Session H63: Physics of Microbiomes and Microbial Communities II

Modeling the influence of metabolic trade-offs on microbiota diversity

Metagenomics has revealed huge diversity in nature, with thousands of microbial species coexisting in microbiota. However, classical resource-competition models predict that the number of species in steady coexistence cannot exceed the number of resources. To investigate the role of environmental conditioning and trade-offs in promoting diversity, we physically modeled the population dynamics of microbes that compete for resources in a chemostat. The model reproduces several notable features of natural ecosystems, including high diversity, keystone species, and characteristics of neutral theory, despite an underlying non-neutral competition for resources. Do metabolic trade-offs still promote diversity if nutrient supplies vary in time or if populations are spatially structured? The answer is yes in both cases. Serial dilutions preserve diversity, but with a surprising non-monotonic dependence on nutrient supply. Spatial structure selects one diverse solution, rather than a degenerate set. Importantly, we find that temporal or spatial variation permit diversity even when trade-offs are only approximate.   

The motility can drive spatial exclusion and promote coexistence in bacterial populations

Bacterial cells encountered in nature rarely live in isolation, they share and compete for space and nutrients with cohabitant microbial communities. They are also known to explore their surroundings and exhibit motility. Despite the ubiquity of motile phenotypes, the fundamental role of bacterial dispersal in the formation of diverse microbial communities and coexistence in spatial habitats have not been elucidated. In this study, we investigated the motility-driven competition for resources between two strains resulting in strong negative frequency-dependent-selection, i.e. each strain becomes fitter than the other when low in frequency. The observed lack of competitive exclusion is a direct consequence of the active segregation: few fast movers can forage and rapidly colonize in virgin territories of the habitat whereas few fast-grower cells can proliferate at the initial contact position. We showed that the coexistence breaks down when the initial contact area is as large as the habitat size or the nutrients become available homogeneously. Our findings demonstrate that motility can foster coexistence between bacterial populations displaying growth-dispersal trade-off in competition for nutrients and space.   

Single cell segmentation in microbiome imaging

Microbes in nature often live in communities with intricate spatial organization. Recent developments in molecular barcoding strategies and confocal spectral imaging have enabled spatially resolved and highly multiplexed phylogenetic measurements in these communities. However, quantitative analysis of these information-rich imaging dataset remains difficult, primarily due to bottlenecks in accurate single cell segmentation. Here, we present our approach to segment spectral images of environmental microbiome using information contained in the neighborhood of each voxel. We will discuss preliminary segmentation results and quantitative analysis of the spatial organization of microbial communities at the single cell level.   

Community coexistence and stability: insights from a mediator-explicit model of microbial interactions

Communities of interacting microbes impact our health and environment. For example, microbes in our gut microbiota can collectively (but not as individual species) confer resistance against pathogen colonization. How species form a community is thus an important question for maintaining or manipulating human-associated communities for improved health outcomes.

We formulate and experimentally constrain a model that explicitly incorporates chemical compounds (e.g. metabolites or waste-products) that can mediate microbial interactions. In a continuous-growth setting where resources are supplied (similar to a bioreactor or gut microbiota), our model highlights facilitation and self-restraint as interactions that contribute to coexistence. We show that when interactions are strong, coexistence and stability are determined primarily by the topology of facilitation and inhibition influences and not the strengths of influences. Importantly, we show that consumption of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.   

Examining Pairwise and Multi-Species Interactions in Larval Zebrafish

The microbial communities resident in animal intestines are composed of dozens to hundreds of species and play important roles in host health and disease. The determinants of microbial composition, which may include physical characteristics or biochemical interactions, remain largely unknown. Further, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are needed to explain community assembly. It is also unclear how spatial organization plays a role in determining the make up of these complex communities.
To address this, we consider commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a combination of dissection and plating assays and 3-dimensional live imaging, we demonstrate the construction of communities of 1 to 5 species and test whether outcomes from 2-species competitions contain enough information to predict the abundances in more complex communities. We also quantify changes in species’ spatial distributions induced by the presence of other species, which may explain correlations in their abundances.   

