Principles and Applications of Soil Microbiology

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1 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 b I : o t h e k SchnittspahnstraBe 10 D Darmstadt 1nv.-Nr. Prentice Hall Upper Saddle River New Jersey 07458

2 Brief Contents PART 1 HABITAT AND ORGANISMS Chapter 1 Introduction and Historical Perspective 3 2 The Soil Habitat 21 3 Bacteria and Archaea 44 4 Fungi 72 5 Eukaryotic Algae and Cyanobacteria 94 6 Protozoa and Nematodes Viruses Microbial Ecology Molecular Genetic Analysis in Soil Ecology 168 PART 2 MICROBLALLY MEDIATED TRANSFORMATIONS IN SOIL Chapter 10 "Microbial Metabolism Transformations of Carbon and Soil Organic Matter Formation Transformations of Nitrogen Biological Dinitrogen (N 2 ) Fixation: Introduction and Nonsymbiotic Biological Dinitrogen (N 2 ) Fixation: Symbiotic Transformations of Sulfur Transformations of Other Elements 369 PART 3 APPLIED AND ENVIRONMENTAL TOPICS Chapter 17 The Rliizosphere and Spermosphere Mycorrhizal Symbioses Biological Control of Plant Pathogens and Nematodes Biochemistry and Metabolism of Xenobiotics Bioremediation of Contaminated Soils Composting of Organic Wastes Global Gases 498 Glossary/Index 517

3 List of Methods xiv Preface xv List of Contributors xvii Acknowledgments xix < About the Editors xx Chapter Quotations 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

4 vii Chapter 2 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 94. Classification 94 ^ Major Groups Found in Soil 96 Morphology and Reproduction 99

5 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 v Distribution 124 ' > 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 '< Genetic Consequences of Viral Infection 140 J Enumeration, Isolation, and Characterization ofviruses 141 Survival of Viruses in Soil 143, Importance of Viruses 144 Some Future Prospects for Soil Virology 145 Summary 147 Cited References 147 Study Questions 148 Chapter 8 Microbial Ecology 149 Nature of Soil Organisms and Their Interactions 150 Influence of Plants on Soil Organisms 150 Growth Characteristics of Soil Microorganisms 151 Interactions Between Soil Organisms 157 Diversity in Soil Microbial Populations 161 Summary 166

6 IX Cited References 166 Study Questions 167 Chapter 9 Molecular Genetic Analyses in Soil Ecology 168 Methodologies 169 Detection of Specific DNA Sequences in Soil 180 Applications of Molecular Analyses in Soil Microbiology 181 Summary 184 Cited References 184 Study Questions 185 PART 2 MICROBIALLY MEDIATED TRANSFORMATIONS IN SOIL 187 Chapter 10 Microbial Metabolism 189 An Overview of Microbial Metabolism 189 The Chemical Foundations of Metabolism 194 The Role of Enzymes in Metabolism 198 Production of ATP 203 Glycolysis 205 Fermentation 206 Respiration 207 Phototrophy 212 Carbon Nutrition 214 Integration of Metabolic Pathways 215 Summary 216, Cited References 217 General References 217 Study Questions 217 Chapter 11 Carbon Transformations and Soil Organic Matter Formation 218 Significance of Microbes to Carbon Cycling 219 Nature of Organic Materials Added to Soil 221 Decomposition of Naturally Occurring Organic Materials 228 Decomposition Activity of Microorganisms 235 Soil Organic Matter (SOM) 246 Summary 256 Cited References 256 General References 257 Study Questions 258

