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Index
Ecosystem Science and Applications
Title Page
Copyright Page
Acknowledgments
Acronyms
Table of Contents
List of Tables
Table of Figures
Table of Contents
Part I - Context of Soil and Plant Analysis
Chapter 1 - Overview of Soil and Plant Analysis for Forest Ecosystems
1.1 Soils are Physically, Chemically andBiologically Complex
Part II - Introductory Methods in Soil and Plant Analyses
Chapter 2 - Field Characterization of Soils to Establish Sampling Protocols
2.1 Soil Sampling Design and Methods
2.1.1 Introduction to Sampling Design
2.1.1.1 Accuracy, Bias, and Precision
2.1.1.2 General Considerations on Soil Sampling
2.1.1.3 Common Sampling Tools and Techniques
2.1.1.4 Soil Sample Preparation
2.1.2 Soil Sample Process Procedure
2.1.2.1 Sample Variability—Number of Samples Required
Chapter 3 - Plant Tissue Characterization
3.1 Tissue Sampling
3.2 Tissue Preparation and LaboratoryExtraction
Chapter 4 - Introduction: Laboratory Practices
4.1 General Laboratory Protocol
4.1.1 Safety
4.1.2 Laboratory Water
4.1.3 Clean-up
4.1.4 Waste Disposal
Part III - Soil Physical, Chemical and Biological Analyses
Chapter 5 - Methods for Analyzing Soil Physical Characteristics
5.1 Soil Moisture
5.1.1 Direct Methods of Estimating Soil Moisture and Soil WaterPotential
5.1.2 Procedure to Determine Gravimetric Water Concentrations
5.2 Soil Bulk Density
5.2.1 Soil Bulk Density Methods
5.3 Soil Texture (Particle Size Analysis orMechanical Analysis)
5.3.1 Soil Texture Methods
5.3.1.1 Soil Texture Procedure: Bouyoucos Hydrometer Method
5.4 Soil Water Potential
5.4.1 Pressure Plate Apparatus Procedure: Soil Moisture ReleaseCurve
Chapter 6 - Soil Chemical Characterization
6.1 Soil pH
6.1.1 Measuring pH
6.1.2 The Care of pH Electrodes
6.2 Electrical Conductivity (EC)
6.2.1 Saturated Paste Extract Procedure: Electrical Conductivity
6.3 Ion Exchange in Soils
6.3.1 Cation Exchange Capacity
6.3.2 Exchangeable Cations
6.3.3 Extraction Procedures for Exchangeable Cations and CationExchange Capacity
6.4 Exchangeable Soil Acidity
6.4.1 Extraction Procedures for Exchangeable Soil Acidity
6.4.1.1 Exchangeable Acidity (Barium Chloride—Triethanolamine Method)
6.4.1.2 Exchangeable Acidity (Potassium Chloride Method)
6.5 Extractable Inorganic Soil Nitrogen
6.5.1 Extraction Methods for Inorganic Soil Nitrogen
6.5.1.1 Single Extraction Procedure: Extractable Inorganic Nitrogen
6.5.1.2 Double Extraction Procedure: Mechanical Vacuum Extractor
6.6 Soil Phosphorus
6.6.1 Methodology for Measuring Soil Phosphorus
6.6.2 Procedure: Extractable Inorganic Phosphorus
6.7 Soil Carbon and Organic Matter
6.7.1 Dry Combustion Procedure: Total Soil Carbon and Nitrogen
6.7.2 Loss on Ignition (LOI) Procedure: Total Soil Organic Matter
6.7.3 Walkley-Black Procedure: Soil Carbon
6.8 Selective Dissolution of Iron and Aluminum
6.8.1 Extraction Procedure: Organically Complexed Iron andAluminum
6.8.2 Extraction Procedure: Non-crystalline Soil Iron and AluminumOxides
