Biology subjects

soyer, o. s.

Publications and source records attributed to soyer, o. s..

9 recordsLinked to original sources

bioRxiv2026

Emergent particle collection by cyanobacteria through gliding motility and filament buckling

Cyanobacterial macrostructures such as mats, aggregates, and stromatolites are observed in diverse habitats. These structures incorporate organic and inorganic matter and form microenvironments enabling biochemical transformations. Macrostructures are found to be associated with motile, filamentous cyanobacteria, but to what extent, and how filament motility can drive macrostructure formation is unclear. To address this question, we study macrostructure formation in a well-characterised freshwater cyanobacterial community dominated by the filamentous cyanobacterium Fluctiforma draycotensis. We discover an emergent particle collection behaviour that results in aggregate macrostructures composed of a solid core surrounded by an outer layer dominated by entangled cyanobacterial filaments. We show that the particle collection and subsequent aggregate formation result from the gliding motility of the cyanobacteria. Developing a novel 3D model of active filament movement, we analyse how filament morphology and mechanical properties affect movement dynamics, particle collection, and filament entanglement. We predict that particle collection requires filaments above a certain length and flexibility. We confirm the resulting prediction of length dependence of particle collection behavior with shortened filaments of F. draycotensis and naturally short Pseudanabaena sp. filaments. Together, our results show that filamentous cyanobacteria can use gliding motility to actively engineer their environments through particle collection and macrostructure formation, and that this ability is confined to a part of the filament phase space in terms of length and flexibility. These insights will allow better prediction of macrostructure formation in natural habitats and specific cyanobacterial species, and the engineering of cyanobacterial macrostructures for biotechnological applications.

biophysics↗

bioRxiv2026

Enrichment of convergent metabolic functions in microbial communities through imposed and emergent environmental niches

Microbial community composition is determined by numerous factors, including environmental filtering, biotic interactions, and stochasticity. Disentangling the relative contribution of these distinct processes is a fundamental problem for microbial ecology. Towards addressing it, here we used controlled experiments on replicate freshwater communities that vary individual factors, and used contig-based metagenomics methods to capture functional composition independently from uneven genome recovery across taxa. After repeated sub-culturing in minimal media lacking organic carbon but containing nitrate and vitamins, communities with distinct initial compositions consistently converged toward similar taxonomic structures and metabolic functions. These included oxygenic photosynthesis and nitrate metabolism, consistent with the imposed growth regime, and also showed reproducible enrichment of anoxygenic photosynthesis, vitamin biosynthesis and degradation pathways. These patterns indicate strong environmental filtering during assembly while also revealing a consistent role for emergent environments arising from microbial activity and metabolic interactions. To more directly test specific environmental drivers, we initiated replicate cultures from a single community and propagated them in the original medium and in variants lacking vitamins or both vitamins and nitrates. Only nitrate removal produced a distinct and statistically significant shift in both composition and function, with nitrate-free communities enriched for cyanobacterial nitrogen fixation and supporting metabolic functions in heterotrophs. Together, these results support a hierarchy of environmental filters determining community outcomes and provide a quantitative framework for predicting and steering community function through rational environmental design.

microbiology↗

bioRxiv2025

Co-substrate induced nonlinear flux switching at branch-points can explain overflow metabolism

Metabolic overflow is pervasive from microbes to tumors: as glucose consumption increases, cells switch from respiration to respirofermentation with excretion of organic acids or ethanol. How do cells regulate their fluxes to implement this switch? Using simplified models of a branch point, we found that three independent "built-in" mechanisms can each enable flux switching at a branch point: differential enzyme kinetics at the two branches, allosteric regulation of a branch enzyme, and asymmetric co-substrate (e.g. NADH/NAD+) usage across the two branch point re-actions. Notably, the co-substrate mechanism achieves several fold higher sensitivity, which can be further enhanced by the other two mechanisms. We then applied this theory to the yeast pyruvate branch point underpinning overflow metabolism by developing a compartmentalized model with or without NADH dynamics in cytoplasm and in mitochondria. Crucially, only models that included NADH dynamics recapitulated experimental data: (a) NADH level increases nonlinearly with increasing glucose influx; (b) this increase occurs at a lower glucose threshold than that for overflow; and (c) glucose threshold for overflow increases when NADH oxidase is expressed in mitochondria but not in cytosol. Thus, cosubstrates are not merely passive carriers of chemical groups; their asymmetric utilization at a branch point offers an intrinsic, network-embedded regulatory layer that synergises with enzyme-based control. Beyond explaining overflow metabolism in yeast, this theory offers a metabolic engineering strategy for re-routing flux through manipulating co-substrates.

systems biology↗

bioRxiv2023

Can Single Cell Respiration be Measured by Scanning Electrochemical Microscopy (SECM)?

