Methods of Soil Enzymology
DESCRIPTION
Methods in Soil Enzymology provides the first comprehensive set of vetted methods for studying enzymes in soils. Main topics include activity assays, enzyme extraction, and synthetic enzyme complexes. Each method covered includes background informaton, step-by-step descriptions of the procedure, and special comments regarding nuances, pitfalls, and interpretation of the method. Learn the latest research methods, including enzyme extraction methods and procedures for creating synthetic enzyme complexes, as well as the newest ways to use small-scale and high-throughput methods for enzyme activity assays. In the tradition of SSSA methods books, Methods of Soil Enzymology features a comprehensive approach with a focus on ease of use.
CONTENTS
Chapter 1
A Brief History of Soil Enzymology Research 1
Richard P. Dick and Richard G. Burns
1–1 Introduction 1
1–2 The Early Years 1
1–3 Soil Enzyme Methodology 2
1–4 Origins and Distribution of Enzymes In Soil 7
1–5 Relationship of Enzyme Activity to Biological Properties In Soils 13
1–6 Applications and Ecosystems Services 15
1–7 Summary 19
Chapter 2
Ecology of Extracellular Enzyme Activities and Organic Matter Degradation in Soil: A Complex Community-Driven Process 35
Matthew D. Wallenstein and Richard G. Burns
2–1 Introduction 35
2–2 Substrate and Enzyme Diversity in Soils 37
2–3 Location and Stability of Extracellular Soil Enzymes 40
2–5 Regulation of Extracellular Enzyme Production 46
2–6 Conclusions 48
Chapter 3
Kinetics of Soil Enzyme Reactions 57
Warren A. Dick
3–1 Introduction 57
3–2 Michaelis–Menten Kinetics 58
3–3 Determination of the Kinetic Constants Km and Vmax 60
3–4 Comments Related to Michaelis–Menten Kinetics 60
3–5 Simple Competitive and Noncompetitive Inhibition of Enzymes and Enzyme Kinetics 62
3–6 Partial Competitive and Partial Noncompetitive Inhibition Kinetic Models 65
3–7 Application of Kinetic Models 67
3–8 Summary 69
Chapter 4
Development of a Soil Enzyme Reaction Assay 71
Warren A. Dick
4–1 Introduction 71
4–2 Factors of a Valid Soil Enzyme Assay 72
4–3 Summary 84
Chapter 5
Sampling and Pretreatment of Soil before Enzyme Analysis 85
Nicola Lorenz and Richard P. Dick
5–1 Introduction 85
5–2 Soil Sample Collection Strategies and Considerations 85
5–3 Sampling Protocol 88
5–4 Sample Handling and Pretreatment 92
Chapter 6
Soil Oxidoreductases and FDA Hydrolysis 103
Jennifer A. Prosser, Tom W. Speir, and Diane E. Stott
6–1 General Introduction 103
6–2 Dehydrogenase 104
6–3 Fluorescein Diacetate Hydrolysis 107
6–4 Phenol Oxidase (Tyrosinase) 110
6–5 Peroxidase 113
6–6 Catechol Oxidase 116
6–7 Catalase 118
Chapter 7
Sulfur Cycle Enzymes 125
Susanne Klose, Serdar Bilen, M. Ali Tabatabai, and Warren A. Dick
7–1 Introduction 125
7–2 Cystathionine Lyase 129
7–3 Arylsulfatase 133
7–4 Rhodanese 137
7–5 Sulfur Oxidation 141
7–6 Sulfate Reduction 146
7–7 Modification of p-Nitrophenol-Based Enzyme Activities for Organic Soils or Forest Organic Horizons 151
Chapter 8
Phosphorus Cycle Enzymes 161
Verónica Acosta-Martínez and M. Ali Tabatabai
8–1 Introduction 161
8–2 Phosphomonoesterases 163
8–3 Phosphodiesterase 168
8–4 Inorganic Pyrophosphatase 172
8–5 Trimetaphosphatase 175
Chapter 9 178
Carbohydrate Hydrolases 185
Shiping Deng and Inna Popova
9–1 Introduction 185
9–2 Glycosidases that Release Monosaccharides (a- and b-Glucosidases, a- and b-Galactosidases, and N-Acetyl-b-Glucosaminidase) 195
9–3 Amylase, Cellulase, Xylanase, Chitinase, and Invertase 198
Chapter 10
Nitrogen Cycle Enzymes 211
Ellen Kandeler, Christian Poll, William T. Frankenberger Jr., and M. Ali Tabatabai
10–1 Introduction 211
10–2 Amidohydrolases (Urease, l-Asparaginase, l-Glutaminase, and Amidase) 212
10–3 Ammonium Oxidation 226
10–4 Denitrification Enzyme Activity and Nitrate Reductase 229
10–5 Arylamidase 233
Chapter 11
Activities of Proteolytic Enzymes 247
Loretta Landi, Giancarlo Renella, Laura Giagnoni, and Paolo Nannipieri
11–1 Introduction 247
11–2 Principles 252
11–3 Assay Methods 252
Chapter 12
Biologically Active Compounds in Soil: Plant Hormones and Allelochemicals 261
Serdar Bilen, Jeong Jin Kim, and Warren A. Dick
12–1 Introduction 261
12–2 ACC Oxidase 262
12–3 Tryptophan-Dependent Auxin Production 265
12–4 Myrosinase 268
vii
Chapter 13
Enzyme Activities of Root Tips and in situ Profiles of Soils and Rhizospheres 275
Melanie D. Jones, Denise D. Brooks, Pierre-Emmanuel Courty, Jean Garbaye, Pauline F. Grierson, and Karin Pritsch
13–1 Introduction 275
13–2 Methodology for Soil Imprinting of Enzyme Activity 279
13–3 Extracellular Enzyme Activity Profiles of Individual Excised Absorbing Roots 296
Chapter 14
Microplate Fluorimetric Assay of Soil Enzymes 311
Shiping Deng, Hojeong Kang, and Chris Freeman
14–1 Introduction 311
14–2 Principles 313
14–3 Enzyme Assays using Fluorescence Quantification─ b-Glucosidase, b-N-acetyl-glucosaminidase, acid phosphomonoesterase, and arylsulfatase 313
14–5 Comments 315
Chapter 15
Stabilizing Enzymes as Synthetic Complexes 319
Liliana Gianfreda and Maria A. Rao
15–1 Principles 320
15–2 Preparation and Characterization of Synthetic Enzymatic Complexes 325
15–3 Adsorption 326
15–4 Enzyme Complexes with Organic and Organo–Mineral Supports 340
15–5 Chemical Binding 350
15–6 Entrapment of Enzymes in Humic and Humic-Like Complexes 358
Chapter 16
Enzyme Extraction from Soil 371
Flavio Fornasier, Yves Dudal, and Herve Quiquampoix
16–1 Introduction 371
16–2 Extraction with Water 375
16–3 Extraction with Acetate Buffer 376
16–4 Extraction with Phosphate Buffer 377
16–5 Extraction with Pyrophosphate 379
16–6 Extraction with Triton X-100 and Bovine Serum Albumin 380
Index 385
contents
