Introduction to Biofilm Engineering

Introduction to Biofilm Engineering
ACS Symposium Series1323
	Introduction to Biofilm Engineering
		Library of Congress Cataloging-in-Publication Data
Foreword
Preface
	1
Quorum Sensing in Pseudomonas aeruginosa and Its Relationship to Biofilm Development
	1 Introduction
	2 Common Molecular Pathways Used by Bacteria for QS
		Figure 1. Generalized model of a bacterial QS system.
	3 QS Systems in P. aeruginosa
		Figure 2. Schematic diagram of the interconnected las, rhl, pqs, and iqs QS systems and their relationship to biofilm development in P. aeruginosa. (A) Schematic representation of the four QS signaling networks in P. aeruginosa. (B) Schematic of biofilm development regulated by QS relevant to panel (A). See text for details.
	4 QS-Regulated Factors Influencing Biofilm Formation in P. aeruginosa
	4.1 Las- and Rhl-Controlled Factors
	4.2 PQS-Controlled Factors
	4.3 IQS-Controlled Factors
	5 Environmental Parameters Influencing QS-Mediated Biofilm Formation
	5.1 Nutrition
	5.2 pH
	5.3 Anoxic Conditions
	5.4 Hydrodynamics
	6 Concluding Remarks
	Acknowledgments
	References
Quorum Sensing in Pseudomonas aeruginosa and Its Relationship to Biofilm Development
	References
		2
Role of Exopolysaccharides in Biofilm Formation
	Introduction
		Figure 1. Different stages of biofilm development.
	EPSs
	Bacterial Polysaccharides
	Aggregative Polysaccharides
		Figure 2. Graphical representation of EPSs found in ECM: (A) PIA, (B) Pel, (C) colanic acid, (D) levan, (E) Psl, (F) alginate, (G) cellulose, (H) mannan-glucan complex, (I) galactomannan, (J) α-1,3glucan, (K) β-1,3 glucan, and (L) galactosaminogalactan. Parentheses represent repeating units while subscript indicates frequency.
		Figure 3. Proposed structural assembly of Psl synthetic complex and schematic representation of Psl synthesis.
		Figure 4. Proposed structural assembly of alginate biosynthetic complex.
	Architectural Polysaccharides
	Fungal EPSs
	Proteins
	Extracellular DNA
	Lipids
	Role of EPSs
	Biofilm Development and Maintenance
	Dual-Species Biofilm
	Antifungal Resistance
	QS Molecules
	Formation of Biological Soil Crusts
	Techniques for Study of EPSs
		Figure 5. A schematic representation of techniques used for characterization of different components of ECM.
	EPS as Novel Drug Target
	Conclusion and Future Prospective
	References
Role of Exopolysaccharides in Biofilm Formation
	References
		3
Biofilm-Biology-Informed Biofilm Engineering for Environmental Biotechnology
	Introduction
	Biofilm Life Cycle
		Figure 1. The biofilm life cycle. Reproduced with permission from ref. 18. Copyright 2018 Springer Nature.
	Microbial Attachment
	Biofilm Maturation
	Biofilm Dispersal
	Biofilm Matrix
		Figure 2. The biofilm matrix. (A) A model of biofilm formed on a solid surface. (B) The matrix mainly comprises proteins, DNA, and polysaccharides. Adapted with permission from ref. 16. Copyright 2018 Springer Nature.
	Chemical Signaling Systems in Biofilm Development
	C-di-GMP
		Figure 3. Structure and physiological functions of c-di-GMP. The cellular level of bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is regulated by DGCs with GGDEF domains and specific PDEs with EAL or HD-GYP domains. The c-di-GMP signaling networks coordinate many biological processes, including motility, virulence, biofilm formation, and cell cycle. Adapted with permission from ref. 69. Copyright 2018 Springer Nature.
