The extraction and analysis of sedimentary ancient DNA (sedaDNA) from Pleistocene and Holocene sediments could potentially revolutionise palaeoecology and biostratigraphy over the next decade. This potential is growing because it has been shown that a) there is preservation of sedaDNA well outside the sub-Arctic and Arctic biomes, b) the costs are reducing, c) the number of laboratories has increased, and most importantly, d) the techniques, such as metabarcoding and shot gun sequencing, are becoming more robust (both in reliability and specificity) and deeper (in taxonomic coverage). At present, and probably for some considerable time to come, sedaDNA will be used alongside microscopic proxies such as pollen, diatoms, foraminifera and insects but it has the potential to be far more specific in characterising local biotic conditions, climatic reconstructions and impact of human activities. This session invites papers using sedaDNA from sediments or soils from any site from lakes to marine deposits and any time period. Methodological papers are also welcome.

Convener: Kathleen Stoof-Leichsenring | Co-conveners: Laura S. Epp, Mikkel Winther Pedersen
| Attendance Mon, 04 May, 16:15–18:00 (CEST)

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Session materials Download all presentations (142MB)

Chat time: Monday, 4 May 2020, 16:15–18:00

Chairperson: Kathleen, Laura, Mikkel
D618 |
Inger Alsos and the ECOGEN and IceAGenT teams

Arctic and alpine species are disproportionally affected by climate change, and knowledge about their ability to survive or disperse is essential for their long-term conservation. Ancient sedimentary DNA (sedaDNA) has improved as a proxy for reconstructing past floras, and may now be applied in high throughput analyses. Our lab has analysed, or is in the process of analysing, sedaDNA from ~40 long (up to 26 000 years old) and 11 short (0-1000 years old) lake sediment cores from the Europe (Alps, Norway, Svalbard, Iceland, Polar Urals). Both general and site-specific patterns have emerged from these data. For example, the taxa recorded in sedaDNA often indicate a warmer climate than that which has been inferred based on pollen records; this is in concordance with macrofossil evidence. Also, the limits of past northern tree lines may have been underestimated based on pollen studies. Some heathland species, such as Vaccinium spp. and Empetrum, often show a time lag in arrival compared with other species with similar climatic requirements. Thus, despite the fact that they have berries and therefore are well adapted to long-distance dispersal by birds, our data show they are constrained from rapid responses to climate changes. Other patterns are site-specific. For example, we see a stepwise doubling of floristic richness from the Last Glacial Maximum to the Holocene in the Polar Urals, which is barely detectable in the pollen analyses. Further, the majority of taxa with a mainly arctic-alpine distributions survived the early-Holocene climate warming, when shrub and trees entered the region, probably due to a very heterogeneous landscape that allows co-existence of species with different requirements. In contrast, arctic-alpine taxa disappear from the catchment a subset of the lakes studied in North Norway after shrub and forest expansion. Linking this type of information to characteristics of these biogeographic regions may provide useful when planning for future nature reserves. In the near future, the combination of many sites, complete DNA reference libraries, and emerging molecular methods will allow for the tracking of individual species through time and space.

How to cite: Alsos, I. and the ECOGEN and IceAGenT teams: Ancient sedimentary DNA reveals long-term impact of climate change on northern flora, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-9605, https://doi.org/10.5194/egusphere-egu2020-9605, 2020.

D619 |
Laura Parducci, Kevin Nota, Willy Tinner, Jacqueline van Leeuwen, Pim van der Knaap, Dirk Sachse, Zuobing Liang, Achim Brauer, Markus J. Schwab, Xuery Zhao, Aldo Marchetto, Andrea Lami, and Sabine Wulf

We used shotgun DNA sequencing of the full metagenome preserved in varved lake sediments from southern Italy (Lago Grande di Monticchio) to investigate the whole diversity of taxonomic groups present. We combine sedimentary aDNA and pollen data as well as other biological multi-proxy data and tested if it was possible to correlate the relative abundances of plants and other biological communities to distinct climatic shifts that occurred between the Late Glacial and Holocene. In addition, we used the metabarcoding technique to compare the two sequencing approaches specifically for plants.

Our studies showed that the inhibition of DNA replication was almost absent in older (full glacial) sediment samples while it increased substantially in more recent samples. DNA provides a strong signal of plant community changes and a large number of new plant taxa were recorded. A comparison between sequencing approaches and proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are often recorded by DNA and that DNA provides important complementary information to that collected from palaeoecological analyses. Nevertheless, increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the metagenomic approach.

How to cite: Parducci, L., Nota, K., Tinner, W., van Leeuwen, J., van der Knaap, P., Sachse, D., Liang, Z., Brauer, A., Schwab, M. J., Zhao, X., Marchetto, A., Lami, A., and Wulf, S.: Shotgun DNA, pollen and biological multi-proxy analysis of Lateglacial lake sediments from Monticchio, Italy, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-19272, https://doi.org/10.5194/egusphere-egu2020-19272, 2020.

