The fourth edition of Soil Microbiology, Ecology and Biochemistry updates this widely used reference as the study and understanding of soil biota, their function, and the dynamics of soil organic matter has been revolutionized by molecular and instrumental techniques, and information technology. Knowledge of soil microbiology, ecology and biochemistry is central to our understanding of organisms and their processes and interactions with their environment. In a time of great global change and increased emphasis on biodiversity and food security, soil microbiology and ecology has become an increasingly important topic. Revised by a group of world-renowned authors in many institutions and disciplines, this work relates the breakthroughs in knowledge in this important field to its history as well as future applications. The new edition provides readable, practical, impactful information for its many applied and fundamental disciplines. Professionals turn to this text as a reference for fundamental knowledge in their field or to inform management practices. - New section on "e;Methods in Studying Soil Organic Matter Formation and Nutrient Dynamics"e; to balance the two successful chapters on microbial and physiological methodology- Includes expanded information on soil interactions with organisms involved in human and plant disease- Improved readability and integration for an ever-widening audience in his field- Integrated concepts related to soil biota, diversity, and function allow readers in multiple disciplines to understand the complex soil biota and their function
Front Cover 1
Soil Microbiology, Ecology, and Biochemistry 4
Copyright 5
Contents 6
Contributors 16
Preface 18
Chapter 1: Soil Microbiology, Ecology, and Biochemistry: An Exciting Present and Great Future Built on Basic Knowledge and Unifying Concepts 22
I. Scope and Challenges 22
II. The Controls and Unifying Principles in our Field 24
III. The Special Role of Accessibility and Spatial Scaling of Biota and Soil Organic Matter 25
IV. Soil Organic Matter as a Control and Informational Storehouse of Biotic Functions 29
V. Biotic Diversity and Microbial Products 30
VI. Unifying Concepts 31
References 34
Chapter 2: The Soil Habitat 36
I. Introduction 36
II. Soil Genesis and Formation of the Soil Habitat 38
A. Soil Profile 40
III. Physical Aspects of Soil 40
A. Soil Texture 41
B. Aggregation of Soil Mineral Particles 42
IV. Soil Habitat and Scale of Observation 45
A. Scale of Soil Habitat 45
B. Pore Space 46
V. Soil Solution Chemistry 49
A. Soil pH 49
B. Soil Redox 50
C. Soil Aeration 52
VI. Environmental Factors, Temperature, and Moisture Interactions 54
A. Soil Temperature 54
B. Soil Water 56
References 34
Chapter 3: The Bacteria and Archaea 62
I. Introduction 62
II. Phylogeny 63
A. Cultivated Organisms 63
B. Uncultivated Organisms 64
C. Phylogeny and Function 70
III. General Features of Prokaryotes 71
IV. Cell Structure 72
A. Unicellular Growth Forms 72
B. Filamentous and Mycelial Growth 74
C. Cell Walls 75
D. Internal Structure 77
E. Motility 79
V. Metabolism and Physiology 79
A. The Diversity of Prokaryotic Metabolism 79
B. Carbon and Energy Sources 81
C. Oxygen Requirements 82
D. Substrate Utilization 83
E. Autochthony and Zymogeny 85
F. Oligotrophy, Copiotrophy, and the r-K Continuum 87
G. Facultative Activities 87
VI. Biodegradation Capacity 89
A. Cellulose 89
B. Pollutants 90
VII. Differentiation, Secondary Metabolism, and Antibiotic Production 92
VIII. Conclusion 93
References 34
Chapter 4: The Soil Fungi: Occurrence,
98
I. Introduction 98
II. Phylogeny 99
A. Definition of Eumycota 99
B. Present Phylogeny 101
C. Novel Lineages 104
III. Occurrence 105
A. Extremophiles, Distribution Across the Planet 105
B. Biomass, Growth, and Abundance 107
IV. Biodiversity 108
