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TRANSCRIPT
Second Edition
Environmental
Microbiologyfor Engineers
Volodymyr Ivanov
CRC PressTaylor &Francis CroupBoca Raton London NewYork
CRC Press is an imprint of the
Taylor & Francis Croup, an informa business
Contents
Preface xxvii
Author xxix
Chapter 1 Microorganisms 1
Systems 1
Self-Organized Systems 1
Life as Self-Organized Growth of Biomass 1
Cells 2
Organisms and Microorganisms 3
Size of Microorganisms 3
Biology 3
Microbiology 3
Environmental Microbiology 4
Why Are Microbes Used in Environmental Engineering? 4
Organisms of Importance in Environmental Microbiology 4
Viruses 5
Subviral Particles 6
Importance of Viruses in Environmental and Civil Engineering 6
Prokaryotes 6
Bacteria and Archaea 7
Importance of Prokaryotes in Environmental
and Civil Engineering 7
Fungi 8
Importance of Fungi in Environmental and Civil Engineering 9
Algae 10
Importance of Algae in Environmental Engineering 10
Protozoa 12
Importance of Protozoa for Environmental Engineering 13
Chapter 1 Quiz 13
Chapter 2 Static Biochemistry 15
Static and Dynamic Biochemistry 15
Chemical Features of Life 15
Balance of Elements 15
Covalent Bonds 16
Organic Compounds and Functional Groups 16
Polarity of Chemical Bonds 16
Water 17
pH of Solutions 17
Intermolecular Forces 17
ziii Contents
Hydrophobic Substances and Hydrophobic Forces 18
Stereoisomers 18
Biological Monomers and Polymers 18
Monosaccharides 20
Oligosaccharides and Polysaccharides 21
Lipids and Membranes 22
Lipid Membranes 22
Membrane Melting and Freezing 22
Amino Acids and Proteins 23
Structure of a Protein Molecule 23
Globular and Fibrous Proteins 27
Denaturation of Proteins 29
Enzymes 29
Coenzymes 29
Nucleotides 30
Cyclic Nucleotides 30
Oligonucleotides 31
DNA Structure 31
DNA Melting 32
DNA as a Carrier of Genetic Information 33
DNA Sequences and Sequencing 35
RNA 35
mRNA 36
tRNA 36
Genetic Code 36
rRNA and Translation 36
16S rRNA 37
Functions of rRNA in the Ribosome 37
miRNA 37
Summary of the Functions of Monomers and Polymers in a Cell 37
Chapter 2 Quiz 39
Chapter 3 Dynamic Biochemistry 41
Levels of Metabolism 41
Biochemical Reactions 41
Major Features of Enzymes 41
Mechanism of Enzymatic Catalysis 42
Specificity of Enzymes 42
Inactivation of Enzymes 42
Classification of Enzymes 42
Environmental Applications of Microbial Enzymesand Coenzymes 44
Coenzymes 44
Units of Enzymatic Activity 45
Control of Individual Biochemical Reactions 45
Contents ix
Effect of Noncompetitive Inhibitors on Enzymatic Activity 46
Effect of Competitive Inhibitors on Enzymatic Activity 46
Control of a Group of Biochemical Reactions 46
Regulation of Enzymatic Activity in the Sequence of Enzymes 47
Regulation of Enzyme Synthesis and Degradation 47
Metabolic Blocks 48
Control of Metabolic Blocks 49
Cyclic AMP and GMP as Whole-Cell Regulators of Metabolism.... 50
Temporal Control of Cell Metabolism 50
Nitric Oxide as Controller of Metabolism 50
Quorum Sensing 51
Control of Metabolism in the Biosphere 51
Chapter 3 Quiz 52
Chapter 4 Biooxidation and Bioreduction 53
Oxidation-Reduction 53
Oxidation Numbers 54
Oxidation of Carbon 55
Oxidation-Reduction during Fermentation 55
Energy 55
Two Sources of Biological Forms of Energy 56
Chemotrophy 56
Chemotrophic Oxidation-Reduction Reactions 57
Chemotrophy: Fermentation 57
Chemotrophy: Anaerobic (Anoxic) Respiration 58
Chemotrophy: Aerobic Respiration 58
Phototrophy 58
Oxygenic and Anoxygenic Phototrophic Oxidation-Reduction
Reactions 58
Electron-Transfer Chain 59
Proton Motive Force 59
Oxidative Phosphorylation 60
Biological Forms of Energy 60
