Mike Kahn and Svetlana Yurgel, molecular biologists in Washington State University’s Institute of Biological Chemistry, have a challenge on their hands that involves one of the most abundant, but also difficult to obtain, substances on earth.

Nearly 80 percent of the atmosphere is nitrogen, and even that is only 7 percent of the total nitrogen on earth. However, most of it is locked up in rock. Only a tiny fraction of 1 percent of the total nitrogen is accessible to plants in the soil and in a form that can be used by living things.

And living things need nitrogen in a big way. Nitrogen is a key component of nucleic acids (a major component of DNA) and proteins, so it is about as essential as things get.

We get most of our nitrogen from plants or from animals that eat plants. But before plants can use nitrogen, the atmospheric gas must be “fixed,” changed to a more reactive form, and there are only a few ways that it can be fixed.

Lightning can fix atmospheric nitrogen. Volcanoes can release it from rock. But most nitrogen is fixed either through symbiosis between bacteria and legumes or through synthetic production.

By themselves, rhizobia bacteria search for nutrients and grow slowly. However, if legume plants, such as peas, lentils, and alfalfa, are growing in the vicinity, the rhizobia invade their roots. The infected roots develop growths called nodules that house the bacteria. In exchange for food and energy, the bacteria start fixing nitrogen for the plant.

Nitrogen produced synthetically through industrial chemistry called the Haber-Bosch process is the nitrogen that supplies the majority of modern agriculture. But like most good things, it also has a downside. Prime among these is the growing cost. Not only does the process rely on natural gas for hydrogen, but the high pressure and temperature of the process require enormous amounts of energy. Then of course is the transportation cost. Eighty percent of the nitrogen fertilizer used in the U.S. is imported. Add the cost of applying it at current fuel prices and it becomes expensive. Still, growing crops at current production levels without synthetic N can be, while not impossible, difficult.

With the help of their symbiotic bacteria, legumes do a fine job not only of fixing nitrogen for themselves but for subsequent plants, also. But only up to a point. For example, says Kahn, in the Midwest, a crop of lentils one year can produce enough extra nitrogen for a crop of wheat that follows, producing 40–50 bushels per acre. But lentils, which are grown as a rotational crop on the Palouse, cannot produce enough nitrogen to support a typical wheat yield in this area of 100 bushels or more.

What Kahn would like to do is fool the legume into thinking it needs more nitrogen than it has, so it would produce more nitrogen than it is actually able to use.

This is no easy task. Kahn has been working on similar strategies for the past couple decades. In spite of his work and that of others, much remains to be learned. For example, the signaling mechanism the plant uses to tell the bacteria how much N it needs is not well understood at all.

Also, persuading a legume and its bacteria to produce more N is not a simple matter of adjusting a metabolic governor so it produces nitrogen faster. Nitrogen fixation is a very energy-expensive reaction, perhaps the most expensive in nature. Producing more N would likely mean the plant would yield less seed.

Kahn does now have an advantage that was lacking in his earlier work. His colleague, Yurgel, recently discovered a mutant rhizobium that they hope will provide the key. For some reason, the bacteria produce nitrogen just fine. But the plant doesn’t turn green.

“We think what’s probably happening is the bacteria is making something with the N that the plant doesn’t know how to use,” says Kahn. “Our notion is that it [the mutant bacterium] is a little bit broken.”

Another piece to the puzzle is the mutant gene in the bacteria. It happens to be the gene that is involved in sensing the bacteria’s nitrogen status.

A clue! you say, with good reason. But just a clue.

Let’s back up a little. Kahn says the common, happy-family version of nitrogen-fixing symbiosis is probably not true. Plant and bacteria work together in symbiotic harmony, bacteria making nitrogen, plant getting green, and everybody’s happy, happy, happy.

Well, says Kahn, “Natural systems tend not to work strictly by altruism.” If this were the case, organisms would be much more vulnerable to parasitism. “Cheaters do prosper.” Organisms have ways, he says, of sanctioning non-cooperating cooperators.

So this leads us to Kahn’s wildest hypothesis:

Let’s say the bacterium wants to sanction the plant, for whatever reason. The most obvious way is to stop fixing nitrogen. But if they do that, they may have a problem. Nitrogen fixation is inactivated by oxygen. The bacteria deal with this by burning all the oxygen in the system in the process of fixing the nitrogen. (Remember the high energy.) So by fixing nitrogen, they’re creating the conditions that allow them to fix nitrogen. And what happens if they stop fixing nitrogen? They destroy the conditions they need to fix nitrogen.

So how can the bacteria not give nitrogen to the plant and still fix nitrogen?

One possibility is that they put the nitrogen in chemicals the plant can’t use. So the plant continues to tell the bacteria it needs nitrogen, because it does, even while the bacteria are pumping nitrogen to the plant in a form the plant can’t use. The plant is trying to cooperate. It’s doing everything it can to support bacterial nitrogen fixation. And nitrogen is getting fixed.

But because the bacteria’s sensor is broken, the system has a serious case of miscommunication. The plant is telling the bacteria to make nitrogen, but the bacteria can’t understand the signal and do something with the nitrogen besides feeding the plant. The plant is getting plenty of nitrogen, but it can’t use it in the form the bacteria supplies. It is like having canned soup and no can opener.

There must, thinks Kahn, be some way to exploit this communication breakdown. If the plant can glean some nitrogen, but tell the bacteria to keep pumping out more than the system needs, voila! More nitrogen for next year’s crop.