Metabarcoding lake sediments: taphonomy and representation of contemporary vegetation in environmental DNA (eDNA) records

Abstract

21Metabarcoding of lake sediments may reveal current and past biodiversity, but little is known 22 about the degree to which taxa growing in the vegetation are represented in environmental DNA 23 (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA 24 at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 25 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA 26 records, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m 27 away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of 28 the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside 29 the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, 30 and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. 31 Detection rate and taxonomic resolution varied among plant families and functional groups with good 32 detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The 33 representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and 34

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

“…3). This relationship probably reflects the significant role of biomass production that has been described in previous studies 2,40 . However, phases (d) and (f) do not follow this pattern.…”

“…In addition, poor DNA preservation might also be explained by low water depth that engenders high temperatures and oxygenation at the lake bottom. Higher detection probability of taxa has been demonstrated in studies of deeper lakes in boreal to alpine environments in Northern Norway 40 . In Lake Serre de l'Homme, better in-lake preservation conditions are assumed to have existed from 300-100 cal.…”

“…At least four of these plants live in wet environments (Athyrium sp., Caltha sp., Saliceae and Filipendula ulmaria). The proximity or good connection between these wet environments and the lake might have favoured DNA transfer of plants that grow in these environments, such as DNA from the aquatic plants 28,40 that appear throughout the Serre de l'Homme record (successions of Myriophyllum sp., Sparganium sp. and Potamogeton sp.…”

“…Whereas taphonomic processes are relatively well-understood for pollen and plant macro-remains, their understanding for lake sedDNA is still limited 2,8,37 , especially for extracellular DNA, which by definition excludes the DNA from pollen and plant macro-remains. However, a recent review 2,19 , along with two studies that compared modern vegetation with pollen and DNA analyses from surface sediments from a large set of lakes in different vegetation environments (tundra to forest-tundra environments 39 ; boreal and alpine 40 ) have suggested the following: (1) pollen does not significantly contribute to DNA records, (2) the DNA has a local origin and probably has a similar source as the macrofossils, (3) aquatic plants are well-represented, (4) taxa detection seems to depend on the distance to lakeshore, the relief and its abundance (biomass) in the vegetation, (5) different physical and chemical sediment characteristics might have an impact on the DNA preservation. These studies targeted both intra and extracellular DNA, of which the respective contribution to the sediments remains unclear 2 while the taphonomic processes affecting each of these DNA pools can be expected to differ.…”

Clitellate worms (Annelida) in lateglacial and Holocene sedimentary DNA records from the Polar Urals and northern Norway

“…While probability statistics may be used to inform the likelihood of a record to represent a true positive, they require an independent record for calibration (Alsos et al . ). Thus, without records of bones, detection when there are low read numbers and few PCR repeats should be interpreted with caution.…”