Data from: evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community
Cite this dataset
Thorpe, Amy et al. (2023). Data from: evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community [Dataset]. Dryad. https://doi.org/10.5061/dryad.q83bk3jpw
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 less than 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.
README: Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community
https://doi.org/10.5061/dryad.q83bk3jpw
This dataset includes the occurrence of phytoplankton genera identified with microscopy in Esthwaite Water from 1945 to 2010.
Phytoplankton in surface water samples collected from Esthwaite Water on a weekly/fortnightly basis from 1945-2010 were identified and enumerated with microscopy. Counts were grouped at the genus level, converted to presence-absence, summed by year and normalised by the number of sampling occasions per year.
Description of the data and file structure
- Annual genus occurrence
- This file is a matrix containing the frequency of occurrence of each phytoplankton genus identified from 1945 to 2010
- Rows are genera
- Columns are years
- Sampling frequency
- This file contains the number of sampling occassions per year from 1945 to 2010 during which a water sample was collected for phytoplankton monitoring
- This data is used to normalise the frequency of occurrence to account for variable sampling effort
- Phytoplankton taxonomy
- This file contains the taxonomic classification (domain, kingdom, phylum, class, order, family and genus) of phytoplankton identified in the water samples
Links to related datasets
A long-term monitoring record of physicochemical conditions in Esthwaite Water is available at: https://doi.org/10.5285/87360d1a-85d9-4a4e-b9ac-e315977a52d3
Raw 18S rRNA gene sequences used to construct a sedimentary DNA record of the phytoplankton community in Esthwaite Water are deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB66188 (https://www.ebi.ac.uk/ena/browser/view/PRJEB66188).
Methods
This dataset contains the long-term microscopy-based monitoring record of phytoplankton genus occurrence in Esthwaite Water. This record has been compared with a sedimentary DNA (sedDNA) record of the phytoplankton community to evaluate the performance of sedDNA in palaeolimnology.
Phytoplankton in surface water samples collected from Esthwaite Water on a weekly/fortnightly basis from 1945-2010 were identified and enumerated with microscopy. Counts were grouped at the genus level, converted to presence-absence, summed by year and normalised by the number of sampling occasions per year.
Funding
Natural Environment Research Council, Award: NE/R016429/1, UK-SCAPE
Leverhulme Trust, Award: PRG-2018-110, PhD studentship