Sedimentary ancient DNA: Exploring methods of ancient DNA analysis for different taxonomic groups

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12%matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNAmay be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation. PLOSONE | https://doi.org/10.1371/journal.pone. 0195403 April 17, 2018 1 / 23 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 Citation: Alsos IG, Lammers Y, Yoccoz NG, J rgensen T, Sjögren P, Gielly L, et al. (2018) Plant DNAmetabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE 13(4): e0195403. https://doi.org/10.1371/ journal.pone. 0195403 Editor: Christopher Carcaillet, Ecole Pratique des Hautes Etudes, FRANCE Received:December 21, 2017 Accepted:March 21, 2018 Published: April 17, 2018 Copyright: 2018 Alsos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files except the raw data files, which are available from Dryad using the following DOI: 10.5061/ dryad.g72v731. Funding: The work was supported by the Research Council of Norway (grant nos. 213692/F20, 250963/F20 and 230617/E10 to Alsos). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.