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

Amy C. Thorpe*, Eleanor B. Mackay, Tim Goodall, James A. Bendle, Stephen J. Thackeray, Stephen C. Maberly, Daniel S. Read*

*Corresponding author for this work

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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
Original languageEnglish
JournalMolecular ecology resources
Early online date23 Nov 2023
Publication statusE-pub ahead of print - 23 Nov 2023

Bibliographical note

We thank fieldworkers past and present for collecting data for the long-term monitoring records, and the Freshwater Biological Association for collection of earlier records. We are also thankful to Alice Hardman for assistance with collecting and sectioning the sediment core, and Katharine Moss and Grace Duffy for assistance in the field. DSR, SCM, SJT and EBM were supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability. Monitoring of Esthwaite Water is also supported by UK-SCAPE. ACT was supported by the Leverhulme Trust Grant, PRG-2018-110.


  • time‐series
  • Lake
  • phytoplankton
  • palaeolimnology
  • sedDNA


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