Marine Biology

, 164:128 | Cite as

Seawater environmental DNA reflects seasonality of a coastal fish community

  • Eva Egelyng Sigsgaard
  • Ida Broman Nielsen
  • Henrik Carl
  • Marcus Anders Krag
  • Steen Wilhelm Knudsen
  • Yingchun Xing
  • Tore Hejl Holm-Hansen
  • Peter Rask Møller
  • Philip Francis ThomsenEmail author
Original Paper


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.


Common Eider Mute Swan European Perch Atlantic Herring Mock Sample 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

227_2017_3147_MOESM1_ESM.pdf (1.9 mb)
Supplementary material 1 (PDF 1922 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Eva Egelyng Sigsgaard
    • 1
    • 2
  • Ida Broman Nielsen
    • 1
  • Henrik Carl
    • 2
  • Marcus Anders Krag
    • 3
  • Steen Wilhelm Knudsen
    • 2
  • Yingchun Xing
    • 1
    • 4
  • Tore Hejl Holm-Hansen
    • 3
  • Peter Rask Møller
    • 2
  • Philip Francis Thomsen
    • 1
    Email author
  1. 1.Centre for GeoGenetics, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
  2. 2.Section for Evolutionary Genomics, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
  3. 3.Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
  4. 4.Natural Resource and Environment Research CenterChinese Academy of Fishery SciencesBeijingChina

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