Research

Individual PhD research projects

Project 1: Enhanced nutrient utilization efficiency through development of ‘system feeds’ (Wageningen University, The Netherlands)
PhD student: Eliza Syropoulou
PIs: Fotini Kokou, Detmer Sipkema
Aquafeed diet formulation in the current era is a great challenge due to the reduction of fish meal inclusion, which may affect nutrient digestibility as well as waste production. Such metabolic wastes may differ in C:N ratio, therefore affecting the microbial populations in the fish gut, but also in the nitrifying and denitrifying biofilters and the rearing water. Therefore, microbial community and its management are crucial for the stabilization of culture environment, an efficient waste management, and fish welfare, especially for closed systems such as recirculating systems. Here seabass diets will be evaluated in terms of fish and system performance, focusing on the carbon fraction of the feeds (type of fibers). The feeds will be developed to adjust the nutrients ratio for optimal removal of waste (with partner organisation ARC). The effects of diet composition on microbiota diversity and functionality (nitrifiying, denitrifying, heterotrophic microbes), system and filter performance (i.e nitrogen removal rates, stability), and fish welfare (in collaboration with CSIC), will be measured. Research outcomes will provide feeds for optimal fish growth, biofilter performance and overall environmental performance of aquaculture systems.

Project 2: Development of next-generation probiotics for aquaculture (Wageningen University, The Netherlands)
PhD student: Valentina Romboli
PIs: Detmer Sipkema, Fotini Kokou
Currently probiotics used in aquaculture are often derivatives of human probiotics of which the efficacy and fate in aquaculture are poorly characterised. ‘Healthy’ salmon and oyster aquaculture systems will be used as inoculum to isolate potential probiotic strains. Depending on the disease target aerobic (water/gills) or anaerobic (gut) strains will be selected for. Pure strains or minimal microbial consortia will be compiled to generate a microbial biobank. Efficacy to inhibit growth of known (shell)fish bacterial pathogens, such as Aeromonas salmonicida, Flexibacter columnaris, Vibrio vulnificus and the eukaryote Neoparamoeba perurans, causative agent of amoebic gill disease in salmon, will be assessed in challenge assays; first in vitro, subsequently in vivo in collaboration with IFREMER and NOFIMA (links to Projects 1, 3, 5). The expected result is a number of single species or minimal microbial communities to be used as more effective next-generation probiotics in aquaculture. Market potential of these new probiotics will be investigated in collaboration with ESR11 (ABSint).

Project 3: The genetics of disease outbreaks in mussels (Ifremer- La Tremblade, France)
PhD student: Ajithkumar
PIs: Lionel Dégremont, Abdellah Benabdelmouna, Jean-Baptiste Lamy
Recent disease outbreaks in Mytilus edulis and M. galloprovincialis leading to high mortality remain unexplained although poor cytogenetic quality of mussels and the presence of virulent Vibrio strains have been observed during this phenomenon. The major aim in EATFish is to identify the heritability and the genetic correlations associated with growth and resistance to spring disease outbreaks in M. edulis and M. galloprovincialis. Preliminary results have shown that mussel survival increased by 34-48% after one generation of selection in M. edulis. Here, we will investigate the genetic basis for resistance to the main mussels species cultivated in France and Belgium (offshore sites of Partner Organisation CG), as well as their hybrids. Subsequently, mussels of each species showing high resistance and high vulnerability levels will be crossed and phenotyped, and subjected to controlled challenge tests (by co-habitation with mussels exposed in the field). These results will aid the mussel industry to better understand the etiology of the disease and sustain their production by using resistant mussels. Exploitation of the data and knowledge transfer to the breeding industry will be done through a secondment at SYSAAF.

Project 4: To define microbial biomarkers for fish mucosal health (CSIC, Torre de la Sal, Spain)
PhD student: Maria del Socorro Toxqui-Rodriguez
PIs: Ariadna Sitja-Bobadilla, Jaume Perez-Sanchez, Carla Piazzon
Fish mucosal samples will be used for microbiota profiling in terms of diversity and functional capacity of the fish  microbiome. Changes in the microbiota of Sparus aurata (the gilthead sea bream) in response to biotic factors (host genetics, presence of pathogens) and abiotic factors (water temperature, diet [collaboration CCMAR]) will be determined and linked to fish health and performance indicators to understand the means by which certain microbial taxa and genes relate to host health. The combination of metagenome and metatranscriptome studies [collaboration WU] with immune cell composition and activation in the gut and gills and general performance indicators (growth, feed conversion and physical activity monitored by implanted biosensors) will create a complete package of information that can be extrapolated to assess health markers. In silico predictive modelling (discriminant analyses, Bayesian networks) will allow to define a core microbiota or microbiota-profile biomarkers, associated to different heath status or farming interventions. A major aim is to assess whether these particular biomarkers can be identified and exploited to increase fish health and performance, or to be used as early indicators to adapt aquaculture management procedures [collaboration Nofima].

