Ecology at the ecosystem level has both necessitated and benefited from new methods and technologies as well as those adapted from other disciplines. With the ascendancy of ecosystem science and management, the need has arisen for a comprehensive treatment of techniques used in this rapidly-growing field. Methods in Ecosystem Science answers that need by synthesizing the advantages, disadvantages and tradeoffs associated with the most commonly used techniques in both aquatic and terrestrial research. The book is divided into sections addressing carbon and energy dynamics, nutrient and water dynamics, manipulative ecosystem experiements and tools to synthesize our understanding of ecosystems. Detailed information about various methods will help researchers choose the most appropriate methods for their particular studies. Prominent scientists discuss how tools from a variety of disciplines can be used in ecosystem science at different scales.
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Foreword v Acknowledgments vii Contributors xix Introduction. Methods in Ecosystem Science: Progress, Tradeoffs, and Limitations 1(2) Osvaldo E. Sala Robert B. Jackson Harold A. Mooney Robert W. Howarth References 3(2) Part
1. Carbon and Energy Dynamics 5(154) Stand Structure in Terrestrial Ecosystems 7(24) Frank W. Davis Dar Roberts Introduction 7(1) Methodological Approaches 7(1) Models of Canopy Architecture 8(3) Remote Sensing Instrumentation for Indirect Methods 11(7) Portable Ground Instruments 11(1) Aerial Remote Sensing 12(6) Approaches for Estimating Stand Structure 18(7) Canopy Height 19(1) Vertical Foliar Distribution 19(2) Stand Density 21(1) Cover and Leaf Area 22(1) Biomass 23(1) Three-Dimensional Structure 24(1) References 25(6) Methods of Estimating Aboveground Net Primary Productivity 31(13) Osvaldo E. Sala Amy T. Austin Introduction 31(2) Methods to Estimate ANPP in Fast Turnover Ecosystems 33(3) Estimates of Aboveground Biomass 35(1) Methods to Estimate ANPP in Slow Turnover Ecosystems 36(1) Errors Associated with Estimates of ANPP 37(4) Optimal Methodology to Estimate ANPP 41(1) Summary 41(1) References 42(2) Global Terrestrial Gross and Net Primary Productivity from the Earth Observing System 44(14) Steven W. Running Peter E. Thornton Ramakrishna Nemani Joseph M. Glassy Introduction 44(1) Theoretical Basis for the Algorithm for Global NPP 44(6) Relating NPP and APAR 45(1) Relating APAR and NDVI 45(1) Biophysical Variability of ε 45(1) Parameterization of ε with Global BIOME-BGC Simulations 46(4) Algorithm Implementation Logic in EOS 50(3) Satellite-Derived Input Variables 50(1) Final NPP Algorithm 51(2) Validation of Global NPP 53(2) Summary 55(1) References 55(3) Methods of Estimating Belowground Net Primary Production 58(14) William K. Lauenroth Introduction 58(1) Concepts 58(1) Methods 59(6) Biomass 59(1) Ingrowth Cores 60(1) Isotopes 61(1) Carbon Balance 62(1) Nitrogen Balance 63(1) Minirhizotrons 63(2) Uncertainty in Estimates of BNPP 65(4) Summary 69(1) References 69(3) The Measurement of Primary Production in Aquatic Ecosystems 72(14) Robert W. Howarth Anthony F. Michaels Introduction 72(2) Light and Dark Bottle Oxygen Technique 74(1) Carbon-14 Technique 75(2) Problems and Challenges with Light and Dark Bottle and Carbon-14 Techniques 77(2) In Situ Diel Approaches 79(3) Remote Sensing Techniques 82(1) References 82(4) Benthic Respiration in Aquatic Sediments 86(18) Bo Thamdrup Donald E. Canfield Introduction 86(2) Total Benthic Mineralization, Flux Measurements 88(1) Other Total Mineralization Assays 89(1) Respiratory Pathways, Oxygen Respiration 90(1) Nitrate Reduction 91(1) Manganese and Iron Reduction 92(3) Sulfate