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 deposition. We detect a higher lake level and water conductivity in the Early Holocene (c. 10,700–7000 cal yrs BP) compared to other periods, supported by the dominance of Stephanodiscus sp. and Stuckenia pectinata. Further climate warming towards the Mid-Holocene (7000–4700 cal yrs BP) led to a shallowing of Lake Satagay, an increase of the submerged macrophyte Ceratophyllum, and a decline of planktonic diatoms. In the Late Holocene (c. 4700 cal yrs BP–present) stable shallow water conditions are confirmed by small fragilarioid and staurosiroid diatoms dominating the lake. Lake Satagay has not yet reached the final stage of alaas development, but satellite imagery shows an intensification of anthropogenic land use, which in combination with future warming will likely result in a rapid desiccation of the lake.

Methods
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 plant EMBL reference databases were built by using in silico PCR (Ficetola et al. 2010) with diatom and plant specific primers, respectively, on the EMBL Nucleotide Sequence Database (Release 143, April 2020). Plant DNA query sequences were matched against the plant EMBL Nucleotide Sequence Database and the Arctic and Boreal vascular plant and bryophytes database (Willerslev et al. 2014, Soininen et al. 2015, Sønstebø et al. 2010). The taxonomic assignment of diatoms was based on 98–100% similarity to at least one entry of the diatom EMBL reference database and taxonomic assignment of plants was based on a 100% similarity between query sequences and the arctic and plant EMBL reference database.

Reference: 

Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E (2015) OBITOOLS: a unix-inspired software package for DNA metabarcoding. Mol Ecol Res 16: 176–182. 10.1111/1755-0998.12428.
Ficetola, G.F., Coissac, E., Zundel, S. Riaz, S., Shehzad, W., Bessiere, J., Taberlet, P., Pompano, F. (2010) An In silico approach for the evaluation of DNA barcodes. BMC Genomics 11, 434. https://doi.org/10.1186/1471-2164-11-434
Soininen, E. M.; Gauthier, G.; Bilodeau, F.; Berteaux, D.; Gielly, L.; Taberlet, P.; Gussarova, G.; Bellemain, E.; Hassel, K.; Stenøien, H. K.; Epp, L.; Schrøder-Nielsen, A.; Brochmann, C.; Yoccoz, N. G. Highly Overlapping Winter Diet in Two Sympatric Lemming Species Revealed by DNA Metabarcoding. PLoS ONE 2015, 10 (1), e0115335. https://doi.org/10.1371/journal.pone.0115335.
Sønstebø, J. H., Gielly, L., Brysting, A. K., Elven, R., Edwards, M., Haile, J., et al. (2010). Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Mol. Ecol. Resour. 10, 1009–1018. doi: 10.1111/j. 1755-0998.2010.02855.x
Stoof-Leichsenring K, Epp L, Trauth M, Tiedemann R (2012) Hidden diversity in diatoms of Kenyan Lake Naivasha: A genetic approach detects temporal variation. Mol Ecol 21: 1918–1930. 10.1111/j.1365-294X.2011.05412.x.
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast TrnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35 (3): e14–e14. https://doi.org/10.1093/nar/gkl938.
Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergård M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen M, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjær KH, Orlando L, Brochmann C, Taberlet P (2014) Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506 (7486): 47–51. https://doi.org/10.1038/nature12921.