Introduction What Are Soils? p. 3 Introduction p. 3 Soil Genesis p. 4 Rock Weathering or Decay p. 4 Importance of Soil Texture p. 5 Input of Organic Matter into Soils and Aggregation p. 7 Migration Processes p. 8 Biogeochemical Processes in Soils p. 8 Energy and Carbon p. 8 Nitrogen and Phosphorus p. 10 Biotic Interactions Involving Soil Microorganisms p. 11 Competition Versus Facilitation p. 11 The Example of Mycorrhizas p. 12 Integrative Considerations on Functions of Microorganisms in Specific Soil Compartments Release oftransgenic Organisms as a Toolto Trace Effects of Ecological Disruptions on Soil Microorganisms p. 13 p. 13 Soil Pollution by Heavy Metals as a More Complex Disruption p. 14 Understanding Complex Functional Domains in Soil Habitats p. 15 Conclusion or Back to Biodiversity of Soil Microbes p. 15 References p. 16 Microbial Diversity in Soils p. 19 Introduction p. 19 Origin of Microbial Diversity p. 20 Oxygen Revolution p. 21 Origin of the First Eukaryotes p. 22 Types of Soil Microorganisms p. 22 Eubacteria p. 24 Archaebacteria p. 29 Fungi p. 31 Algae p. 33 Microbial Diversity and Biological Spheres p. 33 The Detritusphere p. 34 The Drilosphere p. 34 The Porosphere p. 35 The Aggregatusphere p. 35 The Rhizosphere p. 36 Microbial Diversity and Chemical Transformation p. 37 Nitrogen Transformation p. 38 Phosphorus Transformation p. 39 Sulfur Transformation p. 41
Iron Transformation p. 42 Microbial Diversity and Biotic Interactions p. 42 Conclusion p. 47 References p. 49 Microorganisms and Soil Genesis Role of Microorganisms in Wear Down of Rocks and Minerals p. 59 Rock Weathering or Rock Wear Down? p. 59 Carbon Dioxide and Rock Wear Down p. 63 Balance of Carbon Dioxide Sources and Sinks p. 68 Rock Wear Down as a Potential Carbon Dioxide Sink p. 70 The Fractal Dimension of Biological Rock Wear Down p. 71 Calcium Carbonate and Silicate Wear Down, Dissolution and Precipitation With Special Reference to Biological Rock Degradation p. 74 Conclusions p. 79 References p. 80 Humification and Mineralization in Soils p. 85 Definitions and Introduction p. 85 Soil Organic Matter Resources p. 86 Plant Compounds p. 87 Microbial Compounds p. 89 Black Carbon p. 90 Mineralization and Humification Pathways p. 91 Factors Affecting Decomposition and Mineralization p. 92 Humification Processes p. 95 Conclusions p. 102 References p. 104 Importance of Microorganisms for Soil Aggregation p. 107 Introduction p. 107 Evidence of the Role of Soil Microorganisms p. 108 Microbial Metabolites Responsible for Soil Aggregation p. 110 Polysaccharides p. 110 Glomalin p. 111 Lipids p. 112 Manipulation of Microbially Mediated Processes to Improve Soil Aggregation p. 113 The Rhizosphere Microbial Community p. 113 Organic Residues p. 113 Inoculation with Microorganisms p. 114 Conclusion p. 115 References p. 115 Microorganisms and Biogeochemical Processes in Soils Microbial Energetics in Soils p. 123 Introduction p. 123
