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Abstract
Microbial Ecology of Activated Sludge, written for both microbiologists and engineers, critically reviews our current understanding of the microbiology of activated sludge, the most commonly used process for treating both domestic and industrial wastes. The contributors are all internationally recognized as leading research workers in activated sludge microbiology, and all have made valuable contributions to our present understanding of the process.
The book pays particular attention to how the application of molecular methods has changed our perceptions of the identity of the filamentous bacteria causing the operational disorders of bulking and foaming, and the bacteria responsible for nitrification and denitrification and phosphorus accumulation in nutrient removal processes. Special attention is given to how it is now becoming possible to relate the composition of the community of microbes present in activated sludge, and the in situ function of individual populations there, and how such information might be used to manage and control these systems better. Detailed descriptions of some of these molecular methods are provided to allow newcomers to this field of study an opportunity to apply them in their research. Comprehensive descriptions of organisms of interest and importance are also given, together with high quality photos of activated sludge microbes.
Activated sludge processes have been used globally for nearly 100 years, and yet we still know very little of how they work. In the past 15 years the advent of molecular culture independent methods of study have provided tools enabling microbiologists to understand which organisms are present in activated sludge, and critically, what they might be doing there. Microbial Ecology of Activated Sludge will be the first book available to deal comprehensively with the very exciting new information from applying these methods, and their impact on how we now view microbiologically mediated processes taking place there. As such it will be essential reading for microbial ecologists, environmental biotechnologists and engineers involved in designing and managing these plants. It will also be suitable for postgraduate students working in this field.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Half Title | 1 | ||
| Title | 3 | ||
| Copyright | 4 | ||
| Table of contents | 5 | ||
| Preface | 7 | ||
| Contributors | 11 | ||
| Chapter 1: An overview of the microbes in activated sludge | 17 | ||
| INTRODUCTION | 17 | ||
| The need for wastewater treatment | 17 | ||
| A brief history of wastewater treatment | 19 | ||
| THE ACTIVATED SLUDGE PROCESS | 20 | ||
| GENERAL FEATURES AND CHARACTERISTICS OF MICROBES RELEVANT TO ACTIVATED SLUDGE SYSTEMS | 22 | ||
| WHAT IS MICROBIOLOGY? | 23 | ||
| HOW DO WE STUDY MICROBES? | 23 | ||
| WHAT ARE THESE MICROBES? | 25 | ||
| Some cell biology | 25 | ||
| Subcellular organisation: the viruses | 25 | ||
| Cellular organisms | 25 | ||
| CELLS WITH A NON-EUKARYOTIC ORGANIZATION | 28 | ||
| STRUCTURAL FEATURES OF ‘PROKARYOTIC’ CELLS | 31 | ||
| HOW DO WE DIVIDE THESE GROUPS UP? | 31 | ||
| Outer cell layers | 35 | ||
