Principles and Applications of Soil Microbiology

Principles and Applications of Soil Microbiology

Edited by

David M. Sylvia JefFry J. Fuhrmann Peter G. Hartel David A. Zuberer Technische Universitat Darmstadt FACHBEREICH 10 — BIOLOGIE — B i bI:ot h ek— SchnittspahnstraBe 10 D-64287 D a r m s t a d t

1nv.-Nr.

Prentice Hall Upper Saddle River New Jersey 07458

Brief Contents PART 1 HABITAT AND ORGANISMS Chapter 1 Introduction and Historical Perspective 2

The Soil Habitat

3

Bacteria and Archaea

4

Fungi

44

72

5 Eukaryotic Algae and Cyanobacteria 6 ™

Protozoa and Nematodes

7 Viruses

3

21

94

114

132

8

Microbial Ecology

149

9

Molecular Genetic Analysis in Soil Ecology

168

PART 2 MICROBLALLY MEDIATED TRANSFORMATIONS IN SOIL Chapter 10 "Microbial Metabolism

189

11 Transformations of Carbon and Soil Organic Matter Formation 12 Transformations of Nitrogen

13 Biological Dinitrogen (N2) Fixation: Introduction and Nonsymbiotic 14 Biological Dinitrogen (N2) Fixation: Symbiotic 15 Transformations of Sulfur

322

346

16 Transformations of Other Elements

369

PART 3 APPLIED AND ENVIRONMENTAL TOPICS Chapter 17 18

The Rliizosphere and Spermosphere Mycorrhizal Symbioses

389

408

19 Biological Control of Plant Pathogens and Nematodes 20

Biochemistry and Metabolism of Xenobiotics

21 Bioremediation of Contaminated Soils 22

Composting of Organic Wastes

23

Global Gases

Glossary/Index

517

498

218

259

482

469

447

427

295

Contents

List of Methods

xiv

Preface xv List of Contributors Acknowledgments

xvii xix

< About the Editors Chapter Quotations

xx xxii

PART 1

HABITAT AND ORGANISMS

1

Chapter 1

Introduction and Historical Perspective

3

The Soil Habitat 3 The Nature of Cellular Organisms 4 Classification of Organisms 4 Organisms in the Soil 7 The Historical Context of Soil Microbiology 9 Current and Future Directions 15 Summary 18 Cited References 19 General References 20 Worldwide Web Sites of Interest to Soil Microbiology 20 Study Questions 20

Contents Chapter 2

vii The Soil Habitat

21

Soil Description 21 Soil Physical Characteristics 24 Soil Chemical Characteristics 29 Soil Abiotic^Factors 35 Summary 42 Cited References 42 Study Questions 43

Chapter 3

Bacteria and Archaea

44

Classification 44 Structure and Function of Bacterial Cells 46 Mechanisms of Gene Modification and Transfer 57 Nutrition and Metabolism of Soil Bacteria 59 Ecology bf Soil Bacteria 62 , The Actinomycetes 65 Quantifying Bacterial Populations 66 Summary 69 Cited References 70 General References 70 Study Questions 71

Chapter 4

Fungi

72

iFungal Cell Structure 72 Growth and Reproduction, with Reference to Taxonomy 73 Nutritional Patterns 83 Genetic Patterns 85 Dispersal Patterns 88 Ecological Interactions 90 Summary 91 Cited References 91 General References 92 Study Questions 92

Chapter 5

Eukaryotic Algae and Cyanobacteria Classification 94

^

Major Groups Found in Soil 96 Morphology and Reproduction 99

94.

viii

Contents Physiology 100 Ecology 103, Soil Formation and Quality 108

.

Summary 111 Cited References 111 General References 113 Study Questions 113 Chapter 6 ^

Protozoa and Nematodes

114

Classification 114 Feeding Behavior 119 Distribution 124

v

'•>

Function 127 Summary 129 Cited References 130 General References 130

"

Study Questions 131

Chapter 7

Viruses

132

The Viral Genome 133 Classification of Viruses 134 Types of Bacterial Virus Life Cycles 138 '