BG2.6

EDI
Reconstruction of past ecosystems using sedimentary ancient DNA: Applications, method developments, analytic pipelines and data management

Sedimentary ancient DNA (sedaDNA) is an established proxy used to investigate the past biota, including community reconstruction, detection of richness, and eco-functional shifts. It has provided a much more detailed understanding of overall ecosystem changes and its relation to environmental variability from decadal to millennial time scales. The potential of sedaDNA data to comprehend past ecosystems is rapidly accelerating because of a.) increasing DNA reference databases, b.) increasing applications in case studies addressing different paleoecological scientific questions, c.) the use and development of new protocols for high-throughput sequencing technologies, d.) the establishment of stringent bioinformatic pipelines to improve data analyses and authenticate ancient molecular signals e.) the development of sedaDNA data management tools allowing comprehensive and summarizing sedaDNA data interpretation. This session invites contributions covering terrestrial and marine applications of sedaDNA in paleoecology, including methodological renewals, bioinformatic pipelines and data management.

Convener: Kathleen Stoof-Leichsenring | Co-conveners: Eric Capo, Vilma PerezECSECS
vPICO presentations
| Wed, 28 Apr, 11:45–12:30 (CEST), 15:30–17:00 (CEST)

Session assets

Session materials

vPICO presentations: Wed, 28 Apr

Chairpersons: Kathleen Stoof-Leichsenring, Vilma Perez
11:45–11:47
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EGU21-13501
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ECS
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solicited
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Kevin Nota, Ludovic Orlando, Alexis Marchesini, Matteo Girardi, Cristiano Vernesi, and Laura Parducci

The current main methodologies for identifying DNA fragments in ancient environmental samples are metabarcoding and shotgun sequencing which present strong advantages and limitations. Target capture is a promising method for enriching shotgun libraries for target organisms and might be able to combine the advantages from metabarcoding and shotgun sequencing into a single method. Target capture operates by hybridising DNA fragments in a sample to synthetic RNA-baits which share enough homology (≥85 %). These RNA-baits contain a magnetic molecule which is used to pull the hybridised fragments of interest to a magnet, allowing for the non-hybridised molecules to be washed away. The RNA-baits are designed according to prior knowledge of target sequences. Target capture does not require a PCR amplification step to amplify fragments using taxon-specific primers, and it might, therefore, be less prone to PCR amplification biases.

We designed a bait-set for capturing two barcoding plastidial genes matK and rbcL for all the species in four major plant orders: Asterales, Fagales, Pinales, and Poales. These orders are species-rich and/or difficult to identify to low taxonomic levels (family, genus or species) using metabarcoding. Our objectives were: 1) to design a universal method for trimming and selecting sequences for bait design using online sequence repositories, 2) to investigate a potential capture bias of species with a low GC-content (proportion of guanine and cytosine nucleotides) and 3) to investigate taxonomic resolution of target capture compared to metabarcoding. Because species with an overall low GC content (<32%) might be less efficiently captured than species with a higher GC content, we used mock communities with a known proportion of amplicons fragment size distribution and GC content. Further, we used sequence data simulations to investigate taxonomic resolution using varies species pools.

How to cite: Nota, K., Orlando, L., Marchesini, A., Girardi, M., Vernesi, C., and Parducci, L.: Shotgun barcode baiting: capturing barcoding genes from environmental samples for species identification, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13501, https://doi.org/10.5194/egusphere-egu21-13501, 2021.

11:47–11:49
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EGU21-14474
Inger Alsos, Youri Lammers, Sofia E Kjellman, Marie K. F. Merkel, Emma M Bender, Alexandra Rouillard, Egill Erlendsson, Esther Ruth Guðmundsdóttir, Ívar Örn Benediktsson, Wesley R Farnsworth, Skafti Brynjólfsson, Guðrún Gísladóttir, Sigrún Dögg Eddudóttir, and Anders Schomacker

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 ¾ 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 (Landnám), 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.

How to cite: Alsos, I., Lammers, Y., Kjellman, S. E., Merkel, M. K. F., Bender, E. M., Rouillard, A., Erlendsson, E., Guðmundsdóttir, E. R., Benediktsson, Í. Ö., Farnsworth, W. R., Brynjólfsson, S., Gísladóttir, G., Eddudóttir, S. D., and Schomacker, A.: Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until Landnám, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14474, https://doi.org/10.5194/egusphere-egu21-14474, 2021.

11:49–11:51
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EGU21-14114
Matthew Power, Sarah Crump, Gifford Miller, Michael Bunce, and Morten Allentoft

The recent development and refinement of the molecular toolkit to detect ancient DNA in sediment samples (sedaDNA) has allowed the high-resolution reconstruction of ancient ecological communities dating back thousands of years. Specifically, DNA from lake sediment has been used to derive continuous records of ecological community changes through variable paleoenvironmental conditions. These paleoecological reconstructions can be an important tool for understanding how ecosystems may respond to current and future warming, but reliable methods for taxonomic detection are needed in order make optimal use of these bioarchives. In this study, metabarcoding assays targeting mammal, bird, and marine fauna have been carried out across a sediment core collected from Lake Qaupat, Baffin Island, Arctic Canada. While Lake Qaupat is currently ~30 m above sea level, it is located below the local marine limit related to isostatic adjustment after deglaciation. Consequently, initial sediment accumulation is in a marine environment, Combined results from the DNA assays indicate a transitional period over which marine-based fauna are systematically replaced by more terrestrial-based fauna. This transition occurs at a predicted age of 7.4 ± 0.2 ka. This research builds on previous studies to develop Baffin Island paleorecords in an effort to inform future changes to the Arctic system in the context of a rapidly warming world. Ultimately these data will be useful in better informing climate models and how taxa may move, adapt or be extirpated from arctic regions[GHM1] [SC2] .[SC3] 

How to cite: Power, M., Crump, S., Miller, G., Bunce, M., and Allentoft, M.: Detection of a marine to terrestrial transition in lake sediment from Baffin Island, Arctic Canada, using sedimentary DNA, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14114, https://doi.org/10.5194/egusphere-egu21-14114, 2021.

11:51–11:53
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EGU21-16451
Mary Edwards, Charlotte Clarke, Nancy Bigelow, Peter Heintzman, Ben Potter, Inger Alsos, and Joshua Reuther

About 14,000 years ago, on the cusp of major environmental changes that affected the distribution of animals, vegetation cover and hydrology, humans entered interior Alaska for the first time.  A sedimentary ancient DNA (sedaDNA) record from a lake in the Tanana valley, which lies close to several of the oldest dated archaeological sites, documents plant community changes over the past ca. 15,000 years and makes an important contribution towards resolving late MIS-2 floristic composition of the northern, ice-free region of northwest North America.  Macroscopic charcoal and sediment properties provide further information on changes in climate and fire regimes.

