Environmental microbiology /

Preface p. xv
The Authors p. xvii
Contributing Authors p. xix
Chapter 1 Introduction to Environmental Microbiology Raina M. Maier and Ian L. Pepper and Charles P. Gerba
1.1 Introduction p. 1
1.2 An Historical Perspective p. 1
1.3 Modern Environmental Microbiology p. 4
1.4 Purpose and Organization of This Text p. 5
Chapter 2 Microorganisms in the Environment Kelly A. Reynolds and Ian L. Pepper
2.1 Viruses p. 7
2.2 Bacteria p. 19
2.3 Fungi p. 31
2.4 Alage p. 34
2.5 Protozoa p. 34
Questions and Problems p. 40
References and Recommended Readings p. 40
Chapter 3 Bacterial Growth Raina M. Maier
3.1 Growth in Pure Culture in a Flask p. 43
3.2 Continuous Culture p. 51
3.3 Growth under Aerobic Conditions p. 52
3.4 Growth under Anaerobic Conditions p. 55
3.5 Growth in the Environment p. 56
Questions and Problems p. 59
References and Recommended Readings p. 59
Chapter 4 Terrestrial Environments Raina M. Maier and Ian L. Pepper
4.1 Introduction p. 61
4.2 Porous Media p. 61
4.3 Soil and Subsurface Environments p. 70
4.4 General Characteristics of Microorganisms in Porous Media p. 74
4.5 Microbial Activities in Porous Media p. 77
4.6 Microorganisms in Surface Soils p. 79
4.7 Microorganisms in Shallow Subsurface Environments p. 83
4.8 Microorganisms in Deep Subsurface Environments p. 85
Questions and Problems p. 88
References and Recommended Readings p. 89
Chapter 5 Aeromicrobiology Scot E. Dowd and Raina M. Maier
5.1 Introduction p. 91
5.2 Important Airborne Pathogens p. 91
5.3 Important Airborne Toxins p. 93
5.4 Nature of Bioaerosols p. 93
5.5 The Atmosphere p. 94
5.6 Aeromicrobiological Pathway p. 95
5.7 Mathematical Modeling p. 100
5.8 Sampling Devices for the Collection of Bioaerosols p. 103
5.9 Microbial Survival in the Air p. 105
5.10 Extramural Aeromicrobiology p. 107
5.11 Intramural Aeromicrobiology p. 111
5.12 Bioaerosol Control p. 113
5.13 Biosafety in the Laboratory p. 115
5.14 Other Areas of Interest p. 120
Chapter 6 Aquatic and Extreme Environments Scot E. Dowd and David C. Herman and Raina M. Maier
6.1 Introduction p. 123
6.2 Microbial Habitats in the Aquatic Environment p. 123
6.3 Aquatic Environments p. 130
6.4 Environmental Determinants That Govern Extreme Environments p. 140
6.5 Aquatic Microbes in the News p. 143
Questions and Problems p. 145
References and Recommended Readings p. 145
Chapter 7 Microbial Transport Deborah T. Newby and Ian L. Pepper and Raina M. Maier
7.1 Introduction p. 147
7.2 Factors Affecting Microbial Transport p. 148
7.3 Factors Affecting Transport of DNA p. 162
7.4 Novel Approaches to Facilitate Microbial Transport p. 163
7.5 Methodology for Studying Transport p. 166
7.6 Models for Microbial Transport p. 172
Questions and Problems p. 173
References and Recommended Readings p. 174
Chapter 8 Environmental Sample Collection and Processing Ian L. Pepper and Charles P. Gerba and Raina M. Maier
8.1 Soils and Sediments p. 177
8.2 Water p. 186
8.3 Detection of Microorganisms on Fomites p. 190
Questions and Problems p. 194
References and Recommended Readings p. 194
Chapter 9 Microscopic Techniques Timberley M. Roane and Ian L. Pepper
9.1 History of Microscopy p. 195
9.2 Theory of Microscopy p. 195
9.3 Basic Microscopic Techniques p. 197
9.4 In Situ Soil Microscopy p. 200
9.5 In Situ Detection with Molecular Probes and Epifluoresence Microscopy p. 201
9.6 Direct Bacterial Counts p. 202
9.7 Estimation of Biomass Using Microscopic Counts p. 204
9.8 Advanced Microscopic Techniques p. 204
Questions and Problems p. 211
References and Recommended Readings p. 211
Chapter 10 Cultural Methods Karen C. Josephson and Charles P. Gerba and Ian L. Pepper
10.1 Cultural Methods for Enumeration of Bacteria p. 213
10.2 Cultural Media for Bacteria p. 218
10.3 Cultural Methods for Fungi p. 224
10.4 Cultural Methods for Algae and Cyanobacteria p. 225
10.5 Cell Culture-Based Detection Methods for Viruses p. 227
Questions and Problems p. 232
References and Recommended Readings p. 232
Chapter 11 Physiological Methods David C. Herman and Raina M. Maier
11.1 Introduction p. 235
11.2 Measuring Microbial Activity in Pure Culture p. 236
11.3 Choosing the Appropriate Activity Measurement for Environmental Samples p. 243
11.4 Carbon Respiration p. 243
11.5 Incorporation of Radiolabeled Tracers into Cellular Macromolecules p. 257
11.6 Adenylate Energy Charge p. 258
11.7 Enzyme Assays p. 259
Questions and Problems p. 263
References and Recommended Readings p. 263
Chapter 12 Immunological Methods Scot E. Dowd and Raina M. Maier
12.1 Introduction p. 267
12.2 What Is an Antibody? p. 267
12.3 Immunoassays p. 273
Questions and Problems p. 284
References and Recommended Readings p. 284
