Soil Enzymology (eBook)

Soil Enzymology 3
Preface 5
Contents 9
Contributors 13
Chapter 1: Soil Enzyme: The State-of-Art 17
1.1 Introduction 17
1.2 Soil: A Physical Point of View 18
1.2.1 Particle Shape and Size 18
1.2.2 Textural Classes 18
1.2.3 Colors 19
1.2.4 Density 19
1.2.5 Pore Space 19
1.2.6 Plasticity and Cohesion 19
1.2.7 Soil Temperature and Heat 20
1.2.8 Soil Water 20
1.3 Soil: A Chemical Point of View 20
1.3.1 Organic Matter 20
1.3.2 Humus 21
1.3.3 Soil Colloids 21
1.4 Soil: A Biological Point of View 21
1.4.1 Kind of Soil Organisms 22
1.4.1.1 Eubacteria 22
1.4.1.2 Fungi 24
Decomposers 24
Mutualists 24
Pathogens 24
1.4.1.3 Algae 25
1.4.2 Population Density 25
1.4.3 Bacterial Activity 25
1.4.3.1 Energetics of Nitrification 26
1.5 Enzymes 27
1.6 Soil Enzymes 27
1.6.1 Amylase 29
1.6.2 beta-Glucosidase 29
1.6.3 Cellulase 30
1.6.4 Laccase 30
1.6.5 Chitinase 31
1.6.6 Dehydrogenase 31
1.6.7 Phosphatase 32
1.6.8 Protease 33
1.6.9 Urease 33
1.6.10 Arylsulphatase 33
1.7 Conclusion 34
References 34
Chapter 2: Role of Enzymes in Maintaining Soil Health 40
2.1 Introduction 40
2.2 Soil Enzymes 41
2.2.1 Kind of Soil Enzymes 41
2.2.1.1 Constitutive 41
2.2.1.2 Inducible 41
2.2.2 Origin and State of Soil Enzymes 42
2.2.3 Importance of Soil Enzymes 42
2.2.4 Application of Soil Enzymes 42
2.3 Soil Health 43
2.3.1 Definition 43
2.3.2 Aspects of Soil Health 44
2.3.3 Interpretation of Soil Health 44
2.3.4 Pressures on Soil Health Towards Impacts 45
2.4 Indicators of Soil Health 46
2.4.1 Microorganism as Indicators of Soil Health 46
2.4.2 Soil Enzymes as Indicators of Soil Health 46
2.5 Potential Roles of Soil Enzymes in Maintaining Soil Health 47
2.5.1 Amylase 47
2.5.2 Arylsulphatases 48
2.5.3 beta-Glucosidase 48
2.5.4 Cellulases 49
2.5.5 Chitinase 50
2.5.6 Dehydrogenase 50
2.5.7 Phosphatases 51
2.5.8 Proteases 51
2.5.9 Urease 52
2.6 Conclusion 52
References 53
Chapter 3: Agricultural and Ecological Significance of Soil Enzymes: Soil Carbon Sequestration and Nutrient Cycling 58
3.1 Introduction 58
3.2 Soil Enzymes for Organic Matter Decomposition and Nutrient Cycling 59
3.2.1 Soil Enzymes of Primary Interest 59
3.2.2 Lignocellulolytic Enzymes as Predictors of Organic Matter Decomposition 60
3.2.3 Enzymes as Indicators of Soil Nutrient Availability 61
3.3 Microbial Enzyme Production as Affected by Organic Carbon and Nutrient Availability 61
3.3.1 Positive and Negative Feedback Mechanisms 61
3.3.2 Microbial Resource Reallocation 63
3.3.3 Microbial Nutrient Demand 64
3.4 Soil Enzyme Activity in Relation to the Quantity and Quality of Soil Organic Matter 65
3.5 Agricultural and Ecological Significance of Soil Enzymes in Soil Carbon Sequestration 65
3.5.1 Assessing Carbon Efflux in Peatlands Under Global Climate Change 65
3.5.2 Predicting Soil Carbon Sequestration in Temperate Forests 66
3.5.3 Understanding Soil Carbon Storage Potential in Semi-arid Grasslands 69
3.5.4 Restoring Soil Organic Matter from the Perspective of Soil Enzymes 70
3.6 Conclusions 71
References 72
Chapter 4: Enzymes in Forest Soils 76
4.1 Introduction 76
4.2 Distribution of Enzymes in the Soil Profile 77
4.3 Spatial Variability of Enzyme Activities in Soils 78
4.4 Factors Affecting Soil Enzyme Activities 80
4.4.1 Producers of Extracellular Enzymes 80
