Soil Microbiology, Ecology and Biochemistry
Eldor A. Paul
Soil Microbiology, Ecology and Biochemistry - 4th ed - Amsterdam : Academic Press, 2015. - 582p.,
bout the Editor
Eldor Paul
Eldor Paul
Eldor A. Paul is a Senior Research Scientist at the Natural Resources Ecology Laboratory at Colorado State University, Fort Collins and Professor Emeritus at Michigan State University, East Lansing. During his time at Michigan State, he was professor of Soil Microbiology and Biochemistry, and Crop and Soil Sciences. He earned degrees from the University of Alberta and the University of Minnesota. His research focuses on the dynamics of soil organic matter and the microbial ecology of soil. Dr. Paul is a Fellow of ASA, SSSA, the Canadian Society of Soil Science, and the American Association for the Advancement of Science.
Table of Contents
Preface
Chapter 1: Soil Microbiology, Ecology, and Biochemistry: An Exciting Present and Great Future Built on Basic Knowledge and Unifying Concepts
Abstract
I Scope and Challenges
II The Controls and Unifying Principles in our Field
III The Special Role of Accessibility and Spatial Scaling of Biota and Soil Organic Matter
IV Soil Organic Matter as a Control and Informational Storehouse of Biotic Functions
V Biotic Diversity and Microbial Products
VI Unifying Concepts
Chapter 2: The Soil Habitat
Abstract
I Introduction
II Soil Genesis and Formation of the Soil Habitat
III Physical Aspects of Soil
IV Soil Habitat and Scale of Observation
V Soil Solution Chemistry
VI Environmental Factors, Temperature, and Moisture Interactions
Chapter 3: The Bacteria and Archaea
Abstract
I Introduction
II Phylogeny
III General Features of Prokaryotes
IV Cell Structure
V Metabolism and Physiology
VI Biodegradation Capacity
VII Differentiation, Secondary Metabolism, and Antibiotic Production
VIII Conclusion
Chapter 4: The Soil Fungi: Occurrence, Phylogeny, and Ecology
Abstract
Acknowledgments
I Introduction
II Phylogeny
III Occurrence
IV Biodiversity
V Fungal Communities
VI Functions
VII Fungus-like Organisms and Soil Food Webs
Chapter 5: Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function
Abstract
Acknowledgments
I Introduction
II Overview of Faunal Biodiversity in Soils
III Microfauna
IV Mesofauna
V Macrofauna
VI Roles of Soil Fauna in Ecosystems
VII Summary
Chapter 6: Molecular Approaches to Studying the Soil Biota
Abstract
I Introduction
II Types and Structures of Nucleic Acids
III Nucleic acid Analyses in Soil Ecology Studies
IV Direct Molecular Analysis of Soil Biota
V Biosensors and Marker Gene Technologies
VI Extraction of Nucleic Acids (DNA/RNA)
VII Choosing Between DNA and RNA for Studying Soil Biota
VIII Analysis of Nucleic Acid Extracts
IX Partial Community Analyses—PCR-based Assays
X Level of Resolution
XI Factors that May Affect Molecular Analyses
XII Future Promise
Chapter 7: Physiological and Biochemical Methods for Studying Soil Biota and Their Functions
Abstract
I Introduction
II Scale of Investigations and Collection of Samples
III Storage and Pretreatment of Samples
IV Microbial Biomass
V Compound-Specific Analyses of Microbial Biomass and Microbial Community Structure
VI Isotopic Composition of Microbial Biomass and Signal Molecules
VII Physiological Analyses
VIII Activities of Enzymes
IX Imaging Microbial Activities
X Functional Diversity
Chapter 8: The Spatial Distribution of Soil Biota
Abstract
I Introduction
II The Biogeography of Soil Biota
III Vertical Distribution Within the Soil Profile
IV Microscale Heterogeneity in Microbial Populations
V Drivers of Spatial Heterogeneity
VI Summary
Chapter 9: The Metabolic Physiology of Soil Microorganisms
Abstract
I Introduction
II Foundations of Microbial Metabolism
III Metabolic Classification of Soil Organisms
IV Cellular Energy Transformations
