Plants, like all living things, need nitrogen to build amino acids and other essential biomolecules. Although nitrogen is the most abundant element in air, the molecular form of nitrogen found there is largely unreactive. To become useful to plants, that nitrogen must first be "fixed," or busted out of its molecular form and linked with hydrogen to make ammonia. The plants can then get at it by catalyzing reactions with ammonia.

But plants can't fix nitrogen. Bacteria can.

Some legumes and a few other plants have a symbiotic relationship with certain bacterial species. The plants build specialized structures on their roots called nodules to house and feed the bacteria, which in turn fix nitrogen for the plants and assure them a steady supply of ammonia. Only 10 families of plants have the ability to do this, and even within these families, most genera opt out. Ever since the symbiosis was discovered in 1888, plant geneticists have wondered: why? If you could ensure a steady supply of nitrogen for use, why wouldn't you?

A global consortium of geneticists sequenced and compared the genomes of 37 plants—some symbiotic, some not; some that build nodules, some not; some agriculturally relevant, some not—to try to find out what was going on. The group's genetic analysis of the conundrum was reported in Science.

The authors considered three possible influences on the presence of the plant-bacterial partnership: (1) an ancestor underwent a predisposition event that allowed the symbiosis to evolve; (2) symbiosis independently evolved multiple times; and (3) symbiosis was also independently lost multiple times.

They figured that any genes required for a predisposing event would be present in all of the nodulating species, and found only in them and their clade—the other plants descended from the same forbears. They found zero genes meeting this criterion. So if a predisposing event did happen, it did so by coopting extant genes instead of via new ones.

Then they looked for the expansion of a gene family in symbiotic plants, since this is one method by which a trait can evolve multiple times. They didn’t find genes like this either.

To see if genes governing symbiosis had been lost—which seems weird, since nitrogen fixation is so vital—they looked for genes found only in nodulating species and plants outside their clade but not in most non-nodulating species within their clade. The existence of such a gene would imply that an ancestor would have had it but the non-modulating species would have lost it along the way.

Lo and behold, a gene called NIN (named for its function, Nodule Inception) fit the bill. The non-nodulating species had the same genes surrounding NIN as their nodulating cousins, but eight different deletion events had erased the NIN gene from different species. One other gene, also required to house the symbiotic bacteria, followed a similar pattern.

"Use it or lose it" applies to genes as much as (or maybe even more than) anything else. Genes involved in biological processes are lost if the trait they confer is unused or unnecessary. For most of the time that plants have lived on this planet, nitrogen has been limiting, so symbiosis should have been favored. But it was jettisoned at least eight different times. Maybe it was too energetically costly for most plants to keep: maybe housing and feeding the bacteria wasn't worth it, or non-nitrogen fixing bacteria took advantage and moved in.

Synthetic biologists are currently working to engineer nitrogen fixation into crops—it's a worthy goal, as it could decrease the use of fossil fuels to manufacture nitrogen fertilizer and prevent the runoff of said fertilizer into water sources. But they should bear in mind that, when left to their own devices, plants got rid of their ability to fix nitrogen time and time again.

Science, 2018. DOI: 10.1126/science.aat1743 (About DOIs).