| |
| |
| Preface | |
| |
| |
| Acknowledgments | |
| |
| |
| |
| Overview of Microbiology | |
| |
| |
| |
| History, Geology, and Microbiology | |
| |
| |
| |
| Geology--An Observational Science | |
| |
| |
| |
| Microbiology--An Experimental Science | |
| |
| |
| |
| Ground-Water Chemistry and Subsurface Microbiology | |
| |
| |
| |
| Subsurface Microbiology and the Geosciences | |
| |
| |
| |
| Subsurface Microbiology and Microbial Ecology | |
| |
| |
| |
| Subsurface Microbiology and Contaminant Biodegradation | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Microorganisms Present in the Ground-Water Environment | |
| |
| |
| |
| The Bacteria | |
| |
| |
| |
| The Eucarya | |
| |
| |
| |
| Eucaryotes in Ground-Water Systems | |
| |
| |
| |
| The Archaea | |
| |
| |
| |
| The Viruses | |
| |
| |
| |
| Viral Ecology | |
| |
| |
| |
| Viruses in Ground-Water Systems | |
| |
| |
| |
| Bacteria in Ground-Water Systems | |
| |
| |
| |
| Classifying Bacteria | |
| |
| |
| |
| Gram-Negative Bacteria Found in Ground-Water Systems | |
| |
| |
| |
| Gram-Positive Bacteria in Ground-Water Systems | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Bacterial Growth | |
| |
| |
| |
| Bacterial Reproduction | |
| |
| |
| |
| Population Growth Kinetics | |
| |
| |
| |
| Environmental Conditions and Bacterial Growth | |
| |
| |
| |
| Temperature | |
| |
| |
| |
| Water | |
| |
| |
| |
| Molecular Oxygen | |
| |
| |
| |
| pH | |
| |
| |
| |
| Osmotic Pressure | |
| |
| |
| |
| Techniques for Culturing Bacteria | |
| |
| |
| |
| Design of Growth Media | |
| |
| |
| |
| Isolating Bacteria from Environmental Samples | |
| |
| |
| |
| Enumerating Bacteria | |
| |
| |
| |
| Viable Counting Procedures | |
| |
| |
| |
| Direct Counting Procedures | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Bacterial Metabolism | |
| |
| |
| |
| Thermodynamics and Bacterial Metabolism | |
| |
| |
| |
| ATP Synthesis-Storing Energy | |
| |
| |
| |
| Electron Transport Systems--Releasing Energy | |
| |
| |
| |
| Chemiosmosis--Harnessing Energy from Electron Transport | |
| |
| |
| |
| The Role of Enzymes | |
| |
| |
| |
| Energy-Releasing Pathways of Geochemical Importance | |
| |
| |
| |
| Lactate and Acetate Fermentations | |
| |
| |
| |
| Ferredoxins and the Production of Hydrogen and Acetate in Fermentation | |
| |
| |
| |
| Methanogenic Pathways | |
| |
| |
| |
| Sulfate Reduction | |
| |
| |
| |
| Fe(III) Reduction | |
| |
| |
| |
| Nitrate Reduction | |
| |
| |
| |
| Oxygen Reduction--Aerobic Metabolism | |
| |
| |
| |
| Biosynthesis | |
| |
| |
| |
| Amino Acids | |
| |
| |
| |
| Carbohydrates | |
| |
| |
| |
| Lipids | |
| |
| |
| |
| Chemolithotrophy | |
| |
| |
| |
| Hydrogen Oxidizers | |
| |
| |
| |
| Sulfide Oxidizers | |
| |
| |
| |
| Iron Oxidizers | |
| |
| |
| |
| Ammonia-Oxidizing (Nitrifying) Bacteria | |
| |
| |
| |
| Autotrophic CO[subscript 2] Fixation | |
| |
| |
| |
| Metabolic Control of Geochemical Processes | |
| |
| |
| |
| Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Bacterial Genetics | |
| |
| |
| |
| DNA--Its Structure and Organization | |
| |
| |
| |
| RNA--Its Structure and Organization | |
| |
| |
| |
| Transcription | |
| |
| |
| |
| Translation--Making Proteins | |
| |
| |
| |
| Gene Expression and Regulation | |
| |
| |
| |
| Induction | |
| |
| |
| |
| Repression | |
| |
| |
| |
| Mutations | |
| |
| |
| |
| Mutagenic Agents | |
| |
| |
| |
| Transposable Genetic Material | |
| |
| |
| |
