E-Book, Englisch, 624 Seiten
Reihe: Maier and Pepper Set
Pepper / Gerba / Gentry Environmental Microbiology
2. Auflage 2011
ISBN: 978-0-08-091940-9
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark
E-Book, Englisch, 624 Seiten
Reihe: Maier and Pepper Set
ISBN: 978-0-08-091940-9
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark
For microbiology and environmental microbiology courses, this leading textbook builds on the academic success of the previous edition by including a comprehensive and up-to-date discussion of environmental microbiology as a discipline that has grown in scope and interest in recent years. From environmental science and microbial ecology to topics in molecular genetics, this edition relates environmental microbiology to the work of a variety of life science, ecology, and environmental science investigators. The authors and editors have taken the care to highlight links between environmental microbiology and topics important to our changing world such as bioterrorism and national security with sections on practical issues such as bioremediation, waterborne pathogens, microbial risk assessment, and environmental biotechnology.
WHY ADOPT THIS EDITION?
New chapters on:
• Urban Environmental Microbiology
• Bacterial Communities in Natural Ecosystems
• Global Change and Microbial Infectious Disease
• Microorganisms and Bioterrorism
• Extreme Environments (emphasizing the ecology of these environments)
• Aquatic Environments (now devoted to its own chapter- was combined with Extreme Environments)
Updates to Methodologies:
• Nucleic Acid -Based Methods: microarrays, phyloarrays, real-time PCR, metagomics, and comparative genomics
• Physiological Methods: stable isotope fingerprinting and functional genomics and proteomics-based approaches
• Microscopic Techniques: FISH (fluorescent in situ hybridization) and atomic force microscopy
• Cultural Methods: new approaches to enhanced cultivation of environmental bacteria
• Environmental Sample Collection and Processing: added section on air sampling
Autoren/Hrsg.
Weitere Infos & Material
1;Front Cover;1
2;Environmental Microbiology;4
3;Copyright Page;5
4;Contents;8
5;Preface;16
6;Acknowledgments;18
7;The Authors;20
8;Contributing Authors;22
9;Part I: Review of Basic Microbiological Concepts;24
9.1;Chapter 1. Introduction to Environmental Microbiology;26
9.1.1;1.1 Introduction;26
9.1.2;1.2 An Historical Perspective;26
9.1.3;1.3 Modern Environmental Microbiology;29
9.1.4;1.4 Purpose and Organization of This Text;30
9.2;Chapter 2. Microorganisms;32
9.2.1;2.1 Classification of Organisms;33
9.2.2;2.2 Eubacteria;33
9.2.2.1;2.2.1 Cell Envelope;34
9.2.2.2;2.2.2 Cytoplasm;37
9.2.2.3;2.2.3 Glycocalyx;39
9.2.2.4;2.2.4 Appendages;39
9.2.2.5;2.2.5 Endospores;39
9.2.2.6;2.2.6 Information Transfer;40
9.2.2.7;2.2.7 Metabolism;41
9.2.3;2.3 The Archaea;43
9.2.3.1;2.3.1 Archaean Habitats;44
9.2.3.2;2.3.2 Archaean Function;44
9.2.4;2.4 Fungi;45
9.2.4.1;2.4.1 Fungal Structure;45
9.2.4.2;2.4.2 Fungal Diversity;46
9.2.4.3;2.4.3 Ecological Considerations;47
9.2.5;2.5 Slime Molds;48
9.2.6;2.6 Protozoa;48
9.2.6.1;2.6.1 Structure and Function;48
9.2.6.2;2.6.2 Physiological and Ecological Considerations;49
9.2.7;2.7 Algae;49
9.2.7.1;2.7.1 Cell Structure;50
9.2.7.2;2.7.2 Physiological and Ecological Considerations;50
9.2.8;2.8 Viruses;51
9.2.8.1;2.8.1 Infective Nature of Viruses;52
9.2.8.2;2.8.2 Procaryotic Viruses;53
9.2.8.3;2.8.3 Eucaryotic Viruses;55
9.2.9;2.9 Other Biological Entities;56