For sedaDNA analysis, we amplified a short locus of the plant chloroplast genome in all samples, and a total of 167 vascular plant and 14 bryophyte taxa were detected in the lake sedaDNA record. A rich herbaceous flora, including taxa typical of open tundra habitats, dominates the record until ca. 14,000 cal yr BP; diverse grass taxa are present, and Salicaceae is recorded in every sample in this period. This flora continued (though with compositional changes) as a dominant element in the following period, which was also characterized by the presence of shrub and/or tree birch, and which ended with the establishment of coniferous forest ca. 10,000-11,000 yr BP. This last change is also reflected in sediment organic content, sedimentation rate, and the addition of a diverse range of shrubs, sub-shrubs, boreal forbs, spore-plants and aquatic macrophytes, all reflecting profound alterations in both terrestrial and lacustrine plant communities. Macro-charcoal is present in all floristic zones, with higher concentrations afterca. 14,000 yr BP, indicating that both deciduous and evergreen woody communities burned.  

This lake record provides a picture of key landscape-scale changes experienced by early human populations.SedaDNA results obtained from contemporaneous cultural and non-cultural layers at nearby archaeological sites in the Tanana Valley can provide further complementary information on natural resource use by early human communities in response to a changing environment. The loessal sediments at these archaeological sites present challenges to sedaDNA studies, including anthropogenic disturbance of the matrix, rootlet penetration, and unfrozen conditions for around four months of the year that may accelerate bacterial degradation and fragmentation of DNA. We present here some preliminary results from these archaeological localities.

How to cite: Edwards, M., Clarke, C., Bigelow, N., Heintzman, P., Potter, B., Alsos, I., and Reuther, J.: Late Quaternary vegetation dynamics in interior Alaska revealed by sedimentary ancient DNA (sedaDNA) from lake sediment and unfrozen (loessic) archaeological sediments, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-16451, https://doi.org/10.5194/egusphere-egu21-16451, 2021.

11:53–11:55
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EGU21-14881
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ECS
Sisi Liu, Kathleen R. Stoof-Leichsenring, Luise Schulte, Heike H. Zimmermann, Steffen Mischke, and Ulrike Herzschuh

Climate change and associated species interactions are responsible for many vital mechanisms governing the dynamics of ecological communities. However, the long-term contribution of environmental conditions and species connections to community assembly remain mostly unknown. Here, we present changes of terrestrial and freshwater communities based on metagenomic shotgun data retrieved from lacustrine sediments of an alpine freshwater lake on the south-eastern Tibetan Plateau (Hengduan Mountains) covering the past 15,100 thousand years (ka). Terrestrial assemblages between 15.1-14 ka are explained by the harsh environment and facilitative interactions due to diverse cushion plants, while the abundant ice-age algae (Nannochloropsis and N. limnnetica) indicate dominance of glacial meltwaters. A sharp decrease in alpine herbs (e.g Asteraceae, Carex and Poaceae) corresponded to competitive interactions with the colonization of woody plants (Salicaceae, Salix, Rhododendron and R. delavayi) since 14 ka, leading to a decline of large herbivores (Bovidae and Bos mutus) that predominated. Meanwhile, the disappearance of ice-age algae and the expansion of submerged plants (e.g., Potamogeton, P. perfoliatus, Myriophyllum, and M. spicatum) are consistent with an increase in temperature and a plentiful supply of nutrients due to weathering and soil erosion. The loss of submerged plants during the late Holocene (~3.6 ka) is probably related to environmental deterioration; however, it could also be related to the Cyanobacteria boom. Our study highlights that shotgun sequencing of lake sediments is an important tool for exploring ecological processes of communities in the past.

How to cite: Liu, S., R. Stoof-Leichsenring, K., Schulte, L., H. Zimmermann, H., Mischke, S., and Herzschuh, U.: Terrestrial-aquatic ecosystem links on the Tibetan Plateau inferred from sedaDNA shotgun sequencing, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14881, https://doi.org/10.5194/egusphere-egu21-14881, 2021.

11:55–11:57
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EGU21-13710
Wei Shen, Sisi Liu, Kathleen R. Stoof-Leichsenring, Jeremy Courtin, Steffen Mischke, and Ulrike Herzschuh

The eastern Tibetan Plateau, particularly the Hengduan Mountains and Sanjiangyuan region, is a biodiversity hotspot also known for its sensitivity to climate change. How these vegetation communities assembled since the Last Glacial Maximum is still unclear. Here we present new results from plant metabarcoding of sediments from Lake Ximencuo (Nianbaoyeze Mountains, Sanjiangyuan region) covering the last 18 ka and compare them with records from Lake Naleng (Hengduan Mountains).  We investigate temporal changes of within-site and between-site alpha and beta diversities. Both sites show the highest richness between 14 and 10 ka when alpine meadows covered the areas while richness was rather low in forested periods during the early Holocene. Ordination results support that the vegetation composition was relatively low between-site beta-diversities indicate that the vegetation composition was relatively similar in the two study areas before the Holocene, particularly during the early late-glacial when alpine steppes dominated. The maximal between-site beta-diversity occurred between 10 and 8 ka when environmental filtering was most relevant, as suggested by the dominating turnover component. The nestedness component of beta-diversity reached a maximum during the middle Holocene indicating that between-site differences during this period possibly originated from e.g., dispersal limitation.

How to cite: Shen, W., Liu, S., Stoof-Leichsenring, K. R., Courtin, J., Mischke, S., and Herzschuh, U.: Vegetation composition in Sanjiangyuan region compared with Hengduan Mountains (eastern Tibetan Plateau) since the Last Glacial Maximum revealed by plant metabarcoding of sedimentary ancient DNA, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13710, https://doi.org/10.5194/egusphere-egu21-13710, 2021.

11:57–11:59
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EGU21-4697
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ECS
Eric Capo and the sedaDNA scientific community

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.

How to cite: Capo, E. and the sedaDNA scientific community: Unifying the sedaDNA scientific community, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4697, https://doi.org/10.5194/egusphere-egu21-4697, 2021.

11:59–12:01
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EGU21-8030
Sara Harðardóttir, Connie Lovejoy, Marit-Solveig Seidenkrantz, and Sofia Ribeiro

Arctic sea ice is declining at an unprecedented pace as the Arctic Ocean heads towards ice-free summers within the next few decades. Because of the role of sea ice in the Earth System such as ocean circulation and ecosystem functioning, reconstructing its past variability is of great importance providing insight into past climate patterns and future climate scenarios. Today, much of our knowledge of past sea-ice variability derives from a relatively few microfossil and biogeochemical tracers, which have limitations, such as preservation biases and low taxonomic resolution. Marine sedimentary ancient DNA (marine sedaDNA) has the potential to capture more of the arctic marine biodiversity compared to other approaches. However, little is known about how well past communities are represented in marine sedaDNA. The transport and fate of DNA derived from sea-ice associated organisms, from surface waters to the seafloor and its eventual incorporation into marine sediment records is poorly understood.  Here, we present results from a study applying a combination of methods to examine modern and ancient DNA to material collected along the Northeast Greenland Shelf. We characterized the vertical export of genetic material by amplicon sequencing the hyper-variable V4 region of the 18S rDNA at three water depths, in surface sediments, and in a dated sediment core.  The amplicon sequencing approach, as currently applied, includes some limitations for quantitative reconstructions of past changes such as primer competition, PCR errors, and variation of gene copy numbers across different taxa. For these reasons we quantified amplicons from a single species, the circum-polar sea ice dinoflagellate Polarella glacialis in the marine sedaDNA, using digital droplet PCR. The results will increase our understanding on the taphonomy of DNA in sea ice environments, how sedimentation differs among taxonomic groups, and provide indications to potentially useful marine sedaDNA-based proxies for climate and environmental reconstructions.

