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Book Details
Abstract
The Perfect Slime presents the latest state of knowledge and all aspects of the Extracellular Polymeric Substances, (EPS) matrix – from the ecological and health to the antifouling perspectives. The book brings together all the current material in order to expand our understanding of the functions, properties and characteristics of the matrix as well as the possibilities to strengthen or weaken it. The EPS matrix represents the immediate environment in which biofilm organisms live. From their point of view, this matrix has paramount advantages. It allows them to stay together for extended periods and form synergistic microconsortia, it retains extracellular enzymes and turns the matrix into an external digestion system and it is a universal recycling yard, it protects them against desiccation, it allows for intense communication and represents a huge genetic archive. They can remodel their matrix, break free and eventually, they can use it as a nutrient source. The EPS matrix can be considered as one of the emergent properties of biofilms and are a major reason for the success of this form of life. Nevertheless, they have been termed the “black matter of biofilms” for good reasons. First of all: the isolation methods define the results. In most cases, only water soluble EPS components are investigated; insoluble ones such as cellulose or amyloids are much less included. In particular in environmental biofilms with many species, it is difficult to impossible isolate, separate the various EPS molecules they are encased in and to define which species produced which EPS. The regulation and the factors which trigger or inhibit EPS production are still very poorly understood. Furthermore: bacteria are not the only microorganisms to produce EPS. Archaea, Fungi and algae can also form EPS. This book investigates the questions, What is their composition, function, dynamics and regulation? What do they all have in common?
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| Contents | v | ||
| Preface | xiii | ||
| Chapter 1: The perfect slime – and the “dark matter” of biofilms | 1 | ||
| ABSTRACT | 1 | ||
| 1.1 WHAT IS ‘PERFECT’? | 1 | ||
| 1.2 THE MATRIX: BASIS FOR THE EMERGENT PROPERTIES OF BIOFILMS | 2 | ||
| 1.3 THE “DARK MATTER OF BIOFILMS” | 8 | ||
| 1.3.1 What influences EPS production and how can it be managed? | 9 | ||
| 1.3.2 Where and by which mechanisms are hydrophobic substances sorbed in the matrix? | 9 | ||
| 1.3.3 What are the mechanisms behind water retention? | 9 | ||
| 1.3.4 Can the permeability of biofouling layer be engineered in membrane technology? | 9 | ||
| 1.3.5 Which are the interactions of the various EPS components? | 10 | ||
| 1.3.6 What is the function of complex EPS components? | 10 | ||
| 1.3.7 Which EPS components contribute to matrix stability and how can we predict it? | 10 | ||
| 1.4 CHAOS AND FUNCTION – SELF-ORGANIZATION | 10 | ||
| ACKNOWLEDGEMENTS | 11 | ||
| REFERENCES | 11 | ||
| Chapter 2: EPS – a complex mixture | 15 | ||
