eDNA water sampling
Environmental DNA (eDNA) is the collective term for any DNA left behind or released into the environment (water, sediment etc.) by organisms. eDNA is a combination of DNA present in living cells or conserved in organelles, in tissue fragments shed by organisms or in secretions (such as faeces, mucous or slime) as well as DNA released through the natural decay process.
The analysis of eDNA in an environmental sample can be used to infer the presence or absence of organisms in an ecosystem and has emerged as a promising tool for biodiversity assessments. eDNA analysis is typically quicker and less labour-intensive compared to traditional sampling methods such as visual surveys and is a less invasive method than capture approaches.
When a water sample is collected, it will contain eDNA from multiple organisms. We can filter a water sample and collect the eDNA on a filter (left). This DNA is then extracted from cellular debris etc. and a specific region of the DNA is amplified using specific DNA barcode markers. The use of genetic markers allows the simultaneous detection of multiple taxa in one sample through an approach called metabarcoding. These short sections of DNA are then sequenced to determine the order of nucleotides. Following quality control steps, the sequences are then compared to a reference sequence database which allows sequences to be assigned to a taxonomic group.
eDNA sampler RoCSI
The eDNA sampler – also known as the Robotic Cartridge Sampling Instrument (RoCSI) – developed by the National Oceanography Centre (NOC), is an autonomous sampling device for filtering predetermined volumes of water and preserving the filters in situ. The main advantage of this is that seawater samples can be collected at a high resolution, larger volumes of water can be filtered easily and the filters can be immediately preserved ensuring a high quality sample is collected for eDNA metabarcoding analysis. During the iMirabilis2 cruise, RoCSI will be deployed in the autonomous underwater vehicle (AUV) Autosub6000 for the first time to autonomously collect water column samples for eDNA analysis.