ALBERT

Note: Contents Acknowledgments 1 Introduction to environmental DNA (eDNA) 1.1 Definitions 1.2 A brief history of eDNA analysis 1.3 Constraints when working with eDNA 1.4 Workflow in eDNA studies and main methods used 1.5 Environmental DNA as a monitoring tool 2 DNA metabarcode choice and design 2.1 Which DNA metabarcode? 2.2 Properties of the ideal DNA metabarcode 2.3 In silica primer design and testing 2.3.1 Prerequisites 2.3.2 Reference sequences: description, filtering, and formatting for ecoPrimers 2.3.3 In silica primer design with ecoPrimers 2.3.3.1 'Ihe ecoPrimers output 2.3.4 In silica primer testing with ecoPCR 2.3.4.1 The ecoPCR output 2.3.4.2 Filtering of the ecoPCR output 2.3.4.3 Evaluation of primer conservation 2.3.4.4 Taxonomic resolution and Bs index 2.4 Examples of primer pairs available for DNA metabarcoding 3 Reference databases 3.1 Extracting reference databases from EMBL/GenBank/DDBJ 3.1.1 Downloading a local copy of EMBL 3.1.2 Identifying sequences corresponding to the relevant metabarcode 3.2 Marker-specific reference databases 3.2.1 Nuclear rRNA gene reference databases 3.2.2 Eukaryote-specific databases 3.3 Building a local reference database 3.3.1 PCR-based local reference database 3.3.2 Shotgun-based local reference database 3.4 Current challenges and future directions 4 Sampling 4.1 The cycle of eDNA in the environment 4.1.1 State and origin 4.1.2 Fate 4.1.3 Transport 4.2 Sampling design 4.2.1 Focusing on the appropriate DNA population 4.2.2 Defining the sampling strategy 4.3 Sample preservation 5 DNA extraction 5.1 From soil samples 5.2 From sediment 5.3 From litter 5.4 From fecal samples 5.5 From water samples 6 DNA amplification and multiplexing 6.1 Principle of the PCR 6.2 Which polymerase to choose? 6.3 The standard PCR reaction 6.4 The importance of including appropriate controls 6.4.1 Extraction negative controls 6.4.2 PCR negative controls 6.4.3 PCR positive controls 6.4.4 Tagging system controls 6.4.5 Internal controls 6.5 PCR optimization 6.6 How to limit the risk of contamination? 6.7 Blocking oligonucleotides for reducing the amplification of undesirable sequences 6.8 How many PCR replicates? 6.9 Multiplexing several metabarcodes within the same PCR 6.10 Multiplexing many samples on the same sequencing lane 6.10.1 Overview of the problem 6.10.2 Strategy 1: single-step PCR with Illumina adapters 6.10.3 Strategy 2: two-step PCR with Illumina adapters 6.10.4 Strategy 3: single-step PCR with tagged primers 7 DNA sequencing 7.1 Overview of the first, second, and third generations of sequencing technologies 7.2 The Illumina technology 7.2.1 Library preparation 7.2.2 Flow cell, bridge PCR, and clusters 7.2.3 Sequencing by synthesis 7.2.4 Quality scores of the sequence reads 8 DNA metabarcoding data analysis 8.1 Basic sequence handling and curation 8.1.1 Sequencing quality 8.1.1.1 The pros and cons of read quality-based filtering 8.1.1.2 Quality trimming software 8.1.2 Paired-end read pairing 8.1.3 Sequence demultiplexing 8.1.4 Sequence dereplication 8.1.5 Rough sequence curation 8.2 Sequence classification 8.2.1 Taxonomic classification 8.2.2 Unsupervised classification 8.2.3 Chimera identification 8.3 Taking advantages of experimental controls 8.3.1 Filtering out potential contaminants 8.3.2 Removing dysfunctional PCRs 8.4 General considerations on ecological analyses 8.4.1 Sampling effort and representativeness 8.4.1.1 Evaluating representativeness of the sequencing per PCR 8.4.1.2 Evaluating representativeness at the sampling unit or site level 8.4.2 Handling samples with varying sequencing depth 8.4.3 Going further and adapting the ecological models to metabarcoding 9 Single-species detection 9.1 Principle of the quantitative PCR (qPCR) 9.1.1 Recording amplicon accumulation in real time via fluorescence measurement 9.1.2 The typical amplification curve 9.1.3 Quantification of target sequences with the Ct method 9.2 Design and testing of qPCR barcodes targeting a single species 9.2.1 1he problem of specificity 9.2.2 qPCR primers and probe 9.2.3 Candidate qPCR barcodes 9.3 Additional experimental considerations 9.3.1 General issues associated with sampling, extraction, and PCR amplification 9.3.2 The particular concerns of contamination and inhibition 10 Environmental DNA for functional diversity 10.1 Functional diversity from DNA metabarcoding 10.1.1 Functional inferences 10.1.2 Targeting active populations 