Permafrost-thaw lake development in Central Yakutia: sedimentary ancient DNA and element analyses from a Holocene sediment record ...

• Main Authors: Baisheva, Izabella, Levina, Sardana, Biskaborn, Boris K., Vyse, Stuart A., Heim, Birgit, Pestryakova, Luidmila, Glückler, Ramesh, Herzschuh, Ulrike, Stoof-Leichsenring, Kathleen R.
• Format: Dataset
• Language: English
• Published: Dryad 2022
• Subjects: FOS Earth and related environmental sciences; sedaDNA; metabarcoding; lake sediment core; Central Yakutia; Siberia; Permafrost; alaas; thaw-lake; Diatoms; Plants; macrophytes; Earth-Surface Processes; Aquatic Science; Alaas; Boyer; permafrost; Thermokarst; Yakutia
• Online Access: https://dx.doi.org/10.5061/dryad.vq83bk3w5; https://datadryad.org/stash/dataset/doi:10.5061/dryad.vq83bk3w5

In Central Yakutia (Siberia) livelihoods of local communities depend on alaas (thermokarst depression) landscapes and the lakes within. Development and dynamics of these alaas lakes are closely connected to climate change, permafrost thawing, catchment conditions, and land use. To reconstruct lake development throughout the Holocene we analyze sedimentary ancient DNA (sedaDNA) and biogeochemistry from a sediment core from Lake Satagay, spanning the last c. 10,800 calibrated years before present (cal yrs BP). SedaDNA of diatoms and macrophytes and microfossil diatom analysis reveal lake formation earlier than 10,700 cal yrs BP. The sedaDNA approach detected 42 amplicon sequence variants (ASVs) of diatom taxa, one ASV of Eustigmatophyceae (Nannochloropsis), and 12 ASVs of macrophytes. We relate diatom and macrophyte community changes to climate-driven shifts in water level and mineral and organic input, which result in variable water conductivity, in-lake productivity, and sediment deposition. We detect a ... : SedaDNA was extracted using Dneasy PowerSoil and Dneasy PowerSoil Max DNA Isolation Kit. Extracted DNA was combined and concentrated using a GeneJet PCR purification Kit. Primers for the amplification of diatoms targeted a diagnostic short diatom metabarcode (primers: diat_rbcL705 and diat_rbcL808, Stoof-Leichsenring et al. 2012). For plant DNA metabarcoding we used standard primers targeting the chloroplast trnL P6 loop (Taberlet et al. 2007). PCRs for diatom and plant metabarcoding were run in three replicates along with No Template Controls (NTCs) to control chemical contamination of PCR chemicals. Purification of PCRs was done using MinElute. Samples containing diatoms and plants DNA were sequenced in paired-end mode (2x 150 bp) on an Illumina NextSeq 500 platform at an external sequencing service. We used the Obitools pipeline as described in Boyer et al. 2015, but applied the updated version Obitools3 (see detailed usage description here: https://git.metabarcoding.org/obitools/obitools3). Diatom and ...