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Ground-Water Microbiology
and Geochemistry
Table of Contents
Preface
Acknowledgements
Part I.- Overview of Microbiology
Chapter 1.-- History, Geology, and Microbiology
1.1 Geology--An Observational Science
1.2 Microbiology--An Experimental Science
1.3 Ground-Water Chemistry and Subsurface Microbiology
1.3.1 Subsurface Microbiology and the Geosciences
1.3.2 Subsurface Microbiology and Microbial Ecology
1.3.3 Subsurface Microbiology and Contaminant Biodegradation
1.4 Chapter Summary
Questions to Consider
Chapter 2.-- Microorganisms Present in The Ground-water Environment
2.1 The Bacteria
2.2 The Eucarya
2.2.1 Eucaryotes in Ground-Water Systems
Giardia and Cryptosporidium
2.3 The Archaea
2.4 The Viruses
2.4.1 Viral Ecology
2.4.2 Viruses in Ground-Water Systems
2.5 Bacteria in Ground-Water Systems
2.5.1 Classifying Bacteria
Criteria Used to Classify Bacteria
2.5.2 Gram-Negative Bacteria Found in Ground-Water Systems
Aerobic Gram-Negative Rods
Aerobic Gram-Negative Cocci
Facultatively Anaerobic Gram-Negative Rods
Anaerobic Gram-Negative Rods
2.5.3 Gram-Positive Bacteria in Ground-Water Systems
Coryneform Bacteria
Spore-Forming Rods
2.6 Chapter Summary
Questions to Consider
Chapter 3.--Bacterial Growth
3.1 Bacterial Reproduction
3.2 Population Growth Kinetics
3.3 Environmental Conditions and Bacterial Growth
3.3.1 Temperature
3.3.2 Water
3.3.3 Molecular Oxygen
3.3.4 pH
3.3.5 Osmotic Pressure
3.4 Techniques for Culturing Bacteria
3.4.1 Design of Growth Media
Carbon Sources
Nitrogen Sources
Phosphorus and Inorganic Nutrients
Electron Acceptors
Selective Growth Using Culture Media
3.4.2 Isolating Bacteria from Environmental Samples
Rich Versus Dilute Media
3.5 Enumerating Bacteria
3.5.1 Viable Counting Procedures
3.5.2 Direct Counting Procedures
3.6 Chapter Summary
Questions to Consider
Chapter 4.--Bacterial Metabolism
4.1 Thermodynamics and Bacterial Metabolism
4.2 ATP Synthesis-Storing Energy
4.3 Electron Transport Systems--Releasing Energy
4.4 Chemiosmosis--Harnessing Energy from Electron Transport
4.5 The Role of Enzymes
4.6 Energy-Releasing Pathways of Geochemical Importance
4.6.1 Lactate and Acetate Fermentations
4.6.2 Ferredoxins and the Production of Hydrogen and Acetate in Fermentation
4.6.3 Methanogenic Pathways
4.6.4 Sulfate Reduction
4.6.5 Fe(III) Reduction
4.6.6 Nitrate Reduction
4.6.7 Oxygen Reduction--Aerobic Metabolism
4.7 Biosynthesis
4.7.1 Amino Acids
4.7.2 Carbohydrates
4.7.3 Lipids
4.8 Chemolithotrophy
4.8.1 Hydrogen Oxidizers
4.8.2 Sulfide Oxidizers
4.8.3 Iron Oxidizers
4.8.4 Ammonia Oxidizing (Nitrifying) Bacteria
4.8.5 Autotrophic CO2 Fixation
4.9 Metabolic Control of Geochemical Processes
4.10 Summary
Questions to Consider
Chapter 5 Bacterial Genetics
5.1 DNA--Its Structure and Organization
5.2 RNA--Its Structure and Organization
5.3 Gene Expression and Regulation
5.3.1 Induction
5.3.2 Repression
5.4 Mutations
5.4.1 Mutagenic Agents
5.4.2 Transposable Genetic Material
5.5 Natural Genetic Exchanges
5.5.1 Recombination
Transformation
Transduction
5.6 DNA Technology
5.6.1 Analyzing DNA
Restriction nucleases
Sequencing DNA
Hybridization
5.6.3 DNA Cloning
The Polymerase Chain Reaction
Denaturing Gradient Gel Electrophoresis (DGGE)
5.7 Genetic Engineering
5.7.1 Plasmids
5.7.2 Vectors
Plasmid vectors
Phage vectors
5.8 Applications of DNA Technology