	Quorum Sensing
		Figure 4. Typical QS circuits : (A) A Gram-negative one-component and (B) two-component QS system; (C) A Gram-positive one-component and (D) two-component QS system. Reproduced with permission from ref. 76. Copyright 2019 Oxford University Press.
	Matrix-Targeted Biofilm Engineering
	Direct Manipulation of Matrix Components for Biofilm Engineering
		Figure 5. Surface display of GOx on yeast in MFC mediates biocatalysis by the oxidation of glucose. Reproduced with permission from ref. 91. Copyright 2018 American Chemical Society.
		Figure 6. Surface display of redox sensor roGFP in S. oneidensis MR1 by genetically fusing to BpfA. (A) Localization of BpfA-roGFP on the cell surface. The fluorescence (green) observed at 405 nm excitation is induced by the oxidation of roGFP fused to BpfA upon exposure to 10 mM H2O2 for 1 h. (B) Depth-resolved extracellular redox status within S. oneidensis MR-1 BpfA‐roGFP biofilm is indicated in terms of the ratiometric fluorescence change (405/488 nm) with the biofilm depth. Reproduced with permission from ref. 92. Copyright 2018 John Wiley and Sons.
		Figure 7. Biofilm matrix immobilization of enzymes by modification of curli fibers. (A) E. coli expresses CsgA fused to the 13 amino acid SpyTag (CsgA-ST), which self-assembles into curli fibers on the cell surface. (B) The polymer matrix is covalently modified with an enzyme, amylase, fused to SpyCatcher. The peptide-protein (SpyTag-SpyCatcher) coupling through covalent bond formation ensures the immobilization of enzyme on biofilm matrix. (C) Engineered biofilm-matrix-mediated extracellular biocatalysis occurs on the catalytic fibers. Reproduced with permission from ref. 98. Copyright 2018 John Wiley and Sons.
	Indirect Approaches To Manipulate Biofilm Matrix
		Figure 8. (A) Rates of cell detachment from the biofilms of S. oneidensis MR-1 WT and strain CP2-1-S1 before Cr(VI) addition and after 12 h exposure to Cr(VI). (B) Amounts of Cr accumulated in the biofilms over time. Reproduced with permission from ref. 103. Copyright 2019 American Society for Microbiology.
	C-di-GMP-Targeted Biofilm Engineering
		Figure 9. Genetic programming of catalytic P. putida biofilms for enhancing biodegradation of haloalkanes. (A) The gene circuits, including a cyclohexanone inducible c-di-GMP circuit and an alkyl halide degradation pathway. (B) The performance of engineered P. putida for the degradation of haloalkane. Reproduced with permission from ref. 115. Copyright 2018 Elsevier.
	QS-Targeted Biofilm Engineering
	Conclusions and Future Prospects
		Figure 10. Schematic illustration of the biofilm life cycle and potential targets for biofilm engineering.
	Acknowledgments
	References
Biofilm-Biology-Informed Biofilm Engineering for Environmental Biotechnology
	References
		4
Medical Biofilms
	What Are Biofilms?
		Figure 1. Single-species bacterial biofilms (A and B), and multiple-species bacterial biofilms (C and D). White arrows indicate bacterial cells embedded in the matrix. Adapted with permission from reference 6. Kedar Diwakar Mandakhalikar Copyright 2018.
		Figure 2. Schematic representation of biofilm formation. (i) Reversible attachment of planktonic bacteria to surfaces. (ii) Irreversible attachment to surfaces. (iii) Formation of the external matrix. (iv) Biofilms acquire a three-dimensional structure. (v) Biofilm detachment. Reproduced with permission from reference 10. Sara M. Soto Copyright 2014.
	Encrustation as a Complication of Biofilm
		Figure 3. Encrustation in ex vivo urinary catheters. (A) Deposition of mineral salts near the eye and the balloon of Foley catheter. (B) Partial and (C) complete blockage of urinary catheter lumen due to encrustation.
	Where Do Medical Biofilms Form?
