Biogeochemistry of Wetlands: Science and Applications

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Title
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Contents
Preface
Acknowledgments
Authors
Chapter 1 Introduction
Chapter 2 Basic Concepts and Terminology
	2.1 Introduction
	2.2 Chemistry
		2.2.1 Aqueous Chemistry
			2.2.1.1 Concentration Units
		2.2.2 Acids and Bases
		2.2.3 Equilibrium Constant
		2.2.4 Thermodynamics
			2.2.4.1 Influence of pH
		2.2.5 Oxidation–Reduction Reactions
			2.2.5.1 Oxidation–Reduction
			2.2.5.2 Oxidation State or Number
		2.2.6 Balancing Oxidation–Reduction Reactions
	2.3 Biology
		2.3.1 Microbial Cell
		2.3.2 Microbial Classification
		2.3.3 Chemistry of Biological Molecules
		2.3.4 Metabolic Reactions
		2.3.5 Enzymes
		2.3.6 Biochemical Kinetics
	2.4 Isotopes
		2.4.1 Radioactive Isotopes and Decay
		2.4.2 Half­Life
		2.4.3 Stable Isotopes
	2.5 Terminology in Soil Science
		2.5.1 Master Soil Horizon
		2.5.2 Properties Used in Soil Description
		2.5.3 Soil Taxonomy
		2.5.4 Physical Properties
		2.5.5 Chemical Properties
	2.6 Units
	Study Questions
	Further Readings
Chapter 3 Biogeochemical Characteristics
	3.1 Introduction
	3.2 Types of Wetlands
		3.2.1 Coastal Wetlands
		3.2.2 Inland Wetlands
	3.3 Wetland Hydrology
	3.4 Wetland Soils
		3.4.1 Physical Characteristics
		3.4.2 Biochemical Characteristics
		3.4.3 Biological Characteristics
	3.5 Wetland Vegetation
	3.6 Biogeochemical Features of Wetlands
		3.6.1 Presence of Molecular Oxygen in Restricted Zones
		3.6.2 Sequential Reduction of Other Inorganic Electron Acceptors
		3.6.3 Aerobic Soil–Floodwater Interface
		3.6.4 Exchanges at the Soil–Water Interface
		3.6.5 Presence of Hydrophytic Vegetation
	3.7 Types of Wetland/Hydric Soils
		3.7.1 Waterlogged Mineral Soils
		3.7.2 Organic Soils (Histosols)
		3.7.3 Marsh Soils
		3.7.4 Paddy Soils
		3.7.5 Subaqueous Soils
		3.7.6 Hydric Soils
	3.8 Summary
	Study Questions
	Further Readings
Chapter 4 Electrochemical Properties
	4.1 Introduction
	4.2 Theoretical Relationships
		4.2.1 E° vs. log K
		4.2.2 pe vs. Eh
	4.3 Measurement of Eh
	4.4 Eh–pH Relationships
	4.5 Buffering of Redox Potential (Poise)
	4.6 Measurement of Redox Potentials
		4.6.1 Construction of Platinum Electrodes
		4.6.2 Standardization of Electrodes
		4.6.3 Redox Potentials in Soils
	4.7 pH
		4.7.1 Soil pH
		4.7.2 Floodwater pH
		4.7.3 pH Effects
	4.8 Redox Couples in Wetlands
		4.8.1 Intensity
		4.8.2 Capacity
	4.9 Redox Gradients in Soils
	4.10 Specific Conductance
	4.11 Summary
	Study Questions
	Further Readings
Chapter 5 Carbon
	5.1 Introduction
	5.2 Major Components of the Carbon Cycle in Wetlands
		5.2.1 Plant Biomass Carbon (Net Primary Productivity)
		5.2.2 Particulate Organic Matter (Detrital and Soil)
		5.2.3 Microbial Biomass Carbon
		5.2.4 Dissolved Organic Matter
		5.2.5 Gaseous Forms of Carbon
	5.3 Organic Matter Accumulation
