Robert L. Tate

Soil Microbiology (eBook, ePUB)

• Format: ePub

Produktbeschreibung

An updated text exploring the properties of the soil microbial community Today, the environmentally oriented specialties of microbiology are shifting from considering a single or a few microbial species to focusing on the entire microbial community and its interactions. The third edition of Soil Microbiology has been fully revised and updated to reflect this change, with a new focus on microbial communities and how they impact global ecology. The third edition still provides thorough coverage of basic soil microbiology principles, yet the textbook also expands students' understanding of the role the soil microbial community plays in global environmental health and human health. They can also learn more about the techniques used to conduct analysis at this level. Readers will benefit from the edition's expanded use of figures and tables as well as the recommendations for further reading found within each chapter. * Considers the impact of environmental perturbations on microbial community structure as well as the implications for soil system functions * Discusses the impact of soil microbial communities on food and health related issues * Emphasizes the importance of soil microbial communities on the sustainability of terrestrial ecosystems and solutions to global issues This third edition is a suitable text for those studying soil microbiology and soil ecology at the undergraduate or graduate level. It also serves as a valuable reference tool for professionals working in the fields of reclamation and soil management.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 592
• Erscheinungstermin: 21. Oktober 2020
• Englisch
• ISBN-13: 9781119114246
• Artikelnr.: 60477111

Autorenporträt

DR. TATE is Professor Emeritus at Rutgers University and held appointments in the Department of Environmental Sciences and the Environmental and Occupational Health Sciences Institute. The author conducted research at the leading edge of soil microbiology and taught soil microbiology and related courses. He is a fellow of the two leading scientific societies serving soil microbiologists (Soil Science Society of America, Agronomy Society). Dr. Tate served as the Editor-in-Chief of Soil Science and editor of the Journal of the Soil Science Society of America. At Rutgers, he was the Director of the undergraduate Environmental Science Program and Chair of the Department of Environmental Sciences.

Inhaltsangabe

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