Chapter 1 BASICS OF MICROBIOLOGY 1
1.1 The Cell 2
1.2 Taxonomy and Phylogeny 4
1.3 Prokaryotes 6
1.3.1 Bacteria 7
1.3.2 Archaea 21
1.4 Eukarya 22
1.4.1 Fungi 22
1.4.2 Algae 26
1.4.3 Protozoa 31
1.4.4 Other Multicellular Microorganisms 34
1.5 Viruses 36
1.6 Infectious Disease 37
1.7 Biochemistry 42
1.8 Enzymes 43
1.8.1 Enzyme Reactivity 46
1.8.2 Regulating the Activity of Enzymes 51
1.9 Energy Capture 51
1.9.1 Electron and Energy Carriers 51
1.9.2 Energy and Electron Investments 54
1.10 Metabolism 55
1.10.1 Catabolism 58
1.10.2 Anabolism 76
1.10.3 Metabolism and Trophic Groups 80
1.11 Genetics and Information Flow 80
1.12 Deoxyribonucleic Acid(DNA) 82
1.12.1 The Chromosome 84
1.12.2 P1asmids 87
1.12.3 DNA Replication 87
1.13 Ribonucleic Acid(RNA) 88
1.13.1 Transcription 88
1.13.2 Messenger RNA(mRNA) 90
1.13.3 Transfer RNA(tRNA) 90
1.13.4 Translation and the Ribosomal RNA(rRNA) 91
1.13.5 Translation 92
1.13.6 Regulation 94
1.14 Phylogeny 94
1.14.1 The Basics of Phylogenetic Classification 97
1.15 Microbial Ecology 99
1.15.1 Selection 100
1.15.2 Exchange of Materials 102
1.15.3 Adaptation 107
1.16 Tools to Study Microbial Ecology 110
1.16.1 Traditional Enrichment Tools 111
1.16.2 Molecular Tools 112
1.16.3 Multispecies Modeling 119
1.17 Bibliography 120
1.18 Problems 121
Chapter 2 STOICHIOMETRY AND BACTERIAL ENERGETICS 126
2.1 An Example Stoichiometric Equation 126
2.2 Empirical Formulas for Microbial Cells 128
2.3 Substrate Partitioning and Cellular Yield 130
2.4 Energy Reactions 132
2.5 Overall Reactions for Biological Growth 141
2.5.1 Fermentation Reactions 145
2.6 Energetics and Bacterial Growth 150
2.6.1 Free Energy ofthe Energy Reaction 151
2.7 Yield Coefficient and Reaction Energetics 155
2.8 Oxidized Nitrogen Sources 159
2.9 Bibliography 161
2.10 Problems 161
Chapter 3 MICROBIAL KINETICS 165
3.1 Basic Rate Expressions 165
3.2 Parameter Values 168
3.3 Basic Mass Balances 171
3.4 Mass Balances on Inert Biomass and Volatile Solids 175
3.5 Soluble Microbial Products 176
3.6 Nutrients and Electron Acceptors 183
3.7 Input Active Biomass 186
3.8 Hydrolysis of Particulate and Polymeric Substrates 188
3.9 Inhibition 191
3.10 Other Alternate Rate Expressions 197
3.11 Bibliography 198
3.12 Problems 199
Chapter 4 BIOFILM KINETICS 207
4.1 Microbial Aggregation 207
4.2 Why Biofilms? 208
4.3 The Idealized Biofilm 208
4.3.1 Substrate Phenomena 210
4.3.2 The Biofilm Itself 213
4.4 The Steady-State Biofilm 214
4.5 The Steady-State-Biofilm Solution 215
4.6 Estimating Parameter Values 220
4.7 Average Biofilm SRT 225
4.8 Completely Mixed Biofilm Reactor 225
4.9 Soluble Microbial Products and Inert Biomass 228
4.10 Trends in CMBRPerformance 231
4.11 Normalized Surface Loading 233
4.12 Nonsteady-State Biofilms 239
4.13 Special-Case Biofilm Solutions 245
4.13.1 Deep Biofilms 246
4.13.2 Zero-Order Kinetics 246
4.14 Bibliography 247
4.15 Problems 248
Chapter 5 REACTORS 261
5.1 Reactor Types 261
5.1.1 Suspended-Growth Reactors 262
5.1.2 Biofilm Reactors 264
5.1.3 Reactor Arrangements 266
5.2 Mass Balances 267
5.3 A Batch Reactor 270
5.4 A Continuous-Flow Stirred-Tank Reactor with Effluent Recycle 273
5.5 A Plug-Flow Reactor 275
5.6 A Plug-Flow Reactor with Effluent Recycle 277
5.7 Reactors with Recycle of Settled Cells 280
5.7.1 CSTR with Settling and Cell Recycling 280
5.7.2 Evaluation of Assumptions 286
5.7.3 Plug-Flow Reactor with Settling and Cell Recycle 287
