The Creativity of Microbes

In my last post, I wrote about how our genes work in networks, much like circuits made of elements wired together in various ways. As genes are accidentally duplicated, mutated, and rewired, old networks can give rise to new ones. It’s pretty clear our ancestors could have never become particularly complex if not for this sort of network evolution. As they acquired nerves, muscles, and other tissues, animals needed to organize more and more genes into new circuits. But in saying this I don’t mean to imply that single-celled microbes, such as bacteria, live without gene networks. Far from it. In fact, in many ways bacteria are more adept at network engineering than we are.

Evolution has engineered the networks of bacteria with many of the same tricks that produced our own. As one bacterium divides into two, all sorts of mistakes can creep into its duplicating DNA. As one generation inherits gene networks from its parents, the networks can slowly change.

But bacteria can also do something else we virtually never do: they can swap genes. The genes may be carried by viruses that jump from one bacterial host to another; in other cases, bacteria slurp up DNA from dead microbes and insert it into their own genomes. In still other cases, genes can spontaneously slice themselves out of one genome and get inserted in the DNA of a distantly related species. The most famous example of this process is antibiotic resistance. One reason that resistant bacteria can spread so quickly in a hospital is that inheritance is not the only way these microbes can get hold of the genes that can fight off a drug. Every now and then, the genes get transferred from one species to another; the lucky bugs that receive them soon outcompete their cousins who lack the defense. Horizontal gene transfer, as it’s known, may involve a single gene or an entire network of genes. And when two networks arrive in an alien genome, they can combine together into a bigger network that can do something entirely new. Horizontal gene transfer gives bacteria an extra dimension of creativity.

Our penchant for pollution has given bacteria a new opportunity to flaunt this extra creativity. Over billions of years, they evolved the ability to eat just about any source of carbon on the planet. But in the past century we have created synthetic chemicals that bacteria have never faced before (or faced in only tiny amounts). In many cases, these chemicals kill off most of the bacteria that encounter them. Over the years, though, strains have emerged that can not only survive exposure to these pollutants but can even devour them. Scientists have unpacked the genomes of these hardy microbes to figure out how they evolved a solution so quickly. It turns out that microbes are swapping genes and gene networks, and then assembling them into networks that can handle the chemical at hand. Last year, for example, scientists looked at the bacteria that thrive in ground water near a Texas Air Force base polluted with fuel. One strain of bacteria there can break down chlorobenzene with a series of enzymes. This chlorobenzene-destroying network actually is the product of two smaller networks that can each be found in other bacteria strains in the same ground water. One turns chlorinated benzenes into another compound known as chlorocatechol. The other breaks chlorocatechol down into smaller molecules. Only in the strain studied by the scientists did these two networks come together to create an entirely new kind of metabolism.

These bacteria show an evolutionary nimbleness we will never enjoy. But it may be possible to harness them to clean up the messes we make.

(For more information, see this fascinating survey in the March issue of Nature Review Genetics.)