5.8.1 Insulin Production
5.8.2 Enhanced Biodegradation
Aliphatic Petroleum Hydrocarbons
Aromatic Hydrocarbons
5.9 DNA Technology in Subsurface Microbiology
5.9.1 Phylogenetic Analysis of Fe(III)-reducing Bacteria
5.9.2 Using DNA Probes to Find Contaminant-Degrading Microorganisms
5.9.3 Release of Genetically Engineered Microorganisms to the Environment
5.10 Summary
Questions to Consider
Chapter 6 Microbial Ecology of Ground-water Systems
6.1 Scope of Subsurface Microbial Ecology
6.2 Methods in Subsurface Microbial Ecology
6.2.1 Culture Methods
6.2.2 Direct Observation
6.2.3 Phospolipid Fatty Acid Analysis
6.2.4 Activity Measurements in Microcosms
6.2.5 Geochemical Methods
6.2.6 Molecular Microbial Ecology
6.3 Microbial Diversity and Niches in Aquifer Systems
6.3.1 Measurement of Diversity
6.3.2 Niches and Sources of Microbial Diversity
6.3.3 Stress and Microbial Diversity
6.4 Population Interactions
6.4.1 Neutralism
6.4.2 Commensalism
6.4.3 Synergism and Symbiosis
6.4.4 Competition
6.4.5 Antagonism, Parasitism, and Predation
6.5 r and K Strategies in Microbial Ecosystems
6.5.1 r and K Strategies in the Aquifer Environment
6.6 Chapter Summary
Questions to Consider
Chapter 7 Abundance And Distribution of Bacteria in The Subsurface
7.1 Classification of Subsurface Environments
7.2 The Unsaturated Zone
7.2.1 The Unsaturated Zone as a Microbial Habitat
Moisture and Gas Content
7.2.2 Biomass Measurements in Soil Microbiology
Direct Microscopy
Chemical Techniques
Activity Measurements
Other Measures of Biomass and Activity
7.2.3 Distribution of Bacteria in the Unsaturated Zone
The Soil Zone
The Intermediate Unsaturated Zone
The Deep Unsaturated Zone
7.3 Local Flow Systems
7.3.1 Local Flow Systems as a Microbial Habitat
7.3.2 Distribution of Bacteria in Local Flow Systems
7.4 Intermediate Flow Systems
7.4.1 Intermediate Flow Systems as a Microbial Habitat
7.4.2 Distribution of Bacteria in Intermediate Flow Systems
7.4.3 Microbial Processes in Confining Beds
7.5 Regional Flow systems
7.5.1 Early Observations from Petroleum Reservoirs
7.5.2 Distribution of Bacteria in Regional Flow Systems
Culture Techniques
Geochemical Methods
Molecular Methods
7.7 Chapter Summary
Chapter 8 Microbiological Sampling of Subsurface Environments
8.1 Sampling the Unsaturated Zone
8.1.1 Hand Augering
8.1.2 Air Drilling and Coring
8.2 Sampling Local Flow Systems
8.2.1 Split Spoon Sampling
8.2.2 Push-tube (Shelby tube) sampling methods
8.2.3 Direct Push Sampling
8.2.4 Aseptic Technique With Split-spoon, Shelby Tube, and Direct Push Sampling
Tool Contamination
Down-hole Contamination
8.3 Sampling Intermediate and Regional Systems
8.3.1 Mud Rotary Drilling
8.3.2 Drilling Fluids
Density
Viscosity
Yield Point
Gel Strength
Fluid-loss control
Lubricity
8.3.3 Mud-Rotary Coring
Equipment Used for Mud-Rotary Coring
The Role of the Driller
Drilling Fluid Technology and Coring
8.4 Drilling-fluid Contamination of Cored Sediments
8.4.1 Downhole Saturation Contamination
8.4.2 Core Seepage contamination
8.4.3 Core-fracture Contamination
8.4.4 Evaluating Drilling Fluid Contamination
Drilling Fluid as a Tracer
Chemical Additive Tracers
Particulate Tracers
Biological Tracers
8.5 Sampling Ground Water for Microorganisms
8.6 Chapter Summary
Questions to Consider
Chapter 9 Biogeochemical Cycling in Ground-water Systems
9.1 The Oxygen Cycle
