Root nodules of Discaria (Order: Rosales), a non-legume species capable of nitrogen-fixing symbiosis.

Root nodules of Discaria (Order: Rosales), a non-legume species capable of nitrogen-fixing symbiosis.

© IRD / Sergio Svistoonoff

Nitrogen-fixing symbioses reveal themselves


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Recent research has revealed the origin and evolution of symbiotic relationships between certain plants and soil bacteria in order to use atmospheric nitrogen. This knowledge could ultimately contribute to the development of sustainable agriculture minimising the use of chemical fertilisers.

The comparative analysis of the genomes of several plants sheds light on the origin of root symbioses. This natural phenomenon links certain plants to soil bacteria capable of capturing atmospheric nitrogen. The relationship significantly optimises the mineral nutrition of the plants in question. “Despite the significant advantage of this symbiotic relationship, only legumes and a few other parent species from the orders Fagales, Rosales and Cucurbitales, are capable of developing this symbiosis”, explains Valérie Hocher, expert in plant molecular physiology at IRD. “By combining study of the genome with study of relationships and evolution, the phylogenomic approach undertaken within an international scientific consortium1, gives us a clearer picture2.

Making the most of atmospheric nitrogen

Nitrogen is vital to all living organisms. While it accounts for nearly 80% of the earth’s atmosphere, plants are incapable of using it directly in its gaseous form. They must take it in a form available in soil. They are therefore sensitive to their naturally high levels of nitrogen or possible enrichment into nitrogen fertilisers, synthesised by the chemical industry using fossil energy sources. Certain plant species form relationships with diazotrophic bacteria3, which allows them to grow in low-nitrogen environments, by making the most of the atmosphere’s inexhaustible reserves. To do this, they develop specific root organs called nodules, which enable the transfer to the plant of the atmospheric nitrogen made available by the action of their bacterial partners.

To understand the evolution mechanisms behind nitrogen-fixing symbioses, the genomes of 37 species, whether or not they are capable of developing this relationship, were compared”, states the researcher. 27 of them come from genomic databases and 10 including legumes, Fagales, Rosales and Cucurbitales were sequenced on this occasion.

Casuarina (order Fagales), here in Mboro, Senegal, grows in particularly poor environments thanks to the development of a nitrogen-fixing symbiosis.

© IRD / Alexandre Tromas

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An advantage that is often lost

These analyses confirmed that the predisposition to the formation of nitrogen-fixing symbioses existed in an ancestor common to all species capable of developing nodules. The genome comparison surprisingly revealed that the ability to form a nitrogen-fixing symbiosis was lost in multiple species, some of which are of agricultural value such as apples or strawberries, as attested by the presence of a gene previously identified for its key role in the bacterial association process. This one, known as NIN, is found in the genome of all plants that form root nodules. It is however missing or found in a fragmented form in the genome of most species studied which are now incapable of forming this symbiosis.

The loss of this advantageous ability remains unexplained. It means however that the symbiotic disposition may have been unfavourable in certain circumstances. One suggested hypothesis is the hijacking of the symbiosis by “cheater” parasitic bacteria which do not provide nitrogen. As a result, the loss of this property would provide an advantageous selectional feature.

The implications of this research largely exceed knowledge about the evolution of plants”, the physiologist points out. “It is consistent with the trend towards sustainable agriculture, minimising the use of chemical fertilisers, and aims at transferring or using nitrogen-fixing symbiosis for the benefit of cultivated species of major agricultural value.” Perhaps tomorrow’s cereals will grow without artificial fertiliser thanks to partner bacteria…


1. Involving thirteen institutions from eight countries, including the IRD’s Symbiosis of tropical actinorhizal plants team, from UMR LSTM 040

2. M. Griesmann, Y. Chang, X. Liu, Y. Song, G. Haberer, M. B. Crook, B. Billault-Penneteau, D. Lauressergues, J. Keller, L. Imanishi, Y. P. Roswanjaya, W. Kohlen, P. Pujic, K. Battenberg, N. Alloisio, Y. Liang, H. Hilhorst, M. G. Salgado, V. Hocher, H. Gherbi, S. Svistoonoff, J. J. Doyle, S. He, Y. Xu, S. Xu, J. Qu, Q. Gao, X. Fang, Y. Fu, P. Normand, A. M. Berry, L. G. Wall, J-M. Ané, K. Pawlowski, X. Xu, H. Yang, M. Spannagl, K. F. X. Mayer, G. K. Wong, M. Parniske, P.-M. Delaux, S. Cheng (2018) Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis Science, 24 mai 2018 ; DOI : 10.1126/science.aat1743

3. Atmospheric nitrogen-fixing microorganisms

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