ADVANCES IN APPLIED MICROBIOLOGY
CONTENTS CHAPTER 1: BACTERIAL EXTRACELLULAR POLYSACCHARIDES IN BIOFILM FORMATION AND FUNCTION DIBYAJIT LAHIRI, MOUPRIYA NAG, BANDITA DUTTA, ANKITA DEY AND RINA RANI RAY 1 1 INTRODUCTION 1 2 EXOPOLYSACCHARIDES ASSOCIATED WITH THE MATRIX OF BIOFILM VARIOUS TYPES OF ARCHITECTURAL POLYSACCHARIDES ASSOCIATED WITH THE BIOFILM 1 3 VARIATION IN STRUCTURAL COMPONENTS OF BACTERIAL EPS 1 4 EPS VARIATION IN GRAM-POSITIVE AND GRAM-NEGATIVE BACTERIA GRAM-POSITIVE BACTERIA GRAM-NEGATIVE BACTERIA 1 5 VARIOUS METHODS OF EXOPOLYSACCHARIDE EXTRACTION FROM THE MATRIX OF BIOFILM 1 6 FUNCTIONAL ATTRIBUTES OF EPS ADHESION/COHESION/GENETIC MATERIAL TRANSFER SYMBIOSIS DEVELOPMENT OF PATHOGENICITY SOURCE OF NUTRITION PROTECTION FROM ANTIMICROBIALS 1 7 MECHANISM OF FORMATION OF MICROBIAL AGGREGATES BY EXTRACELLULAR POLYMERIC SUBSTANCES (EPS) INTRACELLULAR ADHESION BY EPS CONDITIONS INFLUENCING EPS FORMATION AND ACTION 1 8 APPLICATIONS OF EPS IN BIOTECHNOLOGY 1 9 CONCLUSION REFERENCES CHAPTER 2: PSEUDOMONAS PUTIDA BIOFILM: DEVELOPMENT AND DYNAMICS SOUGATA GHOSH, BHAVTOSH A KIKANI AND RAYMOND J TURNER 2 1 INTRODUCTION 2 2 BIOFILM FORMATION 2 3 FACTORS AFFECTING PSEUDOMONAS PUTIDA BIOFILM DYNAMIC NATURE FLAGELLA STARVATION STRESS 2 4 GENETICS OF PSEUDOMONAS PUTIDA BIOFILM 2 5 BIOFILM CONTROL STRATEGIES PHYSICAL METHODS CHEMICAL METHODS BIOLOGICAL METHODS 2 6 CONCLUSIONS AND FUTURE PERSPECTIVES CHAPTER 3: BIOFILM MATRIX PROTEINS SURBHI SHARMA, MUKESH MEENA, AVINASH MARWAL AND PRASHANT SWAPNIL 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 CHAPTER 4: MICROBIAL BIOFILM—A MODERN SUSTAINABLE APPROACH FOR BIOREMEDIATION IN 21ST CENTURY HIREN K PATEL, JAYESH RUPARELIA, NENSI K THUMAR AND AZARUDDIN V GOHIL 4 1 INTRODUCTION THE NATURE OF NATURAL BIOFILMS PROPERTIES OF BIOFILMS TYPES OF BIOFILM 4 2 BIOFILM FORMATION SUPPORTS IN BIOFILM-BASED PROCESSES REVERSIBLE ATTACHMENT IRREVERSIBLE ATTACHMENT BIOFILM MATURATION DETACHMENT FACTORS AFFECTING BIOFILM DEVELOPMENT 4 3 APPLICATION WASTEWATER TREATMENT BIOFILMS FOR THE PRODUCTION OF INDUSTRIAL CHEMICALS OTHER USES OF BIOFILMS 4 4 PROCESSES BASED ON BIOFILM TECHNOLOGY FOR WASTEWATER TREATMENT TRICKLING FILTER ROTATING BIOLOGICAL CONTACTOR MICROBIOLOGY CONSTRUCTED WETLAND SYSTEM MEMBRANE BIOFILM REACTORS FLUIDIZED-BED BIOFILM REACTORS 4 5 CONCLUSION CHAPTER 5: BACILLUS SUBTILIS-BASED BIOFILMS MIR SAHIDUL ALI, JONATHAN TERSUR ORASUGH AND DIPANKAR CHATTOPADHYAY 5 1 INTRODUCTION BACILLUS SUBTILIS AS A MODEL ORGANISM FOR STUDYING BIOFILM FORMATION 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 THE GENETIC CIRCUITRY OF BACILLUS SUBTILIS BIOFILM FORMATION 5 4 BIOFILM’S RESEARCH IN LABORATORY 5 5 QUORUM SENSING AND MICROBIAL BIOFILMS DIFFERENT SYSTEMS FOR SENSING A QUORUM 5 6 ENGINEERED BACILLUS SUBTILIS BIOFILMS 5 7 THE FUTURE OF BIOFILM DEVELOPMENT RESEARCH 5 8 CONCLUSION CHAPTER 6: A REVIEW ON THE CONTAMINATION CAUSED BY BACTERIAL BIOFILMS AND ITS