Production of Biological Energy in Photosynthesis 60
ATP Yield from Oxidative Phosphorylation 61
ATP Production and Yield from Fermentation 62
ATP Yield from Lithotrophy 63
Long-Term Energy Storage in Cells 63
Relation to Oxygen and Generation of Energy 63
Chapter 4 Quiz 64
Chapter 5 Biodegradation 67
Biodegradation and Biotransformation 67
Biochemical Reactions of Biodegradation 67
Aerobic, Anoxic, and Anaerobic Biodegradation 68
X Contents
Biodegraded Substances 68
Biodegradation Rates of Natural Substances 68
Biodegradation Rates Correlate with Turnover Rates 68
Degradation of Storage Polysaccharides 68
Biodegradation of Structural Polysaccharides 69
Biodegradation of Hemicellulose and Pectin 70
Biodegradation of Cellulose 70
Biodegradation of Lignin 70
White-Rot Fungi 71
Biodegradation of Chitin 72
Degradation of Proteins 72
Degradation of Amino Acids 72
Degradation of Nucleic Acids 72
Degradation of Lipids 73
Biodegradation of Chemicals 73
Degradation of Aliphatic Hydrocarbons 73
Degradation of Aromatic Hydrocarbons 73
Biodegradation of Benzene, Toluene, Ethylbenzene, and Xylene 75
Bioremediation of Soil and Water Polluted by BTEX Chemicals 75
Xenobiotics 75
Degradative Plasmids 76
Biodegradation of Chlorinated Hydrocarbons 76
Products of Degradation of Aromatic Hydrocarbons 78
Nonbiodegradable and Biodegradable Polymers 79
Polylactic Acid and Polyhydroxyalkanoates 80
Chapter 5 Quiz 80
Chapter 6 Molecular Biology and Genetics 83
Metabolic Blocks of Biosynthesis 83
Energy for Biosynthesis 83
Balance of Energy 83
Excess of Biological Energy 84
Number of Enzymes 84
Genes 85
Noncoding RNA Genes 85
Chromosomes 85
Genomes 85
Genomes of Chloroplasts and Mitochondria 85
The Genome in Comparison with a Book 85
Flow of Genetic Information 86
Genetics, Molecular Biology, Bioinformatics, and Epigenetics 86
Collection of DNA Sequences 87
Nucleus and Nucleoid 87
Plasmids 87
Transposons 88
Contents xi
DNA Replication 88
Speed of DNA Replication 88
Transcription 89
Translation 89
Genetic Code 89
Genome Changes 89
Natural Genetic Recombination in Prokaryotes 90
Conjugation 90
Transformation 91
Transduction 91
Horizontal Gene Transfer 91
DNA Reparation and Mutations 91
Chemical Mutagens 91
Physical Mutagens 91
Biological Mutagens 92
Genetic Adaptation of Microbial Population to ChangedEnvironment 92
Chapter 6 Quiz 92
Chapter 7 Bioagents of Environmental and Engineering Bioprocesses 95
Hierarchy of Life 95
Cell Aggregates 95
Microbial Communities and Ecosystems 95
Shapes of Individual and Connected Prokaryotic Cells 95
Prokaryotic Cell Shapes as Evolutionary Adaptation to Environment.... 97
Inner Structure of Prokaryotic Cells 97
Intracellular Inclusions in Prokaryotic Cells 97
Outer Components of Prokaryotic Cells 99
Cytoplasmic Membrane 99
Vulnerability of the Cytoplasmic Membrane 100
Prokaryotic Cell Walls 100
Origin of Gram-Negative Cells 100
Origin of Gram-Positive Cells 100
Flagella, Fimbriae, and Pili 101
Outer Membrane, Lipopolysaccharides, and S-Layer 101
Glycocalyx and Capsule 101
Anabiotic Prokaryotic Cells 102
Structure of Eukaryotic Cells 102
Organelles 102
Chapter 7 Quiz 103
Chapter 8 Reproduction, Proliferation, and Growth 105
Reproduction of Viruses 105
Reproduction of Prokaryotes 105
xii Contents
Vegetative Reproduction of Microscopic Eukaryotes 105
Asexual and Sexual Reproduction of Microscopic Eukaryotes 107
Cell Growth and the Cell Division Cycle 107
Coordination of Cell Cycle Events 108
Periods of Exotrophy and Endotrophy in the Cell Cycle 108
Cell Differentiation 109
Growth and Proliferation of Cell Populations 109
Generation Time and Number of Generations 109
