S o i l M ic r o b io lo g y

Second Edition
Robert L. Tate III
Rutgers University
John Wiley & Sons, Inc.
New York | Chichester | Weinheim | Brisbane | Singapore | Toronto
Contents
Preface v
Preface to the First Edition vii
Contents ix
Introduction xx
The Soil Ecosystem: Physical and
Chemical Boundaries
1.1 The Soil Ecosystem 5
1.1.1 Soil Defined 6
1.1.2 Designation of Soil Ecosystems 8
1.1.3 Implications of Definition of the Soil
Ecosystem 11
1.2 The Micro-Ecosystem 12
1.2.1 Interaction of Individual Soil Components with
the Biotic System 13
1.2.1.1 Clay and Ecosystem Function 14
1.2.1.2 Humic Substances and Ecosystem
Function 20
1.2.2 Soil Aggregate Structure and Biological
Systems 24
1.2.2.1 Native Soil Aggregate Structure and Its Impact
on Ecosystem Function 24
1.2.2.2 Separation of Soil Particulates by Density
Fractionation 29
1.3 The Macro-Ecosystem 30
xi
1.4 Concluding Comments
References 33
32
The S o i l Ec o sy stem:
Bi o l o g i c al Par ti c i pants
37
2.1
2.2
2.3
2.4
2.5
2.6
2.7
The Living Soil Component 38
2.1.1 Biological and Genetic Implications of
Occurrence of Living Cells in Soil 38
2.1.1.1 Gene Pool Potential 39
2.1.1.2 Cell Structure and Biochemical Stability
in Soil 44
2.1.1.3 Resting Structures and Soil Respiration 44
2.1.1.4 Soil Mineral Transformation by
Microbial Cells 45
2.1.1.5 Microbial Link to Aboveground
Communities 46
2.1.2 Impl i c ati o ns o n M i c r o b i al Properties o f
Handl i ng o f S o il Samples 46
Measurement of Soil Microbial Biomass 47
The Nature of the Soil Inhabitants 57
Autecological Soil Microbiology 58
2.4.1 Viable Counts/Enrichment Cultures
2.4.2 Intrinsic Limitations of Viable Count
Procedures 63
2.4.3 DNA Hybridization/PCR Procedures
2.4.4 Expression of Population Density per
Unit of Soil 66
2.4.5 Products o f S o il Autec o l o g i c al Research 66
Principles and Products of Synecological Research 68
Interphase between Study of the Individual and Community
Microbiology 68
Concluding Comments 69
References 70
59
64
M i c r o b i al Di ver si ty o f S o i l Ec o sy stems
76
3.1 Cl assi c al S tudi es o f S o i l M i c r o b i al Di ver si ty :
Numer i c al Taxo no my 77
3.2 Bi o c hemi c al M easur es o f S o i l M i c r o b i al Di ver si ty 79
3.3 M etab o l i c Di ver si ty o f S o i l S y stems 80
3.4 Pho spho l i pi d Fatty Acid Anal y si s 86
3.5 Nuc l ei c Ac i d-Based Anal y si s o f S o i l M i c r o b i al
Di ver si ty 87
Contents xi i i
3.6 Co nc l usi o ns: Uti l i ty and Li mi tati o ns o f Di ver si ty
Anal y si s Pr o c edur es 89
Refer enc es 90
Energy Tr ansfo r mati o ns and
M etab o l i c Ac ti vi ti es o f S o i l M i c r o b es 95
4. 1 M i c r o b i al Gro wth Ki neti c s in S o i l 96
4.1.1 Microbial Growth Phases: Laboratory-Observed
Microbial Growth Compared to Soil Population
Dynamics 98
4.1.2 Mathematical Representation of Soil Microbial
Growth 104
4.1.3 Uncoupling Energy Production from Microbial
Biomass Synthesis 108
4.2 Implications of Microbial Energy and Carbon Transformation
Capacities on Soil Biological Processes 109
4.2.1 Energy Acquisition in Soil Ecosystems 110
4.2.2 Microbial Contributions to Soil Energy and
Carbon Transformations 114
4.3 Concluding Comments 119
Refer enc es 121
Pr o c ess Co ntr o l in S o i l 125
5.1 Microbial Response to Abiotic Limitations:
General Considerations 127
5.1.1 Definition of Limitations to Biological
Activity 127
5.1.2 Elucidation of Limiting Factors in
Soil 130
5.2 Impact of Individual Soil Properties on
Microbial Activity 133
5.2.1 Availability of Nutrients 133
5.2.2 Moisture 139
5.2.3 Aeration 147
5.2.4 Redox Potential 148
5.2.5 pH 149
5.2.6 Temperature 152
5.3 Microbial Adaptation to Abiotic Stress 155
5.4 Concluding Comments 156
References 156
Contents xv
S o il Enzymes as Indicators of
Ecosystem Status
159
6.1 Philosophical Basis for the Study of Soil Enzymes 161
6.2 Basic Soil Enzyme Properties 164