Reduction 95(1) Methanogenesis 96(1) Conclusions 97(1) References 97(7) Decomposition and Soil Organic Matter Dynamics 104(13) G. Philip Robertson Eldor A. Paul Introduction 104(2) Plant Litter Decomposition 106(4) Fine Litter Decomposition Rates 106(3) Woody Detritus 109(1) Reciprocal Transplants and Standard Substrates 109(1) Soil Organic Matter Dynamics 110(3) Soil Organic Matter Stores 110(1) Physical Fractionation of Soil Organic Matter 110(1) Biological Soil Organic Matter Fractions 111(2) Use of Tracers 113(1) References 113(4) Stable Isotope Tracers and Mathematical Models in Soil Organic Matter Studies 117(21) Ronald Amundson W. Troy Baisden Introduction 117(1) Soil Organic Matter Pools and Dynamics 117(2) SOM Pools 117(1) SOM Additions 118(1) SOM Losses 118(1) Internal SOM Transfers 119(1) SOM Transformations 119(1) Stable Carbon Isotopes in Organic Matter 119(9) Well-Mixed One Box Model of C Isotopes in SOM 119(3) Uses of Well-Mixed Box Models in SOM C Studies 122(1) Models for Vertical Variations in the δ13C Value of SOM 123(5) Stable Nitrogen Isotopes in Organic Matter 128(6) Well-Mixed One Box Soil Ecosystem Model of N Isotopes 129(3) Use of N Isotopes in SOM as a Tracer 132(1) Model of Vertical Variations in δ15N Value of SOM 132(2) Conclusions 134(1) References 134(4) Microbial Carbon Cycling in Pelagic Ecosystems: Microbial Methods for Ecosystem Scientists 138(13) Jonathan J. Cole Introduction 138(1) Abundance and Biomass 139(4) Epifluorescent Direct Count 140(1) Sample Preservation 141(1) Count by Flow Cytometry 141(1) Active and Inactive Cells 141(1) Cell Size and Biomass 142(1) Growth and Respiration of Planktonic Bacteria 143(3) Bacterial Secondary Production 143(1) Bacterial Respiration 144(1) Uptake and Turnover of Specific Substrates 144(1) Substrates Supporting Bacterial Growth 144(2) Conclusions 146(1) References 147(4) Herbivory in Terrestrial Ecosystems 151(8) Martin Oesterheld Samuel J. McNaughton Introduction 151(1) Consumption 151(3) Animal-Based Methods 151(1) Plant-Based Methods 152(2) Differential Use of the Two Approaches 154(1) Effect of Herbivores on Primary Production 154(2) Compensatory Growth 154(1) Approaches 155(1) References 156(3) Part
2. Nutrient and Water Dynamics 159(130) Canopy Fluxes 161(20) John B. Moncrieff Paul G. Jarvis Ricardo Valentini Introduction 161(1) The Canopy Scale 161(5) The Surface Boundary Layer 161(2) Net Ecosystem Exchange 163(1) Flux Footprint 164(2) Methodologies 166(8) Aerodynamic Method 167(1) Energy Balance/Bowen Ratio 167(1) Eddy Covariance 168(6) Conditional Sampling 174(1) Errors in Long-Term Measurements of Fluxes of Carbon and Water 174(1) Related Techniques 175(2) Conclusions 177(1) References 177(4) Assessing Ecosystem-Level Water Relations Through Stable Isotope Ratio Analyses 181(18) James R. Ehleringer John Roden Todd E. Dawson Introduction 181(1) Stable Isotopes: Natural Abundances and δ Notation 181(1) Isotope Ratio Mass Spectrometry 181(2) Meteoric Water Line 183(1) Evaporative Enrichment 183(1) Methods for Water Sampling, Extraction, and Analysis 184(2) Water Sample Collection and Storage 184(1) Soil, Leaf, and Stem Water Extraction 185(1) δD Analysis of Water 185(1) δ18O Analysis of Water 186(1) Methods for Leaf and Stem Organic Matter Sampling, Extraction, and Analysis 186(3) Total Tissue Versus Cellulose Analysis 186(1) Leaf Sampling Considerations 187(1) Tree Ring Separation and Cellulose Purification 187(1) δ13C Analysis of Organic Matter 188(1) δD Analysis of Organic Matter 189(1) δ18O Analysis of Organic Matter 189(1) Short-Term, Ecosystem Process-Level Applications 189(4) Partitioning of Water Resources Among Plants Within