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Chemical warfare and symbiosis between bacteria and plants (PhD project 2012)

(Application closes 12th December 2012)

Colonisation by bacteria of the zone surrounding plant roots (rhizosphere) is crucial to plant productivity. In spite of its importance rhizosphere colonization is poorly understood but recent advances in genome sequencing and analysis makes it possible to address this complex topic in exciting new ways. Global food security depends on sustainably maximising crop yield whilst decreasing use of costly fertilizers which cause release of the potent greenhouse gas N2O from soils. The largest input of fixed nitrogen in the biosphere comes from the biological reduction of atmospheric N2 to ammonium, mainly through Rhizobium–legume symbioses, within which bacteria reduce N2 to ammonia for supply to the host. This frees many of the world’s major crops (e.g. soybeans, alfalfa, and peas) from nitrogenous fertilizer application and transferring nodulation to non-legume crops is a long term goal almost certain to trigger a second, environmentally sustainable, green-revolution. However, only the bacterial symbiont fixes N2 so for successful transfer we must also understand how rhizobia grow in the rhizosphere of plants and colonize their roots. To understand this we have produced a comprehensive transcription map of R. leguminosarum grown in the rhizosphere of 3 different plants (1) but the regulatory circuits controlling this transcription network is unknown. However, among the 200-genes 3x up-regulated in the rhizosphere of all 3 plant hosts there are 7 master regulators and we will determine how they control bacterial colonisation of the rhizosphere. This will involve genetic analysis of these regulators using mutational analysis, microarray analysis, Chip-seq, Network analysis, ligand screening and colonisation assays. Our aim therefore is to understand the chemical signals that govern warfare and symbiosis between plants and microbes. This is a joint project between Professor Philip Poole and Dr Tony Miller and will be based in Molecular Microbiology at the John Innes Centre.
 1.            Ramachandran V, East  AK, Karunakaran R, Downie JA, & Poole PS (2011) Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biology, in press.

Funding will cover a stipend and fees up to UK and EU level, and is available for a maximum of 4 years to UK nationals and EU nationals. The current stipend for 2011/12 is £ 13,590 per annum. International students are eligible for the funding but will need to find their own support to cover the extra fees charged to overseas students. Successful applicants will be interviewed as part of our Studentship Competition. Application deadline: 12 December 2011. For further information please contact philip.poole@jic.ac.uk or visit our website http://www.rhizobium.net/position.htm. To apply please visit the 'How to Apply' page on our website: http://www.jic.ac.uk/students/admissions.htm

 

Increasing legume nitrogen fixation to feed the world (PhD project 2012)

(Application closes 12th December 2012)

Global food security depends on sustainably maximising crop yield whilst decreasing use of costly fertilizers which cause release of the potent greenhouse gas N2O from soils. The largest input of fixed nitrogen in the biosphere comes from the biological reduction of atmospheric N2 to ammonium, mainly through Rhizobium–legume symbioses, within which bacteria reduce N2 to ammonia for supply to the host. This frees many of the world’s major crops (e.g. soybeans, alfalfa, and peas) from nitrogenous fertilizer application and transferring nodulation to non-legume crops is a long term goal almost certain to trigger a second, environmentally sustainable, green-revolution. However, only the bacterial symbiont fixes N2 so for successful transfer we must also understand which nodule factors induce N2-fixation in rhizobia.
          This a joint project between Professor Philip Poole in Molecular Microbiology at the John Innes Centre and Dr Nick Watmough at the University of East Anglia. We propose to use a combination of genetics and biochemistry to investigate how the bacteria, rhizobia, energise the reduction of N2 to NH3 to maximise growth yield of the plant. The successful applicant will investigate the genetic regulation, protein chemistry and biophysical properties of the FixAB/CX complex which shuttles electrons from an energy source to the enzyme nitrogenase. We have already shown that by manipulating aspects of this process we can increase N2 fixation by up to 35% so we now aim to understand how this achieved. Furthermore, we want to understand what consequences enhanced N2-fixation will have for increased legume production as part of environmentally sustainable agriculture.