Depletion Zone Following the Spread of a Bacterial Colony

Many species of bacteria have developed strong abilities to spread on solid surfaces, via a mode of motility called swarming. This study focuses on the swarming, or colony expansion, of a human pathogen Pseudomonas aeruginosa, on an agar surface. We observed occurrence and spread of a central region where the thickness of the bacteria containing fluid film notably drops after the colony has spread to cover most of the agar plate. We call this region “depletion zone”, where bacterial density is lower than the outer region. We propose that occurrence of a depletion zone within an expanding bacterial colony is a de-wetting phenomenon. It is caused by a higher concentration of surface-active molecules, most likely surfactants, that have been secreted by bacteria and accumulated in the central region of the colony. These molecules infiltrate the agar underneath, reducing the surface tension of the agar surface in the central region, causing a radially outward flow to the extent that most of the bacteria laden fluids clear out. In essence, we offer a physical model to a phenomenon prone to misinterpretation by invoking chemotaxis or quorum sensing.
  

Emergence of order and structure in biofilms growing in fluid shear

In many situations bacteria aggregate to form biofilms: dense, surface-associated, three-dimensional structures populated by cells embedded in matrix. Biofilm architectures are sculpted by mechanical processes including cell growth, cell-cell interactions and external forces. Using single-cell live imaging in combination with simulations we characterize the cell-cell and cell-flow interactions that generate Vibrio cholerae biofilm morphologies. Our results demonstrate the importance of dynamics at multiple scales in determining the architectures of biofilms in flow.   

Role of confinement in growing bacterial colonies

Bacterial colonies are abundant in biological and artificial environments, and they are frequently subject to various types of confinement. Yet, the role of confinement, especially from the mechanical perspective, is still not clear. Here, using molecular dynamics simulations and continuum modelling, we demonstrate that the combination of confinement and growth gives rise to strongly anisotropic stress, resulting in the emergence of global nematic order.   

Mechanical interactions in growing yeast colonies

Microbial populations often assemble in dense populations in which proliferating individuals exert mechanical forces on the nearby cells. Here, we use yeast strains whose doubling times depend differently on temperature to show that physical interactions among cells affect the competition between different genotypes in growing yeast colonies. Our experiments demonstrate that these physical interactions have two related effects: they cause the prolonged survival of slower-growing strains at the actively-growing frontier of the colony and cause faster-growing strains to increase their frequency more slowly than expected in the absence of physical interactions. These effects also promote the survival of slower-growing strains and the maintenance of genetic diversity in colonies grown in time-varying environments. The three-dimensional structure of these colonies reflects the history of the environments experienced by the colonies, and the survival of strains depends on the geometry of the colony perimeter. A continuum model inspired by overdamped hydrodynamics reproduces the experiments and predicts that the strength of natural selection depends on the width of the actively growing layer at the colony frontier. We verify these predictions experimentally.   

Dynamic self-organization of microorganisms far from equilibrium

We report ultrafast laser-induced dynamic self-organization of quasi-2D confined solutions of e.coli, m.luteus, s.cerevisiae, and p.aeruginosa far from equilibrium. The laser beam has no interaction with the microorganisms; it only creates thermal gradient-induced convective flows in their growth medium. By precisely controlling these flows, we have been able to form aggregates with predetermined sizes and geometries, and manipulate the adaptive behavior of microorganisms under ‘noisy’ environments. We further demonstrate if and how these microorganisms can withstand harsh physical conditions. Last, we showcase separation of gram positive and gram negative bacteria from an initially homogenous mix.   

Effect of cellular and environmental conditions on bacterial collective oscillation

Collective oscillation in biology is ubiquitous and often arises from coupling between individual oscillators in phase space. Previously, we discovered a novel type of collective oscillatory motion in bacterial suspensions, which arises from weak synchronization and diffusive coupling between random trajectories but does not require individual oscillators. However, it is unclear what determines the intrinsic oscillation frequency in the system. Here we manipulate the cellular and environmental conditions to systematically to identify potential factors controlling the oscillation frequency. Our results will provide necessary information to fully understand the collective oscillatory motion and suggest new directions for active matter engineering.   

Emergent oscillations in dense adaptive cell populations

Dynamical quorum sensing is one of the simplest group behaviours in cell populations, where collective oscillations emerge via mutual signaling when cells reach beyond a critical density. While some examples have been extensively studied, their biological function remains confounding, sug- gesting a non-functional origin of collective oscillations. Here, by considering the response of cells to the extracellular signal and vice versa, we develop a quantitative theory for the phenomenon, and present a necessary condition for collective oscillations in a communicating population. We further show that a sufficient condition for oscillations is fulfilled by cells with adaptive signaling systems, which are ubiquitous in biology. These general results were elucidated from non-equilibrium thermodynamic principles, where stimulated energy release from active cells drives oscillations in the medium. The unexpected link between adaptation and oscillation is shown to underlie several known examples of dynamical quorum sensing, and as such may also be a source of inadvertent group behaviour in large populations of living organisms.