	5.4 Characteristics of Detritus and Soil Organic Matter
		5.4.1 Non­Humic Substances
			5.4.1.1 Carbohydrates
		5.4.2 Phenolic Substances
		5.4.3 Humic Substances
	5.5 Decomposition
		5.5.1 Leaching and Fragmentation
		5.5.2 Photolysis
		5.5.3 Extracellular Enzyme Hydrolysis
		5.5.4 Catabolic Activity
			5.5.4.1 Aerobic Catabolism
			5.5.4.2 Anaerobic Catabolism
			5.5.4.3 Aerobic vs. Anaerobic Catabolism
	5.6 Organic Matter Turnover
		5.6.1 Decomposition Rates
	5.7 Regulators of Organic Matter Decomposition
		5.7.1 Quality and Quantity of Organic Matter
		5.7.2 Microbial Communities and Biomass
		5.7.3 Water Table or Soil Aeration Status
		5.7.4 Availability of Electron Acceptors with Higher Reduction Potentials
		5.7.5 Nutrient Availability
		5.7.6 Temperature
	5.8 Environmental and Ecological Significance
	5.9 Functions of Organic Matter in Soils
	5.10 Summary
	Study Questions
	Further Readings
Chapter 6 Oxygen
	6.1 Introduction
	6.2 Soil Gases
	6.3 Oxygen–H2O Redox Couple
		6.3.1 Oxygen Diffusion Rate
		6.3.2 Soil Oxygen Content
	6.4 Sources of Oxygen
	6.5 Aerobic­Anaerobic Interfaces
	6.6 Oxygen Consumption
		6.6.1 Oxygen as a Reactant
		6.6.2 Oxygen as an Electron Acceptor
	6.7 Summary
	Study Questions
	Further Readings
Chapter 7 Adaptation of Plants to Soil Anaerobiosis
	7.1 Introduction
	7.2 Distribution of Wetland Plants
	7.3 Mechanisms of Flood Tolerance
		7.3.1 Metabolic Adaptations
		7.3.2 Morphological/Anatomical Adaptations
			7.3.2.1 Roots
			7.3.2.2 Pneumatophores
			7.3.2.3 Lenticels
			7.3.2.4 Intercellular Airspaces
		7.3.3 Aerenchyma Formation
		7.3.4 Intercellular Oxygen Concentration
	7.4 Mechanisms of Oxygen Movement in Wetland Plants
		7.4.1 Diffusion
		7.4.2 Mass Flow
	7.5 Oxygen Release by Plants
	7.6 Measurement of Radial Oxygen Loss
	7.7 Soil Phytotoxic Accumulation Effects on Plant Growth
		7.7.1 Greenhouse Gas Emissions: Methane
		7.7.2 Greenhouse Gas Emissions: Nitrous Oxide
	7.8 Oxidizing Power of Plant Roots
		7.8.1 Root Iron Plaque Formation
	7.9 Effect of Intensity and Capacity of Soil Reduction on Wetland Plant Functions
		7.9.1 Effect of Soil Reduction Intensity
		7.9.2 Relationship of Reduction Intensity with Root Porosity and Radial Oxygen Loss
		7.9.3 Effect of Soil Reduction Intensity on Nutrient Uptake
		7.9.4 Soil Reduction Capacity Effects on Carbon Assimilation and Radial Oxygen Loss
	7.10 Summary
	Study Questions
	Further Readings
Chapter 8 Nitrogen
	8.1 Introduction
	8.2 Forms of Nitrogen
		8.2.1 Inorganic Nitrogen
		8.2.2 Organic Nitrogen
	8.3 Major Storage Compartments
		8.3.1 Plant Biomass Nitrogen
		8.3.2 Particulate Organic Nitrogen
		8.3.3 Microbial Biomass Nitrogen
		8.3.4 Dissolved Organic Nitrogen
		8.3.5 Inorganic Forms of Nitrogen
		8.3.6 Gaseous Forms of Nitrogen
	8.4 Redox Transformations of Nitrogen
	8.5 Nitrogen Fixation
		8.5.1 Regulators of Dinitrogen Fixation
		8.5.2 Nitrogen Fixation Rates
	8.6 Nitrogen Assimilation by Vegetation
