Sedimentary ancient DNA: a new paleogenomic tool for reconstructing the history of marine ecosystems

Nguyen, Ngoc-Loi; Devendra, Dhanushka; Szymańska, Natalia; Greco, Mattia; Angeles, Inès Barrenechea; Weiner, Agnes; Ray, Jessica L.; Cordier, Tristan; Schepper, Stijn De; Pawłowski, Jan; Pawłowska, Joanna

doi:10.3389/fmars.2023.1185435

Cited by 6 publications

(5 citation statements)

References 140 publications

(211 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…highly sensitive ddPCR. This can simplify data in comparison to metabarcoding or metagenomics (Gielings et al, 2021; Nguyen et al, 2023) and our analyses suggest that it can deliver reliable information on ecological changes by narrowing the focus on ecologically relevant key species that are used as proxies and in indices for ecosystem status. Such simple approaches could be implemented in monitoring and management relatively easily.…”

Section: Discussionmentioning

confidence: 96%

“…for separate basins in marine systems. This shortcoming can potentially be addressed through the use of paleoecological archives, from which the history of ecosystems and their constituent species can be studied through the fossil record (Nguyen et al, 2023; Wingard et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Focusing on highly variable genomic markers, sedaDNA offers the potential for high taxonomic resolution, discriminating between sister species and reaching population level (Epp et al, 2018;Lammers et al, 2021). It also includes taxa that are not well-preserved in the fossil record (Nguyen et al, 2023), such as a number of phytoplankton taxa lacking rigid structures. Among these are dinoflagellates, which, together with diatoms, represent a dominant group of phytoplankton world-wide (Bi et al, 2021;Kang et al, 2021;Zhang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Decoding the Baltic Sea's Past and Present: A simple Molecular Index for Ecosystem Assessment

Schmidt,

Roman,

Andren

et al. 2024

Preprint

View full text Add to dashboard Cite

Marginal sea ecosystems, such as the Baltic Sea, are severely affected by anthropogenic pressures, such as climate warming, pollution, and eutrophication, which increased in the course of the past century. Biodiversity monitoring data and assessment of environmental status in such systems have typically been carried out only for the past few decades, if at all, and knowledge on pre-impact stability and good ecological status is limited. An extension of monitoring time series can potentially be achieved through analyses of paleoecological records, e.g. for phytoplankton, which form the base of the food web and are highly susceptible to environmental changes. Within the phytoplankton community, dinoflagellates and diatoms play a significant role as primary producers, and their relative dominance in the spring bloom, calculated as Dia/Dino index, is used as an indicator for the environmental status of the Baltic Sea. To extend time series on the dominance patterns and include non-fossilized dinoflagellates, we here establish a simple droplet digital PCR (ddPCR) reaction on ancient DNA from sediment cores that decodes phytoplankton dynamics. We focus on two common spring bloom species, the diatom Skeletonema marinoi and the dinoflagellate Apocalathium malmogiense, for which we evaluate a DNA based dominance index. It performs very well in comparison to DNA metabarcoding and modern monitoring and can elucidate past species dominance across the past century in three basins of the Baltic and across millennia in two of these basins. For the past century, we see a dominance shift already starting before the mid-20th century in two of the Baltic Sea basins, thus substantially predating current monitoring programs. Shifts are only partly coeval among the cores and the index shows different degrees of stability. This pattern is confirmed across millennia, where a long-term stable relationship between the diatom and the dinoflagellate is observed in the Eastern Gotland Basin, while data from the Gulf of Finland bear testimony to a much more unstable relationship. This confirms that good ecological status based on the dominance pattern of diatoms and dinoflagellates must be established locally and exemplifies how sediment core DNA can be employed to extend monitoring data.

show abstract

Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Decoding the Baltic Sea's Past and Present: A simple Molecular Index for Ecosystem Assessment

Schmidt,

Roman,

Andren

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…To date, studies employing aeDNA as a climate and biodiversity proxy in sediments mostly focused on lacustrine deposits (Nguyen et al, 2023), with a marked increase in aeDNA research on marine deposits observed recently (e.g., De Schepper et al, 2019;Selway et al, 2022;Zimmermann et al, 2020Zimmermann et al, , 2021, including latest reports of 1-million years old diatom DNA isolated from a marine sediment core (Armbrecht et al, 2022) and record 2-million years old DNA from Kap København formation, which in part includes old marine sediments (Kjaer et al, 2022). Although fossilizing taxa (e.g., foraminifera, diatoms, and coccolithophores) offer a well-established proxy for marine paleoclimate reconstructions, aeDNA adds to a deeper understanding of past ecosystem structure, capturing diversity beyond the fossilized repository and often complementing it (Lejzerowicz et al, 2013;Parducci et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Recovering short DNA fragments from minerals and marine sediments: A comparative study evaluating lysis and isolation approaches