4.4.2 Soil Chemistry and Nutrient Availability 80
4.4.3 Seasonality 81
4.4.4 Soil Moisture Content 82
4.5 Litter Decomposition in Forest Ecosystems 83
4.6 Conclusions 84
References 84
Chapter 5: Extracellular Enzymes in Sensing Environmental Nutrients and Ecosystem Changes: Ligand Mediation in Organic Phospho 89
5.1 Introduction 89
5.2 Biogeochemistry of Phosphorus 91
5.2.1 Inorganic Phosphate 92
5.2.2 Organic Phosphorus 94
5.3 Reactions Involving Organic Phosphorus in Soils 95
5.3.1 Chemical Processes 95
5.3.1.1 Adsorption-Precipitation 95
5.3.1.2 Autohydrolysis and Metal-Mediated Hydrolysis 97
5.3.2 Biological Processes Involved in Organic P Solubilization and Degradation 99
5.3.2.1 Mineralization of Environmental Biological Tissues Containing Organic P 99
5.3.2.2 Mycorrhizal Associations 100
5.3.2.3 Extracellular Phosphohydrolases 101
Enzymatic Dephosphorylation of Uncomplexed Organic Phosphate Monoesters 101
Ligand Mediation of (or Chemically-Assisted) Enzymatic Dephosphorylation of Complexed Organic Phosphate Monoesters 102
5.4 An In Vitro Method to Emulate Ligand-Based Plant and Microbial Solubilization and Mineralization of Organic P Pools in Soil 106
5.5 Conclusions 108
References 110
Chapter 6: Importance of Extracellular Enzymes for Biogeochemical Processes in Temporary River Sediments during Fluctuating Dr 117
6.1 Introduction 117
6.2 The Response of Benthic Microbial Communities to Drought: A Matter of Survival 119
6.3 Benthic Microbial Community Awakening After Flooding 124
6.4 Conclusions 127
References 129
Chapter 7: Soil Enzymes as Indication of Soil Quality 132
7.1 Introduction 132
7.2 Soil Enzymes: Classification, Sources, States, Affecting Factors and Activation or Inhibition 135
7.2.1 Enzyme Classification 135
7.2.2 Sources of Soil Enzymes 136
7.2.3 States 136
7.2.4 Affecting Factors 137
7.2.5 Enzyme Inhibition and Activation 137
7.3 Indication of Soil Enzymes 138
7.3.1 Soil Enzymes as Pollution Indicators 141
7.3.2 Soil Enzymes as Ecosystems Perturbations Indicators 144
7.3.3 Soil Enzymes as Agricultural Practices Indicators 146
7.4 Conclusion 152
References 153
Chapter 8: Enzyme Activities in the Rhizosphere of Plants 162
8.1 Introduction 162
8.2 Effect of Root Exudates on Rhizosphere Soil Enzyme Activities 165
8.3 The Role of Lytic Enzymes and Plant Growth Regulators 166
8.4 Effect of Soil Management and Heavy Metals on Rhizosphere Soil Enzyme Activities 169
8.5 Impact of Salinity on Rhizosphere Enzyme Activities 171
8.6 Conclusions 173
References 174
Chapter 9: Lignocellulose-Degrading Enzymes in Soils 180
9.1 Introduction 180
9.2 Degradation of Cellulose and Hemicelluloses 181
9.3 Enzymes Degrading Lignin and Humic Substances 182
9.4 Lignocellulolytic Systems of Soil Microorganisms 183
9.5 Lignocellulolytic Enzymes in Different Ecosystems 185
9.5.1 Polar and Mountainous Soils 186
9.5.2 Boreal Forests 187
9.5.3 Temperate Forests 188
9.5.4 Evergreen Forests 188
9.5.5 Grasslands 189
9.5.6 Arable Soils 189
9.5.7 Wetlands 190
9.5.8 Arid and Desert Soils 190
9.6 Factors Affecting Lignocellulose Degradation in Soils 191
9.7 Molecular Biology of Enzymes in Soils 192
9.8 Conclusions 193
References 193
Chapter 10: Heterophase Synthesis of Humic Acids in Soils by Immobilized Phenol Oxidases 200
