Project

Comprehensive literature about ancient DNA studies from sedimentary archives - by the sedaDNA scientific society

Goal: This tool is an updated and comprehensive database about the scientific literature related to sed-ancient-DNA studies. This initiative comes from the sedaDNA scientific society https://ercapo.wixsite.com/sedadna-society

Updates
0 new
1
Recommendations
0 new
3
Followers
0 new
167
Reads
8 new
1480

Project log

Eric Capo
added a research item
Locations of sampling sites from sedimentary ancient environmental DNA (aeDNA) studies. aeDNA is DNA that has degraded into short fragments, exhibits post-mortem damage signatures, and is recovered from a non-living tissue, organism, or environmental sample. Here we focus on sedimentary archives with contiguous records such as lake and marine sediments, permafrost, middens, cave sediments, soils, and incidental associated surface sediment samples used to interpret sedimentary archives. Studies span historic and ancient time periods using a variety of DNA-based methods (i.e., metabarcoding, shotgun sequencing, target capture, qPCR, ddPCR, and others) to study taxa from microorganisms to plants and mammals.
Eric Capo
added 9 research items
The temporal trajectory of lake microbial communities is still rarely investigated over timescales that encompass the full history of an aquatic ecosystem and, therefore, its response to global or local long-term environmental changes. Thanks to the development of molecularbased procedures in paleoecology, it is today possible to assess changes in lake microbial communities via the extraction and sequencing of DNA molecules preserved in sedimentary archives. Here we applied an 18S-metabarcoding approach on sedimentary DNA obtained from four Swedish mountain lakes to assess the temporal variations of microbial eukaryotic communities over the last 10,000 years. The coupling of DNA data with sediment geochemistry and paleoclimatic data allow us to pinpoint when and to what extent environmental changes impacted these lake ecosystems. This study highlights the strong impact of catchment geology (bedrock and vegetation cover) on the shaping of lake microbial communities suggesting that - at least in a long-term perspective - species sorting may act more intensely than dispersal in these mountain lakes. While providing novel indications about the pioneer communities of those natural systems, data was also used to evaluate the effects of long-term climatic fluctuations on lake microbial communities, a continuous pressure known to impact such communities but still rarely studied over long-term time scales.
PaleoEcoGen is a new working group that was launched with the aim of bringing together scientists from around the world who use ancient environmental DNA (ancient eDNA) as a novel proxy to examine the response of past biological communities to environmental changes (pastglobalchanges.org/paleoecogen). We are particularly interested in exploiting the added value of these emerging ancient eDNA tools to advance our knowledge of critical transitions in Earth's Quaternary history. To this end, we aim to stimulate and enhance international ancient eDNA research by organizing topical work-shops to discuss new methodologies in the field (including synthetic analyses and model-ing approaches), and to coordinate research efforts for bigger picture analyses that, ultimately, will help to inform conservation efforts and future biodiversity assessments.
Based on the coupling between paleoecology and high-throughput sequencing of DNA, we analyzed the sedimentary records from two lakes (Lake Annecy and Lake Bourget, French Alps) in order to reconstruct the temporal dynamics of their microbial eukaryotes communities. We aimed to reveal the effects of environmental changes in these two lakes both similarly subject to air temperature fluctuations and differently exposed to phosphorus concentration during the last century (between 10 and 15 µg.L-1 in Lake Annecy; up to 100 µg.L-1 in Lake Bourget). The results showed that a large number of microbial eukaryotes OTUs were recovered from the sedimentary records mainly distributed within ciliophora, fungi, dinophyceae and chlorophyta in both lakes. Common responses were observed regarding the impact of the air temperature increase in the late 1980s, with notably the increase in the relative abundance of dinophyceae in the 2 lakes. The changes in terms of richness and relative abundance of microbial eukaryotes groups related to eutrophication were found to depend on the level of phosphorus concentration (i.e., threshold effect). Network analysis revealed temporal patterns of OTUs co-occurrence driven by environmental changes. Overall, our data shows that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes, allowing the study of numerous microbial eukaryotes groups that were traditionally not considered in paleo-reconstructions.
