UNC plant genetics research could lead to more phosphate-efficient crops

Phosphate is a key nutrient vital for best crop yields, but the global supply is limited and could peak in 30 years. This UNC research details how soil bacteria enhance phosphate-seeking in plants to aid plant survival.

Media Contact: Mark Derewicz, 919-923-0959, mark.derewicz@unch.unc.edu

March 15, 2017

CHAPEL HILL, NC – Scientists at the University of North Carolina have made a discovery that could lead to more efficient agricultural use of phosphate, an essential plant nutrient with a limited global supply. 

The finding, published this week in Nature, centers on a molecular switch in plants, PHR1, a gene known to trigger the spreading of roots and other responses to help plants find and absorb phosphate in low-phosphate soil conditions. The scientists discovered that when PHR1 activates this phosphate stress response, it also suppresses plant immune defenses against bacteria and other microbes in the soil.

“This is one of just a few examples in plant biology research where we’ve been able to see an interplay between plant nutritional stress and the plant immune system, and in this case we’ve been able to nail down the molecular factors involved,” said senior author Jeffery L. Dangl, PhD, the John N. Couch Distinguished Professor of Biology and adjunct professor of microbiology and immunology at the UNC School of Medicine.

Dangl and colleagues found evidence that soil bacteria can make use of this tradeoff between nutrient-seeking and immune defense, potentially to help establish symbiotic relationships with plants.

“Some bacteria live happily on the surface of, and inside, plant roots,” said Dangl, who is also a Howard Hughes Medical Institute Investigator. “And bacteria seem to enhance this phosphate stress response, in part simply by competing for phosphate but also by actively ‘telling’ the plant to turn on its phosphate stress response.”

This work raises the possibility of “probiotic,” microbe treatments for plants to increase their efficient use of phosphate. This has major implications. Phosphate in a form plants can use has a limited global supply, and at least one scientific analysis has predicted “peak phosphate” – when supply fails to keep up with demand – just 30 years from now. This could translate into a decreased rate of crop yield as the world population continues to climb.

In recent plant biology studies, there have been hints of a relationship between plant phosphate levels and immune system activity – a relationship that some microbes can manipulate.

In the new study, Dangl and colleagues delved more deeply into this relationship, using mutant versions of Arabidopsis thaliana, a weed also known as thale cress or mouse ear cress that has long been the standard “lab rat” of plant biology research.

In one set of experiments, Dangl’s team found that Arabidopsis plants with mutant versions of the PHR1 gene not only had impaired phosphate stress responses, but also developed different communities of microbes in and around their roots when grown in a local native North Carolina soil. This was the case even in an environment of plentiful phosphate – where phosphate competition wouldn’t have been a factor – hinting that something else was happening in the plants to trigger the growth of different microbial communities. The researchers found similar results studying PHL1, a protein closely related to PHR1 with similar but weaker functions.

In another set of experiments, in lab-dish conditions, the researchers colonized roots of sterile-grown normal Arabidopsis plants with a set of 35 bacterial species isolated from roots of plants grown previously in the same native soil. In these ‘re-colonized’ plants, the phosphate stress response increased when exposed to a low-phosphate condition.

“There was a huge enhancement of the phosphate stress response in the presence of these microbes,” Dangl said.

Then Dangl’s lab ran the same experiment in mutant plants that lacked functional PHR1 and PHL1. They found no significant increase in markers of the phosphate stress response, indicating that the enhancement worked via these “switch” proteins.

Investigating further, the team showed that PHR1 – and probably to a lesser extent PHL1 – not only activates the phosphate stress response but also triggers a pattern of gene expression that reduces immune activity, and thus makes it easier for resident microbes to survive.

The findings suggest, firstly, that many soil-dwelling microbes have figured out how to get along with their plant hosts, at least in part by activating PHR1/PHL1 to suppress immune responses to them. Secondly, Dangl’s team thinks these microbes may even be necessary for plants to respond normally to low-phosphate conditions. It could be possible, then, to harness this relationship – via probiotic or related crop treatments – to enable plants to make do with less phosphate.

“Phosphate is a limited resource and we don’t use it very efficiently now,” Dangl said. “As part of fertilizer, a lot of phosphate runs off into waterways where it can adversely affect river and marine ecosystems. It would be better if we could use phosphate in a way that’s more efficient.”

He and his colleagues are now trying to determine more details of how some soil microbes appear to live symbiotically with their plant hosts.

“Under high levels of phosphate, these microbes don’t induce the phosphate stress response, but they still somehow fail to activate the plant immune system,” Dangl said. “So, bacteria are able to stay in place and thus stay available to help the plant when a low-phosphate condition occurs. How do they reach that détente with the immune system? We’re still trying to figure that out.”

The lead authors of the study were postdoctoral researchers Gabriel Castrillo, PhD, and Paulo José Pereira Lima Teixeira, PhD, and graduate student Sur Herrera Paredes. Other co-authors were Theresa F. Law, Meghan E. Feltcher, Omri M. Finkel, PhD, Piotr Mieczkowski, PhD, Corbin D. Jones, PhD, all of UNC; former UNC postdoc Natalie W. Breakfield, PhD; and Laura de Lorenzo, PhD, and Javier Paz-Ares, PhD, of Spain’s Centro Nacional de Biotecnología. 

The National Institutes of Health, the National Science Foundation, the U.S. Department of Energy, the U.S. Department of Agriculture, the Howard Hughes Medical Institute, and the Gordon and Betty Moore Foundation supported this research.

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