How to cite: Harðardóttir, S., Lovejoy, C., Seidenkrantz, M.-S., and Ribeiro, S.: Sea ice protists in arctic marine sedaDNA records: origins, diversity, and vertical export of DNA from the sea surface to the seafloor , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8030, https://doi.org/10.5194/egusphere-egu21-8030, 2021.

12:01–12:03
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EGU21-3587
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ECS
Danielle Grant, Kristine Steinsland, Sigrid Mugu, Katrine Sandnes Skaar, Umer Z. Ijaz, Ulysses Ninneman, Jessica Louise Ray, and Stijn De Schepper

The Last Interglacial (LIG, ~128–116ka) was characterized by a warmer climate, increased sea level, and a reduced Greenland ice sheet compared to today. Climate projections suggest our future climate may resemble LIG conditions if anthropogenic climate change progresses unabated. Previous studies have identified key shifts in the Labrador Sea oceanography and climate before, during, and after the LIG, making this time interval an exciting target for exploring high-latitude marine ecological dynamics. In recent years, the application of sedimentary ancient DNA (sedaDNA) has provided new glimpses into past ocean and climate conditions. Here, we have explored sedaDNA alongside other, traditional, paleoceanography proxies, to better understand the changing Labrador Sea biome across climate transitions and in a globally warmer world. We have generated a sedaDNA record from a giant piston core at the Eirik Drift (Labrador Sea). Our sedaDNA record, dating back to ~135 ka, was sampled at 4 cm depth intervals and covers the glacial-interglacial transition, as well as the LIG. SedaDNA was purified using a commercial spin column kit and analysed using a metabarcoding approach targeting the V7 hypervariable region of the eukaryote small subunit RNA. Illumina MiSeq analysis of metabarcoding libraries revealed PCR-amplifiable eukaryotic DNA throughout the investigated downcore section. Shifts in relative taxon abundance and alpha- and beta-diversity metrics paralleled shifts in foraminifer isotope records (δ18Ο), palynological assemblages, and biomarkers suggesting that the molecular genetic signal preserved in downcore sediments shows promise for identifying ecological shifts across the LIG. We are currently investigating the potential utility of specific taxa identified in the sedaDNA record to act as indicators of the glacial-interglacial transition. This study strengthens the growing potential of marine sedaDNA as a supplemental proxy for climate reconstructions in the Late Quaternary.

How to cite: Grant, D., Steinsland, K., Mugu, S., Sandnes Skaar, K., Ijaz, U. Z., Ninneman, U., Louise Ray, J., and De Schepper, S.: The Last Interglacial in the Labrador Sea: a sedimentary ancient DNA investigation , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3587, https://doi.org/10.5194/egusphere-egu21-3587, 2021.

12:03–12:05
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EGU21-14809
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ECS
Ines Barrenechea Angeles, Luc Beaufort, Daniel Ariztegui, and Jan Pawlowski

Sedimentary ancient DNA (sedaDNA) is becoming a paleo-proxy of choice for many marine environments. However, there are few studies from tropical sites and even fewer from tropical marine sediments exposed to factors damaging the DNA such as elevated sea surface water temperature or UV radiation. Here, we report successful extraction of DNA from a marine sedimentary core retrieved from the Bismarck Sea, off New Papua Guinea, where the mean annual temperature is about 29°C. The core MD05-2920 covers the last 385 000 years. We analyzed samples from 20 layers, where the isotopic measures of δ18O isotopic composition of benthic foraminifera show significant palaeoceanographic changes from glacial to interglacial periods. We apply a metabarcoding approach using specific 18S primers for planktonic foraminifera, diatoms, and radiolarians. Even if the amount of DNA declines throughout the core, the patterns of successional changes in species communities of these three taxonomic groups are well archived. Our study shows that it is possible to reconstruct the planktonic community even from very old sedaDNA samples from a tropical marine sedimentary core.

How to cite: Barrenechea Angeles, I., Beaufort, L., Ariztegui, D., and Pawlowski, J.: Using sedaDNA to reconstruct planktonic communities across 385’000 years old marine sedimentary core from a tropical sea., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14809, https://doi.org/10.5194/egusphere-egu21-14809, 2021.

12:05–12:07
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EGU21-4003
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ECS
Akhtar-E Ekram, Rebecca Hamilton, Matthew Campbell, Chloe Plett, Sureyya Kose, James Russell, Janelle Stevenson, and Marco Coolen

Several studies have shown that ancient plant-derived DNA can be extracted and sequenced from lake sediments and complement the analysis of fossil pollen in reconstructing past vegetation responses to climate variability and anthropogenic perturbations. The majority of such studies have been performed on Holocene lakes located in cooler higher latitude regions whereas similar studies from tropical lakes are limited. Here, we report a ~1 Ma record of vegetation changes in tropical Lake Towuti (Sulawesi, Indonesia) through parallel pollen and sedimentary ancient DNA (sed aDNA) analysis. Lake Towuti is located in a vegetation biodiversity hotspot and in the centre of the Indo Pacific Warm Pool (IPWP), which comprises the world’s warmest oceanic waters and influences globally important climate systems. In the context of global change, the surface area of the IPWP is rapidly expanding. Lake Towuti is of particular interest since it provides a unique opportunity to obtain a long-term record of IPWP-controlled climate-ecosystem interactions and ecosystem resilience. Stratigraphic analysis of fossil pollen vs. sequencing of preserved chloroplast DNA (cpDNA) signatures (i.e., trnL-P6) both revealed that Lake Towuti experienced significant vegetation changes during the transition from a landscape initially characterized by active river channels, shallow lakes and swamps into a permanent lake ~1 Ma ago. Both proxies marked a predominance of trees or shrubs during most of Lake Towuti’s history, but the trnL-P6 barcoding approach revealed a much higher relative abundance of remote montane conifers, which likely have produced large amounts of chloroplast-rich airborne pollen that were subsequently buried in the sedimentary record. The pollen record showed a higher relative abundance of evergreen tropical forest vegetation, whereas the trnL-P6 record revealed a higher relative abundance of predominantly wetland herbs that must have entered the lake from the local catchment in the form of chloroplast-rich litter. Furthermore, the sedimentary record was rich in presumably wind-derived chloroplast-lacking fern spores, while fern trnL-P6 was only sporadically detected. Only through trnL-P6 barcoding, fern-derived biomass in the sedimentary record could be identified as Schizaeaceae, which is a primitive tropical grass-like fern family often associated with swampy or moist soils. Unlike pollen, trnL-P6 could identify grasses at clade and subfamily levels and confirmed that the majority of grasses in the area represented wet climate C3 grasses or those that can switch between C3 and C4 carbon fixation pathways, whereas grasses that can only perform C4 carbon fixation, indicative of dry climate conditions, were not detected. At least for sediments deposited prior to the Last Glacial Maximum, neither pollen nor trnL-P6 revealed significant vegetation changes between alternating layers of lacustrine green and red sideritic clays thought to have been deposited during orbitally controlled wetter vs. drier periods. These preliminary results suggest that vegetation in this tropical biodiversity hotspot may be relatively resilient to long-term variations in IPWP hydrology.

