Soil Microbiology

Preface xv Introduction 1 1 Soil Ecosystems: Physical and Chemical Boundaries 5 1.1 Soil as an Ecosystem 11 1.1.1 Soil System Function 12 1.1.2 Soil Formation and the Microbial Community 15 1.1.3 Implications of Definition of the Soil Ecosystem 18 1.2 The Micro-ecosystem 19 1.2.1 Interaction of Individual Soil Components with the Biotic System 19 1.2.2 Aboveground and Belowground Communities and Soil Ecosystem Synergistic Development 31 1.3 The Macro-ecosystem 37 1.4 Concluding Comments 39 2 The Soil Ecosystem: Biological Participants 45 2.1 The Living Soil Component 45 2.1.1 Biological and Genetic Implications of Occurrence of Living Cells in Soil 46 2.1.2 Implications of Microbial Properties for Handling of Soil Samples 55 2.2 Measurement of Soil Microbial Biomass 56 2.2.1 Direct Counting Methods 58 2.2.2 ATP Measure of Soil Microbial Biomass 59 2.2.3 Soil Aerobic Respiration Measurements 60 2.2.4 Chloroform Fumigation (Extraction and Incubation) Technique 61 2.2.5 Limitations of Microbial Biomass Measurements 64 2.3 The Nature of Soil Inhabitants 65 2.4 Autecology and Soil Microbiology 66 2.4.1 Limitations to Autecological Research 67 2.4.2 Autecological Methods 67 2.4.3 PCR for Quantification of Soil Microbes 72 2.4.4 Expression of Population Density per Unit of Soil 78 2.4.5 Products of Soil Autecological Research 78 2.5 Principles and Products of Synecological Research 79 2.6 Interphase Between Study of Individual and Community Microbiology 80 2.7 Concluding Comments 81 3 Microbial Diversity of Soil Ecosystems 89 3.1 Classical Culture-Based Studies of Soil Microbial Diversity 90 3.1.1 Value of Culture-Based Studies of Soil Microbial Diversity 90 3.1.2 Limitations of Culture-Based Studies of Soil Microbial Diversity 90 3.1.3 The Challenge of Defining Bacterial Species 91 3.1.4 Alternatives to Bacterial Strain Isolation 92 3.2 Surrogate Measures of Soil Microbial Diversity 92 3.3 Diversity Surrogates: Physiological Profiling 93 3.3.1 Physiological Profiling of Isolates 93 3.3.2 Community-Level Physiological Profiling 94 3.3.3 Value of Community-Level Physiological Profiling 95 3.3.4 Limitations of Community Level Physiological Profiling 95 3.4 Diversity Surrogates: Phospholipid Fatty Acid Analysis 96 3.4.1 PLFA Analysis of Isolates 96 3.4.2 Community PLFA Analysis 97 3.4.3 Value of PLFA Analysis 98 3.4.4 Limitations of PFLA Analysis 98 3.5 Nucleic Acid-Based Analyses of Soil Microbial Diversity 98 3.5.1 Nucleic Acid Based Analysis of Isolates 99 3.5.2 Community Nucleic Acid Analysis 99 3.5.3 DNA Extraction 100 3.5.4 Analysis of Community DNA 101 3.6 PCR-Based Methods 101 3.6.1 Clone Library Sequencing 101 3.6.2 DNA-Based Fingerprinting Techniques 102 3.6.3 High-Throughput Amplicon Sequencing 103 3.6.4 Limitations of PCR-Based Methods 105 3.7 Metagenomics 105 3.7.1 Limitations of Metagenomics 106 3.8 Conclusions: Utility and Limitations of Diversity Analysis Procedures 107 4 Energy Transformations Supporting Growth and Survival of Soil Microbes 115 4.1 Microbial Growth Kinetics in Soil 116 4.2 Microbial Growth Phases: Laboratory-Observed Microbial Growth Compared to Soil Population Dynamics 120 4.3 Mathematical Representation of Soil Microbial Growth 126 4.4 Uncoupling Energy Production from Microbial Biomass Synthesis 130 4.5 Implications of Microbial Energy and Carbon Transformation Capacities for Soil Biological Processes 132 4.5.1 Energy Acquisition in Soil Ecosystems 132 4.5.2 Microbial Contribution to Soil Energy and Carbon Transformation 136 4.6 Concluding Comments 143 5 Process Control in Soil 149 5.1 Microbial Response to Abiotic Limitations: General Considerations 151 5.1.1 Definition of Limitations to Biological Activity 151 5.1.2 Elucidation of Limiting Factors in Soil 153 5.2 Impact of Individual Soil Properties on Microbial Activity 157 5.2.1 Availability of Nutrients 158 5.2.2 Soil Water 164 5.2.3 Aeration 172 5.2.4 Redox Potential 173 5.2.5 pH 175 5.2.6 Temperature 178 5.3 Microbial Adaptation to Abiotic Stress 180 5.4 Concluding Comments 181 6 Soil