Biodiversity in agricultural production systems /

Table Of Contents:
Introduction xvii

Gero Benckiser and Sylvia Schnell
Chapter 1 Diversity in Crop Production Systems 1(20)

Bernd Honermeier

1.1 Diversity of Crop Plants 1(5)

1.1.1 Cereals and Pseudocereals 1(2)

1.1.2 Oil Seed Crops 3(1)

1.1.3 Pulses, Root Crops, and Tuber Crops 3(1)

1.1.4 Sugar Plants 3(1)

1.1.5 Diversity of Medicinal and Spice Plants 4(2)

1.2 Effect of Plant Cultivation on Biodiversity 6(11)

1.2.1 Management of Crop Rotations 6(3)

1.2.2 Use of Allelopathy 9(1)

1.2.3 Cropping Systems 10(1)

1.2.4 Soil Tillage 11(2)

1.2.5 Cultivation of Genetically Modified Plants 13(2)

1.2.6 Precision Farming 15(2)

References 17(4)
Chapter 2 Agrodiversity: Genetic Diversity in Crops and Cropping Systems 21(20)

Jutta Ahlemeyer, Rod J. Snowdon, Frank Ordon, and Wolfgang Friedt

2.1 Diversity and Plant Breeding 21(1)

2.2 Measuring Molecular Diversity 21(2)

2.2.1 Isozymes 22(1)

2.2.2 DNA Markers 22(1)

2.3 Genetic Diversity in Modern Breeding Material 23(11)

2.3.1 Barley (Hordeum vulgare) 23(2)

2.3.2 Rapeseed (Brassica napus) 25(9)

2.4 Conclusions 34(1)

References 34(7)
Chapter 3 Soil Space Diversity and Its Dynamics: Qualitative and Quantitative Considerations 41(28)

Hans-J枚rg Vogel and Ulrich Babel

3.1 Introduction 41(2)

3.2 Observable Structure at Different Scales 43(11)

3.2.1 Imaging Techniques 43(1)

3.2.2 The Evidence of Structure At Any Scale 44(10)

2.3 Concepts of Hierarchical Organization of Structure across Scales 54(5)

3.3.1 Observation Scale and Resolution of the Instrument 54(1)

3.3.2 Minimum Characteristic Length and REV-Length of the Structure 54(2)

3.3.3 Structure and Texture 56(1)

3.3.4 Macroscopic Homogeneity 57(1)

3.3.5 Discrete and Continuous Hierarchy 58(1)

3.3.6 Fractal Structures 58(1)

2.4 Quantification of Structure and Diversity 59(7)

3.4.1 General Remarks on Image Analysis 59(1)

3.4.2 Basic Measures (Minkowski Numbers) 59(4)

3.4.3 Extension to Minkowski Functions 63(3)

2.5 Conclusions and Final Remarks 66(1)

References 66(3)
Chapter 4 Microbial Communities Introduced through Organic Amendments and by Air-Transport into Agricultural Soils 69(12)

Udo J盲ckel and Peter K盲mpfer

4.1 Introduction 69(1)

4.2 Microorganisms in Organic Wastes 70(1)

4.3 Microbial Community in Composts 71(3)

4.4 Airborne Microorganisms Released by Composts 74(1)

4.5 Anaerobic Digesters 74(1)

4.6 Dairy Wastes and Microbial Diveristy 75(2)

References 77(4)
Chapter 5 Discerning the Diversity of Soil Prokaryotes (Bacteria and Archaea) and Their Impact on Agriculture 81(20)

Christoph C. Tebbe and Michael Schloter

5.1 Prokaryotes in Soil: A Story of Success 81(1)

5.2 The Problem of Diversity Measurements of Soil Prokaryotes 82(2)

5.3 Accessing the Nonculturable Majority of Soil Prokaryotes 84(1)

5.4 The Dominant Prokaryotic Groups in Soil 85(4)

5.5 The Impact of Agriculture on Soil Prokaryotic Diversity: A View on Structure 89(1)

5.6 The Limitations of Structural Diversity Measurements: The Need for Functional Diversity Measurements 90(1)

5.7 The Impact of Agriculture on Soil Prokaryotic Diversity: A View on Functional Diversity in the Nitrogen Cycle 91(2)

5.8 Conclusions 93(1)

Acknowledgments 93(1)

References 93(8)
Chapter 6 Microbial Diversity in the Rhizosphere: Highly Resolving Molecular Methodology to Study Plant-Beneficial Rhizosphere Bacteria 101(30)

