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

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 deposi..., 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/obi...,
The datasets* are prepared for the manuscripts: Baisheva et al. (2022): \"Permafrost-thaw lake development in Central Yakutia – Sedimentary ancient DNA and element analyses from a Holocene sediment record\" (submitted) and Glückler et al. (2022): \"Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies\" (preprint). Also included is the processing of the raw sequencing data using bioinformatics tools.
*The datasets were uploaded into two separate directories containing data and scripts. Each directory contains two main folders APMG_32 (Diatoms) and APMG_33 (Plants). Files of APMG_32 and APMG_33 after downloading have to be merged in the same folder, so the structure of datasets looks like as it is given below:
1)      APMG_32 contains several folders and files of different format:
00.   APMG-32_Metadata - Metadata information including lake geographic coordinates, sample depths and ages, laboratory codes and used primer tag combinati...

西伯利亚雅库特中部地区的本土社区生计依赖于阿拉斯（alaas，热融洼地）景观及其内部湖泊。这些阿拉斯湖泊的发育与动态变化与气候变化、多年冻土融化、流域条件以及土地利用密切相关。为重建全新世以来的湖泊发育历史，我们对萨塔盖湖（Lake Satagay）的沉积物岩芯开展了沉积古DNA（sedimentary ancient DNA, sedaDNA）与生物地球化学分析，该岩芯覆盖了过去约10800个校准年（calibrated years before present, cal yrs BP）。

对硅藻和大型植物的沉积古DNA以及微化石硅藻分析显示，湖泊形成时间早于10700 cal yrs BP。该沉积古DNA方法共检测到42个硅藻分类群的扩增子序列变体（amplicon sequence variants, ASVs）、1个真色藻纲（Eustigmatophyceae，Nannochloropsis）的ASV，以及12个大型植物的ASV。我们将硅藻与大型植物群落的变化归因于气候驱动的水位变化、矿物与有机质输入变化，这些变化进而导致水体电导率、湖内生产力及沉积物沉积……

沉积古DNA提取使用了Dneasy PowerSoil与Dneasy PowerSoil Max DNA分离试剂盒。提取得到的DNA经合并后，使用GeneJet PCR纯化试剂盒进行浓缩。硅藻扩增靶向一段诊断性的短硅藻元条形码（引物：diat_rbcL705与diat_rbcL808，Stoof-Leichsenring等，2012）。针对植物DNA元条形码测序，我们采用靶向叶绿体trnL P6环的标准引物（Taberlet等，2007）。硅藻与植物元条形码的PCR反应均设置3次重复，并设置无模板对照（No Template Controls, NTCs）以控制PCR试剂的化学污染。PCR产物纯化使用MinElute试剂盒完成。携带硅藻与植物DNA的样本在外部测序服务机构的Illumina NextSeq 500平台上以双端模式（2×150 bp）进行测序。我们采用Boyer等（2015）所述的Obitools分析流程，但使用了更新后的Obitools3版本（详细使用说明见：https://git.metabarcoding.org/obitools/obi...）

本数据集服务于两篇学术论文：Baisheva等（2022）的《西伯利亚雅库特中部多年冻土融化湖泊发育——来自全新世沉积记录的沉积古DNA与元素分析》（已投稿），以及格吕克勒（Glückler）等（2022）的《西伯利亚雅库特中部全新世野火与植被动态：基于湖沉积物代用指标重建》（预印本）。数据集同时包含使用生物信息学工具处理的原始测序数据。

*数据集被上传至两个独立的目录，分别包含数据与脚本。每个目录均包含两个主要文件夹：APMG_32（硅藻组）与APMG_33（植物组）。下载APMG_32与APMG_33的文件后需合并至同一文件夹，数据集结构如下所示：
1) APMG_32包含多个不同格式的文件夹与文件：
00. APMG-32_Metadata——元数据信息，涵盖湖泊地理坐标、样品深度与年代、实验室编码以及所用引物标签组合……