D620 |
Luise Schulte, Nadine Bernhardt, Kathleen Stoof-Leichsenring, Heike Zimmermann, Luidmila Pestryakova, Laura Epp, and Ulrike Herzschuh

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the earth. To be able to predict future responses of these forests to a changing climate, it is important to understand also past dynamics of larch populations. One well-preserved archive to study vegetation changes of the past is sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores. We studied a lake sediment core covering 6700 calibrated years BP, from the Taymyr region in northern Siberia. To enrich the sedaDNA for DNA of our focal species Larix, we combine shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of Larix. Variation in the chloroplast reads confirm an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. In this time span, both species can be detected at the site, although larch populations have decreased from a forested area to a single-tree tundra at present. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.

How to cite: Schulte, L., Bernhardt, N., Stoof-Leichsenring, K., Zimmermann, H., Pestryakova, L., Epp, L., and Herzschuh, U.: Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-19733, https://doi.org/10.5194/egusphere-egu2020-19733, 2020.

D621 |
Stijn De Schepper, Jessica Louise Ray, Lisa Griem, Nicolas Van Nieuwenhove, Danielle Magann Grant, Kristine Steinsland, Katrine Sandnes Skaar, and Umer Zeeshan Ijaz

Long sedimentary ancient DNA (sedaDNA) records from the marine environment are at present a curiosity and their utility in paleoceanographic research is not yet fully explored. Nevertheless, a few studies indicate that this ecogenetic repository represents an untapped source of new information with which paleoclimatic and paleoceanographic variability can be more deeply explored. We have generated a sedaDNA record from a 19.6 m-long sediment core in the Labrador Sea (Eirik Drift, south of Greenland). The record extends from the early Holocene to Marine Isotope Stage 5 (ca. 130,000 years ago), and we characterized several important climatic transitions in this time interval using stable isotope stratigraphy, ice-rafted detritus counts, and dinoflagellate cyst census counts. The primary goal of this investigation was to query the sedaDNA record for a biological indication of the last and penultimate deglaciation, as well as Heinrich events identified between 65,000 and 25,000 years ago. Our metabarcoding strategy targeted a broad diversity of eukaryotic organisms through amplification of the V7 hypervariable region of the small subunit ribosomal RNA (SSU rRNA) gene. The preliminary sedaDNA results indicate that eukaryote ancient DNA is present in all samples investigated, including those dating back to Marine Isotope Stage 5. Furthermore, we identified abundance shifts in Protaspidae (cercozoa), diatoms, dinoflagellates, and marine stramenopiles (amongst others) that may be linked to changes in paleoceanography during the last two deglaciations as well as Heinrich events (HE3, HE4).

How to cite: De Schepper, S., Ray, J. L., Griem, L., Van Nieuwenhove, N., Grant, D. M., Steinsland, K., Sandnes Skaar, K., and Ijaz, U. Z.: A sedimentary ancient DNA approach to elucidate the Labrador Sea paleoceanography over the last ~130,000 years, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-10928, https://doi.org/10.5194/egusphere-egu2020-10928, 2020.

D622 |
Ines Barrenechea Angeles, Luc Beaufort, Daniel Ariztegui, and Jan Pawlowski

In the last ten years, sedimentary ancient DNA (sedaDNA) becomes a new proxy for paleoceanographic analyses that provide information about large range of non-fossilized taxa. Usually, the sediment samples destinated for sedaDNA study are immediately frozen after collection or stored in special buffer to preserve the DNA. However, there are many cores that have been collected long time before the advent of paleogenomics and that are commonly refrigerated and stored at 4°C. Here, we test whether such cores can be used as a source of ancient DNA, by analysing the sedaDNA samples from 36 meters long marine gravity core that was stored during 14 years at 4 °C. The core MD05-2920 was retrieved during the MD148/PECTEN – Images XII cruise, in Bismarck Sea, off New Papua Guinea, and records the past 385 ka. We analysed samples from 20 layers spanning the interval from 1.6 ka to 384 ka, where isotopic measures of ∂18O showed significant paleoceanographic changes. We started by analysing a universal eukaryotic marker, the V9 (170 bp) region of the 18S rRNA. However, the obtained datasets were dominated by sequences belonging to species of fungi and amoebae that probably originated from post-collection storage. More data were obtained by using markers specific to selected marine taxa, such as foraminifera, radiolaria, and diatoms. The analysis of these data show clearly that the DNA is preserved in marine sediment down to 385 ka old layers. Our study also shows a possibility to exploit the sedaDNA from refrigerated material stored in cores repositories.

