Biology subjects

Ursell, T.

Publications and source records attributed to Ursell, T..

4 recordsLinked to original sources

bioRxiv2021

Bacterial bioconvection confers context-dependent growth benefits and is robust under varying metabolic and genetic conditions

Microbial communities often respond to environmental cues by adopting collective behaviors--like biofilms or swarming--that benefit the population. Bioconvection is a distinct and robust collective behavior wherein microbes locally gather into dense groups and subsequently plume downward through fluid environments, driving flow and mixing on scales thousands of times larger than an individual cell. Though bioconvection was observed more than 100 years ago, effects of differing physical and chemical inputs, as well as its potential selective advantages to different species of microbes, remain largely unexplored. In the canonical microbial bioconvector Bacillus subtilis, density inversions that drive this flow are setup by vertically oriented oxygen gradients that originate from an air-liquid interface. In this work, we develop Escherichia coli as a complementary model organism for the study of bioconvection. We show that for E. coli and B. subtilis, bioconvection confers a context-dependent growth benefit with clear genetic correlates to motility and chemotaxis. We found that fluid depth, cell concentration, and carbon availability have complimentary effects on the emergence and timing of bioconvective patterns, and whereas oxygen gradients are required for B. subtilis bioconvection, we found that E. coli deficient in aerotaxis ({Delta}aer) or energy-taxis ({Delta}tsr) still bioconvect, as do cultures that lack an air-liquid interface. Thus, in two distantly related microbes, bioconvection confers context-dependent growth benefits, and E. coli bioconvection is robustly elicited by multiple types of chemotaxis. These results greatly expand the set of physical and metabolic conditions in which this striking collective behavior can be expected and demonstrate its potential to be a generic force for behavioral selection across ecological contexts.

biophysics↗

bioRxiv2020

Competitive ecosystems are robustly stabilized by structured environments

Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetic mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that physical structure stabilizes large competitive ecological networks, even with significant differences in the strength of competitive interactions between species. We show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the generic stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility. AUTHOR SUMMARYNatural environments often have many species competing for the same resources and frequently one species will out-compete others. This poses the fundamental question of how a diverse array of species can coexist in a resource limited environment. Among other mechanisms, previous studies examined how interactions between species - like cooperation or predation - could lead to stable biodiversity. In this work we looked at this question from a different angle: we used computational models to examine the role that the environment itself might play in stabilizing competing species. We modeled how species arrange themselves in space when the environment contains objects that alter the interfaces along which competing species meet. We found that these structured environments stabilize species coexistence, across a range of density of those objects and in a way that was robust to differing strengths of interspecies competition. Thus, in addition to biological factors, our work presents a generic mechanism by which the environment itself can influence ecological outcomes and biodiversity.

ecology↗

bioRxiv2019

Rapid and directed group motility in B. subtilis does not rely on individual motility or chemotaxis

Microbes routinely face the challenge of acquiring territory and resources on wet surfaces. Cells move in large groups inside thin, surface-bound water layers, often achieving speeds of 30 {micro}m/s within this environment, where viscous forces dominate over inertial forces (low Reynolds number). The canonical Gram-positive bacterium Bacillus subtilis is a model organism for the study of collective migration over surfaces with groups exhibiting motility on length scales three orders of magnitude larger than themselves within a few doubling times. Genetic and chemical studies clearly show that the secretion of endogenous surfactants and availability of free surface water are required for this fast group motility. Here we show that: (i) water availability is a sensitive control parameter modulating an abiotic jamming-like transition that determines whether the group remains fluidized and therefore collectively motile, (ii) groups self-organize into discrete layers as they travel, (iii) group motility does not require proliferation, rather groups are pulled from the front, and (iv) flow within expanding groups is capable of moving material from the parent colony into the expanding tip of a cellular dendrite with implications for expansion into regions of varying nutrient content. Together, these findings illuminate the physical structure of surface-motile groups and demonstrate that physical properties, like cellular packing fraction and flow, regulate motion from the scale of individual cells up to length scales of centimeters.

biophysics↗

bioRxiv2018

Structured environments fundamentally alter dynamics and stability of ecological communities

The dynamics and stability of ecological communities are intimately linked with the specific interactions - like cooperation or predation - between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Though natural communities existing in physically unstructured environments is rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. To address this gap, we used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics. We find that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local pinning of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades. These results indicate that the stability of microbial communities strongly depends on the structural environment in which they reside. Therefore, a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.\n\nSIGNIFICANCEMany microbial communities of ecological and medical importance reside in complex and heterogeneous environments, such as soils or intestinal tracts. While many studies consider the effects of flow or chemical gradients in structuring these communities, how the physical structure of the environment shapes community dynamics and outcomes remains poorly understood. Using simulations of competitive microbial communities, we show that stability and dynamics qualitatively shift in environments with complex surface structures compared to open isotropic environments. Therefore, in addition to biochemical interactions between species, our work suggests that the physical structure of the environment is an equally important determinant of dynamics and stability in microbial communities, in a manner dependent on the specific patterns of interactions within that community.

ecology↗