Philip Poole

Senior Research Fellow in Plant Sciences (Somerville); Professor of Plant Microbiology
Dept Plant Sciences

Research Description

The general areas in which my group works are bacterial genetics and molecular biology of plant associated bacteria. Our emphasis is to study the physiology of bacterial growth and survival in the rhizosphere and how they establish symbiotic interactions with plants. A further focus of our work is the physiology and biochemistry of nitrogen fixation in legume nodules. Most recently we have been studying how bacteria attach to and colonise roots and have developed methods to open up the whole area of how plants control the microbial 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. Nature solved the N-limitation problem via evolution of biological nitrogen fixation (BNF) in bacteria (called diazotrophs), which reduce atmospheric N2 to ammonia (NH3) that is assimilated into biological molecules.  BNF is carried out by a complex of three proteins (nitrogenase), encoded by nifH, nifD and nifK, which are assembled and activated by an additional 17 genes. Some plants, including most legumes and a few non-legumes, have evolved the ability to form intimate, nitrogen-fixing symbioses with diazotrophs (rhizobia in the case of legumes), whereby large populations of diazotrophs are accommodated within living plant cells that provide nutrients to the bacteria in exchange for ammonia produced by nitrogenase.  The plant host also protects oxygen-labile nitrogenase from inactivation by reducing free-oxygen.  Symbiotic nitrogen fixation (SNF) 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 the grasses such as maize/corn, rice, wheat and sorghum do not establish intimate nitrogen-fixing endo-symbioses with diazotrophs and thus require addition of nitrogen to sustain yields.

Why study the root micro biome? 

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,S,P) 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 molecules 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 raft 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.

  • Tkacz, A. & Poole, P. (2015) Role of root microbiota in plant productivity. J. Exp. Bot. (2015) 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
  • 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.
  • 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.
  • 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 (3): pp 464-478. doi:10.1111/mmi.12670
  • Udvardi, M and Poole, P.S. (2013). Transport and Metabolism in Legume Root Nodules.
    Annual Review of Plant Biology 64: 781-805.
  • Turner,T.R, James,E.K. and Poole,P.S. (2013) The plant microbiome.
    Genome Biology 14:209-218
  • Untiet,V., Karunakaran, R., Maria Krämer, M., Poole, P., Priefer, U., an Prell J. (2013). ABC transport is inactivated by the PTSNtr under potassium limitation in Rhizobium leguminosarum 3841.
    PLOS One, 8(5) e64682.
  • Karunakaran, R., East, A and Poole, P.S. (2013) Malonate catabolism does not drive nitrogen fixation in legume nodules.
    Appl Env Microbiol 79 (14) 4496-4498.
  • Turner, T. R., Karunakaran , R, Walshaw, J., Heavens, D., Alston, M., Swarbreck,D., Osbourn, A., Grant,A., and Poole, P.S. (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants.
    ISME J., 7, 2248–2258

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