eDNA metabarcoding: a realistic perspective
Year: 2013
Type: dissertation
Abstract: The classic DNA barcoding approach, first described by Hebert et al. in 2003, was not able to fulfill all\nthe promises made at the time. Some challenges remained; for instance the ability of DNA barcoding to\nidentify specimens accurately up to species level. Now, the research field of DNA\nbarcoding has diversified itself and new DNA barcoding methods have been developed. These methods\nwere not only applicable to taxonomic research, but scientists realized that new forms of DNA barcoding\n(eDNA barcoding, metabarcoding and eDNA metbabarcoding) could be very well used in ecological\nresearch. For this thesis, the main promises of (e)DNA (meta)barcoding and the remaining limitations\nhave been investigated in order to find a realistic perspective on the (e)DNA (meta)barcoding approach.\neDNA could be used for the identification of species when only part of the species is present in the\nenvironment. Another promise of eDNA barcoding is that with eDNA barcoding it should be possible to\nidentify species which cannot be morphologically identified. eDNA usually involves shorter, degraded\nDNA samples and this is highly compatible to a new, advanced method for DNA sequencing: Next-\nGeneration Sequencing. With NGS, multiple DNA samples could be analyzed simultaneously, fast and\naccurately. The development of NGS facilitated the emergence of (e)DNA metabarcoding, which could\npotentially identify all the organisms present in an ecosystem. For these new forms of DNA barcoding,\nnew techniques had to be developed. Ordinary barcodes were too long and minibarcodes were needed;\nthe use of NGS involves shorter read lengths than Sanger sequencing. Since the emergence of NGS\ntechniques around 2005, DNA sequencing becomes faster and less expensive and the amount of reads\nper run is increasing. All this data needs to be analyzed and bioinformatics tools could help with this.\nAlthough (e)DNA (meta)barcoding seems very promising for the future, there are still many\nlimitations and gaps that need to be filled. Some limitations concern sampling issues: how large should\nthe sample be in order to represent the biodiversity in the area correctly? Furthermore, the (e)DNA\nneeds to be extracted from the soil and this could influence the results. Other limitations concern the\nuse of different barcodes and reference databases. There is an ongoing search for new primers and\nbarcodes, and new reference libraries have to be constructed. Techniques used for (e)DNA\n(meta)barcoding could also be limiting for achieving good results. PCR and NGS could influence the\nrelative quantities of (e)DNA and the ratio DNA:species. Bioinformatics tools have to be improved to\nprocess the large amounts of data generated by NGS and for species assignment. Lastly, there are some\nextra limitations when (e)DNA is used. Not all species excrete eDNA in their environment, and when the\neDNA is too much degraded it will bias the results. Furthermore, it is hard to be sure whether the eDNA\nfound in the samples belongs to species which are still present in the area or if it belongs to species\nwhich are already extinct. Due to the limitations mentioned above, it is not yet possible to conduct a reliable eDNA\nmetabarcoding analysis. However, research is going full steam ahead and the current limitations do not\nseem insuperable. Combined with the fact that every year, NGS is becoming faster and cheaper, the\neDNA metabarcoding approach could become available to ecologists around the world.
Author: S. Moinier
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W37101343