Methods in Ecosystem Science

Springer Science+Business Media, LLC

Osvaldo E. Sala Robert B. Jackson Harold A. Mooney Robert W. Howarth Editors

Methods in Ecosystem Science Foreword by Eugene P. Odum

With 90 Illustrations

Springer

Osvaldo E. Sala lFEVA Catedra de Ecologia Facultad de Agronomia Universidad de Buenos Aires Av. San Martin 4453 Buenos Aires 1417 Argentina

Harold A. Mooney Department of Biological

Sciences Stanford University Stanford, CA 94305 USA

Robert B. Jackson Department of Biology and Nicholas

School of the Environment Phytotron Building Duke University Durham, NC 27708 USA

Robert W. Howarth Program in Biogeochemistry and

Environmental Change Section of Ecology and Systematics Corson Hall Cornell University Ithaca, NY 14853 USA

Cover illustration: Diagram developed by A. T. Austin and O. E. Sala representing the different scales of study in ecosystem science. Tbe questions asked by the ecosystem scientist will determine the scale of study and the variables to be evaluated, which range from interpretation of satellite imagery at the global scale to microbial populations in a milliliter of water or a gram of soil. A multidisciplinary approach and a broad range of methodology are necessary to address the newest challenges in eco­system science.

Library of Congress Cataloging-in-Publication Data Methods in ecosystem science / editors, Osvaldo E. Sala ... [et al.].

p. cm Includes bibliographical references and index (p. ). ISBN 978-0-387-98743-9 ISBN 978-1-4612-1224-9 (eBook) DOI 10.1007/978-1-4612-1224-9 I. Ecology. I. Sala, Osvaldo E.

QH54 J.M43 2000 577-dc21

Printed on acid-free paper.

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~ 2000 Springer Science+Business Media New York Originally published by Springer-VerlagNew York, Inc. in 2000 Softcover reprint ofthe hardcover 1 SI edition 2000 All rights reserved. This work may not be translated or copied in whole or in part without the written permissionofthepublisher( Springer Science+Business Media New York ),

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Foreword

The ecosystem is the first (or lowest) unit in the molecule-to-ecosphere levels­of-organization hierarchy that is complete, that is, has all of the components, biological and physical, necessary for survival. Accordingly, it is the basic unit around which to organize both theory and practice in ecology. As the shortcom­ings of the "piecemeal" short-term technological and economic approaches to dealing with complex environmental problems become ever more evident with each passing year, ecosystem management emerges as the challenge for the pres­ent and future.

As ecologists and resource managers move up from the species and population levels to the ecosystem level, the biological ecologist needs the help of the physi­cal scientist when it comes to methods, as is evident in the layout of this book on ecosystem methods. About half of the 51 authors of the 26 chapters are chem­ists, hydrologists, limnologists, soil scientists, and others associated with ecology and environmental and resource sciences departments and schools rather than biology departments. Many of these are not current members of the Ecological Society of America.

Chapters are about evenly divided between aquatic and terrestrial environments in the four sections: 1, energetics (ten chapters); 2, nutrient and water cycling (eight chapters); 3, experimental approaches (six chapters); and 4, modeling (two chapters). Measurement of organic production is a special focus. Primary pro­duction is easier to measure by gaseous exchange in water than on land. Gross production is very difficult to measure on land, especially in large biomass eco­systems such as forests, so attention is focused on net primary production (four chapters). Estimating productivity at the biome and global levels by satellite re­mote sensing is very promising, but such estimates have to be ultimately cali­brated by "ground truth" measurement.

In this era of multiauthored books, we can say that this one has a very high author diversity! The message is that measurements at the ecosystem and land­scape levels require a lot of team effort.

