arXiv subjects

Takuro Shimaya

Publications and source records attributed to Takuro Shimaya.

5 recordsLinked to original sources

arXiv2024

Smectic-like bundle formation of planktonic bacteria upon nutrient starvation

Bacteria aggregate through various intercellular interactions to build biofilms, but the effect of environmental changes thereupon remains largely unexplored. Here, by using an experimental device that overcomes past difficulties, we observed the collective response of Escherichia coli aggregates against dynamic changes in the growth condition. We discovered that nutrient starvation caused bacterial cells to arrange themselves into bundle-shaped clusters, developing a structure akin to that of smectic liquid crystal. The degree of the smectic-like bundle order was evaluated by a deep learning approach. Our experiments suggest that both the depletion attraction by extracellular polymeric substances and the growth arrest are essential for the bundle formation. Since these effects of nutrient starvation at the single-cell level are common to many bacterial species, bundle formation might also be common collective behavior that bacterial cells may exhibit under harsh environments.

physics.bio-ph↗

arXiv2024

Emergence of bacterial glass

Densely packed, motile bacteria can adopt collective states not seen in conventional, passive materials. These states remain in many ways mysterious, and their physical characterization can aid our understanding of natural bacterial colonies and biofilms as well as materials in general. Here, we overcome challenges associated with generating uniformly growing, large, quasi-two-dimensional bacterial assemblies by a membrane-based microfluidic device and report the emergence of glassy states in two-dimensional suspension of Escherichia coli. As the number density increases by cell growth, populations of motile bacteria transition to a glassy state, where cells are packed and unable to move. This takes place in two steps, the first one suppressing only the orientational modes and the second one vitrifying the motion completely. Characterizing each phase through statistical analyses and investigations of individual motion of bacteria, we find not only characteristic features of glass such as rapid slowdown, dynamic heterogeneity and cage effects, but also a few properties distinguished from those of thermal glass. These distinctive properties include the spontaneous formation of micro-domains of aligned cells with collective motion, the appearance of an unusual signal in the dynamic susceptibility, and the dynamic slowdown with a density dependence generally forbidden for thermal systems. Our results are expected to capture general characteristics of such active rod glass, which may serve as a physical mechanism underlying dense bacterial aggregates.

cond-mat.stat-mech↗

arXiv2022

Tilt-induced polar order and topological defects in growing bacterial populations

Rod-shaped bacteria, such as Escherichia coli, commonly live forming mounded colonies. They initially grow two-dimensionally on a surface and finally achieve three-dimensional growth. While it was recently reported that three-dimensional growth is promoted by topological defects of winding number $+1/2$ in populations of motile bacteria, how cellular alignment plays a role in non-motile cases is largely unknown. Here, we investigate the relevance of topological defects in colony formation processes of non-motile E. coli populations, and found that both $\pm 1/2$ topological defects contribute to the three-dimensional growth. Analyzing the cell flow in the bottom layer of the colony, we observe that $+1/2$ defects attract cells and $-1/2$ defects repel cells, in agreement with previous studies on motile cells, in the initial stage of the colony growth. However, later, cells gradually flow toward $-1/2$ defects as well, exhibiting a sharp contrast to the existing knowledge. By investigating three-dimensional cell orientations by confocal microscopy, we find strong vertical tilting of cells near the defects. Crucially, this leads to the emergence of a polar order in the otherwise nematic two-dimensional cell orientation. We extend the theory of active nematics by incorporating this polar order and the vertical tilting, which successfully explains the influx toward $-1/2$ defects in terms of a polarity-induced force. Our work reveals that three-dimensional cell orientations may result in drastic changes in properties of active nematics, especially those of topological defects, which may be generically relevant in active matter systems driven by cellular growth instead of self-propulsion.

cond-mat.soft↗

arXiv2021

Scale invariance of cell size fluctuations in starving bacteria

In stable environments, cell size fluctuations are thought to be governed by simple physical principles, as suggested by recent findings of scaling properties. Here, by developing a microfluidic device and using E. coli, we investigate the response of cell size fluctuations against starvation. By abruptly switching to non-nutritious medium, we find that the cell size distribution changes but satisfies scale invariance: the rescaled distribution is kept unchanged and determined by the growth condition before starvation. These findings are underpinned by a model based on cell growth and cell cycle. Further, we numerically determine the range of validity of the scale invariance over various characteristic times of the starvation process, and find the violation of the scale invariance for slow starvation. Our results, combined with theoretical arguments, suggest the relevance of the multifork replication, which helps retaining information of cell cycle states and may thus result in the scale invariance.

q-bio.CB↗

arXiv2019

Lane formation and critical coarsening in a model of bacterial competition

We study competition of two non-motile bacterial strains in a three-dimensional channel numerically, and analyze how their configuration evolves in space and time. We construct a lattice model that takes into account self-replication, mutation, and killing of bacteria. When mutation is not significant, the two strains segregate and form stripe patterns along the channel. The formed lanes are gradually rearranged, with increasing length scales in the two-dimensional cross-sectional plane. We characterize it in terms of coarsening and phase ordering in statistical physics. In particular, for the simple model without mutation and killing, we find logarithmically slow coarsening, which is characteristic of the two-dimensional voter model. With mutation and killing, we find a phase transition from a monopolistic phase, in which lanes are formed and coarsened until the system is eventually dominated by one of the two strains, to an equally mixed and disordered phase without lane structure. Critical behavior at the transition point is also studied and compared with the generalized voter class and the Ising class. These results are accounted for by continuum equations, obtained by applying a mean field approximation along the channel axis. Our findings indicate relevance of critical coarsening of two-dimensional systems in the problem of bacterial competition within anisotropic three-dimensional geometry.

q-bio.PE↗