Soil Microbiology, Ecology and BiochemistryEdited by
- Eldor Paul, Colorado State University, Ft. Collins, U.S.A.
- Eldor Paul, Colorado State University, Ft. Collins, U.S.A.
Now in its third edition, this classic textbook includes basic concepts and applications in agriculture, forestry, environmental science, and a new section entirely devoted to ecology. This revised and updated edition guides students through biochemical and microbial processes in soils and introduces them to microbial processes in water and sediments. Soil Microbiology, Ecology, and Biochemistry serves as an invaluable resource for students in biogeochemistry, soil microbiology, soil ecology, sustainable agriculture, and environmental amelioration.
Undergraduate students in soil science, soil microbiology, agronomy, and related disciplines. Faculty, graduate students and researchers at institutions with strong programs and libraries at institutions with departmens in all these disciplines.
Hardbound, 552 Pages
Published: December 2006
Imprint: Academic Press
"This is a comprehensive text for the study of soil ecology. It covers the subject in sufficient depth for an advanced undergraduate or post graduate course in soil microbiology and biochemistry...the reader soon begins to relate the discussions to plant health and fruit development. The topics are covered to a depth that addresses a wide range of readers, from those who wish an overview of the subject to those who need to know the fundamental microbiology or biochemistry. The 18 chapters are divded into five broad subject areas, starting with background and continuing through the soil biota, interactions, biochemistry, and concluding with the impact of human processes. There is little current appreciation of the impact of cultivation on soil ecosystems, thus we employ few strategies to manage these systems to our advantage. A book like this is food for though." - Gary Strachan, in FRUIT GROWER
- I BACKGROUND1 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 Reading2 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 ReadingII SOIL BIOTA3 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 Reading4 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 References5 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 Reading6 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 Reading7 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 abundance2. Biology and ecology3. Influence on soil processes4. Earthworm effects on ecosystems C. Ants D. Termites VIII. Summary ReferencesIII CONCEPTS AND INTERACTIONS8 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 Readings9 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 References10 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 ReadingIV BIOCHEMISTRY AND BIOGEOCHEMISTRY12 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 Reading13 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 References14 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 Reading16 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 ReadingV. 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 erosionB. 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 Reading18 Soil Microbiology, Ecology, and Biochemistry for the 21st CenturyJ.P. SchimelI. IntroductionII. Soil Community Ecology- Controls over Population and Community DynamicsIII. Microbial Life at the Microbial Scale - The Microbial LandscapeIV. A Whole Profile PerspectiveV. Scaling to the EcosystemVI. ApplicationVII. ConclusionsReferences