Anton Hartmann, Kornelia Smalla, and Jan S酶rensen

6.1 The Rhizosphere: A Very Special Soil Habitat 102(1)

6.2 Methods to Study Microbial Diversity in Soil and Rhizosphere 103(7)

6.2.1 Cultivation-Based Methods 103(1)

6.2.2 Analysis of the Total Microbial Community 103(4)

6.2.2.1 Phenotypic Fingerprints: BIOLOG Substrate Utilization Patterns 103(1)

6.2.2.2 Chemotypic Fingerprints: Phospholipid Fatty Acid (PLFA) Patterns 104(1)

6.2.2.3 Genotypic (Genetic) Fingerprints (Ribosomal and Metabolic Genes) 104(3)

6.2.3 Analysis of the Active Microbial Community 107(3)

6.2.3.1 Bromodeoxyuridine (BrdU) Method 107(1)

6.2.3.2 Stable Isotope Probing 107(1)

6.2.3.3 Reverse Transcriptase PCR (RT-PCR) 108(1)

6.2.3.4 Dot-Blot Hybridization 108(1)

6.2.3.5 Fluorescence In Situ Hybridization (FISH) 108(1)

6.2.3.6 Confocal Laser Scanning Microscopy (CLSM) 109(1)

6.3 Plant-Beneficial Rhizosphere Bacteria 110(9)

6.3.1 Symbiotic Nitrogen Fixing Bacteria in Agriculture 110(3)

6.3.1.1 Rhizobium鈥揕egume Symbioses 110(1)

6.3.1.2 Diversity of Rhizobia 111(1)

6.3.1.3 Host Specificity in Rhizobia鈥揕egume Symbioses 112(1)

6.3.1.4 Competitive Inoculant Strains 112(1)

6.3.1.5 Unrevealed Diversity of Rhizobia and Novel Symbiotic Nitrogen-Fixing Symbioses 113(1)

6.3.2 Plant Growth Promoting Rhizobacteria (PGPR) 113(3)

6.3.2.1 Nitrogen-Fixing PGPR 114(1)

6.3.2.2 Non-Nitrogen-Fixing PGPR 114(2)

6.3.3 Plant-Protecting Rhizobacteria 116(34)

6.3.3.1 Induction of Plant Systemic Resistance 116(1)

6.3.3.2 Biological Control of Plant Diseases 117(1)

6.3.3.3 Diversity of Novel Plant-Protecting Bacteria 118(1)

6.4 Summary and Perspectives 119(1)

References 120(11)
Chapter 7 Diversity of Biofilms and Their Formation Processes 131(18)

Michael W. Falk and Stefan Wuertz

7.1 What Constitutes a Biofilm? 131(1)

7.2 Origins of Biofilm Research 132(1)

7.3 Analytical Tools to Investigate Biofilms 133(2)

7.4 Highly Structured Biofilm Communities 135(1)

7.5 Formation and Development of Biofilms in Soil 136(2)

7.6 Prevalence and Diversity of Biofilms in Soil 138(2)

7.7 Prevalence and Diversity of Biofilms in the Rhizosphere for Agricultural Systems 140(1)

7.8 Additional Areas of Biofilm Interest in Agricultural Systems 141(1)

7.9 Conclusions 141(1)

References 142(7)
Chapter 8 Diversity of Soil Fungi 149(16)

Guido Fischer

8.1 What Are Soil Fungi? 149(1)

8.2 Introduction 149(1)

8.3 Ecological Aspects of Fungal Diversity 150(4)

8.3.1 Diversity of Arbuscular Mycorrhiza: A Model for the Saprophytes? 150(1)

8.3.2 Diversity of Hyphomycetes: Interactions within the Trophic Level 151(2)

8.3.3 Interactions with Other Trophic Levels 153(1)

8.3.4 Impact of Antropogenic Activity 153(1)

8.4 Species Richness and Diversity in Agricultural Environments 154(3)

8.4.1 Data from Culture-Based Techniques 154(1)

8.4.2 Data from Molecular Methods 155(2)

8.4.3 Comparison of Biodiversity Assessed by Culture-Based and Molecular Techniques 157(1)

8.5 Species Richness and Diversity in Nonagricultural Environments 157(2)

8.6 Conclusions 159(1)

References 160(5)
Chapter 9 Diversity of Chytrids 165(24)

