Next Generation Biomonitoring: Part 1

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NEXT GENERATION BIOMONITORING: Part 1, Volume 58, the latest release in the Advances in Ecological Research series, is the firstpart of a thematic on ecological biomonitoring, including specific chapters that cover Aquatic volatile metabolomics – using trace gases to examine ecological processes, Next generation approaches to rapid monitoring Bio-aerosol and the link between human health and environmental microbiology, NGB in Canadian wetlands, Monitoring the biodiversity and functioning of terrestrial systems via high resolution trace gas fluxes, and Computational approaches to gathering biomonitoring data from social media platforms: a superior solution to next generation biomonitoring challenges. Front Cover Next Generation Biomonitoring: Part 1 Copyright Contents Contributors Preface Acknowledgements Chapter One: Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis 1. Introduction 2. How Are Ecological Networks Useful for Biomonitoring? 2.1. Traditional Biomonitoring Is Typically Descriptive and Rarely Provides an Understanding of the Underlying Mechanisms ... 2.2. Ecological Networks Provide a Framework to Describe and Monitor Ecological Processes and Ecosystem Functions 2.3. Ecological Network Structure Characterizes Ecosystem Properties 2.4. Knowledge of Ecological Networks Helps to Assess the Effect(s) of Environmental Changes on Ecosystem Processes and A ... 2.5. The Robustness of Networks of Ecological Networks: Applications for Understanding Species and Habitat Loss, Restorat ... 3. Ecological Networks Can Be Challenging to Build Using Conventional Approaches 4. Combining NGS With ENA: Opportunities and Challenges 4.1. Using NGS to Construct Ecological Networks 4.2. PCR Bias and Abundance Estimation in NGS Community Analyses 4.3. NGS Without a Prior PCR Step 4.4. Detection of Species Interactions Using Molecular Tools 4.5. How to Deal With Interactions Not Directly Resolved by NGS: Are Species Association Networks Species Interaction Net ... 5. Machine Learning as a Way to Rapidly Build Molecular Ecological Networks in a Rapid and Reliable Way? 5.1. Learning Ecological Networks From Data 5.2. Exploiting eDNA-Derived Information as a Source for Network Data 6. NGS Network Data Sharing 6.1. The Importance of a Dedicated NGS Network Database: Linking DNA Sequences and Ecological Interactions to Limit Speci ... 6.2. Reconstructing Ecological Networks With Different Predicting Methods of Species Interactions 6.3. Do Only Sequences and Species Interactions/Cooccurrences Matter in a NGS Network Database? 6.4. An Example Output From a NGS Network Database: Phylogenetically Structured Networks 6.5. Improving Network Ecology Research With a NGS Network Database 7. Conclusion: Towards the Construction of Multilayer Networks in Ecology Using NGS 7.1. Towards Larger, Highly Resolved Networks 7.2. NGS Networks to Link Above- and Belowground Ecosystems, as Well as Eukaryotes and Prokaryotes 7.3. Biomonitoring of Ecosystems With Multilayer Phylogenetically Structured Networks Acknowledgements Glossary References Further Reading Chapter Two: Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomo ... 1. State and Fate of Aquatic Ecosystems 2. Advancement of Aquatic Biomonitoring With a Focus on Europe 3. A DNA-Based Next Generation of Aquatic Biomonitoring? 3.1. Revolutions in Sequencing Technology Drive Academic Progress 3.2. Metabarcoding and Other Genetic Approaches for Bioassessment 4. The Grand Challenges for Next-Generation Aquatic Biomonitoring 4.1. Genetic Data Cannot Deliver All Information Required by Legislation 4.2. Adjusting the Reference Conditions 4.3. Stressor-Biodiversity Relationships 4.4. Technological Progress Hampers Continuity and Demands Standardisation 4.5. Costs and Accessibility: A Janus-Headed Debate? 