REMEDIATION SUBHASISH DUTTA AND JOYANI BHATTACHARJEE 6 1 INTRODUCTION 6 2 STEPS ASSOCIATED IN BIOFILM FORMATION 6 3 INFECTIONS ASSOCIATED WITH BIOFILM FORMATION DEVICE RELATED BIOFILM INFECTIONS NONDEVICE RELATED BIOFILM FORMATION 6 4 FEW BACTERIAL BIOFILM MODELS ESCHERICHIA COLI BACILLUS SUBTILIS PSEUDOMONAS AERUGINOSA 6 5 VARIOUS WAYS TO COMBAT BACTERIAL BIOFILM FORMATION USAGE OF SORTIES AS AN ANTIADHESION REMOVAL OF INFECTED FOREIGN BODIES TREATMENT OF INFECTED CENTRAL VENOUS CATHETER EARLY DETECTION OF BIOFILM FORMATION USAGE OF NANOPARTICLES FOR THE REMOVAL OF BACTERIAL BIOFILM BACTERICIDAL SURFACES USAGE OF MICROORGANISM RESPONSIVE MAGNETIC NANOPARTICLES BASED ON SILVER/GENTAMICIN FOR BIOFILM DISRUPTION USAGE OF SUPERPARAMAGNETIC IRON OXIDE ENCAPSULATING POLYMERASE NANOCARRIERS FOR THE BIOFILMS REMOVAL 6 6 CONCLUSION FURTHER READING CHAPTER 7: PSEUDOMONAS PUTIDA BIOFILMS NAHID REHMAN AND ANJANA PANDEY 7 1 INTRODUCTION 7 2 BIOFILM FORMATION BY PSEUDOMONAS PUTIDA MECHANISM 7 3 DEVELOPMENT AND DISPERSAL OF MATURE BIOFILM 7 4 PROPERTIES OF BIOFILMS EXTRACELLULAR MATRIX QUORUM SENSING 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 CHAPTER 8: MECHANISMS OF COMPETITION IN BIOFILM COMMUNITIES PRAGATI THAKUR AND SHOBANA SUGUMAR 8 1 INTRODUCTION 8 2 EXPLOITATIVE COMPETITION 8 3 INTERFERENCE COMPETITION INTERFERENCE MEDIATED BY THE HELP OF ANTIMICROBIAL ELEMENTS COMPETITION SENSING HYPOTHESIS AND QUORUM SENSING MECHANISMS BIOFILM AND MATRIX-ASSOCIATED CHANGES FRUITING BODIES AND MICROBIAL COMPETITION INTERFERENCE MEDIATED BY THE HELP OF CONTACT-DEPENDENT INTERFERENCE OUTER MEMBRANE EXCHANGES 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 CHAPTER 9: ESCHERICHIA COLI BIOFILMS ANKURITA BHOWMIK, SANGITA JANA, ARUNIMA BHATTACHARJEE, TUSHAR KANTI DUTTA AND ASHWINI CHAUHAN 9 1 INTRODUCTION 9 2 SEEING THE SURFACE CONTACTING THE SURFACE TEMPORARY ATTACHMENTS TO SURFACES: REVERSIBLE BINDING ROBUST ADHESION TO SURFACES: FIMBRIAE-MEDIATED IRREVERSIBLE ATTACHMENT 9 3 CONSTRUCTING THE MATURE BIOFILM SURFACE BIOMOLECULES CONTRIBUTING TO BIOFILM STRUCTURES BIOFILM MATRIX COMPONENTS 9 4 REGULATED FORMATION OF BIOFILM COORDINATED TENDENCY TO ADHERE TO A SURFACE REGULATORY NETWORK FOR PRIMARY INTERPLAY WITH SURFACES REGULATION WITHIN E COLI BIOFILMS 9 5 CONCLUSIONS ACKNOWLEDGMENTS CHAPTER 10: ROLE OF MICROBIAL BIOFILMS IN BIOREMEDIATION OF ORGANIC POLLUTANTS IN AQUATIC BODIES SLIPA KANUNGO, PUNEET KUMAR SINGH, LOPAMUDRA RAY, DEBASMITA CHAKRABORTY AND RITESH PATTNAIK 10 1 INTRODUCTION 10 2 QUORUM SENSING-DEPENDENT BIOFILM 10 3 ORGANIC POLLUTANTS: ORIGIN AND IMPLICATIONS IN AQUATIC BODIES SYNTHETIC CHEMICALS INDUSTRIAL EFFLUENTS 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 ASSIMILATION OF NUTRIENTS ADSORPTION OF CONTAMINANTS 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 CHAPTER 11: BACTERIAL EXTRACELLULAR POLYMERIC SUBSTANCES IN BIOFILM MATRIX JAYASHREE SHANMUGAM, MAYAKKANNAN GOPAL, SHRUTHI