BSc Thesis Subjects

BSc Subjects AFI July 2018

Aquaculture topics

AFI-1. Control of sea lice infections in salmon culture

A commonly claimed external effect of aquaculture is the transmission of infectious diseases to wild fish stocks. A frequently cited example of this is the infection of wild salmon by sea lice from salmon farms. Management of the disease risk to wild salmon populations requires an understanding both of the disease transmission mechanisms and the control incentives faced by fish farmers. To evaluate this issue you need to understand and describe the interaction between sea lice population dynamics, fish population dynamics, aquaculture, and wild capture salmon fisheries.

The student will execute a literature study on the different strategies that can be effective in controlling sea lice.

Supervision: Geert Wiegertjes

Contact: Geert Wiegertjes (

Number of possible students: 1

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AFI-2.Amoebic gill disease in salmon

Amoebic gill disease (AGD) is a gill disorder found in marine fish, but primarily affecting salmon. The disease is well known in Tasmania, Australia, but in recent years the disease has been a growing problem in Ireland, and has also been identified in France, Norway, USA, Canada and most recently Scotland. AGD is caused by a protozoan amoeba species. The parasite causes a proliferative response in the gill epithelium. Normally oxygen would diffuse through the thin epithelium, which it can't do when the epithelium is thickened. In the parts of the gill affected, the fish effectively can't breathe. Once on a farm, these amoebae divide exponentially, so clinical disease can develop quickly. As of yet there is no cure for the disease, but if outbreaks are carefully managed, as the water temperature cools, the disease generally resolves. Bathing whole cages in freshwater is the most recognised treatment in Tasmania, but this is expensive and technically difficult to achieve. The industries in Scotland, Ireland and Tasmania are presently researching possible treatment strategies. Early intervention is likely key to avoiding losses.

The student will execute a literature study on the different strategies that can be effective in controlling Amoebic gill disease in salmon.

Supervision: Geert Wiegertjes

Contact: Geert Wiegertjes (

Number of possible students: 1

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AFI-3. Are fish feeds safe: Effects of mycotoxins on fish species.

Mycotoxins are toxic secondary metabolites produced by moulds. They can be found mainly on agricultural commodities and produced before and/or after harvest; during transportation or storage. Mycotoxins came to the attention of aquaculture during the 60s with outbreaks of aflatoxicosis at hatchery-reared rainbow trout in the USA. However, nowadays the concern of fish feeds contamination with mycotoxins gained more attention as the climate change, and the trend to replace expensive animal proteins such as fishmeal by cheaper plant ingredients and by-products have increased the probability of contamination. In animals including fish, ingestion of mycotoxin-contaminated feeds has been associated with organ failure, carcinogenicity, neurotoxicity, immune suppression, reproductive and developmental toxicity. The most prevalent mycotoxin in aquafeed ingredients in Europe is deoxynivalenol (DON), produced by Fusarium species. The contamination of fish feeds with DON is usually associated with symptoms like decreased feed intake and animal performance, gastrointestinal haemorrhaging, inflammation and alteration of the immune response, while at the cellular level with inhibition of protein, DNA and RNA synthesis.

Work: Literature study about the mechanisms that lead to the adverse effect of DON on fish species.

Supervision: Vivi Koletsi (& Johan Schrama)

Contact: Vivi Koletsi ( or Johan Schrama (

Number of possible students: 1

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AFI-4.What makes a shrimp eat?

The replacement of fishmeal by plant ingredients is a key issue in shrimp farming. Besides the nutritional value, fishmeal plays an important role in attractability and palatability of the diets. Alternative attractants and feeding stimulants should therefore be sought for. To test if a product works as an attractant for shrimp, behavioural tests have been developed, but optimization is needed.

In this study, the student will optimize behavioural tests, to study attractability of diets for white leg shrimp (Litopenaeus vannamei).

Supervision: Marit Nederlof

Contact: Marit Nederlof (

Number of possible students: 1

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AFI-5. How feed and water exchange level influence fish gut microbiota and functionality?

