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Enhancing plant productivity using engineered microbes

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  • Full or part time
    Dr T Howard
    Prof M Knight
    Dr Maria del Carmen Montero Calasanz
    Dr J Stach
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The productivity and resilience of agricultural systems faces multiple challenges including from climate change, increasing demand and the need for more sustainable sources of fertilisers. In this project, you will investigate the role that engineered bacterial endophytes - microbes that live harmlessly within plant tissues - might play in mitigating these threats. Currently, plant productivity in natural and agricultural systems is greatly enhanced through plant/microbe interactions. Examples include the nitrogen-fixing bacteria associated with legumes, root-associated mycorrhizal fungi and endophytes that synthesise anti-herbivory chemicals within their host’s leaves. To date, however, our agricultural systems benefit from evolved symbiosis, rather than designed (or engineered) symbiosis.

In this project you will develop a bacterial species suitable for use as a synthetic biology model organism. You will use the latest in sequencing technologies, bioinformatics and functional genomics to examine the genetic make-up of a bacterial endophyte available in our laboratory. You will use statistical optimisation combined with laboratory automation to design, build, test and optimise protocols and genetic resources required for robust engineering of this species. You will use these tools and information to study the response of the host plant to endophyte colonisation within the laboratory. From this you will gain skills in the quantification of transcriptional and secondary messenger signalling. Together, these skills will allow you to lay the groundwork for the development of novel tools for plant science.

This PhD is appropriate for a student with interests in both microbiology and plant sciences who wishes to study plant/microbial interactions at the cellular and molecular level.

Applications should be made by emailing [Email Address Removed] with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – clearly stating your first choice project, and optionally 2nd and 3rd ranked projects, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University. Applications not meeting these criteria will be rejected.
In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to [Email Address Removed]. A blank copy of this form can be found at:
Informal enquiries may be made to [Email Address Removed]

Funding Notes

This is a 4 year BBSRC studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.


ACS Synthetic Biology (2019), 8, 1175-1186 Rapid, heuristic discovery and design of promoter collections in non-model microbes for industrial applications

Plant & Cell Physiology (2019) 60(3): 538-548 Increases in absolute temperature stimulate free calcium concentration elevations in the chloroplast

New Phytologist (2018) 217(4): 1598-1609. Predicting plant immunity gene expression by identifying the decoding mechanism of calcium signatures

Scientific Reports (2018) 8, 525 Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

ACS SynBio (2018) 7: 1676-1684 Design of experiments methodology to build a multifactorial statistical model describing the metabolic interactions of alcohol dehydrogenase isozymes in the ethanol biosynthetic pathway of the yeast Saccharomyces cerevisiae

Int J Syst Evol Microbiol. (2018) 68: 2800-2806 Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., plant growth promoting endophytes isolated from the halophyte plant Arthrocnemum macrostachyum

Transgenic Research (2018) 27(4): 355-366. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae).

Front Microbiol. (2017) 19: 2501 Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae

PNAS (2013) 110: 7636-7641 Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli

Int J Syst Evol Microbiol (2013) 63: 4386-4395 Chryseobacterium hispalense sp. nov., a plant growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium

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