GROUND-WATER MICROBIOLOGY AND GEOCHEMISTRY

Transcription

1 J8Q5-900 GROUND-WATER MICROBIOLOGY AND GEOCHEMISTRY Second Edition Francis H. Chapelle United States Geological Survey JOHN WILEY & SONS, INC. New York / Chichester / Weinheim / Brisbane / Singapore / Toronto

2 CONTENTS Preface Acknowledgments xv xvii I. OVERVIEW OF MICROBIOLOGY 1 1. 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 / 30 Questions to Consider / MICROORGANISMS PRESENT IN THE GROUND-WATER ENVIRONMENT The Bacteria / 33

3 Vi CONTENTS 2.2 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 / 56 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 / 80 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 / 88

4 CONTENTS Vii 4.6 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(m) 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 2 Fixation / Metabolic Control of Geochemical Processes / Summary / 114 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 / 137

5 ViM CONTENTS 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 / 147 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 / 183 Questions to Consider / 184

6 CONTENTS ix II. 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 Row Systems / Chapter Summary / 221 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 / 231

7 X CONTENTS 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 / 247 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 / 280 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 / 295

8 CONTENTS Xi 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 / 319 Questions to Consider / 319 III. 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 / 338

9 Xii CONTENTS 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 / 346 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 / 360, 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 / 378

10 CONTENTS Xiii 12.8 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 / 401 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 / 438

11 XiV CONTENTS Degradation of Chlorinated Herbicides / Degradation of Chlorophenolic Compounds / Summary / 443 Questions to Consider / 444 References 446 Index 469