Getting to the root of the global food crisis

Increasing legume use in agriculture is essential for sustainably feeding the worlds ballooning population. Legumes are the only crops that are able to capture nitrogen from the air to make their own ammonia fertilizer to promote growth and high protein yields. The main way of reducing excessive meat and dairy consumption for humans is therefore to eat more legumes, as beans and pulses. However, legumes rely on a symbiosis with bacteria in their roots, called rhizobia to turn the nitrogen in air into ammonia fertiliser inside small nodules on the roots of the plants. The rhizobia come from the soil surrounding roots and there is a mighty competition for the best rhizobia to gain entry to the root nodules instead of cheating bacteria that give little to the plant.

For the first time, a team of researchers from the Department of Plant Sciences have developed a high-throughput method that allows identification of the best rhizobia at the single nodule level. Published in the journal PNAS, this finding has the potential to revolutionise the search for the best rhizobia.

Marcela Mendoza-Suárez, lead author of the paper, said: “Selecting the best rhizobia for the legume crops that farmers grow will be of fundamental importance for reducing environmental problems that result from the overuse of the nitrogen-based fertilisers.”

Effectiveness at producing ammonia fertilizer and competitiveness to get inside nodules are independent of each other,. Furthermore, these properties are difficult to measure, so there are few studies evaluating them at the same time. Therefore, the identification of the best rhizobia, known as elite strains is extremely difficult.

“You may have a very good sports team who perform exceptionally at home, but once that team competes in a different city or in a different country, they no longer have that home advantage,” explains Mendoza-Suárez. “No matter how good they were at home, during an away game they are playing in unfamiliar territory. This tricky situation, in the world of the symbiosis between a  legume and rhizobia, is known as the competition problem.”

Using a simple synthetic biology approach, where dozens of rhizobia are individually tagged the team have developed a novel method that assesses the rates of ammonia fertilizer production in single nodules and identifies which rhizobia are living inside these nodules.

This results in a flexible system that is extremely successful in the selection of elite rhizobia for legumes such as peas and beans. The aim is to transfer this system to many other rhizobia and legumes to select the winning strains that increase the yield and protein content of the plants.

Dr Carmen Sánchez-Cañizares, who also worked on the paper, said: "This work is the result of a multidisciplinary team where, with our defined skills, we all contributed to Marcela’s PhD work. This publication is a turning point in the area of bacterial inoculants. As a natural follow-up from my PhD work, where only two strains could be assessed together in a competition experiment, this novel approach gives now a step further in several directions, allowing the identification of multiple barcoded-strains at the same time they are assessed in nitrogen fixation and success in competing with native rhizobia. Not only that but due to its simplicity in terms of equipment needed, this genetic tool could be used in any lab worldwide.”

Professor Phil Poole, PI of the Rhizosphere Lab, adds: “This project began as a challenge from agronomists for academic scientists to produce something useful in the real world. It was worked on by a dedicated group of young scientists who once again show the division between pure and applied science is often artificial.”