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Schematic illustration of change in relative abundance of DNA due to taphonomic processes. This figure illustrates the processes affecting DNA distribution, degradation and/or preferential preservation during the transitions from the pelagic to the benthic zones, and from the surface sediment to the deeper sediment. The approximate timescales of preservation of different fractions of the sediment record is also illustrated.

Schematic illustration of change in relative abundance of DNA due to taphonomic processes. This figure illustrates the processes affecting DNA distribution, degradation and/or preferential preservation during the transitions from the pelagic to the benthic zones, and from the surface sediment to the deeper sediment. The approximate timescales of preservation of different fractions of the sediment record is also illustrated.

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DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These n...

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... from viruses to mammals, can be preserved in lake and marine sediments (Fig. 1). However, the degree to which they faithfully reflect changing abundance and community composition varies enormously depending on taxon preservation capacity 4 , the depositional environment, including sedimentation rate, and distance to the depositional site (Fig. ...
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... wellpreserved archives covering multiple trophic levels and with strict age-control are unique to aquatic sites with undisturbed sedimentation. Temporal genetic signals of change can also be analysed by extracting total sedimentary DNA (Box 1). Similar to other biomarkers, DNA may be archived in aquatic sediments, but as described below (see Fig. 2), the degree to which this occurs depends heavily on deposition and preservation conditions. Thus, sediment-archived DNA may be either extracellular, in dead tissue/cells, or inside living organisms (within dormant propagules or active microbes). Each of these sources of DNA can be used for detecting genetic change that reflects ...
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... for white fish in a Swedish lake 69 . eDNA approaches therefore offer the potential to assess the impact of environmental change across taxonomic groups, over long temporal scales, and potentially with a taxonomic resolution unavailable by traditional microfossil approaches. However, many authors have also highlighted limitations 70 (see also Fig. 2) and questioned the reliability of DNA archives from sediments as a stand-alone proxy 71 . Instead, most researchers advocate a combination of DNA evidence and palaeoecological approaches as the way forward (i.e. using DNA as one proxy within a multiproxy study) 70,72,73 . Indeed, as indicated in the previous section, the mechanisms of ...
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... Fungi and Viruses. Bacteria, Archaea and to a lesser extent Fungi, pose both an opportunity and a threat to the field of sed-eDNA. The opportunity is that, as for other organisms, their sed-eDNA can be used for temporal reconstruction of communities, with at least two requirements: firstly, that the environment is favourable to preservation (Fig. 2); secondly, that the DNA is from a group that would be present and functional in the water column but not the sediment. The threat comes from the ability of many microorganisms to function in sediments, with two primary, interconnected effects: (1) they increase the bioavailability and degradation of organic matter, including DNA and ...
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... from viruses to mammals, can be preserved in lake and marine sediments (Fig. 1). However, the degree to which they faithfully reflect changing abundance and community composition varies enormously depending on taxon preservation capacity 4 , the depositional environment, including sedimentation rate, and distance to the depositional site (Fig. ...
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... wellpreserved archives covering multiple trophic levels and with strict age-control are unique to aquatic sites with undisturbed sedimentation. Temporal genetic signals of change can also be analysed by extracting total sedimentary DNA (Box 1). Similar to other biomarkers, DNA may be archived in aquatic sediments, but as described below (see Fig. 2), the degree to which this occurs depends heavily on deposition and preservation conditions. Thus, sediment-archived DNA may be either extracellular, in dead tissue/cells, or inside living organisms (within dormant propagules or active microbes). Each of these sources of DNA can be used for detecting genetic change that reflects ...
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... for white fish in a Swedish lake 69 . eDNA approaches therefore offer the potential to assess the impact of environmental change across taxonomic groups, over long temporal scales, and potentially with a taxonomic resolution unavailable by traditional microfossil approaches. However, many authors have also highlighted limitations 70 (see also Fig. 2) and questioned the reliability of DNA archives from sediments as a stand-alone proxy 71 . Instead, most researchers advocate a combination of DNA evidence and palaeoecological approaches as the way forward (i.e. using DNA as one proxy within a multiproxy study) 70,72,73 . Indeed, as indicated in the previous section, the mechanisms of ...