Project 5: Genetics of amoebic gill disease resistance and gill health (Nofima, Ås, Norway)
PhD student: Afees Ajasa
PIs: Marie Lillehammer, Ingrid Olesen
Nofima’s Department of Breeding and Genetics is seeking one dedicated and enthusiastic PhD candidate to conduct research within quantitative genetic and statistical genomics for gill health in Atlantic salmon. The main tasks of this position is to search for alternative phenotyping methods for gill health that are non-invasive, objective and accurate and to perform quantitative genetics and genomics analysis to facilitate effective selective breeding for improved gill health in salmon. Further information on this PhD project can be found here.

Project 6: A nutritional approach to improve fish robustness (CCMAR, Faro, Portugal)
PhD student: Ibon Garcia-Gallego
PIs: Sofia Engrola, Claudia Aragao
FAO is responding to the “Blue Revolution” by promoting aquaculture as the solution to improve food security, and nutrition while increasing biological efficiency and optimizing the production cycle. To face this challenge, it is important to develop resilient aquaculture practices, which increase productivity, maintain healthy ecosystems, and ensure a sustainable consumption pattern. Nutrition is the most important factor that determines both growth and development of animals, with a direct impact in the gastrointestinal tract (GIT). CCMAR will target dietary strategies that will improve fish robustness, to understand the biological pathways that mediate the relationships between growth, nutrition, and metabolism. Dietary strategies will be developed in collaboration with Partner Organisation Skretting (ARC). The GIT of fish is modulated by diet type, the initial microbiota adapts over time and is shaped by the availability of different nutrients. The impact of diet on fish gut microbiota and identification of microbial biomarkers related to host robustness will be done in collaboration with Partner CSIC. Growth plasticity, oxidative biology, protein metabolism, and the microbiome-gut axis will be key targets for the PhD proposal. Experimental species: gilthead seabream (Sparus aurata) and Senegalese sole (Solea senegalensis).

Project 7: Gene silencing in fish eggs (HAFOGVATN, Reykjavik, Iceland)
PhD student:
PI: Ragnar Johannsson
Application deadline: The potential of a novel gene silencing technique (non-GMO) to prevent sexual maturation will be explored for Atlantic salmon (Salmo salar). Preventing sexual maturation may be a remedy against genetic introgression from farmed salmon in wild fish salmon. A molecular transporter, Vivo, can carry the Morpholino oligomer across the chorion of fish eggs, enter the embryo and reach target cells. This causes primordial germ-cell mis-migration and differentiation into somatic cells and arrested development of germ cells. The method has been found to produce a generation of infertile zebrafish. Furthermore, the bath-immersion technology has given promising results in rainbow trout (84% sterility) and will now be tested for the first time on Atlantic salmon. With gene silencing we intend to fully develop the method where >98% sterility is achieved and that the method can be used on a commercial scale based on protocols from the project. The project will include grow-out experiments on an experimental scale as well as assessing the exploitation potential at industrial scale (secondment MG) for proof of concept.

Project 8: Integrated Multi-Trophic Aquaculture (BMRS, Bantry, Ireland)
PhD student: Thomas Juhasz
PIs: Julie Maquire, Luke Wilson
Seaweed, lumpfish and sea urchin will be assessed for their performance in poly-culture in Bantry Bay, SW Ireland, with a particular focus on the culture of echinoderms. Testing criteria will include environmental parameters, growth, food conversion ratio and health and welfare of co-cultured species. The impact of microbial processes in IMTA performance will be assessed in collaboration with Wageningen University. The performance of each system will be compared with previous mono-culture data. The IMTA systems will be evaluated to determine the practicality and applicability of the new infrastructure and species mix chosen. Also, the effect of each of the systems on the environment, the quality and production of the cultured organisms and the time/effort and cost involved will be assessed and compared with the unmodified situation. The successful student will have a background in marine biology/aquaculture and work well in a multidisciplinary team. They should be confident in both analytical lab and running field experiments. Hatchery experience (echinoderm or other shellfish or seaweed) and experience in productivity measurements will be an advantage. The PhD student will be based at BMRS and registered for their PhD at University College Cork. Two secondments are also planned to Wageningen University and the University of Stirling.

