Geomicrobiology: Molecular and Environmental Perspective (eBook)

Preface 6
Contents 8
List of Authors 10
Chapter 1: Chemoautotrophic Origin of Life: The Iron–Sulfur World Hypothesis 16
Introduction 16
Retrodicting the Origin from the Chemical Elements of Life 18
On the Minimal Organization of the Pioneer Organism 21
Metabolic Reproduction and Evolution of the Pioneer Organism 23
Volcanic Flow Setting of the Pioneer Organism 26
Experimental Synthetic Reactions 30
Activated Acetic Acid Thioester 30
Pathways to a-Hydroxy Acids and a-Amino Acids 31
Activation of a-Amino Acids and Peptide Cycle 31
Emergence of the Genetic Machinery and Enzymatization of the Metabolism 32
Cellularization 34
Inorganic Cells? 34
Lipid Synthesis 35
Surface Lipophilization 36
Semi-cellular Structures 38
Origin of Chemiosmosis 38
Pre-cells and the Dawn of Speciation 39
Divergence of the Domains Bacteria and Archaea 42
Divergence of the Domain Eukarya 45
Natural-Historic Considerations 46
References 47
Chapter 2: Evolution of Metabolic Pathways and Evolution of Genomes 51
The Microbial Role in Geochemistry 51
Origin and Evolution of Metabolic Pathways 55
From Ancestral to Extant Genomes 55
The Primordial Metabolism 56
The Role of Duplication and Fusion of DNA Sequences in the Evolution of Metabolic Pathways in the Early Cells 57
The Starter Types 57
The Explosive Expansion of Metabolism in the Early Cells 57
Gene Duplication 57
Fate of Duplicated Genes 58
Gene Fusion 59
Hypotheses on the Origin and Evolution of Metabolic Pathways 60
The Retrograde Hypothesis 60
The Patchwork Hypothesis 61
The Role of Horizontal Gene Transfer in the Evolution of Genomes and Spreading of Metabolic Functions 62
The Nitrogen Cycle 63
Nitrification 64
Denitrification 65
Anaerobic Ammonia Oxidation (ANAMMOX) 65
Ammonification 65
Nitrogen Fixation: A Paradigm for the Evolution of Metabolic Pathways 65
Is Nitrogen Fixation an Ancestral Character? 67
How Many Genes were Involved in the Ancestral Nitrogen Fixation? 68
How Did the nif Genes Originate and Evolve? 68
Which were the Molecular Mechanisms Involved in the Spreading of Nitrogen Fixation? 75
Conclusions 77
References 79
Chapter 3: Novel Cultivation Strategies for Environmentally Important Microorganisms 83
The Significance of Culture-Based Approaches 83
Basic Requirements of the Bacterial Cell 84
Principles of the Selective Enrichment 86
Improved Classical and Advanced Cultivation Methods 88
Determining Potential Growth Substrates 88
Mimicking the Chemical Composition in the Natural Environment 90
Effect of Cyclic Adenosine Monophosphate (cAMP) 92
Mimicking the Physical Structure and Heterogeneity of the Natural Environment: Polymer Matrices, Solid Surfaces and Defined Laboratory Gradient Systems 93
Removal of Inhibitors and Avoiding the Formation of Toxic Compounds and Oxygen Radicals 94
Removal or Selective Inhibition of Bacterial Competitors 96
Exploiting Positive Interactions Between Bacteria: Cocultivation and Dialysis Cultures 97
Techniques for the Isolation of Individual Cells 98
References 101
Chapter 4: Environmental Proteomics: Studying Structure and Function of Microbial Communities 104
Introduction 104
Open Questions in Microbial Ecology 104
Historical Retrospective of “Omics” Technologies 105
Environmental Proteomics – A Babylonian Confusion? 107
Potential Applications of Environmental Proteomics 107
State-of-the-Art Proteomics Technologies 108
Sample Preparation 108
Protein/Peptide Separation and Mass Spectrometry Analyses 110
Data Analysis and Protein Identification 111
Data Evaluation 112
Current Environmental Proteomics Studies – Where Are We So Far? 112
Community Proteomics of Marine Symbionts of Riftia pachyptila 112
Whole-Community Proteomics of Richmond Acid Mine Drainage (AMD) Mixed Biofilms 114
Proteome Analyses of Waste Water Treatment Plants and Activated Sludge 114
Community Proteomics of Animal and Human Intestinal Tracts 115
Metaproteome Analyses of Ocean Water 115
Metaproteome Studies of Highly Complex Groundwater and Soil Environments 116
Future Perspectives and Final Remarks 116
Improvements of Mass Spectrometer Sensitivity and Accuracy 117
Quantitative Metaproteomics – Dream or Reality? 117
Final Remarks 118
References 118
Chapter 5: Analysis of Microbial Communities by Functional Gene Arrays 122
Introduction 122
Functional Gene Array Development 123
Comparison of FGA to Other High-Throughput Genomic Technologies 124
Design and Development of Geochip 126
