Microbiology and chemistry for environmental scientists and engineers

Microbiology and Chemistry for Environmental Scientists and Engineers......Page 2
Preface to the second edition......Page 8
Acknowledgements......Page 10
Contents......Page 4
1.1 Origins of microbiology......Page 11
1.2 History of sanitary microbiology......Page 13
1.3 Principles of microbiology......Page 22
References and further reading......Page 25
2.1 Introduction......Page 27
2.2.1 Nuclear material......Page 28
2.2.2 Cytoplasm......Page 29
2.2.4 Cytoplasmic membrane......Page 30
2.2.5 Cell wall......Page 31
2.2.6 External features of the bacterial cell......Page 32
2.3 Identification of bacteria......Page 34
2.3.2 Colony morphology......Page 35
2.3.3 Physiology......Page 37
2.4 Classification of bacteria......Page 38
2.4.4 Budding and/or appendaged bacteria......Page 39
2.4.7 Gram-negative aerobic rods and cocci......Page 40
2.4.10 Gram-negative cocci......Page 41
2.4.13 Methane producing bacteria......Page 42
2.4.17 Actinomycetes and related organisms......Page 43
Further reading......Page 44
3.2 Algae......Page 45
3.2.1 Morphology......Page 47
3.2.2 Reproduction......Page 49
3.2.3 Classification......Page 50
3.3 Protozoa......Page 52
3.3.1 Morphology......Page 54
3.3.2 Reproduction......Page 55
3.3.3 Classification......Page 57
3.4 Fungi......Page 60
3.4.2 Reproduction......Page 61
3.4.3 Classification......Page 63
References and further reading......Page 65
4.2 Viruses......Page 66
4.2.1 Morphology......Page 67
4.2.2 Reproduction......Page 69
4.3.1 Rotifera......Page 70
References and further reading......Page 71
5.2 Safety precautions in microbiological laboratories......Page 73
5.3.1 Sterilization......Page 74
5.3.3 Inoculation and aseptic transfer......Page 76
5.4.1 Culture media......Page 77
5.4.2 Types of culture......Page 78
5.4.3 Isolation of pure cultures......Page 79
5.5 Microscopy......Page 80
5.6.1 Total counts......Page 81
5.6.2 Viable counts......Page 82
5.6.4 Enumeration in water analysis......Page 83
5.7 Staining methods......Page 84
5.7.3 Capsules......Page 85
5.7.4 Flagella......Page 86
5.8.1 Biochemical oxygen demand......Page 87
5.8.2 Mutagenicity testing......Page 89
References and further reading......Page 90
6.2 The atom......Page 91
6.2.2 Electronic configuration......Page 92
6.3.1 General properties......Page 94
6.3.3 Ionization potential......Page 96
6.4.1 Ionic bonding......Page 97
6.4.2 Covalent bonding......Page 99
6.4.4 Oxidation number/valency......Page 101
6.5.3 Normality......Page 103
6.6.1 Stoichiometry......Page 104
6.6.3 Acids and bases......Page 105
6.6.4 Dissociation of water......Page 106
6.6.5 Buffers......Page 107
6.7 Laws of chemistry......Page 108
6.9 Oxidation-reduction redox reactions......Page 110
References and further reading......Page 112
7.2 The carbon atom......Page 113
7.2.1 General properties of organic compounds......Page 114
7.2.2 Formulae......Page 115
7.3.1 Alkanes......Page 117
7.3.2 Alkenes......Page 120
7.3.3 Alkynes......Page 123
7.3.4 Alcohols......Page 124
7.3.5 Aldehydes and ketones......Page 127
7.3.6 Carboxylic acids......Page 130
7.3.7 Esters......Page 133
7.3.8 Ethers......Page 134
7.4.1 Amines......Page 135
7.4.2 Amides......Page 136
7.5.1 Nomenclature......Page 137
7.5.3 Chlorinated benzene compounds......Page 138
7.6 Heterocyclic compounds......Page 140
7.6.1 Nomenclature......Page 141
References and further reading......Page 142
8.1 Introduction......Page 143
8.2 Isomerism......Page 144
8.3.1 Structure......Page 145
8.3.2 Function......Page 146
8.4.1 Structure......Page 152
8.4.2 Function......Page 154
8.5.1 Structure......Page 157
8.5.2 Function......Page 160
8.6.1 Structure......Page 162
References and further reading......Page 163
9.1 Introduction......Page 164
9.2.1 Reversible reactions......Page 165
9.2.2 Coupling of reactions......Page 167
9.2.3 Biochemical energy coupling......Page 168
9.3 Energy-yielding metabolism......Page 169
9.3.1 Substrate level phosphorylation: glycolysis......Page 170
9.3.2 Aerobic respiration......Page 173
9.3.3 Anaerobic fermentation......Page 176
9.3.4 Implications of respiratory and fermentative metabolism......Page 177
9.3.5 Photosynthetic energy-yielding metabolism......Page 178
9.4 Biosynthesis......Page 181
9.4.1 Polysaccharide synthesis......Page 183
9.4.2 Nucleic acid synthesis......Page 184
References and further reading......Page 186
10.2 Mathematical description of growth......Page 187
10.3 Growth curve......Page 190
10.4.1 Substrate concentration......Page 192
10.4.2 Temperature......Page 194
10.5 Continuous cultivation......Page 195
10.5.1 Control of growth rate by dilution rate......Page 196
10.5.2 Cell maintenance......Page 198
10.6 Growth on two substrates......Page 199
10.7 Mixed cultures......Page 201
References and further reading......Page 203
11.2 The water molecule......Page 204