	8.7 Organic Nitrogen Accumulation
	8.8 Mineralization of Organic Nitrogen
		8.8.1 Chemical Composition of Organic Nitrogen
		8.8.2 C:N Ratio Concept
		8.8.3 Microbial Degradation of Organic Nitrogen
		8.8.4 Regulators of Organic Nitrogen Mineralization
	8.9 Ammonia Adsorption–Desorption
	8.10 Ammonia Fixation
	8.11 Ammonia Volatilization
		8.11.1 Physicochemical Reaction
		8.11.2 Regulators of Ammonia Volatilization
	8.12 Aerobic Ammonia Oxidation
		8.12.1 Chemoautotrophic Prokaryotes
		8.12.2 Methane­Oxidizing Bacteria
		8.12.3 Heterotrophic Bacteria and Fungi
		8.12.4 Regulators of Ammonium Oxidation
	8.13 Anaerobic Ammonium Oxidation
		8.13.1 Other Processes of Anaerobic Ammonium Oxidation
	8.14 Nitrate Reduction
		8.14.1 Denitrification
		8.14.2 Nitrifier Denitrification
		8.14.3 Aerobic Denitrification
		8.14.4 Chemodenitrification
		8.14.5 Dissimilatory Nitrate Reduction to Ammonia
		8.14.6 Regulators of Nitrate Reduction
		8.14.7 Nitrate Reduction Rates in Wetlands and Aquatic Systems
	8.15 Nitrogen Processing by Wetlands
		8.15.1 Ammonium Flux
		8.15.2 Nitrate Flux
	8.16 Environmental and Ecological Significance
	8.17 Summary
	Study Questions
	Further Readings
Chapter 9 Phosphorus
	9.1 Introduction
	9.2 Phosphorus Accumulation in Soils
		9.2.1 Why Does Phosphorus Added to Wetlands Accumulate in Soils?
	9.3 Phosphorus Forms in the Water Column and Soil
		9.3.1 Phosphorus Speciation
		9.3.2 Water Column
		9.3.2 Soil
	9.4 Inorganic Phosphorus
	9.5 Phosphorus Sorption by Soils
		9.5.1 Adsorption–Desorption
			9.5.1.1 Isotherm Concepts
		9.5.2 Phosphorus Sorption Isotherms
			9.5.2.1 Linear Equation
			9.5.2.2 Freundlich Equation
			9.5.2.3 Langmuir Equation
			9.5.2.4 Single­Point Isotherm
			9.5.2.5 Quantity (Q)/Intensity (I) Relationships
		9.5.3 Precipitation and Dissolution
		9.5.4 Regulators of Phosphorus Retention and Release
	9.6 Organic Phosphorus
		9.6.1 Forms of Organic Phosphorus
		9.6.2 Chemical Characterization of Organic Phosphorus
	9.7 Phosphorus Uptake and Storage in Biotic Communities
		9.7.1 Microorganisms
		9.7.2 Periphyton
		9.7.3 Vegetation
	9.8 Mineralization of Organic Phosphorus
		9.8.1 Abiotic Degradation and Stabilization of Organic Phosphorus
			9.8.1.1 Leaching of Soluble Organic Phosphorus
			9.8.1.2 Noncatalyzed Hydrolysis of Phosphate Esters
			9.8.1.3 Photolysis
			9.8.1.4 Stabilization of Organic Phosphorus
		9.8.2 Enzymatic Hydrolysis of Organic Phosphorus
			9.8.2.1 Phosphatases or Monoesterases
			9.8.2.2 Phosphodiesterases
		9.8.3 Microbial Activities and Phosphorus Release
		9.8.4 Regulators of Organic Phosphorus Mineralization
	9.9 Biotic and Abiotic Interactions on Phosphorus Mobilization
		9.9.1 Phosphorus–Iron–Sulfur Interactions
		9.9.2 Periphyton–Phosphate Interactions
		9.9.3 Biotic and Abiotic Interactions of Fe and Ca with Phosphorus
		9.9.4 Gaseous Loss of Phosphorus
	9.10 Phosphorus Exchange between Soil and Overlying Water Column
