Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA (Developments in Paleoenvironmental Research, 21)

Preface
Aims and Scope of Developments in Paleoenvironmental Research Series
Editor and Board of Advisors of Developments in Paleoenvironmental Research Book Series
	Series Editor
	Advisory Board
Safety Considerations and Caution
Contents
Contributors
About the Editors
Chapter 1: Using Lake Sedimentary DNA to Reconstruct Biodiversity Changes
	References
Chapter 2: The Sources and Fates of Lake Sedimentary DNA
	Introduction
	Effects of Taphonomic Processes on DNA Fractions Archived in Lake Sediments
		Concentrations of inDNA and exDNA Fractions in Lake Sediments
		Efficiencies of Extraction Methods
		Molecular Inventories from inDNA and exDNA Fractions
	DNA Degradation and Preservation in the Environment
		Effects of Physico-Chemical Conditions on DNA Degradation
		DNA Binding on Particles: Implications for Lake sedDNA Studies, Mechanisms and Factors
			Binding Mechanisms Between DNA and Minerals
			Factors Controlling the Binding on Minerals
			DNA Binding on Organic Compounds and Carbonaceous Materials
		Early Diagenesis in the Sedimentary Column: Effects on DNA Concentration and Taxonomic Diversity
		Taxa-Dependent Preservation of Sedimentary DNA
	Terrestrial DNA in Lake Sediments
		DNA Production and Sources
			“Primary Source” of DNA
			Soil DNA, a “Secondary and Primary Source” of DNA
				Spatial Representativeness of the DNA Signals
				DNA Distribution in a Soil Profile
		Transfer of Terrestrial DNA and Spatial Representativeness of the Records
	Aquatic DNA in Lake Sediments
		Sources of Aquatic DNA: Production and Spatial Variability
			Habitats of Aquatic Organisms
			Variability in DNA Detection Linked to Biomass and Spatio-Temporal Distribution of Organisms and Abiotic Factors
		Transfer of Aquatic DNA to Sediments
	Summary
	References
Chapter 3: The Sedimentary Ancient DNA Workflow
	Introduction
	Ethical Considerations
	Fieldwork
	Sediment Storage
	Subsampling
	DNA Extraction
	Data Generation Strategies
		Endpoint PCR
		Amplicon
		Metagenomics
		Sequencing
	Data Pre-processing and Denoising
	Identification and Validation
		Identification
		Validation
	Environmental and Evolutionary Analysis
		Environmental Analysis
		Evolutionary Analysis
	Data and Script Availability
	Future Directions
	Summary
	References
Chapter 4: Bacterial and Archaeal DNA from Lake Sediments
	Introduction
		Lake Sediments as Microbial Niches and Prokaryotic DNA Repositories
		Assembly of Lake Sediment Microbiomes
		Lacustrine Stratigraphy and Preservation of Sedimentary DNA
		Buried Alive in Lacustrine Sediment Archives
	Taxonomic Assemblages and Metabolic Guilds from Source to Sink
		Allochthonous Versus Autochthonous Microorganisms in Lake Sediments
			Environmental Processes: Dispersal, Dormancy and Resuscitation of Microbial Seed Banks
			Taxonomy: Primary Versus Secondary Producers in the Microbial Loop
		Stratified Microbial Communities in Shallow Subsurface Sediments
			Environmental Processes: Imprints of Successive Respiration Modes and Fermentation
			Charismatic Microbial Guilds in Shallow Sediments: Denitrifiers, Sulfate Reducers, Syntrophs, Methanogens
			Vertical Distribution of Microbial Taxa in Recent Sediments from Two Geochemically Distinct Lakes
		Slow Growers and Persistent Prokaryotes in Deep Lake Sediments
			Environmental Processes: Fermentation of Residual Substrates, Necromass and DNA Turnover
			Populations that Live and Persist at the Thermodynamic Limit of Life
			Prokaryotic Assemblages of the Deep Biosphere Persisting in Lake Sediments Older than 50 Ka
		Anthropogenic Expansion of Adaptive and Versatile Ubiquists
