Soil Microbiology

Inbunden, Engelska, 2020

AvRobert L. Tate

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An updated text exploring the properties of the soil microbial communityToday, 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 functionsDiscusses the impact of soil microbial communities on food and health related issuesEmphasizes the importance of soil microbial communities on the sustainability of terrestrial ecosystems and solutions to global issuesThis 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.

Produktinformation

Utgivningsdatum2020-11-16
Mått158 x 231 x 31 mm
Vikt1 021 g
FormatInbunden
SpråkEngelska
Antal sidor592
Upplaga3
FörlagJohn Wiley and Sons Ltd
ISBN9780470311103

Tillhör följande kategorier

Geovetenskap inom Naturvetenskap och teknik
Biologi inom Naturvetenskap och teknik
Biovetenskap inom Naturvetenskap och teknik

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.

Preface xvIntroduction 11 Soil Ecosystems: Physical and Chemical Boundaries 51.1 Soil as an Ecosystem 111.1.1 Soil System Function 121.1.2 Soil Formation and the Microbial Community 151.1.3 Implications of Definition of the Soil Ecosystem 181.2 The Micro-ecosystem 191.2.1 Interaction of Individual Soil Components with the Biotic System 191.2.2 Aboveground and Belowground Communities and Soil Ecosystem Synergistic Development 311.3 The Macro-ecosystem 371.4 Concluding Comments 392 The Soil Ecosystem: Biological Participants 452.1 The Living Soil Component 452.1.1 Biological and Genetic Implications of Occurrence of Living Cells in Soil 462.1.2 Implications of Microbial Properties for Handling of Soil Samples 552.2 Measurement of Soil Microbial Biomass 562.2.1 Direct Counting Methods 582.2.2 ATP Measure of Soil Microbial Biomass 592.2.3 Soil Aerobic Respiration Measurements 602.2.4 Chloroform Fumigation (Extraction and Incubation) Technique 612.2.5 Limitations of Microbial Biomass Measurements 642.3 The Nature of Soil Inhabitants 652.4 Autecology and Soil Microbiology 662.4.1 Limitations to Autecological Research 672.4.2 Autecological Methods 672.4.3 PCR for Quantification of Soil Microbes 722.4.4 Expression of Population Density per Unit of Soil 782.4.5 Products of Soil Autecological Research 782.5 Principles and Products of Synecological Research 792.6 Interphase Between Study of Individual and Community Microbiology 802.7 Concluding Comments 813 Microbial Diversity of Soil Ecosystems 893.1 Classical Culture-Based Studies of Soil Microbial Diversity 903.1.1 Value of Culture-Based Studies of Soil Microbial Diversity 903.1.2 Limitations of Culture-Based Studies of Soil Microbial Diversity 903.1.3 The Challenge of Defining Bacterial Species 913.1.4 Alternatives to Bacterial Strain Isolation 923.2 Surrogate Measures of Soil Microbial Diversity 923.3 Diversity Surrogates: Physiological Profiling 933.3.1 Physiological Profiling of Isolates 933.3.2 Community-Level Physiological Profiling 943.3.3 Value of Community-Level Physiological Profiling 953.3.4 Limitations of Community Level Physiological Profiling 953.4 Diversity Surrogates: Phospholipid Fatty Acid Analysis 963.4.1 PLFA Analysis of Isolates 963.4.2 Community PLFA Analysis 973.4.3 Value of PLFA Analysis 983.4.4 Limitations of PFLA Analysis 983.5 Nucleic Acid-Based Analyses of Soil Microbial Diversity 983.5.1 Nucleic Acid Based Analysis of Isolates 993.5.2 Community Nucleic Acid Analysis 993.5.3 DNA Extraction 1003.5.4 Analysis of Community DNA 1013.6 PCR-Based Methods 1013.6.1 Clone Library Sequencing 1013.6.2 DNA-Based Fingerprinting Techniques 1023.6.3 High-Throughput Amplicon Sequencing 1033.6.4 Limitations of PCR-Based Methods 1053.7 Metagenomics 1053.7.1 Limitations of Metagenomics 1063.8 Conclusions: Utility and Limitations of Diversity Analysis Procedures 1074 Energy Transformations Supporting Growth and Survival of Soil Microbes 1154.1 Microbial Growth Kinetics in Soil 1164.2 Microbial Growth Phases: Laboratory-Observed Microbial Growth Compared to Soil Population Dynamics 1204.3 Mathematical Representation of Soil Microbial Growth 1264.4 Uncoupling Energy Production from Microbial Biomass Synthesis 1304.5 Implications of Microbial Energy and Carbon Transformation Capacities for Soil Biological Processes 1324.5.1 Energy Acquisition in