Surprising genetic diversity found among cleanup microbes

Researchers have uncovered a broad genetic diversity among members of a bacterial genus, using a cutting-edge “systems” approach that might one day help scientists choose the right microbe for environmental cleanups.

Employing modern genomics and proteomics techniques, the researchers found that Shewanella, an adaptable genus of bacteria found both in the oceans and on land, was more diverse than traditional microbiology approaches would suggest (P Natl Acad Sci USA 2009; doi:10.1073/pnas.0902000106).

“With many classical techniques, some of these bacterial strains would be indistinguishable from one another”, explains lead researcher Kostas Konstantinidis (Georgia Institute of Technology, Atlanta), “but when we gave them different heavy metals to grow on, some
expressed completely different proteins, even though they supposedly belong to the same genus.”

Because of their ability to metabolize a variety of metals and compounds, Shewanella holds promise as an environmental cleanup organism that could mitigate toxic spills or serve as
a pollution indicator. Determining which species of Shewanella would work best for cleaning up a certain toxin requires understanding their ability to metabolize certain the toxins into something not harmful to other organisms.

Using traditional microbiology techniques that focus on genetic material in the ribosome, the site of protein synthesis in bacteria, Konstantinidis and his colleagues found ten different strains in the Shewanella genus. But when they analyzed the bacteria using genomics (an analysis of the entire genome) and proteomics (an analysis of the full range of proteins produced by the bacteria), the researchers found greater diversity.

Some bacteria that were lumped into a single strain shared only 70% of the same genes. Nearly half of the 10,000 genes in the genus were found only in certain strains, and the assortment of proteins each strain produced was greater than that predicted by their genetic differences.

“We’re trying to get more scientific about doing this”, continues Konstantinidis. “During the past couple of decades, we mostly studied one gene at a time, but now we study a whole cell at a time, with all the genes and all the protein pathways that are expressed.”

Konstantinidis points out that systems-level approaches – as whole organism approaches that employ genomics and proteomics are typically called – could be used to determine which Shewanella strain might best be used for cleaning up certain toxic compounds.

Conversely, by measuring the activity of certain Shewanella genes or proteins, scientists might be able to use the bacteria to determine whether a toxin is present in a certain location.

Published in Frontiers in Ecology and the Environment