| Description |
xii, 253 pages : illustrations (chiefly color) ; 26 cm |
| Contents |
Machine generated contents note: 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 silico primer design and testing -- 2.3.1. Prerequisites -- 2.3.2. Reference sequences: description, filtering, and formatting for ecoPrimers -- 2.3.3. In silico primer design with ecoPrimers -- 2.3.3.1. The ecoPrimers output -- 2.3.4. In silico 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 |
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Note continued: 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 |
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Note continued: 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 |
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Note continued: 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 |
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Note continued: 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. The 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 |
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Note continued: 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 detectability of eDNA in freshwater ecosystems -- 12.1.1. Production -- 12.1.2. Persistence |
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Note continued: 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. Detectability, 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 -- 15. Paleoenvironments -- 15.1. Lake sediments -- 15.1.1. Pollen, macrofossils, and DNA metabarcoding -- 15.1.2. Plants and mammals from Lake Anterne |
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Note continued: 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 |
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Note continued: 17.2. Methodological and experimental specificities of eDNA diet analyses -- 17.2.1.eDNA sources -- 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 metazoan 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. Single-marker approach -- 19.1.2. Multiplex approach |
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Note continued: 19.2. Shotgun-based metabarcoding -- 19.2.1. Without enrichment by capture -- 19.2.2. With enrichment by capture -- 19.3. Toward more standardization -- 19.3.1. For sound comparisons across studies -- 19.3.2. For environmental monitoring -- 19.4. Next-generation reference databases -- 19.5. Open questions -- 19.5.1. What will be the impact of new sequencing technologies on eDNA analysis? -- 19.5.2. Will some specific repositories be developed for DNA metabarcoding? -- 19.5.3. Will metabarcoding provide quantitative results? -- 19.5.4. Will metabarcoding be fully integrated into ecological models and theories? -- 19.5.5. How do we train students and managers to effectively integrate this tool into academic and operational ecological research and monitoring? |
| Summary |
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning - Provided by publisher |
| Bibliography |
Includes bibliographical references (pages 223-246) and index |
| Subject |
Microbial ecology -- Research
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Molecular microbiology -- Research
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DNA, Fossil -- Analysis
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Environmental monitoring
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Biodiversity -- Research
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| LC no. |
2017959944 |
| ISBN |
9780198767220 |
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0198767226 |
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9780198767282 |
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0198767285 |
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