How to cite: Ekram, A.-E., Hamilton, R., Campbell, M., Plett, C., Kose, S., Russell, J., Stevenson, J., and Coolen, M.: A 1 Ma record of climate-induced vegetation changes using sed aDNA and pollen in a biodiversity hotspot: Lake Towuti, Sulawesi, Indonesia, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4003, https://doi.org/10.5194/egusphere-egu21-4003, 2021.

12:07–12:09
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EGU21-1700
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ECS
René Dommain, Morgan Andama, Molly M. McDonough, Natalia A. Prado, Tobias Goldhammer, Richard Potts, Jesús E. Maldonado, John Bosco Nkurunungi, and Michael G. Campana

Most of the Earth’s biodiversity is concentrated in the tropics. While the ultimate causes of this geographic pattern remain to be established, ongoing anthropogenic impacts in the tropical belt lead to rapid losses of species diversity. Ancient DNA approaches may help in deciphering temporal patterns in the diversification of tropical biota and could potentially provide historical baseline data on the diversity and distribution of species in anthropogenically modified landscapes. However, studies of sedimentary ancient DNA (sedaDNA) are thus far extremely rare in tropical settings and consequently its value as a conservation tool for tropical ecosystems remains to be tested systematically. To address this issue we present meta-genomic records of shot-gun sequenced sedimentary ancient DNA (sedaDNA) from several sediment cores from the equatorial Bwindi-Impenetrable Forest in Uganda. Because Bwindi is one the most diverse rainforests in Africa and its biota is well documented (including endangered species such Mountain Gorilla and Chimpanzee) it is well suited for a baseline study. We describe the taxonomic composition of sedaDNA from Bwindi for the past 2200 years at an average resolution of 50 years – one of the first comprehensive sedaDNA records of plant and animal taxa from a tropical rainforest. We specifically address the following questions: 1) How precisely can the taxonomic level of shotgun-sequenced tropical sediments be resolved at present? 2) What is the effect of temperature, acidity, nutrient availability, elemental and lithological sediment composition, and burial age on the degradation of DNA? Taxonomic assignments are based on three metagenomic classifiers and four reference databases and their reliability tested against local pollen and modern animal occurrence data. We find that 92.3% of our metagenomic data is taxonomically not identifiable due to the substantial underrepresentation of tropical taxa in genomic reference databases. Yet at ordinal level we reconstruct typical afrotropical assemblages, which do not decline in diversity over time. Our comprehensive set of ecological and sedimentological parameters including sediment age, surface water chemistry, pH, soil temperature, sediment density, sediment water and organic matter content, XRF elemental chemistry, nutrient concentrations, and magnetic susceptibility reveals that DNA degradation cannot be explained by any sedimentary parameter alone, is at Bwindi independent of sediment type, and most likely primarily driven by burial age, suggesting that DNA taphonomic models need to be site-specific in tropical environments. The viability of sedaDNA as a conservation-biology tool requires comprehensive genomic surveys of tropical biota to drastically improve the taxonomic representativeness of DNA reference databases.

How to cite: Dommain, R., Andama, M., McDonough, M. M., Prado, N. A., Goldhammer, T., Potts, R., Maldonado, J. E., Nkurunungi, J. B., and Campana, M. G.: Biodiversity and DNA degradation patterns recorded in a 2200-year-long sequence of sedimentary ancient DNA from the afrotropical Bwindi Impenetrable Forest, Uganda, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1700, https://doi.org/10.5194/egusphere-egu21-1700, 2021.

12:09–12:11
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EGU21-14979
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ECS
Marina A. Morlock, Saúl Rodriguez-Martinez, Doreen Yu-Tuan Huang, Nicole Glaus, Hendrik Vogel, Flavio S. Anselmetti, and Jonatan Klaminder

Mountain ecosystems are particularly sensitive to soil erosion and it is critical to better understand how climate and human activities can be linked to erosion in the alpine environment. To explore this link across time, we combine sedimentary ancient DNA (sedaDNA) analyses with erosion proxies to assess the timing and type of animal husbandry in the Eastern Alps and its impact on hill-slope processes and vegetation. With its clear and continuous erosion history, the sediment record contained in Lake Grosssee, Switzerland, is ideally suited to resolve key stages in ecosystem change and anthropogenic land use since the last glaciation. Initial results show that sedaDNA can successfully detect key species in today’s ecosystem and suggest significant changes in mammal and plant diversity across the Holocene. DNA of domestic animals such as cattle and sheep has been the dominant in the past 4,000 years BP, which coincides with frequent and intensive erosion events in this period. Our record promises a detailed history of anthropogenic activities and terrestrial ecosystem change across the Holocene, which will help to determine how erosion, land use, and climate shape alpine ecosystems through time.

How to cite: Morlock, M. A., Rodriguez-Martinez, S., Huang, D. Y.-T., Glaus, N., Vogel, H., Anselmetti, F. S., and Klaminder, J.: Holocene human-environment interactions and their link to erosion in the Eastern Alps, inferred from sedaDNA, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14979, https://doi.org/10.5194/egusphere-egu21-14979, 2021.

12:11–12:13
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EGU21-6072
Charline Giguet-Covex, Manon Bajard, Wentao Chen, Kevin James Walsh, Pierre-Jérôme Rey, Erwan Messager, David Etienne, Pierre Sabatier, Francesco Gentile Ficetola, Ludovic Gielly, Claire Blanchet, Christophe Guffond, Fabien Arnaud, and Jérôme Poulenard

Past trajectories of alpine agro-ecosystems are legacies that we should consider in the context of current global changes. By integrating archaeology, history and multi-proxy palaeoenvironmental records including lake sediment DNA, we reconstructed the precise nature of agro-pastoral activities and their interactions with the landscape evolution (erosion and vegetation) in the Northwestern Alps, across an altitudinal gradient ranging from 880 and 2440 m a.s.l. We demonstrate that the origins of current vegetation cover in the “Alpages” date to the Mid to Late Bronze Age. However, at the lower limit of the subalpine belt and below this zone, the first significant plant cover changes date to a later period, from the Early to High Middle Ages. From the Bronze Age, we see also anthropogenic disturbances of the natural erosion cycle, especially on some sites in the subalpine belt. This erosion became generalized across all sites during the Roman period. Then, decreasing anthropogenic impacts on the erosion are recorded everywhere, which suggests the beginning of efficient soil management strategies, with protection of the soil resource. This important tipping point arose from the High to Late Middle Ages, when activities and practices are changing.

How to cite: Giguet-Covex, C., Bajard, M., Chen, W., Walsh, K. J., Rey, P.-J., Messager, E., Etienne, D., Sabatier, P., Ficetola, F. G., Gielly, L., Blanchet, C., Guffond, C., Arnaud, F., and Poulenard, J.: Mountain agro-ecosystems long-term trajectories in the North Western Alps, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6072, https://doi.org/10.5194/egusphere-egu21-6072, 2021.