V Examples of Soil Microbial Transformations
VI A Simplified View of Soil Microbial Metabolism
Chapter 10: The Ecology of the Soil Biota and their Function
Abstract
I Introduction
II Mechanisms that Drive Community Structure
III Consequences of Microbial Community Structure for Ecosystem Function
IV Conclusion
Chapter 11: Plant-Soil Biota Interactions
Abstract
Acknowledgments
I Soil Biota
II The Rhizosphere: Ecological Network of Soil Microbial Communities
III New Insights into Root/Soil Microbes Through Metagenomic/Metatranscriptomic Approaches
IV An Important Rhizospheric Component: The Mycorrhizal Fungi
V The Contribution of Fungal Genome Projects
VI Summary
Chapter 12: Carbon Cycling: The Dynamics and Formation of Organic Matter
Abstract
I Introduction
II Geological Carbon Cycle
III Biological C Cycle
IV Organic Matter
V Quantity, Distribution, and Turnover of Carbon in Soil and Sediments
VI Role of Climate Change on the Global C Cycle
VII Future Considerations
Chapter 13: Methods for Studying Soil Organic Matter: Nature, Dynamics, Spatial Accessibility, and Interactions with Minerals
Abstract
I Introduction
II Quantifying Soil Organic Matter
III Fractionation Methods
IV Characterization Methods
V Visualization Methods
VI Methods to Measure the Turnover Rate of SOM
Chapter 14: Nitrogen Transformations
Abstract
I Introduction
II Nitrogen Mineralization and Immobilization
III Nitrification
IV Inhibition of Nitrification
V Denitrification
VI Other Nitrogen Transformations in Soil
VII Nitrogen Movement in the Landscape
Chapter 15: Biological N Inputs
Abstract
Acknowledgments
I Global N Inputs
II Biological Nitrogen Fixation
III Free Living N2-Fixing Bacteria
IV Associative N2-Fixing Bacteria
V Phototrophic Bacteria
VI Symbiotic N2-Fixing Associations Between Legumes and Rhizobia
VII Microbial Ecology of BNF
VIII Biotechnology of BNF
Chapter 16: Biological Cycling of Inorganic Nutrients and Metals in Soils and Their Role in Soil Biogeochemistry
Abstract
I Introduction
II Nutrient Needs of Soil Microorganisms
III Effect of Microorganisms on Element Cycles
IV Examples of Interconnections Between Microbial Community/Activity and Element Cycles
Chapter 17: Modeling the Dynamics of Soil Organic Matter and Nutrient Cycling
Abstract
I Introduction
II Reaction Kinetics
III Modeling Soil Carbon and Nutrient Dynamics
IV Model Classification and Comparison
V Model Parameterization
VI Model Selection Methods
VII Conclusion
Chapter 18: Management of Soil Biota and Their Processes
Abstract
I Introduction
II Changing Soil Organism Populations and Processes
III Alternative Agricultural Management
IV The Potential for Managing Microorganisms and their Processes
V Concluding Comments on Microbial Ecology
Index
Description
The fourth edition of Soil Microbiology, Ecology and Biochemistry updates this widely used reference as the study and understanding of soil biota, their function, and the dynamics of soil organic matter has been revolutionized by molecular and instrumental techniques, and information technology. Knowledge of soil microbiology, ecology and biochemistry is central to our understanding of organisms and their processes and interactions with their environment. In a time of great global change and increased emphasis on biodiversity and food security, soil microbiology and ecology has become an increasingly important topic.
Revised by a group of world-renowned authors in many institutions and disciplines, this work relates the breakthroughs in knowledge in this important field to its history as well as future applications. The new edition provides readable, practical, impactful information for its many applied and fundamental disciplines. Professionals turn to this text as a reference for fundamental knowledge in their field or to inform management practices.