SAMPATKUMAR AND S ARUNA SHARMILI 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 B SUBTILIS POLYSACCHARIDE PSEUDOMONAS AERUGINOSA (PEL) P AERUGINOSA PSL 11 10 REGULATION OF EXTRACELLULAR POLYSACCHARIDES 11 11 FUTURE DIRECTIONS AND PERSPECTIVES FURTHER READINGS CHAPTER 12: ALGAL BIOFILMS: POTENTIAL WASTEWATER TREATMENT APPLICATIONS AND BIOTECHNOLOGICAL SIGNIFICANCE KANISHKA SRIVASTAVA, SWETA SINGH, MEENAKSHI SINGH, FARZIN PARABIA AND K CHANDRASEKHAR 12 1 INTRODUCTION WHAT IS ALGAL BIOFILM? SPECIES FORMING THE ALGAL BIOFILM APPLICATIONS OF ALGAL BIOFILM HOW TO FORM ALGAL BIOFILM IN THE LAB? 12 2 CHARACTERIZATION OF ALGAL-BASED BIOFILMS NATURAL INHABITANTS CULTIVATED ALGAL CULTURES CONSORTIA OF ALGAL BACTERIA STRUCTURAL ORGANIZATION OF ALGALBACTERIAL BIOFILMS 12 3 GROWTH CONDITIONS FOR BIOFILM PRODUCTION LIGHT ENERGY TEMPERATURE NUTRIENTS SUBSTRATUM EXTRACELLULAR POLYMERIC SUBSTANCES 12 4 ROLE OF ENVIRONMENTAL AND BIOLOGICAL INTERACTIONS SPECIES COMPOSITION COLONIZATION RATES BACTERIAL-ALGAL INTERACTION 12 5 WASTEWATER TREATMENT AND ALGAL BIOMASS PROCESSING ALGAL BIOFILM PHOTOBIOREACTOR REVOLVING ALGAL BIOFILM REACTOR CARBON DIOXIDE FIXATION ON ALGAL BIOFILMS ALGAL BIOFILM MEDIATED BIOREMEDIATION 12 6 ADVANTAGES OF ALGAL-BIOFILMS AND THEIR BIOTECHNOLOGICAL SIGNIFICANCE 12 7 CONCLUSION CHAPTER 13: ANTIMICROBIAL TOLERANCE IN BIOFILMS JAYA CHAWLA AND ANUPAMA SHRIVASTAV 13 1 INTRODUCTION 13 2 ANTIMICROBIAL TOLERANCE HOW ARE ANTIMICROBIALS DIFFERENT FROM ANTIBIOTICS? ANTIMICROBIAL CLASSIFICATION 13 3 BIOFILMS EPS BIOFILM FORMATION: THE DEVELOPMENT STAGES OF BIOFILMS FACTORS ASSOCIATED WITH BIOFILM FORMATION MIXED SPECIES OF BIOFILMS 13 4 BIOCIDES TYPES OF BIOCIDES DIVISION OF BIOCIDES 13 5 DIVERSE BIOCIDES CHEMISTRIES HALOGENS PHENOLICS QUATERNARY AMMONIUM COMPOUNDS ALDEHYDES PLANT ESSENTIAL OILS PEROXIDES 13 6 BIOFILMS AND ANTIMICROBIAL TOLERANCE ANTIMICROBIAL TOLERANCE IN BIOFILMS AND ITS MIXED SPECIES (EXAMPLE OF REDUCED BIOFILM SUSCEPTIBILITY) ANTIMICROBIAL TOLERANCE—CORRELATION WITH BIOFILM AGE 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 CHAPTER 14: BIOFILM-BASED ANTIMICROBIAL TOLERANCE AND RESISTANCE APOORVA SHARMA, SAANYA YADAV, SAKSHAM GARG AND SMITA RASTOGI VERMA 14 1 INTRODUCTION 14 2 ANTIMICROBIAL TOLERANCE VERSUS ANTIMICROBIAL RESISTANCE 14 3 TYPES OF ANTIMICROBIAL RESISTANCE MECHANISMS INTRINSIC MECHANISMS ACQUIRED AND ADAPTIVE MECHANISMS HETERORESISTANCE 14 4 TYPES OF ANTIMICROBIAL TOLERANCE TOLERANCE BY SLOW GROWTH TOLERANCE BY LAG (TBL) 14 5 FACTORS INVOLVED IN RECALCITRANCE OF BIOFILMS TO ANTIMICROBIAL AGENTS PERSISTER CELLS FAILURE OR DELAY IN PENETRATION OF ANTIBIOTICS PHYSIOLOGICAL HETEROGENEITY TOXINANTITOXIN MODULES EFFLUX PUMPS ENVIRONMENT AND NUTRIENTS STARVATION MUTATIONS 14 6 COMBATING ANTIMICROBIAL TOLERANCE/RESISTANCE ESSENTIAL OILS PHAGE THERAPY LIPIDS QUORUM SENSING INHIBITORS COMBINATION THERAPY ANTIMICROBIAL PEPTIDES BIOSURFACTANTS 14 7 CONCLUSION AND DISCUSSION