Biology subjects

Gros, O.

Publications and source records attributed to Gros, O..

7 recordsLinked to original sources

bioRxiv2026

Polyploid Achromatium sp. expresses protein variants based on environmental cues

Achromatium spp. are giant bacteria harboring hundreds of non-clonal chromosomes per cell. The allelic divergence they exhibit could be a mechanism to enable fine-tuned responses to environmental changes, enabling this organism to broaden its ecological range. However, while ubiquitous in freshwater and marine environments, Achromatium has not been obtained in culture, leaving the role and functioning of its genomic and proteomic diversity poorly understood. Here, we incubated freshly collected freshwater Achromatium under three temperature conditions to conduct comparative mass spectrometry-based proteomics experiments. These were interpreted against an Achromatium-specific protein atlas developed from curated published and new assemblies from marine and freshwater environments. This de novo assembled atlas allowed a twenty-fold increase in the number of identified proteins compared to mass spectrometry data searches against the UniProt database. Predicted proteins from the Achromatium atlas were grouped into orthologs, 5% of which showed temperature-associated detection of distinct protein variants within the group. This provides the first indication that Achromatium uses distinct protein variants under different environmental conditions, enabling it to swiftly respond to environmental changes through differential expression from its cache of chromosomes.

microbiology↗

bioRxiv2025

Organosulfur cycling in the multi-partner symbiosis between lucinid bivalves, sulphur-oxidizing symbionts, and Endozoicomonas

Organosulfur compounds play an important role in chemotaxis, stress protection, and nutrition in many marine symbioses. Lucinidae, an ancient and species-rich family of marine bivalves, host chemosynthetic sulphur-oxidising bacteria within gill epithelial cells, and is well-known for its contribution to inorganic sulphur cycling in marine sediments worldwide. Little is known about organosulfur transformations by lucinid-associated microbiota or the hosts potential contribution. Here, we integrated field measurements, genomics, transcriptomics, and experimental assays to investigate organosulfur cycling in three lucinid species from temperate and tropical environments. Concentrations of the osmolyte dimethylsulphoniopropionate (DMSP) in lucinids were typically much higher than in their surrounding environment, and varied with host species and season, but not with symbiont abundance. Indeed, candidate DMSP synthesis DSYB genes were expressed by the animal hosts implying that the host may be the source of DMSP. Furthermore, a newly identified and isolated Candidatus Endozoicomonas endolucinida symbiont was capable of DMSP catabolism to dimethylsulphide (DMS), which could be further syntrophically oxidised by the sulphur-oxidising symbionts that encode methanethiol oxidase genes in their genomes. Finally, incubation experiments supported a combined role of the host and its associated microbiome in organosulfur cycling during stress, with the highest DMSP concentrations measured when holobionts were incubated with antibiotics under anoxic conditions. This study identified a previously unrecognised microbial partner in lucinid symbioses and revealed its potential organosulphur-based metabolic interactions with both the host and the sulphur-oxidising symbionts, highlighting the capacity of these widespread associations to influence global organosulfur cycling.

ecology↗

bioRxiv2025

Microscopy Nodes: versatile 3D microscopy visualization with Blender

Effective visualization of 3D microscopy data is essential for communicating biological results. While scientific 3D rendering software is specifically designed for this purpose, it often lacks the flexibility found in non-scientific software like Blender, which is a free and open-source 3D graphics platform. However, loading microscopy data in Blender is not trivial. To bridge this gap, we introduce Microscopy Nodes, an extension for Blender that enables the seamless integration of large microscopy data. Microscopy Nodes provides efficient loading and visualization of up to 5D microscopy data from Tif and OME-Zarr files. Microscopy Nodes supports various visualization modes including volumetric, isosurface, and label-mask representations, and offers additional tools for slicing, annotation, and dynamic adjustments. By leveraging Blenders advanced rendering capabilities, users can create high-quality visualizations that accommodate both light and electron microscopy. Microscopy Nodes makes powerful, clear data visualization available to all researchers, regardless of their computational experience, and is available through the Blender extensions platform with comprehensive tutorials.

cell biology↗

bioRxiv2024

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliate Zoothamnium niveum and its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup, Z. niveum holds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.

microbiology↗

bioRxiv2024

Spherical harmonics texture extraction for versatile analysis of biological objects

