Elucidating Population Structures of an Emerging Pathogen Affecting Global Fisheries - Biosciences - NERC GW4+ DTP PhD studentship Ref: 2809

About the award

This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP).  The GW4+ DTP consists of the Great Western Four alliance of the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus six Research Organisation partners:  British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, the Met Office, the Natural History Museum and Plymouth Marine Laboratory.  The partnership aims to provide a broad training in earth and environmental sciences, designed to train tomorrow’s leaders in earth and environmental science. For further details about the programme please see http://nercgw4plus.ac.uk/

The studentships will provide funding for a stipend which is currently £14,553 per annum for 2017-2018, research costs and UK/EU tuition fees at Research Council UK rates for 42 months (3.5 years) for full-time students, pro rata for part-time students.


Lead supervisor: Dr Mark van der Giezen

Co-Supervisor: Dr Stephen Short

Co-Supervisor: Dr Grant Stentiford 

Co-Supervisor: Dr Kelly Bateman


Location: Streatham Campus, Exeter

Project description:

Global farmed and wild caught crustaceans add 10bn kg to protein production a year with first sale value of >£20bn. However, disease limits future growth and sustainability. Pathogens such as the dinoflagellate Hematodinium are the most significant factor limiting food security in this sector (Stentiford et al 2014).

Hematodinium is lethal to its host (Stentiford and Shields 2005). However, our studies revealed differential host responses to distinct isolates. Some isolates induced no immune response, resulting in severe parasitaemia, while for others, the host responded and resisted infection (Daniels et al., unpubl.). Current genetic markers cannot separate strains and tools to discriminate disease and non-disease-causing forms do not exist. Sequencing Hematodinium genomes is not feasible due to genome size. However, a powerful next generation sequencing method, RADSeq, can reveal genome-wide genetic markers without whole genome sequencing (see Davey et al. 2011).

Project Aims and Methods:

Overall aim:
This project will enable the discrimination between emerging virulent and non-virulent strains of the major crustacean parasite Hematodinium. This is a direct requirement when defining pathogens in a legislative context and will protect UK fisheries.


Discriminate between virulent and non-virulent Hematodinium strains in order to provide strain specific markers and allow regulators to make informed decisions regarding border protection against movement of pathogenic strains.

Investigate the molecular basis of divergent immune responses to Hematodinium isolates. This will enhance our understanding of crustacean immunity and inform strategies for producing infection-resistant stocks.

Work to be carried out and outcomes:

Use RADSeq technology to provide taxonomic resolution for Hematodinium isolates from geographically distinct host populations to discriminate between virulent and non-virulent strains (verified by histopathology). Our data will map the emergence of pathogenic strains onto environmental change drivers to develop a forecasting tool for predicting emerging threats (Stentiford et al. 2014).

RADseq will be used on the type species from the type host at the type location (Hematodinium perezi in the shore crab Carcinus maenas from the English Channel) and compared with numerous global isolates from different hosts (lobster, edible crab, snow crab, blue crab and giant mud crab). By defining key SNP markers, we will provide the first toolbox to discriminate Hematodinium strains.

Use comparative RNASeq to investigate the molecular basis of the divergent Hematodinium immune evasion capabilities. Investigating the molecular basis of host response variability will be facilitated by combining the parasite transcriptomes with our existing genomic and transcriptomic resources for the type host C. maenas, including the characterised immune system pathways (Verbruggen et al. 2015). Studies of haemocytic response following Hematodinium infection suggests immune evasion is the result of molecular mimicry (Rowley et al. 2015). Therefore, comparative RNASeq will reveal candidate factors that underlie the evasion mechanism. This would be a major step towards engineering tangible approaches for mitigating the economic consequences of Hematodinium, whether via improved monitoring, immunostimulant treatments or breeding strategies that produce resistant crustacean stocks (via the National Lobster Hatchery, one of our collaborators).


The candidate is ambitious and wants to make a positive change to our world which faces a multitude of challenges. The applicant ideally has an animal biology background with molecular experience and knowledge of mathematical modeling would be a strong plus. Overall, the candidate needs to be a team player.

