Practical Atlas for Bacterial Identification, Second Edition

Cover Page......Page 1
About The Cover......Page 3
Title: Practical Atlas For Bacterial Identification......Page 4
ISBN 9781420087970......Page 5
Dedication......Page 6
Contents......Page 7
List Of Tables......Page 13
List Of Figures......Page 15
List Of Plates......Page 20
Preface......Page 24
Some Further Thoughts......Page 27
Acknowledgments......Page 28
Author......Page 29
1.1 Introduction to Layering of Bacterial Communities......Page 30
1.2 Factors Significantly Influencing Bacterial Activities and Nutrient Cycles......Page 33
1.3 Bacteria: Human Perspectives......Page 35
2.1 Historical Overview......Page 40
2.2 Challenges of Classifying "Unculturables"......Page 42
2.3 Evolutionary Trends toward Bacterial Diversity......Page 43
2.4 Two-Dimensional Grid Definition of Bacterial Communities......Page 44
2.5 Establishment of Grid Location Points for Bacterial Atlas......Page 49
2.6 Summary of Bacterial Community Grid Positioning Atlas Principles......Page 50
3.1 Historical Overview......Page 52
3.2 Definitions of Alpha-Based Bacterial Consortia......Page 56
3.3 Alpha One: Bionucleating Dispersed Consorms [ FPL ( fmv: fcP) 22- 04]......Page 59
3.4 Alpha Two: Organic Bioconcreting Consorms [ FPL ( fmv: fcP) 22- 16]......Page 60
3.5 Alpha Three: Inorganic Bioconcreting Consorms [ FPL ( fmv: fcP) 13- 21)......Page 61
3.6 Alpha Four: Carbon- Reducing Consorms [ FPL ( fmv: fcP) 06- 27]......Page 62
3.8 Alpha Six: Hyperbaric Disp ersed Bionucleating Consorms [ FPL ( fmv: fcP) 01- 03]......Page 63
3.9 Summary......Page 64
4.1 I ntroduction......Page 66
4.2.1 Principal Alpha One Consormial Activities......Page 67
4.3 Alpha Two: Organic Bionucleating Consorms ( FPL 2, 22- 16)......Page 68
4.3.1 Principal Alpha Two Consormial Activities......Page 69
4.4 Alpha Three: Inorganic Bionucleating Consorms ( FPL 3, 13- 21)......Page 73
4.4.1 Principal Alpha Three Consormial Activities......Page 74
4.5 Alpha Four: Carbon- Reducing Consorms ( FPL 4, 06- 27)......Page 78
4.5.1 Principal Alpha Four Consormial Activities......Page 79
4.6.1 Principal Alpha Five Consormial Activities......Page 81
4.7 Alpha Six: Hyperbaric Disp ersed Bionucleating Consorms ( FPL 6, 01- 03)......Page 82
5.1 Introduction......Page 84
5.2 Defining Bacteriologically Dominated Consorms......Page 85
5.3 Categorization of Consorms......Page 86
5.3.1 Location within Environment......Page 87
5.3.2 Generated Colors......Page 88
5.3.3 Texture and Porosity......Page 91
5.3.4 Inorganic and Organic Chemistry......Page 93
5.3.5 Water Form and Content......Page 95
5.3.7 Identification of Recovered Bacterial Consorms......Page 96
5.3.8 Time-Scaled Maturation......Page 97
6.1 Introduction......Page 100
6.2 Identification of Consorms......Page 101
6.3 Determining Probability of Consormial Activity......Page 102
6.4 Symptoms of Consormial Intrusions......Page 106
6.5 Quantification of Consormial Intrusions into Environment......Page 107
6.6 Causes and Eff ects of Consorm Intrusions in Impacted Environment......Page 108
6.7 Consorm Sampling Protocols......Page 112
7.1 I ntroduction......Page 114
7.2 D efining Bacterial Consorms by Form, Function, and Habitat......Page 115
1, 19-06 FOM (Foam)......Page 117
1, 19-12 SN O (Snow)......Page 118
2, 19-07 BCH (Bronchitis)......Page 119
2, 15-07 CLS (Cloudiness)......Page 120
2, 15-18 CLW (Colloidal Water)......Page 121
2, 10-08 KDS (Kidney Stones)......Page 122
2, 09-15 MIC (Microb iolog ically Influenced Corrosion)......Page 123
2, 19-21 PLG (Plugg ing)......Page 124
2, 06-18 ROE (Rotten Egg s)......Page 125
2, 22-07 SHN (Sheen)......Page 126
2, 24-13 TCT (Thatch)......Page 127
2, 07-20 ULC (Ulcers)......Page 128
3, 10-21 BPL (Black Plug Layer)......Page 129
3, 19-03 CR B (Carbo nates)......Page 130
3, 06-16 CRS (Corrosion)......Page 131
