The Bacteria Whisperer

The Bacteria Whisperer

Bonnie Bassler discovered a secret about microbes that the science world has missed for centuries. The bugs are talking to each other. And plotting against us.

Issue 11.04 - April 2003
By Steve Silberman
[www.wired.com]

Trim and hyperkinetic at 40, Bonnie Bassler is often mistaken for a graduate student at conferences. Five mornings a week at dawn, she walks a mile to the local YMCA to lead a popular aerobics class. When a representative from the MacArthur Foundation phoned last fall, the caller played coy at first, asking Bassler if she knew anyone who might be worthy of one of the foundation's fellowships, popularly known as genius grants. "I'm sorry," Bassler apologized, "I don't hang out with that caliber of people."

The point of the call, of course, was that Bassler - an associate professor of molecular biology at Princeton - is now officially a genius herself. More than a decade ago, she began studying a phenomenon that even fellow biologists considered to be of questionable significance: bacterial communication. Now she finds herself at the forefront of a major shift in mainstream science.

The notion that microbes have anything to say to each other is surprisingly new. For more than a century, bacterial cells were regarded as single-minded opportunists, little more than efficient machines for self-replication. Flourishing in plant and animal tissue, in volcanic vents and polar ice, thriving on gasoline additives and radiation, they were supremely adaptive, but their lives seemed, well, boring. The "sole ambition" of a bacterium, wrote geneticist François Jacob in 1973, is "to produce two bacteria."

New research suggests, however, that microbial life is much richer: highly social, intricately networked, and teeming with interactions. Bassler and other researchers have determined that bacteria communicate using molecules comparable to pheromones. By tapping into this cell-to-cell network, microbes are able to collectively track changes in their environment, conspire with their own species, build mutually beneficial alliances with other types of bacteria, gain advantages over competitors, and communicate with their hosts - the sort of collective strategizing typically ascribed to bees, ants, and people, not to bacteria.

Last year, Bassler and her colleagues unlocked the structure of a molecular language shared by many of nature's most fearsome particles of mass destruction, including those responsible for cholera, tuberculosis, pneumonia, septicemia, ulcers, Lyme disease, stomach cancer, and bubonic plague. Now even Big Pharma, faced with a soaring number of microbes resistant to existing drugs, is taking notice of her work.

What Bassler and other pioneers in her field have given us, however, is more than a set of potential drug targets. Their discoveries suggest that the ability to create intricate social networks for mutual benefit was not one of the crowning flourishes in the invention of life. It was the first.

The bobtail squid lives in the knee-deep coastal shallows in Hawaii, burying itself in the sand during the day and emerging to hunt after dark. On moonlit nights, the squid's shadow on the sand should make it visible to predators, but it possesses a "light organ" that shines with a blue glow, perfectly matching the amount of light shining down through the water.

The secret of the squid's ability to simulate moonlight is a densely packed community of luminescent bacteria called Vibrio fischeri. Minutes after birth, a squid begins circulating seawater through a hollow chamber in its body. The water contains millions of species of microbes, but cilia in the squid's light organ expel all but the V. fischeri cells. Fed with oxygen and amino acids, they multiply and begin to emit light. Sensors on the squid's upper surface detect the amount of illumination in the night sky, and the squid adjusts an irislike opening in its body until its shadow on the sand disappears. Each morning, the squid flushes out most of its cache of glowing vibrios, leaving enough cells to start the cycle anew.

In the early '60s, Woody Hastings, a microbiologist at the University of Illinois, noticed a curious thing about the V. fischeri grown in his lab. The bacterial population would double every 20 minutes, but the amount of the cells' light-producing enzyme, called luciferase, would stay the same for four or five hours, dispersed among more and more cells. Only when the bacterial population had vastly increased would the flask begin to glow brightly.

From the perspective of a single V. fischeri cell, delaying light production makes sense. The emission of photons is metabolically expensive, as biologists say, and the puny glow of a lone organism is apt to be overlooked in the vastness of the ocean. So how do the cells know when they have reached critical mass? One of Hastings' students, Ken Nealson, theorized that they were secreting a chemical that accumulates in their environment until the group reaches some threshold density. He christened this unknown molecule an "autoinducer." Nealson's hunch turned out to be correct, and the chemical process by which V. fischeri keep track of their own numbers - determining, like a group of senators, that enough members are present to take a vote - was eventually dubbed "quorum sensing."