Specific Growth Rate 110
Stoichiometry of Microbial Growth 110
Cell Age and Cell Trophic State Distributions in Microbial
Populations Ill
Quantification of Microbial Biomass 112
Microscopic Enumeration 112
Flow Cytometry Enumeration 112
Physical Methods of Microbial Biomass Measurement 113
Chemical Methods of Microbial Biomass Measurement 113
Physiological Methods of Microbial Biomass Measurement 113
Biological Methods of Cell Enumeration: Plate Count 114
Biological Methods of Cell Enumeration: Most Probable
Number Count 114
Enumeration of Cells and Viral Particles at Low
Concentrations 115
Molecular-Biological Methods of Microbial Biomass
Quantification 116
Chapter 8 Quiz 116
Chapter 9 Microbial Ecology 119
Ecosystems 119
Levels of Ecosystems 119
Ecosystem Boundaries 119
Boundaries of Unicellular Organisms 119
Boundaries of Multicellular Aggregates 120
Boundaries of Microbial Communities in Environmental
Engineering Systems 121
Diversity of a Microbial Ecosystem 121
Quantification of Ecosystem Diversity 121
Diversity in an Anaerobic Digester 122
Types of Interactions in Microbial Ecosystems 122
Population Density Determines Interaction Type 123
Commensalism 123
Mutualism 124
Interactions of Microorganisms in Cellular Aggregates 126
Positive Interactions between Animals and Microorganisms 126
Contents
Symbiotic Mutualism 126
Positive Interactions between Plants and Microorganisms 127
Symbiosis of Plants and Microorganisms 127
Neutral Competition 127
Amensalism 127
Antagonism 128
Predation 128
Parasitism 128
Microbial Parasites of Plants 128
Microbial Parasites of Human and Animals 129
Effects of Nutrients on Biotic Elements 129
Effects of Nutrients on Yield 129
Effect of Starvation on Microorganisms 130
Effect of Oxygen on Biotic Elements 130
Anoxic Microorganisms 131
Effect of Temperature on Growth 131
Effect of pH on Growth 131
Effect of Osmotic Pressure on Growth 131
Natural Death of Microorganisms 132
Fate of Microorganisms Released into the Environment 132
Chapter 9 Quiz 132
Chapter 10 Classification of Viruses and Microorganisms 135
Biological Classification 135
Units of Biological Classification 135
Names of Species 135
Classification of Viruses 135
Groups of Viruses 136
Importance of Viruses for Environmental Engineering 136
Isolation and Collection of Microbial Strains 136
Microbial Collections 137
Classification of Microorganisms 137
Phenotypic Characteristics 138
Genotypic Classification 138
Phylogenetic Classification 138
G+C Content in DNA and Genotypic Classification 139
Comparison of the Steps in Phenotypic and PhylogeneticIdentification of Strains 139
Phylogenetic Groups of Prokaryotes 139
Classification of Microscopic Fungi 141
Classification of Microscopic Algae 142
Classification of Protozoa 142
Chapter 10 Quiz 143
References 144
xiv Contents
Chapter 11 Physiological Classification of Prokaryotes 145
Physiology of Prokaryotes 145
Three Types of Chemotrophic Energy Generation 145
Three Types of Phototrophic Energy Generation 145
Evolution of the Earth's Atmosphere and Prokaryotes 146
Contradictions between rRNA-Based PhylogeneticClassification and Physiological Classification of Prokaryotes 146
Absence of Predictive Power in rRNA-Based PhylogeneticClassification 147
Parallelism in Evolution of Genes 147
Periodic Table of Prokaryotes 147
Origin of Prokaryotes in Aquatic, Terrestrial, and Extreme
Environments 148
Phototrophic Prokaryotes in the Periodic Table 149
Reasons for Evolutionary Parallelism in the Periods of the
Periodic Table of Prokaryotes 149
Geological Synchronization of the Periods in the Periodic Table
