Gene sequencing explains why natural bioremediation 'bug' has big appetite for chlorinated pollutants

Jan 6 2005

"The born-to-dechlorinate bug" is what Cornell University researchers called Dehalococcoides ethenogenes Strain 195 when they found the bacterium obligingly detoxifying the pollutant PCE, or perchloroethylene (a chlorinated solvent used for dry cleaning), in sludge from an Ithaca, N.Y., sewage treatment plant.

Their discovery led to two questions: Might cultures of the naturally occurring microorganism serve as bioremediation agents to clean up sites where solvents such as PCE and TCE (trichloroethylene) -- used to clean metal parts -- had been dumped or spilled? And what on earth had the bug been eating before synthetic chlorinated compounds were invented some 50 years ago?

Sequencing of the Strain 195 genome at the Institute for Genomic Research (TIGR), Rockville, Md., which is reported in the latest issue of the journal Science (Jan. 7, 2005), helps resolve the second question. An up-and-coming bioremediation industry, based on Strain 195, answers the first.

"Strain 195 has a relatively small genome, only about a third the size of E. coli's in base pairs, but it's a highly adaptable one with clusters of genes called mobile genetic elements," says Cornell professor of microbiology Stephen H. Zinder. He named and studied Strain 195 after James M. Gossett, Cornell professor of civil and environmental engineering, found the enterprising organism in sewage sludge.

"Just by picking up these mobile genetic elements from other bacteria, Dehalococcoides strains seem able to adapt and to take advantage of opportunities as they present themselves," Zinder notes.

The genomic analysis showed how various Dehalococcoides strains are able to make enzymes called reductive dehalogenases to dechlorinate chlorobenzenes, chloronapthalenes, polychlorinated biphenyls and dibenzodioxins -- by turning the genes on and off as the organism detects something appetizing. Since Strain 195 requires diverse nutrients in its growth medium, it was a surprise when the genome sequence showed genes for fixing nitrogen and remnants of genes for fixing carbon dioxide, Zinder notes. "It once must have been a much more independent organism," he observes.

Another biochemical trick for the deceptively simple and unremarkable looking bacterium, Zinder says, is that "it has five different hydrogenases -- it is highly adapted to using hydrogen."When Zinder and Gossett first published news of the discovery in Science (June 6, 1997), Zinder said the anaerobic bacterium detoxifies PCE via a reduction process that leaves little more than ethylene, the natural gas that causes fruit to ripen.

But what were Dehalococcoides bacteria doing for a living before humans devised chlorinated solvents, the highly effective cleaning compounds that also are potentially carcinogenic chemicals and now pose a significant threat in the environment? The Cornell researchers think Strain 195's genetic antecedents were reducing some of the hundreds -- or even thousands -- of natural chlorinated compounds that existed long before we came up with Martinizing.

"Some natural halogenated compounds are made by marine algae," Zinder observes. "We have a saying in the microbiological world: Everything is everywhere. So wherever chlorinated compounds popped up, maybe some form of Dehalococcoides adapted to dechlorinate it."

Or maybe Bruce Springsteen should sing "Born to Dechlorinate," considering that New Jersey has at least one industrial cleanup site where Dehalococcoides is living the "runaway American dream." Zinder points to a map of the United States displaying contaminated sites at which naturally occurring Dehalococcoides has been found.

However, Dehalococcoide is not found at all sites with chlorinated pollutants -- and at those sites bioremediation fails to neutralize a compound that still has two chlorine atoms left on it. Several companies are now marketing tests for Dehalococcoides and even cultures that can be added to groundwater to hasten the process. Some cleanup sites are on air force bases and naval air stations, which explains why the Department of Defense has been interested enough to fund the research.

For a bug that thrives in nature, Strain 195 and other Dehalococcoides varieties are proving difficult to culture in the laboratory, the Cornell microbiologist acknowledges. Together, the academic and corporate researchers are learning more about Dehalococcoides husbandry. For example, it seems to like a cocktail of acetate, vitamin B-12 and extracts of mixed microbial cultures as nutrients. One bioremediation company even adds molasses to the elixir it injects into pollution sites.

Since their Strain 195 discovery was not patentable, the academic scientists have not profited from their research -- except in scientific acclaim.

Future patents are unlikely, Zinder adds, "because Dehalococcoides apparently is intractable to genetic engineering. That's all right. It's doing a pretty good job of engineering itself."