Environmental RNA in Marine Systems – eRNAmaris

Wider research context: Large-scale scientific bottom trawl surveys are still the method of choice to investigate fish-stock densities in marine systems, despite their negative impacts on the environment. The analysis of eDNA, which is becoming a common biomonitoring tool in many aquatic habitats and might replace bottom trawling, fails in providing good population estimates for marine fish. A reason is the stability of eDNA over elevated timespans in the environment, facilitating diffusion of eDNA signals over long distances and conflicting with estimating the size of local populations. Recently eRNA analysis was proposed as a potential alternative due to its faster environmental degradation which should enhance local population estimates. However, only little is known on the actual properties of eRNA. Therefore, we propose to conduct the first eRNA study on marine fish, to explore the potential of eRNA in overcoming the limitations of eDNA analysis in marine systems.
Research questions: This proposal addresses three key questions: (1) How do shedding and decay rates of different eRNA types (mRNA, rRNA) compare to those of eDNA? (2) Can the analysis of eRNA help to overcome shortcomings of eDNA analysis in marine systems? (3) How can hydrodynamic drift models improve the ability of eDNA/eRNA analysis to deliver non-invasive spatio-temporally highly resolved information on marine fish population densities?
Approach: The questions above will be addressed by an experimental design following three consequential steps. First, base-line data on the abundance and stability of eRNA in marine environments will be obtained from experiments with different fish species. Second, this data will be used to develop and parametrise a hydrodynamic diffusion/advection model describing eDNA/eRNA transport in the ocean, aiming to increase the predictive power of eDNA/eRNA analysis for fish-stock estimates. Active fish movement will be integrated into the model to evaluate its relative importance compared to eDNA/eRNA transport. Third, the new approaches will be evaluated using field data collected using bottom trawling and eDNA/eRNA during two dedicated and two opportunistic field surveys in the Bay of Biscay.
Level of originality: Being the first study on eRNA of marine vertebrates, this project will be a front runner in bringing this new approach into the science and application of nucleic-acid based biomonitoring. Only by combining the complementary expertise of the French and Austrian project partners, will it be possible to conduct this comprehensive project investigating the potentials of eRNA-based biomonitoring in marine systems.
Primary researchers involved: The project builds on the expertise of Daniela Sint (PI-AT) and Michael Traugott (Univ. of Innsbruck, AT), being specialists in the analysis of degraded DNA/RNA traces from environmental samples and Verena Trenkel (PI-FR) and Robin Faillettaz (Ifremer, FR) – experts in marine science and modelling.