Fish environmental DNA is more concentrated in aquatic sediments than surface water

By C. Turner, K. Uy, R. Everhart. 2015

513 citations recorded by the source corpus.

Abstract Genetic identification of aqueous environmental DNA (eDNA) provides site occupancy inferences for rare aquatic macrofauna that are often easier to obtain than direct observations of organisms. This relative ease makes eDNA sampling a valuable tool for conservation biology. Research on the origin, state, transport, and fate of eDNA shed by aquatic macrofauna is needed to describe the spatiotemporal context for eDNA-based occupancy inferences and to guide eDNA sampling design. We tested the hypothesis that eDNA is more concentrated in surficial sediments than in surface water by measuring the concentration of aqueous and sedimentary eDNA from an invasive fish, bigheaded Asian carp ( Hypophthalmichthys spp.), in experimental ponds and natural rivers. We modified a simple, low-cost DNA extraction method to yield inhibitor-free eDNA from both sediment and water samples. Carp eDNA was 8–1800 times more concentrated per gram of sediment than per milliliter of water and was detected in sediments up to 132 days after carp removal – five times longer than any previous reports of macrobial eDNA persistence in water. These results may be explained by particle settling and/or retarded degradation of sediment-adsorbed DNA molecules. Compared to aqueous eDNA, sedimentary eDNA could provide a more abundant and longer-lasting source of genetic material for inferring current-or-past site occupancy by aquatic macrofauna, particularly benthic species. However, resuspension and transport of sedimentary eDNA could complicate the spatiotemporal inferences from surface water sampling, which is currently the predominant eDNA-based approach. We discuss these implications in the context of conservation-oriented monitoring in aquatic ecosystems.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/02409980ca45a282ea804f4a2ba51c16dbe7e25a

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Citations in the corpus

DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity (2017, background): “Aquatic sediments are generally characterized by relatively high DNA concentrations in comparison to concentrations in the water column (Eichmiller et al. 2014; Turner et al. 2015), and most of this is thought to be extracellular DNA as demonstrated in marine sediments (Corinaldesi et al.”
Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America (2017, result): “(2015) used laboratory studies to evaluate where crayfish eDNA was most prevalent, finding most frequent detections for the species Procambarus zonangulus (Hobbs & Hobbs, 1990) in sediments rather than surface waters, similar to results for some fish species (Turner et al., 2015).”
Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus) (2015, background): “Recent observations on the distribution of carp eDNA in sediments, reported in this special issue by Turner et al. (2014), indicate that sediments are likely to be an important compartment for eDNA preservation.”
Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting (2017, methodology): “Collecting sediments instead of water samples can also be an option as Turner et al. (2015) found that for bigheaded Asian carp, eDNA is more concentrated in sediments than surface water.”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, background): “…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 et al., 2015; Turner et al., 2015; Pearman et al., 2016).”
Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation (2018, background): “Although this relatively short persistence is ideal for studies of current biodiversity (Lindahl 1993), eDNA in sediments can persist far longer and is often present at much higher concentration than is eDNA in the water column (Turner et al. 2015).”
Effective monitoring of freshwater fish (2019, methodology): “Environmental DNA (‘eDNA’ hereafter) is based on the presence DNA of fishes in water samples originating from mucus and faeces, the sloughing off of cells from their gut lining, and the decomposition of dead individuals (Davison et al., 2016; Jerde et al., 2011; Turner et al., 2015).”
Efficacy of Environmental DNA to Detect and Quantify Brook Trout Populations in Headwater Streams of the Adirondack Mountains, New York (2017, background): “2015), possibly due to differences in DNA settling rates, dilution, and/or degradation (Turner et al. 2015).”
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “However, the potential release of ‘‘ancient’’ eDNA from bottom sediments to the water column (Turner et al. 2015) might also complicate the use of aquatic eDNA as strict contemporary biodiversity surveys.”