9.2.9.1;2.9.1 Viroids;56
9.2.9.2;2.9.2 Prions;56
9.2.10;References;57
9.3;Chapter 3. Bacterial Growth;60
9.3.1;3.1 Growth in Pure Culture in a Flask;61
9.3.1.1;3.1.1 The Lag Phase;61
9.3.1.2;3.1.2 The Exponential Phase;62
9.3.1.3;3.1.3 The Stationary Phase;63
9.3.1.4;3.1.4 The Death Phase;64
9.3.1.5;3.1.5 Effect of Substrate Concentration on Growth;65
9.3.2;3.2 Continuous Culture;67
9.3.3;3.3 Growth in the Environment;69
9.3.3.1;3.3.1 The Lag Phase;70
9.3.3.2;3.3.2 The Exponential Phase;70
9.3.3.3;3.3.3 The Stationary and Death Phases;70
9.3.4;3.4 Mass Balance of Growth;72
9.3.4.1;3.4.1 Aerobic Conditions;73
9.3.4.2;3.4.2 Anaerobic Conditions;75
9.3.5;Questions and Problems;76
9.3.6;References and Recommended Readings;77
10;Part II: Microbial Environments;78
10.1;Chapter 4. Earth Environments;80
10.1.1;4.1 Earth's Living Skin;80
10.1.2;4.2 Physicochemical Characteristics of the Earth Environment;81
10.1.2.1;4.2.1 Earth Environments;81
10.1.2.2;4.2.2 The Solid Phase;82
10.1.2.3;4.2.3 The Liquid Phase;90
10.1.2.4;4.2.4 Soil Atmosphere;92
10.1.3;4.3 Soil as a Microbial Environment;93
10.1.3.1;4.3.1 Biotic Stresses;93
10.1.3.2;4.3.2 Abiotic Stresses;93
10.1.4;4.4 Microorganisms in Surface Soils;94
10.1.4.1;4.4.1 Bacteria;94
10.1.4.2;4.4.2 Actinomycetes;94
10.1.4.3;4.4.3 Fungi;96
10.1.4.4;4.4.4 Algae;97
10.1.4.5;4.4.5 Protozoa;97
10.1.5;4.5 Distribution of Microorganisms in Soil;98
10.1.6;4.6 Microorganisms in Subsurface Environments;99
10.1.6.1;4.6.1 Microorganisms in Shallow Subsurface Environments;100
10.1.6.2;4.6.2 Microorganisms in Deep Subsurface Environments;100
10.1.7;Questions and Problems;104
10.1.8;References and Recommended Readings;104
10.2;Chapter 5. Aeromicrobiology;106
10.2.1;5.1 Introduction;106
10.2.2;5.2 Important Airborne Pathogens;106
10.2.3;5.3 Important Airborne Toxins;107
10.2.4;5.4 Aerosols;108
10.2.5;5.5 Nature of Bioaerosols;110
10.2.6;5.6 Aeromicrobiological Pathway;110
10.2.6.1;5.6.1 Launching;111
10.2.6.2;5.6.2 Transport;111
10.2.6.3;5.6.3 Deposition;112
10.2.7;5.7 Microbial Survival in the Air;114
10.2.7.1;5.7.1 Relative Humidity;114
10.2.7.2;5.7.2 Temperature;115
10.2.7.3;5.7.3 Radiation;115
10.2.7.4;5.7.4 Oxygen, OAFs, and Ions;115
10.2.8;5.8 Extramural Aeromicrobiology;115
10.2.8.1;5.8.1 Agriculture;115
10.2.8.2;5.8.2 Waste Disposal;117
10.2.9;5.9 Intramural Aeromicrobiology;118
10.2.9.1;5.9.1 Buildings;118
10.2.9.2;5.9.2 Public Health;119
10.2.9.3;5.9.3 Hospitals and Laboratories;119
10.2.10;5.10 Bioaerosol Control;120
10.2.10.1;5.10.1 Ventilation;120
10.2.10.2;5.10.2 Filtration;120
10.2.10.3;5.10.3 Biocidal Control;120
10.2.10.4;5.10.4 Isolation;121
10.2.11;5.11 Biosafety in the Laboratory;121
10.2.11.1;5.11.1 Biological Safety Cabinets;121
10.2.11.2;5.11.2 Biosafety Laboratories;123
10.2.12;Questions and Problems;124
10.2.13;References and Recommended Readings;124
10.3;Chapter 6. Aquatic Environments;126
10.3.1;6.1 Introduction;126
10.3.2;6.2 Microbial Habitats in the Aquatic Environment;126
10.3.2.1;6.2.1 Planktonic Environment;126
10.3.2.2;6.2.2 Benthic Habitat;128
10.3.2.3;6.2.3 Microbial Mats;130
10.3.2.4;6.2.4 Biofilms;130
10.3.3;6.3 Aquatic Environments;133
10.3.3.1;6.3.1 Freshwater Environments;133
10.3.3.2;6.3.2 Brackish Water;138
10.3.3.3;6.3.3 Marine Water;138
10.3.3.4;6.3.4 Subterranean Water;140
10.3.4;6.4 Aquatic Microbes in the News;140
10.3.4.1;6.4.1 Shotgun Sequencing Reveals Secrets about the Sargasso Sea;140
10.3.4.2;6.4.2 Aquatic Microbes: Food for the Future;142
