Biology subjects

Stocker, R.

Publications and source records attributed to Stocker, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Microcalorimetry reveals bacterial motility as an expensive trait during starvation

Quantifying the energetic costs of cellular traits is important to understand their evolutionary constraints and ecological function. However, direct measurements of energy expenditure of distinct traits are rare. Here, we present direct measurements of the power dissipation due to bacterial flagellar motility using microcalorimetry, based on measuring the power dissipation of a motile population and a non-motile mutant. For the single-flagellated marine bacterium \textit{Vibrio coralliilyticus}, we determined the power dissipated by motility in cultures to be 0.91 W/mL/OD. Per swimming cell this amounts to 2.0E-15 W, or a turnover of 2.5E4 ATP molecules per second. The power dissipated for motility equals 35 % of total metabolism during starvation, indicating this is likely the most expensive cellular trait during starvation. The dissipation for motility is in good agreement with that predicted using resistive force theory, indicating that any thermodynamic inefficiencies upstream of the flagellar motor, such as metabolic inefficiencies, are small. We further show that the multiflagellated bacterium Escherichia coli dissipates 0.70 W/mL/OD when in motility buffer, comparable to marine bacteria despite the much lower swimming speed, and hence indicating lower efficiency of swimming. Finally, we show that the energy spent by Vibrio coralliilyticus on motility can have major consequences on their survival under starvation, causing a 40 % reduction in survival after 3 weeks of starvation of a motile compared to non-motile mutant. These results reveal the large costs involved in an individual trait that shapes microbial life in heterogeneous environments.

biophysics↗

bioRxiv2026

Widespread attraction of marine bacteria to the macroalgae-derived polysaccharide fucoidan

Fucoidan is the second most abundant polysaccharide in brown macroalgae, contributing up to 50% of the dissolved organic matter released daily from these algae into the ocean, substantially influencing the marine carbon cycle. Due to its complex chemical structure, fucoidan is highly resistant to microbial degradation and accumulates on the surface of macroalgae, where it contributes to regulating their microbiome. Here, we used a range of microfluidic assays to quantify the chemotactic and physiological responses of marine bacteria to fucoidan. Our results reveal that all the strains tested (14 out of 14) are attracted to fucoidan produced by two different species of brown macroalgae. Attraction occurred only at high fucoidan concentrations (0.1 to 1 mg/mL), such as those expected in the immediate vicinity of algal surfaces, whereas low concentrations elicited no response or modest chemorepulsion. Although fucoidan did not support bacterial growth under our experimental conditions, it did not impair the utilization of other carbon sources. Together, these findings suggest that fucoidan gradients can act as chemical cues guiding marine bacteria toward the nutrient-rich microenvironment of macroalgal surfaces, pointing to a potential ecological role of fucoidan in shaping macroalgal microbiota, bacterial behavior, and ultimately carbon cycling in the ocean.

microbiology↗

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↗

bioRxiv2026

Chromatin- and actin-mediated mitochondrial streaming leads to patterning of mitochondrial distribution in oocytes

Mitochondria are highly dynamic organelles, and their spatiotemporal organization is strictly regulated. While it has long been recognized that mitochondria in ovulated oocytes are concentrated in the spindle hemisphere, the mechanism remains unknown. Through live cell imaging and modelling, we have discovered three features of mitochondrial dynamics in the ooplasm: (i) actin-driven cortical mitochondrial streaming is delimited to the boundary of the polarized spindle hemisphere; (ii) distinct from bulk cytoplasmic streaming, mitochondrial streaming occurs bilaterally and perpendicular to the long axis of the MII spindle and, (iii) mitochondria movement from the cytoplasm to the polarized cortex is via MYO19-mediated chromatin-associated channel around the spindle midzone. This directionality in mitochondrial streaming patterns the ooplasm of the spindle cortex, creating mitochondria-rich and mitochondria-poor regions. These features explain the establishment of the polar gradient of mitochondria in MII oocytes and may provide new insight into the spatiotemporal organization of mitochondria in cells.

cell biology↗

bioRxiv2026

Opposing range-dependent interactions create complex spatial patterns of antibiotic tolerance in multispecies biofilms

