Methods in Ecosystem Science

Ecology at the ecosystem level uses new methods and technologies as well as those adapted from other disciplines. This text synthesizes the advantages, disadvantages and tradeoffs associated with the most commonly used techniques in both aquatic and terrestrial research.

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.