PhD students

Background of the project
The global population is on the rise and with this increase comes multiple climatic as well as food security issues. Anthropogenic activity has caused a widespread increase of greenhouse gases including rising CO₂ levels. Microalgae play a crucial role in mitigating rising CO₂ levels through sequestration while also serving as a valuable resource in aquaculture. Their biochemical composition can be altered by environmental stressors such as CO₂ levels and photoperiod, impacting their nutritional value. In marine fish larviculture, microalgae enhance live feeds like rotifers and Artemia, improving larval growth, survival, and microbiome development. The "green water technique" further supports larval health by enriching the rearing environment. Optimizing microalgae nutrient profiles for both live feeds and water quality can significantly improve fish larval growth, survival, and long-term robustness.

About the project
The project will encompass all aspects of teleost larval rearing. I will begin by applying various abiotic stressors to the microalgae culture of multiple species to manipulate the omega-3 polyunsaturated fatty acids (DHA, EPA) profile which are essential in early larval development. I will follow the microalgal culture trials by culturing and enriching live feeds (rotifers and Artemia) with the cultured microalgae and analyzing their nutrient retention efficiency. Lastly, I will culture finfish larvae while utilizing the results from the live feeds trial and condition the water with the cultured microalgae in an attempt to enhance larval growth, development, and survival.

Perspectives
The potential gained perspectives of the PhD project are to 1) address how microalgae species respond to various stressors in terms of growth, nutrient profile, and physio-chemical interactions, 2) promote growth and survival of finfish larvae through live feed nutrition and water conditioning and to better understand the mechanisms and interactions behind the growth and survival, 3) discover the short and the long-term effects on larval growth, development, and robustness from initial early nutrition and environmental exposure.

Supervisors
Ivar Lund & Anne Johanne Tang Dalsgaard, DTU Aqua

Background of the project
Nitrogen waste is a major concern in the aquaculture industry, as it can create toxic environments for fish and may lead to eutrophication in receiving water bodies. In aquaculture systems, dissolved nitrogen waste primarily originates from fish excretion, particularly in the form of ammonia. The amount of ammonia produced by fish largely depends on the amino acid composition of the feed. Both excesses and deficiencies of amino acids can negatively affect growth performance and nitrogen metabolism in fish. Therefore, optimizing diets to achieve balanced compositions of both essential amino acids (EAAs) and non-essential amino acids (NEAAs) is considered as a key to regulating not only protein retention for growth but also to mitigating the environmental impact of nitrogen‐rich effluents. Commercial aquafeeds are designed to meet the dietary requirements for essential amino acids; however, the composition of non-essential amino acids is generally not considered.

About the project
The project aims to investigate and develop nitrogen-optimized feed to reduce nitrogen excretion, improve protein retention and feed utilization in rainbow trout (Onchorynchus mykiss). At the beginning of the project, digestibility trials will be conducted to determine the apparent digestibility (ADC) of amino acids, protein, ash, fat, moisture and phosphorus. Based on the digestibility data of raw materials, R&D feed will be formulated with different amino acids profiles (focus on NEAAs) and tested in the mass balance trials for 6-8 weeks in recirculating aquaculture system (RAS) to estimate the optimized diets for rainbow trout. Beside optimized amino acid profiles, the project also aims to investigate the bioavailability of amino acid isomers (DL-amino acids) as well as the role of mammalian target of rapamycin complex 1(mTORC1) in protein synthesis and the normal growth development in rainbow trout.

Perspectives
The project is expected to provide new insights into the role of nitrogen-optimized feed for reducing nitrogen excretion and enhancing fish welfare. These findings may later be translated into industrial applications to reduce the environmental footprint of feed and contribute to more sustainable production practices.

Supervisors
Anne Johanne Tang Dalsgaard & Kylian Manon Eggink, DTU Aqua

Background of the project
Rainbow trout (Oncorhynchus mykiss) is one of the most important species in European aquaculture, contributing significantly to global finfish production. As aquaculture intensifies, improving fish health, welfare, and sustainability has become increasingly important. The gut microbiome plays a critical role in fish immunity and disease resistance, particularly during early development when microbial communities are first established. Although fish hatch with a largely sterile gastrointestinal tract, microbial colonisation occurs rapidly and is influenced by the surrounding environment, egg-associated microbes, and feeding practices. Disruptions to the microbiome can increase susceptibility to disease, inflammation, and mortality, highlighting the importance of establishing beneficial microbial communities early in life.

