Sclerotia Grains in Soils: A New Perspective from Pedosclerotiology (Progress in Soil Science)

This book introduces what sclerotia grains are, and where and how they exist in soils, by compiling the results obtained from the studies on fungal sclerotia formed by Cenococcum geophilum ( Cg ) and related species, the visible black small grains persistent for a few thousand to ten thousands of years in forest soils and sediments. The chapters contain the results and discussions on the ecological distribution and regulating factors, characteristics, and function of Cg sclerotia grains, carried out by researchers from soil geography, soil science, soil microbiology, physiology, forestry, analytical chemistry, environmental chemistry, material science, and related disciplines. The anatomy of sclerotia grains in soil was realized in terms of interdisciplinary joint researches, which resulted in deepening understanding of the ecological function of the mesoscale organic component in soils. This book covers the natural history of sclerotia in soils, pedo-sclerotiology. Preface 7 Contents 10 Contributors 12 Chapter 1: Introduction 14 1.1 Sclerotia: Fungal Propagule or Soil Grain? 15 1.2 Melanized Sclerotia Grains Found in Forest Soils 17 1.3 Sclerotia Grains in Earth Sciences Studies 21 1.4 Conclusion 24 References 25 Chapter 2: Fungal Communities of Sclerotia Grains from Forest Soils 29 2.1 Introduction 30 2.1.1 Molecular Methods for Identification of Sclerotia-Associated Fungi 31 2.2 Analysis of Sclerotia-Associated Fungal Communities by T-RFLP Profiling 32 2.2.1 Materials and Methods 32 2.2.2 Results and Discussion 33 2.2.2.1 Sclerotia Grain Density 33 2.2.2.2 Identification of Sclerotia-Associated Fungi by Molecular Methods 34 2.3 Fungal Community Analysis by Culture and Molecular Methods in Sclerotia from Forest Soil on Mt. Ontake, Gifu Prefecture, J... 36 2.3.1 Material and Methods 36 2.3.1.1 Soil Sampling and Collection of Sclerotia 36 2.3.1.2 Creation of Clone Library for Identification of Fungal Species 37 2.3.1.3 Isolation of Fungi by Culturing 38 2.3.1.4 Isolates ́ Ability to Form Sclerotia and Sclerotial Morphology 38 2.3.2 Results and Discussion 38 2.3.2.1 Identification of Isolates by the Clone Library Method 38 2.3.2.2 Identification of Isolates by the Culture Method 40 2.3.2.3 Morphology of Sclerotia Formed by Isolates 41 2.4 Conclusion 42 References 43 Chapter 3: Relationships Between Soil Mesofauna, Ectomycorrhizal Fungi, and Sclerotia in Forest Soils 47 3.1 Introduction 47 3.2 Community Profiles of Ectomycorrhizal Fungi Consumed by Soil Mesofauna 49 3.2.1 Materials and Methods 49 3.2.1.1 Study Area and Soil Sampling Techniques 49 3.2.1.2 Soil Mesofauna Extraction 49 3.2.1.3 Isolation of Fungal DNA from Soil Mesofauna 51 3.2.1.4 Statistical Analyses 52 Mesofaunal Diversity 52 Diversity of Fungal Communities 52 3.2.2 Results and Discussion 53 3.2.2.1 Soil Mesofauna Characteristics 53 3.2.2.2 Community Profiles of Fungi Consumed by Soil Mesofauna 54 3.2.2.3 Predominance of Acari and Collembola and Their Roles in the Soil Ecosystem 54 3.3 Relationship Between Sclerotia and Mesofauna in Forest Soils Based on Ectomycorrhizal Fungal Community Profiles 61 3.3.1 Materials and Methods 61 3.3.1.1 Fungal Community Profiles in Soil 61 3.3.1.2 Soil pH and Exchangeable Aluminum Content 63 3.3.2 Results and Discussion 63 3.3.2.1 Ectomycorrhizal Fungal Community Profiles of Sclerotia, Soil Mesofauna, and Soil Samples 63 3.3.2.2 Environmental Factors Regulating Sclerotia Formation 66 3.4 Model of Relationship Between Sclerotia Formation and Soil Mesofauna Mediated Via Ectomycorrhizal Fungi 67 3.5 Conclusion 70 References 72 Chapter 4: Sclerotia Grains as Bacterial Carriers in Soil 75 4.1 Introduction 75 4.2 Bacterial Habitat in Sclerotia Grains 77 4.3 Washing Treatment for Bacterial Isolation from Sclerotia Grains 78 4.4 Bacterial Colonization of Sclerotia Grains 80 4.4.1 Materials and Methods 80 4.4.1.1 Soil Sampling and Collection of Ontake Sclerotia 80 4.4.1.2 Isolation and Identification of Bacteria Inside Sclerotia 80 4.4.1.3 Comparison of Sclerotia Before and After Autoclaving 80 4.4.1.4 Sclerotia Colonization Trial 81 4.4.2 Results 81 4.4.2.1 Comparison of Sclerotia Before and After Autoclaving 81 4.4.2.2 Isolation and Identification of Bacteria Inside Ontake Sclerotia 81 4.4.2.3 Sclerotia Colonization 83 4.4.3 Discussion 85 4.5 Conclusions 86 References 87 Chapter 5: Chemical Characterization of Sclerotia Grains Collected from a Volcanic Ash Soil Profile in Japan 88 5.1 Introduction 89 5.2 Preparation of Standard Samples 89 5.3 Grain Size, Volume, and Specific Gravity of Sclerotia 90 5.4 Elemental Analysis by Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM-EDS) 