Soil Ecosystems 1324.5.2 Microbial Contribution to Soil Energy and Carbon Transformation 1364.6 Concluding Comments 1435 Process Control in Soil 1495.1 Microbial Response to Abiotic Limitations: General Considerations 1515.1.1 Definition of Limitations to Biological Activity 1515.1.2 Elucidation of Limiting Factors in Soil 1535.2 Impact of Individual Soil Properties on Microbial Activity 1575.2.1 Availability of Nutrients 1585.2.2 Soil Water 1645.2.3 Aeration 1725.2.4 Redox Potential 1735.2.5 pH 1755.2.6 Temperature 1785.3 Microbial Adaptation to Abiotic Stress 1805.4 Concluding Comments 1816 Soil Enzymes: Basic Principles and Their Applications 1856.1 A Philosophical Basis for the Study of Soil Enzymes 1876.2 Basic Soil Enzyme Properties 1926.3 Principles of Enzyme Assays 1966.4 Enzyme Kinetics 2026.5 Distribution of Enzymes in Soil Organic Components 2066.6 Ecology of Extracellular Enzymes 2106.7 Concluding Comments 2127 Microbial Interactions and Community Development and Resilience 2177.1 Common Concepts of Microbial Community Interaction 2207.2 Classes of Biological Interactions 2227.2.1 Neutralism 2237.2.2 Positive Biological Interactions 2237.2.3 Negative Biological Interactions 2277.3 Trophic Interactions and Nutrient Cycling 2357.3.1 Soil Flora and Fauna 2357.3.2 Earthworms: Mediators of Multilevel Mutualism 2387.4 Importance of Microbial Interactions to Overall Biological Community Development 2397.5 Management of Soil Microbial Populations 2417.6 Concluding Comments: Implications of Soil Microbial Interactions 2428 The Rhizosphere/Mycorrhizosphere 2518.1 The Rhizosphere 2528.1.1 The Microbial Community 2548.1.2 Sampling Rhizosphere Soil 2568.1.3 Plant Contributions to the Rhizosphere Ecosystem 2588.1.4 Benefits to Plants Resulting from Rhizosphere Populations 2638.1.5 Plant Pathogens in the Rhizosphere 2648.1.6 Manipulation of Rhizosphere Populations 2658.2 Mycorrhizal Associations 2688.2.1 Mycorrhizae in the Soil Community 2718.2.2 Symbiont Benefits from Mycorrhizal Development 2738.2.3 Environmental Considerations 2758.3 The Mycorrhizosphere 2768.4 Conclusion 2789 Introduction to the Biogeochemical Cycles 2879.1 Introduction to Conceptual and Mathematical Models of Biogeochemical Cycles 2899.1.1 Development and Utility of Conceptual Models 2909.1.2 Mathematical Modeling of Biogeochemical Cycles 2959.2 Specific Models of Biogeochemical Cycles and Their Application 2979.2.1 The Environmental Connection 3009.2.2 Interconnectedness of Biogeochemical Cycle Processes 3029.3 Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance 3069.4 General Processes and Participants in Biogeochemical Cycles 3079.5 Measurement of Biogeochemical Processes: What Data Are Useful? 3099.5.1 Assessment of Biological Activities Associated with Biogeochemical Cycling 3099.5.2 Soil Sampling Aspects of Assessment of Biogeochemical Cycling Rates 3109.5.3 Environmental Impact of Nutrient Cycles 3119.5.4 Example of Complications in Assessing Soil Nutrient Cycling: Nitrogen Mineralization 3129.6 Conclusions 31510 The Carbon Cycle 32110.1 Environmental Implications of the Soil Carbon Cycle 32310.1.1 Soils as a Source or Sink for Carbon Dioxide and Methane 32410.1.2 Diffusion of Soil Carbon Dioxide to the Atmosphere 32510.1.3 Managing Soils to Augment Organic Matter Contents 32710.1.4 Carbon Recycling in Soil Systems 32810.2 Biochemical Aspects of the Soil Carbon Cycle 32910.2.1 Individual Components of Soil Organic Carbon Pools 33010.2.2 Analysis of Soil Organic Carbon Fractions 33710.2.3 Structural versus Functional Analysis 33910.2.4 Microbial Mediators of Soil Carbon Cycle Processes 34210.3 Kinetics of Soil Carbon Transformations 34410.4 Conclusions: Management of the Soil Carbon Cycle 34811 The Nitrogen Cycle: Mineralization, Immobilization, and Nitrification 35511.1 Nitrogen Mineralization 35911.1.1 Soil Organic Nitrogen Resources 35911.1.2 Assessment of Nitrogen Mineralization 36111.2 Nitrogen Immobilization 36211.2.1 Process Definition and Organisms Involved 36211.2.2 Impact of Nitrogen Immobilization Processes on Plant Communities 36211.2.3 Measurement of Soil Nitrogen Immobilization Rates 36511.3 Quantitative Description of Nitrogen Mineralization Kinetics 36611.4 Microbiology of Mineralization 37011.5 Environmental