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 and sediment properties might affect DNA records 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 insights derived from this approach elucidate and assess issues relating to 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 a 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 but help the record of these human activities. 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”).

Is a Central Sediment Sample Sufficient? Exploring Spatial and Temporal Microbial Diversity in a Small Lake

“…Unfortunately, long-term monitoring data are scarce. An emerging technique that can contribute historic data is the application of molecular biological methods to sediment core analysis [19]. Employing molecular techniques, e.g., metabarcoding and droplet digital PCR (ddPCR), allows reconstruction of historical cyanobacteria communities using phylogenetic marker genes like the 16S ribosomal RNA (16S rRNA) but also functional genes (such as the mcy gene cluster) identified in sediment samples [6,7].…”

The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda

“…As predicted by current models of DNA preservation (e.g., Dabney et al, 2013b;Kistler et al, 2017), the vast majority of DNA content loss occurs rapidly after deposition in the Mubwindi Swamp (Figures 6, 7). Not only was there a sharp decline in DNA content below the top meter of bioactive sediment, we observed very few eukaryotic sequences, even in sites of recent elephant activity, suggesting that deposited DNA degrades rapidly in the acidic and warm (17-21 • C) swamp environment (Giguet-Covex et al, 2019). Based on laboratory and field experiments, acidic, warm conditions are known to promote DNA hydrolysis and are non-conducive to long-term DNA preservation (Lindahl and Nyberg, 1972;Lindahl, 1993;Strickler et al, 2015;Kistler et al, 2017;Seymour et al, 2018).…”

“…Taxa in red indicate likely taxonomic misassignments since these taxa are unknown in the area. processes, and cross-validation of our results, in the Mubwindi Swamp (Armbrecht et al, 2019;Giguet-Covex et al, 2019).…”

“…The deposition of DNA in a sedimentary basin and its representation of the locally present biota are influenced by the abundance of the locally present species, their biomass, their genome length, transport processes and by chance (but see Andersen et al, 2012;Yoccoz et al, 2012;Giguet-Covex et al, 2019). Four possible sources provide DNA to the sediments of Mubwindi Swamp including (1) DNA from micro-and macro-organisms living in the sediment, (2) DNA from organisms living on or utilizing the surface of the swamp, (3) DNA derived via streams and runoff from the catchment of the swamp (see Giguet-Covex et al, 2019), and (4) DNA derived by deposition from the air (e.g., pollen grains: Parducci et al, 2005). Given these sources, DNA extracted from the sediments will be a mixture of modern and ancient DNA.…”

“…The role of DNA leaching in saturated sediments needs to be examined since the polarity of DNA molecules should promote its degradation by hydrolysis (Lindahl, 1993;Pääbo et al, 2004). Given these issues, a much better understanding of transport, deposition, preservation and degradation of sedimentary DNA in the tropics is needed (Domaizon et al, 2017;Giguet-Covex et al, 2019).…”