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Revolutionary Rhizobia

Posted Nov. 10, 2014

Noble Research Institute scientists attempt to decipher the complex relationship between plants and bacteria in a bold new approach that could affect nitrogen use challenges
udvardi research team
Plant Biology Division Director Michael Udvardi, Ph.D., (center) leads a research team seeking to create beneficial plant-bacteria partnerships.

"We're trying to learn from nature by looking at the nitrogen fixation process in legumes."

Michael Udvardi, Ph.D.,
senior vice president and director, plant biology division

lab test
Senior Research Associate Ivone Torres-Jerez prepares a laboratory test as Udvardi observes.
green millet
Green millet (Setaria viridis) will be used as a model plant in the Udvardi laboratory's rhizobia research.

Plants would die without nitrogen.

The nutrient is necessary for healthy growth and is a key ingredient in the manufacture of molecules the plants need, including chlorophyll (and is why nitrogen-starved plants turn yellow). Yet despite the fact that plants live in an invisible cloud of nitrogen gas it makes up 78 percent of the Earth's atmosphere the element in the air is inaccessible to most of them.

Throughout most of human history, farmers have had to nourish their crops with other forms of nitrogen, like that deposited into the soil from weathered rocks or tilled into fields with plant and animal waste. Only legumes, through the aid of microbes that work their way into the cells of a plant's roots, are able to turn nitrogen from the air into compounds a plant can use, a process known as nitrogen fixation.

In 1909, German chemist Fritz Haber revolutionized agriculture by pioneering a process that converts nitrogen from the air (which exists in a form called di-nitrogen, because two nitrogen atoms are chemically stuck together) into ammonia that can be applied as fertilizer. Over the next century, crop yields skyrocketed as farmers harvested from nitrogen-enriched soil to meet the needs of rising world population.

Problem is, this abundance has come at a cost. Experts predict that by 2015, farmers will be adding 190 million tons of nitrogen into the world's soils. But crops only use about half of it. The excess runs off into lakes and rivers, and eventually into the ocean.

Nitrogen washed into the sea fuels the growth of algae that suck oxygen and other nutrients from the water. Each year, a "dead zone" at the mouth of the Mississippi River forms in the Gulf of Mexico, a semi-lifeless pool where the oxygen levels are so poor that little marine life can survive. Unused nitrogen also escapes back into the atmosphere as nitrous oxide, a so-called "greenhouse gas." And, as the recent explosion in West, Texas, tragically showed, fertilizer manufacture produces compounds that are hazardous to store.

A novel approach

Scientists at Noble Research Institute are working to solve these problems by coming up with ways to make nitrogen available to plants without the need to add so much extra to the soil. If more plants could use the tricks of legumes and fix nitrogen themselves, the world might reduce its dependency on industrial fertilizer. The secret is creating new bacteria-plant partnerships.

"We're trying to learn from nature by looking at the nitrogen fixation process in legumes," said Michael Udvardi, Ph.D., director of Noble's Plant Biology Division. "We want to apply it to non-legumes."

If successful, the development of new nitrogen-fixing bacteria and plant-microbe partnerships could also help farmers in countries where fertilizer is too expensive to buy. In poorer nations, Udvardi said, crop yields are a fraction of those in the United States.

One of the first steps has been to figure out the secrets of rhizobia, the soil bacteria that fix nitrogen naturally in legumes. The relationship between rhizobia and legumes has become so synchronized over millions of years that both plant and bacteria thrive best when they have each other. (In fact, the name rhizobia itself is a combination of the Greek words for "root" and "life.")

Rhizobia live naturally in soil. When a legume is planted into the ground, the root sends out chemical signals that attract the bacteria. Through a back-and-forth chemical conversation between microbe and plant, the root develops special structures called nodules where the bacteria "infect" the plant's cells and begin to multiply.

The relationship is mutually beneficial. The plant supplies the bacteria with carbon and other nutrients that it uses for its own metabolism. The bacteria supply nitrogen (in the form of ammonia) the plant needs to make molecules necessary for its growth and survival.

By figuring out which plant and bacterial genes are important for symbiotic nitrogen fixation by rhizobia in legumes, researchers might be able to recreate a nitrogen-fixation system for crops like wheat or corn, which is the greatest consumer of nitrogen fertilizer. "We hope to engineer nitrogen-fixation genes into bacteria that form relationships with plants naturally," Udvardi said.

The road forward

A $2.5 million grant from the National Science Foundation and the Biotechnology and Biological Sciences Research Council in the United Kingdom allows Udvardi and his collaborators to explore this. (The project is split among researchers at the Noble Research Institute, Montana State University, the University of Wisconsin-Madison and the Massachusetts Institute of Technology in the U.S., and the John Innes Center and Oxford University in the UK.)

One approach would be to genetically alter a form of rhizobia to allow the same chemical crosstalk that takes place in legumes to happen in another species. Another possibility is enabling other bacteria to work like rhizobia.

"There's a suite of microorganisms that will colonize plants, but they aren't really supplying nitrogen," said John Peters of Montana State University, who is also working on the project. "Typically they're not feeding the plant with significant amounts of fixed nitrogen. What we're trying to do is strengthen these associations."

But first the genetic instructions involved in the nitrogen fixation process have to be identified. Then the researchers must figure out how active these genes need to be and in what metabolic systems of the bacterial cell. For example, if the bacteria produce ammonia, scientists want to be sure that it is ferried on to the plant and not used by the microbe itself.

"This is the first time a group of scientists have come together to try to manipulate both the plant and the bacteria," Udvardi said. "If we can work out the rules of engagement the ways microbes and plants can live together we can develop novel nitrogen-fixing systems to reduce the amount of nitrogen fertilizer used in agriculture, which will be a win-win situation for agriculture and the environment."

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