| The cell walls of Bacteria and Archaea | 35 | ||
| The cytoplasmic membranes of Bacteria and Archaea | 37 | ||
| Organization of DNA in Bacteria and Archaea | 38 | ||
| Genetic recombination and horizontal gene transfer in ‘prokaryotes’ | 38 | ||
| Horizontal or lateral gene transfer | 39 | ||
| Intracellular inclusion bodies in ‘prokaryotes’ | 40 | ||
| Vacuoles in ‘prokaryotic’ cells | 41 | ||
| Motility in organisms with ‘prokaryotic’ cells | 41 | ||
| Do ‘prokaryotic’ cells possess a cytoskeleton? | 41 | ||
| CELLS WITH A EUKARYOTIC ORGANIZATION | 42 | ||
| The cell walls of eukaryotic microbes | 43 | ||
| The membranes of eukaryotic microbes | 43 | ||
| Organelles in eukaryotic microbes | 43 | ||
| The nuclear arrangement in eukaryotic microbes | 45 | ||
| Cytoskeletal elements in eukaryotic microbes | 45 | ||
| Conclusions | 45 | ||
| A BRIEF DESCRIPTION OF THE FUNGI | 45 | ||
| A BRIEF DESCRIPTION OF THE ALGAE AND PROTOZOA | 52 | ||
| ALGAE | 52 | ||
| THE PROTOZOA | 53 | ||
| A COMPREHENSIVE SINGLE CLASSIFICATION OF ALL THE EUKARYA | 53 | ||
| HOW DO THESE MICROBES GROW? | 54 | ||
| MECHANISMS CELLS USE FOR GENERATING ENERGY | 54 | ||
| Chemoorganoheterotrophs | 56 | ||
| Chemolithoautotrophs | 58 | ||
| Photolithoautotrophs | 61 | ||
| THE GROWTH AND NUTRITION OF MICROBES | 62 | ||
| THE GROWTH KINETICS OF MICROBES | 63 | ||
| Batch culture systems | 64 | ||
| KINETIC ANALYSIS OF BATCH CULTURES | 65 | ||
| How can we determine values for K⊂s and μmax? | 66 | ||
| UTILISATION OF SUBSTRATES IN BATCH CULTURE | 67 | ||
| KINETIC ANALYSIS OF CHEMOSTAT CULTURES | 69 | ||
| UTILISATION OF SUBSTRATES IN CONTINUOUS CULTURE | 70 | ||
| THE CONTROL AND PREVENTION OF MICROBIAL GROWTH | 71 | ||
| CONCLUSIONS | 72 | ||
| Chapter 2: The activated sludge process | 73 | ||
| INTRODUCTION | 73 | ||
| What do these systems need to deal with? | 73 | ||
| WASTE DISPOSAL SYSTEMS OR WATER RESOURCES FOR RECYCLING? | 75 | ||
| WHAT ABOUT DISPOSAL OF THE SLUDGE? | 76 | ||
| THE CURRENT STATE OF THE ACTIVATED SLUDGE PROCESS | 77 | ||
| DESIGN CONFIGURATIONS FOR FULL-SCALE ACTIVATED SLUDGE SYSTEMS: THE ENGINEER’S PERSPECTIVE | 78 | ||
| CONVENTIONAL ACTIVATED SLUDGE PLANTS REMOVING ORGANIC CARBON | 78 | ||
| PLUG FLOW SYSTEMS | 78 | ||
| COMPLETELY MIXED SYSTEMS | 80 | ||
| CONTACT STABILIZATION | 80 | ||
| EXTENDED AERATION SYSTEMS | 81 | ||
| PACKAGED PLANTS | 82 | ||
| HIGH RATE TREATMENT SYSTEMS | 82 | ||
| MULTISTAGE TREATMENT SYSTEMS | 82 | ||
| ACTIVATED SLUDGE PROCESS DESIGNED FOR NITROGEN (N) REMOVAL | 82 | ||
| PROCESS CONFIGURATIONS IN SYSTEMS REMOVING NITROGEN | 83 | ||
| The R-D-N and Biodenitro processes | 85 | ||
| NOVEL N REMOVAL PROCESSES | 86 | ||
| ACTIVATED SLUDGE SYSTEMS REMOVING NITROGEN AND PHOSPHORUS | 87 | ||
| OTHER EBPR SYSTEMS | 90 | ||
| SEQUENCING BATCH REACTORS (SBR) | 91 | ||
| FULL SCALE SBR DESIGN AND OPERATION | 92 | ||
| MEMBRANE BIOREACTORS (MBR) | 92 | ||
| AEROBIC GRANULE TECHNOLOGY | 93 | ||
| THE FUTURE FOR ACTIVATED SLUDGE PLANT DESIGN? | 95 | ||
| MONITORING THE PROCESS – THE ENGINEERS’ REQUIREMENTS | 95 | ||
| Influent flow data and hydraulic load | 95 | ||
| Influent alkalinity and pH | 96 | ||
| Dissolved oxygen and redox levels | 96 | ||