10.3.5;Questions and Problems;143
10.3.6;References and Recommended Readings;143
10.4;Chapter 7. Extreme Environments;146
10.4.1;7.1 Low Temperature Environments;147
10.4.1.1;7.1.1 McMurdo Dry Valleys, Antarctica;147
10.4.2;7.2 High Temperature Environments;149
10.4.2.1;7.2.1 Geothermal Hot Springs;149
10.4.3;7.3 Desiccation and UV Stress;151
10.4.3.1;7.3.1 The Atacama Desert, Chile;151
10.4.4;7.4 Environments Based on Chemoautotrophy;153
10.4.4.1;7.4.1 Deep-Sea Hydrothermal Vents;153
10.4.5;7.5 Acidic Environments;155
10.4.5.1;7.5.1 Acid Mine Drainage;155
10.4.6;Questions and Problems;156
10.4.7;References;157
11;Part III: Detection, Enumeration, and Identification;158
11.1;Chapter 8. Environmental Sample Collection and Processing;160
11.1.1;8.1 Soils and Sediments;160
11.1.1.1;8.1.1 Sampling Strategies and Methods for Surface Soils;161
11.1.1.2;8.1.2 Sampling Strategies and Methods for the Subsurface;162
11.1.1.3;8.1.3 Sample Processing and Storage;164
11.1.2;8.2 Water;167
11.1.2.1;8.2.1 Sampling Strategies and Methods for Water;167
11.1.2.2;8.2.2 Processing Water Samples for Virus Analysis;168
11.1.2.3;8.2.3 Processing Water Samples for Detection of Bacteria;170
11.1.2.4;8.2.4 Processing Water Samples for Detection of Protozoan Parasites;171
11.1.3;8.3 Air;172
11.1.3.1;8.3.1 Sampling Devices for the Collection of Air Samples;172
11.1.4;8.4 Detection of Microorganisms on Fomites;176
11.1.5;Questions and Problems;177
11.1.6;References and Recommended Readings;177
11.2;Chapter 9. Microscopic Techniques;180
11.2.1;9.1 History of Microscopy;180
11.2.2;9.2 Theory of Microscopy;180
11.2.3;9.3 Visible Light Microscopy;182
11.2.3.1;9.3.1 Types of Light Microscopy;182
11.2.3.2;9.3.2 Sample Preparation;185
11.2.4;9.4 Fluorescence Microscopy;186
11.2.4.1;9.4.1 Direct Counts;187
11.2.4.2;9.4.2 Fluorescent Immunolabeling;188
11.2.4.3;9.4.3 Fluorescent In Situ Hybridization;188
11.2.4.4;9.4.4 Confocal Laser Scanning Microscopy;190
11.2.4.5;9.4.5 Flow Cytometry;190
11.2.5;9.5 Electron Microscopy;190
11.2.5.1;9.5.1 Scanning Electron Microscopy;190
11.2.5.2;9.5.2 Transmission Electron Microscopy;192
11.2.5.3;9.5.3 Elemental Analysis;193
11.2.6;9.6 Scanning Probe Microscopy;194
11.2.6.1;9.6.1 Atomic Force Microscopy;194
11.2.7;9.7 Imaging;194
11.2.8;Questions and Problems;194
11.2.9;References;195
11.3;Chapter 10. Cultural Methods;196
11.3.1;10.1 Cultural Methods for Isolation and Enumeration of Bacteria;196
11.3.1.1;10.1.1 Enumeration and Isolation Techniques;196
11.3.1.2;10.1.2 Plating Methods;197
11.3.1.3;10.1.3 Most Probable Number Technique;198
11.3.2;10.2 Culture Media for Bacteria;199
11.3.2.1;10.2.1 General Media Used for Culturing Bacteria;199
11.3.2.2;10.2.2 New Approaches to Enhanced Cultivation of Soil Bacteria;206
11.3.3;10.3 Cultural Methods for Fungi;207
11.3.4;10.4 Cultural Methods for Algae and Cyanobacteria;208
11.3.5;10.5 Cell Culture–Based Detection Methods for Viruses;209
11.3.6;Questions and Problems;211
11.3.7;References and Recommended Readings;211
11.4;Chapter 11. Physiological Methods;214
11.4.1;11.1 Introduction;214
11.4.2;11.2 Measuring Microbial Activity in Pure Culture;215
11.4.2.1;11.2.1 Substrate Utilization;215
11.4.2.2;11.2.2 Terminal Electron Acceptors;218
11.4.2.3;11.2.3 Cell Mass;219
11.4.2.4;11.2.4 Carbon Dioxide Evolution;220
11.4.3;11.3 Choosing the Appropriate Activity Measurement for Environmental Samples;221
11.4.4;11.4 Carbon Respiration;221
