ALBERT

Note: Contents: The Theory of Externalities and Public Goods: The Lifework of Richard Cornes ; Efficiency in Contests Between Groups ; Multiple-Aggregate Games ; Strategic Coalition Formation in Global Public Good Provision ; Evolution of Consistent Conjectures in Semi-aggregative Representation of Games, with Applications to Public Good Games and Contests ; Mixed-Strategy Kant-Nash Equilibrium and Private Contributions to a Public Good ; Social Creation of Pro-social Preferences for Collective Action ; Community Size and Public Goods in Hume’s Treatise of Human Nature ; Decentralized Leadership ; Debt NeutralityWithout Altruism: Voluntary Contributions to Public Goods as ‘Operative Linkages’ ; Counterterrorism: A Public Goods Approach ; Linguistic Assimilation and Ethno-religious Conflict ; International Carbon Trade and National Taxes: Distributional Impacts of Double Regulation ; Thinking Local but Acting Global? The Interplay Between Local and Global Internalization of Externalities ; Showdown in Schönau: A Contest Case Study

Note: Contents ISOLA Code for Multiple-Point Source Modeling—Review / Jiří Zahradník and Efthimios Sokos Seismic Moment Tensors in Anisotropic Media: A Review / Václav Vavryčuk The Frequency-Domain Moment-Tensor Inversion: Retrieving the Complete Source Moment-Tensor Spectra and Time Histories / Xiaoning Yang, Brian W. Stump and Mason D. Macphail Berkeley Seismic Moment Tensor Method, Uncertainty Analysis, and Study of Non-double-couple Seismic Events / Douglas S. Dreger Estimating Stability and Resolution of Waveform Inversion Focal Mechanisms / S. Scolaro, C. Totaro, D. Presti, Sebastiano D’Amico, G. Neri and B. Orecchio The Method of Cataclastic Analysis of Discontinuous Displacements / Yu. L. Rebetsky and A. Yu. Polets Challenges in Regional Moment Tensor Resolution and Interpretation / Simone Cesca and Sebastian Heimann The Role of Moment Tensors in the Characterization of Hydraulic Stimulations / Ismael Vera Rodriguez, James Rutledge and Sergey Stanchits Constrained Moment Tensors: Source Models and Case Studies / Jan Šílený Seismic Deformation Derived from Moment Tensor Summation: Application Along the Hellenic Trench / Anastasia Kiratzi, Christoforos Benetatos and Filippos Vallianatos Estimation of Empirical Green’s Tensor Spatial Derivative Elements: A Preliminary Study Using Strong Motion Records in Southern Fukui Prefecture, Japan / Michihiro Ohori Retrieval of the Seismic Moment Tensor from Joint Measurements of Translational and Rotational Ground Motions: Sparse Networks and Single Stations / Stefanie Donner, Heiner Igel, Céline Hadziioannou and the Romy group Overview of Moment Tensor Analysis in New Zealand / John Ristau Applications of Moment Tensor Solutions to the Assessment of Earthquake Hazard in Canada / J. F. Cassidy, H. Kao, John Ristau and A. Bent Intraplate Earthquakes in Europe—Source Parameters from Regional Moment Tensor Analysis / Jochen Braunmiller Source Characteristics of the January 8, 2013 (M W = 5.7) and May 24, 2014 (M W = 6.8) North Aegean Earthquakes Sequence / Doğan Kalafat, Kıvanç Kekovalı and Ali Pınar Investigating the Focal Mechanisms of the August 4th, 2003, Mw 7.6, South Orkney Islands Earthquake and its Aftershocks Sequence / M. P. Plasencia Linares, M. Guidarelli, M. Russi and G. F. Panza Waveform Modelling of 2009 Bhutan Earthquake of Magnitude 6.1 (Mw) Using Local Network Data of North East India / Santanu Baruah and Midusmita Boruah Resolving the Tectonic Stress by the