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Publications in Natural Sciences by NOMIS researchers

Glacier-fed stream diatoms (Bacillariophyta) from the Rwenzori Mountains, Uganda, with the description of one new species from the genus Neidium

NOMIS Researcher(s)

Published in

April 8, 2025

Glacier-fed streams (GFSs) are harsh environments hosting unique, highly specialized communities. Interestingly, glaciers and their GFSs are also present in Earth’s tropical regions, where environmental characteristics contrast with GFS conditions elsewhere. Yet, despite the unique and isolated nature of tropical GFSs, little is known about their inhabitants, even though they may disappear later this century with ongoing climate change. Here, we examined diatom communities from one of the last tropical African GFSs in the Rwenzori Mountains, Uganda, to characterize the composition and diversity of this unique system. Six sediment-associated biofilm samples were collected from two reaches of a stream draining the Mt. Stanley Glacier, and the resident diatom communities were studied morphologically using light and scanning electron microscopy, as well as through the sequencing of amplicons from extracted DNA (18S and rbcL). In general, morphological results agree well with barcoding results, but each individually provides irreplaceable insights. In total, we identify 24 morphotypes utilizing light microscopy, 101 diatom Amplicon Sequence Variants (ASVs) using 18S sequences, and 65 ASVs with rbcL. Across approaches, common genera include Achnanthidium, Psammothidium, Neidium, Cymbopleura, Eunotia, and Pinnularia. However, only about half of the diversity could be assigned to the species level across methodologies, including several of the most common taxa, indicating a high level of uniqueness. Accordingly, one of the most common taxa encountered is described here as a new species, Neidium rwenzoriense sp. nov. Our results emphasize the Rwenzori Mountains as a global hotspot for endemism, and the novelty of disappearing tropical GFSs as diatom habitats.

Research field(s)
Conservation Biology, Ecology, Environmental Sciences

DOI
10.1080/0269249X.2025.2474765

Glaciers are not just blocks of ice — plans to save them mustn’t overlook their hidden life

NOMIS Researcher(s)

Published in

March 24, 2025

As glaciers begin to disappear, technological fixes to slow or halt ice melt are emerging. But regulations are urgently required before these fixes are used widely.

Research field(s)
Conservation Biology, Environmental Sciences

DOI
10.1038/d41586-025-00897-4

Microtubules in Asgard archaea

NOMIS Researcher(s)

Published in

March 21, 2025
Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear.
Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies.
Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.

Partnership(s)

Research field(s)
Molecular Biology, Evolutionary Biology, Microbiology

DOI
10.1016/j.cell.2025.02.027

BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation

NOMIS Researcher(s)

Published in

March 8, 2025

Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation.

Partnership(s)
,

Research field(s)
Molecular Biology, Biophysics

DOI
10.1016/j.celrep.2025.115387

Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors

NOMIS Researcher(s)

Published in

March 1, 2025

High kinetic inductance superconductors are gaining increasing interest for the realisation of qubits, amplifiers and detectors. Moreover, thanks to their high impedance, quantum buses made of such materials enable large zero-point fluctuations of the voltage, boosting the coupling rates to spin and charge qubits. However, fully exploiting the potential of disordered or granular superconductors is challenging, as their inductance and, therefore, impedance at high values are difficult to control. Here, we report a reproducible fabrication of granular aluminium resonators by developing a wireless ohmmeter, which allows in situ measurements during film deposition and, therefore, control of the kinetic inductance of granular aluminium films. Reproducible fabrication of circuits with impedances (inductances) exceeding 13 kΩ (1 nH per square) is now possible. By integrating a 7.9 kΩ resonator with a germanium double quantum dot, we demonstrate strong charge-photon coupling with a rate of gc/2π = 566 ± 2 MHz. This broadly applicable method opens the path for novel qubits and high-fidelity, long-distance two-qubit gates.

