Biology subjects

Stoof-Leichsenring, K.

Publications and source records attributed to Stoof-Leichsenring, K..

7 recordsLinked to original sources

bioRxiv2026

Taxon-resolved sources of organic carbon preserved in lake sediments using the sedaDNA GenC pipeline

Organic carbon (OC) burial in lakes is an important component of the global carbon cycle, but the source organisms of preserved OC remain poorly resolved. Here we develop the genC pipeline, which combines sedimentary ancient DNA concentrations, read-based taxonomic assignments, and group-specific priors for DNA and cellular carbon content to derive OCDNA-projected, a semi-quantitative proxy for the magnitude and taxonomic composition of preserved sedimentary OC. We apply genC to six high-latitude lake records spanning the last 30,000 years. OCDNA-projected broadly agrees with independent proxies for total organic carbon and aquatic contribution, supporting its reliability. Our results indicate that environmental conditions, especially warming, rather than preservation alone, are the main drivers of preserved OC variation. Terrestrial sources, mainly woody plants, dominate lake sediment OC. Eukaryotic algae as well as aquatic and terrestrial bacteria become more important during the warmer Holocene. These results establish sedaDNA as a taxonomically resolved tool for reconstructing long-term changes in preserved lake-sediment OC.

paleontology↗

bioRxiv2025

Capture probe, metabarcoding, or shotgun sequencing: which best reflects local vegetation?

O_LIMetabarcoding is the most widely applied method for studying plant communities using environmental DNA, with shotgun sequencing and capture probes being alternative methods. Any methods ability to detect and correctly identify plant taxa may vary with DNA preservation, DNA reference library and the size of the local flora, making it difficult to compare results from different environments. C_LIO_LIHere we compare these methods using lake surface-sediments from Northern Fennoscandia with the PhyloNorway genome skim reference library (1500 taxa) that includes almost all species of the regional flora. We also undertook vegetation surveys from around the lakes to estimate the true positive detection rate, identify false positive detections, and provide optimal filtering cut-off thresholds for the three methods. C_LIO_LIOptimal filter cutoffs were one PCR replicate and 3 reads for metabarcoding, and 3.2x10e-6 and 5.6x10e-6 of queried reads, respectively, for the shotgun and capture probe data. Applying these thresholds, the rate of false positives was too high for reliable identification at species level based on shotgun (49%) and capture probes (62%), whereas it was low for metabarcoding (5-12%). All methods were reliable at genus and family levels after applying the optimal filtering thresholds (<4% false positives). Our results show that metabarcoding on average detects 2.1 times as many true positive taxa as shotgun sequencing, and 6.4 times as many taxa as capture probes. Proportions of filtered metabarcoding and shotgun reads were significantly related to abundance categories from vegetation surveys, but this was not the case for capture probe data. C_LIO_LIWe expect the false positive rate of shotgun sequencing to decrease with increasing genome completeness in the reference libraries, and be advantageous for highly degraded DNA with fragments too short for metabarcoding. At present, metabarcoding provides the highest detectability and taxonomic resolution for correct identification of vascular plants. C_LI

ecology↗

bioRxiv2025

DNA virus-host patterns in lake and marine environments over the last glacial cycle

Viruses are crucial to population control, biogeochemical cycling, and host evolution, making them essential for ecosystem function. Here, we explore long-term virus-host interactions in lake and marine environments across the late Pleistocene and Holocene. We analysed sedimentary ancient DNA (sedaDNA) from five Siberian lakes and four Subarctic/Antarctic marine cores to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 0.089% (357 161 reads) of mapped reads across 2084 taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes in virus communities from the Pleistocene to the Holocene, supporting the inference that sedaDNA can reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs known from published literature to infect bacterial, archaeal, or eukaryotic hosts, and assessed their associations using co-variation patterns. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded rapidly after the Bering Strait opened, potentially due to absent viral infection. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study shows that sedaDNA can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem- specific responses to environmental change.

