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Tables of Contents for Methods in Ecosystem Science
Chapter/Section Title
Page #
Page Count
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