Possible PhD project in Ulrike Mathesius Lab

Engineering rhizosphere signals for improved nitrogen-fixing symbioses in legumes –

Many legumes form a symbiosis with nitrogen-fixing rhizobia that can alleviate the need for nitrogen fertiliser.
Rhizobia are attracted to the root by signals exuded from the root, these include flavonoids, a class of phenolic metabolites that occur inside the plant and in the rhizosphere. Many of the genes required for flavonoid synthesis are known, and some flavonoid transporters that are responsible for rhizosphere exudation have also recently been identified.
This project will genetically modify synthesis and/or transport of specific flavonoids into the rhizosphere to alter the attraction and activation of rhizobia prior to the establishment of symbiosis.
One problem with efficient nodulation in legumes is that effective rhizobia are out-competed by ‘cheaters’ as well unspecific bacteria in the soil, and therefore a stronger selection and retention of the most efficient nitrogen-fixing strains by the host is important.
Genetic modification of the flavonoid pathway will be combined with metabolomics of flavonoid exudates extracted from rhizosphere soil and testing for the activation of nodulation genes by the altered exudates.
We will then use metagenomics to characterise the changes in the microbiome of the rhizosphere to examine how altered flavonoid exudation of specific metabolites alters abundance of specific symbionts and other bacteria.
It is increasingly being recognised that the symbiosis with rhizobia can be improved by ‘helper bacteria’ present in the rhizosphere, and it would be interesting to test if these other bacteria (or fungi) respond to similar signals as rhizobia, as the associations could have co-evolved.
Possible outcomes include identification of key genes that alter exudates, and identification of signals that control attraction/retention of rhizobia as well as ‘helper bacteria’. The helper bacteria could be developed into new consortia of inoculants.
As an alternative, a similar strategy of rhizosphere engineering could be employed to identify signals in non-legumes that recruit bacteria that either protect plants from abiotic stress or help with associative nitrogen fixation.


The ARC Training Centre for Accelerated Future Crops Development is funded by the Australian Research Council under its Industrial Transformation Training Hubs Program to run from 2022 to 2027.

It is a collaboration of universities, government research agencies and the Australian grains sector’s key stakeholders in training, R&D, social engagement, responsible innovation, breeding, marketing and delivery.

It also has international partners in gene-editing, SynBio, crop breeding, and, other partnerships for co-developing deep technologies to transform the agriculture industry and global food security.