11.4.4.1;11.4.1 Measurement of Respiratory Gases, CO[sub(2)] and O[sub(2)], in Laboratory and Field Studies;222
11.4.4.2;11.4.2 The Application of Respiration Measurements in Environmental Microbiology;225
11.4.4.3;11.4.3 Tracer Studies to Determine Heterotrophic Potential;230
11.4.4.4;11.4.4 Anaerobic Respiration as an Indicator of Microbial Activity;232
11.4.5;11.5 Incorporation of Radiolabelled Tracers into Cellular Macromolecules;232
11.4.5.1;11.5.1 Incorporation of Thymidine into DNA;233
11.4.5.2;11.5.2 Incorporation of Leucine into Protein;233
11.4.6;11.6 Adenylate Energy Charge;234
11.4.7;11.7 Enzyme Assays;235
11.4.7.1;11.7.1 Dehydrogenase Assay;235
11.4.8;11.8 Stable Isotope Probing;238
11.4.9;11.9 Functional Genomics and Proteomics-Based Approaches;238
11.4.9.1;11.9.1 Functional Genomics;238
11.4.9.2;11.9.2 Proteomics;240
11.4.10;Questions and Problems;242
11.4.11;References and Recommended Readings;244
11.5;Chapter 12. Immunological Methods;248
11.5.1;12.1 Introduction;248
11.5.2;12.2 What Is an Antibody?;249
11.5.2.1;12.2.1 Antibody Diversity;250
11.5.2.2;12.2.2 Antibody Specificity;250
11.5.2.3;12.2.3 Antibody Affinity;250
11.5.2.4;12.2.4 Polyclonal and Monoclonal Antibodies;251
11.5.2.5;12.2.5 Antiglobulins;251
11.5.3;12.3 Immunoassays;253
11.5.3.1;12.3.1 Fluorescent Immunolabeling;255
11.5.3.2;12.3.2 Enzyme-Linked Immunosorbent Assays;256
11.5.3.3;12.3.3 Competitive ELISA;257
11.5.3.4;12.3.4 Immunomagnetic Separation Assays;258
11.5.3.5;12.3.5 Western Immunoblotting Assays;259
11.5.3.6;12.3.6 Immunoaffinity Chromatography Assays;260
11.5.3.7;12.3.7 Immunocytochemical Assays;261
11.5.3.8;12.3.8 Immunoprecipitation Assays;262
11.5.4;Questions and Problems;263
11.5.5;References and Recommended Readings;264
11.6;Chapter 13. Nucleic Acid–Based Methods of Analysis;266
11.6.1;13.1 Structure and Complementarity of Nucleic Acids;266
11.6.2;13.2 Obtaining Microbial Nucleic Acids from the Environment;268
11.6.2.1;13.2.1 Extraction of Nucleic Acids from Environmental Samples;268
11.6.3;13.3 Gene Probes and Probing;269
11.6.3.1;13.3.1 Colony Hybridization or Lifts;271
11.6.3.2;13.3.2 Southern and Northern Hybridizations;271
11.6.3.3;13.3.3 Fluorescent In Situ Hybridization (FISH);274
11.6.3.4;13.3.4 Microarrays;274
11.6.3.5;13.3.5 Phyloarrays;277
11.6.4;13.4 Polymerase Chain Reaction;277
11.6.4.1;13.4.1 The Steps of PCR;277
11.6.4.2;13.4.2 Design of Primers;281
11.6.4.3;13.4.3 PCR Detection of Specific and Universal Genes;281
11.6.4.4;13.4.4 RT-PCR;282
11.6.4.5;13.4.5 ICC-PCR;283
11.6.4.6;13.4.6 Seminested, Nested, and Multiplex PCR;284
11.6.4.7;13.4.7 PCR Fingerprinting;286
11.6.4.8;13.4.8 Real-time PCR;286
11.6.4.9;13.4.9 Advantages and Disadvantages of PCR;289
11.6.5;13.5 Recombinant DNA Techniques;289
11.6.5.1;13.5.1 Cloning;289
11.6.5.2;13.5.2 Metagenomics;291
11.6.5.3;13.5.3 Sequence Analysis;293
11.6.5.4;13.5.4 Comparative Genomics;293
11.6.6;13.6 Restriction Fragment Length Polymorphism Analysis;294
11.6.6.1;13.6.1 Theory and Concept;294
11.6.6.2;13.6.2 RFLP Analysis of Whole Genomes;294
11.6.6.3;13.6.3 RFLP Analysis of PCR Sequences;295
11.6.6.4;13.6.4 Fluorescent Fragment Length Polymorphism Techniques;295
11.6.6.5;13.6.5 Pulsed Field Gel Electrophoresis;297
11.6.6.6;13.6.6 Advantages and Disadvantages of RFLP and PFGE Analyses;298
11.6.7;13.7 Denaturing/Temperature Gradient Gel Electrophoresis;298
11.6.7.1;13.7.1 Theory and Concept;298
11.6.7.2;13.7.2 Advantages and Disadvantages of DGGE/TGGE;299
11.6.8;13.8 Plasmid Analysis;300
11.6.8.1;13.8.1 Theory and Concept;300
