Biology subjects

Harms, L.

Publications and source records attributed to Harms, L..

5 recordsLinked to original sources

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↗

bioRxiv2024

Dynamic land-plant carbon sources in marine sediments inferred from ancient DNA

Terrigenous organic matter in marine sediments is considered a significant long-term carbon sink, yet our knowledge regarding its source taxa is severely limited. Here, we leverage land-plant ancient DNA from six globally distributed marine sediment cores covering the Last Glacial-Holocene transition as a proxy for the share, accumulation rate, preservation, and composition of terrigenous organic matter. We show that the spatial and temporal plant composition as revealed by sedaDNA records reflects mainly the vegetation dynamics of nearby continents as revealed by comparison with pollen from land archives. However, we also find indications of a global north-to-south translocation of sedaDNA. The plant composition shows that upland vegetation is strongly underrepresented in the record compared to riverine and coastal sources. We also find that plant sedaDNA has a higher accumulation rate in samples from the Late Glacial, which is characterized by high runoff and mineral load. Thus plant DNA in marine sediments allows for new perspectives on the global linkages between the terrestrial and marine carbon cycle which would benefit from a more quantitative understanding of DNA preservation and dispersal. This represents the basis of how climate change and land-use change translate into carbon-sink dynamics and also informs about natural carbon-capture solutions.

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↗

bioRxiv2019

Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima

Saccharina latissima is an economically and ecologically relevant kelp species in Europe and North America. In kelps, the sexuality is expressed during the haploid life stage and the microscopic gametophytes exhibit significant sexual dimorphism. To understand the sex-dependent impact of temperature on the gametophyte stage, we analyzed for the first time, gene expression profiles of male and female gametophytes at three different temperatures (4{degrees}C, 12{degrees}C and 20{degrees}C) characteristic for the species distribution range by using RNA-sequencing. We identified several differentially expressed genes between sexes; while female biased genes were enriched in general metabolism and energy production, male biased genes function within cell cycle and signaling. In our study, temperature modulated sex-biased gene expression, with only a small percentage of differentially expressed genes consistently male (7%) or female-biased (12%) at the three temperatures. Female gametophytes responded stronger to higher temperatures than males, suggesting that males are more heat tolerant. Differences between S. latissima and other brown algal gender-dependent gene expression might mirror the different evolutionary and ecological contexts. Genomic information on kelp gametophyte is still scarce and thus this study adds to our knowledge on sex differences in abiotic stress responses in macroalgae at the transcriptomic level.\n\nHighlightThe transcriptomic basis for sexual dimorphism and associated metabolic needs are described for the kelp Saccharina latissima. Temperature modulates sex-biased gene expression resulting in a stronger stress response in females.

plant biology↗

bioRxiv2019

The effect of NMDA-R antagonist, MK-801, on Neuronal Mismatch along the Auditory Thalamocortical System

Efficient sensory processing requires that the brain is able to maximize its response to unexpected stimuli, while suppressing responsivity to expected events. Mismatch negativity (MMN) is an auditory event-related potential that occurs when a regular pattern is interrupted by an event that violates the expected properties of the pattern. MMN has been found to be reduced in individuals with schizophrenia in over 100 separate studies, an effect believed to be underpinned by glutamate N-methyl-D-aspartate receptor (NMDA-R) dysfunction, as it is observed that NMDA-R antagonists also reduce MMN in healthy volunteers. The aim of the current study is to examine this effect in rodents. Using single unit recording in specific auditory areas using methods not readily utilized in humans, we have previously demonstrated that neuronal indices of rodent mismatch responses recorded from thalamic and cortical areas of the brain can be decomposed into a relatively simple repetition suppression and a more sophisticated prediction error process. In the current study, we aimed to test how the NMDA-R antagonist, MK-801, affected both of these processes along the rat auditory thalamocortical pathway. We found that MK-801 had the opposite effect than expected, and enhanced thalamic repetition suppression and cortical prediction error. These single unit data correlate with the recordings of local field responses. Together with previous data, this study suggests that our understanding of the contribution of NMDA-R system to MMN generation is far from complete, and also has potential implications for future research in schizophrenia.\n\nSignificance StatementIn this study, we demonstrate that an NMDA-R antagonist, MK-801, differentially affects single neuron responses to auditory stimuli along the thalamocortical axis by increasing the response magnitude of unexpected events in the auditory cortex and intensifying the adaptation of responses to expected events in the thalamus. Thus, we provide evidence that NMDA-R antagonists alter the balance between prediction-error and repetition suppression processes that underlie the generation of mismatch responses in the brain, and these effects are differentially expressed at different levels of auditory processing. As effects of MK-801 were in the opposite direction to our expectations, it demonstrates that our understanding of role of NMDA-R in synaptic plasticity and the neural processes underpinning MMN generation are far from complete.

neuroscience↗