Living conditions during early life (larval and fingerling rearing) influence fish performance during grow-out. Larvae and fingerling can be reared in flow-trough or recirculation systems. In flow-through, metabolites and wastes are daily added and removed. In consequence, the microbial community in the rearing water is reduced with water exchange, while growth of the microbial community is stimulated each time the fish is fed. This cause constant shifts in the microbial community abundance and composition. In contrast, in a recirculation system with minimum water exchange, fluctuations in water quality are minor and a constant and mature microbial community develops in the water column. This project investigates the effect of a constant (mature) or a changing (imature) microbial community during early live on fish performance during grow-out.
The transfer of fish from the hatchery to grow-out facilities exposes fishl to a new living environment. This transfer is often accompanied with a high level of mortality.

The student is asked to analyse existing literature on how conditions during hatchery rearing (with focus on daily water exchange and solid removal) influences the ability of fish to cope with the transfer to and subsequent performance during grow-out.

Supervision: Marc Verdegem & Yale Deng (

Contact: Marc Verdegem (

Number of possible students: 1.

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AFI-6. Abundance and roles of fungi in the aquatic food web.

Globally, the bulk of aquaculture production is produced in earthen ponds. An advantage of ponds is the presence of an aquatic food web. The latter helps in maintaining water quality and provides natural foods that contribute to fish production. In terrestrial soils, fungi are (on a weight basis) by far the largest fraction of microorganisms present in the food web, where they act as decomposers of organic matter, pathogens or beneficial symbionts, and a lot is known about their roles. Fungi are also an important component of the microbiota in ponds. However, little is known about the role of fungi in ponds.

As part of a larger study, aiming to optimize the contribution of natural foods in aquaculture ponds to fish production, we ask the student to execute a literature study on the presence and role of fungi in ponds, with focus on aquaculture pond systems.

Supervision: Vinasyiam Apriana & Marc Verdegem

Contact: Marc Verdegem (

Number of possible students: 1

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AFI-7. Body building by diet: muscle fibre growth dynamics in Nile tilapia affected by diet.

The freshwater cichlid Nile tilapia (Oreochromis niloticus) is among the main fish species farmed worldwide and has seen rapid increase in production in the past 20 years. Feed represents half of the operational costs of most Nile tilapia farms. Adequate feed formulation is therefore an important aspect of successful tilapia farming. Feed quality is often evaluated in terms of growth efficiency (i.e. body mass increase for a given amount of feed intake). Body mass increase of growing fish mainly results from muscle growth. In Nile tilapia as in many teleost species, post-embryonic muscle growth results from both recruitment of new muscle fibres (hyperplasia) and enlargement of existing ones (hypertrophy). Both mechanisms are somewhat flexible and differently regulated by a variety of factors including diet composition. Little is known about the effect of diet composition on muscle fibre growth dynamics in Nile tilapia. Muscle fibre growth dynamics may affect feed efficiency and fish fillet (i.e. muscle) quality.
An experiment will be conducted in early 2019 in which 16 diets differing in their macronutrient profile (protein/lipid/carbohydrate) will be fed to 60 grams Nile tilapia. Muscle samples will be collected to quantify muscle fibre hyperplasia and hypertrophy rate during the experiment.

Student’s mission: 1) assist in performing the histological analyses of Nile tilapia muscle samples and 2) perform statistical analyses to determine the effect of dietary macronutrient profile on muscle fibre growth dynamics in Nile tilapia.

Supervision: Gauthier Konnert and Johan Schrama

Contact: Johan Schrama (

Number of possible students:2

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Fisheries/fish ecology topics

AFI-8. Selective fishing, balanced harvesting and sustainability of fisheries and ecosystems: the effects of selective fishing on species and sizes to fish communities.

