Soil Microbiology

by Tate, Robert L.

• ISBN13: 9780471317913
• ISBN10: 0471317918
• Edition: 2nd
• Format: Hardcover
• Copyright: 2000-01-24
• Publisher: Wiley

Summary

* A strong emphasis on research in real-world settings as well as theoretical concerns

Author Biography

<b>ROBERT L. TATE III, PhD</b>, is Professor of Soil Microbiology in the Department of Environmental Science at Rutgers University in New Brunswick, New Jersey. He is the author of a number of books on soil microbiology, including Microbial Ecology and Soil Organic Matter.

Table of Contents

Preface	v
Preface to the First Edition	vii
Contents	ix
Introduction	xx
The Soil Ecosystem: Physical and Chemical Boundaries	1	(36)
The Soil Ecosystem	5	(7)
Soil Defined	6	(2)
Designation of Soil Ecosystems	8	(3)
Implications of Definition of the Soil Ecosystem	11	(1)
The Micro-Ecosystem	12	(18)
Interaction of Individual Soil Components with the Biotic System	13	(1)
Clay and Ecosystem Function	14	(6)
Humic Substances and Ecosystem Function	20	(4)
Soil Aggregate Structure and Biological Systems	24	(1)
Native Soil Aggregate Structure and Its Impact on Ecosystem Function	24	(5)
Separation of Soil Particulates by Density Fractionation	29	(1)
The Macro-Ecosystem	30	(2)
Concluding Comments	32	(5)
References	33	(4)
The Soil Ecosystem: Biological Participants	37	(39)
The Living Soil Component	38	(9)
Biological and Genetic Implications of Occurrence of Living Cells in Soil	38	(1)
Gene Pool Potential	39	(5)
Cell Structure and Biochemical Stability in Soil	44	(1)
Resting Structures and Soil Respiration	44	(1)
Soil Mineral Transformation by Microbial Cells	45	(1)
Microbial Link to Aboveground Communities	46	(1)
Implications on Microbial Properties of Handling of Soil Samples	46	(1)
Measurement of Soil Microbial Biomass	47	(10)
The Nature of the Soil Inhabitants	57	(1)
Autecological Soil Microbiology	58	(10)
Viable Counts/Enrichment Cultures	59	(4)
Intrinsic Limitations of Viable Count Procedures	63	(1)
DNA Hybridization/PCR Procedures	64	(2)
Expression of Population Density per Unit of Soil	66	(1)
Products of Soil Autecological Research	66	(2)
Principles and Products of Synecological Research	68	(1)
Interphase between Study of the Individual and Community Microbiology	68	(1)
Concluding Comments	69	(7)
References	70	(6)
Microbial Diversity of Soil Ecosystems	76	(19)
Classical Studies of Soil Microbial Diversity: Numerical Taxonomy	77	(2)
Biochemical Measures of Soil Microbial Diversity	79	(1)
Metabolic Diversity of Soil Systems	80	(6)
Phospholipid Fatty Acid Analysis	86	(1)
Nucleic Acid-Based Analysis of Soil Microbial Diversity	87	(2)
Conclusions: Utility and Limitations of Diversity Analysis Procedures	89	(6)
References	90	(5)
Energy Transformations and Metabolic Activities of Soil Microbes	95	(30)
Microbial Growth Kinetics in Soil	96	(13)
Microbial Growth Phases: Laboratory-Observed Microbial Growth Compared to Soil Population Dynamics	98	(6)
Mathematical Representation of Soil Microbial Growth	104	(4)
Uncoupling Energy Production from Microbial Biomass Synthesis	108	(1)
Implications of Microbial Energy and Carbon Transformation Capacities on Soil Biological Processes	109	(10)
Energy Acquisition in Soil Ecosystems	110	(4)
Microbial Contributions to Soil Energy and Carbon Transformations	114	(5)
Concluding Comments	119	(6)
References	121	(4)
Process Control in Soil	125	(34)
Microbial Response to Abiotic Limitations: General Considerations	127	(6)
Definition of Limitations to Biological Activity	127	(3)
Elucidation of Limiting Factors in Soil	130	(3)
Impact of Individual Soil Properties on Microbial Activity	133	(22)
Availability of Nutrients	133	(6)
Moisture	139	(8)
Aeration	147	(1)
Redox Potential	148	(1)
pH	149	(3)
Temperature	152	(3)
Microbial Adaptation to Abiotic Stress	155	(1)
