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

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.

Personal specification

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

Funding details 

ARIES studentships are subject to UKRI terms and conditions(opens in a new window). 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. 

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