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Find a PhD at SAMS

We have currentlyTWO funded PhD opportunities:

As a new initiative in 2018, the Bermuda Institute of Ocean Sciences is funding research as part of XL Catlin’s Ocean Risk Scholarships to examine and quantify risks to ecosystems, businesses and people from the changes taking place in the ocean. The project will seek to improve HAB early warning skill for the benefit of the aquaculture industry.

Wild fish catches have been static for the last 25 years, and the growing shortfall in fish supply must be met by aquaculture. Hence, with an increasing global demand for protein, the size of coastal aquaculture is increasing dramatically worldwide with an estimated value of €75 billion.

One of the largest, but currently unquantified risks to coastal aquaculture is that from Harmful Algal Blooms (HABs). The effects of these blooms are two-fold.

1) Mortalities of farmed fish, with associated financial consequences.

2) Human illness through biotoxins via shellfish consumption.

The potential large scale impact of HABs was vividly illustrated by the blooms of Pseudochatonella that caused mass mortality of farmed fish in Chile in 2016. The blooms killed 39 million salmon mostly in Reloncavi Sound and Fjord. This reflected a harvest weight of 100,000 metric tons and a value of US $800 million (Anderson et al. 2017).

HABs are not a single entity. Harmful genera/species all have different ecology and life cycles and hence a single one size fits all risk assessment is not appropriate. Most HAB organisms are dinoflagellates but some are diatoms. Blooms of some organisms occur locally from excystment of resting cysts within the sediment. Other genera are thought to be holoplanktonic with blooms initiating offshore and being advectively transported to coast. While some HAB genera are autotrophic, gaining their energy from photosynthesis and their nutrition from mineral nutrients, others are mixotrophic, supplementing their nutrition by heterotrophically ingesting prey cells (Reguera et al. 2012).

Fortunately, the number of harmful organisms is limited. In the UK the genera AlexandriumDinophysis and Pseudo-nitzschia are of most concern to shellfish aquaculture through their production of saxitoxin (paralytic shellfish poisoning), okadaic acid and derivatives (diarrhetic shellfish poisoning) and domoic acid (amnesic shellfish poisoning).

UK farmed fish mortality most frequently results from the species Karenia mikimotoi and spiney diatoms of the genus Chaetoceros.

With the exception of a few locations where HABs can be linked to anthropogenic nutrient loadings (e.g. from waste water or sewage effluent), blooms are spatially and temporally variable and are thought to be dependent on a number of interacting environmental drivers (Gowen et al. 2012).  Most HABs, including those in Scotland, occur naturally and are not directly anthropogenically generated. Prevention of HAB events in aquaculture areas is therefore not possible. Mitigation of their impact is therefore necessary, and is best achieved through understanding of when and where events will occur and early warning that allows remedial action to be undertaken (moving fish cages, early harvesting of shellfish or delay in harvesting until toxins depurate).

Two forms of improved HAB risk assessment are needed:

1) Better understanding of the long term and likely changes in key HAB species/genera and their link to environmental conditions in different regions 

2) Methods to model the short term development of HABs at aquaculture sites to allow action to be taken in response to these events.

While funding constraints has increasingly limited the collection of multi-year high resolution data sets, we are fortunate that phytoplankton and HABs in particular have bucked this trend with a number of data sources being available. These include:

1) Continuous Plankton Recorder data collected from plankton tows over a large spatial scale for many years.

2) HAB Regulatory monitoring data. For example, 1996 in Scottish waters harmful phytoplankton have been monitored at aquaculture sites. Since 2005 this monitoring has been on a weekly basis at ~ 40 sites. Similar monitoring programmes are operated in outer EU countries and elsewhere. 

3)  The harmful algal event database HAEDAT records harmful algal events since 2003 in ICES countries. 

These and other HAB data provide an excellent data resource to study the temporal and spatial variability in the key harmful algal genera of concern to aquaculture. Their analysis in conjunction with measured or modelled environmental information related to (for example) chlorophyll, water temperature, salinity, currents, rainfall, stratification etc. provide the potential to evaluate how different HAB genera or species will respond to climate change and to develop models of these processes.


Burrows, Professor Michael, SAMS

Davidson, Professor Keith, SAMS

Professor Martin Edwards, MBA

The project

Year 1: Literature review; Assemble data sets of relevance to UK aquaculture from CPR, regulatory and other sources; Initial assessment of spatial and temporal trends of different HAB species; Initial correlation of HAB events and abundances with potential environmental drivers

Year 2: Develop spatially and temporally resolved statistical models of HAB likelihood from observed associations in datasets assembled in Year 1, including predicting the risks of extreme and damaging HAB events; 3 month placement with CASE partner

Year 3: Expansion of analysis to other geographical areas with HAB/aquaculture problems; Production of research papers and thesis


Funding notes

The studentship is funded by an XL Catlin Ocean Risk Scholarship through the Bermuda Institute of Ocean Sciences.