Research field(s)
Nanoscience & Nanotechnology, Quantum

DOI
10.1038/s41467-025-57252-4

Large closed-basin lakes sustainably supplied phosphate during the origins of life

NOMIS Researcher(s)

Published in

February 19, 2025

The origin of life on Earth required a supply of phosphorus (P) for the synthesis of universal biomolecules. Closed lakes may have accumulated high P concentrations on early Earth. However, it is not clear whether prebiotic P uptake in such settings would then have been sustainable. We show that large closed-basin lakes can combine high P concentrations at steady state with extremely high rates of biological productivity. Our case study is Mono Lake in California, which has close to 1 millimolar dissolved P at steady state despite extremely high rates of biological productivity, in contrast to smaller closed basins where life is scarce. Hence, large closed-basin lakes offer an environment where high rates of prebiotic P productivity can plausibly coexist with high steady-state P concentrations. Such lakes should have readily formed on the heavily cratered and volcanically active surface of early Earth.

Partnership(s)
,

Research field(s)
Physics & Astronomy

DOI
10.1126/sciadv.adq0027

Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb

NOMIS Researcher(s)

Published in

February 11, 2025

Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics.

Research field(s)
Quantum

DOI
10.1103/PhysRevLett.134.063601

Visually guided in vivo single-cell electroporation for monitoring and manipulating mammalian hippocampal neurons

NOMIS Researcher(s)

Published in

February 10, 2025

Sparse, single-cell labeling approaches enable high-resolution, high signal-to-noise recordings from subcellular compartments and intracellular organelles and allow precise manipulations of individual cells and local circuits while minimizing complex changes associated with global network manipulations. However, thus far, only a limited number of approaches have been developed to label single cells with unique combinations of genetically encoded indicators, target deep cortical structures or sustainably use the same chronic preparation for weeks. Here we developed a method to deliver plasmids selectively to single pyramidal neurons in the mouse dorsal hippocampus using two-photon visually guided in vivo single-cell electroporation to address these limitations. This method allows long-term plasmid expression in a controlled number of individual pyramidal neurons, facilitating subcellular resolution imaging, intracellular organelle tracking, monosynaptic input mapping, plasticity induction and targeted whole-cell patch-clamp recordings.

Research field(s)
Neuroscience, Molecular Biology

DOI
10.1038/s41596-024-01099-4

Predicting climate-change impacts on the global glacier-fed stream microbiome

NOMIS Researcher(s)

Published in

February 1, 2025

The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth’s major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a ‘greener’ future of the world’s GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.

Research field(s)
Conservation Biology, Ecology, Environmental Sciences

DOI
10.1038/s41467-025-56426-4

Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment

NOMIS Researcher(s)

Published in

January 30, 2025

Human accelerated regions (HARs) have been implicated in human brain evolution. However, insight into the genes and pathways they control is lacking, hindering the understanding of their function. Here, we identify 2,963 conserved gene targets for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs). Conserved gene targets are enriched for neurodevelopmental functions and are overrepresented among differentially expressed genes (DEGs) identified in human NSCs (hNSCs) and chimpanzee NSCs (cNSCs) as well as in human versus non-human primate brains. Species-specific gene targets do not converge on any function and are not enriched among DEGs. HAR targets also show cell-type-specific expression in the human fetal brain, including in outer radial glia, which are linked to cortical expansion. Our findings support that HARs influence brain evolution by altering the expression of ancestral gene targets shared between human and chimpanzee rather than by gaining new targets in human and facilitate hypothesis-directed studies of HAR biology.

Research field(s)
Bioinformatics, Developmental Biology, Evolutionary Biology

DOI
10.1016/j.cell.2025.01.007

Tropical forest clearance impacts biodiversity and function, whereas logging changes structure

NOMIS Researcher(s)

Published in

January 9, 2025

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: (i) structure and environment, (ii) species traits, (iii) biodiversity, and (iv) ecosystem functions. Responses were highly heterogeneous and often complex and nonlinear. Variables that were directly impacted by the physical process of timber extraction, such as soil structure, were sensitive to even moderate amounts of logging, whereas measures of biodiversity and ecosystem functioning were generally resilient to logging but more affected by conversion to oil palm plantation.

Research field(s)
Conservation Biology, Forestry, Ecology, Environmental Sciences

DOI
10.1126/science.adf9856

Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

NOMIS Researcher(s)

Published in

January 2, 2025

Glacier-fed streams (GFS) feature among Earth’s most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.

