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

doi:10.1111/1755-0998.13903

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

Earth and Environmental Sciences

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Abstract

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 language	English
Journal	Molecular ecology resources
Early online date	23 Nov 2023
DOIs	https://doi.org/10.1111/1755-0998.13903
Publication status	E-pub ahead of print - 23 Nov 2023

Bibliographical note

Acknowledgements:
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.

Keywords

time‐series
Lake
phytoplankton
palaeolimnology
sedDNA

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

abstract = "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",

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note = "Acknowledgements: 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.",

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AU - Maberly, Stephen C.

AU - Read, Daniel S.

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AB - 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

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KW - sedDNA

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DO - 10.1111/1755-0998.13903

M3 - Article

SN - 1755-0998

JO - Molecular ecology resources

JF - Molecular ecology resources

ER -

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

Abstract

Bibliographical note

Keywords

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