of Prokaryotes 150
Practical Importance of the Periodic Table of Prokaryotes 151
Chapter 11 Quiz 151
Chapter 12 Groups of Anaerobic Prokaryotes 153
The 24 Major Physiological Groups of Prokaryotes 153
Gram-Negative (Aquatic) Chemotrophic Fermenting Bacteria 153
Gram-Positive (Terrestrial) Chemotrophic Fermenting Bacteria 155
Chemotrophic Fermenting Archaea 156
Gram-Negative (Aquatic) Phototrophic Bacteria That Use
Products of Fermentation as Electron Donors 156
Gram-Positive (Terrestrial) Phototrophic Bacteria That Use
Products of Fermentation as Electron Donors 156
Phototrophic Archaea That Use Products of Fermentation as
Electron Donors 156
Chapter 12 Quiz 157
Chapter 13 Groups of Anoxic Prokaryotes 159
Gram-Negative (Aquatic), Chemotrophic, Anoxic Bacteria 159
Dissimilatory Sulfate-Reducing Bacteria 159
Iron-Reducing Bacteria 162
Denitrifying Bacteria 163
Gram-Positive (Terrestrial), Chemotrophic, Anoxic Bacteria 163
Chemotrophic, Anoxic Archaea (Methanogens) 164
Gram-Negative (Aquatic), Phototrophic, Anoxic Bacteria 164
Gram-Positive (Terrestrial), Phototrophic, Anoxic Bacteria 165
Contents xv
Phototrophic Archaea That Use Products of Anoxic Respiration
as Electron Donors 165
Chapter 13 Quiz 166
Chapter 14 Groups of Microaerophilic and Facultative Aerobic/Anaerobic
Prokaryotes 167
Evolutionary Adaptations of Facultative Aerobic/Anaerobic and
Microaerophilic Prokaryotes 167
Gram-Negative (Aquatic), Chemotrophic, Facultative Aerobic/
Anaerobic Bacteria 167
Gram-Negative (Aquatic), Chemotrophic, MicroaerophilicBacteria 170
Gram-Positive (Terrestrial), Chemotrophic, Facultative Aerobic/
Anaerobic and Microaerophilic Bacteria 171
Chemotrophic, Facultative Aerobic/Anaerobic and
Microaerophilic Archaea 171
Gram-Negative (Aquatic), Phototrophic, Facultative Aerobic/
Anaerobic and Microaerophilic Bacteria 171
Gram-Positive (Terrestrial), Phototrophic, Facultative Aerobic/
Anaerobic and Microaerophilic Bacteria 172
Phototrophic, Facultative Aerobic/Anaerobic and
Microaerophilic Archaea 172
Chapter 14 Quiz 172
Chapter 15 Groups of Aerobic Prokaryotes 173
Functions of Aerobic Prokaryotes 173
Pseudomonads and Their Relatives 173
Slime-Producing Bacteria 173
Phosphate-Accumulating Bacteria 175
Nitrogen-Fixing Bacteria 175
Methanotrophs 175
Oligotrophs 175
Bacterial Parasites of Bacteria 176
Rhizobia 176
Gram-Negative, Chemotrophic, Aerobic Pathogens 176
Ammonium-Oxidizing Chemolithotrophs (Nitrifying Bacteria) 177
Sulfur-Oxidizing, Chemolithotrophic Bacteria 178
Iron- and Manganese-Oxidizing Bacteria 179
Gram-Positive (Terrestrial), Chemotrophic, Aerobic Bacteria 179
Chemotrophic, Aerobic Archaea 180
Gram-Negative (Aquatic), Phototrophic, Aerobic Bacteria 180
Gram-Positive (Terrestrial), Phototrophic, Aerobic Bacteria 181
Phototrophic, Aerobic Archaea 181
Chapter 15 Quiz 181
xvi Contents
Chapter 16 Public Health and Water Disinfection 183
Saprophytic, Pathogenic, and Opportunistic Microbes 183
Parasites of Humans and Animals 183
Stages of Infectious Disease 183
Transmission of Infection 183
Patterns and Extent of Infectious Disease 184
Cooperation between Epidemiologists and Civil Engineers 184
Infections via Vectors 184
Factors of Microbial Pathogenicity 185
Exotoxins 185
Enterotoxins 185
The Problem of Opportunistic Bacteria in Environmental
Biotechnology 185
Waterborne Pathogens 186
Detection of Waterborne Pathogenic Viruses 186
Waterborne Pathogenic Bacteria 186
Fate of Pathogens Released into the Environment 186
Waterborne Pathogenic Protozoa 187
Indicator Microorganisms 187
Coliforms as Indicators of Fecal Pollution 188
Other Indicators of Fecal Pollution 188
