Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

Abstract

Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp) eDNA fragments degrades beyond detectability within days.Although further studies are needed to validate the eDNA approach in varying environmental conditions, our findings provide a strong proof-of-concept with great perspectives for future monitoring of marine biodiversity and resources.

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

“…The eDNA is therefore likely to be primarily of local origin and the probability of detecting nonresident species decreases with distance from those species distributions, consistent with the only other field eDNA survey of marine fishes to date (Thomsen et al . 2012a). We found significant differences in eDNA community composition and relative abundance of taxa between adjacent habitat types and by distance from shore within a habitat type, indicating that sampling locations in close proximity (~60 m) had distinct eDNA assemblages.…”

“…2007), only recently has the technique been used to survey higher eukaryotes including fishes (Thomsen et al . 2012a,b; Jerde et al . 2013), mammals (Andersen et al .…”

“…2014), and to a lesser extent biodiversity profiling (Thomsen et al . 2012a,b), but uses of this technique for field ecology and conservation have lagged due to unknown error rates of detection and spatial resolution of eDNA in the field.…”

“…The ocean imposes an additional set of physical and chemical constraints affecting eDNA distribution and detection probability; currents, tides, wind and salinity all impact eDNA degradation rates and persistence in seawater (Thomsen et al . 2012a; Barnes et al . 2014).…”

Trends and frontiers for the science and management of the oceans

“…At the other extreme, the emergence of environmental DNA (eDNA), whereby traces of organisms in the water column, be it emanating from mucus, faeces or even urine, provide a remarkably sensitive way to detect the presence of species, including those that are rare and therefore diffi cult to sample through conventional means [15]. Samples of seawater from the coast of Denmark, for example, detected a suite of fi sh species -as expected -but also the presence of transient birds, thereby providing an ecosystem-wide perspective on biodiversity [16]. Thus, new technology is reinvigorating longstanding questions of biodiversity.…”