Sunday, April 1, 2012

Apparently, Bacteria have ears...

Bacteria have an endless ability to amaze. Even plain old Escherichia coli, the workhorse organism of thousands of labs—an organism that, in my youth, I thought too boring and well-known to be worth focusing a career on—still generates research that leaves us dumbstruck and groping for explanations. Nowadays, as often as not, these surprises turn up on the fringes of science and don’t really affect our understanding of how the world works. However, they do make us pause and scratch our heads—sometimes at the result itself, other times at why the initial experiments were done. So, we have findings from Czech researchers about how E. coli in “heavy” water (enriched for the deuterium isotope of hydrogen, 2H2O) grow faster than they do in normal water. We have the finding from an astrobiology group that growth in zero gravity causes changes in the expression of almost half of E. coli’s genes. And now, a new report suggests that E. coli can actually sense and respond to sound—in a word, bacteria can hear.

The finding, like many in the history of science, is an example of Pasteur’s dictum about fortune favoring the prepared mind. In this case, the mind belongs to Felix Balatro of Miskatonic University. He was actually testing a pet hypothesis about whether Bacteria could learn.

Of course, one would not expect terribly deep thinking from a bacterium. Nor would you expect deep thinking from the flatworm Planaria—however, this has been demonstrated using a T-maze. A T-maze is the simplest possible maze: the worm can go forward from the bottom of the T to the top, then it can turn left or right. If the reward is consistently on the right, then the little guys start turning right more than half of the time. Balatro had the rather crazy idea that bacteria could do the same trick. One problem he had to solve was a matter of scale: a planarial T-maze is a few centimeters long, a distance that would take a couple of generations for E. coli to swim. Fortunately, advances in microfluidics and techniques borrowed from semiconductor production enabled him to produce a T-maze of millimeter scale, with exactly equal concentrations of an attractant (aspartate) at each branch of the maze.

Now, the first piece of luck for Balatro was that he didn’t really think this through. Planaria, being flatworms, have a clearly defined left and right. They crawl, instead of swimming. So, the right side of the T-maze corresponds only to the right side of the flatworm’s body. Not so with E. coli. They swim, and spiral and loop and frequently tumble as they swim, so they “know not their right hand from their left.” Anyone knowing this basic fact of E. coli’s biology knows that this experiment would fail—but Balatro, either through ignorance or (more likely) stubbornness, pushed ahead.

Amazingly, E. coli seemed to learn to turn right. Balatro ran his cells through the T-maze, and collected the cells that made it to the right side of the maze. Using some nifty microfluidic devices, he let these cells reproduce for one generation, and ran them through the maze again. Again he selected the cells that turned right, and let them grow again…and again, and again, for approximately a thousand generations. After this time, when he ran a thousand cells through the maze, he found that between 60 and 70% of the cells would turn right.

This result is completely, totally, 100% unbelievable. Being a good scientist, Balatro didn’t believe it. Suspecting some barely perceptible turbulence in his test chamber, he turned the microfluidic slide upside down in the microscope—and obtained the same result. He wondered if the bacteria were somehow responding to light, so he blacked out his lab and ran the cells through the maze with the microscope’s lights out—and again found that nearly three quarters of the cells turned right.

Magnetotaxis—the ability to sense and respond to the Earth’s magnetic field—is not unknown among the bacteria, so Balatro tried to test this. “Right” in his original maze corresponded to south-southeast. He spent a day rearranging the tangle of pumps and controllers surrounding the apparatus so that “right” now corresponded to north-northwest, and he must have experienced a mixture of surprise and elation when he found that now, 75% of his cells got to the T and turned left!

Balatro’s celebratory mood was presumably deflated when he shared his results with his colleague, D. Avril Poisson. She looked through the microscope at the maze, coolly removed a magnet from a nearby refrigerator door, and set it upon the stage. The resulting magnetic field was many times stronger than the Earth’s, and the bacteria did not change their behavior at all. In fact, when Balatro ran the experiment in her presence, the bacteria seemed to forget everything—they got to the T, and half turned left, half turned right.

Here’ was Balatro’s second piece of luck. It had to do with a combination of his intellect and his personal eccentricities. I got to know one of Balatro’s PhD committee members when I was in graduate school, and she described him as “one of the most brilliant and…um…uh…ehhh…I guess you could say lateral thinkers I’ve met.” He apparently lived in the lab, only going home to shower; he spent a fair amount of his time in lab stoned, and he spent absolutely all of his time in lab, awake or asleep, with the stereo blasting the Grateful Dead at deafening volume. He even ditched one thesis advisor (and, thus one field of study and one future career) for another solely because his newly chosen advisor was deaf and didn’t mind the noise—and so oncology’s loss was microbiology’s gain.

