Soil Microbiology and Sustainable Crop Production

Soils into which crop plants root and from which they obtain essential minerals and water contain huge arrays of microbes. Many have highly beneficial effects on crop growth and productivity, others are pathogens causing diseases and losses to yield and quality, a few microbes offer protection from these pathogenic forms and others have little or no effect. These intimate and often complex inter-relationships are being explored with increasing success providing exciting opportunities for increasing crop yields and quality in sustainable harmony with the populations of beneficial soil microbes and to the detriment of pathogens. This book explores current knowledge for each of these aspects of soil microbiology and indicates where future progress is most likely to aid in increasing crop productivity by means which are environmentally benign and beneficial.Advanced first degree, post-graduate students, post-doctoral researchers, lecturers, research-leaders, consultants, advisors, crop practitioners and policy makers involved with crop agronomy, biological control, plant pathology, plant breeding, agriculture, soil science, environmental interactions and conservation, and others requiring up to date knowledge of the impact of soil microbiology on sustainable crop production will find this book invaluable. Springer Cover 1 Soil Microbiology and Sustainable Crop Production 4 ISBN 9789048194780 5 Preface 6 Contents 10 Contributors 12 Chapter 1: The Nature of Sustainable Agriculture 16 Introduction 16 Recent Challenges in the Global Foodscape 18 Land Degradation and It Impact on Sustainability 20 Chemical Degradation 22 Amelioration of Charge Degradation 27 Addressing Soil Physical Degradation 33 Transforming the Agricultural Landscape 36 References 37 Chapter 2: The Microbiology of Natural Soils 42 Introduction 42 Methods of Study 43 Soil as a Habitat 44 Survey of Ecosystems 45 Tropical Forests 46 Neotropics: Amazonia, Costa Rica, Hawaii 47 Conclusions: Neotropics 56 Tropics of Africa, Southeast Asia, and Oceania 56 Conclusions: Old World Tropics 61 Wetlands 62 Soil Microbial Communities and Changing Agricultural Management Regimes 64 Conclusion 66 References 67 Chapter 3: Soil Microbiology and Nutrient Cycling 74 Introduction 74 The Global Biogeochemical Cycle of Carbon 78 Organic Matter in Soils and Its Turnover 78 Factors Controlling Decomposition 81 Substrate Quality 82 Organisms 83 Environmental Conditions 84 The Biogeochemical Cycle of Nitrogen 86 Nitrogen Mineralization 86 Nitrogen Fixation 88 Denitrification 90 Nitrification 91 Microbial Contributions to Phosphorus Cycling in Soil 92 Concluding Remarks 92 References 93 Chapter 4: The Role of Microbial Communities in the Formation and Decomposition of Soil Organic Matter 96 Introduction 96 Importance of Soil Microbial Community Composition and Diversity 102 Interactions Between Microorganisms and Soil Fauna 109 Impacts of Nutrient Inputs on Microbial Mineralisation 113 Microorganism-Nutrient Relationships 114 Mechanisms for Nutrient Effect on the Decomposition of Soil Organic Matter 114 Effects of Nutrient Addition on Decomposition of Soil Organic Matter Components 116 Microbial Origin of Soil Organic Matter 118 References 123 Chapter 5: Intimate Associations of Beneficial Soil Microbes with Host Plants 134 Introduction 134 Mycorrhizas 136 The Main Types of Mycorrhizas 136 Arbuscular Mycorrhiza (AM) 138 Ectomycorrhiza (ECM) 140 Orchid Mycorrhiza 140 Ericoid Mycorrhiza 140 Arbuscular Mycorrhiza (AM): Development and Function 141 Cycle of AM Development 141 Improvement of Plant Phosphorus Uptake by AM Fungi 145 Increase of Plant Drought Tolerance 146 Increase of Plant Resistance to Pathogens 147 Bacterial Endosymbionts of Mycorrhizal Fungi 148 Legume-Rhizobia Root-Nodule (RN) Symbiosis 149 Specificity of RN Symbiosis 149 Development and Functioning of RN 152 Developmental Genetics of RN and AM Symbioses 157 Developmental Genetics of RN Symbiosis 159 Plant Genes Implicated in AM Development 160 The Use of Model Legumes for Studying Molecular Genetics of Symbioses 163 General Scheme of Functioning of the Common Symbiosis Pathway 164 Plant Receptors Involved in Nodule Formation 167 Cytokinin Signalling and Reception in Legumes 170 Autoregulation of RN and AM Symbioses Development 