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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.
By Steve Silberman
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' quorumsensing 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 50year 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."