Concluding Comments	156	(3)
References	156	(3)
Soil Enzymes as Indicators of Ecosystem Status	159	(30)
Philosophical Basis for the Study of Soil Enzymes	161	(3)
Basic Soil Enzyme Properties	164	(5)
Principles of Enzyme Assays	169	(6)
Enzyme Kinetics	175	(5)
Distribution of Enzymes in Soil Organic Components	180	(3)
Ecology of Extracellular Enzymes	183	(2)
Concluding Comments	185	(4)
References	185	(4)
Microbial Interactions and Community Development and Resilience	189	(29)
Common Concepts of Microbial Community Interaction	192	(2)
Classes of Biological Interactions	194	(12)
Neutralism	195	(1)
Positive Biological Interactions	195	(3)
Negative Biological Interactions	198	(8)
Trophic Interactions and Nutrient Cycling	206	(4)
Soil Flora and Fauna	207	(2)
Earthworms: Mediators of Multilevel Mutualism	209	(1)
Importance of Microbial Interactions to Overall Biological Community Development	210	(2)
Management of Soil Microbial Populations	212	(1)
Concluding Comments: Implications of Soil Microbial Interactions	213	(5)
References	214	(4)
The Rhizosphere/Mycorrhizosphere	218	(35)
The Rhizosphere	219	(16)
The Microbial Community	221	(2)
Sampling Rhizosphere Soil	223	(1)
Plant Contributions to the Rhizosphere Ecosystem	224	(5)
Benefits to Plants Resulting from Rhizosphere Populations	229	(2)
Plant Pathogens in the Rhizosphere	231	(1)
Manipulation of Rhizosphere Populations	232	(3)
Mycorrhizal Associations	235	(8)
Mycorrhizae in the Soil Community	238	(1)
Symbiont Benefits from Mycorrhizal Development	239	(2)
Environmental Considerations	241	(2)
The Mycorrhizosphere	243	(1)
Conclusions	244	(9)
References	244	(9)
Introduction to the Biogeochemical Cycles	253	(31)
Conceptual and Mathematical Models of Biogeochemical Cycles	255	(7)
Development and Utility of Conceptual Models	255	(4)
Mathematical Modeling of Biogeochemical Cycles	259	(3)
Specific Conceptual Models of Biogeochemical Cycles and Their Application	262	(9)
The Environmental Connection	265	(3)
Interconnectedness of Biogeochemical Cycle Processes	268	(3)
Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance	271	(1)
General Processes and Participants in Biogeochemical Cycles	272	(2)
Measurement of Biogeochemical Processes: What Data Are Meaningful?	274	(6)
Assessment of Biological Activities Associated with Biogeochemical Cycling	274	(1)
Soil Sampling Aspects of Assessment of Biogeochemical Cycling Rates	275	(1)
Environmental Impact of Nutrient Cycles	276	(1)
Examples of Complications in Assessing Soil Nutrient Cycling: Nitrogen Mineralization	277	(3)
Conclusions	280	(4)
References	280	(4)
The Carbon Cycle	284	(30)
Environmental Implications of the Soil Carbon Cycle	286	(5)
Soils as a Source or Skin for Carbon Dioxide	287	(1)
Diffusion of Soil Carbon Dioxide to the Atmosphere	288	(1)
Managing Soils to Augment Organic Matter Contents	289	(1)
Carbon Recycling in Soil Systems	290	(1)
Biochemical Aspects of the Carbon Cycle	291	(14)
Individual Components of Soil Organic Carbon Pools	292	(7)
Analysis of Soil Organic Carbon Fractions	299	(2)
Structural vs Functional Analysis	301	(3)
Microbial Mediators of Soil Carbon Cycle Processes	304	(1)
Kinetics of Soil Carbon Transformations	305	(4)
Conclusions: Management of the Soil Carbon Cycle	309	(5)
References	310	(4)
The Nitrogen Cycle: Soil-Based Processes	314	(33)
Nitrogen Mineralization	318	(3)
Soil Organic Nitrogen Resources	318	(2)
Assessment of Nitrogen Mineralization	320	(1)
Nitrogen Immobilization	321	(4)
Process Definition and Organisms Involved	321	(1)
Impact of Nitrogen Immobilization Processes on Plant Communities	321	(3)
Measurement of Soil Nitrogen Immobilization Rates	324	(1)
Quantitative Description of Nitrogen Mineralization Kinetics	325	(4)
Microbiology of Mineralization	329	(1)
Environmental Influences on Nitrogen Mineralization	329	(1)
