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

Abstract

eDnA refers to DnA extracted from an environmental sample with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDnA records. to investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil samples were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, samples were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the samples as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. overall, these results illustrate the potential of eDnA analyses for identifying the recent (< 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. the capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales. Environmental DNA (eDNA) is a complex mixture of genetic material present in environmental samples. 1-4 During the last several decades, eDNA studies have significantly improved our ability to detect a range of organisms, including macroorganisms, plants, animals and even to reconstruct paleo communities. 5,6 Detection of taxa present in an eDNA sample can be accessed with a general approach based on target PCR (polymerase chain reaction) called "DNA metabarcoding". 7 This method was successfully applied in a wide range of environmental samples collected from soil compartments, 8 freshwater ecosystems, 9,10 marine environnements 11 as well as for palaeoenvironnemental reconstructions of aquatic and terrestrial ecosystems. 12-14 eDNA studies conducted on soils are assumed to analyze particles of eDNA originating from organism remains, organic matter, or from extra-cellular DNA molecules bound to soil compounds, such as clay. 15 In principle, eDNA can remain in soil or sediments for long periods as eDNA bound to clay was shown to be protected

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

“…PCR replicability was calculated as the mean proportion of detections in PCR replicates across all taxa within a sample. from grapevine are still detected in high quantity despite the crop already being strongly decreased 60 years ago [302]. The frequency of positive PCRs and the detection probability of domestic mammals was significantly higher with the Amicons (AmTaberlet2012 method), confirming their usefulness.…”

Combining spectroscopy and magnetism with geochemical tracers to improve the discrimination of sediment sources in a homogeneous subtropical catchment

“…A significant proportion of the most productive soils around the world are found under these conditions, and this situation strengthens the need to develop new approaches to discriminate between these land use-based sources. Alternative tracers such as environmental DNA (Foucher et al, 2020) and compound specific stable isotopes (CSSI) (Blake et al, 2012) may provide a powerful alternative to trace the contribution of specific land use sources to sediment. However, technical solutions allowing for the global application of these methods still need to be developed (Brandt et al, 2018;.…”

Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples

“…A recent study by Foucher et al . 49 showed that eDNA cultivated at 20–30 cm underground might remain for 6 or 7 years. Our results showed that the persistence time scale of eDNA at the soil surface was relatively shorter, possibly because the absorption of soil particles, weathering, and UV effects at the soil surface may have promoted DNA degradation.…”