Metabarcoding is a method of sequencing the DNA barcodes of many different organisms in parallel.
Classic DNA barcoding is of limited use for biodiversity surveys for two main reasons. First, it is too slow and expensive for generating large-scale data across diverse groups (e.g. arthropods other invertebrates) because it requires a separate sequencing reaction for each specimen. Second, it can’t be used on samples that contain DNA from a mixture of related species (e.g. environmental samples).
Metabarcoding solves this problem by using High Throughput Sequencing on community DNA to identify diverse taxa in a single reaction. When metabarcoding is applied to environmental samples, such as water, it is known as eDNA metabarcoding.
The principle steps in a metabarcoding pipeline are:
(1) Extract community DNA from your sample
(2) PCR amplify the barcode region using general primers optimised for your target taxon group (e.g. fish / arthropods / molluscs)
(3) Sequence the amplified DNA on a high throughput sequencing platform such as the Illumina MiSeq
(4) Bioinformatically process the raw sequence data to obtain a species x sample table that can be used for ecological analysis
USE FOR impact assessment
Several studies have demonstrated that the majority of species in a sample can be recovered using metabarcoding (Hajibabaei et al., 2011; Yu et al., 2012; Carew et al., 2013), and that ecological information is recovered accurately (Yu et al., 2012; Ji et al., 2013).
Metabarcoding enables the responses of thousands of species to be assessed quickly and cheaply, yielding high-resolution data on environmental change over time and space. This is extremely powerful for impact assessment.