10.2 Metagenomics and metatranscriptomics: sequencing more than a barcode 10.2.1 General sampling constraints 10.2.1.1 Optimization of the number of samples 10.2.1.2 Enrichment in target organisms 10.2.1.3 Enrichment in functional information 10.2.2 General molecular constraints 10.2.3 From sequences to functions 10.2.3.1 Assembling (or not) a metagenome 10.2.3.2 Sorting contigs or reads in broad categories 10.2.3.3 Extracting functional information via taxonomic inferences 10.2.3.4 Functional annotation of metagenomes 11 Some early landmark studies 11.1 Emergence of the concept of eDNA and first results on microorganisms 11.2 Examining metagenomes to explore the functional information carried by eDNA 11.3 Extension to macroorganisms 12 Freshwater ecosystems 12.1 Production, persistence, transport, and delectability of eDNA in freshwater ecosystems 12.1.1 Production 12.1.2 Persistence 12.1.3 Transport/ diffusion distance 12.1.4 Detectability 12.2 Macroinvertebrates 12.3 Diatoms and microeukaryotes 12.4 Aquatic plants 12.5 Fish, amphibians, and other vertebrates 12.5.1 Species detection 12.5.2 Biomass estimates 12.6 Are rivers conveyer belts of biodiversity information? 13 Marine environments 13.1 Environmental DNA cycle and transport in marine ecosystems 13.2 Marine microbial diversity 13.3 Environmental DNA for marine macroorganisms 14 Terrestrial ecosystems 14.1 Delectability, persistence, and mobility of eDNA in soil 14.2 Plant community characterization 14.3 Earthworm community characterization 14.4 Bacterial community or metagenome characterization 14.5 Multitaxa diversity surveys 1 5 Paleoenvironments 15.1 Lake sediments 15.1.1 Pollen, macrofossils, and DNA metabarcoding 15.1.2 Plants and mammals from Lake Anteme 15.1.3 Viability in the ice-free corridor in North America 15.2 Permafrost 15.2.1 Overview of the emergence of permafrost as a source of eDNA 15.2.2 Large-scale analysis of permafrost samples for reconstructing past plant communities 15.3 Archaeological midden material 15.3.1 Bulk archaeological fish bones from Madagascar 15.3.2 Midden from Greenland to assess past human diet 16 Host-associated microbiota 16.1 DNA dynamics 16.2 Early molecular-based works 16.3 Post-holobiont works 17 Diet analysis 17.1 Some seminal diet studies 17.1.1 Proof of concept-analyzing herbivore diet using next-generation sequencing 17.1.2 Assessing the efficiency of conservation actions in Bialowieza forest 17.1.3 Characterizing carnivore diet, or how to disentangle predator and prey eDNA 17.1.4 Analyzing an omnivorous diet, or integrating several diets in a single one 17.2 Methodological and experimental specificities of eDNA diet analyses 17.2.1 eDNAsources 17.2.1.1 Feces 17.2.1.2 Gut content 17.2.1.3 Whole body 17.2.2 Quantitative aspects 17.2.2.1 Relationship between the amount of ingested food and DNA quantity in the sample 17.2.2.2 Quantifying DNA with PCR and next-generation sequencing 17.2.2.3 Empirical correction of abundances 17.2.3 Diet as a sample of the existing biodiversity 17.2.4 Problematic diets 18 Analysis of bulk samples 18.1 What is a bulk sample? 18.2 Case studies 18.2.1 Bulk insect samples for biodiversity monitoring 18.2.2 Nematode diversity in tropical rainforest 18.2.3 Marine metawan diversity in benthic ecosystems 18.3 Metabarcoding markers for bulk samples 18.4 Alternative strategies 19 The future of eDNA metabarcoding 19.1 PCR-based approaches 19.1.1 Singl

Note: Contents Preface Acknowledgement Gold Supporters Silver Supporters I Introduction Why OpenDroneMap? What You Can Do with OpenDroneMap The Key To Becoming a Successful User II Getting Started Installing The Software Hardware Requirements Installing on Windows Installing on macOS Installing on Linux Basic Commands and Troubleshooting Hello, WebODM! Processing Datasets Dataset Size File Requirements Process Tasks Output Results Share With Others Export To Another WebODM Manage Plugins Change The Look & Feel Create New Users Manage Permissions How Does WebODM Process Images? The Processing Pipeline Load Dataset Structure From Motion Multi View Stereo Meshing Texturing Georeferencing Digital Elevation Model Processing Orthophoto Processing Task Options in Depth build-overviews cameras crop debug dem-decimation dem-euclidean-map dem-gapfill-steps dem-resolution depthmap-resolution dsm dtm end-with fast-orthophoto gcp help ignore-gsd matcher-distance matcher-neighbors max-concurrency