Key Features
New section on "Methods in Studying Soil Organic Matter Formation and Nutrient Dynamics" to balance the two successful chapters on microbial and physiological methodology
Includes expanded information on soil interactions with organisms involved in human and plant disease
Improved readability and integration for an ever-widening audience in his field
Integrated concepts related to soil biota, diversity, and function allow readers in multiple disciplines to understand the complex soil biota and their function
9780124159556
Soil microbiology;
Soil ecology; Soil biochemistry;
579.175 / PAU
Soil Microbiology, Ecology and Biochemistry - 4th ed - Amsterdam : Academic Press, 2015. - 582p.,
bout the Editor
Eldor Paul
Eldor Paul
Eldor A. Paul is a Senior Research Scientist at the Natural Resources Ecology Laboratory at Colorado State University, Fort Collins and Professor Emeritus at Michigan State University, East Lansing. During his time at Michigan State, he was professor of Soil Microbiology and Biochemistry, and Crop and Soil Sciences. He earned degrees from the University of Alberta and the University of Minnesota. His research focuses on the dynamics of soil organic matter and the microbial ecology of soil. Dr. Paul is a Fellow of ASA, SSSA, the Canadian Society of Soil Science, and the American Association for the Advancement of Science.
Table of Contents
Preface
Chapter 1: Soil Microbiology, Ecology, and Biochemistry: An Exciting Present and Great Future Built on Basic Knowledge and Unifying Concepts
Abstract
I Scope and Challenges
II The Controls and Unifying Principles in our Field
III The Special Role of Accessibility and Spatial Scaling of Biota and Soil Organic Matter
IV Soil Organic Matter as a Control and Informational Storehouse of Biotic Functions
V Biotic Diversity and Microbial Products
VI Unifying Concepts
Chapter 2: The Soil Habitat
Abstract
I Introduction
II Soil Genesis and Formation of the Soil Habitat
III Physical Aspects of Soil
IV Soil Habitat and Scale of Observation
V Soil Solution Chemistry
VI Environmental Factors, Temperature, and Moisture Interactions
Chapter 3: The Bacteria and Archaea
Abstract
I Introduction
II Phylogeny
III General Features of Prokaryotes
IV Cell Structure
V Metabolism and Physiology
VI Biodegradation Capacity
VII Differentiation, Secondary Metabolism, and Antibiotic Production
VIII Conclusion
Chapter 4: The Soil Fungi: Occurrence, Phylogeny, and Ecology
Abstract
Acknowledgments
I Introduction
II Phylogeny
III Occurrence
IV Biodiversity
V Fungal Communities
VI Functions
VII Fungus-like Organisms and Soil Food Webs
Chapter 5: Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function
Abstract
Acknowledgments
I Introduction
II Overview of Faunal Biodiversity in Soils
III Microfauna
IV Mesofauna
V Macrofauna
VI Roles of Soil Fauna in Ecosystems
VII Summary
Chapter 6: Molecular Approaches to Studying the Soil Biota
Abstract
I Introduction
II Types and Structures of Nucleic Acids
III Nucleic acid Analyses in Soil Ecology Studies
IV Direct Molecular Analysis of Soil Biota
V Biosensors and Marker Gene Technologies
VI Extraction of Nucleic Acids (DNA/RNA)
VII Choosing Between DNA and RNA for Studying Soil Biota
VIII Analysis of Nucleic Acid Extracts
IX Partial Community Analyses—PCR-based Assays
X Level of Resolution
XI Factors that May Affect Molecular Analyses
XII Future Promise
Chapter 7: Physiological and Biochemical Methods for Studying Soil Biota and Their Functions
Abstract
I Introduction
II Scale of Investigations and Collection of Samples
III Storage and Pretreatment of Samples
IV Microbial Biomass
V Compound-Specific Analyses of Microbial Biomass and Microbial Community Structure
VI Isotopic Composition of Microbial Biomass and Signal Molecules
VII Physiological Analyses
VIII Activities of Enzymes
IX Imaging Microbial Activities
X Functional Diversity
Chapter 8: The Spatial Distribution of Soil Biota
Abstract
I Introduction
II The Biogeography of Soil Biota
III Vertical Distribution Within the Soil Profile
IV Microscale Heterogeneity in Microbial Populations
V Drivers of Spatial Heterogeneity
VI Summary
Chapter 9: The Metabolic Physiology of Soil Microorganisms
Abstract
I Introduction
II Foundations of Microbial Metabolism
III Metabolic Classification of Soil Organisms
IV Cellular Energy Transformations
V Examples of Soil Microbial Transformations
