Application of Biofilms in Applied Microbiology

Front Cover
Application of Biofilms in Applied Microbiology
Copyright Page
Contents
List of contributors
1 Bacterial extracellular polysaccharides in biofilm formation and function
1.1 Introduction
1.2 Exopolysaccharides associated with the matrix of biofilm
1.2.1 Various types of architectural polysaccharides associated with the biofilm
1.2.1.1 Bacterial alginates
1.2.1.2 Cellulose
1.2.1.3 Poly-N-acetyl glucose amine
1.2.1.4 Capsular polysaccharides
1.2.1.5 Levan
1.2.1.6 Colonic acid
1.2.1.7 Vibrio polysaccharide
1.3 Variation in structural components of bacterial EPS
1.4 EPS variation in gram-positive and gram-negative bacteria
1.4.1 Gram-positive bacteria
1.4.2 Gram-negative bacteria
1.5 Various methods of exopolysaccharide extraction from the matrix of biofilm
1.6 Functional attributes of EPS
1.6.1 Adhesion/cohesion/genetic material transfer
1.6.2 Symbiosis
1.6.3 Development of pathogenicity
1.6.4 Source of nutrition
1.6.5 Protection from antimicrobials
1.7 Mechanism of formation of microbial aggregates by Extracellular Polymeric Substances (EPS)
1.7.1 Intracellular adhesion by EPS
1.7.2 Conditions influencing EPS formation and action
1.8 Applications of EPS in biotechnology
1.9 Conclusion
References
2 Pseudomonas putida biofilm: development and dynamics
2.1 Introduction
2.2 Biofilm formation
2.3 Factors affecting Pseudomonas putida biofilm
2.3.1 Dynamic nature
2.3.2 Flagella
2.3.3 Starvation stress
2.4 Genetics of Pseudomonas putida biofilm
2.5 Biofilm control strategies
2.5.1 Physical methods
2.5.1.1 Radiation
2.5.1.2 Temperature
2.5.1.3 Other approaches
2.5.2 Chemical methods
2.5.2.1 Aggressive chemicals
2.5.2.2 Quaternary ammonium compounds
2.5.2.3 Surfactants
2.5.2.4 Natural products
2.5.2.5 Antimicrobial peptides
2.5.2.6 Quorum sensing inhibitors
2.5.2.7 Metals
2.5.2.8 Nanoparticles
2.5.2.9 Surface coatings
2.5.2.10 Tolerance to chemical approaches
2.5.3 Biological methods
2.5.3.1 Bacteriophages
2.5.3.2 Enzyme-mediated disruption
2.5.3.3 Combination strategy
2.6 Conclusions and future perspectives
References
3 Biofilm matrix proteins
3.1 Introduction
3.2 Biofilm matrix
3.3 Biofilm matrix proteins
3.4 Accumulation-associated protein
3.5 Rugosity and biofilm structure modulator A
3.6 Biofilm-associated protein
3.7 Biofilm-surface layer protein
3.8 GlcNAc-Binding protein A
3.9 Techniques to extract extracellular matrix from bacterial biofilms
3.10 Conclusion
Acknowledgment
Conflict of interest statement
References
4 Microbial Biofilm—a modern sustainable approach for bioremediation in 21st century
4.1 Introduction
4.1.1 The nature of natural biofilms
4.1.2 Properties of biofilms
4.1.3 Types of biofilm
4.1.3.1 Single-species biofilm
4.1.3.2 Bacterial biofilm
4.1.3.3 Fungal biofilm
4.1.3.4 Algal biofilms
4.1.3.5 Protozoa biofilms
4.1.3.6 Multiple-species biofilm
4.2 Biofilm formation
4.2.1 Supports in biofilm-based processes
4.2.2 Reversible attachment
4.2.3 Irreversible attachment
4.2.4 Biofilm maturation
4.2.5 Detachment
4.2.6 Factors affecting biofilm development
4.2.6.1 Biofilm resistance
4.3 Application
4.3.1 Wastewater treatment
4.3.1.1 Removal of organic pollutants
4.3.1.2 Removal of inorganic pollutants
4.3.1.3 Removal of micropollutants
4.3.2 Biofilms for the production of industrial chemicals
4.3.3 Other uses of biofilms
4.4 Processes based on biofilm technology for wastewater treatment
4.4.1 Trickling filter
4.4.2 Rotating biological contactor microbiology
4.4.3 Constructed wetland system
4.4.4 Membrane biofilm reactors
4.4.5 Fluidized-bed biofilm reactors
4.5 Conclusion
References
5 Bacillus subtilis-based biofilms
5.1 Introduction
5.1.1 Bacillus subtilis as a model organism for studying biofilm formation
5.1.2 Global regulators determining the physiology of subpopulations of biofilm cells
5.2 General model for biofilm development on substrate
5.3 Environmental influences on biofilm development
5.3.1 The genetic circuitry of Bacillus subtilis biofilm formation
5.4 Biofilm’s research in laboratory
5.5 Quorum sensing and microbial biofilms
5.5.1 Different systems for sensing a quorum