Enzymes: Basic Principles and Their Applications 185 6.1 A Philosophical Basis for the Study of Soil Enzymes 187 6.2 Basic Soil Enzyme Properties 192 6.3 Principles of Enzyme Assays 196 6.4 Enzyme Kinetics 202 6.5 Distribution of Enzymes in Soil Organic Components 206 6.6 Ecology of Extracellular Enzymes 210 6.7 Concluding Comments 212 7 Microbial Interactions and Community Development and Resilience 217 7.1 Common Concepts of Microbial Community Interaction 220 7.2 Classes of Biological Interactions 222 7.2.1 Neutralism 223 7.2.2 Positive Biological Interactions 223 7.2.3 Negative Biological Interactions 227 7.3 Trophic Interactions and Nutrient Cycling 235 7.3.1 Soil Flora and Fauna 235 7.3.2 Earthworms: Mediators of Multilevel Mutualism 238 7.4 Importance of Microbial Interactions to Overall Biological Community Development 239 7.5 Management of Soil Microbial Populations 241 7.6 Concluding Comments: Implications of Soil Microbial Interactions 242 8 The Rhizosphere/Mycorrhizosphere 251 8.1 The Rhizosphere 252 8.1.1 The Microbial Community 254 8.1.2 Sampling Rhizosphere Soil 256 8.1.3 Plant Contributions to the Rhizosphere Ecosystem 258 8.1.4 Benefits to Plants Resulting from Rhizosphere Populations 263 8.1.5 Plant Pathogens in the Rhizosphere 264 8.1.6 Manipulation of Rhizosphere Populations 265 8.2 Mycorrhizal Associations 268 8.2.1 Mycorrhizae in the Soil Community 271 8.2.2 Symbiont Benefits from Mycorrhizal Development 273 8.2.3 Environmental Considerations 275 8.3 The Mycorrhizosphere 276 8.4 Conclusion 278 9 Introduction to the Biogeochemical Cycles 287 9.1 Introduction to Conceptual and Mathematical Models of Biogeochemical Cycles 289 9.1.1 Development and Utility of Conceptual Models 290 9.1.2 Mathematical Modeling of Biogeochemical Cycles 295 9.2 Specific Models of Biogeochemical Cycles and Their Application 297 9.2.1 The Environmental Connection 300 9.2.2 Interconnectedness of Biogeochemical Cycle Processes 302 9.3 Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance 306 9.4 General Processes and Participants in Biogeochemical Cycles 307 9.5 Measurement of Biogeochemical Processes: What Data Are Useful? 309 9.5.1 Assessment of Biological Activities Associated with Biogeochemical Cycling 309 9.5.2 Soil Sampling Aspects of Assessment of Biogeochemical Cycling Rates 310 9.5.3 Environmental Impact of Nutrient Cycles 311 9.5.4 Example of Complications in Assessing Soil Nutrient Cycling: Nitrogen Mineralization 312 9.6 Conclusions 315 10 The Carbon Cycle 321 10.1 Environmental Implications of the Soil Carbon Cycle 323 10.1.1 Soils as a Source or Sink for Carbon Dioxide and Methane 324 10.1.2 Diffusion of Soil Carbon Dioxide to the Atmosphere 325 10.1.3 Managing Soils to Augment Organic Matter Contents 327 10.1.4 Carbon Recycling in Soil Systems 328 10.2 Biochemical Aspects of the Soil Carbon Cycle 329 10.2.1 Individual Components of Soil Organic Carbon Pools 330 10.2.2 Analysis of Soil Organic Carbon Fractions 337 10.2.3 Structural versus Functional Analysis 339 10.2.4 Microbial Mediators of Soil Carbon Cycle Processes 342 10.3 Kinetics of Soil Carbon Transformations 344 10.4 Conclusions: Management of the Soil Carbon Cycle 348 11 The Nitrogen Cycle: Mineralization, Immobilization, and Nitrification 355 11.1 Nitrogen Mineralization 359 11.1.1 Soil Organic Nitrogen Resources 359 11.1.2 Assessment of Nitrogen Mineralization 361 11.2 Nitrogen Immobilization 362 11.2.1 Process Definition and Organisms Involved 362 11.2.2 Impact of Nitrogen Immobilization Processes on Plant Communities 362 11.2.3 Measurement of Soil Nitrogen Immobilization Rates 365 11.3 Quantitative Description of Nitrogen Mineralization Kinetics 366 11.4 Microbiology of Mineralization 370 11.5 Environmental Influences on Nitrogen Mineralization 370 11.6 Nitrification 372 11.6.1 Identity of Bacterial Species that Nitrify 373 11.6.2 Benefits to the Microorganism from Nitrification 374 11.6.3 Quantification of Nitrifiers in Soil Samples 374 11.6.4 Discrepancies between Population Enumeration Data and Field Nitrification