Use of metabarcoding to detect non-indigenous species in Danish harbors: methods comparison
Sapkota, R.; Winding, A.; Staehr, P.A.U.; Andersen, N.R.; Buur, H.; Hablützel, P.I. (2023). Use of metabarcoding to detect non-indigenous species in Danish harbors: methods comparison. Scientific Report from DCE – Danish Centre for Environment and Energy, 267. Aarhus University, DCE – Danish Centre for Environment and Energy: Aarhus. 30 pp.
Part of: Scientific Report from DCE – Danish Centre for Environment and Energy. Aarhus University, DCE – Danish Centre for Environment and Energy: Aarhus. ISSN 2245-0203
This report provides a comparison of non-indigenous species (NIS) in the marine environment detected using three different methods: conventional monitoring, and two eDNA molecular based methods: qPCR and metabarcoding. Conventional NIS detection is limited in early rapid detection of NIS, and eDNA are proposed as an alternative method, as eDNA is less invasive, is supposed to cover a larger area and potentially with a high level of detection. In the monitoring of NIS in six Danish harbors in 2021 by conventional methods and NIS specific qPCR detection systems for 23 species, eDNA was collected from three stations in each of the six harbors. This eDNA was used for metabarcoding with three different primer sets: 18S rDNA, cytochrome oxidase I (COI) and 12S rDNA, targeting eukaryotes, invertebrates and fish, respectively. The results show a higher number of NIS detected by metabarcoding followed by conventional and qPCR techniques. Only three NIS were found by all three methods, while metabarcoding found 23 unique species. While metabarcoding has advantages compared to conventional and qPCR analyses; metabarcoding results are sensitive to the applied bioinformatics pipelines which should be standardized and optimized along with the reference databases of the marine species in Danish and regional waters.
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