How to cite: Barrenechea Angeles, I., Beaufort, L., Ariztegui, D., and Pawlowski, J.: Exploring diversity of marine eukaryotes across 385 ka old gravity core using sedaDNA, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-17545, https://doi.org/10.5194/egusphere-egu2020-17545, 2020.

D623 |
| Highlight
Katharina Dulias, Juliette Knockaert, Charline Giguet-Covex, and Kevin Walsh

Archaeologists working in high altitude-zones in the Alps where faunal remains were absent have until relatively recently, been reliant on palynology in order to infer the probable presence of pastured animals. The development of sedimentary ancient DNA (sedaDNA) analysis has changed this. We are now able, if taphonomic conditions permit, to identify the presence and absence of specific domesticated animals as well as changes in vegetation communities that were a consequence of pastoral activity. Over the past decade, lake sediment DNA has been used by an increasing number of studies to trace past agricultural activities, human presence and landscape changes.

More recently, lake sedaDNA sequencing has proven applicable to investigate the relative impact of human activities, such as transhumance pastoralism, on the vegetation in the catchment of lakes in the Western French Alps and the domestic species used at different time periods. Thus, providing a new outlook on the anthropogenic effect on alpine landscapes.

Our use of sedaDNA is one element in a project designed to elucidate the evolution of transhumance in the Western Alps. While the sequential isotope analyses from domesticated herbivore teeth facilitate our comprehension of seasonal pastoral mobility, the sedaDNA complements this work via its potential for inferring which pastures were frequented and the effect of livestock presence on these environments. This combined approach can demonstrate not only the existence of pastoral practises in the region, but also reconstruct the movement patterns as well as the direct impact of transhumance pastoralism in the Western Alps in a wide chronological and spatial frame.

With the application of advanced bioinformatic techniques, we combine previous data on past and present vegetation with our findings. The genetic data was obtained through the established method of metabarcoding, which is a relevant tool for reconstructing palaeoenvironments. Using the same approach with additional quantitative PCR analysis for mammalian sedaDNA offers even more detailed insights into the presence and possible abundance of domestic species in the lake catchment area.

This application can demonstrate the potential of sedaDNA in reconstructing palaeoenvironments and its relevance in conceptualising long-term ecosystem changes relating to human and non-human agencies.

How to cite: Dulias, K., Knockaert, J., Giguet-Covex, C., and Walsh, K.: The use of sedimentary ancient DNA from lakes in tracing human-environment interactions in the Western Alps, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-21944, https://doi.org/10.5194/egusphere-egu2020-21944, 2020.

D624 |
| Highlight
Charline Giguet-Covex, Qi Lin, Ludovic Gielly, Fabien Arnaud, and Ke Zhang

More than 80% of shallow lake ecosystems in the Yangtze floodplain suffer significant disturbances from the 50’s, especially eutrophication. These environmental degradations and subsequent loss of services are related with the important and rapid development of the agriculture, industry, urban areas and the population boom in the region. Lake Taihu is one of the largest lakes of the floodplain and represents an important water resource (for drinking and fishing) for the population of the two big cities on the lake shore. This lake experimented two shifts toward the degradation of the trophic state: one in the 50-60’s and a second in 80’s.

In order to document the causes of these ecological shifts, we applied the DNA metabarcoding approach on lake sediments and focused on plants as proxy of land use. Whereas this proxy has been successfully applied in many lakes over the world, it has never been tested in large shallow lakes and not in China either.

We show important changes in land use in 50’s and 80’s related with agricultural developments (i.e. intensification) and urban expansion, respectively. In fact, in the 50’s crop plants are increasing (rapeseed and/or cabbage, rice and/or wheat, barley and Poaceae) whereas in 80’s, we record the development of several plants associated to gardens (e.g. ornamental species). Moreover, this last period is characterised by the presence of trees mostly cultivated along stream banks to protect dikes against erosion. Between the 80’s and the years 2000, the plant diversity recorded in the sediment strongly increase, which may be due to higher detrital inputs (i.e. more efficient DNA transfer). The timing in land-use changes corresponds to the main shifts in lake trophic state.

How to cite: Giguet-Covex, C., Lin, Q., Gielly, L., Arnaud, F., and Zhang, K.: Recent ecological trajectory of lake Taihu and land-use history reconstructed from lake sediment DNA , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-3011, https://doi.org/10.5194/egusphere-egu2020-3011, 2020.

