DOI: 10.5061/dryad.sbcc2frc9
title: Data from: Erosion regime controls sediment environmental DNA-based community reconstruction

description: Analysis of environmental DNA detected in lake sediments shows promise to
 become a great paleoecological technique that can provide detailed
 information about organism communities living in past environments.
 However, when interpreting sedimentary environmental DNA records, it is of
 crucial importance to separate ecosystem responses to large-scale
 environmental change from ‘noise’ caused by changes in sediment provenance
 or potential post-depositional DNA mobility. In this study, we show that
 plant and mammalian communities reconstructed from sediments are strongly
 affected by sediment provenance, but unaffected by vertical mobility of
 DNA after sediment deposition. We observe that DNA from aquatic plants was
 abundant in background sediment, while embedded detrital event layers
 (sediment deposited under erosion events) primarily contained terrestrial
 plants; hence, vertical mobility of aquatic plant DNA across sediment
 layers was negligible within our studied lakes. About 33% of the
 identified terrestrial plant genera were only found in detrital sediment
 suggesting that sediment origin had a strong impact on the reconstructed
 plant community. Similarly, DNA of some mammalian taxa (Capra hircus,
 Ursus arctos, Lepus, Felis) were only or preferentially found in detrital
 event layers. Temporal changes across the Holocene were the main drivers
 of change for reconstructed plant communities, but sediment type was the
 second most important factor of variance. Our results highlight that
 erosion and sediment provenance need to be considered when reconstructing
 past mammalian and plant communities using environmental DNA from lake
 sediments.
description: The uploaded material contains
 sediment DNA metabarcoding data targeting plants (trnL gene) and mammals
 (16S gene). It consists of two data sets: Plant and mammalian DNA sequences from a
 Holocene sediment sequence that was retrieved from Lake Grosssee,
 Flumserberg, Eastern Switzerland.
 Plant and mammalian DNA
 sequences from surface sediments that were recovered from seven lakes
 across the Central Alps. 
 The samples in each data set
 are paired to contain a sample of hemipelagic background sediment and a
 detrital event layer deposited during a heavy precipitation event, which
 is of similar age compared to the background
 sediment. All DNA libraries include extraction blanks
 (named ‘K1_date’ and ‘K2_date’ for each of the extraction runs,
 respectively), which were run along the extractions with no sediment
 input, as well as PCR negatives (named ‘Neg1-8’), which contain PCR mix
 and primers, but no DNA. Sample tags are dual-unique (twin tagging) and
 hence, PCR blanks are not specifically outlined in the ngs files (that is,
 unused tag combinations in a library). More information on sample
 labelling and pairing can be found in the file
 ‘SampleInfo.xlsx’. Coring and sampling
 A sediment sequence spanning
 the Holocene was retrieved from Lake Grosssee, Flumserberg, Eastern
 Switzerland, with a percussion piston-coring system (Uwitec, Austria) in
 2017. Five 3-m-long core segments were recovered with a horizontal offset
 of 1 m and by using a vertical offset by 0.5 m down to 8 m sediment depth.
 The established composite section uses the highest-quality sediments from
 these core segments and spans 7.73 m. Cores were split lengthwise and kept
 in a fridge until subsampling for sediment DNA analysis in 2021. Dark,
 organic-rich sediments are interpreted to represent hemi-pelagic
 background sedimentation, while reddish siliciclastic beds are interpreted
 as flood event deposits (Glaus, 2018). In 2016, a strong summer
 thunderstorm at Lake Grosssee triggered high runoff in all streams
 entering the lake as well as overland flow across the alpine meadows,
 leading to the deposition of a 2.5-cm-thick layer in the lake. The
 Holocene record contains more than 100 comparable event layers ranging
 from 0.2-10 cm in thickness, of which the youngest could be correlated to
 documented flood events in the region (Glaus, 2018). Nine of these event
 layers together with adjacent background sediments were sampled for eDNA
 analysis. Average age difference in the sample pairs is 102 years, based
 on an age-depth model, which was built on 17 radiocarbon dates from
 terrestrial plant macrofossils (Dwileski, 2022). The sample pairs span an
 age range from modern to around 8,000 calibrated years before present
 (cal. yrs BP). Surface sediments were taken with a gravity
 corer (Uwitec, Austria) from the lake’s depocentre in seven lakes across
 the Central Alps in 2020. Cores were kept in a fridge until splitting and
 subsampling for sediment DNA analysis in 2021. Event layers were
 identified visually, based on characteristics such as fining-upward
 sequences, high minerogenic content in contrast to organic-rich
 surrounding sediment, and the local abundance of plant macrofossils.
