Comparative analyses of 18S rDNA regions for assessing the eukaryotic community in ancient lake sediment samples

Abstract The study of ancient sedimentary DNA (sedaDNA) aims to reconstruct the past environments and understand the historical biodiversity in or around aquatic ecosystems. The 18S ribosomal RNA gene (18S rDNA) is usually the target for discerning a broad spectrum of eukaryotic organisms, mainly microbial. Depending on the scientific context, metabarcoding of three hypervariable gene regions (V4, V7, and V9) are the most used alternatives for characterizing aquatic communities. Here, we evaluate the pros and cons of the three regions using sedaDNA samples up to about 3300 years old from a high mountain lake sediment. In samples with sufficient DNA content (ca. 1 µg DNA/g wet sediment) and preservation, V4, the longest region, provides community reconstructions richer in taxa. However, when DNA deterioration becomes more pronounced (i.e., > 1300-year-old samples in this study), the performance of the shortest V9 region is more satisfactory. The V7 region provides intermediate results. The three regions show biases concerning high taxonomic ranks, with V7 and V9 regions performing similarly. Microbial eukaryotes are better assessed than metazoans, and Kinetoplastea (Euglenozoa) are particularly persistent in ancient samples.