Soil Microbiology
, by Tate, Robert L.
- ISBN: 9780470311103 | 047031110X
- Cover: Hardcover
- Copyright: 11/24/2020
The environmentally oriented specialties of microbiology are in the midst of a major paradigm shift from a focus on single or a few key microbial species to consideration of the entirety of the microbial community and its interactions. This fully revised and updated edition focuses on the importance of soil microbial communities to sustainability of terrestrial ecosystems and solutions to global problems. Basic principles are covered, and details of the finer points of processes and their implications have been updated. This is a one-of-a-kind reference for advanced students and professionals.
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.
Dedication
Preface
Introduction
Soil Ecosystems: Physical and Chemical Boundaries
Soil as an Ecosystem
Soil System Function
Soil Formation and the Microbial Community
Implications of Definition of the Soil Ecosystem
The Micro-Ecosystem
Interactions of Individual Soil Components with the Biotic System
Clay and Ecosystem Function
Humic Substances and Ecosystem Function
Aboveground and Belowground Communities and Ecosystem Synergetic Development
Soil Aggregate Structure Development and Its Impact on Ecosystem Development
Separation of Soil Particulates by Density Fractionation
The Macro-Ecosystem
Concluding Comments
References
The Soil Ecosystem: Biological Participants
The Living Soil Component
Biological and Genetic Implications of Occurrence of Living Cells in Soil
Gene Pool Potential
Cellular Replication and Soil Properties
Cell Structure and Biological Stability in Soil
Resting Structure and Soil Respiration
Microbial Activity and Soil Properties
Microbial Links to Aboveground Community
Implications of Microbial Properties of Handling of Soil Samples
Measurement of Soil Microbial biomass
Direct Counting Measurements
ATP Measurement and Soil Microbial Biomass
Soil Aerobic Respiration Measurements
Chloroform Fumigation (Extraction and Incubation Technique)
Limitation of Microbial Biomass Measurements
The Nature of Soil Inhabitants
Autecology and Soil Microbiology
Limitations of Autecological Research
2.4.1. Autecological Methods
2.4.2. Viable Counts/Enrichment Cultures
2.4.2.1. Most Probable Number Procedures
2.4.2.2. Sources of Error in Viable Count procedures
2.4.2.3. Interpretation of Viable Count Data
2.4.3. PCR for Quantification of Soil Microbes
2.4.3.1. SYBR method for Real-Time PCR
2.4.3.2. Taq-Man Method for Real Time PCR
2.4.3.3. Applications of Quantitative Real Time PCR for Soil Microbiology
2.4.3.4. Limitations of q PCR Approaches
2.4.4. Expression of Population Density per Unit of Soil
2.4.5. Products of Soil Autoecological Research
2.5. Principles and Products of Synecological Research
2.6. Interphase between Study of Individual and Community Microbiology
2.7. Concluding Comments.
References
Microbial Diversity in Soil Ecosystems
Classical Culture-Based Studies of Soil Microbial Diversity
Value of Culture-Based Studies of Soil Microbial Diversity
Limitations of Culture-Based Studies of Soil Microbial Diversity
The Challenge of defining Bacterial Species
Alternatives to Bacterial Strain Isolation
Surrogate Measures of Soil Microbial Diversity
Diversity Surrogates: Physiological Profiling
Physiological Profiling of Isolates
Community Level Physiological Profiling
Value of Community Level Physiological Profiling
Limitations of Community Level Profiling
Diversity Surrogates: Phospholipid Fatty Analysis (PLFA)
PLFA Analysis of Isolates
Community PLFA Analysis
Limitations of Phospholipid Fatty Acid Analysis
Nucleic Acid Based Analysis of Soil Microbial Diversity
Nucleic Acid Based Analysis of Soil Microbial Isolates
Community Nucleic Acid Analysis
DNA Extraction
Analysis of Community DNA
PCR Based Methods
Values and Limitations of Clone Library Sequencing
DNA Based Fingerprinting Techniques
Value and Limitations of DNA Based Fingerprinting Techniques
High Through Put Amplicon Sequence
3.7. Metagenomes
3.10. Conclusions: Utility and Limitations of Diversity Analysis Procedures
References
Energy Transformations Supporting Growth and Survival of Soil Microbes
Microbial Growth Kinetics in Soil
Microbial Growth Phases: Laboratory-Observed Microbial Growth Compared to Soil Population Dynamics
Mathematical Representation of Soil Microbial Growth
Uncoupling Energy Production from Microbial Biomass Synthesis
Implications of Microbial Energy and Carbon Transformation Capacities on Soil Biological Processes
Energy Acquisition in Soil Ecosystems
Microbial Contribution to Soil Energy and Carbon Transformation
Concluding Comments
References
Process Control in Soil
Microbial Response to Abiotic Limitations: General Considerations
Definition of Limitations to Biological Activity
Elucidation of Limiting Factors in Soil
Impact of Individual Soil Properties on Microbial Activity
Availability of Nutrients
Soil Water
Aeration
Redox Potential
pH
Temperature
Microbial Adaptation to Abiotic Stress
Concluding Comments
References
Soil Enzymes: Basic Principles and their Applications
A Philosophical Basis for the Study of Soil Enzymes
Basic Soil Enzyme Properties
Principles of Enzyme Assays
Enzyme Kinetics
Distribution of Enzymes in Soil Organic Components
Ecology of Extracellular Enzymes
Concluding Comments
References
Microbial Interactions and Community Development and Resilience
Common Concepts of Microbial Community Interaction
Classes of Biological Interactions
Neutralism
Positive Biological Interactions
Negative Biological Interactions
Trophic Interactions and Nutrient Cycling
Soil Flora and Fauna
Earthworms: Mediators of Multilevel Mutualism
Importance of Microbial Interactions to Overall Biological Community Development
Management of Soil Microbial Populations
Concluding Comments: Implications of Soil Microbial Interactions
References
The Rhizosphere/Mycorrhizosphere
The Rhizosphere
The Microbial Community
Sampling Rhizosphere Soil: What is Representative Soil Sample?
