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Find a PhD at SAMS

We currently have 3 fully funded PhD vacancys:

Organism and ecological impacts of electrofishing in Scottish shallow coastal habitats

Over the last decade, electrofishing has developed in shallow marine coastal sites around Scotland. The principal targets are two species of razor clam (Ensis siliqua and Ensis magnus). These shellfish command high prices in the Far East which has driven a fishery that has increased substantially since the mid-1990s reaching a value of around £3 million per annum and extracting 400-500 tonnes of razors per annum. Electrofishing is preferred by the fishers because it produces a cleaner and hence more valuable product compared with other harvest techniques, such as dredging. It is also claimed that electrofishing is more benign from an environmental view but there is limited scientific evidence to support this. Some research has been conducted on the short-term impacts of electrofishing on razor clams and other non-target benthic organisms. These studies suggested that impacts are limited with razor clams being observed to rebury a few minutes after the electrical field has passed. Non-target organisms such as juvenile flatfish, starfish and crabs were either temporarily stunned or apparently unaffected. On the other hand there is anecdotal evidence that electrofished razor clams do not ‘depurate’a as well as those harvested using other techniques. This suggests that electrofishing may affect the physiology of the clams in the short and possibly medium-term.

Although previously illegal under the EU Common Fisheries Policy, the Scottish Government has established a tightly controlled research-scale trial electrofishery for razor clams in a number of locations around Scotland. The impacts of the trial fisheries on the Ensis stocks are being monitored by Marine Scotland Science. However, concerns remain about potential longer-term impacts on both smaller and under-sized razor clams that are not collected, and on the wider benthic ecosystem, especially with industry pressure to open out wider areas to electrofishing.

The aim of the project will be to conduct laboratory and field-studies to address these issues.

The proposed project addresses the SUPER DTP focus on sustainable exploitation and blue growth. The longer term impacts of electrofishing on these habitats have not been investigated and are thus unknown. This aspect requires urgent investigation and assessment before the technique becomes more widespread in the commercial fisheries. The project thus clearly addresses the theme Biodiversity and ecosystem function: Ecosystem services, ecology and conservation, not only of the razor clam stocks themselves but also of their habitat and associated shallow sub-tidal communities.

The project has the potential to include a variety of laboratory and field based approaches:-

1. Aquarium based experiments comparing the growth, filtration and other physiological performance indicators of razor clams and other non-target organisms collected using electrofishing with samples which have been collected by alternate means. Organisms will be marked using suitable tags (visible elastomer for flatfish, starfish etc.), external marking of the shell for bivalves and maintained in mixed groups so that compared subjects experience the same environmental conditions.
2. Physiological performance measures may include measurements of growth, filtration clearance rates for filtration feeding organisms (razor clams and other bivalves), swimming activity rates assessed using SAMS video observation facility (flatfish and decapods), oxygen uptake rates using respirometry, muscle energy metabolites and protein profiles.
3. Field sampling within and adjacent to the Scottish experimental electrofishing areas to investigate whether there are any detectable impacts on the wider benthic communities from electrofishing activity.
4. The student will also have the opportunity to work with Marine Scotland Science’s Assessment team in terms of analysing background data on the trial fisheries. Such data include fishing intensity, catch records and information on sizes of shellfish being landed.
5. Marine Scotland Science are also collecting shells from the experimental fisheries and are interested in the student applying methods of age determination to establish age-length relationships, and growth characteristics for razor clams in the different fishing areas. These data could be used in stock production models and potentially age-based stock assessment methods.

a Depuration (purification) is a process by which shellfish are held in tanks of clean seawater under conditions that maximize the natural filtering activity. This results in purging of intestinal contents including microbial contaminants such as E. coli thus reducing chances of contamination of the shellfish when eaten.

Funding Notes

Funded by NERC Studentships awarded to the SUPER Doctoral Training Partnership. The SUPER DTP partner Universities are St Andrews University, Aberdeen University, Edinburgh Napier University, Heriot-Watt University, the University of the Highlands and Islands, Stirling University, University of Strathclyde and the University of the West of Scotland. Underpinning these research partners, providing additional training and projects are Marine Scotland, Scottish Natural Heritage, and the James Hutton Institute, among a total of 40 stakeholder organisations including industry and government agencies and international collaborators.

The start date of this project is: 5th October 2020

The 3½ year studentships cover:
• Tuition fees each year (for 2019/20 this is currently £4,327 for full-time study)
• A maintenance grant each of around £15,000 per annum (for full-time study)
• Funding for research training
• Part-time study is an option, with a minimum of 50% of full-time effort being required.

Applicants should normally have, or be studying for:
• A postgraduate Master’s degree from a degree-awarding body recognised by the UK government, or equivalent, or
• A first or upper second class honours degree from a degree awarding body recognised by the UK government, or equivalent, or
• Other qualifications or experience that affords sufficient evidence of an applicant’s ability to work at the academic level associated with doctoral study.