Inversion of Earthquake Focal Mechanisms. Application in the Region of Greece. A Tutorial / Ioannis G. Kassaras and Vasilis Kapetanidis Relative Locations of Clustered Earthquakes in the Sea of Marmara and States of Local Stresses in the East of the Central Marmara Basin / Yasemin Korkusuz Öztürk and Nurcan Meral Özel Focal Mechanisms of Earthquakes and Stress Field of the Earth Crust in Azerbaijan / G. J. Yetirmishli and S. E. Kazimova Seismotectonic Crustal Strains of the Mongol-Baikal Seismic Belt from Seismological Data / Alena Seredkina and Valentina Melnikova The Stress State of Seismic Areas of the Central and East Asia / Yu. L. Rebetsky, A. Yu. Polets, O. A. Kuchay and N. A. Sycheva The Significance of Crustal Velocity Model in Moment Tensor Solutions: A Case Study of Yedisu Earthquakes / Fatih Turhan, Musavver Didem Cambaz and Jiří Zahradník An Overview of the Seismicity and Tectonics of the Black Sea / Doğan Kalafat Coulomb Stress Changes in the Area of December 2013–January 2014 Sannio-Matese Seismic Sequence (Southern Italy) / Santanu Baruah and Sebastiano D’Amico Active Faulting in the Earth’s Crust of the Baikal Rift System Based on the Earthquake Focal Mechanisms / Vladimir A. Sankov and Anna A. Dobrynina Quaternary Stress Field and Faulting in the Western Part of the Catanzaro Trough (Calabria, Southern Italy) / F. Brutto, F. Muto, M. F. Loreto, Sebastiano D’Amico, N. De Paola, V. Tripodi and S. Critelli A Seismogenic Zone Model for Seismic Hazard Studies in Northwestern Africa / J. A. Peláez, J. Henares, M. Hamdache and C. Sanz de Galdeano A Trial Modeling of Perturbed Repeating Earthquakes Combined by Mathematical Statics, Numerical Modeling and Seismological Observations / Keisuke Ariyoshi, Shunichi Nomura, Naoki Uchida and Toshihiro Igarashi Getting Started with GMT: An Introduction for Seismologists / Matthew R. Agius Devices for a Rotational Ground Motion Measurement / Leszek R. Jaroszewicz and Anna Kurzych

Note: Contents Part I Regional Initiatives 1 South/Southeast Asia Research Initiative (SARI): A Response to Regional Needs in Land Cover/Land Use Change Science and Education / Krishna Prasad Vadrevu 2 SERVIR: Connecting Earth Observation Satellite Data to Local Science Applications / Africa Flores, Dauna S. Coulter, Ashutosh S. Limaye, and Daniel Irwin Part II Biomass Burning, Air Pollution and Impacts 3 Emission of Toxic Air Pollutants and Greenhouse Gases from Crop Residue Open Burning in Southeast Asia / Nguyen Thi Kim Oanh, Didin Agustian Permadi, Nguyen Phan Dong, and Dang Anh Nguyet 4 Impacts of Biomass Burning Emissions on Tropospheric NO2 Vertical Column Density over Continental Southeast Asia / Syuichi Itahashi, Itsushi Uno, Hitoshi Irie, Jun-Ichi Kurokawa, and Toshimasa Ohara 5 Observations of Asian Dust and Agricultural Fire Smoke Episodes: Transport and Impacts on Regional Air Quality in Southeast China / Yonghua Wu, Yong Han, and Tijian Wang 6 Spatio-Temporal Analysis of Land and Forest Fires in Indonesia Using MODIS Active Fire Dataset / Israr Albar, I. Nengah Surati Jaya, Bambang Hero Saharjo, Budi Kuncahyo, and Krishna Prasad Vadrevu 7 Severe Air Pollution Due to Peat Fires During 2015 Super El Niño in Central Kalimantan, Indonesia / Hiroshi Hayasaka and Alpon Sepriando 8 Forest and Land Fires in Riau Province: A Case Study in Fire Prevention Policy Implementation with Local Concession Holders / Bambang Hero Saharjo and Alex Yungan 9 Biomass Burning Emissions Variation from Satellite-Derived Land Cover, Burned Area, and