Research field(s)
Biology, Evolutionary Biology

DOI
10.1038/s41564-024-01874-9

Diversity and biogeography of the bacterial microbiome in glacier-fed streams

NOMIS Researcher(s)

Published in

January 1, 2025

The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth’s major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

Research field(s)
Biology, Evolutionary Biology

DOI
10.1038/s41586-024-08313-z

Alzheimer’s disease-associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain

NOMIS Researcher(s)

Published in

December 19, 2024

INTRODUCTION: While there may be microbial contributions to Alzheimer’s disease (AD), findings have been inconclusive. We recently reported an AD-associated CD83(+)microglia subtype associated with increased immunoglobulinG4(IgG4) in the transverse colon (TC).

METHODS: We used immunohistochemistry (IHC), IgG4 repertoire profiling, and brain organoid experiments to explore this association.

RESULTS: CD83(+) microglia in the superior frontal gyrus (SFG) are associated with elevated IgG4 and human cytomegalovirus (HCMV) in the TC, anti-HCMV IgG4 in cerebrospinal fluid, and both HCMV and IgG4 in the SFG and vagal nerve. This association was replicated in an independent AD cohort. HCMV-infected cerebral organoids showed accelerated AD pathophysiological features (Aβ42 and pTau-212) and neuronal death.

DISCUSSION: Findings indicate complex, cross-tissue interactions between HCMV and the adaptive immune response associated with CD83(+)microglia in persons with AD. This may indicate an opportunity for antiviral therapy in persons with AD and biomarker evidence of HCMV, IgG4, or CD83(+)microglia.

Research field(s)
Genetics & Heredity, Neurology & Neurosurgery, Biology

DOI
10.1002/alz.14401

Synaptic basis of feature selectivity in hippocampal neurons

NOMIS Researcher(s)

Published in

December 18, 2024

A central question in neuroscience is how synaptic plasticity shapes the feature selectivity of neurons in behaving animals1. Hippocampal CA1 pyramidal neurons display one of the most striking forms of feature selectivity by forming spatially and contextually selective receptive fields called place fields, which serve as a model for studying the synaptic basis of learning and memory. Various forms of synaptic plasticity have been proposed as cellular substrates for the emergence of place fields. However, despite decades of work, our understanding of how synaptic plasticity underlies place-field formation and memory encoding remains limited, largely due to a shortage of tools and technical challenges associated with the visualization of synaptic plasticity at the single-neuron resolution in awake behaving animals. To address this, we developed an all-optical approach to monitor the spatiotemporal tuning and synaptic weight changes of dendritic spines before and after the induction of a place field in single CA1 pyramidal neurons during spatial navigation. We identified a temporally asymmetric synaptic plasticity kernel resulting from bidirectional modifications of synaptic weights around the induction of a place field. Our work identified compartment-specific differences in the magnitude and temporal expression of synaptic plasticity between basal dendrites and oblique dendrites. Our results provide experimental evidence linking synaptic plasticity to the rapid emergence of spatial selectivity in hippocampal neurons, a critical prerequisite for episodic memory.

Research field(s)
Neuroscience

DOI
10.1038/s41586-024-08325-9

Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19

NOMIS Researcher(s)

Published in

December 11, 2024

SARS-CoV-2 infection is associated with long-lasting neurological symptoms, although the underlying mechanisms remain unclear. Using optical clearing and imaging, we observed the accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis of human COVID-19 patients, persisting long after viral clearance. Further, biomarkers of neurodegeneration were elevated in the cerebrospinal fluid from long COVID patients, and proteomic analysis of human skull, meninges, and brain samples revealed dysregulated inflammatory pathways and neurodegeneration-associated changes. Similar distribution patterns of the spike protein were observed in SARS-CoV-2-infected mice. Injection of spike protein alone was sufficient to induce neuroinflammation, proteome changes in the skull-meninges-brain axis, anxiety-like behavior, and exacerbated outcomes in mouse models of stroke and traumatic brain injury. Vaccination reduced but did not eliminate spike protein accumulation after infection in mice. Our findings suggest persistent spike protein at the brain borders may contribute to lasting neurological sequelae of COVID-19.

