Papers

Bacteria solve the problem of crowding by moving slowly

Nature Physics

Movie by Oliver Meacock

Bacteria typically live attached to surfaces in dense collectives containing billions of cells. To expand into new territory, many different strains use tiny grappling hooks called pili to pull themselves along. Here we show that a fast-moving strain (engineered to express more pili) are overtaken and outcompeted by the slower-moving wild-type strain at high cell densities. 

Using theory developed to study liquid crystals, we demonstrate that this effect is mediated by the physics of topological defects, points where cells with different orientations meet one another. We show that the physics of active liquid crystals can exert a fundamental limit on the speed of motility within crowds of bacteria. 

Cells that exceed this critical threshold are unstable to verticalization upon collision, causing fast-moving cells to become trapped within the interior of colonies where nutrients are scarce. However, bacteria that move more slowly as individuals are able to avoid this fate and therefore can outcompete faster moving cells.

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Chain formation can enhance the vertical migration of phytoplankton through turbulence

Science Advances

Many species of motile phytoplankton can actively form long multicellular chains by remaining attached to one another after cell division. 

While chains swim more rapidly than single cells of the same species, chain formation also markedly reduces phytoplankton’s ability to maintain their bearing. This suggests that turbulence, which acts to randomise swimming direction, could sharply attenuate a chain’s ability to migrate between well-lit surface waters during the day and deeper nutrient-rich waters at night. 

Here, we use numerical models to investigate how chain formation affects the migration of phytoplankton through a turbulent water column. 

Unexpectedly, we find that the elongated shape of chains helps them travel through weak to moderate turbulence much more effectively than single cells, and isolate the physical processes that confer chains this ability. 

Our findings provide a new mechanistic understanding of how turbulence can select for phytoplankton with elongated morphologies and may help explain why turbulence triggers chain formation.

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A model of strongly biased chemotaxis reveals the trade-offs of different bacterial migration strategies

Mathematical Medicine and Biology

Recent experiments from our group demonstrated swimming and biofilm bacteria employ fundamentally different strategies to generate chemotaxis: swimming cells typically suppress reorientations when moving up a chemoattractant gradient, whereas biofilm cells increase reorientations when moving down a chemoattractant gradient. The reason for this difference remains unknown. 

Here we develop a mathematical framework to understand how these different chemotactic strategies affect the distribution of cells at the population level. 

Current continuum models typically assume a weak bias in the reorientation rate and are not able to distinguish between these two strategies, so we derive a model for strong chemotaxis that resolves how both the drift and diffusive components depend on the underlying chemotactic strategy. 

This new model reveals that the strategy employed by swimming cells yields a larger chemotactic drift, but the strategy used by biofilm cells allows them to more tightly aggregate where the chemoattractant is most abundant. 

This new modelling framework provides new quantitative insights into how the different chemical landscapes experienced by swimming and biofilm cells each selects for a different way to generate chemotaxis.

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Microbial competition in porous environments can select against rapid biofilm growth

Proceedings of the National Academy of Sciences, USA

Approximately 97% of bacteria on Earth live in porous environments like soil, sediments, and aquifers where they form surface attached biofilms. In this paper, we use microfluidic experiments, mechanistic models, and evolutionary game theory to show that these bacteria face a fundamental dilemma. 

In porous environments cells rely on flow for nutrients and dispersal, however, as they grow they tend to reduce to their access to flow, diverting it instead to competitors. The interaction between biofilms and porous media hydrodynamics thus select for bacteria that grow more slowly, which stands in sharp contrast with classical theory. 

These new insights may give us the tools to rationally engineer microbial communities for important functions, like cleaning up polluted water or enhancing oil extraction.

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Single-cell chemotaxis during biofilm formation

Proceedings of the National Academy of Sciences, USA

Bacteria living in surface attached structures known as biofilms play a central role in human infection and facilitate many important processes in the environment. 

In this paper, we show that single attached cells can sense chemical gradients and use this information to guide their movement along surfaces using tiny grappling hooks called pili. This ability allows cells to move to greener pastures, where food is more abundant. 

