List of Tables ............................................... xiii
List of Figures ................................................ xv
List of Plates ................................................ xxi
Preface ....................................................... xxv
Acknowledgments .............................................. xxix
Author ....................................................... xxxi
Chapter 1 Bacterial Communities by Location and Function ....... 1
1.1 Introduction to Layering of Bacterial
Communities .................................... 1
1.2 Factors Significantly Influencing Bacterial
Activities and Nutrient Cycles ................. 4
1.3 Bacteria: Human Perspectives ................... 6
Chapter 2 Common Bacteriologically Initiated Events ........... 11
2.1 Historical Overview ........................... 11
2.2 Challenges of Classifying "Unculturables" ..... 13
2.3 Evolutionary Trends toward Bacterial
Diversity ..................................... 14
2.4 Two-Dimensional Grid Definition of Bacterial
Communities ................................... 15
2.5 Establishment of Grid Location Points for
Bacterial Atlas ............................... 20
2.6 Summary of Bacterial Community Grid
Positioning Atlas Principles .................. 21
Chapter 3 Bacteria Are Everywhere: Classification of Alpha
Groups of Bacterial Consorms ........................ 23
3.1 Historical Overview ........................... 23
3.2 Definitions of Alpha-Based Bacterial
Consortia ..................................... 27
3.3 Alpha One: Bionucleating Dispersed Consorms
[FPL (FMV:FCP) 22-04] ......................... 30
3.4 Alpha Two: Organic Bioconcreting Consorms
[FPL (FMV:FCP) 22-16] ......................... 31
3.5 Alpha Three: Inorganic Bioconcreting
Consorms [FPL (FMV:FCP) 13-21] ................ 32
3.6 Alpha Four: Carbon-Reducing Consorms
[FPL (FMV:FCP) 06-27] ......................... 33
3.7 Alpha Five: Carbon-Oxidizing Consorms
[FPL (FMV:FCP) 13-07] ......................... 34
3.8 Alpha Six: Hyperbaric Dispersed Bionucleating
Consorms [FPL (FMV:FCP) 01-03] ................ 34
3.9 Summary ....................................... 35
Chapter 4 Preliminary Differentiation of Alpha Bacterial
Consorms ............................................ 37
4.1 Introduction .................................. 37
4.2 Alpha One: Bionucleating Dispersed Consorms
(FPL 1, 22-04) ................................ 38
4.2.1 Principal Alpha One Consormial
Activities .............................. 38
4.3 Alpha Two: Organic Bionucleating Consorms
(FPL 2, 22-16) ................................ 39
4.3.1 Principal Alpha Two Consormial
Activities .............................. 40
4.4 Alpha Three: Inorganic Bionucleating
Consorms (FPL 3, 13-21) ....................... 44
4.4.1 Principal Alpha Three Consormial
Activities .............................. 45
4.5 Alpha Four: Carbon-Reducing Consorms
(FPL 4, 06-27) ................................ 49
4.5.1 Principal Alpha Four Consormial
Activities .............................. 50
4.6 Alpha Five: Carbon-Oxidizing Consorms
(FPL 5, 13-07) ................................ 52
4.6.1 Principal Alpha Five Consormial
Activities .............................. 52
4.7 Alpha Six: Hyperbaric Dispersed
Bionucleating Consorms (FPL 6,01-03) .......... 53
Chapter 5 Environmental Dynamics of Bacterial Consorms ........ 55
5.1 Introduction .................................. 55
5.2 Defining Bacteriologically Dominated
Consorms ...................................... 56
5.3 Categorization of Consorms .................... 57
5.3.1 Location within Environment ............. 58
5.3.2 Generated Colors ........................ 59
5.3.3 Texture and Porosity .................... 62
5.3.4 Inorganic and Organic Chemistry ......... 64
5.3.5 Water Form and Content .................. 66
5.3.6 Odors Emanating from Consorms ........... 66
5.3.7 Identification of Recovered Bacterial
Consorms ................................ 67
5.3.8 Time-Scaled Maturation .................. 68
Chapter 6 Bacterial Consormial Challenges ..................... 71
6.1 Introduction .................................. 71
6.2 Identification of Consorms .................... 72
6.3 Determining Probability of Consormial
Activity ...................................... 73
6.4 Symptoms of Consormial Intrusions ............. 77
6.5 Quantification of Consormial Intrusions into
Environment ................................... 78
6.6 Causes and Effects of Consorm Intrusions in
