Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation

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, eDNA may 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.</p

Characteristics of lakes where vegetation surveys and lake sediment DNA analyses were performed.

<p>Characteristics of lakes where vegetation surveys and lake sediment DNA analyses were performed.</p

Lake depth versus detection probability.

<p>Relationship between lake depth and probability that a species present in the vegetation and detected at least once by eDNA is detected by eDNA in a given lake. The relationship is modelled as a logit function and back-transformed to the probability scale.</p

Read numbers per taxa and per lake, and the sum per taxa for all lakes.

<p>Read numbers per taxa and per lake, and the sum per taxa for all lakes.</p

Match between records of taxa in the sedimentary eDNA in relation to vegetation surveys.

<p>a) Number of records in the sedimentary eDNA in relation to vegetation survey distance. b) Percentage records in eDNA in relation to abundance in vegetation surveys. c) Variation in percentage data among families with >11 eDNA records. d) Variation in percentage of taxa detected among lakes. Percentages in b), c) and d) refers to percentage of taxa recorded in the vegetation that potentially could be identified with the DNA barcode used. Note that DNA of more taxa were likely recorded but filtered out (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195403#pone.0195403.s002" target="_blank">S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195403#pone.0195403.s005" target="_blank">S4</a> Tables)–these numbers are only shown in Fig b).</p

Location of the studied lakes in Norway.

<p>Location of the studied lakes in Norway.</p

Study lakes in northern Norway.

<p>a) A-tjern, b) Brennskogtjørna, c) Einletvatnet, d) Finnvatnet, e) Gauptjern, f) Jula Jävrí, g) Lakselvhøgda, h) Lauvås, i) Øvre Æråsvatnet, j) Paulan Jávri, k) Rottjern, l) Tina Jørgensen sampling surface sediments with Kajak corer. Photo: I.G. Alsos.</p

Multivariate ordination (non symmetric correspondence analysis; NSC) of the 11 lakes.

<p>The ordination is based on taxa recorded in the vegetation (a) and eDNA (b). Note that lakes in tall forbs birch/pine mixed forest (A-tjern, Rottjern, Gauptjern are clustered together in both plots; so are also Einletvatnet and Øvre Æråsvatnet (both mire/birch forest at the island Andøya), whereas some lake with poorer DNA records show some differences in clustering.</p

Metabarcoding of modern soil DNA gives a highly local vegetation signal in Svalbard tundra

Environmental DNA retrieved from modern soils (eDNA) and late-Quaternary palaeosols and sediments (aDNA and sedaDNA) promises insight into the composition of present and past terrestrial biotic communities, but few studies address the spatial relationship between recovered eDNA and contributing organisms. Svalbard’s vascular plant flora is well known, and a cold climate enhances preservation of eDNA in soils. Thus, Svalbard plant communities are excellent systems for addressing the representation of plant eDNA in soil samples. In two valleys in the inner fjord region of Spitsbergen, we carried out detailed vegetation surveys of circular plots up to a 4-m radius. One or three near-surface soil samples from each plot were used for extraction and metabarcoding of soil-derived eDNA. Use of PCR replicates and appropriate filtering, plus a relevant reference metabarcode catalogue, provided taxon lists that reflected the local flora. There was high concordance between taxa recorded in plot vegetation and those in the eDNA, but floristic diversity was under-sampled, even at the scale of a 1-m radius plot. Most detected taxa grew within &lt; 0.5–1.0 m of the sampling point. Taxa present in vegetation but not in eDNA tended to occur further from the sampling point, and most had above-ground cover of &lt; 5%. Soil-derived eDNA provides a highly local floristic signal, and this spatial constraint should be considered in sampling designs. For palaeoecological or archaeological studies, multiple samples from a given soil horizon that are spatially distributed across the area of interest are likely to provide the most complete picture of species presence