 Sample pairs were spaced 1.5 cm apart, on average.
 DNA extraction and
 sequencing Sample pairs for sediment DNA analysis were
 taken using sterile sampling equipment in a lab where no polymerase chain
 reactions (PCR) are performed. We cleaned the core surfaces before
 subsampling and avoided sediment touching with the core liner. Samples of
 background sediments span across 2 cm, while event samples are an
 integration of the respective event layer (spanning 1-10
 cm). DNA from 0.5 g of wet sediment was extracted in
 a dedicated clean lab for ancient DNA analysis with a Qiagen PowerSoil Pro
 kit, following the manufacturer’s instructions, but incubating the samples
 on a shaker overnight at 60°C (lysis step). Two extractions were done per
 sediment depth and two negative extraction controls were added to each
 extraction batch run to detect potential contamination during extraction.
 DNA from all extracts, including extraction controls, was amplified in 4
 PCR replicates, yielding 8 replicates per sediment depth. PCR reagents are
 summarised in Table 1. Plant DNA was amplified with primers targeting the
 P6 loop region of the chloroplast trnL gene (g, 5’-GGGCAATCCTGAGCCAA-3’;
 and h, 5’-CCATTGAGTCTCTGCACCTATC-3’; Taberlet et al. (2006)). The PCR
 protocol included 45 cycles of a denaturing step (95°C, 30 s), an
 annealing temperature of 55°C (30 s), and an elongation step at 72°C (30
 s). Mammalian DNA was amplified with primers targeting the mitochondrial
 16S gene (MamP007F, 5’-CGAGAAGACCCTATGGAGCT-3’; MamP007R,
 5’-CCGAGGTCRCCCCAACC-3’; Giguet-Covex et al. (2014)) with a human blocker
 (MamP007_B_Hum1, 5’-GGAGCTTTAATTTATTAATGCAAACAGTACC-C3spacer 3’). The PCR
 protocol included 45 cycles (as suggested by Giguet-Covex et al. (2014))
 of a denaturing step (95°C, 30 s), an annealing temperature of 50°C (30
 s), and an elongation step at 72°C (30 s). Primers were twin-tagged on the
 5’ end using a unique combination of 12 bp long nucleotide sequence with
 at least three mismatches (Binladen et al., 2007), plus 4 additional
 random nucleotides. The twin-tagging approach was applied to avoid effects
 of tag jumping, which can greatly distort eDNA interpretations
 (Rodriguez-Martinez et al., 2023). On each PCR 96-well plate, we randomly
 arranged 7-8 PCR negatives to trace possible cross-contamination during
 PCR. After PCR, samples, PCR negatives, and extraction blanks were pooled
 by plate (equivolume) and purified with a QIAQuick PCR purification kit
 (Qiagen, Germany). Whenever possible, sediment sample pairs were extracted
 on the same day and arranged in the same library to avoid any bias through
 downstream analyses. Library preparation was done by Novogene (UK)
 following the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB
 #E7645) without the PCR enrichment step and samples were sequenced on an
 Illumina NovaSeq 6000 PE150 platform. Libraries with the same primer tags
 were sequenced on separate sequencing lanes to avoid the effects of index
 hopping. Table 1 Reagents used for PCR reactions to amplify plant
 and mammalian DNA, respectively.   Plants(trnL g/h primers) 
 Mammals(MamP007-F/-R primers) 
 Reaction volume 20
 µl 25 µl 
 10X PCR buffer (Qiagen,
 Germany) 1 1 
 dNTPs
 (Qiagen, Germany) 0.2
 mM 0.2 mM 
 MgCl2 (Qiagen, Germany)
 1.5 mM
 in PCR buffer + 0.5 mM 1.5 mM in PCR
 buffer + 1.5 mM Bovine Serum
 Albumin (BSA; Thermo Scientific, USA) 4
 µg 4 µg 
 Primers 0.4
 µM 0.4 µM 
 DNA 1
 µl 2 µl 
 HotStartTaq Polymerase (Qiagen,
 Germany) 1.25 U 0.625
 U Human
 blocker - 2
 µM 
 References
 Binladen, J., Gilbert, M. T.,
 Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., and Willerslev,
 E., 2007, The use of coded PCR primers enables high-throughput sequencing
 of multiple homolog amplification products by 454 parallel sequencing:
 PLoS One, v. 2, no. 2, p. e197. Dwileski, A., 2022, Holocene vegetation change
 in the eastern Swiss Alps (Grosssee, SG): Effects of climate and human
 impact [Master of Sciences: University of Basel.