| Mixed liquor suspended solids (MLSS) and mixed liquor volatile suspended solids (MLVSS) | 96 | ||
| Sludge loading or food/microorganisms ratio (F/M ratio) | 96 | ||
| Sludge age or sludge residence time (SRT) or mean cell residence time (MCRT) | 97 | ||
| MONITORING THE PROCESS – THE CHEMIST’S REQUIREMENTS | 97 | ||
| MONITORING THE CHEMICAL PROPERTIES OF THE INFLUENT AND EFFLUENT | 98 | ||
| The amount of organic material entering or leaving the plant (organic loading) | 98 | ||
| The BOD⊂5 test | 98 | ||
| The COD test | 99 | ||
| The amount of nitrogenous material in the influent | 100 | ||
| TKN/COD ratio | 100 | ||
| MONITORING THE PROCESS – THE MICROBIOLOGIST’S REQUIREMENTS | 100 | ||
| AUTOMATIC ON-LINE MONITORING OF ACTIVATED SLUDGE SYSTEMS | 101 | ||
| MODELLING THE ACTIVATED SLUDGE PROCESS | 102 | ||
| Activated sludge model no. 1 (ASM1) | 102 | ||
| Incorporating enhanced biological phosphorus removal (EBPR) processes into ASM models | 104 | ||
| Activated sludge model no. 3 (ASM3) | 104 | ||
| Combining ASM models with structured metabolic models | 105 | ||
| Model calibration and wastewater characterisation | 106 | ||
| ADVANCES AND FUTURE DIRECTIONS IN ASM MODELLING | 107 | ||
| Microbial population dynamics | 107 | ||
| Linking activated sludge models with the entire WWTP | 107 | ||
| Biofilm, granular and membrane bioreactor (MBR) processes | 108 | ||
| The presence of micropollutants | 109 | ||
| Empirical and hybrid models | 109 | ||
| Chapter 3: Microbial communities in activated sludge plants | 111 | ||
| INTRODUCTION | 111 | ||
| MICROBIAL POPULATIONS IN ACTIVATED SLUDGE – THEIR LOCATION | 112 | ||
| The floc | 113 | ||
| Aerobic granules | 115 | ||
| METHODS FOR STUDYING MICROBIAL POPULATIONS IN ACTIVATED SLUDGE | 116 | ||
| Sampling populations | 116 | ||
| Micromanipulation | 116 | ||
| Differential centrifugation | 117 | ||
| Flow cytometry | 117 | ||
| Culturing activated sludge organisms | 118 | ||
| Identifying and quantifying populations in activated sludge | 118 | ||
| FISH | 119 | ||
| qPCR based methods | 120 | ||
| Other quantification methods | 121 | ||
| Detecting viable cells in activated sludge | 121 | ||
| Detecting and identifying active cells in activated sludge and measuring their activities | 122 | ||
| Following changes in activated sludge community composition | 124 | ||
| Resolving population structure/function relationships in activated sludge communities | 125 | ||
| THE ACTIVATED SLUDGE MICROBIAL COMMUNITY COMPOSITION | 125 | ||
| Viruses and bacteriophages | 125 | ||
| Bacteria and Archaea | 127 | ||
| The extent of the biodiversity of activated sludge bacterial communities? | 127 | ||
| ACTIVATED SLUDGE PLANT COMMUNITY STRUCTURE | 129 | ||
| The Archaea | 129 | ||
| Chemoorganoheterotrophic bacteria | 129 | ||
| Function of these populations? | 130 | ||
| Denitrifying bacteria | 130 | ||
| Polymer degrading bacteria | 131 | ||
| Iron bacteria | 131 | ||
| Sulfate reducing bacteria | 132 | ||
| PHA accumulating bacteria | 132 | ||
| The glycogen accumulating organisms (GAO) | 132 | ||
| The PAO | 133 | ||
| Chemolithoautotrophic bacteria | 133 | ||
| The nitrifying organisms | 133 | ||
| The sulphur oxidizing bacteria | 135 | ||
| Cyanobacteria | 135 | ||
