Soil Microbiology

by Tate, Robert L.

• ISBN13: 9780470311103
• ISBN10: 047031110X
• Edition: 3rd
• Format: Hardcover
• Copyright: 2020-11-24
• Publisher: Wiley-Blackwell

Summary

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.

Author Biography

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.

Table of Contents

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