Emission Factors in Vietnam / Kristofer Lasko and Krishna Prasad Vadrevu 10 Enhancement of Fire Early Warning System in Vietnam Using Spatial Data and Assimilation / Ba Tung Nguyen, Khac Phong Do, Nguyen Le Tran, Quang Hung Bui, Thi Nhat Thanh Nguyen, Van Quynh Vuong, and Thanh Ha Le 11 Greenhouse Gas Budget of Terrestrial Ecosystems in Monsoon Asia: A Process-Based Model Study for the Period 1901–2014 / Akihiko Ito and Motoko Inatomi 12 Simulations of Emissions, Air Quality, and Climate Contribution in Southeast Asia for March and December / Teerachai Amnuaylojaroen, Mary C. Barth, Gabriele Pfister, and Cindy Bruyere 13 Study of Lower Tropospheric Ozone over Central and Eastern China: Comparison of Satellite Observation with Model Simulation / Sachiko Hayashida, Satoko Kayaba, Makoto Deushi, Kazuyo Yamaji, Akiko Ono, Mizuo Kajino, Tsuyoshi Thomas Sekiyama, Takashi Maki, and Xiong Liu 14 Multi-scale Simulations of Atmospheric Pollutants Using a Non-hydrostatic Icosahedral Atmospheric Model / Daisuke Goto, Teruyuki Nakajima, Dai Tie, Hisashi Yashiro, Yousuke Sato, Kentaroh Suzuki, Junya Uchida, Shota Misawa, Ryoma Yonemoto, Tran Thi Ngoc Trieu, Hirofumi Tomita, and Masaki Satoh 15 Project MANTRA: Multi-platform ANalysis of TRace Gases and Aerosols with a Focus on Atmospheric CO2 Measurements for Southeast Asia / Ronald C. Macatangay 16 Dry Deposition of Reactive Nitrogen Species in Tropics / Reema Tiwari and Umesh Kulshrestha Part III Aerosol Pollution 17 Aerosols and Climate Change: Present Understanding, Challenges, and Future Outlook / S. Ramachandran 18 Organic Aerosols in South and East Asia: Composition and Sources / Chandra Mouli Pavuluri and Kimitaka Kawamura 19 Shortwave Radiation, Climate Change, and Anthropogenic Aerosols in China / Tadahiro Hayasaka 20 Conceptualizing How Severe Haze Events Are Impacting Long-Term Satellite-Based Trend Studies of Aerosol Optical Thickness over Asia / Zhao Yang Zhang, Man Sing Wong, and James R. Campbell 21 Aerosol Properties over Kuching, Sarawak from Satellite and Ground- Based Measurements / Arnis Asmat, Khairunnisa Abdul Jalal, and Siti Noratiqah Mohd Deros 22 Investigating the Aerosol Type and Spatial Distribution During Winter Fog Conditions over Indo-Gangetic Plains / Muhammad Fahim Khokhar and Naila Yasmin 23 Satellite Aerosol Optical Depth over Vietnam - An Analysis from VIIRS and CALIOP Aerosol Products / Vinh T. Tran, Ha V. Pham, Thanh T. N. Nguyen, Thanh X. Pham, Quang Hung Bui, Anh X. Nguyen, and Thuy T. Nguyen 24 Satellite Remote Sensing of Aerosols and Gaseous Pollution over Pakistan / Salman Tariq and Zia Ul-Haq Part IV Land Use/Cover Change and Impacts 25 The Impact of Land Cover and Land Use Change on the Indian Monsoon Region Hydroclimate / Dev Niyogi, Subashini Subramanian, U. C. Mohanty, C. M. Kishtawal, Subimal Ghosh, U. S. Nair, M. Ek, and M. Rajeevan 26 Decadal Land-Cover Changes in China and Their Impacts on the Atmospheric Environment / Mengmeng Li and Yu Song 27 Analyzing the Influence of Urban Growth on Thermal Environment Through Demographic, Environmental, and Physical Parameters in Bangladesh / Yogesh Kant, Saiful Azim, and Debashis Mitra 28 Ecosystem Carbon Stock, Atmosphere, and Food Security in Slash-and-Burn Land Use: A Geospatial Study in Mountainous Region of Laos / Yoshio Inoue 29 Spatial Modeling of Land Cover/Land Use Change and Its Effects on Hydrology Within the Lower Mekong Basin / Kel N. Markert, Robert E. Griffin, Ashutosh S. Limaye, and Richard T. McNider 30 Land–Atmosphere Interactions in South Asia: A Regional Earth Systems Perspective / Venkataramana Sridhar and Prasanth Valayamkunnath Erratum Index