More recently, scientists have begun to understand that the importance of cell-to-cell communication goes far beyond mere head counting. Many things that bacteria do, it turns out, are orchestrated by cascades of molecular signals. One such behavior is the formation of spores that make bacteria more resistant to antibiotics. Another is the unleashing of virulence. For disease-causing pathogens like Staphylococcus aureus, waiting for a quorum to assemble before getting down to business has distinct benefits. A few microbes dribbling out toxins in a 200-pound host will succeed only in calling down the furies of the immune system. En masse, they can do serious damage. The first "sleeper cells" were bacterial cells.

Hastings, who is now at Harvard, admits that he underestimated the significance of what he saw in his lab. He assumed that quorum sensing was limited to the marine microbes he was studying. "I accepted the view that these bacteria were in a very specific situation," he says, with a burr of regret. "It doesn't take much reflection to think this must occur elsewhere."

The conclusion that only highly evolved organisms have the ability to act collectively proved to be a stubborn prejudice, however. On several occasions, Nealson tried to publish a diagram in microbiology journals illustrating cell-to-cell signaling in V. fischeri, but peer reviewers rejected it. Bacteria just don't do this, the critics told him.

Bassler proved that they did, by discovering that V. fischeri were not the only chatty microbes in the sea.

As an undergraduate at UC Davis, Bassler decided that she wanted to become a veterinarian. But there was a problem: Dissections in biology class made her faint. She also loathed the rote memorization of lists of muscles and bones. Then she volunteered to work in a biochemistry lab. "I was planning to cure cancer," she recalls, smiling, "then I discovered that bacteria were these totally fantastic creatures."

In 1990, she joined geneticist Mike Silverman for postdoctoral work at the Agouron Institute in La Jolla, California. Microbial light was in the water; the institute was located on a cliff above the Pacific Ocean, where luminescent organisms sparkled on balmy nights. It was Silverman and a graduate student, Joanne Engebrecht, who had mapped the quorum-sensing circuit in Vibrio fischeri by cloning the genes that made luciferase.

At Agouron, Bassler turned her attention to another marine organism, Vibrio harveyi. Unlike V. fischeri, these cells live in the open ocean or in the gut tracts of fish, in bacterial consortia composed of many different species. While the pampered existences of symbiotic V. fischeri are dully predictable, the lives of cosmopolitan V. harveyi are more like ours - having to make sense, minute to minute, of swarms of changing conditions.

Like V. fischeri cells, V. harveyi light up when their own population reaches quorum density. But if a "soup" made of extracts of other species of bacteria is introduced into a V. harveyi culture, they glow as well.

Bassler determined that what looked like one signaling system was actually two: The first sensed the presence of other V. harveyi cells, and the second received signals from many other kinds of bacteria. She and her colleagues created mutant "reporter strains" of V. harveyi - capable of responding to only one signal or the other - to tease the two circuits apart.

The work required an intensity perfectly suited to Bassler, who obsesses about everything - her weight, her guilt that she hasn't put in enough hours at the lab, and especially her bacteria, which she speaks of with unabashed awe. "Did you know that 'vibrio' means vibrate? Unlike E. coli, which are fat and sleepy, these guys zip around under the microscope," she gushes. "Each bacterium in a species is perfect for the niche in which it resides, and if one survives, the whole species survives. They're better than us. They're the ultimate, stripped-down version of life."

Silverman, who is now retired, recalls that while Bassler was "starry-eyed and deferential" to him when she first arrived at his lab, she was soon advancing the research further than he had hoped. "Once she got some traction, she really started pulling," he says.

But in part because Bassler's cute glow-in-the dark microbes seemed to have little impact on the health or commercial success of humankind, her discoveries were considered a sideline curiosity in the world of mainstream science. Just before Bassler left Agouron, she recalls, "I was in the lab, streaking out my bacteria, and I thought, 'I love this job. But I'm gonna be selling shoes at Thom McAnn's next year, because Mike and I are the only people who care about this.'"

Bassler had more reasons to be optimistic than she knew. In 1994, she was hired as an associate professor at Princeton. Thomas Silhavy, who chaired the search committee, admired how far she had pushed the young science of quorum sensing in such a short time. "Figuring out that there were two circuits was a difficult problem, and Bonnie solved it," he says. "It was a gutsy move. Now the whole field rests on it."

