BSc Thesis Subjects

If you are considering taking on a Bachelor Thesis at AFI, please stop by during our Meet & Greet every first Tuesday of the month, between 13:00 and 14:00 in Zodiac E0243. Even if you only have a broad idea of your plans, you are most welcome! We are happy to think along with you, and discuss whether we can agree on a topic that suits you.

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 (office.afi@wur.nl), stating your subject of interest in one sentence. You then will be directed to an AFI staff member to explore thesis options.

On this page an overview of current Bachelor thesis subjects is presented. Please be aware that research might be finished or altered. Agreement on a topic will always be discussed first.

Aquaculture topics

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AFI-1. The mucus of fish as a parameter for fish health

The fish mucus layers are the main surface of exchange between fish and the environment, and these mucus layers possess important biological and ecological functions. For instance, mucus plays a major role against fish infections. Much research has focused on the study of fish mucus bioactive molecules (e.g., antimicrobial peptides and immune-related molecules) and associated microbiota due to their potential in aquaculture and human medicine. However, the different bioactive molecules in the mucus can also be indicative of the health status of fish. A disbalance, a deficit or an excess of specific compounds or molecules might indicate for instance an infection. A better understanding and overview of the different bioactive molecules can aid in the establishment of less invasive methods to investigate the fish health, by analysing composition of mucus of fish.
Work: One student will execute a literature study on different bioactive molecules in mucus of fish and the importance of these molecules for fish health. A second student can, based on the work of the first student, continue with a panel of bioactive molecules in the fish mucus that can serve as parameters of health, and execute a literature study on the differences between species in these bioactive molecules.

Supervision: Jules Petit
Contact: Jules Petit (jules.petit@wur.nl)
Number of possible students: 2


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AFI-2. More inflammation with PUFAs from micro-algae?

As an alternative to fish oil or plant oil, oil with both omega-3 fatty acids EPA / DHA can be produced from natural marine algae. A further advantage is that the mico-algal oil can be highly purified containing ≥50% EPA / DHA, whilst fish oils usually contain 20-28% EPA / DHA. The algal oil could enable the animal nutrition industry to keep up with the increasing demand for EPA / DHA omega-3 fatty acids without pressuring global fish stocks, while contributing to healthy animal nutrition. Micro-algae can reach much higher content and natural balanced of EPA / DHA, and thus algae oil can be considered a promising sustainable alternative for fish oil to support fish growth. However, the effect of micro-algal oils on fish health have not been examined. Fish cannot synthesize omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFA) de novo, and cannot convert n-6 to n-3 PUFAs. Thus, the dietary n-3/n-6 PUFA ratio is decisive for the ratio of n-3/n-6 PUFA in the tissue and their corresponding metabolites. The ratio of PUFA is important: eicosanoids derived from n-6 PUFAs have pro-inflammatory properties and eicosanoids derived from n-3 PUFAs have anti-inflammatory properties. Resolution of inflammation has historically been viewed as a passive process, occurring as a result of the withdrawal of pro-inflammatory signals. Only recently has it been established that inflammation resolution is an active process with a distinct set of chemical mediators. Resolvins and protectins are recently identified molecules being generated from ω-3 PUFA precursors and can orchestrate the timely resolution of inflammation.

Work: The student will execute a literature study on the effect of the ratio of n-3/n-6 PUFA on fish health
Supervision: Geert Wiegertjes
Contact: Geert Wiegertjes (geert.wiegertjes@wur.nl)
Number of possible students: 1

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AFI-3. Short Chain Fatty Acids in the intestine of fish: immuno-modulation through the gut?

SCFAs are fatty acids with less than six carbon atoms and produced as end products of fermentation of dietary fibres by the intestinal microbiota. In mammals, a lot of studies have been performed on the immuno-modulatory effects of these SCFAs. The reduction of inflammation in the lungs of mice fed with a high-fibre diets, which was shown to act via a SCFA produced in the intestine, is an interesting example of such immuno-modulation. Up to date, little is known about the immuno-modulatory effects of SCFAs in fish and their effects on the overall health of fish. If these SCFAs have similar effects in fish, supplementation of the feed with SCFAs can be of interest to modify the general health of fish.

Work: Executing a literature study on the presence of SCFAs in fish intestine and the effects on fish health and try to delineate the knowledge gap present in the field of fish health and SCFAs.

Supervision: Jules Petit
Contact: Jules Petit (jules.petit@wur.nl)
Number of possible students: 1

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AFI-4. Is trout really carbohydrate intolerant (diabatic)? Effect of protein determination on carbohydrate digestibility.

Literature has shown that carbohydrate digestibility in trout and other carnivorous fish species is mostly limited and has been attributed to low inclusions in the natural diet of these fish. However, the determination of carbohydrates in fish diets has also been debated as this is mostly considered as the rest fraction after subtracting protein, fat and ash from the dry matter. In some cases, starch is also analysed and then this carbohydrate fraction can be divided into starch and non-starch polysaccharides (NSP). But because total carbohydrates and NSP are rest fractions, they depend on the analysis (and analysis error) of the other macronutrients.
Protein determination is commonly done by analysing nitrogen and multiplying this by 6.25 (the jones factor based on the assumption that amino acids contain on average 16% nitrogen). However, studies in the past have shown that this factor is not appropriate for all raw materials due to differences in amino acid composition. Additionally, some raw materials contain other nitrogen containing compounds like chitin in insect meal. As mentioned above, this could influence the determination of dietary carbohydrates and carbohydrate digestibility in scientific studies. It would therefore be more appropriate to use the level of total amino acids to calculate the true protein factor for protein determination.

