Rheosensing: how bacteria feel the flow

Combining techniques and perspectives led to insights into how bacterial cells interact with their mechanical environment.

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May 17, 2019

The paper published in Nature Microbiology can be found here: https://www.nature.com/articles/s41564-019-0455-0

This story is largely the product of combination. Technically, we combined the power of microfluidics and transcriptomics. Intellectually, we combined ideas from molecular biology, physics, and engineering. While the combination of techniques was relatively seamless, the combination of intellectual viewpoints took more work. Luckily, the individuals involved in this project were able to balance their desire for field-specific rigor with the excitement of interdisciplinary science. Ultimately, hours of intense conversation and debate led us to understand each other's viewpoints more clearly and move science forward.

Bacterial cells have a remarkable ability to sense environmental cues to optimize their behavior in changing environments. While it has been known for decades that chemical cues affect bacterial behavior in a multitude of ways, it has recently become apparent that mechanical cues also affect bacterial behavior. Shear flow is frequently associated with environments where bacteria thrive, such as the bloodstream and urinary tract. Therefore, we asked a relatively simple question: how does shear flow affect bacterial gene expression? Using a novel experimental approach that combined microfluidics (to apply shear flow) and transcriptomics (to measure gene expression), we discovered that the pathogenic bacterium Pseudomonas aeruginosa is able to sense and respond to shear flow through a process we named rheosensing (as -rheo is Greek for flow). 

Pseudomonas aeruginosa rapidly induces gene expression when subjected to shear flow. The top row of pictures represent induction of a fluorescence reporter in relation to the amount of time they have been subjected to shear flow.

The idea that micron-scale bacterial cells can sense shear flow is exciting to biologists, physicists, and engineers alike. However, I have learned that we find it exciting for different reasons and use different terms to describe it. Not surprisingly, biologists view the problem through the lens of the bacteria, while engineers seem to view the problem through the lens of the fluid. Surprisingly, at least to me, physicists and engineers do not agree on the terms used to define fluid flow. In my experience, physicists prefer to think in velocities and forces, while engineers prefer to think in rates and stresses. While these differences are subtle and perhaps unimportant, they do present a conceptual barrier to overcome during the collaborative process. 

Differences also provide a remarkable opportunity. What I view as the most important conclusion from our paper (rheosensing does not measure force) was a direct result of a conversation that brought together vastly different perspectives. At the time, we were working with the assumption that bacterial rheosensing was measuring the force of flow (known as shear force). This assumption was based off the simple intuition to associate flow with force and the fact that some eukaryotic cell types are known to sense shear force. However, in that meeting, the non-biologists in the room pointed out that the formula for shear force was quite simple and included only two variables: shear rate and viscosity. Based off this suggestion, I went back to the lab and experimentally altered the two parameters independently. Rheosensing scaled with shear rate but not viscosity. Our assumption was wrong. 

As we move to understand more about how bacteria interact with their mechanical environment, we should continue to lean on interdisciplinary collaborations and search for "simple" experiments that are only simple because they combine established technologies and ideas. 

Note: The artwork above was created by Matilda Luk.

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Joseph Sanfilippo

Post-doc, Princeton University

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