Methods in Ecosystem Science: Progress, Tradeoffs, and Limitations.- References.- 1. Carbon and Energy Dynamics.- 1 Stand Structure in Terrestrial Ecosystems.- Methodological Approaches.- Models of Canopy Architecture.- Remote Sensing Instrumentation for Indirect Methods.- Portable Ground Instruments.- Aerial Remote Sensing.- Approaches for Estimating Stand Structure.- Canopy Height.- Vertical Foliar Distribution.- Stand Density.- Cover and Leaf Area.- Biomass.- Three-Dimensional Structure.- References.- 2 Methods of Estimating Aboveground Net Primary Productivity.- Methods to Estimate ANPP in Fast Turnover Ecosystems.- Estimates of Aboveground Biomass.- Methods to Estimate ANPP in Slow Turnover Ecosystems.- Errors Associated with Estimates of ANPP.- Optimal Methodology to Estimate ANPP.- Summary.- References.- 3 Global Terrestrial Gross and Net Primary Productivity from the Earth Observing System.- Theoretical Basis for the Algorithm for Global NPP.- Relating NPP and APAR.- Relating APAR and NDVI.- Biophysical Variability of ?.- Parameterization of ? with Global BIOME-BGC Simulations.- Algorithm Implementation Logic in EOS.- Satellite-Derived Input Variables.- Final NPP Algorithm.- Validation of Global NPP.- Summary.- References.- 4 Methods of Estimating Belowground Net Primary Production.- Concepts.- Methods.- Biomass.- Ingrowth Cores.- Isotopes.- Carbon Balance.- Nitrogen Balance.- Minirhizotrons.- Uncertainty in Estimates of BNPP.- Summary.- References.- 5 The Measurement of Primary Production in Aquatic Ecosystems.- Light and Dark Bottle Oxygen Technique.- Carbon-14 Technique.- Problems and Challenges with Light and Dark Bottle and Carbon-14 Techniques.- In Situ Diel Approaches.- Remote Sensing Techniques.- References.- 6 Benthic Respiration in Aquatic Sediments.- Total Benthic Mineralization, Flux Measurements.- Other Total Mineralization Assays.- Respiratory Pathways, Oxygen Respiration.- Nitrate Reduction.- Manganese and Iron Reduction.- Sulfate Reduction.- Methanogenesis.- Conclusions.- References.- 7 Decomposition and Soil Organic Matter Dynamics.- Plant Litter Decomposition.- Fine Litter Decomposition Rates.- Woody Detritus.- Reciprocal Transplants and Standard Substrates.- Soil Organic Matter Dynamics.- Soil Organic Matter Stores.- Physical Fractionation of Soil Organic Matter.- Biological Soil Organic Matter Fractions.- Use of Tracers.- References.- 8 Stable Isotope Tracers and Mathematical Models in Soil Organic Matter Studies.- Soil Organic Matter Pools and Dynamics.- SOM Pools.- SOM Additions.- SOM Losses.- Internal SOM Transfers.- SOM Transformations.- Stable Carbon Isotopes in Organic Matter.- Well-Mixed One Box Model of C Isotopes in SOM.- Uses of Well-Mixed Box Models in SOM C Studies.- Models for Vertical Variations in the ?13C Value of SOM.- Stable Nitrogen Isotopes in Organic Matter.- Well-Mixed One Box Soil Ecosystem Model of N Isotopes.- Use of N Isotopes in SOM as a Tracer.- Model of Vertical Variations in ?15N Value of SOM.- Conclusions.- References.- 9 Microbial Carbon Cycling in Pelagic Ecosystems: Microbial Methods for Ecosystem Scientists.- Abundance and Biomass.- Epifluorescent Direct Count.- Sample Preservation.- Count by Flow Cytometry.- Active and Inactive Cells.- Cell Size and Biomass.- Growth and Respiration of Planktonic Bacteria.- Bacterial Secondary Production.- Bacterial Respiration.- Uptake and Turnover of Specific Substrates.- Substrates Supporting Bacterial Growth.- Conclusions.- References.- 10 Herbivory in Terrestrial Ecosystems.- Consumption.- Animal-Based Methods.