5.8 Using Alternate Rate Models 289
5.9 Linking Stoichiometric Equations to Mass Balance Equations 289
5.10 Engineering Design of Reactors 292
5.11 Reactors in Series 296
5.12 Bibliography 300
5.13 Problems 300
Chapter 6 THE ACTIVATED SLUDGE PROCESS 307
6.1 Characteristics of Activated Sludge 308
6.1.1 Microbial Ecology 308
6.1.2 Oxygen and Nutrient Requirements 311
6.1.3 Impacts of Solids Retention Time 312
6.2 Process Configurations 313
6.2.1 Physical Configurations 313
6.2.2 Oxygen Supply Modifications 319
6.2.3 Loading Modifications 322
6.3 Design and Operating Criteria 323
6.3.1 Historical Background 324
6.3.2 Food-to-Microorganism Ratio 324
6.3.3 Solids Retention Time 326
6.3.4 Comparison of Loading Factors 329
6.3.5 Mixed-Liquor Suspended Solids,the SVI,and the Recycle Ratio 330
6.3.6 Eckenfelder and McKirney Equations 334
6.4 Aeration Systems 335
6.4.1 Oxygen-Transfer and Mixing Rates 335
6.4.2 Diffused Aeration Systems 338
6.4.3 Mechanical Aeration Systems 339
6.5 Bulking and Other Sludge-Settling Problems 340
6.5.1 Bulking Sludge 340
6.5.2 Foaming and Scum Control 344
6.5.3 Rising Sludge 345
6.5.4 Dispersed Growth and Pinpoint Floc 345
6.5.5 Viscous Bulking 346
6.5.6 Addition of Polymers 346
6.6 Activated Sludge Design and Analysis 346
6.7 Analysis and Design of Settlers 353
6.7.1 Activated-Sludge Properties 353
6.7.2 Settler Components 355
6.7.3 Loading Criteria 360
6.7.4 Basics of Flux Theory 362
6.7.5 State-Point Analysis 368
3.7.6 Connecting the Settler and Aeration Tank 374
6.7.7 Limitations of State-Point Analysis 374
6.8 Centrifugal Separations 375
6.9 Membrane Separations 375
6.10 Bibliography 378
6.11 Problems 380
Chapter 7 LAGOONS 394
7.1 Aerated Lagoons 394
7.2 Stabilization Lagoons 400
7.3 Types of Stabilization Lagoons 401
7.4 Aerobic Stabilization Lagoons 402
7.4.1 Basic Equations 403
7.4.2 Solar Energy Input and Utilization Efficiency 405
7.4.3 BODLRemoval 407
7.4.4 Kinetics of Phototrophic Growth 412
7.4.5 Facultative Stabilization Lagoons 416
7.4.6 Surface BOD5Loading Rates 416
7.4.7 First-Order Kinetics 417
7.5 Anaerobic Stabilization Lagoons 422
7.6 Series Operation 423
7.7 Coliform Reduction 424
7.8 Lagoon Design Details 427
7.9 Removing Suspended Solids fromtheLagoonEffluent 427
7.10 Wetlands Treatment 429
7.11 Bibliography 430
7.12 Problems 431
Chapter 8 AEROBIC BIOFILM PROCESSES 434
8.1 Biofilm Process Considerations 435
8.2 Trickling Filters and Biological Towers 438
8.3 Rotating Biological Contactors 451
8.4 Granular-Media Filters 456
8.5 Fluidized-Bed and Circulating-Bed Biofilm Reactors 457
8.6 Hybrid Biofilm/Suspended-Growth Processes 463
8.7 Bibliography 464
8.8 Problems 465
Chapter 9 NITRIFICATION 470
9.1 Biochemistry and Physiology of Nitrifying Bacteria 470
9.2 Common Process Considerations 474
9.3 Activated Sludge Nitrification:One-Sludge Versus Two-Sludge 474
9.4 Biofilm Nitrificafion 483
9.5 Hybrid Processes 486
9.6 The Role of the Input BODL:TKN Ratio 488
9.7 The ANAMMOX Process 488
9.8 Bibliography 489
9.9 Problems 490
Chapter 10 DENITRIFICATION 497
10.1 Physiology of Denitrifying Bacteria 497
10.2 Tertiary Denitrification 501
10.2.1 Activated Sludge 503
10.2.2 Biofilm Processes 506
10.3 One-Sludge Denitrification 508
10.3.1 Basic One-Sludge Strategies 509
10.3.2 Variations on the Basic One-Sludge Processes 512
10.3.3 Quantitative Analysis of One-Sludge Denitrification 515
10.4 Bibliography 524