merge mesh-octree-depth mesh-point-weight mesh-samples mesh-size min-num-features mve-confidence opensfm-depthmap-method opensfm-depthmap-min-patch-sd orthophoto-bigtiff orthophoto-compression orthophoto-cutline orthophoto-no-tiled orthophoto-resolution pc-classify pc-csv pc-ept pc-filter pc-las rerun rerun-all rerun-from resize-to skip-3dmodel sm-cluster smrf-scalar smrf-slope smrf-threshold smrf-window split split-overlap texturing-data-term texturing-keep-unseen-faces texturing-nadir-weight texturing-outlier-removal-type texturing-skip-global-seam-leveling texturing-skip-hole-filling texturing-skip-local-seam-leveling texturing-skip-visibility-test texturing-tone-mapping time use-3dmesh use-exif use-fixed-camera-params use-hybrid-bundle-adjustment use-opensfm-dense verbose version Ground Control Points Creating a GCP file using POSM GCPi Using GCP files How GCP files work Flying Tips Fly Higher Fly on Overcast Days Fly Between 10am and 2pm Fly at Different Elevations and Capture Multiple Angles Fly on Calm Days Increase Overlap Set Drone to Hover While Taking Images Check Camera Settings III Advanced Usages The Command Line Command Line Basics Using ODM Processed Files Owned By Root Add New Processing Nodes to WebODM Batch Geotagging of Images Using Exiftool Further Readings Docker Essentials Docker Basics Managing Containers Managing Images Managing Volumes Docker-Compose Basics Managing Disk Space Changing Entrypoint Assigning Names To Containers Jumping Into Existing Containers Making Changes Without Rebuilding Images Camera Calibration Option 1: Use an Existing Camera Model Option 2: Generate a Camera Model From a Calibration Target Taking Pictures of a Calibration Target Extracting a Camera Profile Manually Writing a cameras.json File Bonus: Checking Your LCP File by Manually Removing Geometric Distortion Processing Large Datasets Split-Merge Options Local Split-Merge Distributed Split-Merge Using Image Groups and GCPs Limitations The NodeODM API Launching a NodeODM Instance NodeODM Configuration Using the API with cURL Remove a Task API Specification Automated Processing With Python Getting Started Example 1: Hello NodeODM Example 2: Process Datasets Concluding Remarks API Reference Glossary About the Author

Note: Contents Chapter 1 Introdution Chapter 2 Origins Building a Planet, Shaping the Oceans Water, Salt, and Circulation Life, Oxygen, and Carbon Chapter 3 Controls On change Orbital and Solar Changes Greenhouse Gases Plate Tectonics Impacts Chapter 4 Snowball earth and the explosions of life Into the Freezer Out of the Freezer, Into a Greenhouse A Tale of Two Explosions Reverberations Chapter 5 Oceans On acid About Acidification Acidification in Action Chapter 6 The age of reptiles Choking Oceans Salty Giants Chapter 7 Winter is coming Reconstructing Sea-Level Change The Great Northern Ice Ages Ocean Controls on CO2 A Seesaw in the Ocean Chapter 8 Future Oceans and climate Our Carbon Emissions Consequences Epilogue Acknowledgments Bibliography Index

Note: Contents -- Foreword -- Acknowledgments -- Introduction -- Part I Overview of Satellite Datasets -- Chapter 1 A Tour of Current Satellite Missions and Products -- 1.1 History of Computational Scientific Visualization -- 1.2 Brief Catalog of Current Satellite Products -- 1.2.1 Meteorological and Atmospheric Science -- 1.2.2 Hydrology -- 1.2.3 Oceanography and Biogeosciences -- 1.2.4 Cryosphere -- 1.3 The Flow of Data from Satellites to Computer -- 1.4 Learning Using Real Data and Case Studies -- 1.5 Summary -- References -- Chapter 2 Overview of Python -- 2.1 Why Python? -- 2.2 Useful Packages for Remote Sensing Visualization -- 2.2.1 NumPy -- 2.2.2 Pandas -- 2.2.3 Matplotlib -- 2.2.4 netCDF4 and h5py -- 2.2.5 Cartopy -- 2.3 Maturing Packages -- 2.3.1 xarray -- 2.3.2 Dask -- 2.3.3 Iris -- 2.3.4 MetPy -- 2.3.5 cfgrib and eccodes -- 2.4 Summary -- References -- Chapter 3 A Deep Dive into Scientific Data Sets -- 3.1 Storage -- 3.1.1 Single Values -- 3.1.2 Arrays -- 3.2 Data Formats -- 3.2.1 Binary -- 3.2.2 Text -- 3.2.3 Self-Describing Data Formats -- 3.2.4 Table-Driven Formats -- 3.2.5 geoTIFF -- 3.3 Data Usage -- 3.3.1 Processing Levels -- 3.3.2 Product Maturity -- 3.3.3 Quality Control -- 3.3.4 Data Latency -- 3.3.5 Reprocessing -- 3.4 Summary -- References -- Part II Practical Python Tutorials for Remote Sensing -- Chapter 4 Practical Python Syntax -- 4.1 "Hello Earth" in Python -- 4.2 