Phosphorus in Action (eBook)

Preface 6
Reference 9
Contents 10
Contributors 12
Part I: Methods 18
Chapter 1: Soil Organic Phosphorus Speciation Using Spectroscopic Techniques 19
1.1 Introduction 19
1.1.1 Why Spectroscopy? 20
1.2 Solution 31P NMR Spectroscopy 22
1.2.1 Sample Preparation 24
1.2.2 Sensitivity 26
1.2.3 Resolution 28
1.2.3.1 Identification of P Species 28
1.2.4 Quantitation 31
1.3 Solid-State 31P NMR SpectroscopySolid-state 31P NMR spectroscopy 33
1.3.1 Sample Preparation 34
1.3.2 Sensitivity 35
1.3.3 Resolution 36
1.3.4 Quantitation 37
1.4 P XANES Spectroscopy 38
1.4.1 Sample Preparation 40
1.4.2 Sensitivity 40
1.4.3 Resolution 40
1.4.4 Quantitation 42
1.5 Conclusions 45
1.6 Future Directions 46
References 47
Chapter 2: Characterization of Phosphorus Forms in Soil Microorganisms 53
2.1 Microorganisms as a Pool of Phosphorus in Soil 53
2.2 Cultivation and Extraction Methods 56
2.2.1 Culturing of Microorganisms 56
2.2.2 Extraction of Microorganisms from Soil 57
2.3 Methods for Analysis of Chemical Forms of Phosphorus 58
2.3.1 Total P 58
2.3.2 P Speciation Using 31P NMR 59
2.3.3 P Speciation by Chromatographic, Spectrometric, Staining, and Enzymatic Techniques 60
2.3.3.1 P in DNA and RNA 60
2.3.3.2 P in Lipids 61
2.3.3.3 P in Metabolites 62
2.3.3.4 P in Teichoic Acids and Other Compounds 63
2.4 Phosphorus Forms in Cultured and Extracted Soil Microorganisms 63
2.4.1 Analysis of P Forms in Pure Cultures Using 31P NMR 63
2.4.2 Analysis of P Forms in Microbial Cells Extracted from a Ferralsol 65
2.5 Conclusions and Outlook 68
References 69
Chapter 3: The Use of Tracers to Investigate Phosphate Cycling in Soil-Plant Systems 74
3.1 Introduction 74
3.2 Use of P Radioisotopes to Study Soil Processes and to Probe Soil P Pools 76
3.2.1 Isotopic Dilution of P in Soil-Solution Systems: The Principles 77
3.2.2 Isotopic Dilution of Phosphate Ions in Soil-Solution Systems: Selected Applications 80
3.2.2.1 Assessment of Availability of Phosphate Ions for Plants 80
3.2.2.2 Quantification of Phosphate Mineralized from Soil Organic Matter and from Soil Microorganisms 82
3.2.3 Isotopic Dilution of Phosphate Ions in Soil-Solution Systems: Limits and Answers 85
3.2.3.1 Measuring Very Low Concentrations of Phosphate Ions in Solution 85
3.2.3.2 Are P Radioisotopes Irreversibly Fixed in Soils That Sorb Very High Amounts of Phosphate Ions? 86
3.2.4 Application of Isotopic Dilution Techniques to Soil-Plant Systems 87
3.3 Use of P Radioisotopes to Trace the Fate of P Sources in the Soil-Plant System 89
3.3.1 Labeling the P Source (Direct Labeling Technique) 89
3.3.2 Labeling the Plant-Available Soil Phosphate (Indirect Labeling Technique) 90
3.4 Using P Radioisotopes to Assess Foraging Strategies of AMF 91
3.5 Can the Isotopic Composition of Oxygen Bound to Phosphorus Be Used to Study Biological P Transformations in Soil-Plant Syst 94
3.5.1 What Do We Know Already? 94
3.5.2 What Should Be Done to Apply This Approach to Soil-Plant Systems? 97
3.6 Concluding Remarks and Research Needs 98
References 99
Chapter 4: Molecular Approaches to the Study of Biological Phosphorus Cycling 107
4.1 Introduction 107
4.2 DNA Extraction 107
4.2.1 Soil Samples 107
4.2.2 Plants and Hyphae 109
4.2.3 Rolling Cycle Amplification 109
