Soil Microbiology and Biochemistry

About this book

This revised and updated text guides students through biochemical and microbial processes in soils and introduces them to microbial processes in water and sediments. This classic teaching text includes basic concepts and applications in agriculture, forestry, ecology, and environmental science. It can also be an invaluable resource for research in biogeochemistry, microbiology, sustainable agriculture, and environmental amelioration.

The Third Edition has been expanded from 13 to 19 chapters including such topics as bioremediation, molecular biology of soil, biodiversity of soil organisms, and the impact of global climate change on soil microhabitats. Furthermore, the lead author has decided to recruit contibuted chapters from leading soil microbiologists and agronomists.

New to this edition:
- New section on Ecology integrated with biochemistry and microbiology
- Sections on exciting new methodology such as tracers, molecular analysis and computers that will allow great advances in this field
- Six new chapters: bioremediation, soil molecular biology, biodiversity, global climate change, basic physiology and ecological interpretations
- Expanded with contributions from leading soil microbiologists and agronomists on both fundamental and applied aspects of the science
- Full-color figures
- Includes a website with figures for classroom presentation use

Contents

I BACKGROUND

1 Soil Microbiology, Ecology and Biochemistry in Perspective
E.A. Paul
I. General History and Scope
II. Soil Microbiology
III. Soil Ecology
IV. Soil Biochemistry
V. In Perspective
References and Suggested Reading

2 The Soil Habitat
R. P. Voroney
I. Introduction
II. Soil Genesis and Formation of the Soil Habitat
A. Soil Profile
III. Physical Aspects of Soil
A. Soil Texture
B. Soil Structure
IV. Soil Habitat Scale and Observation
A. Scale of Soil Habitat
B. Pore Space
C. Soil Solution Chemistry
D. Soil pH
E. Soil Temperature
F. Soil Water Content
G. Environmental Factors, Temperature and Moisture Interactions
References and Suggested Reading

II SOIL BIOTA

3 Physiological and Biochemical Methods for Studying Soil Biota and Their Function
E. Kandeler
I. Introduction
II. Scale of Investigations and Collection of Samples
III. Storage and Pre-treatment of Samples
IV. Microbial Biomass
A. Chloroform Fumigation Incubation and Extraction Methods
B. Substrate-Induced Respiration
C. Isotopic Composition of Microbial Biomass
V. Signature Molecules as a Measure of Microbial Biomass and Microbial Community Structure
A. ATP as a Measure of Active Microbial Biomass
B. Microbial Membrane Components and Fatty Acids
C. Respiratory Quinones as a Measure of Structural Diversity
D. Ergosterol as a Measure of Fungal Biomass
E. Lipopolysaccharides, Glycoproteins and Cell Walls
F. Growth Rates from Signature Molecules
VI. Physiological Analyses
A. Culture-based Studies
B. Isolation and Characterization of Specific Organisms
C. Soil Organic Matter Decomposition and Respiration
D. N Mineralization
VII. Activities and Location of Enzymes
A. Spectrophotometric Methods
B. Fluorescence Methods
C. Techniques for Imaging the Location of Enzymes
VIII. Functional Diversity
References and Suggested Reading

4 Molecular Methods for Studying Soil Ecology
J.E. Thies
I. Introduction
II. Types and Structures of Nucleic Acids
III. Use of Nucleic Acid Analyses for Soil Ecology Studies
IV. Direct Molecular Analysis of Soil Biota
A. Nucleic Acid Hybridization
B. Confocal Microscopy
V. Biosensors and Marker Gene Technologies
VI. Extraction of Nucleic Acids (DNA/RNA)
VII. Choosing Between DNA and RNA for Soil Ecology Studies
VIII. Analysis of Nucleic Acid Extracts
A. DNA:DNA Re-association Kinetics
B. Microarrays
C. Restriction Fragment Length Polymorphism (RFLP) Analysis
D. Cloning
E. DNA Sequencing
F. Stable Isotope Probing
IX. Partial Community Analyses - PCR-Based Assays
A. Electrophoresis of Nucleic Acids
B. PCR Fingerprinting
C. Similarity Analyses
X. Level of Resolution
XI. Other Factors That May Affect Molecular Analyses
A. Sample Handling
B. Soil Chemical Factors
C. Sampling Scale
XII. Summary
References

5 The Prokaryotes
K. Killham and J.I. Prosser
I. Introduction
II. Phylogeny
A. Cultivated Organisms
B. Uncultivated Organisms
C. Phylogeny and Function
III. General Features of Prokaryotes
IV. Cell Structure
A. Unicellular Growth Forms
B. Filamentous and Mycelial Growth
C. Cell Walls
D. Internal Structure
E. Motility
V. Metabolism and Physiology
A. C and Energy Sources
B. Oxygen Requirements
C. Substrate Utilisation
D. Autochthony and Zymogeny
E. Oligotrophy, Copiotrophy and the r-K Continuum
F. Facultativeness
VI. Biodegradation Capacity
A. Cellulose
B. Pollutants
VII. Differentiation, Secondary Metabolism and Antibiotic Production
VIII. Conclusion
References and Suggested Reading

