Legume plants are unique in their ability to produce specialised root nodules, which host bacteria called rhizobia that convert atmospheric nitrogen into nutrients. Previous research showed that a genetic program for initiating the development of lateral – or secondary – roots also underpins the same process that triggers the formation of these nodules. But the question remained around the additional genetic factors that confer nodule identity as distinct from lateral roots.

By gene expression profiling and imaging the model legume Medicago truncatula, research carried out as part of the Enabling Nutrient Symbioses in Agriculture (ENSA) project showed that two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) family of genes determine the identity of bacterial induced lateral root organs as nodules. This group of factors was previously predominantly known to define the organs and tissues that produce flowers and stems.

We now understand that LSH1 and LSH2 are instrumental in forming a group of cells that are infectable and habitable by nitrogen-fixing bacteria early during nodule development.

Critical to this discovery were deep tissue imaging techniques and induction protocols that allowed researchers to study nodule development at an early stage.

Studying legumes such as Medicago is challenging because the root is twice as thick as Arabidopsis, the model plant typically used by developmental biologists. The early formation of root nodules happens deep within the plant’s tissue, making it difficult to image. The combination of time-resolved microscopy “seeing,” and gene expression studies allowed us to link our observation at a cellular level with molecular processes. This was a powerful tool for generating working hypotheses, which helped identify these novel but not yet identified nodule organ identity regulators.

The research ultimately shed light on the very genesis of legumes’ ability to fix nitrogen. This helps to further the mission of ENSA to understand and then recreate nutrient symbiosis to eventually engineer more self-sufficient, productive and sustainable crop plants, reducing the need for synthetic fertiliser.