	Medical Biofilms Associated with Medical Devices
	Medical Biofilms Not Associated with Foreign Body
	Dental Biofilms
	Biofilms and Wounds
	Other Clinically Relevant Biofilms
	Why Are Medical Biofilms Important?
	How Can Biofilms Be Prevented or Treated?
	Treatment
	Prevention
	Conclusion
	References
Medical Biofilms
	References
		5
Surface Engineering Approaches for Controlling Biofilms and Wound Infections
	Introduction
		Figure 1. PubMed-indexed literature citations for biofilm formation on biomedical devices and antimicrobial surface modification.
	Wound Infections and Their Consequences in the Biomedical Field
	Mechanism of Biofilm Formation
		Figure 2. Schematic representation of the steps involved in biofilm formation.
	Properties Responsible for Bacterial Adhesion
		Figure 3. Factors affecting bacterial adhesion and biofilm formation.
	Environmental Conditions
	Material Surface Properties
	Characteristics of the Adhering Bacteria
	Surface Modification Approaches
	Altering Physicochemical Surface Properties
		Figure 4. Simplified representation of physicochemical engineering strategies and their effects on bacterial adhesion.
	Surface Roughness and Topography
	Surface Free Energy
	Surface Charge
	Antiadhesive Surfaces
		Figure 5. Simplified representation of antiadhesive engineering strategies for inhibiting bacterial adhesion.
	Bioactive Coating
		Figure 6. Simplified representation of bioactive engineering strategies for bacteriostatic or bactericidal activity.
	Organic Coatings
	Inorganic Coatings
	Antimicrobial Coatings
		Figure 7. Simplified representation of antimicrobial engineering strategies for bacteriostatic or bactericidal activity.
	Surface-Bound Antimicrobial Substance
	Loading and Release of an Antimicrobial Substance from the Surface
	Other Surface Engineering Strategies
	Take-Home Message for Surface Engineering
	Conclusion
	References
Surface Engineering Approaches for Controlling Biofilms and Wound Infections
	References
		6
Nanomaterials for Antibiofilm Activity
	Nanotechnology Strategy for Antibiofilm Activity
	Parameters To Control Biofilm Formation
	Types of Nanomaterials for Antibiofilm Activity
	Lipid-Based Nanoparticles
		Figure 1. Liposome–bacterium interactions, P. aeruginosa (fluorescent microscopic image). (a) Free rhodamine B, penetration into the bacterial cells. (b) Transparent microscopy image. (c) Rhodamine-liposomes and bacterial cell interaction (red light emission of bacterial cell membranes). (d) Transparent microscopy image. Reproduced with permission from reference 20. Copyright 2009 Elsevier.
	Polymeric Nanoparticles
		Figure 2. (a) Schematic diagram of the synthesis of CS-Au@MMT NPs and their use in disruption of mature biofilm. Fluorescence micrographs of (b) E. coli and (c) S. aureus stained with PI (red fluorescence: dead bacteria) and SYTO9 (green fluorescence: live bacteria) after treatment with CS, CS-Au, and CS-Au@MMT. (d) Minimal inhibitory concentration (MIC) of different nanocomposites against E. coli (left columns) and S. aureus (right columns). (e) Antibacterial activity of nanocomposites against E. coli and S. aureus. (f) SEM images of E. coli and S. aureus after treatment with CS-Au@MMT. Reproduced with permission from reference 33. Copyright 2018 Elsevier.
	Metal-Based Nanoparticles
	Mechanisms of Nanoparticles for Biofilm Control
		Figure 3. Schematic illustration of plausible molecular mechanisms of AgNPs in opposition to bacterial cells. Reproduced with permission from reference 49. Copyright 2015 Elsevier.
