Investigate How Bacterial Hosts Control Domesticated Viral Machines to Drive Horizontal Gene Transfer in Marine Environments?

Project Code: LE_JIC_ARIES27

Investigate How Bacterial Hosts Control Domesticated Viral Machines to Drive Horizontal Gene Transfer in Marine Environments?

Project Code: LE_JIC_ARIES27

Project Description

Supervisors

Professor Tung Le, John Innes Centre – contact me

Professor Jonathan Todd, Quadram Institute & UEA

Dr Ngat Tran, John Innes Centre

 

Scientific Background:

Horizontal gene transfer (HGT) is a major driver of bacterial evolution, shaping adaptation at both species and community levels. While HGT by plasmids, transposons and bacteriophages are well understood, HGT by gene transfer agents (GTAs) is under-explored and under-appreciated. GTAs are phage-derived particles that package random fragments of the host chromosome and transfer them to neighboring cells. Unlike bacteriophages, they are non-infectious/non-replicative and instead represent remarkable examples of viral machinery domesticated by bacteria i.e. a selfless virus.

Despite their widespread distribution in marine Alphaproteobacteria, fundamental questions remain: why have bacteria retained these inherently dangerous systems, how are they regulated, how abundant are they in marine environments, and what ecological benefits do they provide?

Ruegeria pomeroyi DSS-3, a producer of functional gene transfer agents (RpGTA), is an excellent model to answer these questions. R. pomeroyi plays a pivotal role in marine carbon, sulfur and nitrogen cycling by recycling phytoplankton-derived organic matter in the phycosphere. We hypothesize that these transient nutrient-rich hotspots support dense microbial communities/biofilms where GTA-mediated gene exchange accelerate adaptation and influence the ocean ecosystem.

 

Research Methodology

By integrating molecular genetics, cell imaging, and marine metagenomics and metatranscriptomics, the student will investigate how the host controls viral systems to drive gene exchange.

Aim 1. Define the regulatory network controlling RpGTA production

Aim 2. Identify the ecological signals that trigger GTA production

Aim 3. Determine the abundance, expression and diversity of GTAs in marine Roseobacter communities by deep metagenomic and metatranscriptomic sequencing

 

Training:

Based primarily in the Le lab at the JIC, the student will receive interdisciplinary training in bacterial genetics, molecular biology, biochemistry, genomics (ChIP-seq, RNA-seq, Tn-seq) and live-cell imaging. The Todd lab, a world leader in R. pomeroyi biology and marine sulphur cycling, will provide complementary expertise in marine microbial ecology, metagenomic sampling and bioinformatics. Additional mentoring and training in specialised methodologies, experimental design and data analysis will be provided by long-term postdoc and scientific platform scientists at the JIC, Quadram Institute and UEA.

 

Person Specification:

Applicants should hold, or expect to obtain, a first degree in biology, microbiology, Molecular biology or a related discipline.

References

  • Todd, J.D., Kirkwood, M., Newton-Payne, S., Johnston, A.W.B. (2012). DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3. The ISME journal, 6, 223-226.
  • Banks, E.J., Bárdy, P., Tran, N.T., Nguyen, P.M., Stojilković, B., Gozzi, K., Maqbool, A., and Tung Le (2026). A bacterial CARD-NLR-like immune system controls the release of gene transfer agents. Nature Microbiology https://doi.org/10.1038/s41564-026-02316-4. )
  • Tran NT, Tung Le. (2023) Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination. Nature Communications, 15, 4749 (2024). https://doi.org/10.1038/s41467-024-49114-2
  • Carrión, O., Li, C.-Y., Peng, M., Wang, J., Pohnert, G., Azizah, M., Zhu, X.-Y., Curson, A.R.J., Wang, Q., Walsham, K.S., Zhang, X.-H., Monaco, S., Harvey, J.M., Chen, X.-L., Gao, C., Wang, N., Wang, X.-J., Wang, P., Giovanonni, S.J., Lee, C.-P., Suffridge, C.P., Zhang, Y., Luo, Z., Wang, D., Todd, J.D., Zhang, Y.-Z. (2023). DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms. Nature Microbiology, 8, 2326-2337.
  • Fu, H.-H., Wang, M.-C., Wang, Z.-Q., Sang, Y.-H., Li, Z.-K., Li, F.-F., Liu, J.-R., Qin, Q.-L., Zhu, X.-Y., Wang, N., Wan, J.-J., Teng, Z.-J., Zhang, W.-P., Gates, A.J., Li, C.-Y., Todd, J.D., Zhang, Y.-Z. (2026). Regulation of DMSP organosulfur cycling in ubiquitous Roseobacter marine bacteria. The EMBO Journal, 45, 1980-1996.

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2027. The closing date for applications is 23:59 on 16 December 2026.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£21,805 p.a. for 2026/27) 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