Variable Assignment and Arithmetic -- 4.3 Lists -- 4.4 Importing Packages -- 4.5 Array and Matrix Operations -- 4.6 Time Series Data -- 4.7 Loops -- 4.8 List Comprehensions -- 4.9 Functions -- 4.10 Dictionaries -- 4.11 Summary -- References -- Chapter 5 Importing Standard Earth Science Datasets -- 5.1 Text -- 5.2 NetCDF -- 5.2.1 Manually Creating a Mask Variable Using True and False Values. -- 5.2.2 Using NumPy Masked Arrays to Filter Automatically -- 5.3 HDF -- 5.4 GRIB2 -- 5.5 Importing Data Using Xarray -- 5.5.1 netCDF -- 5.5.2 Examining Vertical Cross Sections -- 5.5.3 Examining Horizontal Cross Sections -- 5.5.4 GRIB2 using Cfgrib -- 5.5.5 Accessing Datasets Using OpenDAP -- 5.6 Summary -- References -- Chapter 6 Plotting and Graphs for All -- 6.1 Univariate Plots -- 6.1.1 Histograms -- 6.1.2 Barplots -- 6.2 Two Variable Plots -- 6.2.1 Converting Data to a Time Series -- 6.2.2 Useful Plot Customizations -- 6.2.3 Scatter Plots -- 6.2.4 Line Plots -- 6.2.5 Adding Data to an Existing Plot -- 6.2.6 Plotting Two Side-by-Side Plots -- 6.2.7 Skew-T Log-P -- 6.3 Three Variable Plots -- 6.3.1 Filled Contour Plots -- 6.3.2 Mesh Plots -- 6.4 Summary -- References -- Chapter 7 Creating Effective and Functional Maps -- 7.1 Cartographic Projections -- 7.1.1 Geographic Coordinate Systems -- 7.1.2 Choosing a Projection -- 7.1.3 Some Common Projections -- 7.2 Cylindrical Maps -- 7.2.1 Global Plots -- 7.2.2 Changing Projections -- 7.2.3 Regional Plots -- 7.2.4 Swath Data -- 7.2.5 Quality Flag Filtering -- 7.3 Polar Stereographic Maps -- 7.4 Geostationary Maps -- 7.5 Creating Maps from Datasets Using OpenDAP -- 7.6 Summary -- References -- Chapter 8 Gridding Operations -- 8.1 Regular One-Dimensional Grids -- 8.2 Regular Two-Dimensional Grids -- 8.3 Irregular Two-Dimensional Grids -- 8.3.1 Resizing -- 8.3.2 Regridding -- 8.3.3 Resampling -- 8.4 Summary -- References -- Chapter 9 Meaningful Visuals through Data Combination -- 9.1 Spectral and Spatial Characteristics of Different Sensors -- 9.2 Normalized Difference Vegetation Index (NDVI) -- 9.3 Window Channels -- 9.4 RGB -- 9.4.1 True Color -- 9.4.2 Dust RGB -- 9.4.3. Fire/Natural RGB -- 9.5 Matching with Surface Observations -- 9.5.1 With User-Defined Functions -- 9.5.2 With Machine Learning. -- 9.6 Summary -- References -- Chapter 10 Exporting with Ease -- 10.1 Figures -- 10.2 Text Files -- 10.3 Pickling -- 10.4 NumPy Binary Files -- 10.5 NetCDF -- 10.5.1 Using netCDF4 to Create netCDF Files -- 10.5.2 Using Xarray to Create netCDF Files -- 10.5.3 Following Climate and Forecast (CF) Metadata Conventions -- 10.6 Summary -- Part III Effective Coding Practices -- Chapter 11 Developing a Workflow -- 11.1 Scripting with Python -- 11.1.1 Creating Scripts Using Text Editors -- 11.1.2 Creating Scripts from Jupyter Notebook -- 11.1.3 Running Python Scripts from the Command Line -- 11.1.4 Handling Output When Scripting -- 11.2 Version Control -- 11.2.1 Code Sharing though Online Repositories -- 11.2.2 Setting up on GitHub -- 11.3 Virtual Environments -- 11.3.1 Creating an Environment -- 11.3.2 Changing Environments from the Command Line -- 11.3.3 Changing Environments in Jupyter Notebook -- 11.4 Methods for Code Development -- 11.5 Summary -- References -- Chapter 12 Reproducible and Shareable Science -- 12.1 Clean Coding Techniques -- 12.1.1 Stylistic Conventions -- 12.1.2 Tools for Clean Code -- 12.2 Documentation -- 12.2.1 Comments and Docstrings -- 12.2.2 README File -- 12.2.3 Creating Useful Commit Messages -- 12.3 Licensing -- 12.4 Effective Visuals -- 12.4.1 Make a Statement -- 12.4.2 Undergo Revision -- 12.4.3 Are Accessible and Ethical -- 12.5 Summary -- References -- Conclusion -- Appendix A Installing Python -- A.1. Download Tutorials for This Book -- A.2. Download and Install Anaconda -- A.3. Package Management in Anaconda -- Appendix B Jupyter Notebook -- B.1. Running on a Local Machine (New Coders) -- B.2. Running on a Remote Server (Advanced) -- B.3. Tips for Advanced Users -- B.3.1. Customizing Notebooks with Configuration Files -- B.3.2. Starting and Ending Python Scripts -- B.3.3. Creating Git Commit Templates. -- Appendix C Additional Learning Resources -- Appendix D Tools -- D.1. Text Editors and IDEs -- D.2. Terminals -- Appendix E Finding, Accessing, and Downloading Satellite Datasets -- E.1. Ordering Data from NASA EarthData -- E.2. Ordering Data from NOAA/CLASS -- Appendix F Acronyms -- Index -- EULA.

