Call number:
9780191079993 (e-book)
Type of Medium:
12
Pages:
1 online resource (254 pages)
Edition:
First edition
ISBN:
9780191079993 (e-book)
URL:
https://ebookcentral.proquest.com/lib/gfz-potsdam/detail.action?docID=5255026
Language:
English
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
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