Probe Design 126
Target Preparation 127
Hybridization 128
Image Analysis 128
Data Analysis 129
Important Issues for Microarray Application 130
Application of GeoChip for Microbial Community Analysis 132
Summary 134
References 135
Chapter 6: Probing Identity and Physiology of Uncultured Microorganisms with Isotope Labeling Techniques 140
Introduction 140
The Principle of Substrate-Mediated Isotope Labeling Techniques 141
Community-Wide Screening Approaches 143
Stable Isotope Probing of Phospholipid-Derived Fatty Acids 143
Stable Isotope Probing of Nucleic Acids (DNA/RNA-SIP) 146
Directed Phylogenetic Oligonucleotide Probe-Based Approaches: From Communities to Single Cells 148
What to Keep in Mind When Using rRNA-Targeted Oligonucleotide Probes/Primers 148
The Magnetic Beads-Probe-Based rRNA Capture Approach 149
Sequence Specific Primer Extension RNA Analysis (SeSPERA) 149
Isotope Microarrays 150
Fluorescence In Situ Hybridization Combined with Microautoradiography 151
Fluorescence In situ Hybridization Combined with Raman-Microspectroscopy 152
Whole Cell Hybridization and Secondary Ion Mass Spectrometry 153
Conclusions 154
References 155
Chapter 7: The Geomicrobiology of Arsenic 159
Introduction 159
Arsenic in the Environment 160
Arsenic in Biological Systems 162
Uptake of Arsenic from the Environment 163
Arsenic Tranformation Mechanisms 163
Arsenic Oxidation 163
Arsenic Reduction 165
Methylation 167
Demethylation 168
Applying Molecular and Microbiological Tools to the Study of Microbial Arsenic Transformation 168
Cultivation Methods 169
Culture Independent Methods 169
Functional Gene Detection 170
(Meta)proteomics 171
(Meta)genomics 172
Contributions from the Study of Microbial Arsenic Transformation 173
Biogeochemical Cycling 174
Bioremediation 174
Exobiology 175
Conclusions 175
References 177
Chapter 8: Bioinformatics and Genomics of Iron- and Sulfur-Oxidizing Acidophiles 181
“Omics”, What Does that Mean? 182
Genomics 184
Transcriptomics 185
Proteomics 186
Acidithiobacillus ferrooxidans 186
Genomics 186
Proteomics 187
Transcriptomics 188
Acidithiobacillus thiooxidans and Acidithiobacillus caldus 190
Acidithiobacillus caldus 190
Comparative Genomics Between the Acidithiobacilli 191
Leptospirillum spp. 192
Ferroplasma spp. 193
Metallosphaera sedula 194
Sulfolobus spp. 195
Sulfolobus acidocaldarius 195
Sulfolobus solfataricus 195
Sulfolobus tokodaii 196
From the Microbial Communities to Protein Analysis 196
Conclusion 197
References 198
Chapter 9: The Geomicrobiology of Catastrophe: A Comparison of Microbial Colonization in Post-volcanic and Impact Environments 205
The Geological Context 206
Phototrophs and Endolithic Habitats in the Post-volcanic Environment 208
Culture-Independent Analysis 209
Culture-Dependent Observations on the Phototroph Population in Volcanic Glasses 215
Effects of Position in TAS Diagram on Endolithic Colonization 217
Phototrophs and Endolithic Habitats in the Post-impact Environment 219
Comparison of Endolithic Colonization in the Post-volcanic and Impact Environments 223
Post-volcanic and Impact Succession 225
References 226
Chapter 10: Microbial Diversity of Cave Ecosystems 230
The Karst Habitat 232
Exploration History and Microbiological Methods 233
Distribution of Microbial Groups by Cave Type 235
Natural and Impact-Associated Communities in Epigenic Caves 238
Microbial Communities from Hypogenic Caves 241
The Future of Cave Microbial Diversity Research 243
References 244
Chapter 11: Statistical Evaluation of Bacterial 16S rRNA Gene Sequences in Relation to Travertine Mineral Precipitation and Water Chemistry at Mammoth Hot Springs, Yellowstone National Park, USA 250
Geological Setting of Mammoth Hot Springs 252
Materials and Methods 254
Results 255
Discussion 258
References 259
Chapter 12: Compositional, Physiological and Metabolic Variability in Microbial Communities Associated with Geochemically Diverse, Deep-Sea Hydrothermal Vent Fluids 261
Introduction 261
Method for Thermodynamic Calculation of Available Energy Metabolisms 263
Case Studies 268
Kairei Hydrothermal Field in the Central Indian Ridge (CIR) 268
Geological Settings and Physical–Chemical Characteristics of Hydrothermal Fluids 268
Microbial Communities in the Chimney Structures and the Fluids 270
Thermodynamic Potentials of Various Chemolithotrophic Energy Metabolisms 272
Mariner Hydrothermal Field in the Lau Basin (LB) 274
Geological Settings and Physical–Chemical Characteristics of Hydrothermal Fluids 274