Gande,

Hassenrück,

Žure

et al. 2024

Environmental DNA

View full text Add to dashboard Cite

Marine sediments as excellent climate archives, contain among other biomolecules substantial amounts of extracellular DNA. Through mineral binding, some of the DNA remains protected from degradation which aids its preservation. While this pool of DNA represents genomic ecosystem fingerprints spanning over millions of years, the capability of current DNA extraction methods in recovering mineral‐bound DNA remains poorly understood. We evaluated current sedimentary DNA extraction approaches and their ability to recover short DNA fragments from artificially created DNA‐mineral complexes involving pure clay minerals or quartz, as well as from different types of natural marine sediments. We separately investigated lysis (DNA release) and isolation steps (purification of DNA) comparing five different lysis buffers across two commonly used DNA isolation approaches: silica magnetic beads and liquid‐phase organic extraction and purification. The choice of lysis buffer significantly impacted the amount of recovered mineral‐bound DNA and facilitated selective desorption of DNA fragments. High molarity EDTA and phosphate lysis buffers recovered on average an order of magnitude more DNA from clay minerals than other tested buffers, while both isolation approaches recovered comparable amounts of DNA. In marine sediments, however, liquid‐phase organic extraction caused inhibitory effects in subsequent downstream applications (e.g., PCR), across all assessed DNA extracts, while silica magnetic beads induced inhibition only in half of the tested DNA extracts. Thus, the isolation approach, together with the lysis buffer, played a decisive role in successful library preparation with lysis buffer choice ultimately impacting final library fragment distribution. With this study, we underscore the critical importance of lysis buffer selection to maximize the recovery of mineral‐bound DNA and show its profound impact on recovered fragment lengths in sedimentary DNA extractions, a crucial factor alongside existing isolation approaches in facilitating high‐quality DNA extracts for downstream analysis related to ancient environmental DNA research.

show abstract

“…To date, studies employing aeDNA as a climate and biodiversity proxy in sediments mostly focused on lacustrine deposits (Nguyen et al 2023), with a marked increase in aeDNA research on marine deposits observed recently (e.g., De Schepper et al 2019, Zimmermann et al 2020, Zimmermann et al 2021, Selway et al 2022, including latest reports of 1-million old diatom DNA isolated from marine sediment core (Armbrecht et al 2022) and a record 2-million old DNA from Kap København formation, which in part includes old marine sediments (Kjaer et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Recovering short DNA fragments from minerals and marine sediments: a comparative study evaluating lysis and isolation approaches

Gande,

Hassenrück,

Žure

et al. 2023

Preprint

View full text Add to dashboard Cite

Marine sediments as excellent climate archives, contain among other biomolecules substantial amounts of extracellular DNA. Through mechanisms of binding to various minerals, some of the DNA stays protected from degradation and remains preserved. While this pool of DNA represents genomic ecosystem fingerprints spanning over millions of years, the capability of current DNA extraction methods in recovering mineral-bound DNA remains poorly understood. We evaluated current sedimentary DNA extraction approaches and their ability to desorb and extract short DNA fragments from pure clay and quartz minerals as well as from different types of marine sediments. We separately investigated lysis (DNA release) and isolation steps (purification of DNA) comparing five different types of lysis buffers across two commonly used DNA isolation approaches: silica magnetic beads and liquid-phase organic extraction and purification. The choice of lysis buffer significantly impacted the amount of recovered mineral-bound DNA and facilitated selective desorption of DNA fragments. High molarity EDTA and phosphate lysis buffers recovered on average an order of magnitude more DNA from clay than other tested buffers, while both isolation approaches recovered comparable amounts of DNA. However, organic extraction caused an inhibitory effect in subsequent downstream applications (e.g., PCR), across all assessed sediment DNA extracts while silica magnetic beads induced inhibition only in half of the tested DNA extracts. Furthermore, we demonstrate that both, the isolation approach and the lysis buffer play a decisive role in successful library preparation and that lysis buffer choice impacted the final library fragment distribution. With this study, we underscore the critical importance of lysis buffer selection to maximize the recovery of mineral-bound DNA in sedimentary DNA extractions and show its profound impact on recovered fragment lengths, a crucial factor alongside existing isolation approaches in facilitating high-quality DNA extracts for downstream analysis related to ancient environmental (aeDNA) research.

show abstract

Sedimentary ancient DNA: a new paleogenomic tool for reconstructing the history of marine ecosystems

Cited by 6 publications

References 140 publications

Decoding the Baltic Sea's Past and Present: A simple Molecular Index for Ecosystem Assessment

Decoding the Baltic Sea's Past and Present: A simple Molecular Index for Ecosystem Assessment

Recovering short DNA fragments from minerals and marine sediments: A comparative study evaluating lysis and isolation approaches

Recovering short DNA fragments from minerals and marine sediments: a comparative study evaluating lysis and isolation approaches

Contact Info

Product

Resources

About