3, 20-28 FRD (Ferric-Rich Depo sits)......Page 132
3, 15-28 MGN (Manganese Nodules)......Page 133
3, 10-30 PGI (Pig Iron)......Page 134
3, 19-21 PLG (Plugg ing)......Page 135
3, 10-10 SBL (Sand Boils)......Page 137
3, 15-17 TCL (Tubercles)......Page 138
4, 04-20 CDR (Carbo n Dioxide Reducers)......Page 139
4, 06-22 BNG (Biog enic Natural Gas)......Page 140
4 01-28 OIL (Oil)......Page 141
4, 07-19 PET (Peat)......Page 142
5, 15-10 GHY (Gas Hydrates)......Page 143
8.2 Determination of Consormial Activity by ATP Analysis......Page 144
8.3 RASI Protocol for Determining Potential ATP Activity......Page 146
8.3.1 Differentiation of RASI Procedures......Page 148
8.3.2 RASI -MIDI Protocols for Identifying Bacterial Consorms......Page 149
9.1 Introduction......Page 152
9.2 Development of BART to Determine Bacterial Activity......Page 153
9.3 BART SetUp......Page 155
9.4 Red Cap: Iron-Related Bacteria ( IRB BART)......Page 157
9.4.1 Qualitative Interpretation of IR B Reaction Patterns......Page 158
9.5 Black Cap: Sulfate-Reducing Bacteria ( SRB BART)......Page 160
9.6 Lime Green Cap: Slime-Forming Bacteria ( SLYM BART)......Page 162
9.7 Dark Blue Cap: Heterotrophic Bacteria ( HAB BART)......Page 164
9.8 Grey Cap: Denitrifying Bacteria ( DN BART)......Page 165
9.9 White Cap: Nitrifying Bacteria ( N BART)......Page 166
9.10 Purple Cap: Acid- Producing Bacteria ( APB BART)......Page 168
9.11 Yellow Cap: Fluorescent Pseudomonad Bacteria ( FLOR BART)......Page 169
9.12.1 Comparison of BART, HPC, and ATP......Page 170
9.12.3 Comparison of BART and Other Microbiological Tests......Page 171
10.2 Differentiation of Grid At las into Six Major Consormial Groups......Page 174
10.3 Alpha One: Bionucleating Disp ersed Consorms......Page 175
10.4 Alpha Two: Organic Bionucleating Consorms......Page 178
10.5 Alpha Three: Inorganic Bioconcreting Consorms......Page 182
10.6 Alpha Four: Carbon Reducing Consorms......Page 184
10.7 Alpha Five: Carbon Oxidizing Consorms......Page 187
10.9 Differentiation of Major Consorms by Grid Positions and BART Reactions......Page 189
11.1 Introduction......Page 204
11.3 Limitations of Animal Habitats on Gridded At las......Page 207
11.4 Limitations of Plant Habitats on Gridded At las......Page 208
11.6 Dominant Microbiological Eukaryotic Domains......Page 210
11.7 Bacterial Consorms Associated with Plant Activities......Page 212
11.8 Bacterial Consorms Associated with Non- Herbivoral Intest inal Streaming......Page 214
11.9 Bacterial Consorms Involved in Spoilage of Foods......Page 216
11.10 Mammalian Consormial Non-Enteric Pathogens on Gridded Atlas......Page 218
11.11 Bacterial Consorms Associated with Water Quality Issues......Page 219
11.12 Bacterial Consorms Involved in Oil, Gas, and Coal Production in Geological Media......Page 220
11.13 Bacterial Consormial Interceptors in Upward Migration of Hydrocarbons......Page 221
11.14 Bacterial Intercept ion of Groundwater Flows in Porous and Fractured Media......Page 222
12.2 1, 22- 03 CLD ( Clouds)......Page 226
12.3 1, 16- 12 ICE ( Ice)......Page 228
12.4 3, 18- 25 CCR ( Concretions)......Page 229
12.5 3, 18- 19 OCR ( Ochres)......Page 230
12.6 3, 06- 24 PTG ( Pitt ing)......Page 235
12.7 3, 03- 19 PFR ( Perforation)......Page 238
12.8 2, 09- 15 MIC ( Microbiologically Influenced Corrosion)......Page 240
12.9 3, 10- 21 BPL ( Black Plug Layers)......Page 243
12.10 3, 10- 27 BBR (" Blueberries")......Page 245
12.11 3, 19- 26 RST ( Rust icles)......Page 246
12.12 1, 19- 06 FOM ( Foam)......Page 248
12.14 3, 18- 14 LSL ( Lateral Slime Layer)......Page 250
12.15 5. 15- 10 GHY ( Gas Hydrates)......Page 251
12.16 Culturing Bacterial Consorms......Page 252
12.17 Rehabilitation......Page 254
12.18 Monitoring Methodologies......Page 258
Suggestions for Further Reading......Page 264
Appendix: Alpha Two TraditionalAtlas Concept......Page 268
Index......Page 318
Back Page......Page 325