Fundamentals of Soil Ecology

Second Edition

Fundamentals

of

Soil

Ecology

Second Edition

Fundamentals

of

Soil

Ecology

David C. Coleman

D. A. Crossley, Jr.

Paul F. Hendrix

Institute of Ecology

University of Georgia

Athens, Georgia

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Library of Congress Cataloging-in-Publication Data

Coleman, David C., 1938–

Fundamentals of soil ecology / David C. Coleman, D.A. Crossley, Jr.,

Paul F. Hendrix.—2nd ed.

p. cm.

Includes bibliographical references and index.

ISBN 0-12-179726-0 (alk. paper)

1. Soil ecology. 2. Soil biology. I. Crossley, D. A. II. Hendrix,

Paul F. III. Title.

QH541.5.S6C65 2004

577.5¢7—dc22

2004046994

British Library Cataloguing in Publication Data

A catalogue record for this book is available from the British Library

ISBN: 0-12-179726-0

For all information on all Academic Press publications

visit our website at www.academicpressbooks.com

PRINTED IN THE UNITED STATES OF AMERICA

04 05 06 07 08 09987654321

Contents

Preface to the Second Edition xi

Preface to the First Edition xiii

1 Historical Overview of Soils and the Fitness

of the Soil Environment 1

The Historical Background of Soil Ecology 1

Water as a Constituent of Soil 4

Elemental Constitution of Soil 9

How Soils Are Formed 9

Profile Development 11

Soil Texture 13

Clay Mineral Structure 15

Soil Structure 16

Soils as Suppliers of Ecosystem Services 20

Summary 20

2 Primary Production Processes in Soils: Roots

and Rhizosphere Associates 23

Introduction 23

The Primary Production Process 23

Methods of Sampling 25

Destructive Techniques 25

The Harvest Method 25

Isotope-Dilution Method 28

Root-Ingrowth Technique 28

Nondestructive Techniques 30

Additional Sources of Primary Production 34

Symbiotic Associates of Roots 34

Mycorrhizal Structure and Function 36

v

Ecosystem-Level Consequences of ECM Function 37

Actinorhiza 38

Carbon Allocation in the Root/Rhizosphere 38

Carbon Allocation Costs of Development and Maintenance

of Symbiotic Associations with Roots 42

Future Directions for Research on Roots and Mycorrhizal

Function and Biodiversity 44

Summary 46

3 Secondary Production: Activities of

Heterotrophic Organisms—Microbes 47

Introduction 47

Compounds Being Decomposed 48

Microbial Activities in Relation to Catabolism in

Soil Systems 48

Microbial Abundance and Distribution in Soil 53

Techniques for Measuring Microbial Communities 57

Direct Measures of Numbers and Biomass 57

Indirect Measures of Biomass 59

Chemical Methods 59

The Chloroform Fumigation and Incubation (CFI)

Technique 59

The Chloroform Fumigation and Extraction (CFE)

