The corn vari­ety Sierra Mixe grows aer­ial roots that pro­duce a sweet mucus that feeds bac­te­ria. The bac­te­ria, in turn, pull nitro­gen out of the air and fer­til­ize the corn. If sci­en­tists can breed this trait into con­ven­tional corn, it could lead to a rev­o­lu­tion in agri­cul­ture. Photo from Wiki­me­dia Com­mons /​CC BY 4.0.

In the 1980s, Howard-​Yana Shapiro, now chief agri­cul­tural offi­cer at Mars, Incor­po­rated, was look­ing for new kinds of corn. He was in the Mixes Dis­trict of Oax­aca in south­ern Mex­ico, the area where the pre­cur­sors to maize (aka corn) first evolved, when he located some of the strangest corn ever seen. Not only was it 16 to 20 feet tall, dwarf­ing the 12-​foot stuff in Amer­i­can fields, it took six to eight months to mature, far longer than the 3 months needed for con­ven­tional corn. Yet it grew to those impres­sive heights in what can char­i­ta­bly be called poor soil, with­out the use of fer­til­izer.. But the strangest part of the corn was its aer­ial roots – green and rose-​colored, finger-​like pro­tru­sions stick­ing out of the corn’s stalk, drip­ping with a clear, syrupy gel.

Shapiro sus­pected that those mucousy fin­gers might be the Holy Grail of agri­cul­ture. He believed that the roots allowed this unique vari­ety of corn, dubbed Sierra Mixe and locally bred over hun­dreds or even thou­sands of years, to pro­duce its own nitro­gen, an essen­tial nutri­ent for crops that is usu­ally applied as fer­til­izer in epic amounts.

The idea seemed promis­ing, but with­out DNA tools to look into the specifics of how the corn was mak­ing nitro­gen, the dis­cov­ery was shelved. Nearly two decades later, in 2005, Alan B. Ben­nett of the Uni­ver­sity of Cal­i­for­nia, Davis — along with Shapiro and other researchers — began using cutting-​edge tech­nol­ogy to look into the nitrogen-​fixing prop­er­ties of the phlegmy corn, find­ing that indeed, bac­te­ria liv­ing in the mucus were pulling nitro­gen from the air, trans­mut­ing it into a form the corn could absorb.

Now, in 2018, after over a decade of field research and genetic analy­sis, the team has pub­lished their work in the jour­nal PLOS Biol­ogy. If the nitrogen-​fixing trait could be bred into con­ven­tional corn, allow­ing it to pro­duce even a por­tion of its own nitro­gen, it could reduce the cost of farm­ing, reduce green­house gas emis­sions and halt one of the major pol­lu­tants in lakes, rivers and the ocean. In other words, it could lead to a sec­ond nitro­gen rev­o­lu­tion.

The syn­thetic pro­duc­tion of nitro­gen may be the great­est achieve­ment of the 20th cen­tury. The dis­cov­ery of the Haber-​Bosch process and its refine­ments, in which nitro­gen is stripped out of the air under high heat and pres­sure in the pres­ence of a cat­a­lyst, has led to three sep­a­rate Nobel prizes. And they are well deserved. It’s esti­mated that crop yields more than dou­bled between 1908 and 2008, with syn­thetic nitro­gen fer­til­izer respon­si­ble for up to half that growth. Some researchers have tied the mas­sive growth in human pop­u­la­tion in the last sev­enty years to the increased use of nitro­gen fer­til­izer. With­out it, we’d have to farm almost four times as much land or have bil­lions of fewer peo­ple in the world.

But pro­duc­ing all that nitro­gen has con­se­quences. It’s esti­mated that mak­ing fer­til­izer via the Haber-​Bosch process uses between 1 and 2 per­cent of the world’s energy, emit­ting lots of green­house gases. And syn­thetic nitro­gen rou­tinely washes off fields into water­ways, lead­ing to mas­sive algae blooms that suck up all the oxy­gen, killing fish and other organ­isms. So much nitro­gen goes into rivers and streams that large dead zones have devel­oped at the mouths of the world’s rivers, includ­ing one in the Gulf of Mex­ico that last year was the size of New Jer­sey. Mark Sut­ton of the UK Cen­tre for Ecol­ogy and Hydrol­ogy calls nitro­gen “the God­fa­ther of pol­lu­tion” — its effects are every­where, but you never really see the cul­prit.

