Environmental Microbiology

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Academic Press, 2009 - Science - 598 pages
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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
 

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As a student working out of this book, it is not one I would recommend. It is a difficult read, even if you have a solid background in enviromental science, it is still very difficult to follow.

Contents

Introduction to Environmental Microbiology
3
13 MODERN ENVIRONMENTAL MICROBIOLOGY
6
14 PURPOSE AND ORGANIZATION OF THIS TEXT
7
Microorganisms
9
21 CLASSIFICATION OF ORGANISMS
10
221 Cell Envelope
11
222 Cytoplasm
14
223 Glycocalyx
16
1433 Ammonia Assimilation Immobilization and Ammonification Mineralization
302
1434 Nitrification
305
1435 Nitrate Reduction
306
144 SULFUR CYCLE
309
1441 Sulfur Reservoirs
310
1442 Assimilatory Sulfate Reduction and Sulfur Mineralization
311
1444 Sulfur Reduction
313
145 IRON CYCLE
314

226 Information Transfer
17
227 Metabolism
18
23 THE ARCHAEA
20
231 Archaean Habitats
21
24 FUNGI
22
242 Fungal Diversity
23
243 Ecological Considerations
24
25 SLIME MOLDS
25
262 Physiological and Ecological Considerations
26
271 Cell Structure
27
28 VIRUSES
28
281 Infective Nature of Viruses
29
282 Procaryotic Viruses
30
283 Eucaryotic Viruses
32
29 OTHER BIOLOGICAL ENTITIES
33
REFERENCES
34
Bacterial Growth
37
31 GROWTH IN PURE CULTURE IN A FLASK
38
312 The Exponential Phase
39
313 The Stationary Phase
40
314 The Death Phase
41
315 Effect of Substrate Concentration on Growth
42
32 CONTINUOUS CULTURE
44
33 GROWTH IN THE ENVIRONMENT
46
331 The Lag Phase
47
34 MASS BALANCE OF GROWTH
49
341 Aerobic Conditions
50
342 Anaerobic Conditions
52
QUESTIONS AND PROBLEMS
53
REFERENCES AND RECOMMENDED READINGS
54
Microbial Environments
55
Earth Environments
57
42 PHYSICOCHEMICAL CHARACTERISTICS OF THE EARTH ENVIRONMENT
58
422 The Solid Phase
59
423 The Liquid Phase
67
424 Soil Atmosphere
69
43 SOIL AS A MICROBIAL ENVIRONMENT
70
44 MICROORGANISMS IN SURFACE SOILS
71
443 Fungi
73
444 Algae
74
45 DISTRIBUTION OF MICROORGANISMS IN SOIL
75
46 MICROORGANISMS IN SUBSURFACE ENVIRONMENTS
76
461 Microorganisms in Shallow Subsurface Environments
77
QUESTIONS AND PROBLEMS
81
Aeromicrobiology
83
53 IMPORTANT AIRBORNE TOXINS
84
54 AEROSOLS
85
55 NATURE OF BIOAEROSOLS
87
561 Launching
88
563 Deposition
89
57 MICROBIAL SURVIVAL IN THE AIR
91
572 Temperature
92
582 Waste Disposal
94
59 INTRAMURAL AEROMICROBIOLOGY
95
592 Public Health
96
510 BIOAEROSOL CONTROL
97
5104 Isolation
98
5112 Biosafety Laboratories
100
QUESTIONS AND PROBLEMS
101
Aquatic Environments
103
622 Benthic Habitat
105
623 Microbial Mats
107
63 AQUATIC ENVIRONMENTS
110
632 Brackish Water
115
634 Subterranean Water
117
Food for the Future
119
QUESTIONS AND PROBLEMS
120
Extreme Environments
123
71 LOW TEMPERATURE ENVIRONMENTS
124
72 HIGH TEMPERATURE ENVIRONMENTS
126
73 DESICCATION AND UV STRESS
128
74 ENVIRONMENTS BASED ON CHEMOAUTOTROPHY
130
75 ACIDIC ENVIRONMENTS
132
QUESTIONS AND PROBLEMS
133
REFERENCES
134
Detection Enumeration and Identification
135
Environmental Sample Collection and Processing
137
811 Sampling Strategies and Methods for Surface Soils