Technique 60

Physiological Methods: SIR Technique 61

Additional Physiological Methods of Measuring Microbial

Activity 61

Enzyme Assays and Measures of Biological Activities in

Soils 63

DirectMethods of Determining Soil Microbial Activity 66

Soil Sterilization and Partial Sterilization Techniques 67

Conceptual Models of Microbes in Soil Systems 67

Root–Rhizosphere Microbe Models and Experiments 67

Soil Aggregation Models 69

Models: Organism and Process-Oriented 74

Summary 77

4 Secondary Production: Activities of

Heterotrophic Organisms—The Soil Fauna 79

Introduction 79

The Microfauna 83

vi Contents

Methods for Extracting and Counting Protozoa 86

Distribution of Protozoa in Soil Profiles 87

Impacts of Protozoa on Ecosystem Function 87

The Mesofauna 89

Rotifera 89

Features of Body Plan and General Ecology 89

Nematoda 90

Nematode Feeding Habits 90

Nematode Zones of Activity in Soil 93

Nematode Extraction Techniques 94

Tardigrada 95

Microarthropods 98

Collembola 101

Families of Collembola 103

Population Growth and Reproduction 107

Collembolan Feeding Habits 107

Collembolan Impacts on Soil Ecosystems 108

Acari (Mites) 109

Oribatid Mites 111

Abundance and Diversity of Oribatid Mites 114

Population Growth 116

Oribatid Feeding Habits 116

Oribatid Impacts on Soil Ecosystems 119

Prostigmatic Mites 119

Mesostigmatic Mites 122

Astigmatic Mites 124

Other Microarthropods 128

Protura 128

Diplura 129

Microcoryphia 130

Pseudoscorpionida 130

Symphyla 131

Pauropoda 133

Enchytraeidae 133

The Macrofauna 141

Macroarthropods 141

Importance of the Macroarthropods 141

Isopoda 143

Diplopoda 145

Chilopoda 146

Scorpionida 147

Araneae 149

Opiliones 151

Solifugae 152

Contents vii

Uropygi 152

The Pterygote Insects 153

Coleoptera 154

Hymenoptera 159

Diptera 161

Isoptera 162

Other Pterygota 166

Gastropoda 167

Sampling Techniques for Gastropods 168

Oligochaeta—Earthworms 169

Earthworm Distribution and Abundance 170

Biology and Ecology 171

Influence on Soil Processes 176

Earthworm Management 178

Earthworm Sampling and Identification 179

General Attributes of Fauna in Soil Systems 181

Faunal Feedbacks on Microbial Community Composition

and Diversity 182

Summary 184

5 Decomposition and Nutrient Cycling 187

Introduction 187

Integrating Variables 188

Resource Quality, Climate, and Litter Breakdown 190

Dynamics of Litter Breakdown 192

Direct Measurement of Litter Breakdown 194

Patterns of Mass Loss During Decomposition 201

Effects of Fauna on Litter Breakdown Rates 204

Nutrient Movement During Decomposition 206

Nutrient Cycling Links in Soil Systems 215

Role of Soil Fauna in Organic Matter Dynamics and

Nutrient Turnover 216

Faunal Impacts in Applied Ecology—Agroecosystems 220

Applied Ecology in Forested Ecosystems 222

Summary 225

6 Soil Food Webs: Detritivory and Microbivory

in Soils 227

Introduction 227

Physiological Ecology of Soil Organisms 229

viii Contents

Energy Available for Detrital Food Chains and Webs 231

Arenas of Interest 236

A Hierarchical Approach to Organisms in Soils 237

Future Research Prospects 241

Summary 246

7 Soil Biodiversity and Linkages

to Soil Processes 247

Introduction 247

Biodiversity in Soils and Its Impacts on Terrestrial

Ecosystem Function 247

Heterogeneity of Carbon Substrates and Effects on Soil

Biodiversity 259

Impacts of Species Richness on Ecosystem Function 259

Models, Microcosms, and Soil Biodiversity 263

Experimental Additions and Deletions in Soil Biodiversity

Studies 265

Problems of Concern in Soil Biodiversity Studies 266

Why Is Soil Diversity So High? 269

Biogeographical Trends in Diversity of SoilOrganisms 269

8 Future Developments in Soil Ecology 271

Introduction 271

Roles of Soils in Carbon Sequestration 271

Roles of Soils in the Global Carbon Cycle 275

Problems in Modeling Soil Carbon Dynamics 279

Biological Interactions in Soils and Global Change 281

Ecology of Invasive Species in Soil Systems: An Increasing

Problem in Soil Ecology 285

Soils and “Gaia”: Possible Mechanisms for Evolution of

“the Fitness of the Soil Environment?” 289

Soil Ecology in the Third Millennium 293

9 Laboratory and Field Exercises

in Soil Ecology 299

Introduction 299

Minirhizotron Studies 299

Principle 299

Contents ix

Description of a Minirhizotron 299

Installation of the Minirhizotrons 300

Observation and Recording 300

Getting Data from the Videotape 300

Tracing Technique 300

Automated Root Length Measures 301

Soil Respiration Studies 301

Principle 301

Materials and Supplies Needed 301

Procedure 302

Calculations 302

Litter Decomposition Studies 303

Principle 303

Litterbag Construction 304

Calculations 305

Analyses for Soil Microbial Biomass 305

The Chloroform-Fumigation K2SO4-Extraction

Method 305

Principle 305

Preparation and Handling of Potassium Sulfate 306

Sample Preparation 306

Potassium Sulfate Extractions 306

Chloroform Fumigation 306

Chloroform Removal 307

Calculations 307

Sampling and Enumeration of Nematodes 308

Principle 308

Sampling Considerations 308

Sampling Tool and Precautions 309

Nematode Extraction: Baermann Funnel Method 309

Principle 309