Bacteriological Quality of Water 188
Protozoan and Viral Pathogens 188
Detection of Pathogens in the Environment 189
Removal and Killing of Pathogens 189
Control of Microbial Death in Water 189
Thermal Treatment of Water 190
Pasteurization and Sterilization 190
Sterilization by Electromagnetic Radiation 190
Sterilization by Filtration 191
Conservation 191
Disinfectants and Antiseptics 191
Antibiotics 191
Disinfection 191
Resistance of Different Microbial Groups to Disinfection 192
Comparison of Chemical Disinfectants 192
UV Disinfection of Water 193
Chemical Interference with Disinfection of Water 193
Physical Interference with Disinfection of Water 193
Chapter 16 Quiz 193
Chapter 17 Biotechnological Processes 195
Biotechnology 195
Environmental Biotechnology 195
Contents
Comparison of Biotechnological Treatment
with Other Methods 195
Applicability of Environmental Biotechnology 196
Combination of Biotechnology with Other Methods 196
Bioprocesses Used in Environmental Biotechnology 197
Stages of Biotechnological Processes 197
Upstream Processes in Environmental Biotechnology 197
Pretreatment in Biotechnology 197
Medium Preparation 198
Medium Components 198
Preparation of Equipment 198
Preparation of Inoculum 199
Core Process in Environmental Biotechnology 199
Semi-Closed and Open Systems of Cultivation 199
Batch Culture 200
Continuous Cultivation 200
Chemostat 200
Plug-Flow Systems 201
Suspended Biomass Bioreactors 202
Continuous Systems with Internal Recycling or Retention
of Biomass 202
Microbiological Methods Used in Environmental Engineering 203
Isolation of Pure Cultures 204
Selection of Microorganisms 204
Theoretical Selection 205
Selection of an Enrichment Culture 205
Selective Pressure 205
Autoselection Mechanisms 205
Instability of Autoselected Features 206
Selection of an Ecosystem 206
Construction of Genetically Engineered Microorganisms 206
Steps for Artificial Recombination of DNA 207
Application of Genetic Engineering in Environmental
Engineering 207
Physical Boundary of an Artificial Ecosystem 207
Chemical Boundary of an Artificial Ecosystem 208
Macro- and Microenvironments 208
Effect of Nutrients on Growth Rate 208
Downstream Processes 208
Microbial Aggregates 209
Structure of Microbial Aggregates 209
Sedimentation of Cellular Aggregates 209
Selection of Microbial Aggregates by Settling Time 210
Chapter 17 Quiz 210
xviii Contents
Chapter 18 Aquatic Systems and Water Biotreatment 213
Microorganisms of the Hydrosphere, Lithosphere,and Atmosphere 213
Functions of Microorganisms in the Hydrosphere 213
The Biogeochemical Carbon Cycle 214
The Biogeochemical Nitrogen Cycle 214
The Biogeochemical Phosphorus Cycle 215
The Biogeochemical Sulfur Cycle 215
The Biogeochemical Iron Cycle 216
Stratification in Aquatic Ecosystems 217
Sources of Water Pollution 217
Eutrophication of Water in Reservoirs 218
Signs of Eutrophication 218
Treatment of Storm Water in Artificial (Constructed) Wetlands 219
Stages of Treatment of Raw Drinking Water 219
Pollutants of Water That Can Be Removed by Biotreatment 219
Biological Instability of Water 220
Chemical Removal of Sources of Biological Instability 221
Biological Removal of Sources of Biological Instability 221
Disadvantages of Bioremoval of Sources of Biological
Instability 221
BOM in Water 221
Chemical Oxygen Demand, Biological Oxygen Demand,
and Total Organic Carbon 222
Measurement of BOM 222
Bioremoval of Sources of Biological Instability 223
Fixed-Bed Biofilters 223
Fluidized-Bed Biofilm Reactors 224
Biofiltration of Water through Soil 224
Organic Micropollutants of Water 224