Chapter 13 Nucleic Acid-Based Methods of Analysis Elizabeth M. Marlowe and Karen L. Josephson and Ian L. Pepper
13.1 Structure and Complementarity of Nucleic Acids p. 287
13.2 Obtaining Microbial Nucleic Acids from the Environment p. 289
13.3 Nucleic Acid-Based Methods p. 290
Questions and Problems p. 315
References and Recommended Readings p. 316
Chapter 14 Biogeochemical Cycling Raina M. Maier
14.1 Introduction p. 319
14.2 Carbon Cycle p. 321
14.3 Nitrogen Cycle p. 331
14.4 Sulfur Cycle p. 340
Questions and Problems p. 345
References and Recommended Readings p. 345
Chapter 15 Consequences of Biogeochemical Cycles Gone Wild David C. Herman and Raina M. Maier
15.1 Introduction p. 347
15.2 Microbially Influenced Corrosion p. 347
15.3 Acid Mine Drainage and Metal Recovery p. 350
15.4 Biomethylation of Metals and Metalloids p. 352
15.5 Nitrous Oxide and Earth's Atmosphere p. 354
15.6 Nitrate Contamination of Groundwater p. 356
15.7 Biogenesis of Halomethanes and Other Organohalogens p. 358
15.8 Composting p. 358
Questions and Problems p. 360
References and Recommended Readings p. 360
Chapter 16 Microorganisms and Organic Pollutants Raina M. Maier
16.1 Introduction p. 363
16.2 Environmental Law p. 364
16.3 The Overall Process of Biodegradation p. 365
16.4 Relationship between Contaminant Structure, Toxicity, and Biodegradability p. 368
16.5 Environmental Factors Affecting Biodegradation p. 375
16.6 Biodegradation of Organic Pollutants p. 377
16.7 Bioremediation p. 394
Questions and Problems p. 400
References and Recommended Readings p. 400
Chapter 17 Microorganisms and Metal Pollutants Timberley M. Roane and Ian L. Pepper
17.1 Cause for Concern p. 403
17.2 Metals Defined p. 404
17.3 Sources of Metals p. 405
17.4 Metal Bioavailability in the Environment p. 406
17.5 Metal Toxicity Effects on the Microbial Cell p. 408
17.6 Mechanisms of Microbial Metal Resistance and Detoxification p. 408
17.7 Methods for Studying Metal-Microbial Interactions p. 413
17.8 Adverse Effects of Microbial Metal Transformations p. 415
17.9 The Benefits of Metal-Microbial Interactions p. 416
17.10 Physical/Chemical Methods of Metal Remediation p. 418
17.11 Innovative Microbial Approaches in the Remediation of Metal-Contaminated Soils and Sediments p. 418
17.12 Innovative Microbial Approaches in the Remediation of Metal-Contaminated Aquatic Systems p. 421
Questions and Problems p. 422
References and Recommended Readings p. 423
Chapter 18 Beneficial and Pathogenic Microbes in Agriculture Ian L. Pepper
18.1 Overview p. 425
18.2 Beneficial Root-Microbial Interactions p. 429
18.3 Pathogenic Microbes in Agriculture p. 439
Questions and Problems p. 445
References and Recommended Readings p. 445
Chapter 19 Environmentally Transmitted Pathogens Patricia Rusin and Carlos E. Enriquez and Dana Johnson and Charles P. Gerba
19.1 Environmental Transmitted Pathogens p. 447
19.2 Bacteria p. 449
19.3 Parasitology p. 459
19.4 Viruses p. 472
Questions and Problems p. 484
References and Recommended Readings p. 485
Chapter 20 Indicator Microorganisms Charles P. Gerba
20.1 The Concept of Indicator Organisms p. 491
20.2 Total Coliforms p. 491
20.3 Fecal Coliforms p. 496
20.4 Fecal Streptococci p. 496
20.5 Clostridium perfringens p. 497
20.6 Heterotrophic Plate Count p. 497
20.7 Bacteriophage p. 499
20.8 Other Indicator Organisms p. 500
20.9 Standards and Criteria for Indicators p. 500
Questions and Problems p. 502
References and Recommended Readings p. 503
Chapter 21 Domestic Wastes and Waste Treatment Charles P. Gerba
21.1 Domestic Wastewater p. 505
21.2 Modern Wastewater Treatment p. 508
21.3 Oxidation Ponds p. 520
21.4 Septic Tanks p. 521
21.5 Land Application of Wastewater p. 522
21.6 Wetlands and Aquaculture Systems p. 524
21.7 Solid Waste p. 528
Questions and Problems p. 532
References and Recommended Readings p. 533
Chapter 22 Drinking Water Treatment and Distribution Charles P. Gerba
22.1 Water Treatment Processes p. 535
22.2 Water Distribution Systems p. 538
22.3 Assimilable Organic Carbon p. 539
Questions and Problems p. 541
References and Recommended Readings p. 541
Chapter 23 Disinfection Charles P. Gerba
23.1 Thermal Destruction p. 543
23.2 Kinetics of Disinfection p. 544
23.3 Factors Affecting Disinfectants p. 546
23.4 Halogens p. 547
23.5 Ozone p. 550
23.6 Metal Ions p. 551
23.7 Ultraviolet Disinfection p. 552
23.8 Photodynamic Inactivation p. 554
23.9 Gamma and High-Energy Irradiation p. 554
Questions and Problems p. 555
References and Recommended Readings p. 555
Chapter 24 Risk Assessment Charles P. Gerba
24.1 The Concept of Risk Assessment p. 557
24.2 Elements of Risk Assessment p. 557
24.3 The Process of Risk Assessment p. 560
24.4 Microbial Risk Assessment p. 564
Questions and Problems p. 570
References and Recommended Readings p. 570