4.3 Molecular Approaches Using the Sequences of SSU rRNA and ITS Regions 110
4.3.1 Clone Libraries 110
4.3.2 PCR-DGGE 110
4.3.3 Restriction Fragment Length Polymorphism 112
4.4 Methods Targeting Active Microbes and Functional Genes 112
4.4.1 RNA Extraction 112
4.4.2 Analysis of Functional Genes by DNA-Based Techniques 113
4.4.3 Quantitative Real-Time PCR: Quantification Technology for SSU rRNA and Transcripts of Functional Genes 113
4.4.4 Fluorescence In Situ Hybridization 114
4.4.5 Stable Isotope Probing 114
4.4.6 Bromodeoxyuridine Immunocapture 115
4.4.7 Phosphate-Reporter Bacteria 115
4.5 Methods for Analysis of Plant Functions 115
4.5.1 Phosphatase Activities 116
4.5.2 Organic Acid Exudation from Plant Roots 117
4.5.3 Phosphate Transporters 117
4.5.4 Exudation of Antibiotic Compounds and Enzymes 118
4.5.5 Quantitative RT-PCR 118
4.6 Novel Technologies: Omics Analyses for P Cycling 118
4.6.1 Microarrays 118
4.6.2 Metagenomics and the Next Generation of DNA Sequencers 119
4.6.3 Proteomics and Metabolomics 121
4.7 Conclusions 121
References 122
Chapter 5: Modelling Phosphorus Dynamics in the Soil-Plant System 126
5.1 Introduction 126
5.1.1 Building a Mathematical Model 128
5.1.2 Aims of This Chapter 128
5.2 Modelling Case Studies 129
5.2.1 P Uptake by Mycorrhizal Roots 129
5.2.1.1 Aim of the Model 129
5.2.1.2 Model Description 129
5.2.1.3 Results 131
5.2.1.4 Discussion and Outlook 131
5.2.2 P Uptake by a Root System 133
5.2.2.1 Aim of the Model 133
5.2.2.2 Model Description 133
5.2.2.3 Results 136
5.2.2.4 Discussion and Outlook 136
5.2.3 P Uptake and Crop Response to Soil P Levels 137
5.2.3.1 Aim of the Model 137
5.2.3.2 Model Description 138
Module 1: Modelling Crop Growth and Crop P Demand 138
Module 2: Modelling Soil P Supply to Crops 139
Module 3: Modelling P Uptake by the Root System According to Crop P Demand and Soil P Supply 140
Integration and Feedback Loop 141
5.2.3.3 Results 141
5.2.3.4 Discussion and Outlook 142
5.3 Summary 143
References 143
Part II: Processes 147
Chapter 6: Role of Mycorrhizal Symbioses in Phosphorus Cycling 148
6.1 Introduction 148
6.1.1 Mycorrhizal Symbiosis: Definition, Partners, Diversity 148
6.1.2 Mycorrhizal Functioning 150
6.2 Different Forms of P in the Soil and Their Accessibility to Mycorrhizas 153
6.2.1 Forms of P 153
6.2.2 Kinetics of P Acquisition by Hyphae 153
6.2.3 Access to Recalcitrant P Forms, Weathering, and Mineralization 155
6.2.4 Mycorrhizas as Compound-Specific Filters 160
6.3 Translocation of P Within the Hyphae and Its Release to the Plants 160
6.3.1 Transport Within the Hyphae 160
6.3.2 Release of P to the Plant 161
6.3.3 Consequences of Mycorrhizal P Acquisition for the Plants and for Maintenance of Mutualism 161
6.4 Functional Diversity of Mycorrhizas with Respect to P Uptake 163
6.5 Human Impact on the Mycorrhizal Pathway of P Acquisition by Plants 163
6.6 Conclusions 165
References 166
Chapter 7: Solubilization of Phosphorus by Soil Microorganisms 180
7.1 Introduction 180
7.2 P in the Soil Environment 181
7.2.1 Sources of Soil P Capable of Microbial Solubilization 181
7.2.1.1 Inorganic P 182
7.2.1.2 Organic P 183
Soil Organic Matter 183
Organic Soil Additives 184
7.3 P-Solubilizing Mechanisms 185