This work sheds new light into how biofilms function and presents a new tool to manipulate them to our advantage.

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Turbulent fluid acceleration generates clusters of gyrotactic microorganisms

Physical Review Letters

In this contribution we use a combination of experiments and modeling to demonstrate that fluid acceleration can 'hijack' phytoplankton's ability to sense the direction of gravity.  We find this new biophysical mechanism induces cells to swim into regions of enhanced fluid vorticity, triggering multifractal patchiness. While the magnitude of fluid acceleration only becomes comparable to gravity at very large turbulent dissipation rates, this mechanism may help understand phytoplankton population dynamics in biofuel production facilities, where turbulence is often more energetic than within natural aquatic environments.

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Turbulence drives microscale patches of motile phytoplankton

Nature Communications

Centimetre-scale patchiness in the distribution of marine phytoplankton increases the efficacy of many important ecological interactions by enhancing the rate at which cells encounter one another and their predators. 

We show that turbulent fluid motion, whose effect is customarily associated with mixing in the ocean, instead generates intense small-scale patchiness in the distribution of motile phytoplankton. 

This motility-driven ‘unmixing’ offers an explanation for why motile cells are often more patchily distributed than non-motile cells and provides a mechanistic framework to understand how turbulence, whose strength varies profoundly in marine environments, impacts ocean productivity.

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Division by fluid incision: Biofilm patch development in porous media

Physics of Fluids

A winner of the American Physical Society's Milton Van Dyke Award, this image illustrates that the interaction of bacterial biofilm (green) and fluid flow (red) generates striking patterns of preferential channelization in a porous microfluidic device that mimics soil.  A full article on this phenomena is currently in preparation.

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Thin Phytoplankton Layers: Characteristics, Mechanisms, and Consequences

Annual Review of Marine Science

'Thin layers' are a spectacular form of patchiness in the distribution of phytoplankton. By confining a large number of primary producers to small depth intervals, these structures act as oases for higher trophic levels in a ocean where resources are often too scarce to permit survival.

In this review article, we survey the salient features of thin layers, the mechanisms at play and mathematical techniques used to infer them in the field, and their impacts on the marine ecosystem. We argue that the time is ripe for the development of a quantitative, predictive framework to better understand their occurrence and, consequently, their ecological repercussions.

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Gyrotaxis in a steady vortical flow

Physical Review Letters

We show that gyrotactic motility within a vortical flow leads to tightly clustered aggregations of microorganisms. Two dimensionless numbers, characterising the relative swimming speed and stability against overturning by shear, govern the coupling between motility and flow. Exploration of parameter space revealed a striking array of patchiness regimes. 

We find that patches form under conditions typical of small-scale marine turbulence, suggesting that this mechanism may be responsible for observed microscale heterogeneity in the distribution of phytoplankton.

Microbial alignment in flow changes ocean light climate

Proceedings of the National Academy of Sciences, USA

Whirls of E. coli

The growth of microbial cultures in the laboratory is often informally assessed with a quick flick of the wrist: dense suspensions of microorganisms produce translucent ‘swirls’ when agitated. Here, we rationalise the mechanism behind this phenomenon and show that the same process may affect the propagation of light through the upper ocean.

Tumbling for Stealth?

Science

In this perspective article, we comment on the implications of a recent article by Polin et al. that found the phytoplankton Chlamydomonas reinhardtii can actively synchronise and desynchronise its flagella to swim in a "run and tumble" manner reminiscent of the enteric bacteria E. coli. We suggest this movement behaviour might be a strategy to reduce predator encounter rates.

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Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers

Science

Thin layer development via gyrotactic trapping.

In this paper we demonstrate that thin layers of phytoplankton can be generated by a coupling between motility, cell morphology, and hydrodynamic shear; a process we call 'gyrotactic trapping.'  Using a suite of physical experiments and modeling, we show that the vertical motility of phytoplankton is inhibited in regions of enhanced shear and leads to dense aggregations of phytoplankton. e

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