10.1 Introduction 200
10.2 Synthesis of Humic Substances from Soluble Precursors 201
10.2.1 Enzymatic Catalysis 202
10.2.1.1 Occurrence of Phenol Oxidases in Soils 203
10.2.1.2 Phenol Oxidase Distribution among Soil Phases 204
10.2.1.3 Synthesis of Humic Substances in the Aqueous Phase 205
10.2.1.4 Synthesis of Humic Substances on the Solution/Solid Interface 207
10.2.2 Abiotic Heterogeneous Catalysis 212
10.3 Conclusions 214
References 215
Chapter 11: Fungal Oxidoreductases and Humification in Forest Soils 219
11.1 Introduction 219
11.2 The Origin of HSs 220
11.3 Major Fungal Oxidative Enzymes 221
11.3.1 Peroxidases 221
11.3.2 Laccase and Tyrosinase 222
11.4 Humification Activities of Fungi in Wood and Soil 223
11.4.1 Wood Decomposers 224
11.4.1.1 Soft-rot Ascomycetes: Production of Large Soluble Fragments 224
11.4.1.2 Brown-rot Fungi: Formation of Humic Acids from Partially Oxidized Lignin 226
11.4.1.3 White-rot Fungi: Production of Small Soluble Polyphenols (Structural Units) and FAs 226
11.4.2 Litter and Soil-inhabiting Fungi 228
11.4.2.1 Microfungi: Lignocellulose and Humus Solubilization, Synthesis of Melanins, and HS 228
11.4.2.2 Saprotrophic Basidiomycetes: Production of the ``White-Rot´´ Humus and FA-like Compounds 229
11.4.3 Symbiotic Fungi 230
11.4.3.1 Ectomycorrhiza 231
11.4.3.2 Lichens 232
11.5 Conclusions 234
References 235
Chapter 12: Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function 241
12.1 Introduction 241
12.2 The Evolutionary Economics of Extracellular Enzyme Production 243
12.3 Controls on Microbial Allocation to Enzyme Production 243
12.3.1 Microbial Demand 243
12.3.2 Enzyme Regulation 244
12.4 Resource Availability in Soil 245
12.5 Implications of Enzyme Allocation 247
12.5.1 Protection of Investment 247
12.5.2 Enzyme Responses to Global Environmental Change 248
12.5.2.1 Increase in Atmospheric CO2 249
12.5.2.2 Increases in N Deposition 250
12.5.2.3 Changes in Temperature and Moisture 251
12.6 Conclusions 251
References 252
Chapter 13: Controls on the Temperature Sensitivity of Soil Enzymes: A Key Driver of In Situ Enzyme Activity Rates 256
13.1 Introduction 256
13.2 What Controls Enzyme Temperature Sensitivity? 257
13.2.1 Enzyme Conformation 257
13.2.2 Modeling Enzyme Kinetics 259
13.2.3 Michaelis-Menten Model 260
13.2.4 Enzyme Binding to Soil Particles 262
13.3 Indirect Effects of Temperature on Enzyme Activities 263
13.4 Temperature Sensitivity of Extracellular Enzymes under Field Conditions 263
13.5 Conclusions 265
References 266
Chapter 14: Actinomycetes: Sources for Soil Enzymes 270
14.1 Introduction 270
14.2 Keratinases 272
14.3 Pectinases 273
14.4 Xylanases 275
14.5 Lipases 276
14.6 Conclusion 278
References 279
Chapter 15: Organo-Mineral-Enzyme Interaction and Soil Enzyme Activity 281
15.1 Introduction 281
15.2 History of Enzyme-Organo-Mineral Interaction Studies 282
15.3 Enzyme-Mineral Interactions 284
15.4 Enzyme-Organic Matter Interactions 289
15.5 Mineral-Organic Matter-Enzyme Synergistic Interactions 292
15.6 Consequences of Organo-Mineral-Enzyme Interactions 295
15.7 Conclusion 296
References 296
Chapter 16: The Influence of Pesticides on Soil Enzymes 303
16.1 Introduction 303
16.2 Pesticides and Soil 304
16.3 Soil Enzymes 307
16.4 Pesticides and Soil Enzymes 310