	9.11 Phosphorus Memory by Soils and Sediments
	9.12 Summary
	Study Questions
	Further Readings
Chapter 10 Iron and Manganese
	10.1 Introduction
	10.2 Storage and Distribution
	10.3 Eh–pH Relationships
		10.3.1 Iron
		10.3.2 Manganese
	10.4 Reduction of Iron and Manganese
		10.4.1 Microbial Communities
		10.4.2 Biotic and Abiotic Reduction
			10.4.2.1 Biotic Reduction
			10.4.2.2 Abiotic Reduction
		10.4.3 Forms of Iron and Manganese
			10.4.3.1 Iron
			10.4.3.2 Manganese
			10.4.3.3 Complexation of Iron and Manganese with Dissolved Organic Matter
			10.4.3.4 Mobile and Immobile Pools of Iron and Manganese
	10.5 Oxidation of Iron and Manganese
		10.5.1 Microbial Communities
		10.5.2 Biotic and Abiotic Oxidation
			10.5.2.1 Iron
			10.5.2.2 Manganese
	10.6 Mobility of Iron and Manganese
	10.7 Ecological Significance
		10.7.1 Nutrient Regeneration/Immobilization
			10.7.1.1 Organic Matter Decomposition and Nutrient Release
			10.7.1.2 Phosphorus Release or Retention
			10.7.1.3 Coprecipitation of Trace Elements with Iron and Manganese Oxides
			10.7.1.4 Siderophores and Complexation of Iron and Manganese Oxides
		10.7.2 Ferromanganese Nodules
		10.7.3 Root Plaque Formation
		10.7.4 Wetting and Drying: Hydrologic Fluctuations
		10.7.5 Ferrolysis
		10.7.6 Methane Emissions
	10.8 Summary
	Study Questions
	Further Readings
Chapter 11 Sulfur
	11.1 Introduction
	11.2 Major Storage Compartments
	11.3 Forms of Sulfur
	11.4 Oxidation–Reduction of Sulfur
	11.5 Assimilatory Sulfate and Elemental Sulfur Reduction
	11.6 Mineralization of Organic Sulfur
	11.7 Electron Acceptor–Reduction of Inorganic Sulfur
		11.7.1 Dissimilatory Sulfate Reduction
		11.7.2 Role of Sulfur in Energy Flow
		11.7.3 Measurement of Sulfate Reduction in Wetland Soils
		11.7.4 Regulators of Sulfate Reductions
	11.8 Sulfide Toxicity
	11.9 Electron Donor–Oxidation of Sulfur Compounds
	11.10 Biogenic Emission of Reduced Sulfur Gases
	11.11 Sulfur–Metal Interactions
	11.12 Exchange between Soil and Water Column
	11.13 Sulfur Sinks
	11.14 Environmental and Ecological Significance
	11.15 Summary
	Study Questions
	Further Readings
Chapter 12 Metals/Metalloids
	12.1 Introduction
	12.2 Biogeochemical Regulators of Metal Availability and Transformation
		12.2.1 Sorption and Precipitation
		12.2.2 Interaction with Organic Matter
		12.2.3 Interaction with Clay Minerals
		12.2.4 Biotic Transformations
		12.2.5 Redox Potential and pH of Soils and Sediments
	12.3 Mercury–Methyl Mercury
	12.4 Arsenic
	12.5 Copper
	12.6 Zinc
	12.7 Selenium
	12.8 Chromium
	12.9 Cadmium
	12.10 Lead
	12.11 Nickel
	12.12 Summary
	Study Questions
	Further Readings
Chapter 13 Toxic Organic Compounds
	13.1 Introduction
	13.2 Abiotic Pathways
		13.2.1 Redox Potential–pH
		13.2.2 Hydrolysis
		13.2.3 Sorption to Suspended Solids and the Substrate Bed
			13.2.3.1 Effect of Colloidal Organic Matter in Surface Water on Sorption in Wetlands
