Soil Microbiology

Name: Soil Microbiology
Brand: Wiley
Price: 114.99 EUR
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Robert L. Tate(Autor*in)

Wiley (Verlag)

3. Auflage

Erschienen am 8. Oktober 2020

592 Seiten

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Inhalt

Cover
Title Page
Copyright Page
Contents
Preface
Introduction
Chapter 1 Soil Ecosystems: Physical and Chemical Boundaries
1.1 Soil as an Ecosystem
1.1.1 Soil System Function
1.1.2 Soil Formation and the Microbial Community
1.1.3 Implications of Definition of the Soil Ecosystem
1.2 The Micro-ecosystem
1.2.1 Interaction of Individual Soil Components with the Biotic System
1.2.2 Aboveground and Belowground Communities and Soil Ecosystem Synergistic Development
1.3 The Macro-ecosystem
1.4 Concluding Comments
References
Chapter 2 The Soil Ecosystem: Biological Participants
2.1 The Living Soil Component
2.1.1 Biological and Genetic Implications of Occurrence of Living Cells in Soil
2.1.2 Implications of Microbial Properties for Handling of Soil Samples
2.2 Measurement of Soil Microbial Biomass
2.2.1 Direct Counting Methods
2.2.2 ATP Measure of Soil Microbial Biomass
2.2.3 Soil Aerobic Respiration Measurements
2.2.4 Chloroform Fumigation (Extraction and Incubation) Technique
2.2.5 Limitations of Microbial Biomass Measurements
2.3 The Nature of Soil Inhabitants
2.4 Autecology and Soil Microbiology
2.4.1 Limitations to Autecological Research
2.4.2 Autecological Methods
2.4.3 PCR for Quantification of Soil Microbes (see Figure 2.7)
2.4.4 Expression of Population Density per Unit of Soil
2.4.5 Products of Soil Autecological Research
2.5 Principles and Products of Synecological Research
2.6 Interphase Between Study of Individual and Community Microbiology
2.7 Concluding Comments
References
Chapter 3 Microbial Diversity of Soil Ecosystems
3.1 Classical Culture-Based Studies of Soil Microbial Diversity
3.1.1 Value of Culture-Based Studies of Soil Microbial Diversity
3.1.2 Limitations of Culture-Based Studies of Soil Microbial Diversity
3.1.3 The Challenge of Defining Bacterial Species
3.1.4 Alternatives to Bacterial Strain Isolation
3.2 Surrogate Measures of Soil Microbial Diversity
3.3 Diversity Surrogates: Physiological Profiling
3.3.1 Physiological Profiling of Isolates
3.3.2 Community-Level Physiological Profiling
3.3.3 Value of Community-Level Physiological Profiling
3.3.4 Limitations of Community Level Physiological Profiling
3.4 Diversity Surrogates: Phospholipid Fatty Acid Analysis
3.4.1 PLFA Analysis of Isolates
3.4.2 Community PLFA Analysis
3.4.3 Value of PLFA Analysis
3.4.4 Limitations of PFLA Analysis
3.5 Nucleic Acid-Based Analyses of Soil Microbial Diversity
3.5.1 Nucleic Acid Based Analysis of Isolates
3.5.2 Community Nucleic Acid Analysis
3.5.3 DNA Extraction
3.5.4 Analysis of Community DNA
3.6 PCR-Based Methods
3.6.1 Clone Library Sequencing
3.6.2 DNA-Based Fingerprinting Techniques
3.6.3 High-Throughput Amplicon Sequencing
3.6.4 Limitations of PCR-Based Methods
3.7 Metagenomics
3.7.1 Limitations of Metagenomics
3.8 Conclusions: Utility and Limitations of Diversity Analysis Procedures
References
Chapter 4 Energy Transformations Supporting Growth and Survival of Soil Microbes
4.1 Microbial Growth Kinetics in Soil
4.2 Microbial Growth Phases: Laboratory-Observed Microbial Growth Compared to Soil Population Dynamics
4.3 Mathematical Representation of Soil Microbial Growth
4.4 Uncoupling Energy Production from Microbial Biomass Synthesis
4.5 Implications of Microbial Energy and Carbon Transformation Capacities for Soil Biological Processes
4.5.1 Energy Acquisition in Soil Ecosystems
4.5.2 Microbial Contribution to Soil Energy and Carbon Transformation
4.6 Concluding Comments
References
Chapter 5 Process Control in Soil
5.1 Microbial Response to Abiotic Limitations: General Considerations
5.1.1 Definition of Limitations to Biological Activity
5.1.2 Elucidation of Limiting Factors in Soil
5.2 Impact of Individual Soil Properties on Microbial Activity
