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Genetic Control of the symbiosis

Team GenetSYM / Pascal Ratet



Plants interact with a wide diversity of microorganisms, some being beneficial and other detrimental (pathogenic). Beneficial associations include fungal and bacterial symbiosis but also interactions with beneficial microorganisms like bacteria that are called Plant Growth Promoting Rhizobacteria (PGPR). The association with nitrogen fixing rhizobia is restricted mostly to legume plants. It has probably evolved from the ancient symbiosis with beneficial fungi such as mycorrhiza.

            Grain (such as peas, faba beans, soybean, chickpea) and forage (alfalfa, clover, lupinus) legume plants are important crops worldwide for both animal and human consumption as they are major protein sources. Legumes are also rich in a range of secondary plant compounds and other high added value compounds that open new fields of legume use for non-food purposes (bio-active molecules, bioenergy, biopolymers…). Legumes are grown in rotation with other crops for their capacity to restore soil fertility in organic farming practices. Their use in agriculture can reduce the application of nitrogen fertilizers, as they can grow in nitrogen deficient soils. Establishment of a symbiotic interaction between legume plants and beneficial soil bacteria, collectively named rhizobia, occurs when the soil nitrogen source is limiting and leads to the de-novo formation of symbiotic nodules, generally formed on roots of the plants. Nodules host bacteria that fix atmospheric nitrogen and make it available for the plant (figure 1). This symbiotic association thus allows the plant to overcome nitrogen limitation. In return, the plant furnishes carbon derivatives to its invaders.


Figure 1. The legume model Medicago truncatula, grown in soil (a) or in in vitro conditions (b) is able to establish a symbiotic interaction with rhizobia such as Sinorhizobium medicae. Bacteria are hosted in nodules formed by the roots (c). The blue arrow points to a nodule.


The first steps of this symbiotic association and the formation of the symbiotic organ have been described in details but organ identity and later steps of the interaction related to bacterial accommodation and immunity are less understood. Rhizobia often invade the plant root using specialized symbiotic structures called infection threads. In the mature nitrogen fixing nodule, the rhizobia reside in symbiotic nodule cells within organelle-like structures, called symbiosomes. In contrast to what is generally observed during microbial invasion, legumes do not elicit apparent defense reactions during symbiosis despite that the bacterial population reaches massive densities in nodules. In addition, in nature the nodules are hosting other bacteria called nodule endophytes.

            Our team is studying the mechanisms governing beneficial plant-microbe interactions, how the symbiotic interface (nodules) is built and the role of plant immunity in these interactions, mainly in the legumes-rhizobia symbiosis. We are also initiating a project with cereal endophytes. We study the consequences of these interactions in multiple microbe interactions involving endophytes and pathogens and see how they can be used to improve the benefit of the beneficial interactions for the plant. Understanding these multipartite interactions will help to better understand the complex interactions that plants are facing in fields or in the wild.

            The team has pioneered the development of Tnt1 mutagenesis in the model legume plant Medicago truncatula (figure 1) (d'Erfurth et al., 2003 ; Tadege et al., 2005 ; Tadege et al., 2008 ; Pislariu et al., 2012) together with the isolation of Medicago mutants and transformation of Medicago (Cosson et al., 2015). The team is using reverse and forward genetic strategies to study plant microbe interactions including legume-rhizobium interactions.


The main axes of research developed by the team are: 

  • The symbiotic organ identity: how nodules are formed and how their identity (nodule versus root identity) is genetically controlled by the NBCL (NOOT-BOP-COCH-like) genes? As an extension of this project we are studying the role of the NBCL genes in organ identity in monocot plants.
  • Symbiosis and immunity: How the plant can deal with a massive colonization of rhizobia (chronic infection)? Emphasis is made on signalling events that are involved in bacterial perception and control of the immune response in the symbiotic organ. The role of the defense hormones in this process is studied using Medicago mutants. Finally, we are also studying the role of senescence in the immune response.
  • Characterization of bacterial endophytes: We are characterizing Medicago nodule endophytes that are not rhizobia, as well as wheat root endophytes.



  • d'Erfurth I., Cosson V., Eschstruth A., Lucas H., Kondorosi A., Ratet P. (2003). Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J. 34(1):95-106. doi:  10.1046/j.1365-313X.2003.01701.x.
  • Pislariu C.I., Murray J.D., Wen J., Cosson V., Muni R.R., Wang M., Benedito V.A., Andriankaja A., Cheng X., Jerez I.T., Mondy S., Zhang S., Taylor M.E., Tadege M., Ratet P., Mysore K.S., Chen R., Udvardi M.K. (2012). A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.  Plant Physiol. 159(4):1686-99. doi: 10.1104/pp.112.197061. 
  • Tadege M., Ratet P., Mysore K.S. (2005) Insertional mutagenesis: a Swiss Army knife for functional genomics of Medicago truncatula. Trends Plant Sci. 10(5):229-35. doi: 10.1016/j.tplants.2005.03.009.