11.6.8.2;13.8.2 Advantages and Disadvantages of Plasmid Analyses;300
11.6.9;13.9 Reporter Genes;300
11.6.9.1;13.9.1 Theory and Concept;300
11.6.9.2;13.9.2 Specific Reporter Gene Systems;301
11.6.9.3;13.9.3 Advantages and Disadvantages of Reporter Genes;303
11.6.10;Questions and Problems;304
11.6.11;References and Recommended Readings;304
12;Part IV: Microbial Communication, Activities, and Interactions with Environment and Nutrient Cycling;308
12.1;Chapter 14. Biogeochemical Cycling;310
12.1.1;14.1 Introduction;310
12.1.1.1;14.1.1 Biogeochemical Cycles;310
12.1.1.2;14.1.2 Gaia Hypothesis;310
12.1.2;14.2 Carbon Cycle;312
12.1.2.1;14.2.1 Carbon Reservoirs;312
12.1.2.2;14.2.2 Carbon Fixation and Energy Flow;313
12.1.2.3;14.2.3 Carbon Respiration;313
12.1.3;14.3 Nitrogen Cycle;322
12.1.3.1;14.3.1 Nitrogen Reservoirs;323
12.1.3.2;14.3.2 Nitrogen Fixation;323
12.1.3.3;14.3.3 Ammonia Assimilation (Immobilization) and Ammonification (Mineralization);325
12.1.3.4;14.3.4 Nitrification;328
12.1.3.5;14.3.5 Nitrate Reduction;329
12.1.4;14.4 Sulfur Cycle;332
12.1.4.1;14.4.1 Sulfur Reservoirs;333
12.1.4.2;14.4.2 Assimilatory Sulfate Reduction and Sulfur Mineralization;334
12.1.4.3;14.4.3 Sulfur Oxidation;334
12.1.4.4;14.4.4 Sulfur Reduction;336
12.1.5;14.5 Iron Cycle;337
12.1.5.1;14.5.1 Iron Reservoirs;337
12.1.5.2;14.5.2 Iron in Soils and Sediments;337
12.1.5.3;14.5.3 Iron in Marine Environments;338
12.1.5.4;14.5.4 Iron Oxidation;339
12.1.5.5;14.5.5 Iron Reduction;340
12.1.6;Questions and Problems;340
12.1.7;References and Recommended Readings;341
12.2;Chapter 15. Consequences of Biogeochemical Cycles Gone Wild;342
12.2.1;15.1 Introduction;342
12.2.2;15.2 Microbially Influenced Corrosion;343
12.2.2.1;15.2.1 Metal Corrosion;343
12.2.2.2;15.2.2 Microbially Induced Concrete Corrosion;345
12.2.3;15.3 Acid Mine Drainage and Metal Recovery;346
12.2.3.1;15.3.1 Acid Mine Drainage;346
12.2.3.2;15.3.2 Metal Recovery;348
12.2.3.3;15.3.3 Desulfurization of Coal;349
12.2.4;15.4 Biomethylation of Metals and Metalloids;349
12.2.5;15.5 Nitrous Oxide and Earth's Atmosphere;350
12.2.6;15.6 Nitrate Contamination of Groundwater;352
12.2.7;15.7 Composting;353
12.2.8;Questions and Problems;355
12.2.9;References and Recommended Readings;355
12.3;Chapter 16. Microbial Communication: Bacteria–Bacteria and Bacteria–Host;358
12.3.1;16.1 Introduction;358
12.3.2;16.2 Communication via Quorum Sensing in Gram-Negative Bacteria;359
12.3.2.1;16.2.1 N-Acyl Homoserine Lactones (AHLs);359
12.3.2.2;16.2.2 Quorum Sensing in Agrobacterium tumefaciens, a Ubiquitous Plant Pathogen;360
12.3.2.3;16.2.3 Quorum Sensing and Cross-Talk;362
12.3.3;16.3 Signaling in Gram-Positive Bacteria;363
12.3.3.1;16.3.1 ?-Butyrolactones;364
12.3.3.2;16.3.2 Peptide Signaling;364
12.3.4;16.4 Other Types of Signaling;365
12.3.4.1;16.4.1 Autoinducers-2 and -3;365
12.3.4.2;16.4.2 Eavesdropping on the Party Line;365
12.3.4.3;16.4.3 Bacterial Communication Interference;366
12.3.4.4;16.4.4 Interkingdom Communication;367
12.3.4.5;16.4.5 Host–Bacterial Communication;368
12.3.5;16.5 Summary and Core Concepts;368
12.3.6;Questions and Problems;368
12.3.7;References and Recommended Readings;368
12.4;Chapter 17. Bacterial Communities in Natural Ecosystems;370
12.4.1;17.1 Bacterial Communities;370
12.4.2;17.2 Bacterial Diversity in Natural Systems;371
12.4.2.1;17.2.1 What is a Species?;371
12.4.2.2;17.2.2 Diversity in Soil;371
12.4.2.3;17.2.3 Diversity in the Ocean;372