But we can’t just quit nitro­gen with­out see­ing major reduc­tions in agri­cul­ture. While bet­ter man­age­ment and farm­ing prac­tices can help keep it out of water­ways, those strate­gies aren’t enough to fix nitrogen’s eco­log­i­cal prob­lems. That’s why researchers have for decades won­dered if there was a way to help cereal crops like corn and wheat pro­duce their own nitro­gen.

The idea is not as far­fetched as it sounds. Lots of plants, in par­tic­u­lar legumes like soy­beans, peanuts and clover, have a sym­bi­otic rela­tion­ship with Rhi­zo­bium bac­te­ria, which pro­duce nitro­gen for them. The plants grow root nod­ules where the bac­te­ria take up res­i­dence and sip on plant sug­ars while con­vert­ing nitro­gen in the air into a form the plants can use. If a sim­i­lar sym­bi­otic rela­tion­ship could be found that works in cereal crops like corn and wheat, researchers believe we could reduce our use of the pol­lu­tant.

That’s why the mucus corn is so impor­tant, and why Ben­nett and his team spent eight years study­ing and re-​studying the bac­te­ria and gel to con­vince them­selves that the corn was indeed able to pro­duce its own nitro­gen. Using DNA sequenc­ing, they were able to show the microbes in the slime car­ried genes for fix­ing nitro­gen and demon­strated the gel the corn excretes, which is high sugar and low oxy­gen, is per­fectly designed to encour­age nitro­gen fix­a­tion. Using five dif­fer­ent tests they showed that the nitro­gen pro­duced by the microbes then made its way into the corn, pro­vid­ing 30 to 80 per­cent of the plant’s needs. They then pro­duced a syn­thetic ver­sion of the slime and seeded it with the microbes, find­ing that they pro­duced nitro­gen in that envi­ron­ment as well. They even grew Sierra Mixe in Davis, Cal­i­for­nia, and Madi­son, Wis­con­sin, show­ing that it could per­form its spe­cial trick out­side its home turf in Mex­ico.

“This mech­a­nism is totally dif­fer­ent from what legumes use,” Ben­nett says, adding it may exist in other crops as well. “It’s cer­tainly con­ceiv­able that sim­i­lar types of sys­tems exist in many cere­als. Sorghum, for exam­ple, has aer­ial roots and mucilage. Maybe oth­ers have more sub­tle mech­a­nisms that occur under­ground that could exist more widely. Now that we’re aware, we can look for them.”

Co-​author Jean Michel-​Ane from the Uni­ver­sity of Wis­con­sin, Madi­son, agrees that this dis­cov­ery opens up all types of new pos­si­bil­i­ties. “Engi­neer­ing corn to fix nitro­gen and form root nod­ules like legumes has been a dream and strug­gle of sci­en­tists for decades. It turns out that this corn devel­oped a totally dif­fer­ent way to solve this nitro­gen fix­a­tion prob­lem. The sci­en­tific com­mu­nity prob­a­bly under­es­ti­mated nitro­gen fix­a­tion in other crops because of its obses­sion with root nod­ules,” he says in a state­ment. “This corn showed us that nature can find solu­tions to some prob­lems far beyond what sci­en­tists could ever imag­ine.”

It turns out that nature has even more nitrogen-​producing tricks up her sleeve that researchers are just get­ting a han­dle on. There are sev­eral other ongo­ing projects aimed at get­ting cereal and veg­etable crops to do the Haber-​Bosching for us. One of the most promis­ing is the use of endo­phytes, or microor­gan­isms like bac­te­ria and fungi that live in the inter­cel­lu­lar spaces of plants. Uni­ver­sity of Wash­ing­ton researcher Sharon Doty got inter­ested in the organ­isms a cou­ple decades ago. She was study­ing wil­low and poplar trees, which are among the first trees to grow on dis­turbed land after events like a vol­canic erup­tion, floods or rock­fall. These trees were grow­ing out of river gravel, with hardly any access to nitro­gen in the soil. Inside their stems, how­ever, Doty found endo­phytes that fixed the nitro­gen for the trees, no root nod­ules nec­es­sary. Since then, she’s teased out dozens of var­i­ous endo­phyte strains, many of which help plants in sur­pris­ing ways. Some pro­duce nitro­gen or phos­pho­rus, another impor­tant nutri­ent, while oth­ers improve root growth and some allow plants to sur­vive in drought or high-​salt con­di­tions.