	Antibiofilm Devices Based on Nanomaterials
	Summary
	References
Nanomaterials for Antibiofilm Activity
	References
		7
Extremophilic Biofilms: Exploring the Prospects
	1 Introduction
	2 Steps of Biofilm Formation
	2.1 Biofilm Attachment
	2.2 Biofilm Formation
	2.3 Dispersal of Biofilm
		Figure 1. Steps involved in biofilm formation.
	2.4 Traits of Biofilm in Different Stages
	2.5 Factors Regulating the Fate of Biofilm
	3 Types of Extremophiles, Their Biofilms, and EPS
	3.1 Thermophiles, Their Biofilms, and EPS
	3.2 Psychrophiles, Their Biofilms, and EPS
	3.3 Halophiles, Their Biofilms, and EPS
	3.4 Acidophiles, Their Biofilms, and EPS
	3.5 Alkaliphiles, Their Biofilms, and EPS
	3.6 Barophiles, Their Biofilms, and EPS
	3.7 Radiophiles, Their Biofilms, and EPS
		Figure 2. Extremophiles and the triggers for their biofilm formation.
	4 Scope and Hurdles in Commercial EPS Production by Extremophiles
	4.1 Factors Affecting the Commercial Production of Extremophilic EPSs
	5 Future Perspectives
	6 Conclusions
	References
Extremophilic Biofilms: Exploring the Prospects
	References
		8
Microbial Electroactive Biofilms
	Introduction
		Figure 1. Schematic of a typical bioelectrochemical system showing the EAB at the anode and cathode surfaces.
	Electroactive Microorganisms and Biofilms
	Anodic Electroactive Biofilms
	Cathodic Electroactive Biofilms
	Electron Transfer Mechanisms in Electroactive Biofilms
	Mechanisms of Electron Transfer in Anodic EABs
		Figure 2. The proposed Mtr and Pcc EET pathways. In the metal-reducing (Mtr) pathway of Shewanella oneidensis MR-1 (a) and the porin–cytochrome (Pcc) pathways of Geobacter sulfurreducens (b), electrons are transferred from quinol (QH2) in the cytoplasmic membrane, through the periplasm, and across the outer membrane to the bacterial surface, where MtrC transfers electrons to surface iron atoms directly through its solvent-exposed heme iron atom (inset of a; brown sphere). For simplicity, OmcA on the bacterial surface and flavins are not shown in a. Reproduced with permission from ref 86). Copyright Macmillan Publishers Limited, part of Springer Nature 2016 Nature Reviews Microbiology.
		Figure 3. Schematic of an EAB formed on the anode, showing the distribution of outer membrane cytochromes, pili, and EPS.
		Figure 4. Tapping atomic force microscopy phase images of S. oneidensis MR-1 cells after producing bacterial nanowires in the perfusion flow system. The sample is fixed and air-dried before atomic force microscopy imaging. (Scale bar: 2 μm). (Insets) In vivo fluorescence images of the same cells/nanowires at the surface/solution interface in the perfusion platform. The cells and the nanowires are stained by the membrane stain FM 4-64FX. (Scale bar: 1 μm). The morphologies observed range from vesicle chains (A) to partially smooth filaments incorporating vesicles (B). (C) Transmission electron micrographs of G. metallireducens strain Aro-5. A and B reproduced with permission from ref. 99. Copyright 2010 National Academy of Sciences, U.S.A. C reproduced with permission from ref. 100. Copyright 2018 American Society for Microbiology.
	Mechanisms of Electron Transfer in Cathodic EABs
	Tools and Techniques Used To Study Electroactive Biofilms
		Figure 5. (a) SEM image of Shewanella oneidensis MR-1 biofilm on the anode surface. (b) Confocal laser scanning microscopy of a fully-grown biofilm on a gold interdigitated microelectrode array (scale bar: 10 μm.) (c) Cyclic voltammogram of acetate metabolizing G. sulfurreducens biofilm. Scan rate: 5 mV/s, 268 h. Inset: first derivatives of the voltammetric curve showing the midpoint potential detectable in catalytic waves of mature biofilms. (d) Nyquist diagrams corresponding to anodic biofilm (mixed culture) at different times of growth: (a) week 1 and (b) week 20. a: Reproduced with permission from ref. 134. Copyright (2013) The Royal Society of Chemistry. b: Reproduced with permission from ref. 87. Copyright (2012) PNAS: National Academy of Sciences. c: Reproduced with permission from ref. 122. Copyright (2008) The Royal Society of Chemistry. d: Reproduced with permission from ref. 123. Copyright (2014) Biomed Central.