6.3 Principles of Enzyme Assays 169
6.4 Enzyme Kinetics 175
6.5 Distribution of Enzymes in Soil Organic Components 180
6.6 Ecology of Extracellular Enzymes 183
6.7 Concluding Comments 185
References 185
Microbial Interactio ns and Community
Development and Resilience
189
7.1 Common Concepts of Microbial Community Interaction 192
7.2 Classes of Biological Interactions 194
7.2.1 Neutralism 195
7.2.2 Positive Biological Interactions 195
7.2.3 Negative Biological Interactions 198
7.3 Trophic Interactions and Nutrient Cycling 206
7.3.1 Soil Flora and Fauna 207
7.3.2 Earthworms: Mediators of Multilevel
Mutualism 209
7.4 Importance of Microbial Interactions to Overall Biological
Community Development 210
7.5 Management of Soil Microbial Populations 212
7.6 Concluding Comments: Implications of Soil Microbial
Interactions 213
References 214
The Rhizosphere/Mycorrhizosphere
218
8.1 The Rhizosphere 219
8.1.1 The Microbial Community 221
8.1.2 Sampling Rhizosphere Soil 223
8.1.3 Plant Contributions to the Rhizosphere
Ecosystem 224
8.1.4 Benefits to Plants Resulting from Rhizosphere
Populations 229
8.1.5 Plant Pathogens in the Rhizosphere 231
8.1.6 Manipulation of Rhizosphere Populations 232
8.2 Mycorrhizal Associations 235
8.2.1 Mycorrhizae in the Soil Community 238
8.2.2 Symbiont Benefits from Mycorrhizal
Development 239
8.2.3 Environmental Considerations 241
8.3 The Mycorrhizosphere 243
8.4 Conclusions 244
References 244
Intr o duc ti o n to the Bi o g eo c hemi c al Cy c l es 2 5 3
9.1 Conceptual and Mathematical Models of Biogeochemical
Cycles 255
9.1.1 Development and Utility of Conceptual
Models 255
9.1.2 Mathematical Modeling of Biogeochemical
Cycles 259
9.2 Specific Conceptual Models of Biogeochemical Cycles and
Their Application 262
9.2.1 The Environmental Connection 265
9.2.2 Interconnectedness of Biogeochemical
Cycle Processes 268
9.3 Biogeochemical Cycles as Sources of Plant Nutrients for
Ecosystem Sustenance 271
9.4 General Processes and Participants in Biogeochemical
Cycles 272
9.5 Measurement of Biogeochemical Processes:
What Data Are Meaningful? 274
9.5.1 Assessment of Biological Activities Associated
with Biogeochemical Cycling 274
9.5.2 Soil Sampling Aspects of Assessment of
Biogeochemical Cycling Rates 275
9.5.3 Environmental Impact of Nutrient Cycles 276
9.5.4 Examples of Complications in Assessing Soil
Nutrient Cycling: Nitrogen Mineralization 277
9.6 Conclusions 280
References 280
10 The Carbon Cycle 284
10.1 Environmental Implications of the Soil
Carbon Cycle 286
10.1.1 Soils as a Source or Sink for Carbon
Dioxide 287
Contents xvi i
J.0.1.2 Diffusion of Soil Carbon Dioxide to the
Atmosphere 288
10.1.3 Managing Soils to Augment Organic Matter
Contents 289
10.1.4 Carbon Recycling in Soil Systems 290
10.2 Biochemical Aspects of the Carbon Cycle 291
10.2.1 Individual Components of Soil Organic
Carbon Pools 292
10.2.2 Analysis of Soil Organic Carbon Fractions 299
10.2.3 Structural vs Functional Analysis 301
10.2.4 Microbial Mediators of Soil Carbon Cycle
Processes 304
10.3 Kinetics of Soil Carbon Transformations 305
10.4 Conclusions: Management of the Soil
Carbon Cycle 309
References 310
12
11.6.6 Environmental Properties Limiting
Nitrification 335
11.7 Concluding Observations: Control of the Internal Soil
Nitrogen Cycle 340
References 341
Ni tr o g en Fi xati o n: The Gateway to
S o i l Ni tr o g en Cy c l i ng 347
The Ni tr o g en Cy c l e: S o i l -Based
Pr o c esses 314
11.1 Nitrogen Mineralization 318.
11.1.1 Soil Organic Nitrogen Resources 318
11.1.2 Assessment of Nitrogen Mineralization 320
11.2 Nitrogen Immobilization 321
11.2.1 Process Definition and Organisms
Involved 321
11.2.2 Impact of Nitrogen Immobilization Processes
on Plant Communities 321
11.2.3 Measurement of Soil Nitrogen Immobilization
Rates 324
11.3 Quantitative Description of Nitrogen Mineralization
Kinetics 325