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... Fungi and Viruses. Bacteria, Archaea and to a lesser extent Fungi, pose both an opportunity and a threat to the field of sed-eDNA. The opportunity is that, as for other organisms, their sed-eDNA can be used for temporal reconstruction of communities, with at least two requirements: firstly, that the environment is favourable to preservation (Fig. 2); secondly, that the DNA is from a group that would be present and functional in the water column but not the sediment. The threat comes from the ability of many microorganisms to function in sediments, with two primary, interconnected effects: (1) they increase the bioavailability and degradation of organic matter, including DNA and ...
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... from viruses to mammals, can be preserved in lake and marine sediments (Fig. 1). However, the degree to which they faithfully reflect changing abundance and community composition varies enormously depending on taxon preservation capacity 4 , the depositional environment, including sedimentation rate, and distance to the depositional site (Fig. ...
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... wellpreserved archives covering multiple trophic levels and with strict age-control are unique to aquatic sites with undisturbed sedimentation. Temporal genetic signals of change can also be analysed by extracting total sedimentary DNA (Box 1). Similar to other biomarkers, DNA may be archived in aquatic sediments, but as described below (see Fig. 2), the degree to which this occurs depends heavily on deposition and preservation conditions. Thus, sediment-archived DNA may be either extracellular, in dead tissue/cells, or inside living organisms (within dormant propagules or active microbes). Each of these sources of DNA can be used for detecting genetic change that reflects ...
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... for white fish in a Swedish lake 69 . eDNA approaches therefore offer the potential to assess the impact of environmental change across taxonomic groups, over long temporal scales, and potentially with a taxonomic resolution unavailable by traditional microfossil approaches. However, many authors have also highlighted limitations 70 (see also Fig. 2) and questioned the reliability of DNA archives from sediments as a stand-alone proxy 71 . Instead, most researchers advocate a combination of DNA evidence and palaeoecological approaches as the way forward (i.e. using DNA as one proxy within a multiproxy study) 70,72,73 . Indeed, as indicated in the previous section, the mechanisms of ...
Context 12
... Fungi and Viruses. Bacteria, Archaea and to a lesser extent Fungi, pose both an opportunity and a threat to the field of sed-eDNA. The opportunity is that, as for other organisms, their sed-eDNA can be used for temporal reconstruction of communities, with at least two requirements: firstly, that the environment is favourable to preservation (Fig. 2); secondly, that the DNA is from a group that would be present and functional in the water column but not the sediment. The threat comes from the ability of many microorganisms to function in sediments, with two primary, interconnected effects: (1) they increase the bioavailability and degradation of organic matter, including DNA and ...

Citations

... In the past, fi eld studies on dinofl agellate cysts are generally focused on the surface sediments for mapping the distribution and abundance of cysts of important species, investigating species diversity of cyst assemblage in a region of concern, and confi rming the cyst presence for some species with particular importance (Luo et al., 2018;Limoges et al., 2020;Liu et al., 2020aLiu et al., , b, 2021Mertens et al., 2020;Van Nieuwenhove et al., 2020;Hu et al., 2021Hu et al., , 2022, whereas sediment cores representing a valuable archive of phytoplankton communities are usually used to reconstruct past environmental changes (Keafer et al., 1992;Dai et al., 2012;Ellegaard et al., 2013Ellegaard et al., , 2020Bringué et al., 2016;García-Moreiras et al., 2018;Kim et al., 2018;Price et al., 2018;de Freitas et al., 2020;Li et al., 2021;Siano et al., 2021). Cultures established from reviving dinofl agellate resting cysts collected from sediment cores have been used to evaluate the impact of environmental changes on the physiology, genetic structure, and diversity in various species Klouch et al., 2016;Lundholm et al., 2017;Kremp et al., 2018;Delebecq et al., 2020;Ellegaard et al., 2020;Girault et al., 2021). ...