9.1.1 Oxygen Cycling in Ground-Water Systems
9.2 The Carbon Cycle
9.2.1 The Integrated Carbon, Oxygen, and Hydrogen Cycles
9.2.2 Carbon Cycling in Ground-Water Systems
Local Flow Systems
9.3 The Nitrogen Cycle
9.3.1 Nitrogen Cycling in Ground Water Systems
Animal Excrement and Manures
Sewage Effluents
Nitrogen Fertilizers
Municipal Wastes
Distinguishing Sources of Nitrogen Contamination
Nitrate Accumulation Due to Dry-land Farming Practices
9.4 The Iron Cycle
9.4.1 Iron Cycling in Aquatic Sediments
9.4.2 Iron Cycling in Ground-Water Systems
Wells and Iron-Oxidizing Bacteria
High-Iron Concentrations in Ground Water
9.5 The Sulfur Cycle
9.5.1 Sulfur Cycling in Ground-Water Systems
Sulfide Oxidation in an Oxygenated Aquifer
Sulfate Reduction in Sulfate Mineral-Free Aquifers
Sulfate Reduction in Sulfate Mineral-Bearing Aquifers
9.6 Chapter Summary
Questions to Consider
Chapter 10 Oxidation-reduction Processes in Ground-water Systems
10.1 Overview of Redox Geochemistry
10.1.1 The Equilibrium Approach
10.1.2 The Kinetic Approach
10.1.3 Redox Processes in Ground-Water Systems
10.2 Describing Kinetic Redox Processes in Ground-Water Systems
10.2.1 Identifying Electron Donors
10.2.2 Identifying Electron Acceptors
Microbial Ecology and Competitive Exclusion
10.3 Identifying Terminal Electron-Accepting Processes (TEAPs) in the Environment
10.3.1 Redox Zonation in Aquatic Sediments
10.3.2 Redox Zonation in Ground-Water Systems
10.4 Redox Processes in Pristine Ground-Water Systems
10.4.1 Black Creek Aquifer of South Carolina
10.4.2 Floridan Aquifer of Georgia
10.5 Redox Processes in Contaminated Ground-Water Systems
10.5.1 A Petroleum Hydrocarbon-Contaminated Aquifer, Charleston, South Carolina
10.5.2 A Mixed Petroleum Hydrocarbon/Chlorinated Solvent-Contaminated Aquifer, Plattsburgh, New York
10.5.3 Complications Associated With Small-Scale Redox Zones
10.6 Kinetic Modeling of Redox Processes
10.6.1 Electron Flow in Ground-Water Systems
10.6.2 Developing Kinetic Models of Microbial Redox Processes
10.7 Chapter Summary
Questions to Consider
Chapter 11 Microbial Acclimation to Ground-water Contamination
11.1 Microbial Response to Environmental Changes
11.2 Mechanisms of Acclimation
11.2.1 Induction
Induction of Hydrocarbon-Degrading Enzymes
11.2.2 Catabolite Repression
Catabolite Repression of Organic Compound Oxidation
11.2.3 Genetic Mutations
11.2.4 Acclimation to Available Electron Acceptors
11.2.5 Production of Proteins in Response to Chemical Stresses
11.3 Factors Affecting Microbial Acclimation
11.3.1 Rates of Acclimation
11.3.2 Concentration Effects
11.3.3 Cross-Acclimation of Xenobiotic Compounds
11.3.4 Chemical Structure of Xenobiotics
11.4 Acclimation to Xenobiotics in Ground-water Systems
11.4.1 Acclimation Response in a Contaminated Aquifer
11.4.2 Acclimation Response in Pristine Aquifer Sediments
11.4.3 Acclimation of Eucaryotic Microorganisms
11.4.4 Acclimation in Bioremediation Technology
11.5 Acclimation to Metal Toxicity
11.5.1 Metal Detoxitication Mechanisms
Metal Binding
Biotransformations
Metal Deposition
11.5.2 Plasmid-Encoded Metal Resistance Mechanisms
11.5.3 Acclimation to Mercury Toxicity
11.6 Summary
Questions to Consider
Chapter 12 Biodegradation And Bioremediation of Petroleum Hydrocarbons
In Ground-water Systems
12.1 Composition of Crude Oil
12.2 Petroleum Refining And Fuel Blending