Applicants with experience of maintaining marine shellfish in aquaria and of conducting controlled experiments on marine organisms in aquaria and/or of undertaking fisheries field research are encouraged to apply.

Project specific enquiries: clive.fox@sams.ac.uk

General enquiries: Graduate School Office gradresearch@uhi.ac.uk

 

Understanding and exploiting stoichiogenomics to harness reactive nitrogen in sustainable food production systems

Aquaculture is the fastest growing food production sector in the world, however global aquaculture needs to double in size over the next decade to keep pace with the ever-rising demand for quality protein. Nitrogen, the main constituent of protein, is one of the most critical and valuable elements globally. Current aquaculture practices are characterised by inefficiencies in nitrogen use and globally, aquaculture is contributing to net nitrogen loading to the environment, with concomitant negative impacts on the environment and human health. As aquaculture intensifies, the volume of waste produced will increase in direct proportion to aquaculture production, however presently, there are limited solutions to deal with N-rich waste.

This research will develop innovative systems, based on the recovery of valuable resources, to pioneer sustainable food production systems and catalyse a new revolution in the nitrogen cycle. Rather than promoting technologies that result in the permanent removal of nitrogen, this research will explore the potential to exploit the genomic capacity and functional potential of microbial communities within marine sediments and deposit feeder gut microbiomes to upcycle waste N into high value biomass as organic nitrogen.

Understanding and exploiting genomics and concomitantly proteomics is a fundamental theme underpinning the research. Through a close partnership with the commercial partner, Great British Prawns Ltd, an innovative company producing high value prawns in a marine recirculating aquaculture systems (RAS), the student will use discovery science and stoichiogenomics to demonstrate how genome level responses of sediment and deposit feeder microbiomes, in response to anthropogenic Nr pollution, can be manipulated and exploited to engineer low-cost systems, that provide a myriad of solutions to the current global challenges facing the agro-industry sector.

The PhD student will work within the framework of Elemental Stoichiometry to understand the structure, organisation, function and interaction of microbial communities in deposit feeder gut, soil and sediment microbiomes. A stoichioproteomic analysis of microbial communities from different environments, including agriculture, aquaculture and engineered bioremediation systems will be undertaken using annotated sequencing data from soils, sediment and bioremediation systems currently available through the Earth Microbiome Project. Long-term growth trials of the polychaete Alitta virens reared on waste from a prawn Recirculating Aquaculture System (RAS) will be coupled with integrative microbiome research to explore the role of the ‘system microbiome’ (soil, sediment and gut microbiomes of deposit feeders), and the role they play in elemental nutrient cycling and the global N budget.

The PhD student will be primarily based at the Scottish Association for Marine Science in Oban, under the supervision of UKRI Future Leaders Fellow Dr Georgina Robinson, with additional supervision from Dr Mary Doherty, University of the Highlands and Islands and Dr Katherine Duncan, University of Strathclyde and will undertake a 3-month placement with the commercial partner GBP Ltd in Balfron. The student will receive training in a novel inter-disciplinary scientific area, providing expertise in sample collection, microbiome sequencing, molecular techniques and cutting edge transcriptomics and proteomics methodologies as well as bioinformatics and modelling.

Funding Notes

Funded by NERC Studentships awarded to the SUPER Doctoral Training Partnership. The SUPER DTP partner Universities are St Andrews University, Aberdeen University, Edinburgh Napier University, Heriot-Watt University, the University of the Highlands and Islands, Stirling University, University of Strathclyde and the University of the West of Scotland. Underpinning these research partners, providing additional training and projects are Marine Scotland, Scottish Natural Heritage, and the James Hutton Institute, among a total of 40 stakeholder organisations including industry and government agencies and international collaborators.

The start date of this project is: 5th October 2020

The 3½ year studentships cover:
• Tuition fees each year (for 2019/20 this is currently £4,327 for full-time study)
• A maintenance grant each of around £15,000 per annum (for full-time study)
• Funding for research training
• Part-time study is an option, with a minimum of 50% of full-time effort being required.

Applicants should normally have, or be studying for:
• A postgraduate Master’s degree from a degree-awarding body recognised by the UK government, or equivalent, or
• A first or upper second class honours degree from a degree awarding body recognised by the UK government, or equivalent, or
• Other qualifications or experience that affords sufficient evidence of an applicant’s ability to work at the academic level associated with doctoral study.

Project specific enquiries: mary.doherty@uhi.ac.uk

General enquiries: Graduate School Office gradresearch@uhi.ac.uk

Unlocking the enigma of Scottish harbour porpoise fine-scale habitat use

Harbour porpoises (Phocoena phocoena) are the most abundant and widespread cetacean in Scottish waters but are vulnerable to anthropogenic pressures such as noise from aquaculture and wind farm construction, bycatch in fisheries, and climate change. As a result, various national and international laws and agreements aim to protect porpoises from these pressures. In addition to general protection and inclusion in decision making processes, porpoises were the reason for the designation of one of Europe’s largest protected areas, the cSAC along the west coast of Scotland in 2018.