The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences in the spatial distribution of image intensity. Multiple methods exist for quantifying the intensity distribution - or image texture - across objects in natural images. However, many of these texture extraction methods do not directly adapt to 3D microscopy data. Here, we present Spherical Texture extraction, which measures the variance in intensity per angular wavelength by calculating the Spherical Harmonics or Fourier power spectrum of a spherical or circular projection of the angular mean intensity of the object. This method provides a 20-value characterization that quantifies the scale of features in the spherical projection of the intensity distribution, giving a different signal if the intensity is, for example, clustered in parts of the volume or spread across the entire volume. We apply this method to different systems and demonstrate its ability to describe various biological problems through feature extraction. The Spherical Texture extraction characterizes biologically defined gene expression patterns in Drosophila melanogaster embryos, giving a quantitative read-out for pattern formation. Our method can also quantify morphological differences in Caenorhabditis elegans germline nuclei, which lack a predefined pattern. We show that the classification of germline nuclei using their Spherical Texture outperforms a convolutional neural net when training data is limited. Additionally, we use a similar pipeline on 2D cell migration data to extract polarization direction, quantifying the alignment of fluorescent markers to the migration direction. We implemented the Spherical Texture method as a plugin in ilastik, making it easy to install and apply to any segmented 3D or 2D dataset. Additionally, this technique can also easily be applied through a Python package to provide extra feature extraction for any object classification pipeline or downstream analysis. Author summaryWe introduce a novel method to extract quantitative data from microscopy images by precisely measuring the distribution of intensities within objects in both 3D or 2D. This method is easily accessible through the object classification workflow of ilastik, provided the original image is segmented into separate objects. The method is specifically designed to analyze mostly convex objects, focusing on the variation in fluorescence intensity caused by differences in their shapes or patterns. We demonstrate the versatility of our method by applying it to very different biological samples. Specifically, we showcase its effectiveness in quantifying the patterning in D. melanogaster embryos, in classifying the nuclei in C. elegans germlines, and in extracting polarization information from individual migratory cells. Through these examples, we illustrate that our technique can be employed across different biological scales. Furthermore, we highlight the multiple ways in which the data generated by our method can be used, including quantifying the strength of a specific pattern, employing machine learning to classify diverse morphologies, or extracting directionality or polarization from fluorescence intensity.

bioinformatics↗

bioRxiv2022

A centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles

Cells of most bacterial species are around 2 {micro}m in length, with some of the largest specimens reaching 750 {micro}m. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Ca. Thiomargarita magnifica, a bacterium with an average cell length greater than 9,000 {micro}m that is visible to the naked eye. We found that these cells grow orders of magnitude over theoretical limits for bacterial cell size through unique biology, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes in daughter cells. These features, along with compartmentalization of genomic material and protein synthesis in membrane-bound organelles, indicate gain of complexity in the Thiomargarita lineage, and challenge traditional concepts of bacterial cells. One Sentence SummaryCa. T. magnifica are compartmentalized centimeter-long bacteria

cell biology↗

bioRxiv2021

Ehrlichia ruminantium uses its transmembrane protein Ape to adhere to host bovine aortic endothelial cells

AO_SCPLOWBSTRACTC_SCPLOWEhrlichia ruminantium is an obligate intracellular bacterium, transmitted by ticks of the genus Amblyomma and responsible for heartwater, a disease of domestic and wild ruminants. High genetic diversity of E. ruminantium strains hampers the development of an effective vaccine against all strains present in the field. In order to develop strategies for the control of heartwater through both vaccine and alternative therapeutic approaches, it is important to first gain a better understanding of the early interaction of E. ruminantium and its host cell. Particularly, the mechanisms associated with bacterial adhesion remain to be elucidated. Herein, we studied the role of E. ruminantium membrane protein ERGA_CDS_01230 (UniProt Q5FFA9), a probable iron transporter, in the adhesion process to host bovine aortic endothelial cells (BAEC). The recombinant version of the protein ERGA_CDS_01230, successfully produced in the Leishmania tarentolae system, is O-glycosylated. Following in vitro culture of E. ruminantium in BAEC, the expression of CDS ERGA_CDS_01230 peaks at the extracellular infectious elementary body stages. This result suggest the likely involvement of ERGA_CDS_01230, named hereafter Ape for Adhesion protein of Ehrlichia, in the early interaction of E. ruminantium with its host cells. We showed using flow cytometry and scanning electron microscopy that beads coated with recombinant ERGA_CDS_01230 (rApe) adheres to BAEC. In addition, we also observed that rApe interacts with proteins of the cell lysate, membrane and organelle fractions. Additionally, enzymatic treatment degrading dermatan and chondroitin sulfates on the surface of BAEC is associated with a 50% reduction in the number of bacteria in the host cell after a developmental cycle, indicating that glycosaminoglycans seem to play a role in the adhesion of E. ruminantium to the host cell. Finally, Ape induces a humoral response in vaccinated animals. Globally, our work identifying the role of Ape in E. ruminantium adhesion to host cells makes it a gold vaccine candidate and represents a first step toward the understanding of the mechanisms of cell invasion by E. ruminantium.

microbiology↗