EastBio: Who’s there? Unbiased microbiome assessment during Atlantic salmon seawater transfer.

Details

This fully funded, 4-year PhD project is part of a competition funded by the BBSRC EASTBIO Doctoral Training Partnership.

Aquaculture is the fastest growing food sector globally, but continued sustainable expansion in line with projected food security estimates is hampered by issues with fish health and disease. Understanding how aquaculture practices impact fish immune system function and resilience is key to addressing these issues.

Atlantic salmon is the most valuable finfish species cultured worldwide, with production in Scotland alone valued at over £1.2 billion in 2025. An anadromous species they spend periods of their life cycle in freshwater (FW) as parr, and in saltwater (SW) as smolts. The transition between FW and SW is enabled by a suite of changes known collectively as smoltification. In the aquaculture industry, this sensitive SW transition period is associated with high levels of mortality, undesirable for the fish, and for industry productivity. Alternative practices involved gradual introduction to SW through a brackish water transition period.

Depression of the Atlantic salmon immune system during smoltification has been identified through transcriptomics, likely due to redirection of resources to osmoregulation. An important component of the teleost immune system is the symbiotic microbial communities (bacteria, archaea, viruses and fungi) that inhabit mucosal surfaces. Collectively known as the microbiome, these microbial communities contribute to defence against potential pathogens in the surrounding water. Distinct shifts in microbiome communities in important osmoregulatory mucosal tissues including gill and skin have been identified following transfer to sea, but traditional assessment using 16S rRNA amplification does not capture the full microbial communities, only bacteria and archaea, and are biased by primer set selection.

In this project we will assess microbiome communities in water, gill and skin samples during smoltification and following transfer to SW, assessing the impact of sudden or gradual SW transfer regimes. The candidate will undertake a 3-month internship with a commercial diagnostic company (Esox Biologics) where they will be trained in using their proprietary metagenomic Detect platform which enables holistic microbiome identification without bias by sequencing all DNA identified in a sample with no prior assumptions. Traditional 16S rRNA sequencing will be used to supplement and compare. Quantitative PCR-based transcriptomic analysis will be conducted in parallel and integrative analysis conducted to assess interactions between immune transcriptome and microbiome.

The successful applicant will learn a range of transferrable molecular biology skills including DNA / RNA extraction, metagenomic and quantitative PCR transcriptomic analysis, bioinformatics skills as well as gaining hands on experience in a commercial facing diagnostic company.

This is a CASE studentship (Collaborative Awards in Science and Engineering). CASE studentships involve students enhancing their training by spending three to 18 months with a CASE partner in a workplace outside of the academic environment. The CASE partner for this project is esoxbiologics.com.

Please note, your application may be shared with any external partners of this PhD Studentship.

This project is available for part-time study (Home/UK students only).

Interested applicants should contact the lead supervisor to discuss the project prior to applying. You can do this by selecting the first listed name at the top of this advert and sending your enquiry. Alternatively, you can search for the supervisor through the University of Aberdeen staff directory and email them directly.

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ELIGIBILITY:

Applicants should hold a minimum of a 2:1 UK Honours degree (or international equivalent) in a relevant subject. Those with a 2:2 UK Honours degree (or international equivalent) may be considered, provided they have (or are expected to achieve) a Distinction or Commendation at master’s level.

We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

All students must meet the eligibility criteria as outlined in the UKRI guidance on funding for postgraduate training and development. This guidance should be read in conjunction with the Terms and conditions for training funding – UKRI.

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APPLICATION PROCEDURE

For full details and to download the application form, visit: https://biology.ed.ac.uk/eastbio/how-to-apply

Please note that you may only apply for one EASTBIO project.

1. Application submission

Submit your complete application by 23:59 GMT on 16th November 2026 to smmsn-pgrenquiries@abdn.ac.uk.

Send your application as a single email with the subject line: “EASTBIO Application – [Your Name]”

“EASTBIO Application – [Your Name]”

2. Required documents

Your application email must include the following:

• Completed EASTBIO application form
• Academic certificates and transcripts
• Two references (one reference may be non-academic)

3. References

All references must be provided using the official EASTBIO reference form (available here).

References can be either:

• Included with your application, or
• Sent directly by referees to smmsn-pgrenquiries@abdn.ac.uk with the subject line: “EASTBIO Reference – [Your Name]”

All references must be received by 23:59 GMT on 16th November 2026.

It is the applicant’s responsibility to ensure both references are submitted by the deadline, as we cannot request them on your behalf.

Important notes

• No research proposal is required.
• Do not include any additional documents (for example, school certificates, conference papers, or dissertations).
• Incomplete applications or those including unnecessary materials will not be considered.
• Due to workload constraints, we are unable to follow up on missing documents or process incomplete applications.
• All candidates will be notified of the outcome of their application.

For any questions or assistance with the application process, please contact smmsn-pgrenquiries@abdn.ac.uk.

Funding Notes

This fully funded, four-year PhD project is offered as part of a competition within the EASTBIO BBSRC Doctoral Training Partnership. The opportunity is open to both UK and international applicants, although the proportion of international students recruited through the EASTBIO DTP is capped at 30% by UKRI BBSRC.

EASTBIO studentships provide a tax-free UKRI doctoral stipend (estimated at £22,437 for the 2027/28 academic year), a training grant of £5,000 per year for the first three years (and £1,500 in the fourth year), and a travel and conference allowance of £230 per year.

Please note that EASTBIO is unable to fund visa costs or associated healthcare surcharges for international students