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Waves of Berkeley Lab responders deploy omics to track Deepwater Horizon cleanup microbes
Date:6/21/2012

the microbes responded to the influx of oil. They focused on the community's expressed functional information or metatranscriptome. In addition, they isolated single cells to identify the predominant microbial members in the deep ocean oil plume. Using the latter technique, they were able to assemble a draft genome of what they say is the first deep-sea, oil-eating bacterium from a single cell.

Jansson's postdoctoral fellow Olivia Mason collected deep water samples from the oil plume that appeared during the Deepwater Horizon spill 1.5 kilometers and 11 km from the wellhead and the samples were analyzed by a team of scientists back at the Berkeley Lab. Mason extracted DNA and RNA from the samples and at the DOE JGI, researchers led by Microbial Program head Tanja Woyke and Metagenome Program head Susannah Tringe subjected the samples to deep sequencing approaches, generating billions of bases of data for each sample. Mason analyzed the resulting metagenomic (DNA) and metatranscriptomic (RNA) sequences to reveal genes for functions such as hydrocarbon degradation. Data analysis revealed an abundance of genes involved in the degradation of alkanes, as well as genes involved in degradation of aromatic compounds. A separate group under DOE JGI Microbial Program head Tanja Woyke worked to isolate and sequence three cells of Oceanospirillales bacteria, two of which they were able to co-assemble into a draft genome.

Mason then searched against a database of microbial proteins known to be involved in the pathways for breaking down hydrocarbons. The results suggested that the microbes responding to the plume were predominantly Oceanospirillales bacteria, able to break down cyclohexanes.

Jansson said that the results suggest a succession of microbes acted on the oil spill, degrading different fractions. "I think what we're seeing are these waves of community members and this is known to happen in the ocean. We probably have a bloom of alkane degra
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Contact: David Gilbert
degilbert@lbl.gov
924-296-5643
DOE/Joint Genome Institute
Source:Eurekalert

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