A. Estimates of Species Richness 108
B. Fungal Dispersal and Biogeography 109
V. Fungal Communities 110
A. Definition 110
B. Abiotic Drivers 110
C. Biotic Drivers 113
VI. Functions 115
A. Introduction 115
B. Nutrient Cycling 116
1. Enzymes/Decomposition 116
2. Nitrogen 118
3. Phosphorus 118
C. Bioremediation 119
VII. Fungus-like Organisms and Soil Food Webs 119
References 34
Chapter 5: Soil Fauna: Occurrence,
132
I. Introduction 133
II. Overview of Faunal Biodiversity in Soils 133
III. Microfauna 135
A. Protozoa 135
1. Methods for Extracting and Counting Protozoa 138
2. Impacts of Protozoa on Ecosystem Function 139
3. Distribution of Protozoa in Soil Profiles 140
B. Rotifera 140
IV. Mesofauna 141
A. Nematoda 141
1. Nematodes in Soil Food Webs 143
2. Food Sources for Nematodes 144
3. Zones of Nematode Activity in Soil 145
4. Nematode Extraction Techniques 146
B. Microarthropods 146
1. Determining the Trophic Position of Microarthropods 147
C. Enchytraeids 148
1. Food Sources of Enchytraeids 149
2. Distribution and Abundance of Enchytraeids 149
3. Extraction of Enchytraeids 150
V. Macrofauna 151
A. Macroarthropods 151
B. Oligochaeta (Earthworms) 153
1. Earthworm Distribution and Abundance 154
2. Biology and Ecology 154
3. Influence on Soil Processes 155
4. Earthworm Effects on Ecosystems 156
C. Formicidae (Ants) 156
D. Termitidae (Termites) 157
VI. Roles of Soil Fauna in Ecosystems 158
VII. Summary 160
References 34
Further reading 170
Chapter 6: Molecular Approaches to
172
I. Introduction 172
II. Types and Structures of Nucleic Acids 174
III. Nucleic acid Analyses in Soil Ecology Studies 175
IV. Direct Molecular Analysis of Soil Biota 176
A. Nucleic Acid Hybridization 176
B. Confocal Microscopy 179
V. Biosensors and Marker Gene Technologies 180
VI. Extraction of Nucleic Acids (DNA/RNA) 180
VII. Choosing Between DNA and RNA for Studying Soil Biota 182
VIII. Analysis of Nucleic Acid Extracts 183
A. DNA:DNA Reassociation Kinetics 183
B. Microarrays 183
C. Restriction Fragment Length Polymorphism (RFLP) Analysis 185
D. Cloning and Sequencing 186
E. Stable Isotope Probing 187
IX. Partial Community Analyses-PCR-based Assays 190
A. Electrophoresis of Nucleic Acids 192
B. PCR Fingerprinting 193
C. Metagenomics 194
D. Metatranscriptomics 197
X. Level of Resolution 199
XI. Factors that May Affect Molecular Analyses 200
XII. Future Promise 201
References 34
Chapter 7: Physiological and Biochemical Methods for Studying Soil Biota and Their Functions 208
I. Introduction 209
II. Scale of Investigations and Collection of Samples 209
III. Storage and Pretreatment of Samples 213
IV. Microbial Biomass 213
A. Fumigation Incubation and Fumigation Extraction Methods 213
B. Substrate-Induced Respiration 214
V. Compound-Specific Analyses of Microbial Biomass and Microbial Community Structure 215
A. ATP as a Measure of Active Microbial Biomass 215
B. Microbial Membrane Components and Fatty Acids 216
C. Phospholipid Etherlipids 219
D. Respiratory Quinones 219
E. Ergosterol as a Measure of Fungal Biomass 219
F. Gene Abundance as a Measure of Biomass of Specific Groups of Soil Microorganisms 220
G. Component-Specific Analyses of Microbial Products 221
VI. Isotopic Composition of MICROBIAL Biomass and Signal Molecules 222
A. Isotopic Composition of Microbial Biomass 222
B. Stable-Isotope Probing of Fatty Acids, Ergosterol, and Nucleic Acids 223
C. Growth Rates from Signature Molecules and Leucine/Thymidine Incorporation 224
VII. Physiological Analyses 225
A. Culture Studies 225
B. Isolation and Characterization of Specific Organisms 226
C. Microbial Growth and Respiration 227
D. Nitrogen Mineralization 229
VIII. Activities of Enzymes 230
A. Spectrophotometric Methods 233
B. Fluorescence Methods 234
IX. Imaging Microbial Activities 235