About the project
This PhD project aims to investigate how early-life microbial conditions influence gut microbiome development, stability, and fish health in rainbow trout. Initially, germ-free eggs will be exposed to different microbial environments, including low-microbial conditions, conventional recirculating aquaculture systems (RAS), and faecal inoculations from healthy adult fish. Microbiome development will be tracked using nanopore sequencing, alongside measurements of growth, survival, and overall performance. The second phase will examine the interaction between host genetics and microbiome development using genetically distinct trout lines with varying resistance to Flavobacterium columnare. This will help determine how genetic background and microbial exposure contribute to disease resistance and microbiome composition. Finally, microbiome variation across Danish rainbow trout farms will be analysed to provide one of the first systematic studies of microbiome development in Danish aquaculture systems.

Perspectives
The project is expected to improve understanding of how microbiomes establish and influence fish health and welfare throughout production. The findings may support the development of improved rearing strategies that optimise early-life microbial conditions, strengthen disease resistance, reduce mortality and antibiotic use, and enhance the sustainability and economic efficiency of aquaculture production.

Supervisors
Sanni-Leea Aalto & Manuel Gesto Rodriguez, DTU Aqua

Background of the project
Concern for animal welfare in husbandry has grown, yet fish farm guidelines remain in their early stages. Intensive land-based practices involve frequent handling and environmental challenges that cause fish stress. Delivering good welfare requires understanding fish responses to these practices and identifying reliable indicators. 

About the project
This study will investigate how operational welfare indicators (OWIs) relate to stress and welfare states in rainbow trout (Oncorhynchus mykiss) during on-farm operations, transport, and slaughter. Welfare will be assessed in real commercial settings from two perspectives: OWIs (usually external damage to the fish) and physiological parameters, which capture the internal stress response triggered by poor conditions at each production stage. Together, these methods will build a comprehensive picture of which OWIs most effectively reflect poor welfare states in rainbow trout depending on the farming phase. The result will present the links between operational indicators to actual welfare status.

Perspectives
Concern for animal welfare in husbandry has grown, yet fish farm guidelines remain in their early stages. Intensive land-based practices involve frequent handling and environmental challenges that cause fish stress. Delivering good welfare requires understanding fish responses to these practices and identifying reliable indicators. 

Supervisors
Manuel Gesto & Peter Vilhelm Skov, DTU Aqua

Background of the project
While aquaculture is essential for meeting the growing demand for food while reducing pressure on wild fish stocks, intensive aquaculture systems generate nutrient-rich effluent that requires treatment. At the same time, there is increasing interest in the red macroalgae genus Asparagopsis, which has been found to substantially reduce methane emissions when fed in small amounts to ruminant livestock such as cattle. Combining the cultivation of Asparagopsis spp. with aquaculture effluent treatment could create a circular approach that recovers nutrients while producing a valuable climate-mitigation product.

About the project
Together with the company Maripure ApS, this Industrial PhD project investigates the cultivation of Asparagopsis spp. using nutrient-rich water from recirculating aquaculture systems (RAS) for the production of methane-reducing compounds. The project will first determine the conditions required to optimize seaweed growth and bromoform production when cultivated in aquaculture effluent. Cultivation will then be scaled up to larger photobioreactor systems, with particular focus on monitoring seaweed growth and physiological condition using spectroscopy technologies. By creating correlation models, hyperspectral imaging and fluorometry will be explored as non-invasive tools for monitoring biomass and detecting stress, with the aim of supporting automated cultivation.

Perspectives
As this approach has not been previously studied, this project will demonstrate how the Asparagopsis cultivation industry can turn a waste stream into a resource, contributing to a more circular and sustainable aquaculture system that will support large-scale seaweed production. The project will also contribute to improved monitoring and automation of seaweed cultivation, facilitating future industrial production.

Supervisors
Carlos O. Letelier Gordo (principal), DTU Aqua, Esther Savina, DTU Aqua, Thomas Stenum (principal), Maripure ApS & Lucas Lyst Thiesen, Force Technology