Bioremoval of Endocrine Disruptors from Water 225
Bioremoval of Petroleum Hydrocarbons and Their Derivatives
from Water 225
Bioremoval of Halogenated Compounds from Water 226
Sucralose in Water 227
Taste and Odor Compounds of Microbial Origin 227
Arsenic in Water 228
Nitrate and Nitrite in Water 228
Heterotrophic Denitrification of Drinking Water 228
Autotrophic Denitrification 229
Conditions for Denitrification 229
Bioreduction of Perchlorate in Drinking Water 230
Iron and Manganese in Water 230
Chapter 18 Quiz 230
Reference 232
Contents XIX
Chapter 19 Anaerobic and Anoxic Treatment of Wastewater 233
Oxygen and Energy Generation 233
Anaerobic Digestion of Organic Matter 233
Microbiology of Anaerobic Digestion of Biopolymers 234
Biogas Collection and Use 235
Optimal Conditions for Anaerobic Digestion of Organic Waste 236
Interaction between Methanogenesis and Sulfate Reduction 236
Comparison of Anaerobic and Aerobic Digestionof Organic Waste 236
Bioreactors Used in Anaerobic Wastewater Treatment 237
Stirred Tank Reactors for Anaerobic Digestion of Organics 237
UASB Reactors 237
Septic Tanks 238
Anaerobic Processes in Landfills 238
Anaerobic Degradation of Xenobiotics by Fermenting Bacteria 238
Anoxic Bioprocesses 238
Nitrate Reduction in Water and Wastewater Treatment 239
Nitrate Reduction in Microbially Enhanced Oil Recovery 239
Nitrate Reduction in Soil Bioremediation 240
Nitrate Reduction in Geotechnical Improvement of Soil 240
Iron Reduction in Water, Wastewater, and Groundwater
Treatment 240
Sulfate Reduction in Water and Wastewater Treatment 241
Dehalogenating Bacteria 242
Combined Anaerobic/Aerobic Biotreatment of Wastes 242
Biotechnological Treatment of Heavy Metal-ContainingWaste and Radionuclide-Containing Waste 243
Chapter 19 Quiz 244
Chapter 20 Aerobic Treatment of Wastewater 247
Domestic Wastewater 247
Industrial Wastewater 247
Aeration 247
Objectives of Aerobic Wastewater Biotreatment 247
Aerobic Treatment of Wastewater 248
Conventional Biotreatment in Aerobic Tanks 248
Organic Load of Aerobic Treatment 249
Activated Sludge Settleability 249
Activated Sludge Recycling 250
Microorganisms of Activated Sludge 251
Floes of Activated Sludge 251
Filamentous Bacteria in Activated Sludge Floes 251
Control of Filamentous Bulking of Activated Sludge 252
Foaming 252
XX Contents
Suspended Microbial Aggregates (Granules) Used in Aerobic
Treatment of Wastewater 253
Removal of Nutrients from Wastewater 254
Aerobic Reactors 255
Aerobic Treatment of Wastewater with Low Concentrations
of Hazardous Substances 256
Aerobic Digestion of Activated Sludge 256
Combinations of Aerobic Treatment of Wastewater
with Other Treatments 256
Application of Microaerophilic Microorganisms in
Biotechnological Treatments 257
Aerobic Biofilm Reactors 257
Development of Biofilm in Aerobic Biofilm Reactors 258
Chapter 20 Quiz 258
Chapter 21 Value-Added By-Products of Environmental Engineering 261
Organic Wastes as Raw Material for BiotechnologicalTransformation 261
Biotechnological Products from Organic Wastes 261
Production of Enzymes from Wastes 261
Production of Organic Acids 264
Production of Flavors 265
Production of Polysaccharides 265
Edible Mushroom Production 265
Production of Biodegradable Plastics 266
Production of Animal Feed 266
Use of Organic Waste for the Production of Fungi for
Soil Bioremediation 266
Solid-State Fermentation of Agricultural and
Food Processing Wastes 267
Production of Fuel Ethanol 267
Production of Hydrogen, Methane, and Biodiesel 268
Production of Organic Fertilizer 268
Biorecovery of Metals from Mining and Industrial Wastes 268