Rates 376 11.6.5 Sources of Ammonium and Nitrite for Nitrifiers 377 11.6.6 Environmental Properties Limiting Nitrification 377 11.7 Concluding Observations: Control of the Internal Soil Nitrogen Cycle 381 12 Nitrogen Fixation: The Gateway to Soil Nitrogen Cycling 389 12.1 Biochemistry of Nitrogen Fixation 391 12.1.1 The Process 391 12.1.2 The Enzyme, Nitrogenase 394 12.1.3 Measurement of Biological Nitrogen Fixation in Culture and in the Field 396 12.2 General Properties of Soil Diazotrophs 401 12.2.1 Free-Living Diazotrophs 401 12.2.2 Examples of Function of Nonsymbiotic Diazotrophs in Soil Ecosystems 404 12.2.3 Diazotrophs in Rhizosphere Populations 404 12.2.4 Dizaotrophs in Flooded Ecosystems 408 12.3 Conclusions 409 13 Biological Nitrogen Fixation 415 13.1 Rhizobium–Legume Symbioses 416 13.1.1 Grouping of Rhizobial Strains 416 13.1.2 Rhizobial Contributions to Nitrogen Fixation 418 13.1.3 Nodulation of Legumes 419 13.1.4 Plant Control of Nodule Formation 423 13.2 Manipulation of Rhizobium–Legume Symbioses for Ecosystem Management 424 13.3 Rhizobial Inoculation Procedures 426 13.3.1 Inocula Delivery Systems 426 13.3.2 Survival of Rhizobial Inocula 427 13.3.3 Biological Interactions in Legume Nodulation 432 13.4 Nodule Occupants: Indigenous vs Foreign 432 13.5 Actinorhizal Associations 434 13.6 Conclusions 436 14 Denitrification 447 14.1 Pathways for Biological Reduction of Soil Nitrate 448 14.2 Biochemical Properties of Denitrification 450 14.2.1 Carbon and Energy Sources for Denitrifiers 450 14.2.2 Induction of Synthesis of Nitrogen Oxide Reductases 451 14.3 Environmental Implications of Nitrous Oxide Formation 452 14.4 Microbiology of Denitrification 453 14.4.1 Assessment of Soil Denitrifier Populations 453 14.4.2 General Traits of Denitrifiers 454 14.4.3 Generic Identity of Denitrifiers 455 14.5 Quantification of Nitrogen Losses from an Ecosystem via Denitrification 456 14.5.1 Nitrogen Balance Studies 456 14.5.2 Use of Nitrogen Isotopes to Trace Soil Nitrogen Transformations 458 14.5.3 Soil Nitrogen Oxide Transformations 459 14.5.4 Acetylene Block Method for Assessing Denitrification Processes in Soil 460 14.6 Environmental Factors Controlling Denitrification Rates 462 14.6.1 Nature and Amount of Organic Matter 462 14.6.2 Nitrate Concentration 464 14.6.3 Aeration/Moisture 464 14.6.4 pH 465 14.6.5 Temperature 466 14.6.6 Interaction of Limitations to Denitrification in Soil Systems 467 14.7 Conclusions 467 15 Fundamentals of the Sulfur, Phosphorus, and Mineral Cycles 477 15.1 Sulfur in the Soil Ecosystem 477 15.2 Biogeochemical Cycling of Sulfur in Soil 479 15.3 Biological Sulfur Oxidation 482 15.3.1 Microbiology of Sulfur Oxidation 482 15.3.2 Environmental Conditions Affecting Sulfur Oxidation 486 15.4 Biological Sulfur Reduction 488 15.4.1 Anaerobic Biodegradation 490 15.4.2 Reducing Acidity of Acid Mine Drainage 490 15.4.3 Reduction of Complications of Metal Contamination in Soil 490 15.5 Mineralization and Assimilation of Sulfurous Substances 491 15.6 The Phosphorus Cycle 492 15.7 Microbially Catalyzed Soil Metal Cycling 494 15.7.1 Interactions of Soil Metals with Living Systems 495 15.7.2 Microbial Response to Elevated Metal Loading 497 15.7.3 Microbial Modifications of Metal Mobility in Soils 498 15.7.4 Managing Soils Contaminated with Toxic Metals 501 15.8 Conclusion 502 16 Soil Microbes: Optimizers of Soil System Sustainability and Reparation of Damaged Soils 511 16.1 Foundational Concepts of Bioremediation 514 16.1.1 Bioremediation Defined 514 16.1.2 Conceptual Unity of Bioremediation Science 515 16.1.3 Complexity of Remediation Questions 516 16.2 The Microbiology of Bioremediation 517 16.2.1 Microbes as Soil Remediators 518 16.2.2 Substrate–Decomposer Interactions 519 16.2.3 Microbial Inoculation for Bioremediation 528 16.3 Soil Properties Controlling Bioremediation 532 16.3.1 Physical and Chemical Delimiters of Biological Activities 532 16.3.2 Sequestration and Sorption Limitations to Bioavailability 536 16.4 Concluding Observations 538 Concluding Challenge 545 Index 549