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Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

Hänfling, Bernd; Lawson Handley, Lori; Read, Daniel S.; Hahn, Christoph; Li, Jianlong; Nichols, Paul; Blackman, Rosetta C.; Oliver, Anna; Winfield, Ian J.

Authors

Dr Bernd Haenfling B.Haenfling@hull.ac.uk
Senior Lecturer/ Chair of the Evolutionary Biology Group (EvoHull)

Lori Lawson Handley

Daniel S. Read

Christoph Hahn

Jianlong Li

Paul Nichols

Rosetta C. Blackman

Anna Oliver

Ian J. Winfield

Abstract

Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net data set available in the UK. Seventy-eight 2L water samples were collected along depth profile transects, gill-net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill-net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.

Publication Date 2016-07
Journal Molecular ecology
Print ISSN 0962-1083
Electronic ISSN 1365-294X
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 25
Issue 13
Pages 3101-3119
Institution Citation Hänfling, B., Lawson Handley, L., Read, D. S., Hahn, C., Li, J., Nichols, P., …Winfield, I. J. (2016). Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular ecology, 25(13), 3101-3119. https://doi.org/10.1111/mec.13660
DOI https://doi.org/10.1111/mec.13660
Keywords eDNA, Environmental DNA, Metabarcoding, Fish monitoring, Lakes, Lentic systems, EC water framework directive
Publisher URL http://onlinelibrary.wiley.com/doi/10.1111/mec.13660/abstract
Additional Information Authors' accepted manuscript of article: Hänfling, B., Lawson Handley, L., Read, D. S., Hahn, C., Li, J., Nichols, P., Blackman, R. C., Oliver, A. and Winfield, I. J. (2016), Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol Ecol, 25: 3101–3119. doi:10.1111/mec.13660

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