PDRA job opportunity – Posted Nov 27th 2019

Engineering synthetic signalling between plants and microbes

 With the human population estimated to reach 9.8 billion people by 2050, the looming nitrogen (N) crisis, stemming from the intensive use of fertilisers in agriculture, requires urgent global action. Massive synthesis and application of fertiliser N has a large energy cost, causes CO2 release and results in large-scale loss of reduced N to the environment. This has doubled reactive N in the atmosphere, and run-off of excess nitrate pollutes rivers and oceans causing eutrophication and O2-depleted dead zones [1, 2].  Use of legumes, which in association with rhizobia can fix up to 200 kg N per ha, as crops and for forage are potential ways to improve both N efficiency and the sustainability of agriculture. Using legumes in crop rotation can be of great benefit, but much of our agricultural productivity depends on high-yielding cereals, such as wheat, maize, rice and barley. Attempts are therefore underway to utilise N2-fixing bacteria on roots or inside engineered nodules of cereals to provide ammonia to plants, in order to improve N efficiency and reduce external fertiliser application [1, 2]. Currently we cannot control bacterial infection of cereals, N2 fixation and N release from bacteria to plants, nor can we prevent promiscuous transfer of N2-fixing bacteria to weeds. This led to our work to develop synthetic N2-fixing symbioses to deliver N to crop [3]. In summary (Fig.1), rhizopine produced and secreted by the plant (step 1), is transported into a bacterium, binds its cognate regulator MocR to induce the master regulator of N2 fixation nifA(step 2), switching on nif to fix N2 to ammonia. Concomitantly, rhizopine represses glnA and hence ammonia assimilation (Step 3), promoting ammonia secretion to the plant rather than bacterial assimilation. To establish true two-way communication rhizopine should also control a bacterial signal such as LCOs or COs, which control multiple aspects of plant development, including nodule formation in cereals. Rhizopine can also be used to control a raft of bacterial genes key in plant-microbe interactions, including hormone biosynthesis, phosphate solubilisation, antibiotic and antifungal compound synthesis.

Fig. 1. Synthetic symbioses between plants and bacteria. Box 1, Rhizopine synthesised in the plant is secreted and transported into a bacterium and binds to MocR; Box 2, MocR induces nifA which induces N2 fixation; Box 3, MocR represses glnA resulting in ammonia secretion; Box 4, MocR induces nodD resulting in production of LCO or CO as a reverse signal to the plant. Green arrows, induction; red arrows repression. The diagram is a composite of work achieved (e.g. rhizopine synthesis and secretion by plants) and objectives of this proposal (e.g. fine control of nifA, glnA, nodD).

This project has recently been funded by a new grant from the BBRSC for a 3-year full time post-doctoral research fellow. The successful candidate will develop tools needed for controlling and fine-tuning synthetic signalling between plants and microbes and apply these to engineering N2 fixation and secondary metabolite production. He/she will join a large multidisciplinary group at the Department of Plant Sciences, University of Oxford working on understanding bacterial root colonisation and microbiome function, regulation of N2 fixation and the use of synthetic biology to engineer plant microbe interactions. Contact Phil Poole for further details. Lab website:


  1. Geddes, B.A., Ryu, M.H., Mus, F., Garcia Costas, A., Peters, J.W., Voigt, C.A., and Poole, P. (2015). Use of plant colonizing bacteria as chassis for transfer of N2-fixation to cereals. Curr Opin Biotechnol 32, 216-222.
  2. Mus, F., Crook, M.B., Garcia, K., Garcia Costas, A., Geddes, B.A., Kouri, E.D., Paramasivan, P., Ryu, M.-H., Oldroyd, G.E.D., Poole, P.S., et al. (2016). Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Applied and Environmental Microbiology 82, 3698-3710.
  3. Geddes, B.A., Paramasivan, P., Joffrin, A., Thompson, A.L., Christensen, K., Jorrin, B., Brett, P., Conway, S.J., Oldroyd, G.E.D., and Poole, P.S. (2019). Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nature Communications 10, 3430.