Using nature’s miracle bugs to help feed the world

By Edmund L. Andrews

Nitrogen-based fertilizer has been the linchpin of modern agriculture for the past century.

It’s nitrogen that increases crop yields, and makes grass greener and gardens more opulent. The chemical industry extracts 100 million metric tons of it from the atmosphere each year.

But producing the kind of nitrogen that’s useful for plants requires enormous amounts of energy – temperatures of 1000 degrees Fahrenheit at extremely high pressure. It’s a significant contributor of greenhouse gas emissions and many other forms of pollution.

Now, researchers at Stanford Engineering have developed a way to leverage nature’s own processes to produce plant-ready nitrogen at room temperature. They did it by tinkering with the genetic machinery of bacteria that already form symbiotic relationships with cereal crops like corn, wheat and rice.

Indeed, the researchers were able to create what amounts to a genetic on-off switch for converting atmospheric nitrogen into ammonia, an important source of nitrogen for plants. When the modified bacteria were cultivated alongside plants, they generated both measurable increases in plant health and growth.

“We’ve made use of something that nature has come up with to symbiotically feed our plants,” says Tim Schnabel, a PhD candidate in bioengineering at Stanford who carried out much of the work. “Instead of working against nature with synthetic chemicals, we’re working with nature to solve one of the grand challenges in sustainably producing enough food for the world.”

Since the earliest breakthroughs in genetic engineering in the early 1970s, scientists have dreamed of getting microbes to produce abundant plant-ready nitrogen. In what’s often described as a small miracle, many bacteria that colonize around the roots of plants convert nitrogen from the atmosphere into ammonia at ambient temperatures.

In nature, however, the microbes that colonize cereal plants don’t make much more ammonia than they need for themselves. They use most of it to make glutamine, a key amino acid that’s a building block for proteins and for life itself.

Despite decades of effort, genetic engineers have been unable to turn the microbes into sustainable, high-volume fertilizer factories because of the complex regulation surrounding nitrogen metabolism.

Until now, perhaps. Schnabel teamed up with Elizabeth Sattely, an associate professor of chemical engineering at Stanford and a Howard Hughes Medical Institute investigator, to design a new strategy to help achieve the goal. To prove their concept, they delved deep into the nitrogen machinery of Azospirillum brasilense, a bacterial strain that lives alongside many food crops.

“The advantage of engineering with a microbe is that you can use it with a hundred different plants and they can all do better,” says Schnabel. Indeed, the nitrogen project is part of broader research on the vast array of microbes that occupy the biome in and around plants. The microbes get nutrients from the plants and return the favor in all kinds of other ways, from fending off predators to producing hormones. In effect, the microbes give plants a huge array of additional capabilities to survive and thrive in tough environments.

Writing in the journal Applied and Environmental Microbiology, Schnabel and Sattely document that their genetically modified bacteria not only produced much more ammonia than normal but also sparked faster growth in neighboring plants.

The key was in modifying the mechanism that regulates what the bacteria do with the ammonia they make. That mechanism combines the ammonia with glutamate molecules to make glutamine.

Schnabel and Sattely inserted a new gene to largely deactivate the glutamine production. That leaves the ammonia in its original form, but it also spurs the cell to make even more because it senses that it needs to make more glutamine. With nowhere else to go, the excess ammonia seeps out the cell membranes and into the plant roots.

Schnabel and Sattely were able to measure the increased ammonia production and then confirm its impact on plant growth. Using isotopes to label the nitrogen gas that the bacteria were receiving, they were able to track its conversion to ammonia and its assimilation into the plants. And it had an impact: The plants that were cultivated alongside the modified bacteria added 54% more biomass and 74% more chlorophyll than the plants that were not.

Sattely and Schnabel caution that challenges remain. The most daunting is the ability of microbes to evolve rapidly in a world where survival goes to the fittest. If the engineered bacteria are less robust and can’t compete well, because they’re using energy to make nitrogen that they give away, they will inevitably start adapting to stop doing that.

The researchers were able to slow that process by adding an extra copy of the modified gene. It takes longer to mutate multiple genes, so the microbes maintain high ammonia production much longer as well.

But the real key going forward may be that the modified gene is “tunable” – it can be switched on and off by adding or withholding a compound that activates the gene. “We can envision turning it on and off every 24 hours if we wanted to,” Schnabel says. “These are logic gates, so you can engineer whatever control mechanism you want.”

That’s important, because adaptation back toward less nitrogen production only happens when the switch is turned on. In the long run, the key may lie in designing microbes that can both produce lots of nitrogen and take proper care of themselves.