Note: Cover -- Title Page -- Copyright Page -- Contents -- Series Preface -- Preface -- List of Contributors -- Chapter 1 Introduction: Working Across Scales to Project Soil Biogeochemical Responses to Climate -- 1.1. Context -- 1.2. Soil Responses to Environmental Conditions at Diverse Scales: Organic Matter Transformations and Feedbacks to Climate -- 1.2.1. Organic Matter at the Microscale -- 1.2.2. Organic Matter at the Mesocosm Scale -- 1.2.3. Organic Matter at the Plot and Decadal Scale -- 1.2.4. Organic Matter at Ecosystem to Landscape Scales Across Years to Decades -- 1.3. Recent Empirical Investigations of Soil Responses to Environmental Conditions at Diverse Scales: Mineral Weathering -- 1.3.1. Mineral Weathering at the Column or Mesocosm Scale -- 1.3.2. Mineral Weathering at the Ecosystem to Landscape Scale Across Diverse Temporal Scales -- 1.4. Cross-Scale Discrepancies: Two Examples of Nonlinearities That Challenge Predictive Abilities -- 1.5. Models as a Means of Integrating Across Disciplines and Scales -- 1.6. Conclusions -- Acknowledgments -- References -- SECTION 1 Molecular-scale Processes and Critical Reactions -- Chapter 2 The Science and Semantics of "Soil Organic Matter Stabilization" -- 2.1. The Cycling of Organic Matter in Soil -- 2.2. What Is "Stability?" -- 2.2.1. The Paradigm of Chemical Stability (I): Humification and Humic Substances -- 2.2.2. The Paradigm of Chemical Stability (II): Litter Quality -- 2.2.3. The Paradigm of Chemical Stability (III): Molecular Complexity and Activation Energies -- 2.2.4. The Paradigm of Chemical Stability (IV): Plastics and Black Carbon -- 2.3. The Paradigm of Sorptive Protection/Interactions -- 2.4. The Paradigm of Accessibility: Aggregation -- 2.5. The Paradigm of Accessibility: How Location Matters -- 2.6. Microbial Metabolic Performance as a Factor in Soil Carbon Cycling. , 2.7. Habitat Properties as Logistical Constraints -- 2.8. Habitat Properties and Reactant Supply -- 2.8.1. Habitat Properties Determine the Thermodynamics of Decomposition -- 2.8.2. Decomposition and Decomposer Needs: Microbial Carbon Use Efficiency -- 2.8.3. Decomposition and Decomposer Needs: Resource Stoichiometry -- 2.8.4. Plants as an Interested Party in Soil Organic Matter Decomposition -- 2.9. Conclusions -- References -- Chapter 3 Interconnecting Soil Organic Matter with Nitrogen and Phosphorus Cycling -- 3.1. Soil Organic Matter: The Key Player for Controlling Nutrient Cycling -- 3.2. Nitrogen -- 3.2.1. Introduction -- 3.2.2. Biological N Fixation -- 3.2.3. Organic N Stabilization and Depolymerization -- 3.2.4. Microbial Utilization of N in Soils -- 3.2.5. Microbial N Oxidation and Reduction -- 3.2.6. Plant N Uptake as a Function of Resource Availability -- 3.3. Phosphorus -- 3.3.1. Introduction -- 3.3.2. Abiotic Processes -- 3.3.3. Organic P Dynamics and P Recycling -- 3.3.4. Microbial P in Soil -- 3.3.5. Plant and Microbial Strategies for P Uptake -- 3.3.6. Plant P Uptake as Related to Internal Plant Nutritional Status and Soil P Availability -- 3.4. Conclusions -- References -- Chapter 4 Plant-Derived Macromolecules