Biology subjects

Slomka, J.

Publications and source records attributed to Slomka, J..

6 recordsLinked to original sources

bioRxiv2026

Bacterial capture and lysis on diatom spines reveal a suspension-feeding strategy

Phytoplankton contribute nearly half of global primary production and play a central role in ocean biogeochemistry. Although traditionally viewed as phototrophs, a growing body of evidence indicates that many phytoplankton are mixotrophic, supplementing photosynthesis with heterotrophic acquisition of nutrients and organic matter. Yet, the mechanisms enabling heterotrophic feeding in diatoms remain poorly understood. Here, we show that the chitinous spines of the diatom Conticribra weissflogii can serve as attachment sites for the bacterium Marinobacter adhaerens. Cryo-electron tomography and viability staining revealed that a substantial fraction of spine-associated M. adhaerens undergoes lysis. Consistent with bacterial lysis on the spines, Raman spectroscopy showed that diatom cells bearing spine-associated bacteria acquired more bacteria-derived nitrogen than uncolonized cells. Although microfluidic assays revealed a low bacterial affinity for the spines, our results suggest that attachment can be promoted by fucoidan deposits identified on the spines - a compound for which bacteria showed significantly higher binding affinity than chitin - as well as by their geometry, which encounter rate calculations show to be particularly efficient at intercepting bacteria. Together, these findings reveal a previously undescribed form of suspension-feeding in phytoplankton, reminiscent of the role of zooplankton pseudopods in prey capture. Diatom spines intercept bacteria from the surrounding water, retain them near the cell surface, and facilitate subsequent nutrient acquisition, probably through bacterial lysis. Our results expand the functional repertoire of diatom spines beyond defense and buoyancy, identifying spine-mediated bacterial capture as a previously overlooked pathway contributing to phytoplankton mixotrophy.

microbiology↗

bioRxiv2025

A universal surface functionalization technique to chemically enhance live microbial cells

Microbial surface functionalization is a powerful strategy for endowing microbes with novel, non-genetic functions. However, existing methods are often species-specific, limited in scope, and compromise cell viability. Here, we present a universal and modular platform for high-density, reproducible surface functionalization across diverse microbial species--including Gram-positive, Gram-negative, aerobic, and anaerobic bacteria--using multiple molecular classes such as fluorophores, enzymes, and nucleic acids. Our method preserves cell viability, and achieves 50x higher functionalization efficiency than previous methods with a standardized protocol applicable to any azide-containing molecule. Applications of the method show reproducible and tunable phenotypic outcomes at the single-cell level: fluorophore labeling yielded adjustable fluorescence, {beta}-lactamase conferred scalable antibiotic resistance, and DNA coatings modulated adhesion and aggregation. This platform provides quantitative, non-genetic control over microbial phenotypes and complements genetic engineering approaches. It enables new possibilities for microbial design in biotechnology, medicine, and environmental applications where genetic modification is impractical or undesirable.

microbiology↗

bioRxiv2025

Precise 3D Tracking of Highly Non-planar Eukaryotic Flagellar Beating Patterns using Digital Holographic Microscopy

Precise tracking of the rapid and complex three-dimensional movement of eukaryotic flagella is important for understanding their roles in cellular motility, sensory functions, and resource acquisition. Yet, achieving accurate 3D kinematic reconstruction of flagellar beating patterns, particularly highly non-planar ones, remains challenging. Here we present holoV3C, a method based on Digital Holographic Microscopy (DHM) that allows precise, label-free 3D tracking of highly non-planar eukaryotic flagella with high temporal resolution. This algorithm leverages phase anomaly detection to provide a combination of high temporal and axial resolution, with 0.25 m for beating mouse sperm flagella and down to 53 nm for polystyrene particles, across large sampling volumes in a computationally efficient manner. Algorithmic validation is performed by tracking mouse sperm flagella over time, capturing approximately 600 points along a single flagellum to achieve high axial resolution. Furthermore, we apply holoV3C to reconstruct the highly non-planar beating dynamics of the 200-nm-diameter flagellum of the protist Reclinomonas americana with a temporal resolution of 200 frames per second. By enabling 3D tracking of non-planar eukaryotic flagella, holoV3C can yield important insights to advance our understanding of flagellar dynamics, opening new avenues in the study of microorganism motility and its ecological roles.

biophysics↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2024

Salmonids exhibit an acute behavioral response to heterothermal environments

Most fish species are ectothermic and rely on behavioral strategies to control their body temperature in heterothermal environments. Both thermotaxis and thermokinesis have been suggested as important underlying mechanisms. However, to what extent these behaviors allow fish to respond to rapid (timescales of minutes) and strong thermal disturbances, like those caused by anthropogenic water releases into natural freshwater systems, is poorly understood. Here, we quantify this response for a salmonid species with a novel laboratory approach coupled with image-based tracking. We exposed brown trout parr (Salmo trutta), acclimated to 12 {degrees}C, to rapidly forming cold- and warm-water interfaces with temperatures ranging from 4 to 20 {degrees}C. We found that fish actively avoided colder water ([≤]8 {degrees}C) through a rapid response that combined thermotaxis and thermokinesis. In contrast, fish did not avoid warmer water and frequently crossed interfaces having temperature contrasts of up to 8 {degrees}C. This study shows that brown trout parr swiftly deploy multiple behavioral strategies to minimize exposure to cold water and take advantage of warm water, illustrating their capability to cope with rapidly occurring thermal alterations.

biophysics↗

bioRxiv2022

A microfluidic platform for characterizing the structure and rheology of biofilm streamers

Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults. When ambient flow is present, this viscoelastic scaffold can take a streamlined shape, forming biofilm filaments suspended in flow, called streamers. Streamers significantly disrupt the fluid flow by causing rapid clogging and affect transport in aquatic environments. Despite their relevance, the structural and rheological characterization of biofilm streamers is still at an early stage. In this work, we present a microfluidic platform that allows the reproducible growth of biofilm streamers in controlled physico-chemical conditions and the characterization of their biochemical composition, morphology, and rheology in situ. We employed isolated micropillars as nucleation sites for the growth of single biofilm streamers under the continuous flow of a diluted bacterial suspension. By combining fluorescent staining of the EPS components and epifluorescence microscopy, we were able to characterize the biochemical composition and morphology of the streamers. Additionally, we optimized a protocol to perform hydrodynamic stress tests in situ, by inducing controlled variations of the fluid shear stress exerted on the streamers by the flow. Thus, the reproducibility of the formation process and the testing protocol make it possible to perform several consistent experimental replicates that provide statistically significant information. By allowing the systematic investigation of the role of biochemical composition on the structure and rheology of streamers, this platform will advance our understanding of biofilm formation.

biophysics↗