| ABSTRACT | 15 | ||
| 2.1 INTRODUCTION | 15 | ||
| 2.2 MICROBIAL POLYSACCHARIDE COMPOSITION | 17 | ||
| 2.3 POLYSACCHARIDE STRUCTURE | 19 | ||
| 2.4 PHYSICAL PROPERTIES | 21 | ||
| 2.5 POLYSACCHARIDE INTERACTIONS | 21 | ||
| REFERENCES | 23 | ||
| Chapter 3: The extracellular matrix – an intractable part of biofilm systems | 25 | ||
| ABSTRACT | 25 | ||
| 3.1 INTRODUCTION | 25 | ||
| 3.2 CHALLENGES | 26 | ||
| 3.3 BIOFILM MATRIX ANALYSIS | 30 | ||
| 3.4 BIOFILM MATRIX CONSTITUENTS | 31 | ||
| 3.4.1 Polysaccharides | 31 | ||
| 3.4.2 Proteins | 31 | ||
| 3.4.3 Amyloids | 32 | ||
| 3.4.4 Extracellular nucleic acids | 33 | ||
| 3.4.5 Amphiphilic compounds | 35 | ||
| 3.4.6 Membrane vesicles | 35 | ||
| 3.4.7 Refractory compounds | 37 | ||
| 3.5 BACTERIAL EXTRACELLULAR BIOLOGY | 37 | ||
| 3.6 BIOFILM MATRIX FUNCTIONALITY | 40 | ||
| 3.6.1 Architecture | 40 | ||
| 3.6.2 Protection | 42 | ||
| 3.6.3 Cryo- and Osmo-protection | 42 | ||
| 3.6.4 Sorption | 42 | ||
| 3.6.5 Precipitation | 42 | ||
| 3.6.6 Adhesion | 42 | ||
| 3.6.7 Repellent | 43 | ||
| 3.6.8 Cohesion | 43 | ||
| 3.6.9 Connectivity | 43 | ||
| 3.6.10 Activity | 43 | ||
| 3.6.11 Surface-activity | 44 | ||
| 3.6.12 Information | 44 | ||
| 3.6.13 Competition | 45 | ||
| 3.6.14 Nutrition | 45 | ||
| 3.6.15 Motility | 46 | ||
| 3.6.16 Transportation | 46 | ||
| 3.6.17 Communication | 47 | ||
| 3.6.18 Conduction | 47 | ||
| 3.6.19 Redox-activity | 47 | ||
| 3.6.20 Dispersion | 48 | ||
| 3.7 EMERGING VIEWS OF THE BIOFILM MATRIX | 48 | ||
| REFERENCES | 49 | ||
| Chapter 4: The transition from bacterial adhesion to the production of EPS and biofilm formation | 61 | ||
| ABSTRACT | 61 | ||
| 4.1 INTRODUCTION | 62 | ||
| 4.2 THE TRANSITION FROM BACTERIAL ADHESION TO BIOFILM FORMATION | 63 | ||
| 4.3 BACTERIAL SURFACE SENSING AND CELL WALL DEFORMATION | 64 | ||
| 4.4 METHODS TO STUDY BACTERIAL CELL WALL DEFORMATION | 65 | ||
| 4.4.1 Macroscopic bio-optical fluorescence imaging | 65 | ||
| 4.4.2 Atomic force microscopy | 65 | ||
| 4.4.3 Surface thermodynamic approach | 66 | ||
| 4.5 BACTERIAL SURFACE SENSING AND THE ROLE OF EPS IN BIOFILMS | 67 | ||
| 4.5.1 Bacterial surface sensing and EPS production | 67 | ||
| 4.5.2 Role of EPS in biofilms | 68 | ||
| 4.5.2.1 EPS and resistance of biofilms against mechanical attack | 69 | ||
| 4.5.2.2 EPS and resistance of biofilms against chemical attack | 69 | ||
| 4.5.2.3 Lubricating properties of EPS in biofilms | 70 | ||
| 4.6 METHODS TO STUDY BIOFILM COMPOSITION AND STRUCTURE | 70 | ||
| 4.6.1 Microscopic structure of biofilms | 70 | ||
| 4.6.2 Composition of biofilms | 70 | ||
| 4.6.3 Viscoelastic properties of biofilms | 71 | ||
| 4.6.4 Lubricating properties of biofilms with and without EPS | 71 | ||
| 4.7 CONCLUDING COMMENTS | 71 | ||
| REFERENCES | 72 | ||
| Chapter 5: Genetics and regulation of EPS formation in Pseudomonas aeruginosa | 79 | ||
| ABSTRACT | 79 | ||
| 5.1 INTRODUCTION | 79 | ||
| 5.1.1 Biofilm formation by Pseudomonas aeruginosa | 80 | ||
| 5.2 PSL (POLYSACCHARIDE SYNTHESIS LOCUS) | 86 | ||
| 5.2.1 Psl composition and structure | 86 | ||