| Protozoa | 135 | ||
| Fungi | 136 | ||
| Algae | 137 | ||
| Metazoa | 137 | ||
| FACTORS AFFECTING SURVIVAL OF AN ORGANISM IN ACTIVATED SLUDGE SYSTEMS | 137 | ||
| An organism’s specific growth rate (μ) | 137 | ||
| Tolerance to abiotic factors and toxic chemicals | 139 | ||
| An ability to contribute to floc formation | 139 | ||
| An ability to withstand starvation conditions | 140 | ||
| HORIZONTAL GENE TRANSFER IN ACTIVATED SLUDGE COMMUNITIES | 140 | ||
| MANIPULATING THE MICROBIAL COMMUNITY IN ACTIVATED SLUDGE PLANTS | 141 | ||
| Chapter 4: Protozoa in activated sludge processes | 143 | ||
| INTRODUCTION | 143 | ||
| OCCURRENCE IN PLANTS | 143 | ||
| Ciliates | 144 | ||
| Flagellates | 145 | ||
| Amoebae | 146 | ||
| Pathogenic and parasitic protozoa | 147 | ||
| THE ROLE OF PROTOZOA IN ACTIVATED SLUDGE PLANTS | 148 | ||
| PROTOZOA AS INDICATORS OF PLANT PERFORMANCE | 150 | ||
| POPULATION DYNAMICS OF ACTIVATED SLUDGE PROTOZOA | 153 | ||
| ACKNOWLEDGEMENT | 154 | ||
| Chapter 5: Factors affecting the bulking and foaming filamentous bacteria in activated sludge | 155 | ||
| INTRODUCTION | 155 | ||
| REASONS FOR INADEQUATE SOLIDS SEPARATIONS IN CLARIFIERS | 156 | ||
| Bulking sludge and its properties | 156 | ||
| HOW DO WE PREDICT WHETHER PLANTS WILL SUFFER FROM FOAMING AND BULKING? | 157 | ||
| Foaming | 157 | ||
| Bulking | 159 | ||
| Filament quantification methods in bulking sludge | 159 | ||
| FISH based quantification methods for monitoring bulking | 159 | ||
| WHAT SELECTIVE PRESSURES ARE THOUGHT TO FAVOR THE FILAMENTOUS BACTERIA IN ACTIVATED SLUDGE? | 160 | ||
| The microbiological approach | 160 | ||
| Surveying filament populations in plants | 160 | ||
| So are survey data helpful? | 162 | ||
| The engineering approach | 163 | ||
| The kinetic and metabolic selection theories | 163 | ||
| The kinetic selection theory | 163 | ||
| The storage selection theory | 164 | ||
| The metabolic selection theory | 164 | ||
| The NO⊂x inhibition selection theory for low F/M filaments | 164 | ||
| WHAT EVIDENCE IS THERE TO SUPPORT THESE SELECTION THEORIES? | 165 | ||
| THE ECOLOGY OF FILAMENTS IN ACTIVATED SLUDGE; WHAT OTHER FACTORS MIGHT ALSO DETERMINE THEIR INFLUENCE ON PLANT PERFORMANCE? | 178 | ||
| Tolerance to abiotic factors | 178 | ||
| Temperature | 178 | ||
| pH | 179 | ||
| pO⊂2 | 179 | ||
| Redox potential | 179 | ||
| Metabolic attributes of filaments | 179 | ||
| Implicit selective factors | 182 | ||
| Chapter 6: The current taxonomic status of the filamentous bacteria found in activated sludge plants | 185 | ||
| INTRODUCTION | 185 | ||
| 1. CLASSIFICATION | 185 | ||
| The ‘prokaryotic’ species – an artificial concept | 186 | ||
| Principles of classification | 187 | ||
| 2. NOMENCLATURE | 188 | ||
| 3. IDENTIFICATION | 189 | ||
| APPROACHES TO IDENTIFICATION | 189 | ||
| CHARACTERS USED IN THE CLASSIFICATION AND IDENTIFICATION OF BACTERIA | 190 | ||
| GENOTYPIC CHARACTERS | 190 | ||
| PHENOTYPIC CHARACTERS | 191 | ||
| SO HOW DO WE CLASSIFY AND IDENTIFY THE FILAMENTOUS BACTERIA? | 191 | ||
| LACK OF AVAILABILITY OF PURE CULTURES | 192 | ||
| CHARACTERIZATION OF FILAMENTS | 197 | ||
| HOW DO WE IDENTIFY THESE FILAMENTS? | 201 | ||
| NAMING THESE FILAMENTS? | 201 | ||
