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Systems Biology Provides Clues to Bacteria with Bioremediation Potential

NEW YORK (GenomeWeb News) – An American research team has taken a systems biology approach to understanding the diversity found in Shewanella — a bacterial genus touted for its bioremediation potential.

The researchers brought together genomic, proteomic, and physiological data for ten Shewanella strains in order to get a better sense of how genotype relates to phenotype. The work, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, suggests relationships between the strains are more complicated than previously appreciated, with related strains not necessarily sharing the same functions.

"[T]raditional microbiological approaches would suggest that the physiology and phenotype of these Shewanella bacteria are very similar, if not identical, but that is not true," lead author Kostas Konstantinidis, an environmental microbiology and genomics researcher at the Georgia Institute of Technology, said in a statement.

In the past, a great deal of bacterial classification has been based on phenotype, physiology, and comparisons between known species. But the genetic aspect of this classification has usually been limited to sequence data from 16S rRNA genes. Now, researchers are integrating information from genomic and proteomic work to clarify this bacterial classification.

"The powerful genomic tools now available provide the opportunity for a much more detailed and informative evaluation of the relationship between genetic and phenotypic similarity," the researchers explained.

To do this, the team used genome sequence data generated by researchers from the US Department of Energy's Joint Genome Institute for ten Shewanella strains. The researchers also employed mass spectrometry to get proteomic data for the same strains grown under different environmental conditions.

When they assessed the average nucleotide identity between any two of the ten Shewanella genomes, the researchers found that the most closely related pair — Shewanella sp. MR-4 and MR-7 — had an ANI value of roughly 98.4 percent. That pair was closely followed by S. putrefaciens strains W3-18-1 and CN-31, which had an ANI of about 96.5 percent.

On the other hand, most of the Shewanella strains shared less than 70 percent ANI with the four most divergent Shewanella strains: S. frigidimarina NCIMB400, S. denitrificans OS217, S. loihica PV-4, and S. amazonensis SB2B.

Of the 9,782 non-redundant protein-coding genes that have been annotated in the ten genomes, the researchers noted, just 22 percent or so appeared to be core genes present in all of the strains. Meanwhile, a third of the genes were shared between at least two strains and nearly half were unique to one of the strains.

Unexpectedly though, the strains with the highest ANI didn't necessarily share the most expressed genes. Instead, the researchers speculated that strains' adaptations to particular environments played a larger role in the bugs' functional repertoire, although more closely related strains tended to have similar proteins.

"These findings suggest that similarity in gene regulation and expression constitutes an important factor for determining phenotypic similarity or dissimilarity among the very closely related Shewanella genomes," Konstantinidis said in a statement.

And, the researchers noted, while the majority of genes found in the Shewanella genomes reflected the evolutionary history of the strains being examined, many of the bugs' key functions were not necessarily shared with other members of the same lineage. Instead, horizontal gene transfer, including the transfer of genomic islands, appears to have significantly contributed to Shewanella functions.

"If you put that strain in an environment that contains high concentrations of uranium, that microbe is likely to acquire the genes that accept uranium from a nearby strain, in turn preventing uranium from spreading as the groundwater flows," Konstantinidis explained.

The researchers are in the process of replicating their results and conceded that the current study has limitations — including a restricted set of growth conditions and an incomplete understanding of what some of the Shewanella genes do.

Still, the team expressed enthusiasm that their results may prove useful for understanding how certain Shewanella strains acquired their bioremediation-related skills — and for selecting strains best-suited to cleaning up specific environments.

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