Piranha to Petunia

Cataloguing with the Darwin Decimal System

RNA model
Ribose sugars and phosphate backbones combine with base pairs in the familiar helix.
Credit: Darryl Leja/Access Excellence.

From person to piranha to petunia, it’s pretty easy to spot different species in the human-scale part of the plant and animal kingdoms. But a new study shows that species differences aren’t so clear, at least as currently measured, when it comes to microscopic bacteria.

MSU researchers have spotted significant differences in genetic libraries among thought-to-be similar bacteria strains. The results, published this week in the journal the Proceedings of the National Academy of Sciences, suggest that new definitions are needed to catalogue bacteria – single-celled organisms with at least a 3.5 billion-year history.

"It’s important to point out the importance of these small microbes on Earth; even though they are small, their mass in soil and water is equal to that of all plants," said MSU microbiologist James Tiedje, one of the study’s authors. "Furthermore, they are responsible for recycling the key elements of life so life on Earth can continue."

DNA, used by all life including bacteria to store genetic information, is a double-stranded molecule. When a given DNA molecule is split in two, for instance by heating it up, its two strands will spontaneously find each other, or reassociate, when the temperature drops.

Scientists have long exploited this fact in their rough rule-of-thumb approach for saying just what makes up a species of bacteria. Single strands of DNA from two bacteria are mixed together. If most of these strands reassociate – specifically, if 70 percent of strands from bacteria A come together with strands from bacteria B – then the two bacteria strains are said to members of the same species.

Matching genetic letters is equivalent to biochemical editing
Credit: www.lbl.gov

Tiedje and his MSU colleague, microbiologist Konstantinos Konstantinidis, set out to put this mix and match approach to the test. The two scientists selected 70 related bacteria whose genomes, or complete genetic libraries, had been fully sequenced.

A sequenced genome gives scientists what amounts to a card catalogue guide to an organism’s genetic information.

The MSU scientists downloaded the already-sequenced bacteria genomes from a variety of sites on the Internet. Then they did some cross-card catalogue comparisons.

To their surprise, many bacteria that are considered members of the same species by the current mix and match approach, often share as few as 65 percent of their genes. Humans, in comparison, share 75 percent of their genes with fish.

Relation between species in tree of life showing key kingdoms. Credit: UCLA

No one’s calling for the species rules to be rewritten so that humans are lumped with their distant underwater relatives. And when it comes to bacteria, the authors say, the current species definition appears to be too liberal.

Much of the differences between genetically-similar bacteria appear to be the result of environmental pressures. E. coli bacteria, for instance, exists everywhere from the intestines of warm blooded animals to paper mills. Any new way of tallying up bacteria species should "accommodate the ecological distinctiveness of the organisms," the authors write.

"The point is about the value of a correct understanding of species – people expect a species to have certain traits and live in certain habitats," said Tiedje, whose work is also supported by the Michigan Agricultural Experiment Station. "If the species definition is not reasonably predictive of this, then it loses its value. This can be important for pathogen identification, quarantine or biotechnology, for example."

Konstantinidis and Tiedje also noted that even bacteria with genetic card catalogues that were as much as 99 percent similar had enough outward differences to be separate species. This shouldn’t come as a shock. Humans and chimpanzees, in comparison, share 98.7 percent of their DNA. But that small difference at the genetic level results in a big difference when it comes to outward appearance.

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