Application of Biofilms in Applied Microbiology

308 Pages·2022·5.405 MB·English

by  Maulin P. Shah

Application of Biofilms in
Applied Microbiology
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Developments in Applied Microbiology and Biotechnology
Application of Biofilms in
Applied Microbiology
Edited by
Maulin P. Shah
Industrial Wastewater Research Laboratory,
Division of Applied & Environmental Microbiology,
Enviro Technology Limited, Ankleshwar, Gujarat, India
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Contents
List of contributors...............................................................................................xv
Chapter 1:Bacterial extracellular polysaccharides in biofilm formation and
function................................................................................................ 1
Dibyajit Lahiri, Moupriya Nag, Bandita Dutta, Ankita Dey and
Rina Rani Ray
1.1 Introduction...........................................................................................................1
1.2 Exopolysaccharides associated with the matrix of biofilm.....................................3
1.2.1 Various types of architectural polysaccharides associated
with the biofilm..........................................................................................3
1.3 Variation in structural components of bacterial EPS..............................................9
1.4 EPS variation in gram-positive and gram-negative bacteria.................................10
1.4.1 Gram-positive bacteria..............................................................................10
1.4.2 Gram-negative bacteria.............................................................................11
1.5 Various methods of exopolysaccharide extraction from the
matrix of biofilm.................................................................................................12
1.6 Functional attributes of EPS................................................................................13
1.6.1 Adhesion/cohesion/genetic material transfer.............................................14
1.6.2 Symbiosis.................................................................................................14
1.6.3 Development of pathogenicity..................................................................15
1.6.4 Source of nutrition....................................................................................15
1.6.5 Protection from antimicrobials..................................................................15
1.7 Mechanism of formation of microbial aggregates by Extracellular
Polymeric Substances (EPS)................................................................................16
1.7.1 Intracellular adhesion by EPS...................................................................17
1.7.2 Conditions influencing EPS formation and action.....................................17
1.8 Applications of EPS in biotechnology.................................................................18
1.9 Conclusion...........................................................................................................20
References...................................................................................................................20
v
vi Contents
Chapter 2:Pseudomonas putida biofilm: development and dynamics.................... 25
Sougata Ghosh, Bhavtosh A. Kikani and Raymond J. Turner
2.1 Introduction.........................................................................................................25
2.2 Biofilm formation................................................................................................27
2.3 Factors affecting Pseudomonas putida biofilm....................................................28
2.3.1 Dynamic nature.........................................................................................29
2.3.2 Flagella.....................................................................................................29
2.3.3 Starvation stress........................................................................................31
2.4 Genetics of Pseudomonas putida biofilm.............................................................32
2.5 Biofilm control strategies.....................................................................................32
2.5.1 Physical methods......................................................................................33
2.5.2 Chemical methods.....................................................................................34
2.5.3 Biological methods...................................................................................40
2.6 Conclusions and future perspectives....................................................................42
References...................................................................................................................43
Chapter 3:Biofilm matrix proteins ....................................................................... 51
Surbhi Sharma, Mukesh Meena, Avinash Marwal and Prashant Swapnil
3.1 Introduction.......................................................................................................51
3.2 Biofilm matrix...................................................................................................53
3.3 Biofilm matrix proteins......................................................................................54
3.4 Accumulation-associated protein........................................................................54
3.5 Rugosity and biofilm structure modulator A......................................................56
3.6 Biofilm-associated protein.................................................................................57
3.7 Biofilm-surface layer protein.............................................................................57
3.8 GlcNAc-Binding protein A................................................................................58
3.9 Techniques to extract extracellular matrix from bacterial biofilms.....................59
3.10 Conclusion.........................................................................................................59
Acknowledgment.........................................................................................................59
Conflict of interest statement.......................................................................................59
References...................................................................................................................60
Chapter 4:Microbial Biofilm—a modern sustainable approach for
bioremediation in 21st century ............................................................ 65
Hiren K. Patel, Jayesh Ruparelia, Nensi K. Thumar and Azaruddin V. Gohil
4.1 Introduction.........................................................................................................65
4.1.1 The nature of natural biofilms...................................................................67
Contents vii
4.1.2 Properties of biofilms................................................................................67
4.1.3 Types of biofilm.......................................................................................68
4.2 Biofilm formation................................................................................................71
4.2.1 Supports in biofilm-based processes.........................................................72
4.2.2 Reversible attachment...............................................................................73
4.2.3 Irreversible attachment..............................................................................74
4.2.4 Biofilm maturation....................................................................................74
4.2.5 Detachment...............................................................................................74
4.2.6 Factors affecting biofilm development......................................................75
4.3 Application..........................................................................................................76
4.3.1 Wastewater treatment................................................................................76
4.3.2 Biofilms for the production of industrial chemicals..................................80
4.3.3 Other uses of biofilms...............................................................................80
4.4 Processes based on biofilm technology for wastewater treatment........................81
4.4.1 Trickling filter..........................................................................................82
4.4.2 Rotating biological contactor microbiology..............................................82
4.4.3 Constructed wetland system......................................................................83
4.4.4 Membrane biofilm reactors.......................................................................84
4.4.5 Fluidized-bed biofilm reactors..................................................................86
4.5 Conclusion...........................................................................................................87