Marie-Eve Monchamp
added a research item
Freshwater ecosystems are under new and increasing threats from anthropogenic change. Ability to detect and predict consequences of environmental perturbations on ecosystem function and water quality is limited by the lack of empirical data over relevant time scales. Paleoecological records present a unique opportunity to broaden understanding of ecological transitions over decadal to millennial timescales. This study tested the occurrence of regime shifts to track changes throughout the lake food web beyond the typical instrumental era, using both “traditional” paleoecological proxies (e.g., microzoo-plankton, zoobenthos, and pigments) and more recently developed molecular genetic methods (sedimentary DNA). We used sediment cores from the perialpine Lake Joux (Swiss Jura), where the history of human settlement and land-use practices in the catchment has been well documented since the Medieval period. Paleoecological evidence revealed an abrupt and unprecedented biological reorganization in the second half of the 20th century, following several centuries of relatively stable communities despite growing human pressure. Time-varying autoregression computed using dynamic linear modelling identified this transition, triggered by the onset of rapid cultural eutrophication in the 1950s, as a true regime shift. Since this time, despite decades of re-oligotrophication, biotic communities of Lake Joux have not returned to pre-disturbance composition, most likely due to other confounding factors, including climate warming, that may prevent the lake from returning to an earlier equilibrium state. Paleoecological reconstruction further suggested that cladocerans responded earlier to disturbance, which is highly relevant for lake monitoring and management strategies.
Joanna Gauthier
added a research item
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.
Jamie Wood
added a research item
Knowledge about the diets of New Zealand's extinct moa (Aves: Dinornithiformes) is heavily biased towards just three species (Dinornis robustus, Megalapteryx didinus and Pachyornis elephantopus), which represent about 90% of all identified coprolites and gizzard content samples. By comparison, the diets of the other six moa species are poorly known. Here, we report the discovery of a new coprolite deposit attributed to little bush moa (Anomalopteryx didiformis) based on DNA barcoding and former moa species distributions. The deposit is the southernmost site from which moa coprolites have been recovered and just the second to contain mid-Holocene specimens. Moreover, the deposit provides the longest known temporal span (∼2200 years) of moa coprolites within a stratigraphic context. Pollen and plant DNA from the coprolites, as well as associated plant macrofossils, indicate that the deposit spans a period when the forest canopy was transitioning from Podocarpaceae to silver beech (Lophozonia menziesii) dominance about 6800–4600 years ago. Our analysis of coprolite content supports the current hypothesis that little bush moa browsed trees and shrubs within the forest understorey, but provides new evidence that ferns were also an important part of their diet. Based on this finding, we suggest that moa might once have played a previously unrecognised role in the dispersal of ground fern spores throughout New Zealand forests.
Heike H. Zimmermann
added 2 research items
We traced diatom composition and diversity through time using diatom-derived sedimentary ancient DNA (sedaDNA) from eastern continental slope sediments off Kamchatka (North Pacific) by applying a short, diatom-specific marker on 63 samples in a DNA metabarcoding approach. The sequences were assigned to diatoms that are common in the area and characteristic of cold water. SedaDNA allowed us to observe shifts of potential lineages from species of the genus Chaetoceros that can be related to different climatic phases, suggesting that pre-adapted ecotypes might have played a role in the long-term success of species in areas of changing environmental conditions. These sedaDNA results complement our understanding of the long-term history of diatom assemblages and their general relationship to environmental conditions of the past. Sea-ice diatoms (Pauliella taeniata [Grunow] Round & Basson, Attheya septentrionalis [Østrup] R. M. Crawford and Nitzschia frigida [Grunow]) detected during the late glacial and Younger Dryas are in agreement with previous sea-ice reconstructions. A positive correlation between pennate diatom richness and the sea-ice proxy IP25 suggests that sea ice fosters pennate diatom richness, whereas a negative correlation with June insolation and temperature points to unfavorable conditions during the Holocene. A sharp increase in proportions of freshwater diatoms at ∼11.1 cal kyr BP implies the influence of terrestrial runoff and coincides with the loss of 42% of diatom sequence variants. We assume that reduced salinity at this time stabilized vertical stratification which limited the replenishment of nutrients in the euphotic zone.
Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest‐tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species‐specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.