	Applications of Electroactive Biofilms
	Conclusions and Future Prospects
	Abbreviations
	References
Microbial Electroactive Biofilms
	References
		9
Biofilms and Microbiologically Influenced Corrosion in the Petroleum Industry
	Biofilm Formation
		Figure 1. The steps of biofilm formation and maturation. A) Initial attachment—planktonic cells initiate a reversible attachment to a surface mediated by pili and flagella. B) Irreversible attachment—cells shed their pili and flagella and begin producing components of the biofilm matrix (EPS, DNA, lipids, and proteins). C) Biofilm maturation—cells begin to grow and replicate. Microbial diversity increases as new genera contact the biofilm and are incorporated into the community. D) Metabolic stratification—as the biofilm grows and develops, the community members will create niche environments as nutrients are taken up at the outer edge and metabolic end products are released and diffuse deeper into the biofilm. E) Dispersal—mature biofilms begin shedding mobile planktonic cells into the environment to form new biofilms and begin the cycle again.
	Biofilms in the Petroleum Industry
	Microbiologically Influenced Corrosion
	Chemical Microbiologically Influenced Corrosion
		Figure 2. Schematic of chemical reactions associated with cMIC.
	Electrical Microbiologically Influenced Corrosion
		Figure 3. eMIC highlighting A) electron uptake via microbial nanowires, B) direct electron uptake, and C) conductive iron scale transfer of electrons to microbes throughout the crust. The release of electrons causes solubilization of the iron, which reacts abiotically with hydrogen sulfide and bicarbonate, settling out as iron scales.
	Concentration Cells
		Figure 4. Concentration cell depicting A) an oxygen gradient, which forms when active microbes consume oxygen, primarily at the surface, and prevent oxygen from reaching the metal surface and B) a metal concentration cell, which traps solubilized metal ions, preventing contact with the metal surface. The concentration cells create an anodic environment under the biofilm, allowing electrons to flow to the cathodic regions around the biofilm where they are consumed and drive corrosion forward.
	Microbial Biocide Resistances
	Eradication of Biofilms
	Biocide Corrosion Control
	Conclusion
	References
Biofilms and Microbiologically Influenced Corrosion in the Petroleum Industry
	References
		10
Antibiotic Resistance in Biofilms
	Introduction
		Figure 1. Different mechanisms of antibiotic resistance.
	Biofilms and Clinical Relevance
	Difference between Biofilm and Planktonic Phenotypes
	Mechanism of Antibiotic Tolerance and Resistance in Biofilms
	Extracellular Matrix: More Than a Shield
		Figure 2. ECM of a biofilm and its components.
	Biofilm Physiology: Link to Resistance
		Figure 3. Heterogeneity of biofilm lifestyle.
	Host Immune Suppression
		Figure 4. Host immune suppression of a biofilm. (1) and (2) represent the process by which the innate immune system can phagocytose the planktonic cells. (3) and (4) represent the fate of the immune cells once encountered by the biofilm. (3) illustrates the immune cell death by the biofilm cells, and (4) points to the location where the immune cells are trapped in the biofilm matrix and are made dysfunctional.
	Conclusions, Future Directions, and Scope
	Acknowledgments
	References
Antibiotic Resistance in Biofilms
	References
		11
Spectral Fingerprinting of Escherichia coli C and Micrococcus luteus Biofilms by Enhanced Darkfield-Hyperspectral Imaging Microscopy
	Introduction
	Methods
	Sample Preparation and Biofilm Formation on Glass Slides
	ED-HSI
		Figure 1. CytoViva ED-HSI microscopy set up and its characteristics.