| Natural Genetic Exchanges | |
| |
| |
| |
| Recombination | |
| |
| |
| |
| DNA Technology | |
| |
| |
| |
| Analyzing DNA | |
| |
| |
| |
| DNA Cloning | |
| |
| |
| |
| Genetic Engineering | |
| |
| |
| |
| Plasmids | |
| |
| |
| |
| Vectors | |
| |
| |
| |
| Applications of DNA Technology | |
| |
| |
| |
| Insulin Production | |
| |
| |
| |
| Enhanced Biodegradation | |
| |
| |
| |
| DNA Technology in Subsurface Microbiology | |
| |
| |
| |
| Phylogenetic Analysis of Fe(III)-Reducing Bacteria | |
| |
| |
| |
| Using DNA Probes to Find Contaminant-Degrading Microorganisms | |
| |
| |
| |
| Release of Genetically Engineered Microorganisms to the Environment | |
| |
| |
| |
| Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Microbial Ecology of Ground-Water Ststems | |
| |
| |
| |
| Scope of Subsurface Microbial Ecology | |
| |
| |
| |
| Methods in Subsurface Microbial Ecology | |
| |
| |
| |
| Culture Methods | |
| |
| |
| |
| Direct Observation | |
| |
| |
| |
| Phospolipid Fatty Acid Analysis | |
| |
| |
| |
| Activity Measurements in Microcosms | |
| |
| |
| |
| Geochemical Methods | |
| |
| |
| |
| Molecular Microbial Ecology | |
| |
| |
| |
| Microbial Diversity and Niches in Aquifer Systems | |
| |
| |
| |
| Measurement of Diversity | |
| |
| |
| |
| Niches and Sources of Microbial Diversity | |
| |
| |
| |
| Stress and Microbial Diversity | |
| |
| |
| |
| Population Interactions | |
| |
| |
| |
| Neutralism | |
| |
| |
| |
| Commensalism | |
| |
| |
| |
| Synergism and Symbiosis | |
| |
| |
| |
| Competition | |
| |
| |
| |
| Antagonism, Parasitism, and Predation | |
| |
| |
| |
| r and K Strategies in Microbial Ecosystems | |
| |
| |
| |
| r and K Strategies in the Aquifer Environment | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Microbial Processes in Pristine Ground-Water Systems | |
| |
| |
| |
| Abundance and Distribution of Bacteria in the Subsurface | |
| |
| |
| |
| Classification of Subsurface Environments | |
| |
| |
| |
| The Unsaturated Zone | |
| |
| |
| |
| The Unsaturated Zone As a Microbial Habitat | |
| |
| |
| |
| Biomass Measurements in Soil Microbiology | |
| |
| |
| |
| Distribution of Bacteria in the Unsaturated Zone | |
| |
| |
| |
| Local Flow Systems | |
| |
| |
| |
| Local Flow Systems as a Microbial Habitat | |
| |
| |
| |
| Distribution of Bacteria in Local Flow Systems | |
| |
| |
| |
| Intermediate Flow Systems | |
| |
| |
| |
| Intermediate Flow Systems As a Microbial Habitat | |
| |
| |
| |
| Distribution of Bacteria in Intermediate Flow Systems | |
| |
| |
| |
| Microbial Processes in Confining Beds | |
| |
| |
| |
| Regional Flow systems | |
| |
| |
| |
| Early Observations from Petroleum Reservoirs | |
| |
| |
| |
| Distribution of Bacteria in Regional Flow Systems | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Microbiological Sampling of Subsurface Environments | |
| |
| |
| |
| Sampling the Unsaturated Zone | |
| |
| |
| |
| Hand Augering | |
| |
| |
| |
| Air Drilling and Coring | |
| |
| |
| |
| Sampling Local Flow Systems | |
| |
| |
| |
| Split Spoon Sampling | |
| |
| |
| |
| Push-Tube (Shelby Tube) Sampling Methods | |
| |
| |
| |
| Direct Push Sampling | |
| |
| |
| |
| Aseptic Technique with Split-Spoon, Shelby Tube, and Direct Push Sampling | |
| |
| |
| |
| Sampling Intermediate and Regional Systems | |
| |
| |
| |
| Mud Rotary Drilling | |
| |
| |
| |
| Drilling Fluids | |
| |
| |
| |
| Mud-Rotary Coring | |
| |
| |
| |