Eric Capo
added a research item
Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruct past biota. One way to pursue this goal is by unifying the sedaDNA scientific community. Here, we present a few initiatives taken over the last years to transmit information, augment our knowledge about best practices and method standardisation related to sedaDNA analysis and strengthen collaborations between research groups. Also, we discuss tools and ideas that could be used to increase the visibility of sedaDNA research by the scientific community. Finally, we would like to use this opportunity to discuss with the audience about new strategies to unify experts from different research fields - including paleoecology, paleolimnology, paleoceanography, molecular ecology, aquatic ecology, terrestrial ecology, microbial ecology - around the use of sedaDNA.
Eric Capo
added a research item
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.
Alexandra Rouillard
added a research item
Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to infer patterns of colonisation and Holocene vegetation development. Our cores from lakes Torfdalsvatn and Nykurvatn span the last c. 12,000 cal. yr BP and c. 8600 cal. yr BP, respectively. With near-centennial resolution, we identified a total of 191 plant taxa, with 152 taxa identified in the sedimentary record of Torfdalsvatn and 172 plant taxa in the sedimentary record of Nykurvatn. The terrestrial vegetation at Torfdalsvatn was first dominated by bryophytes, arctic herbs such as Saxifraga spp. and grasses. Around 10,100 cal. yr BP, a massive immigration of new taxa was observed, and shrubs and dwarf shrubs became common whereas aquatic macrophytes became dominant. At Nykurvatn, all dominant taxa occurred already in the earliest samples; shrubs and dwarf shrubs were more abundant at this site than at Torfdalsvatn. There was an overall steep increase both in the local and regional species pool until 8000 cal. yr BP, by which time 3/4 of all taxa identified had arrived. In the period 4500-1000 cal. yr BP, a few new taxa of bryophytes, graminoids and forbs are identified. The last millennium, after human settlement of the island (Landnam), is characterised by a sudden disappearance of Juniperus communis, but also reappearance of some high arctic forbs and dwarf shrubs. Notable immigration during the Holocene coincides with periods of dense sea-ice cover, and we hypothesise that this may have acted as a dispersal vector. Thus, although ongoing climate change might provide a suitable habitat in Iceland for a large range of species only found in the neighbouring regions today, the reduction of sea ice may in fact limit the natural colonisation of new plant species.
Camille Thomas
added 2 research items
The Dead Sea Deep Drilling Project allowed to retrieve a continuous sedimentary record spanning the two last glacial cycles. This unique archive, in such an extreme environment, has allowed for the development of new proxies and the refinement of already available paleoenvironmental studies. In particular, the interaction of the lake and sediment biosphere with elements and minerals that constitute paleoclimatic proxies has been emphasized. Although life is pushed to its extremes in the Dead Sea environment, several studies have highlighted the impact of microbial activity on this harsh milieu. The paradox is that the identity and means of adaptation of these organisms are largely ignored. We also know relatively little on the way this extreme ecosystem has evolved with time, and how it will react to growing pressure. Constraining this gap should allow to gain precision on the use of paleoenvironmental studies, and also assess the impact of human activity and climate change on a rare ecosystem. In this study, we use halite, the main evaporitic phase during arid periods in the Dead Sea basin and extract ancient DNA from their fluid inclusions, in order to characterize the ancient life of the Holocene Dead Sea. With the aid of an accurately designed protocol, we obtained fossil bacterial and archaeal 16S rRNA gene sequences that illustrate that the main microbial actors of the present Dead Sea have been present in the lake for a relatively long period, emphasizing the stability of this extreme environment. Additionally, we show that current phylotypes of the deep biosphere are present within the obtained fluid inclusions sequences, which would support seeding of the deep biosphere from the water column. Finally, we shed light on putative new actors of the sulfur cycle involving both archaea and bacteria, which could play an unexpected role in the reduction of sulfur species. Together, these data provide new research avenues for both geologists and biologists working in this extreme environment, and help understanding the evolution of the Dead Sea ecosystem with time.