Ecosystems 189(2) Using δD and δ18O Water Pulses and Interpretation of Mixing Models 191(1) Water-Use Efficiency 192(1) Short-Term, Regional Process-Level Applications Across Ecosystems 193(1) Recycling of Water Among and Between Ecosystems 193(1) δ18O of Atmospheric Carbon Dioxide 193(1) Long-Term, Temporal Scaling of Ecosystem Processes 193(1) Decadal-to-Century: Tree Rings 193(1) Millennial: Caliche 194(1) Animals 194(1) Short-Term Indicators of Water Source 194(1) Long-Term Indicators of Water Source 194(1) References 195(4) Measuring Water Availability and Uptake in Ecosystem Studies 199(16) Robert B. Jackson Laurel J. Anderson William T. Pockman Introduction 199(1) Theory and Currencies for Measuring Water in the Environment 199(2) Methods for Estimating Plant and Soil Moisture 201(6) Gravimetric Measurements of θm and θv 201(1) Techniques for Direct Measurement of ψ 202(2) Time Domain Reflectometry 204(2) Remotely Sensed Data Using Microwave Radiometers 206(1) Estimating the Vegetative Component of Ecosystem Water Fluxes 207(3) Sap Flow Measurements 208(1) Whole Root/Shoot Hydraulic Conductance 209(1) Summary 210(1) References 211(4) Nutrient Transformations 215(20) John M. Stark Introduction 215(2) Non-Isotope Methods 217(6) Net Rate Measurements with Inhibitors 217(4) Rate Measurements Obtained from Nutrient Budgets 221(1) Net Rate Measurements with ``Super Sinks 221(1) Rate Measurements Using Substrate Analogs 222(1) Isotope Methods 223(8) Tracer Measurements 223(1) Isotope Dilution Measurements 224(5) Estimation of Rates by Modeling Methods 229(1) Natural Abundance Isotope Methods 230(1) Application of Methods to Other Nutrient Transformations 231(1) References 231(4) Biogenic Trace Gas Exchanges 235(14) Pamela Matson Allen Goldstein Approaches for Estimation of Fluxes 235(7) Enclosure Methods 236(6) Micrometeorological Approaches 242(1) Analytical Methods for Trace Gases 242(2) Multiple Approaches for Understanding and Estimating Fluxes 244(1) References 244(5) Ecosystem Nutrient Balance and Dynamics 249(16) Kate Lajtha Introduction 249(1) Input--Output Ecosystem Budgets at the Watershed Scale 250(3) Atmospheric Inputs 251(1) Stream Outputs 252(1) Other Budget Approaches 253(5) Stand-Level Budgets Using Lysimetry 253(3) Monolith Lysimetry and Sandbox Experiments 256(2) Nitrogen-15 Studies at the Ecosystem Scale 258(1) References 259(6) Deposition of Nutrients and Pollutants to Ecosystems 265(12) Lars O. Hedin Role of Atmospheric Deposition 265(1) Vectors of Delivery 266(1) Scales of Inquiry 266(1) Wet Deposition 267(1) Dry Deposition 268(2) Cloud Deposition 270(1) Mass-Balance Techniques 271(1) Stable Isotope and Other Tracer Techniques 272(1) Summary and Prospects 273(1) References 274(3) Landscape and Regional Biogeochemistry: Approaches 277(12) Ingrid C. Burke Introduction 277(1) Pattern Analysis: Design for Field Studies 278(2) Stratified Sampling and Discrete Units 278(1) Sampling Continuous Variation 279(1) Spatially Explicit Analyses 280(2) Field Analyses 280(1) Modeling Movement 281(1) Extrapolating to the Regional or Landscape Scale 282(1) Field Analysis 282(1) Modeling 283(1) Summary 283(1) References 284(5) Part