X. Functional Diversity 237
References 34
Chapter 8: The Spatial Distribution
244
I. Introduction 244
II. The Biogeography of Soil Biota 244
III. Vertical Distribution Within the Soil Profile 249
IV. Microscale Heterogeneity in Microbial Populations 254
V. Drivers of Spatial Heterogeneity 257
VI. Summary 262
References 34
Further Reading 170
Chapter 9: The Spatial Distribution
266
I. Introduction 266
II. Foundations of Microbial Metabolism 267
A. Stoichiometry 267
B. Redox Reactions 268
C. Energetics 270
D. Role of Enzymes in Metabolism 272
III. Metabolic Classification of Soil Organisms 273
IV. Cellular Energy Transformations 276
A. Substrate-Level Versus Oxidative Phosphorylation 276
B. How ATP Production Varies for Different Metabolic Classes of Soil Microorganisms 277
V. Examples of Soil Microbial Transformations 279
A. Organotrophy 279
B. Lithotrophy 283
C. Phototrophy 286
VI. A Simplified View of Soil Microbial Metabolism 287
A. Model of Interconnected Cycles of Electrons 288
B. The Anoxygenic Cycle 288
C. The Oxygenic Cycle 289
References 34
Further Reading 170
Chapter 10: The Ecology of the Soil Biota
294
I. Introduction 294
II. Mechanisms that Drive Community Structure 296
A. Physiological Limitations to Survival 297
B. Intraspecific Competition 299
C. Dispersal in Space and Time 301
D. Interspecific Competition 303
E. Direct Effects of Exploitation 304
F. Indirect Effects of Exploitation 306
G. Mutualistic Interactions 307
H. Community Impacts on Abiotic Factors 308
I. Community Variation Among Soil Habitats 309
J. Changes in Community Structure Through Time 310
K. Historical and Geographic Contingency Leads to Biogeography 311
III. Consequences of Microbial Community Structure for Ecosystem Function 313
A. Energy Flow 315
B. Nutrient Cycles 318
C. Emergent Properties 321
IV. Conclusion 323
References 34
Chapter 11: Plant-Soil Biota Interactions 332
I. Soil Biota 332
II. The Rhizosphere: Ecological Network of Soil Microbial Communities 333
III. New Insights into Root/Soil Microbes Through Metagenomic/Metatranscriptomic Approaches 336
IV. An Important Rhizospheric Component: The Mycorrhizal Fungi 343
V. The Contribution of Fungal Genome Projects 349
VI. Summary 350
References 34
Chapter 12: Carbon Cycling: The Dynamics
360
I. Introduction 360
II. Geological Carbon Cycle 361
III. Biological C Cycle 363
A. Photosynthesis 364
B. Decomposition of Plant and Microbial Products 366
C. Cytoplasmic Constituents of Plants and Microorganisms 367
D. Plant and Microbial Lipids 368
E. Starch 370
F. Hemicelluloses, Pectins, and Cellulose 370
G. Lignin 375
H. Plant Secondary Compounds 377
I. Roots and Root-Derived Materials 378
J. Cell Walls of Microorganisms 379
IV. Organic Matter 381
A. Substrates for OM Formation 381
B. Theories of SOM Stabilization 384
C. Aggregate Protection of OM Fractions in Soil 388
D. SOM Maintenance 389
V. Quantity, Distribution, and Turnover of Carbon in Soil and Sediments 390
A. Terrestrial Soil C Stocks 393
B. Ocean C Pools 394
VI. Role of Climate Change on the Global C Cycle 395
A. Results from Elevated CO2 Studies 395
B. Soil Processes in a Warmer Climate 395
C. Methane in the C Cycle 396
D. Elevated CO2 and Ocean Processes 397
VII. Future Considerations 398
References 34
Further reading 170
Chapter 13: Methods for Studying Soil
404
I. Introduction 405
II. Quantifying Soil organic matter 407
III. Fractionation Methods 407
A. Chemical and Thermal Fractionation 408
1. Extraction Methods 408
1.1. Dissolved Organic Matter 409
1.2. Solubility in Bases and Acids: Humic Substances and Extracts 409
2. Hydrolysis Methods 410
3. Oxidation Methods 411
4. Destruction of the Mineral Phase 412
5. Calorimetric Methods 412
B. Physical Fractionation 412
1. Introduction and Definitions 412
2. Soil Dispersion 413