Many microbial communities form multispecies biofilms where cells interact through diffusible molecules. In these biofilms, multiple interactions, often with opposing effects, occur simultaneously, yet we lack quantitative frameworks to predict how they combine to shape community functions. Here, we hypothesized that complex spatial patterns can emerge when opposing interactions have distinct spatial ranges. To test this, we studied how two Pseudomonas aeruginosa exoproducts, HQNO and rhamnolipids, jointly modulate Staphylococcus aureus antibiotic tolerance by respectively increasing and decreasing it. Using microfluidics-based imaging, we quantified spatial-tolerance patterns at single-cell resolution and found that tolerance indeed shows a complex spatial pattern: S. aureus cells survived treatment only at intermediate distances from P. aeruginosa, while cells closer or farther away did not. Combining experiments and modelling, we showed that this remarkable pattern emerges because rhamnolipids have a stronger but short-ranged effect, while HQNO has a weaker but longer-ranged effect. We found that spatial arrangement affects overall tolerance by shifting the balance between the two opposing interactions. Finally, using bioprinting, we confirmed that HQNO and rhamnolipids modulate tolerance in highly mixed biofilms. In more segregated biofilms, spatial arrangement still strongly modulated tolerance, but independently of these compounds, suggesting additional interactions. Together, our results show that spatial-tolerance patterns emerge from the combined effect of opposing range-dependent interactions and cannot be predicted from either alone. By predicting how opposing interactions jointly determine community properties, our framework provides a foundation for understanding and ultimately engineering microbiome functions.

systems biology↗

bioRxiv2026

Heritable diel energy reserves enhance diatom growth

Diatoms are important drivers of marine primary production and biogeochemistry1-4. Compared to other phytoplankton groups, diatoms divide more asynchronously (i.e., divisions occur in a manner that is less aligned with the diel cycle) under non-limiting conditions, resulting in divisions occurring during both day and night5-16. However, the mechanisms and rates of asynchronous division have remained elusive. Here, using microfluidics-based time-resolved cell tracking, we measure the growth dynamics of individual cells of the diatom Thalassiosira pseudonana and show that cells growing mostly during the dark phase achieve rapid generation times (8 hours), dividing as fast as cells growing fully in light. We found that this remarkable ability of rapid growth in the dark is a consequence of the light history of both the cell and its parent cell, as light history controls the amount of photosynthetic energy the cell has stored in the form of the polysaccharide chrysolaminarin when entering the night. Furthermore, a mathematical model of this mechanism yields an up to 14% increase in the daily asynchronous population growth rate compared to growth without diel energy reserves when nutrients are non-limiting. This results in an up to 17-fold predicted increase in cell abundance over a typical 10-day diatom bloom, the maximal growth advantage of heritable chrysolaminarin during exponential phases of growth. By directly demonstrating and quantifying the benefit of chrysolaminarin under different diel conditions, this work provides a mechanistic understanding of how heritable diel energy reserves contribute to the rapid growth of diatom populations in the ocean. Beyond the specific discovery of the role of heritable energy reserves, we anticipate that our experimental approach can be broadly utilized in phytoplankton research by providing a blueprint to study phytoplankton physiology and ecology at the single-cell level, revealing novel mechanisms normally obscured in bulk growth assays.

microbiology↗

bioRxiv2025

Breaching the diatom frustule: Alteromonas macleodii triggers protoplast emergence and programmed necrotic-like cell death in the oceanic diatom Thalassiosira rotula

Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. While the role of bacteria in recycling organic matter is well established, their potential to actively induce algal death remains poorly understood. Here we examined the interaction between the bloom-forming diatom Thalassiosira rotula and a known member of its microbiome, Alteromonas macleodii. Microscopy revealed that A. macleodii breached the diatoms silica frustule, inducing >95% of diatom cells to emerge from their shells within 72 hours, exposing protoplasts to lysis and exploitation. This algicidal interaction is species-specific and contact-dependent. Dual transcriptomics revealed programmed necrotic-like cell death underpins T. rotulas terminal morphological change, alongside bacterial upregulation of motility, chemotaxis, and coordinated metabolism to exploit the diatom host. These findings indicate the presence of a programmed necrosis-like pathway in diatoms, akin to that known in mammals. They also reveal a novel algicidal strategy, recasting A. macleodii as a specialized antagonist capable of influencing bloom termination and removing the ballast provided by diatom frustules, thereby reshaping carbon cycling in the ocean.

