BSc Thesis Subjects

BSc Subjects AFI July 2018

Aquaculture topics

AFI-1. Fish mucus stops pathogens and more?

Fish mucus layers are the main surface of exchange between fish and the environment, and they possess important biological and ecological functions. Mucins are a family of high molecular weight, heavily glycosylated proteins produced by epithelial tissues and are important for fish skin, gills, intestine and more. Mucins' key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers. Fish mucus plays a major role against fish infections, and research has mostly 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, external fish mucus surfaces also play important roles in social relationships between conspecifics (fish shoaling, spawning synchronisation, suitable habitat finding, or alarm signals) and in interspecific interactions such as prey-predator relationships, parasite–host interactions, and symbiosis.

Work: The student will execute a literature study on the different roles and importance of mucus for fish health.
Supervision: Geert Wiegertjes
Contact: Geert Wiegertjes (geert.wiegertjes@wur.nl)
Number of possible students: 1

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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. 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 (vivi.koletsi@wur.nl) or Johan Schrama (johan.schrama@wur.nl)
Number of possible students: 1

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AFI-4. Tilapia culture species for aquaculture.

Commonly cultured African cichlid (Pseudocrenilabrinae) species belong to genera Oreochromis, Sarotherodon and Tilapia, which as a group are referred to as tilapia species. These species are endemic to Africa and the Middle east, each species having its own natural distribution area. To avoid cross contamination between species, some African countries restrict the species that can be cultured on their territory, and forbid import of non-endemic species. In this study, we concentrate on Africa below the equator. Today, Nile tilapia (Oreochromis niloticus) represents more than 95% of the global aquaculture production of tilapia species. Through domestication and selection, fast growing strains of Nile tilapia are now available, but this is less the case for other tilapia species. Species with farming potential include Mozambique tilapia (O. mossambicus), black tilapia (O. placidus), three-spotted tilapia (O. andersonii), greenhead tilapia (O. macrochir), red-breast tilapia (T. rendalli) and banded tilapia (T. sparrmanii). All these species have been cultured and their growth has been reported in literature. For the species mentioned above, you are asked to make a literature study on reported growth rates, culture practices (stocking densities, diet preferences) and productions achieved. You also make an overview of the natural occurrence area of each species, and where each species is allowed to be cultured in your study area. Based on the information gathered, make a ranking of which species are most promising for aquaculture.

Supervision and contact: Marc Verdegem (marc.verdegem@wur.nl)
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 (yale.deng@wur.nl)
Contact: Marc Verdegem (marc.verdegem@wur.nl)
Number of possible students: 1.

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FI-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 (marc.verdegem@wur.nl)
Number of possible students: 1

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AFI-7. 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 and has seen rapid increase in production in the past 20 years. Feed represents half of the operational costs of most Nile tilapia farms. Thus, feed efficiency is an important aspect of fish farms resource-use efficiency. Improving feed efficiency requires knowledge of the nutritional requirements and growth potential of fish. The latter has been mainly evaluated in terms of daily body mass increase for Nile tilapia, a major aquaculture species. In growing fish, body mass gain mainly results from accretion of white muscle tissue. Interestingly, post-embryonic growth of fish muscle results from both enlargement of existing fibres (hypertrophy) and recruitment of new ones (hyperplasia). Unlike terrestrial farm species (mammals and birds), fish show persistent hyperplasia after hatching (i.e. birth), especially in species reaching large ultimate size. Muscle fibre hyperplasia and hypertrophy are somewhat flexible mechanisms which duration and intensity have been only partially described for Nile tilapia. The regulation and respective contribution of hyperplasia and hypertrophy to muscle growth in Nile tilapia will be investigated in a 6 months in vivo experiment to be conducted from June to November 2019. Muscle samples will be collected to quantify muscle fibre hyperplasia and hypertrophy rate during the experiment.

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

Supervision: Gauthier Konnert and Johan Schrama
Contact: Johan Schrama (johan.schrama@wur.nl)
Number of possible students:2

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AFI-8. Energy storage strategy: Where do fish mainly store energy?

Growth in fish requires protein, lipid and minerals to build up bones and body mass. This process is fuelled by energy. Energy is also required for a wide range of daily activities like swimming, searching for food or even attacking preys. Fish can yield energy from protein, lipid and carbohydrates in diets or energy storages in different body compartments like liver, muscle or abdominal fat. Most interestingly, different fish species have different strategies to store energy in the form of protein or fat in different compartments depending feeding behaviours, swimming styles and living habitats. Eels mainly store fat in muscles while fat is mainly deposited in the abdominal part of African catfish (Clarias gariepinus). It is not clear whether the rest compartment (i.e., head, skins, skeleton) can play as a major substrate for energy storage in this species. An experiment with four diets (protein-rich diet, starch-rich diet, lipid-rich diet, and lipid-starch-rich diet) and two feeding levels (low and high) will be conducted in the middle of 2019 to investigate differences in energy storage among four key compartments: liver, viscera (including gallbladder, spleen and gonads), fillets and the rest (including head, skin and bones) in African catfish.

Student’s tasks: 1) To conduct the chemical composition analysis of the four body compartments in African catfish and 2) To performance statistical analyses to see the effect of diets and feeding levels on energy (nutrients) storage among the four body compartments in African catfish. 3) conduct literature assessment of impact of diet on location of nutrient deposition in fish.
Supervision: Thuat Phan and Johan Schrama
Contact: Johan Schrama (johan.schrama@wur.nl) or Thuat Phan (thuat.phan@wur.nl)
Number of possible students: 1 

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Fisheries/fish ecology topics

AFI-9. 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-10. 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 (Leo.Nagelkerke@wur.nl)
Number of possible students: 1-3 (1 per geographical location)

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AFI-11. 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

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

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

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

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.