Chapter 7 - Total Plant and Soil Nutrient Analysis (Digestion)
7.1 Wet Oxidation Method
7.2 Dry Oxidation Method
7.3 Total Dissolved Carbon and Nitrogen inWater
7.4 Modified Kjeldahl Digest Procedure: Sulfuric Acid Digest for “Total” Nutrients
7.5 “Total” Nutrient Analysis Procedure:Dry Ashing Followed by Nitric Acid Digest
7.6 Total Dissolved Nitrogen in WaterProcedure: Persulfate Oxidation
Chapter 8 - Soil Biology Characterization
8.1 Soil Microbes
8.1.1 Archaea and Bacteria
8.1.2 Fungi
8.1.3 Soil Algae and Cyanobacteria (Blue-green Algae)
8.2 Methods for Determining Soil MicrobialDiversity and Populations—Numbers andBiomass
8.2.1 Direct Culture, Microscopy and Image Analysis
8.2.2 Microbial Numbers and Microbial Biomass
8.3 Mycorrhizas
8.3.1 Types of Mycorrhizas
8.3.2 Sampling Mycorrhizas
8.3.2.1 Sampling Design
8.3.2.2 Collection of Root and Soil Samples
8.3.2.3 Storage of Samples
8.3.2.4 Determining Mycorrhizas in Samples
8.3.3 Determination of Mycorrhizal Fungal Species
8.3.3.1 Analysis of Sporocarps and Spores
8.3.3.2 Morphotypes of Ectomycorrhizas
8.3.3.3 Trap Cultures for Arbuscular Mycorrhizal Fungi
8.3.3.4 DNA and Biochemical Techniques
8.3.4 Ectomycorrhizal Quantification
8.3.5 Identification of Ectomycorrhizal Sporocarps
8.3.6 Quantification of Arbuscular Mycorrhizal Colonization
8.3.6.1 Staining
8.3.6.2 Grid-line Intersection Method with a Dissecting Microscope
8.4 Indirect Indices for Soil Biological Activity
8.4.1 Soil Respiration
8.4.1.1 CO2 Gas Sampling
8.4.1.2 The Soda Lime Technique
8.4.2 Decomposition Rates of Litter
8.4.2.1 Fine Litter
8.4.2.2 Woody Debris
8.4.2.3 Fine Woody Debris
8.4.2.4 Coarse Woody Debris (CWD)
8.4.2.5 Standard Substrates
8.4.2.6 Calculation of Decomposition Rates
8.4.3 Soil Enzymes
8.4.4 Functional Biodiversity—Phospholipid Ester-linked Fatty Acids(PLFA) and Substrate Utilization Profiles
8.4.5 Molecular Tools for Ecological Systems
8.4.5.1 DNA Extraction from Soil
8.4.5.2 PCR
8.4.5.3 Restriction Length Fragment Polymorphism RFLP
8.4.5.4 Primers
8.4.5.5 Gel Electrophoresis
8.4.5.6 DNA Sequencing
8.4.5.7 Metagenomics and Transcriptomics
8.5 Soil Invertebrates
8.5.1 Macrofauna with Emphasis on Earthworms
8.5.1.1 Extraction Methods
8.5.2 Mesofauna
8.5.2.1 Mites and Collembola
8.5.2.2 Enchytraeids
8.5.3 Microfauna
8.5.3.1 Protozoans
8.5.3.2 Rotifers
8.5.3.3 Tardigrades
8.5.3.4 Microfauna-Nematodes
8.6 Nitrogen Transformations
8.6.1 Nitrogen Fixation
8.6.1.1 Acetylene Reduction
8.6.1.2 N Accretion through Time
8.6.1.3 15N Based Methods
8.6.2 Denitrification
8.6.2.1 The Acetylene Inhibition Method
8.6.2.2 15N Tracer Methods
8.6.2.3 Direct N2 Quantification
8.6.2.4 Mass Balance Approaches
8.6.2.5 Stable Isotope Approaches
8.6.2.6 Approaches using in situ Gradients in Environmental Tracers
8.6.2.7 Molecular Approaches
Appendices
Appendix A Statistics Example
Appendix B Quality Assurance/ Quality Control
Appendix C Example Format for Field and Laboratory Data Sheets
References
Subject Index
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