- Plant-Based Methods.- Differential Use of the Two Approaches.- Effect of Herbivores on Primary Production.- Compensatory Growth.- Approaches.- References.- 2. Nutrient and Water Dynamics.- 11 Canopy Fluxes.- The Canopy Scale.- The Surface Boundary Layer.- Net Ecosystem Exchange.- Flux Footprint.- Methodologies.- Aerodynamic Method.- Energy Balance/Bowen Ratio.- Eddy Covariance.- Conditional Sampling.- Errors in Long-Term Measurements of Fluxes of Carbon and Water.- Related Techniques.- Conclusions.- References.- 12 Assessing Ecosystem-Level Water Relations Through Stable Isotope Ratio Analyses.- Stable Isotopes: Natural Abundances and ? Notation.- Isotope Ratio Mass Spectrometry.- Meteoric Water Line.- Evaporative Enrichment.- Methods for Water Sampling, Extraction, and Analysis.- Water Sample Collection and Storage.- Soil, Leaf, and Stem Water Extraction.- ?D Analysis of Water.- ?18O Analysis of Water.- Methods for Leaf and Stem Organic Matter Sampling, Extraction, and Analysis.- Total Tissue Versus Cellulose Analysis.- Leaf Sampling Considerations.- Tree Ring Separation and Cellulose Purification.- ?13C Analysis of Organic Matter.- ?D Analysis of Organic Matter.- ?18O Analysis of Organic Matter.- Short-Term, Ecosystem Process-Level Applications.- Partitioning of Water Resources Among Plants Within Ecosystems.- Using ?D and ?18O Water Pulses and Interpretation of Mixing Models.- Water-Use Efficiency.- Short-Term, Regional Process-Level Applications Across Ecosystems.- Recycling of Water Among and Between Ecosystems.- ?18O of Atmospheric Carbon Dioxide.- Long-Term, Temporal Scaling of Ecosystem Processes.- Decadal-to-Century: Tree Rings.- Millennial: Caliche.- Animals.- Short-Term Indicators of Water Source.- Long-Term Indicators of Water Source.- References.- 13 Measuring Water Availability and Uptake in Ecosystem Studies.- Theory and Currencies for Measuring Water in the Environment.- Methods for Estimating Plant and Soil Moisture.- Gravimetric Measurements of ?m and ?v.- Techniques for Direct Measurement of ?.- Time Domain Reflectometry.- Remotely Sensed Data Using Microwave Radiometers.- Estimating the Vegetative Component of Ecosystem Water Fluxes.- Sap Flow Measurements.- Whole Root/Shoot Hydraulic Conductance.- Summary.- References.- 14 Nutrient Transformations.- Non-Isotope Methods.- Net Rate Measurements with Inhibitors.- Rate Measurements Obtained from Nutrient Budgets.- Net Rate Measurements with Super Sinks.- Rate Measurements Using Substrate Analogs.- Isotope Methods.- Tracer Measurements.- Isotope Dilution Measurements.- Estimation of Rates by Modeling Methods.- Natural Abundance Isotope Methods.- Application of Methods to Other Nutrient Transformations.- References.- 15 Biogenic Trace Gas Exchanges.- Approaches for Estimation of Fluxes.- Enclosure Methods.- Micrometeorological Approaches.- Analytical Methods for Trace Gases.- Multiple Approaches for Understanding and Estimating Fluxes.- References.- 16 Ecosystem Nutrient Balance and Dynamics.- Input-Output Ecosystem Budgets at the Watershed Scale.- Atmospheric Inputs.- Stream Outputs.- Other Budget Approaches.- Stand-Level Budgets Using Lysimetry.- Monolith Lysimetry and Sandbox Experiments.- Nitrogen-15 Studies at the Ecosystem Scale.- References.- 17 Deposition of Nutrients and Pollutants to Ecosystems.- Role of Atmospheric Deposition.- Vectors of Delivery.- Scales of Inquiry.- Wet Deposition.- Dry Deposition.- Cloud Deposition.- Mass-Balance Techniques.- Stable Isotope and Other Tracer Techniques.- Summary and Prospects.