Project 9: Market opportunities, consumer segmentation, perception and communication strategies of aquaculture products (Aarhus University, Denmark)
PhD student: Sezgin Tunca
PI: Karen Brunso
Based on analysis of consumer perceptions and preferences, a cross-cultural segmentation study will be conducted and form the basis for determining market opportunities, with a particular focus on aquaculture products based on lower trophic levels, such as marine plants and marine invertebrates (in collaboration with BMRS), that up to now are related to as ‘less’ tasteful. With point of departure based on attractiveness of consumer food-related life-style segments, new and targeted communication strategies will be tested in order to examine how consumers perceive messages, and how new aquaculture products are perceived, accepted and provide market opportunities. This will be done via surveys as well as experimental ‘set-ups’ such as conjoint analysis and testing of reactions to different stimuli in collaboration with retail Partner Organisation CG. All together this will contribute to estimations of market opportunities of new aquaculture products. An exploitation plan for aquacultured seaweeds and marine invertebrates will be made in collaboration with ABSint. Further information about this project can be found here.

Project 10: Analysis of market position of differentiated aquaculture products and associated public perception (University of Western Brittany, Brest, France)
PhD student:
PIs: Bertrand Le Gallic, Estelle Masson
A broad study of economic scenarios and consumer perception of diversified aquaculture produce will be explored to assess the market potential of premium class, organic and/or otherwise certified products. The poultry sector with a diversified market with respect to certifications related to animal welfare and environmental impact will serve as reference (in collaboration with partner organisation SYSAAF). For aquaculture produce, the focus will be on salmon and different sectors along the value chain (from fisheries and aquaculture producers (MG) via processing companies, wholesalers, retailers (CG) to direct marketing to mobile fishmongers and restaurants) will be explored. These analyses also include long-term predictions about the viability of certain products, for example premium or organically farmed salmon products. Particular attention will be paid to the perceptions and social acceptance of production systems (including the use of sterilised salmon) quality of the products and labelling schemes.

Project 11: Capturing the value of marine aquaculture (ABS-int, Bruges, Belgium)
PhD student: vacancy. Open for application till 30-6-2022 here.
PI: Thomas Vanagt
Ground-breaking science is no guarantee for successful valorisation of research results. Turning a research result into a product or process that can be profitable requires a number of actions that are not related to science as such, yet are linked to for instance finance, marketing and business partnerships. The ESR will look at existing successful aquaculture companies (e.g. MG and ARC), and assess how they implement innovation. However, we will also interview key staff of ventures that were not successful in order to understand the risk factors of the aquaculture business. A business model canvas will be completed for a set of companies from different sections of the aquaculture value chain and common elements will be identified (in collaboration with associated industrial platforms EATIP and the Federation of Norwegian Industries (through Advisory Board memberships of Iciar Martinez and Petter Arnesen) and partner organisation SYSAAF). All of the results will be compiled in a set of guidelines on valorisation for aquaculture researchers and implemented in The Case in the EATFish training programme. Specific innovation scenarios based on ESR research proposals from WP2 will be assessed for their valorisation potential: e.g. probiotics (WU, ESR2), aquaculture feed innovations (WU, ESR1, CCMAR), in collaboration with ESR2 WU) and potential other valorisation opportunities that will be identified in EATFish. Finally, the ESR will explore innovative finance structures to combine offshore aquaculture licenses with other blue growth activities. More specifically, we will focus on offshore wind farms of partner organisation CG, and produce a case study for how a multi-use concession zone could be financed for large scale wind, aquaculture and nature conservation purposes. Further information on this project can be found here.