7.3.1 P Release Mediated by Changes in pH 186
7.3.2 P Release Mediated by Organic Acid Anions 187
7.3.3 Exopolysaccharide-Mediated Release of P 189
7.3.4 Siderophore-Mediated Release of P 190
7.3.5 Enzyme-Mediated Release of P 190
7.3.6 Release of P Held in P-Solubilizing Microorganisms 192
7.4 P-Solubilizing Organisms 193
7.4.1 Bacteria 193
7.4.2 Non-mycorrhizal Fungi 194
7.4.3 Actinomycetes 195
7.4.4 Protozoa 195
7.4.5 Mesofaunal Interactions 196
7.5 Significance of PSM in the Field and Potential for Management 196
7.6 Conclusions and Future Research Directions 199
References 200
Chapter 8: Role of Soil Macrofauna in Phosphorus Cycling 210
8.1 Introduction 210
8.2 Earthworms 211
8.2.1 Phosphorus Contents and Forms in Earthworm Biogenic Structures 211
8.2.2 Phosphorus Dynamics and Availability in Earthworm Casts 212
8.2.3 Surface-Cast Erosion and Phosphorus Transfer 214
8.3 Termites 216
8.3.1 Phosphorus Contents in Termite Mounds 216
8.3.2 Phosphorus Dynamics and Availability in Termite Mounds 217
8.3.3 Termite Mounds and Phosphorus Transfer 218
8.4 Conclusion 219
References 219
Chapter 9: Role of Phosphatase Enzymes in Soil 225
9.1 Introduction 225
9.2 Determination of Soil Phosphatase Activities 226
9.3 Range and Kinetic Properties 229
9.4 Limitations of the Present Enzyme Assays 232
9.5 Role of Phosphatase in Organic P Mineralisation in Soil and the Effect of Inorganic P 235
9.6 Phosphatase Activities of Bulk and Rhizosphere Soil and the Origin of Phosphatases in Soil 236
9.7 Effects of Soil Handling, Soil Properties, Agricultural Management and Pollutants on Soil Phosphatase Activities 238
9.7.1 Effects of Soil Handling and Soil Properties on Phosphatase Activities 239
9.7.2 Effect of Agricultural Management, Forest Practices and Fire on Soil Phosphatases 240
9.7.3 Effects of Pollutants on Soil Phosphatase Activities 241
9.8 Stabilisation of Extracellular Phosphatases in Soil by Interaction with Surface-Reactive Particles or by Entrapment Within 243
9.9 Conclusions and Future Research Needs 245
References 246
Chapter 10: Phosphorus Nutrition: Rhizosphere Processes, Plant Response and Adaptations 254
10.1 Introduction 254
10.2 Root and Rhizosphere Responses of Plants to P Deficit 256
10.2.1 Morphological Adjustment of Roots to P Deficiency 256
10.2.2 Formation of Root Hairs in Response to P Deficit 256
10.2.3 Release of Extracellular Organic Anions 257
10.2.4 Release of Extracellular Phosphatase 258
10.3 Coordinating Plant Responses to Variations in P Supply 262
10.4 Response of Plants to P Re-supply 265
10.5 Can P Starvation and Re-supply Responses Be Genetically Manipulated for Agricultural Benefit? 267
10.6 Concluding Remarks 271
References 271
Part III: Ecosystems and Management 281
Chapter 11: Biological Phosphorus Cycling in Grasslands: Interactions with Nitrogen 282
11.1 Introduction 282
11.1.1 P Cycle in Grassland Ecosystems 283
11.1.2 Aims of the Chapter 284
11.2 Direct N-P Interactions in Grasslands 284
11.2.1 Influence of N-P Interaction on Grassland Production 284
11.2.2 Analysis of N-P Interaction Using the Nutrient Index Approach 285
11.2.2.1 The Plant Nutrient Index Approach 285
11.2.2.2 Relationships Between Nutrition Indices and Growth: Analysis of N-P Interaction 288
