Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [30]
E. coli can also settle down and build a microbial city. Scientists have long been aware that bacteria can form a cloudy layer of scum on their flasks, known as a biofilm. Biofilms simply annoyed biologists at first. But a closer look revealed biofilms to be marvelously intricate structures. All microbes can make biofilms, and scientists suspect that the vast majority of microbes spend most of their lives in one. Biofilms form slimy coats on river bottoms, on the ocean floor, at the bottom of acid-drenched mine shafts, and on the inner walls of our intestines.
Biofilms may be everywhere, but studying them is not a simple matter. Scientists have had to ditch their flasks and petri dishes and think of new kinds of experiments. Some have built special chambers with warm flowing water to mimic the human gut. Under the right conditions, E. coli will settle down inside them and begin to build its biofilm. As the bacteria drift through the chamber, some alight on the bottom. Normally the microbes immediately let go and swim on, but sometimes they settle down instead. Some experiments suggest that E. coli make this decision if they detect other E. coli nearby. They sense their fellow microbes by the chemicals they release—not just serine and other sorts of waste but special molecules that serve as signals and can change the way other E. coli behave.
Once a group of E. coli has committed itself to forming a biofilm, the microbes start to build sticky fibers to snag one another and pull together into a tight cluster. They’re joined by more floating E. coli, and the cluster grows. They begin to squirt a rubbery slime from their pores, entombing themselves in a matrix. As the biofilm takes shape, it does not form a flat sheet. It grows looming towers, broad pedestals, and a network of crisscrossing avenues. All of these changes require each microbe to switch hundreds of genes on and off in a complicated, coordinated fashion. E. coli biofilms are in some ways like our bodies. A biofilm may not get up and walk around on two legs. But, like our cells, it forms collectives in which different cells take on different jobs and work together to promote their shared survival.
A biofilm of E. coli
Scientists are still trying to figure out exactly why E. coli bothers to build biofilms. An individual microbe must make a great sacrifice to join the effort, spending a lot of its precious energy to build the glue that will join it to other microbes. If an individual E. coli should happen to get stuck deep inside the biofilm, it will have a harder time getting food than it would have if it remained floating free. These costs may be outweighed by benefits. Biofilms may provide E. coli with sustenance and protection. Biofilms can withstand harsh swings of the environment. Viruses may have a harder time penetrating biofilms than infecting single cells. Antibiotics are a thousand times weaker against biofilms than against individual microbes.
Biofilms may also allow bacteria to work together to catch food. Nutrients may get caught in the rubbery slime of biofilms and flow down canals to reach out-of-the-way microbes. Bacteria can also work cooperatively in biofilms by dividing their labors. The ones near the surface can get more food and oxygen than the ones buried deep inside. But they also face more stress. The E. coli nestled at the base of a biofilm may slip into a state of suspended animation, a kind of microbial seed bank. From time to time they may break off from the biofilm and drift away, becoming free-floating individuals or settling back down on the gut to build a new biofilm.
Humans, the supremely social species, don’t cooperate just to build cities and help their fellow humans. They also cooperate to wage war. And here again E. coli mirrors our social life. We build