| CURRENT CLASSIFICATIONS OF THE FILAMENTOUS BACTERIA | 201 | ||
| CURRENT STATUS OF FILAMENT IDENTIFICATION PROCEDURES | 204 | ||
| WHICH IDENTIFICATION METHOD IS BEST? | 205 | ||
| MICROSCOPIC IDENTIFICATION METHODS | 205 | ||
| Chapter 7: Microbiology of bulking | 207 | ||
| INTRODUCTION | 207 | ||
| THE ABUNDANCE AND OCCURENCE OF BULKING IN ACTIVTATED SLUDGE SYSTEMS | 208 | ||
| Surveys based on morphological identification | 208 | ||
| Surveys based on FISH probing | 210 | ||
| The most abundant filamentous species in municipal and industrial WWTP | 215 | ||
| BULKING CONTROL METHODS | 216 | ||
| SPECIFIC, BIOENGINEERING METHODS FOR BULKING CONTROL | 218 | ||
| Outside factors affecting composition of activated sludge | 218 | ||
| Wastewater composition | 218 | ||
| Temperature, pH, toxic compounds | 219 | ||
| Intrinsic factors | 220 | ||
| Biomass retention time ΘX | 220 | ||
| Actual substrate concentration in reactor | 220 | ||
| Dissolved oxygen, organic substrate, nutrients, pH and temperature in aeration basins | 223 | ||
| Control measures based on ecophysiological features of bulking filamentous bacteria | 224 | ||
| Non-specific, abiotic methods of bulking control | 227 | ||
| Elimination of the filamentous population | 227 | ||
| Increase of sedimentation velocities | 228 | ||
| Compensation of slow settling velocities | 230 | ||
| Chapter 8: Foaming | 231 | ||
| INTRODUCTION | 231 | ||
| OCCURRENCE AND INITIAL STUDIES | 232 | ||
| PROBLEMS ASSOCIATED WITH FOAMING | 232 | ||
| WHICH MICROBES ARE IN FOAM? | 233 | ||
| Microscopic identification and relative incidence of foam microbes | 233 | ||
| Isolation and identification in pure culture | 237 | ||
| The importance of bacterial identification | 240 | ||
| MOLECULAR APPROACHES | 240 | ||
| DETERMINING CAUSATIVE ORGANISMS | 245 | ||
| QUANTIFYING FILAMENTS AND MYCOLATA IN FOAMS | 247 | ||
| Filaments in activated sludge | 247 | ||
| Quantifying Mycolata using microscopy and colony counts | 247 | ||
| Antibody stains and molecular methods | 248 | ||
| Thresholds for foaming | 248 | ||
| TAXONOMY OF FOAM-FORMING ORGANISMS | 249 | ||
| Mycolic acid-containing Actinobacteria – the Mycolata | 249 | ||
| Current classification | 250 | ||
| Candidatus ‘M. parvicella’ | 250 | ||
| HOW IS FOAM FORMED? | 256 | ||
| Gas bubbles | 256 | ||
| Hydrophobicity | 257 | ||
| Surfactants (surface active agents) | 258 | ||
| FACTORS AFFECTING GROWTH OF FOAM FORMERS | 259 | ||
| Nutrient requirements | 259 | ||
| Oxygen | 260 | ||
| Temperature | 261 | ||
| pH | 262 | ||
| MCRT | 262 | ||
| HOW DO FOAM FORMERS COMPETE IN ACTIVATED SLUDGE? | 263 | ||
| r-K strategy? | 263 | ||
| Growth at the air-water interface | 264 | ||
| Foam trapping | 265 | ||
| Enrichment in the foam layer | 265 | ||
| MEASUREMENT OF FOAMING POTENTIAL AND STABILITY | 266 | ||
| General methods | 266 | ||
| Methods applied to activated sludge | 266 | ||
| FOAM CONTROL METHODS | 269 | ||
| Manipulation of biomass retention time | 269 | ||
| Use of chemicals and antifoam agents | 270 | ||
| Physical methods | 272 | ||
| Addition of supernatant from anaerobic digesters | 273 | ||
| Kinetic and metabolic selection | 273 | ||
| CONCLUSIONS | 274 | ||