171 Associations of Roots with Plant Growth-Promoting Rhizobacteria (PGPR) 172 Nutritional Associations 173 Defensive Associations 174 Mutually Beneficial Associations of Plants with Endophytic Bacteria 178 Synergism of the Beneficial Soil Microbes in the Rhizosphere 180 Adaptive Evolution of the Mutually Beneficial Plant–Microbe Symbioses 181 New Approaches of Application of Mutually Beneficial Plant–Microbe Systems in Sustainable Agriculture 186 Development of New Types of Microbial Inocula 187 Legumes in Sustainable Agriculture 188 Legume Breeding to Improve Their Symbiotic Effectiveness 188 Analysis of Genetic Variability of Pea with Respect to its Effectiveness of Interactions with Beneficial Soil Microbes 189 Breeding to Improve Pea Symbiotic Effectiveness 190 Conclusions 190 References 191 Chapter 6: Soil-Borne Pathogens and Their Interactions with the Soil Environment 212 Introduction 212 The Impact of Soil-Borne Pathogens on Crops 214 Quantifying Losses 215 Evaluating Losses 218 Mitigation by Manipulating Husbandry 222 Rotation 222 Soil Type 225 Primary Cultivation: Tillage3 228 Secondary Cultivation 230 Soil Acidity and Alkalinity (Hydrogen Ion Content, pH) 232 Nutrient Status 235 Water Management 242 Sowing and Planting Times 245 Soil Solarisation 246 Cover, Trap and Biofumigation Cropping 248 Organic Additives 250 Characteristics of Soil Microbial Communities 255 Inoculum Potential 255 Entry and Colonisation 258 Pathogenesis 260 Characterising Sustainability Through Suppressive Soils 263 Integrative Pathogen Management 267 References 271 Chapter 7: The Impact of Land-Use Practices on Soil Microbes 288 Introduction 288 Measuring the Soil Microbial Community 289 Size 289 Composition 291 Activity 291 Physical Arrangement 291 Genotype 293 Phenotype 294 Functional Capability 294 Conventional Agriculture 295 Cultivation 295 Fertilisation 296 Pesticides 296 Livestock Management: Pastures 296 Sustainable Agriculture 297 Minimal or No Tillage and Organic Agriculture 297 Soil Amendments: Biochar 297 Animal Manures, Sewage Sludge and Other Organic Wastes 298 Use of Plant Growth Promoting Rhizobacteria (PGRP) 299 Impact of Civil Engineering, Mineral Extraction and Other Forms of Extreme Disturbance 300 Changes During Disturbance 301 Changes During Topsoil Storage 301 Recovery After Disturbance 302 Relationship Between Soil Microbial Community and Other Parameters 302 Effects of Management 303 Concluding Remarks 305 References 306 Chapter 8: The Effects of Plant Breeding on Soil Microbes 312 Introduction 312 Breeding for Modified Nutrient Uptake 313 Associative and Symbiotic Nitrogen Fixation 313 Arbuscular Mycorrhiza 314 Phosphorus Efficiency 315 Manganese Efficiency and Availability 317 Other Plant Breeding Effects 318 Glucosinolates in Brassicas 318 Transgenic Plants with Increased Resistance Against Damage by Pathogens or Insects 320 Control of Rhizoctonia 322 Conclusions 322 References 324 Chapter 9: Utilizing Soil Microbes for Biocontrol 330 Introduction 330 The Role of Soil Microbes in Biocontrol 330 Disease Suppression Using Composts 331 Pest Suppression Using Compost 332 Suppressive Soils 333 Take-All Suppression 333 Fusarium Suppressive Soils 334 Augmentation with Selected Bioactives 334 Insect Pests 335 Entomopathogenic Fungi 335 Entomopathogenic Bacteria 338 Antibiosis/Toxins 338 Plant Parasitic Nematodes 340 Microbial Plant Pathogens 343 Parasitism 343 Antibiosis/Toxins 346 Competition 348 Space and Nutrients 349 Iron Competition 349 Non-pathogenic and Hypovirulent Strains 350 Induced Resistance 351 Constraints to Successful Biological Control 352 Abiotic Factors 352 Soil Type 352 Soil Temperature 353 Osmotolerance 354 Carbon and Nitrogen 354 Soil pH 355 Interactions Between Soil Abiotic Factors 356 Biotic Factors 357 Production and Formulation 359 Fungal Inoculum 359 Bacterial Inoculum 360 The Way Forward 362 Characteristics of Successful Biocontrol Agents 362 Identification and Selection of Desired Traits 366 Insect Pests 366 Microbial Pathogens 367 Ecological Data 367 Integrated Control 368 Conclusions 370 References 371 Chapter 10: How Will Climate Change Impact Soil Microbial Communities? 