Phil Poole

Department of Plant Sciences

University of Oxford

South Parks Road

Oxford, OX1 3RB, UK


Tel +44 (0) 1865 275023

Professor of Plant Microbiology

Phil’s research focusses on interactions between plant roots and microbes in the rhizosphere. He has a particular interest in symbiotic nitrogen fixation.

His group studies the physiology of bacterial growth and survival in the rhizosphere, colonisation of roots and how bacteria establish symbiotic interactions with plants. A further focus of his research is the physiology and biochemistry of nitrogen fixation in legume nodules. Recently he has developed new methods to study how plants control the plant root microbiome.

Why study nitrogen fixation? Availability of nitrogen (N) is one of the principal elements limiting growth and development of crops, particularly in agricultural soils for plant production of food, feed, fibre and fuel. Over-use of nitrogenous fertilisers has led to catastrophic effects on the environment through run-off from the site of application into streams and rivers. Nature solved the N-limitation problem through the evolution of biological nitrogen fixation (BNF) in bacteria (called diazotrophs), organisms which reduce atmospheric N2 to ammonia that is then assimilated by the plant. Legumes and a few non-leguminous plants, have evolved the ability to form intimate nitrogen-fixing symbioses with diazotrophs (rhizobia in the case of legumes). BNF provides upwards of 200 kg N per hectare per year for some legumes. Thus legumes, including various bean and pea species and forages like alfalfa, have become an integral part of sustainable agricultural systems. Unfortunately, many of our most important food species, including grasses such as maize/corn, rice, wheat and sorghum do not establish nitrogen-fixing endo-symbioses with diazotrophs and thus require nitrogenous fertilisers to sustain yields. Ways to engineering association of these plants with nitrogen-fixing bacteria are being studied (Synthetic Symbioses).

In India, legumes are an especially valuable and often under-exploited resource. Crops, such as pigeon pea (Cajanus cajan), are able to fix nitrogen, thus removing the need for expensive and ecologically disastrous nitrogenous fertilisers. This crop is the main protein source for more than one billion people and although moderately drought-resistant it suffers from poor nodulation by rhizobia. A research project, India-UK Nitrogen Fixation Centre (IUNFC) was recently funded by BBSRC-DBT to tackle this problem as part of a £10M programme UK-India Virtual Joint Centres in Agricultural Nitrogen.

Why study the root microbiome? The interaction between micro-organisms and roots in the nutrient-rich rhizosphere is a key determinant of plant productivity, with rhizosphere micro-organisms essential to nutrient (e.g. N, sulphur and phosphorous) and carbon cycling. There is growing evidence for a two-way dialogue in which plants manipulate the rhizosphere microbial community and this in turn alters plant growth. Plants may exude 10-20% of fixed carbon via their roots, including both small organic and signalling molecules. Export on this scale must offer a significant fitness benefit to the plant, via alterations in the rhizosphere microbial community structure and/or functioning, and is likely to involve co-evolved mutualistic relationships between plants and microbes. So root microbes are critical in a range of processes essential to nutrient cycling including methane, and nitrous oxide release (both are potent greenhouse gases), nitrogen fixation, as well as altering plant growth and agricultural productivity. Opening up this area using both plant and bacterial genetics and environmental microbiology to study microbial communities is a focus of our work.




Recent Relevant Publications: 

Hood, G., Karunakaran, R., Downie, J.A. & Poole P. (2015) MgtE From Rhizobium leguminosarum Is a Mg2+ Channel Essential for Growth at Low pH and N2 Fixation on Specific Plants. Mol. Plant Microbe Interact. Nov 25: MPMI07150166R. [Epub ahead of print]

Geddes, B. A., Ryu, M-H., Mus, F., Garcia Costas, A., Peters, J. W., Voigt, C. A. &  Poole, P. (2015) Use of plant colonizing bacteria as chassis for transfer of N2-fixation to cereals. Current Opinion in Biotechnology 32;216-222.

Tkacz, A. & Poole, P. (2015) Role of root microbiota in plant productivity. J. Exp. Bot. 66 (8): 2167-2175. This article appears in: Special Issue: Roots to Global Food Security

Tkacz, A., Cheema, J., Chandra, G., Grant, A. & Poole, P. S. (2015) Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. The ISME Journal doi:10.1038/ismej.2015.41

Garcia-Fraile, P., Seaman, J.C., Karunakaran, R., Edwards, A., Poole, P.S. & Downie, J.A. (2015) Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant and Soil 390: 251-264.

Frederix, M., Edwards, A., Swiderska, A., Stanger, A., Karunakaran, R., Williams, A., Abbruscato, P., Sanchez-Contreras, M., Poole, P.S. & Downie, J.A. (2014) Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. Molecular Microbiology 93: 464-78.

Turner, T.R., Karunakaran, R., Walshaw, J., Heavens, D., Alston, M., Swarbreck,D., Osbourn, A., Grant, A. & Poole, P.S. (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. The ISME Journal 7: 2248-2258.