From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo‐diversity in sedimentary ancient DNA over the last ~14,500 years

Abstract

Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

“…This approach provides information about Holocene and Late Pleistocene biota, including taxa that leave no morphologically identifiable remains preserved in lakes (see [13] for review). Thus far, the most common investigated aquatic organisms in sedaDNA studies have been photosynthetic bacteria and phytoplankton [18,34,[66][67][68][69][70][71][72][73][74][75][76][77][78][79][80][81]. Although macrophytes and some algal groups are typically well detected in sedaDNA plant surveys [24][25][26]81,82], there are few papers reporting the presence of zooplanktonic DNA [83,84] and fish DNA from lake sediments [85][86][87].…”

New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

“…However, since 2008, researchers have successfully tracked organisms derived from terrestrial environments, using bulk sediments and focusing on the analysis of extracellular or total DNA 19 . These studies on bulk sediments targeted plants 20–29 , mammals 24,30 , humans and/or animal specific faecal bacteria 30–35 , and more recently other eukaryotes, such as fungi and worms 5,36 . The aim of such research includes the reconstruction of past biodiversity, vegetation cover, landscape, and climate changes, the nature of agro-pastoral activities and the relationships between humans and landscapes.…”

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene

“…While past climate changes impacted the aquatic biota in both a large peri-alpine and a small arctic lake, the effects of eutrophication on the perialpine lake were stronger and partly overprinted the influence of climate forcing [13,29]. Despite this large potential of studying ancient DNA in sediment archives, there are only a few time series of aquatic microbial eukaryotic communities covering the entire Holocene [30,31] and none concerning boreal or alpine lakes.…”