12.4.3;17.3 Functional Diversity and the Resilience of Bacterial Communities;373
12.4.3.1;17.3.1 Soil Bacterial Communities;373
12.4.3.2;17.3.2 Soil–Plant–Microbe Interactions;374
12.4.4;17.4 Microbial Diversity and Natural Products;376
12.4.5;Questions and Problems;378
12.4.6;References and Recommended Readings;378
12.5;Chapter 18. Global Change and Microbial Infectious Disease;380
12.5.1;18.1 Environmental Human Pathogenic Microbes;380
12.5.1.1;18.1.1 Indigenous Pathogens of Soilborne Origin;382
12.5.1.2;18.1.2 Water-Based and Airborne Human Pathogenic Microbes;383
12.5.2;18.2 Routes of Exposure;383
12.5.2.1;18.2.1 What We Breathe;383
12.5.2.2;18.2.2 What We Eat;383
12.5.2.3;18.2.3 What We Drink;384
12.5.3;18.3 Environmental Change and Microbial Infectious Diseases;385
12.5.3.1;18.3.1 Global Climate Change and Microbial Infectious Disease;385
12.5.3.2;18.3.2 Urbanization and Deforestation;386
12.5.4;Questions and Problems;386
12.5.5;References and Recommended Readings;386
12.6;Chapter 19. Microbial Transport;388
12.6.1;19.1 Factors Affecting Microbial Transport;388
12.6.1.1;19.1.1 Microbial Filtration;389
12.6.1.2;19.1.2 Physiological State;389
12.6.1.3;19.1.3 Microbial Adhesion—The Influence of Cell Surface Properties;390
12.6.1.4;19.1.4 Impact of pH on Microbial Transport;394
12.6.1.5;19.1.5 Impact of Ionic Strength on Transport;394
12.6.1.6;19.1.6 Cellular Appendages;395
12.6.1.7;19.1.7 Hydrogeological Factors;396
12.6.1.8;19.1.8 Persistence and Activity of Introduced Microbes;398
12.6.2;19.2 Factors Affecting Transport of DNA;398
12.6.3;19.3 Novel Approaches to Facilitate Microbial Transport;399
12.6.3.1;19.3.1 Ultramicrobacteria;399
12.6.3.2;19.3.2 Surfactants;399
12.6.3.3;19.3.3 Gene Transfer;400
12.6.4;19.4 Microbial Transport Studies;400
12.6.4.1;19.4.1 Column Studies;400
12.6.4.2;19.4.2 Field Studies;401
12.6.4.3;19.4.3 Tracers;402
12.6.5;19.5 Models for Microbial Transport;403
12.6.5.1;19.5.1 Advection–Dispersion Models;403
12.6.5.2;19.5.2 Filtration Models;404
12.6.6;Questions and Problems;404
12.6.7;References and Recommended Readings;405
13;Part V: Remediation of Organic and Metal Pollutants;408
13.1;Chapter 20. Microorganisms and Organic Pollutants;410
13.1.1;20.1 Introduction;410
13.1.2;20.2 Environmental Law;411
13.1.3;20.3 The Overall Process of Biodegradation;413
13.1.4;20.4 Contaminant Structure, Toxicity, and Biodegradability;416
13.1.4.1;20.4.1 Genetic Potential;416
13.1.4.2;20.4.2 Toxicity;417
13.1.4.3;20.4.3 Bioavailability;417
13.1.4.4;20.4.4 Contaminant Structure;419
13.1.5;20.5 Environmental Factors Affecting Biodegradation;420
13.1.5.1;20.5.1 Redox Conditions;420
13.1.5.2;20.5.2 Organic Matter Content;421
13.1.5.3;20.5.3 Nitrogen;421
13.1.5.4;20.5.4 Other Environmental Factors;421
13.1.6;20.6 Biodegradation of Organic Pollutants;422
13.1.6.1;20.6.1 Pollutant Sources and Types;422
13.1.6.2;20.6.2 Aliphatics;425
13.1.7;20.7 Bioremediation;437
13.1.7.1;20.7.1 Addition of Oxygen or Other Gases;439
13.1.7.2;20.7.2 Nutrient Addition;440
13.1.7.3;20.7.3 Sequential Anaerobic-Aerobic Degradation;441
13.1.7.4;20.7.4 Addition of Surfactants;441
13.1.7.5;20.7.5 Addition of Microorganisms or DNA;441
13.1.8;Questions and Problems;442
13.1.9;References and Recommended Readings;442
13.2;Chapter 21. Microorganisms and Metal Pollutants;444
13.2.1;21.1 Metals in the Environment;444
13.2.2;21.2 Cause for Concern;445
13.2.3;21.3 Metals Defined;445
13.2.3.1;21.3.1 The Essential Metals;446
13.2.3.2;21.3.2 The Toxic Metals;446
13.2.3.3;21.3.3 The Nontoxic Nonessential Metals;446