Note: Contents Part I Arctic Climate and Greenland 1 Arctic Climate Change, Variability, and Extremes / John E. Walsh 2 Precipitation Characteristics and Changes / Hengchun Ye, Daqing Yang, Ali Behrangi, Svetlana L. Stuefer, Xicai Pan, Eva Mekis, Yonas Dibike, and John E. Walsh 3 Snow Cover - Observations, Processes, Changes, and Impacts on Northern Hydrology / Ross Brown, Philip Marsh, Stephen Déry, and Daqing Yang 4 Evaporation Processes and Changes Over the Northern Regions / Yinsheng Zhang, Ning Ma, Hotaek Park, John E. Walsh, and Ke Zhang 5 Greenland Ice Sheet and Arctic Mountain Glaciers / Sebastian H. Mernild, Glen E. Liston, and Daqing Yang Part II Hydrology and Biogeochemistry 6 Regional and Basin Streamflow Regimes and Changes: Climate Impact and Human Effect / Michael Rawlins, Daqing Yang, and Shaoqing Ge 7 Hydrologic Extremes in Arctic Rivers and Regions: Historical Variability and Future Perspectives / Rajesh R. Shrestha, Katrina E. Bennett, Daniel L. Peters, and Daqing Yang 8 Overview of Environmental Flows in Permafrost Regions / Daniel L, Peters, Donald J. Baird, Joseph Culp, Jennifer Lento, Wendy A. Monk, and Rajesh R. Shrestha 9 Yukon River Discharge Response to Seasonal Snow Cover Change / Daqing Yang, Yuanyuan Zhao, Richard Armstrong, Mary J. Brodzik, and David Robinson 10 Arctic River Water Temperatures and Thermal Regimes / Daqing Yang, Hoteak Park, Amber Peterson, and Baozhong Liu 11 Changing Biogeochemical Cycles of Organic Carbon, Nitrogen, Phosphorus, and Trace Elements in Arctic Rivers / Jonathan O'Donnell, Thomas Douglas, Amanda Barker, and Laodong Guo 12 Arctic Wetlands and Lakes-Dynamics and Linkages / Kathy L. Young, Laura Brown, and Yonas Dibike 13 River Ice Processes and Changes Across the Northern Regions / Daqing Yang, Hotaek Park, Terry Prowse, Alexander Shiklomanov, and Ellie McLeod Part III Permafrost and Frozen Ground 14 Permafrost Features and Talik Geometry in Hydrologic System / Kenji Yoshikawa and Douglas L. Kane 15 Ground Temperature and Active Layer Regimes and Changes / Lin Zhao, Cangwei Xie, Daqing Yang, and Tingjun Zhang 16 Permafrost Hydrology: Linkages and Feedbacks / Tetsuya Hiyama, Daqing Yang, and Douglas L. Kane 17 Permafrost Hydrogeology / Barret L. Kurylyk and Michelle A. Walvoord Part IV Ecosystem Change and Impact 18 Greenhouse Gases and Energy Fluxes at Permafrost Zone / Masahito Ueyama, Hiroki Iwata, Hideki Kobayashi, Eugénie Euskirchen, Lutz Merbold, Takeshi Ohta, Takashi Machimura, Donatella Zona, Walter C. Oechel, and Edward A. G. Schuur 19 Spring Phenology of the Boreal Ecosystems / Nicolas Delbart 20 Diagnosing Environmental Controls on Vegetation Greening and Browning Trends Over Alaska and Northwest Canada Using Complementary Satellite Observations / Youngwook Kim, John S. Kimball, Nicholas Parazoo, and Peter Kirchner 21 Boreal Forest and Forest Fires / Yongwon Kim, Hideki Kobayashi, Shin Nagai, Masahito Ueyama, Bang-Yong Lee, and Rikie Suzuki 22 Northern Ecohydrology of Interior Alaska Subarctic / Jessica M. Young-Robertson, W. Robert Bolton, and Ryan Toohey 23 Yukon River Discharge-NDVI Relationship / Weixin Xu and Daqing Yang Part V Cross-System Linkage and Integration 24 River Freshwater Flux to the Arctic Ocean / Alexander Shiklomanov, Stephen Déry, Mikhail Tretiakov, Daqing Yang, Dmitry Magritsky, Alex Georgiadi, and Wenqing Tang 25 River Heat Flux into the Arctic Ocean / Daqing Yang, Shaoqing Ge, Hotaek Park, and Richard L. Lammers 26 Cold Region Hydrologic Models and Applications / Hotaek Park, Yonas Dibike, Fengge Su, and John Xiaogang Shi 27 Regional Climate Modeling in the Northern Regions / Zhenhua Li, Yanping Li, Daqing Yang, and Rajesh R. Shrestha 28 High-Resolution Weather Research Forecasting (WRF) Modeling and Projection Over Western Canada, Including Mackenzie Watershed / Yanping Li and Zhenhua Li 29 Responses of Boreal Forest Ecosystems and Permafrost to Climate Change and Disturbances: A Modeling Perspective / Shuhua Yi and Fengming Yuan 30 Future Trajectory of Arctic System Evolution / Kazuyuki Saito, John E. Walsh, Arvid Bring, Ross Brown, Alexander Shiklomanov, and Daqing Yang Correction to: Arctic Hydrology, Permafrost and Ecosystems / Daqing Yang, and Douglas L. Kane

