Abstract
Artificial coastal structures associated with coastal defences, energy generation, ports, marinas and other developments, are known to support lower levels of biodiversity than natural coastal environments and tend to be hotspots of invasive non-native species (INNS). In the present study, we attempted to detect INNS through both quantitative (q)PCR and metabarcoding of environmental (e)DNA from seawater samples. A mitochondrial COI based species-specific qPCR assay was developed and deployed to detect Didemnum vexillum, a colonial tunicate that has successfully become established at coastal sites across Europe. Our targeted qPCR assay was able to detect D. vexillum in eDNA seawater samples from all sampled sites where it is currently found in Ireland and Wales. Through metabarcoding of the same eDNA samples, we detected an established INNS at all sites but not D. vexillum even in locations where it is present. We conclude that our qPCR approach is effective for sensitive and targeted screening for specific INNS at coastal sites including those with artificial structures, and while metabarcoding is a less sensitive approach it is a valuable tool to detect a broad taxonomic range of native and non-native species.
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Data availability
Raw sequences will be made available on Zenodo. These data are also stored in University College Dublin data repositories and will be made available on request from the corresponding author.
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Acknowledgements
Thanks to Jen Coughlan and Gary Gillespie from UCD for field assistance, and to marina management and staff for access, during sample collection. Further, we thank the Conwy Harbour master and Holyhead Port Authority, Hannah Earp & Holly Date for assistance with sampling.
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This research was completed as part of the Ecostructure project (part-funded by the European Regional Development Fund through the Ireland Wales Cooperation Programme 2014–2020).
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LMG assisted in study design, performed genetic benchwork, undertook genetic and statistical analyses and wrote the draft manuscript. LMG, PRB and SRV performed fieldwork and secured samples. JC was the main lead for the study and conceived the study with input from LMG, PB, SV, SRJ and TC. All authors LGM, PRB, SRV, JEI, SRJ, TPC and JC assisted in planning, critical analysis and development of all drafts and the final manuscript.
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Gargan, L.M., Brooks, P.R., Vye, S.R. et al. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biol Invasions 24, 635–648 (2022). https://doi.org/10.1007/s10530-021-02672-8
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DOI: https://doi.org/10.1007/s10530-021-02672-8