School of Biological and Chemical Sciences

Unravelling the genomic basis of bacterial symbiosis in deep-sea annelid worms

Project description

Mutualistic relationships between bacteria and complex organisms have repeatedly evolved and this has allowed host organisms to exploit new environments and foods. Humans also establish mutual ‘symbiotic’ associations with bacteria, mostly in our skin and digestive tract, and when altered, these symbioses can cause serious diseases, such as obesity, diabetes, and cancers. Which cellular and genetic mechanisms control bacterial symbiosis? How do these mechanisms evolve over time? How does its change contribute to animal evolution? Dr Martin’s lab studies how a unique group of worms capable of living in some of the most extreme environments on Earth can inform these questions. 

Siboglinid annelid worms (e.g. Riftia and Osedax) are able to live in particularly extreme environments including deep sea hydrothermal vents and carcases thanks to a particular symbiosis: as juveniles, these annelids acquire bacteria from the environment (Hilario et al 2011). This ultimately induces a drastic developmental change where they degenerate their guts and rely entirely on the bacterial symbionts to produce the essential nutrients they require for survival. This represents one of the most extreme and fascinating cases of symbiosis in the animal kingdom. 

A PhD studentship is available in Dr Martin’s group to study how siboglinid genomes evolve during adaptation to bacterial symbiosis and extreme deep-sea environments. In collaboration with Dr Lee Henry – whose group studies the evolution of host–symbiont relationships – and Dr Yannick Wurm – whose group studies evolutionary genomics of emerging model systems –, the project will generate and characterise genome and transcriptome assemblies of different siboglinid worms to untangle the molecular changes associated with their ecological adaptation to symbiosis and deep-sea environments. Dr Martin’s lab works with a variety of annelid species at the experimental and computational level, and thus the successful applicant will also have some opportunity to develop his/her own research directions based on interests and skills, given that these fall within the expertise of the supervisor and align with on-going research projects. 

We are looking for a highly self-motivated and enthusiastic candidate with a strong interest in animal genomics and evolution, and with previous computational experience (literacy in Unix and programming languages such as R or python). The project will involve experimental and computational approaches, as well as molecular biology and embryological techniques. The successful applicant will also have the opportunity to present their work at national and international conferences, and to collaborate with other research groups at an international and interdisciplinary level. Training will be available to help the student develop proficiency in computational analyses of next-generation sequencing datasets (e.g., genome assembly and annotation, RNA-seq analyses, molecular evolution, gene family evolution). 

Location: Dr Martin’s group, together with Dr Henry’s and Dr Wurm’s labs, are based in the Organismal Biology Department at Queen Mary University of London (Mile End campus). Queen Mary is a Russell Group University, a college of the University of London located in London’s vibrant East End (10 min bicycle ride to Tower Bridge; 10 min walking to Victoria Park; 30 min walking to Shoreditch nightlife). It benefits from state-of-the-art equipment and expertise in next-generation sequencing technologies, genomics, and bioinformatics. 

For more information about Dr Martin’s research profile, please see For more information on Dr Henry’s and Dr Wurm’s research profiles, please see and


The studentship will cover UK/EU tuition fees and provide an annual tax-free maintenance allowance for 3 years at the Research Council rate (£16,777 in 2018/19).

Eligibility and applying

Applications are invited from candidates with, or expecting to be awarded, a degree (UK 1st or 2:1 or equivalent qualification) in a relevant area (e.g. biology, biochemistry, biomedicine, bioinformatics). Although not essential, ideally applicants will have a Master’s degree, or appropriate relevant work experience. Experience in bioinformatics is highly desirable. Students outside the UK are required to provide evidence of their proficiency in English language skills. 

Informal enquiries are encouraged and can be made by email to Dr Chema Martin (). Formal applications should be made online by the stated deadline and should include a statement of purpose (motivation letter), a CV, transcripts, and two referee details. 

Apply Online


  • Hilario, A. et al. New perspectives on the ecology and evolution of siboglinid tubeworms. PLoS One 6, e16309, doi:10.1371/journal.pone.0016309 (2011).