138
812 Sampling Strategies and Methods for the Subsurface
139
813 Sample Processing and Storage
141
82 WATER
144
822 Processing Water Samples for Virus Analysis
145
823 Processing Water Samples for Detection of Bacteria
147
824 Processing Water Samples for Detection of Protozoan Parasites
148
83 AIR
149
84 DETECTION OF MICROORGANISMS ON FOMITES
153
QUESTIONS AND PROBLEMS
154
Microscopic Techniques
157
93 VISIBLE LIGHT MICROSCOPY
159
932 Sample Preparation
162
94 FLUORESCENCE MICROSCOPY
163
941 Direct Counts
164
942 Fluorescent Immunolabeling
165
944 Confocal Laser Scanning Microscopy
167
952 Transmission Electron Microscopy
169
953 Elemental Analysis
170
96 SCANNING PROBE MICROSCOPY
171
REFERENCES
172
Cultural Methods
173
1012 Plating Methods
174
1013 Most Probable Number Technique
175
102 CULTURE MEDIA FOR BACTERIA
176
1022 New Approaches for Enhanced Cultivation of Soil Bacteria
183
103 CULTURAL METHODS FOR FUNGI
184
104 CULTURAL METHODS FOR ALGAE AND CYANOBACTERIA
185
105 CELL CULTUREBASED DETECTION METHODS FOR VIRUSES
186
QUESTIONS AND PROBLEMS
188
Physiological Methods
191
112 MEASURING MICROBIAL ACTIVITY IN PURE CULTURE
192
1122 Terminal Electron Acceptors
195
1123 Cell Mass
196
1124 Carbon Dioxide Evolution
197
113 CHOOSING THE APPROPRIATE ACTIVITY MEASUREMENT FOR ENVIRONMENTAL SAMPLES
198
1141 Measurement of Respiratory Gases CO2 and O2 in Laboratory and Field Studies
199
1142 The Application of Respiration Measurements in Environmental Microbiology
202
1143 Tracer Studies to Determine Heterotrophic Potential
207
1144 Anaerobic Respiration as an Indicator of Microbial Activity
209
1151 Incorporation of Thymidine into DNA
210
116 ADENYLATE ENERGY CHARGE
211
117 ENZYME ASSAYS
212
118 STABLE ISOTOPE PROBING
215
1192 Proteomics
217
QUESTIONS AND PROBLEMS
219
REFERENCES AND RECOMMENDED READINGS
221
Immunological Methods
225
122 WHAT IS AN ANTIBODY?
226
1221 Antibody Diversity
227
1224 Polyclonal and Monoclonal Antibodies
228
123 IMMUNOASSAYS
230
1231 Fluorescent Immunolabeling
232
1232 EnzymeLinked Immunosorbent Assays
233
1233 Competitive ELISA
234
1234 Immunomagnetic Separation Assays
235
1235 Western Immunoblotting Assays
236
1236 Immunoaffinity Chromatography Assays
237
1237 Immunocytochemical Assays
238
1238 Immunoprecipitation Assays
239
QUESTIONS AND PROBLEMS
240
REFERENCES AND RECOMMENDED READINGS
241
Nucleic AcidBased Methods of Analysis
243
132 OBTAINING MICROBIAL NUCLEIC ACIDS FROM THE ENVIRONMENT
245
133 GENE PROBES AND PROBING
246
1331 Colony Hybridization or Lifts
248
1333 Fluorescent In Situ Hybridization FISH
251
1335 Phyloarrays
254
1342 Design of Primers
258
1344 RTPCR
259
1345 ICCPCR
260
1346 Seminested Nested and Multiplex PCR
261
1347 PCR Fingerprinting
263
1349 Advantages and Disadvantages of PCR
266
1352 Metagenomics
268
1353 Sequence Analysis
270
136 RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS
271
1363 RFLP Analysis of PCR Sequences
272
1365 Pulsed Field Gel Electrophoresis
274
1366 Advantages and Disadvantages of RFLP and PFGE Analyses
275
1372 Advantages and Disadvantages of DGGETGGE
276
138 PLASMID ANALYSIS
277
1392 Specific Reporter Gene Systems
278
1393 Advantages and Disadvantages of Reporter Genes
280
QUESTIONS AND PROBLEMS