3. Manipulative Ecosystem Experiments 289(82) Nutrient Manipulations in Terrestrial Ecosystems 291(17) Valerie T. Eviner F. Stuart Chapin III Charles E. Vaughn Introduction 291(1) Ecological Questions Addressed by Nutrient Addition 291(1) Nature of Nutrient Limitation 292(1) Commonly Limiting Nutrients 293(1) Single Versus Multiple Nutrient Limitation 293(1) Experimental Design 293(7) General Approach 293(1) Experimental Setup 294(1) Experimental Design 294(1) Time Scale of Response 295(1) Addition Rates 295(1) How to Add? 295(1) Form of Nutrients Added 296(1) Nitrogen 296(2) Phosphorus 298(1) Potassium 299(1) Sulfur 299(1) Isotopes 300(2) Alternatives to Nutrient Addition Experiments 302(1) Summary and Conclusions 303(1) References 303(5) Biotic Manipulation of Aquatic Ecosystems 308(10) Daniel E. Schindler Brian R. Herwig Stephen R. Carpenter Introduction 308(1) Manipulation of Species 308(2) Species Removals 308(1) Species Introductions 309(1) Habitat Manipulations 310(1) Macrophyte Restoration and Removal in Lakes 310(1) Restoration of Other Structural Features 311(1) Wetland Restoration 311(1) Simulation Modeling, Manipulation Strength, and Statistical Power 311(2) Future Prospects 313(2) Field Guide to Keystones 313(1) Humans and Ecosystems 313(1) Adaptive Management 314(1) References 315(3) Biotic Manipulations Involving Belowground Animals 318(12) Diana H. Wall O. James Reichman Introduction 318(1) Soil Biota 318(2) Exclusions as Biotic Manipulations 320(2) Physical Exclusion Methods 320(1) Chemical Exclusions 321(1) Natural Gradients as Treatments 322(1) Habitat Manipulations 323(1) Physical Alteration 323(1) Introductions and Transplants 323(1) Resource Manipulations 324(1) Laboratory Studies 324(1) Summary 325(1) References 325(5) Assessing the Effects of Acidification on Aquatic Ecosystems: Insights from Lake Experiments 330(11) Thomas M. Frost Janet M. Fischer Introduction 330(1) The Chemistry of Acidification 331(1) What Controls the Anthropogenic Acidification of Aquatic Ecosystems? 331(1) Ecological Consequences of Acidification 332(1) Smaller-Scale Experiments to Evaluate the Effects of Acidification 332(2) Large-Scale Experiments to Evaluate the Effects of Acidification 334(4) References 338(3) Large-Scale Water Manipulations 341(12) Paul J. Hanson Introduction 341(1) Active Versus Passive Manipulations 342(1) Artificial Rainfall 343(1) Throughfall Interception 344(1) Verification of Water Treatments 345(3) Measurement Approaches 345(1) Dealing with Spatial Variation 346(2) Collection of Adequate Weather Data 348(1) Confounding Issues 348(1) Plot Size and Edge Effects 348(1) Statistical Replication 349(1) Conclusions 349(1) References 350(3) Ecosystem Climate Manipulations 353(18) Karin P. Shen John Harte Introduction 353(1) Global Climate Change and Ecosystems 353(2) Methods of Ecosystem Climate Manipulation 355(9) Laboratory Methods: Growth Chambers 355(1) Field Manipulations: General Considerations 356(1) Field Manipulations: Warming Experiments 357(5) Field Methods: Other Climate Variables 362(1) Field Methods: Enhancing UV-B Radiation 363(1) General Recommendations 364(1) References 365(6) Part
4. Synthesis and Conclusions 371(36) Ecosystem Modeling 373(16) Herman H. Shugart Introduction 373(1) Lexical Phase 373(1) Parsing Phase 374(1) Modeling Phase 375(6) A Simple Population Model 376(1) Compartment Models and Material Flow 376(2) Formulation of Compartment Models for Ecosystem Studies 378(3) Analysis Phase 381(2) Model Validation 381(1) Sensitivity Analysis 381(2) Stability Analysis 383(1) Future Directions: Multiple Commodity Models and Individual-Based Models 383(3) Multiple Commodity Models 383(2) Individual-Based Models 385(1) Conclusions 386(1) References 386(3) Stoichiometric Analysis of Pelagic Ecosystems: The Biogeochemistry of Planktonic Food Webs 389(18) James J. Elser Introduction 389(1) Biogeochemical Structure of Planktonic Food Webs 390(7) Dynamics Under Stoichiometric Constraints: The Andersen Model 397(3) What About the Microbes? 400(1) Methodological Issues 401(1) Applications 402(1) Implications 403(1) References 404(3) Index 407
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