11.3 Indirect N-P Interactions 289
11.3.1 Indirect Interactions Related to Grassland Vegetation Types 289
11.3.1.1 Definition of Plant Functional Types and Grassland Vegetation Types from Plant Functional Traits 289
11.3.1.2 Relationships Between Response Traits and Fertility Gradients 290
11.3.1.3 Relationships Between Plant Functional Types and Nutrient Cycling 293
11.3.2 Effects of P on Biological Nitrogen Fixation 294
11.4 Analyzing the Effect of Herbivores on N and P Cycles in Grassland Ecosystems 294
11.5 Conclusion 296
References 297
Chapter 12: Biological Phosphorus Cycling in Arctic and Alpine Soils 302
12.1 Introduction 302
12.2 Characteristics of Arctic and Alpine Soils 303
12.3 P Availability and Uptake in Arctic and Alpine Soils 304
12.3.1 P Forms and Distribution in Arctic Soils 304
12.3.2 P Forms and Distribution in Alpine Soils 306
12.3.3 P Mineralization Dynamics in Arctic and Alpine Soils 308
12.3.4 Seasonal Dynamics of Arctic and Alpine Plant P Uptake 310
12.3.5 The Role of Phosphatases in P Acquisition 311
12.4 P Limitation in Arctic and Alpine Soils 313
12.4.1 Case Studies from Arctic P Addition Experiments 313
12.4.2 Case Studies from Alpine P Addition Experiments 316
12.5 Conclusions 318
References 320
Chapter 13: Phosphorus Nutrition of Forest Plantations: The Role of Inorganic and Organic Phosphorus 324
13.1 Introduction 324
13.2 Phosphorus Fertilization of Forest Plantations 326
13.3 Phosphorus Dynamics in Forest Ecosystems 329
13.3.1 Phosphorus Pools and Cycling in the Forest Floor 330
13.3.2 Organic P in Forest Soils 331
13.3.3 Availability of Organic P in Forest Ecosystems 333
13.3.4 Impact of Organic Acids on Phosphorus Dynamics in Forest Soils 335
13.4 Summary and Implications to Tree P Nutrition 338
References 338
Chapter 14: Phosphorus Cycling in Tropical Forests Growing on Highly Weathered Soils 346
14.1 Introduction 346
14.2 The P Cycle in Tropical Soils 349
14.2.1 Tropical Soil P: Inputs 349
14.2.1.1 Parent Material 349
14.2.1.2 Atmospheric Inputs 351
14.2.2 Tropical Soil P: Internal Cycling and Transformations 353
14.2.2.1 Mineralization 353
14.2.2.2 Sorption 357
14.2.3 Biological Responses to Low P Availability 360
14.2.4 Tropical Soil P: Losses 361
14.3 Nutrient Limitation in Tropical Forests 364
14.4 Global Change and Soil P in the Tropics 366
14.5 Conclusions 367
References 368
Chapter 15: Biological Phosphorus Cycling in Dryland Regions 377
15.1 Introduction 377
15.2 Inputs and Losses of P in Drylands 377
15.3 Distribution and Redistribution of P in Drylands 380
15.3.1 Horizontal Redistribution of P and Materials Affecting P Availability 380
15.3.1.1 Wind 380
15.3.1.2 Water 382
15.3.1.3 Wildlife, Livestock, and Human Settlements 382
15.3.2 Vertical Redistribution of P 383
15.3.2.1 Animal Activity 383
15.3.2.2 Ants and Termites 384
15.3.2.3 Dung Beetles 385
15.3.2.4 Mammals and Reptiles 385
15.3.2.5 Plants 385
15.4 Controls on P Bioavailability in Drylands 386
15.4.1 Abiotic and Microbial Controls on P Bioavailability 387
15.4.2 Biocrust Controls on P Availability 389
15.4.2.1 Secretion of Extracellular Polysaccharides, Organic Acids, and Chelators 389
15.4.2.2 Secretion of Phosphatases 390
15.4.3 Fungi as Connectors 391