Recovery of Phosphate and Ammonia 269
Chapter 21 Quiz 269
Chapter 22 Biotreatment of Industrial Hazardous Wastes 271
Electron Donors and Acceptors in Biotreatments 271
Energetic Efficiency of Biooxidation-Bioreduction 271
Aerobic Treatment of Xenobiotics 271
Secondary Hazardous Waste 272
Treatment of Wastewater with Low Concentrations
of Hazardous Substances 272
Contents XXI
Biodegradation Using Co-oxidation/Cometabolism 272
Combination of Aerobic Treatment with Other Treatments 272
Biotreatment of Hazardous Waste by Anaerobic FermentingBacteria 273
Landfilling of Hazardous Solid Waste 273
Combined Anaerobic/Aerobic Biotreatment of Hazardous
Industrial Waste 273
Optimization of Hazardous Waste Biodegradation 274
Optimal Temperatures for Biodegradation of Hazardous Waste 274
Optimal pH for Biodegradation of Hazardous Waste 275
Enhancement of Biodegradation by Nutrients 275
Enhancement of Biodegradation by Growth Factors 276
Increase of Bioavailability of Contaminants 276
Enhancement of Biodegradation by Enzymes 276
Enhancement ofBiodegradation by Aeration and Oxygen Supply 276
Enhancement of Biodegradation by Oxygen Radicals 277
Enhancement of Biodegradation by Electron Acceptors Other
Than Oxygen 277
Bioenhancement of the Treatment of Hazardous Waste 278
Application of Acclimated Microorganisms 278
Selection and Use of Pure Cultures 278
Construction of Microbial Communities 279
Construction of Genetically Engineered Microorganisms 279
Environmental Engineering Applications of Recombinant
Strains of Microorganisms 280
Application of Microbial Aggregates and Immobilized
Microorganisms 280
Chemical Gradients in Microbial Aggregates 280
Chapter 22 Quiz 281
Chapter 23 Solid Wastes and Soil Biotreatment 283
Solid Wastes 283
Treatment of Solid Wastes 283
Landfills 283
Biological Reactions of Decay in Landfills 284
Sewage Sludge Processing 284
Composting 285
Microbiology of Composting 285
Bulking Agents 286
Types of Composting Systems 286
Optimal Parameters for Composting 287
Composting a Mixture of Wastes 288
Vermicomposting 289
Scale of Composting 289
Public Health Aspects of Composting 289
xxii Contents
Odor Control in Composting 289
Composting of Hazardous Organic Wastes 290
Soil 290
Organic Matter in Soil 290
Microbial Activity and Soil 290
Soil and the Biodegradation of Xenobiotics 291
Toxic Pollutants of Soil 291
Sources of Soil Pollution 291
Leakage from Underground Storage Tank Facilities 292
Landfill Leachate 292
Bioremediation 292
Soil and Groundwater Bioremediation 292
Landfarming, Land Treatment, and Plant Bioremediation 292
Onsite and In Situ Soil and Groundwater Bioremediation 293
Excavation and Composting of Contaminated Soil 293
Slurry-Phase Bioremediation in Bioreactors 293
Gas Cleaning 294
Pretreatment of Contaminated Soil 294
Steps in Microbial Culture Development for Slurry-PhaseBioremediation 294
Advantages of Soil Bioremediation 294
Disadvantages of Soil Bioremediation 295
Bioremediation and Biodecontamination of Construction Sites
through Biocementation 295
Artificial Protective Geochemical Barrier 296
Chapter 23 Quiz 296
Chapter 24 Construction Biotechnology 299
Introduction 299
Bioagents Used in Construction Biotechnology 299
Construction Biotechnology Methods 299
Microbial Biogeotechnics 300
Reasons for Microbial Applications in Geotechnical Engineering 300
Major Applications of Microorganisms for Ground Improvement 300
Bioclogging 302
Biocementation 302
Chemical Grouting 302
Biogrouting 302
Microbial Processes for Bioclogging with Organic Material 302
Microbial Processes for Bioclogging with Inorganic Material 303
Clogging with Microbial Polysaccharides 303