Donald A. Klein

9.1 What Are Chytrids? 165(4)

9.2 Assessing Biodiversity 169(6)

9.2.1 General Applications in the Microbial World 169(1)

9.2.2 Diversity and the Species Concept in the Chytrids 170(2)

9.2.3 Methodological Aspects of Diversity Assessment 172(3)

9.3 Description of Chytrid Biodiversity in Agricultural Systems 175(4)

9.3.1 Chytrids As Saprophytes 175(2)

9.3.2 Chytrids As Biotrophs 177(1)

9.3.2.1 Plant Interactions 177(1)

9.3.2.2 Animal Interactions 177(1)

9.3.3 Microbial Interactions 178(1)

9.3.4 Summary: Biodiversity in Agricultural Systems 178(1)

9.4 Structural and Functional Relationships of Chytrids 179(1)

9.5 Factors Controlling Chytrid Biodiversity 180(1)

9.6 Future Research Needs: Biodiversity and the Chytrids 181(1)

9.7 Summary 181(1)

Acknowledgments 182(1)

References 182(7)
Chapter 10 Diversity of Arbuscular Mycorrhizal Fungi 189(16)

Philipp Franken and Eckhard George

10.1 Introduction 189(1)

10.2 Genotypic Variation 190(1)

10.3 Phenotypic Variation 191(3)

10.4 Biodiversity in Ecosystems 194(2)

10.5 Conclusion 196(1)

Acknowledgments 197(1)

References 197(8)
Chapter 11 Diversity of Protozoa 205(10)

Stuart S. Bamforth

11.1 Protozoan Biodiversity 206(3)

11.1.1 Protozoan Groups 206(1)

11.1.2 Methods of Study 206(2)

11.1.3 Protozoa as Bioindicators 208(1)

11.1.4 Protozoan Biodiversity in Agricultural Production Systems 208(1)

11.2 Structure and Functional Relationships 209(1)

11.2.1 Bacteria and Fungi 209(1)

11.2.2 Interaction with Plants: The Rhizosphere 210(1)

11.2.3 Nematodes 210(1)

11.2.4 Earthworms 210(1)

11.3 Factors Controlling Biodiversity 210(2)

11.3.1 Cultivation Management 210(1)

11.3.2 Fertilizers 211(1)

11.3.3 Biocides 211(1)

11.3.4 Soil Compaction 211(1)

11.3.5 Soil Restoration and Conservation 211(1)

11.3.6 Summary 211(1)

References 212(3)
Chapter 12 Diversity of Nematodes 215(22)

Gregor W. Yeates

12.1 Introduction 215(1)

12.2 Nematode Diversity 215(5)

12.2.1 Food, Energy, and Feeding Type Classification 217(1)

12.2.2 Effects of Nematode Feeding 218(2)

12.2.3 Nematodes in Biological Control of Agricultural Pests 220(1)

12.3 Diverse Nematodes of Each Feeding Group Coexist 220(2)

12.4 Species Diversity and Functional Diversity of Nematode Assemblages 222(3)

12.5 Management Practices and the Nematode Assemblage 225(5)

12.6 Overview 230(1)

Acknowledgment 231(1)

References 231(6)
Chapter 13 Diversity of Tardigrada 237(12)

Kunihiro Seki and Daiki D. Horikawa

13.1 Introduction 237(1)

13.2 Cryptobiosis 237(7)

13.2.1 Anhydrobiosis 238(5)

13.2.1.1 Induction of Anhydrobiosis 239(1)

13.2.1.2 Metabolic State and Longevity of Anhydrobiosis 240(1)

13.2.1.3 Sugar and Protein Accumulation 240(1)

13.2.1.4 Revival from Anhydrobiosis 241(1)

13.2.1.5 Ecological Significance of Anhydrobiosis 241(1)

13.2.1.6 Tolerance to Extreme Environments 242(1)

13.2.2 Cryobiosis 243(1)

13.2.2.1 Effects of Cooling Rate on Cryobiotic Survival 243(1)

13.2.2.2 Effects of Cooling Periods on Survival 243(1)

13.2.2.3 Cryoprotectants 243(1)

13.2.3 Similarity between Anhydrobiosis and Cryobiosis 244(1)

13.3 Future Research on Cryptobiosis 244(1)

13.4 Conclusion 244(1)

References 245(4)
Chapter 14 Diversity of Lumbricid Earthworms in Temperate Agroecosystems 249(14)

