Evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community

Thorpe, Amy C. ORCID: https://orcid.org/0000-0003-0210-2767; Mackay, Eleanor B. ORCID: https://orcid.org/0000-0001-5697-7062; Goodall, Tim ORCID: https://orcid.org/0000-0002-1526-4071; Bendle, James A.; Thackeray, Stephen J. ORCID: https://orcid.org/0000-0003-3274-2706; Maberly, Stephen C. ORCID: https://orcid.org/0000-0003-3541-5903; Read, Daniel S. ORCID: https://orcid.org/0000-0001-8546-5154. 2024 Evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community. Molecular Ecology Resources, 24 (2), e13903. 15, pp. https://doi.org/10.1111/1755-0998.13903

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Official URL: https://doi.org/10.1111/1755-0998.13903

Abstract/Summary

Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1111/1755-0998.13903
UKCEH and CEH Sections/Science Areas:	Soils and Land Use (Science Area 2017-) Water Resources (Science Area 2017-)
ISSN:	1755-098X
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link.
Additional Keywords:	lake, palaeolimnology, phytoplankton, sedDNA, time-series
NORA Subject Terms:	Ecology and Environment Biology and Microbiology
Related URLs:	Dataset Dataset Dataset
Date made live:	05 Dec 2023 16:34 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/536330

Item Type:

Publication - Article

Digital Object Identifier (DOI):

https://doi.org/10.1111/1755-0998.13903

UKCEH and CEH Sections/Science Areas:

Soils and Land Use (Science Area 2017-)
Water Resources (Science Area 2017-)

ISSN:

1755-098X

Additional Information. Not used in RCUK Gateway to Research.:

Open Access paper - full text available via Official URL link.

Additional Keywords:

lake, palaeolimnology, phytoplankton, sedDNA, time-series