			Environmental Processes: Pollutant Loading, Eutrophication, and Excess Nutrient
			Microbial Mitigation of Anthropogenic Pressures: Sulfur and Iron Oxidizers, Methylotrophs, Methanotrophs, Anammox Bacteria, Opportunists
			Indicators of Excess Nutrient in Lake Sediments Downstream Urbanized Catchments
	Research Perspectives and Methodological Considerations
		Prokaryotic Sedimentary DNA as an Indicator of Past and Current Environmental Shifts
		Meta-Omics Adapted to Limnogeology and Stratigraphic Studies
			Parallel Field Sampling for Limnogeology and Microbiology
			Selective Extractions of Nucleic Acid Fractions
			Targeted PCR Assays for Linking Taxonomy to Functions, Fluorescence Techniques
			Metagenomics and Metatranscriptomics
			On-Site Contamination Control and Core Sampling
	Summary
	References
Chapter 5: Cyanobacterial DNA from Lake Sediments
	Introduction
		Diversity and Distribution of Cyanobacteria
		Physiological and Morphological Traits of Cyanobacteria Favoring Their Dominance
		Current Trends in the Frequency and Magnitude of Cyanobacterial Blooms
	Sediment Deposition of Cyanobacteria
		Taphonomic Processes: Production, Sedimentation, and Preservation of Cyanobacterial DNA in Sediments
		Cyanobacterial Signal in Lacustrine Sediments: Dead or Alive?
	SedDNA-Based Approaches: A Means of Reconstructing Past Cyanobacterial Histories
		An Expanded Representation of Phylum Cyanobacteria: Contribution of sedDNA Analyses
		The Use of sedDNA to Track Anthropogenic-Induced Change: Impact of climate and Pollution on Cyanobacteria Abundance, Community Structure and Taxonomic Composition
		The Use of sedDNA in Evaluating the Temporal Dynamics of Potentially Toxic Cyanobacteria
	Methodological Considerations
	Future Directions
	Summary
	References
Chapter 6: Protist DNA from Lake Sediments
	Introduction
	Protist Ecology
		Taxonomic and Functional Diversity of Protists
		Protists Diversity Across Biomes
		Role of Protists in Aquatic Ecosystems
			Phototrophic Protists
			Heterotrophic Protists
	SedDNA Analysis of Protist Communities
		Workflow of the sedDNA Approach to Study Past Lake Protists
			Selection of Coring Sites
			Sediment Quantity
			DNA Extraction from the Sediment Matrix
			Molecular Techniques
			Resurrection Ecology
			Technical Replicates
		Taphonomy of Protist DNA from Sources to Sediments
		Reliability of the Molecular Signal
		Signal from Sediment-Living Protists
			Environmental Changes in the Anthropocene
			Holocene Records
			Biogeography
			Long-Term Perspective on Protist Biodiversity
			Protists as Potential Paleo-Indicators
	Summary
	References
Chapter 7: Diatom DNA from Lake Sediments
	Introduction
	Diatoms as Ecological Indicators
	Evolution, Taxonomy and Identification of Diatoms
	Environmental and Sedimentary DNA of Diatoms
		Established Metabarcoding Approaches for Diatoms
		Comparison of Microfossil and sedDNA Diatom Data and Their Limitations and Biases
		Diatom Resting Stages and Their Potential to Investigate Past Diatom Population Genetics
	Advances for Paleoecological Research
	Emerging Topics and Future Directions
		Technical Advancements in Metabarcoding
		Ecosystem Level Approaches Including Diatoms
		Quantitative Use of Environmental DNA
	Summary
	References
Chapter 8: Aquatic Vegetation DNA from Lake Sediments
	Introduction
		Importance to Reconstruct Aquatic Vegetation
		Proxies for Aquatic Vegetation Reconstruction
		Aquatic Vegetation and Its Ecology
		Grounds for Further Research
	Detection and Identification of Aquatic Macrophytes with Molecular Methods
		Methodological Approaches (Metabarcoding, Shotgun Sequencing, Targeted Capture)
		Representation of Aquatic Plants in sedDNA Data
