
Republic of Korea

Puneet Singh Chauhan
Division of Plant Microbe Interactions
CSIR-National Botanical Research Institute
Lucknow, India

G.C. Daniels
Alberta Agriculture and Forestry
Crop Diversification Centre South
Brooks, Canada

Deepak Dwivedi
Department of Microbiology
Barkatullah University
Bhopal, India

Mohammad Faizan
Department of Botany
Aligarh Muslim University
Aligarh, India

Ahmad Faraz
Department of Botany
Aligarh Muslim University
Aligarh, India

Rodolfo García-Contreras
Universidad Nacional Autónoma de México
Department of Microbiology and Parasitology
Faculty of Medicine
Mexico City, Mexico

Elisabeth Grohmann
Department of Life Sciences and Technology
Beuth University of Applied Sciences Berlin
Berlin, Germany

Govind Gupta
Department of Microbiology
Barkatullah University
Bhopal, India

Michael W. Harding
Alberta Agriculture and Forestry
Crop Diversification Centre South
Brooks, Canada

Kusum Harjai
Department of Microbiology
Panjab University
Chandigarh, India

Shamsul Hayat
Department of Botany
Aligarh Muslim University
Aligarh, India

Fohad Mabood Husain
Department of Food Science and Nutrition
College of Food and Agriculture Sciences
King Saud University
Riyadh, Saudi Arabia

Huma Jafri
Department of Agricultural Microbiology
Aligarh Muslim University
Aligarh, India

Rajendran Janani
Rhizosphere Biology Laboratory
Department of Microbiology
Bharathidasan University
Tiruchirappalli, India

Sadaf Kalam
Molecular Plant-Microbe Interaction Lab
Department of Plant Sciences
School of Life Sciences
University of Hyderabad
Hyderabad, India

Ashraf A. Khan
Division of Microbiology (HFT-250)
National Center for Toxicological Research
U.S. Food and Drug Administration
Jefferson, Arkansas, USA

Masudulla Khan
Division of Plant pathology and Biocontrol
Department of Botany
Aligarh Muslim University
Aligarh, India

M.E. Khan
School of Chemical Engineering
Yeungnam University
Republic of Korea

Mohammad Shavez Khan
Department of Agricultural Microbiology
Faculty of Agricultural Sciences
Aligarh Muslim University
Aligarh, India

Mohd Sajjad Ahmad Khan
Department of Biology
College of Medicine
Imam Abdulrahman Bin Faisal University, Dammam
Saudi Arabia

Mayuri Khare
Department of Microbiology
Barkatullah University
Bhopal, India

Meenu Mahaeshewari
Department of Agricultural Microbiology
Faculty of Agricultural Sciences
Aligarh Muslim University
Aligarh, India

Lyriam L.R. Marques
MicroBio SMARTS
Calgary, Canada

Alexander Cardoso Machado
Environmental Biotechnology Laboratory
West Zone State University – Uezo
RJ, Brazil

Mohd. Oves
Faulty of Science
Centre of Excellence in Environmental Studies
King Abdul Aziz University
Jeddah, Saudi Arabia

Daniel Padilla-Chacón
Colegio de Postgraduados
Campus Montecillo
Posgrado de Botánica
Montecillo, Mexico City, Mexico

Alwar Ramanujam Padmavathi
Department of Biotechnology
Alagappa University
Karaikudi, India

Nanotec-PSU Center of Excellence on Drug Delivery System and Department of Pharmaceutical Technology
Faculty of Pharmaceutical Sciences
Prince of Songkla University
Hat Yai, Songkhla, Thailand

Shunmugiah Karutha Pandian
Department of Biotechnology
Alagappa University
Karaikudi, India

Vânia Lúcia Muniz de Pádua
Environmental Biotechnology Laboratory
West Zone State University – Uezo
RJ, Brazil

John Pichtel
Ball State University
Natural Resources and Environmental Management, Muncie, USA

Faizan Abul Qais
Department of Agricultural Microbiology
Aligarh Muslim University
Aligarh, India

Velu Rajesh Kannan
Rhizosphere Biology Laboratory
Department of Microbiology
Bharathidasan University
Tiruchirappalli, India

Kendra P. Rumbaugh
Department of Surgery
Texas Tech University Health Sciences Center
Lubbock, Texas, USA

Neha Sabharwal
Department of Microbiology
Panjab University
Chandigarh, India

Gamini Seneviratne
Microbial Biotechnology Unit
National Institute of Fundamental Studies (NIFS)
Kandy, Sri Lanka

Byron Shore
Nautilus Environmental
Calgary, Canada

Zaki Anwar Siddiqui
Division of Plant Pathology and Biocontrol,
Department of Botany
Aligarh Muslim University
Aligarh, India

Arpita Singh
Division of Plant Microbe Interactions
CSIR-National Botanical Research Institute
Lucknow, India

Vinod Singh
Department of Microbiology
Barkatullah University
Bhopal, India

Sunil Kumar Snehi
Department of Microbiology
Barkatullah University
Bhopal, India

John B. Sutherland
Division of Microbiology (HFT-250)
National Center for Toxicological Research
U.S. Food and Drug Administration
Jefferson, Arkansas, USA

Ankita Vaishampayan
Beuth University of Applied Sciences Berlin
Department of Life Sciences and Technology
Berlin, Germany

P.C. Wijepala
Microbial Biotechnology Unit
National Institute of Fundamental Studies (NIFS)
Kandy, Sri Lanka