References...................................................................................................................88
Chapter 5:Bacillus subtilis-based biofilms............................................................ 93
Mir Sahidul Ali, Jonathan Tersur Orasugh and Dipankar Chattopadhyay
5.1 Introduction.........................................................................................................93
5.1.1 Bacillus subtilis as a model organism for studying biofilm formation.......94
5.1.2 Global regulators determining the physiology of subpopulations
of biofilm cells..........................................................................................94
5.2 General model for biofilm development on substrate...........................................95
5.3 Environmental influences on biofilm development..............................................96
5.3.1 The genetic circuitry of Bacillus subtilis biofilm formation......................97
5.4 Biofilm’s research in laboratory...........................................................................97
5.5 Quorum sensing and microbial biofilms..............................................................99
5.5.1 Different systems for sensing a quorum....................................................99
5.6 Engineered Bacillus subtilis biofilms.................................................................100
5.7 The future of biofilm development research......................................................101
5.8 Conclusion.........................................................................................................101
Acknowledgment.......................................................................................................102
References.................................................................................................................102
viii Contents
Chapter 6:A review on the contamination caused by bacterial biofilms
and its remediation............................................................................105
Subhasish Dutta and Joyani Bhattacharjee
6.1 Introduction.......................................................................................................105
6.2 Steps associated in biofilm formation................................................................106
6.3 Infections associated with biofilm formation.....................................................110
6.3.1 Device related biofilm infections............................................................110
6.3.2 Nondevice related biofilm formation......................................................114
6.4 Few bacterial biofilm models.............................................................................115
6.4.1 Escherichia coli.......................................................................................115
6.4.2 Bacillus subtilis.......................................................................................116
6.4.3 Pseudomonas aeruginosa.........................................................................117
6.5 Various ways to combat bacterial biofilm formation..........................................117
6.5.1 Usage of sorties as an antiadhesion.........................................................118
6.5.2 Removal of infected foreign bodies........................................................118
6.5.3 Treatment of infected central venous catheter.........................................118
6.5.4 Early detection of biofilm formation.......................................................119
6.5.5 Usage of nanoparticles for the removal of bacterial biofilm....................119
6.5.6 Bactericidal surfaces...............................................................................120
6.5.7 Usage of microorganism responsive magnetic nanoparticles
based on silver/gentamicin for biofilm disruption...................................121
6.5.8 Usage of Superparamagnetic iron oxide encapsulating polymerase
nanocarriers for the biofilms removal.....................................................121
6.6 Conclusion.........................................................................................................123
References.................................................................................................................123
Further reading...........................................................................................................125
Chapter 7: Pseudomonas putida biofilms...........................................................127
Nahid Rehman and Anjana Pandey
7.1 Introduction.......................................................................................................127
7.2 Biofilm formation by Pseudomonas putida........................................................128
7.2.1 Mechanism..............................................................................................128
7.3 Development and dispersal of mature biofilm....................................................129
7.4 Properties of biofilms........................................................................................130
7.4.1 Extracellular matrix................................................................................130
7.4.2 Quorum sensing......................................................................................131
7.4.3 Biofilms are less susceptible to antimicrobial agents..............................132
7.5 Factors affecting biofilm formation....................................................................132
Contents ix
7.6 Benefits of biofilm.............................................................................................132
7.7 Possible eradication strategies............................................................................133
7.8 Challenges in the eradication of biofilms...........................................................133
References.................................................................................................................134
Chapter 8:Mechanisms of competition in biofilm communities...............................135
Pragati Thakur and Shobana Sugumar
8.1 Introduction.....................................................................................................135
8.2 Exploitative competition..................................................................................136
8.3 Interference competition..................................................................................137
8.3.1 Interference mediated by the help of antimicrobial elements................138
8.3.2 Competition sensing hypothesis and quorum sensing mechanisms........139
8.3.3 Biofilm and matrix-associated changes.................................................140
8.3.4 Fruiting bodies and microbial competition............................................140
8.3.5 Interference mediated by the help of contact-dependent interference..........141
8.3.6 Outer membrane exchanges..................................................................142
8.3.7 Type VI secretion systems....................................................................142
8.4 Studying single and multi-species populations.................................................143
8.5 Genetic aspects of competition........................................................................143
8.6 Models for defining different means of competition........................................144
8.7 Techniques for assessment of biofilm..............................................................145
8.8 Quantification and qualification for screening biofilm competition
formation of biofilms for study........................................................................147
8.9 Microfluidics....................................................................................................147
8.10 Microscopic imaging techniques for biofilm study...........................................148
8.11 Transcriptomics and genomics in biofilm study...............................................149
8.12 Concluding remarks.........................................................................................150
References.................................................................................................................150
Chapter 9:Escherichia coli biofilms....................................................................153
Ankurita Bhowmik, Sangita Jana, Arunima Bhattacharjee,
Tushar Kanti Dutta and Ashwini Chauhan
9.1 Introduction.......................................................................................................153
9.2 Seeing the surface..............................................................................................156
9.2.1 Contacting the surface.............................................................................156
9.2.2 Temporary attachments to surfaces: reversible binding...........................156
9.2.3 Robust adhesion to surfaces: fimbriae-mediated irreversible
attachment...............................................................................................156