281
Microbial Communication Activities and Interactions with Environment and Nutrient Cycling
285
Biogeochemical Cycling
287
142 CARBON CYCLE
289
1422 Carbon Fixation and Energy Flow
290
143 NITROGEN CYCLE
299
1431 Nitrogen Reservoirs
300
1453 Iron in Marine Environments
315
1454 Iron Oxidation
316
1455 Iron Reduction
317
REFERENCES AND RECOMMENDED READINGS
318
Consequences of Biogeochemical Cycles Gone Wild
319
152 MICROBIALLY INFLUENCED CORROSION
320
1522 Microbially Induced Concrete Corrosion
322
153 ACID MINE DRAINAGE AND METAL RECOVERY
323
1532 Metal Recovery
325
1533 Desulfurization of Coal
326
155 NITROUS OXIDE AND EARTHS ATMOSPHERE
327
156 NITRATE CONTAMINATION OF GROUNDWATER
329
157 COMPOSTING
330
QUESTIONS AND PROBLEMS
332
Microbial Communication BacteriaBacteria and BacteriaHost
335
162 COMMUNICATION VIA QUORUM SENSING IN GRAMNEGATIVE BACTERIA
336
1622 Quorum Sensing in Agrobacterium tumefaciens a Ubiquitous Plant Pathogen
337
1623 Quorum Sensing and CrossTalk
339
163 SIGNALING IN GRAMPOSITIVE BACTERIA
340
1631 Butyrolactones
341
164 OTHER TYPES OF SIGNALING
342
1643 Bacterial Communication Interference
343
1644 Interkingdom Communication
344
1645 HostBacterial Communication
345
Bacterial Communities in Natural Ecosystems
347
172 BACTERIAL DIVERSITY IN NATURAL SYSTEMS
348
1723 Diversity in the Ocean
349
173 FUNCTIONAL DIVERSITY AND THE RESILIENCE OF BACTERIAL COMMUNITIES
350
1732 SoilPlantMicrobe Interactions
351
174 MICROBIAL DIVERSITY AND NATURAL PRODUCTS
353
QUESTIONS AND PROBLEMS
355
Global Change and Microbial Infectious Disease
357
1811 Indigenous Pathogens of Soilborne Origin
359
1812 Waterbased and Airborne Human Pathogenic Microbes
360
1823 What We Drink
361
183 ENVIRONMENTAL CHANGE AND MICROBIAL INFECTIOUS DISEASES
362
1832 Urbanization and Deforestation
363
Microbial Transport
365
1911 Microbial Filtration
366
1913 Microbial AdhesionThe Influence of Cell Surface Properties
367
1914 Impact of pH on Microbial Transport
371
1916 Cellular Appendages
372
1917 Hydrogeological Factors
373
1918 Persistence and Activity of Introduced Microbes
375
193 NOVEL APPROACHES TO FACILITATE MICROBIAL TRANSPORT
376
1933 Gene Transfer
377
1942 Field Studies
378
1943 Tracers
379
195 MODELS FOR MICROBIAL TRANSPORT
380
1952 Filtration Models
381
REFERENCES AND RECOMMENDED READINGS
382
Remediation of Organic and Metal Pollutants
385
Microorganisms and Organic Pollutants
387
202 ENVIRONMENTAL LAW
388
203 THE OVERALL PROCESS OF BIODEGRADATION
390
204 CONTAMINANT STRUCTURE TOXICITY AND BIODEGRADABILITY
393
2042 Toxicity
394
2044 Contaminant Structure
396
205 ENVIRONMENTAL FACTORS AFFECTING BIODEGRADATION
397
2052 Organic Matter Content
398
206 BIODEGRADATION OF ORGANIC POLLUTANTS
399
2062 Aliphatics
402
2063 Alicyclics
406
207 BIOREMEDIATION
414
2071 Addition of Oxygen or Other Gases
416
2072 Nutrient Addition
417
2073 Sequential AnaerobicAerobic Degradation
418
QUESTIONS AND PROBLEMS
419
Microorganisms and Metal Pollutants
421
212 CAUSE FOR CONCERN
422
2131 The Essential Metals
423
214 METAL SOURCES
424
215 METAL SOLUBILITY BIOAVAILABILITY AND SPECIATION
425
2151 Metal Chemistry
426
2152 CationExchange Capacity
427
217 MECHANISMS OF MICROBIAL METAL RESISTANCE AND DETOXIFICATION
429
