Soil Microbiology and Sustainable Crop Production (eBook)

Soil Microbiology andSustainable Crop Production 3
Preface 5
Contents 9
Contributors 11
Chapter 1: The Nature of Sustainable Agriculture 15
Introduction 15
Recent Challenges in the Global Foodscape 17
Land Degradation and It Impact on Sustainability 19
Chemical Degradation 21
Amelioration of Charge Degradation 26
Addressing Soil Physical Degradation 32
Transforming the Agricultural Landscape 35
References 36
Chapter 2: The Microbiology of Natural Soils 40
Introduction 40
Methods of Study 41
Soil as a Habitat 42
Survey of Ecosystems 43
Tropical Forests 44
Neotropics: Amazonia, Costa Rica, Hawaii 45
Conclusions: Neotropics 54
Tropics of Africa, Southeast Asia, and Oceania 54
Conclusions: Old World Tropics 59
Wetlands 60
Soil Microbial Communities and Changing Agricultural Management Regimes 62
Conclusion 64
References 65
Chapter 3: Soil Microbiology and Nutrient Cycling 71
Introduction 71
The Global Biogeochemical Cycle of Carbon 75
Organic Matter in Soils and Its Turnover 75
Factors Controlling Decomposition 78
Substrate Quality 79
Organisms 80
Environmental Conditions 81
The Biogeochemical Cycle of Nitrogen 83
Nitrogen Mineralization 83
Nitrogen Fixation 85
Denitrification 87
Nitrification 88
Microbial Contributions to Phosphorus Cycling in Soil 89
Concluding Remarks 89
References 90
Chapter 4: The Role of Microbial Communities in the Formation and Decomposition of Soil Organic Matter 93
Introduction 93
Importance of Soil Microbial Community Composition and Diversity 99
Interactions Between Microorganisms and Soil Fauna 106
Impacts of Nutrient Inputs on Microbial Mineralisation 110
Microorganism-Nutrient Relationships 111
Mechanisms for Nutrient Effect on the Decomposition of Soil Organic Matter 111
Effects of Nutrient Addition on Decomposition of Soil Organic Matter Components 113
Microbial Origin of Soil Organic Matter 115
References 120
Chapter 5: Intimate Associations of Beneficial Soil Microbes with Host Plants 131
Introduction 131
Mycorrhizas 133
The Main Types of Mycorrhizas 133
Arbuscular Mycorrhiza (AM) 135
Ectomycorrhiza (ECM) 137
Orchid Mycorrhiza 137
Ericoid Mycorrhiza 137
Arbuscular Mycorrhiza (AM): Development and Function 138
Cycle of AM Development 138
Improvement of Plant Phosphorus Uptake by AM Fungi 142
Increase of Plant Drought Tolerance 143
Increase of Plant Resistance to Pathogens 144
Bacterial Endosymbionts of Mycorrhizal Fungi 145
Legume-Rhizobia Root-Nodule (RN) Symbiosis 146
Specificity of RN Symbiosis 146
Development and Functioning of RN 149
Developmental Genetics of RN and AM Symbioses 154
Developmental Genetics of RN Symbiosis 156
Plant Genes Implicated in AM Development 157
The Use of Model Legumes for Studying Molecular Genetics of Symbioses 160
General Scheme of Functioning of the Common Symbiosis Pathway 161
Plant Receptors Involved in Nodule Formation 164
Cytokinin Signalling and Reception in Legumes 167
Autoregulation of RN and AM Symbioses Development 168
Associations of Roots with Plant Growth-Promoting Rhizobacteria (PGPR) 169
Nutritional Associations 170
Defensive Associations 171
Mutually Beneficial Associations of Plants with Endophytic Bacteria 175
Synergism of the Beneficial Soil Microbes in the Rhizosphere 177
Adaptive Evolution of the Mutually Beneficial Plant–Microbe Symbioses 178
New Approaches of Application of Mutually Beneficial Plant–Microbe Systems in Sustainable Agriculture 183
Development of New Types of Microbial Inocula 184
Legumes in Sustainable Agriculture 185
Legume Breeding to Improve Their Symbiotic Effectiveness 185
Analysis of Genetic Variability of Pea with Respect to its Effectiveness of Interactions with Beneficial Soil Microbes 186
Breeding to Improve Pea Symbiotic Effectiveness 187
Conclusions 187
References 188
Chapter 6: Soil-Borne Pathogens and Their Interactions with the Soil Environment 209
Introduction 209
The Impact of Soil-Borne Pathogens on Crops 211
Quantifying Losses 212
Evaluating Losses 215
Mitigation by Manipulating Husbandry 219
Rotation 219
Soil Type 222
Primary Cultivation: Tillage3 225