Students tasks: 1) write a small literature review on the jones factor versus a true protein factor, and influence on carbohydrate determination, 2) make a small database containing true protein factors in different raw materials, 3) asses the effect of using the true protein factor instead of the jones factor on carbohydrate digestibility in diets containing different raw materials.

Supervision: Ruben Groot (Alltech Coppens) and Johan Schrama
Contact: Johan Schrama (johan.schrama@wur.nl)
Number of possible students: 1

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AFI-5. Do fish have diarrhea?

Faeces consistency has a significant impact on water quality in closed farming systems. Indeed, diarrhea-like faeces increase the concentration of total suspended solids (TSS) affecting system performance, animal health and environmental eutrophication. Digesta properties (dry matter, osmolarity, pH) of fish throughout the gastrointestinal tract (GIT) and faecal consistency during excretion variate among fish species. The GIT is typically subdivided into: esophagus, stomach, proximal intestine (with or without pyloric caeca), middle intestine, posterior intestine and rectum. During digestion, numerous fluids are secreted along the GIT (e.g. HCl, bile and pancreatic fluids), which have to be reabsorbed when the chyme moves from the stomach into the intestine where nutrient hydrolysis and absorption occur. Water balance over the entire GIT has an impact on faeces quality and may result in diarrhea-like faeces when a lot of water is excreted together with the faeces. Therefore, investigating and comparing physiological responses concerning water reabsorption in different compartments of the digestive tract will help to better understand the variation in faeces and chyme characteristics among fish species steering focus of future research.

Work: sampling of the GIT of various fish species from nature (collected from e.g. fish market) in order to detect chyme properties (dry matter, osmolarity, pH) and faecal consistency along the GIT. Literature review and comparison with field data collection. Also consider the impact of freezing fish for storage on dry matter analysis.

Supervision: Elisa Ciavoni, Peter Horstmann (& Johan Schrama)
Contact: Elisa Ciavoni (elisa.ciavoni@wur.nl), Peter Horstmann (peter.horstmann@wur.nl), Johan Schrama (johan.schrama@wur.nl)
Number of possible students: 1

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AFI-6. Fish body building: muscle fibre growth dynamics in Nile tilapia.

The freshwater cichlid Nile tilapia (Oreochromis niloticus) is among the main fish species farmed worldwide. The rapid growth of Nile tilapia makes it an attractive species for fish farmers. Growth is an important read-out parameter when breeding new tilapia strains or testing new feeds. Tilapia growth is driven by accretion of white muscle tissue (i.e. fillet). Yet, growth is often simply evaluated in terms of body weight gain, without considering muscle growth dynamics. In fish, new muscle fibres can be recruited after hatching, conversely to mammals which are born with a definite number of muscle fibres. Fish muscle tissue growth is the result of both the recruitment of new fibres (hyperplasia) and the enlargement of existing ones (hypertrophy). The duration and extent of both mechanisms are not well known for Nile tilapia but may have important implications for growth potential or nutrient requirements across life stages. To fill this gap, a 6 months experiment was conducted at WUR fish facility (CARUS-ARF). Muscle samples were collected from Nile tilapia with body weight ranging from 5 to 700 grams. Through histological analysis of these samples, a precise description of Nile tilapia muscle fibre growth dynamics (hyperplasia and hypertrophy) will be made.

Student’s missions: 1) write a short literature review on muscle growth dynamics in fish, 2) assist in performing the histological analyses of Nile tilapia muscle samples, and 3) statistical analysis.

Supervision: Gauthier Konnert and Johan Schrama
Contact: Johan Schrama (johan.schrama@wur.nl)
Number of possible students:1

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AFI-7. How to make a good well-balanced feed for African catfish?

Proper formulation of animal feeds requires information on the nutrient content and digestibility of common ingredients. This is a prerequisite for estimating requirement for these specific nutrients. Generally, there is limited information in literature on nutrient digestibility in fish compared to terrestrial farm animals, most especially regarding the amino acid digestibility of potential feed ingredients. This also is the case for African catfish, which is of great economic importance in Africa and worldwide. Currently in Africa, the culture of African catfish is increasing due to enhanced local demand, but the lack of adequate data on digestibility of common ingredients used in feed formulation has deterred the development of least cost feedstuff for this species. Furthermore, there are limited information on the essential amino acid (EAA) requirement of this species. The requirement for specific essential amino acids is linked to their absorption rate in the gut, which can be influenced by the rate of transport of food in the digestive tract. This contributes to the time of release of nutrients to the body, which in turn can influence optimum utilization. Knowledge on the difference in digestion and absorption rates of nutrients as affected by ingredients characteristics is essential for improving amino acid utilization efficiency in fish. This will enable us to understand the mechanisms of the kinetics of digestion on nutrient utilization. Therefore, the student will conduct a literature search on 1) Amino acid digestibility of common ingredients in African catfish 2) Essential amino acid requirement of African catfish 3) Kinetics of digestion and adsorption of AA in different segments of the gut.