| Chapter 9: The microbiology of nitrogen removal | 275 | ||
| INTRODUCTION | 275 | ||
| CHEMOLITHOAUTOTROPHIC AMMONIA-OXIDIZING BACTERIA AND ARCHAEA | 278 | ||
| Phylogeny and habitats of the ammonia oxidizers | 278 | ||
| Physiology of ammonia oxidation | 280 | ||
| Ammonia-oxidizing bacteria and wastewater treatment | 281 | ||
| CHEMOLITHOAUTOTROPHIC NITRITE-OXIDIZING BACTERIA | 282 | ||
| Phylogeny and habitats of the nitrite oxidizers | 282 | ||
| Physiology of nitrite oxidation | 284 | ||
| Nitrite oxidizers and wastewater treatment | 284 | ||
| DENITRIFICATION AND DENITRIFYING BACTERIA | 287 | ||
| Diversity and physiology of the denitrifiers | 287 | ||
| Denitrifying bacteria and wastewater treatment | 288 | ||
| ANAEROBIC AMMONIUM OXIDATION (ANAMMOX) | 293 | ||
| Phylogeny and physiology of anaerobic ammonium oxidizers | 293 | ||
| Anammox organisms and wastewater treatment | 295 | ||
| Chapter 10: The microbiology of phosphorus removal | 297 | ||
| INTRODUCTION | 297 | ||
| THE DISCOVERY AND APPLICATION OF EBPR | 298 | ||
| BIOCHEMICAL TRANSFORMATIONS AND METABOLIC MODELS | 298 | ||
| Biochemical transformations | 298 | ||
| Comeau-Wentzel model | 299 | ||
| Mino model | 300 | ||
| Denitrifying PAO (DPAO) | 301 | ||
| STORAGE POLYMERS IN EBPR | 301 | ||
| Polyphosphate and its metabolism | 301 | ||
| Polyphosphate | 301 | ||
| Functions of polyP | 302 | ||
| PolyP metabolism and polyphosphate kinase | 302 | ||
| PPK1 in model bacteria | 303 | ||
| Other enzymes involved in polyP metabolisms | 304 | ||
| Exopolyphosphatase | 304 | ||
| Phosphotransferase | 305 | ||
| Polyhydroxyalkanoates | 305 | ||
| Glycogen | 306 | ||
| THE ROLE AND NECESSITY OF THE ANAEROBIC ZONE | 306 | ||
| THE MICROBES RESPONSIBLE FOR EBPR – CULTURE-DEPENDENT APPROACHES | 307 | ||
| MOLECULAR BIOLOGY TECHNIQUES USED IN STUDYING EBPR MICROBIAL ECOLOGY | 308 | ||
| CANDIDATUS ‘ACCUMULIBACTER PHOSPHATIS’ | 311 | ||
| Identification and confirmation of Accumulibacter as a bona fide PAO | 311 | ||
| Distribution patterns, population dynamics, and ecology of Accumulibacter | 313 | ||
| Ecophysiology of Accumulibacter | 314 | ||
| Population ecology of Accumulibacter | 314 | ||
| Species delineation with Accumulibacter | 315 | ||
| The nitrate reduction conundrum | 316 | ||
| The Accumulibacter genome | 317 | ||
| Metabolic reconstruction | 318 | ||
| Carbon metabolism in Accumulibacter | 318 | ||
| Phosphate metabolism | 319 | ||
| The imprint of phage | 320 | ||
| Post-genomic insights | 321 | ||
| OTHER PAO | 322 | ||
| Actinobacterial PAO | 322 | ||
| Dechloromonas-related PAO | 324 | ||
| OTHER EBPR COMMUNITY MEMBERS | 324 | ||
| GLYCOGEN ACCUMULATING NON-POLYP ORGANISMS (GAO) | 325 | ||
| GAO phylogeny (Figure 10.11) | 326 | ||
| Culture-Dependent Approaches | 326 | ||
| Candidatus ‘Competibacter phosphatis’ | 326 | ||
| Defluviicoccus vanus – related GAO | 328 | ||
| other GOA | 329 | ||
| Physiological differentiation between GAO and PAO | 329 | ||
| Glycogen degradation pathway | 330 | ||
| Mechanisms for organic carbon uptake | 330 | ||
| Nitrate and nitrite utilization by GAO | 330 | ||
| Competition between GAO and PAO | 332 | ||
| COD/P ratio | 332 | ||
| Carbon Source | 332 | ||
| pH | 334 | ||