Eugene P. Odum Institute of Ecology University of Georgia Athens, GA 30602 USA

v

Acknowledgments

This book had its intellectual origin during a productive sabbatical leave at Stan­ford University where most of the editors met and freely discussed ideas about science in general and ecology in particular. At that time, we realized that there was a gap in ecology and that a book synthesizing methods in ecosystem science was badly needed. From the origin of the idea until completion of the book, we benefited from the help and encouragement of many people and institutions. We are deeply indebted to Amy Austin for her constant support, encouragement, and insightful discussions. We are very grateful to the authors for producing such high-quality chapters and for tolerating our multiple demands. We want to thank our responsible reviewers who, with their anonymous work, assured the excellent quality of all the chapters. Janet Slobodien provided excellent guidance and sup­port throughout this project. We specially want to thank Anne Schram, Jazmin Vrsalovic, and Christian Micieli who contributed in many ways to the completion of this project. Finally, the Guggenheim and Mellon Foundations, the University of Buenos Aires, CDNICET, and the Inter-American Institute for Global Change Research supported DES while the U.S. Department of Energy supported RBJ during the period when the ideas for this book fermented.

Osvaldo Sala Roblackson Hal Mooney Bob Howarth

vii

Contents

Foreword v Acknowledgments vii Contributors xix

Introduction. Methods in Ecosystem Science: Progress, Tradeoffs, and Limitations 1 Osvaldo E. Sala, Robert B. Jackson, Harold A. Mooney, and Robert W. Howarth

References 3

Part 1. Carbon and Energy Dynamics 5

1 Stand Structure in Terrestrial Ecosystems 7 Frank W. Davis and Dar Roberts

Introduction 7 Methodological Approaches 7 Models of Canopy Architecture 8 Remote Sensing Instrumentation for Indirect Methods 11

Portable Ground Instruments 11 Aerial Remote Sensing 12

Approaches for Estimating Stand Structure 18 Canopy Height 19 Vertical Foliar Distribution 19 Stand Density 21 Cover and Leaf Area 22 Biomass 23 Three-Dimensional Structure 24

References 25

2 Methods of Estimating Aboveground Net Primary Productivity 31 Osvaldo E. Sala and Amy T. Austin

Introduction 31 Methods to Estimate ANPP in Fast Turnover Ecosystems 33

Estimates of Aboveground Biomass 35

ix

x Contents

Methods to Estimate ANPP in Slow Turnover Ecosystems 36 Errors Associated with Estimates of ANPP 37 Optimal Methodology to Estimate ANPP 41 Summary 41 References 42

3 Global Terrestrial Gross and Net Primary Productivity from the Earth Observing System 44 Steven W. Running, Peter E. Thornton, Ramakrishna Nemani, and Joseph M. Glassy

Introduction 44 Theoretical Basis for the Algorithm for Global NPP 44

Relating NPP and APAR 45 Relating APAR and NDVI 45 Biophysical Variability of e 45 Parameterization of e with Global BIOME-BGC Simulations 46

Algorithm Implementation Logic in EOS 50 Satellite-Derived Input Variables 50 Final NPP Algorithm 51

Validation of Global NPP 53 Summary 55 References 55

4 Methods of Estimating Belowground Net Primary Production 58 William K. Lauenroth

Introduction 58 Concepts 58 Methods 59

Biomass 59 Ingrowth Cores 60 Isotopes 61 Carbon Balance 62 Nitrogen Balance 63 Minirhizotrons 63

Uncertainty in Estimates of BNPP 65 Summary 69 References 69

5 The Measurement of Primary Production in Aquatic Ecosystems 72 Robert W. Howarth and Anthony F. Michaels

Introduction 72 Light and Dark Bottle Oxygen Technique 74 Carbon-14 Technique 75 Problems and Challenges with Light and Dark Bottle and Carbon-14 Techniques 77 In Situ Diel Approaches 79 Remote Sensing Techniques 82 References 82

Contents

6 Benthic Respiration in Aquatic Sediments Eo Thamdrup and Donald E. Canfield

Introduction 86

86

Total Benthic Mineralization, Flux Measurements 88 Other Total Mineralization Assays 89 Respiratory Pathways, Oxygen Respiration 90 Nitrate Reduction 91 Manganese and Iron Reduction 92 Sulfate Reduction 95 Methanogenesis 96 Conclusions 97 References 97

7 Decomposition and Soil Organic Matter Dynamics 104 G. Philip Robertson and Eldor A. Paul

Introduction 104 Plant Litter Decomposition 106

Fine Litter Decomposition Rates 106 Woody Detritus 109 Reciprocal Transplants and Standard Substrates 109

Soil Organic Matter Dynamics 110 Soil Organic Matter Stores 110 Physical Fractionation of Soil Organic Matter 110 Biological Soil Organic Matter Fractions 111 Use of Tracers 113

