PhD Opportunities (X 5) at the Institute of Aquaculture

Industry-academia PhD projects at the Institute of Aquaculture

 The Institute of Aquaculture is a world leading research institute with a strong cross-disciplinary portfolio integrating research dealing with animal health, genetics, nutrition, biotechnology, production, environmental and socio-economic sustainability. We are pleased to offer 5 fully-funded full-time PhD studentships at the Institute. Each PhD studentship has strong links with the aquaculture industry with 50% of the studentship funded by our industry partners. Further background describing the Institute of Aquaculture staff, teaching and research can be found at

PhD project titles

 1. Control of Salmon Gill poxvirus on Aquafarms in Scotland. Principal supervisor; Professor Manfred Weidmann (, industry partner Cooke Aquaculture.

Note: This PhD must begin no later than March 2018

 Background: Gill disease in salmon suspected to be caused by a pox virus has been documented in Norway since the 1990’s. During the investigation of material from some acute gill disease in salmon from Norwegian aquafarms the whole genome of the new Salmon gill poxvirus was determined by NGS in 2015 (Gjessing 2015). It since has emerged that SGPV is the most ancient species of pox virus located at the base of phylogenetic tree of pox viruses of the Chordapoxvirinae infecting vertebrates. It appears to be widely prevalent in wild salmon (46 %) and in brood fish (83 %) and it seems very likely it has been introduced to farmed salmon through use of freshwater from anadromous water bodies in hatcheries (Garseth 2017). Currently published work seems to indicate a wide spread prevalence of SGPV in farmed salmon combined with rare diseae. Disease seems to erupt when stress stimuli impact on the salmon possibly causing immune-depression thus allowing for enhanced SGPV replication. SGPV has been detected by PCR in fish of hatcheries on the Scottish West Coast. In order to understand the situation better and to establish correlates between the presence of SGPV and disease in salmon throughout the production cycle several basic methods need to be established. This project will try to develop tools for diagnostics and surveillance of SGPV to develop monitoring for SGPV gill disease into a tool for general health monitoring of salmon hatcheries.


2. Characterization of the smoltification process in modern aquaculture systems and triploid Atlantic salmon. Principal supervisor; Professor Herve Migaud ( and industry partner AquaGen Scotland Ltd.

The process of parr-smolt transformation (PST) plays also an important role on Atlantic salmon robustness at sea. PST is synchronised by changes in day length invariably coupled with prevailing water temperature. PST is characterised by a huge number of morphological, enzymatic, endocrine and immune related functions, and upon completion ensures sea transfer readiness. One of the major changes is in the activation of chloride cells which differentially express enzymes (NKA) which function to maintain water and ion homeostasis in the differing osmotic environments. The completion of PST is marked by transition from the freshwater isoform to the seawater isoform, permitting maintenance of osmotic balance at sea. This process is energetically driven, and key development thresholds must be met in order to successfully achieve PST. However, while regimes are routinely used in the industry, assessing PST as a trait remains problematic and there is a need to better characterize this critical physiological process in salmon. This is especially relevant due to increasing size of smolts reared in large Recirculation Aquaculture Systems (RAS) transferred to sea earlier than ever before and the implementation of triploidy as a mean to produce sterile stocks to prevent potential cross-breeding with wild stocks following escapees and enhance productivity.

The PhD project will therefore investigate the effect of ploidy, energetic/adiposity status, environmental manipulation and body size on the smoltification trait through phenotypic and transcriptomic comparisons between environmental regimes to identify gene markers of smoltification that could be used as a monitoring and selection tool. Analyses of gills, liver, skin/mucus and possibly gut and blood will be performed as these are playing important roles in osmoregulation but also mucosal immunity. Finally, the project will also study the impact of sub-optimal smoltification (failed smolts or de-synchrony) on fish robustness at sea.

3. Evaluating efficacy of prophylactic health products (PHP) for intensive-shrimp (Litopenaeus vannamei) culture under commercial production conditions in Andhra Pradesh, India. Principal supervisor; Dr Francis Murray (, industry partner ANANDA Group AP.

