Fish environmental DNA is more concentrated in aquatic sediments than surface water
Summary
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 [...]
Summary
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 sedimentadsorbed
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.