Note: Contents 1 Introduction 1.1 Why Numerical Ecology? 1.2 Why R? 1.3 Readership and Structure of the Book 1.4 How to Use This Book 1.5 The Data Sets 1.5.1 The Doubs Fish Data 1.5.2 The Oribatid Mite Data 1.6 A Quick Reminder About Help Sources 1.7 Now It Is Time 2 Exploratory Data Analysis 2.1 Objectives 2.2 Data Exploration 2.2.1 Data Extraction 2.2.2 Species Data: First Contact 2.2.3 Species Data: A Closer Look 2.2.4 Ecological Data Transformation 2.2.5 Environmental Data 2.3 Conclusion 3 Association Measures and Matrices 3.1 Objectives 3.2 The Main Categories of Association Measures (Short Overview) 3.2.1 Q Mode and R Mode 3.2.2 Symmetrical or Asymmetrical Coefficients in Q Mode: The Double-Zero Problem 3.2.3 Association Measures for Qualitative or Quantitative Data 3.2.4 To Summarize 3.3 Q Mode: Computing Dissimilarity Matrices Among Objects 3.3.1 Q Mode: Quantitative Species Data 3.3.2 Q Mode: Binary (Presence-Absence) Species Data 3.3.3 Q Mode: Quantitative Data (Excluding Species Abundances) 3.3.4 Q Mode: Binary Data (Excluding Species Presence-Absence Data) 3.3.5 Q Mode: Mixed Types Including Categorical (Qualitative Multiclass) Variables 3.4 R Mode: Computing Dependence Matrices Among Variables 3.4.1 R Mode: Species Abundance Data 3.4.2 R Mode: Species Presence-Absence Data 3.4.3 R Mode: Quantitative and Ordinal Data (Other than Species Abundances) 3.4.4 R Mode: Binary Data (Other than Species Abundance Data) 3.5 Pre-transformations for Species Data 3.6 Conclusion 4 Cluster Analysis 4.1 Objectives 4.2 Clustering Overview 4.3 Hierarchical Clustering Based on Links 4.3.1 Single Linkage Agglomerative Clustering 4.3.2 Complete Linkage Agglomerative Clustering 4.4 Average Agglomerative Clustering 4.5 Ward's Minimum Variance Clustering 4.6 Flexible Clustering 4.7 Interpreting and Comparing Hierarchical Clustering Results 4.7.1 Introduction 4.7.2 Cophenetic Correlation 4.7.3 Looking for Inteipretable Clusters 4.8 Non-hierarchical Clustering 4.8.1 k-means Partitioning 4.8.2 Partitioning Around Medoids (PAM) 4.9 Comparison with Environmental Data 4.9.1 Comparing a Typology with External Data (ANOVA Approach) 4.9.2 Comparing Two Typologies (Contingency Table Approach) 4.10 Species Assemblages 4.10.1 Simple Statistics on Group Contents 4.10.2 Kendall's W Coefficient of Concordance 4.10.3 Species Assemblages in Presence-Absence Data 4.10.4 Species Co-occurrence Network 4.11 Indicator Species 4.11.1 Introduction 4.11.2 IndVal: Species Indicator Values 4.11.3 Correlation-Type Indices 4.12 Multivariate Regression Trees (MRT): Constrained Clustering 4.12.1 Introduction 4.12.2 Computation (Principle) 4.12.3 Application Using Packages mvpart and MVPARTwrap 4.12.4 Combining MRT and IndVal 4.13 MRT as a Monothetic Clustering Method 4.14 Sequential Clustering 4.15 A Very Different Approach: Fuzzy Clustering 4.15.1 Fuzzy c-means Using Package cluster's Function fanny () 4.15.2 Noise Clustering Using the vegclust () Function 4.16 Conclusion 5 Unconstrained Ordination 5.1 Objectives 5.2 Ordination Overview 5.2.1 Multidimensional Space 5.2.2 Ordination in Reduced Space 5.3 Principal Component Analysis (PCA) 5.3.1 Overview 5.3.2 PCA of the Environmental Variables of the Doubs River Data Using rda () 5.3.3 PCA on Transformed Species Data 5.3.4 Domain of Application of PCA 5.3.5 PCA Using Function PCA. newr () 5.3.6 Imputation of Missing