Exploring the genome architecture of plastic-degrading bacteria
Funded PhD Project (UK and EU students only)
Centre for Enzyme Innovation, School of Biological Sciences
7 February 2020
This project is now closed. The details below are for information purposes only. View our current projects here.
Applications are invited for a fully-funded four year PhD studentship to commence in October 2020.
Established in 2019, the Centre for Enzyme Innovation (CEI) focuses on the discovery, engineering and deployment of enzymes with potential application to the sustainability aspects of the circular economy.
The studentship is available to UK and EU students only and covers tuition fees and an annual maintenance grant of £15,009 (UKRI 2019/20 rate) for three years. University funding will be made available to offer extensions into a 4th year where this will maximise scientific output and boost research careers. Funds of £7,500 per annum are available to cover research expenses and support attendance at workshops and conferences.
This studentship will explore the genomic context of bacteria exhibiting evidence of utilisation of plastic polymers as a carbon source. Specifically, work on the project will:-
- Extract DNA from complex multi-organism metagenomic samples.
- Perform directed evolutionary growth on a range of synthetic polymer substrates.
- Use cutting-edge metagenomic DNA sequencing approaches to profile whole-genome bacterial sequences at different stages of directed growth.
- Employ advanced bioinformatics approaches to identify genomic loci enriched by directed evolution.
- Combine data with existing knowledge and databases to identify genomic loci and candidate enzymes associated with degradation and metabolism of synthetic plastics.
- Characterise promising candidate enzymes using X-ray crystallography (utilising the Diamond Light Source synchrotron), NMR spectroscopy, differential scanning calorimetry (DSC) and molecular dynamics (MD) simulations.
This project brings together expertise within the Centre for Enzyme Innovation with the common goal of addressing one of our most imminent global challenges; plastic pollution (1-5). Everyday plastics such as poly(ethylene terephthalate), or PET, are highly versatile but the chemical properties that make them so useful also make them highly resistant to natural biodegradation.
However, there is hope. Nature has found a way to evolve enzymatic solutions to allow naturally occurring microorganisms to survive on these man-made materials. Harnessing these enzymatic pathways, and replicating the methods developed in the environment through evolution will provide us with novel targets in our pipeline. Our aim is to profile these evolutionary solutions at the genomic level to understand the key components that allow specific microorganisms to thrive on these complex polymers in the environment.
Building upon parallel research projects currently running in our laboratories on the depolymerisation of natural and synthetic solid polymers (1-5), we will use cutting-edge DNA sequencing technologies to profile changes in the genome that occur over successive generations of bacteria fed on polymers of interest.
The successful candidate will join a growing team of postgraduate students, technical and research staff working together within our recently-established Centre for Enzyme Innovation. In addition to a full program of training provided by the Graduate School, specialist training will be provided for a range of in-house instruments and techniques, including analysis of high-throughput DNA sequencing data. You will be supported by the CEI team of postdoctoral researchers with skills in bioinformatics, molecular modelling, structural biology and enzymology. There may be opportunities for travel for field work, laboratory visits and training at specialist facilities.
This work will have applications in:
- Development of potential enzymatic solutions for tackling the current plastic crisis.
- Understanding evolutionary mechanisms utilised by microorganisms to become highly specialised at survival in distinct niches.
- Understanding the genomic context of enzyme evolution and development of a systematic DNA sequencing resource.
- Austin HP et al. (2018) Characterization and engineering of a plastic-degrading aromatic polyesterase. PNAS 115(19):E4350-E4357.
- Kern M et al. (2013) Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance. PNAS 18;110(25):10189-94
- Watts J. Schreier H, McDonald R, Marden CL 2017 Investigation into the fungal diversity within different regions of the gastrointestinal tract of Panaque nigrolineatus, a wood-eating fish AIMS Microbiology 3: 749-761.
- Besser, K. et al., (in press) Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans. Nature Communications.
- McDonald R, Zhang F, Watts J, Schreier H 2015 Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus. ISME Journal 9: 2712-2724.
The project requires a candidate with a good first degree (minimum 2.1 or equivalent) in a project-relevant discipline such as Biology, Microbiology or Biochemistry. Potential applicants with a Masters-level qualification, or equivalent experience in a relevant field, are strongly encouraged to apply. English language proficiency at a minimum of IELTS band 6.5 with no component score below 6.0.
We are looking for a talented student with a strong background in biology, microbiology and molecular biology, with an interest in the application of bioinformatics techniques. Good computer literacy is also required, and a background in bioinformatics and computer programming is encouraged. Candidates should have a desire to excel as a disciplined scientist within a cohesive research team. Familiarity with the concept of high-throughput DNA sequencing will also be an advantage. We will provide specialist training in the range of skills required for this project.
How to apply
Informal enquiries are encouraged and can be made to Dr Sam Robson on email@example.com or 023 9284 2144 or Dr. Joy Watts firstname.lastname@example.org or 023 9284 6211, quoting both the project code and the project title. For administrative and admissions enquiries please contact email@example.com.
When you are ready to apply, you can use our online application form making sure you submit a personal statement, proof of your degrees and grades, details of two referees, proof of your English language proficiency and an up-to-date CV.
Our ‘How to Apply’ page offers further guidance on the PhD application process.
If you want to be considered for this funded PhD opportunity you must quote project code PHBM5180220 when applying.
Interview date: Week commencing Monday 2nd March 2020