New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

Abstract

Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation might affect DNA archiving via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new knowledge from this approach concern the DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).

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.…”

“…The long term persistence of residues of some species could partly explain the temporal inconsistence recorded in some palaeoenvironmental studies. 14,22 In addition to the crop taxa detected with the eDNA analyses, results obtained at the Fromonvilliers and Louroux sites both indicated a significant contribution of weeds to the total number of reads. Weeds were characterized by a larger diversity than the cultivated species in almost all the studied plots (90% at the Fromonvilliers site and 50% for the Louroux site), and were identified with more eDNA reads in a large number of plots (e.g.…”

“…Nevertheless, particular attention should be paid to the potential release of past cultivated crop eDNA stored in soil, in particular hardly degradable eDNA from grapevine or other woody species. 22 The targeting of the exact plant species grown on the soils delivering sediment to the riverine and lacustrine systems through the analysis of eDNA is particularly powerful and promising to improve our understanding of sediment transfer processes and to design effective erosion control measures. Furthermore, the current research demonstrated that this technique was able to identify weeds, which opens novel perspectives to investigate the resistance of these plants to herbicides by studying their detection in sedimentary sequences.…”

“…Furthermore, Yoccoz et al 8 demonstrated the absence of DNA sequences in a meadow that was never cultivated located 1 km away from the formerly cultivated plots. This result suggests that the locally produced biomass contributes the large majority of the soil DNA at a given location and that long-distance transport can be not significant 22 .…”

Sediment source fingerprinting: benchmarking recent outputs, remaining challenges and emerging themes

“…However, there remain several methodological challenges that require further research. In particular, upper organic and mineral topsoil layers were shown to be enriched in plant DNA compared with deeper soil horizons, which may complicate the use of this technique in catchments dominated by sub-soil erosion (Giguet-Covex et al 2019 ).…”