5.6 Engineered Bacillus subtilis biofilms
5.7 The future of biofilm development research
5.8 Conclusion
Acknowledgment
References
6 A review on the contamination caused by bacterial biofilms and its remediation
6.1 Introduction
6.2 Steps associated in biofilm formation
6.3 Infections associated with biofilm formation
6.3.1 Device related biofilm infections
6.3.1.1 Dental biofilm formation
6.3.1.2 Contact lens
6.3.1.3 Central venous catheter
6.3.1.4 Urinary tract
6.3.2 Nondevice related biofilm formation
6.3.2.1 Periodontitis
6.3.2.2 Osteomyelitis
6.4 Few bacterial biofilm models
6.4.1 Escherichia coli
6.4.2 Bacillus subtilis
6.4.3 Pseudomonas aeruginosa
6.5 Various ways to combat bacterial biofilm formation
6.5.1 Usage of sorties as an antiadhesion
6.5.2 Removal of infected foreign bodies
6.5.3 Treatment of infected central venous catheter
6.5.4 Early detection of biofilm formation
6.5.5 Usage of nanoparticles for the removal of bacterial biofilm
6.5.6 Bactericidal surfaces
6.5.7 Usage of microorganism responsive magnetic nanoparticles based on silver/gentamicin for biofilm disruption
6.5.8 Usage of Superparamagnetic iron oxide encapsulating polymerase nanocarriers for the biofilms removal
6.6 Conclusion
References
Further reading
7 Pseudomonas putida biofilms
7.1 Introduction
7.2 Biofilm formation by Pseudomonas putida
7.2.1 Mechanism
7.3 Development and dispersal of mature biofilm
7.4 Properties of biofilms
7.4.1 Extracellular matrix
7.4.2 Quorum sensing
7.4.3 Biofilms are less susceptible to antimicrobial agents
7.5 Factors affecting biofilm formation
7.6 Benefits of biofilm
7.7 Possible eradication strategies
7.8 Challenges in the eradication of biofilms
References
8 Mechanisms of competition in biofilm communities
8.1 Introduction
8.2 Exploitative competition
8.3 Interference competition
8.3.1 Interference mediated by the help of antimicrobial elements
8.3.2 Competition sensing hypothesis and quorum sensing mechanisms
8.3.3 Biofilm and matrix-associated changes
8.3.4 Fruiting bodies and microbial competition
8.3.5 Interference mediated by the help of contact-dependent interference
8.3.6 Outer membrane exchanges
8.3.7 Type VI secretion systems
8.4 Studying single and multi-species populations
8.5 Genetic aspects of competition
8.6 Models for defining different means of competition
8.7 Techniques for assessment of biofilm
8.8 Quantification and qualification for screening biofilm competition formation of biofilms for study
8.9 Microfluidics
8.10 Microscopic imaging techniques for biofilm study
8.11 Transcriptomics and genomics in biofilm study
8.12 Concluding remarks
References
9 Escherichia coli biofilms
9.1 Introduction
9.2 Seeing the surface
9.2.1 Contacting the surface
9.2.2 Temporary attachments to surfaces: reversible binding
9.2.3 Robust adhesion to surfaces: fimbriae-mediated irreversible attachment
9.2.3.1 Type I fimbriae
9.2.3.2 Curli fimbriae
9.2.3.3 Conjugative pili
9.3 Constructing the mature biofilm
9.3.1 Surface biomolecules contributing to biofilm structures
9.3.2 Biofilm matrix components
9.4 Regulated formation of biofilm
9.4.1 Coordinated tendency to adhere to a surface
9.4.2 Regulatory network for primary interplay with surfaces
9.4.2.1 CpxAR system
9.4.2.2 RcsCDB system
9.4.2.3 EnvZ/OmpR system
9.4.2.4 Role of small molecules in biofilm formation
9.4.3 Regulation within E. coli biofilms
9.4.3.1 Role of central carbon flux in biofilm regulation
9.5 Conclusions
Acknowledgments
References
10 Role of microbial biofilms in bioremediation of organic pollutants in aquatic bodies
10.1 Introduction
10.2 Quorum sensing-dependent biofilm
10.3 Organic pollutants: origin and implications in aquatic bodies
10.3.1 Synthetic chemicals
10.3.1.1 Antibacterial agents
10.3.1.2 Parasiticides
10.3.1.3 Pesticides
10.3.2 Industrial effluents
10.3.2.1 Pharmaceutical industries
10.3.2.2 Paper mill industries
10.3.2.3 Pesticide industries
10.4 Impact of synthetic chemicals and pesticides on aquatic ecosystem
10.5 Microbial diversity in aquatic biofilm
10.6 Role of biofilm in bioaugmentation of pollutants