		Factors Affecting the Detection and Preservation of Aquatic Macrophyte sedDNA
	Applications of sedaDNA to Macrophyte Ecological Research
		Detecting Plant Dispersal, Establishment, and Survival
		Reconstruction of Past Aquatic Vegetation Communities
		Reconstructing Past Environments
		Detection and Monitoring of Invasive Plants
		Reconstruct Past Trophic Networks
	Summary
	References
Chapter 9: Aquatic Animal DNA from Lake Sediments
	Introduction
	Zooplankton Population and Community Dynamics
		Preservation of Zooplankton Resting Stages and DNA in Sediments
		Examining External Stressors as Drivers of Zooplankton Population or Community Dynamics
		Zooplankton-Parasite Studies
		Moving Beyond Ephippial DNA
	Aquatic Vertebrate Population and Community Dynamics
		PCR-Based Approaches
			Fishes
			Other Vertebrates and Their Parasites
		Vertebrate Reads Detected via Shotgun Sequencing
	Summary
	References
Chapter 10: Terrestrial Plant DNA from Lake Sediments
	Introduction
		Advantages of Palaeoecological Studies Using sedDNA Compared with Pollen and Macrofossils
		Representation of Terrestrial Taxa in sedDNA and Taphonomy of DNA
		Molecular Ecology Approaches Used to Detect Floral Diversity (Metabarcoding, Shotgun and Capture Probe)
		Bias in sedDNA Methods on Past Floral Reconstructions
	Applications of sedDNA Approaches
		Reconstructing Past Vegetation
		Plant Dispersal and Establishment
		Reconstructing Arctic and Alpine Ecosystems
		Tracing Single Species and Intraspecific Variation
		Detection of Human Impact on Vegetation and Domesticated Taxa
	Future Directions
	Summary
	References
Chapter 11: Terrestrial Fauna and Hominin DNA from Sedimentary Archives
	The Environmental DNA of Ancient Animals
	The Taphonomy and Magnitude of Animal eDNA Shedding
	The Spatial Distribution of eDNA from Animals
	Challenges in Contextual Authentication
	Detecting Stratigraphically Decontextualized sedDNA
	Where to Look for Ancient Animal eDNA?
	Caves and Rock Shelters
	Lakes and Swamp Areas
	Permafrost and Periglacial Sediments
	Archaeological Sites
	Animal sedDNA Recovery, Targeting, and Sequencing
	Considerations to Be Made in the Lab When Processing Materials for Animal sedDNA
	Shotgun Metagenomics
	PCR Metabarcoding
	Capture Enrichment
	Bioinformatic Considerations
	Data Processing and Analysis
	Realistic End Products of Animal sedDNA Research
	Determining Presence/Absence of Species Through Time with sedDNA
	Can We Estimate Animal Biomass Abundance from sedDNA Data?
	Genome Assembly and Phylogenetics
	Conclusion: the Future of Animal sedDNA Research
	Summary
	References
Chapter 12: An Overview of Biodiversity and Network Modeling Approaches: Applications to Sedimentary DNA Records
	Introduction
	Food-web Structures
		Network Analyses
		Traits, Phylogeny and Unmeasured Predictors
	Biodiversity
		Diverging Responses Among Trophic Levels
		Threshold Responses and Abrupt Changes
	Integrating Analyses of Food-web Structures and Biodiversity
	Summary
	References
Chapter 13: Perspectives and Future Developments Within Sedimentary DNA Research
	Introduction
		Trajectories
	Experimental Design, Taphonomy, Sampling and DNA Extraction
		Planning
		Taphonomy
		Sampling
		Community Driven Science
		Age Estimation
		DNA Source
		DNA Extraction
	Metabarcoding
	Metagenomics
	Standards and Ethics
	The Unknown Future
	Summary
	References
Correction to: Terrestrial Plant DNA from Lake Sediments
	Correction to: Chapter 10 in: E. Capo et al. (eds.), Tracking Environmental Change Using Lake Sediments, Developments in Paleoenvironmental Research 21, https://doi.org/10.1007/978-3-031-43799-1_10
Glossary, Acronyms and Abbreviations
Index