Secondary Cultivation 227
Soil Acidity and Alkalinity (Hydrogen Ion Content, pH) 229
Nutrient Status 232
Water Management 239
Sowing and Planting Times 242
Soil Solarisation 243
Cover, Trap and Biofumigation Cropping 245
Organic Additives 247
Characteristics of Soil Microbial Communities 252
Inoculum Potential 252
Entry and Colonisation 255
Pathogenesis 257
Characterising Sustainability Through Suppressive Soils 260
Integrative Pathogen Management 264
References 268
Chapter 7: The Impact of Land-Use Practices on Soil Microbes 284
Introduction 284
Measuring the Soil Microbial Community 285
Size 285
Composition 287
Activity 287
Physical Arrangement 287
Genotype 289
Phenotype 290
Functional Capability 290
Conventional Agriculture 291
Cultivation 291
Fertilisation 292
Pesticides 292
Livestock Management: Pastures 292
Sustainable Agriculture 293
Minimal or No Tillage and Organic Agriculture 293
Soil Amendments: Biochar 293
Animal Manures, Sewage Sludge and Other Organic Wastes 294
Use of Plant Growth Promoting Rhizobacteria (PGRP) 295
Impact of Civil Engineering, Mineral Extraction and Other Forms of Extreme Disturbance 296
Changes During Disturbance 297
Changes During Topsoil Storage 297
Recovery After Disturbance 298
Relationship Between Soil Microbial Community and Other Parameters 298
Effects of Management 299
Concluding Remarks 301
References 302
Chapter 8: The Effects of Plant Breeding on Soil Microbes 307
Introduction 307
Breeding for Modified Nutrient Uptake 308
Associative and Symbiotic Nitrogen Fixation 308
Arbuscular Mycorrhiza 309
Phosphorus Efficiency 310
Manganese Efficiency and Availability 312
Other Plant Breeding Effects 313
Glucosinolates in Brassicas 313
Transgenic Plants with Increased Resistance Against Damage by Pathogens or Insects 315
Control of Rhizoctonia 317
Conclusions 317
References 319
Chapter 9: Utilizing Soil Microbes for Biocontrol 325
Introduction 325
The Role of Soil Microbes in Biocontrol 325
Disease Suppression Using Composts 326
Pest Suppression Using Compost 327
Suppressive Soils 328
Take-All Suppression 328
Fusarium Suppressive Soils 329
Augmentation with Selected Bioactives 329
Insect Pests 330
Entomopathogenic Fungi 330
Entomopathogenic Bacteria 333
Antibiosis/Toxins 333
Plant Parasitic Nematodes 335
Microbial Plant Pathogens 338
Parasitism 338
Antibiosis/Toxins 341
Competition 343
Space and Nutrients 344
Iron Competition 344
Non-pathogenic and Hypovirulent Strains 345
Induced Resistance 346
Constraints to Successful Biological Control 347
Abiotic Factors 347
Soil Type 347
Soil Temperature 348
Osmotolerance 349
Carbon and Nitrogen 349
Soil pH 350
Interactions Between Soil Abiotic Factors 351
Biotic Factors 352
Production and Formulation 354
Fungal Inoculum 354
Bacterial Inoculum 355
The Way Forward 357
Characteristics of Successful Biocontrol Agents 357
Identification and Selection of Desired Traits 361
Insect Pests 361
Microbial Pathogens 362
Ecological Data 362
Integrated Control 363
Conclusions 365
References 366
Chapter 10: How Will Climate Change Impact Soil Microbial Communities? 382
Introduction 382
Microbial Response to Climate Change 384
Response to Specific Changes in Climate 386
Impact of Increasing Temperature 386
Impact of Elevated Carbon Dioxide 389
Impact of Changing Soil Moisture 390
Changing Agricultural Management Regimes and Soil Microbial Communities 392
Linking the Structure and Function of Microbial Communities in Changing Landscapes 393
Caveats and Conclusions 394
Climate Modulators and Native Regimes 394
Importance of Study Context and Length 395
Conclusions 396
References 397
Chapter 11: Evaluating the Economic and Social Impact of Soil Microbes 407
Introduction 407
Social and Economic Impacts of Soil Microbes 409
Economic Impacts 409
Social Impacts 411
Box 1 Soil Health and Social and Economic Well-being 412
Ecosystem Functions 413
Supporting Functions 415
Regulating Functions 415
Case Studies 416
Adoption of No-Till and Conservation Farming Practices in Australia 416
Soil Improvement in Sub-Saharan Africa 419
Summary 420
References 421
Index 426