Impacted Environment .......................... 79
6.7 Consorm Sampling Protocols .................... 83
Chapter 7 Detailed Identification of Bacterial Consorms ....... 85
7.1 Introduction .................................. 85
7.2 Defining Bacterial Consorms by Form,
Function, and Habitat ......................... 86
1, 22-03 CLD (Clouds) ......................... 88
1, 17-15 CMT (Comets) ......................... 88
1, 19-06 FOM (Foam) ........................... 88
1, 16-12 ICE (Ice) ............................ 89
1, 16-03 LNG (Lightning) ...................... 89
1, 19-12 SNO (Snow) ........................... 89
2, 12-17 ABS (Abscesses) ...................... 90
2, 13-10 BOL (Boils) .......................... 90
2, 19-07 BCH (Bronchitis) ..................... 90
2, 08-20 CBC (Carbuncles) ..................... 91
2, 11-14 CCD (Carietic Condition) ............. 91
2, 15-07 CLS (Cloudiness) ..................... 91
2, 11-18 CHR (Cholera) ........................ 92
2, 16-13 CLB (Coliform Bacteria) .............. 92
2, 15-18 CLW (Colloidal Water) ................ 92
2, 18-13 DRR (Diarrhea) ....................... 93
2, 10-12 FCB (Fecal Coliform Bacteria) ........ 93
2, 07-23 FEC (Feces) .......................... 93
2, 10-08 KDS (Kidney Stones) .................. 93
2, 22-12 LMN (Luminescent Bacteria) ........... 94
2, 09-15 MIC (Microbiologically Influenced
Corrosion) ....................... 94
2, 18-16 NCR (Necrosis) ....................... 95
2, 22-21 PMP (Pimples) ........................ 95
2, 19-21 PLG (Plugging) ....................... 95
2, 23-14 PEY (Pink Eye) ....................... 96
2, 16-18 PUS (Pus) ............................ 96
2, 06-18 ROE (Rotten Eggs) .................... 96
2, 14-15 ROT (Rotting) ........................ 97
2, 16-21 RZZ (Rhizosphere) .................... 97
2, 22-07 SHN (Sheen) .......................... 97
2, 23-21 SKN (Skin) ........................... 98
2, 11-16 SLT (Silt) ........................... 98
2, 21-22 SLM (Slime) .......................... 98
2, 24-13 TCT (Thatch) ......................... 98
2, 15-13 TBD (Turbidity) ...................... 99
2, 07-20 ULC (Ulcers) ......................... 99
2, 12-07 URN (Urinary Tract Infections) ...... 100
2, 12-13 WLT (Wilt) .......................... 100
3, 10-21 BPL (Black Plug Layer) .............. 100
3, 10-27 BBR (Blueberries) ................... 101
3, 03-16 BWR (Black Water) ................... 101
3, 19-03 CRB (Carbonates) .................... 101
3, 05-27 CGG (Clogging) ...................... 102
3, 06-16 CRS (Corrosion) ..................... 102
3, 18-25 CCR (Concretions) ................... 103
3, 20-28 FRD (Ferric-Rich Deposits) .......... 103
3, 22-18 IPN (Iron Pan) ...................... 104
3, 18-14 LSL (Lateral Slime Layer) ........... 104
3, 15-28 MGN (Manganese Nodules) ............. 104
3, 18-19 OCR (Ochres) ........................ 105
3, 10-30 PGI (Pig Iron) ...................... 105
3, 03-19 PFR (Perforation) ................... 106
3, 06-24 PTG (Pitting) ....................... 106
3, 19-21 PLG (Plugging) ...................... 106
3, 19-26 RST(Rusticles) ...................... 108
3, 10-10 SBL (Sand Boils) .................... 108
3, 15-17 TCL (Tubercles) ..................... 109
4, 05-25 BAP (Black Asphaltene-Rich Plugs) ... 110
4, 04-20 CDR (Carbon Dioxide Reducers) ....... 110
4, 05-17 COL (Coal)* ......................... 111
4, 06-22 BNG (Biogenic Natural Gas) .......... 111
4, 03-13 BSR (Black Smokers) ................. 112
4, 01-28 OIL (Oil) ........................... 112
4, 07-19 PET (Peat) .......................... 113
5, 15-I0GHY (Gas Hydrates) ................... 114
Chapter 8 Biochemical Methods for Identification of
Consorms ........................................... 115
8.1 Introduction ................................. 115
8.2 Determination of Consormial Activity by ATP
Analysis ..................................... 115
8.3 RASI Protocol for Determining Potential ATP
Activity ..................................... 117
8.3.1 Differentiation of RASI Procedures ..... 119
8.3.2 RASI-MIDI Protocols for Identifying
Bacterial Consorms ..................... 120
Chapter 9 Identifying Bacterial Consorms Using BART .......... 123
9.1 Introduction ................................. 123
9.2 Development of BART to Determine Bacterial
Activity ..................................... 124
9.3 BART Setup ................................... 126
9.4 Red Cap: Iron-Related Bacteria (IRB BART) .... 128