13.2.4;21.4 Metal Sources;447
13.2.4.1;21.4.1 Anthropogenic Sources;447
13.2.4.2;21.4.2 Natural Sources;447
13.2.5;21.5 Metal Solubility, Bioavailability and Speciation;448
13.2.5.1;21.5.1 Metal Chemistry;449
13.2.5.2;21.5.2 Cation-Exchange Capacity;450
13.2.5.3;21.5.3 Redox Potential;450
13.2.5.4;21.5.4 pH;450
13.2.6;21.6 Metal Toxicity Effects on the Microbial Cell;450
13.2.7;21.7 Mechanisms of Microbial Metal Resistance and Detoxification;452
13.2.7.1;21.7.1 General Mechanisms of Metal Resistance;453
13.2.7.2;21.7.2 Metal-Dependent Mechanisms of Resistance;453
13.2.8;21.8 Methods for Studying Metal–Microbial Interactions;455
13.2.8.1;21.8.1 Culture Medium;455
13.2.8.2;21.8.2 Measurement of Total, Soluble, and Bioavailable Metal;456
13.2.9;21.9 Microbial Metal Transformations;457
13.2.9.1;21.9.1 Oxidation–Reduction;457
13.2.9.2;21.9.2 Methylation;458
13.2.10;21.10 Physicochemical Methods of Metal Remediation;458
13.2.11;21.11 Microbial Approaches in the Remediation of Metal-Contaminated Soils and Sediments;460
13.2.12;21.12 Microbial Approaches in the Remediation of Metal-Contaminated Aquatic Systems;461
13.2.13;Questions and Problems;462
13.2.14;References and Recommended Readings;463
14;Part VI: Water- and Foodborne Pathogens;466
14.1;Chapter 22. Environmentally Transmitted Pathogens;468
14.1.1;22.1 Environmentally Transmitted Pathogens;468
14.1.2;22.2 Bacteria;470
14.1.2.1;22.2.1 Salmonella;470
14.1.2.2;22.2.2 Escherichia coli and Shigella;471
14.1.2.3;22.2.3 Campylobacter;472
14.1.2.4;22.2.4 Yersinia;473
14.1.2.5;22.2.5 Vibrio;474
14.1.2.6;22.2.6 Helicobacter;475
14.1.2.7;22.2.7 Legionella;476
14.1.2.8;22.2.8 Opportunistic Bacterial Pathogens;477
14.1.2.9;22.2.9 Blue-Green Algae;478
14.1.3;22.3 Parasitology;480
14.1.3.1;22.3.1 Protozoa;481
14.1.3.2;22.3.2 Nematodes;488
14.1.3.3;22.3.3 Cestodes (Taenia saginata);490
14.1.3.4;22.3.4 Trematodes (Schistosoma mansoni);490
14.1.4;22.4 Viruses;492
14.1.4.1;22.4.1 Enteric Viruses;492
14.1.4.2;22.4.2 Respiratory Viruses;498
14.1.5;22.5 Fate and Transport of Pathogens in the Environment;502
14.1.6;Questions and Problems;503
14.1.7;References and Recommended Readings;504
14.2;Chapter 23. Indicator Microorganisms;508
14.2.1;23.1 The Concept of Indicator Organisms;508
14.2.2;23.2 Total Coliforms;509
14.2.2.1;23.2.1 The Most Probable Number (MPN) Test;510
14.2.2.2;23.2.2 The Membrane Filter (MF) Test;510
14.2.2.3;23.2.3 The Presence–Absence (P–A) Test;510
14.2.3;23.3 Fecal Coliforms and Escherichia coli;513
14.2.4;23.4 Fecal Streptococci;513
14.2.5;23.5 Clostridium Perfringens;514
14.2.6;23.6 Heterotrophic Plate Count;514
14.2.7;23.7 Bacteriophage;515
14.2.8;23.8 Other Potential Indicator Organisms;516
14.2.9;23.9 Standards and Criteria for Indicators;517
14.2.10;23.10 Microbial Source Tracking;519
14.2.11;Questions and Problems;521
14.2.12;References and Recommended Readings;521
15;Part VII: Wastewater Treatment and Disinfection;524
15.1;Chapter 24. Wastewater Treatment and Biosolids Reuse;526
15.1.1;24.1 The Nature of Wastewater (Sewage);526
15.1.2;24.2 Modern Wastewater Treatment;529
15.1.2.1;24.2.1 Primary Treatment;529
15.1.2.2;24.2.2 Secondary Treatment;529
15.1.2.3;24.2.3 Tertiary Treatment;534
15.1.2.4;24.2.4 Removal of Pathogens by Sewage Treatment Processes;534
15.1.2.5;24.2.5 Removal of Organics and Inorganics by Sewage Treatment Processes;536
15.1.3;24.3 Oxidation Ponds;536
15.1.4;24.4 Septic Tanks;538
15.1.5;24.5 Land Application of Wastewater;539
