Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years

Abstract

Although the use of genetic analyses of sedimentary DNA to track changes in biodiversity has increased over the last decade, questions remain as to how well DNA captures past ecological conditions. Even less is known about how extracellular and intracellular DNA are archived in lake sediments and whether the two fractions yield similar information. Here we characterized the changes of micro-eukaryotic communities over the past ~200 years in Cultus Lake (British Columbia, Canada), for which a rich body of limnological data and a pre-existing multi-proxy paleolimnological study exist. We generated and analyzed 18S rRNA gene amplicons and found that extracellular and intracellular DNA provided different insights, with the preservation of extracellular DNA compromised in sediments older than ~30 years. Principal Coordinates and indicator species analyses based on intracellular DNA showed that changes in micro-eukaryotic diversity occurred at similar time periods as those identified with the classical paleolimnological study. For instance, decreases of Opisthokonta amplicons occurred during years with elevated numbers of sockeye salmon spawners, which might be associated with an increase of herbivory by juvenile sockeye salmon. Furthermore, two diatom species identified morphologically exhibited similar temporal dynamics to two diatom taxa identified genetically, suggesting that sedimentary DNA can track past diatom species changes as well as micro-eukaryotic community changes. Overall, our study provides insights into the use of extracellular and intracellular DNA in sedimentary records and showed that sedimentary DNA enriches our understanding of micro-eukaryotic community changes over centennial time scales.

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

“…Several studies combined the genetic approach with microscopic analysis to assess the long‐term dynamic of diatom communities, while also exploring the similarities, differences and complementarity of the two methods (Anslan et al, 2022; Dulias et al, 2017; Epp et al, 2011; Gauthier et al, 2022; Huang et al, 2020; Kang et al, 2021; Stoof‐Leichsenring et al, 2012; Stoof‐Leichsenring, Dulias, et al, 2020; Stoof‐Leichsenring, Pestryakova, et al, 2020). Beyond the methodological advancements, insights into the response of the diatom communities to environmental changes were also gained from these analyses, including shifts in diatom community structure, diversity, and the occurrence of particular genetic lineages.…”

“…Several studies combined the genetic approach with microscopic analysis to assess the long-term dynamic of diatom communities, while also exploring the similarities, differences and complementarity of the two methods (Anslan et al, 2022;Dulias et al, 2017;Epp et al, 2011;Gauthier et al, 2022;Huang et al, 2020;Kang et al, 2021;Stoof-Leichsenring et al, 2012;Stoof-Leichsenring, Dulias, et al, 2020;.…”

“…To our knowledge, sedDNA studies specifically targeting chlorophytes are still rare (Fonseca et al, 2022). However, the reconstruction of the long-term dynamic of microbial eukaryotic communities was successful at recovering archived DNA of chlorophytes (Capo et al, 2016(Capo et al, , 2017Gauthier et al, 2022;Ibrahim et al, 2021), providing insight into the response of this specific group of algae to environmental change. In Lake Bourget (France), relative abundance of Chlamydomonas sp.…”

Sediment core DNA-Metabarcoding and chitinous remain identification: Integrating complementary methods to characterise Chironomidae biodiversity in lake sediment archives

“…However, a further obvious application of a sedDNA metabarcoding approach for identifying Chironomidae samples would be exploring truly ancient sedDNA from longer sediment sequences encompassing extended sections of the sedimentation history of lakes. Similar studies targeting plant or mammal DNA have recently been conducted (e.g., Garces-Pastor et al, 2022;Gauthier et al, 2022;Giguet-Covex et al, 2014) and have shown that sedDNA analyses of lake sediment samples can provide information on past vegetation change, species assemblage compositions and past presence of livestock and other grazers in the vicinity of lakes.…”