Joann K. Whalen and C.A. Fox

14.1 Introduction 249(1)

14.2 Taxonomic Diversity of Lumbricid Earthworms 249(1)

14.3 Functional Diversity of Lumbricid Earthworms 250(3)

14.4 Effect of Agriculture on Earthworm Diversity 253(4)

14.4.1 Tillage 253(1)

14.4.2 Cropping Systems and Residue Management 254(1)

14.4.3 Fertilizers and Pesticides 255(2)

14.5 Earthworm Diversity and Agroecosystem Function 257(1)

14.6 Conclusions and Future Directions 258(1)

References 258(5)
Chapter 15 Soil Enzymes: Spatial Distribution and Function in Agroecosystems 263(24)

Ellen Kandeler and Richard P. Dick

15.1 Introduction 263(1)

15.2 Sources of Extracellular Enzymes in Soils 264(1)

15.3 Spatial Distribution of Enzymes in Soils 265(7)

15.3.1 Micro-Scale Distribution 265(4)

15.3.2 Meso-Scale Distribution 269(3)

15.3.3 Macro-Landscape Distribution 272(1)

15.4 Methods for Studying Enzyme Activities in Soils 272(2)

15.5 Response of Soil Enzymes to Environmental Change 274(4)

15.5.1 Elevation of Carbon Dioxide and Trace Gas Emissions 275(2)

15.5.2 Soil Management 277(1)

15.6 Conclusions 278(1)

References 279(8)
Chapter 16 Metabolic Diversity of Microorganisms in Agricultural Soils 287(30)

Stefan Ratering, Gero Benckiser, and Sylvia Schnell

16.1 Introduction 287(1)

16.2 Carbon Substrate Diversity in Agriculture 288(1)

16.3 Substrate Degradation 289(8)

16.3.1 Degradation of Carbohydrate Polymers and Sugars 290(2)

16.3.2 Degradation of Lipids and Hydrocarbons 292(3)

16.3.3 Aromatic Compounds and Lignin Degradation 295(2)

16.4 Reduction of Various Electron Acceptors 297(1)

16.5 Autotrophic Metabolic Diversity 298(1)

16.6 Production of Secondary Metabolites in Agricultural Soil 299(2)

16.7 Methods to Access Metabolic Diversity 301(1)

16.8 Consequences of Lost Metabolic Diversity 302(1)

16.9 Postscript 303(1)

References 303(14)
Chapter 17 Gaseous Emissions (CO2, CH,, N2O, and NO) from Diverse Agricultural Production Systems 317(32)

Arvin R. Mosier and Tim Parkin

17.1 Introduction 318(3)

17.1.1 CO2 318(1)

17.1.2 CH4 318(1)

17.1.3 N2O 319(1)

17.1.4 NOx 319(1)

17.1.5 Chapter Objectives 320(1)

17.2 Production and Consumption of CO2, CH4, N2O, and NO 321(9)

17.2.1 Production and Consumption of CO, 321(3)

17.2.1.1 Root Contributions to Soil CO2 Flux 321(1)

17.2.1.2 Organic Matter Decomposition Contribution to Soil CO2 Flux 321(1)

17.2.1.3 Temperature 322(1)

17.2.1.4 Water 323(1)

17.2.1.5 Substrate 323(1)

17.2.2 CH4 324(2)

17.2.2.1 CH4 Production in Soils 325(1)

17.2.2.2 CH4 Transport 325(1)

17.2.2.3 CH4 Oxidation 325(1)

17.2.3 N2O and NO 326(4)

17.2.3.1 Process-Level Controls on Gaseous Emissions of N 327(1)

17.2.3.2 Nitrification 327(1)

17.2.3.3 Chemodenitrification 328(1)

17.2.3.4 Biological Denitrification 328(2)

17.3 Crop Production and Trace Gas Exchange 330(6)

17.3.1 Relevance of Soil CO2 Measurements 330(1)

17.3.1.1 Soil C Change 330(1)

17.3.1.2 Ecosystem Processes 330(1)

17.3.2 Flooded Rice 331(1)

17.3.3 Annual Emissions of CH4, N2O, and NO from Rice鈥揥heat Cropping Systems 332(1)

17.3.4 Trace Gas Exchange in Temperate and Tropical Upland Crops 333(26)

17.3.4.1 Sugar Cane 334(1)

17.3.4.2 Cotton, Maize, and Wheat 334(1)

17.3.4.3 Impact of Crop on N,O Emissions in Scotland 335(1)

17.4 Impact of Tillage on N2O, CH4, and Soil Organic Carbon in Cropped Soils 336(3)

17.5 Impact of Soil Freeze/Thaw on N,O Flux 339(1)

17.6 Concluding Remarks 339(1)

References 340(9)
Chapter 18 Principles Behind Order and Sustainability in Natural Successions and Agriculture 349(36)