- References.- 18 Landscape and Regional Biogeochemistry: Approaches.- Pattern Analysis: Design for Field Studies.- Stratified Sampling and Discrete Units.- Sampling Continuous Variation.- Spatially Explicit Analyses.- Field Analyses.- Modeling Movement.- Extrapolating to the Regional or Landscape Scale.- Field Analysis.- Modeling.- Summary.- References.- 3. Manipulative Ecosystem Experiments.- 19 Nutrient Manipulations in Terrestrial Ecosystems.- Ecological Questions Addressed by Nutrient Addition.- Nature of Nutrient Limitation.- Commonly Limiting Nutrients.- Single Versus Multiple Nutrient Limitation.- Experimental Design.- General Approach.- Experimental Setup.- Experimental Design.- Time Scale of Response.- Addition Rates.- How to Add?.- Form of Nutrients Added.- Nitrogen.- Phosphorus.- Potassium.- Sulfur.- Isotopes.- Alternatives to Nutrient Addition Experiments.- Summary and Conclusions.- References.- 20 Biotic Manipulation of Aquatic Ecosystems.- Manipulation of Species.- Species Removals.- Species Introductions.- Habitat Manipulations.- Macrophyte Restoration and Removal in Lakes.- Restoration of Other Structural Features.- Wetland Restoration.- Simulation Modeling, Manipulation Strength, and Statistical Power.- Future Prospects.- Field Guide to Keystones.- Humans and Ecosystems.- Adaptive Management.- References.- 21 Biotic Manipulations Involving Belowground Animals.- Soil Biota.- Exclusions as Biotic Manipulations.- Physical Exclusion Methods.- Chemical Exclusions.- Natural Gradients as Treatments.- Habitat Manipulations.- Physical Alteration.- Introductions and Transplants.- Resource Manipulations.- Laboratory Studies.- Summary.- References.- 22 Assessing the Effects of Acidification on Aquatic Ecosystems: Insights from Lake Experiments.- The Chemistry of Acidification.- What Controls the Anthropogenic Acidification of Aquatic Ecosystems?.- Ecological Consequences of Acidification.- Smaller-Scale Experiments to Evaluate the Effects of Acidification.- Large-Scale Experiments to Evaluate the Effects of Acidification.- References.- 23 Large-Scale Water Manipulations.- Active Versus Passive Manipulations.- Artificial Rainfall.- Throughfall Interception.- Verification of Water Treatments.- Measurement Approaches.- Dealing with Spatial Variation.- Collection of Adequate Weather Data.- Confounding Issues.- Plot Size and Edge Effects.- Statistical Replication.- Conclusions.- References.- 24 Ecosystem Climate Manipulations.- Global Climate Change and Ecosystems.- Methods of Ecosystem Climate Manipulation.- Laboratory Methods: Growth Chambers.- Field Manipulations: General Considerations.- Field Manipulations: Warming Experiments.- Field Methods: Other Climate Variables.- Field Methods: Enhancing UV-B Radiation.- General Recommendations.- References.- 4. Synthesis and Conclusions.- 25 Ecosystem Modeling.- Lexical Phase.- Parsing Phase.- Modeling Phase.- A Simple Population Model.- Compartment Models and Material Flow.- Formulation of Compartment Models for Ecosystem Studies.- Analysis Phase.- Model Validation.- Sensitivity Analysis.- Stability Analysis.- Future Directions: Multiple Commodity Models and Individual-Based Models.- Multiple Commodity Models.- Individual-Based Models.- Conclusions.- References.- 26 Stoichiometric Analysis of Pelagic Ecosystems: The Biogeochemistry of Planktonic Food Webs.- Biogeochemical Structure of Planktonic Food Webs.- Dynamics Under Stoichiometric Constraints: The Andersen Model.- What About the Microbes?.- Methodological Issues.- Applications.- Implications.- References.