Microbial Communities in the Chimney Structures 275
Thermodynamic Potentials of Various Chemolithotrophic Energy Metabolisms 276
Iheya North Hydrothermal Field in the Okinawa Trough (OT) 278
Geological Settings and Physical–Chemical Characteristics of Hydrothermal Fluids 278
Microbial Communities in the Fluids and Chimney Structures 279
Thermodynamic Potentials of Various Chemolithotrophic Energy Metabolisms 280
TOTO Caldera Field in the Mariana Volcanic Arc (MVA) 282
Geological Settings and Physical–Chemical Characteristics of Hydrothermal Fluids 282
Microbial Community in the Sulfur Chimney 283
Thermodynamic Potentials of Various Chemolithotrophic Energy Metabolisms 284
Inter-Fields Comparison of Variability in Thermodynamic Energy State and Microbial Community 285
Conclusions and Perspectives 289
References 290
Chapter 13: The Molecular Geomicrobiology of Bacterial Manganese(II) Oxidation 294
Introduction 294
Manganese(III,IV) Oxide Formation 295
Bacterial Manganese(II) Oxidation 295
The Molecular Microbiology of Manganese(II) Oxidation 298
Mn(II) Oxidation by Bacillus sp. Strain SG-1 Spores 298
MCO Enzymes Identified as the Mn(II) Oxidase in Other Genera 301
A Calcium-Binding Heme Peroxidase Involved in Mn(II) Oxidation 302
The Mn(II) Oxidase of Pseudomonas putida GB-1 Remains Elusive 304
The Molecular Complexity of Bacterial Mn Oxidation 306
Environmental Perspectives 308
Suboxic Zones of Anoxic and Seasonally Anoxic Basins: Mn(III) Is Important! 308
The Columbia River Estuary: Identification of the Environmental Mn Oxidase 310
Implications and Future Directions 311
References 311
Chapter 14: Role of Microorganisms in Banded Iron Formations 318
Composition, Occurance, and Spatial/Temporal Distribution of BIF’S 318
Mineralogy 318
Tectonic Setting 319
Spatial and Temporal Distribution 320
Microbial and Chemical Processes Generating BIF Source Sediment 320
Oxidation of Fe(II) by Cyanobacterial O2 320
UV-Photooxidation Model 323
Direct Biological Oxidation of Fe2+ by Anoxygenic Phototrophic Fe(II)-Oxidizing Bacteria 324
Post-Depositional Processes (Including Microbial Activity) in BIF 325
Limitation of Microbial Processes in BIF’s by Nutrients and Trace Metals 327
Mechanisms of Altering Iron and Silica Mineral Layering – A Potential Role of Microorganisms? 328
Conclusions 330
References 330
Chapter 15: Synergistic Roles of Microorganisms in Mineral Precipitates Associated with Deep Sea Methane Seeps 334
Methane Production and Methane Hydrate Formation 336
Biogenic Methane Production through Methanogenesis 336
Thermogenic Methane Production 338
Geothermal Methane Production Through Serpentinization of Ultramafic Rocks 338
Methane Hydrate Formation and Dissociation 339
Anaerobic Oxidation of Methane (AOM) at the Sulfate-Methane Transition (SMT) Zone 340
Mineral Precipitates 342
Precipitation of Pyrite and Graphitic Carbon 342
Precipitations of Carbonate Minerals 345
Geological Records and Biosignatures 350
References 351
Chapter 16: Bacterial Degradation of Polychlorinated Biphenyls 356
PCB Biodegradation 357
Anaerobic Degradation of PCB 357
Aerobic Degradation of PCB 364
Concluding Remarks 369
References 370
Chapter 17: Role of Clay and Organic Matter in the Biodegradation of Organics in Soil 376
Soil Contaminant Interactions – Bioavailability and Biodegradation 378
Clays and Clay Minerals 379
Sorption and Desorption Phenomena of Clays and Clay Minerals 381
The Effect of Clays on the Mobility and Activity of Microorgansims in Soil 385
Impact of Clay on Biodegradation 387
Conclusions 389
References 389
Chapter 18: Electrodes as Electron Acceptors, and the Bacteria Who Love Them 394
Is an Electrode a Defined Habitat? 395
What Bacteria Can Use Electrodes as Electron Acceptors? 396
What Does It Take to Use an Electrode? 398
Some Examples of the Relationship Between Potential and Electron Transfer Rates 400
Similarities with the Thermodynamics of Metal Reduction 402
Conclusions 403
References 404
Chapter 19: The Biogeochemistry of Biomining 409
Principles and Practices of Biomining 409
A Brief History of Biomining 414
Geochemical Aspects 415
Mechanisms of Mineral Dissolution 420
Diversity and Interactions of Biomining Microorganisms 423
Bioleaching Microbial Communities 424
Metal Recovery Technologies 428
Challenges and Opportunities 429
Bioleaching Minerals Using Saline and Brackish Waters 429
Bioleaching Chalcopyrite 430
Complex Ores and Mine Wastes 430
Oxidized Ores 431
References 432
Index 435