| 5.2.2 Psl synthesis | 87 | ||
| 5.2.3 Transcriptional regulation of Psl | 88 | ||
| 5.2.4 Post-transcriptional regulation of Psl | 90 | ||
| 5.3 PEL (PELLICLE FORMATION) | 91 | ||
| 5.3.1 Pel composition and structure | 92 | ||
| 5.3.2 Pel synthesis | 92 | ||
| 5.3.3 Transcriptional regulation of Pel | 93 | ||
| 5.3.4 Post-transcriptional regulation of Pel | 94 | ||
| 5.4 ALGINATE | 95 | ||
| 5.4.1 Alginate composition and structure | 95 | ||
| 5.4.2 Alginate synthesis | 95 | ||
| 5.4.3 Transcriptional regulation of alginate | 96 | ||
| 5.4.4 Post-transcriptional regulation of alginate | 100 | ||
| 5.5 CONCLUSIONS AND PERSPECTIVES | 102 | ||
| REFERENCES | 102 | ||
| Chapter 6: Amyloids – a neglected child of the slime | 113 | ||
| ABSTRACT | 113 | ||
| 6.1 INTRODUCTION | 114 | ||
| 6.2 VISUALIZATION OF AMYLOIDS AND THEIR ABUNDANCE IN BIOFILMS | 116 | ||
| 6.3 ONLY A FEW FUNCTIONAL AMYLOIDS HAVE BEEN CHARACTERIZED | 118 | ||
| 6.3.1 Curli fimbriae | 118 | ||
| 6.3.1.1 Biological role | 118 | ||
| 6.3.1.2 Biogenesis | 120 | ||
| 6.3.1.3 Biotechnological applications | 120 | ||
| 6.3.2 Functional amyloids of Pseudomonas (Fap) | 121 | ||
| 6.3.2.1 Biological role | 121 | ||
| 6.3.2.2 Biogenesis | 122 | ||
| 6.3.3 TasA from Bacillus | 123 | ||
| 6.3.3.1 Biological role | 123 | ||
| 6.3.3.2 Biogenesis | 123 | ||
| 6.3.4 Other EPS-associated functional amyloids | 123 | ||
| 6.4 ISOLATION AND CHARACTERIZATION OF FUNCTIONAL AMYLOIDS | 125 | ||
| 6.5 CONCLUDING REMARK | 127 | ||
| REFERENCES | 127 | ||
| Chapter 7: Bacterial exopolysaccharides from unusual environments and their applications | 135 | ||
| ABSTRACT | 135 | ||
| 7.1 INTRODUCTION | 135 | ||
| 7.2 EPS FROM DEEP SEA HYDROTHERMAL VENTS | 136 | ||
| 7.3 EPS FROM COLD ENVIRONMENTS | 138 | ||
| 7.4 EPS FROM MICROBIAL MATS | 139 | ||
| 7.5 BIOMEDIAL APPLICATIONS OF EPS | 141 | ||
| 7.6 EPS AS ANTIBIOFILM AGENT | 142 | ||
| 7.7 EPS AS BIODETOXIFIERS | 144 | ||
| 7.8 EPS AND..... BLACK PEARLS | 145 | ||
| 7.9 EPS IN EOR/MEOR | 147 | ||
| 7.10 EPS IN COSMETICS | 148 | ||
| 7.11 CONCLUSIONS | 148 | ||
| REFERENCES | 149 | ||
| Chapter 8: Mechanical properties of biofilms | 153 | ||
| ABSTRACT | 153 | ||
| 8.1 INTRODUCTION | 154 | ||
| 8.2 MECHANICAL BACKGROUND | 155 | ||
| 8.2.1 Hookean solids and newtonian fluids | 157 | ||
| 8.2.2 Non-linear behaviour | 158 | ||
| 8.2.3 Viscoelasticity | 158 | ||
| 8.2.4 Rheology of viscoelastic materials | 159 | ||
| 8.2.4.1 Creep and relaxation tests | 159 | ||
| 8.2.4.2 Dynamic test | 160 | ||
| 8.2.4.3 Modelling viscoelasticity | 161 | ||
| 8.3 BIOFILM MECHANICS | 162 | ||
| 8.3.1 Macrorheological studies | 163 | ||
| 8.3.2 Microrehological studies | 165 | ||
| 8.4 BIOFILM DETACHMENT | 166 | ||
| 8.5 MATERIAL MODELLING OF BIOFILM MECHANICS | 168 | ||
| 8.6 ARE BIOFILM MECHANICS AND FUNCTION CORRELATED? | 170 | ||
| ACKNOWLEDGMENTS | 172 | ||
| REFERENCES | 172 | ||
| Chapter 9: Travelling through slime – bacterial movements in the EPS matrix | 179 | ||
| ABSTRACT | 179 | ||
| 9.1 INTRODUCTION: BACTERIAL MOVEMENTS INVOLVED IN THE BIOFILM LIFE-CYCLE | 179 | ||
