Orkun S. Soyer

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.

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.

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.

Cyanobacteria are key contributors to biogeochemical cycles through photosynthesis and carbon fixation. In filamentous, multicellular cyanobacteria, these functions can be influenced through gliding motility, which enables filaments to localise in response to light and also form aggregates. Here, we use the aggregate-forming species Fluctiforma draycotensis to study gliding motility dynamics in detail. We find that filaments move in curved and straight trajectories interspersed with reorientation or reversal of direction. Most reversals take a few seconds, but some take substantially longer, resulting in a long-tailed distribution of stoppage times. Mean filament speeds range around a micron per second with a relatively uniform distribution against filament length, implying that all or a fixed proportion of cells in a filament contribute to movement. We implement a biophysical model that can recapitulate these findings. Model simulations show that for filaments to reverse quickly, cells in a filament must achieve high coordination of the direction of the forces that they generate. To seek experimental support for this prediction, we track individual cells in a filament. This reveals that cells’ translational movement is fully coupled with their rotation along the long axis of the filament, and that cellular movement remains coordinated throughout a reversal. For some filaments, especially longer ones, however, we also find that cellular coordination can be lost, and filaments can form buckles that can twist around themselves, resulting in plectonemes. The experimental findings and the biophysical model presented here will inform future studies of individual and collective filament movement.

1 Metabolic behaviours of cells, such as metabolic overflow, involve regulation of metabolic fluxes across different pathways. Two well-established concepts in flux regulation are transcriptional regulation, involving changes in enzyme levels through gene regulation, and allosteric regulation, involving changes in enzyme catalytic activities through metabolite binding. Here, we describe an additional mechanism arising through co-substrate usage around metabolic branch points. Using models of different branch-point motifs, we find that asymmetric usage of a given co-substrate by reactions at and around a branch point induces flux switching at that branch point as influx increases. This provides cells with an inherent ‘self-regulation’ embedded in the architecture of metabolic pathways. We then develop a specific model of the yeast pyruvate branch point involving NADH usage. Using this model, we show that co-substrate based flux switching can explain experimental data on yeast metabolic overflow at high glucose influx, as well as how altering NADH dynamics shifts the initiation point of metabolic overflow. We conclude that asymmetric co-substrate utilisation around branch points provides an inherent regulatory mechanism that could explain observed relations between cosubstrate dynamics and metabolic behaviours. Additionally, the presented theory and its extensions will provide a model-based approach to manipulating co-substrate dynamics for metabolic engineering.

Cyanobacteria are key contributors to biogeochemical cycles through photosynthesis and carbon fixation. In filamentous, multicellular cyanobacteria these functions can be influenced through gliding motility, which enables filaments to localise in response to light and also form aggregates. Here, we use the aggregate forming species Fluctiforma draycotensis to study gliding motility dynamics in detail. We find that filaments move in curved and straight trajectories interspersed with re-orientation or reversal of direction. Most reversals take few seconds but some take substantially longer, resulting in a long-tailed distribution of stoppage times. Mean filament speeds range around a micron per second with a relatively uniform distribution against filament length, implying that all or fixed proportion of cells in a filament contribute to movement. We implement a biophysical model that can recapitulate these findings. Model simulations show that for filaments to reverse quickly, cells in a filament must achieve high coordination of the direction of the forces that they generate. To seek experimental support of this prediction, we track individual cells in a filament. This reveals that cells’ translational movement is fully coupled with their rotation along the long-axis of the filament, and that cellular movement remains coordinated throughout a reversal. For some filaments, especially longer ones, however, we also find that cellular coordination can be lost, and filaments can form buckles that can twist around themselves, resulting in plectonemes. The experimental findings and the biophysical model presented here will inform future studies of individual and collective filament movement.

This work presents an experimental platform combining scanning ion conductance microscopy (SICM) with confocal laser scanning microscopy (CLSM), using intra- and extracellular pH indicator dyes to study the impact of acid delivery on individual HeLa cells within a population. The proton gradient generated by the SICM delivery is highly confined by the action of the media buffer, making the challenge local. Temporal and spatial aspects of the delivery are modeled by simulations, allowing for pH gradients across individual cells, even within a group, to be calculated. We find a strong dependency between the intracellular pH and the extracellular pH gradient imposed by local acid delivery. Postdelivery intracellular pH recovery depends on the extent of the acid challenge, with cells exposed to lower pH not returning to basal intracellular pH values after the extracellular pH recovers. This is a unique method for concentration-gradient challenge studies of cell populations that will have broad applications in cell biology. SICM can be used to deliver different chemicals and enables a wide range of local conditions to be applied across a cell population, for which the effects can be investigated at the single-cell level.

Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via metatranscriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.

Many species of soil fungi grow in the form of branched networks that enable long-range communication and mass flow of nutrient. These networks play important roles in the soil ecosystem as a major decomposer of organic materials. While there have been investigations on the branching of the fungal networks, their long-term growth dynamics in space and time is still not very well understood. In this study, we monitor the spatio-temporal growth dynamics of the plant-promoting filamentous fungus Serendipita indica for several days in a controlled environment within a microfluidic chamber. We find that S. indica cells display synchronized growth oscillations with the onset of sporulation and at a period of 3 h. Quantifying this experimental synchronization of oscillatory dynamics, we show that the synchronization can be recapitulated by the nearest neighbour Kuramoto model with a millimetre-scale cell–cell coupling. The microfluidic set-up presented in this work may aid the future characterization of the molecular mechanisms of the cell–cell communication, which could lead to biophysical approaches for controlling fungi growth and reproductive sporulation in soil and plant health management.