3. Particle Fractionation 415
4. Aggregate Fractionation 416
IV. Characterization Methods 418
A. Wet Chemical Methods for Analyses of Biochemical SOM Constituents 418
1. Carbohydrates 419
2. Aromatic Compounds 419
3. Aliphatic Compounds 420
4. Organic Nitrogen 420
B. Spectroscopic Methods to Characterize Functional Groups of SOM 421
1. Infrared Spectroscopy 421
2. Solid-State NMR Spectroscopy 422
C. Molecular Analysis of SOM 423
V. Visualization Methods 423
A. Light Microscopy 424
B. Scanning Electron Microscopy 424
C. Transmission Electron Microscopy 426
D. Atomic Force Microscopy 426
E. X-Ray Spectro-Microscopy 427
F. NanoSIMS 427
G. X-Ray Computed Microtomography 429
VI. Methods to Measure the Turnover Rate of SOM 429
A. Soil Incubation and Modeling of CO2 Evolution 429
B. Decomposition of Organic Materials Added to Soil 430
C. 13C Natural Abundance 431
D. 14C Dating 432
E. Compound-Specific Assessment of SOM Turnover 432
References 34
Chapter 14: Nitrogen Transformations 442
I. Introduction 442
II. Nitrogen Mineralization and Immobilization 445
III. Nitrification 448
A. The Biochemistry of Autotrophic Nitrification 449
B. The Diversity of Autotrophic Nitrifiers 450
C. Heterotrophic Nitrification 453
D. Environmental Controls of Nitrification 454
IV. Inhibition of Nitrification 456
V. Denitrification 456
A. Denitrifier Diversity 457
B. Environmental Controls of Denitrification 459
VI. Other Nitrogen Transformations in Soil 460
VII. Nitrogen Movement in the Landscape 462
References 34
Further Reading 170
Chapter 15: Biological N Inputs 468
I. Global N Inputs 468
II. Biological Nitrogen Fixation 470
A. Measuring BNF 474
III. Free Living N2-Fixing Bacteria 475
IV. Associative N2-Fixing Bacteria 476
V. Phototrophic Bacteria 476
VI. Symbiotic N2-Fixing Associations Between Legumes and Rhizobia 477
A. Formation of the Legume Symbiosis 478
B. Rhizobial Nodulation Genes 480
C. Plant Nodulation Genes 482
D. Development of BNF and Nitrogen Assimilatory Processes in Nodules 484
E. Symbiotic Associations between Actinorhizal Plants and Frankia 485
VII. Microbial Ecology of BNF 487
VIII. Biotechnology of BNF 488
References 34
Suggested Reading 170
Chapter 16: Biological Cycling of Inorganic Nutrients and Metals in Soils and Their Role in Soil Biogeochemistry 492
I. Introduction 492
II. Nutrient Needs of Soil Microorganisms 493
III. Effect of Microorganisms on Element Cycles 496
A. Phosphorus Cycle 496
B. Sulfur Cycle 500
C. Iron Cycle 504
D. Cycles of Other Elements 508
IV. Examples of Interconnections Between Microbial Community/Activity and Element Cycles 511
A. Element Cycles During Early Soil Development 511
B. Coupling of Iron and Sulfur Transformations in Acid Mine Drainage 515
C. Integration of Element Cycles in Wetland Systems 516
References 34
Chapter 17: Modeling the Dynamics
526
I. Introduction 526
II. Reaction Kinetics 527
A. Zero-Order Reactions 527
B. First-Order Reactions 528
C. Enzyme Kinetics 529
D. Microbial Growth 530
III. Modeling Soil Carbon and Nutrient Dynamics 533
A. Analytical Models 533
B. Substrate-Enzyme-Microbe Models 538
C. Cohort Models 539
D. Multicompartmental Models 540
E. Nutrient Dynamics Models 541
F. Ecosystem and Earth System Models 543
G. Case Studies 543
1. Century/DayCent 545
2. The DeNitrification-DeComposition Model 546
3. Ecosys 547
IV. Model Classification and Comparison 548
V. Model Parameterization 549
VI. Model Selection Methods 552
VII. Conclusion 554
References 34
Suggested Reading 170
Chapter 18: Management of Soil Biota
560
I. Introduction 560
II. Changing Soil Organism Populations and Processes 562
A. Tillage and Erosion 562
B. Rangeland and Forest Health 565
III. Alternative Agricultural Management 568
A. Organic Agriculture 568
B. Biodynamic Agriculture and Charcoal 571