... In the past, fi eld studies on dinofl agellate cysts are generally focused on the surface sediments for mapping the distribution and abundance of cysts of important species, investigating species diversity of cyst assemblage in a region of concern, and confi rming the cyst presence for some species with particular importance (Luo et al., 2018;Limoges et al., 2020;Liu et al., 2020aLiu et al., , b, 2021Mertens et al., 2020;Van Nieuwenhove et al., 2020;Hu et al., 2021Hu et al., , 2022, whereas sediment cores representing a valuable archive of phytoplankton communities are usually used to reconstruct past environmental changes (Keafer et al., 1992;Dai et al., 2012;Ellegaard et al., 2013Ellegaard et al., , 2020Bringué et al., 2016;García-Moreiras et al., 2018;Kim et al., 2018;Price et al., 2018;de Freitas et al., 2020;Li et al., 2021;Siano et al., 2021). Cultures established from reviving dinofl agellate resting cysts collected from sediment cores have been used to evaluate the impact of environmental changes on the physiology, genetic structure, and diversity in various species Klouch et al., 2016;Lundholm et al., 2017;Kremp et al., 2018;Delebecq et al., 2020;Ellegaard et al., 2020;Girault et al., 2021). However, the numbers of dinofl agellate cysts remaining viable in long-buried sediments and the mechanisms behind it still need to be explored. ...
... In the past, changes of species composition in sediments have been used to assess environmental changes including eutrophication, changes in salinity, or oxygen concentration (Dale et al., 1999; Ellegaard et al., 2013Ellegaard et al., , 2020Bringué et al., 2016;García-Moreiras et al., 2018;Li et al., 2021;Siano et al., 2021). The adaptive responses of dinofl agellate species might be infl uenced by anthropogenic activities or climate changes, and revealing the evolutionary processes in a species is very important to understanding the genetic structure of populations. ...
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Many marine dinoflagellates can form resting cysts as part of their life cycle, which may be buried in sediment and remained viable for over 150 years, as the longest record in the literature. However, only a very limited number of cyst species have been revived from long-buried sediments and investigated in regard to a possible shift in the intra-specific genetic structure of a species detected from the historical record at a particular location. Here, we report a successful germination of three species of resting cysts that were sampled from the depth dated back to 1941 ± 18 AD from a 44-cm sediment core from the East China Sea. Seven isolates were established from germination of single cyst isolation or multi-cyst germinations. LSU rRNA gene or ITS sequences of these strains were obtained, then they were identified to be Biecheleria brevisulcata (five strains), Biecheleriopsis adriatica (one strain), and Scrippsiella donghaienis (one strain) according to their morphologies and rRNA gene sequences. Biecheleria brevisulcata strain 1, Bps. adriatica strain 21, and S. donghaienis strain 23 were examined in detail with LM and SEM, and analyzed with HPLC for their pigment compositions, and genetic diversity. We also confirmed the presence of a resting cyst of Bps. adriatica in the field for the first time. The LSU rRNA gene-based genetic distances of Bps. adriatica from that obtained from water sample, single-cell PCR sequencing for the cysts isolated from the surface sediment of the same sea area and that reported from other regions during the recent years, and ITS-based genetic distances of S. donghaienis from that obtained from cysts isolated from the surface sediment of the same location and that reported from other regions during the recent years indicated that the intra-specific genetic structure of each species in the sampling area may have shifted during the last 70 years. Our work confirms that B. brevisulcata, Bps. adriatica, and S. donghaienis, all described as new species around 2010, have inhabited the East China Sea for about 70 years. The present work reports the first retrieval of the viability of dinoflagellate resting cysts long-buried in the coastal sediments of China, which will facilitate further study on the historical occurrences of other harmful dinoflagellates and their relevance to the regional climate and environmental changes in China.
... For example, the eDNA in the marine sediments can not only reflect the biogenesis processes on different time scales, but also provide information on biodiversity and genetic diversity of different ecosystems in both ancient and modern times [74]. In addition, eDNA could be used to obtain past climate and environmental information through a taxa analysis, and it promises to be a very powerful tool for predicting future environmental changes and the function of the ecosystem [75]. ...
Article
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In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
... Such studies in the future could be greatly reinforced by the extraction of DNA from resting eggs [23,206,207]. We expect that eDNA from bottom sediments [208,209] will be also applied in such studies in the future, but such technologies are only recently being fine-tuned (and a proper taxonomically curated database of comparative sequences is vital). ...