Plant Contributions to the Rhizosphere Ecosystem
Benefits to Plants Resulting from Rhizosphere Populations
Plant Pathogens in the Rhizosphere
Manipulation of Rhizosphere Populations
Mycorrhizal Associations
Mycorrhizae in the Soil Community
Symbiont Benefits from Mycorrhizal Development
Environmental Considerations
The Mycorrhizosphere
Conclusions
References
Introduction to the Biogeochemical Cycles
Introduction to Conceptual and Mathematical Models of Biogeochemical Cycles
Development and Utility of Conceptual Models
Mathematical Modeling of Biogeochemical Cycles
Specific Conceptual Models of Biogeochemical Cycles and Their Application
The Environmental Connection
Interconnectedness of Biogeochemical Cycle Process
Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance
General Processes and Participants in Biogeochemical Cycles
Measurement of Biogeochemical Processes: What Data Are Useful?
Assessment of Biological Activities Associated with Biogeochemical Cycling
Soil Sampling Aspects of Assessment of Biogeochemical Cycling Rates
Environmental Impact of Nutrient cycles
Examples of Complications in Assessing Soil Nutrient Cycling: Nitrogen Mineralization
Conclusions
References
The Carbon Cycle
Environmental Implications of the Soil Carbon Cycle
Soils as a Source or Sink for Carbon Dioxide
Diffusion of Soil Carbon Dioxide to the Atmosphere
Managing Soils to Augment Organic Matter Contents
Carbon Recycling in Soil Systems
Biochemical Aspects of the Carbon Cycle
Individual Components of Soil Organic Carbon Pools
Analysis of Soil Organic Carbon Fractions
Structural vs. Functional Analysis
Microbial Mediators of Soil Carbon Processes
Kinetics of Soil Carbon Transformations
Conclusions: Management of the Soil Carbon Cycle
References
The Nitrogen Cycle: Mineralization, Immobilization, and Nitrification
Nitrogen Mineralization
Soil Organic Nitrogen Resources
Assessment of
11.2 Nitrogen Immobilization
Process Definition and Organisms Involved
11.22 Impact of Nitrogen Immobilization Processes on Plant Communities
11.2.3. Measurements of 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 Microorganisms from Nitrification
11.6.3. Quantification of Nitrifiers in Soil sample
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
11.67 Concluding Observations: Control of the Internal Soil Nitrogen Cycle
References
12 Nitrogen Fixation: The Gateway to Soil Nitrogen Cycling
12.1 Biochemistry of Nitrogen Fixation
12.1.1. The Process
The Enzyme, Nitrogenase
Measurements of Biological Nitrogen Fixation in Culture and in the Field
General Properties of Soil Diazotrophs
Free Living Diazotrophs examples of Function of Non-Symbiotic Diazotrophs in Soil Systems
Diazotrophs in Rhizosphere Populations
Diazotrophs in Flooded Ecosystems
12.5 Conclusion
13. Biological Nitrogen Fixation
Rhizobium-Legume Associations
13.1.1. Grouping of Rhizobial Strains
13.1.2. Rhizobium Contributions to Nitrogen Fixation
13.1.3. Nodulation of Legumes
13.1.4. Plant Controls on Nodulation
13.2. Manipulation of Rhizobium-Legume Symbioses for Ecosystem Management
Rhizobium 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
Actinorhizal Associations
Conclusions
References
Denitrification
14.1. Pathways for Biological Reduction of Soil Nitrate
14.2. Biochemical Properties of Denitrification
14.3 Microbiology of Denitrification
14.4 Quantification of Nitrogen Losses from an Ecosystem via Denitrifiation
14.5.1. Nitrogen Balance
14.5.2. Use of Nitrogen Isotopes to Trace Soil Nitrogen Transform
14.5.3. Soil Nitrogen Oxide Transformations
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. Interation of Limitations to Denitrification in Soil Systems
14.7. Concluding Comments
References
15. Fundamentals of the Sulfur, Phosphorus, and Mineral Cycles
15.1. Sulfur in Soils
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
15.5 Mineralization and Assimilation of Sulfurous Substances
15.6. The Phosphorus Cycle
15.7. Microbial Catalyzed Soil Metal Cycling
15.71 Interactions of Soil Metals with Living Systems
15.72 Microbial Response to Elevated Metal Loading
15.73. Microbial Modifications of Metal Mobility in Soils
Managing Soils Contaminated with Metals
15.8 Conclusions
References
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
16.2.1Microbes as Soil Remediators
16.2.2 Substrate-Decomposer Interactions
16.2.3. Microbial Inoculation for Bioremediation
16.3 Soil Properties Controlling Bioremediation1
16.31Physical and Chemical Delimiters of Biological Activities
16.32 Sequestration and Sorptive Limitations to Bioavailability
16.3 Concluding Observations
References
Concluding Challenge
Index
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