Development of genetic tools for rhizosphere engineering

Dr Timothy Haskett
Research Fellow 2019

Dr Timothy Haskett
University of Oxford

Agricultural productivity in the developed world is sustained through supplementation of crops with chemically synthesised fertilisers and biocides that are unintentionally detrimental to human and environmental health. By contrast, these chemicals are largely unavailable in developing countries, restricting crop yields. With the world’s population projected to increase by 2.2-billion over the next 30 years, rising food demands mandate that we consider more sustainable agricultural practices.

Exploitation of plant growth-promoting rhizobacteria (PGPR) that naturally occupy the rhizosphere environment (plant root and proximal soil) represents one of the most environmentally friendly alternatives to the use of chemicals in agriculture. These bacteria promote plant growth by enhancing nutrient availability, alleviating stress, stimulating physiological development and deterring pathogens. Owing to recent developments in the characterisation of genetic mechanisms underlying PGPR traits, engineering ‘dominant’ PGPR is now becoming a realistic strategy to enhance plant-growth promotion. However, progress in this field has been largely hindered by the lack of genetic tools available to artificially regulate engineered genes. 

The Rhizosphere and Giles Oldroyd groups (at Oxford and Cambridge, respectively) recently developed a novel synthetic plant-microbe signalling circuit specifically designed for this purpose. In this system, transgenic plants harbour a biosynthesis pathway for the signalling molecule rhizopine, and a narrow group of engineered ‘rhizobial’ alpha-proteobacteria carry a genetic sensor to perceive rhizopine and activate gene expression.


“Exploitation of plant growth-promoting rhizobacteria represents one of the most environmentally friendly alternatives to the use of chemicals in agriculture”

Host-plant dependent regulation of engineered PGPR traits ensures that;

i) bacteria do not promiscuously promote growth of non-target weed species; and

ii) the bacterial energy cost incurred by heterologous gene expression is minimised. Currently, rhizopine signalling lacks fine-tuned control and is functionally restricted to small group of alpha-proteobacteria.

Here, I propose to couple rhizopine-signalling with a series of genetic logic gates to achieve the dynamic and conditional control over gene expression needed to engineer complex PGPR traits. I will also adapt rhizopine-signalling for function in diverse bacteria, as this will be critical for engineering PGPR traits in different hosts. These adaptations to rhizopine-signalling circuitry will prompt crucial advances towards engineering an efficate, manipulatable rhizosphere and will be beneficial for numerous applications in synthetic biology.