Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense.

In symbiotic plant-microbe interactions, the host invests considerable amounts of resources in the microbial partner. If the microbe does not reciprocate with a comparable symbiotic benefit, it is regarded as a cheater. The host responds to cheaters with negative feedback mechanisms (sanctions) to prevent fitness deficits resulting from being exploited. We study sanctioning in the symbiosis between Medicago truncatula and the nitrogen-fixing rhizobium Sinorhizobium meliloti. We manipulated the exchange of resources between the partners in three ways: by using mutant rhizobia defective in nitrogenase; replacing nitrogen in the atmosphere with argon gas; and supplying rich nitrogen fertilizer to the host. We follow the consequences of simulated cheating by examining the metabolome and proteome of both partners. We find that sanctioning occurs at multiple levels. In particular, we observe repression of essential symbiotic functions and changes in central metabolism that are likely to be relevant for microbial fitness and that could therefore contribute to sanctioning. In addition, sanctioning triggers a broad panel of defense markers. A thorough understanding of the multilevel phenomenon of sanctioning will be essential for its genetic dissection and for the breeding of elite legume crops with efficient symbiosis.