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No. 133: eDNA in environmental monitoring

Winding, A., Bang-Andreasen, T., Hansen, L.H., Panitz, F., Krogh, P.H., Krause-Jensen, D., Stæhr, P., Nicolaisen, M., Hendriksen, N.B., Sapkota, R., Santos, S. & Andersen, L.W.:2019. eDNA in environmental monitoring. Aarhus University, DCE – Danish Centre for Environment and Energy, 40 pp. Technical Report No. 133. http://dce2.au.dk/pub/TR133.pdf

Summary

The use of environmental DNA (eDNA) for environmental monitoring has been presented as a technique to replace existing traditional monitoring techniques, being faster, easier and more accurate. Both the technical and economic development in the area is currently very fast and ambitions for the use of eDNA for environmental monitoring are high. In both aquatic and terrestrial environments detection of specific species or group of organisms as well as biodiversity assessment have shown promising results with eDNA. How-ever, several technological and data assessment issues have to be resolved prior to full implementation in environmental monitoring. Sharing, harmonizing and consolidating the available knowledge are therefore of prime importance in order to develop standardized procedures throughout all the steps of the process (e.g. sampling, DNA extraction, amplification primers and conditions, bioinformatic analysis) including handling of false positives and negatives. Databased scientific literature clearly demonstrates that even though sampling might be easier and faster, sequencing library preparation is still costly, although continuously decreasing, while standardized bioinformatics procedures (pipelines) make bioinformatic analyses more efficient. 
eDNA-based results generally show different aspects of the environmental state with increasing detailed knowledge on a different scale than traditional monitoring. This applies both to biodiversity and species-specific occurrence and abundance. The conventional long time series of environmental monitoring is of high value and great care should be taken not to compromise these without careful evaluation of the benefits of moving to eDNA approaches. If we convert all environmental monitoring to eDNA and stop collecting specimens for collections, we lose the possibility of certain studies requiring e.g. long time series. Therefore, it is recommended to perform parallel monitoring with eDNA-based techniques and the traditional monitoring until sufficient experience and data have been obtained to be able to follow the environmental state back to the time before eDNA monitoring.
Future techniques will probably allow metabarcoding based on longer reads thanks to advances in sequencing technologies. Another branch of eDNA analysis is expected to focus on direct sequencing of eDNA omitting PCR and the biases associated with this. In addition, the bioinformatics analyses are anticipated to be standardized and detailed in standard operating procedures. In situ monitoring will most likely be possible, either through autonomous samplers coupled with qPCR assays or portable sequencers.