Project 12: Model-based assessment of ecosystem services in aquaculture (Hungarian University of Agriculture and Life Sciences – Research Institute for Fisheries and Aquaculture (HAKI), Szarvas, Hungary)
PhD student
PIs: Gergó Gyalog, Emese Bekefi, Bela Halasi-Kovacs
Mapping and measuring ecosystem services (e.g. maintenance of biodiversity, nutrient removal, carbon sequestration and storage, etc.) of extensive aquaculture technologies are considered to be vital in formulating policies and regulations affecting the development of the European fish farming sector. Within this PhD topic, mapping and model-based assessment of pond aquaculture and other low-trophic farming practices are planned to be undertaken. Work is planned to start on the basis of already developed assessment frameworks (e.g. 4-step MAES framework of EC). Emphasis will be put on selecting and delineating case study sites, as definition of appropriate system boundaries is still a challenge. For the case study sites, utilizing PPS modelling framework, a combined model describing quantitative biophysical processes and qualitative features, will be implemented. The applied framework makes possible the integrated assessment of quantitative variables in combination with qualitative data derived from stakeholder perception. GIS modules for integration of field data into prognosis and estimation maps are planned to be utilized to present results. The prospective PhD student is expected to have flexibility to work in a multidisciplinary team. Experience in wetland ecology/mechanistic modelling/GIS software (QGIS, ArcGIS) would be an advantage.

Project 13: Societal perception of aquaculture in Europe (University of Stirling, UK)
PhD student: Mausam Budhathoki
PI: Dave Little
Within Europe, perceptions of aquaculture have often been seen to be ill-informed leading to lack of social license that has hampered interest in, and growth of the sector. This is despite the rise of certification and ever stricter regulations at national and EU levels that have supported the sector to make real strides in sustainability. In parallel , however, appetites for European farmed seafood internationally have become an important part of the growth that has occurred, particularly in rapidly growing economies where seafood is a dietary staple. Furthermore, and  largely as an outcome of the technical innovation in the salmon sector, a major market for aquaculture related products and services has developed supporting growth in aquaculture outside of Europe  and where the practice is growing most rapidly. This project will conduct a global analysis of the drivers for the trade, assessing the role of the governance in place in Europe in affecting consumers perceptions of seafood value internationally. Value chain and Life Cycle Analyses will be used in tandem to assess benefits and sustainability credentials. The impacts of innovation in both EU and the overseas markets will be investigated to assess threats and further opportunities for future mutually beneficial trade.

Project 14: Improved aquaculture governance to enhance sustainability through the use of decision support systems (University of Stirling, UK)
PhD student: Amalia Krupandan
PI: Trevor Telfer
Decision support tools and frameworks will be refined, based on existing systems developed for H2020 project Tapas, for a number of EATFish aquaculture case studies. Different types of aquaculture systems ranging from intensive e.g. land-based recirculating aquaculture systems at WUand commercial farms of MG) to extensive (e.g. offshore farming at multi-use platforms by Partner Organisation CG, integrated multi-trophic aquaculture at BMRS, fresh-water pond farming at NARIC) and management practices (e.g.  use of veterinary medicinal products)  will be investigated for their environmental impact using tools such as life cycle assessment. In addition, the environmental impact of dual use (e.g. offshore windfarms + aquaculture) will be assessed and compared to single use. Guidelines for spatial modelling of site selection and suitability will be developed taking into account physical, social, production and ecological carrying capacity to ensure sustainability of the site during initial production and expansion. Then, it will be assessed how sustainability can be linked to economic feasibility (WP3) and potential technological innovations (WP2) and international accreditation standards, and national licensing procedures to synthesise a policy advise on European aquaculture.

Project 15: Determining the role of marine spatial planning in aquaculture development (University College Cork, Ireland)
PhD student: Stacy-Ann Gray
PIs: Anne Marie O’Hagan, Tom Doyle
Maritime Spatial Planning is at the initial stages of implementation across the EU, with all coastal member states legally required to have MSP in place by 2021. Aquaculture is one of the sectors that can be included in MSP, according to Article 8 (Directive 2014/89/EU) but different approaches to planning across the EU mean that in some countries aquaculture planning is addressed through terrestrial spatial planning systems whereas in others it may be incorporated into marine planning systems. This project will explore the systems already in place, how these interact with each other, how consenting/licensing outcomes are influenced by extant planning systems, and if there are differences between nearshore and offshore aquaculture production as a result of planning processes. The project will include engaging with industry stakeholders, such as Partner Organisation CG who operates offshore windfarms, and competent authorities to establish how they have or will include aquaculture in their Maritime Spatial Plans. It will be determined what planning model best facilitates current aquaculture development. In addition, all the findings will then be used to make recommendations on how spatial planning could best be used to facilitate European aquaculture development in future and how these can be aligned with other maritime/aquatic activities.