Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems

Abstract

Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may, therefore, help reveal biodiversity changes in past ecosystems. Lake sediments contain the DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We re-evaluated various commonly used metabarcoding primers, and we developed a novel PCR primer combination for fungal metabarcoding to produce a short amplicon, thus accounting for amplification bias due to the degradation of ancient DNA. In silico PCRs showed higher diversity using this new primer combination, compared with previously established fungal metabarcoding primers. We analyzed data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2-22 years after coring; we, therefore, examined the degradation effects of ancient DNA and storage time-related bias affecting fungal communities. Amplicon lengths showed considerable variation within and between the major divisions of fungi, for example, amplicons of Basidiomycota were significantly longer than those of Mucoromycota; however, we observed no significant effect of sample age on amplicon length and GC content, suggesting the robustness of our results. We also found no indication of post-coring fungal growth during storage regarding the proportions of common mold taxa, which would otherwise distort conclusions on past fungal communities.Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, whereas typical aquatic taxa were only represented to a negligible extent, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities.

Investigating the effects of anthropogenic stressors on lake biota using sedimentary DNA

“…Long‐term changes in fungal communities using the sed DNA approach have been recently used to track catchment dynamics related to environmental changes (Talas et al, 2021; von Hippel et al, 2021). Using a fungal‐specific assay, data on diverse fungal assemblages were retrieved from a series of lake sediment cores in Siberia (Seeber et al, 2022). In this case, most fungal sequences taxonomically annotated were from terrestrial taxa, thereby supporting the changes observed in fungi diversity and assemblage composition recovered from the sediment are closely associated to terrestrial vegetation changes.…”

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

“…With the development of next-generation sequencing technologies (Glenn, 2011;Metzker, 2010;Shendure and Ji, 2008), metabarcoding has shown a great potential for reconstructing long-term changes in different biological groups. Several sets of universal PCR primers suitable for sedaDNA studies have been designed for plants (Taberlet et al, 2007), mammals (Giguet-Covex et al, 2014), fish (Miya et al, 2015), fungi (Seeber et al, 2022), diatoms (Stoof-Leichsenring et al, 2012), ostracods (Echeverría-Galindo et al, 2021), and bacteria (Belle and Parent, 2019). Metabarcodes amplified by these primers offer the opportunity to identify the target groups at high taxonomic levels (e.g., species level), and the bias in taxonomic resolution between different taxa can be further complemented by specific primers.…”

Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change

“…Using both blocking oligos increases detection of mammals and also co-amplifies birds, fish, amphibians and worms (figure 1). Additional organisms, such as diatoms, fungi and lichens, can be amplified through the use of dedicated primers [65][66][67], giving a broader spectrum of biodiversity. Having multiple trophic levels allows a more comprehensive tracing of ecosystem dynamics.…”