Nitrification	330	(10)
Identity of Bacterial Species That Nitrify	331	(1)
Benefits to the Microorganism from Nitrification	332	(1)
Quantification of Nitrifiers in Soil Samples	333	(1)
Discrepancies Between Population Enumeration Data and Field Nitrification Rates	334	(1)
Sources of Ammonium and Nitrite for Nitrifiers	335	(1)
Environmental Properties Limiting Nitrification	335	(5)
Concluding Observations: Control of the Internal Soil Nitrogen Cycle	340	(7)
References	341	(6)
Nitrogen Fixation: The Gateway to Soil Nitrogen Cycling	347	(27)
Biochemistry of Nitrogen Fixation	349	(9)
The Process	349	(3)
The Enzyme, Nitrogenase	352	(2)
Measurements of Biological Nitrogen Fixation in Culture and in the Field	354	(4)
General Properties of Soil Diazotrophs	358	(3)
Free-Living Diazotrophs	361	(2)
Function of Diazotrophs in Native Ecosystems	363	(6)
Nitrogen-Fixing Bacteria Among Rhizosphere Populations	363	(4)
Nitrogen Fixation in Flooded Ecosystems	367	(2)
Conclusions	369	(5)
References	369	(5)
Symbiotic Nitrogen Fixation	374	(30)
Rhizobium-Legume Association	375	(8)
Grouping of Rhizobial Strains	376	(1)
Rhizobial Contributions to Nitrogen Fixation	377	(1)
Nodulation of Legumes	378	(4)
Plant Controls of Nodulation	382	(1)
Manipulation of Rhizobium-Legume Symbioses for Ecosystem Management	383	(2)
Rhizobial Inoculation Procedures	385	(6)
Inocula Delivery Systems	385	(1)
Survival of Rhizobial Inocula	386	(4)
Biological Interactions in Legume Nodulation	390	(1)
Nodule Occupants: Indigenous Versus Foreign	391	(1)
Actinorhizal Associations	392	(2)
Conclusions	394	(10)
References	395	(9)
Dentrification	404	(29)
Pathways for Biochemical Reduction of Soil Nitrate	405	(2)
Biochemical Properties of Dentrification	407	(2)
Environmental Implications of Nitrous Oxide Formation	409	(1)
Microbiology of Denitrification	410	(3)
Quantification of Nitrogen Losses from an Ecosystem via Denitrification	413	(6)
Nitrogen Balance Studies	413	(2)
Use of Nitrogen Isotopes to Trace Soil Nitrogen Movement	415	(1)
Disappearance of Endogenous or Added Nitrogen Oxides	416	(1)
Acetylene Block Method for Assessing Denitrification Processes in Soil	417	(2)
Environmental Factors Controlling Denitrification Rates	419	(5)
Nature and Amount of Organic Matter	419	(1)
Nitrate Concentration	420	(1)
Aeration/Moisture	421	(1)
pH	422	(1)
Temperature	423	(1)
Interactions of Limitations to Denitrification in Soil Systems	423	(1)
Concluding Comments	424	(9)
References	424	(9)
Sulfur, Phosphorus, and Mineral Cycles	433	(31)
Sulfur in the Soil Ecosystem	433	(1)
Biogeochemical Cycling of Sulfur in Soil	434	(4)
Biological Sulfur Oxidation	438	(6)
Microbiology of Sulfur Oxidation	438	(4)
Environmental Conditions Affecting Sulfur Oxidation	442	(2)
Biological Sulfur Reduction	444	(2)
Mineralization and Assimilation of Sulfurous Substances	446	(1)
The Phosphorus Cycle	447	(2)
Microbially Catalyzed Soil Metal Cycling	449	(8)
Interactions of Metals with Living Systems	449	(3)
Microbial Response to Elevated Metal Loadings	452	(1)
Microbial Modification of Metal Mobility in Soils	453	(3)
Managing Soils Contaminated with Metals	456	(1)
Conclusions	457	(7)
References	457	(7)
Principles of Bioremediation	464	(31)
Foundational Concepts of Bioremediation	466	(3)
Bioremediation Defined	466	(1)
Conceptual Unity of Bioremediation Science	467	(1)
Complexity of Remediation Questions	468	(1)
The Microbiology of Bioremediation	469	(13)
Microbes as Soil Remediators	470	(1)
Substrate-Decomposer Interactions	471	(8)
Microbial Inoculation for Bioremediation	479	(3)
Soil Properties Controlling Bioremediation	482	(6)
Physical and Chemical Delimiters of Biological Activities	483	(4)
Sequestration and Sorption Limitations to Bioavailability	487	(1)
Concluding Observations	488	(7)
References	489	(6)
Concluding Challenge	495	(4)
Index	499