11.3.1 Biochemical oxygen demand BOD......Page 205
11.3.2 Reaeration......Page 207
11.3.3 Chemical oxygen demand COD......Page 208
11.4.2 Alkalinity......Page 209
11.5 Hardness and metal ions in water......Page 210
11.5.1 Metal ions......Page 212
11.6.1 Nitrogen......Page 213
11.6.2 Phosphorus......Page 214
11.7 Water quality standards......Page 215
11.7.1 Microbiological standards......Page 216
11.7.2 Chemical standards......Page 218
References and further reading......Page 222
12.2 The hydrologic cycle......Page 223
12.3 Surface water chemistry......Page 226
12.3.2 Weathering processes......Page 227
12.3.3 Precipitation......Page 231
12.3.5 Chemical characteristics of seawater......Page 232
12.4 Precipitation chemistry......Page 233
12.4.2 Dry deposition......Page 234
12.4.4 Wet deposition......Page 236
12.4.5 Acid rain......Page 237
12.5.1 Groundwater storage......Page 239
12.5.2 Chemical characteristics of groundwater......Page 242
12.5.3 Ion exchange......Page 245
References and further reading......Page 246
13.1 Introduction......Page 247
13.2 Sources of pollutants......Page 248
13.2.1 Point sources......Page 249
13.2.2 Non-point sources......Page 250
13.3 Groundwater pollution......Page 252
13.3.1 Behaviour of pollutants in groundwater......Page 253
13.4 Marine pollution......Page 254
13.5 Physical pollutants......Page 255
13.5.2 Thermal pollution......Page 256
13.6.1 Black and Grey List substances......Page 257
13.6.3 Heavy metals......Page 258
13.6.5 Drinking water......Page 259
13.6.7 Organochlorine compounds......Page 260
13.6.8 Polychlorinated biphenyls PCBs......Page 261
13.6.10 Organophosphorus compounds......Page 262
13.6.11 Organotin compounds......Page 263
13.6.12 Polycyclic aromatic hydrocarbons PAHs......Page 265
13.7 Toxic pollutants......Page 266
13.7.3 Acidity/alkalinity......Page 267
References and further reading......Page 268
14.2.1 Composition of domestic sewage......Page 269
14.2.3 Primary sedimentation......Page 270
14.4.1 Process description......Page 271
14.4.2 Operational parameters......Page 272
14.5 Substrate removal and growth in biomass recycle systems......Page 275
14.6 Biological activities in activated sludge......Page 277
14.6.1 Microbial composition of activated sludge......Page 278
14.6.2 Flocculation......Page 280
14.6.3 Bulking and related phenomena......Page 282
14.6.5 Nitrification......Page 285
14.7 Operational modifications......Page 287
14.8 Design modifications......Page 289
14.9.1 Process description......Page 290
14.9.2 Operational parameters......Page 291
14.9.3 Substrate removal and growth......Page 292
14.9.4 Biological activities in percolating filters......Page 294
14.9.5 Design modifications......Page 295
References and further reading......Page 297
15.1 Introduction......Page 298
15.2.2 Operational parameters......Page 299
15.3.1 Microbial composition of digesting sludge......Page 301
15.3.3 Biochemistry of anaerobic digestion......Page 302
15.3.4 Stability of anaerobic digestion......Page 305
15.3.5 Microbial growth parameters......Page 306
15.4.2 Facultative ponds......Page 307
15.4.3 Anaerobic ponds......Page 309
References and further reading......Page 310
16.2.1 Salvage......Page 311
16.2.3 Biological degradation......Page 312
16.3 Microbiology of composting......Page 313
16.4 Fate of pathogens during composting......Page 316
References and further reading......Page 317
17.2 Trade effluent control......Page 318
17.3.1 Inhibition......Page 320
17.3.2 Incidental removal......Page 321
17.3.3 Biodegradation of specific pollutants......Page 322
17.4 Aerobic treatment processes......Page 326
17.4.1 Bioaugmentation......Page 328
17.5.1 Suspended biomass systems......Page 329
17.5.2 Fixed film processes a Anaerobic filter......Page 331
17.5.3 Multistage phase-separated systems......Page 332
References and further reading......Page 333
18.2.1 Bacterial metabolism at low substrate concentrations......Page 335
18.2.3 Biodegradability testing......Page 336
18.3 Degradation in heterogeneous environments......Page 338
18.4 Microbial activity in trace heavy metal cycling......Page 340
18.5.1 Limiting nutrients......Page 342
18.5.2 Causes of eutrophication......Page 343
18.5.3 Effects of eutrophication......Page 344
18.6 Microbiological indicators of pollution......Page 346
References and further reading......Page 347
19.1 Introduction......Page 348
19.2 Modes of entry and transmission of pathogens......Page 349
19.3 Diseases caused by waterborne pathogens......Page 351
19.3.1 Bacterial infections......Page 353
19.3.2 Viral infections......Page 359
19.3.3 Parasitic protozoan infections......Page 361
19.3.4 Parasitic worm infections......Page 363
Further reading......Page 365
20.2 Water treatment processes......Page 367
20.3 Disinfection......Page 371
20.3.2 Chlorination......Page 372
20.3.4 Other disinfectants......Page 376
References and further reading......Page 377