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Improved bacterial chassis for engineering of microbial strains for bioremediation of contaminated sites

   School of Biological Sciences

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  Prof C French  No more applications being accepted  Self-Funded PhD Students Only

About the Project

*The difference between international and UK fee rate will be covered by the University of Edinburgh for successful candidates*

Supervisors: Christopher French, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh ([Email Address Removed]) and Zhenmei Lu, Institute of Microbiology, College of Life Sciences, Zhejiang University ([Email Address Removed])

An MSc degree is not a requirement.

Project details

A great deal of land is heavily contaminated with multiple pollutants including refractory organic compounds and heavy metals, and many industries produce wastewaters and other waste materials containing complex mixtures of such substances. Biological processes using engineered microorganisms can be used to remove organic contaminants, and even convert them to value-added products (1, 2, 3, 4), but the target pollutants together with co-occurring substances such as heavy metals can be highly toxic to the types of microorganisms which are normally used as a starting point for such engineered pathways. In this project we will aim to develop new host organisms for engineered bioremediation and waste valorization pathways, using soil organisms such as Pseudomonas sp., and Sphingomonas sp., which naturally possess high tolerance to organic compounds, and engineering them further to enhance their stress tolerance and ability to stably support engineered metabolic pathways. We will then test the engineered strains for their ability to survive in environments containing realistic mixtures of pollutants, to dominate such environments in the face of competition from other organisms, and to achieve effective transformation of target compounds in such mixed systems. The results from this project will form a basis for future work to develop novel engineered microbial strains which can reduce the burden of chemical contamination of land and water.

Techniques used in this project will include bioinformatic analysis of stress-resistance determinants, bacterial genome sequence analysis, DNA assembly and bacterial genome engineering, microbial community analysis, and chemical analysis techniques.

 PI Websites

Christopher French

 Zhenmei Lu

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Funding Notes

The difference between international and UK fee rate will be covered by the University of Edinburgh for successful candidates. Successful candidates will be required to provide evidence of funding to cover the UK fee rate, plus living expenses of approximately £15k per year.


[1] Werner AZ, Clare R, Mand TD et al., Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440. Metab Eng. 2021, 67: 250-261.
[2] Henson WR, Meyers AW, Jayakody LN et al., Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production. Metab Eng. 2021, 68: 14-25.
[3] Kim DH, Han DO, Shin KI et al., One-pot chemo-bioprocess of PET depolymerization and recycling enabled by a biocompatible catalyst, betaine. ACS Catal. 2021, 11: 3996-4008.
[4] Chen FYH, Jung HW, Tsuei CY et al., Converting Escherichia coli to a synthetic methylotroph growing solely on methanol. Cell. 2020, 182: 933–946.

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