C. Crop Rotations and Green Manures 572
IV. The Potential for Managing Microorganisms and their Processes 573
A. Management of Native and Introduced Microorganisms 573
B. Managing Microbial Populations as Agents of Biological Control 575
C. Control of Insects 577
D. Weed Control 578
E. Use of Synthetic and Natural Compounds to Modify Soil Communities or Functions 579
F. Composting 581
G. Manipulating Soil Populations for Bioremediation Xenobiotics 583
V. Concluding Comments on Microbial Ecology 586
References 34
Suggested Reading 170
Index 594
The Soil Habitat
R.P. Voroney; R.J. Heck School of Environmental Sciences, University of Guelph, Ontario, Canada
Abstract
The soil environment is the most complex habitat on earth and provides a range of habitats that support an enormous population of soil organisms. This chapter describes the key physical and chemical features of the soil habitat that govern the biodiversity and activity of this population. The habitat provided by the soil is characterized by heterogeneity, is measured across scales from nanometers to kilometers, and differs in chemical, physical, and biological characteristics in both space and time. The nature of the habitat is determined by the intensity of the interaction of geology, climate, and vegetation and is a biochemical product of the organisms participating in its genesis.
Keywords
Critical zone
Pedosphere
Solum
Fine-earth fraction
Soil colloids
Aggregates
Spatial heterogeneity
Habitable pore space
Temperature-water potential
Chapter Contents
I. Introduction 15
II. Soil Genesis and Formation of the Soil Habitat 17
A. Soil Profile 19
III. Physical Aspects of Soil 19
A. Soil Texture 20
B. Aggregation of Soil Mineral Particles 21
IV. Soil Habitat and Scale of Observation 24
A. Scale of Soil Habitat 24
B. Pore Space 25
V. Soil Solution Chemistry 28
A. Soil pH 28
B. Soil Redox 29
C. Soil Aeration 31
VI. Environmental Factors, Temperature, and Moisture Interactions 33
A. Soil Temperature 33
B. Soil Water 35
References 39
I Introduction
Soil, the naturally occurring unconsolidated mineral and organic material at the earth's surface, provides an essential natural resource for living organisms. It is a central component of the earth's critical zone and deserves special status due to its role in regulating the earth's environment, thus affecting the sustainability of life on the planet. The soil environment is the most complex habitat on earth. This complexity governs soil biodiversity, as soil is estimated to contain one-third of all living organisms and regulates the activity of the organisms responsible for ecosystem functioning and evolution. The concept that the earth’s physicochemical properties are tightly coupled to the activity of the living organisms it supports was proposed in the early 1970s by James Lovelock and Lynn Margulis as the Gaia hypothesis. They theorized that the earth behaves as a superorganism, with an intrinsic ability to control its own climate and chemistry and thus maintain an environment favorable for life. Soil has the intrinsic ability to both support terrestrial life and provide a habitat for the interdependent existence and evolution of organisms living within it. In 2011, scientists embarked on a Global Soil Biodiversity Initiative to assess soil life in all biomes across the globe for the essential ecosystem services that soils provide (i.e., plant biomass production, decomposition, and nutrient cycling) and to identify where soil quality is endangered due to human activities. The ultimate goal of the initiative was to guide environmental policy for sustainable land management (Soil Stories, The Whole Story, http://youtube.com/watch?v?Ego6LI-IjbY; see online supplemental material at: http://booksite.elsevier.com/9780124159556).