D625 |
Tony Brown, Thierry Fonville, Helen Mackay, Maarten van Hardenbroek, and Inger Alsos

Lowland lakes in Scotland and Ireland have been heavily impacted by human activity since the Neolithic due to forest clearance, agriculture and lakeside settlement. Whilst plant macrofossils, pollen and other microfossils, especially diatoms, have been able to outline these changes many uncertainties remain about the origin and exact nature of these impacts. Obtaining independent measures of both vascular plants and mammals (and other animals) allows for more taxonomically precise reconstructions and the study of long-term biotic interactions. Lipid biomarkers, such as faecal steroids and bile acids, can both validate the mammal DNA, and also indicate the magnitude of agricultural and human lake inputs into the lake ecosystem. Our initial work focused on small artificial islands (crannogs) common in the Celtic parts of the UK. Unusually strong sedaDNA and lipid biomarker results from both plants and animals are believed to result from the creation of a biogeochemical halo around the crannogs due to the direct input of bone and viscera, rapid organic and clastic sedimentation, and a lack of disturbance. The human activities on the artificial islands, such as slaughter, butchery and feasting, caused severe eutrophication of the smaller lakes, which only partially recovered after the abandonment of the sites. Similar but less pronounced effects can be seen at lake-side settlement sites in larger lakes and away from archaeological sites which reflect catchment-wide influences. This paper will present data from crannogs, lake-side sites and from a new study of lakes on small islands on the Celtic Seaboard. These island sites are being studied to test the narrative of ‘marginality’ and a perceived lack of resilience in small islands during the last two thousand years. Overall our sedaDNA and steroid results complement data from both archaeological excavation, survey and traditional palaeoenvironmental proxies to provide a more detailed and comprehensive image of the environment in which our ancestors were operating, the changes they had on their ecosystems and our inheritance of this today.

How to cite: Brown, T., Fonville, T., Mackay, H., van Hardenbroek, M., and Alsos, I.: Getting it Together: Combining plant and mammal DNA with Lipid Biomarkers from Irish and Scottish Lakes, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-4846, https://doi.org/10.5194/egusphere-egu2020-4846, 2020.

D626 |
Anastasia Poliakova, Lena M. Håkansson, Anders Schomacker, Sandra Garces Pastor, and Inger Greve Alsos

Ancient DNA metabarcoding applied together with the investigations of the plant macro-remains, pollen, spores and non-pollen palynomorphs (NPP), open new perspectives and give better taxonomical resolution, allowing to obtain more precise and specific data on the local environment conditions and their changes. So far, only three multiproxy studies that involve both molecular and palaeobotanical/palynological methods are available for the high Arctic archipelago Svalbard. We intend to contribute filling this gap. Therefore, a field trip to Svalbard was undertaken in September, 2019, and three sediment cores were retrieved from the Tenndammen lake (N 78°06.118; E 15°02.024, 7 m asl) which is a small and shallow water body (ca 2.5 m depth). The lake is located in the valley of Colesdalen, a well-known Svalbard’s biodiversity hot spots and a home for about seven to ten thermophilic plant species.

To investigate the Holocene to modern vegetation history of this place, the 85cm core Te2019 was chosen, it was described for lithology, X-rayed, µXRF-scanned, line-scan photographed with high resolution and sampled for sedaDNA, pollen, spores and NPP studies as well as for studies on plant macrofossils. Ten 14C AMS dates were taken in order to establish an age-depth model. The DNA record contains around 100 taxa, most findings of those are supported by pollen studies (Asteraceae, Betula, Brassicaceae, Salix, Saxifraga, Vaccinium/Ericaceae) and by spores (Equisetum and Bryophyta). In addition, various fungi spores were identified. Investigations of plant macro-remains well support findings of the aquatic (i.e. Warnstorfia fluitans) and terrestrial mosses (e.g. Aulacomnium conf. turgidum, Bryum spp., Distichium capillaceum, Calliergon richardsonii, Scorpidium cossonii, Sphagnum spp., Rhizomnium spp.). Besides, fragments of Salix and Betula leaves and fruit parts, various leaf, stem tissues and flower fragments of Saxifraga species were found within the samples from the same depths with the correspondence to DNA records. Three DNA zones (SvDNA 1 – SvDNA3) and  one subzone within the earliest zone (SvDNA-1a – SvDNA-1b) were established. Relations between DNA, pollen and macrofossil zones were studied. This study is performed within the “Future ArcTic Ecosystems” (FATE) research program: Initiative for investigation on drivers of diversity and future scenarios from ethnoecology, contemporary ecology and ancient DNA.

How to cite: Poliakova, A., Håkansson, L. M., Schomacker, A., Garces Pastor, S., and Alsos, I. G.: Ancient plant DNA, macro- and microfossil studies of the lake sediments from the High Arctic lake Tenndammen, Svalbard, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5444, https://doi.org/10.5194/egusphere-egu2020-5444, 2020.