Values in PCA 5.4 Correspondence Analysis (CA) 5.4.1 Introduction 5.4.2 CA Using Function cca () of Package vegan 5.4.3 CA Using Function CA. newr () 5.4.4 Arch Effect and Detrended Correspondence Analysis (DCA) 5.4.5 Multiple Correspondence Analysis (MCA) 5.5 Principal Coordinate Analysis (PCoA) 5.5.1 Introduction 5.5.2 Application of PCoA to the Doubs Data Set Using cmdscaleO and vegan 5.5.3 Application of PCoA to the Doubs Data Set Using pcoa () 5.6 Nonmetric Multidimensional Scaling (NMDS) 5.6.1 Introduction 5.6.2 Application to the Doubs Fish Data 5.6.3 PCoA or NMDS? 5.7 Hand-Written PCA Ordination Function 6 Canonical Ordination 6.1 Objectives 6.2 Canonical Ordination Overview 6.3 Redundancy Analysis (RDA) 6.3.1 Introduction 6.3.2 RDA of the Doubs River Data 6.3.3 Distance-Based Redundancy Analysis (db-RDA) 6.3.4 A Hand-Written RDA Function 6.4 Canonical Correspondence Analysis (CCA) 6.4.1 Introduction 6.4.2 CCA of the Doubs River Data 6.5 Linear Discriminant Analysis (LDA) 6.5.1 Introduction 6.5.2 Discriminant Analysis Using Ida () 6.6 Other Asymmetric Analyses 6.6.1 Principal Response Curves (PRC) 6.6.2 Co-correspondence Analysis (CoCA) 6.7 Symmetric Analysis of Two (or More) Data Sets 6.8 Canonical Correlation Analysis (CCorA) 6.8.1 Introduction 6.8.2 Canonical Correlation Analysis Using CCorA () 6.9 Co-inertia Analysis (CoIA) 6.9.1 Introduction 6.9.2 Co-inertia Analysis Using Function coinertia () of ade4 6.10 Multiple Factor Analysis (MFA) 6.10.1 Introduction 6.10.2 Multiple Factor Analysis Using FactoMineR 6.11 Relating Species Traits and Environment 6.11.1 The Fourth-Corner Method 6.11.2 RLQ Analysis 6.11.3 Application in R 6.12 Conclusion 7 Spatial Analysis of Ecological Data 7.1 Objectives 7.2 Spatial Structures and Spatial Analysis: A Short Overview 7.2.1 Introduction 7.2.2 Induced Spatial Dependence and Spatial Autocorrelation 7.2.3 Spatial Scale 7.2.4 Spatial Heterogeneity 7.2.5 Spatial Correlation or Autocorrelation Functions and Spatial Correlograms 7.2.6 Testing for the Presence of Spatial Correlation: Conditions 7.2.7 Modelling Spatial Structures 7.3 Multivariate Trend-Surface Analysis 7.3.1 Introduction 7.3.2 Trend-Surface Analysis in Practice 7.4 Eigenvector-Based Spatial Variables and Spatial Modelling 7.4.1 Introduction 7.4.2 Distance-Based Moran's Eigenvector Maps (dbMEM) and Principal Coordinates of Neighbour Matrices (PCNM) 7.4.3 MEM in a Wider Context: Weights Other than Geographic Distances 7.4.4 MEM with Positive or Negative Spatial Correlation: Which Ones should Be Used? 7.4.5 Asymmetric Eigenvector Maps (AEM): When Directionality Matters 7.5 Another Way to Look at Spatial Structures: Multiscale Ordination (MSO) 7.5.1 Principle 7.5.2 Application to the Mite Data - Exploratory Approach 7.5.3 Application to the Detrended Mite and Environmental Data 7.6 Space-Time Interaction Test in Multivariate ANOVA, Without Replicates 7.6.1 Introduction 7.6.2 Testing the Space-Time Interaction with the sti Functions 7.7 Conclusion 8 Community Diversity 8.1 Objectives 8.2 The Multiple Facets of Diversity 8.2.1 Introduction 8.2.2 Species Diversity Measured by a Single Number 8.2.3 Taxonomic Diversity Indices in Practice 8.3 When Space Matters: Alpha, Beta and Gamma Diversities 8.4 Beta Diversity 8.4.1 Beta Diversity Measured by a Single Number 8.4.2 Beta Diversity as the Variance of the Community Composition Table: SCBD and LCBD Indices 8.4.3 Partitioning Beta Diversity into Replacement, Richness Difference and Nestedness Components 8.5 Functional Diversity, Functional Composition and Phylogenetic Diversity of Communities 8.5.1 Alpha Functional Diversity 8.5.2 Beta Taxonomic, Phylogenetic and Functional Diversities 8.6 Conclusion Bibliography Index