11.4 Microbiology of Mineralization 329
11.5 Environmental Influences on Nitrogen Mineralization 329
11.6 Nitrification 330 ,
11.6.1 Identity of Bacterial Species That Nitrify 331
11.6.2 Benefits to the Microorganism from
Nitrification 332
11.6.3 Quantification of Nitrifiers in Soil Samples 333
11.6.4 Discrepancies Between Population Enumeration
Data and Field Nitrification Rates 334
11.6.5 Sources of Ammonium and Nitrite for
Nitrifiers 335
12.1 Biochemistry of Nitrogen Fixation 349
12.1.1 The Process 349
12.1.2 The Enzyme, Nitrogenase 352
12.1.3 Measurements of Biological Nitrogen Fixation
in Culture and in the Field 354
12.2 General Properties of Soil Diazotrophs 358
12.3 Free-Living Diazotrophs 361
12.4 Function of Diazotrophs in Native Ecosystems 363
12.4.1 Nitrogen-Fixing Bacteria Among Rhizosphere
Populations 363
12.4.2 Nitrogen Fixation in Flooded Ecosystems 367
12.5 Conclusions 369
References 369
13 S y mb i o ti c Ni tr o g en Fi xati o n 374
13.1 Rh/zob/um-Legume Association 375
13.1.1 Grouping of Rhizobial Strains 376
13.1.2 Rhizobial Contributions to Nitrogen
Fixation 377
13.1.3 Nodulation of Legumes 378
13.1.4 Plant Controls of Nodulation 382
13.2 Manipulation of Rhizobium-Legume Symbioses for
Ecosystem Management 383
13.3 Rhizobial Inoculation Procedures 385
13.3.1 Inocula Delivery Systems 385
13.3.2 Survival of Rhizobial Inocula 386
13.3.3 Biological Interactions in Legume
Nodulation 390
13.4 Nodule Occupants: Indigenous Versus Foreign 391
13.5 Actinorhizal Associations 392
13.6 Conclusions 394
References 395
Contents x i x
Deni tr i fi c ati o n 404
14.1
14.2
14.3
14.4
14.5
14.6
14. 6
Pathways for Biochemical Reduction of Soil Nitrate 405
Biochemical Properties of Denitrification 407
Environmental Implications of Nitrous Oxide
Formation 409
Microbiology of Denitrification 410
Quantification of Nitrogen Losses from an Ecosystem via
Denitrification 413
14.5.1 Nitrogen Balance Studies 413
14.5.2 Use of Nitrogen Isotopes to Trace Soil Nitrogen
Movement 415
14.5.3 Disappearance of Endogenous or Added
Nitrogen Oxides 416
14.5.4 Acetylene Block Method for Assessing
Denitrification Processes in Soil 417
Environmental Factors Controlling Denitrification
Rates 419
14.6.1 Nature and Amount of Organic Matter 419
14.6.2 Nitrate Concentration 420
14.6.3 Aeration/Moisture 421
14.6.4 pH 422
14.6.5 Temperature 423
14.6.6 Interactions of Limitations to Denitrification
in Soil Systems 423
Concluding Comments 424
References 424
15.8
Loadings 452
15.7.3 Microbial Modification of Metal Mobility in
Soils 453
15.7.4 Managing Soils Contaminated with
Metals 456
Co nc l usi o ns 457
Refer enc es 457
16 Pr i nc i pl es of Bi o r emedi ati o n 464
16.1
16.2
16.3
16.4
Foundational Concepts of Bioremediation 466
16.1.1 Bioremediation Defined 466
16.1.2 Conceptual Unity of Bioremediation
Science 467
16.1.3 Complexity of Remediation Questions 468
The Microbiology of Bioremediation 469
16.2.1 Microbes as Soil Remediators 470
16.2.2 Substrate-Decomposer Interactions 471
16.2.3 Microbial Inoculation for Bioremediation 479
Soil Properties Controlling Bioremediation 482
16.3.1 Physical and Chemical Delimiters of Biological
Activities 483
16.3.2 Sequestration and Sorption Limitations to
Bioavailability 487
Concluding Observations 488
References 489
Concluding Challenge 495
S ul fur , Phosphorus, and M i ner al Cycles 4 3 3
15.1 Sulfur in the Soil Ecosystem 433
15.2 Biogeochemical Cycling of Sulfur in Soil 434
15.3 Biological Sulfur Oxidation 438
15.3.1 Microbiology of Sulfur Oxidation 438
15.3.2 Environmental Conditions Affecting Sulfur
Oxidation 442
15.4 Biological Sulfur Reduction 444
15.5 Mineralization and Assimilation of Sulfurous
Substances 446
15.6 The Phosphorus Cycle 447
15.7 Microbially Catalyzed Soil M etal Cycling 449
15.7.1 Interactions of Metals with Living Systems 449
15.7.2 Microbial Response to Elevated Metal
Index 499