Biology subjects

Stoof-Leichsenring, K. R.

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

10 recordsLinked to original sources

bioRxiv2026

Microbial priming controls terrestrial carbon burial in marine sediments

Marine sediments are a globally important sink for organic carbon of both marine and terrestrial origin, yet far less terrestrial carbon is ultimately buried than rivers deliver to the ocean margins. This long-standing "terrestrial carbon conundrum" has resisted explanation, largely because conventional bulk proxies cannot distinguish marine, terrestrial and microbial-degrader carbon pools. Here we use sedimentary ancient DNA from five records spanning the Bering Sea to the Sea of Okhotsk over the past 30,000 years to reconstruct organic carbon resolved simultaneously by taxonomy and habitat. Integrating these taxon-resolved carbon estimates with environmental proxies across the last glacial-interglacial cycle, we find that terrestrial carbon burial is governed not only by supply but by biogeochemical interactions previously documented only in soils. Microbial processing splits into two competing pathways: under priming, marine organic matter fuels the degradation of terrestrial organic matter, whereas under preferential substrate utilization microbes consume marine organic matter and spare terrestrial carbon. Both pathways are triggered only once marine organic-matter availability crosses a critical, temperature-governed threshold. This temperature-sensitive cascade reveals a previously unrecognized vulnerability of the ocean's carbon sink to global warming.

biochemistry↗

bioRxiv2026

Forest expansion and open vegetation responses during the past 14 ka at Zhagaer Co on the eastern Tibetan Plateau

Forest expansion and retreat are key drivers of alpine ecosystem dynamics, yet it remains unclear how forest expansion shapes alpine plant communities and whether alpine assemblages that re-emerge after forest decline resemble those of the Late Glacial. Here, we integrate sedimentary ancient DNA (sedaDNA) and pollen records from Zhagaer Co on the eastern Tibetan Plateau to reconstruct vegetation changes over the past [~]14 ka. Using Picea abundance as a proxy for forest cover, we apply constrained ordination of sedaDNA-inferred plant communities to identify plant taxa as "winners" and "losers" of forest expansion and compare the composition of loser taxa between the late Glacial and late Holocene cold-open phases. Our results show that forest expansion during the early to mid-Holocene favoured woody and forest-margin taxa (e.g. Rhododendron, Salicaceae), while suppressing alpine forbs and graminoids (e.g. Carex, Thalictrum), consistent with patterns expected under ecological filtering. However, late Holocene reopening did not fully restore a late Glacial-like alpine community; instead, it was characterised by a stronger contribution of alpine meadow and shrub taxa. This difference may reflect contrasting environmental backgrounds, including higher atmospheric CO2 levels during the late Holocene, ecological legacies of prior forest expansion, and increasing human influence. These findings suggest that forest expansion may lead to long-term restructuring of alpine plant assemblages, and that late Holocene cooling did not simply restore late Glacial alpine communities but instead produced a distinct alpine ecosystem state. Together, these results highlight the long-term legacy of treeline dynamics in shaping alpine ecosystem trajectories.

ecology↗

bioRxiv2025

Dynamic connectivities of plant metacommunities at a millennial time-scale: the Beringia testbed

Ecological connectivity shapes ecosystem responses to climate change and is thought to underpin stability, yet its millennial-scale dynamics remain poorly resolved. We asked how spatial and temporal connectivity of plant metacommunities changed over the last 40 ka and which processes drove it. We analysed and compiled plant sedimentary DNA from 20 lake cores across Beringia (Siberia, Alaska) to investigate community dynamics and, for a high-resolution subset, applied beta- and zeta-diversity to track connectivity. Vegetation changed coherently across the glacial-Holocene transition, with trait shifts mirroring functional composition. Connectivity peaked during the late MIS3 and Last Glacial Maximum--likely aided by the Bering Land Bridge, mass effects and facilitation--collapsed during the Deglacial with rapid turnover, and rebounded in the Holocene as shrub and boreal communities expanded. Temporal zeta within sites exceeded spatial zeta, indicating strong local persistence and resilience. Tundra sites uninvaded by forest maintained continuous species pools. Overall, these patterns underscore the value of a metacommunity perspective for assessing millennial-scale connectivity changes.

ecology↗

bioRxiv2025

Arctic defaunation initiated a cascade of mammal-plant interaction shift through dispersal dynamics

