Biology subjects

Amchin, D. B.

Publications and source records attributed to Amchin, D. B..

2 recordsLinked to original sources

bioRxiv2022

Microbial mutualism generates multistable and oscillatory growth dynamics

Microbial communities typically comprise multiple different species with an intricate network of interactions, ranging from competitive to cooperative, between them. How does the nature of these inter-species interactions impact overall community behavior? While the influence of purely competitive interactions is well-studied, the opposite case of mutualistic interactions--which are also prevalent in many naturally-occurring communities--is poorly understood. Here, we address this gap in knowledge by mathematically modeling a well-mixed two-species community of aerobes and anaerobes having mutualistic metabolic interactions between them. Despite the simplicity of the model, we find that it reproduces three characteristic experimental findings. In particular, in response to changes in the fluxes of exogenously-supplied carbon and oxygen, the community adopts two distinct stable states with differing fractions of aerobes and anaerobes. These states are bistable, capable of arising under identical environmental conditions; transitions between the two are therefore history-dependent and can give rise to oscillations in the bacterial and chemical concentrations. Moreover, using the model, we establish biophysical principles describing how oxygen depletion and nutrient sharing jointly dictate the characteristics of the different states as well as the transitions between them. Altogether, this work thus helps disentangle and highlight the pivotal role of mutualism in governing the overall stability and functioning of microbial communities. Moreover, our model provides a foundation for future studies of more complex communities that play important roles in agriculture, environment, industry, and medicine.

systems biology↗

bioRxiv2020

Chemotactic Migration of Bacteria in Porous Media

Chemotactic migration of bacteria--their ability to direct multicellular motion along chemical gradients--is central to processes in agriculture, the environment, and medicine. However, studies are typically performed in homogeneous media, despite the fact that many bacteria inhabit heterogeneous porous media such as soils, sediments, and biological gels. Here, we directly visualize the migration of Escherichia coli populations in 3D porous media. We find that pore-scale confinement is a strong regulator of chemotactic migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the dynamics and morphology of the migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous environments. Statement of SignificanceTypical studies of bacterial motility focus on cells in homogeneous media; however, many bacteria inhabit tight porous media such as soils, sediments, and biological gels. This paper demonstrates how confinement in a porous medium fundamentally alters the chemotactic migration of Escherichia coli. We find that cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the overall dynamics and morphology of a migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. This work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous porous environments.

biophysics↗