 Giguet-Covex, C., Pansu, J.,
 Arnaud, F., Rey, P. J., Griggo, C., Gielly, L., Domaizon, I., Coissac, E.,
 David, F., Choler, P., Poulenard, J., and Taberlet, P., 2014, Long
 livestock farming history and human landscape shaping revealed by lake
 sediment DNA: Nat Commun, v. 5, p. 3211.
 Glaus, N., 2018, Holocene
 flood events and sediment flux in Alpine lake Grosssee (Flumserberg,
 Switzerland) [Master of Science: University of Bern,
 Switzerland. Rodriguez-Martinez, S., Klaminder, J., Morlock,
 M. A., Dalen, L., and Huang, D. Y., 2023, The topological nature of tag
 jumping in environmental DNA metabarcoding studies: Mol Ecol Resour, v.
 23, no. 3, p. 621-631. Taberlet, P., Coissac, E., Pompanon, F., Gielly,
 L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C.,
 and Willerslev, E., 2006, Power and limitations of the chloroplast trn L
 (UAA) intron for plant DNA barcoding: Nucleic Acids Research, v. 35, no.
 3, p. e14-e14.
description: Raw sequencing data in .fq.gz
 format. Files need to be decompressed and can be run through an Obitools3
 pipeline, for example.
description: # Erosion regime controls sediment environmental DNA-based community
 reconstruction *** Analysis of environmental DNA detected in lake
 sediments shows promise to become a great paleoecological technique that
 can provide detailed information about organism communities living in past
 environments. However, when interpreting sedimentary environmental DNA
 records, it is of crucial importance to separate ecosystem responses to
 large-scale environmental change from ‘noise’ caused by changes in
 sediment provenance or potential post-depositional DNA mobility. In this
 study, we show that plant and mammalian communities reconstructed from
 sediments are strongly affected by sediment provenance, but unaffected by
 vertical mobility of DNA after sediment deposition. We observe that DNA
 from aquatic plants was abundant in background sediment, while embedded
 detrital event layers (sediment deposited under erosion events) primarily
 contained terrestrial plants; hence, vertical mobility of aquatic plant
 DNA across sediment layers was negligible within our studied lakes. About
 33% of the identified terrestrial plant genera were only found in detrital
 sediment suggesting that sediment origin had a strong impact on the
 reconstructed plant community. Similarly, DNA of some mammalian taxa
 (Capra hircus, Ursus arctos, Lepus, Felis) were only or preferentially
 found in detrital event layers. Temporal changes across the Holocene were
 the main drivers of change for reconstructed plant communities, but
 sediment type was the second most important factor of variance. Our
 results highlight that erosion and sediment provenance need to be
 considered when reconstructing past mammalian and plant communities using
 environmental DNA from lake sediments. ## Description of the data and file
 structure The uploaded material contains sediment DNA metabarcoding data
 targeting plants (trnL gene) and mammals (16S gene). It consists of two
 data sets: * Plant and mammalian DNA sequences from a Holocene sediment
 sequence that was retrieved from Lake Grosssee, Flumserberg, Eastern
 Switzerland. * Plant and mammalian DNA sequences from surface sediments
 that were recovered from seven lakes across the Central Alps. The samples
 in each data set are paired to contain a sample of hemipelagic background
 sediment and a detrital event layer deposited during a heavy precipitation
 event, which is of similar age compared to the background sediment. All
 DNA libraries include extraction blanks (named ‘K1\_date’ and ‘K2\_date’
 for each of the extraction runs, respectively), which were run along the
 extractions with no sediment input, as well as PCR negatives (named
 ‘Neg1-8’), which contain PCR mix and primers, but no DNA. Sample tags are
 dual-unique (twin tagging) and hence, PCR blanks are not specifically
 outlined in the ngs files (that is, unused tag combinations in a library).
 More information on sample labelling and pairing can be found in the file
 ‘Morlock\_MA\_eDNA\_SampleInformation.xlsx’. For more information, please
 contact Marina Morlock: marina.morlock@umu.se or marina.morlock@hotmail.de
 ## Sharing/Access information This dataset is part of the article Morlock,
 MA, Rodriguez-Martinez, S, Huang, D Y-T, and Klaminder, J 2023. Erosion
 regime controls sediment environmental DNA-based community reconstruction.
 Environmental DNA, DOI: 10.1002/edn3.458