| Drilling Fluid Contamination of Cored Sediments | |
| |
| |
| |
| Down-Hole Saturation Contamination | |
| |
| |
| |
| Core Seepage Contamination | |
| |
| |
| |
| Core-fracture Contamination | |
| |
| |
| |
| Evaluating Drilling Fluid Contamination | |
| |
| |
| |
| Sampling Ground Water for Microorganisms | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Biogeochemical Cycling in Ground-Water Systems | |
| |
| |
| |
| The Oxygen Cycle | |
| |
| |
| |
| Oxygen Cycling in Ground-Water Systems | |
| |
| |
| |
| The Carbon Cycle | |
| |
| |
| |
| The Integrated Carbon, Oxygen, and Hydrogen Cycles | |
| |
| |
| |
| Carbon Cycling in Ground-Water Systems | |
| |
| |
| |
| The Nitrogen Cycle | |
| |
| |
| |
| Nitrogen Cycling in Ground-Water Systems | |
| |
| |
| |
| The Iron Cycle | |
| |
| |
| |
| Iron Cycling in Aquatic Sediments | |
| |
| |
| |
| Iron Cycling in Ground-Water Systems | |
| |
| |
| |
| The Sulfur Cycle | |
| |
| |
| |
| Sulfur Cycling in Ground-Water Systems | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Oxidation-Reduction Processes in Ground-Water Systems | |
| |
| |
| |
| Overview of Redox Geochemistry | |
| |
| |
| |
| The Equilibrium Approach | |
| |
| |
| |
| The Kinetic Approach | |
| |
| |
| |
| Redox Processes in Ground-Water Systems | |
| |
| |
| |
| Describing Kinetic Redox Processes in Ground-Water Systems | |
| |
| |
| |
| Identifying Electron Donors | |
| |
| |
| |
| Identifying Electron Acceptors | |
| |
| |
| |
| Identifying Terminal Electron-Accepting Processes (TEAPs) in the Environment | |
| |
| |
| |
| Redox Zonation in Aquatic Sediments | |
| |
| |
| |
| Redox Zonation in Ground-Water Systems | |
| |
| |
| |
| Redox Processes in Pristine Ground-Water Systems | |
| |
| |
| |
| Black Creek Aquifer of South Carolina | |
| |
| |
| |
| Floridan Aquifer of Georgia | |
| |
| |
| |
| Redox Processes in Contaminated Ground-Water Systems | |
| |
| |
| |
| A Petroleum Hydrocarbon-Contaminated Aquifer, Charleston, South Carolina | |
| |
| |
| |
| A Mixed Petroleum Hydrocarbon/Chlorinated Solvent-Contaminated Aquifer, Plattsburgh, New York | |
| |
| |
| |
| Complications Associated with Small-Scale Redox Zones | |
| |
| |
| |
| Kinetic Modeling of Redox Processes | |
| |
| |
| |
| Electron Flow in Ground-Water Systems | |
| |
| |
| |
| Developing Kinetic Models of Microbial Redox Processes | |
| |
| |
| |
| Chapter Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Microbial Processes in Contaminated Ground-Water Systems | |
| |
| |
| |
| Microbial Acclimation to Ground-Water Contamination | |
| |
| |
| |
| Microbial Response to Environmental Changes | |
| |
| |
| |
| Mechanisms of Acclimation | |
| |
| |
| |
| Induction | |
| |
| |
| |
| Catabolite Repression | |
| |
| |
| |
| Genetic Mutations | |
| |
| |
| |
| Acclimation to Available Electron Acceptors | |
| |
| |
| |
| Production of Proteins in Response to Chemical Stresses | |
| |
| |
| |
| Factors Affecting Microbial Acclimation | |
| |
| |
| |
| Rates of Acclimation | |
| |
| |
| |
| Concentration Effects | |
| |
| |
| |
| Cross-Acclimation of Xenobiotic Compounds | |
| |
| |
| |
| Chemical Structure of Xenobiotics | |
| |
| |
| |
| Acclimation to Xenobiotics in Ground-Water Systems | |
| |
| |
| |
| Acclimation Response in a Contaminated Aquifer | |
| |
| |
| |
| Acclimation Response in Pristine Aquifer Sediments | |
| |
| |
| |
| Acclimation of Eucaryotic Microorganisms | |
| |
| |
| |
| Acclimation in Bioremediation Technology | |
| |