Ultramicroelectrode (UME), or - equivalently - microelectrode, probes are increasingly used for single-cell measurements of cellular properties and processes, including physiological activity, such as metabolic fluxes and respiration rates. Major challenges for the sensitivity of such measurements include: (i) the relative magnitude of cellular and UME fluxes (manifested in the current); and (ii) issues around the stability of the UME response over time. To explore the extent to which these factors impact the precision of electrochemical cellular measurements, we undertake a systematic analysis of measurement conditions and experimental parameters for determining single cell respiration rates, via the oxygen consumption rate (OCR) at single HeLa cells. Using scanning electrochemical microscopy (SECM), with a platinum UME as the probe, we employ a self-referencing measurement protocol, rarely employed in SECM, whereby the UME is repeatedly approached from bulk solution to a cell, and a short pulse to oxygen reduction reaction (ORR) potentials is performed near the cell and in bulk solution. This approach enables the periodic tracking of the bulk UME response to which the near-cell response is repeatedly compared (referenced), and also ensures that the ORR near the cell is performed only briefly, minimizing the effect of the electrochemical process on the cell. SECM experiments are combined with a finite element method (FEM) modeling framework, to simulate oxygen diffusion and the UME response. Taking a realistic range of single cell OCR to be 1x10-18 to 1x10-16 mol s-1, results from the combination of FEM simulations and self-referencing SECM measurements show that these OCR values are at - or below - the present detection sensitivity of the technique. We provide a set of model-based suggestions for improving these measurements in the future, but highlight that extraordinary improvements in the stability and precision of SECM measurements will be required if single cell OCR measurements are to be realized. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/538172v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@14a6e59org.highwire.dtl.DTLVardef@192d44borg.highwire.dtl.DTLVardef@afb2caorg.highwire.dtl.DTLVardef@103131b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactions

Understanding how microbial communities maintain stable compositional diversity is key for predicting community function. Studies from species pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence coexistence, but the relevance of these factors in more complex communities is unclear. Model systems often lack multi-species complexity, thereby making it difficult to study community diversity temporally. Here we used a spatially-organised cyanobacterial enrichment community to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found that the community maintains relatively high diversity, with 17 co-existing bacterial species. Using short and long read shotgun metagenomics sequencing from different time point samples, we have reconstructed complete genomes. Genomic annotation of these species revealed complementary metabolic functions involving carbon breakdown and vitamin biosynthesis suggesting interactions amongst community members. Using isolated species, we provide experimental support for carbon provision through cyanobacterial slime and growth on the component substrates by representative members of the Proteobacteria and Actinobacteriota phyla. Additionally, we experimentally show vitamin provision and uptake between prototrophic and auxotrophic members. We also found genomic capability for (an)oxygenic photosynthesis and sulfur cycling in several species. We show consistent formation of oxygen gradients across photogranule structures, supporting niches that can sustain these specific metabolic functions. These findings indicate that spatial niche formation and metabolic interactions enable maintenance of community compositional stability and diversity. SIGNIFICANCE STATEMENTMicrobes exist as species-diverse communities in nature and understanding their stability is an open challenge in microbial ecology. We established and maintained a spatially-organised, photosynthetic microbial community from a freshwater reservoir through long-term culturing in laboratory medium. We found that this community maintained a taxonomically-diverse set of 17 bacterial species. Combining genomic and physiological assays, we characterised a novel filamentous cyanobacterium capable of carbohydrate-rich slime secretion supporting growth of other microbes. We predict inter-species vitamin exchanges and identify sulfur cycling and alternative types of photosynthesis that are likely to be favoured in oxygen-free zones identified within the spatial structures. Our findings indicate that metabolic interactions and spatial structures can enable stable microbial coexistence in natural ecosystems.