D627 |
Sofia Ribeiro, Sara Hardardottir, Jessica Louise Ray, Stijn De Schepper, Audrey Limoges, Connie Lovejoy, and Marit-Solveig Seidenkrantz

As we move towards a “blue” Arctic Ocean in the summer within the next decades, predicting the full range of effects of climate change on the marine arctic environment remains a challenge. This is partly due to the paucity of long-term data on ocean-biosphere-cryosphere interactions over time and partly because, today, much of our knowledge on past ocean variability derives from microfossil and biogeochemical tracers that all have considerable limitations such as preservation biases and low taxonomic resolution or coverage.

Recent studies have revealed sedaDNA as a potential “game-changer” in our ability to reconstruct past ocean conditions, due to the preservation of DNA at low temperatures, and the possibility to capture a much larger fraction of the Arctic marine biome diversity than with classical approaches. However, while sedaDNA has been used in terrestrial, archeological, and lake studies for some years, its application to marine sediment records is still in its infancy.

Here, we will present new results from material recently collected along the two Arctic Ocean outflow shelves off Greenland (Greenland Sea/Fram Strait and Northern Baffin Bay/Nares Strait). We have used a combination of modern and ancient DNA methods applied to seawater, surface sediments, and sediment cores covering the past ca. 12 000 years with the objectives of: 1) characterizing the vertical export of sea ice-associated genetic material through the water column and into the sediments following sea ice melt and 2) exploring the potential of sedaDNA from the circum-polar sea ice dinoflagellate Polarella glacialis as a new sea ice proxy. For the first objective, we followed a comparative metabarcoding approach while the second objective included designing species-specific primers followed by gene copy number quantification by a droplet digital PCR assay. 

We argue that sedaDNA will have a critical role in expanding the Paleoceanography “toolbox” and lead to the establishment of a new cross-disciplinary field.


How to cite: Ribeiro, S., Hardardottir, S., Ray, J. L., De Schepper, S., Limoges, A., Lovejoy, C., and Seidenkrantz, M.-S.: The dawn of Molecular Genetics in Paleoceanography: tracing Arctic change during the Holocene with marine sedaDNA records from Greenland , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-7131, https://doi.org/10.5194/egusphere-egu2020-7131, 2020.

D628 |
Dilli Prasad Rijal, Peter D. Heintzman, Youri Lammers, Nigel Gilles Yoccoz, Tony Gavin Brown, Kelsey Lorberau, Dorothee Ehrich, Iva Pitelkova, Tomasz Goslar, Jostein Bakke, Kari Anne Bråthen, and Inger Greve Alsos

Understanding the dynamics of biodiversity in the past will contribute to a better informed inference of future biodiversity. Palaeoecological patterns in biodiversity are mainly preserved in natural archives such as lake sediments. Using ancient DNA from the sediment of 10 lakes from northern Fennoscandia, we analysed terrestrial plant diversity pattern for the entire Holocene, and how these patterns correspond to drivers of change such as temperature and biota. We modeled temporal trends in taxonomic richness and turnover using generalized additive models (GAM). We included delta oxygen isotope values from North Greenland Ice Core Project as a proxy for regional temperature, and the presence of dominant woody species as biotic drivers of terrestrial plant diversity.  

Results show a general tendency of an increase in species richness from the early Holocene onwards, but this pattern is asynchronous across the lakes, with some lakes having a peak in diversity in the mid-Holocene (8,000-6,000 cal. BP), late Holocene (~2,500 cal. BP), or in recent times. The turnover decreases in most of the lakes throughout the Holocene. Meanwhile, it consistently increases in a few lakes. With some exceptions, temperature and biotic variable differentially affects the richness and turnover across the lakes. Our study from multiple lakes and heterogeneous habitats may be able to identify the main drivers of past biodiversity changes in these systems. As a result, it may help us to understand the mechanisms of change so that the impacts of current climate change and biotic factors on biodiversity may be assessed.


Author's list and affiliations:

Dilli Prasad Rijal1, Peter D. Heintzman2, Youri Lammers2, Nigel Gilles Yoccoz1, Tony Gavin Brown2,3, Kelsey Lorberau1, Dorothee Ehrich1, Iva Pitelkova2, Tomasz Goslar4, Jostein Bakke5, Kari Anne Bråthen1, Inger Greve Alsos2

1Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.

2The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.

3School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.4

4Faculty of Physics, Adam Mickiewicz University, Poznan, Poland

5Department of Earth Science, University of Bergen, 5020 Bergen, Norway

How to cite: Rijal, D. P., Heintzman, P. D., Lammers, Y., Yoccoz, N. G., Brown, T. G., Lorberau, K., Ehrich, D., Pitelkova, I., Goslar, T., Bakke, J., Bråthen, K. A., and Alsos, I. G.: Temporal pattern of terrestrial plant diversity in northern Fennoscandia, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-12257, https://doi.org/10.5194/egusphere-egu2020-12257, 2020.