10.6.1 Assimilation of nutrients
10.6.2 Adsorption of contaminants
10.6.3 Biodegradation of contaminants
10.7 Mechanism of pollutant removal via use of microbial consortia
10.8 Constraints of biofilm-based bioremediation
10.9 Conclusion and future perspective
Acknowledgment
Conflict of interest statement
References
11 Bacterial extracellular polymeric substances in biofilm matrix
11.1 Introduction
11.2 Extracellular polysaccharides as an integral part of bacterial biofilms
11.3 Colanic acid
11.4 Cellulose
11.5 Alginate
11.6 Levan
11.7 Capsular polysaccharides
11.8 Intercellular adhesion of polysaccharides
11.9 Vibrio polysaccharide
11.9.1 B. subtilis polysaccharide
11.9.2 Pseudomonas aeruginosa (Pel)
11.9.3 P. aeruginosa Psl
11.10 Regulation of extracellular polysaccharides
11.11 Future directions and perspectives
References
Further readings
12 Algal biofilms: potential wastewater treatment applications and biotechnological significance
12.1 Introduction
12.1.1 What is algal biofilm?
12.1.2 Species forming the algal biofilm
12.1.3 Applications of algal biofilm
12.1.4 How to form algal biofilm in the lab?
12.2 Characterization of algal-based biofilms
12.2.1 Natural inhabitants
12.2.2 Cultivated algal cultures
12.2.2.1 Requirements for the cultivation of algae
12.2.2.2 Algae production methods
12.2.3 Consortia of algal bacteria
12.2.4 Structural organization of algal–bacterial biofilms
12.3 Growth conditions for biofilm production
12.3.1 Light energy
12.3.2 Temperature
12.3.3 Nutrients
12.3.4 Substratum
12.3.5 Extracellular polymeric substances
12.4 Role of environmental and biological interactions
12.4.1 Species composition
12.4.2 Colonization rates
12.4.3 Bacterial-algal interaction
12.5 Wastewater treatment and algal biomass processing
12.5.1 Algal biofilm photobioreactor
12.5.2 Revolving algal biofilm reactor
12.5.3 Carbon dioxide fixation on algal biofilms
12.5.4 Algal biofilm mediated bioremediation
12.6 Advantages of algal-biofilms and their biotechnological significance
12.7 Conclusion
References
13 Antimicrobial tolerance in biofilms
13.1 Introduction
13.2 Antimicrobial tolerance
13.2.1 How are antimicrobials different from antibiotics?
13.2.2 Antimicrobial classification
13.3 Biofilms
13.3.1 EPS
13.3.2 Biofilm formation: the development stages of biofilms
13.3.3 Factors associated with biofilm formation
13.3.4 Mixed species of biofilms
13.4 Biocides
13.4.1 Types of biocides
13.4.2 Division of biocides
13.5 Diverse biocides chemistries
13.5.1 Halogens
13.5.2 Phenolics
13.5.3 Quaternary ammonium compounds
13.5.4 Aldehydes
13.5.5 Plant essential oils
13.5.6 Peroxides
13.6 Biofilms and antimicrobial tolerance
13.6.1 Antimicrobial tolerance in biofilms and its mixed species (example of reduced biofilm susceptibility)
13.6.2 Antimicrobial tolerance—correlation with biofilm age
13.6.3 Components influencing biofilm susceptibility
13.7 Biofilms responsible for taking part in principle of infection
13.8 Tolerance mechanism of biofilm includes
13.9 Conclusion
References
14 Biofilm-based antimicrobial tolerance and resistance
14.1 Introduction
14.2 Antimicrobial tolerance versus antimicrobial resistance
14.3 Types of antimicrobial resistance mechanisms
14.3.1 Intrinsic mechanisms
14.3.2 Acquired and adaptive mechanisms
14.3.3 Heteroresistance
14.4 Types of antimicrobial tolerance
14.4.1 Tolerance by slow growth
14.4.2 Tolerance by lag (tbl)
14.5 Factors involved in recalcitrance of biofilms to antimicrobial agents
14.5.1 Persister cells
14.5.2 Failure or delay in penetration of antibiotics
14.5.3 Physiological heterogeneity
14.5.4 Toxin–antitoxin modules
14.5.5 Efflux pumps
14.5.6 Quorum sensing
14.5.7 Environment and nutrients
14.5.8 Starvation
14.5.9 Mutations
14.6 Combating antimicrobial tolerance/resistance
14.6.1 Essential oils
14.6.2 Phage therapy
14.6.3 Phenolics
14.6.4 Lipids
14.6.5 Peroxides
14.6.6 Quorum sensing inhibitors
14.6.7 Combination therapy
14.6.8 Antimicrobial peptides
14.6.9 Quaternary ammonium compounds
14.6.10 Biosurfactants
14.7 Conclusion and discussion
References
Index
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