microbiology↗

bioRxiv2021

ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks

MotivationSpatial organisation plays an important role in the function of many biological systems, from cell fate specification in animal development to multi-step metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the in silico testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling. ResultsHere, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chastes existing capabilities. In particular, ChemChaste enables: (i) simulation of an arbitrary number of spatially diffusing chemicals; (ii) spatially heterogeneous chemical diffusion coefficients; and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chastes core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modelling bulk chemical reactions and their coupling with intracellular reactions. Availability and implementationChemChaste is a free, open-source C++ library, available via GitHub at https://github.com/OSS-Lab/ChemChaste under the BSD license. ContactO.Soyer@warwick.ac.uk or a.g.fletcher@sheffield.ac.uk

systems biology↗

bioRxiv2021

Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner.

The fluorescent benzothiazole Thioflavin T (ThT) has a high binding affinity to protein aggregates and is used as a marker for the study of this process, most commonly in the context of neurodegenerative disease research and diagnosis. Recently, this same dye was shown to indicate membrane potential in bacteria due to its cationic nature. This finding prompted a question whether ThT fluorescence is linked to the membrane potential in mammalian cells, which would be important for appropriate utilisation of ThT in research and diagnosis. Here, we show that ThT localises into the mitochondria of HeLa cells in a membrane-potential dependent manner. Specifically, ThT colocalised in cells with a well-established mitochondrial membrane-potential indicator Tetramethylrhodamine methyl ester (TMRM) and gave similar temporal responses as TMRM to treatment with a protonophore, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP). Additionally, we found that presence of ThT together with exposure to blue light ({lambda}=405 nm) exposure, but neither factor alone, caused depolarisation of mitochondrial membrane potential. This depolarisation effect was recapitulated by a mathematical model implementing the potential-dependent distribution of ThT and its light-dependent binding in mitochondria. These results show that ThT can act as a membrane potential dye in mammalian cells, when used at low concentrations and with low blue-light exposure, while it causes dissipation of the mitochondrial membrane potential at higher concentrations and in the presence of blue light excitation. This conclusion motivates a re-evaluation of ThTs use at micromolar range in live-cell analyses, while indicating that this dye can enable future studies on the potential connections between membrane potential dynamics and protein aggregation.

cell biology↗

bioRxiv2021

Multi-site enzymes as a mechanism for bistability in reaction networks

Here, we focus on a common class of enzymes that have multiple substrate-binding sites (multi-site enzymes), and analyse their capacity to generate bistable dynamics in the reaction systems that they are embedded in. Using mathematical techniques, we show that the inherent binding and catalysis reactions arising from multiple substrate-enzyme complexes creates a potential for bistable dynamics in a reaction system. We construct a generic model of an enzyme with n substrate binding sites and derive an analytical solution for the steady state concentration of all enzyme-substrate complexes. By studying these expressions, we obtain a mechanistic understanding for bistability and derive parameter combinations that guarantee bistability and show how changing specific enzyme kinetic parameters and enzyme levels can lead to bistability in reaction systems involving mjulti-site enzymes. Thus, the presented findings provide a biochemical and mathematical basis for predicting and engineering bistability in multi-site enzymes.

systems biology↗

bioRxiv2020

Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria

This paper reports on the use of scanning ion conductance microscopy (SICM) to locally map the ionic properties and charge environment of two live bacterial strains: the gramnegative Escherichia coli and the gram-positive Bacillus subtilis. SICM results find heterogeneities across the bacterial surface, and significant differences among the grampositive and -negative bacteria. The bioelectrical environment of the B. subtilis was found to be considerably more negatively charged compared to E. coli. SICM measurements, fitted to a simplified finite element method (FEM) model, revealed surface charge values of -80 to -140 mC m-2 for the gram-negative E. coli. The gram-positive B. subtilis show a much higher conductivity around the cell wall, and surface charge values between -350 and -450 mC m-2 were found using the same simplified model. SICM was also able to detect regions of high negative charge near B. subtilis, not detected in the topographical SICM response and attributed to extracellular polymeric substance. To further explore how the B. subtilis cell wall structure can influence the SICM current response, a more comprehensive FEM model, accounting for the physical properties of the gram-positive cell wall, was developed. The new model provides a more realistic description of the cell wall and allowed investigation of the relation between its key properties and SICM currents, building foundations to further investigate and improve understanding of the gram-positive cellular microenvironment. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

microbiology↗