References 113

8 Stable Isotope Tracers and Mathematical Models in Soil Organic Matter Studies 117 Ronald Amundson and W. Troy Baisden

Introduction 117 Soil Organic Matter Pools and Dynamics 117

SOM Pools 117 SOM Additions 118 SOM Losses 118 Internal SOM Transfers 119 SOM Transformations 119

Stable Carbon Isotopes in Organic Matter 119 Well-Mixed One Box Model of C Isotopes in SOM 119 Uses of Well-Mixed Box Models in SOM C Studies 122 Models for Vertical Variations in the Ol3C Value of SOM 123

Stable Nitrogen Isotopes in Organic Matter 128 Well-Mixed One Box Soil Ecosystem Model of N Isotopes 129 Use of N Isotopes in SOM as a Tracer 132 Model of Vertical Variations in 015N Value of SOM 132

Conclusions 134 References 134

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xii Contents

9 Microbial Carbon Cycling in Pelagic Ecosystems: Microbial Methods for Ecosystem Scientists 138 Jonathan J. Cole

Introduction 138 Abundance and Biomass 139

Epifluorescent Direct Count 140 Sample Preservation 141 Count by Flow Cytometry Active and Inactive Cells Cell Size and Biomass

141 141

142 Growth and Respiration of Planktonic Bacteria 143

Bacterial Secondary Production 143 Bacterial Respiration 144 Uptake and Turnover of Specific Substrates 144 Substrates Supporting Bacterial Growth 144

Conclusions 146 References 147

10 Herbivory in Terrestrial Ecosystems 151 MartIn Oesterheld and Samuel J. McNaughton

Introduction 151 Consumption 151

Animal-Based Methods 151 Plant-Based Methods 152 Differential Use of the Two Approaches 154

Effect of Herbivores on Primary Production 154 Compensatory Growth 154 Approaches 155

References 156

Part 2. Nutrient and Water Dynamics 159

11 Canopy Fluxes 161 John B. Moncrieff, Paul G. Jarvis, and Ricardo Valentini

Introduction 161 The Canopy Scale 161

The Surface Boundary Layer Net Ecosystem Exchange Flux Footprint 164

Methodologies 166 Aerodynamic Method 167 Energy BalancelBowen Ratio Eddy Covariance 168 Conditional Sampling 174

161 163

167

Errors in Long-Term Measurements of Fluxes of Carbon and Water 174 Related Techniques 175 Conclusions 177 References 177

Contents xiii

12 Assessing Ecosystem-Level Water Relations Through Stable Isotope Ratio Analyses 181 James R. Ehleringer, John Roden, and Todd E. Dawson

Introduction 181 Stable Isotopes: Natural Abundances and 0 Notation 181 Isotope Ratio Mass Spectrometry 181 Meteoric Water Line 183 Evaporative Enrichment 183 Methods for Water Sampling, Extraction, and Analysis 184

Water Sample Collection and Storage 184 Soil, Leaf, and Stem Water Extraction 185 oD Analysis of Water 185 0180 Analysis of Water 186

Methods for Leaf and Stem Organic Matter Sampling, Extraction, and Analysis 186

Total Tissue Versus Cellulose Analysis 186 Leaf Sampling Considerations 187 Tree Ring Separation and Cellulose Purification 187 o13C Analysis of Organic Matter 188 oD Analysis of Organic Matter 189 0180 Analysis of Organic Matter 189

Short-Term, Ecosystem Process-Level Applications 189 Partitioning of Water Resources Among Plants Within Ecosystems 189 Using oD and 0180 Water Pulses and Interpretation of Mixing Models 191 Water-Use Efficiency 192

Short-Term, Regional Process-Level Applications Across Ecosystems 193

Recycling of Water Among and Between Ecosystems 193 0180 of Atmospheric Carbon Dioxide 193

Long-Term, Temporal Scaling of Ecosystem Processes 193 Decadal-to-Century: Tree Rings 193 Millennial: Caliche 194

Animals 194 Short-Term Indicators of Water Source 194 Long-Term Indicators of Water Source 194