Note: Contents 1 Curves, Maps and Hotspots: The Diversity and Distribution of Araneomorph Spiders in the Neotropics / Adalberto J. Santos, Antonio D. Brescovit, Márcia de Oliveira-Tomasi, Philip Russo, and Ubirajara Oliveira 2 Behavior and Biology of Mygalomorphae / Fernando Pérez-Miles and Carlos Perafán 3 Neotropical Arachnological Collections: Basic Tools for the Development of Spider Research / Antonio D. Brescovit, Oscar Francke, Álvaro Laborda, Griselda Montiel Parra, Cristina Scioscia, Miguel Simó, and Carlos Víquez Núñez 4 Habitat Selection and Dispersal / Dinesh Rao 5 Dispersal Strategies, Genetic Diversity, and Distribution of Two Wolf Spiders (Araneae, Lycosidae): Potential Bio-Indicators of Ecosystem Health of Coastal Dune Habitats of South America / Leticia Bidegaray-Batista, Miquel Arnedo, Ana Carlozzi, Carolina Jorge, Patricio Pliscoff, Rodrigo Postiglioni, Miguel Simó, and Anita Aisenberg 6 Webs: Diversity, Structure and Function / Sean J. Blamires, Shichang Zhang, and I-Min Tso 7 Spider–Plant Interactions: An Ecological Approach / João Vasconcellos-Neto, Yuri Fanchini Messas, Hebert da Silva Souza, German Antonio Villanueva-Bonila, and Gustavo Quevedo Romero 8 Spiders as Plant Partners: Complementing Ant Services to Plants with Extrafloral Nectaries / Kleber Del-Claro, Vanessa Stefani, Larissa Nahas, and Helena Maura Torezan-Silingardi 9 Foraging Strategies of Cursorial and Ambush Spiders / Rodrigo H. Willemart and Mariángeles Lacava 10 Trophic Niches and Trophic Adaptations of Prey-Specialized Spiders from the Neotropics: A Guide / Stano Pekár, Luis Fernando García, and Carmen Viera 11 Spiders Associated with Agroecosystems: Roles and Perspectives / Marco Antonio Benamú, Mariángeles Lacava, Luis Fernando García, Martín Santana, and Carmen Viera 12 Sexual Selection in Neotropical Spiders: Examples from Selected Groups / Luiz Ernesto Costa-Schmidt, María José Albo, Fedra Bollatti, Franco Cargnelutti, Lucía Calbacho-Rosa, Sofía Copperi, Nelson Ferretti, Matías Izquierdo, and Alfredo V. Peretti 13 Parental Care and Sociality / Carmen Viera and Ingi Agnarsson 14 Plasticity and Cognition in Spiders / Hilton F. Japyassú 15 Anti-Predator Strategies / Felipe M. Gawryszewski 16 Host Behavioural Manipulation of Spiders by Ichneumonid Wasps / Marcelo O. Gonzaga, Thiago G. Kloss, and Jober F. Sobczak

Note: Contents 1 General Chemical Concepts Introduction Periodic Table and Element Groups Chemical Bonding Chemical Reactions, Stoichiometry, and Kinetics Equilibrium, Steady-State, and Residence Time General Concepts of Organic Chemistry Aqueous Solubility and Polarity Diffusion and Osmotic Potential Freezing Exclusion and Concentration of Solutes Defining Dissolved and Particulate Phases SI Units and Concentrations Ionic Charge Balance Stable Isotope Chemistry 2 Soil Biogeochemistry Introduction Soil Formation and Pedogenesis Soil Classification Soil Texture and Coarse Fragments Soil Moisture Mineralogy Physical-Chemical Features of Clays and Other Soil Colloids Clay Colloids Humic Colloids Chemical Processes in Soils Ion Exchange and Adsorption in Soils Soil Ion Exchange Chemistry and Base Saturation Acidification Complexation Leaching Dissolution and Precipitation Reactions Comparative Analysis of Soil Chemical Properties Soil Exchange Chemistry