Porpoises are found in a range of habitats throughout Scottish waters. However, these habitats are not used equally with some favoured year round and others at particular times. This project will seek to understand the drivers for these differences, making use of existing datasets collected using passive acoustic monitoring (PAM). PAM is a commonly used technique to establish presence and relative abundance of echolocating porpoises in specific locations over extended time periods, using fixed or towed underwater acoustic detectors (hydrophones). Across both the east and west coasts, several projects have been collecting PAM data from fixed stations for up to a decade. While these data have all been collected for slightly different purposes, they have all used similar methods and so this project seeks to consider them at a more holistic level to better understand porpoise ecology and how and why porpoises use different environments. Most Scottish PAM studies to date have focused on large-scale trends in usage, however their use has also revealed intriguing patterns of habitat use that vary at fine-scales (<1km). Some of these differences have been found to occur over subtly different seabed habitats, depths and time scales. Integrating these data with environmental parameters is likely to help reveal and provide insights into which fundamental ecological and/or anthropogenic drivers underpin porpoise distribution and habitat use in Scottish waters.

In this project, the student will have the opportunity to combine and explore previously independent datasets collected for a variety of reasons from across Scotland. Doing so will provide opportunities to better understand biases in standard survey methods and reveal wider patterns of habitat use by porpoises. In addition there may be the opportunity to collect new data to better test some of the environmental relationships that emerge. Discoveries associated with this project have the potential to provide information for conservation management efforts particularly in terms of improving monitoring strategies.

With this project bringing together previously disparate datasets, the student will need to be willing to deal with large datasets and the inherent challenges these bring (particularly extensive manipulation and error-checking). Thus the applicant will need to demonstrate excellent attention to detail and organisational skills. Analysis of these datasets will likely involve sophisticated statistical modelling approaches, and a strong candidate will possess excellent numeracy skills and be familiar with advanced quantitative analytical approaches. Familiarity with programming (such as R or Matlab) and multivariate statistics would be a bonus. Experience in underwater acoustics, PAM analysis and practical experience studying small cetaceans in temperate coastal environments may be beneficial but are not essential.

The student will benefit from an experienced supervisory team, which will be led by Prof. Ben Wilson (SAMS-UHI) and will also include Dr. Kate Brookes (Marine Scotland), Dr. Steven Benjamins (SAMS-UHI) and Prof. Paul Thompson (University of Aberdeen). The student will join the SAMS team working on Scottish marine vertebrates, acoustics and behaviour under Prof. Wilson, but will be expected to also spend time at the other partner institutions to facilitate analysis of PAM datasets held by them and to develop working relationships with colleagues working in different areas of marine science.

Funding notes

Funded by NERC Studentships awarded to the SUPER Doctoral Training Partnership. The SUPER DTP partner Universities are St Andrews University, Aberdeen University, Edinburgh Napier University, Heriot-Watt University, the University of the Highlands and Islands, Stirling University, University of Strathclyde and the University of the West of Scotland. Underpinning these research partners, providing additional training and projects are Marine Scotland, Scottish Natural Heritage, and the James Hutton Institute, among a total of 40 stakeholder organisations including industry and government agencies and international collaborators.

The start date of this project is: 5th October 2020

The 3½ year studentships cover:
• Tuition fees each year (for 2019/20 this is currently £4,327 for full-time study)
• A maintenance grant each of around £15,000 per annum (for full-time study)
• Funding for research training
• Part-time study is an option, with a minimum of 50% of full-time effort being required.

Applicants should normally have, or be studying for:
• A postgraduate Master’s degree from a degree-awarding body recognised by the UK government, or equivalent, or
• A first or upper second class honours degree from a degree awarding body recognised by the UK government, or equivalent, or
• Other qualifications or experience that affords sufficient evidence of an applicant’s ability to work at the academic level associated with doctoral study.

Numerate applicants who are familiar with advanced quantitative analytical approaches are encouraged to apply.

Project specific enquiries: ben.wilson@sams.ac.ukor steven.benjamins@sams.ac.uk

General enquiries: Graduate School Office gradresearch@uhi.ac.uk

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

  • >The genetic stabilit of microalgal strains used in biofuel production (Dr Michele Stanley)
  • >Modelling the hydrodynamics of large scale macroalgae cultivation (Dr Michele Stanley)
  • >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.

Eligibility

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.

PhD application guidance SAMS 2019-20

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

  • >Completed application form.
  • >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.

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

By post
Academic Registry Officer: Post Graduate
The Scottish Association for Marine Science
Oban
Argyll PA37 1QA
UK

OR

By Email
phd@sams.ac.uk

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, Anna Kane:

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)