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Schematic illustration of eDNA taphonomic processes in the marine environment. These processes involve eDNA distribution, degradation, and/or preferential preservation during the transition from the pelagic to the benthic zones, and from the water-sediment interface into subsurface sediment.

Schematic illustration of eDNA taphonomic processes in the marine environment. These processes involve eDNA distribution, degradation, and/or preferential preservation during the transition from the pelagic to the benthic zones, and from the water-sediment interface into subsurface sediment.

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Article
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Sedimentary ancient DNA (sedaDNA) offers a novel retrospective approach to reconstructing the history of marine ecosystems over geological timescales. Until now, the biological proxies used to reconstruct paleoceanographic and paleoecological conditions were limited to organisms whose remains are preserved in the fossil record. The development of a...

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... The hypothesis and its propositions presented in this paper provide a first exploration of some of the factors that might inhibit the introduction of LBF from the IPR to the ACR regions (and perhaps vice versa) by natural processes. This model has an advantage over most other early historical biotic dispersion accounts in supplying specific temporal parameters that can be tested using such methods as radiocarbon dating of foraminiferal assemblages and other organisms from cores [118], comparative studies of genetic diversity [86] sedimentary ancient DNA analyses in the sediment cores from the key regions [128]. ...
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The larger benthic foraminifera is a group of marine protists harbouring symbiotic algae, that are geographically confined to shallow tropical and subtropical waters, often associated with coral reefs. The resulting controls on availability of habitat and rates of dispersion make these foraminifers, particularly the genus Amphistegina, useful proxies in the study of invasive marine biota, transported through hull fouling and ballast water contamination in modern commercial shipping. However, there is limited information on the importance of these dispersal mechanisms for foraminifers in the Pre-Industrial Era (pre-1850) for the Atlantic and Caribbean region. This paper examines possible constraints and vectors controlling the invasion of warm-water taxa from the Indo-Pacific region to the Atlantic and Caribbean region. Heterostegina depressa, first described from St. Helena, a remote island in the South Atlantic, provides a test case. The paper postulates that invasions through natural range expansion or ocean currents were unlikely along the possible available routes and hypothesises that anthropogenic vectors, particularly sailing ships, were the most likely means of transport. It concludes that the invasion of the Atlantic by H. depressa was accomplished within the Little Ice Age (1350–1850 C.E.), during the period between the start of Portuguese marine trade with east Africa in 1497 and the first description of H. depressa in 1826. This hypothesis is likely applicable to other foraminifers and other biota currently resident in the Atlantic and Caribbean region. The model presented provides well-defined parameters that can be tested using methods such as isotopic dating of foraminiferal assemblages in cores and genetic indices of similarity of geographic populations.
... The degradation of short DNA and RNA fragments in the environment is mainly due to hydrolysis and oxidative damage 24 . Environmental DNA in the ancient environment is also referred to as sedimentary ancient DNA (sedaDNA) 25,26 , and in previous studies, the physicochemical properties of the sediment were thought to play an important role in the preservation of sedaDNA 26 . It has been experimentally demonstrated that clayey sediments have high DNA content under low-temperature and anoxic conditions 27 , and that clay enhances the DNA adsorption capacity of the sediment 28 . ...
... The degradation of short DNA and RNA fragments in the environment is mainly due to hydrolysis and oxidative damage 24 . Environmental DNA in the ancient environment is also referred to as sedimentary ancient DNA (sedaDNA) 25,26 , and in previous studies, the physicochemical properties of the sediment were thought to play an important role in the preservation of sedaDNA 26 . It has been experimentally demonstrated that clayey sediments have high DNA content under low-temperature and anoxic conditions 27 , and that clay enhances the DNA adsorption capacity of the sediment 28 . ...
... There is also some debate that the binding of DNA is weaker in sand than in other sediment types 27 . The relationship between the characteristics of seabed sediment and the preservation of sedaDNA over time is not well understood 26 , and this is an issue for the future. However, the presence of small amounts of DNA derived from marine organisms in the sandy part of the tsunami deposit indicates that this sediment contains allochthonous genetic information. ...