12:13–12:15
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EGU21-15285
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ECS
Sandra Garces Pastor, Youri Lammers, Peter D. Heintzman, Antony Gavin Brown, Willy Tinner, Christoph Schwörer, Oliver Heiri, Fabian Rey, Martina Heer, Astrid Rutzer, Sébastien Lavergne, Eric Coissac, Pierre Taberlet, Jean-Paul Theurillat, and Inger G. Alsos

The increase in plant species richness in the Alps over the last century has been described as a direct response to climate warming. Alpine ecosystems are expected to have an upward displacement of vegetation, resulting in shifts of species ranges, high replacement rates, and species loss. To apply proper management measures, it is necessary to understand how drivers of change affect species and ecosystem tipping points. Palaeoecological studies allow us to understand how species responded to similar situations in the past. However, such studies are often challenged by proxy preservation and taxonomic resolution. Metabarcoding approaches based on sedimentary ancient DNA (sedaDNA) can overcome these caveats. 

Here we use plant sedaDNA and the new PhyloAlps taxonomic reference database, which covers 4500 plant taxa from the Alps, to explore alpine floral diversity of Sulseewlii, a subalpine lake in the Central Alps (Switzerland). We present a 12,000 year record of vegetational composition and structural changes in a subalpine ecosystem. To disentangle the relationship between climate and vegetation, we used a novel local temperature reconstruction inferred from chironomids of the same lake. We also used coprophilous fungal spores and charcoal, together with pastoral and arable indicators, to infer human pressure. 

With 377 identified taxa, including 140 at species level, Sulseewlii has yielded the richest dataset of plant sedaDNA to date and emphasizes the Alps as an important biodiversity hotspot in Europe. Out of the identified taxa, 91 are indicators that allowed us to reconstruct the vegetation stages and altitudinal shifts of the main vegetation groups. Total taxonomic richness increases from the onset of the Holocene and has a similar pattern to subalpine-montane DNA taxa, with three marked drops at 8200, 3200, and ~500 cal yr BP. Plant sedaDNA registered a marked transition from alpine to subalpine communities at the onset of the Holocene. The highest proportions of montane taxa occurred during the Holocene climatic optimum (9,000-6,000 cal yr BP). Finally, a shift back to subalpine-montane species with some lowland influence occurs as we approach the present.

How to cite: Garces Pastor, S., Lammers, Y., Heintzman, P. D., Gavin Brown, A., Tinner, W., Schwörer, C., Heiri, O., Rey, F., Heer, M., Rutzer, A., Lavergne, S., Coissac, E., Taberlet, P., Theurillat, J.-P., and G. Alsos, I.: Exceptionally rich sedaDNA record from a subalpine lake in the Central Alps reveals plant responses to climate change and human land use, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15285, https://doi.org/10.5194/egusphere-egu21-15285, 2021.

12:15–12:30
Chairpersons: Eric Capo, Vilma Perez
15:30–15:32
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EGU21-372
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ECS
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solicited
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Tyler J. Murchie, Alistair J. Monteath, George S. Long, Emil Karpsinski, Scott Cocker, Grant Zazula, Ross MacPhee, Duane Froese, and Hendrik Poinar

The multitude of factors alleged to have contributed to the late Quaternary mass extinction of some two-thirds of Earth’s megafauna is complicated by the coarse record of buried macro-fossils. In response, micro-methods such as ancient DNA have been increasingly able to augment discontinuous palaeontological records to investigate the relative timings of vegetation turnover versus megafaunal extirpations—all in the absence of biological tissues. Here, we present sedimentary ancient DNA data retrieved using the PalaeoChip Arctic-1.0 bait-set diachronically identifying fauna and flora from permafrost cores recovered from the Klondike region of central Yukon, Canada dating between 30,000–6000 calendar years BP. We observe a substantial turnover in ecosystem composition between 13,000–10,000 BP with the rise of woody shrubs and the disappearance of mammoth-steppe vegetation. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) from multiple samples thousands of years after their last dated macro-fossils, possibly as late as the mid-Holocene.

How to cite: Murchie, T. J., Monteath, A. J., Long, G. S., Karpsinski, E., Cocker, S., Zazula, G., MacPhee, R., Froese, D., and Poinar, H.: Ecological turnover and megafaunal ghost ranges during the Pleistocene-Holocene transition in central Yukon, Canada as revealed by palaeoenvironmental DNA, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-372, https://doi.org/10.5194/egusphere-egu21-372, 2020.

15:32–15:34
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EGU21-15432
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ECS
Scarlett Zetter, Sandra Garcés Pastor, Youri Lammers, Andreas Tribsch, Antony G. Brown, Eric Coissac, Sébastian Lavergne, Peter D. Heintzman, and Inger G. Alsos

The Alps contain highly biodiverse ecosystems including a large number endemic flora. As a result of climate change and anthropogenic activities, such ecosystems are at risk from upward vegetation displacement and species loss. Extensive archaeological research in the Eastern Alps has documented human settlement from ~5500 years ago driven by salt and copper mining; which has caused significant impact on the ecosystems through mining, deforestation, and pastoral farming. To elucidate the effects of climate change and anthropogenic activities on plant biodiversity, multi-proxy reconstructions have been carried out throughout the Western Alps . Despite this research, the palaeoecological history of the Eastern Alps is relatively understudied. Consequently, we are limited in our understanding of how climate change and human impact have affected past biodiversity and the formation of the contemporary vegetation in this region. Here, we focus on the Austrian sub-alpine lake, Großer Winterleitensee located at the Easternmost margin of the Alps; only locally glaciated during the Pleistocene. We applied sedimentary ancient DNA (sedaDNA) metabarcoding to reconstruct Holocene plant community dynamics within the lake catchment. These data, in conjunction with local temperature reconstructions, sediment elemental composition, magnetic susceptibility, and loss-on-ignition analyses, allowed us to identify key intervals of plant diversity change. Two such intervals begin at samples dated ~5500 cal. yr BP and ~2200 cal. yr BP, coinciding with Neolithic and Iron Age settlement phases in the area. Palaeoecological reconstructions of plant biodiversity and their responses to climate change and anthropogenic pressures may be able to provide essential information for future conservation purposes.

 
 
 

How to cite: Zetter, S., Garcés Pastor, S., Lammers, Y., Tribsch, A., Brown, A. G., Coissac, E., Lavergne, S., Heintzman, P. D., and Alsos, I. G.: Holocene reconstruction of plant communities and impacts of human activity from sedaDNA in the Austrian Alps., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15432, https://doi.org/10.5194/egusphere-egu21-15432, 2021.