12.3 Movement And Separation of Petroleum Hydrocarbons in Ground-water Systems
12.3.1 Density-driven Migration of Hydrocarbons
12.3.2 Solubility and Hydrocarbon Separation in Ground-Water Systems
12.4 Microbial Degradation of Aliphatic Hydrocarbons
12.4.1 Methane Oxidation
12.4.2 Oxidation of n-alkanes
Beta-oxidation
Methyl Group Oxidation
12.4.3 Alkene Oxidation and Reduction
12.4.4 Branched Aliphatics
12.5 Microbial Degradation of Alicyclic Hydrocarbons
12.5.1 Pathways for Cyclohexanol Degradation
Application to Environmental Studies
12.6 Microbial Degradation of Aromatic Hydrocarbons
12.6.1 Benzene Degradation
Ortho and Meta Cleavage of Catechol
12.6.2 Degradation of Alkyl Benzenes
Aerobic Degradation of Aromatic Hydrocarbons by Subsurface Bacteria
12.6.3 Degradation of Polycyclic Aromatic Compounds
12.6.4 Anaerobic Degradation of Aromatic Hydrocarbons
Degradation of Toluene and Benzene Under Methanogenic Conditions
Degradation of Toluene Under Fe(III)-Reducing Conditions
Degradation of Alkyl Benzenes Under Denitrifying Conditions
12.6.5 Biodegradation of Alkyl Ethers
12.7 Microbial Degradation of Petroleum Hydrocarbons in Ground-water Systems
12.7.1 Aerobic Degradation of BTX Compounds
12.7.2 Anaerobic Degradation of BTEX Compounds
12.8 Bioremediation of Petroleum Hydrocarbon Contamination in Ground-water Systems
12.8.1 Marine Oil Spills and the Biodegradation of Petroleum Hydrocarbons
12.8.2 Microbial Degradation Processes in Shallow Water-Table Aquifers
12.8.3 Engineered Bioremediation of Petroleum Hydrocarbons in Ground Water Systems
12.8.4 Monitored Natural Attenuation of Petroleum Hydrocarbons
12.8.5 Estimating Biodegradation Rates in Ground-Water Systems
12.9 Summary
Questions to Consider
Chapter 13 Biodegradation and Bioremediation of Halogenated Organic Compounds in Ground-water Systems
13.1 Chemistry And Uses of Halogenated Organic compounds
13.1.1 Alphatic Compounds
13.1.2 Monocyclic Aromatic Compounds
13.1.3 Polychlorinated Biphenols
13.1.4 Organochlorine Insecticides
13.1.5 Chlorinated Herbicides
13.1.6 Chlorinated Phenols
13.2 Microbial Degradation of Halogenated Organic Compounds
13.2.1 Chlorinated Ethenes
Reductive Dechlorination
Aerobic Oxidation
Anaerobic Oxidation
Aerobic Cometabolism
Redox Conditions and the Biodegradation of Chlorinated Ethenes in Ground-Water Systems
13.2.2 Chlorinated Benzenes
Aerobic Degradation
Anaerobic Degradation
13.2.3 Polychlorinated Biphenyls
13.2.4 Organochlorine Insecticides
13.2.5 Chlorinated Herbicides
13.2.6 Chlorinated Phenols
Aerobic Degradation
Anaerobic Degradation
13.3 Biodegradation of Halogenated Organic Compounds in Ground-water Systems
13.3.1 Reductive and Oxidative Biodegradation Patterns for Chlorinated Ethenes
Biodegradation Patterns in an Oxic Aquifer, Albany, Georgia
Biodegradation Patterns in an Oxic Aquifer Contaminated with Fuels and Solvents, Plattsburgh, New York
13.3.2 Cometabolic Degradation of Chlorinated Ethenes
Savannah River Site Demonstration Project
13.3.3 Degradation Patterns of Alkyl Halide Insecticides
EDB Contamination, Hawaii
Pesticide Contamination, Long Island
13.3.4 Degradation Patterns of Chlorobenzenes
13.3.5 Degradation of Chlorinated Herbicides
13.3.6 Degradation of Chlorophenolic Compounds
13.4 Summary
Questions to Consider
References
Index
Preface
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