5.2.1 Availability of Nutrients
5.2.2 Soil Water
5.2.3 Aeration
5.2.4 Redox Potential
5.2.5 pH
5.2.6 Temperature
5.3 Microbial Adaptation to Abiotic Stress
5.4 Concluding Comments
References
Chapter 6 Soil Enzymes: Basic Principles and Their Applications
6.1 A Philosophical Basis for the Study of Soil Enzymes
6.2 Basic Soil Enzyme Properties
6.3 Principles of Enzyme Assays
6.4 Enzyme Kinetics
6.5 Distribution of Enzymes in Soil Organic Components
6.6 Ecology of Extracellular Enzymes
6.7 Concluding Comments
References
Chapter 7 Microbial Interactions and Community Development and Resilience
7.1 Common Concepts of Microbial Community Interaction
7.2 Classes of Biological Interactions
7.2.1 Neutralism
7.2.2 Positive Biological Interactions
7.2.3 Negative Biological Interactions
7.3 Trophic Interactions and Nutrient Cycling
7.3.1 Soil Flora and Fauna
7.3.2 Earthworms: Mediators of Multilevel Mutualism
7.4 Importance of Microbial Interactions to Overall Biological Community Development
7.5 Management of Soil Microbial Populations
7.6 Concluding Comments: Implications of Soil Microbial Interactions
References
Chapter 8 The Rhizosphere/Mycorrhizosphere
8.1 The Rhizosphere
8.1.1 The Microbial Community
8.1.2 Sampling Rhizosphere Soil
8.1.3 Plant Contributions to the Rhizosphere Ecosystem
8.1.4 Benefits to Plants Resulting from Rhizosphere Populations
8.1.5 Plant Pathogens in the Rhizosphere
8.1.6 Manipulation of Rhizosphere Populations
8.2 Mycorrhizal Associations
8.2.1 Mycorrhizae in the Soil Community
8.2.2 Symbiont Benefits from Mycorrhizal Development
8.2.3 Environmental Considerations
8.3 The Mycorrhizosphere
8.4 Conclusion
References
Chapter 9 Introduction to the Biogeochemical Cycles
9.1 Introduction to Conceptual and Mathematical Models of Biogeochemical Cycles
9.1.1 Development and Utility of Conceptual Models
9.1.2 Mathematical Modeling of Biogeochemical Cycles
9.2 Specific Models of Biogeochemical Cycles and Their Application
9.2.1 The Environmental Connection
9.2.2 Interconnectedness of Biogeochemical Cycle Processes
9.3 Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance
9.4 General Processes and Participants in Biogeochemical Cycles
9.5 Measurement of Biogeochemical Processes: What Data Are Useful?
9.5.1 Assessment of Biological Activities Associated with Biogeochemical Cycling
9.5.2 Soil Sampling Aspects of Assessment of Biogeochemical Cycling Rates
9.5.3 Environmental Impact of Nutrient Cycles
9.5.4 Example of Complications in Assessing Soil Nutrient Cycling: Nitrogen Mineralization
9.6 Conclusions
References
Chapter 10 The Carbon Cycle
10.1 Environmental Implications of the Soil Carbon Cycle
10.1.1 Soils as a Source or Sink for Carbon Dioxide and Methane
10.1.2 Diffusion of Soil Carbon Dioxide to the Atmosphere
10.1.3 Managing Soils to Augment Organic Matter Contents
10.1.4 Carbon Recycling in Soil Systems
10.2 Biochemical Aspects of the Soil Carbon Cycle
10.2.1 Individual Components of Soil Organic Carbon Pools
10.2.2 Analysis of Soil Organic Carbon Fractions
10.2.3 Structural versus Functional Analysis
10.2.4 Microbial Mediators of Soil Carbon Cycle Processes
10.3 Kinetics of Soil Carbon Transformations
10.4 Conclusions: Management of the Soil Carbon Cycle
References
Chapter 11 The Nitrogen Cycle: Mineralization, Immobilization, and Nitrification
11.1 Nitrogen Mineralization
11.1.1 Soil Organic Nitrogen Resources
11.1.2 Assessment of Nitrogen Mineralization
11.2 Nitrogen Immobilization
11.2.1 Process Definition and Organisms Involved
11.2.2 Impact of Nitrogen Immobilization Processes on Plant Communities
11.2.3 Measurement of Soil Nitrogen Immobilization Rates
11.3 Quantitative Description of Nitrogen Mineralization Kinetics
11.4 Microbiology of Mineralization
11.5 Environmental Influences on Nitrogen Mineralization
11.6 Nitrification
11.6.1 Identity of Bacterial Species that Nitrify
11.6.2 Benefits to the Microorganism from Nitrification
11.6.3 Quantification of Nitrifiers in Soil Samples