Article
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We examined the potential of environmental DNA (eDNA) for identifying tsunami deposits in the geological record using lake-bottom sediments in the Tohoku region, Japan. The presence of eDNA from marine organisms in a lacustrine event deposit provides very strong evidence that the deposit was formed by an influx of water from the ocean. The diverse DNA assemblage in the deposit formed by the 2011 Tohoku-oki tsunami included DNA of marine origin indicating that eDNA has potential as an identifying proxy for tsunami deposits. Subsequently, we examined the applicability of eDNA for recognizing paleo-tsunami events using the deposits formed by the 869 CE Jogan tsunami and a prehistoric event (2400–2900 cal year BP). The taxa detected in the tsunami deposits were markedly different from those of the background sediments. Many taxa that were represented in the Jogan tsunami deposit were also detected in the layer immediately above the tsunami deposit. This layer was indistinguishable from the overlying peat by visual observation, but the eDNA results suggest that it is likely to be a muddy tsunami deposit. The results of this study indicate that eDNA has the potential to elucidate the origin of event deposits that have been difficult to identify.
... Throughout their lifetime organisms shed DNA into the environment; this genetic material can be deposited and incorporated into marine sediments, which accumulated over time preserves an archive of past biodiversity. Analysis of this ancient environmental DNA (eDNA) is an approach that is becoming increasingly common to study past marine ecosystems [9]. The analysis of marine sediment archives has enabled the reconstruction of past fish abundances [10], revealed marine ecosystem change as a result of both natural [11] and anthropogenic [12] forcings, and reconstructed previously undescribed marine ecosystems from millions of years ago [11,13]. ...
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Human activities are affecting marine biodiversity globally by accelerating extinction rates, altering ecosystem conditions, and changing community structures. These changes can only be understood through establishing the ecosystem state prior to significant anthropogenic impact, and by disentangling the anthropogenic effect from natural climatic changes. Here, we reconstruct marine biodiversity in Iceland across three millennia (1315 BCE-1785 CE), encompassing periods of climatic fluctuation and human settlement, to explore the comparative effect of natural and anthropogenic forces on marine biodiversity. We performed 18S metabarcoding of ancient environmental DNA from two sediment cores collected from northern Icelandic shelf seas, integrating local climatic records, population estimates and zooarchaeological remains from published sources to estimate the influence of climatic and anthropogenic impacts. Against the backdrop of increasing human populations and marine exploitation, we observe no large-scale taxonomic shifts or anthropogenic biodiversity changes across the period. In contrast, we found a positive correlation between herring ( Clupea harengus ) detection rates and proxy-reconstructed sea surface temperature, suggesting a role for climate in shaping marine biodiversity. Overall, our data suggest that despite impacts on terrestrial ecosystems and the development of a substantial export fishery across the study period, Icelandic society may have had a limited effect on marine biodiversity.
... Many meiofauna specimens were retrieved, including nematodes, copepods and plentiful kinorhynchs. Kinorhynchs were manually picked out from the bubble and blot extract and divided into thirds which were (1) preserved in 100% ethanol and frozen in -80 C for molecular study (2) preserved in a solution of 4% formaldehyde (10% formalin) for morphological study and (3) kept alive in seawater and sediment for culturing attempts, all under the Artsdatabanken project Scalidophora of Norway. The second sampling event took place on the 3 rd of July at 20.40 UTC. ...
Technical Report
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R/V Helmer Hanssen is an ice class research vessel owned by UiT The Arctic University of Norway. The HHUMLT24 cruise onboard R/V Helmer Hanssen was an initiative by The Arctic University Museum of Norway (UMAK, UiT). Sampling was conducted for the following four projects: 1. The Scalidophora of Norway, 2. The role of microRNAs in animal evolution, 3. The diversity of benthic fauna around Svalbard and the Barents Sea, 4. Reconstruction of past ecosystems using sedimentary ancient DNA. For the first project, which aimed to sample scalidophoran fauna, primarily kinorhynchs, for the Scalidophora of Norway project funded by Artsdatabanken, box cores were taken. The second project employed plankton nets, box cores, and a triangular dredge. The third project used samples from box cores, plankton nets, and a triangular dredge to collect marine macrofauna for the museum collections. All macrofauna present in plankton nets, box cores, and triangular dredge samples were photographed, and records were uploaded to GBIF. The fourth project took gravity cores. The cruise leader was Andreas Altenburger (UiT).
