A genus of bacteria that plays a crucial role in the functioning of the marine ecosystem has a genome loaded up with DNA that doesn't make proteins. While this is a common feature of animals and plants, it has not been seen before among bacteria. The scientists who discovered this anomaly have no explanation yet, but expect that finding one may tell us a lot about an exceptionally important, but neglected, microbe.
Trichodesmium brings life to vast stretches of the open ocean that would otherwise be barren. It has the capacity to “fix” nitrogen, converting the N2 molecules in the atmosphere to ammonium, which can then be used by other life forms. The six species of Trichodesmium are the prime fixers of nitrogen in warm but nutrient depleted waters across tropical and subtropical regions.
The huge Trichodesmium blooms that sometimes occur, and are visible from space, have earned the bacterium the nickname “sea sawdust.” Darwin attributed the name the Red Sea to the presence of large Trichodesmium erythraeum blooms, although this etymology is disputed.
It was for their importance, rather than an anticipation of anything unusual about the Trichodesmium genome, that Dr. Eric Webb of the University of Southern California decided to sequence the bacteria's DNA. He found that 63.8% of T. erythraeum's genome coded for proteins. Webb and his PhD student Nathan Walworth reported the result in Proceedings of the National Academy of Sciences, having confirmed that other Trichodesmium species are similar.
For an animal, 63.8% would be an impressively high percentage. Only 1-2% of the human genome is coding DNA, while the puffer fish is unusually high by animal standards at 10-15%.
By bacterial standards, however, 64% is extraordinarily low. In general, 85% is a more typical figure, and the proportion is higher among oligotrophs—species that survive were nutrient levels are low. This leaves a lot of room for non-coding DNA, which oligotrophs normally find takes too much energy to produce. But for the members of the Trichodesmium genus, the non-coding components are packed together into large sections that are highly conserved.
"The unique evolutionary path reflected in this genome contradicts nearly all accounts of free-living microbial genome architectures to date," said Walworth. "Different evolutionary paths are foundational to all arenas of biology, including biotechnology, so it is important for the field to be cognizant of different paths a living organism can take to achieve ecological success."
"Our study adds another wrinkle to this enigmatic organism's story," says Webb.
Webb and Walworth speculate that the huge blooms that characterize Trichodesmium make the species more likely to experience genetic drift, which leaves a trace in additional non-coding DNA. They think this is only part of the explanation, however, with Webb saying, “Since there are many other bloom-forming cyanobacteria that do not have expanded non-coding space, blooming ecology is likely not the whole story. Right now we speculate that interactions with other undefined organisms might also be important.”