         This project has been shortlisted for a Norwich Research Park Studentship. Funding will cover a stipend and fees up to UK and EU level, and is available for a maximum of 4 years to UK nationals and EU nationals. The current stipend for 2011/12 is £ 13,590 per annum. International students are eligible for the funding but will need to find their own support to cover the extra fees charged to overseas students. Successful applicants will be interviewed as part of our Studentship Competition. Application deadline: 12 December 2011. For further information please contact philip.poole@jic.ac.uk or visit our website http://www.rhizobium.net/position.htm. To apply please visit the 'How to Apply' page on our website: http://www.jic.ac.uk/students/admissions.htm

 

Differentiation of Rhizobium to form bacteroids
(Open trawl Ph.D. students)

 

The infection of legume hosts by rhizobia is typically initiated by rhizobia attaching to root hairs. This is followed by a complex developmental pathway that results in the formation of root nodules. The differentiated form of rhizobia present in root nodules (bacteroids), obtain dicarboxylic acids (succinate, fumarate and malate) as a carbon and energy source from the plant (1-3). It has always been assumed that these dicarboxylic acids are oxidised by the TCA-cycle to provide electrons and ATP for N2-reduction to ammonium and the bacteroids simply secrete the ammonium to the plant.  A major  reassessment of this was caused by our demonstration that both ammonium and alanine are secreted by bacteroids  (4), which is supported by our recent work showing that bacteroids can completely stop all assimilation of ammonium (5).  However, we also demonstrated that an even  more complex exchange is required with an obligate requirement for amino acid uptake by nodule bacteria via the ABC transporters Aap and Bra (6). Unravelling this conundrum was complicated by Aap and Bra transporting a wide range of amino acids. However, by constraining the solute specificity of Bra we showed that only branched chain amino acids need to be supplied to bacteroids by the plant (7-8). Preventing branched chain amino acid uptake by bacteroids leads to amino acid starvation; causing a failure to fully develop, reduced size and endoreduplication of their chromosomes. This phenomenon was named symbiotic auxotrophy because R. leguminosarum only becomes auxotrophic when in symbiosis with the plant and is caused by the shut-down of amino acid synthesis by bacteroids. It has led us to propose that bacteroids can be considered to be organelles (9). We demonstrated that this developmental pathway is regulated by a number of factors including BacA (10) and as part of a large programme to understand the development of bacteroids we dissected the transcriptional changes that occur over time as bacteroids develop (10-11). A major breakthrough in this has been to recognise that many of the early transcriptional changes in developing bacteroids (~50%) also occur in free-living rhizosphere bacteria (12). Once these shared transcriptional changes are removed the changes specific to developing bacteroids are revealed. For the first time this has enabled us to initiate a project to specifically examine the early development genes in bacteroid formation. We are now investigating the regulatory network that governs bacteroid development using transcriptional regulator mutants, microarrays, Chip-seq, and biochemical analysis.

  

1.            Mulley G, et al. (2010) Pyruvate is synthesized by two pathways in pea bacteroids with different efficiencies for nitrogen fixation. J. Bacteriol. 192(19):4944-4953.

2.            Prell J & Poole P (2006) Metabolic changes of rhizobia in legume nodules. Trends Microbiol. 14(4):161-168.

3.            White J, Prell J, James EK, & Poole P (2007) Nutrient sharing between symbionts. Plant Physiol. 144(2):604-614.

4.            Allaway D, et al. (2000) Identification of alanine dehydrogenase and its role in mixed secretion of ammonium and alanine by pea bacteroids. Mol. Microbiol. 36(2):508-515.

5.            Mulley G, et al. (2011) Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally down-regulating transport of organic nitrogen sources. Mol. Microbiol. 80:149-167.

6.            Lodwig EM, et al. (2003) Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature 422:722-726.

7.            Prell J, et al. (2009) Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc. Natl. Acad. Sci. USA 106:12477-12482.

8.            Prell J, et al. (2010) Role of symbiotic auxotrophy in the Rhizobium-legume symbioses. PLoS ONE 5(11):e13933.

9.            Oldroyd G, Murray J, Poole PS, & Downie JA (2011) The rules of engagement in the legume-rhizobial symbiosis. Annual Review of Genetics 45:119-144.

10.          Karunakaran R, et al. (2010) BacA Is Essential for Bacteroid Development in Nodules of Galegoid, but not Phaseoloid, Legumes. (Translated from English) J. Bacteriol. 192(11):2920-2928 (in English).

11.          Karunakaran R, et al. (2009) Transcriptomic analysis of Rhizobium leguminosarum b.v. viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J. Bacteriol. 191(12):4002-4014.

12.          Ramachandran V, East  AK, Karunakaran R, Downie JA, & Poole PS (2011) Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biology, in press.

 

 

For further information contact Philip Poole. This page was last updated on 20-Oct-2011. Positions similar to these may become available subject to funding.  General information about my group and other projects can be found here.