15:34–15:36
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EGU21-16231
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ECS
Lasse Topstad, Charlotte Clarke, Jan Mangerud, John-Inge Svendsen, Haflidi Haflidason, and Inger Greve Alsos

Throughout the late Quaternary, the vegetation of Polar Urals (Russia) endured dramatic changes in climate, but still seems to have maintained a high, yet compositionally dynamic species richness. A recent study of Lake Bolshoe Schuchye (187 m a.s.l., Clarke et al. 2019 Sci. Rep.) suggests that this region was an important refugium for arctic-alpine plant taxa during the Early Holocene forest expansion. Whether the survival of taxa and the turnover of species and functional groups was consistent throughout the region or dependent on local conditions remains unknown. Here, we present reconstructed plant assemblage dynamics spanning the past 22,000 years based on metabarcoding of sedimentary ancient DNA (sedaDNA) cored from Maloe Schuchye (287 m a.s.l.). The record is compared to the neighboring lake Bolshoe Schuchye in terms of how taxonomic richness and composition of functional groups developed through time. Throughout the study period, several large-scale vegetation changes occur in both cores, however, identified at slightly delayed time intervals for the higher altitude site Maloe Schuchye, based on the CONISS clustering. The total richness was higher in Maloe Schuchye (274 taxa) compared to Bolshoe Schuchye (191 taxa), and the average richness was higher in Maloe Schuchye throughout the period. The largest difference in taxonomic richness between the two lakes was during the Last Glacial Maximum (LGM) and Late Glacial periods, when Maloe Schuchye had considerable higher richness of forbs and graminoids than Bolshoe Schuchye. Despite these contrasting diversity patterns, the time of arrival of taxa highly align in the two records. Thermophilic plant taxa occur slightly earlier in the lower altitude Bolshoe Schuchye lake record, as expected. Further, the survival and persistence of arctic-alpine taxa is similar in the two catchments, confirming the importance of this region for long-term survival or arctic-alpine species.

How to cite: Topstad, L., Clarke, C., Mangerud, J., Svendsen, J.-I., Haflidason, H., and Greve Alsos, I.: Contrasting patterns of vegetation compositing and species diversity over 22 000 years in two adjacent artic-alpine catchments, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-16231, https://doi.org/10.5194/egusphere-egu21-16231, 2021.

15:36–15:38
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EGU21-15265
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ECS
Yi Wang, Lisa Gutbrod, Myriam Schmid, and Laura Epp

Lake sedimentary ancient DNA has become a recognized source of information on past biodiversity change, but our understanding of its distribution and taphonomy is still limited. Here we collected 40 surface sediment samples from Lake Constance in southern Germany and characterized sedimentary DNA (sedDNA) heterogeneity through four metabarcoding PCRs on general eukaryotes, vascular plants, cyanobacteria and copepods.  We observed the variability of overall sedDNA being strongly correlated with sediment sample geographical locations, although this pattern varies within taxonomic groups. Specifically, geographical coordination and water depth explain 10.7% variability of terrestrial vascular plant sedDNA distribution, but the distribution of copepods is patchy and not correlated with sampling locations. Out study indicates that sedDNA is not distributed uniformly across the lake but rather linked to the movement of lake water and the local presence of the organisms.

How to cite: Wang, Y., Gutbrod, L., Schmid, M., and Epp, L.: Metarbarcoding reveals distribution patterns of DNA in surface sediments of a large lake , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15265, https://doi.org/10.5194/egusphere-egu21-15265, 2021.

15:38–15:40
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EGU21-14835
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ECS
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Weihan Jia, Kathleen Stoof-Leichsenring, Sisi Liu, Kai Li, Sichao Huang, Xingqi Liu, Jian Ni, Xianyong Cao, Luidmila Pestryakova, Steffen Mischke, and Ulrike Herzschuh

Lake sedimentary DNA (sedDNA) is an established tool to trace past changes in vegetation composition and plant diversity. However, little is known about the relationships between sedimentary plant DNA and modern vegetational and environmental conditions. In this study, we investigate i) the relationships between the preservation of sedimentary plant DNA and environmental variables, ii) the modern analogue of ancient plant DNA assemblages archived in lake sediments, and iii) the usability of sedimentary plant DNA for characterization of terrestrial and aquatic plant composition and diversity based on a large dataset of PCR-amplified plant DNA data retrieved from 259 lake surface sediments from the Tibetan Plateau and Siberia. Our results indicate the following: i) Lake-water electrical conductivity and pH are the most important variables for the preservation of plant DNA in lake sediments. We expect the best preservation conditions for sedimentary plant DNA in small deep lakes characterized by high water conductivities (≥100 μS cm-1) and neutral to slightly alkaline pH conditions (7–9). ii) Plant DNA metabarcoding is promising for palaeovegetation reconstruction in high mountain regions, where shifts in vegetation are solely captured by the sedDNA-based analogue matching and fossil pollen generally has poor modern analogues. However, the biases in the representation of some taxa could lead to poor analogue conditions. iii) Plant DNA metabarcoding is a reliable proxy to reflect modern vegetation types and climate characteristics at a sub-continental scale. However, the resolution of the trnL P6 loop marker, the incompleteness of the reference library, and the extent of sedDNA preservation are still the main limitations of this method. iv) Plant DNA metabarcoding is a suitable proxy to recover modern aquatic plant diversity, which is mostly affected by July temperature and lake-water conductivity. Ongoing warming might decrease macrophyte richness in the Tibetan Plateau and Siberia, and ultimately threaten the health of these important freshwater ecosystems. To conclude, sedimentary plant DNA presents a high correlation with modern vegetation and may therefore be an important proxy for reconstruction of past vegetation.

How to cite: Jia, W., Stoof-Leichsenring, K., Liu, S., Li, K., Huang, S., Liu, X., Ni, J., Cao, X., Pestryakova, L., Mischke, S., and Herzschuh, U.: Metabarcoding of modern sedimentary DNA from the Tibetan Plateau and Siberia as a training dataset for vegetation reconstructions, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14835, https://doi.org/10.5194/egusphere-egu21-14835, 2021.

15:40–15:42
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EGU21-8589
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ECS
Cécilia Barouillet, Julie Rotschi, Jean-Philippe Jenny, Andrea Lami, David Etienne, and Isabelle Domaizon

The use of molecular biology tools in paleolimnological investigations provides promising opportunities to study the long-term dynamic of a broad spectrum of organisms and obtain a more comprehensive overlook at the overall lake biodiversity. In this study, we reconstruct the long-term dynamic of pigmented communities of three peri-alpine lakes (Leman, Annecy and Bourget) using the analysis of traditional paleolimnological proxies (i.e. diatom frustules, pigments) and quantitative PCR (qPCR) analysis of sedimentary DNA (sed-aDNA). We then compare the results with the phytoplankton data from decadal long limnological surveys. The goal being 2-fold: (1) to consolidate and reinforce the quantitative estimates derived from qPCR analysis of sed-aDNA, (2) reconstruct the long-term dynamics and identify the timing of changes of the pigmented communities in these lakes. We will present the preliminary results of this study and discuss the potential of this type of multi-proxy analysis to strengthen the application of molecular tools in paleolimnology.

How to cite: Barouillet, C., Rotschi, J., Jenny, J.-P., Lami, A., Etienne, D., and Domaizon, I.: Reconstructing the long-term dynamic of pigmented communities in freshwater ecosystems using qPCR, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8589, https://doi.org/10.5194/egusphere-egu21-8589, 2021.