D629 |
Peter Seeber, Ulrike Herzschuh, Beth Shapiro, Hendrik Poinar, Duane Froese, and Laura Epp

The Arctic is currently experiencing dramatic ecosystem changes with immediate effects on biodiversity. Sedimentary ancient DNA is a unique and valuable source of information on ecosystem changes over a long temporal scale. Understanding these past changes may help predict the relative impacts of climate change, herbivory, and anthropogenic effects on present ecosystems. In the BiodivERsA project “Future ArcTic Ecosystems” (FATE), we aim to assess changes in past herbivore abundance over large spatial (circumarctic) and temporal (Last Glacial Maximum until today) scales using three (semi-)quantitative methods on sedimentary ancient DNA of plants, herbivores, and herbivore proxies (i.e. coprophilous fungi and parasites) – metabarcoding, hybridization capture enrichment, and droplet digital PCR (ddPCR).

Metabarcoding was applied to DNA of plants and also of coprophilous fungi as proxies of herbivore abundance. This approach is an established and important tool for assessing biodiversity from recent environmental DNA; however, quantification of specific taxa may be complicated due to inherent methodological biases (e.g. amplification efficiency due to primer bias), and our current understanding of the factors affecting potential quantification by metabarcoding is still limited. Moreover, ancient DNA is highly fragmented, which may prevent PCR amplification altogether. As an alternative, target enrichment by hybridization capture is a method that does not depend on target PCR amplification and is typically not affected by DNA fragmentation. Furthermore, hybridization capture can be used to target numerous genetic markers of a vast range of highly diverse taxa. We are using hybridization capture to enrich DNA of a range of herbivore species and numerous proxy organisms. Metabarcoding and hybridization capture can be applied to a vast taxonomic range and may be used quantitatively based on relative sequencing read abundance; however, the respective read abundance may be confounded by random and systematic errors and other biases. We are therefore using an additional quantification method – ddPCR – on several selected taxa, which is taxon-specific but facilitates highly accurate quantification of template DNA molecules in a given sample. The combined taxonomic and quantitative results of these three approaches are used to generate highly resolved datasets on past vegetation and herbivores, which allows us to reconstruct past vegetation changes over large spatial (circumarctic) and temporal (Last Glacial Maximum until today) scales.

Detailed inferences on herbivore abundance and reconstructing past ecological conditions may be important for ecosystem management and conservation in the face of accelerating changes in Arctic ecosystems due to global climate change.

How to cite: Seeber, P., Herzschuh, U., Shapiro, B., Poinar, H., Froese, D., and Epp, L.: Quantification of past arctic herbivore populations from ancient sedimentary DNA by hybridization capture enrichment, metabarcoding, and droplet digital PCR, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-16933, https://doi.org/10.5194/egusphere-egu2020-16933, 2020.

D630 |
Sandra Garces Pastor, Peter D. Heintzman, Youri Lammers, Scarlett Zetter, Antony Gavin Brown, Kevin Walsh, Charline Giguet Covex, Willy Tinner, Christoph Schwörer, Oliver Heiri, Sébastien Lavergne, Eric Coissac, Boris Vannière, Isabelle Jouffroy-Bapicot, Andreas Tribsch, and Inger G. Alsos

Climate change has already started to rapidly transform ecosystems. Predicted scenarios of future ecosystem changes inferred from contemporary ecological data may be uncertain, as these records do not provide the temporal depth needed to understand how ecosystems have responded to past periods of climatic changes and human pressure. However, palaeoecological approaches allow for the reconstruction of past ecosystem changes, including the composition of plant communities, thereby enabling researchers to improve models of future climatic change impacts.

Lakes located in high-mountain ranges, such as the Alps, are suitable ecosystems for studying long-term species turnover and environmental shifts driven by past climate changes, as they preserve a wealth of palaeoecological information in its sediment archives. The Alpine ecosystems are expected to be affected by ongoing climate warming, prompting an upward displacement of vegetation, elevated replacement rates and species losses, with projected increased intensity of impacts in the future.

Previous studies of the Alps have used pollen and macrofossil evidence to infer past vegetation dynamics. However, microscopic morphological determinations are time-consuming and some inferences have been limited by low taxonomic resolution and the biased preservation of identifiable remains. Ancient DNA from organisms is also often preserved in the sediment (sedaDNA), which can rapidly be detected and analysed using metabarcoding approaches. Together with a novel, region-specific barcode reference database for the flora of the Alps (PhyloAlps; 4500 taxa), we can bypass the morphological limitations of previous palaeobotanical studies and refine taxonomic resolution, often to the species level.

To investigate the origin and impact of past environmental changes in alpine ecosystems throughout the Holocene, we performed a multi-proxy reconstruction of 9 lake sediment cores from the Western Alps (France, Italy and Switzerland). Using metabarcoding, we reconstructed the plant community composition and used XRF, magnetic susceptibility, and loss-on-ignition data to understand lacustrine dynamics during the Holocene for each lake. We will present the major findings from these analysed records, the general ecosystem shifts inferred, and the impacts of perturbations caused by human pressure and climatic changes.

