The Loom

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.)


  1. #1 mary freeman
    March 7, 2004

    Wonderfully full and compact–I admire your writing! Your essay made me think of this poem of mine:


    New snow is floating down darkly on old:
    Its shadows are deep. I think of viruses’
    Dominion of man, how they raised him up
    In their own conceit while he ran amok
    Building his cities, their image conceived
    As his own–the viral paradigm divine.
    Three billennia ago it happened,
    They devised the plan: “We’ll let the apes grow
    Fringey types, let ’Sapiens take dominion–
    Let him live. As aphids to ants they’ll be
    To us”–this was before the aphids arrived
    Of course, and they were speaking Metaphor,
    The language of viruses long ago,

    In a fission they saw it, saw him rise
    To Parnassus, test the bonds that bound him,
    Discover his power’s use and license
    Saw him, finally, discovering them–
    The viral invasion, the ooze sublime.
    There in deepening, darkest endurance,
    In apocalyptic throes they triumphed,
    Preoccupied: “As molds to gravity
    They’ll be like to us, gravely intent on
    Purposes only the holy inspire!” –
    They saw him in their lowly image shine.
    Like old snow brightened by new, the viruses
    Gleam in the shadows, and dream the divine

  2. #2 Nic Tamzek
    March 12, 2004

    Well, I don’t have a poem, but I would like to mention that the evolution of catabolic pathways is the perfect example of the evolution of “irreducible comlexity” in modern times, which as you will recall is exactly the thing that the Intelligent Design folks say can’t evolve.

    (1) These catabolic pathways typically break down “xenobiotic” compouds that humans have only recently introduced into the environment

    (2) These compounds are typically environmentally persistent toxins. Sometimes they are pesticides or herbicides, or by-products of other nasty compounds like explosives. Much of the the research on the evolution of the degradation pathways is done by military-funded labs, because the military has a big problem with polluted ground on military bases where chemical weapons, explosives, etc. were stored.

    (3) The degradation pathways typically have multiple required proteins in the breakdown process. Often the compounds contain e.g. aromatic rings protected by tightly-binding atoms such as chlorine, and stripping off the chlorines and then breaking open the rings are all required before a non-toxic “eat-able” carbon chain is produced.

    Some example papers:
    * Copley, S. D. (2000). Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochemical Sciences V25(N6): 261-265. Source:

    * Johnson, G. R., Jain, R. K. and Spain, J. C. (2002). Origins of the 2,4-Dinitrotoluene Pathway. Journal of Bacteriology 184(15): 4219-4232. Source:

    * (Atrazine pathway evolution) Sadowsky, M. J., Tong, Z., de Souza, M. and Wackett, L. P., 1998. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J Bacteriol. 180 (1), 152-158. URL:

    * (Atrazine pathway evolution) Seffernick, J. L. and Wackett, L. P., 2001. Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry. 40 (43), 12747-12753. URL:

    The McAdams et al. Nature Reviews Genetics paper you linked to mentions studies like these, and also last year’s paper in Nature by Lenski et al. that did a computer simulation of the evolution of an “irreducibly complex” system. McAdams et al. don’t miss the chance to take a swipe at Intelligent Design:

    These experiments are particularly valuable as they show how straightforward evolutionary mechanisms of mutation and selection can produce steady increases in organism complexity without invoking ‘intelligent design’.

    So far, the ID folks seem to be saying that the computer simulation is irrelevant for [insert obscure hair-splitting here], and they seem to hope that if they completely ignore the studies on the evolution of catabolic pathways for xenobiotic compounds, the studies will just go away. I would not bet on their strategy over the long term. But then again, the ID folks appeal entirely to the public and avoid discussions with the relevant scientific experts like the plague, and their strategy seems be having some success lately. I’m glad that there are at least a few people like Carl Zimmer around to help get the word out.