6 Fungi and Eukaryotic Algae
R. G. Thorn and M. D. J. Lynch
I. Introduction
II. Classification, Characteristics, and Ecological Roles in Soil
A. Fungus-like Protists
B. Fungi (Chytridiomycota, Glomeromycota, Zygomycota, Ascomycota and Basidiomycota)
C. Eukaryotic Algae
References and Suggested Reading

7 Fauna: The Engine for Microbial Activity and Transport
D. C. Coleman and D. H. Wall
I. Introduction
II. The Microfauna
A. Methods for Extracting and Counting Protozoa
B. Impacts of Protozoa on Ecosystem Function
C. Distribution of Protozoa in Soil Profiles
III. Rotifera
IV. Nematoda
A. Nematode Feeding Habits
B. Zones of Nematode Activity in Soil
C. Nematode Extraction Techniques
V. Microarthropods
VI. Enchytraeids
VII. Macrofauna
A. Macroarthropods
1. Importance of the macroarthropods
B. Oligochaeta -- Earthworms
1. Earthworm distribution and abundance
2. Biology and ecology
3. Influence on soil processes
4. Earthworm effects on ecosystems
C. Ants
D. Termites
VIII. Summary
References
III CONCEPTS AND INTERACTIONS

8 The Ecology of Soil Organisms
S. J. Morris and C. Blackwood
I. Introduction
II. Mechanisms That Drive Community Structure
A. Physiological Limits
B. Intraspecific Competition
C. Dispersal in Space and Time
D. Predicting Population Growth
E. Interspecific Competition
F. Direct Effects of Exploitation
G. Indirect Effects of Exploitation
H. Mutualisms
I. Abiotic Factors
J. Changes in Community Structure through Time and Space
K. Historical and Geographic Contingency
L. Hierarchical Community Assembly Rules
III. Ecosystem Dynamics
A. Energy Flow
B. Carbon, Nutrient and Water Cycles
C. Emergent Properties
IV. Conclusion
References and Suggested Readings

9 The Physiology and Biochemistry of Soil Organisms
W. B. Mcgill
I. Introduction
II. Metabolic Classifications Of Soil Organisms
A. Electrons and ATP
B. Substrate-Level Phosphorylation
C. Electron Transport Phosphorylation
D. Overview of mechanisms to generate ATP and reducing equivalents
III. Examples of Soil Microbial Transformations
A. Nitrogen Fixation
B. Aerobic chemo-lithotrophic examples
1. Oxidation of H₂S with reduction of CO₂
2. Oxidation of N with reduction of CO₂
C. Oxidation of Reduced C
IV. How Can the Microbial Contributions Be Viewed in a Simplified and Unified Concept?
A. A model of interconnected cycles of electrons
B. The Anoxygenic Cycle
C. The Oxygenic Cycle
References

10 The Ecology of Plant-Microbial Mutualisms
J. Powell and J. Klironomos
I. Introduction
II. Roots as an Interface for Plant-Microbial Mutualisms
III. Mycorrhizal Symbioses
IV. Symbioses Involving N-Fixing Organisms
V. Interactions among Mutualists
VI. Interactions with Pathogens
VII. Implications for Plant Populations and Communities
VIII. Challenges in the Study of Interactions
IX. Conclusions
References and Suggested Reading

11 Spatial Distribution of Soil Organisms
S. D. Frey
I. Introduction
II. Geographical Differences in Soil Biota
III. Association of Soil Organisms with Plants
IV. Spatial Heterogeneity of Soil Organisms
V. Vertical Distribution within the Soil Profile
VI. Microscale Heterogeneity in Microbial Populations
References and Suggested Reading

IV BIOCHEMISTRY AND BIOGEOCHEMISTRY

12 Carbon Cycling and Formation of Soil Organic Matter
W. Horwath
I. Introduction
II. Long-Term Carbon Cycle
III. The Short-Term C Cycle
IV. Ecosystem C Cycling
V. Composition and Turnover of C Inputs to Soil
A. Plant and Microbial Components and Their Decomposition
1. Plant and Microbial Lipids
2. Starch
3. Hemicelluloses, Pectins and Cellulose
4. Lignin
5. Other Plant Cell Wall Carbohydrates and Proteins
6. Plant Secondary compounds
7. Roots and Root Exudates
8. Cell Walls of Microorganisms
VI. Soil Organic Matter
A. Soil Organic Matter Formation
B. Classical Fractions of Soil Organic Matter
C. Physical Analysis of Soil Organic matter Fractions
D. Structure of Soil Organic Matter
VII. Quantity and Distribution of Organic Matter in Soils
VIII. Role of Methane in the C Cycle
IX. Future Considerations
References and Suggested Reading