microbiology↗

bioRxiv2025

GUARDIANS OF THE CELL: COCCOSPHERE PREVENTS OPPORTUNISTIC BACTERIA ATTACK IN HEAVY CALCIFYING COCCOLITHOPHORE

Coccolithophores are responsible for 40-60% of marine calcium carbonate production. This occurs through the biomineralization of extracellular calcium carbonate plates that encase the cell in a structure called the coccosphere. Despite its central role in ocean biogeochemistry, the function of coccolithophore calcification remains unresolved. One hypothesis is that the coccosphere acts as a physical shield, deterring predators and microbes. While its protective role has been investigated against grazers and viruses, its function in bacterial defense remains untested. Here, we investigate the interaction between heavily calcified Coccolithus braarudii and the bacterial pathogen Phaeobacter inhibens, known for its lethal Jekyll and Hyde relationship with the bloom-forming Gephyrocapsa huxleyi. We find that in C. braarudii, no P. inhibens pathogenicity is observed--unless the algae are decalcified. Upon decalcification, the relationship with P. inhibens becomes pathogenic, leading to algal cell death. Mortality of decalcified cells is specific to interactions with P. inhibens and is attachment-mediated: no toxicity is observed when cells are exposed to P. inhibens supernatant or to growth-inhibiting concentrations of indole-3-acetic acid-- identified in the P. inhibens-G. huxleyi system. Attachment requirement is further supported by scanning electron microscopy, which reveals extensive bacterial colonization on decalcified but not on calcified C. braarudii with P. inhibens. These findings provide the first experimental evidence that the coccosphere acts as a physical barrier against bacterial attack, underscoring its defensive role in coccolithophores.

microbiology↗

bioRxiv2025

Synergy in viral-bacterial coinfection expedites algal bloom demise

Algal blooms are hotspots for diverse microbial interactions affecting bloom dynamics. Viral infections often regulate the demise of these blooms, recycling >25% of oceanic fixed carbon. Although these blooms collapse synchronously, only 10-30% of algal cells show active viral infection, suggesting additional mortality agents. Using microbial communities from natural coccolithophore blooms, we discovered that bacteria significantly enhanced virus-mediated algal mortality. We quantified this interaction using two novel metrics: the Synergy Index (SI) measuring viral-bacterial interaction strength, and the Benefit Index (BI) assessing changes in bacterial fitness. We identified Alteromonas bacteria as drivers of viral-bacterial coinfection with consistently high SI and BI. In natural communities, Alteromonas exhibited chemoattraction towards infected algal cells, leading to their enrichment in bloom demise particles. This viral-bacterial synergy represents a previously unrecognized mortality agent controlling bloom termination, modulating the balance between the carbon-recycling viral shunt and the carbon-exporting viral shuttle pathways, likely influencing global carbon cycling.

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↗

bioRxiv2025

When less is not more: Limits to the evolution of metabolic dependence in spatially structured microbial communities

In microbial communities, evolutionary processes can lead to loss of biosynthetic pathways, creating metabolic dependencies. The Black Queen Hypothesis suggests that such gene loss can confer a fitness advantage by reducing metabolic burden. However, how these dependencies evolve at the level of individual cells in spatially structured communities remains poorly understood. We used a combination of microfluidic single-cell imaging and mathematical modeling to examine the early fate of auxotrophic mutants within E. coli populations. We found that without external amino acids, auxotroph growth is strongly constrained by low amino acid leakage from wildtype neighbors, and further reduced when they form local clusters that drain this limited amino acid pool. A growth advantage was only observed when amino acids were added or when leakage from wildtypes exceeded a threshold. Together, our results reveal insights into determinants of mutant invasion fitness and the trade-offs between reducing metabolic costs and maintaining metabolic autonomy. HighlightsO_LISingle-cell imaging reveals how auxotrophs fare in spatially structured populations C_LIO_LIAuxotrophs grow slowly due to low amino acid leakage from wildtype neighbors C_LIO_LIMutant clustering intensifies local amino acid depletion and reduces auxotroph growth C_LIO_LIModel identifies leakage threshold required for auxotroph invasion from rare C_LI

evolutionary biology↗

bioRxiv2025

Risk-reward trade-off in motility endurance generates dichotomy in search strategies among copiotrophic marine bacteria

Coptiotrophic marine bacteria contribute significantly to carbon storage in the ocean by remineralizing organic carbon present in nutrient-rich hotspots amidst oligotrophic waters. Motility is both highly beneficial and costly in such environments, presenting copiotrophs with a risk-reward trade-off in search behavior. Here we studied the motility endurance of 26 marine isolates using video microscopy and cell tracking over two days of carbon starvation. We found that this cost-benefit trade-off results in a distinct dichotomy among marine bacteria: risk-averse copiotrophs ceased motility within hours ( limostatic), whereas risk-prone copiotrophs converted 10% of their biomass per day into energy to retain motility for the two days of observation ( limokinetic). We identified a genomic component of this dichotomy, sufficiently robust to predict the response of additional species with 83% accuracy and the prevalence of both strategies in the ocean. This dichotomy can facilitate the incorporation of the bacterial contribution in ocean carbon cycle models.

microbiology↗

bioRxiv2025

Extracellular polymeric substance degradation shapes microbial community diversity