| 9.2 EXISTENCE OF FLAGELLA PROPELLED MOTILE BACTERIAL SUBPOPULATIONS IN THE EPS MATRIX | 181 | ||
| 9.3 EXPLOITATION OF BACTERIAL MOTILITY IN BIOFILM CONTROL | 184 | ||
| 9.3.1 Enhanced biocide action | 185 | ||
| 9.3.2 Delivery of antibacterials | 186 | ||
| 9.3.2.1 Targeting cell viability within biofilms | 186 | ||
| 9.3.2.2 Targeting matrix integrity within biofilms | 188 | ||
| 9.4 FUTURE LINES OF INVESTIGATIONS | 189 | ||
| ACKNOWLEDGEMENTS | 189 | ||
| REFERENCES | 189 | ||
| Chapter 10: Why and how biofilms cause biofouling – the “hair-in-sink”-effect | 193 | ||
| ABSTRACT | 193 | ||
| 10.1 INTRODUCTION | 194 | ||
| 10.2 MATERIALS AND METHODS | 195 | ||
| 10.2.1 Experimental set-up | 195 | ||
| 10.2.2 Feed water | 196 | ||
| 10.2.3 Optical coherence tomography (OCT) | 197 | ||
| 10.2.4 Biofilm thickness | 197 | ||
| 10.3 RESULTS | 197 | ||
| 10.3.1 Biofouling layer formation: filtration or biofilm growth? | 197 | ||
| 10.3.2 Impact of permeate flux change on biofilm hydraulic resistance and thickness? | 198 | ||
| 10.3.3 Understanding the reason of hydraulic resistance of biofilms: Model for the mechanism of water permeation | 200 | ||
| 10.4 DISCUSSION | 203 | ||
| ACKNOWLEDGEMENTS | 204 | ||
| REFERENCES | 204 | ||
| Chapter 11: Unique and baffling aspects of the matrix: EPS syneresis and glass formation during desiccation | 207 | ||
| ABSTRACT | 207 | ||
| 11.1 INTRODUCTION | 208 | ||
| 11.2 THE CHALLENGE OF DESICCATION | 208 | ||
| 11.2.1 Desiccation at the level of cells and individual molecules | 208 | ||
| 11.2.2 EPS and hydration-maintenance | 209 | ||
| 11.3 MICROBIAL MATS: AN EPS-MACROSTRUCTURE HAVING MICROSCALE ARCHITECTURE | 211 | ||
| 11.3.1 Mat systems | 211 | ||
| 11.3.1.1 An EPS-based analog of Earth’s earliest life | 211 | ||
| 11.3.2 Present-day mats | 211 | ||
| 11.3.2.1 Anhydrophilic hypersaline environments | 211 | ||
| Active-growth and permeable EPS | 212 | ||
| 11.3.2.2 Higher-salinity, syneresis and development of EPS hydrophobic-skin | 212 | ||
| Enhanced EPS Production during Water-Limitation | 212 | ||
| Potential mechanisms for ion-exclusion during high salinities | 214 | ||
| Syneresis in EPS gel matrix? | 214 | ||
| 11.3.2.3 Desiccation protection by EPS glass formation | 215 | ||
| Compatible-solutes in EPS | 215 | ||
| Maintaining steric conformation of extracellular biomolecules during desiccation | 216 | ||
| Two major hypotheses | 216 | ||
| Glass-formation or vitrification | 217 | ||
| Formation of an organic glass and trehalose? | 218 | ||
| 11.3.2.4 Rehydration and rapid resumption of activities | 219 | ||
| Preservation of cellular and extracellular activities | 219 | ||
| 11.4 CONCLUSIONS | 219 | ||
| ACKNOWLEDGEMENTS | 220 | ||
| REFERENCES | 220 | ||
| Chapter 12: Extracellular factors involved in biofilm matrix formation by Rhizobia | 227 | ||
| ABSTRACT | 227 | ||
| 12.1 OVERVIEW OF RHIZOBIA AND THEIR SYMBIOTIC RELATION WITH LEGUMES | 227 | ||
| 12.2 RHIZOBIAL BIOFILM FORMATION | 228 | ||
| 12.3 RHIZOBIAL COMPONENTS OF THE BIOFILM MATRIX | 229 | ||