13 Nitrogen Transformations
G.P. Robertson and P.M. Groffman
I. Introduction
II. Nitrogen Mineralization and Immobilization
A. Environmental control of mineralization / immobilization
III. Nitrification
A. The Biochemistry of Autotrophic Nitrification
B. The Diversity of Autotrophic Nitrifiers
C. Heterotrophic Nitrification
D. Environmental Controls of Nitrification
IV. Inhibition of Nitrification
V. Denitrification
A. Denitrifier Diversity
B. Environmental Controls of Denitrification
VI. Other Nitrogen Transformations in Soil
VII. Nitrogen Movement in the Landscape
References

14 Biological N Inputs
P. J. Bottomley and D. D. Myrold
I. Global N Inputs
II. Biological Nitrogen Fixation
A. Measuring BNF
III. Free Living N₂-Fixing Bacteria
IV. Associative N₂-Fixing Bacteria
V. Phototrophic Bacteria
VI. Symbiotic N₂ Fixing Associations between Legumes and Rhizobia
A. Formation of the Symbiosis
B. Rhizobial Nodulation Genes
C. Plant Nodulation Genes
D. Development of BNF and Nitrogen Assimilatory Processes in Nodules
E. Symbiotic associations between actinorhizal plants and Frankia
VII. Biotechnology of BNF
VIII. Acknowledgements
References and Suggested Reading

15 Soil Biogeochemical Cycling of Inorganic Nutrients and Metals
A. F. Plante
I. Introduction
II. Phosphorous
A. The Soil Phosphorous Cycle
B. Nature and Forms of Phosphorous in Soil
C. Biological Importance of Phosphorous
D. Microbial Transformations of Phosphorous
1. Mineralization
2. Immobilization
3. Oxidation and reduction
4. Solubilization
III. Sulfur
A. The Soil Sulfur Cycle
B. Nature and Forms of Sulfur in Soil
C. Biological Importance of Sulfur
D. Microbial Transformations of Sulfur
1. Mineralization
2. Immobilization
3. Oxidation
4. Reduction
5. Volatilization
IV. Micronutrients and Trace Metals
A. Micronutrient and Trace Metal Cycling in Soil
B. Nature and Forms in Soil
C. Biological Importance
D. Microbial Transformations
1. Oxidation and reduction
a. Oxidation of Fe and Mn
b. Reduction of Fe and Mn
c. Reduction of other metals
2. Biomethylation transformations
V. Environmental Significance of P, S and Metal Biogeochemistry
A. Eutrophication
B. Acid Sulfate Soils
C. Acid Mine Drainage
D. Heavy Metal Mining Using Microbes
E. Microbial Corrosion of Buried Iron and Concrete Pipes
VI. Conclusion: Microorganisms as Unifiers of Elemental Cycles in Soil
References and Suggested Reading

16 The Dynamics of Soil Organic Matter and Nutrient Cycling
A.F. Plante and W.J. Parton
I. Introduction
II. Reaction Kinetics
A. Zero-order Reactions
B. First-order Reactions
C. Enzymatic Kinetics
D. Microbial Growth
III. Modeling the Dynamics of Decomposition and Nutrient Transformations
A. Simple Models
B. Multi-compartmental Models
1. Rothamsted Model
2. van Veen and Paul Model
3. The Century Model
C. Alternative SOM Models
D. Models of Non-C Nutrient Elements
E. Ecosystem Models: Interactions of Nutrient Cycling and SOM Dynamics
IV. Establishing Pool Sizes and Kinetic Constants
V. Model Selection and Evaluation
References and Suggested Reading

V. THE MANAGEMENT OF SOIL ORGANISMS

17 Management of Organisms and Their Processes in Soils
J. L. Smith and H. P. Collins
I. Introduction
II. Changing Soil Organism Populations and Processes
A. Tillage and erosion
B. Rangeland and Forest Health
III. Alternative Agricultural Management
A. Organic Agriculture
B. Bio-dynamic Agriculture
C. Composting
D. Crop Rotations and Green Manures
IV. The Potential for Managing Microorganisms and Their Processes
A. Management of Native and Introduced Microorganisms
B. Managing Microbial Populations as Agents of Biological Control
C. Control of insects
D. Weed control
E. Use of Synthetic and Natural Compounds to Modify Soil Communities or Functions
F. Manipulating Soil Populations for Bioremediation Xenobiotics
V. Concluding Comments on Microbial Ecology
VI. References and Suggested Reading

18 Soil Microbiology, Ecology, and Biochemistry for the 21st Century
J.P. Schimel
I. Introduction
II. Soil Community Ecology- Controls over Population and Community Dynamics
III. Microbial Life at the Microbial Scale - The Microbial Landscape
IV. A Whole Profile Perspective
V. Scaling to the Ecosystem
VI. Application
VII. Conclusions
References

Customer Reviews

Biography

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.