References 195

13 Measuring Water Availability and Uptake in Ecosystem Studies 199 Robert B. Jackson, Laurel J. Anderson, and William T. Pockman

Introduction 199 Theory and Currencies for Measuring Water in the Environment 199 Methods for Estimating Plant and Soil Moisture 201

Gravimetric Measurements of 9m and 9v 201 Techniques for Direct Measurement of 'II 202 Time Domain Reflectometry 204 Remotely Sensed Data Using Microwave Radiometers 206

xiv Contents

Estimating the Vegetative Component of Ecosystem Water Fluxes 207 Sap Flow Measurements 208 Whole Root/Shoot Hydraulic Conductance 209

Summary 210 References 211

14 Nutrient Transformations 215 John M. Stark

Introduction 215 Non-Isotope Methods 217

Net Rate Measurements with Inhibitors 217 Rate Measurements Obtained from Nutrient Budgets 221 Net Rate Measurements with "Super Sinks" 221 Rate Measurements Using Substrate Analogs 222

Isotope Methods 223 Tracer Measurements 223 Isotope Dilution Measurements 224 Estimation of Rates by Modeling Methods 229 Natural Abundance Isotope Methods 230

Application of Methods to Other Nutrient Transformations 231 References 231

15 Biogenic Trace Gas Exchanges 235 Pamela Matson and Allen Goldstein

Approaches for Estimation of Fluxes 235 Enclosure Methods 236 Micrometeorological Approaches 242

Analytical Methods for Trace Gases 242 Multiple Approaches for Understanding and Estimating Fluxes 244 References 244

16 Ecosystem Nutrient Balance and Dynamics 249 Kate Lajtha

Introduction 249 Input-Output Ecosystem Budgets at the Watershed Scale 250

Atmospheric Inputs 251 Stream Outputs 252

Other Budget Approaches 253 Stand-Level Budgets Using Lysimetry 253 Monolith Lysimetry and Sandbox Experiments 256

Nitrogen-15 Studies at the Ecosystem Scale 258 References 259

17 Deposition of Nutrients and Pollutants to Ecosystems 265 Lars O. Hedin

Role of Atmospheric Deposition 265 Vectors of Delivery 266 Scales of Inquiry 266

Contents xv

Wet Deposition 267 Dry Deposition 268 Cloud Deposition 270 Mass-Balance Techniques 271 Stable Isotope and Other Tracer Techniques 272 Summary and Prospects 273 References 274

18 Landscape and Regional Biogeochemistry: Approaches 277 Ingrid C. Burke

Introduction 277 Pattern Analysis: Design for Field Studies 278

Stratified Sampling and Discrete Units 278 Sampling Continuous Variation 279

Spatially Explicit Analyses 280 Field Analyses 280 Modeling Movement 281

Extrapolating to the Regional or Landscape Scale 282 Field Analysis 282 Modeling 283

Summary 283 References 284

Part 3. Manipulative Ecosystem Experiments 289

19 Nutrient Manipulations in Terrestrial Ecosystems 291 Valerie T. Eviner, F. Stuart Chapin III, and Charles E. Vaughn

Introduction 291 Ecological Questions Addressed by Nutrient Addition 291 Nature of Nutrient Limitation 292

Commonly Limiting Nutrients 293 Single Versus Multiple Nutrient Limitation 293

Experimental Design 293 General Approach 293 Experimental Setup 294 Experimental Design 294 Time Scale of Response 295 Addition Rates 295 How to Add? 295 Form of Nutrients Added 296 Nitrogen 296 Phosphorus 298 Potassium 299 Sulfur 299

Isotopes 300 Alternatives to Nutrient Addition Experiments 302 Summary and Conclusions 303 References 303

xvi

20 Biotic Manipulation of Aquatic Ecosystems 308 Daniel E. Schindler, Brian R. Herwig, and Stephen R. Carpenter

Introduction 308 Manipulation of Species 308

Species Removals 308 Species Introductions 309

Habitat Manipulations 310 Macrophyte Restoration and Removal in Lakes 310 Restoration of Other Structural Features 311 Wetland Restoration 311

Simulation Modeling, Manipulation Strength, and Statistical Power 311 Future Prospects 313

