The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

The emergence of DNA analyses of lake sediments has opened up many new areas of inquiry, including the study of taxa that were traditionally not considered in paleolimnology because they do not leave distinct morphological fossils. Here, we discuss the potential and challenges associated with the study of DNA in paleolimnology to address critical research questions in lacustrine ecology. We examine some recent applications by highlighting studies that have quantified centennial to millennial-scale dynamics, and that considered a diversity of planktonic groups, including bacteria, phytoplankton and zooplankton. We also summarize the main methodological precautions to be taken into account for implementing these types of DNA analyses. Based on our review of the literature focused on the analysis of DNA preserved in lake sediments, the emerging topics we have identified include: (1) the spread, establishment and effect of invasive species, (2) past fish population dynamics, (3) interactions within lacustrine communities, identified through network analyses, (4) potential application of metabarcoding for transfer functions. There are many new and exciting questions that could be addressed using DNA preserved in lake sediment and this will no doubt be an area of continued expansion in the field of paleolimnology for many years to come

1. Summer thermal stratification is thought to be one of the key structuring physical factors for north temperate lake zooplankton. Shifts associated with climate change may lead to altered thermocline depths in stratified lakes through changes to (i) wind stress and associated water column mixing or (ii) air temperature and precipitation. The effects of thermocline deepening through these two scenarios were simulated in a whole-lake experiment to assess the effects on the phenology, biomass and mean body size of the zooplankton. 2. The thermocline of a three-basin dimictic lake was deepened to 7-8 m in one basin using a lake mixer. Through heat transfer, the thermocline of the adjacent basin was deepened to 6-7 m, while the third basin served as an unmanipulated control (4-5 m deep thermocline). Zooplankton community dynamics were followed weekly in a control year and in two experimental years. A before-after-control-impact (BACI) statistical protocol was used to assess the effects of two treatments: Deepening and Deepening+Mixing. 3. Thermocline depth was the main factor influencing zooplankton changes. The biomass and late-season dominance by smaller-bodied and more fish-evasive species were favoured by deepening, leading to a decline in mean community body size, but an increase in total biomass. 4. While many effects could be attributed to thermocline deepening, additional or exacerbated responses were observed when mixing was also present. This resulted mostly from a loss of the hypolimnetic refuge for zooplankton, which accentuated predation effects by warm-water fish on larger cladocerans. Overall, our treatments promoted top-down (predation) effects that increased over the 2 years of the experiment.

Paleolimnological studies are central for identifying long-term changes, yet many studies rely on bioindicators that deposit detectable subfossils in sediments, such as diatoms and cladocerans. Emerging DNA-based approaches are expanding the taxonomic diversity that can be investigated. However, as sedimentary DNA-based approaches are expanding rapidly, calibration work is required to determine the advantages and limitations of these techniques. In this study, we assessed the congruence between morphological and DNA-based approaches applied to sediment trap samples for diatoms and crustaceans using both intracellular and extracellular DNA. We also evaluated which taxa are deposited in sediment traps from the water column to identify potential paleolimnological bioindicators of environmental variations. Based on 18S rRNA gene amplicons, we developed and analyzed a micro-eukaryotic, monthly time series that spanned 3 years and was comprised of paired water column and sediment trap samples from Cultus Lake, British Columbia, Canada. Comparisons of assemblages derived from our genetic and morphological analyses using RV coefficients revealed significant correlations for diatoms, but weaker correlations for crustaceans. Intracellular DNA reads correlated more strongly with diatom morphology, while extracellular DNA reads correlated more strongly with crustacean morphology. Additional analyses of amplicon sequence variants shared between water and sediment trap samples revealed a wide diversity of taxa to study in paleolimnology, including Ciliophora, Dinoflagellata, Chytridiomycota, Chrysophyceae, and Cryptophyceae. Partial RDAs identified significant environmental predictors of these shared assemblages. Overall, our study demonstrates the effectiveness of DNA-based approaches to track community dynamics from sediment samples, an essential step for successful paleolimnological studies.

Peri-urban lakes offer many valued ecosystem services, but their vulnerability to climate change and anthropogenic disturbances increases with expanding human populations. As the effects and interactions of multiple stressors on lakes can lead to unexpected outcomes, affecting societal and ecological values, it is necessary to evaluate ecosystem trajectories and respective drivers in peri-urban lakes. BetterPowered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation management practices could thus be applied to preserve ecosystem services of periurban lakes. We conducted a multi-proxy paleolimnological study on Cultus Lake, British Columbia, a Canadian peri-urban lake experiencing cultural eutrophication, to reconstruct a comprehensive ecological trajectory of the lake over the past ~200 years. We also integrated historical data as well as historical archival information to identify the potential drivers of the changes. We identified ca. 1800-1900 CE as a reference period, reflected in muted variations across most paleo-indicators. Minor increases in sedimentary δ 15 N ca. 1880-1940 CE coincided with the onset of anthropogenic modifications to the Cultus Lake watershed. Signs of early eutrophication were evident by ca. 1940 CE, as indicated by increases in all sedimentary pigments. By ca. 1970-1990 CE, elevated concentrations of sedimentary cyanobacterial pigments and changes in diatom species assemblages highlighted the potential interactive effects of multiple stressors, including cultural eutrophication, climate warming and declines in the endangered Cultus Lake sockeye salmon population. Recent (ca. 1990 declines in sedimentary pigments and increases in cladoceran fluxes suggested an increase in top-down control of the lake food web. From the collection of changes observed in the past ~200 years in our study, it is clear that Cultus Lake and its associated ecosystem services would benefit from abatement of nutrient loadings from terrestrial and atmospheric sources. Our study emphasizes the complexity and interactivity of drivers in peri-urban lake ecosystems and the necessity of long-term perspectives to contextualize modern ecological conditions to inform lake and watershed management.