DOI: 10.5061/dryad.41ns1rnh0
title: Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years

description: Although the use of genetic analyses of sedimentary DNA to track changes
 in biodiversity has increased over the last decade, questions remain as to
 how well DNA captures past ecological conditions. Even less is known about
 how extracellular and intracellular DNA are archived in lake sediments and
 whether the two fractions yield similar information. Here we characterized
 the changes of micro‐eukaryotic communities over the past ~200 years in
 Cultus Lake (British Columbia, Canada), for which a rich body of
 limnological data and a pre‐existing multi‐proxy paleolimnological study
 exist. We generated and analyzed 18S rRNA gene amplicons and found that
 extracellular and intracellular DNA provided different insights, with the
 preservation of extracellular DNA compromised in sediments older than
 ~30 years. Principal Coordinates and indicator species analyses based on
 intracellular DNA showed that changes in micro‐eukaryotic diversity
 occurred at similar time periods as those identified with the classical
 paleolimnological study. For instance, decreases of Opisthokonta amplicons
 occurred during years with elevated numbers of sockeye salmon spawners,
 which might be associated with an increase of herbivory by juvenile
 sockeye salmon. Furthermore, two diatom species identified morphologically
 exhibited similar temporal dynamics to two diatom taxa identified
 genetically, suggesting that sedimentary DNA can track past diatom species
 changes as well as micro‐eukaryotic community changes. Overall, our study
 provides insights into the use of extracellular and intracellular DNA in
 sedimentary records and showed that sedimentary DNA enriches our
 understanding of micro‐eukaryotic community changes over centennial time
 scales.
description: Intracellular and extracellular DNA was extracted from sediment
 samples using the NucleoSpin® Soil kit according to the manufacturer
 instructions (Macherey-Nagel, Düren, Germany). Beforehand, a phosphate
 buffer was used to de-adsord the extracellular DNA fraction from sediment
 particles and the first steps of the commercial DNA extraction kit
 involving lysis were skipped to avoid further degradation of the
 extracellular DNA. PCR amplification were performed to amplify the V7
 region of the 18S rRNA gene and the samples were sent to Genome Quebec for
 library preparation and paired-end (2 x 250bp) sequencing on a MiSeq
 Illumina instrument. The MiSeq reads were then trimmed and filtered, and
 the paired-end reads were merged with the package dada2 in R software.
 Taxonomic assignment was performed using the Protist Ribosomal Reference
 database (PR2)  - SSU rRNA gene database. For more details about the
 methods, refer to Gauthier et al. (2022; doi: 10.1002/edn3.310).
description: # Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake)
 reveals changes in micro‐eukaryotic diversity over the past \~200 years ##
 Description of the data and file structure This following data files were
 submitted: 1\) SampleDescription_CultusLakeSedimentCore.csv: a sample
 description with subsample of sediments and age estimation 2\)
 TaxonomyTable_CultusLakeSedimentCore.csv: the taxonomy of the ASV
 identified with the 18S rRNA gene primers 3\)
 V7-18SrRNAsequences_CultusLakeSedimentCore.fasta: the fasta file with the
 DNA sequence of each ASV 4\) ASVTable_CultusLakeSedimentCore.csv: the
 number of sequences of the ASVs in each sample
 **SampleDescription_CultusLakeSedimentCore.csv** *SampleID*: Number given
 to the sample for its location in the core. The A means that it was the A
 replicate analysed for metabarcoding (collected A and B replicates), and S
 or P means that it is extracellular (supernatant) or intracellular
 (pellet). S and P were used because of the process to separate both DNA
 fraction during the DNA extraction, i.e. after addition of NaP buffer to
 deadsorb the extracellular to the sediment matrix and centrifugation. The
 supernatant contains mostly extracellular DNA while the pellet contained
 intracellular DNA. *SedimentIntervalDepth_Top_cm*: the top of the sediment
 interval collected in cm; 0cm being the top of the core (more recent
 sediments) *SedimentIntervalDepth_Bottom_cm*: the bottom of the sediment
 interval collected in cm *SedimentInterval_MidDepth_cm*: the middle of the
 sediment interval collected in cm *AgeModelEstimatedYear*: The estimated
 year of the sediment sample according to the Constant rate of supply (CRS)
 model *SedimentYear*: year of the sediment sample used for statistical
 analyses *DNAfraction*: indicates whether the DNA was extracted as
 extracellular of intracellular DNA
 **TaxonomyTable_CultusLakeSedimentCores.csv** *asvCode*: Code of ASV
 attributed during the bioinformatic process The taxonomy of the ASVs
 includes the levels of Kingdom, Phylum, Subphylum, Class, Order, Family,
 Genus and Species. The taxonomy was obtained using the reference database
 PR2 – SSU rRNA gene version 4.10.0 (Guillou et al. 2013). Guillou, L.,
 Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C.,
 Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J. R.,
 Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H., Lara, E., le
 Bescot, N., Logares, R., ... Christen, R. (2013). The protist ribosomal
 reference database (PR2): A catalog of unicellular eukaryote small
 sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41,
 D597–D604. [https://doi.org/10.1093/](https://doi.org/10.1093/)
 nar/gks1160 **V7-18SrRNAsequences_CultusLakeSedimentCores.fasta** This
 fasta file contained the asv code and its associated V7 18S rRNA gene
 sequence. **ASVTable_CultusLakeSedimentCore.csv** *SampleID*: same as in
 the file SampleDescription_CultusLakeSedimentCore.csv *DNAfraction*:
 indicates whether the DNA was extracted as extracellular of intracellular
 DNA The other columns represent each asv and the lines contained the
 number of sequences of the ASVs for each sample.