Delivering plastic degrading genes into contaminated soils using bacterial megaplasmids

Delivering plastic degrading genes into contaminated soils using bacterial megaplasmids

Project Description

Supervisors

Professor Jacob Malone, John Innes Centre

Dr Andrew Truman, John Innes Centre

Professor Neil Dixon, Manchester Institute of Biotechnology, University of Manchester

 

Scientific Background

Soil contamination with plastics and other pollutants causes significant challenges in terms of environmental containment and restoration. For example, the food-safe plastic PET is found throughout the terrestrial ecosystem, where it can persist for decades. Biodegradation has great potential as a cost-effective, environmentally friendly solution to plastic contamination, and is subject to substantial research interest. We recently discovered a set of plasmid-encoded regulatory genes that have the curious ability to manipulate the behaviour of their host bacteria, dramatically increasing the rate of gene transfer between different bacteria. By combining these genes with plastic biodegradation loci, we can produce plasmids with the ability to effectively drive biodegradation traits into contaminated soil communities.

 

Research Methodology

The successful applicant will use a combination of molecular and environmental microbiology, bioinformatics and bioremediation assays to identify new plasmid regulatory genes and determine how they manipulate bacteria. This knowledge will enable them to design, build and test a series of synthetic biodegradation plasmids with enhanced abilities to spread within complex microbial communities, and to metabolise contaminating xenobiotics. Finally, they will assess the impact of their novel plasmids on the efficiency of bioremediation, alongside the short and longer-term impacts of plasmid introduction on the microbial communities of contaminated agricultural soils.

The project will ultimately lead to a molecular-level understanding of plasmid regulation and its role in controlling plasmid spread and pollutant bioremediation in complex microbial communities. Plasmid regulatory genes are widespread among divergent plasmids in a wide variety of bacterial hosts, suggesting that these genes may control bacterial lifestyle, evolution and horizontal gene transfer in a range of different environments.

 

Training

The project will be hosted at the internationally recognised John Innes Centre, in collaboration with the Manchester Institute for Biotechnology, providing cutting-edge research facilities and a stimulating research and training environment alongside world-leading scientists in the fields of molecular microbiology and microbial biotechnology. They will be part of a friendly, collaborative research team and will gain excellent training in molecular biology, environmental microbiology and bioremediation science. The combination of transferrable, technical skills associated with the project will make the successful candidate highly employable, in industry or academia.

 

Person Specification

Acceptable first degree subjects: BSc or equivalent in biochemistry, biology, microbiology, environmental sciences, or other related bioscience subjects.

Project code: MALONE_JI_ARIES26

References

  • Plasmids manipulate bacterial behaviour through translational regulatory crosstalk C Thompson, J Hall, …& JG Malone, PLoS Biology (2023) 21 (2), e3001988
  • Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities SM Bird, S Ford, ... JG Malone…& MA Brockhurst, FEMS Microbiology Ecology (2023) 99 (4), fiad027
  • Mechanisms of Plasmid Behavioral Manipulation JG Malone & CMA Thompson, DNA and Cell Biology (2024) 43 (3), 105-107
  • Complex waste stream valorization through combined enzymatic hydrolysis and catabolic assimilation by Pseudomonas putida M Chacon, G Alvarez-Gonzalez, …& N Dixon, Trends in Biotechnology (2025) 43 (3), 647-672
  • Genetic Bioaugmentation‐Mediated Bioremediation of Terephthalate in Soil Microcosms Using an Engineered Environmental Plasmid, A Marquiegui–Alvaro, A Kottara, …& N Dixon, Microbial Biotechnology (2025) 18 (1), e70071

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2026. The closing date for applications is 23:59 on 7 January 2026.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£20,780 p.a. for 2025/26) and a research training and support grant (RTSG). A limited number of studentships are available for international applicants, with the difference between 'home' and 'international' fees being waived by the registering university. Please note, however, that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK, such as visa costs or the health surcharge.
  • ARIES postgraduate researchers (PGRs) benefit from bespoke training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis. International applicants should check whether there are any conditions of visa or immigration permission that preclude part-time study. All advertised project proposals have been developed with consideration of a safe, inclusive and appropriate research and fieldwork environment with respect to protected characteristics. If you have any concerns, please contact us.
  • For further information, please contact the supervisor. To apply for this Studentship, follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential and will be stored on the UEA SharePoint server. Data will not be shared with those involved in making decisions on the award of Studentships and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be asked to complete the form by the University to which you apply.
  • ARIES studentships are subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. Please see https://www.ukri.org/publications/terms-and-conditions-for-training-funding/ for more information.

Apply Now

Apply now via the  University of East Anglia Application Portal