Recently, the discovery of active microbial life in deep-sea sediments has triggered a rapid development of the field known as the “deep biosphere.” Geomicrobiological investigations in lacustrine basins have also shown a substantial microbial impact on lake sediments similar to that described for the marine record. Although only 30 % of the lake sites drilled by the International Continental Drilling Program (ICDP) have included microbial investigations, these lakes cover a relatively wide range of salinities (from 0.15 to 33.8 %), pH (from 6.0 to 9.8) and environmental conditions (from very arid to humid subtropical conditions). Here, we analyze results of very recent ICDP lake sites including subsurface biosphere research from southern Patagonia (Laguna Potrok Aike) to the Levantine area (Dead Sea) as well as the East Anatolian high plateau (Lake Van) and Macedonia (Lake Ohrid). These various settings allow the examination of the impact of contrasting environments on microbial activity and their subsequent role during early diagenesis. Furthermore, they permit the identification of biosignatures of former microbial activity recorded in the sediments as well as investigating the impact of microbes in biogeochemical cycles. One of the general outcomes of these preliminary investigations is data to support the hypothesis that microbes react to climatically driven environmental changes that have a direct impact on their subsurface distribution and diversity. This is clear at conspicuous levels associated with well-known climatic periods such as the Medieval Climatic Anomaly or the Little Ice Age. Although more research is needed, this relationship between prevailing microbial assemblages and different climatic settings appears to dominate the lacustrine sites studied until to date.
Eric Capo
added a project reference
Eric Capo
added an update
My aim is to collect papers and add columns with various informations about these research works (studied ecosystems, time periods, goals of the papers, targeted organisms, methods used etc) and to update regularly this table.
Alternatively, I am looking for a better way to have an online table that could be editable by everyone. If you know about such (free) tools, please let me know.
 
Laura Parducci
added 2 research items
Ancient DNA (aDNA) in lake sediments opens novel approaches to a better understanding of past environmental changes in aquatic and terrestrial ecosystems. The lake sediment sequences of Hässeldala and Atteköpsmosse in southern Sweden form two excellent records to investigate the wide spectrum of aquatic and terrestrial floral, faunal and microbial remains that existed between 17000 and 11000 years ago. aDNA were extracted from 26 sediment samples and shotgun metagenomic libraries were constructed in aDNA dedicated facilities at the Centre for GeoGenetics, Copenhagen. Here we present preliminary results from the currently ongoing bioinformatic processing of the shotgun metagenomic dataset. The analyzed samples cover past cold and warm time intervals and thus have the potential to provide a high-resolution reconstruction of ancient biological diversity under very different climatic scenarios.
The final stages of the Last Glacial in the Northern Hemisphere, between 19 and 11.7 thousand years before present, were punctuated by distinct and alternating warmer and colder climate states before Interglacial temperatures were attained, which in turn strongly influenced past vegetation. One of the best studied Lateglacial lake sedimentary record in Sweden is derived from the ancient lake of Hässeldala Port where several recent multi-proxy sediment studies and detailed chronological frameworks allowed reconstructing local and regional environmental conditions and summer temperatures between specific periods in great detail. Here we used shotgun DNA sequencing of the full metagenome preserved in the Hässeldala sedimentary record to investigate the whole diversity of taxonomic groups present in the lake sediment. We combine sedimentary aDNA, pollen and macrofossil studies and succeeded in correlating the relative abundances of plant communities to distinct climatic shifts that occurred between 14 and 10.5 ka BP.
Charlotte L. Clarke
added a research item
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
Private Profile
added 2 research items
Past bacterial diversity of a paleosol was reconstructed using metabarcoding of paleo environmental DNA (PalEnDNA). The paleosol was subsampled from a sediment core which was excavated from a palaeo beach-ridge located 2.6 km away from present sea shore and identified that it was deposited under marine influence ∼6000 years ago, using geological proxies. The bacterial community contained 37 bacterial phyla and dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, and Chloroflexi. The bacterial community was a mix-up of marine and terrestrial population, and thereby diversity was higher than marine populations. The result shows metabarcoding of PalEnDNA can effectively reconstruct past bacterial community structure.