10.5 Problems 525
Chapter11 PHOSPHORUS REMOVAL 535
11.1 Normal Phosphorus Uptake into Biomass 535
11.2 Precipitation by Metal-Salts Addition to a Biological Process 537
11.3 Enhanced Biological Phosphorus Removal 539
11.4 Bibliography 545
11.5 Problems 547
Chapter12 DRINKING-WATER TREATMENT 550
12.1 Aerobic Biofilm Processes to Eliminate Biological Instability 551
12.1.1 BOM Measurement Techniques 553
12.1.2 Removing Inorganic Sources of Biological Instability 554
12.1.3 Biofilm Pretreatment 555
12.1.4 Hybrid Biofiltration 558
12.1.5 Slow Biofiltration 561
12.2 Release of Microorganisms 561
12.3 Biodegradation of Specific Organic Compounds 562
1 2.4 Denitrification 563
12.5 Bibliography 566
12.6 Problems 567
Chapter 13 ANAEROBIC TREATMENT BY METHANOGENESIS 569
13.1 Uses for Methanogenic Treatment 570
13.2 Reactor Configurations 573
13.2.1 Completely Mixed 573
13.2.2 Anaerobic Contact 575
13.2.3 Upflow and Downflow Packed Beds 576
13.2.4 F1uidized and Expanded Beds 577
13.2.5 Upflow Anaerobic Sludge Blanket 578
13.2.6 Miscellaneous Anaerobic Reactors 579
13.3 Process Chemistry and Microbiology 581
13.3.1 Process Microbiology 581
13.3.2 Process Chemistry 585
13.4 Process Kinetics 604
13.4.1 Temperature Effects 604
13.4.2 Reaction Kinetics for a CSTR 606
13.4.3 Complex Substrates 609
13.4.4 Process Optimization 614
13.4.5 Reaction Kinetics for Biofilm Processes 616
13.4.6 Kinetics with Hydrolysis as the Limiting Factor 618
13.5 Special Factors for the Design of Anaerobic Sludge Digesters 622
13.5.1 Loading Criteria 623
13.5.2 Mixing 624
13.5.3 Heating 625
13.5.4 Gas Collection 626
13.5.5 Performance 626
13.6 Bibliography 627
13.7 Problems 629
Chapter 14 DETOXIFICATION OF HAZARDOUS CHEMICALS 637
14.1 Factors Causing Molecular Recalcitrance 639
14.1.1 Molecular Structure 640
14.1.2 Environmental Conditions 640
14.1.2 Microorganism Presence 640
14.2 Syntheric Organic Chemical Classes 643
14.3 Energy Metabolism Versus Cometabolism 647
14.4 Electron Donor Versus Electron Acceptor 648
14.5 Minimum Substrate Concentration(Smin) 651
14.6 Biodegradation of Problem Environmental Contaminants 653
14.6.1 Syntheric Detergents 653
14.6.2 Pesticides 654
14.6.3 Hydrocarbons 657
14.6.4 Chlorinated Solvents and Other Halogenated Aliphatic Hydrocarbons 663
14.6.5 Chlorinated Aromatic Hydrocarbons 673
14.6.6 Explosives 678
14.6.7 General Fate Modeling for Organic Chemicals 680
14.6.8 Inorganic Elements 682
14.7 Summary 685
14.8 Bibliography 685
14.9 Problems 689
Chapter 15 BIOREMEDIATION 695
15.1 Scope and Characteristics of Contaminants 696
15.1.1 Organic Compounds 697
15.1.2 Mixtures of Organic Compounds 699
15.1.3 Mixtures Created by Codisposal 702
15.2 Biodegradability 705
15.3 Contaminant Availability for Biodegradation 705
15.3.1 Sorption to Surfaces 706
15.3.2 Formation of a Nonaqueous Phase 708
15.4 Treatability Studies 711
15.5 Engineering Strategies for Bioremediation 713
15.5.1 Site Characterization 713
15.5.2 Engineered In Situ Bioremediation 714
15.5.3 Intrinsic In Situ Bioremediation and Natural Attenuation 717
15.5.4 In Situ Biobarriers 718
15.5.5 Ex Situ Bioremediation 719
15.5.6 Phytoremediation 720
15.5.7 Bioremediation of Gas-Phage VOCs 721
15.6 Evaluating Bioremediation 722
15.7 Bibliography 725
15.8 Problems 728
Appendix A FREE ENERGIES OF FORMATION FOR VARIOUS CHEMICAL SPECIES,25° 730
Appendix B NORMALIZED SURFACE-LOADING CURVE 739