Case Award Description:

The project fits Cefas’ Food Security Directorate science plan to 2020, particularly the Aquatic Animal Health Science Theme. Cefas focuses strongly on detection and description of aquatic animal pathogens in support of UK trade policies. Hematodinium recently emerged in global aquaculture and is a significant pathogen of wild (fished) crustaceans. Little is known about its genome or host interaction. A focus on that aspect of Hematodinium life history is pertinent and may lead to control strategies to protect UK trade. 


The applicants have a strong cross-site relationship and co-supervised numerous UG, PG and PDRA staff. The student will receive first class training in fish biology, disease mechanisms, molecular biology and bioinformatics. The student will attend international conferences, scientific meetings and participate in outreach activities, further encouraging networking skills. In addition, the University of Exeter runs a Researcher Development Programme within its Employability and Graduate Development unit informed by the national Vitae Researcher Development Framework. At Cefas, students benefit from hands on experience of operational science in a government agency environment. This all will aid post-doctoral employment on completion.


Gentekaki,E., Curtis,B., Stairs,C., Klimes,V., Elias,M., Salas,D., Herman,E., Eme,L., Arias,M.C., Hilliou,F., Klute,M., Suga,H., Malik,S.-B., Pightling,A., Kolisko, M., Rachubinski,R., Schlacht,A., Tsaousis,A., Archibald,J., Ball,S.G., Dacks,J., Clark,G., van der Giezen, M. and A.J. Roger (2017) Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol., 15(9): e2003769

Read, B.A., Kegel, J., Klute, M.J., Kuo, A., Lefebvre, S.C., Maumus, F. … , van der Giezen, M., … and I.V. Grigoriev (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 499: 209-213.

Small, H.J., Reece, K.S., Shields, J.D., Bateman, K., Stentiford, G.D. (2012) Morphological and molecular characterization of Hematodinium perezi (Dinophyceae: Syndiniales), a dinoflagellate parasite of the harbour crab, Liocarcinus depurator. Journal of Eukaryotic Microbiology 59, 54–66.

Stentiford, G.D., Shields, J.D. (2005) A review of the parasitic dinoflagellates Hematodinium species and Hematodinium-like infections in marine crustaceans. Diseases of Aquatic Organisms 66, 47-70.

Stentiford, G.D., Green, M.,  Bateman, K.S., Small, H.J., Neil, D.M., Feist, S.W. (2002) Infection by a Hematodinium-like parasitic dinoflagellate causes Pink Crab Disease (PCD) in the edible crab Cancer pagurus.  Journal of Invertebrate Pathology, 79, (3), 179-191.

Entry requirements:        

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK.   Applicants with a Lower Second Class degree will be considered if they also have Master’s degree.  Applicants with a minimum of Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

All applicants would need to meet our English language requirements by the start of the  project http://www.exeter.ac.uk/postgraduate/apply/english/.

Applicants who are classed as International for tuition fee purposes are not eligible for funding.


Application deadline:7th January 2018
Value:£14,553 per annum for 2017-18
Duration of award:per year
Contact: PGR Recruitment Officepgrenquiries@exeter.ac.uk

How to apply

In the application process you will be asked to upload several documents.  Please note our preferred format is PDF, each file named with your surname and the name of the document, eg. “Smith – CV.pdf”, “Smith – Cover Letter.pdf”, “Smith – Transcript.pdf”.

•       CV
•       Letter of application outlining your academic interests, prior research experience and reasons for wishing to
        undertake the project.
•       Transcript(s) giving full details of subjects studied and grades/marks obtained.  This should be an interim transcript
        if you are still studying.
•       If you are not a national of a majority English-speaking country you will need to submit evidence of your current
        proficiency in English.

You will be asked to name 2 referees as part of the application process however we will not contact these people until the shortlisting stage. Your referees should not be from the prospective supervisory team.

The closing date for applications is midnight on 7 January 2018.  Interviews will be held at the University of Exeter between 5 - 16 February 2018.

If you have any general enquiries about the application process please email pgrenquiries@exeter.ac.uk.  Project-specific queries should be directed to the supervisor.

During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates.  These are not limited to, but may include disclosures to:

• the selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from one or more other HEIs;

• administrative staff at one or more other HEIs participating in the relevant programme.

Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.