SAFIPO: Sammenligning av filterporestørrelser for artsspesifikk overvåkning av miljø-DNA i marine vannprøver
Can new filter types provide better results in environmental DNA monitoring? In the SAFIPO project, researchers are investigating whether alternative filters and pore sizes can contribute to better monitoring of environmental DNA.
About the project
For monitoring of environmental DNA from alien species in Danish waters, the ability of different filter types to collect environmental DNA has not yet been tested. It is possible that other pore sizes can contribute to better monitoring of environmental DNA. By testing ten different filter types in several replicates, water samples filtered from Elsinore's Øresund Aquarium are compared. All filter samples are analysed in the same way with the same extraction and the same setup of digital droplet Polymerase Chain Reaction. This is to investigate whether it would be beneficial to switch to a different filter type.
The SAFIPO project is carried out for the Danish Environmental Protection Agency to elucidate whether switching to other filter types with other pore sizes may be beneficial in connection with the monitoring of environmental DNA that has been carried out under the MONIS projects (‘Monitoring of non-indigenous species’) on water samples collected in Danish waters. The MONIS projects include environmental DNA monitoring carried out under the Danish NOVANA programme.
Over the past ten years, monitoring of marine species by means of detection of environmental DNA in water samples has been carried out all over the world. Most projects focus on detecting all environmental DNA in a water sample from many different organisms within a defined taxonomic group, through what is also known as ‘eDNA metabarcoding’. In the MONIS projects, the focus has instead been on detecting a few specific species that are considered alien in Danish waters.
Previous studies that have attempted to compare the ability of different filter types to retain environmental DNA have been based on improving the diversity profile that can be achieved by eDNA metabarcoding. However, because the MONIS projects instead focus on a few, selected, specific species, it is not necessarily the case that the filter types and pore sizes that work best for eDNA metabarcoding are also the best for specific monitoring of individual species' environmental DNA in Danish waters.
The purpose of the trial is therefore to elucidate whether there may be advantages in using other filter types than what has been used in the MONIS projects so far, in relation to the ability of the different filter types and pore sizes to retain environmental DNA from individual species. To make this comparison of filter types as uniform as possible, and without the influence of factors other than filter pore size and type of filter membrane, this comparison of filter units has been carried out on water taken from the Øresund aquarium in Elsinore, where there are a similar number of individuals of different species.
Water from the same aquarium can then be filtered using the same pump system, and the subsequent laboratory part is carried out in the same way for all samples. In the laboratory, the number of environmental DNA molecules per litre of filtered water can then be counted and the different filter types compared. By testing several different detection systems aimed at both fish and invertebrates in the aquarium, the ability of the different filter units to retain environmental DNA molecules can be compared across different species.