Ecological indicators based on quantitative eDNA metabarcoding: the case of marine reserves

Abstract

In a context of marine biodiversity erosion, the need to better understand the effects of overfishing stands out. New genetic techniques such as environmental DNA (eDNA) metabarcoding have emerged and allow the detection of a wider range of species compared to conventional methods, but still fall short of providing reliable abundance estimations and subsequent ecological indicators. In this paper, we propose a combination of metabarcoding and quantitative polymerase chain reaction to obtain the quantity of eDNA molecules per species. This method was used inside and outside six no-take Mediterranean marine reserves to measure the effect of the protection on fish species and build a new indicator. Even if the total quantity of fish eDNA molecules was not different between the inside and outside of the reserves, we detected that cryptobenthic fish eDNA was significantly associated to the outside of reserves. Based on this observation, we propose a novel ecological indicator, the Demerso-pelagic to Benthic fish eDNA Ratio (DeBRa), taking advantage of the eDNA capacity to detect cryptobenthic reef fishes which are often missed by classical surveys. The DeBRa was significantly higher inside reserves, reflecting a higher relative quantity of eDNA molecules belonging to pelagic and demersal fishes under protection against fishing, therefore it appears to be a reliable eDNA-based indicator of human pressure. Furthermore, the DeBRa was not sensitive to habitat or environmental variations and does not require a complete reference database of eDNA sequences since it can rely on sequences assigned at the genus or family scale if possible and necessary.