The scholarship covers fees at the Home/EU rate only, plus a stipend at the RCUK level, for a total of 42 months (including writing-up). Funding is available for students worldwide, however non UK/EU students will be liable for the difference between home/EU and international fees (value TBC for 2018).

Students must be domiciled in the Highlands and Islands transition region during the course of their study to be eligible for funding.


Application notes

Applicants must possess a minimum of an Honours degree at 2:1 and/or a Master’s Degree (or International equivalent) in a relevant subject.

To apply please complete the standard application form, attaching supporting documentation (see subsequent tabs) and send to: phd@sams.ac.uk

Students who applied for this project previously do not need to resubmit their application. 

The project is expected to start on 30th September 2018.

Application deadline: 3 August 2018 ar 5 pm British Summer Time

Interview date: 17 August 2018


Parasitic sea lice pose a persistent challenge to the salmon aquaculture industry in all regions in which it operates, with both ecological and economic impacts (Costello, 2009; Ford & Myers, 2008). Developing a better understanding of their population dynamics, the factors leading to outbreaks, and improving methods of control are a current priority for industrial, regulatory, academic and external stakeholders (Scottish Aquaculture Innovation Centre, 2017). Detection of the early stages of lice infestation is difficult, as the small size of the juvenile lice means they may be missed in routine sampling. Chemical treatments may therefore be applied in a reactionary manner, requiring greater concentrations than would be needed if applied earlier, or if the threat had been avoided by other means such as deployment of physical barriers.

This PhD project will link the outputs from computer models, describing coastal currents and potential dispersal of sea lice in Scottish waters (Adams, Aleynik, & Black, 2016; Salama et al., 2012), with models of lice population dynamics on aquaculture sites themselves (Adams, Proud, & Black, 2015). This will be validated using site lice count data, in order to take the steps necessary to provide a prototype forecasting tool for parasite abundances.

At the present time, we are able to forecast physical conditions (meteorology and current patterns), and resulting dispersal patterns of larval lice, but a lack of site data has prevented development of understanding of the mechanisms for sea lice population dynamics. Over the last year, Marine Harvest have published this data on a monthly basis for their sites.  Working with this data will allow parameterisation of a predictive model for lice abundances, including environmental and management factors. This will allow the development of a forecasting tool that may be used to forecast lice abundances at a regional scale and at fine temporal resolution. Development and validation of such a model would represent a huge leap forward in terms of our understanding of the parasite, but would also offer huge potential benefits to the industry in the longer term, allowing reduced treatment costs and lower environmental impacts.


Supervisory Team


Dr Thomas Adams

Prof Keith Davidson

Dr Philip Gillibrand (Marine Harvest Scotland – industrial partner)

Dr Sandy Murray (Marine Scotland Science)



The studentship is funded by The Scottish Aquaculture Innovation Centre and The DataLab. Marine Harvest Scotland and Marine Science Scotland will support the project through in-kind contributions.

The studentship covers fees at the Home/EU/International rate only, plus a stipend at the UKRI-RCUK level, for a total of 42 months (including writing-up time). Funding is available for students worldwide, however non UK/EU students will be liable for the difference between home/EU and international fees (value TBC. As a guideline, for 2017-18 fees for international students were £14,662).

Students must be domiciled in the Highlands and Islands transition region during the course of their study to be eligible for funding.

The project is expected to start on 1st October 2018 – this may be flexible based on discussion at interview.

Applicants must possess a minimum of an Honours degree at 2:1 and/or a Master’s Degree (or International equivalent) in a relevant subject.



To apply please complete the standard application form, attaching supporting documentation (see 'How to Apply' tab) and send to: phd@sams.ac.uk

DEADLINE: 10th August 2018 5pm BST

Interview date: Week commencing 27th August 2018

Below are some ideas put forward by staff for students who want to self-fund a PhD project:

  • >Using microalgae to strip contaminating phosphates and nitrates from water supplies with (Dr Michele Stanley and Prof John Day)
  • >The genetic stabilit of microalgal strains used in biofuel production (Dr Michele Stanley and Prof John Day)
  • >Modelling the hydrodynamics of large scale macroalgae cultivation (Dr Michele Stanley and Prof John Day)
  • >Oyster culture in Scotland (Drs Adam Hughes and Michele Stanley)
  • >The war of the marine worlds: Do pathogens contribute to the resilience of marine ecosystems against biological invasions? (Dr Claire Gachon)
  • >Genomics of algal defenses against their pathogens (Dr Claire Gachon)
  • >The evolution of pathogenicity among oomycetes: a comparative genomics approach (Dr Claire Gachon)
  • >Implications of large offshore renewables arrays for fisheries (Dr Clive Fox)
  • >Prey selection by gadoid larvae (Dr Clive Fox)
  • >Behaviour of the marine predatory copepod Euchaeta norvegica (Dr Clive Fox)
  • >Reproductive behaviour of a southern copepod in the changing environment of the west of Scotland (Dr Clive Fox)
  • >Feeding preferences of Nephrops larvae (Dr Clive Fox)
  • >Dispersal of early life stages of flatfish on the west of Scotland (Dr Clive Fox and Professor Michael Burrows)
  • >Fine scale passive acoustic tracking of harbour porpoises: investigation of echolocation behaviour and practical applications (Professor Ben Wilson)
  • >Arctic wide zooplankton migration behaviour (Professor Finlo Cottier and Dr Kim Last)
  • >Developing a fjord box model for high latitudes (Professor Mark Inall and Profesor Finlo Cottier)
  • >How does vertical mixing influence ocean-glacier interactions? (Professor Mark Inall and Professor Finlo Cottier

Many PhDs come with full studentships, which cover fees and living expenses, so that students can focus on their research and be expected to complete their studies in 3 or 3.5 years.

Self-funded students will require to have IRO £14,500 per year for living expenses to be in line with RCUK doctoral stipends on top of the fees.

For UHI PhD projects, click here for the current fees.

Most our PhD projects are registered through the University of the Highlands and Islands, and this page outlines the application procedure for UHI PhDs. Please note that we have several other doctoral training partnerships - most notably with the University of Edinburgh, and applications to these programmes follow procedures by other universities. Information regarding these can be found on the individual project adverts.

We adhere strictly to equality and diversity policies during all phases of recruitment so that we find the most talented and motivated students to join us.


To be eligible to study for a PhD at SAMS UHI, who need to possess - in a relevant discipline and from a reputable institution:

  • >A Master's qualification and / or
  • >A Bachelor degree with first class or upper second class honours and / or
  • >Another qualification or substantial experience that demonstrates your academic competence to complete doctoral training successfully (to be approved by the UHI Research Degrees Committee on the recommendation of the SAMS Director).
  • >Additionally, international students whose first language is not English and who do not hold a prior degree obtained in English must hold an IELTS qualification with a score of 6.5 (6+ in writing), gained within two years prior to your registration date.

How to apply

Most importantly you need to have identified an approved PhD project (including a Director of Studies / supervisory team) that you are unquestionably excited by. This can be a ready made project advertised on these pages OR a proposal you have developed with a SAMS supervisor and have funding for.

Gradschool guide for applicants 2017

To apply, you will need to submit the following::

  • >Completed application form (Gradschool application form 2017)
  • >Copies of all official qualification certificates and transcripts. If your official certificates/transcripts are not in English, this must be accompanied by a fully certified translation provided by a professional translator/translation company
  • >For applicants whose first language is not English, an English language test certificate (IELTS or eqv.) is required and the certificate must have been gained within the past 2 years
  • >A copy of the photo page of your passport if you are not a UK national. Also include any pages which indicate a right of abode in the UK.
  • >Copy of all your official degree transcripts (BSc & MSc - as appropriate). If you have not yet completed your degree, please send a transcript showing all your modules and grades.
  • >Two references. Send the Gradschool reference form 2017 reference request form to each referee and ask them to return them to phd@sams.ac.uk before the application deadline

These documents should be sent to reach us by the deadline advertised on each advert.

By post
Fiona Tindall (Academic Registry Officer Post Graduate)

The Scottish Association for Marine Science
Argyll PA37 1QA


By Email

Interview information

The best candidates on paper will be invited for face-to-face interview. Applicants who cannot attend an interview in Oban may be offered Skype interviews.

Most PhD students will want to meet their potential supervisors to discuss the project, their personal suitability and to ascertain that they will be able to work together for a prolonged period of time.

For administrative issues, your first and main point of contact is the postgraduate registry officer, Fiona Tindall:

E: PhD@sams.ac.uk T: +44 (0) 1631 559 000 (reception)
T: +44 (0) 1631 559 427 (direct)

The SAMS graduate school is convened by marine deep-sea ecologist, Dr Bhavani Narayanaswamy:

E: Bhavani.Narayanaswamy@sams.ac.uk T: +44 (0) 1631 559 305 (direct)