Research field(s)
Molecular Biology, Virology, Immunology

DOI
10.1016/j.chom.2024.11.007

If you please, draw me a neuron — linking evolutionary tinkering with human neuron evolution

NOMIS Researcher(s)

Published in

October 1, 2024

Animal speciation often involves novel behavioral features that rely on nervous system evolution. Human-specific brain features have been proposed to underlie specialized cognitive functions and to be linked, at least in part, to the evolution of synapses, neurons, and circuits of the cerebral cortex. Here, we review recent results showing that, while the human cortex is composed of a repertoire of cells that appears to be largely similar to the one found in other mammals, human cortical neurons do display specialized features at many levels, from gene expression to intrinsic physiological properties. The molecular mechanisms underlying human species-specific neuronal features remain largely unknown but implicate hominid-specific gene duplicates that encode novel molecular modifiers of neuronal function. The identification of human-specific genetic modifiers of neuronal function brings novel insights on brain evolution and function and, could also provide new insights on human species-specific vulnerabilities to brain disorders.

Research field(s)
Genetics & Heredity, Evolutionary Biology

DOI
10.1016/j.gde.2024.102260

Gradients of Deposition and In Situ Production Drive Global Glacier Organic Matter Composition

NOMIS Researcher(s)

Published in

September 19, 2024

Runoff from rapidly melting mountain glaciers is a dominant source of riverine organic carbon in many high-latitude and high-elevation regions. Glacier dissolved organic carbon is highly bioavailable, and its composition likely reflects internal (e.g., autotrophic production) and external (i.e., atmospheric deposition) sources. However, the balance of these sources across Earth’s glaciers is poorly understood, despite implications for the mineralization and assimilation of glacier organic carbon within recipient ecosystems. We assessed the molecular-level composition of dissolved organic matter from 136 mountain glacier outflows from 11 regions covering six continents using ultrahigh resolution 21 T mass spectrometry. We found substantial diversity in organic matter composition with coherent and predictable (80% accuracy) regional patterns. Employing stable and radiocarbon isotopic analyses, we demonstrate that these patterns are inherently linked to atmospheric deposition and in situ production. In remote regions like Greenland and New Zealand, the glacier organic matter pool appears to be dominated by in situ production. However, downwind of industrial centers (e.g., Alaska and Nepal), fossil fuel combustion byproducts likely underpin organic matter composition, resulting in older and more aromatic material being exported downstream. These findings highlight that the glacier carbon cycle is spatially distinct, with ramifications for predicting the dynamics and fate of glacier organic carbon concurrent with continued retreat and anthropogenic perturbation.

Research field(s)
Conservation Biology, Biology

DOI
10.1029/2024GB008212

New insights to be gained from a Virtual Ecosystem

NOMIS Researcher(s)

Published in

September 16, 2024

The myriad interactions among individual plants, animals, microbes and their abiotic environment generate emergent phenomena that will determine the future of life on Earth. Here, we argue that holistic ecosystem models – incorporating key biological domains and feedbacks between biotic and abiotic processes and capable of predicting emergent phenomena – are required if we are to understand the functioning of complex, terrestrial ecosystems in a rapidly changing planet. We argue that holistic ecosystem models will provide a framework for integrating the many approaches used to study ecosystems, including biodiversity science, population and community ecology, soil science, biogeochemistry, hydrology and climate science. Holistic models will provide new insights into the nature and importance of feedbacks that cut across scales of space and time, and that connect ecosystem domains such as microbes with animals or above with below ground. They will allow us to critically examine the origins and maintenance of ecosystem stability, resilience and sustainability through the lens of systems theory, and provide a much-needed boost for conservation and the management of natural environments. We outline our approach to developing a holistic ecosystem model – the Virtual Ecosystem – and argue that while the construction of such complex models is obviously ambitious, it is both feasible and necessary.

Research field(s)
Conservation Biology, Ecology, Environmental Sciences

DOI
10.1016/j.ecolmodel.2024.110866

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