7 Chapter 12 Transformations of Nitrogen 259 The Nitrogen Cycle 259 Nitrogen Mineralization (Ammonification) /Immobilization 265 Fate of Ammonium in Soil 271 Nitrification 271 Fate of Nitrate in the Soil Environment Denitrificatioh 282 Summary 291 j Cited References General References 293 Study Questions 293 Chapter 13 Biological Dinitrogen Fixation: Introduction and Nonsymbiotic 295 Historical Background 297 The Significance of Biological Dinitrogen Fixation 297 The Nitrogenase Enzyme Complex 298 The Free-Living Dinitrogen-Fixing Bacteria 303 Factors Affecting Dinitrogen Fixation by Free-Liying Diazotrophs 303 The Associative Dinitrogen-Fixing Bacteria 308 Methods for Measuring Dinitrogen Fixation 315 Summary 318 Cited References 318 General References 320 Study Questions 320 Chapter 14 Biological Dinitrogen Fixation: Symbiotic 322 The Symbiosis Between Legumes and Rhizobia 323 The Infection Process 325 Influence of Environmental Factors 332 Legume Inoculation 336 Other Important Symbiotic Dinitrogen-Fixing Associations 340 Summary 343 Cited References 343 General References 344 Study Questions 344 Chapter 15 Transformations of Sulfur 346 The Sulfur Cycle in Agroecosystems and Terrestrial Environments 349 Microbial Transformations of Sulfur in Soil 352

8 Microbial Oxidation of Inorganic Sulfur Compounds 358 Microbial Reduction of Inorganic Sulfur Compounds 363 Volatilization of Inorganic and Organic Sulfur Compounds from Soil 364 Environmental Aspects of Sulfur Pollutants 365 Summary 365 Cited References 366 General References 367 Study Questions 367 Chapter 16 Transformations of Other Elements 369 Phosphorus 370 Iron, Manganese, Mercury, and Selenium 378 Summary 384 Cited References 385 Study Questions 386 PART 3 APPLIED AND ENVIRONMENTAL TOPICS 387 Chapter 17 The Rhizosphere and Spermosphere 389 The Seed and Root Environment 392 The Rhizosphere Environment 394 Plant-Derived Compounds 395 Microbial Populations of the Rhizosphere 398 Movement of Microflora in the Rhizosphere 400 Faunal Populations 402 Microbe-Plant Interactions in the Rhizosphere 402 Inoculants 404 Modeling Rhizosphere Function 405 Future Research Needs 405 Summary 406 Cited References 406 General References 407 Study Questions 407 Chapter 18 Mycorrhizal Symbioses 408 Global Perspective 409 Types of Mycorrhizae 410 Uptake and Transfer of Soil Nutrients 415

9 ^ Carbon Fluxesjin Mycorrhizal Plants 418 Interactions with Other Soil Organisms 418 Management of Mycorrhizae 420 Problems and Potential for Inoculum Production and Use 421 Summary 423 Cited References 424 General References 425 Study Questions 425 Chapter 19 Biological Control of Soilborne Plant Pathogens and Nematodes 427 Fundamental Biological Control Concepts 428 The Plant-Soil-Microbial Equilibrium 429 Approaches to Biological Control 429 Biological Control with Introduced Antagonists 435 Commercialization of Biocontrol Agents 442 Summary 443 Cited References 444 General References 445 Study Questions 446 Chapter 20 Biochemistry and Metabolism of Xenobiotic Chemicals 447 Xenobiotics: What Are They, and Why Are They Problems? 448 Overview of Xenobiotic Degradation 449 Biochemistry of Xenobiotic Metabolism 455 Summary 466 Cited References 466 Study Questions 467 Chapter 21 Bioremediation of Contaminated Soils 469 Diversity and Magnitude of Soil Contaminants 469 Definitions 470 Criteria for Bioremediation 471 Biological Mechanisms of Transformation 471 Strategies for Bioremediation 472 Case Studies of Bioremediation Strategies 473 Advantages and Disadvantages of Bioremediation 479 The Future of Bioremediation 479 Summary 480

10 xiii Cited References 480 Study Questions 481 Chapter 22 Composting of Organic Wastes 482 ^ TheWhat and Why of Composting 482 Properties of Compostable Wastes 484 Microbial Characteristics of the Composting Process 487 V Progression of the Composting Process 489 Compost Systems 492 * - Compost Testing and Use 494 Summary 495 Cited References 496 General References 497 Study Questions 497 Chapter 23 Global Gases 498 Defining Trace Gases 498 Importance of Global Gases 500 Gases Released from Soils 501 General Controls on Gas Production 503 Carbon-Based Gases 503 Nitrogen-Based Gases 509 Summary 514 Cited References 515 General References 515 Study Questions 515 Glossary/Index 517

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