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Non-indigenous species may pose a threat to native ecosystems worldwide. In aquatic environments, invasives may have a negative impact on human food security and livelihoods. Several water fleas (Crustacea: Branchiopoda: Cladocera) are notorious invasive alien species influencing large freshwater lake systems and even inland seas. In the current review, we discuss the state of knowledge regarding non-indigenous species in the Cladocera and their invasiveness potential in different continents. We argue that the potential impacts and occurrence of cladoceran exotics may be higher than generally assumed. We critically review 79 cases from literature sources, involving 61 cladoceran taxa where records outside of their natural distribution ranges were previously interpreted as invasions. We assessed the probability of natural range expansions versus human-mediated introductions and we discuss several major corridors of invasion. We estimate human-mediated transportations for at least 43 taxa (out of 61; ca 70%), while other cases can be seen as natural expansions of their distribution ranges (not necessarily/not likely human-mediated) and/or taxonomical confusion. We confirm non-indigenous presence in recipient regions for at least 41 cladoceran taxa, of which several are true invasives (i.e., with negative impacts on native ecosystems). The majority are zooplankters with effects on pelagic freshwater ecosystems, yet we also report on introductions by littoral taxa. We argue that cryptic introductions of cladocerans are taking place on a global scale, yet they remain under the radar. We highlight several striking case studies, such as the Ponto–Caspian onychopods that have invaded the Baltic Sea and the Laurentian Great Lakes, and several clones of the anomopod genera Daphnia and Bosmina that have successfully colonised new environments, causing equilibria shifts in native aquatic worlds. At the same time, we dispel some myths about taxa that were misconstrued as invasive in certain localities. Based on our review, the first of its kind for freshwater zooplankton, future environmental monitoring tools including molecular techniques and detailed surveys with rigorous and critical taxonomical assessments may help to provide a clearer picture on the extent of invasiveness of cladocerans.
... The concept of eDNA not only finds its applicability in monitoring the health and eminence of modern ecosystems but also provides a fascinating way to reconstruct past environments to provide a complete overview of ancient ecosystems. For future conservation planning, such reconstructed ecosystems can be utilized for backward testing of climate change models, emergence tracking of invasive species, and the valuation of anthropogenic impacts on ancient biodiversity and landscape [30]. ...
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The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
... Elevated organic matter (OM) content seems to play a crucial role in trapping DNAses to soil colloids and minerals and hence, reducing the degradation speed of exDNA (Cai et al., 2006). In aquatic environments, UV-radiation, dissolved OM-and salt concentrations are additional constraints potentially influencing exDNA decay (Ellegaard et al., 2020;Zhang et al., 2020). In addition, also the bind- Microbial hotspots such as the rhizosphere or bioreactors, but also soils and sediments with high microbial turnover and low clay F I G U R E 2 Recovery and extraction of different DNA types from environmental samples. ...
Article
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The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. We review the fractions of eDNA, describe how to obtain them from environmental samples and present a four‐scenario concept that aims at enhancing spatial and temporal resolution of eDNA‐based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA‐based biodiversity data. Finally, future avenues of research towards eDNA fraction‐specific analyses are outlined to unravel the full potential of eDNA‐based studies targeting micro‐ and macro‐organisms.
... We observed a much higher decline in the number of sequences amplified from extracellular DNA com- Sedimentation rates and mass accumulation rates have increased since the end of the 1990s ( Figure S8.2), which might result in more rapid DNA burial, and then, less prone to degradation. Although extracellular DNA can be adsorbed to sediment particles, reducing its susceptibility to degradation (Corinaldesi et al., 2005;Dell'Anno et al., 2002;, extracellular DNA is more exposed to secreted DNAases as well as uptake by bacteria than intracellular DNA (Ellegaard et al., 2020). Extracellular DNA can play a key role in ecosystem functioning in the first cm of the sediment layers as a P-rich molecule (~10% weight to weight; Dell'Anno & TA B L E 2 RV coefficients to quantify the congruence between PCoA site scores of morphological and DNA-based methods (intracellular and extracellular DNA) for diatom taxa in the core samples . ...
Article
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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.
... Experimental evidence from other ecosystems has shown that genetic variation in natural Daphnia populations allows adaptation to various environmental changes [57][58][59], such as alterations in elemental food quality [60,61], temperature [62], metal concentrations [63] or predation intensity [64]. While natural changes in lake trophic state are generally slow [65], human-caused changes in lake trophic state typically proceed at much higher rates. ...