| |
| |
| Acclimation to Metal Toxicity | |
| |
| |
| |
| Metal Detoxification Mechanisms | |
| |
| |
| |
| Plasmid-Encoded Metal Resistance Mechanisms | |
| |
| |
| |
| Acclimation to Mercury Toxicity | |
| |
| |
| |
| Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Biodegradation and Bioremediation of Petroleum Hydrocarbons in Ground-Water Systems | |
| |
| |
| |
| Composition of Crude Oil | |
| |
| |
| |
| Petroleum Refining and Fuel Blending | |
| |
| |
| |
| Movement and Separation of Petroleum Hydrocarbons in Ground-Water Systems | |
| |
| |
| |
| Density-Driven Migration of Hydrocarbons | |
| |
| |
| |
| Solubility and Hydrocarbon Separation in Ground-Water Systems | |
| |
| |
| |
| Microbial Degradation of Aliphatic Hydrocarbons | |
| |
| |
| |
| Methane Oxidation | |
| |
| |
| |
| Oxidation of n-alkanes | |
| |
| |
| |
| Alkene Oxidation and Reduction | |
| |
| |
| |
| Branched Aliphatics | |
| |
| |
| |
| Microbial Degradation of Alicyclic Hydrocarbons | |
| |
| |
| |
| Pathways for Cyclohexanol Degradation | |
| |
| |
| |
| Microbial Degradation of Aromatic Hydrocarbons | |
| |
| |
| |
| Benzene Degradation | |
| |
| |
| |
| Degradation of Alkyl Benzenes | |
| |
| |
| |
| Degradation of Polycyclic Aromatic Compounds | |
| |
| |
| |
| Anaerobic Degradation of Aromatic Hydrocarbons | |
| |
| |
| |
| Biodegradation of Alkyl Ethers | |
| |
| |
| |
| Microbial Degradation of Petroleum Hydrocarbons in Ground-Water Systems | |
| |
| |
| |
| Aerobic Degradation of BTX Compounds | |
| |
| |
| |
| Anaerobic Degradation of BTEX Compounds | |
| |
| |
| |
| Bioremediation of Petroleum Hydrocarbon Contamination in Ground-Water Systems | |
| |
| |
| |
| Marine Oil Spills and the Biodegradation of Petroleum Hydrocarbons | |
| |
| |
| |
| Microbial Degradation Processes in Shallow Water Table Aquifers | |
| |
| |
| |
| Engineered Bioremediation of Petroleum Hydrocarbons in Ground-Water Systems | |
| |
| |
| |
| Monitored Natural Attenuation of Petroleum Hydrocarbons | |
| |
| |
| |
| Estimating Biodegradation Rates in Ground-Water Systems | |
| |
| |
| |
| Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| |
| Biodegradation and Bioremediation of Halogenated Organic Compounds in Ground-Water Systems | |
| |
| |
| |
| Chemistry and Uses of Halogenated Organic Compounds | |
| |
| |
| |
| Aliphatic Compounds | |
| |
| |
| |
| Monocyclic Aromatic Compounds | |
| |
| |
| |
| Polychlorinated Biphenols | |
| |
| |
| |
| Organochlorine Insecticides | |
| |
| |
| |
| Chlorinated Herbicides | |
| |
| |
| |
| Chlorinated Phenols | |
| |
| |
| |
| Microbial Degradation of Halogenated Organic Compounds | |
| |
| |
| |
| Chlorinated Ethenes | |
| |
| |
| |
| Chlorinated Benzenes | |
| |
| |
| |
| Polychlorinated Biphenyls | |
| |
| |
| |
| Organochlorine Insecticides | |
| |
| |
| |
| Chlorinated Herbicides | |
| |
| |
| |
| Chlorinated Phenols | |
| |
| |
| |
| Biodegradation of Halogenated Organic Compounds in Ground-Water Systems | |
| |
| |
| |
| Reductive and Oxidative Biodegradation Patterns for Chlorinated Ethenes | |
| |
| |
| |
| Cometabolic Degradation of Chlorinated Ethenes | |
| |
| |
| |
| Degradation Patterns of Alkyl Halide Insecticides | |
| |
| |
| |
| Degradation Patterns of Chlorobenzenes | |
| |
| |
| |
| Degradation of Chlorinated Herbicides | |
| |
| |
| |
| Degradation of Chlorophenolic Compounds | |
| |
| |
| |
| Summary | |
| |
| |
| Questions to Consider | |
| |
| |
| References | |
| |
| |
| Index | |