 Background: Shrimp production in India intensified rapidly following the introduction of Litopenaeus vannamei in 2009, output rising from 80,000 MT in 2009 to 426,500 MT in 2015, a 30% YoY rise. Andhra Pradesh (AP) accounts for 66% of all farmed production. In addition to larger firms, best estimates suggest up to 50,000, mostly small-scale farmers are practicing intensive culture creating regulatory challenges, just as greater restrictions on antibiotic use are being imposed in European and American markets. Consequently, farmers have become increasingly dependent on a proliferating range of prophylactic products including pre and probiotics, often of uncertain provenance & efficacy. Probiotics may applied in-feed or directly to the culture environment at different production stages. This study will centre on implementation of hatchery and grow-out trials with ANANDA Group AP (PhD co-sponsors: to assess efficacy of selected ‘high potential’ PHPs compared with biofloc controls. The study design will build on outcomes of the interdisciplinary research project; IMAQulate[1] ( Previous findings indicate broad differences in farm environmental conditions and health management strategies; for example less-well-resourced farmers with limited disease-diagnostic capacity are more likely to apply ‘soil-and water’ probiotics therapeutically in response to adverse water quality indicators. In this study, the performance of hatchery treated juveniles will be followed by ‘on-farm’ assessments noting that manipulation of the gut-microbiome (using in-feed and or pond-soil probiotics) in early life stages may confer life-long immunological benefits with or without additional treatments. The study will also incorporate a full economic cost benefit analyses and regulatory assessment. To contribute to these goals we are seeking a highly motivated candidate willing to work in an interdisciplinary capacity encompassing aquatic health management, epidemiology and (PHP) and market analysis. The student will be based in Bhimavaram, AP to implement trials at the ANANDA groups R&D commercial facilities before moving to the UK (UoS) to write-up in the final year. The student will also be closely affiliated with the IMAQulate project and its on-going work in AP. Fluency in Telegu (the principle language of AP) is an essential criteria.

 4. Improving disease resistance in Rainbow trout to Flavobacterium psychrophilum, the causative agent of Rainbow Trout Fry Syndrome (RTFS). Principal supervisor; Professor Alexandra Adams (, Dr Rowena Hoare (, industry partners AquaGen Scotland Ltd and Dawnfresh Seafoods Ltd.

Background: Rainbow Trout Fry Syndrome (RTFS) has been responsible for substantial economic losses in the rainbow trout industry globally, including the UK, for decades. It is widespread, occurs frequently, and can cause high mortality in fry and larger fish in freshwater hatcheries and on-growing sites. Antibiotics are often used to treat affected stock. Preliminary work has identified two major markers (QTLs) for resistance to RTFS. Both alone and in combination, the QTLs have a highly significant effect in reducing mortality. The survival among fish with the worst and the best combination of marker allele was 31% and 84%, respectively, indicating that there is huge potential for improving disease resistance in rainbow trout to RTFS. This project aims to fine-map the identified QTLs for RTFS resistance to 1) to identify DNA markers more strongly associated to the QTL (and thus, the trait) than the currently ‘best’ DNA markers, and 2) to identify the causative mutations underlying the QTL. Parameters of resistant and susceptible trout will also be investigated using transcriptomic and proteomic technology in an attempt to identify and elucidate the mechanisms of resistance. In addition, rainbow trout eggs (selected for RTFS resistance) will be followed in a longitudinal study to monitor the presence of other important trout diseases.


5. Performance assessment of emergent aquaculture technology: towards enhanced benefits for producers and consumers. Principal supervisor; Professor Dave Little (, industry partner Worldfish, Penang Malaysia.

Background: This PhD project aims to align with and address key research questions associated with the recently approved FISH aquaculture systems cluster of the CGIAR Research Program on Fish Agri-Food Systems (FISH), led by Worldfish. The key research objective will be to develop and deploy an analytical tool and framework that can be applied widely in WorldFish focal countries to assess the performance of any novel aquaculture technology change in terms of economic, environmental and social impacts. The initial focus will be on improved breeds of tilapia and aim to inform trait prioritisation and development but will also embrace other species and systems identified by the FISH program, including performance of improved feeds, health and system design interventions. A key focus will be to assess nutritional outcomes for smallholders and off-farm consumers from different technology/system/management interventions, ensuring economically optimal nutritional values of farmed aquatic animals is retained or improved. This objective is in line with recent concerns about the nutritional value of farmed fish and the need to proactively address emerging buyer and consumer perceptions.

 Applicants are encouraged to contact the principal supervisors listed above for further details of the projects.


Candidates must have a First / Upper Second Class BSc or MSc in a relevant subject. It is not expected that candidates will have experience in all the above techniques, but they will need to demonstrate the aptitude and commitment to be trained and to work in both academic and industry environments. In most cases the applicant will be largely based at the Institute of Aquaculture in Stirling (with the exception of proposal 3 that is 100% in India) but periods of time will be spent at our external facilities and with industry partners as required as required by the project.

 APPLICATION PROCESS: To apply, send a covering letter and up-to-date CV to Deadline for application is the 16th February 2018. Candidates will then be selected and interviewed as requested. The PhD will start ASAP.