2171 General Mechanisms of Metal Resistance
430
218 METHODS FOR STUDYING METALMICROBIAL INTERACTIONS
432
2182 Measurement of Total Soluble and Bioavailable Metal
433
219 MICROBIAL METAL TRANSFORMATIONS
434
2192 Methylation
435
2111 MICROBIAL APPROACHES IN THE REMEDIATION OF METALCONTAMINATED SOILS AND SEDIMENTS
437
2112 MICROBIAL APPROACHES IN THE REMEDIATION OF METALCONTAMINATED AQUATIC SYSTEMS
438
QUESTIONS AND PROBLEMS
439
REFERENCES AND RECOMMENDED READINGS
440
Water and Foodborne Pathogens
443
Environmentally Transmitted Pathogens
445
222 BACTERIA
447
2222 Escherichia coli and Shigella
448
2223 Campylobacter
449
2224 Yersinia
450
2225 Vibrio
451
2226 Helicobacter
452
2227 Legionella
453
2228 Opportunistic Bacterial Pathogens
454
2229 BlueGreen Algae
455
223 PARASITOLOGY
457
2231 Protozoa
458
2232 Nematodes
465
2233 Cestodes Taenia saginata
467
224 VIRUSES
469
2242 Respiratory Viruses
475
225 FATE AND TRANSPORT OF PATHOGENS IN THE ENVIRONMENT
479
QUESTIONS AND PROBLEMS
480
REFERENCES AND RECOMMENDED READINGS
481
Indicator Microorganisms
485
232 TOTAL COLIFORMS
486
2321 The Most Probable Number MPN Test
487
233 FECAL COLIFORMS AND ESCHERICHIA COLI
490
235 CLOSTRIDIUM PERFRINGENS
491
237 BACTERIOPHAGE
492
238 OTHER POTENTIAL INDICATOR ORGANISMS
493
239 STANDARDS AND CRITERIA FOR INDICATORS
494
2310 MICROBIAL SOURCE TRACKING
496
QUESTIONS AND PROBLEMS
498
Wastewater Treatment and Disinfection
501
Wastewater Treatment and Biosolids Reuse
503
242 MODERN WASTEWATER TREATMENT
506
2423 Tertiary Treatment
511
2425 Removal of Organics and Inorganics by Sewage Treatment Processes
513
244 SEPTIC TANKS
515
245 LAND APPLICATION OF WASTEWATER
516
246 WETLANDS AND AQUACULTURE SYSTEMS
518
247 SLUDGE PROCESSING
521
2472 Sludge Processing to Produce Class A Biosolids
522
AN HISTORICAL PERSPECTIVE AND CURRENT OUTLOOK
523
249 METHODS OF LAND APPLICATION OF BIOSOLIDS
524
24101 Other Biological Concerns with Biosolids
525
24102 Risks from Pathogens in Biosolids
527
2411 PATHOGENS IN ANIMAL MANURES
528
REFERENCES AND ADDITIONAL READINGS
529
Drinking Water Treatment
531
252 WATER TREATMENT REQUIREMENTS
533
253 WATER DISTRIBUTION SYSTEMS
534
254 ORGANIC CARBON AND MICROBIAL GROWTH IN DISTRIBUTION SYSTEMS
536
QUESTIONS AND PROBLEMS
538
Disinfection
539
261 THERMAL DESTRUCTION
540
262 KINETICS OF DISINFECTION
541
263 FACTORS AFFECTING DISINFECTANTS
542
264 HALOGENS
545
2643 Chlorine Dioxide
546
265 OZONE
547
267 ULTRAVIOLET DISINFECTION
548
268 PHOTODYNAMIC INACTIVATION
550
QUESTIONS AND PROBLEMS
551
Urban Microbiology
553
Domestic and Indoor Microbiology
555
2712 Food
556
ROLE IN DISEASE SPREAD
558
2721 Occurrence of Pathogens on Fomites
559
QUESTIONS AND PROBLEMS
562
Microorganisms and Bioterrorism
565
281 MICROBIAL AGENTS OF CONCERN AS WEAPONS OF BIOTERRORISM
566
282 BIOTERRORISM AND POTABLE WATER
568
2822 RealTime Monitoring
569
283 BIOTERRORISM AND AGRICULTURE
571
2832 FootandMouth Disease
574
Risk Assessment
575
293 THE PROCESS OF RISK ASSESSMENT
577
2932 Exposure Assessment
578
2933 DoseResponse Assessment
579
2934 Risk Characterization
580
294 MICROBIAL RISK ASSESSMENT
581
QUESTIONS AND PROBLEMS
586
REFERENCES AND RECOMMENDED READINGS
587
Index
589
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