16.5 Conclusions 318
References 319
Chapter 17: Behavior of Enzymatic Activity in Chilean Volcanic Soil and Their Interactions with Clay Fraction 323
17.1 Introduction 323
17.2 Chilean Volcanic Soil 324
17.2.1 Characteristics of Chilean Volcanic Soils 324
17.2.2 Properties of Volcanic Ashes-derived Soils 324
17.2.3 Mechanisms of Enzyme Immobilization in Soil Derived of Volcanic Ash 326
17.2.3.1 Enzyme Immobilization on Andisol Clay Fraction 326
17.2.3.2 Enzyme Immobilization on Ultisol Clay Fraction 328
17.2.3.3 Some Considerations about Model Using Synthetic Complexes Clay-Enzyme 329
17.3 Soil of Enzymatic Activities in Relation with Some Management Practices 330
17.3.1 Soil Enzymatic Activities in Andisols and Ultisols of Southern Chile 330
17.3.1.1 Evaluation of the Effect of Mn and Mo on Acid Phosphatase in a Model System of Andisol 332
17.4 Conclusion 333
References 335
Chapter 18: Screening, Characterisation and Optimization of Microbial Pectinase 339
18.1 Introduction 339
18.2 Structure of Pectin 340
18.3 Materials and Methods 342
18.4 Screening of Pectinolytic Actinomycetes 344
18.5 Assay of Pectinase 344
18.6 Optimization of Pectinase 345
18.7 Designing Model 346
18.8 Conclusion 346
References 347
Chapter 19: Molecular Techniques to Study Polymorphism between Closely Related Microorganisms in Relation to Specific Protein 348
19.1 Introduction to Sebacinales 348
19.2 Techniques to Study Polymorphism 350
19.2.1 Cultivation of Fungi 350
19.2.1.1 Materials 350
19.2.2 Enzyme Assay (Straker and Mitchell 1986) 351
19.2.2.1 Extraction of Protein 351
Equipments 351
Reagents 351
Protein Extraction Buffer (Rosendahl 1994) 351
Procedure 352
19.2.2.2 Optimization of Physical Conditions 352
Equipment 352
Reagent 352
Procedure 352
19.2.2.3 Calculation (see Fig.19.3) 353
Equipment 353
Reagents 353
Procedure 354
19.2.2.4 Determination of Vmax and Km value 354
Equipment 354
Reagents 354
Procedure 354
19.2.2.5 Two-Dimensional PAGE to Show Protein Polymorphism (Gravel and Golaz 1996) 355
Equipment 355
Reagents 355
Preparation of Second Dimension SDS gels 356
19.2.2.6 Silver Staining (Horst 2000 Oakley et al. 1980)
Procedure 357
19.2.3 Non-denatured Protein Polymorphism Study by Native Polyacrylamide Gel Electrophoresis (Walker 1994) 358
19.2.3.1 Equipments 358
19.2.3.2 Reagents 358
19.2.3.3 Loading Buffer 359
19.2.3.4 Gel Staining Solution 359
19.2.3.5 Procedure 360
19.2.3.6 Gel Enzyme Assay (Walker 1996) 360
Reagents 360
Procedure 360
Equipment 360
Enzyme Elution 361
SDS Polyacrylamide Gel Electrophoresis 361
ELF 97 Endogenous Phosphatase Detection (van Aarle 2001) 363
Equipments 363
Reagents 363
Component A 363
Component B 363
Component C 363
Procedure 363
Fast Garnet GBC Staining of Phosphatase Isozymes (Pasteur et al. 1988) 364
19.2.4 Polymorphism Based on Random Amplification of Polymorphic DNA (RAPD) Technique 365
19.2.4.1 Equipment 365
19.2.4.2 Reagents 366
19.2.4.3 Ethidium Bromide (10mg/ml) 366
19.2.4.4 Procedure 367
19.3 Conclusion 368
References 369
Chapter 20: Production of Ligninolytic Enzymes by White-rot Fungi during Bioremediation of Oil-contaminated Soil 371
20.1 Introduction 371
20.2 Materials and Method 374
20.3 Salient Observations 376
20.4 Conclusions 382
References 383
Index 386