	Image Processing and Analysis
		Figure 2. Spectral angle mapper (SAM) analysis flow chart for characterization and quantification of biofoulants 76.
	Results and Discussion
	ED-HSI Analysis of Planktonic E. coli C and M. luteus
		Figure 3. ED-HSIs of planktonic (a) E. coli C and (b) and M. luteus after 12 h incubation at 30 °C.
		Figure 4. Scanning electron micrographs of planktonic (a) E. coli C and (b) M. luteus after 12 h incubation at 30 °C.
		Figure 5. SAM analysis of planktonic E. coli C and M. luteus. The spectral endmembers (i.e., fingerprints) in the VNIR wavelengths associated with each bacterium are mapped on darkfield images (a) and (b), respectively. The spectral fingerprints for E. coli C and M. luteus are displayed in (c) and (d), respectively. The applied threshold for image classification = 0.85.
	ED-HSI Analysis of E. coli C and M. luteus Biofilms
		Figure 6. Spectral mapper analysis and ED images of E. coli C (a, b) and M. luteus (c, d) biofilms on a glass surface at the end of 12 h growth under constant mixing conditions by an orbital shaker at 150 rpm. The endmembers (i.e., spectral fingerprints) in the VNIR wavelengths associated with each bacterium were used to map the biofilms on the surfaces as shown in (a) and (c), respectively. The applied threshold for image classification = 0.85.
		Figure 7. SEM images of (a) E. coli C biofilm and (b) M. luteus biofilm. The images show the inhomogeneities associated with biofilm thickness.
		Figure 8. The difference mean spectrum (or difference spectral fingerprint) of E. coli C and M. luteus biofilms.
	Implications for Biofouling and Bioflim Monitoring
	Acknowledgments
	References
Spectral Fingerprinting of Escherichia coli C and Micrococcus luteus Biofilms by Enhanced Darkfield-Hyperspectral Imaging Microscopy
	References
		12
Mathematical Modeling of Biofilms
	1 Introduction
	2 Main Features of Biofilm Growth in Liquid Environments
	3 Continuum Approach to Mathematical Modeling of Multispecies Biofilms
	4 Attachment and Detachment
		Figure 1. Typical trend of biofilm thickness over time.
	5 Characteristic Coordinates and Integral Equations
		Figure 2. Characteristics (left) and characteristic line from (right).
	6 Free Boundary Value Problems for Multispecies Biofilm Formation and Growth
		Figure 3.  (left) and (right).
	7 Existence and Uniqueness of Solutions
	Theorem 7.1
	Proof
	Property 7.1
	8 Invasion Free Boundary Problem
		Figure 4. Space-time region where .
	Autotrophic Invasion and Colonization
		Figure 5. Biofilm growth obtained one day (left) and two days (right) after the invading process has started.
		Figure 6. Biofilm growth obtained five days (left) and ten days (right) after the invading process has started.
	9 Reactor Free Boundary Problem
		Figure 7. Biofilm reactor.
	10 Conclusions
	References
Mathematical Modeling of Biofilms
	References
		13
Review of Current Applications of Microbial Biopolymers in Soil and Future Perspectives
	Introduction
	Biopolymers for Water Retention
	Biopolymers for Soil Aggregation and Soil Adhesion
	Biopolymers for Nutrient Accumulation and Vegetative Growth
	Biopolymers for Heavy Metal Sorption
	Biopolymers for Soil Stability and Soil Structure
	Future Directions and Perspectives
	Commercial Applications and Global Trends
	Current Implementation Constraints and Future Perspectives
	Perspectives of Implementation for Future Directions
	Summary and Conclusion
	References
Subject Index
	A
	B
	C
	E
	M
	P