New publication on methods comparison

06 April 2023 - Published by Nele Jacobs
A Danish case study covering six major harbors confirms the potential of metabarcoding as a cost-effective monitoring tool for non-indigenous species.

GEANS partners Aarhus University and VLIZ compared conventional monitoring (visual identification), qPCR and metabarcoding in terms of detection potential and analysis costs for monitoring non-indigenous species (NIS).  Six Danish harbors were sampled in 2021, using conventional methods (scraping, sediment, settling plates) and eDNA was collected from water samples and settling plates. eDNA was used for qPCR detection of 23 NIS and metabarcoding using primers sets for 18S rDNA, cytochrome oxidase I (COI) and 12S rDNA, targeting eukaryotes, invertebrates and fish, respectively. The metabarcoding data were analyzed using two different bioinformatics pipelines.

Metabarcoding outperformed conventional and qPCR techniques in the detection of NIS. Only three NIS were found using all three methods, whereas metabarcoding found 23 different species. However, the bioinformatics pipeline used has an effect on the number of species detected. In terms of efficiency, using DNA-based techniques resulted in a substantial reduction of costs and analysis time, when using DNA from water samples. Bulk analyses were both more expensive and time-consuming. Although qPCR appeared to be more sensitive than metabarcoding, the limited number of detection systems makes it difficult to detect new NIS.

Metabarcoding does have clear advantages over conventional and qPCR analyses, but since results are sensitive to the applied bioinformatics pipelines, results should be standardized and optimized. The same applies to the reference databases of the marine species in Danish and regional waters.


Read more:

Sapkota, R., Winding, A., Stæhr, P.A.U., Andersen, N.R., Buur, H., Hablutzel, P. 2023. Use of metabarcoding to detect non-indigenous species in Danish harbours: Methods comparison. Aarhus University, DCE – Danish Centre for Environment and Energy, 30 pp. Technical Report No. 267