More and more evidence appears that selective fishing on species and sizes to target large, mature fish and avoid by-catch of juvenile fish and non-target species as dolphins or turtles has unexpected side effects on fish populations and fish communities. These range from phenotypic and possibly even genotypic effects (fishery-induced evolution) on size and reproductive capacity of species like cod in the North-Sea to an increase in by-catch of sharks, marlins and other species by avoiding dolphins in tuna fisheries in the Eastern Pacific. The selectivity paradigm in fisheries is 50-year old and turns out not to fit very well in an Ecosystem Approach to fisheries. The paradigm is to avoid catching juveniles and only catch fish when they have grown to commercially optimal sizes. However, it ignores trophic relations and predation and the fact that big old fecund female fish (BOFFF’s) are important to maintain stable reproduction. From model studies it appears that non-selective fisheries, in other words, fisheries that fish the whole fish community and target all sizes and species relative to their production, may maintain ecosystem structure and lead to higher long-term yields. An Ecosystem-Approach to Fisheries requires maintenance of ecosystem structure and processes. In that perspective, selectivity regulations on individual species may diminish rather than enhance the sustainability of the fishery and ecosystem. So the selectivity paradigm needs to be reassessed in an ecosystem perspective! This is a large AFI that can be approached in many ways. Specific subjects could be:
1. On by-catch in specific fisheries as the tuna purse seine fisheries; how to assess these in the light of an ecosystem approach?
2. The effects of fishing on juveniles that are discarded?
3. The impact of the ban on discarding by the European Union to force fishers to be more selective?
4. Model based approaches to size selection and what we can learn from those?
5. Fishery induced evolution: has the long term pressure on larger individuals in the plaice fisheries in the North Sea lead to slower growth? And what would that mean for stock recovery now that fishing pressure has reduced?

Possible tasks include literature study, data analysis on specific examples from African lakes (Kariba, Mweru), Tuna fisheries in the Western Pacific or the North-Sea.

Supervision: Paul van Zwieten or Leo Nagelkerke can assist in defining the subject further

First contact: Paul van Zwieten (

Number of possible student subjects: 3

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AFI-9. Eco-morphological feeding traits fish communities.

The potential of an organism to use food resources from its environment is facilitated and limited by its morphological traits. Different traits are relevant for the whole sequence of food utilization, from detection of the prey, through closing in to it, sucking it into the mouth, holding it, reducing its size, swallowing it and finally to digesting it in the stomach and intestine. For all these actions relevant morphological traits have been identified which have a quantitative relationship with performance. Measuring these traits in different fish species enables the ‘translation’ of morphology into a ‘feeding profile’. By combining the feeding profiles of all species that make up a fish community, the whole community can be characterised functionally. This increases our understanding of the functioning of the food web. In this project we make such functional descriptions of the fish communities in different geographical location (e.g., the Dutch Caribbean; African lakes; etc.). Measurements are taken from pictures that are available through FishBase. Based on the measurements feeding profiles will be made and compared to available field data. Comparisons with previously studied fish communities can be performed. Note: several students can (simultaneously) participate in this study.

Activities: morphological measurements on photo material; entering & analysing data; statistical analysis.

Supervision and contact: Leo Nagelkerke (

Number of possible students: 1-3 (1 per geographical location)

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AFI-10. Length and growth of North Sea rays

Demersal fishing generally affect a wide array of species that inhabit the sea floor: not only are the main commercial species caught, other species are caught as bycatch. The populations of these bycatch are affected by the increased mortality caused by fishing. The North Sea harbours several stocks of different ray species which are caught as bycatch in the fisheries for commercially important flatfish stocks. Availability of data that can inform about the abundance or exploitation rates such as length and growth for these ray stocks is limited. In this study, the student will try to estimate growth of different ray species from trawl survey data in the North Sea.

Work: analyses of growth for several ray species. Data is publicly available online.

Supervision: Jan Jaap Poos

Contact: Jan Jaap Poos (

Number of possible students: 1

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Important message

The list of Bsc thesis subjects at Aquaculture and Fisheries is intended to give an impression of possible thesis projects. If you are interested to learn more about aquatic species or subject, and your subject is not listed then contact the chair group (, stating your subject of interest in one sentence. You then will be directed to an AFI staff member to explore thesis options.