BSc Thesis Subjects

BSc Subjects AFI July 2018

AFI-1. Bioflocs, the key to feed more with less: bio-active compounds in biofloc-based aquaculture systems?

The principle of wastewater treatment by bioflocs (BFs) is extensively used in the treatment of domestic- and industrial wastewater (activated suspension systems). BFs are highly porous, amorphous aggregations of microorganisms, particles and other constituents held together by extracellular polymeric substances. The use of BFs is a relatively new approach in aquaculture and is referred to as Biofloc Technology (BFT). The BFs are co-cultured with the cultured species and aid in the conversion of organic and inorganic wastes into microbial biomass. Other than facilitating a favourable water quality in the system the BFs also serve as an additional protein source for filter feeders such as shrimp and tilapia.

The student will execute a literature study on the availability of bio-active compounds produced in bioflocs in fish or shrimp culture systems.

Supervision: Joost van Loo, Ep Eding & Marc Verdegem

Contact: Marc Verdegem (marc.verdegem@wur.nl)

Number of possible students: 1

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AFI-2. Phenotypic plasticity in acclimation mechanisms for improved oxygen uptake in fish: its role in fish ecology and aquaculture.

Due to global warming and eutrophication in natural ecosystems and intensification in closed recirculating aquaculture systems fish are subjected to higher temperatures and low or fluctuating oxygen concentrations. Avoidance or escape from these environmental conditions is often not possible. Acclimation however is. Phenotypic acclimation response mechanisms help fish to acclimate to the an average higher temperatures and lower oxygen concentrations. Indeed, the early life acclimation response of fish to higher temperature might lead to a shift in thermal tolerance window. In fact these early life acclimation mechanisms make fish more robust for temperature and oxygen fluctuations and may improve their performance, health and welfare in ecosystems in transition and intensive aquaculture. The aim of this thesis project will be to review the literature for the role of early life mechanisms in fish determining (epigenetically) the scope for oxygen uptake in later life.

Supervision and contact: Ep Eding (ep.eding@wur.nl)

Number of possible students: 1

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AFI-3. 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 AFIthat 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, Leo Nagelkerke and Adriaan Rijnsdorp 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-4. Required heating and cooling loads in recirculating fish farm, considering biomass and fish shape.

The majority of water heating and cooling systems for aquaculture facilities (indoor fish farm) are designed based on the volume of water in the fish tank that will be used to grow the fish and typically take a very conservative approach when assessing potential heat and/or cooling sources. In this project the relation between fish biomass, system volume and the required heating and cooling capacity needed to maintain a stable and optimal water temperature, is investigated.

Supervision: Ep Eding & Davood Karimi (Davood.karimi@wur.nl)

Contact: Ep Eding (ep.eding@wur.nl)

Number of possible students: 1

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AFI-5. Modelling of heat, CO2 and NH3 production by the fish biomass (stocking density)

The primary modes of heat transfer in fish tanks are conductive heat transfer from the water to the fish and heat transfer from fish to the water. These modes of heat transfer should be integrated in an existing bio-energetic growth model. The model will be used to predict growth, weight gain, body composition, oxygen consumption, carbon dioxide production, heat production, and excretion of faeces and ammonia-N by fish. The outcome of this study will allow us to predict the contribution of the heat production by the fish in the overall heat.

Supervision: Ep Eding & Davood Karimi (Davood.karimi@wur.nl)

Contact: Ep Eding (ep.eding@wur.nl)

Number of possible students: 1

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AFI-6. Diversity and roles of algae in shrimp ponds.

Shrimp ponds contain a complex food web including primary producers (algae) and consumers ranging from bacteria to higher organisms including crustaceans, molluscs and fishes. As part of a broader study on food webs in shrimp ponds, this study focuses on the dynamics of algae communities in aquaculture ponds. Shrimp are grown in high densities in ponds. Because the feed input in ponds is the principal nutrient input it modulates the algae community. The aim of this study is to review the contribution of algae to the energy availability in aquaculture ponds and to evaluate how the presence of the shrimp affects the composition and density of algae communities in the pond over time. A comparison should made between extensive, semi-intensive and intensive pond culture. The student is asked to focus on whiteleg shrimp (Penaeus vannamei) pond systems.

Supervision: Marc Verdegem & Tinh Tran (tinh.tran@wur.nl)

Contact: Marc Verdegem (marc.verdegem@wur.nl)

Number of possible students: 1

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AFI-7. Eco-morphological feeding traits in Caribbean 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 of the Dutch Caribbean. 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 and analysing data, statistical analysis.

