Genome sequences of stinky bacteria
Via Science Daily, and published in manuscript form in the journal Genome Biology, a report on the genome sequencing of a sulfate-reducing bacterium. Now ordinarily, the sequencing of a bacterial genome has become so commonplace, it almost isn’t news anymore, however I honed right in on this one: Desulfovibrio vulgaris. This bacterium is a member of an ubiquitous family of Gram negative curved rods that are found in a number of terrestrial and aquatic (freshwater and marine) environments. I became familiar with genus Desulfovibrio in junior high school when visiting my father’s microbiology lab at the University of Delaware. He, along with his collaborators, studied the related bacterium Desulfovibrio africanus. BIO230 students may complain about some of the smells generated by family Enterobacteriaceae in lab, however that stench pales in comparison to the
sulfur sulfide produced by sulfate reducers. When D. africanus cultures were being grown in Wolf Hall, everybody in the building knew about it!
The present report describes the initial molecular characterization of an organism with significant potential for bioremediation. D. vulgaris is of interest as a model organism for the study of these bacteria, and is well known for its ability to metabolize metals. Because of this trait, many species of Desulfovibrio are extremely undesired in situations like oil drilling, and they speed corrosion of structures such as oil rigs. The organism also holds significant promise, in that it is also effective at metabolizing heavy metals and radioactive nuclides, and so may be able to degrade toxic environmental contaminants.
The availability of the complete, annotated genome sequence opens up the possibility of tailoring the organism to degrade these compounds more efficiently, for the purpose of introducing them into for bioremdiation purposes. Many of the biochemical pathways that might be useful to humans, for instance the ability of an organism to extract and sequester cadmium from the environment for bioremediation, are not turned on all the time in the bacterial cell. Consequently, it is helpful to identify ways that we can direct the organism to turn these pathways on when it is convenient for us. Many of these pathways are turned on by molecular switches; the organism senses a certain stimulus in the environment, which then turns on a gene response pathway. The genome sequence will allow us then to bypass these sensors and create a situation where the response pathway such as scavenging cadmium from the environment is turned on all the time.
The complete genome sequence of Desulfovibrio vulgaris is not the first genome from this genus to be obtained. A quick search at the National Center for Biotechnology Information reveals that a number of isolates from Desulfovibrio are either completely sequenced or are underway, including the 4.2 megabase sequence of D. africanus, although that sequence has not been finalized and published. The availability of multiple, related sequences enables the rapid comparison of a family of highly related species, which in turn can help us to create a more fully engineered strain to help us clean up toxic environments.