How to cite: Garces Pastor, S., D. Heintzman, P., Lammers, Y., Zetter, S., Gavin Brown, A., Walsh, K., Giguet Covex, C., Tinner, W., Schwörer, C., Heiri, O., Lavergne, S., Coissac, E., Vannière, B., Jouffroy-Bapicot, I., Tribsch, A., and G. Alsos, I.: Holocene plant community changes in the Western Alps, as inferred from sedaDNA , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-19336, https://doi.org/10.5194/egusphere-egu2020-19336, 2020.

D631 |
Scarlett Zetter, Sandra Garces Pastor, Youri Lammers, Antony Gavin Brown, Andreas Tribsch, Eric Coissac, Sebastien Lavergne, Peter D. Heintzman, and Inger G. Alsos

The Eastern Alps in Europe have a rich alpine biodiversity and a long archaeological history. However, the palaeoecological record of this region has been relatively understudied, which has limited our understanding of the formation of the contemporary vegetation since the end of the last Ice Age, including the likely impacts of changes in climate and human pressures through pasturing and agriculture. To fill this knowledge gap, we are using plant and mammal sedaDNA taken from five sub-alpine to alpine Holocene lake cores in the Austrian and Italian Eastern Alps: Grosser Winterleitensee, Krummschnabelsee, Mittlerer Kaltenbachsee and Sulzkarsee (Austria), and Laghetti Colbricon (Italy). We will outline our first results on full plant community reconstructions from some lakes and on the mammal presence. Findings from the plant record will allow us for uncovering the Holocene dynamics of plant communities, and for identifying key intervals where biodiversity may have been strongly affected by anthropogenic factors and climate change. The mammal sedaDNA data will also be used to track the presence of domestic livestock through time and therefore provide insight into past human pastoral practices in the region.

How to cite: Zetter, S., Garces Pastor, S., Lammers, Y., Brown, A. G., Tribsch, A., Coissac, E., Lavergne, S., Heintzman, P. D., and Alsos, I. G.: Holocene reconstruction of plant and mammal communities in the Austrian and Italian Alps, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-19582, https://doi.org/10.5194/egusphere-egu2020-19582, 2020.

D632 |
Kathleen R. Stoof-Leichsenring, Sisi Liu, Weihan Jia, Laura S. Epp, Kai Li, Luidmila A. Pestryakova, and Ulrike Herzschuh

In recent decades Arctic and Alpine terrestrial ecosystems experienced an increase in aquatic plant biomass due to global warming, which motivates the investigation of aquatic plant diversity in High Arctic and Alpine regions, whereof so far only sparse data exist. Aquatic plants are important primary producers, food resource and supply habitat structure and thus have been widely used to infer the ecological status of modern lakes. Identification of past aquatic plants using macrofossil records only partly reflects the past community structure due to differences in spatial distribution, preservation and seed abundance of taxa. Thus, in our study we applied sedimentary DNA analyses to detect aquatic plant diversity in modern surface samples of over 200 lakes from various localities across Northern, Eastern and Central Siberia and the Tibetan plateau and selected lake core samples (covering Holocene timescales) from these regions. We applied metabarcoding of the trnL marker and used Illumina technology for NGS amplicon sequencing of PCR products and performed OBITools pipeline for bioinformatic analyses and taxonomic assignment. Firstly, our study aims to evaluate if the trnL marker typically used for detecting terrestrial plant diversity can deliver valuable information on the composition of aquatic plants. Secondly, we will use ordination analyses to test which environmental variables (e.g. lake water depth, pH and conductivity) shape the diversity of genetically detected aquatic plants. Thirdly, we will analyze past genetic aquatic plant diversity from Holocene lake cores and compare it with the modern genetic data set to reconstruct putative drivers of past diversity changes. So far, we identified free-floating (Nymphoides, Ceratophyllum), submerged (Potamogeton sp.), wetland taxa (Caltha, Carex, Juncus) and bryophytes (Sphagnum) in modern and past genetic data sets. Further statistical analyses are pending and will be finalized and presented at EGU.

How to cite: Stoof-Leichsenring, K. R., Liu, S., Jia, W., Epp, L. S., Li, K., Pestryakova, L. A., and Herzschuh, U.: Sedimentary DNA analyses decipher past and present aquatic plant diversity in Siberian and Tibetan lakes, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-20209, https://doi.org/10.5194/egusphere-egu2020-20209, 2020.

