DOI: 10.5061/dryad.q83bk3jpw
title: Data from: evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community

description: 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.
description: 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.
description: # 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](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 1. 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 2. 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 3. 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](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).