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

By P. F. Thomsen, J. Kielgast, L. L. Iversen, Peter R. Møller, M. Rasmussen, Eske Willerslev. PLoS ONE, 2012

980 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8495d19322e91c423642b0b64bc319c0d2db6e34

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Citations in the corpus

Transport Distance of Invertebrate Environmental DNA in a Natural River (2014, neutral): “similar to those from others (range of 3–8, [16,34,35]).”
Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems (2016, neutral): “2013); eDNA in seawater (Thomsen et al. 2012); generalist insectivore diets where the gut contents of any individual may contain many different prey items (Piñol et al.”
Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms (2015, neutral): “The lowest eDNA persistence reported to date was for two species of marine ﬁsh held in laboratory microcosms, where eDNA was undetectable in about 1–7 days (Thomsen et al., 2012a).”
Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting (2017, neutral): “Earlier eDNA experiments using discrete static mesocosms (aquariums or ponds) showed an association between density and amplification rate (Ficetola et al. 2008), density and DNA concentration (Thomsen et al. 2012) and biomass and DNA concentration (Takahara et al. 2012).”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, neutral): “…cell lysis; Taberlet et al., 2012b) for biodiversity monitoring is increasingly applied to water (e.g., Ficetola et al., 2008; Foote et al., 2012; Thomsen et al., 2012; Kelly et al., 2014; Davy et al., 2015; Valentini et al., 2016), soil (Taberlet et al., 2012b), and sediment samples (Guardiola…”
Environmental DNA detects Critically Endangered largetooth sawfish in the wild (2016, positive): “This is consistent with a rapidly growing body of research that is demonstrating the potential of eDNA as a survey technique for rare, threatened and invasive species in both freshwater (Jerde et al. 2011, Sigsgaard et al. 2015) and marine systems (Thomsen et al. 2012).”
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes (2020, positive): “The monitoring of the biodiversity of coral reefs under global changes could benefit from novel solutions with lower costs and broader applicability complementing traditional methods (Thomsen et al., 2012; West et al., 2020).”
The ecology of environmental DNA and implications for conservation genetics (2016, positive): “Sigsgaard et al. (2015) reported that eDNA surveys for endangered fish in Denmark outperformed traditional methods.”
Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods (2018, positive): “64 While these studies detected known target species using specific PCR primers, recent 65 advances in the technology of metabarcoding using universal PCR primers enabled us to 66 elucidate the complete biodiversity using eDNA (Thomsen et al., 2012a; Kelly et al., 2014a; 67 Valentini et al., 2016).”
A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant (2017, neutral): “eDNA is suggested to degrade rapidly in water, with the rate varying among species (Thomsen et al. 2012; Maruyama et al. 2014; Pilliod et al. 2014).”