Eric Capo
added 3 research items
Abstract. The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are underrepresented, rarely exceed the Holocene and contain sparse information about past diversity and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA ( seda DNA) metabarcoding. By amplifying a short, partial rbcL marker, 95.7 % of our sequences are assigned to diatoms across 18 different families with 38.6 % of them being resolved to species and 25.8 % to genus level. Independent replicates show high similarity of PCR products, especially in the oldest samples. Diatom richness is highest in the Late Weichselian and lowest in Mid- and Late-Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice associated diatoms and shows two re-organizations – one after the Last Glacial Maximum and another after the Younger Dryas. Different sequences assigned, amongst others, to Chaetoceros socialis indicate the detectability of intra-specific diversity using seda DNA. We detect no clear pattern between our diatom seda DNA record and the previously published IP<sub>25</sub> record of this core, although proportions of pennate diatoms increase with higher IP<sub>25</sub> concentrations and proportions of Nitzschia cf. frigida exceeding 2 % of the assemblage point towards past sea-ice presence.
The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long‐term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA ‐ historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) ‐ but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries ‐ the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.
Peat bogs located in high mountains are suitable places to study local environmental responses to climate variability. These ecosystems host a large number of eukaryotes with diverse taxonomic and functional diversity. We carried out a metabarcoding study using universal 18S and COI markers to explore the composition of past and present eukaryotic communities of a Pyrenean peat bog ecosystem. We assessed the molecular biodiversity of four different moss micro-habitats along a flood gradient in the lentic Bassa Nera system (Central Pyrenees). Five samples collected from different sediment depths at the same study site were also analysed, to test the suitability of these universal markers for studying paleoecological communities recovered from ancient DNA and to compare the detected DNA sequences to those obtained from the modern community. We also compared the information provided by the sedimentary DNA to the reconstruction from environmental proxies such as pollen and macro-remains from the same record. We successfully amplified ancient DNA with both universal markers from all sediment samples, including the deepest one (~ 10,000 years old). Most of the metabarcoding reads obtained from sediment samples, however, were assigned to living edaphic organisms and only a small fraction of those reads was considered to be derived from paleoecological communities. Inferences from ancient sedimentary DNA were complementary to the reconstruction based on pollen and macro-remains, and the combined records reveal more detailed information. This molecular study yielded promising findings regarding the diversity of modern eukaryotic peat bog communities. Nevertheless, even though information about past communities could be retrieved from sediment samples, preferential amplification of DNA from living communities is a caveat for the use of universal metabarcoding markers in paleoecology.
Jamie Wood
added 7 research items
Paleoparasitology offers a window into prehistoric parasite faunas, and through studying time-series of parasite assemblages it may be possible to observe how parasites responded to past environmental or climate change, or habitat loss (host decline). Here, we use DNA metabarcoding to reconstruct parasite assemblages in twenty-eight ancient rodent middens (or paleomiddens) from the central Atacama Desert in northern Chile. The paleomiddens span the last 50,000 years, and include middens deposited before, during and after the Central Andean Pluvial Event (CAPE; 17.5 - 8.5 ka BP). The CAPE was a period of increased precipitation and vegetation change, which we also demonstrate was associated with changes in local rodent taxa. Thirteen parasite taxa (including lice, mites, ticks, nematodes and cocci-dians) were identified from the middens, nine of which were likely derived from rodent hosts and four from alternative (insect or avian) hosts. The former are consistent with parasites known to infect South American rodent hosts. At our conservative level of high taxonomic rank assignment, the parasites appear to have been resilient to the major perturbations in climate and host taxa associated with the CAPE, and finer taxonomic resolution would be required to detect whether any species turnover occurred within the identified parasite groups. Rodent paleomiddens are fast becoming an unrivaled source of genomic data that can be used to reconstruct past ecosystem change on multiple taxonomic, temporal and spatial scales providing new insights into ecological responses to global change.
