Web Extras: Movie

Making a Microscopic Metropolis
By Alisa Zapp Machalek
Posted December 22, 2008

Biofilms are highly organized, densely populated communities complete with protective walls and a network of pipes that transport nutrients and dispose of wastes. Credit: E. Peter Greenberg
Click for larger image.

Run your tongue across your teeth. Unless you've brushed recently, you probably feel a slimy residue. It's a biofilm—a collection of bacteria that have formed a well-organized microscopic community.

But don't worry. It's normal.

Biofilms form in moist places—stagnant ponds, the hulls of cargo ships, the kitchen sink, and our teeth. They play critically important ecological roles and are useful for some industrial purposes.

But if biofilms form in certain parts of the human body, they can lead to trouble: lung infections, ear infections, tooth decay, clogged medical implants, and other health issues.

On the surface, biofilms look merely like a gooey paste. But their formation is one of the most remarkable phenomena in all of biology.

Free-living bacteria transform from individual cells to specialized members of a community. The genetically identical cells adopt different shapes, properties, and functions to become a walled city that includes systems for transportation, communications, waste disposal, and chemical weapons defense.

Although scientists are actively studying biofilms, they don't know what controls the fate of each bacterial cell and the role it plays in the community.

Those questions spurred an investigation by University of California, San Diego researchers. The results of this study, led by bioengineer Jeff Hasty and physicist Lev Tsimring, will help shed light on how biofilms form—and possibly how we can prevent them from causing harm within our bodies.

First, the San Diego scientists studied how bacteria grow in a confined environment, which is how many bacteria live. To do this, they grew bacteria on a clear chip about the size of a postage stamp. They used a strain of E. coli bacterial cells that cannot move on their own, but through random jostling end up elbowing each other out of the way. The researchers designed the plate so that the rod-shaped bacteria could only grow one layer deep and were forced by tiny walls to stay in a narrow channel.

To begin the experiment, the researchers placed a handful of bacteria in the center of the narrow chamber. Each rod-shaped bacterial cell lengthened, then split in two. These two cells lengthened and split to make four cells, then eight, then 16...

The bacteria doubled their population every 25 to 30 minutes. So within several hours, bacteria filled the whole chamber.

Somewhere along the way, the overall structure of the colony changed. Bacterial cells, originally helter skelter, started to arrange themselves into tidy columns parallel to the container walls.

"The first time we saw this in the experiments, we thought it was the most interesting thing we'd seen in a long time," says Hasty.

But after thinking about it more, a well-ordered structure just made sense. In essence, the bacteria were shoving each other into any available space so they could pack as tightly as possible.

To figure out how the cells move from a haphazard jumble into neat parallel lines, the researchers designed a computer model to simulate bacterial growth and division on a flat surface.

As in the experiment, the virtual bacteria couldn't stack on top of each other and were confined to a narrow channel. But instead of waiting hours for the expanding bacterial colony to fill the channel, the scientists sped up their simulation so it took only a few minutes.

To track the direction each cell faced during the simulation, the scientists developed a color code based on the cell's orientation relative to the walls of the channel. Blue cells were perpendicular to the sides of the container while red ones were parallel.

At the beginning of the simulation, the few starting bacteria were cool blues and greens. As they were bumped and shoved by their neighbors, they spread into a rainbow-colored array of randomly-orientated cells. When they knocked into the sides of the container, the pressing crowd flattened them against the walls, creating a swath of red along each side.

As the colony expanded, more and more bacteria turned orange or red. Within 15 seconds of the simulation, a wave of bacteria, almost all red, spilled out of the top and bottom of the channel (see movie).

The simulation, relying on basic rules of physics, corresponded closely to how real E. coli behave. As a result, the researchers suspect that simple physics is responsible, at least in part, for the structure of biofilms.

Now the question is whether—and, if so, how—the orderly arrangement of cells in a biofilm affects how each cell adopts its new identity in the community.

Hasty and Tsimring see this work as the beginning of a new understanding of how biofilms establish and maintain their architecture. Their study is one of the first to focus on the effects of physical crowding on bacteria.

Next, the researchers hope to investigate whether cellular pushing and shoving plays a role along with other factors necessary for biofilm formation, like sticking to a surface, staying undisturbed for a time, and communicating with chemical messages.