Note: Contents Part I Atmosphere-Ocean Interaction and Physical Oceanography 1 Geostrophic and Wind-Driven Components of the Antarctic Circumpolar Current / Nikolay A. Diansky, Varvara V. Bagatinskaya, Anatoly V. Gusev, and Eugene G. Morozov 2 Multi-jet Structure of the Antarctic Circumpolar Current / Roman Yu Tarakanov 3 Frontal Zone Between Relatively Warm and Cold Waters in the Northern Weddell Sea / Eugene G. Morozov, Viktor A. Krechik, Dmitry I. Frey, Alexander A. Polukhin, Vladimir A. Artemiev, Valentina V. Kasyan, Philipp V. Sapozhnikov, and Rinat Z. Mukhametianov 4 Water Masses, Currents, and Phytoplankton in the Bransfield Strait in January 2020 / Eugene G. Morozov, Dmitry I. Frey, Viktor A. Krechik, Alexander A. Polukhin, and Philipp V. Sapozhnikov 5 Intra-annual Variability of Water Structure in the Atlantic Sector of the Southern Ocean Based on the ECMWF ORA-S3 and OI SST Reanalysis / Yuri V. Artamonov, Elena A. Skripaleva, Alexander V. Fedirko, and Nikolay V. Nikolsky 6 The Circulation and Mixing Zone in the Antarctic Sound in February 2020 / Alexander V. Krek, Elena V. Krek, and Viktor A. Krechik 7 Rogue Waves in the Drake Passage: Unpredictable Hazard / Ekaterina G. Didenkulova, Tatiana G. Talipova, and Efim N. Pelinovsky 8 Water Mass Transformation in the Powell Basin / Alina A. Fedotova and Svetlana V. Stepanova 9 Interannual Variations of Water Mass Properties in the Central Basin of the Bransfield Strait / Alina A. Fedotova and Sergey V. Kashin 10 Sea Surface Temperature and Ice Concentration Analysis Based on the NOAA Long-Term Satellite and Sea-Truth Data in the Atlantic Antarctic / Viktor V. Zamshin and Vladislav A. Shliupikov Part II Chemical Oceanography, Seawater Optical Properties, Productivity and Microbial Processes 11 Hydrochemical Structure of Waters in the Northern Weddell Sea in Austral Summer 2020 / Svetlana V. Stepanova, Alexander A. Polukhin, Gennadii V. Borisenko, Anna L. Chultsova, Evgeniia N. Marina, Oleg S. Popov, Anna M. Seliverstova, Anna V. Vidnichuk, and Petr P. Tishchenko 12 Features and Processes of the Oxygen and pCO2 Dynamics in the Surface Waters in the Western Parts of the Weddell and Scotia Seas (Southern Ocean) / Natalia A. Orekhova, Anna V. Vidnichuk, and Sergey K. Konovalov 13 Earth’s Insolation and Spatiotemporal Variability of Albedo in the Antarctic / Anton A. Bukatov and Margarita V. Babiy 14 Quantitative and Productional Characteristics of Microplankton in the Powell Basin and Bransfield Strait in Summer / Nadezda D. Romanova, Sergey A. Mosharov, Olga V. Vorobieva, and Elena V. Bardyukova 15 Detection of Thermophilic Methanotrophic Microbial Communities in the Water Column of the Bransfield Strait (Antarctica) / Anna L. Ponomareva, Nikita S. Polonik, Aleksandra V. Kim, and Renat B. Shakirov 16 Spectral Bio-optical Properties of Waters in the Bransfield Strait and Powell Basin / Tanya Ya Churilova, Nataliia A. Moiseeva, Tatiana V. Efimova, Vladimir A. Artemiev, Elena Y. Skorokhod, and Anatoly S. Buchelnikov 17 Variability of Seawater Optical Properties in the Adjacent Water Basins of the Antarctic Peninsula in January and February 2020 / Alexandr A. Latushkin, Vladimir A. Artemiev, Anton V. Garmashov, Pavel A. Salyuk, Inna V. Sahling, and Dmitry I. Glukhovets 18 Bio-Optical Models for Estimating Euphotic Zone Depth in the Western Atlantic Sector of the Southern Ocean in the Antarctic Summer / Pavel A. Salyuk, Vladimir A. Artemiev, Dmitry I. Glukhovets, Alexander N. Khrapko, Anatoly V. Grigoriev, Alexandr A. Latushkin, and Nadezda D. Romanova 19 Phycoerythrin Pigment Distribution in the Upper Water Layer Across the Weddell-Scotia Confluence Zone and Drake Passage / Pavel A. Salyuk, Dmitry I. Glukhovets, Alexander Yu. Mayor, Natalia A. Moiseeva, Vladimir A. Artemiev, and Alexander N. Khrapko 20 Nanophytoplankton in the Bransfield Strait: Contribution of Cryptophyta to the Community Abundance and Biomass During Austral Summer / Vladimir S. Mukhanov, Evgeny G. Sakhon, Aleksander A. Polukhin, and Vladimir A. Artemiev Part III Section Marine Ecosystems and Their Oceanographical Background 21 Phytopelagic Communities of the Powell Basin in the Summer of 2020 / Philipp V. Sapozhnikov, Olga Yu. Kalinina, and Tatiana V. Morozova 22 Bioluminescence in the Atlantic Sector of the Southern Ocean Based on the Field Observations and Sounding Data / Aleksandr V. Melnik, Viktor V. Melnikov, Lidiya A. Melnik, Olga V. Mashukova, and Sergei V. Kapranov 23 Parasites as an Inseparable Part of Antarctic and Subantarctic Marine Biodiversity / Tatyana A. Polyakova and Ilya I. Gordeev 24 Spatial Distribution, Species Composition, and Number of Seabirds in the Argentine Basin, Drake Passage, East of Antarctic Peninsula, and Powell Basin in January–March 2020 / Sergey P. Kharitonov, Alexander L. Mischenko, Nikolai B. Konyukhov, Alexander E. Dmitriyev, Andrey V. Tretyakov, Gleb Yu. Pilipenko, Svetlana M. Artemyeva, and Matvey S. Mamayev 25 Spatial Distribution, Species Composition, and Number of Marine Mammals in the Argentine Basin, Drake Passage, East of Antarctic Peninsula, and Powell Basin in January–March 2020 / Sergey P. Kharitonov, Andrey V. Tretyakov, Alexander L. Mischenko, Nikolai B. Konyukhov, Svetlana M. Artemyeva, Gleb Yu. Pilipenko, Matvey