Field Guide to Keystones Humans and Ecosystems Adaptive Management

References 315

313 313

314

21 Biotic Manipulations Involving Belowground Animals 318 Diana H. Wall and O. James Reichman

Introduction 318 Soil Biota 318 Exclusions as Biotic Manipulations 320

Physical Exclusion Methods 320 Chemical Exclusions 321

Natural Gradients as Treatments 322 Habitat Manipulations 323

Physical Alteration 323 Introductions and Transplants 323

Resource Manipulations 324 Laboratory Studies 324 Summary 325 References 325

22 Assessing the Effects of Acidification on Aquatic Ecosystems: Insights from Lake Experiments 330 Thomas M. Frost and Janet M. Fischer

Introduction 330 The Chemistry of Acidification 331 What Controls the Anthropogenic Acidification of Aquatic Ecosystems? 331 Ecological Consequences of Acidification 332 Smaller-Scale Experiments to Evaluate the Effects of Acidification 332

Contents

Large-Scale Experiments to Evaluate the Effects of Acidification 334 References 338

Contents

23 Large-Scale Water Manipulations Paul J. Hanson

Introduction 341

341

Active Versus Passive Manipulations 342 Artificial Rainfall 343 Throughfall Interception 344 Verification of Water Treatments 345

Measurement Approaches 345 Dealing with Spatial Variation 346

Collection of Adequate Weather Data 348 Confounding Issues 348 Plot Size and Edge Effects 348 Statistical Replication 349 Conclusions 349 References 350

24 Ecosystem Climate Manipulations 353 Karin P. Shen and John Harte

Introduction 353 Global Climate Change and Ecosystems 353 Methods of Ecosystem Climate Manipulation 355

Laboratory Methods: Growth Chambers 355 Field Manipulations: General Considerations 356 Field Manipulations: Warming Experiments 357 Field Methods: Other Climate Variables 362 Field Methods: Enhancing UV-B Radiation 363

General Recommendations 364 References 365

Part 4. Synthesis and Conclusions 371

25 Ecosystem Modeling 373 Herman H. Shugart

Introduction 373 Lexical Phase 373 Parsing Phase 374 Modeling Phase 375

A Simple Population Model 376 Compartment Models and Material Flow 376 Formulation of Compartment Models for Ecosystem Studies 378

Analysis Phase 381 Model Validation 381 Sensitivity Analysis 381 Stability Analysis 383

Future Directions: Multiple Commodity Models and Individual-Based Models 383

Multiple Commodity Models 383 Individual-Based Models 385

Conclusions 386 References 386

xvii

xviii Contents

26 Stoichiometric Analysis of Pelagic Ecosystems: The Biogeochemistry of Planktonic Food Webs 389 James J. Elser

Introduction 389 Biogeochemical Structure of Planktonic Food Webs 390 Dynamics Under Stoichiometric Constraints: The Andersen Model 397 What About the Microbes? 400 Methodological Issues 401 Applications 402 Implications 403 References 404

Index 407

Contributors

Ronald Amundson, Division of Ecosystem Sciences, University of California, Berkeley, CA, USA

Laurel J. Anderson, Department of Horticulture, Pennsylvania State University, University Park, PA, USA

Amy T. Austin, IFEVA and CMedra de Ecologfa, Facultad de Agronomfa, Uni­versidad de Buenos Aires, Buenos Aires, Argentina

W. Troy Baisden, Division of Ecosystem Sciences, University of California, Berkeley, CA, USA

Ingrid C. Burke, Department of Forest Sciences, Colorado State University, Fort Collins, CO, USA

Donald E. Canfield, Institute of Biology, Odense University, Denmark

Stephen R. Carpenter, Center for Limnology, University of Wisconsin, Madison, WI, USA

F. Stuart Chapin III, Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA

Jonathan J. Cole, Institute of Ecosystem Studies, Cary Arboretum, AB, Mill­brook, NY, USA

Frank W. Davis, Department of Geography, University of California, Santa Bar­bara, CA, USA

Todd E. Dawson, Center for Stable Isotope Biogeochemistry, Department of In­tegrative Biology, University of California, Berkeley, CA, USA

James R. Ehleringer, Stable Isotope Ratio Facility for Environmental Research, Department of Biology, University of Utah, Salt Lake City, UT, USA

xix

xx Contributors

James J. Elser, Department of Biology, Arizona State University, Tempe, AZ, USA

Valerie T. Eviner, Department of Integrative Biology, University of California, Berkeley, CA, USA