VI A Simplified View of Soil Microbial Metabolism
Chapter 10: The Ecology of the Soil Biota and their Function
Abstract
I Introduction
II Mechanisms that Drive Community Structure
III Consequences of Microbial Community Structure for Ecosystem Function
IV Conclusion
Chapter 11: Plant-Soil Biota Interactions
Abstract
Acknowledgments
I Soil Biota
II The Rhizosphere: Ecological Network of Soil Microbial Communities
III New Insights into Root/Soil Microbes Through Metagenomic/Metatranscriptomic Approaches
IV An Important Rhizospheric Component: The Mycorrhizal Fungi
V The Contribution of Fungal Genome Projects
VI Summary
Chapter 12: Carbon Cycling: The Dynamics and Formation of Organic Matter
Abstract
I Introduction
II Geological Carbon Cycle
III Biological C Cycle
IV Organic Matter
V Quantity, Distribution, and Turnover of Carbon in Soil and Sediments
VI Role of Climate Change on the Global C Cycle
VII Future Considerations
Chapter 13: Methods for Studying Soil Organic Matter: Nature, Dynamics, Spatial Accessibility, and Interactions with Minerals
Abstract
I Introduction
II Quantifying Soil Organic Matter
III Fractionation Methods
IV Characterization Methods
V Visualization Methods
VI Methods to Measure the Turnover Rate of SOM
Chapter 14: Nitrogen Transformations
Abstract
I Introduction
II Nitrogen Mineralization and Immobilization
III Nitrification
IV Inhibition of Nitrification
V Denitrification
VI Other Nitrogen Transformations in Soil
VII Nitrogen Movement in the Landscape
Chapter 15: Biological N Inputs
Abstract
Acknowledgments
I Global N Inputs
II Biological Nitrogen Fixation
III Free Living N2-Fixing Bacteria
IV Associative N2-Fixing Bacteria
V Phototrophic Bacteria
VI Symbiotic N2-Fixing Associations Between Legumes and Rhizobia
VII Microbial Ecology of BNF
VIII Biotechnology of BNF
Chapter 16: Biological Cycling of Inorganic Nutrients and Metals in Soils and Their Role in Soil Biogeochemistry
Abstract
I Introduction
II Nutrient Needs of Soil Microorganisms
III Effect of Microorganisms on Element Cycles
IV Examples of Interconnections Between Microbial Community/Activity and Element Cycles
Chapter 17: Modeling the Dynamics of Soil Organic Matter and Nutrient Cycling
Abstract
I Introduction
II Reaction Kinetics
III Modeling Soil Carbon and Nutrient Dynamics
IV Model Classification and Comparison
V Model Parameterization
VI Model Selection Methods
VII Conclusion
Chapter 18: Management of Soil Biota and Their Processes
Abstract
I Introduction
II Changing Soil Organism Populations and Processes
III Alternative Agricultural Management
IV The Potential for Managing Microorganisms and their Processes
V Concluding Comments on Microbial Ecology
Index
Description
The fourth edition of Soil Microbiology, Ecology and Biochemistry updates this widely used reference as the study and understanding of soil biota, their function, and the dynamics of soil organic matter has been revolutionized by molecular and instrumental techniques, and information technology. Knowledge of soil microbiology, ecology and biochemistry is central to our understanding of organisms and their processes and interactions with their environment. In a time of great global change and increased emphasis on biodiversity and food security, soil microbiology and ecology has become an increasingly important topic.
Revised by a group of world-renowned authors in many institutions and disciplines, this work relates the breakthroughs in knowledge in this important field to its history as well as future applications. The new edition provides readable, practical, impactful information for its many applied and fundamental disciplines. Professionals turn to this text as a reference for fundamental knowledge in their field or to inform management practices.
Key Features
New section on "Methods in Studying Soil Organic Matter Formation and Nutrient Dynamics" to balance the two successful chapters on microbial and physiological methodology
Includes expanded information on soil interactions with organisms involved in human and plant disease
Improved readability and integration for an ever-widening audience in his field
Integrated concepts related to soil biota, diversity, and function allow readers in multiple disciplines to understand the complex soil biota and their function
9780124159556
Soil microbiology;
Soil ecology; Soil biochemistry;
579.175 / PAU