A practical guide to DNA-based methods for biodiversity assessment (original) (raw)

• Book title
• Acknowledgements
• 1. Introduction
  • 1.1 The application of DNA-based methods to biomonitoring
  • 1.2 Document structure
  • 1.3 Sources and states of DNA
• 2. Capture, preservation and extraction of eDNA from water
  • 2.1 Sampling strategy
  • 2.2 Precipitation or filtration
  • 2.3 Filtration method and filter type
  • 2.4 On-site or off-site filtration
  • 2.5 Volume of water
  • 2.6 eDNA preservation strategy for filters
  • 2.7 eDNA extraction from filters
• 3. Preservation and extraction of macroinvertebrate bulk samples
  • 3.1 Preservation methods
  • 3.2 Homogenisation methods
  • 3.3 Non-destructive methods for macroinvertebrate bulk samples
  • 3.4 Considerations for bulk DNA extraction
• 4. Sampling, preservation and extraction of benthic periphytic diatoms
  • 4.1 Sampling benthic biofilms
  • 4.2 Preservation methods
  • 4.3 Considerations for DNA extraction from benthic biofilms
• 5. Sampling, preservation and extraction of soils and sediments
  • 5.1 Collecting the sample
    * 5.1.1 Sample volume
    * 5.1.2 Sampling depth
  • 5.2 Separation of organisms from soils and sediments
  • 5.3 Preservation of sediment samples
  • 5.4 DNA extraction from sediment samples
• 6. Measuring quality and quantity of extracted DNA
  • 6.1 DNA quantification
  • 6.2 Inhibition testing
  • 6.3 Analytical controls used for DNA and eDNA analyses
• 7. Target species detection
  • 7.1 Analysis methods for target species detection
    * 7.1.1 Conventional PCR (cPCR) assays
    * 7.1.2 Quantitative real-time PCR (qPCR)
    * 7.1.3 Droplet digital PCR (ddPCR) assays
  • 7.2 Defining limits of detection (LOD) and quantification (LOQ)
  • 7.3 Species specific primer design and validation
  • 7.4 Quantitative interpretation of results
• 8. Metabarcoding to survey biological communities
  • 8.1 Metabarcoding primer selection
    * 8.1.2 Amplicon length
  • 8.2 Amplicon library preparation
    * 8.2.1 Types of library preparation
  • 8.2.1.1 One-step PCR
  • 8.2.1.2 two-step PCR
  • 8.2.1.3 Ligation-based approach
    * 8.2.2 PCR replication
    * 8.2.3 Choice of polymerase
    * 8.3.1 Purification
    * 8.3.2 Quantification
    * 8.3.3 Amplicon diversity
• 9. Summary and advice
  • 9.1 Factors influencing methodological choices
  • 9.3 Concluding remarks
• 10. Glossary
• 11. References
• 12. Figure information and photo credits

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