9.4.1 Qualitative Interpretation of IRB
Reaction Patterns ...................... 129
9.5 Black Cap: Sulfate-Reducing Bacteria
(SRB BART) ................................... 131
9.6 Lime Green Cap: Slime-Forming Bacteria
(SLYM BART)................................... 133
9.7 Dark Blue Cap: Heterotrophic Bacteria
(HAB BART) ................................... 135
9.8 Grey Cap: Denitrifying Bacteria (DN BART) .... 136
9.9 White Cap: Nitrifying Bacteria (N BART) ...... 137
9.10 Purple Cap: Acid-Producing Bacteria
(APB BART) ................................... 139
9.11 Yellow Cap: Fluorescent Pseudomonad
Bacteria (FLOR BART) ......................... 140
9.12 Comparison of BART and Other
Bacteriological Enumeration Methods .......... 141
9.12.1 Comparison of BART, HPC, and ATP ...... 141
9.12.2 Environmental Technology
Verification (Canada) ................. 142
9.12.3 Comparison of BART and Other
Microbiological Tests ................. 142
Chapter 10 Introduction to Grid-Formatted Bacteriological
Atlas .............................................. 145
10.1 Focal Point Locations for Bacterial
Consorms ..................................... 145
10.2 Differentiation of Grid Atlas into Six
Major Consormial Groups ...................... 145
10.3 Alpha One: Bionucleating Dispersed
Consorms ..................................... 146
10.4 Alpha Two: Organic Bionucleating Consorms .... 149
10.5 Alpha Three: Inorganic Bioconcreting
Consorms ..................................... 153
10.6 Alpha Four: Carbon Reducing Consorms ......... 155
10.7 Alpha Five: Carbon Oxidizing Consorms ........ 158
10.8 Alpha Six: Hyperbaric Dispersed
Bionucleating Consorms ....................... 160
10.9 Differentiation of Major Consorms by Grid
Positions and BART Reactions ................. 160
Chapter 11 Defining Bacterial Consorms in Gridded Atlas
Format ............................................. 175
11.1 Introduction ................................. 175
11.2 Basic fmv: fcP Grid .......................... 178
11.3 Limitations of Animal Habitats on Gridded
Atlas ........................................ 178
11.4 Limitations of Plant Habitats on Gridded
Atlas ........................................ 179
11.5 Dominant Prokaryotic Consormial Domains ...... 181
11.6 Dominant Microbiological Eukaryotic
Domains ...................................... 181
11.7 Bacterial Consorms Associated with Plant
Activities ................................... 183
11.8 Bacterial Consorms Associated with
Non-Herbivoral Intestinal Streaming .......... 185
11.9 Bacterial Consorms Involved in Spoilage of
Foods ........................................ 187
11.10 Mammalian Consormial Non-Enteric Pathogens
on Gridded Atlas ............................. 189
11.11 Bacterial Consorms Associated with Water
Quality Issues ............................... 190
11.12 Bacterial Consorms Involved in Oil, Gas,
and Coal Production in Geological Media ...... 191
11.13 Bacterial Consormial Interceptors in Upward
Migration of Hydrocarbons .................... 192
11.14 Bacterial Interception of Groundwater Flows
in Porous and Fractured Media ................ 193
Chapter 12 Natural Bacteriological Consorms ................... 197
12.1 Introduction ................................. 197
12.2 1, 22-03 CLD (Clouds) ........................ 197
12.3 1, 16-12 ICE (Ice) ........................... 199
12.4 3, 18-25 CCR (Concretions) ................... 200
12.5 3, 18-19 OCR (Ochres) ........................ 201
12.6 3, 06-24 PTG (Pitting) ....................... 206
12.7 3, 03-19 PFR (Perforation) ................... 209
12.8 2, 09-15 MIC (Microbiologically Influenced
Corrosion) ..................... 211
12.9 3, 10-21 BPL (Black Plug Layers) ............. 214
12.10 3, 10-27 BBR ("Blueberries") ................. 216
12.11 3, 19-26 RST (Rusticles) ..................... 217
12.12 1, 19-06 FOM (Foam) .......................... 219
12.13 3, 15-17 TCL (Tubercles) ..................... 221
12.14 3, 18-14 LSL (Lateral Slime Layer) ........... 221
12.15 5, 15-10 GHY (Gas Hydrates) .................. 222
12.16 Culturing Bacterial Consorms ................. 223
12.17 Rehabilitation ............................... 225
12.18 Monitoring Methodologies ..................... 229
Suggestions for Further Reading ............................... 235
Appendix Alpha Two Traditional Atlas Concept ................ 239
Index ......................................................... 289
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