15.1.6;24.6 Wetlands and Aquaculture Systems;541
15.1.7;24.7 Sludge Processing;544
15.1.7.1;24.7.1 Stabilization Technologies;544
15.1.7.2;24.7.2 Sludge Processing to Produce Class A Biosolids;545
15.1.8;24.8 Land Application of Biosolids and Animal Wastes: An Historical Perspective and Current Outlook;546
15.1.8.1;24.8.1 Class A versus Class B Biosolids;546
15.1.9;24.9 Methods of Land Application of Biosolids;547
15.1.10;24.10 Pathogens of Concern in Class B Biosolids;547
15.1.10.1;24.10.1 Other Biological Concerns with Biosolids;548
15.1.10.2;24.10.2 Risks from Pathogens in Biosolids;550
15.1.11;24.11 Pathogens in Animal Manures;551
15.1.12;Questions and Problems;551
15.1.13;References and Additional Readings;552
15.2;Chapter 25. Drinking Water Treatment;554
15.2.1;25.1 Water Treatment Processes;554
15.2.2;25.2 Water Treatment Requirements;556
15.2.3;25.3 Water Distribution Systems;557
15.2.4;25.4 Organic Carbon and Microbial Growth in Distribution Systems;559
15.2.5;Questions and Problems;561
15.2.6;References and Recommended Readings;561
15.3;Chapter 26. Disinfection;562
15.3.1;26.1 Thermal Destruction;563
15.3.2;26.2 Kinetics of Disinfection;564
15.3.3;26.3 Factors Affecting Disinfectants;565
15.3.4;26.4 Halogens;568
15.3.4.1;26.4.1 Chlorine;568
15.3.4.2;26.4.2 Chloramines;568
15.3.4.3;26.4.3 Chlorine Dioxide;569
15.3.4.4;26.4.4 Bromine and Iodine;569
15.3.5;26.5 Ozone;570
15.3.6;26.6 Metal Ions;570
15.3.7;26.7 Ultraviolet Disinfection;571
15.3.8;26.8 Photodynamic Inactivation;573
15.3.9;26.9 Gamma and High-Energy Irradiation;573
15.3.10;Questions and Problems;574
15.3.11;References and Recommended Readings;574
16;Part VIII: Urban Microbiology;576
16.1;Chapter 27. Domestic and Indoor Microbiology;578
16.1.1;27.1 Household Sources of Pathogens;578
16.1.1.1;27.1.1 Air;578
16.1.1.2;27.1.2 Food;579
16.1.1.3;27.1.3 Water;579
16.1.2;27.2 Fomites: Role in Disease Spread;581
16.1.2.1;27.2.1 Occurrence of Pathogens on Fomites;582
16.1.2.2;27.2.2 Persistence of Pathogens on Fomites;582
16.1.3;27.3 Transfer of Pathogens;582
16.1.4;Questions and Problems;585
16.1.5;References and Recommended Readings;585
16.2;Chapter 28. Microorganisms and Bioterrorism;588
16.2.1;28.1 Microbial Agents of Concern as Weapons of Bioterrorism;589
16.2.2;28.2 Bioterrorism and Potable Water;591
16.2.2.1;28.2.1 Real-Time Monitoring in Water Distribution Systems;591
16.2.2.2;28.2.2 Real-Time Monitoring;592
16.2.2.3;28.2.3 Contaminant Transport Mechanisms and Water Quality Modeling;592
16.2.3;28.3 Bioterrorism and Agriculture;594
16.2.3.1;28.3.1 Contamination via Airborne Microbial Agents;594
16.2.3.2;28.3.2 Foot-and-Mouth Disease;597
16.2.4;28.4 Transmission by Fomites;597
16.2.5;References and Recommended Readings;597
16.3;Chapter 29. Risk Assessment;598
16.3.1;29.1 The Concept of Risk Assessment;598
16.3.2;29.2 Elements of Risk Assessment;598
16.3.3;29.3 The Process of Risk Assessment;600
16.3.3.1;29.3.1 Hazard Identification;600
16.3.3.2;29.3.2 Exposure Assessment;601
16.3.3.3;29.3.3 Dose–Response Assessment;602
16.3.3.4;29.3.4 Risk Characterization;603
16.3.4;29.4 Microbial Risk Assessment;604
16.3.5;Questions and Problems;609
16.3.6;References and Recommended Readings;610
17;Index;612
17.1;A;612
17.2;B;613
17.3;C;613
17.4;D;614
17.5;E;614
17.6;F;615
17.7;G;615
17.8;H;615
17.9;I;616
17.10;L;616
17.11;M;616
17.12;N;617
17.13;O;617
17.14;P;617
17.15;Q;618
17.16;R;618
17.17;S;619
17.18;T;620
17.19;U;620
17.20;V;620
17.21;W;621
17.22;X;621
17.23;Z;621