D633 |
Kevin Nota and Laura Parducci

The survival of boreal trees in ice-free cryptic refugia’s at high latitudes during the Last Glacial Maximum has been subjected to a long-standing debate. Norway spruce (Picea abies L. Karst) is generally believed to have recolonised Scandinavia from the east. Spruce appears for the first time in the pollen assemblages in central Sweden around 3000 years before present (yr BP), however, a growing body of macrofossil and genetic evidence suggested that spruce might have survived in ice-free areas around the Norwegian shore or closer to the Weichselian ice sheet than previously thought. These satellite populations may have contributed to the recolonisation of Scandinavia from the west and may be ancestors to the ancient (up to 9550-year-old) but still living clonal spruce trees occurring today in the Scandinavian mountains (e. g. Old Tjikko and Old Rasmus). Genetic research has shown that modern P. abies contain two sequence variants for the maternal inherited mitochondrial mh05 fragment across its Eurasian distribution, of which one is unique to Scandinavia. The Scandinavian variant shows the highest frequency in western Scandinavia and its modern distribution suggests that it was already present before the last glacial period. The Scandinavian variant was also detected in lake sediment dating back to 10300 yr BP at Trøndelag in Central Norway (63°N).

We are using sensitive melting curve qPCR assay and high-throughput sequencing to detect the presence of the Scandinavian variant in several sediment cores covering Scandinavia and north-east & southern Russia. So far, the qPCR melting curve assay detected the Scandinavian variant in peat sediment from northern Finland (~52,000 – 42,000 yr BP), in lake sediments in central Sweden and central Norway (~10,000 – 900 yr BP) and in southern Sweden (~12000 – 11000 yr BP), which is far earlier than currently believed. Additional lakes are being processed and samples positive for the Scandinavian variant will be sequenced to confirm sequence identity. We are also conducting population genetic analysis of the ancient clonal spruce stands to see how these trees are related to the modern spruce forest and weather they have contributed to the recolonization of Scandinavia. The results of this study will increase our understanding of the post glacial colonisation of P. abies in Scandinavia after the Last Glacial Maximum.

How to cite: Nota, K. and Parducci, L.: Early Holocene presences of Norway spruce (Picea abies L. Karst.) at high latitudes in Norway and Sweden: the genetic story of up to 9550 year old spruce clones in the Scandinavian mountains, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-21385, https://doi.org/10.5194/egusphere-egu2020-21385, 2020.

D634 |
Laura S. Epp, Anan Ibrahim, Yi Wang, Lisa Gutbrod, Patrick Bartolin, Franziska Chucholl, Rebecca Kuehner, David Schleheck, and Peter Andreas Seeber

Sedimentary ancient DNA has by now become a recognized source of information on past biodiversity change, but our understanding of its dynamics and taphonomy is still limited. While for environmental DNA in water, dedicated investigations on its provenance and degradation are being increasingly carried out, we know very little about sedimentary DNA, in particular with respect to aquatic organisms. We are therefore conducting investigations on the distribution of DNA in surface sediments and a short sediment core, with a focus on aquatic communities in the large and heterogeneous Lake Constance. Targeted organisms range from phyto- and zooplankton to fish and waterbirds. Initial results and comparison with sightings of rare species indicate that the DNA is not distributed uniformly or widely across the lake, especially for multicellular animals, but rather linked to the local presence of the organisms. This has implications for our understanding of how DNA enters the sediment and for paleoecological inferences derived from these records.

How to cite: Epp, L. S., Ibrahim, A., Wang, Y., Gutbrod, L., Bartolin, P., Chucholl, F., Kuehner, R., Schleheck, D., and Seeber, P. A.: The making of sedimentary DNA: Insights from distribution patterns of DNA in sediments , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-22045, https://doi.org/10.5194/egusphere-egu2020-22045, 2020.

D635 |
Anan Ibrahim, Laura Epp, Axel Meyer, and David schleheck

Algae and macrophytes are two of the main primary producers that interact with higher trophic levels by providing food and habitat.  Their distribution thereby affect the physical and chemical characteristics of the ecosystem and hence act as its bioindicators. The use of multiple molecular markers to capture DNA signals in sediments allow for the reconstruction of their historical communities. We here use metabarcoding of different primers to illustrate the trophic history and the interactions between diatoms, macrophytes and microbial eukaryotes and their response to anthropogenic impacts. Sediment samples were taken from a large deep lake representing different regions of different chemical and physical characteristics. Preliminary data suggest a congruent trophic history using each of the molecular markers and an interaction between the presence of fungal parasites and the prevalence of diatoms.  


How to cite: Ibrahim, A., Epp, L., Meyer, A., and schleheck, D.: Characterizing diatoms and their correlation with the distribution of macrophytes and parasitic Fungi using sedimentary genetic records from lake Constance, Germany, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-22051, https://doi.org/10.5194/egusphere-egu2020-22051, 2020.