eDNA – Metagenomic snapshot sequencing
Metagenomic sequencing has revolutionized the research of biodiversity by enabling the comprehensive analysis of genetic material recovered directly from environmental samples. Similarly, eDNA can provide an overview of the families or genera present in a defined biotope. In contrast to metabarcoding, eDNA metagenomics involves the creation of a DNA library from all the free DNA molecules present, which is then sequenced using NGS. The analysis of this data is much more complex and demanding than for metabarcoding, as it is not a defined section of the genome or mitochondria, but short fragments of entire genomes covering only small parts of complex genomes. The result is an eDNA snapshot of all families or genera present in a defined environment.
As this method does not involve amplification and focuses on genomic DNA, the resulution of the available databases for this method is limited. The available databases are often not sufficiently curated, there are incorrect entries or the sequence data is contaminated with other species. As the variability of the genomes of closely related species is not particularly high, false positives can occur. The short eDNA fragments exacerbate this effect as there are often areas in the genome of related species that are identical or nearly identical. Species may be identified that do not occur regionally. It is often not possible to resolve the results down to the species level. eDNA metagenomics is still very experimental and much better suited to providing an overview of the genera or families present in the study area. Special care should be taken when interpreting the results and must therefore also be checked for plausibility by the customer.
