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The genomic diversity and interactions of symbiotic bacteria in clover crops

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  • Full or part time
    Prof J P W Young
    Dr V Friman
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

This project forms part of a large research consortium project called NCHAIN, led by Aarhus University, Denmark, that seeks to understand and improve production of clover and grass mixtures for animal feed on organic farms. Nitrogen fixation by symbiotic bacteria (rhizobia) in the clover roots is crucial to productivity when inorganic fertiliser is not used. The overall project aims to develop a quantitative model of the nitrogen transfer from rhizobia to clover to grass, taking into account genomic data for all three partners and the interactions between them. The studentship is concerned only with rhizobium diversity, but the student will attend consortium meetings and learn about the wider context.

The student will use a new molecular approach to reveal the genetic diversity and abundance of rhizobia in field populations. The method is based on PCR amplification of key symbiosis-related genes and high-throughput sequencing, and has been developed within another project. The student will have the opportunity to design and implement extensions to survey other genes. They will use these tools to assess the extent to which elite rhizobium strains become established in the field after introduction on seeds, and the impact on the existing rhizobium population. They will also carry out comparative transcriptomics studies on rhizobium isolates that differ in measured traits. In addition, the NCHAIN project will generate a large number of new rhizobial genome sequences, and the student will be encouraged to explore this resource in order to contribute to the consortium aims and also to address wider questions in bacterial genomics. There is scope for expanding the project in a number of directions. For example, (i) are there genes that are overrepresented in rhizobia that colonise the grass rhizosphere (Rhizobium is frequently reported in surveys of the microbiota of nonlegume plants), (ii) what are the effects of the grass, clover and rhizobium genotypes on the general bacterial community in the rhizospheres, (iii) are rhizobium mixes more stable and effective if the strains have complementary resource utilisation profiles?

The Young lab is world leading in the analysis of the genomic diversity of rhizobia, and the Friman lab has expertise in the eco-evolutionary dynamics of species interactions in multi-trophic communities. The rhizobial component of the NCHAIN project will also be supported by another PhD student and two postdocs (one wet lab, one bioinformatic) based in Aarhus, so the student will benefit from interactions as part of this team and will have the opportuntity to spend some time working in Aarhus.

The student will gain expertise in lab-based microbiology and molecular methods and in computer-based analysis of genomic and transcriptomic data. These skills are in considerable demand and will prepare the student for a range of future career options.

Funding Notes

This studentship is fully funded for 3 years (1 October 2016 - 30 September 2019) by the Danish Strategic Research Council and covers: (i) a tax-free stipend of approximately £18,200 a year to cover living costs and tuition fees, (ii) research costs.

How good is research at University of York in Biological Sciences?

FTE Category A staff submitted: 44.37

Research output data provided by the Research Excellence Framework (REF)

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