Soil, Energy and Microorganisms p. 124 Microbial Communities p. 127 Microbial Metabolism in Soil p. 129 Catabolism p. 129 Anabolism p. 131 Soil Organic C, Microbial C and Biological Active C and Interactions with N p. 133 Holistic Approaches to Evaluate Energetic Strategies of Soil Microbial Communities p. 133 Conclusions p. 136 References p. 136 Role of Microorganisms in Carbon Cycling in Soils Introduction p. 139 Carbon Sources p. 140 Spatial Distribution and Protection of Carbon Sources p. 142 Spatial Distribution of Soil Microorganisms and Their Activities p. 143 Microorganisms and Enzymes Involved in C Cycling p. 147 Dynamics of Organic Matter Decomposition in Agroecosystems p. 148 Soil Organic Matter, Below-Ground Processes and Climate Change p. 151 References p. 153 Contribution of Bacteria to Initial Input and Cycling of Nitrogen in Soils p. 159 Introduction p. 159 Nitrogen Transformations in the Soil p. 160 Bacteria Involved in the Nitrogen Cycle p. 162 Nitrogen-Fixing Bacteria p. 162 Nitrifiers p. 164 Nitrate Reducers, Denitrifiers and Nitrite Ammonifiers p. 165 Nitrogen Fluxes p. 167 Biological Nitrogen Fixation p. 168 Nitrogen Mineralization p. 169 Nitrification p. 169 Dissimilatory Nitrate Reduction to Ammonium p. 170 Denitrification p. 171 References p. 172 Influence of Microorganisms on Phosphorus Bioavailability in Soils p. 177 Introduction p. 177 Microbial Effects on Rhizodeposition p. 177 Mechanisms of Microbial Influence on Phosphorus Availability p. 179 Solubilization of Calcium Phosphates p. 179 Mobilization of Iron- and Aluminum-Bound Phosphorus p. 181 Influence on Phosphorus Diffusion p. 182 Release of Phosphorus from Organic Sources p. 183
Interactions Between Microorganisms and Higher Plants from Competition to Symbiosis p. 184 Phosphorus-Mobilizing Microorganisms as Biofertilizers p. 184 Conclusions p. 187 References p. 188 Biotic Interactions Involving Soil Microorganisms Interactions Between Mycorrhizal Fungi and Bacteria to Improve Plant Nutrient Cycling and Soil Structure p. 195 Introduction p. 195 Beneficial Bacteria and Fungi in Agro-and Natural Ecosystems p. 196 Interactions Between Mycorrhizal Fungi and Symbiotic N p. 197 Interactions Between Mycorrhizal Fungi and Phosphate-Solubilizing Bacteria p. 201 Interactions Between Mycorrhizal Fungi and Phytostimulators Azospirillum Bacteria p. 204 Interactions Improving Soil Structure Stabilization p. 205 Conclusions p. 208 References p. 208 Mycorrhizosphere: Strategies and Functions p. 213 Introduction p. 213 The Rhizosphere p. 214 Evolution ofthe Rhizosphere p. 217 Anatomy of the Root Through the Eyes of a Microbiologist p. 218 Production of Chemical Compounds in the Rhizosphere by Plant Roots p. 220 Microbial Diversityin the Rhizosphere p. 222 What Are Mycorrhizal Fungi? p. 223 Types of Mycorrhizal Fungi p. 224 Ectomycorrhiza p. 224 Arbuscular Mycorrhiza p. 224 Ericoid Mycorrhiza p. 225 Arbutoid Mycorrhiza p. 225 Monotropoid Mycorrhiza p. 226 Ect-endomycorrhiza p. 226 Orchidaceous Mycorrhiza p. 226 Functions of Mycorrhizal Fungi p. 227 Arbuscular Mycorrhizal Fungi in Relation to Soil ph p. 228 Arbuscular Mycorrhizal Fungi in Relation to Heavy Metal Stress p. 229 Arbuscular Mycorrhizal Fungi in Relation to Soil Salinity p. 231 Arbuscular Mycorrhizal Fungi in Relation to Water and Drought Stress p. 234 The Mycorrhizosphere p. 235 Interactions in the Mycorrhizosphere p. 237 Interactions at the Pre-Symbiotic Stage p. 237 Interactions at the Post-Symbiotic Stage p. 238