Amid accelerating defaunation, it remains unclear whether the loss of large mammals can trigger ecosystem collapse and through which functional pathways. Using sedimentary ancient metagenomics, we identify an overlooked role of large mammal defaunation in helping drive the collapse of the glacial mammoth-steppe. Network analyses identified rewiring of mammal interactions during the late glacial supporting cascading effects. Crucially, megafaunal-mediated long-distance seed dispersal buffered vegetation turnover during periods of rapid climate warming but weakened with progressive losses of vital dispersal interactions leading to the steppe-tundras transition to open woodland in the early Holocene. Trophic interactions did not offset turnover and became dominant afterwards with the more stable climate. We identified resilient interactions that may support recovery, suggesting the potential of rewilding to restore Arctic ecosystems. One-sentence abstractAncient metagenomics reveals disrupted long-distance seed dispersal helped drive mammoth-steppe collapse and informs Arctic rewilding efforts.

ecology↗

bioRxiv2025

Woody plant encroachment enhances negative interactions in Arctic plant communities over the last 24,000 years

Woody taxa encroachment in the Arctic has been widely observed. However, it remains uncertain how plant interactions are affected by such encroachment due to the lack of long-term observational data. Here, we reconstruct plant composition and functional trait turnover during post-glacial woody encroachment using sedimentary ancient DNA from nine lakes in the Siberia-Alaska region. Environmentally constrained null models are applied to partition plant interactions from the pure environment driven plant co-occurrence signal. Our results show that plant interactions shifted from predominantly positive interactions (e.g. nurse-plant facilitation) during the glacial period to negative interactions (e.g. competition) during the Holocene. This shift coincided with a community transition from herbaceous to woody taxa, leading to an increase in average plant height and root length, as evidenced by leveraging plant trait information. We suggest that climate (an external factor) and plant interactions (an internal process) jointly supported rapid and widespread woody taxa expansion at the end of the last glacial, which may provide an analogy with contemporary "arctic greening". In turn, woody encroachment is likely to constrain the geographical ranges of native species, increasing the risk of local native taxa loss, while enhancing beta diversity.

ecology↗

bioRxiv2024

Phaeocystis blooms caused carbon drawdown during the Antarctic Cold Reversal from sedimentary ancient DNA

The Southern Ocean plays a crucial role in the global carbon budget. Modeling studies propose that the atmospheric CO2 plateau during the Antarctic Cold Reversal (ACR; 14,700 to 12,700 calibrated years before present (cal yr BP)) is related to increased marine productivity. However, proxy evidence relating environmental conditions as well as primary community composition and productivity to carbon drawdown is missing. Our ancient DNA shotgun metagenomic analysis of marine sediments revealed Phaeocystis antarctica (haptophyte) as a key element of the primary producer community. Independent proxy evidence (blooming-related bacteria, Ba/Fe ratio) from the same sediment record point to high productivity in response to enhanced sea-ice seasonality caused by ACR cooling. Post ACR, abrupt Phaeocystis community loss shows how sensitive this ecosystem is to warming, potentially representing a key tipping element that may be further enhanced by the Phaeocystis-related sulfur cycle-climate feedback. As an analogy for present warming, it highlights the importance of regions with high seasonal sea-ice variability and Phaeocystis-dominance, such as the Ross Sea, for stabilizing atmospheric CO2 content. Additionally, our shotgun metagenomic data portray complex Holocene ecosystem establishment including key Antarctic taxa such as penguins, whales, and Antarctic fishes with implications for ongoing conservation efforts.

ecology↗

bioRxiv2023

Early Neolithic forest farming at Seven Springs, Martlesham, Suffolk from sedaDNA and pollen

The importance of small wetlands and springs to Mesolithic cultures is well established. However, few studies have focused on their significance and use by Early Neolithic agro-pastoralists. Here we present a multiproxy palaeoenvironmental analysis, including authenticated sedimentary ancient DNA (sedaDNA), at Seven Springs, Martlesham, UK, indicating that the springs provided an attractive location for pastoral and ritual activity around a palaeochannel surrounded by dense woodland. We demonstrate that sedaDNA can be preserved well within stratigraphically complex wetland sediment sequences, allowing archaeologically valuable insights into crucial periods of change in the prehistoric, where other forms of environmental evidence can be scarce.

ecology↗

bioRxiv2023

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.

ecology↗

bioRxiv2021

Long-term fungus-plant co-variation from multi-site sedimentary ancient DNA metabarcoding in Siberia

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the palaeo-ecosystems at selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. After bioinformatic processing with the OBItools pipeline, we obtained 706 unique fungal operational taxonomic units (OTUs) and 243 amplicon sequence variants (ASVs) for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus compositional and plant diversity changes which will affect forest advance and stability in arctic regions.

ecology↗

bioRxiv2020

Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches, in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA - metabarcoding - focuses on small fragments which cannot resolve Larix to species level nor allow the detailed study of population dynamics. Here we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back up to 6700 years in age from the Taymyr region in northern Siberia. 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 corroborate an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. 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.

ecology↗