Biology subjects

Crump, S.

Publications and source records attributed to Crump, S..

3 recordsLinked to original sources

bioRxiv2025

Ancient metagenomics reveals subglacial microbiomes driven by oxygen availability

Beneath Earths glaciers and ice sheets lies an aquatic realm where ice, water, rock, and microbial life interact, driving chemical reactions that can collectively influence the global carbon cycle, polar oceans, and climate. Efforts to describe subglacial microbiomes have been limited by the challenge of cleanly drilling through hundreds of meters of ice, such that only a few sites have ever been directly sampled. Here we use ancient metagenomics to present the first spatiotemporal characterization of subglacial bacteria and archaea. We extracted DNA from 25 subglacial precipitate samples, sedimentary accumulations of minerals that form in subglacial waters prior to exposure on the surface. The precipitates studied here formed between 16,000 and 570,000 years ago beneath the Antarctic and Laurentide Ice Sheets. We show that postmortem DNA damage patterns can reliably distinguish between ancient subglacial and modern surface taxa, and that this approach can enable reconstruction of subglacial microbiomes across poles and ice ages. Our analysis suggests that subglacial microbiomes are dominated by chemolithoautotrophs, ultra-small microbes, and taxa closely related to those found in deep subsurface or extreme cold and hypersaline environments. These microbiomes split into two distinct clusters distinguished by oxygen availability and redox conditions, irrespective of geography or age. Geochemical measurements of subglacial redox state, measured either indirectly via precipitate calcite Fe and Mn concentrations or directly via water reduction potential, reproduce these same two clusters exactly. Our findings describe how subglacial water redox states are held in balance by microbes, hydrology, and oxygen input from fresh subglacial meltwater, that we interpret to be controlled by the ice sheet response to past climate variations.

genomics↗

bioRxiv2025

TBRS-associated DNMT3A mutations disrupt cortical interneuron differentiation and neuronal networks

Pathogenic mutations in DNMT3A cause Tatton-Brown-Rahman Syndrome (TBRS), a disorder characterized by somatic overgrowth of multiple tissues including the brain and intellectual disability (OGID). Here, we investigated TBRS etiology using new human pluripotent stem cell models, modeling varying levels of TBRS-associated loss of DNMT3A function. We identified lineage-specific overgrowth in TBRS ventral forebrain medial ganglionic eminence (MGE)-like progenitors, due in part to increased signaling through the PIK3/AKT/mTOR pathway that could be modulated to ameliorate this phenotype. By contrast, reduced DNA methylation during MGE-like progenitor differentiation into GABAergic interneurons caused premature expression of neuronal and synaptic genes, triggering precocious neuronal maturation. As a result, TBRS GABAergic neurons exhibited sufficient hyperactivity to alter the development and structure of neuronal networks, likely contributing to the intellectual disability and autism spectrum disorder common to TBRS patients. Together, this work elucidates new roles for DNMT3A-mediated gene repression in human cortical development, identifying critical requirements for regulating GABAergic neuron production and neuronal network function. These findings also support potential relationships between pathogenic mechanisms underlying TBRS and other OGIDs, including PIK3CA-related overgrowth syndrome and Weaver Syndrome, thus providing a foundation for future studies to identify common paradigms to treat these related disorders.

neuroscience↗

bioRxiv2024

Ancient sedimentary DNA shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park

Beaver-based restoration is emerging as a cost-effective conservation and climate adaptation strategy, but efforts are constrained by limited knowledge of pre-colonial beaver distribution and their long-term ecosystem impacts. Here, we apply sedimentary ancient DNA (sedaDNA) techniques to investigate the history of beaver occupancy at three lakes in Grand Teton National Park, Wyoming over the last [~]10 ka, as well as interactions with the local plant community. We documented a dynamic history of beaver presence in two sub-alpine lakes (Taggart and Jenny Lakes) and demonstrate no history of beaver occupancy at the higher-elevation alpine lake (Lake Solitude). Beavers were first detected at Jenny Lake around 7.2 ka and intermittently thereafter. At nearby Taggart Lake, beavers were first detected at [~]5.9 ka and continuously from 5.2 ka onwards. Vegetation metabarcoding revealed a shift in plant community coinciding with beaver establishment in these two sub-alpine lakes, as well as an increase in taxonomic diversity. These changes coincide with regional trends towards wetter conditions. Notably, beavers persist at Taggart Lake during inferred droughts, indicating a potential role in maintaining wetlands through extended periods of climatic stress. Our results demonstrate sedaDNA as a powerful, novel technique for reconstructing past beaver occupancy dynamics.

ecology↗