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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

 

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