... Thus, the sedimentation rates, the mechanical resuspension and the interactions between benthic and pelagic habitats, make the assessment of the dynamics in the proximity of sediments challenging (Giannakourou et al., 2005;Cibic et al., 2022). Moreover, currents, horizontal flow speed, upwelling and depth have been shown to influence the dispersal, transport and sinking rates of eDNA particles, living microorganisms and resting stages, with the potential to be recovered in sediments far from their origin (Harrison et al., 2019;Nooteboom et al., 2019;Nguyen et al., 2023). ...
Article
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Marine sediments host heterogeneous protist communities consisting of both living benthic microorganisms and planktonic resting stages. Despite their key functions in marine ecosystem processes and biogeochemical cycles, their structure and dynamics are largely unknown. In the present study, with a spatially intensive sampling design we investigated benthic protist diversity and function of surface sediment samples from three subregions of the Mediterranean Sea, through an environmental DNA metabarcoding approach targeting the 18S V4 region of rRNA gene. Protists were characterized at the taxonomic level and trophic function, both in terms of alpha diversity and community composition, testing for potential differences among marine subregions and bathymetric groups. Overall, Alveolata and Stramenopiles were the two divisions that dominated the communities. These dominant groups exhibited significant differences among the three Mediterranean subregions in the alpha diversity estimates based on the detected ASVs, for all computed indices (ASV richness, Shannon and Simpson indices). Protist communities were also found to be significantly different in terms of composition at the order rank in the three subregions p-value < 0.01). These differences were mainly driven by Anoecales, Peridiniales, Borokales, Paraliales and Gonyaulacales, which together contributed almost 80% of the average dissimilarity. Anoecales was the dominant order in the Ionian – Central Mediterranean and Adriatic Sea, but with considerably different relative abundances (52% and 36%, respectively), while Borokales was the dominant order in the Western Mediterranean Sea (33%). Similarly, significant differences among the three marine subregions were also highlighted when protist assemblages were examined in terms of trophic function, both in terms of alpha diversity (calculated on the ASVs for each trophic group) and community composition p-value < 0.01. In particular, the Adriatic Sea stood out for having the highest relative abundance of autotrophic/mixotrophic components in the surface sediments analyzed. Conversely, no significant differences in protist assemblages were found among depth groups. This study provided new insights into the taxonomic and trophic composition of benthic protist communities found in Mediterranean surface sediments, revealing geographical differences among regional seas. The results were discussed in relation to the Mediterranean environmental features that could generate the differences among benthic protist communities.
... The latter aspect limits the possibility to investigate dynamics and establish pre-impact reference states and good ecological status (GES) on local scales, i.e. 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). ...
... Moving away from these conserved markers to more variable genomic loci, however, 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. ...
... Here, we use simple species-specific reactions, including a quantitative aspect, i.e. highly sensitive ddPCR. This can simplify data in comparison to metabarcoding or metagenomics (Gielings et al., 2021;Nguyen et al., 2023). Our analyses suggest that this method can provide insights into ecological changes by narrowing the focus on ecologically relevant key species that are used as proxies and in indices for ecosystem status. ...
Article
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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 nonfossilized 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 and across millennia in different basins of the Baltic. 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.
... The potential of the field cannot be denied, however, as interest in sedaDNA for paleoceanographic applications grows so must efforts to establish well-rounded methods. To our knowledge, the isolation of ancient eukaryote DNA from marine sediment cores has been reported in less than 50 metabarcoding records (less than half of which include nextgeneration sequencing; see Williams et al., 2023 andNguyen et al., 2023), and a handful of shot-gun genomics records. These records mostly have a low and often stochastic sampling resolution that cannot in detail assess changes in ecosystems (i.e. ...