Bacteria That Produce Clogging Polysaccharides 303
Clogging with Microbially Induced Precipitates 304
Biobinding 304
Contents xxiii
Microbial Processes of Bioclogging and Biocementation with
Inorganic Compounds 304
Microbially Induced Calcium Carbonate Precipitation 305
Geotechnical Applications of Biocementation 306
Problems of Microbial Cementation and Clogging 306
Physiological Grouping of Chemotrophic Prokaryotes 306
Screening of Microorganisms for Bioclogging and Biocementation... 307
Application of Anaerobic Fermenting Bacteria in Biogeotechnics.... 308
Application of Anoxic Bacteria in Biogeotechnics 308
Application of Facultative Anaerobic Bacteria in Biogeotechnics 308
Application of Microaerophilic Bacteria in Biogeotechnics 309
Application of Aerobic Bacteria in Biogeotechnics 309
General Considerations on Bacterial Applicability in
Geotechnics 309
Biosafety in Biogeotechnics 309
Soil Biotreatment Procedures 310
Biocement and Biogrout Production Biotechnologies 310
Inoculum for Biotreatment of Soil 310
Use of Indigenous Microorganisms in Soil for Biocementation 311
Medium for Microbial Cultivation 311
Soil Biotreatment 312
Microbial Admixtures 312
Construction Bioplastics 313
Chapter 24 Quiz 314
Chapter 25 Microbiology of Air and Air Treatment 317
Bioaerosols 317
Sources of Bioaerosols 317
Viral Aerosols 317
Bacterial Aerosols 317
Fungal Aerosols 318
Mycotoxins 318
Pollen Grain Aerosols 318
Concentration of Aerosols 318
Bioaerosol Sampling 319
Bioaerosols and Indoor Air Quality 319
Fate of Bioaerosols in the Environment 319
Bioaerosols from Wastewater Treatment, Spray Irrigation,and Biotechnological Plants 319
Odors Generated by Wastewater Treatment Plants 320
Treatment of Odorous and Exhaust Gases 320
Aerobic Biotechnological Treatment of Hazardous Waste Gas 321
Biotreatment of Toxic Gas 321
Chapter 25 Quiz 321
xxiv Contents
Chapter 26 Biodeterioration, Biocorrosion, and Biofouling 323
Microbial Biodeterioration 323
Deterioration of Cultural Heritage 323
Microbially Influenced Corrosion 324
Microbial Formation of Acids 325
Biofouling of Membranes 326
Membrane Treatments of Water and Wastewater 326
Mechanisms of Membrane Fouling 326
Types of Foulants 327
Fouling Control 327
Chapter 26 Quiz 327
Chapter 27 Outline and Summary of the Course "Environmental
Microbiology for Engineers" 329
Microorganisms 329
Static Biochemistry 330
Dynamic Biochemistry 330
Biooxidation and Bioreduction 331
Biodegradation 331
Molecular Biology and Genetics 332
Bioagents of Environmental and Engineering Bioprocesses 332
Reproduction, Proliferation, and Growth 333
Microbial Ecology 335
Classifications of Viruses, Prokaryotes, and Eukaryotes 336
Physiological Classification of Prokaryotes 336
Groups of Prokaryotes 337
Public Health and Water Disinfection 338
Biotechnological Processes 340
Aquatic Ecosystems and Water Treatment 341
Anaerobic and Anoxic Wastewater Treatment 341
Aerobic Wastewater Treatment 342
Value-Added By-Products of Environmental Engineering 343
Solid Waste Biotreatment 343
Soil Bioremediation 343
Construction Biotechnology 344
Microbiology of Air and Air Treatment 345
Biodeterioration, Biocorrosion, and Biofouling 345
Chapter 28 Tutorials 347
Tutorial 1: Microorganisms: Cell Size and Shape 347
Tutorial 2: Cell Chemistry and Structure 352
Tutorial 3: Metabolism and Biodegradation 353
Tutorial 4: Growth and Ecology 357
Tutorial 5: Anaerobic Processes 362
Contents xxv
Tutorial 6: Aerobic Processes 367
Tutorial 7: Solid Waste Biotreatment 370
Tutorial 8: Construction Biotechnology 374
Chapter 29 Exam Question Bank 377
Index 401