Gero Benckiser

18.1 Introduction 349(2)

18.2 The Laser: An Example of Self-Organization in the Inanimated World 351(2)

18.3 Viruses: Mediators between the Inanimated and Animated World 353(1)

18.4 Ordering Principles in Plant Cells 354(2)

18.5 Microbial Cell Networks and Control Circuits 356(3)

18.6 Systems of Increasing Complexity and Communication 359(7)

18.6.1 Symbiont鈥揌ost Interaction in Legumes 359(2)

18.6.2 The Rumen, a Homiothermal, Highly Intercommunicating Fermenter 361(3)

18.6.3 The Earthworm Intestinosphere, an Agriculturally Important Flow-Through System 364(2)

18.7 State-Organizing Ants and Their Working-Together Principles 366(6)

18.7.1 Ants in an Agricultural Landscape: Importance and Distribution 366(1)

18.7.2 Genetic and Behavioral Diversity 367(1)

18.7.3 Nest Construction and Pattern Formation 368(1)

18.7.4 Caste Differentiation and Division of Labor 368(1)

18.7.5 Mobility and Order 369(1)

18.7.6 Changing Tasks and Neuronal Modifications 370(1)

18.7.7 Living Together in Self-Organized Patterns 371(1)

18.8 Entropy Reduction on Agroecosystem Scale 372(3)

Postscript 375(1)

References 376(9)
Chapter 19 Food Web Interactions and Modeling 385(14)

John C. Moore, Rodney T. Simpson, Kevin S. McCann, and Peter C. de Ruiter

19.1 Introduction 385(1)

19.2 Soil Food Web Interactions 385(6)

19.2.1 The Connectedness Food Web 386(1)

19.2.2 The Energy Flow Food Web 387(2)

19.2.3 The Interaction Food Web 389(2)

19.3 Modeling the Impacts of Agricultural Practices 391(4)

19.3.1 Effects of Tillage on Soil Organic Matter and Nutrient Dynamics 392(1)

19.3.2 Effects of Tillage on Food Web Structure and Stability 393(2)

19.4 Discussion and Conclusions 395(1)

Acknowledgments 396(1)

References 396(3)
Chapter 20 Soil Quality Assessment and Long-Term Field Observation with Emphasis on Biological Soil Characteristics 399(26)

Hans-Rudolf Oberholzer and Heinrich H枚per

20.1 Introduction 400(1)

20.2 Soil Biological Diversity and Soil Quality 400(10)

20.2.1 Soil Biological Diversity in Soil Protection Legislation 400(2)

20.2.2 Soil Quality As a Set of Functions and Properties 402(5)

20.2.2.1 The Terms Soil Fertility and Soil Quality 402(1)

20.2.2.2 Soil Functions 402(1)

20.2.2.3 Soil Properties and Analytical Parameters 403(1)

20.2.2.4 Relationship between Soil Functions and Soil Properties 404(1)

20.2.2.5 Relationship between Biodiversity and Soil Functions 404(3)

20.2.3 Aspects of Soil Quality Assessment 407(3)

20.2.3.1 Periodicity and Date of Observation 407(1)

20.2.3.2 Choice of a Reference with Respect to Land-Use Systems and Climatic Conditions 408(1)

20.2.3.3 Soil Quality Assessment under Conflicting Land Use 409(1)

20.3 Importance of Biological Properties in Soil Quality Assessment 410(1)

20.3.1 Detection of Effects of Chemical and Physical Changes on Soil Organisms 410(1)

20.3.2 Use of Soil Biological Properties to Define Chemical and Physical Threshold Values 410(1)

20.4 Assessment and Evaluation of Biological Parameters 411(6)

20.4.1 Reference Systems 412(2)

20.4.2 Examples for Assessment and Evaluation 414(3)

20.4.2.1 Assessment of Polluted Soils 414(1)

20.4.2.2 Assessment of Land-Use System 415(2)

20.5 Long-Term Soil Monitoring 417(4)

20.5.1 Criteria for the Choice of Parameters 417(2)

20.5.2 Soil Monitoring in Lower Saxony: An Example of Use 419(2)

20.5.2.1 Materials and Methods 419(1)

20.5.2.2 Results and Discussion: Microbial Biomass as Indicator of Soil Acidification 419(1)

20.5.2.3 Results and Discussion: Microbial Biomass as an Indicator of Carbon Input 420(1)

20.5.2.4 Conclusions from Microbial Biomass Measurements in Soil Monitoring for Future use of Diversity Indicators 421(1)

20.6 Conclusions 421(1)

References 422(3)
Index 425