ecology↗

bioRxiv2023

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Glacier and permafrost shrinkage and land-use intensification threaten diverse mountain wildlife and affect nature conservation strategy. Our understanding of alpine ecological dynamics is, however, insufficient because time series portraying ecosystem complexity adequately are missing. Here, we present an ancient metagenomic record tracing 317 terrestrial and aquatic taxa, including mammals, fish, plants, and microorganisms retrieved from a lake sediment core from the southeastern Tibetan Plateau covering the last 18,000 years. We infer that steppe-meadow turned into woodland at 14 ka (cal BP) controlled by warming-induced cryosphere loss, further driving a change of herbivore dominance from wild yak to deer. Network analyses reveal that root hemiparasitic and cushion plants are keystone taxa, likely altering the terrestrial ecosystem via facilitation. These findings refute the hypothesis of top-down control by large herbivores in the alpine ecosystem. We also find that glacier mass loss significantly contributes to considerable turnover in the aquatic community at 14 ka, transitioning from glacier-related (blue-green) algae to abundant non-glacier-preferring picocyanobacteria, macrophytes, fish, and fish-eating otters. Human impact contributes little to shaping the alpine ecosystems. By applying network analysis, we provide the first sedaDNA-based assessment of the stress-gradient hypothesis. As cryosphere loss is ongoing due to climate warming, prioritizing the protection of habitats with rich nurse plants that aid neighbors in adapting to stressful conditions is likely to be a more beneficial conservation measure than livestock reduction in the Tibetan Plateau. Significance statementMerging ancient metagenomics and network analysis gives new insights into conserving the Tibetan alpine ecosystem under ongoing warming and human perturbations. We investigated the assembly of the Yak steppe-meadow ecosystem and an alpine lake system in response to cryosphere changes over the past [~]18,000 years on the Tibetan Plateau. Large herbivores cannot be a cost-effective natural climate solution to stabilize the Tibetan alpine ecosystem because they are not keystone taxa at the ecosystem scale. Furthermore, there is no support that land use considerably shapes the alpine communities and ecosystems. Protection policy should thus prioritize focus on alpine areas with intense land use and rich in root hemiparasitic and cushion plants because these taxa act as facilitators in the ecosystem.

ecology↗

bioRxiv2023

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals--both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g., > 400K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.

molecular biology↗

bioRxiv2021

Fungal biodiversity in Arctic paleoecosystems assessed by metabarcoding of lake sedimentary ancient DNA

Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may therefore help reveal biodiversity changes in past ecosystems. Lake sediments contain DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We developed a novel PCR primer combination for fungal metabarcoding targeting a short amplicon to account for length bias of amplification due to ancient DNA degradation. In-silico PCRs showed higher diversity using this primer combination than using previously established fungal metabarcoding primers. We analyzed existing data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2-22 years and examined degradation effects of ancient DNA and storage time-related bias in fungal communities. Amplicon size differed between fungal divisions, however, we observed no significant effect of sample age on amplicon length and GC content, suggesting robust results. We also found no indication of post-coring fungal growth during storage distorting ancient fungal communities. Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities.

ecology↗

bioRxiv2020

Plant sedimentary ancient DNA from Far East Russia covering the last 28 ka reveals different assembly rules in cold and warm climates

Woody plants are expanding into the Arctic under a warming climate. The related impact on plant diversity is not well understood because we have only limited knowledge about plant assembly rules and because of a lack of time-series of plant diversity. Here, we applied sedimentary ancient DNA metabarcoding using the plant-specific g and h primers of the trnL gene to a sediment record from Lake Ilirney (central Chukotka Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-dominated steppe-tundra and Saliceae-rich dwarf-shrub tundra communities dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period between 14 and 0 ka. Larix invasion during the late Holocene substantially lagged behind the period of densest vegetation and likely warmest period between 10 and 6 ka. Overall, we discovered the highest richness during 28-23 ka and a second richness peak during 13-10 ka: both periods are characterised by low shrub abundance. The richest communities during the cold pre-14 ka period were phylogenetically clustered, which probably originates from environmental filtering along with niche differentiation under limited resources. In contrast, the richest post-14 ka community was phylogenetically overdispersed, likely originating from an erratic recruitment process in the course of warming. Despite differences in timescale, some of our evidence can be relevant to arctic plant diversity changes. By analogy to the past, we expect a lagged response of tree invasion. In the long-term, ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community but will also cause reduced plant taxonomic richness; however, richness may overshoot in the short-term.

ecology↗