11.6.4 Discrepancies between Population Enumeration Data and Field Nitrification Rates
11.6.5 Sources of Ammonium and Nitrite for Nitrifiers
11.6.6 Environmental Properties Limiting Nitrification
11.7 Concluding Observations: Control of the Internal Soil Nitrogen Cycle
References
Chapter 12 Nitrogen Fixation: The Gateway to Soil Nitrogen Cycling
12.1 Biochemistry of Nitrogen Fixation
12.1.1 The Process
12.1.2 The Enzyme, Nitrogenase
12.1.3 Measurement of Biological Nitrogen Fixation in Culture and in the Field
12.2 General Properties of Soil Diazotrophs
12.2.1 Free-Living Diazotrophs
12.2.2 Examples of Function of Nonsymbiotic Diazotrophs in Soil Ecosystems
12.2.3 Diazotrophs in Rhizosphere Populations
12.2.4 Dizaotrophs in Flooded Ecosystems
12.3 Conclusions
References
Chapter 13 Biological Nitrogen Fixation
13.1 Rhizobium-Legume Symbioses
13.1.1 Grouping of Rhizobial Strains
13.1.2 Rhizobial Contributions to Nitrogen Fixation
13.1.3 Nodulation of Legumes
13.1.4 Plant Control of Nodule Formation
13.2 Manipulation of Rhizobium-Legume Symbioses for Ecosystem Management
13.3 Rhizobial Inoculation Procedures
13.3.1 Inocula Delivery Systems
13.3.2 Survival of Rhizobial Inocula
13.3.3 Biological Interactions in Legume Nodulation
13.4 Nodule Occupants: Indigenous vs Foreign
13.5 Actinorhizal Associations
13.6 Conclusions
References
Chapter 14 Denitrification
14.1 Pathways for Biological Reduction of Soil Nitrate
14.2 Biochemical Properties of Denitrification
14.2.1 Carbon and Energy Sources for Denitrifiers
14.2.2 Induction of Synthesis of Nitrogen Oxide Reductases
14.3 Environmental Implications of Nitrous Oxide Formation
14.4 Microbiology of Denitrification
14.4.1 Assessment of Soil Denitrifier Populations
14.4.2 General Traits of Denitrifiers
14.4.3 Generic Identity of Denitrifiers
14.5 Quantification of Nitrogen Losses from an Ecosystem via Denitrification
14.5.1 Nitrogen Balance Studies
14.5.2 Use of Nitrogen Isotopes to Trace Soil Nitrogen Transformations
14.5.3 Soil Nitrogen Oxide Transformations
14.5.4 Acetylene Block Method for Assessing Denitrification Processes in Soil
14.6 Environmental Factors Controlling Denitrification Rates
14.6.1 Nature and Amount of Organic Matter
14.6.2 Nitrate Concentration
14.6.3 Aeration/Moisture
14.6.4 pH
14.6.5 Temperature
14.6.6 Interaction of Limitations to Denitrification in Soil Systems
14.7 Conclusions
References
Chapter 15 Fundamentals of the Sulfur, Phosphorus, and Mineral Cycles
15.1 Sulfur in the Soil Ecosystem
15.2 Biogeochemical Cycling of Sulfur in Soil
15.3 Biological Sulfur Oxidation
15.3.1 Microbiology of Sulfur Oxidation
15.3.2 Environmental Conditions Affecting Sulfur Oxidation
15.4 Biological Sulfur Reduction
15.4.1 Anaerobic Biodegradation
15.4.2 Reducing Acidity of Acid Mine Drainage
15.4.3 Reduction of Complications of Metal Contamination in Soil
15.5 Mineralization and Assimilation of Sulfurous Substances
15.6 The Phosphorus Cycle
15.7 Microbially Catalyzed Soil Metal Cycling
15.7.1 Interactions of Soil Metals with Living Systems
15.7.2 Microbial Response to Elevated Metal Loading
15.7.3 Microbial Modifications of Metal Mobility in Soils
15.7.4 Managing Soils Contaminated with Toxic Metals
15.8 Conclusion
References
Chapter 16 Soil Microbes: Optimizers of Soil System Sustainability and Reparation of Damaged Soils
16.1 Foundational Concepts of Bioremediation
16.1.1 Bioremediation Defined
16.1.2 Conceptual Unity of Bioremediation Science
16.1.3 Complexity of Remediation Questions
16.2 The Microbiology of Bioremediation
16.2.1 Microbes as Soil Remediators
16.2.2 Substrate-Decomposer Interactions
16.2.3 Microbial Inoculation for Bioremediation
16.3 Soil Properties Controlling Bioremediation
16.3.1 Physical and Chemical Delimiters of Biological Activities
16.3.2 Sequestration and Sorption Limitations to Bioavailability
16.4 Concluding Observations
References
Concluding Challenge
Index
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