Buscot / Varma Microorganisms in Soils: Roles in Genesis and Functions

1. Auflage 2007
ISBN: 978-3-540-26609-9
Verlag: Springer Berlin Heidelberg
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 3, 422 Seiten

Reihe: Soil Biology

For this third volume of the series Soil Biology, internationally renowned scientists shed light on the significant roles of microbes in soil. Key topics covered include: bioerosion, humification, mineralization and soil aggregation; Interactions in the mycorrhizosphere; microbes and plant nutrient cycling; Microbes in soil surface or toxic metal polluted soils; Use of marker genes and isotopes in soil microbiology, and many more.

Autoren/Hrsg.

Varma, Ajit

Buscot, Francois

Inhaltsverzeichnis

1;Preface;5
2;Contents;8
3;Contributors;17
4;Part I Introduction;22
4.1;What Are Soils?;23
4.1.1;1 Introduction;23
4.1.2;2 Soil Genesis;24
4.1.3;3 Biogeochemical Processes in Soils;28
4.1.4;4 Biotic Interactions Involving Soil Microorganisms;31
4.1.5;5 Integrative Considerations on Functions of Microorganisms in Specific Soil Compartments;33
4.1.6;6 Conclusion or Back to Biodiversity of Soil Microbes;35
4.1.7;References;36
4.2;Microbial Diversity in Soils;38
4.2.1;1 Introduction;38
4.2.2;2 Origin of Microbial Diversity;39
4.2.3;3 Types of Soil Microorganisms;41
4.2.4;4 Microbial Diversity and Biological Spheres;52
4.2.5;5 Microbial Diversity and Chemical Transformation;56
4.2.6;6 Microbial Diversity and Biotic Interactions;61
4.2.7;7 Conclusion;66
4.2.8;References;68
5;Part II Microorganisms and Soil Genesis;75
5.1;Role of Microorganisms inWear Down of Rocks and Minerals;76
5.1.1;1 RockWeathering or RockWear Down?;76
5.1.2;2 Carbon Dioxide and RockWear Down;80
5.1.3;3 Balance of Carbon Dioxide Sources and Sinks;85
5.1.4;4 RockWear Down as a Potential Carbon Dioxide Sink;87
5.1.5;5 The Fractal Dimension of Biological RockWear Down;88
5.1.6;6 Calcium Carbonate and SilicateWear Down, Dissolution and PrecipitationWith Special Reference to Biological Rock Degradation;91
5.1.7;7 Conclusions;96
5.1.8;References;97
5.2;Humification and Mineralization in Soils;102
5.2.1;1 Definitions and Introduction;102
5.2.2;2 Soil Organic Matter Resources;103
5.2.3;3 Mineralization and Humification Pathways;108
5.2.4;4 Conclusions;119
5.2.5;References;121
5.3;Importance of Microorganisms for Soil Aggregation;124
5.3.1;1 Introduction;124
5.3.2;2 Evidence of the Role of Soil Microorganisms;125
5.3.3;3 Microbial Metabolites Responsible for Soil Aggregation;127
5.3.4;4 Manipulation of Microbially Mediated Processes to Improve Soil Aggregation;130
5.3.5;5 Conclusion;132
5.3.6;References;132
6;Part III Microorganisms and Biogeochemical Processes in Soils;137
6.1;Microbial Energetics in Soils;138
6.1.1;1 Introduction;138
6.1.2;2 Soil, Energy and Microorganisms;139
6.1.3;3 Microbial Communities;142
6.1.4;4 Microbial Metabolism in Soil;144
6.1.5;5 Holistic Approaches to Evaluate Energetic Strategies of Soil Microbial Communities;148
6.1.6;6 Conclusions;151
6.1.7;References;151
6.2;Role of Microorganisms in Carbon Cycling in Soils;154
6.2.1;1 Introduction;154
6.2.2;2 Carbon Sources;155
6.2.3;3 Spatial Distribution and Protection of Carbon Sources;157
6.2.4;4 Spatial Distribution of Soil Microorganisms and Their Activities;158
6.2.5;5 Microorganisms and Enzymes Involved in C Cycling;162
6.2.6;6 Dynamics of Organic Matter Decomposition in Agroecosystems;163
6.2.7;7 Soil Organic Matter, Below-Ground Processes and Climate Change;166
6.2.8;References;168
6.3;Contribution of Bacteria to Initial Input and Cycling of Nitrogen in Soils;173
6.3.1;1 Introduction;173
6.3.2;2 Nitrogen Transformations in the Soil;174
6.3.3;3 Bacteria Involved in the Nitrogen Cycle;176
6.3.4;4 Nitrogen Fluxes;181
6.3.5;References;186
6.4;Influence of Microorganisms on Phosphorus Bioavailability in Soils;191
6.4.1;1 Introduction;191
6.4.2;2 Microbial Effects on Rhizodeposition;191
6.4.3;3 Mechanisms of Microbial Influence on Phosphorus Availability;193
6.4.4;4 Interactions Between Microorganisms and Higher Plants from Competition to Symbiosis;198
6.4.5;5 Phosphorus-Mobilizing Microorganisms as Biofertilizers;198
6.4.6;6 Conclusions;201
6.4.7;References;202
7;Part IV Biotic Interactions Involving Soil Microorganisms;206