		13.2.4 Photolysis
	13.3 Biotic Pathways
		13.3.1 Acclimation
		13.3.2 Biodegradation
		13.3.3 Cometabolism
		13.3.4 Microbial Accumulation
		13.3.5 Polymerization and Conjugation
	13.4 Metabolism of Organic Compounds
		13.4.1 Hydrolysis
		13.4.2 Oxidation
			13.4.2.1 Hydroxylation
			13.4.2.2 Dealkylation
			13.4.2.3 β­Oxidation
			13.4.2.4 Decarboxylation
			13.4.2.5 Cleavage of Ether Linkage
			13.4.2.6 Epoxidation
			13.4.2.7 Oxidative Coupling
			13.4.2.8 Aromatic Ring Cleavage
			13.4.2.9 Heterocyclic Ring Cleavage
			13.4.2.10 Sulfoxidation
		13.5.3 Reduction
			13.4.3.1 Reductive Dehalogenation
		13.4.4 Synthesis
	13.5 Plant and Microbial Uptake
	13.6 Transport Processes
		13.6.1 Exchange between Soil and Water Column
		13.6.2 Settling and Burial of Particulate Contaminants
		13.6.3 Volatilization
		13.6.4 Runoff and Leaching
	13.7 Regulators
		13.7.1 Effect of Electron Acceptors on Toxic Organic Degradation
		13.7.2 Bacterial Groups
		13.7.3 Effect of Soil Redox–pH Conditions on Degradation
		13.7.4 Burial
	13.8 Summary
	Study Questions
	Further Readings
Chapter 14 Soil and Floodwater Exchange Processes
	14.1 Introduction
	14.2 Advective Flux
		14.2.1 Advective Flux Processes
		14.2.2 Measurement of Advective Flux
			14.2.2.1 Seepage Meters
			14.2.2.2 Piezometer
			14.2.2.3 Salinity/Conductivity
			14.2.2.4 Radium/Radon Isotopes
			14.2.2.5 Dyes
	14.3 Diffusive Flux
		14.3.1 Diffusive Flux Processes
	14.4 Bioturbation
		14.4.1 Macrobenthos Communities
		14.4.2 Benthic Invertebrates and Sediment–Water Interactions
	14.5 Wind Mixing and Resuspension
	14.6 Exchange of Dissolved Solutes Between Soil/Sediment and the Water Column
		14.6.1 Gradient­Based Measurements
		14.6.2 Overlying Water Incubations
			14.6.2.1 Benthic Chambers
			14.6.2.2 Intact Core Flux
	14.7 Sediment Transport Processes
		14.7.1 Sediment/Organic Matter Accretion in Wetlands
		14.7.2 Measurement of Sedimentation or Accretion Rates
			14.7.2.1 Filter Pad Traps
			14.7.2.2 Artificial Marker Horizons
			14.7.2.3 Sedimentation–Erosion Table
			14.7.2.4 Beryllium­7 Dating
			14.7.2.5 Lead­210 Dating
			14.7.2.6 Cesium­137 Dating
			14.7.2.7 Carbon­14 Dating
			14.7.2.8 Application of Sediment Dating
	14.8 Vegetative Flux/Detrital Export
	14.9 Air–Water Exchange
	14.10 Biogeochemical Regulation of Exchange Processes
	14.11 Summary
	Study Questions
	Further Readings
Chapter 15 Coupled Biogeochemical Cycles: An Integrative Approach
	15.1 Introduction
	15.2 Biotic Communities and Interactions
		15.2.1 Microbial Communities
		15.2.2 Periphyton
		15.2.3 Vegetation
	15.3 Coupled Biogeochemical Processes
		15.3.1 Carbon
		15.3.2 Nitrogen
		15.3.3 Phosphorus
		15.3.4 Sulfur
	15.4 Ecological and Environmental Significance
		15.4.1 Wetlands and Climate Change
		15.4.2 Wetlands and Sea Level Rise
		15.4.3 Wetlands and Water Quality
	15.5 Summary
	15.6 Future Directions and Perspectives
References
Index