92 5.5 Major Elements Analysis 92 5.6 Solid-State Cross-Polarization Magic-Angle Spinning 13C Nuclear Magnetic Resonance Spectra 94 5.7 Fourier-Transform Infrared Spectroscopy 94 5.8 27Al Magic-Angle Spinning Nuclear Magnetic Resonance Spectra 95 5.9 X-Ray Diffraction Spectra 96 5.10 Elemental Compositions of Metal in Sclerotium Grains 96 5.11 Conclusions 99 References 99 Chapter 6: Origin of Soil Polysaccharides, and Ectomycorrhizal Fungal Sclerotia as Sources of Forest Soil Polysaccharides 101 6.1 Introduction 102 6.2 Determination of Neutral Saccharides in Soil, and Data Collection 104 6.2.1 Methods for Neutral Saccharide Determination of Soil and Plant Materials 104 6.2.2 Characterization of Monosaccharide Composition by Numerical Index 105 6.2.3 Statistical Analysis and Terminology 105 6.3 Origins of Soil Polysaccharides 105 6.3.1 Comparison of Neutral Monosaccharide Composition Between Plant Materials and Soil 106 6.3.1.1 Monosaccharide Composition of Plant Materials 106 6.3.1.2 Monosaccharide Composition of Soil Polysaccharides 110 6.3.1.3 Comparison of Composition Between Plant and Soil 110 6.3.2 Identification of Neutral Saccharides Synthesized in Soil by Tracer Techniques 114 6.4 Accumulation of Microbial Polysaccharides in Forest Soil 116 6.5 ECM Fungal Sclerotia as Sources of Forest Soil Polysaccharides 117 6.5.1 Monosaccharide Composition of a Forest Soil on Mt. Ontake from Where ECM Fungal Sclerotium Grains Were Collected 118 6.5.2 Neutral Saccharides of ECM Fungal Sclerotia 118 6.5.2.1 Collection of Sclerotium Grain from Soil Sample 118 6.5.2.2 Content and Composition of Neutral Saccharides in Sclerotium Grains 118 6.5.2.3 Quantitative Comparison of Saccharides in ECM Fungal SG to Those in Whole Soil: A Case Study 121 6.5.3 Production and Stability in Soil of ECM Fungal Sclerotial Polysaccharides 122 6.6 Origins of Forest Soil Polysaccharides 123 References 123 Chapter 7: Dating of Sclerotia Grains in Andosol Profiles 128 7.1 Introduction 129 7.2 14C Ages of Sclerotia Grains in Three Andosol Profiles 129 7.2.1 Materials and Methods 129 7.2.2 14C Ages of Sclerotia in Andosol Profiles 131 7.2.2.1 MYK Profile 132 7.2.2.2 ONT and IWK Profiles 134 7.2.2.3 Changes in Total Carbon Content of Soil, Humic Acid, and Sclerotia by 14C Date 134 7.3 Relationship Between 14C Age and Al/C Ratio of Sclerotia Grains 134 7.3.1 Materials and Methods 134 7.3.1.1 Sclerotia Samples 134 7.3.1.2 AMS 14C Dating of Sclerotia 138 7.3.1.3 SEM-EDS Analysis of Sclerotia 140 7.3.2 Results and Discussion 141 7.4 Conclusion 144 References 144 Chapter 8: Micromorphological Features of Sclerotia Grains 147 8.1 Introduction 148 8.2 Materials and Methods 149 8.3 Aluminum Hydroxide Polymorphs 150 8.4 Carbonaceous Granular Particles and Nanoparticles 153 8.5 Spherical Silica Particles 155 8.6 Micro-CT Analysis 156 8.7 Conclusion 157 References 158 Chapter 9: Spatial Distribution of Sclerotia Grains in Forest Soils, Northern and Central Japan 160 9.1 Introduction 161 9.2 Distribution of Sclerotia in Soil Profile 162 9.3 Variation of Sclerotia Distribution in Mt. Chokai 168 9.4 Altitudinal Distribution of Sclerotia in Surface Soils 170 9.5 Concluding Remarks 176 References 178 Chapter 10: Spatial Distribution of Sclerotia Grains in Low-pH Forest Soils, Central Germany 180 10.1 Distribution of Sclerotia Grains in Forest Soil Profiles in the Harz Mountains 181 10.1.1 Introduction 181 10.1.2 Materials and Methods 181 10.1.2.1 Geography and Soil Profiles of the Study Area 181 10.1.2.2 Measurement of Sclerotia Grain Content 183 10.1.2.3 Scanning Electron Microscopy and Energy Dispersive X-ray Spectroscopy of Sclerotia Grains 183 10.1.2.4 Chemical Analyses 183 10.1.2.5 Mineral Analysis 184 10.1.2.6 Soil Ergosterol Analysis 184 10.1.3 Results and Discussion 185 10.1.3.1 Properties of Representative Soil Profiles 185 10.1.3.2 Content of Sclerotia Grains and Soil Ergosterol 189 10.1.3.3 Relationship Between Soil Properties and Sclerotia Grains 189 10.2 Micro-Topographical Distribution in Single Stand Forest Soil 190 10.2.1 Field Sites and Methodology 190 10.2.2 Results and Discussion 192 10.3 Conclusion 198 References 198 Chapter 11: Melanized Sclerotia Grains from Mongolian Steppe Forest Soils 200 11.1 Introduction 201 11.2 Materials and Methods 201 11.2.1 Sampling Area 201 11.2.2 Soil and Sclerotia Grain Analyses 202 11.2.3 Statistical Analysis 204 11.3 Results and Discussion 205 11.3.1 Soil Properties 205 11.3.2 Element Concentrations of Sclerotia Grains and Soil Samples 206 11.3.3 Transfer Factor and Metal Accumulation in Sclerotia 210 11.4 Conclusion 213 References 213 Chapter 12: Sclerotia Grain, a Mesoscale Component of Soil 216 References 219