Article
The human-caused proliferation of cyanobacteria severely impacts consumers in freshwater ecosystems. Toxicity is often singled out as the sole trait to which consumers can adapt, even though cyanobacteria are not necessarily toxic and the lack of nutritionally critical sterols in cyanobacteria is known to impair consumers. We studied the relative significance of toxicity and dietary sterol deficiency in driving the evolution of grazer resistance to cyanobacteria in a large lake with a well-documented history of eutrophication and oligo-trophication. Resurrecting decades-old Daphnia genotypes from the sediment allowed us to show that the evolution and subsequent loss of grazer resistance to cyanobacteria involved an adaptation to changes in both toxicity and dietary sterol availability. The adaptation of Daphnia to changes in cyanobacteria abundance revealed a sterol-mediated gleaner-opportunist trade-off. Genotypes from peak-eutrophic periods showed a higher affinity for dietary sterols at the cost of a lower maximum growth rate, whereas genotypes from more oligotrophic periods showed a lower affinity for dietary sterols in favour of a higher maximum growth rate. Our data corroborate the significance of sterols as limiting nutrients in aquatic food webs and highlight the applicability of the gleaner-opportunist trade-off for reconstructing eco-evolutionary processes.
... 2 of 14 microscopy analyses of fossilized eukaryotes, such as diatoms, foraminifera, dinoflagellate cysts, radiolaria, and coccolithophores (all belonging to the large group of single-celled protists) have been the gold standard to reconstruct paleoenvironments, paleoproductivity and palaeoceanographic conditions (Mudie et al., 2006;O'Brien et al., 2021;Oksman et al., 2019;Weckström et al., 2020;Yasuhara et al., 2020). However, such microfossil-based reconstructions are limited, as only the more robust and fossilized species are preserved in seafloor sediments, meaning that the vast number of soft-bodied organisms that have also thrived in the past ocean are not accounted for (e.g., many flagellates, chlorophytes, haptophytes, ciliates, zooplankton) (Ellegaard et al., 2020;Witkowski et al., 2016). The study of sedimentary ancient DNA (sedaDNA) has the potential to fill this gap and achieve a more complete picture of past marine ecosystems across the whole food web, which will be useful to help improve our understanding of possible future ecosystem responses to climate and ocean changes. ...
... Possibly, the smaller DNA fragments in our samples were more susceptible to degradation than longer ones or were too short to pass our bioinformatics filtering criteria (all fragments <25 bp were removed during data processing); however, this is speculative and only considers the eukaryotic sequences rather than the whole sample. Fragment size is a relatively simple measure for the authenticity of sedaDNA as many factors can influence fragmentation, including chemical and physical properties, taphonomy, and diagenesis (Ellegaard et al., 2020;Giguet-Covex et al., 2019). In ancient bone samples, sample age does not necessarily correlate with increased fragmentation; however, sample age does correlate with increased DNA deamination frequency (Kistler et al., 2017), thus the latter is a more robust approach to assess DNA authenticity. ...
Article
Full-text available
Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo‐environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo‐investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub‐optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non‐ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best‐practice ship‐board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.
... Despite the different taxonomic resolution and preservation of biomolecules, most paleobiological reconstructions have been focused on the analysis of a single biomolecule, either DNA (Pedersen et al., 2015;Ellegaard et al., 2020), proteins (Cappellini et al., 2012;Mackie et al., 2017) or lipids (Schinteie and Brocks, 2017), limiting a comprehensive reconstruction of the past biological composition and ecological scenario of a sample. Therefore, multiproxy approaches based on the analysis of different biomolecules has recently been claimed to address complex biological questions (Cappellini et al., 2018), such as paleoecological reconstructions. ...
Article
Full-text available
Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.
... The relatively young field of resurrection ecology offers a "backward-in-time" approach and can be defined as the revival and study of long-dormant organisms via hatching of dormant life stages. This enables the direct quantification of phenotypes over temporal scales exceeding the average human lifespan [41,42]. Many phytoplankton species form dormant resting stages that sediment at the sea floor after vegetative growth is ceased in the water column. ...
Article
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Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.