Front Cover -- Next Generation Biomonitoring: Part 2 -- Copyright -- Contents -- Contributors -- Preface -- References -- Acknowledgements -- Chapter One: Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencin ... -- 1. Introduction -- 2. Materials and Methods -- 2.1. Mock Communities -- 2.2. Library Preparation for Roche 454 -- 2.3. Library Preparation for Illumina MiSeq -- 2.4. Bioinformatics and Data Analysis -- 2.5. Assigning Taxonomy to OTUs and Dereplicated Sequences -- 3. Results -- 3.1. Sequence and Read Depth -- 3.2. OTU Clustering and the Effect of Singletons -- 3.3. Species Detection -- 3.4. OTU Precision -- 3.5. Impact of Merging and Appending MiSeq Reads on Species Detection and OTU Estimates -- 4. Discussion -- 4.1. Read Depth and Singletons -- 4.2. OTU Clustering -- 4.3. Experimental Design -- 4.4. Implications for Biomonitoring -- 5. Conclusions -- Acknowledgements -- References -- Chapter Two: Linking DNA Metabarcoding and Text Mining to Create Network-Based Biomonitoring Tools: A Case Study on Borea ... -- 1. Introduction -- 1.1. Ecological Networks as Biomonitoring Tools -- 1.2. New Tools to Rapidly Assess Biodiversity and Annotate It With Ecological Information -- 1.3. Freshwater Biodiversity Hotspots as Candidates for Exploring Novel Approaches for Biodiversity Assessment -- 1.4. Exploring the Generation of DNA Ecological Networks for Aquatic Biomonitoring -- 2. Building Heuristic Food Webs for Wetland Biomonitoring: A Case Study -- 2.1. DNA Sample Collection, Metabarcoding, and Bioinformatics Pipeline -- 2.2. Development of Text-Mining Pipeline for Traits of Freshwater Organisms -- 2.3. Evaluation, and Iterative Refinements to Text-Mining Pipeline for Body Size -- 2.4. Rule-Based Procedure for Retrieving Trait Information for Heuristic Food Web Construction.

2.5. Comparing Food Web Properties in Two River Deltas: A Spatiotemporal Comparison -- 3. The Future of Text Mining: New Tools for Rapid Expansion of Food Web Databases and Challenges to Their Widespread Adop ... -- 4. Towards an Open-Source Pipeline for the Rapid Construction and Assessment of Trait-Based Food Webs for Biomonitoring: ... -- 4.1. Advancing Network Approaches for Biomonitoring -- 4.2. The Need for Vastly Expanded Trait Databases -- 4.3. Assessing Uncertainty Within Ecological Networks and Heuristic Food Webs -- 4.4. Assessing the Effectiveness of Heuristic Food Webs at Detecting Environmental Change -- 5. Perspectives: The Future of Biomonitoring -- Acknowledgements -- Appendix -- Glossary -- References -- Further Reading -- Chapter Three: Volatile Biomarkers for Aquatic Ecological Research -- 1. Introduction -- 1.1. Volatilomes: The Volatile Subset of Metabolomes -- 1.2. Volatilomics: Terms and Techniques -- 2. Principal Techniques for Measuring Biogenic Volatiles -- 3. Medical Volatilomics Provides a Blueprint for Ecological Research -- 4. Role of Volatiles in Aquatic Ecological Interactions -- 4.1. Case Study: Volatilomes of Freshwater Phytoplankton -- 5. Application of Volatilomics to Ecological Research: Using Volatilomics to `Direct Environmental Management -- Acknowledgements -- References -- Chapter Four: Noninvasive Analysis of the Soil Microbiome: Biomonitoring Strategies Using the Volatilome, Community Analy ... -- 1. Introduction -- 2. An Overview of the Soil Volatilome -- 2.1. Microbes -- 2.2. Plants -- 2.3. Soils -- 3. Understanding Essex UK Salt Marsh Sediments Through the Volatilome -- 3.1. Methods -- 3.1.1. The Study Sites -- 3.1.2. Sampling the Volatilome and Sediment in the Field -- 3.1.3. Analysing Volatilome and Sediment Samples -- 3.1.4. DNA Extraction and Sequencing.

