Scientists discover genetics of nitrogen fixation in plants - potential implications for future agriculture

Some plants have the capacity to grow well in nutrient poor soils without additional fertilizers. This is the result of a very efficient symbiosis between either nitrogen fixing bacteria that interact with the plant's roots, or between these roots and mycorrhizal fungi. These symbioses allow plants to strongly improve their uptake of nitrogen, phosphorus and water. Now a team of French and German scientists has discovered [*.pdf French/Spanish] the common genetic mechanism at work that allows the elements of the symbiosis to interact.

Their findings might make it possible to transfer the nitrogen fixing capacity of legumes to a wide range of crops that do not have this ability, including maize and rice. Ultimately, this could lead to a massive reduction of inorganic fertilizer consumption. The discovery is reported in the early edition of the Proceedings of the National Academy of Sciences.

The team of researchers from the Institut de Recherche pour le Développement (IRD) and the University of Munich have been collaborating for years on the project. They found that one of the genetic elements of nitrogen fixing plants called SymRK (Symbiosis Receptor Kinase), used by leguminous plants (pea, alfalfa...) to join Rhizobia bacteria and mycorrhizal fungi, is also essential for the establishment of the symbiosis between the tropical tree Casuarina - an actinorhizal plant that thrives in poor sandy soils - and nitrogen fixing bacteria belonging to the genus Frankia. This new understanding unlocks the keys to the genetics of the nitrogen fixing capacity of plants, and could make it possible to apply the mechanism to the development of crops that massively cut back on fertilizers.

Inorganic fertilizers are an essential but expensive input for farmers. World wide consumption of nitrogen fertilizers was around 130 million tonnes in 2007. Phosphate demand stood at around 37 million ton. Prices are rising steadily because of high oil and gas prices. Some crops like maize require large applications that have to be repeated each growing seaon. Particular cropping systems - such as growing nitrogen-fixing crops after other crops - can limit the need for fertilizers marginally and temporarily.

But what if crops like maize and rice could be designed in such a way that they do not require any additional inorganic fertilizers? That would revolutionise agriculture on a global scale and would greatly limit the different types of pollution and ecosystem damage caused by artificial fertilizers. The discovery of the genetic basis for the efficient N2-fixing capacity in plants might make the development of such crops possible.

The association between mycorrhizal fungi and plants is estimated to be more than 400 million years old. It helped plants colonize the land. Today, the symbiosis can be found in more than 80% of the all plant species. More recently, approximately 60 million years ago, a new symbiosis developed between soil bacteria known as rhizobia, and leguminous plants, which granted them the unique capacity to nourish themselves by extracting nitrogen from the air to use it as a nutrient.

Rhizobia establish themselves inside the root nodules of legumes, where they transform nitrogen into ammonium that can be directly taken up by the plant. In return, the plant provides to the micro-organisms with nutrients in the form of complex glucides:
energy :: sustainability :: biomass :: bioenergy :: agriculture :: fertilizer :: nitrogen fixation :: mycorrhizae :: soil microbes :: symbiosis :: molecular biology :: genetics ::

Unlocking the mechanism
For several years, scientists have tried to unlock the genetic mechanisms responsible for these mutually beneficial relations between plants and bacteria on the one hand, and bacteria and fungi on the other.

Already in 2000, IRD researchers discovered a genetic signaling mechanism common to the way in which legumes interact with rhizobia and to the way in which mycorrhizae work. The symbioses use a common genetic element baptized SymRK. This gene intervenes in recognizing Nod factors - the signaling molecules that are crucial for the rhizobia to establish themselves in root nodules.

So-called actinorhizal plants have formed a second group of plants that have acquired the capacity to benefit from a symbiosis with another type of nitrogen-fixing bacteria called Frankia. The genetic mechanisms of these plants' relationship with their symbiont has not been studied in-depth so far.

The actinorhizal plants can be found in disturbed environments, such as volcanic soils or mining terrain and in soils starved of nitrogen, such as sandy moraines.

There are approximately 260 species of actinorhizal plants distributed over 24 genera and 8 families of flowering plants. To study the symbiosis, the French and German researchers were particularly interested in the tropical Casuarina tree, better known under the name filao. Casuarinas thrive at tropical beaches, in poor sandy soils.

Using techniques from molecular biology, the scientists looked for the sequence coding the SymRK gene within the Casuarina genome. Once they identified the gene, they wanted to find out whether it is again responsible for the establishment of the symbiosis between filao and the Frankia bacteria.

To find out, they developed transgenic plants in which the expression of the SymRK gene was strongly reduced. They then compared the capacity of these plants to form symbiotic nodules on their roots with that of wild plants. According to these analyses, the plants whose SymRK gene's potency was reduced, produced half the number of root nodules compared with the control plants. The formation of mycorrhizae also strongly decreased compared with the wild Casuarina trees.

These results indicate that the reduction of the expression of the SymRK gene, in filao, causes a major reduction in its capacity to fix atmospheric nitrogen as well as a reduction of its aptitude to form mycorrhizae. More generally, these conclusions highlight the fact that there is a common genetic element at work in nitrogen fixing plants that seems essential for the installation of the three types of symbiotic associations utilizing bacteria (Rhizobium and Frankia) or mycorrhizal fungi.

Implications
A better comprehension of these genetic mechanisms could contribute, in the years to come, to the development of techniques to transfer the genetic material necessary for the nitrogen fixing capacity to crops that are unable to perform this task, such as cereals like maize and rice.

Whereas rice does establish a symbiotic relation with a mycorrhizal fungus, it is indeed inapt to develop nitrogen fixing nodules. However, by modifying its genome in such a way that rice plants too are capable of feeding off the atmospheric nutrient, it would become possible to significantly limit the nitrogen fertilizer needs in rice cultivation. This would have major economic and environmental effects: reduced production costs for farmers world wide and less pollution from nitrogen runoff.

If the N2-fixing capacity is transferred to all the major grain crops currently produced, world agriculture would be transformed forever.

Translated for Biopact by Laurens Rademakers.

Image: Frankia is genus of nitrogen-fixing bacteria that live in the soil and have a symbiotic relationship with many plants. By focusing on the genome of Frankia, French and German scientists discovered a genetic mechanism responsible for root-fungal and root-bacterial symbioses. Credit: MicrobeWiki.

References:
Hassen Gherbi, Katharina Markmann, Sergio Svistoonoff, Joan Estevan, Daphné Autran, Gabor Giczey, Florence Auguy, Benjamin Péret, Laurent Laplaze, Claudine Franche, Martin Parniske, and Didier Bogusz, "SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and Frankia bacteria", Published online on March 3, 2008, Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.0710618105,

IRD: Un mécanisme génétique universel découvert chez les plantes fixatrices d’azote [*.pdf] - Fiche n°288 - Février 2008

AlphaGalileo: Un mecanismo genético universal descubierto en las plantas fijadoras de nitrógeno - March 7, 2008.