Andisols, developed from late-Quaternary tephra (volcanic ash) deposits and dominated by the nanocrystalline aluminosilicate, allophane, contain large stores of organic matter and are potential reservoirs for DNA. However, DNA recovery from Andisols and other allophane-bearing soils has been difficult and inefficient because of strong chemical bonding between DNA and both allophane and organic matter, and also because much DNA can be encased and physically protected in nanopores in allophane nano/microaggregates. We have therefore developed a new two-step DNA isolation method for allophanic soils and buried paleosols, including those low in clay, which circumvents these problems. The method centres on (1) releasing mainly microbial DNA, and extracellular (unbound) DNA, using an alkaline phosphate buffer (“Rai’s lysis buffer”) that blocks re-adsorption sites on the allophanic materials, and (2) the novel application of acidified ammonium oxalate (Tamm’s reagent) to dissolve the allophane and to release DNA which had been chemically-bound and also which had been protected within nanopores. Ammonium oxalate has not previously been applied to soil DNA extraction. DNA yields up to 44.5 µg g-1 soil (oven-dry basis) were obtained from three field-moist natural allophanic soil samples from northern New Zealand using this two-step method. Following extraction, we evaluated different DNA purification methods. Gel electrophoresis of the extracted DNA followed by gel purification of the DNA from the agarose gel, despite some DNA loss, was the only purification method that removed sufficient humic material for successful DNA amplification using the polymerase chain reaction (PCR) of multiple gene regions. Sequencing of PCR products obtained from a buried allophanic paleosol at 2.2-m depth on a sandy Holocene tephra yielded endemic and exotic plants that differed from the European grasses growing currently on the soil’s surface. This difference suggests that the DNA extraction method is able to access (paleo)environmental DNA derived from previous vegetation cover. Our DNA extraction and purification method hence may be applied to Andisols and allophane-bearing paleosols, potentially offering a means to isolate paleoenvironmental DNA and thus facilitate reconstruction of past environments in volcanic landscapes, datable using tephrochronology, and also aid biodiversity understanding of andic soils and paleosols.
Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo‐informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the inter‐annual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appear to be extraordinarily resilient. In contrast, at longer time scales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically‐induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future. This article is protected by copyright. All rights reserved.
Marco J. L. Coolen
added 33 research items
[1] Holocene sea surface temperatures (SST) of the Black Sea have been reconstructed using sedimentary C37 unsaturated alkenones assumed to be derived from the coccolithophorid haptophyte Emiliania huxleyi, whose fossil coccoliths are an important constituent of the unit I sediments. However, alkenones can also be biosynthesized by haptophyte species that do not produce microscopic recognizable coccoliths. A species-specific identification of haptophytes is important in such U37K′-based past SST reconstructions since different species have different alkenone-SST calibrations. We showed that 18S rDNA of E. huxleyi made up only a very small percentage (less than 0.8%) of the total eukaryotic 18S rDNA within the up to 3600-year-old fossil record obtained from the depocenter (>2000 m) of the Black Sea. The predominant fossil 18S rDNA was derived from dinoflagellates (Gymnodinium spp.), which are predominant members of the summer phytoplankton bloom in the modern Black Sea. Using a polymerase chain reaction/denaturing gradient gel electrophoresis method selective for haptophytes, we recovered substantial numbers of a preserved 458-base-pair (bp)-long 18S rDNA fragment of E. huxleyi from the Holocene Black Sea sediments. Additional fossil haptophyte sequences were not detected, indicating that the E. huxleyi alkenone-SST calibration can be applied for at least the last ∼3600 years. The ancient E. huxleyi DNA was well protected against degradation since the DNA/alkenone ratio did not significantly decrease throughout the whole sediment core and 20% of ∼2700-year-old fossil E. huxleyi DNA was still up to 23,000 base pairs long. We showed that fossil DNA offers great potential to study the Holocene paleoecology and paleoenvironment of anoxic deep-sea settings in unprecedented detail.
Recent work has shown that paleoenvironmental genomics, i.e. the application of genomic tools to analyze preserved DNA in sedimentary records, is a promising approach to reconstruct the diversity of past planktonic communities. This provides information about past ecological and environmental changes. A major advantage of this approach is that individual species, including those that did not leave other characteristic markers, can be identified. In this study, we determined which dinoflagellate marker (i.e. 18S rDNA, dinosterol or dinocysts) provided the most detailed information about the late-Holocene succession of dinoflagellates in an Antarctic Fjord (Ellis Fjord, Vestfold Hills). The preserved rDNA revealed two intervals in the 2750-year-old sediment record. The dinoflagellate diversity was the highest until approximately 1850 cal yr bp and included phylotypes related to known dinosterol producers. A lower concentration of dinosterol in sediments <1850 cal yr bp coincided with a community shift towards a predominance of the autotrophic sea-ice dinoflagellate Polarella glacialis, which is not a source of dinosterol. Remarkably, cultures of P. glacialis are known to produce other diagnostic sterols, but these were not recovered here. In addition, conspicuous resting cysts of P. glacialis were not preserved in the analyzed sediments. Overall, dinocysts were rare and the paleoenvironmental genomics approach revealed the highest diversity of dinoflagellates in Ellis Fjord, and was the only approach that recorded a shift in dinoflagellate composition at approximately 1850 cal yr bp indicative of a colder climate with more extensive ice cover - this timing coincides with a period of changing climate reported for this region.