“There [are] a whole slew of dif­fer­ent microbes that can fix nitro­gen and a broad range of plant species impacted by them,” she says. Her tests have shown that the microbes can dou­ble the pro­duc­tiv­ity of pep­per and tomato plants, improve growth in rice, and impart drought tol­er­ance to trees like Dou­glas firs. Some even allow trees and plants to suck up and break down indus­trial con­t­a­m­i­nants and are now being used to clean up Super­fund sites. “The advan­tage of using endo­phytes is that it’s a really large group. We’ve found strains that work with rice, maize, toma­toes, pep­pers and other agri­cul­tur­ally impor­tant crop plants.”

In fact, endo­phytes might make it into farm­ers’ hands sooner rather than later. The Los Altos, California-​based Intrin­syxBio is com­mer­cial­iz­ing some of Doty’s endo­phytes. Chief Sci­ence Offi­cer John L. Free­man says in an inter­view the com­pany is on track to have a prod­uct ready for mar­ket in 2019. The goal is to deliver sev­eral strains of endo­phytes into plants, most likely by coat­ing the seeds. After those bac­te­ria take up res­i­dence inside the plant, they should pump out about 25 per­cent of the nitro­gen it needs.

Another biotech com­pany, called Pivot Bio, recently announced it is beta test­ing a sim­i­lar solu­tion, using nitrogen-​fixing microbes that grow in the root sys­tems of corn.

The newly emerg­ing field of syn­thetic biol­ogy is also tak­ing a crack at the nitro­gen prob­lem. Boston-​based Joyn Bio, formed last Sep­tem­ber, is a co-​project between Bayer and Ginkgo Bioworks, a biotech com­pany with expe­ri­ence cre­at­ing cus­tom yeasts and bac­te­ria for the food and fla­vor­ing indus­try, among other “designer microbe” projects. Joyn is cur­rently comb­ing through Bayer’s library of over 100,000 microbes to find a host that can suc­cess­fully col­o­nize plants, sim­i­lar to Doty’s endo­phytes. Then they hope to tweak that “host chas­sis” with genes that will allow it to fix nitro­gen. “Rather than rely on nature and find a magic microbe, which we don’t think exists, we want to find our host microbe and fine tune it to do what we need it to do for corn or wheat,” says Joyn CEO Michael Miille.

The Gates Foun­da­tion is also in on the game, sup­port­ing projects attempt­ing to impart the nitrogen-​fixing abil­i­ties of legumes into cere­als. Still other teams are hop­ing that the advent of super­charged quan­tum com­put­ing will open up new realms of chem­istry and iden­tify new cat­a­lysts that will make the Haber-​Bosch process much more effi­cient.

While it’s unlikely that one solu­tion alone will be able to replace 100 per­cent of the syn­thetic fer­til­izer humans use, per­haps together these projects could make a seri­ous dent in nitro­gen pol­lu­tion. Ben­nett hopes that Sierra Mixe and what his team has learned from it will be part of the nitro­gen rev­o­lu­tion, though he admits it’s a very long leap before his slimy corn fin­gers start pro­duc­ing nitro­gen in con­ven­tional crops. He now wants to iden­tify the genes that pro­duce the aer­ial roots and pin down which of the thou­sands of microbes dis­cov­ered in the mucilage are actu­ally fix­ing the nitro­gen.

“I think what we’re doing could be com­ple­men­tary to those [endoyphte and syn­thetic biol­ogy] approaches,” he says. “I think we’ll see many diver­gent strate­gies, and in 5 to 10 years some­thing will emerge that impacts how corn gets nitro­gen.“

Jason Daley is a Madi­son, Wisconsin-​based writer spe­cial­iz­ing in nat­ural his­tory, sci­ence, travel, and the envi­ron­ment. His work has appeared in Dis­cover, Pop­u­lar Sci­ence, Out­side, Men’s Jour­nal, and other magazines.

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