4.6. The Importance of Transdisciplinary Dialogue 5. The Aim of DNAqua-Net 5.1. Networks Among Countries, Across Generations and Disciplines 6. Next-Generation Biomonitoring Opens New Doors Acknowledgements References Chapter Three: Advances in Monitoring and Modelling Climate at Ecologically Relevant Scales 1. Introduction 2. Factors Leading to Variable Microclimates 2.1. Microclimatic Processes 2.1.1. Solar Radiation 2.1.2. Latent-Heat Flux 2.1.3. Sensible Heat Flux (Heat Convection) 2.1.4. Heat Conduction 2.2. Mesoclimatic Processes 2.3. Fine-Scale Variation in Water Availability 3. Organisms and Their Environment 3.1. Individuals and Microclimate 4. Measuring Microclimates 4.1. Measuring Microclimate In Situ 4.1.1. Temperature 4.1.1.1. Operative Temperature Models 4.1.2. Humidity 4.1.3. Radiation 4.1.4. Visible Light and PAR 4.1.5. Wind 4.1.6. Soil Moisture 4.1.7. Ground Truthing and Sensor Calibration 4.1.8. Sampling Design 4.2. Ex Situ Sensing of Microclimate 4.2.1. Remote Sensing of Microclimate Variables 4.2.2. Remote Sensing of Proxy Variables 5. Modelling Microclimates 5.1. Why Model Microclimates? 5.2. Statistical Models 5.3. Mechanistic Models 6. Looking to the Future of Microclimate Ecology 7. Conclusions References Further Reading Chapter Four: Challenges With Inferring How Land-Use Affects Terrestrial Biodiversity: Study Design, Time, Space and Synt ... 1. Introduction 2. Designs of Studies for Assessing Biotic Impacts of Land-Use Change 2.1. Control-Impact (Also Known as Space-for-Time Substitution) 2.2. Extensions of Control-Impact: Chronosequences, After-Control-Impact and Reference-After 2.3. Before-After and After 2.4. Before-After Control-Impact 2.5. Time Series Designs 3. Sampling Considerations 3.1. `Time-for-Time Substitution: Comparability Between Sampling Events 3.2. `Space-for-Time Substitution: Comparability vs Independence 3.3. `Space-for-Space Substitution: Representativeness of Sites 3.4. Replication and Comparability 3.5. Scale 4. Manipulative vs Correlational Approaches 5. Challenges for Syntheses 5.1. Literature Bias: Realms, Regions and Research Fields 5.2. Different Study Designs Can Give Different Results 6. Methods for Syntheses 7. Research Priorities 8. Conclusions Acknowledgements Glossary References Further Reading Chapter Five: Modelling and Projecting the Response of Local Terrestrial Biodiversity Worldwide to Land Use and Related P ... 1. Introduction: Predicts Scientific and Science-Policy Objectives 2. Key Design Decisions and Methods 2.1. Aiming to Collate a Taxonomically and Geographically Representative, Large Database 2.2. Focus on Site-Level Diversity Data 2.3. The Space-for-Time Gambit 2.4. Collating Raw Data Rather Than Results-Based Meta-Analysis 2.5. Land-Use Classes Chosen to Facilitate Global Spatial and Temporal Projections 3. Modelling Considerations 3.1. General Challenges 3.2. Modelling Species-Level Response Variables: oi, ai, and LRRi 3.3. Modelling Site-Level Response Variables: ɑt, ɑp, and ɑf 3.4. Modelling Among-Site Response Variables: βt, βp, and βf 4. Summary of Findings 4.1. Local (ɑ) Diversity 4.2. Spatial Turnover in Assemblage Composition (β Diversity) 4.3. Ecological Characteristics and Land Use 4.4. Policy-Relevant Results 5. Synthesis and Prospects Acknowledgements References Chapter Six: Mapping Mediterranean Wetlands With Remote Sensing: A Good-Looking Map Is Not Always a Good Map 1. Introduction: The Challenges of Monitoring Wetlands Status and Trends With Remote Sensing (RS) Data 1.1. Characteristic 1: Wetland Habitats and Surface Water Dynamics 1.2. Characteristic 2: Artificial vs Natural Wetland Habitats and Their Relevance for Biodiversity 1.3. Characteristic 3: Strong Inter- and Intraannual Variability 2. Delineation and Separation of Habitat Types 2.1. Wetland Habitat Nomenclature 2.2. Quality Images 2.3. Procedures for Interpreting Habitat Classes 2.4. Validation Procedures 2.5. Concluding Remarks 3. Mapping the Water Dynamics of Wetlands 3.1. Mapping Inundated or Open Water Areas 3.2. Images Covering the Whole Hydroperiod 3.3. Validation of Flood Regime Maps 3.4. Concluding Remarks 4. Detection of Trends Over Time 4.1. Uncertainty of Detecting Trends 4.2. Detecting Long-Term Changes When Flooding Extent Varies Interannually 4.3. Biodiversity: Changes in Ecosystem Quality 4.4. Concluding Remarks 5. Conclusions Acknowledgements References Advances in Ecological Research Volume 1-58 Cumulative List of Titles Back Cover