Interactions Between Arbuscular Mycorrhizal Fungi and Plant Growth-Promoting Rhizobacteria p. 239 Interactions Between Arbuscular Mycorrhizal Fungi and N p. 239 Interactions Between Arbuscular Mycorrhizal Fungi and Phosphate-Solubilizing Bacteria p. 240 Interactions Between Arbuscular Mycorrhizal Fungi and Soil-Borne Pathogens p. 242 Conclusion p. 242 References p. 247 Interactions Between Microorganisms and Soil Micro- and Mesofauna p. 253 Introduction p. 253 Interactions in the Detritus Food Web p. 255 Structure of the Decomposer Animal Community p. 255 The Detritus vs. Root Exudate-Based Food Web p. 257 The Bacterial vs. Fungal Food Chain p. 259 The Role of Micro- and Mesofauna as Drivers of Microbial Decomposition Processes p. 260 Feedbacks of Faunal-Microbial Interactions on Plant Growth p. 262 The Bacterial Food Chain p. 263 The Fungal Food Chain p. 265 Conclusions p. 267 References p. 268 Function of Microbes in Specific Soil Compartments Transgenic Rhizospheres of Crop Plants: Their Impact on Indigenous Soil Fungi p. 279 Introduction p. 279 Experiments with Saprotrophic and Mycorrhizal Fungi p. 281 Saprotrophic Microfungi p. 281 Mycorrhizal Fungi p. 283 Conclusions p. 284 References p. 287 Regulation of Microbial Activities in Functional Domains of Roots and Invertebrates p. 291 Introduction p. 291 Determinants of Microbial Activities: The Hierarchical Model p. 291 Microbial Adaptive Strategies: The Sleeping Beauty Paradox p. 293 Predation in Micro-Food Webs p. 293 The External Rumen Strategy p. 294 Internal Mutualisms in Earthworms and Termites p. 295 Selection of Microflora in the Functional Domains of Soil Ecosystem Engineers p. 296 Conclusion and Implications for Soil Management p. 301 References p. 302 Microorganisms of Biological Crusts on Soil Surfaces p. 307 Introduction p. 307 Oxygenic Phototrophs p. 308
Cyanobacteria p. 308 Algae p. 313 Microlichens p. 314 Heterotrophic Organisms p. 316 Bacteria p. 317 Microfungi p. 317 Heterotrophic Protists and Invertebrate Animals p. 319 Conclusions p. 320 References p. 320 Microorganisms in Toxic Metal-Polluted Soils p. 325 Introduction p. 325 Metals in Soils p. 326 Effects of Toxic Metals on Microbial Communities p. 328 Metal Resistance and Tolerance Mechanisms p. 332 Bacteria p. 332 Fungi p. 333 Microbial Transformations of Toxic Metals p. 335 Mobilization p. 335 Immobilization p. 337 Metalloid Transformations p. 339 Biomineralogy of Metal-Microbe Interactions p. 340 Mycorrhizas p. 342 Bioremediation p. 343 Phytoremediation p. 343 Conclusions p. 344 References p. 345 Techniques to Investigate Soil Microorganisms Marker Genes in Soil Microbiology p. 359 Introduction p. 359 Definition of Marker Genes and Their First Applications in Soil Microbiology p. 360 Ribosomal RNA as an Intrinsic Marker p. 362 Polymerase Chain Reaction and Soil-Extracted Nucleic Acids p. 363 Cloning, Sequencing and Profiling Marker Genes from Soil p. 364 Structural and Functional Diversity of Soil Microbial Communities as Seen with Intrinsic Marker Genes p. 367 Expression of Intrinsic Marker Genes and Detection of Gene Transfer Potentials p. 369 Recombinant Marker Genes p. 370 Detection of In Situ Gene Transfer and Gene Expression with RecombinantMarker Genesp. 372 Recombinant Marker Genes as Biosensors p. 373 Conclusions and the Future of Marker Genes p. 374 References p. 375
Assessing Functions of Soil Microbes with Isotopic Measurements p. 383 Introduction p. 383 Natural Abundance Measurements p. 384 Fungi p. 385 Methane Cycling p. 394 Using Isotopic Differences Between C p. 395 Problems with Extrapolating Natural Abundance Cultures to the Field p. 395 Compound-Specific Measurements and Isotopic Tracers p. 396 Conclusions and Future Research p. 397 References p. 398 Subject Index p. 403 Table of Contents provided by Blackwell's Book Services and R.R. Bowker. Used with permission.