S. Mamayev, and Alexander E. Dmitriyev 26 Meat in the Ocean: How Much and Who Is to Blame? / Sergey P. Kharitonov, Andrey V. Tretyakov, and Alexander L. Mischenko 27 Macro- and Mesozooplankton in the Powell Basin (Antarctica): Species Composition and Distribution of Abundance and Biomass in February 2020 / Vladimir A. Yakovenko, Vassily A. Spiridonov, Konstantin M. Gorbatenko, Nickolai V. Shadrin, Ernest Z. Samyshev, and Natalia I. Minkina 28 Application of Autonomous Underwater Vehicles for Research of Ecosystems in the Southern Ocean / Alexander Yu. Konoplin, Alexey I. Borovik, Denis N. Mikhailov, Yuriy V. Vaulin, Alexander F. Scherbatyuk, Alexey A. Boreiko, Roman A. Babaev, Dmitriy A. Bolovin, and Dmitriy I. Tregubenko 29 Heavy Metals and Anthropogenic Radionuclides in the Region of the Antarctic Peninsula / Artem A. Paraskiv, Natalia Yu. Mirzoeva, Nataliya N. Tereshchenko, Vladislav Yu. Proskurnin, Ilya G. Sidorov, Svetlana I. Arkhipova, and Eugene G. Morozov

Note: Contents Part I Introduction to Our Coastal Atmosphere 1 Scope, Uniqueness, and Importance of Our Coastal Atmosphere 2 Atmospheric Composition, Structure, and Evolution Part II Thermodynamics in Our Coastal Atmosphere 3 Energy Transfer and Electromagnetic Radiation 4 Temperature 5 Application of the Gas Laws in Meteorology 6 The Hydrostatic Equation and Adiabatic Processes 7 Atmospheric Moisture 8 Atmospheric Stability and Potential Temperature 9 Measuring and Estimating Atmospheric Stability 10 Using Thermodynamic Diagrams in Meteorology 11 Clouds 12 Precipitation Processes and Types Part III Dynamic Processes in Our Coastal Atmosphere 13 Pressure and Winds 14 Coriolis Effect 15 Effect of Friction 16 Centripetal Acceleration and the Gradient Wind 17 Gravitation 18 The Seven Basic Equations in Weather Forecasting Models 19 Comparison of Weather Forecasting Models and General Circulation Models 20 General Circulation of the Atmosphere Part IV Weather Systems in the Coastal Zone 21 Air Masses 22 Atmospheric Lifting Mechanisms 23 Fronts and the Mid-Latitude Wave Cyclone 24 Thunderstorms 25 Lightning 26 Tornadoes and Waterspouts 27 Advising the Public About the Severe Weather Risk 28 Tropical Cyclones 29 Coastal Flooding 30 Coastal Drought 31 Winter Storms 32 Sea Ice and Weather Systems 33 Summary of Energy Transfer by Atmospheric and Oceanic Motion Part V Atmospheric Boundary Layers and Air-Sea Interaction 34 Introduction to Near-Surface Atmospheric Dynamics 35 The Logarithmic Wind Profile in Neutral Stability Conditions 36 Non-neutral or Diabatic Wind Profile 37 Introduction to the Transition (or Ekman) Layer 38 The Classical Solution to the Atmospheric Ekman Spiral 39 Fundamentals of Air-Sea Interactions 40 Weather Effects on the Coastal Ocean 41 Wind Stress and Turbulent Flux Drag Coefficients Over Water Part VI Air-Sea-Land Interaction 42 Surface Fluxes of Energy, Moisture, and Momentum 43 Sea and Land Breezes 44 Coastal Fog 45 Coastal Upwelling and Weather 46 Atmospheric Impacts on Lake Processes 47 Coastal Jets 48 Atmospheric Optical Effects in the Coastal Zone 49 Solar Radiation in Aquatic Systems Part VII Dispersion and Engineering Applications 50 Meteorology and Climatology of Coastal Cities 51 Atmospheric Dispersion in the Coastal Zone 52 Engineering Aspects of the Wind Profile Appendices References Index

Note: Contents Part I Fundamentals 1 Overview: Antecedents, Motivation and Necessity / Gabriel Cristóbal, Saúl Blanco, and Gloria Bueno 2 Diatom Classifications: What Purpose Do They Serve? / David M. Williams 3 Diatom Taxonomy and Identification Keys / Saúl Blanco 4 Naturally and Environmentally Driven Variations in Diatom Morphology: Implications for Diatom-Based Assessment of Water Quality / Adriana Olenici, C ̆alin Baciu, Saúl Blanco, and Soizic Morin Part II Sensing 5 Microscopic Modalities and Illumination Techniques / J. Piper and T. Piper 6 Light Filtering in Microscopy / J. Piper 7 Automatization Techniques. Slide Scanning / Carlos Sánchez, Jesús Ruiz-Santaquiteria Alegre, José Luis Espinosa Aranda, and Jesús Salido Part III Analysis 8 Segmentation Techniques / Gloria Bueno, Manuel G. Forero, Carlos A. Jacanamejoy, J. Alejandro Libreros, M. Milagro Fernandez-Carrobles, and Oscar Deniz 9 Diatom Feature Extraction and Classification / Noelia Vallez, Anibal Pedraza, Carlos Sánchez, Jesus Salido, Oscar Deniz, and Gloria Bueno 10 Multifocus and Multiexposure Techniques / Harbinder Singh, Gabriel Cristóbal, and Vinay Kumar 11 Stereoscopic Imaging of Diatoms in Light and Electron Microscopy / Robert Sturm 12 Geometric Morphometrics and the Shape of Microscopic Organisms / Ecaterina Fodor and Ovidiu Ioan Hâruta Part IV Applications 13 Water Quality Assessment / A. Goldenberg-Vilar, R. Álvarez-Troncoso, V. Roldán, and Saúl Blanco 14 Diatoms in Forensic Analysis / Eloy Girela-Lopez, Cristina M. Beltran-Aroca, and Herminia García-Mozo 15 Benthic Foraminifera and Diatoms as Ecological Indicators / Xavier Benito Glossary Index

