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DNA-based monitoring of soft sediments
Derycke, S.; Beentjes, K.; Christodoulou, M.; Hansen, J.L.S.; Khodami, S.; Kröncke, I.; Arbizu, P.M.; Sapkota, R.; Staehr, P.A.U.; Van den Bulcke, L.; Winding, A.; De Backer, A. (2023). DNA-based monitoring of soft sediments. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO): Ostend. 57 pp.
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  • Genetic Tools for Ecosystem Health Assessment in the North Sea Region
Auteurs  Top 
  • Derycke, S.
  • Beentjes, K.
  • Christodoulou, M.
  • Hansen, J.L.S.
  • Khodami, S.
  • Kröncke, I.
  • Arbizu, P.M.
  • Sapkota, R.
  • Staehr, P.A.U.
  • Van den Bulcke, L.
  • Winding, A.
  • De Backer, A.
Abstract
    DNA-based monitoring has the potential to provide high resolution biodiversity data from the marine environment at a fraction of the time and costs associated with morphology based monitoring. Yet, proper ground truthing of DNA-based monitoring is needed across different member states to reach harmonization of methods and to pave the way for implementation in national and European monitoring programs. Within the GEANS soft sediment pilot, three case studies were selected in which bulk DNA-based monitoring was conducted in parallel with morphology-based monitoring: 1/ national ecological impact monitoring for aggregate extraction in the Belgian part of the North Sea, 2/ long term monitoring of a North Sea benthos observatory sampled since 1978 in Germany and 3/ impact assessment of mechanical harvesting of lugworms (Arenicola marina) in The Netherlands. The first two case studies showed very consistent results with identical ecological patterns in alpha diversity (number of species, Shannon-diversity) and beta diversity (community composition) compared to traditional morphology based sampling despite the very different objectives of the two studies. Differences between the two methods were situated in the number of species detected - significantly more species were detected with DNA-based monitoring - and in their identity - only 37% (case study 1) and 25% (case study 2) of the species were detected by both methods thereby emphasizing the complementarity of the two methods. The species responsible for the observed differences linked to sand extraction or to the seasonal fluctuations in the long term monitoring study were to some extent shared between the two methods, but each method also had unique indicator species. For the lugworm case study, no data could be obtained because of a failure in the PCR amplification step. This illustrates that DNA-based monitoring may also come with a risk of getting no data and highlights the importance of following accurate field and lab protocols. In a fourth case study, eDNA from the sediment instead of bulk DNA was used to determine macrobenthos as part of the national MSFD monitoring in the Danish part of the North Sea. Here, similar ecological patterns were observed between eDNA-based and morphological data with both methods showing significant differences between the locations and between the two depth zones. However, species lists were completely different between the two methods, illustrating that eDNA from the sediment is not suitable for macrobenthos monitoring related to MSFD assessments. The case studies all tracked time and costs associated with the two methods, and provide empirical evidence that bulk DNA-based monitoring is 26-27% cheaper and 46-66% faster than morphology based monitoring. A SWOT analysis for DNA-based monitoring of macrobenthos was conducted based on our experience with the case studies, and the contribution of GEANS to solve some of the weaknesses and threats are provided. Finally, we provide practical recommendations for performing DNA-based monitoring and highlight the next steps towards implementation of the method for marine soft-bottom environmental monitoring.
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