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Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community
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  • Amy Thorpe,
  • Eleanor Mackay,
  • Tim Goodall,
  • James Bendle,
  • Stephen Thackeray,
  • Stephen Maberly,
  • Daniel Read
Amy Thorpe
UK Centre for Ecology & Hydrology

Corresponding Author:[email protected]

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Eleanor Mackay
UK Centre for Ecology & Hydrology
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Tim Goodall
UK Centre for Ecology & Hydrology
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James Bendle
University of Birmingham
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Stephen Thackeray
UK Centre for Ecology & Hydrology
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Stephen Maberly
UK Centre for Ecology & Hydrology
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Daniel Read
UK Centre for Ecology & Hydrology
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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 identified in the microscopy record were also detected using sedDNA, and sedDNA revealed a previously undetected community of phytoplankton. 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. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of less than 100 years, but the taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, require further research.
06 Mar 2023Submitted to Molecular Ecology Resources
07 Mar 2023Submission Checks Completed
07 Mar 2023Assigned to Editor
07 Mar 2023Review(s) Completed, Editorial Evaluation Pending
15 May 2023Reviewer(s) Assigned
04 Sep 2023Editorial Decision: Revise Minor
25 Sep 20231st Revision Received
27 Sep 2023Submission Checks Completed
27 Sep 2023Assigned to Editor
27 Sep 2023Review(s) Completed, Editorial Evaluation Pending
09 Nov 2023Editorial Decision: Accept