15:42–15:44
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EGU21-6277
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ECS
Bárbara Moguel, Liseth Pérez, Luis David Alcaraz, Socorro Lozano-García, Luis Herrera-Estrella, Jazmín Blaz, Margarita Caballero, María Ávila-Arcos, Juan Pedro Laclette, Israel Muñoz-Velasco, Beatriz Ortega-guerrero, Arturo Becerra, and Claudia Romero-Oliva

For decades, paleoecological studies in lake sediments have focused on reconstructing the environments of the past and explaining phenomena linked to climatic variations. Recent advances in high-throughput DNA sequencing have allowed access to environmental DNA (eDNA) and ancient sedimentary DNA (sedaDNA) as a new and efficient proxy for past and present biodiversity. The basin of Mexico (BM) is located in the central part of the Trans-Mexican Volcanic Belt at 2,200 m a.s.l.; with the southern portion harboring the Chalco sub-basin. Lake Chalco is one of the last remaining natural aquatic ecosystems within the ever-expanding urban area surrounding Mexico City. The paleoenvironmental history of this lake has been previously characterized using sedimentological and geochemical proxies, as well as preserved microfossils (diatoms, pollen) with a temporal framework based on multiple radiocarbon dates. However, information for the remaining taxonomic groups and metabolic pathways remained unexplored. Here, we present the first metagenomics-based study for the Holocene in a high-altitude lake in Central Mexico –Lake Chalco. We explored the relationship between the lake’s paleoenvironmental condition and estimations of taxonomic and metabolic profiles across the sedimentary sequence (2.5 meters long). Multiple biological and abiotic variables revealed three main environmental phases: 1) a cool freshwater lake (FW1: 11,500-11,000 cal years BP), 2) a warm hyposaline lake (HS2: 11,000-6,000 cal years BP), and 3) a temperate, subsaline lake (SS3, <6,000 cal years BP). We describe the structure of the microbiota community and taxonomy richness turnover in the three Holocene paleoenvironmental phases. During the past 12 000 years BP the most abundant domains in Lake Chalco sediments were Bacteria, followed by Archaea, and Eukarya (36,722 genera). The analysis of functional proteins showed high biodiversity with a total of 27,636,243 proteins identified, but it was only possible to annotate 3,227,398 of them. Also, we identified several genes associated with some relevant pathways, such as methanogenesis. Altogether, this study allowed us to reconstruct the natural history of lake Chalco and its surroundings.

How to cite: Moguel, B., Pérez, L., Alcaraz, L. D., Lozano-García, S., Herrera-Estrella, L., Blaz, J., Caballero, M., Ávila-Arcos, M., Laclette, J. P., Muñoz-Velasco, I., Ortega-guerrero, B., Becerra, A., and Romero-Oliva, C.: Past and recent biodiversity profiling in ancient Lake Chalco Mexico by a metagenomics analysis, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6277, https://doi.org/10.5194/egusphere-egu21-6277, 2021.

15:44–15:46
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EGU21-730
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ECS
Anne-Marie Lapointe, Yohanna Klanten, Alexander Culley, Catherine Girard, and Dermot Antoniades
Stuckberry Valley, located on the north shore of Ellesmere Island (Nunavut), approximately 800 km from the North Pole, was impacted by significant climatic variability during the Holocene and is an environment currently undergoing a rapid transition due to rising temperatures. The retreat of the valley’s main glacier resulted in the formation of four lakes, where the age of each lake is inversely related to the distance from the Arctic Ocean. Lacustrine sediments of these lakes represent a treasure-trove of information about past changes in the Stuckberry Valley watershed and provide a "long-term memory" of how the lakes’ responded to these changes. Microbes are the dominant form of life in this environment and thus understanding the diversity and distribution of microorganisms in the lakes’ sediments is essential to better understanding the effects of climate change on episodic and interannual changes in the biology of this valley. The specific objective of the study is to characterize changes over time in the structure of microbial communities by comparing microbial diversity in sediment cores from the four Stuckberry lakes, based on amplicon sequencing of viruses and bacteria. We hypothesize that microbial diversity will vary over time and that these dynamics will reflect past environmental changes in the catchment. We will also assess the differences in microbial diversity between the sediments of the four lakes and identify possible virus-host systems through network analysis. These data will provide new insight into microbial community succession in a region that is on the frontline of climate change.

How to cite: Lapointe, A.-M., Klanten, Y., Culley, A., Girard, C., and Antoniades, D.: Structure of microbial communities in lake sediments of the High Arctic, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-730, https://doi.org/10.5194/egusphere-egu21-730, 2021.

15:46–15:48
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EGU21-6142
John Williams and the Cyberinfrastructure for Ancient Sedimentary DNA Working Group

The number and extent of ancient DNA records from sedimentary environments (sedaDNA) is rapidly increasing, which creates new opportunities for integrative and macroscale investigations into past population, community, and environmental dynamics at unprecedented taxonomic resolution and spatiotemporal extent.  However, fully achieving this potential requires a robust cyberinfrastructure that supports the joint analysis of many sedaDNA records with each other and with genomic reference libraries, the latest geochronological controls and age-depth models, complementary paleoecological and paleoenvironmental proxies, and the most recent and updated DNA reference library for taxonomic identifications.  Any cyberinfrastructure for macroscale data synthesis must address the variety of ancient DNA records (e.g. taxonomic groups, analytical approaches, depositional contexts) and leverage existing resources and standards such as the Neotoma Paleoecology Database, the MGnify and MG-RAST resources for environmental genomics, and the MixS standard for genetic sequences.  In response, a Cyberinfrastructure for Ancient Sedimentary DNA working group has been meeting regularly since summer 2020 to assess the current state of science and informatics, assess needs and gaps, and establish recommendations for next steps forward.  An initial survey found over 420  sites worldwide with published or in-development sedaDNA records, with greatest densities in Eurasia.  Metabarcoding records, including Amplicon Sequence Variant data and derived taxonomic inferences, are a top priority for trial uploads to Neotoma, with pilot uploads underway, because of the relatively small dataset volumes, the widespread application of metabarcoding assays, and potential of integrating these records with other paleoecological data holdings in Neotoma and linked paleodata resources such as Linked Earth and paleoclimatic data at NOAA’s National Centers for Environmental Informatics.  Because taxonomic inferences are heavily conditioned by choice of bioinformatics pipeline and reference databases, a major unmet need is a repository for minimally processed output from raw sequences.  In general, no existing genomics or paleoecological resource meets all needs of the sedaDNA community, although each covers key elements, so there is a good potential of advancing macroscale data syntheses by leveraging and linking existing resources.

How to cite: Williams, J. and the Cyberinfrastructure for Ancient Sedimentary DNA Working Group: Building cyberinfrastructure systems to support integrative, macroscale analyses of sedimentary ancient DNA records: current resources, needs, and opportunities, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6142, https://doi.org/10.5194/egusphere-egu21-6142, 2021.

15:48–15:50
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EGU21-2906
Rosie Everett, Becky Cribdon, Logan Kistler, Roselyn Ware, and Robin Allaby

Authentication of ancient sedimentary DNA (sedaDNA) remains central to the interpretation of the proxy for wider understanding of palaeoecological archives. Distinguishing between in-situ, endogenous sedaDNA from that of contamination or modern material also allows for a wider understanding of taphonomy in the deposition and post-depositional process in the formation of the sedaDNA archive. At current, tools for authentication are reliant on single-taxon input and require a significant number of input sequences to identify an established cytosine deamination rate consistent with ancient DNA. We present the MetaDamage tool: a tool that examines cytosine deamination on a metagenomic scale. In this paper we outline the process of and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data in order to demonstrate the resolution in which MetaDamage can observe deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for initial assessment of the presence of ancient sedaDNA and provides a method for a wider understanding of key questions of preservation for palaeoecological reconstruction.