Competition for and exchange of nutrients play crucial roles in shaping microbial community function and dynamics. Although cross-feeding of small metabolites is known to drive carbon exchange among species, the importance of self-produced extracellular polymeric substances (EPS)-- which include proteins, polysaccharides, DNA, and humic-like substances-- remains less understood. Utilizing chitin-degrading microbial isolates and natural seawater communities, we found that 4-7% of the carbon from chitin degradation is converted into EPS, accounting for nearly a quarter of the exuded carbon. Different sources of EPS were found to select for distinct microbial communities. Through enzyme assays and untargeted metabolomics, we demonstrated that secreted enzymes degrade EPS in multiple steps that influence community diversity: larger oligomers are initially utilized by specialized degraders, while the subsequent breakdown into smaller oligomers, monosaccharides, and amino acids supports non-specialized consumers. These findings highlight the role of EPS as a significant carbon source exchanged between microbes, fueling metabolically diverse populations and enriching our understanding of carbon-mediated microbial interactions.

microbiology↗

bioRxiv2025

Growth in Low Carbon Conditions Reveals Amino-Acid-Coupled Iron Uptake

Bacteria in nature encounter substrates at widely varying concentrations, yet studies of bacterial physiology have focused more on nutrient type than concentration, partly due to challenges in maintaining low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD) to culture bacteria under precisely controlled nutrient conditions, including very low concentrations, in a manner suitable for proteomic analysis. Using the MCCD, we cultured Escherichia coli with a mixture of amino acids as the sole carbon source at three concentrations supporting growth rates spanning a fivefold range. Surprisingly, at the lowest concentration, cells exhibited proteomic signatures of iron shortage despite equal iron levels across conditions. We observed the uptake of labeled iron-histidine and iron-cysteine complexes, indicating that amino acids facilitated iron acquisition and that amino-acid-bound iron is bioavailable to E. coli. These findings reveal a previously unknown mechanism of bacterial iron acquisition that emerged under the flow imposed by the MCCD, which likely diluted the siderophore pool and reduced their efficacy. This work highlights the importance of studying bacterial physiology under low nutrient concentrations and demonstrates how physical conditions, such as flow, shape microbial nutrient acquisition strategies.

microbiology↗

bioRxiv2025

Bacteria induce an amoeboid phase in coccolithophores that persists after bloom collapse

Coccolithophores, who contribute approximately 1-10% of phytoplankton biomass, are crucial players in the oceans biogeochemical cycles. Significant contributions come from bloom-forming species including Gephyrocapsa huxleyi (formerly Emiliania huxleyi), which has served as a model system for investigating algal-bacterial and agal-viral interactions as well as algal fitness responses to environmental changes. Coccolithophores follow a biphasic lifecycle, existing as motile haploid and non-motile diploid phases. Here we characterize a third, amoeboid phase, using a combination of light, electron and phase amplitude modulation (PAM) microscopy. Using time-resolved imaging we captured the rapid morphological transition from a spherical haploid to an elongated motile amoeboid cell. Cell tracking revealed slower and more directional swimming compared to haploid cells. Amoeboid metamorphosis was triggered by exposure to bacteria, including strains isolated from G. huxleyi blooms and known G. huxleyi pathogens, but not by a range of classical phytoplankton stressors, including viral infection and oxidative stress. Further, the sub-population of haploids which switched to the amoeboid phase persisted past the rapid crash of the haploid population. This amoeboid phase was only observed in the primary bloom-forming coccolithophore species G. huxleyi and Geopharycapsa oceanica in stationary phase when exposed to high bacterial concentrations, typical of late-stage algal bloom events. Photophysiology of amoeboid cells was confirmed to be unaltered via PAM microscopy, indicating these cells are metabolically active. These findings highlight a previously uncharacterized morphotype in this important phytoplankton species and suggest that the amoeboid phase could be a bacteria-resistant morphotype following algal bloom collapse.

microbiology↗

bioRxiv2024

Antagonism as a foraging strategy in microbial communities

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients through lysing neighboring cells via contact-dependent antagonism. Using single-cell live imaging and isotopic markers, we found that during starvation the type VI secretion system, which transfers toxins into neighboring cells, increases growth by enabling the uptake of nutrients from lysing cells. In a spatially structured environment, the gradual lysis of just a few target cells allows for the growth of a new antagonist cell. Genomic adaptations in antagonists, characterized by a reduced metabolic gene repertoire, and the prevalence of the type VI secretion system in natural environments, such as global oceans and soils, suggest that bacterial antagonism has the potential to substantially contribute to nutrient transfer within microbial communities across various ecosystems.

microbiology↗

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↗