| 12.3.1 Rhizobial extracellular polysaccharides | 230 | ||
| 12.3.1.1 Exopolysaccharides | 230 | ||
| 12.3.1.2 Capsular polysaccharides | 234 | ||
| 12.3.1.3 Lipopolysaccharide | 235 | ||
| 12.3.1.4 Glucomannan | 236 | ||
| 12.3.1.5 Cellulose | 237 | ||
| 12.3.2 Extracellular proteins | 238 | ||
| 12.3.2.1 Adhesins | 238 | ||
| 12.3.2.2 Lectins | 238 | ||
| 12.3.2.3 Glycanases | 239 | ||
| 12.3.3 Nod factors | 239 | ||
| 12.3.4 Flagella | 240 | ||
| 12.4 CONCLUDING REMARKS | 240 | ||
| ACKNOWLEDGEMENTS | 242 | ||
| REFERENCES | 242 | ||
| Chapter 13: Transparent exopolymeric particles: an important EPS component in seawater | 249 | ||
| ABSTRACT | 249 | ||
| 13.1 INTRODUCTION | 249 | ||
| 13.2 SOURCES AND DISTRIBUTIONS OF TEP IN THE OCEAN | 251 | ||
| 13.2.1 Sources | 251 | ||
| 13.2.2 Distribution in the water column | 253 | ||
| 13.2.3 Enrichment of TEP at the sea surface | 256 | ||
| 13.2.4 TEP in sea ice | 257 | ||
| 13.3 ROLE OF TEP IN THE MARINE MICROBIAL LOOP | 258 | ||
| 13.3.1 TEP and bacteria | 258 | ||
| 13.3.2 TEP and microbial eukaryotes | 259 | ||
| 13.3.3 TEP and zooplankton | 260 | ||
| 13.3.4 TEP and viruses | 261 | ||
| 13.4 CONCLUSIONS | 261 | ||
| ACKNOWLEDGEMENT | 262 | ||
| REFERENCES | 262 | ||
| Chapter 14: Snapshots of fungal extracellular matrices | 269 | ||
| 14.1 SUMMARY | 269 | ||
| 14.2 THE DIVERSE MATRIX OF BIOFILMS | 269 | ||
| 14.3 FUNGAL CELL WALL AND BEYOND | 270 | ||
| 14.3.1 Polysaccharides | 271 | ||
| 14.3.1.1 α-Glucans | 274 | ||
| 14.3.1.2 ß-glucans | 275 | ||
| 14.3.1.3 Mannans: specific in yeasts | 276 | ||
| 14.4 DIVERSE FUNCTIONS OF FUNGAL EPS | 277 | ||
| 14.4.1 Natural functions and their applications | 277 | ||
| 14.4.2 EPS support interactions with solid substrates including minerals | 278 | ||
| 14.4.3 Function of EPS in yeasts and melanised yeast-like fungi | 281 | ||
| 14.4.3.1 Capsule-forming fungi: Cryptococcus species | 283 | ||
| 14.5 NON-POLYSACCHARIDE CONPOUNDS IN THE EXTRACELLULAR MATRIX | 284 | ||
| 14.5.1 Proteins | 284 | ||
| 14.5.2 Glycolipids | 284 | ||
| 14.5.3 Fungal quorum sensing molecules | 285 | ||
| 14.6 DYNAMICS OF THE FUNGAL CELL WALL DEFINES THE EXTRACELLULAR MATRIX IN A CONSTANT INTERPLAY BETWEEN ORGANISMS AND THE ENVIRONMENT | 286 | ||
| 14.7 CONCLUSIONS: HEIGHTENED AWARENESS OF FUNGAL COMPLEXITY AND THEIR ENVIRONMENTAL RELEVANCE | 287 | ||
| ACKNOWLEDEMENTS | 288 | ||
| REFERENCES | 288 | ||
| Chapter 15: Biofilms X-treme: composition of extracellular polymeric substances in Archaea | 301 | ||
| ABSTRACT | 301 | ||
| 15.1 ARCHAEA | 302 | ||
| 15.2 ARCHAEAL BIOFILMS | 303 | ||
| 15.3 EPS ANALYSIS | 304 | ||
| 15.3.1 Static incubation systems | 304 | ||
| 15.3.2 Flow-through systems | 310 | ||
| 15.3.3 Microscopic techniques | 310 | ||
| 15.3.3.1 Fluorescence microscopy | 311 | ||
| 15.4 EPS ISOLATION AND COMPOSITION | 312 | ||
| 15.4.1 EPS isolation of archaeal biofilms | 312 | ||
| 15.4.1.1 Crenarchaeota | 313 | ||
| 15.4.1.2 Euryarchaeota | 313 | ||
| 15.5 CONCLUSIONS | 314 | ||
| ACKNOWLEDGEMENTS | 314 | ||
| REFERENCES | 315 | ||
| Index | 319 |