That field is expanding at an astonishing rate. In the early '90s, papers were published describing cell-to-cell signaling in Agrobacterium tumefaciens, which causes gall tumors in plants, in Erwinia carotovora, the architect of soft rot in carrots, and in a particularly nasty bug called Pseudomonas aeruginosa, which accounts for 10 percent of all infections contracted in hospitals. Often deadly for cystic fibrosis patients, burn victims, and others with impaired immune systems, P. aeruginosa makes itself impervious to antibiotics by surrounding itself with a biofilm - the bacterial equivalent of a fortress. University of Iowa researcher E. Peter Greenberg, whose daughter has cystic fibrosis, determined that the manufacture of biofilms in P. aeruginosa is mobilized by molecular signals.

Some exceptionally opportunistic bugs have learned to hack the network. The staph microbes responsible for toxic shock, for instance, send out molecular signals in order to compete against nearby staph colonies, disabling their rivals' quorum-sensing circuits before they become virulent.

Quorum sensing has profound implications in the war against disease. With the Age of Antibiotics, we launched a brute force assault on pathogenic bacteria, emphasizing drugs that outright kill. This monolithic approach has brought what geneticists call maximum selective pressure to bear on pathogens. In essence, we have given a 50-year course in antibiotic resistance to an enemy that reproduces every 20 minutes. Bassler's research points to new ways of fighting disease that will aim not to kill but to scramble data in the bacterial network. One approach would be to block the receptors that receive the molecular signals so that cells never become virulent; another would target the DNA-replication mechanisms set in motion inside cells when the signals are received.

Once at Princeton, Bassler turned to identifying the elusive molecule that enabled V. harveyi to communicate with other species. In 2002, her team finally nailed it, christening it AI-2 (autoinducer 2). With the help of Princeton's chemistry department, they determined that the AI-2 molecule contains the element boron, trace amounts of which lurk everywhere in the biosphere, though few biological roles for it have ever been found. When they cloned the gene that makes AI-2, they discovered that at least 50 bacterial species possess the genetic machinery to produce the molecule.

To Bassler, AI-2 is bacterial Esperanto: a molecular language for interspecies conversation and conspiracy that has been spoken on earth for more than a million years.

Not everyone is convinced. Last year, Nottingham University's Paul Williams published a paper titled "Bacterial Cell-to-Cell Communication: Sorry, Can't Talk Now - Gone to Lunch!" Williams claims that while AI-2 plays the role of a signaling molecule in V. harveyi, in most organisms, it's garbage - a metabolic byproduct.

As recently as the late '90s, the National Institutes of Health routinely rejected Bassler's grant applications, politely suggesting that she apply again to a different committee the following year. Her most dependable sources of funding were the National Science Foundation and the Office of Naval Research, which is tracking quorum sensing carefully because biofilms degrade naval steel, foul water lines, and slow the progress of ships at sea. "The good news was that you weren't competing with anyone for money," Bassler recalls. "The bad news was that there was no money."

Papers published over the past year by researchers around the world, however, suggest that Bassler is right about AI-2. And now there's a little more money. Bassler's lab got its first NIH grant this year. She may use some of her $500,000 MacArthur windfall to bring scientists from other fields to study the implications of cell-to-cell communication at Princeton. Quorum-sensing research groups are sprouting up in the UK, Germany, Singapore, Sweden, and Brazil, as well as several dozen universities in the US.

For a growing number of researchers, the term "quorum sensing" already feels too narrowly defined. They favor the use of the broader phrase "cell-to-cell signaling" to stress that communication seems to be the rule, rather than the exception, in every domain of life. Some propose that molecular discourse may even have been one of the things that propelled us up the ladder toward becoming the complex creatures we are; the mechanisms that orchestrate the division of labor in bacterial colonies are similar to the signals that regulate the growth and specialization of animal tissues. "How does your heart know itself from your liver?" asks Bassler. "This may be how multicellular organisms evolved in the first place."

While the post-MacArthur buzz has elevated Bassler from an obscure academic into (in her own half-ironic hyperbole) "the queen of quorum sensing," she is refreshingly unpretentious about her new celebrity. She's grateful that her Advanced Genetics course is as popular as her aerobics classes at the Y, but she's still happiest in the lab, among her bioassays and pipettes, where, as she says, there's a surprise in the incubator every morning.

Through Bassler's discoveries, we're learning that those on the lowest rungs of the Darwinian ladder share one of the traits that has, until recently, been thought of as distinctly human: the propensity to create a continuous stream of commentary about the world. As Bassler puts it, for microbial communities, the advent of the cell-to-cell network made "the difference between subsistence farming and living in Manhattan. These guys know self and other, friend and foe, and have been doing biological warfare for over a million years."

Contributing editor Steve Silberman (digaman @wiredmag.com) wrote about the FBI's war on child pornography in Wired 10.10.