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

• Published in: PLOS ONE
• Main Authors: Inger Greve Alsos, Tina Jørgensen, Ludovic Gielly, Per Sjögren, Youri Lammers, Mary E. Edwards, Nigel G. Yoccoz
• Format: Article in Journal/Newspaper
• Language: English
• Published: Public Library of Science 2018
• Subjects: VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480; VDP::Mathematics and natural science: 400::Zoology and botany: 480; Lakes; Sediment; Polymerase chain reaction; Sequence databases; DNA filter assay; Taxonomy; Ancient DNA; Pollen; Research Article; Earth Sciences; Marine and Aquatic Sciences; Bodies of Water; Ecology and Environmental Sciences; Aquatic Environments; Freshwater Environments; Geology; Petrology; Sedimentary Geology; Biology and Life Sciences; Molecular Biology; Molecular Biology Techniques; Artificial Gene Amplification and Extension; Research and Analysis Methods; Database and Informatics Methods; Biological Databases; Bioinformatics; Sequence Analysis; Molecular biology assays and analysis techniques; Computer and Information Sciences; Data Management; Genetics; DNA; Biochemistry; Nucleic acids; Paleontology; Paleogenetics; Plant Science; Plant Anatomy; General Biochemistry; Genetics and Molecular Biology; General Agricultural and Biological Sciences; General Medicine; envir; geo; Alsos; Lammers; Norway; Northern Norway
• Online Access: https://hdl.handle.net/10037/13448; https://doi.org/10.1371/journal.pone.0195403; https://eprints.soton.ac.uk/420176/; http://europepmc.org/articles/PMC5903670; https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0195403&type=printable; https://www.mendeley.com/catalogue/26e041df-30ad-3e8c-9087-8a1f439bed20/; https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195403; https://www.ncbi.nlm.nih.gov/pubmed/29664954; https://munin.uit.no/handle/10037/13448; https://ui.adsabs.harvard.edu/abs/2018PLoSO.1395403A/abstract; https://academic.microsoft.com/#/detail/2800305992; http://europepmc.org/articles/PMC5903670?pdf=render

This is the final version of the following article: Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195403, which can be retrieved from https://doi.org/10.1371/journal.pone.0195403. Licensed CC BY-NC-ND 4.0. 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 ...