Article
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Sedimentary ancient DNA (sedaDNA) analysis is a promising new approach for reconstructing the impact of past climate and environmental changes on marine paleobiodiversity. By recovering, amplifying, and sequencing taxonomically informative sedaDNA fragments preserved in sediments, it is possible to assess the response of a broad range of eukaryote taxa, including non-fossilizing lineages, to past climate change. Here we present a unique marine derived sedaDNA metabarcoding record, spanning the penultimate glacial-interglacial transition across Marine Isotope Stages 6 to 5d (>135-107 ka) from an Eirik Drift core-site in the Labrador Sea. We identified a range of marine groups including dinoflagellates, diatoms, coccolithophores, chlorophytes, and copepods. There were representatives of primary/secondary producers, grazers, and parasites, which may represent remnants of complex ecosystems and ancient food webs. There were significant biodiversity shifts following the penultimate deglaciation and changing sea ice conditions throughout the Last Interglacial. These shifts reflected the striking increase in community richness during periods of seasonal sea ice and reduction under extensive perennial sea ice cover and open ocean. We identify two potential sedaDNA indicator taxa sequences associated with past seasonal sea ice which are most likely pico-eukaryote representatives of Micromonas and Pyramimonas, both green algae with known sea ice associations in modern ecosystems. Our work demonstrates the importance of high resolution marine sedaDNA metabarcoding for unravelling climate-ecosystem linkages and strengthens the potential of sedaDNA signals for past sea ice reconstructions through indicator sequences.
... 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 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). ...
Article
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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.
... The recovery and analysis of environmental DNA (eDNA) from soil cores is an emerging tool for historical reconstructions of coastal plant communities [9][10][11] . When these data are coupled with information on the environmental conditions of a site, a detailed picture of environmental change can emerge 12 . ...
Article
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Anthropogenic activities are causing detrimental changes to coastal plants– namely seagrass, mangrove, and tidal marshes. Looking beyond recent times to past vegetation dynamics is critical to assess the response and resilience of an environment to change. Here, we develop a high-resolution multi-proxy approach, providing a new evidence base to decipher long-term change in coastal plant communities. Combining targeted environmental DNA analysis with chemical analysis of soils, we reconstructed 4,000 years of change at a temperate wetland on Torrens Island South Australia and identified an ecosystem shift that occurred ~ 1000 years ago. What was once a subtidal seagrass system shifted to an intertidal mangrove environment that persists at this site today. We demonstrate that high-resolution historical changes in coastal vegetation can be attained using these proxies. This approach could be applied to other ecosystems to improve the way we protect, conserve, and restore vegetated ecosystems.
... Although first studies started in the late 1990s (Coolen and Overmann, 1998;Willerslev et al., 2003), sedimentary DNA (sedDNA) research has drastically expanded only in recent years . DNA can be recovered from a broad range of environmental samples reflecting past changes including cave systems, terrestrial and wetland soils, as well as lacustrine and marine sediments (Capo et al., 2021a;Dalén et al., 2023;Nguyen et al., 2023). This chapter provides an overview of the research field using DNA recovered from lake sediments to: (i) reconstruct a holistic view of past ecosystems; (ii) highlight major shifts in biological communities; and (iii) understand the responses of biota to environmental stressors. ...
Chapter
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Ecosystems are continuously responding to both natural and anthropogenic environmental change. Lake sediments preserve local and global evidence of these ecological transitions through time. This archived information can yield crucial insights through the reconstruction of past changes over hundreds to many thousands of years. This chapter provides an overview on what lake sedimentary DNA (sedDNA) is, which biological groups can be detected with this novel paleoecological proxy, and the workflow and analytical techniques currently employed in sedDNA research. Finally, the implications of lake sedDNA studies are illustrated through five topics, illustrating how sedDNA can reconstruct lake response to environmental change.