7.1;Interactions Between Mycorrhizal Fungi and Bacteria to Improve Plant Nutrient Cycling and Soil Structure;207
7.1.1;1 Introduction;207
7.1.2;2 Beneficial Bacteria and Fungi in Agro- and Natural Ecosystems;208
7.1.3;3 Interactions Between Mycorrhizal Fungi and Symbiotic N2- Fixing Rhizobial Bacteria;209
7.1.4;4 Interactions Between Mycorrhizal Fungi and Phosphate- Solubilizing Bacteria;213
7.1.5;5 Interactions Between Mycorrhizal Fungi and Phytostimulators Azospirillum Bacteria;216
7.1.6;6 Interactions Improving Soil Structure Stabilization;217
7.1.7;7 Conclusions;220
7.1.8;References;220
7.2;Mycorrhizosphere: Strategies and Functions;225
7.2.1;1 Introduction;225
7.2.2;2 The Rhizosphere;226
7.2.3;3 Evolution of the Rhizosphere;229
7.2.4;4 Anatomy of the Root Through the Eyes of aMicrobiologist;230
7.2.5;5 Production of Chemical Compounds in the Rhizosphere by Plant Roots;232
7.2.6;6 Microbial Diversity in the Rhizosphere;234
7.2.7;7 What Are Mycorrhizal Fungi?;235
7.2.8;8 Types of Mycorrhizal Fungi;236
7.2.9;9 Functions of Mycorrhizal Fungi;239
7.2.10;10 TheMycorrhizosphere;247
7.2.11;11 Interactions in the Mycorrhizosphere;249
7.2.12;12 Conclusion;254
7.2.13;References;259
7.3;Interactions Between Microorganisms and Soil Micro- and Mesofauna;265
7.3.1;1 Introduction;265
7.3.2;2 Interactions in the Detritus FoodWeb;267
7.3.3;3 The Role of Micro- and Mesofauna as Drivers of Microbial Decomposition Processes;272
7.3.4;4 Feedbacks of Faunal–Microbial Interactions on Plant Growth;274
7.3.5;5 Conclusions;279
7.3.6;References;280
8;Part V Function of Microbes in Specific Soil Compartments;288
8.1;Transgenic Rhizospheres of Crop Plants: Their Impact on Indigenous Soil Fungi;289
8.1.1;1 Introduction;289
8.1.2;2 Experiments with Saprotrophic and Mycorrhizal Fungi;291
8.1.3;3 Conclusions;294
8.1.4;References;297
8.2;Regulation of Microbial Activities in Functional Domains of Roots and Invertebrates;301
8.2.1;1 Introduction;301
8.2.2;2 DeterminantsofMicrobialActivities: TheHierarchicalModel;301
8.2.3;3 MicrobialAdaptiveStrategies: TheSleepingBeautyParadox;303
8.2.4;4 Predation in Micro-FoodWebs;303
8.2.5;5 The External Rumen Strategy;304
8.2.6;6 Internal Mutualisms in Earthworms and Termites;305
8.2.7;7 Selection of Microflora in the Functional Domains of Soil Ecosystem Engineers;306
8.2.8;8 Conclusion and Implications for Soil Management;311
8.2.9;References;312
8.3;Microorganisms of Biological Crusts on Soil Surfaces;316
8.3.1;1 Introduction;316
8.3.2;2 Oxygenic Phototrophs;317
8.3.3;3 Heterotrophic Organisms;325
8.3.4;4 Conclusions;329
8.3.5;References;329
8.4;Microorganisms in Toxic Metal- Polluted Soils;333
8.4.1;1 Introduction;333
8.4.2;2 Metals in Soils;334
8.4.3;3 Effects of Toxic Metals on Microbial Communities;336
8.4.4;4 Metal Resistance and Tolerance Mechanisms;340
8.4.5;5 Microbial Transformations of Toxic Metals;343
8.4.6;6 Metalloid Transformations;347
8.4.7;7 Biomineralogy of Metal–Microbe Interactions;348
8.4.8;8 Mycorrhizas;350
8.4.9;9 Bioremediation;351
8.4.10;10 Phytoremediation;351
8.4.11;11 Conclusions;352
8.4.12;References;353
9;Part VI Techniques to Investigate Soil Microorganisms;365
9.1;Marker Genes in Soil Microbiology;366
9.1.1;1 Introduction;366
9.1.2;2 Definition of Marker Genes and Their First Applications in Soil Microbiology;367
9.1.3;3 Ribosomal RNA as an Intrinsic Marker;369
9.1.4;4 Polymerase Chain Reaction and Soil-ExtractedNucleicAcids;370
9.1.5;5 Cloning, Sequencing and Profiling Marker Genes from Soil;371
9.1.6;6 Structural and Functional Diversity of Soil Microbial Communities as Seen with Intrinsic Marker Genes;374
9.1.7;7 Expression of Intrinsic Marker Genes and Detection of Gene Transfer Potentials;376
9.1.8;8 Recombinant Marker Genes;377
9.1.9;9 Detection of In Situ Gene Transfer and Gene Expression with Recombinant Marker Genes;379
9.1.10;10 Recombinant Marker Genes as Biosensors;380
9.1.11;11 Conclusions and the Future of Marker Genes;381
9.1.12;References;382
9.2;Assessing Functions of Soil Microbes with Isotopic Measurements;390
9.2.1;1 Introduction;390
9.2.2;2 Natural Abundance Measurements;391
9.2.3;3 Compound-Specific Measurements and Isotopic Tracers;403
9.2.4;4 Conclusions and Future Research;404
9.2.5;References;405
10;Subject Index;410