- Course overview
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- Environmental DNA
- DNA metabarcoding and its applications
- DADA2 for analysing metabarcoding data
- Taxonomic classification to assess biodiversity
- Statistics principles in data analysis
- Advances in biodiversity exploration
- Open data resources for eDNA
- Bringing data to life: Data management and sharing
- Further learning
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- References
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DNA extraction
For DNA extraction for DNA metabarcoding there are numerous specialised kits to isolate and purify DNA from various environmental samples, such as soil, water, and biological tissues. These kits streamline the process, making it accessible for researchers to obtain high-quality DNA suitable for downstream applications like PCR amplification and sequencing. Key features often include reagents for cell lysis, DNA binding, washing, and elution, optimised for high yield and purity. The effectiveness of the kits often depends on the sample type, so a literature review may be needed before selecting a specific kit.
Chemical lysis methods such as the phenol-chloroform-isoamyl alcohol (IAA) extraction method is a traditional technique that uses organic solvents to separate DNA from proteins and other contaminants, though it requires careful handling due to the hazardous chemicals involved. It is most useful where complete lysis of the sample is required, or to maximise DNA yield. However, most kits perform well in comparison. There are also other homemade protocols available if commercial kits are not available or within budget, for example Mu-DNA extraction methods for a variety of sample types (S Sellers G et al, 2018).
The DNeasy PowerSoil Pro Kit (Qiagen) is widely used for its efficiency in extracting DNA from challenging soil matrices by breaking down complex organic material. It utilises a mechanical lysis method with beads and includes inhibitor removal steps to ensure high-quality DNA.
The ZymoBIOMICS Fecal/Soil DNA Miniprep Kit (Zymo Research) is commonly used for handling both faecal and soil samples, ensuring high-quality DNA extraction through a streamlined process that reduces inhibitor carryover by incorporating mechanical lysis and inhibitor removal technology.
Effective DNA extraction is critical in DNA metabarcoding as it directly impacts the accuracy of biodiversity assessments, species identification, and ecological studies. By providing consistent and reliable results, these kits and methods play a crucial role in environmental DNA (eDNA) research and monitoring programs.
The next step in the metabarcoding workflow after DNA extraction is sequencing. You can proceed to the next page to explore the sequencing strategies that are best suited for your project.