15.4.4 Soil Fauna Controls on P Availability 392
15.4.5 Plant Controls on Soil P 392
15.4.6 Interactions Between Invasive Plants and P Availability 394
15.5 Case Study: Interaction Between Exotic Annual Grasses and Soil P Availability in the Western United States 395
15.5.1 Controls of P on Exotic Annual Plant Distribution 395
15.5.2 The Interaction of Soil P and Bromus tectorum 398
15.6 Climate Change Effects on Biological P Cycling in Drylands 402
15.7 Conclusion 403
References 404
Chapter 16: Effects of Manure Management on Phosphorus Biotransformations and Losses During Animal Production 413
16.1 Introduction 413
16.2 Major Types of Animal Production Systems and Associated Manure Management Systems 414
16.2.1 Extensive Production Systems on Pastures, Rangelands, and Forested Lands 414
16.2.2 Confined Livestock and Poultry Production Systems 415
16.2.2.1 Ruminant Production and Dietary P Balance 415
16.2.2.2 Production of Monogastric Livestock and Dietary P Balance 417
16.3 Manure P Forms and Management-Induced Biotransformations 418
16.3.1 Transformations of P in Semisolid and Liquid Manure Management Systems 418
16.3.1.1 Loss Pathways of P in Liquid Manure Management Systems 423
16.3.2 Transformations of P in Dry Solid Manure Management 424
16.3.2.1 Beef Cattle and Dry Manure Management 424
16.3.2.2 Poultry Manure and Litter Management 426
16.3.3 Loss Pathways of P in Solid Manure Management Systems 427
16.3.3.1 Open Feedlots and Dry Cattle and Poultry Manure Stockpiles 427
16.3.3.2 Losses of P from Grazed Lands 428
16.3.3.3 Loss of P from Land-Applied Manure in Mixed Crop-Livestock Systems 429
16.4 Conclusions 430
References 431
Chapter 17: Management Impacts on Biological Phosphorus Cycling in Cropped Soils 436
17.1 Introduction 436
17.2 Microbial Functions in Cropped Soils 437
17.3 Tillage Impacts on Biological P Cycling 439
17.3.1 Tillage Effects on P Distribution and P Dynamics 440
17.3.2 Interactions Between Tillage, Specific Organisms, and P Dynamics 440
17.3.3 Tillage or No-Tillage: Trade-Offs in the Use of Crop Residues 441
17.4 Fertilizer Inputs: The Form of Nutrient Sources Matters 441
17.4.1 Animal Manure Promotes Microbial P Cycling: A Case Study on Organic Versus Conventional Farming in Switzerland 442
17.4.2 Availability and Quality of Animal Manure and Recycling Fertilizers 445
17.5 Crop Rotation: Higher P-Use Efficiency Through the Integration of Legumes? 446
17.5.1 Legume Strategies for Acquiring P 446
17.5.2 Crop Rotations: Can Succeeding Crops Benefit from Legume P Acquisition Strategies? 448
17.5.2.1 Legume Residues as a P Source 448
17.5.2.2 Improved Soil P Availability Because of Modified Soil Conditions 450
17.5.2.3 Effects Not Related to P 452
17.5.3 Limitations of the Approach to Integrate Legumes in Crop Rotations 452
17.6 Integrated P Management for Sustainable P Use 453
17.7 Final Remarks and Research Needs 455
References 456
Chapter 18: Phosphorus and Global Change 464
18.1 Human Appropriation of P Deposits 464
18.2 P Cycling in Natural and Agro-Ecosystems 466
18.3 Drivers of Changes in Reservoirs and Fluxes 468
18.4 P Cycle and Biofuels 470
18.5 Land Degradation 471
18.6 Concluding Remarks 473
References 473
Appendix - General Conclusions 477
Index 480