Influences on Nitrogen Mineralization 37011.6 Nitrification 37211.6.1 Identity of Bacterial Species that Nitrify 37311.6.2 Benefits to the Microorganism from Nitrification 37411.6.3 Quantification of Nitrifiers in Soil Samples 37411.6.4 Discrepancies between Population Enumeration Data and Field Nitrification Rates 37611.6.5 Sources of Ammonium and Nitrite for Nitrifiers 37711.6.6 Environmental Properties Limiting Nitrification 37711.7 Concluding Observations: Control of the Internal Soil Nitrogen Cycle 38112 Nitrogen Fixation: The Gateway to Soil Nitrogen Cycling 38912.1 Biochemistry of Nitrogen Fixation 39112.1.1 The Process 39112.1.2 The Enzyme, Nitrogenase 39412.1.3 Measurement of Biological Nitrogen Fixation in Culture and in the Field 39612.2 General Properties of Soil Diazotrophs 40112.2.1 Free-Living Diazotrophs 40112.2.2 Examples of Function of Nonsymbiotic Diazotrophs in Soil Ecosystems 40412.2.3 Diazotrophs in Rhizosphere Populations 40412.2.4 Dizaotrophs in Flooded Ecosystems 40812.3 Conclusions 40913 Biological Nitrogen Fixation 41513.1 Rhizobium–Legume Symbioses 41613.1.1 Grouping of Rhizobial Strains 41613.1.2 Rhizobial Contributions to Nitrogen Fixation 41813.1.3 Nodulation of Legumes 41913.1.4 Plant Control of Nodule Formation 42313.2 Manipulation of Rhizobium–Legume Symbioses for Ecosystem Management 42413.3 Rhizobial Inoculation Procedures 42613.3.1 Inocula Delivery Systems 42613.3.2 Survival of Rhizobial Inocula 42713.3.3 Biological Interactions in Legume Nodulation 43213.4 Nodule Occupants: Indigenous vs Foreign 43213.5 Actinorhizal Associations 43413.6 Conclusions 43614 Denitrification 44714.1 Pathways for Biological Reduction of Soil Nitrate 44814.2 Biochemical Properties of Denitrification 45014.2.1 Carbon and Energy Sources for Denitrifiers 45014.2.2 Induction of Synthesis of Nitrogen Oxide Reductases 45114.3 Environmental Implications of Nitrous Oxide Formation 45214.4 Microbiology of Denitrification 45314.4.1 Assessment of Soil Denitrifier Populations 45314.4.2 General Traits of Denitrifiers 45414.4.3 Generic Identity of Denitrifiers 45514.5 Quantification of Nitrogen Losses from an Ecosystem via Denitrification 45614.5.1 Nitrogen Balance Studies 45614.5.2 Use of Nitrogen Isotopes to Trace Soil Nitrogen Transformations 45814.5.3 Soil Nitrogen Oxide Transformations 45914.5.4 Acetylene Block Method for Assessing Denitrification Processes in Soil 46014.6 Environmental Factors Controlling Denitrification Rates 46214.6.1 Nature and Amount of Organic Matter 46214.6.2 Nitrate Concentration 46414.6.3 Aeration/Moisture 46414.6.4 pH 46514.6.5 Temperature 46614.6.6 Interaction of Limitations to Denitrification in Soil Systems 46714.7 Conclusions 46715 Fundamentals of the Sulfur, Phosphorus, and Mineral Cycles 47715.1 Sulfur in the Soil Ecosystem 47715.2 Biogeochemical Cycling of Sulfur in Soil 47915.3 Biological Sulfur Oxidation 48215.3.1 Microbiology of Sulfur Oxidation 48215.3.2 Environmental Conditions Affecting Sulfur Oxidation 48615.4 Biological Sulfur Reduction 48815.4.1 Anaerobic Biodegradation 49015.4.2 Reducing Acidity of Acid Mine Drainage 49015.4.3 Reduction of Complications of Metal Contamination in Soil 49015.5 Mineralization and Assimilation of Sulfurous Substances 49115.6 The Phosphorus Cycle 49215.7 Microbially Catalyzed Soil Metal Cycling 49415.7.1 Interactions of Soil Metals with Living Systems 49515.7.2 Microbial Response to Elevated Metal Loading 49715.7.3 Microbial Modifications of Metal Mobility in Soils 49815.7.4 Managing Soils Contaminated with Toxic Metals 50115.8 Conclusion 50216 Soil Microbes: Optimizers of Soil System Sustainability and Reparation of Damaged Soils 51116.1 Foundational Concepts of Bioremediation 51416.1.1 Bioremediation Defined 51416.1.2 Conceptual Unity of Bioremediation Science 51516.1.3 Complexity of Remediation Questions 51616.2 The Microbiology of Bioremediation 51716.2.1 Microbes as Soil Remediators 51816.2.2 Substrate–Decomposer Interactions 51916.2.3 Microbial Inoculation for Bioremediation 52816.3 Soil Properties Controlling Bioremediation 53216.3.1 Physical and Chemical Delimiters of Biological Activities 53216.3.2 Sequestration and Sorption Limitations to Bioavailability 53616.4 Concluding Observations 538Concluding Challenge 545Index 549