3.1.5. Microbial Community Sequence Analysis -- 3.1.6. 16S rRNA Analysis -- 3.2. Relationships Between Environment, Microbial Community, and the Volatilome -- 3.2.1. Mud Pan Microbial Communities Across Essex Salt Marshes -- 3.2.2. Environmental Conditions in Sediments Within Essex Salt Marshes -- 3.2.3. The Volatilome Across Essex Salt Marshes -- 3.2.4. Tying Together the Environment, Volatilome, and Microbial Communities -- 4. Conclusion -- Acknowledgements -- References -- Further Reading -- Chapter Five: Using Social Media for Biomonitoring: How Facebook, Twitter, Flickr and Other Social Networking Platforms C ... -- 1. Introduction -- 2. Related Work -- 2.1. Automatic Image Classification -- 2.2. Collecting and Labelling Data With a Crowd -- 2.2.1. Peer Production -- 2.2.2. Microworking -- 2.2.3. Gaming and Games-With-a-Purpose -- 2.2.4. Social Computing and Social Networks -- 3. Examples of Biomonitoring Using Social Networking Platforms -- 3.1. Identifying Species in an Image -- 3.2. Identifying New Species -- 3.3. Requesting Observations of a Species -- 3.4. Coordinating Citizen Science Schemes -- 3.5. Observations of Presence -- 3.6. Proliferation of Changing Nomenclature -- 4. Analysis of Posts About Wildlife on Social Networking Platforms -- 4.1. Data Collection and Preparation -- 4.2. Data Analysis -- 4.2.1. User Workload -- 4.2.2. User Activity -- 4.2.3. Thread Response Time, Lifespan and Activity -- 4.2.4. Task Distribution -- 4.3. Accuracy of Image Labelling -- 4.4. Comparison to Microworking -- 5. Discussion -- 5.1. Data Acquisition and Annotation -- 5.2. User Motivation -- 5.3. Task Difficulty -- 5.4. Social Learning and the Expert in the Crowd -- 5.5. Harnessing Collective Intelligence on Social Networking Platforms -- 5.6. Limitations of a Groupsourcing Approach -- 6. Applications -- 7. Future Directions -- 8. Conclusions.

Acknowledgements -- References -- Chapter Six: A Vision for Global Biodiversity Monitoring With Citizen Science -- 1. Introduction -- 2. Citizen Science for Biodiversity Monitoring -- 2.1. The Definition of Citizen Science -- 2.2. Participatory Monitoring as a Citizen Science Approach -- 2.3. Locally Based, Yet Global, Citizen Science -- 3. The Global Need for Biodiversity Monitoring -- 4. The Global Potential for Biodiversity Monitoring With Citizen Science -- 5. Approaches for Biodiversity Monitoring With Citizen Science: Who, What and How? -- 5.1. Who Are the Potential Volunteers? -- 5.2. How Should Biodiversity Be Recorded? -- 5.3. What Should Be Recorded? -- 5.3.1. Different Variables That Can Be Recorded -- 5.3.2. Species-Level Recording: A Benefit or a Constraint? -- 5.4. How Can Technology Support Recording? -- 5.4.1. Data Collection -- 5.4.2. Making Global Databases From Local Datasets -- 5.4.3. Data Analysis and Feedback to Participants -- 5.5. How Should the Data Be Used to Produce Relevant Outputs? -- 6. Case Studies of Steps Towards Global Biodiversity Monitoring With Citizen Science -- 6.1. Assessing Opportunities for Biodiversity Monitoring in Chile With Citizen Science -- 6.2. eBird: Being Relevant to Local Participants While Global in Ambition -- 6.3. Citizen Science With Semistructured Recording: Kenya Bird Map -- 6.4. Codesign of Monitoring Protocols: New Zealand Environmental Community Groups -- 6.5. Zavamaniry Gasy: Making Recording Accessible Through Investment in Training and Internet Platforms -- 6.6. The Importance of Local Advocates to Support Participants: FreshWater Watch -- 6.7. A Proposal for Global Monitoring of Pollinators With Citizen Science -- 7. Conclusion -- Acknowledgements -- References -- Chapter Seven: A Replicated Network Approach to `Big Data' in Ecology -- 1. Introduction: A Need to Detect Ecosystem Change.

1.1. The Problem: Replication -- 1.2. A Potential Solution: Replicated Networks Through Next-Generation Sequencing -- 2. Historical Perspective on Network Analysis -- 2.1. Low-Level Network Properties: Common Metrics of Simple Networks -- 2.2. Higher-Level Properties: Considerations for the Analysis of Complex Replicate Networks -- 2.3. Dynamics: Assessing Disturbance in Complex Replicated Networks -- 3. Promising Future Avenues to `Big Data, Network Analyses of Change -- 3.1. Novel Food Web Profiling -- 3.2. Null Models -- 3.3. Weighted Networks -- 3.4. Multilayer Networks -- 4. Conclusions -- Acknowledgements -- References -- Further Reading -- Advances in Ecological Research Volume 1-59 -- Cumulative List of Titles -- Back Cover.