Materials and Supplies Needed 310

Procedure 310

Killing and Fixing Nematodes with Hot and Cold

Formalin (5%) 311

Materials and Supplies Needed 311

Procedure 311

Sampling and Enumeration of Microarthropods 311

Principle 311

Methods for the Study of Microarthropods 312

Sampling 312

Extraction of Microarthropods from Samples 313

Sample Sorting and Identification 315

x Contents

Contents xi

Sampling and Enumeration of Macroarthropods 317

Principle 317

Methods for Sampling Macroarthropods 317

Sampling 317

Berlese or Tullgren Extraction 318

Flotation 318

Emergence Traps 318

Pitfall Trapping 318

Sampling and Enumeration of Earthworms 320

Principle 320

Collection of Earthworms 320

Passive Techniques 320

Behavioral Techniques 320

Indirect Techniques 323

Identification of Earthworms 323

Sampling and Enumeration of Enchytraeids 323

Principle 323

Collection of Enchytraeids 324

Identification of Enchytraeids 325

References 327

Index 375

Preface to the Second Edition

We endorse all of the comments and observations made in the Preface

to the First Edition of this book. Over the last 8 years, considerable

progress has been made in opening soil processes up for scientific

inquiry, indeed, viewing soils “through a ped darkly” (Coleman, 1985)

and getting away from the simplistic approaches of the “black box” that

prevailed in much of the 20th century.

In the midst of the wonder and awe surrounding the pictures that

have been transmitted across 100 million miles to Earth during 2004

from the two Mars rovers, it is important to point out a basic fallacy in

the discussions over the findings on the surface of Mars. The engineers

and physical scientists in charge of the study persist in calling the Mars

surface material “soil.” As we note many times in our book, biology is the

leading characteristic of soil. Organisms are one of the five major soil￾forming factors, and life itself characterizes a true soil. Anything found

on the surface of Mars—barring totally unexpected news to the

contrary—is no doubt complex and interesting, but it is essentially

weathered parent material, not soil. Arthur C. Clarke came closer with

the title of his science fiction novel Sands of Mars.

On the biological side of soil studies, much progress has been made

recently in elucidating not only biotic function, especially in the case of

bacteria and fungi, but also the identity of which species is performing

what process. We focus primarily on the biological aspects, and devote a

smaller proportion of our total coverage to soil physics and chemistry,

largely because they are discussed extensively in recent treatises by

Hillel (1997) and Brady and Weil (2000).

As a reflection of these new developments, we have singled out Soil

Biodiversity and Linkages to Soil Processes for coverage in its own chap￾ter (Chapter 7) to identify and emphasize one of the areas of burgeoning

research and conservation interest. Also included is a final chapter

(Chapter 9) on laboratory and field exercises that have proven useful in

our course in Soil Ecology at the University of Georgia. We hope they

will be helpful to faculty and students who use this book. We invite our

readers to become “Earth rovers,” and participate in the wonder and

excitement of studying the ecology of soils, a marvelously complex

xiii

milieu. We hope that this textbook, along with other recent ones, such as

the extensive compendium of Lavelle and Spain (2001), will provide the

interested scientist with some of the background necessary to work in

this often difficult but always fascinating field of research. Two col￾leagues who were instrumental in critiquing our first edition, Eugene P.

Odum and Edward T. Elliott, are now deceased, but their influence is

still felt by the soil ecology community and by us. A new generation of

students and postdoctoral fellows from the University of Georgia and

other universities have contributed ideas and inspiration to this effort,

including: Sina Adl, Mike Beare, Heleen Bossuyt, George Brown,

Weixin Cheng, Charles Chiu, Greg Eckert, Christien Ettema, Shenglei

Fu, Jan Garrett, Randi Hansen, Liam Heneghan, Nat Holland, Coeli

Hoover, Shuijin Hu, John Johnston, Keith Kisselle, Sharon Lachnicht,

Karen Lamoncha, Stephanie Madson, Rob Parmelee, Mitchell Pavao￾Zuckerman, Kitti Reynolds, Chuck Rhoades, Breana Simmons, Guang￾long Tian, Petra van Vliet, Thaïs Winsome, Christina Wright, David

Wright, Qiangli Zhang, and our soil ecology colleagues at the University

of Georgia, Colorado State University, Oregon State University, Univer￾sity College Dublin, and at many LTER sites around the world. Any

errors are of course ours, and we would appreciate comments from

readers pointing them out.

We thank our helpful secretary and colleague, Linda Lee Enos, for her

tireless efforts in compiling the tables and figures. Our spouses, Fran,

Dot, and Cathy, deserve credit for their tolerance of this further foray

into the arcane but now ever-more-relevant world of soil biology and

ecology.

David C. Coleman

D. A. Crossley, Jr.

Paul F. Hendrix

Athens, Georgia, February 2004

xiv Preface to the Second Edition