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Researchers Report on Metagenomic Method for Characterizing Bacteria at Bioremediation Site

NEW YORK (GenomeWeb News) – In a paper appearing online today in Science, researchers from the University of California at Berkeley, Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory, and the Pacific Northwest National Laboratory described the slew of microbes that they unearthed through metagenomic sequencing studies of a uranium contaminated site undergoing bioremediation in Colorado.

From groundwater samples collected over several days at the acetate-treated site, the researchers discerned gene sequences that seem to represent dozens of organisms. For 49 of the microbes identified in these samples, they had enough sequence data to produce partial or nearly complete genome sequences, which were subsequently used to start assessing metabolic features in the organisms.

"All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon," authors of the study explained.

By continuing to characterize these bugs and their metabolic capabilities, researchers hope to uncover some of the mechanisms that microbes use to deal with heavy metals and various other toxic contaminants — information that could serve as inspiration for new methods of dealing with environmental contaminants and/or reducing greenhouse gases in the future.

"What these genomes have given us is amazing in terms of being able to look under the hood at the machine of these organisms that we never really knew anything about, except that we saw them in certain types of environments," first author Kelly Wrighton said in a statement.

"We now have information, which is encoded in their genomic DNA, pertaining to what they look like, how they make their living in the environment, and the interactions they have with other organisms," added Wrighton, a post-doctoral researcher in senior author Jill Banfield's earth and planetary science lab at UC Berkeley.

The study focused on an underground aquifer associated with a contaminated mill in Rifle, Col., that was in the process of being bioremediated. In the past, the site had been used to process vanadium and uranium. And because it is located not far from the Colorado River, efforts have been made to convert contaminants to forms that are less likely to leech into this and other neighboring bodies of water.

As part of the site amendment process, the team started by adding acetate to the aquifer, a method used to boost the levels of bacteria that slurp up dissolved metals and, through reduction, turn them into less mobile, insoluble forms.

A few days after this acetate addition, the researchers started collecting water samples from the underground site using 16S ribosomal RNA sequencing and metagenomic sequencing to assess microbial DNA in the samples.

From 16S and metagenomic sequence data generated by Illumina sequencing, the team then assembled genomic profiles for microbes in samples collected five, seven, and 10 days after acetate was added at the site.

Rather than turning up mainly Geobacter bemidjiensis bacteria, which are known for their metal-reducing prowess in acetate-treated sites, researchers found sequences from a variety of other bugs as well — around 87 organisms, by their estimates.

For 49 of the microbes, they produced genome sequences that were between about 67 and 95 percent complete. These included representatives from bacterial divisions, called OD1, OP11, and BD1-5, that tend to turn up in low-oxygen environments as well bacteria from divisions dubbed PER and ACD80.

Using the genetic sequences coupled with some proteomic profiling experiments, the team started delving into the metabolic capabilities of the anaerobic bacteria from the acetate-amended sites — for instance, looking at the methods that various members of the microbe community use to reduce sulfur and assimilate carbon dioxide.

In a bioremediation setting, Banfield explained in a statement, "it is critical not to just detect the relevant genes in subsurface microorganisms, but to know enough about the lifestyles of the organisms with genes of interest so that manipulation of the system enriches specifically for that organism."

The team is reportedly doing metagenomic analyses on additional samples from the Colorado site. By comparing samples collected before and after the acetate addition, for instance, it should be possible to more clearly define the population of microbes that prevailed at the site prior to bioremediation.

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