Arash Komeili charts the course of magnetotactic bacteria
In a laboratory at Koshland Hall, a bobblehead doll of the X-Men character Magneto sits on a shelf near a few dozen tubes and jars of murky pond water. When a visitor stops by, plant and microbial biology professor Arash Komeili grabs a bottle from a countertop and pours a few milliliters of the cloudy water into a test tube. “This is from a stream near my house,” he says, “or maybe Strawberry Creek. It probably contains tens of millions of bacteria.”
He holds a common refrigerator magnet to the tube, and suddenly sludge drifts upward along the side of the glass. Unsatisfied with the display, he quickly prepares a slide with a water droplet and places it under a microscope. On an attached video screen, the bacteria appear as a scattered constellation of black dots. When Komeili holds the magnet up to the slide, the bacteria rush to gather at the edge of the droplet. Like a line of dancers, they follow the magnet, then fall back into disarray when it’s removed from the glass.
If you didn’t know that bacteria could be magnetic, you’re not alone. In fact, Komeili’s work is bringing attention to a once obscure corner of the biological world, and even causing scientists to reevaluate basic facts about the structures of single-celled organisms. Think back to your introductory high school biology class: Bacteria were probably presented to you as one of the earth’s simplest life-forms, lacking nuclei and defined organelles. Look a little deeper than Bio 101, however, and you’ll find that these organisms aren’t really so simple after all.
Specifically, Komeili studies magnetosomes, microscopic structures within bacteria that contain magnetic particles, such as iron, allowing the bacteria to navigate in relation to the earth’s poles, just like Viking mariners using lodestones. “For the bacterial cells, it’s a valuable product because they use it to align in the earth’s magnetic field,” he says, “and then they can navigate the environment along a restricted space.”
Magnetic Marco Polo
Unlike Vikings, bacteria aren’t looking for new lands to conquer, but magnetism does help them find resources and hospitable environments. Take a typical lake, for example, in which oxygen levels are highest near the surface. Magnetotactic bacteria prefer areas with a lower oxygen content, Komeili explains, “so they swim up and down along the magnetic field lines, and then they decide where to stop.” Like playing Marco Polo in a swimming pool, they’re continually sampling their environment to move in more promising directions.
The magnetosome isn’t a true compass, and it can’t tell bacteria exactly where to go—it’s more like the earth’s magnetic field is a train track, and the magnetosome is the train’s wheels. “Then you have an engine and a conductor,” Komeili says, “but you can’t escape those tracks.”
While this navigation technique is exciting in and of itself, Komeili is even more interested in what the presence of magnetosomes reveals about basic cell biology. To begin with, there’s that traditional understanding of bacteria—that they don’t have organelles, the specific functional subunits associated with complex organisms such as plants and animals. “When I was getting my PhD in cell biology,” Komeili says, “that was certainly what I had heard and believed.”
The presence of what is essentially a “magnet factory” within some of these cells doesn’t square with the sort of basic biology that high school students have been taught for generations. The magnetosomes don’t spring up magically, Komeili says. Rather, “the bacteria are making this compartment, and then within that compartment they’re making the magnetic particle.” And that level of complex organization just isn’t something that organisms this simple were thought to be capable of. Until, that is, Komeili and his colleagues began their groundbreaking research.
A blueprint for magnetosomes
Establishing the basic science that undergirds the magnet factory has been the thrust of Komeili’s inquiry. This has been painstaking, multifaceted work that required figuring out the genetics that control the magnetosome formation process. With those basic tools in place, the researchers then began changing one factor at a time in their bacterial “lab rat,” to reverse engineer how the magnetosome is created.
“Over time, we assembled a little blueprint of how magnetosomes are made and how the magnetic particles are made,” Komeili explains. “And the blueprint says, ‘To make the compartment, you need these genes, then to bring in the iron, you need these other genes. And to turn the iron into something solid like a mineral, you need these other genes, and then to put them together in a line, you need these genes.’”
The study of magnetic bacteria is still in its relative infancy. Komeili did a search of PubMed, the scientific database, and between 1975 and the early 2000s only one or two papers per year matched the term “magnetotactic bacteria.” “In the last five or six years, though,” he says, “you have 50 to 75 papers a year with that search term.” And many of those build on the foundational work being done in the Komeili lab.
There is already great promise for practical applications of magnetotactic bacteria. In the field of environmental remediation, they can be used to bind toxic heavy metals such as chromium, neutralizing them and speeding cleanup. Geologists and paleontologists are also eager to do more work with them: The orientation of fossilized magnetic bacteria provides valuable information about continental plates and the history of the earth’s magnetic poles. But perhaps the most exciting potential is in the field of cancer detection and treatment. One of Komeili’s colleagues at Berkeley is Steven Conolly, a professor in the Department of Electrical Engineering and Computer Sciences who is working on a new technology called magnetic particle imaging.
One long-term goal is to use magnetic bacteria DNA to label mammalian cancer cells—essentially creating a living magnetic biomarker of cancer. Researchers already rely on a similar optical genetic reporter, fluorescent proteins. But, as Conolly notes, “tracking cancer with magnetic reporters has great potential because you can see magnetic signals deep inside an animal without worrying about the attenuation of light through layers of tissue.”
Conolly envisions a research measurement device the size of a toaster—simply pop a mouse inside the machine and you could measure tumor volume very quickly, without even making an image. Additionally, magnetic labels could help physicians track the success of immunotherapy treatments, which are often frustratingly invisible once inside a patient. “If we put magnetic reporters on them,” Conolly says, “then we can see them anywhere. It’s like looking for stars at night instead of looking for stars during the day.”
NOTE: In the Northern Hemisphere, traveling northward takes you lower in the water; in the Southern Hemisphere, the opposite is true. Illustration. by Wren McDonald.
Fun with serious science
Back in the laboratory, Komeili’s enthusiasm for basic science is infectious. Although the work is complex and time-consuming, the mood in the lab is light, with frequent social events and holiday parties, not to mention the presence of every possible magnetic toy on the market. That energy extends beyond the lab and into the classroom, where Komeili teaches a well-regarded undergraduate microbiology course that’s small enough to give him plenty of one-on-one time with budding scientists.
And unlike the microbiologists of yesterday, Komeili maintains an active Twitter presence @micromagnets, often highlighting the work of
other people in his field. In part because of his own research—and in part because of his upbeat attitude and collaborative nature—magnetosomes are beginning to gain wide renown.
“Recently I was interviewing a high school student for a scholarship,” Komeili recalls, “and she asked me about my work. When I told her, she said, ‘Oh, we learned about magnetotactic bacteria in AP Biology,’ and I was so excited that I had to run back into the lab and tell everybody.”
When it comes to his graduate students, Komeili is committed to providing a wide range of challenges and opportunities. “This lab wasn’t initially on my radar,” says fifth-year PhD candidate Carly Grant. “But I took a class with Arash, and I decided that what I wanted from grad school was a really good mentor. He’s given me the freedom and support to explore alternative research opportunities and work on projects that excite me.”
The advantages of that freedom go both ways. The notion that bacteria make compartments “is still the most compelling idea that drives me,” Komeili says, “but different people in my lab get excited about different aspects of this field, and that leads them down different paths, and then that gives me whole new ways of getting excited.”