in the Soil -- 4.1. Introduction -- 4.2. Plant Macromolecules as Inputs into the Soil -- 4.2.1. Cellulose and Hemicellulose -- 4.2.2. Lignin -- 4.2.3. Proteins -- 4.2.4. Tannins and Other Polyphenols -- 4.2.5. Cutin, Suberin, and Free Extractable Lipids -- 4.2.6. Other Molecules -- 4.3. Fraction-Specific Molecular Analyses -- 4.3.1. Biomarkers -- 4.3.2. Compound-specific Isotope Analysis (CSIA) -- 4.3.3. Other Complementary Methods -- 4.4. Fate of Plant-Derived Compounds in the Soil -- 4.4.1. Microbial Degradation -- 4.4.2. Abiotic Degradation -- 4.4.3. Movement in the Soil Through Leaching Processes. , 4.4.4. Preservation Mechanisms -- 4.4.5. Turnover of Plant-Derived Molecules -- 4.5. Root- Versus Shoot-Derived Carbon in the Soil -- 4.6. Conclusions -- References -- Chapter 5 Microbe-Biomolecule-Mineral Interfacial Reactions -- 5.1. Introduction -- 5.2. Microbial Colonization of Rock -- 5.2.1. Initial Colonizers of Fresh Mineral Substrate -- 5.3. Mechanisms of Cell Adhesion to Mineral Surfaces -- 5.3.1. Bacterial Surface Geochemistry -- 5.3.2. Bacterial Adhesion at Mineral Surfaces -- 5.4. Mineral Surface Reactions of Extracellular Biomolecules -- 5.4.1. Composition of Extracellular Polymeric Substances (EPS) -- 5.4.2. Adsorption and Fractionation of EPS at Mineral Surfaces -- 5.5. Heteroaggregate Formation -- 5.6. Conclusions and Future Outlook -- References -- SECTION 2 Ecosystem-scale Studies of Ecological Hotspots -- Chapter 6 Greenhouse Gas Emissions in Wetland Rice Systems: Biogeochemical Processes and Management -- 6.1. Introduction -- 6.2. Carbon Biogeochemistry -- 6.2.1. Anaerobic C Pathways -- 6.2.3. Dissolved Organic C -- 6.2.4. CH4 Production, Consumption, and Emission -- 6.2.5. Mitigation Strategies -- 6.3. N Cycles -- 6.3.1. Biogeochemical Pathways -- 6.3.2. N2O Production, Consumption, and Emission -- 6.4. Future Directions -- References -- Chapter 7 The Changing Biogeochemical Cycles of Tundra -- 7.1. Introduction -- 7.2. The Changing Tundra Carbon Cycle -- 7.2.1. Soil Carbon Accumulation -- 7.2.2. Carbon Balance -- 7.2.3. Carbon Inputs -- 7.2.4. Carbon Outputs: CO2 -- 7.2.5. Carbon Outputs: Methane -- 7.3. Changing Tundra Nutrient Cycles -- 7.3.1. Nutrient Limitation -- 7.3.2. Nutrient Stocks -- 7.3.3. The Changing Nitrogen Cycle -- 7.3.4. The Changing Phosphorus Cycle -- 7.3.5. Nutrient Leaching -- 7.3.6. Effects of Fire on Nutrient Cycles -- 7.4. Future Projections -- 7.5. Future Research Directions -- References. , Chapter 8 Linking Sources, Transformation, and Loss of Phosphorus in the Soil-Water Continuum in a Coastal Environment -- 8.1. Phosphorus: An Essential Nutrient Turned into a Contaminant -- 8.2. Transformation of Phosphorus in Soils -- 8.2.1. Transformation of P Pools in Soils Impacted by Agricultural P Loading -- 8.2.2. Formation of Residual and Recalcitrant P Pools in Soils -- 8.3. Surface and Subsurface Flow of Phosphorus from Agricultural Soils to Open Water -- 8.4. Transport of Phosphorus in the Main Channel and Export to Open Waters -- 8.5. Source Tracking of P Released from Soils and Upland Watershed -- 8.6. Implication