Rather than mope about a failed experiment, Balatro realized that only one thing had changed when Poisson had entered the room. Out of hard-learned politeness, he had muted Jerry Garcia’s solo from “Sugaree” at the Rockpalast, 1977, blasting from the speakers in the south end of his lab. Nothing else had changed—nothing about light, the magnetic field, temperature, pH, nutrient or redox gradients, or any of the myriad other things bacteria are known to sense. Just pure, Gratefully Dead sound. Had he discovered phonotaxis?

Of course, Balatro confirmed this result, and spent a lot of time designing experiments that eliminated other possibilities and left the conclusion that his bacteria could hear and turn towards sound. And so we have the paper, given the innocuous title “Novel functions for mechanosensitive channel proteins in an evolved Escherichia coli system,” and slipped into print in the obscure journal Acta Pathologica, Microbiologica et Immunologica Scandinavica. It’s as if Balatro doesn’t want us to notice that he has discovered something incredible.

However, this is a powerful paper; Balatro, working with Poisson, even proposes a plausible mechanism. Sound, at the cellular level, is a mechanical phenomenon—an alternation of high and low pressure. Bacterial cells have mechanosensory proteins in their membranes, and these have been intensively studied for their role in helping cells survive osmotic stresses. These proteins, as they sit in the cell’s membrane, are deformed when the cell membrane is deformed; the change in the protein’s shape causes the protein to send a signal into the cell, resulting in a change in the expression of several genes.

Balatro and Poisson examined the genes for these mechanosensory proteins, mscL and mscS, in the cells that consistently turn towards high-intensity sound, and found that these genes had evolved over the course of generations of selection. The genes had, in fact, recombined with genes for chemotaxis—that is, genes that encoded proteins that sensed food, and directed cells to swim towards higher concentrations of food. The evolved gene encoded a hybrid protein that still sensed mechanical pressure (though this too had changed slightly), but now controlled the cell’s swimming behavior.

This result is curious, and leaves open lots of questions. We still don’t quite understand how sound waves, which should be much larger than a bacterial cell, can have a perceived direction to E. coli—it would be as if we could tell, just using our own senses, what direction a change in barometric pressure came from. There is also the puzzle of how the changes in the pressure-sensing component of the MscL and MscS proteins in these “hearing” bacteria relate to their ability to hear. Information about the structure of these mutant proteins should provide some answers, and Balatro is quite able to get that data rapidly.

Ultimately, like cells growing in Deuterium or microgravity, this is a completely artificial situation, and thus not likely to be of especial biological significance. Still, it’s pretty neat, and a good reminder of both how science progresses and how amazingly extraordinary even “ordinary” bacteria can be.

Mann, L.R., and Moses, V. (1971). Properties of Escherichia coli grown in deuterated media. Folia Microbiol Praha 16 (4): 267-84.

Rosenzweig, J.A., Abogunde, O., Thomas, K., Lawal A., Nguyen, Y-U., Sodipe, A., and Jejelowo, O (2010). Spaceflight and modeled microgravity effects on microbial growth and virulence. Applied Microbiology and Biotechnology 85 (4): 885-891.

Jacobson, A.L, Fried, C., and Horowitz, S.D. (1966) Planarians and memory. Nature 209: 599-601.

Matsunaga, T., and Okamura, Y (2003). Genes and Proteins involved in Bacterial Magnetic Particle Formation. Trends in Microbiology 11(11): 536-41.

Balatro, Felix, and Poisson, D. Avril (2012). Novel functions for mechanosensitive channel proteins in an evolved Escherichia coli system. Acta Pathologica, Microbiologica et Immunologica Scandinavica 120 (4): 4652-4661.

Haswell, Elizabeth, Phillips, R., and Rees, D.C. (2011) Mechanosensitive Channels: What Can They Do and How Do They Do It? Structure 19: 1356-1369.


  1. Dr. Appleman,

    I love reading these posts from you. They always put a huge grin on my face.


  2. Maria-
    I'm very glad to hear it. I enjoy writing about Dr. Balatro and his exploits, and my family will confirm that I'm prone to that sort of thing--to the point where I was often tempted to add such things in class every so often. On my honor, though, I resisted that temptation.

    P.S. How's your Latin? Have you tried translating Felix Balatro?

  3. Dr. Appleman,

    Hah, 'happy fool'. I see what you did there.