Tuesday, January 11, 2005

Mighty motes

It really seems that microbes can do anything. Last week, Kristen Philipkoski of Wired magazine wrote about the publication of the genome sequence of Dehalococcoides ethenogenes in Science (subscription link). These bacteria are capable of breaking down a number of chlorinated pollutants, including tetrachloroethane (PCE), which are among the most prevalant groundwater contaminants in the US. Although this microbe (or its close relatives) has been found growing in the wild at a number of polluted sites, it has been hard to get it to grow in the laboratory, making study of its chlorine-busting activity very difficult.
Philipkoski and the Science authors point out a wrinkle in the natural biology of this microbe: it is pretty heavily specialized for metabolizing compounds which have only existed in significant amounts for about fifty years. Thus, the polluted environment might have in effect created a brand-new ecological niche, which then, via natural selection, stabilized a very recent genomic transfer of the right metabolic capabilities. A peek at at the genome of D. ethenogenes supports this idea: the genome is full of what appear to be fairly recent modifications, including gene duplications and large inserted elements (IEs). Some of the IEs contain chlorine-reducing genes, including the one which confers the ability of this microbe to remove the final chlorine from pollutants. All these genomic changes may have damaged other capabilities of the ancestral microbe, and present-day D. ethenogens survives in the wild via symbiosis with other microbes. It's probably successful mainly because there's very little competition for this niche. An interesting question, given how fast this microbe arose, is whether a second, independent microbe is out there exploiting the same niche elsewhere.

I think these observations can be very good news for the prospect of cleaning up chlorinated compounds from the environment. The genome of this microbe was essentially cobbled together on the quick by natural selection. This gives hope that scientists could do the same artificially, creating new microbes to clean up sites where D. ethenogenes has trouble growing, or even to help detoxify other classes of chlorinated compounds. The Institute for Genomic Research, the main authors of this work, have also looked at other bugs which which can tackle other kinds of pollutants.

The second notion which struck me upon reading this article is that there seems to be literally nowhere on Earth where there is liquid water and not life. E.O. Wilson tackled this idea in some detail in The Future of Life . For me, this suggests that life on Mars, which would require a combination of capabilities not found in Earth microbes , is still a distinct possibility. Microbes continue to be discovered on earth in "improbable" settings. As a recent example, the same issue of Science has a second article discussing sea-floor microbes which grow in the presence of incredibly high levels of magnesium. Michael Faraday's remark that "nothing is too wonderful to be true" seems tailor made for the microbial world.

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