Environmental DNA provides information on sediment sources: A study in catchments affected by Fukushima radioactive fallout

Abstract

An excessive supply of sediment is observed in numerous rivers across the world where it leads to deleterious impacts. Information on the sources delivering this material to waterbodies is required to design effective management measures, and sediment tracing or fingerprinting techniques are increasingly used to quantify the amount of sediment derived from different sources. However, the current methods used to identify the land use contributions to sediment have a limited discrimination power. Here, we investigated the potential of environmental DNA (eDNA) to provide more detailed information on the plant species found in sediment source areas as a next generation fingerprint. To this end, flood sediment deposits (n=12) were collected in 2017 in two catchments impacted by the Fukushima radioactive fallout along differing river sections draining forests, cropland or a mix of both land uses. Conventional fingerprints (i.e. fallout radionuclides and organic matter properties) were also measured in these samples. The conventional fingerprint model results showed that most sediment samples contained a dominant proportion of subsoil material. Nevertheless, the eDNA information effectively discriminated the three above-mentioned groups of sediment, with the dominance of tree, shrub and fern species in sediment sampled in rivers draining forests versus a majority of grass, algae and cultivated plant species in sediment collected in rivers draining cropland.Based on these encouraging results, future research should examine the potential of eDNA in mixed land use catchments where the contribution of topsoil to sediment dominates and where the cultivation of land has not been abandoned in order to better characterize the memory effect of eDNA in soils and sediment.

Investigating the use of fallout and geogenic radionuclides as potential tracing properties to quantify the sources of suspended sediment in a mining catchment in New Caledonia, South Pacific

“…radioactive elements) (Koiter et al 2013). In recent years, these latter have diversified with the emergence of more alternative sediment fingerprinting techniques based on sediment color (Martínez-Carreras et al 2010;Legout et al 2013), pollen plant (Brown et al 2008) or more recently environmental DNA (Ficetola et al 2018;Evrard et al 2019). This diversity in the use of fingerprints has been achieved in conjunction with the improvement of mixing models (e.g.…”

Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes

“…This approach is particularly powerful for understanding the land use and land cover source contributions to sediment transiting river systems and accumulating in lakes and ponds through the design of improved sediment fingerprinting approaches targeting the specific crop types supplying sediment. 20 Furthermore, as eDNA has been recorded in sediment accumulating in lakes over long periods, 22 the current research shows that this technique can be used to reconstruct the impact of the intensification of agricultural practices and the associated land cover change during the twentieth century on soil erosion.…”

“…extracellular DnA analyses. Soil eDNA targeting extracellular eDNA was extracted following the procedure described in Pansu et al 38 and Evrard et al 20 For each sample, approximatively 15 g of air-dried soil was mixed with 15 ml of saturated phosphate buffer (Na 2 HPO 4 ; 0.12 M, pH ≈ 8) for 15 min. Two ml of the mixture was centrifuged (10 min at 10,000 g) and ~ 400 μl of resulting supernatant was kept as starting material for extraction using the NucleoSpin Soil kit (MACHEREY-NAGEL, Düren, Germany), skipping the cell lysis step and following manufacturer's instructions.…”

“…19 The potential of this method has also been demonstrated for sediment source fingerprinting. 20 However, to our knowledge, limited information is available on the DNA memory effect in soils in general, and in intensively cultivated areas in particular. 8,21 The long-term persistence of plant DNA was investigated in Alpine soils with DNA metabarcoding by Yoccoz et al 8 In this study, soil core samples were collected in formerly cultivated plots that were abandoned between 1810 and 1986 in temperate environments.…”

Preface—evaluating the response of critical zone processes to human impacts with sediment source fingerprinting

“…Advances with novel fingerprints such as CSSIs (Blake et al 2012;Reiffarth et al 2016) and environmental DNA (Evrard et al 2019b) may provide direct information regarding changes in cropping or forestry species in a river basin. These next-generation fingerprints may help the sediment source fingerprinting technique move beyond focusing on estimating source contributions to developing a deeper understanding of how multiple processes in the critical zone have been affected by anthropogenic and natural disturbances during the great acceleration.…”