Note: Contents 1 Introduction / Ola M. Johannessen 2 Sea Ice in the Arctic Paleoenvironments / Leonid P. Bobylev and Martin W. Miles 3 Marginal Ice Zone and Ice-Air-Ocean Interactions / Ola M. Johannessen, Stein Sandven, Richard Davy, and Einar O. Olason 4 Changes in Arctic Sea Ice Cover in the Twentieth and Twenty-First Centuries / Elena V. Shalina, Ola M. Johannessen, and Stein Sandven 5 Arctic Sea Ice Thickness and Volume Transformation / Elena V. Shalina, Kirill Khvorostovsky, and Stein Sandven 6 SAR Sea Ice Type Classification and Drift Retrieval in the Arctic / Natalia Y. Zakhvatkina, Denis Demchev, Stein Sandven, Vladimir A. Volkov, and Alexander S. Komarov 7 Sea Ice Drift in the Arctic / Vladimir A. Volkov, Alexandra Mushta, and Denis Demchev 8 Sea Ice Modelling / Matti Leppäranta, Valentin P. Meleshko, Petteri Uotila, and Tatiana Pavlova 9 Operational Forecasting of Sea Ice in the Arctic Using TOPAZ System / Laurent Bertino and Jiping Xie 10 Current and Projected Sea Ice in the Arctic in the Twenty-First Century / Valentin P. Meleshko, Tatiana Pavlova, Leonid P. Bobylev, and Pavel Golubkin 11 Climate Change Impact on the Arctic Economy / Lasse H. Pettersson, Anton G. Kjelaas, Dmitry V. Kovalevsky, and Klaus Hasselmann 12 Annex: SAR Sea Ice Interpretation Guide / Ola M. Johannessen Afterword / Ola M. Johannessen

Note: Contents Volume 1 1 The Climate System: Its Functioning and History / Sylvie Joussaume and Jean-Claude Duplessy 2 The Changing Face of the Earth Throughout the Ages / Frédéric Fluteau and Pierre Sepulchre 3 Introduction to Geochronology / Hervé Guillou 4 Carbon-14 / Martine Paterne, Élisabeth Michel, and Christine Hatté et Jean-Claude Dutay 5 The 40 K/ 40 Ar and 40 Ar/ 39 Ar Methods / Hervé Guillou, Sébastien Nomade, and Vincent Scao 6 Dating of Corals and Other Geological Samples via the Radioactive Disequilibrium of Uranium and Thorium Isotopes / Norbert Frank and Freya Hemsing 7 Magnetostratigraphy: From a Million to a Thousand Years / Carlo Laj, James E. T. Channell, and Catherine Kissel 8 Dendrochronology / Frédéric Guibal and Joël Guiot 9 The Dating of Ice-Core Archives / Frédéric Parrenin 10 Reconstructing the Physics and Circulation of the Atmosphere / Valérie Masson-Delmotte and Joël Guiot 11 Air-Ice Interface: Polar Ice / Valérie Masson-Delmotte and Jean Jouzel 12 Air-Vegetation Interface: Pollen / Joël Guiot 13 Ground-Air Interface: The Loess Sequences, Markers of Atmospheric Circulation / Denis-Didier Rousseau and Christine Hatté 14 Air-Ground Interface: Reconstruction of Paleoclimates Using Speleothems / Dominique Genty and Ana Moreno 15 Air-Interface: d18O Records of Past Meteoric Water Using Benthic Ostracods from Deep Lakes / Ulrich von Grafenstein and Inga Labuhn 16 Vegetation-Atmosphere Interface: Tree Rings / Joël Guiot and Valérie Daux 17 Air-Vegetation Interface: An Example of the Use of Historical Data on Grape Harvests / Valérie Daux 18 Air-Ground Interface: Sediment Tracers in Tropical Lakes / David Williamson 19 Air-water Interface: Tropical Lake Diatoms and Isotope Hydrology Modeling / Florence Sylvestre, Françoise Gasse, Françoise Vimeux, and Benjamin Quesada 20 Air-Ice Interface: Tropical Glaciers / Françoise Vimeux 21 Climate and the Evolution of the Ocean: The Paleoceanographic Data / Thibaut Caley, Natalia Vázquez Riveiros, Laurent Labeyrie, Elsa Cortijo, and Jean-Claude Duplessy Volume 2 22 Climate Evolution on the Geological Timescale and the Role of Paleogeographic Changes / Frédéric Fluteau and Pierre Sepulchre 23 Biogeochemical Cycles and Aerosols Over the Last Million Years / Nathaelle Bouttes, Laurent Bopp, Samuel Albani, Gilles Ramstein, Tristan Vadsaria, and Emilie Capron 24 The Cryosphere and Sea Level / Catherine Ritz, Vincent Peyaud, Claire Waelbroeck, and Florence Colleoni 25 Modeling and Paleoclimatology / Masa Kageyama and Didier Paillard 26 The Precambrian Climate / Yves Goddéris, Gilles Ramstein, and Guillaume Le Hir 27 The Phanerozoic Climate / Yves Goddéris, Yannick Donnadieu, and Alexandre Pohl 28 Climate and Astronomical Cycles / Didier Paillard 29 Rapid Climate Variability: Description and Mechanisms / Masa Kageyama, Didier M. Roche, Nathalie Combourieu Nebout, and Jorge Alvarez-Solas 30 An Introduction to the Holocene and Anthropic Disturbance / Pascale Braconnot and Pascal Yiou 31 From the Climates of the Past to the Climates of the Future / Sylvie Charbit, Nathaelle Bouttes, Aurélien Quiquet, Laurent Bopp, Gilles Ramstein, Jean-Louis Dufresne, and Julien Cattiaux