| Temperature | 335 | ||
| Other Factors | 335 | ||
| Chapter 11: Methods for the examination and characterization of the activated sludge community | 337 | ||
| INTRODUCTION | 337 | ||
| 11.1 MICROSCOPY AND MICROSCOPIC EXAMINATION OF ACTIVATED SLUDGE | 338 | ||
| THE LIGHT MICROSCOPE | 338 | ||
| PRINCIPLES OF THE COMPOUND LIGHT MICROSCOPY | 338 | ||
| Magnification and resolution | 338 | ||
| Setting up the light microscope | 339 | ||
| Lower power (L.P.) Objective (10×) | 339 | ||
| High Power (H.P.) Objective (×40) | 339 | ||
| Oil Immersion (O.I.) objective | 340 | ||
| Important notes | 340 | ||
| COMMON DIFFICULTIES IN MICROSCOPY | 340 | ||
| Inability to obtain a sharp image with the oil immersion object | 340 | ||
| A dark shadow passes into the field with the loss of definition of the image | 340 | ||
| Poor illumination or the field of view in semi-darkness | 341 | ||
| CARE OF THE MICROSCOPE | 341 | ||
| OPTICAL SYSTEMS FOR LIGHT MICROSCOPY | 341 | ||
| Bright field microscopy | 341 | ||
| Phase contrast microscopy | 341 | ||
| Protocol | 342 | ||
| Nomarski interference microscopy | 342 | ||
| Fluorescence microscopy | 342 | ||
| IMAGE ANALYSIS | 342 | ||
| THE ELECTRON MICROSCOPE | 343 | ||
| THE CONFOCAL LASER SCANNING MICROSCOPE (CLSM) | 344 | ||
| 11.2 PREPARATION OF SPECIMENS FOR MICROSCOPY | 345 | ||
| Equipment and materials | 345 | ||
| Sampling of activated sludge, mixed liquors and foams | 345 | ||
| Sample storage | 345 | ||
| Slide handling | 345 | ||
| Preparation of samples for microscopy | 345 | ||
| Air-dried smears | 346 | ||
| Wet mounts | 346 | ||
| Preparation of sludge and foam samples for SEM | 346 | ||
| Procedure | 346 | ||
| 11.3 STAINS USED FOR EXAMINATION OF ACTIVATED SLUDGE SAMPLES | 347 | ||
| Gram stain (differentiation on the basis of cell wall structure) | 347 | ||
| Preparation of reagents | 347 | ||
| Procedure | 348 | ||
| Comments | 348 | ||
| Alternative Gram staining methods | 348 | ||
| Detecting acid fast bacteria | 348 | ||
| Preparation of reagents | 348 | ||
| Procedure | 349 | ||
| Comments | 349 | ||
| Neisser stain (detection of polyP) | 349 | ||
| Preparation of reagents | 349 | ||
| Chapter 12: Descriptions of activated sludge organisms | 469 | ||
| DESCRIPTIONS OF THE FILAMENTOUS BACTERIA IN ACTIVATED SLUDGE | 470 | ||
| Gram negative filaments | 470 | ||
| Alphaproteobacteria | 470 | ||
| Betaproteobacteria | 475 | ||
| Gammaproteobacteria | 478 | ||
| ‘CHLOROFLEXI’ | 482 | ||
| GRAM POSITIVE FILAMENTS | 485 | ||
| Firmicutes (Low mol% G+C) | 485 | ||
| Actinobacteria (High mol% G+C) | 487 | ||
| Candidatus Division TM7 | 494 | ||
| Planctomycetales | 495 | ||
| ‘Bacteroidetes’ | 495 | ||
| FILAMENTOUS BACTERIA OF UNKNOWN TAXONOMIC AFFILIATION | 497 | ||
| PAO, TFO AND PUTATIVE GAO IN EBPR SYSTEMS | 501 | ||
| Chapter 13: Colour image section | 505 | ||
| Figures from Chapter 1 | 506 | ||
| Figures from Chapter 3 | 507 | ||
| Figures from Chapter 4 | 509 | ||
| Figures from Chapter 5 | 512 | ||
| Figures from Chapter 7 | 513 | ||
| Figures from Chapter 9 | 514 | ||
| Figures from Chapter 10 | 515 | ||
| Figures from Chapter 11 | 518 | ||
| Figures from Chapter 12 | 533 | ||
| Chapter 14: References | 553 | ||
| Index | 659 |