Soils (pedosphere) develop at the interface where organisms (biosphere) interact with rocks and minerals (lithosphere), water (hydrosphere), and air (atmosphere), with climate regulating the intensity of these interactions. In terrestrial ecosystems, the soil affects energy, water and nutrient storage and exchange, and ecosystem productivity. Scientists study soil because of the fundamental need to understand the dynamics of geochemical–biochemical–biophysical interactions at the earth's surface, especially in light of recent and ongoing changes in global climate and the impact of human activity. Geochemical fluxes between the hydrosphere, atmosphere, and lithosphere take place over the time span of hundreds to millions of years. Within the pedosphere, biologically induced fluxes between the lithosphere, atmosphere, and biosphere take place over a much shorter time frame, hours and days to months, which complicates the study of soils.
The soil habitat is defined as the totality of living organisms inhabiting soil, including plants, animals, and microorganisms, and their abiotic environment. The exact nature of the habitat in which the community of organisms lives is determined by a complex interplay of geology, climate, and plant vegetation. The interactions of rock and parent material with temperature, rainfall, elevation, latitude, exposure to sun and wind, and numerous other factors, over broad geographical regions, environmental conditions, and plant communities, have evolved into the current terrestrial biomes with their associated soils (Fig. 2.1).
Because soils provide such a tremendous range of habitats, they support an enormous biomass, with an estimated 2.6 × 1029 for prokaryotic cells alone, and harbor much of the earth's genetic diversity. A single gram of soil contains kilometers of fungal hyphae, more than 109 bacterial and archael cells and organisms belonging to tens of thousands of different species. Zones of good aeration may be only millimeters away from areas that are poorly aerated. Areas near the soil surface may be enriched with decaying organic matter and other accessible nutrients, whereas the subsoil may be nutrient poor. The variance of temperature and water content of surface soils is much greater than that of subsoils. The soil solution in some pores may be acidic, yet in others more basic, or may vary in salinity depending on soil mineralogy, location within the landscape, and biological activity. The microenvironment of the surfaces of soil particles, where nutrients are concentrated, is very different from that of the soil solution.
II Soil Genesis and Formation of the Soil Habitat
Soils derived from weathered rocks and minerals are referred to as mineral soils. When plant residues are submerged in water for prolonged periods, biological decay is slowed. Accumulations of organic matter at various stages of decomposition become organic soils and include peat land, muck land, or bogs and fens. Soil can also be formed in coastal tidal marshes or inland water areas supporting plant growth where areas are periodically submerged.
Mineral soils are formed by the physical and chemical weathering of the rocks and minerals brought to the earth's surface by geological processes. They extend from the earth's terrestrial surface into the underlying, relatively unweathered, parent material. The parent material of mineral soils can be the residual material weathered from solid rock masses or the loose, unconsolidated materials that often have been transported from one location and deposited at another by such processes as sedimentation, erosion, and glaciation. The disintegration of rocks into smaller mineral particles is a physical-chemical process brought about by cycles of heating and cooling, freezing and thawing, and also by abrasion from wind, water, and ice masses. Chemical and biochemical weathering processes are enhanced by the presence of water, oxygen, and the organic compounds resulting from biological activity. These reactions convert primary minerals, such as feldspars and micas, to secondary minerals, such as silicate clays and oxides of aluminum, iron, and silica. Soluble constituent elements in inorganic forms provide nutrients to support the growth of various organisms and plants.
The physical and chemical weathering of rocks into fine particles with large surface areas, along with the accompanying release of plant nutrients, initiate the soil-forming process (Fig. 2.2) by providing a habitat for living organisms. The initial colonizers of soil parent material are usually organisms capable of both photosynthesis and N2 fixation. Intimate root-bacterial/fungal/actinomycetal associations with early plants assist with supplying nutrients and water. Products of the biological decay of organic residues accumulate in the surface...
| Erscheint lt. Verlag | 14.11.2014 |
|---|---|
| Sprache | englisch |
| Themenwelt | Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie |
| Naturwissenschaften ► Geowissenschaften ► Geologie | |
| Technik | |
| Weitere Fachgebiete ► Land- / Forstwirtschaft / Fischerei | |
| ISBN-10 | 0-12-391411-6 / 0123914116 |
| ISBN-13 | 978-0-12-391411-8 / 9780123914118 |
| Haben Sie eine Frage zum Produkt? |
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