Soil Distributions of Aluminum Vertical Distributions of Organic Carbon, Nitrogen, and Phosphorus in Soils Forms of Organic Nitrogen in Soils Patterns of Soil Solution Chemistry Integrated Processes of Nutrient Supply and Storage in Soils 3 Microbial Biogeochemistry Introduction Redox Conditions Microbial Nitrogen Transformations Nitrogen Fixation Mineralization or Ammonification Nitrogen Immobilization Nitrification Denitrification Dissimilatory Nitrate Reduction to Ammonium (DNRA) Assimilatory Nitrate Reduction Microbial Sulfur Transformations Mineralization of Organic Sulfur Anaerobic Dissimilatory Sulfate Reduction Assimilatory Sulfate Reduction Microbial Carbon Transformations Fermentation Methane Production Organic Acid Synthesis by Microbes Microbial Processes that Contribute to Bioremediation or Metal Transformations 4 Plant Biogeochemistry Introduction General Plant Chemistry Plant Functional Morphology and Growth Allocation Aboveground Structure and Function Belowground Structure and Function of the Root System Growth Allocation and Root:Shoot Relationships Carbon Fixation, Metabolism, and Plant Production Photosynthesis and Nutrients Photosynthesis and Water Respiration and Metabolism Exchange of Carbon Dioxide in a Forest Ecosystem Energy Budgets and Primary Production Whole-Plant Carbon Cycling and Allocation Metabolic Allocation to Plant Defense Plant Nutrient Cycling Plant Nutrient Absorption Implications of Nutrient Uptake for Acid-Base Chemistry Plant Transport or Translocation of Nutrients Plant Nutrient Resorption Detrital Cycling of Plant Nutrients Plant Canopy Processes Affecting Element Cycling NUE as an Index of Plant Nutrition and Nutrient Cycling Nutrient Limitation Effects of Chemical Stress on Plants Effects of Acidic Deposition on Plant Membrane-Bound Calcium Aluminum Antagonism and Toxicity Stress Plant Responses to Ozone Stress 5 Cycling of Organic Matter Introduction Ecosystem Perspective Storage of Organic Matter in Forest Soils, Biomass, and Woody Debris Soil Organic Matter and Soil Carbon Storage Forest Floor Storage Turnover Rates and Age of Soil Organic Matter Reservoirs Influence of Land Management and Disturbance on SOM Aboveground and Belowground Biomass Coarse Woody Debris Transfers of Organic Matter in Detritus and Solution Aboveground Litterfall Belowground Detrital Inputs From Root Mortality and Turnover Solution Transfers of DOM Decomposition of Organic Matter General Processes of Decomposition Wood Decay Processes Decomposition Rates and Decay Constants Element Cycling Patterns in Decaying Organic Matter Substrate Controls on Decomposition Environmental Controls on Decomposition Biological Influences on Decomposition Transfers of CO2 in the Organic Matter Budget of a Forest Ecosystem 6 Atmospheric Deposition Introduction Atmospheric Chemistry Deposition Processes and Patterns Atmospheric Emissions and Deposition of Sulfur and Nitrogen Measurement and Analysis of Atmospheric Deposition Wet Deposition Dry Deposition Analysis of Precipitation Chemistry Environmental Patterns of Precipitation Chemistry and Atmospheric Deposition Daily Patterns Monthly Patterns Multi-year Trends in Precipitation Chemistry Long-Term Historical Trends in Atmospheric Deposition of Mercury Spatial Patterns: Deposition in North America Spatial Patterns: Influence of Vegetation and Canopy Structure on Atmospheric Deposition Spatial Patterns: Comparison of Atmospheric Deposition at Different Forest Sites Modeling Atmospheric Deposition