How to cite: Everett, R., Cribdon, B., Kistler, L., Ware, R., and Allaby, R.: MetaDamage Tool: Examining post-mortem damage in sedaDNA on a metagenomic scale, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2906, https://doi.org/10.5194/egusphere-egu21-2906, 2021.

15:50–15:52
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EGU21-15995
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ECS
Stefano Meucci, Luise Schulte, Kathleen R. Stoof-Leichsenring, Stefan Kruse, Konstantin Krutovsky, and Ulrike Herzschuh

Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.

How to cite: Meucci, S., Schulte, L., Stoof-Leichsenring, K. R., Kruse, S., Krutovsky, K., and Herzschuh, U.: Hybridization capture of Larix candidate adaptive genes from sedimentary ancient DNA., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15995, https://doi.org/10.5194/egusphere-egu21-15995, 2021.

15:52–15:54
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EGU21-14218
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ECS
Jérémy Courtin, Luise Schulte, Andrei Andreev, Kathleen Stoof-Leichsenring, Matthias Lenz, Martin Melles, and Ulrike Herzschuh

One of the consequences of the amplified warming of the arctic ecosystems is tundra “greening” and northward expansion of Siberian boreal forests. However, it is still challenging to predict how northern tundra biodiversity will change with the ongoing climate warming as models usually overestimate forest invasion. The investigation of Quaternary records spanning different Pleistocene glacial and interglacial cycles can provide unique insights on past diversity dynamics following forest invasion and retreat events. Therefore, by “looking backward to look forward“, reconstruction of past vegetation can help to forecast the effects of global warming on northern biodiversity.

In 2017, a 46 m core was recovered from the Lake Levinson Lessing located in the tundra of the far north Taymyr Peninsula (northern Central Siberia), the upper 38 m of which span the last 62ka continuously and with a rather constant sedimentation rate. A high resolution of 84 subsamples were collected from the lake sediment core with the aim to characterise biodiversity changes between glacials and interglacials in Russian Arctic during Late Quaternary. We studied pollen and non-pollen-palynomorphs and extracted the ancient DNA (sedaDNA), from the same sediment core samples. We also investigated past vegetation composition changes by a plant metabarcoding approach (chloroplast trnL P6 loop). We compared both pollen and sedaDNA signals to reconstruct changes in biodiversity in the Taymyr Peninsula emphasizing changes in diversity during forest invasion and retreat events.

How to cite: Courtin, J., Schulte, L., Andreev, A., Stoof-Leichsenring, K., Lenz, M., Melles, M., and Herzschuh, U.: Effects of forest invasion and retreat on tundra biodiversity inferred from sedimentary ancient DNA of lake Levinson Lessing, Taymyr Peninsula, Russia, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14218, https://doi.org/10.5194/egusphere-egu21-14218, 2021.

15:54–15:56
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EGU21-11048
Kathleen R. Stoof-Leichsenring, Sichao Huang, Luidmila A. Pestryakova, Boris K. Biskaborn, and Ulrike Herzschuh

Sedimentary ancient DNA is a valuable proxy to study ecosystem change during the past. In particular, Arctic lakes provide fantastic archives of well-preserved DNA in lake sediment cores and provide reconstructions of ecosystem change during climate transitions in the past, which help to predict prospective environmental changes under current rapid warming known to be strongest in the Arctic. Our analyses are conducted on a 10 m sediment core from Lake Ilirney, located in Eastern Chukotka, which covers the last 50 ka of major climate transitions from the lake’s development within a warmer period previous to the last glacial towards nowadays. We prepared seventeen single-stranded DNA libraries from different time slices and used shot gun sequencing, an innovative method neglecting target enrichment, to achieve a portray of the past biotic composition. The bioinformatic data analyses included data trimming and merging with Fastp and k-mer based taxonomic classification against the nucleotide database using Kraken2. Preliminary results revealed about 372 bacterial families (about 90.1% of total reads), 651 eukaryotic families (8.7%) and a few Archaea (1.1%). Dominant eukaryotic groups are plants (Saliceae, Poaceae, and Rosaceae), protists (Monodopsidaceae, Oomycota and flagellates), fish (Salmonidae, Cyprinidae), birds (Phasianidae) and mammals (Muridae). Our data confirms compositional changes of plants throughout the last 28 ka known from pollen and metabarcoding analyses of a parallel core. Further, our data revealed most prominent turnover of the eukaryotic key taxa at about 30 and 12 ka which corresponds to the major climatic transitions from glacial-interglacial periods. The detailed investigation of compositional patterns and authenticity of ancient DNA data will improve our understanding of ecosystem change in the Arctic over millennial time scales.

How to cite: Stoof-Leichsenring, K. R., Huang, S., Pestryakova, L. A., Biskaborn, B. K., and Herzschuh, U.: Shot gun sequencing of sedimentary ancient DNA from an Arctic lake reveals ecosystem changes through climate regime transitions over the last 50,000 years , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-11048, https://doi.org/10.5194/egusphere-egu21-11048, 2021.

15:56–15:58
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EGU21-10391
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ECS
Sarah E. Crump, Matthew Power, Bianca Fréchette, Gregory de Wet, Martha K. Raynolds, Jonathan H. Raberg, Morten Allentoft, Michael Bunce, and Gifford H. Miller

The colonization of recently deglaciated landscapes by tundra vegetation during the early Holocene is an important case study for understanding possible rates and patterns of plant migration in a rapidly warming world. Fossil pollen in lake sediment has traditionally served as the primary tool for reconstructing paleovegetation and understanding postglacial biogeography. However, because pollen can be wind-transported long distances and, in some cases, reworked from older deposits on the landscape, pollen-based vegetation histories can sometimes obscure the true history of plant colonization. In contrast, lacustrine sedimentary ancient DNA (sedaDNA) is sourced locally and is less likely to be adequately preserved through reworking events, thus making it a more reliable proxy for determining the precise timing of plant colonization. Here, we present three sedaDNA records from Holocene lake sediment across southern Baffin Island, Arctic Canada, that clarify the timing of postglacial vegetation changes. In particular, DNA from the subarctic shrub Betula (dwarf birch) first appears thousands of years after deglaciation in all three lake catchments, suggesting delayed colonization despite its strong pollen signal in early postglacial sediments. While moderate levels of Alnus (alder) pollen characterize early to mid-Holocene lake sediments from the region, sedaDNA suggests that Alnus was likely not present in any of the three lake catchments during the Holocene. In addition, aquatic plant community changes indicated by sedaDNA faithfully reflect the timing of early Holocene warmth in the region, highlighting the potential utility of aquatic plant DNA as a qualitative temperature proxy. We suggest that ancient plant DNA in lake sediment provides key paleoecological information that is distinct from traditional proxy records, particularly during periods of relatively rapid ecological change like the early Holocene. 

How to cite: Crump, S. E., Power, M., Fréchette, B., de Wet, G., Raynolds, M. K., Raberg, J. H., Allentoft, M., Bunce, M., and Miller, G. H.: Patterns of postglacial vegetation establishment clarified by lacustrine sedaDNA from Baffin Island, Arctic Canada, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10391, https://doi.org/10.5194/egusphere-egu21-10391, 2021.

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