Janet M. Fischer, Department of Biology, Franklin and Marshall College, Lan­caster, PA, USA

Thomas M. Frost, Trout Lake Station, Center for Limnology, University of Wis­consin, Madison, WI, USA

Joseph M. Glassy, Numerical Terradynarnic Simulation Group, School of For­estry, University of Montana, Missoula, MT, USA

Allen Goldstein, Environmental Science, Policy and Management, Division of Ecosystem Sciences, University of California, Berkeley, CA, USA

Paul J. Hanson, Environmental Sciences Division, Oak Ridge National Labora­tory, Oak Ridge, TN, USA

John Harte, Energy and Resources Group, University of California, Berkeley, CA,USA

Lars o. Hedin, Section of Ecology and Systematics, Cornell University, Ithaca, NY, USA

Brian R. Herwig, Illinois Natural History Survey, Center for Aquatic Ecology, Champaign, IL, USA

Robert W. Howarth, Program in Biogeochemistry and Environmental Change, Section of Ecology and Systematics, Cornell University, Ithaca, NY, USA

Robert B. Jackson, Department of Biology and Nicholas School of the Environ­ment, Duke University, Durham, NC, USA

Paul G. Jarvis, Institute of Ecology and Resource Management, University of Edinburgh, Edinburgh, UK

Kate Lajtha, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA

William K. Lauenroth, Department of Rangeland Ecosystem Science and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, USA

Pamela Matson, Department of Geological and Environmental Sciences, Stanford University, Stanford, CA, USA

Samuel J. McNaughton, Biological Research Laboratories, Syracuse University, Syracuse, NY, USA

Contributors xxi

Anthony F. Michaels, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, USA

John B. Moncrieff, Institute of Ecology and Resource Management, University of Edinburgh, Edinburgh, UK

Harold A. Mooney, Department of Biological Sciences, Stanford University, Stan­ford, CA, USA

Ramakrishna Nemani, Numerical Terradynamic Simulation Group, School of Forestry, University of Montana, Missoula, MT, USA

MartIn Oesterheld, IFEVA and Oitedra de Ecologfa, Facultad de Agronomia, Universidad de Buenos Aires, Buenos Aires, Argentina

Eldor A. Paul, Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI, USA

William T. Pockman, Department of Botany, University of New Mexico, Albu­querque, NM, USA

O. James Reichman, Department of Ecology, Evolution, and Marine Biology and National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, USA

Dar Roberts, Department of Geography, University of California, Santa Barbara, CA,USA

G. Philip Robertson, w.K. Kellogg Biological Station, Michigan State University, Hickory Comers, MI, USA

John Roden, Department of Biology, Southern Oregon University, Ashland, OR, USA

Steven W. Running, Numerical Terradynamic Simulation Group, School of For­estry, University of Montana, Missoula, MT, USA

Osvaldo E. Sala, IFEVA and Catedra de Ecologfa, Facultad de Agronomia, Uni­versidad de Buenos Aires, Buenos Aires, Argentina

Daniel E. Schindler, Department of Zoology, University of Washington, Seattle, WA,USA

Karin P. Shen, Energy and Resources Group, University of California, Berkeley, CA,USA

Herman H. Shugart, Department of Environmental Sciences, University of Vir­ginia, Charlottesville, VA, USA

John M. Stark, Department of Biology and the Ecology Center, Utah State Uni­versity, Logan, UT, USA

xxii Contributors

Bo Thamdrup, Max Planck Institute for Marine Microbiology, Bremen, Germany, and Institute of Biology, Odense University, Odense, Denmark

Peter E. Thornton, Numerical Terradynamic Simulation Group, School of For­estry, University of Montana, Missoula, MT, USA

Ricardo Valentini, Department of Forest Science and Environment, University of Tuscia, Viterbo, Italy

Charles E. Vaughn, Hopland Research and Extension Center, University of Cali­fornia, Hopland, CA, USA

Diana H. Wall, Natural Resource Ecology Laboratory and Department of Range­land Ecosystem Science, Colorado State University, Fort Collins, CO, USA