Supervision: Folasade Elesho (& Johan Schrama)
Contact: Johan Schrama (johan.schrama@wur.nl)
Number of possible students: 1

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Fisheries/fish ecology topics

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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 (paul.vanzwieten@wur.nl)
Number of possible student subjects: 3

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AFI-9: 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 (JanJaap.Poos@wur.nl)
Number of possible students: 1 

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AFI-10: How to predict fish feeding from morphology

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, approaching 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 locations (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 (Leo.Nagelkerke@wur.nl)
Number of possible students: 1-3 (1 per geographical location)

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AFI-11. How do we get our river fish back: analysing habitat and the occurrence of young fish?

The lower river Rhine has been extensively modified throughout history, resulting in a drastic loss of habitats for fish and hence the decline or even disappearance of many of its original riverine fish species. Especially floodplains act as a critical spawning and nursery areas for many of these fish species. Therefore, to improve recruitment success of riverine fish, authorities in the Netherlands have reconstructed numerous floodplains since the 1990s. This resulted in improvement of local habitat conditions, but not to the expected increase in abundance and diversity of riverine fishes. Apparently, habitat characteristics are not optimal yet. This not only the case for adult fish, but also for younger life stages, such as larvae and juveniles. To investigate what the optimal conditions for larvae and juveniles of riverine fish are, this project aims at a systematic review of existing literature. This requires collecting, analysing, and synthesising (preferably) quantitative data through literature study. The literature database is largely present. All publications need to be investigated for the relationships of habitat quality parameters, such as pH, conductivity, salinity, water depth, structural complexity etc. with the presence and abundance of riverine fishes. Data need to be collected in a master datafile, and a report with a synthesis to be written.

Activities: analysis of literature; entering & analysing data; synthesising information.
Supervision and contact: Leo Nagelkerke (Leo.Nagelkerke@wur.nl) in cooperation with Twan Stoffers
Number of possible students: 1

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AFI-12. Dynamics of food web in the Baltic Sea

Ecological communities are constantly being reshaped because of changing environmental conditions and strong anthropogenic pressures. Yet, we do not know how the structure of food webs change over time and space. Understanding how changes of species composition affect the structure of ecosystems is vital to guide management and help to preserve ecosystem services. This study focuses on the Baltic Sea ecosystem and uses a comprehensive monitoring program documenting the dynamics of phytoplankton, zooplankton, fish and benthic invertebrates. Given that the current food web depicting the trophic interaction between species in the Baltic Sea is incomplete, the student will first contribute to a literature review to find missing trophic interactions. Then, using ecological network analysis, the student will derive metrics about the structure of the food web, leading to characterize the spatio-temporal dynamic of the structure of Baltic Sea food web.
Activities: literature study, ecological network analysis and time series analysis
Supervision: Romain Frelat & Jan Jaap Poos
Contact: Romain Frelat (romain.frelat@wur.nl)
Number of possible students: 1

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AFI-13. The hidden gem of bottom trawls: toward a new option to assess the dynamics of benthic invertebrates

Long-term bottom trawl surveys monitor the spatio-temporal dynamics of demersal fish communities. During these surveys, bottom trawls also catch some benthic invertebrates from the seafloor. Usually reports from invertebrates are discarded from further analysis. However, little is known about the spatial and temporal dynamics of benthos. The aim of this study is to understand whether data from bottom trawl surveys can inform the distribution of benthic invertebrates. The student will evaluate the consistency of the reporting, and compare it with known seabed habitat maps. If benthic invertebrates are consistently reported, this work could lead to new species distribution maps using machine learning algorithm.

Activities: data exploration, species distribution, spatial analysis (GIS), machine learning (optional)
Supervision: Romain Frelat & Jan Jaap Poos
Contact: Romain Frelat (romain.frelat@wur.nl)
Number of possible students: 1

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AFI-14. Morphological diversity of tropical reef fish

The study of organisms’ morphology remains a fundamental task in ecology given the close relationship among form, function and evolutionary history. A striking example is found in the megadiverse coral reefs where shapes of herbivorous fish reflect their behaviour and interactions with the environment, and thus can reveal their functional role in ecosystem processes. However, the description of shapes is not straightforward and can be very time consuming. Modern morphometrics approaches can help to efficiently characterized the morphology of very diverse fish assemblages. Using pictures from French Polynesia, the student will perform outline analysis of herbivorous fish and quantify the morphological diversity within assemblages. This work will help identify community assembly rules and the role of environmental processes affecting the fish community.

Work: morphological measurements on photo; analysing data; statistical analysis.
Supervision: Romain Frelat & Jan Jaap Poos
Contact: Romain Frelat (romain.frelat@wur.nl)
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 (office.afi@wur.nl), stating your subject of interest in one sentence. You then will be directed to an AFI staff member to explore thesis options.