Sarah E. Crump
added a research item
Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global‐scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic 10Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen‐based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags. Ancient plant DNA in a lake sediment record from the Eastern Canadian Arctic constrains postglacial colonization of dwarf birch to 5,900 years ago, which was ~3,000 years after local deglaciation and at least 1,300 years after other tundra plants were established. We place this vegetation history into a climatic context using lipid biomarker paleothermometry, demonstrating that Betula colonization was delayed relative to peak postglacial warmth. This colonization timing is >2,000 years after birch pollen appears in adjacent lake sediment, highlighting the influence of exotic pollen fluxes on palynological records and underscoring the utility of sedimentary DNA for determining local plant presence.
Eric Capo
added 7 research items
Peat bogs located in high mountains are suitable places to study local environmental responses to climate variability. These ecosystems host a large number of eukaryotes with diverse taxonomic and functional diversity. We carried out a metabarcoding study using universal 18S and COI markers to explore the composition of past and present eukaryotic communities of a Pyrenean peat bog ecosystem. We assessed the molecular biodiversity of four different same record. We successfully amplified ancient DNA with both universal markers from all sediment samples, including the deepest one (* 10,000 years old). Most of the metabarcoding reads obtained from sediment samples, however, were assigned to living edaphic organisms and only a small fraction of those reads was considered to be derived from paleoecological communities. Inferences from ancient sedimentary DNA were complementary to the reconstruction based on pollen and macro-remains, and the combined records reveal more detailed information. This molecular study yielded promising findings regarding the diversity of modern eukaryotic peat bog communities. Nevertheless, even though information about past communities could be retrieved from sediment samples, preferential amplification of DNA from living communities is a caveat for the use of universal metabarcoding markers in paleoecology.
Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.
Paleogenetics provides a powerful framework to reconstruct the long-term temporal dynamics of various biological groups from aquatic sediments. However, validations are still required to ensure the authenticity of the molecular signal obtained from sedimentary DNA. Here, we investigated the effects of early diagenesis on the DNA signal from micro-eukaryotes preserved in sediments by comparing metabarcoding inventories obtained for two sediment cores sampled in 2007 and 2013 respectively. High-throughput sequencing (Illumina MiSeq) of sedimentary DNA was utilized to reconstruct the composition of microbial eukaryotic communities by targeting the V7 region of the 18S rDNA gene. No significant difference was detected between the molecular inventories obtained for the two cores both for total richness and diversity indices. Moreover, community structures obtained for the two cores were congruent as revealed by procrustean analysis. Though most of the eukaryotic groups showed no significant difference in terms of richness and relative proportion according to the core, the group of fungi was found to differ both in terms of richness and relative proportion (possibly due to their spatial heterogeneity and potential activity in sediments). Considering the OTUs level (i.e. Operational Taxonomic Units as a proxy of ecological species), our results showed that, for the older analyzed strata (age: 15–40 years), the composition and structure of communities were very similar for the two cores (except for fungi) and the DNA signal was considered stable. However, for the uppermost strata (age < 15 years), changes of moderate magnitude were detected in the relative abundance of few OTUs. Overall, this study points out that, in Nylandssjön sediments, early diagenesis did not induce marked modifications in the micro-eukaryotic DNA signal, thus opening new perspectives based on the analysis of eukaryotic sedimentary DNA to address scientific issues both in the domains of paleolimnology and microbial ecology. Because this study site is ideal for DNA preservation in sediment (quick sedimentation processes, no sediment resuspension, anoxic conditions at sediment–water interface), the generalization of our conclusions, in particular for less favorable sites, must be considered cautiously.
Eric Capo
added a project goal
This tool is an updated and comprehensive database about the scientific literature related to sed-ancient-DNA studies. This initiative comes from the sedaDNA scientific society https://ercapo.wixsite.com/sedadna-society