Supervision and contact: Leo Nagelkerke (Leo.Nagelkerke@wur.nl)

Number of possible students: 1

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AFI-8. 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 (yale.deng@wur.nl)

Contact: Marc Verdegem (marc.verdegem@wur.nl)

Number of possible students: 1

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AFI-9. 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 (geert.wiegertjes@wur.nl)

Number of possible students: 1

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AFI-10. 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 to be the 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 (geert.wiegertjes@wur.nl)

Number of possible students: 1

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AFI-11. Methods for behavioural tests with shrimp (Litopenaeus vannamei).

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, which are primarily based on the chemosensory capacity of shrimp. Nevertheless it is hypothesized that vision might also play a role, in particular for larger shrimp. In this study, the student will perform behavioural tests with white leg shrimp (Litopenaeus vannamei) to elucidate the role of vision in diet localization (i.e. attractability), and study if the role of sight differs between large and small shrimp.

Supervision: Marit Nederlof

Contact: Marit Nederlof (marit.nederlof@wur.nl)

Number of possible students: 2

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AFI-12. Palatability of formulated shrimp diets

When an ingredient has been identified as an attractant, the next phase is to determine palatability. Shrimp are slow eaters, and nibbling pellets instead of ingesting whole pellets. Exact feed intake is therefore difficult to determine. In this study, the student will develop a method to measure palatability of shrimp diets. A literature study will be done to give an overview of different methods already used to study palatability, and a small experiment can be performed to test methods developed by the student itself.

Supervision: Marit Nederlof

Contact: Marit Nederlof (marit.nederlof@wur.nl)

Number of possible students: 1

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AFI-13. Prospects of cassava peel as aquafeed ingredient in Africa: A review of potential technologies and feeding strategies to improve its nutritional quality for fish.

One of the major challenges confronting African aquaculture is high costs of feeds. This is as a result of continuous reliance on import for the supply of feed ingredients. In order to increase productivity and profitability of aquaculture enterprise, Africa needs to look inward and utilize locally available feed resources in the most sustainable manner. Crop processing generates large quantities of ‘waste’, that can potentially be incorporated into aquafeed. One of such is cassava. Cassava is widely produced in Africa, particularly sub-Saharan Africa. Cassava peel is a by-product of cassava processing, and constitutes menace to the environment due to indiscriminate disposal and improper management. The peels are high in fibre and limited in protein. Therefore, there is need to improve its nutritive quality before being incorporated into aquafeed. This study intends to review the potential technologies (e.g. fermentation) and feed strategies (e.g. feed enzymes) that can be used to increase the nutritional quality of cassava peel in fish. The student is expected to identify major cassava producing countries in sub-Saharan African (with their annual volumes of cassava and cassava peels production) and to review of available technologies (both traditional and modern) and feedings strategies that can be used to improve nutritional quality of cassava peels.

Supervision: Agboola Jeleel

Contact: Marit Nederlof (jeleel.agboola@wur.nl)

Number of possible students: 1

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AFI-14. Dietary amino acid profile in aquaculture diets and its influence on muscle fibre growth dynamics

In order to improve resource-use efficiency, modern aquaculture diets are increasingly supplemented with crystalline amino acids (AAs). Fish growth strongly depends on the accretion of dietary AAs into fillet (i.e. muscle). A balanced supply of essential and non-essential AAs is required for optimal muscle growth. Fish muscle growth differs from that of mammals in that muscle fibre recruitment (hyperplasia) is still taking place after hatching. Therefore, both hyperplasia and hypertrophy (enlargement of existing fibres) contribute to fish growth. The influence of dietary levels of essential AAs such as lysine or methionine on fish muscle growth dynamics (i.e. hyperplasia and hypertrophy) are not well known. Such knowledge will contribute to improve fish feed formulation and dietary AAs retention into fish fillet. An experiment was recently conducted in which 3 diets differing in their amino acid profile were fed to Nile tilapia juveniles. Muscle samples were collected to quantify muscle fibre recruitment and enlargement.

Student’s mission: 1) assist in performing the histological analyses of Nile tilapia muscle samples and 2) prepare a short literature review on the effects of dietary amino acid supplementation on muscle growth dynamics in Nile tilapia.

Supervision: Gauthier Konnert and Johan Schrama

Contact: Johan Schrama (johan.schrama@wur.nl)

Number of possible students:2

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AFI-15. Mycotoxins in fish feeds: Effects of deoxynivalenol (DON) 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.

Student’s mission: Literature study to get information about the mechanisms that lead to the adverse effect of DON on fish species (reduced feed intake, protein synthesis, immunology, histopathology).

Supervision: Vivi Koletsi and Johan Schrama.

Contact: Johan Schrama (johan.schrama@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.