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Seawater environmental DNA reflects seasonality of a coastal fish community

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Abstract

Coastal marine fish populations are in decline due to overfishing, habitat destruction, climate change and invasive species. Seasonal monitoring is important for detecting temporal changes in the composition of fish communities, but current monitoring is often non-existent or limited to annual or semi-annual surveys. In the present study, we investigate the potential of using environmental DNA (eDNA) metabarcoding of seawater samples to detect the seasonal changes in a coastal marine fish community. Water sampling and snorkelling visual census were performed over 1 year (from 23rd of August 2013 to 11th of August 2014) at a temperate coastal habitat in Denmark (55°45′39″N, 12°35′59″E) and compared to long-term data collected over a 7-year period. We used Illumina sequencing of PCR products to demonstrate that seawater eDNA showed compositional changes in accordance with seasonal changes in the fish community. The vast majority of fish diversity observed in the study area by snorkelling was recovered from sequencing, although the overlap between methods varied widely among sampling events. In total, 24 taxa were detected by both methods, while five taxa were only detected using eDNA and three taxa were only detected by snorkelling. A limitation of the applied primers was the lack of resolution to species level in a few diverse families, and varying sequencing depth between samples represents a potential bias. However, our study demonstrates the utility of eDNA for recovering seasonal variation in marine fish communities, knowledge of which is essential for standardised long-term monitoring of marine biodiversity.

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Acknowledgements

This study was funded by the Danish National Research Foundation with Grant DNRF94, which was awarded to Prof. Eske Willerslev. We thank Aage V. Jensen’s foundations, which have funded the National Fish Atlas with Grant 100307-28272. We thank Prof. Eske Willerslev for project support and providing facilities for carrying out the research. We would like to thank Lillian A. Petersen and the National High-throughput DNA Sequencing Centre for help with sequencing. Morten Rasmussen is thanked for providing a custom-made script and bioinformatic assistance during data analysis of the first test sequencing.

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Authors and Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Eva Egelyng Sigsgaard, Ida Broman Nielsen, Yingchun Xing & Philip Francis Thomsen

  2. Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Eva Egelyng Sigsgaard, Henrik Carl, Steen Wilhelm Knudsen & Peter Rask Møller

  3. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Marcus Anders Krag & Tore Hejl Holm-Hansen

  4. Natural Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, China

    Yingchun Xing

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  1. Eva Egelyng Sigsgaard
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  2. Ida Broman Nielsen
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Sigsgaard, E.E., Nielsen, I.B., Carl, H. et al. Seawater environmental DNA reflects seasonality of a coastal fish community. Mar Biol 164, 128 (2017). https://doi.org/10.1007/s00227-017-3147-4

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