Patterns A Case Study of Deposition Inputs to a Forest Ecosystem 7 Mineral Weathering Introduction Ecosystem Context Mineral Weathering Processes Heterogeneous Mineral Weathering at Different Scales Controls on Mineral Weathering Rates Mineralogical Controls Influence of Acidity and Complexing Ligands on Weathering Rates Experimental Effects of Acidity on Weathering Rates Physical Influences on Weathering Rates Biotic Influences on Mineral Weathering Rates Influence of Mineral Dissolution on the Solution Chemistry of Natural Waters Genesis and Weathering of Clays Methods of Estimating Weathering Contributions to Ecosystem Element Budgets Mass Balance Estimation Element Tracers as Indicators of Weathering Rates Weathering Estimation with Mineral Depletion Techniques Comparison of Weathering Estimates Comparison of Weathering in Different Ecosystems 8 Watershed Hydrology Ecosystem and Landscape Perspectives Influence of Geology and Soils on Storage and Movement of Water Soil Hydrologic Properties Water Movement and Streamflow Generation in a Watershed Inferring Stream Hydrology from Stream Chemistry in Small Watersheds Water Balance of a Watershed Ecosystem Measurement Techniques for Ecosystem Water Budgets Components of a Water Budget: Precipitation Inputs Components of a Water Budget: Evapotranspiration (ET) Components of a Water Budget: Hydrologic Storage Components of a Water Budget: Stream Runoff Integrated Analysis of a Water Budget 9 Aqueous Chemistry Introduction An Example of Soil Solution Chemistry: Analysis and Interpretation General Concepts of Aqueous Chemistry Sample Collection and Analysis Selection of Analytical Parameters Alkalinity or Acid Neutralizing Capacity (ANC) Acidity and pH Conductivity Ionic Strength and Ion Activity Influence of Temperature on Solution Equilibria Hydrolysis and Chemical Speciation as a Function of pH Rate-Limited Versus Equilibrium Conditions Differential Anion Mobility Effects of Ecosystem Processes on Solution Chemistry Case Studies: Analysis and Interpretation of Aqueous Chemistry in Natural Waters Controls on the Chemistry of Forest Floor Leachates Comparison of Stream Chemistry Along a Hydrologic Flow Gradient Changes in Solution Chemistry and ANC Generation Along a Watershed Drainage Gradient Effects of Land Use on Watershed Exports of Nutrients in Stream Runoff 10 Integrated Element Cycling Introduction General Concepts of Element Cycling Terminology Comparison of Element Cycles in Terrestrial Ecosystems Nitrogen Cycle Calcium Cycle Aluminum Cycle Nutrient Cycling in Relation to Ecosystem Succession Chemical Input-Output Budgets for Watershed Ecosystems Element Cycling at the Landscape Scale: Exports of N and P from Large Watersheds Element Cycling at the Global Scale Global Nitrogen Cycle Global Carbon Cycle 11 Biogeochemical Models Introduction Considerations in the Development of a Biogeochemical Model Steps in Building a Biogeochemical Model An Introductory Model of Watershed Nitrogen Cycling Applications of Biogeochemical Models TREGRO: A Model to Simulate Plant Responses to Interacting Stresses TEM: A Global Model of Net Primary Productivity The CENTURY Soil Organic Matter Model PnET-BGC: An Integrated Biogeochemical Model Watershed Acidification Models Nutrient Cycling Models Models in Watershed Hydrology 12 Ecosystem Disturbance and Stress Introduction Disturbance and Recovery in the Context of Ecological Succession Effects of Forest Harvesting on Watershed Ecosystems Twenty Years of Recovery Following H