388 Introduction 388 Microbial Response to Climate Change 390 Response to Specific Changes in Climate 392 Impact of Increasing Temperature 392 Impact of Elevated Carbon Dioxide 395 Impact of Changing Soil Moisture 396 Changing Agricultural Management Regimes and Soil Microbial Communities 398 Linking the Structure and Function of Microbial Communities in Changing Landscapes 399 Caveats and Conclusions 400 Climate Modulators and Native Regimes 400 Importance of Study Context and Length 401 Conclusions 402 References 403 Chapter 11: Evaluating the Economic and Social Impact of Soil Microbes 414 Introduction 414 Social and Economic Impacts of Soil Microbes 416 Economic Impacts 416 Social Impacts 418 Box 1 Soil Health and Social and Economic Well-being 419 Ecosystem Functions 420 Supporting Functions 422 Regulating Functions 422 Case Studies 423 Adoption of No-Till and Conservation Farming Practices in Australia 423 Soil Improvement in Sub-Saharan Africa 426 Summary 427 References 428 Index 434 9789048194780,9048194784 Soils into which crop plants root and from which they obtain essential minerals and water contain huge arrays of microbes. Many have highly beneficial effects on crop growth and productivity, others are pathogens causing diseases and losses to yield and quality, only a few microbes offer protection from these pathogenic forms and others have little or no effect. These intimate and often complex inter-relationships are being explored with increasing success providing exciting opportunities for increasing crop yields and quality in sustainable harmony with the populations of beneficial soil microbes and to the detriment of pathogens. This book explores current knowledge for each of these aspects of soil microbiology and indicates where future progress is most likely to aid in increasing crop productivity by means which are environmentally benign and beneficial. Advance first degree, post-graduate students, post-doctoral researchers, lecturers, research-leaders, consultants, advisors, crop practitioners and policy makers involved with crop agronomy, biological control, plant pathology, plant breeding, agriculture, soil science, environmental interactions and conservation, and others requiring up to date knowledge of the impact of soil microbiology on sustainable crop production will find this book valuable.-- BOOK COVER Soils into which crop plants root and from which they obtain essential minerals and water contain huge arrays of microbes. Many have highly beneficial effects on crop growth and productivity, others are pathogens causing diseases and losses to yield and quality, a few microbes offer protection from these pathogenic forms and others have little or no effect. These intimate and often complex inter-relationships are being explored with increasing success providing exciting opportunities for increasing crop yields and quality in sustainable harmony with the populations of beneficial soil microbes and to the detriment of pathogens. This book explores current knowledge for each of these aspects of soil microbiology and indicates where future progress is most likely to aid in increasing crop productivity by means which are environmentally benign and beneficial. Advanced first degree, post-graduate students, post-doctoral researchers, lecturers, research-leaders, consultants, advisors, crop practitioners and policy makers involved with crop agronomy, biological control, plant pathology, plant breeding, agriculture, soil science, environmental interactions and conservation, and others requiring up to date knowledge of the impact of soil microbiology on sustainable crop production will find this book invaluable Front Matter....Pages i-xiv The Nature of Sustainable Agriculture....Pages 1-25 The Microbiology of Natural Soils....Pages 27-57 Soil Microbiology and Nutrient Cycling....Pages 59-80 The Role of Microbial Communities in the Formation and Decomposition of Soil Organic Matter....Pages 81-118 Intimate Associations of Beneficial Soil Microbes with Host Plants....Pages 119-196 Soil-Borne Pathogens and Their Interactions with the Soil Environment....Pages 197-271 The Impact of Land-Use Practices on Soil Microbes....Pages 273-295 The Effects of Plant Breeding on Soil Microbes....Pages 297-314 Utilizing Soil Microbes for Biocontrol....Pages 315-371 How Will Climate Change Impact Soil Microbial Communities?....Pages 373-397 Evaluating the Economic and Social Impact of Soil Microbes....Pages 399-417 Back Matter....Pages 419-436