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We study the clustering of a model cyanobacterium \textit{Synechocystis} into microcolonies. The bacteria are allowed to diffuse onto surfaces of different hardness, and interact with the others by aggregation and detachment. We find that…
Microbial populations in the natural environment are likely to experience growth conditions very different from those of a typical laboratory xperiment. In particular, removal rates of biomass and substrate are unlikely to be balanced under…
Many systems in chemistry, biology, finance and social sciences present emerging features which are not easy to guess from the elementary interactions of their microscopic individual components. In the past, the macroscopic behavior of such…
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
Emergence of regular spatial patterns is a hallmark in living matter ranging from subcellular organelles to developing embryos and to ecosystems. Mechanisms for the formation of ordered spatial patterns in biology often require chemical…
Bacteria evolve in volatile environments and complex spatial structures. Migration, fluctuations and environmental variability therefore have a significant impact on the evolution of microbial populations. Here, we consider a class of…
Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods.…
In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single…
Cells and microorganisms employ dynamic shape changes to enable steering and avoidance for efficient spatial exploration and collective organization. In contrast, active colloids, their synthetic counterparts, currently lack similar…
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes.…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion creates new niches and facilitates such diversity. Nonetheless, it…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Understanding how growth induces form is a longstanding biological question. Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some others have shown the importance of the mechanical properties of bacterial walls…
To model the morphogenesis of rod-shaped bacterial micro-colony, several individual-based models have been proposed in the biophysical literature. When studying the shape of micro-colonies, most models present interaction forces such as…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…