Preliminary evaluation of the performance of eDNA for marine species detection

Environmental DNA (eDNA) is the collective term for DNA molecules that are released from living or dead organisms in the form of blood, skin, mucous, gametes or faeces into the environment. Subsequently eDNA can be extracted from environmental samples such as water, air or.  Techniques employing eDNA are non-invasive (i.e. do not require the direct observation or sampling of an organism), instead relying on DNA found in the environment as a source of information. As a result, eDNA is rapidly emerging as a valuable tool for assessing species presence and biodiversity monitoring. There are two methods for analysing eDNA – metabarcoding and quantitative (q)PCR. Both methods are usually targeting mitochondrial (mt)DNA due to the much higher copy number per cell than nuclear (n)DNA.

While metabarcoding detects multiple species, qPCR is species (or taxanomical group specific). Specific probes and primers bind to target sequences (i.e. specific species) in the eDNA sample.  An advantage of qPCR over metabarcoding is that only targets species specific DNA and not, as metabarcoding, multiple species making qPCR more sensitive and can detect lower concentrations of eDNA.  In addition, it has been used to estimate the relative biomass of the target. However, qPCR cannot detect biodiversity as the method will only target what is being searched for while metabarcoding can target a wide range of taxa simultaneously.

The purpose is to develop and validate species-specific qPCR assays for eDNA and deploy these approaches in ATLAS areas. The sampling will consists of water samples from different depths. Water samples will be filtered and filters preserved until analysed. These objectives are divided into tasks as follows: (i) cold-water coral Lophelia pertusa, (ii) vulnerable deep-sea seamount fish species Hoplostethus atlanticus or Beryx decadactylus, (iii) assess qPCR as a tool for estimating biomass of deep-sea fish species Helicolenus dactylopterus, (iv) qPCR analyses to help identifying seamount hotspots of pelagic biodiversity Thunnus obesus and Mobula tarapacana, and (v) identifying dispersal patterns of hydrothermal vent species Bathymodiolus azoricus, or Mirocaris fortunata or Segonzacia mesatlantic.

Results from a recently accepted study (Gargan et al., in press, Marine Biology) on Mobula tarapacana eDNA from seamounts of the Azores will be presented.