and Future Research Directions -- Acknowledgments -- References -- Chapter 9 Deep Soil Carbon -- 9.1. Introduction -- 9.2. How Much Carbon Is Stored in the Subsoil? -- 9.3. How Does Carbon Accumulate at Depth? -- 9.4. Factors Contributing to Deep Soil Carbon Persistence -- 9.4.1. Climate -- 9.4.2. Parent Material and Time -- 9.4.3. Relief and Soil Redistribution -- 9.4.4. Biota -- 9.5. Vulnerability of Deep Soil Carbon -- 9.5.1. Land Management -- 9.5.2. Climate Change -- 9.5.3. Disturbance of Buried Soils -- 9.6. Improving Predictions of Deep Soil Carbon -- 9.7. Conclusions -- Acknowledgments -- References -- SECTION 3 Modeling Biogeochemical Cycles and Improvement of Ecosystem Resilience -- Chapter 10 Soil Carbon Dynamics and Responses to Environmental Changes -- 10.1. Introduction -- 10.2. Soil C Inventory -- 10.2.1. Top and Deep Soil C Inventory -- 10.2.2. Global Soil C Stock -- 10.2.3. Permafrost - A Huge Soil C Pool -- 10.2.4. Soil C Inventory Methods -- 10.3. Soil C Dynamics -- 10.3.1. Soil C Input Processes -- 10.3.2. Soil C Output Processes -- 10.3.3. Depth-dependent Soil C Balance -- 10.4. Climate Warming and Soil Carbon -- 10.4.1. Temperature Sensitivity of Different Soil Organic C Pools. , 10.4.2. Thermal Acclimation of Soil Organic C Decomposition -- 10.4.3. Soil Organic C Fraction, Composition, and Stability -- 10.5. Precipitation Change and Soil Carbon -- 10.5.1. Precipitation Amounts -- 10.5.2. Seasonal Rainfall Redistribution -- 10.5.3. Extremes and Precipitation Variability -- 10.5.4. Multifactor and Long-term Experiments -- 10.6. Nitrogen Deposition and Soil Carbon -- 10.6.1. Effects of N Deposition on Quantity and Quality of Plant C Input to Soil -- 10.6.2. Effects Caused by Community Composition Changes -- 10.6.3. Effects of N Deposition on Soil Microbial Activity -- 10.6.4. Effects of N Deposition on Soil Physicochemical Properties -- 10.7. Uncertainties in Modeling Soil C Dynamics -- 10.7.1. Model Structures -- 10.7.2. Poor Representation of Microbial Control on Soil C Cycles -- 10.7.3. Poor Representation of Vertical Soil C Cycles in ESMs -- 10.7.4. Underestimated Soil C Turnover Time in ESMs -- 10.8. Outlook: Neglected Facts and Future Research Directions -- 10.8.1. Neglected Facts About Permafrost Processes -- 10.8.2. Neglected Facts About Human Interferences -- 10.8.3. Neglected Facts About Phosphorus Processes -- 10.9. Conclusions -- References -- Chapter 11 Next-generation Soil Biogeochemistry Model Representations: A Proposed Community Open-source Model Farm (BeTR-S) -- 11.1. Introduction -- 11.2. Proposed SOM Model Structure -- 11.2.1. Litter Input and Polymeric OM Hydrolysis (P1) -- 11.2.2. Microbial Physiology, Microbial Population Dynamics, and Macronutrient Controls (P2) -- 11.2.3. Trophic Interactions and Competition (P3) -- 11.2.4. Mineral-Organic Interactions (P4) -- 11.2.5. Soil Chemistry: Cation Exchange Capacity, pH, Redox, and Salinity (P5) -- 11.2.6. Rhizosphere-Bulk Soil Interactions (P6) -- 11.2.7. Soil Structure, Aggregation, Transport (P7). , 11.3. Mathematical Integration and Solution in the BeTR-S Model Farm.