Tough microbes to treat toxins?

Human pollutants can cause drastic decreases in microbial diversity, but the bacteria that survive the contamination may yield clues for how to remove such toxins from the environment, according to a study published in The International Society for Microbial Ecology Journal. This study suggests "that bacteria can survive in highly toxic environments," said linkurl:Mihai Pop,;http://www.cbcb.umd.edu/~mpop/ a bioinformaticist at University of Maryland, who was not involved in the research.

Aircraft Reactor Experiment Building
Oak Ridge National Laboratory
Image: Wikimedia commons,
Lcolson

"[By] knowing which bacteria can live in a contaminated environment, we can start figuring out how to modify them to perform useful bioremediation options," he added, referring to the use of microbes to remove environmental toxins following chemical spills and other pollutants. From the 1950s to 1980s, numerous toxins -- including nitrate, heavy metals, and radionuclides such as uranium and technetium -- were dumped into ponds near Oak Ridge, Tennessee following nuclear weapons testing at the Oak Ridge National Laboratory. These pollutants leached into the groundwater and rocks, causing widespread contamination. A parking lot built in the late 1980s now sits overtop of these ponds to prevent rainwater from entering the ponds and further spreading the pollutants. With a very low pH of 3.5 and one of the highest concentrations of uranium -- which can bind to DNA and cause mutations -- the site has become a toxic environment where most species are unable to survive. Microbiologist linkurl:Chris Hemme;http://ieg.ou.edu/postdocs.html of the University of Oklahoma and an interdisciplinary team of biologists, hydrologists, and geologists analyzed the genetic material derived from environmental samples -- the site's so-called metagenome -- to determine characteristics of a stressed microbial community. Within an area of contaminated groundwater, the researchers identified fewer than 10 species total, compared to about 400 found in the surrounding soil. The contamination "pretty much eliminated diversity in groundwater," said Hemme. "What we are seeing is either the surviving community or re-colonization" with far fewer species than a typical sample of aquatic microorganisms. Correlating the metagenomic results with aspects of the microbes' physiological processes suggested that the contaminated community has evolved in response to the new environmental stressors. First, the microbes demonstrated magnified de-nitrification activity -- the major mechanism of returning nitrogen to the atmosphere from soil and water -- likely in response to the higher nitrate concentrations surrounding the community. In addition, the team detected greater numbers of metal resistance genes, which corresponded with the high levels of heavy metals at the site. "What we see at the site is very rapid adaptation of the community to the environment," said Hemme. By understanding how some microbes not only survive human-related pollutants, but actually process those toxins and eliminate them from the environment, scientists may gain some clues about how to clean up contaminated environments, Hemme said -- a process known as bioremediation. For example, researchers at linkurl:Argonne National Laboratory;http://www.anl.gov/Media_Center/News/2010/news100318.html recently identified a bacteria that "can change uranium into a state that is not water-soluble," Pop said, ensuring it doesn't spread. The current study, which is the first sequenced metagenome of a human-induced pollutant community and one of a handful of metagenomes sequenced from low pH environments, could identify more microbes with potentially useful qualities for bioremediation. This research is "really important for future studies," said linkurl:Rob Edwards,;http://edwards.sdsu.edu/labsite/ a bioinformaticist at University of California San Diego who was not involved in the study. Once more metagenomes are assembled, including those from nearby non-polluted sites, the contaminated sites can be compared in detail to the uncontaminated controls to understand the influence of different environmental factors on the microbial populations. Indeed, Hemme and his colleagues have already begun analyzing the metagenome of a non-contaminated background site also at the Oak Ridge Federal Research Center. By studying the Oak Ridge Federal Research Center site, Hemme said, scientists "really get a comprehensive view of what's happening" in a contaminated system. C. Hemme et al., "Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community," The ISME Journal, published online February 25, 2010, doi:10.1038/ismej.2009.154.
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