Ocean Megafauna Tracking by eDna passive sampling – OMTeDNA

The inventory of marine biodiversity is carried out by direct observation, detection of activity (acoustics) or capture of living organisms, which is often difficult to implement due to the inaccessibility or ecology of the species. An innovative solution used worldwide (known as eDNA) is to collect a water sample in which the DNA fragments are filtered, amplified, sequenced and compared to genetic databases, thus enabling a list of the species present in the sampled environment. Currents, tides and waves contribute to the dispersal of eDNA, but studies show localized vertical and horizontal dispersal, allowing eDNA to give a picture of the species present in the study area. However, such sampling along a standard transect is likely to fail to detect DNA from mobile species that are absent or in low density at the time of water sampling. To address this limitation, this project will develop a method using passive eDNA sampling to inventory marine biodiversity (from bacteria to mobile megafauna), based on the use of submerged eDNA samplers to collect eDNA from the marine environment. Step 1 of the project is to develop prototypes of long-term stable passive eDNA samplers. Material shape, porosity, chemical composition and surface condition will be characterised in relation to DNA adsorption with both intra- and extracellular DNA. These prototypes will then be tested under increasingly complex conditions: (1) in mesocosms with increasing fish densities to test their ability to record these densities and as a function of water immersion times, (2) in a closed inlet to test the detection of low density species (sea turtle) and the fish community in comparison with the traditional eDNA transect/filtration method and (3) in a coastal lagoon communicating with the sea to test the detection of bacteria, phytoplankton and the fish community, also in comparison with the traditional eDNA method. Step 2 of this project aims to validate the detection of a mobile species by a passive sampler network. The experiment consists of secreting known DNA (with a variable secretion flux) from a boat that will perform different trajectories at different speeds to mimic the movement of a mobile species in a passive sampler array. In order to understand the dispersion of DNA between the donor (moving boat) and receiver (sampler network), the water circulation of the study area will be modelled by deploying measurement devices (radio equipped buoys). Step 3 will be the deployment of samplers in the natural environment (e.g., in offshore wind farms, marine protected areas) to assess their frequentation by mobile megafauna, by comparing the performance of passive samplers with classical (eDNA) and complementary (acoustic and video recordings) inventories. The water circulation of the studied area will be modelled (Lagrangian model), based on in situ measurements collected by a network of Acoustic Doppler Current Profilers (ADCP). The objective is also to evaluate the dimensioning of the protocol (number of samplers, distance between samplers, immersion time) in order to propose an optimised sampling plan. This clearly interdisciplinary project will considerably improve knowledge of the life cycle of eDNA (state, dispersion, adsorption), adapt an original methodology (passive samplers) to this rapidly expanding field (eDNA inventory) and thus improve the performance of marine biodiversity monitoring, which is currently under-detected.