Periodic Reporting for period 2 - RASOPTA (Safeguarding future production of fish in aquaculture systems with water recirculation)
Okres sprawozdawczy: 2023-09-01 do 2025-08-31
Production of food for humans is in great demand. Fish represent a significant protein source for human consumption and aquaculture industries have increased their productions globally. But issues with environmental impact persist and there is a need for development of environmentally friendly production systems. Recirculated Aquaculture Systems (RAS) represent such systems, where up to 100% of the water is recirculated and the outlet of nutrients is controlled. In RAS there are different challenges impairing production that were addressed in this project, and the project aimed to train 12 early stage researchers (ESRs) in novel approaches to understand, characterize and control 1) water quality, 2) off-flavours and 3) fish health and welfare.
RASOPTA has recruited and trained 12 doctoral students. WP1 on water quality involved 3 ESRs, WP2 on off-flavour 4 ESRs, and WP3 on fish health and welfare 5 ESRs.
WP1 advanced understanding of biofilters in recirculating aquaculture systems (RAS) and their role in microbial ecology, water quality, and system stability. Using 16S rRNA and metagenomic sequencing, ammonia-oxidizing prokaryotes in commercial biofilters were quantified. In addition to conventional ammonia-oxidizing bacteria, Nitrosopumilus and comammox Nitrospira represented ~50% of ammonia oxidizers. Biofilters acted as barriers against microbial invasions, while partial disinfection reduced protection. A large-scale survey across Norway and the Faroe Islands confirmed low pathogen levels and provided the first detailed characterization of bacterial, archaeal, and fungal communities in RAS.
Experimental biofilter swaps showed that biofilters directly shape microbial composition. Analyses demonstrated lower bacterial growth in RAS than in flow-through systems. Biofilters stabilize microbial communities, reduce carrying capacity after disturbances, and enhance bacterial competition, supporting fish health and system resilience.
Particle management studies evaluated dietary additives. Guar Gum and black soldier fly larvae had no negative effects on juvenile rainbow trout. Inclusion of 3% cork in feed improved particle removal via faecal flotation, enabling efficient surface skimming and enhancing drum filter performance, while reducing nutrient leaching. WP1 also provided the first comprehensive analysis of particle size distributions in large-scale RAS, guiding improved feeding strategies.
WP2 addressed off-flavour generation and removal through four coordinated sub-projects combining microbiology, chemistry, and aquaculture. Geosmin-producing myxobacteria were isolated, and key environmental and genetic factors controlling production identified, enabling targeted mitigation. Odorant uptake and removal under various depuration conditions, and the effects of feed, RAS compartments, and fish species, were investigated. Several previously unreported odorous compounds in RAS were identified.
A novel setup was developed to study odor impressions of compound mixtures, complementing instrumental profiling and allowing faster, more accurate evaluation. These results support improved off-flavour management via control of geosmin-producing bacteria, optimized depuration, and tailored feeding, while expanding molecular-level understanding of odours in aquaculture products.
WP3 focused on fish health and welfare, developing a Fluidigm® chip to detect pathogens, water quality, and off-flavours using water samples. Controlled trials showed transport, hypoxia, overcrowding, and exposure to nanoplastics or pharmaceuticals significantly elevated stress, measurable non-lethally via blood biomarkers. Nanoplastic exposure also led to tissue accumulation, indicating bioaccumulation risk.
Pathogen surveillance in water and air revealed airborne transmission as an underestimated infection route. Molecular monitoring showed eDNA/eRNA concentrations correlated with disease occurrence and mortality, allowing predictive thresholds to be established. Ectoparasite surveys identified diverse pathogenic and commensal species, including Thaparocleidus vistulensis in European catfish. A molecular assay was developed with purified reference DNA for qPCR testing. The Fluidigm® chip was finalized, with assays validated in eDNA and eRNA formats and tested on samples from Denmark, Hungary, and the Faroe Islands. Comparative analyses across water, air, and tissue generated large datasets supporting studies on co-infections and distinguishing eDNA (dead + live organisms) from eRNA (live only).
WP1 advanced understanding of biofilters in recirculating aquaculture systems (RAS) and their role in microbial ecology, water quality, and system stability. Using 16S rRNA and metagenomic sequencing, ammonia-oxidizing prokaryotes in commercial biofilters were quantified. In addition to conventional ammonia-oxidizing bacteria, Nitrosopumilus and comammox Nitrospira represented ~50% of ammonia oxidizers. Biofilters acted as barriers against microbial invasions, while partial disinfection reduced protection. A large-scale survey across Norway and the Faroe Islands confirmed low pathogen levels and provided the first detailed characterization of bacterial, archaeal, and fungal communities in RAS.
Experimental biofilter swaps showed that biofilters directly shape microbial composition. Analyses demonstrated lower bacterial growth in RAS than in flow-through systems. Biofilters stabilize microbial communities, reduce carrying capacity after disturbances, and enhance bacterial competition, supporting fish health and system resilience.
Particle management studies evaluated dietary additives. Guar Gum and black soldier fly larvae had no negative effects on juvenile rainbow trout. Inclusion of 3% cork in feed improved particle removal via faecal flotation, enabling efficient surface skimming and enhancing drum filter performance, while reducing nutrient leaching. WP1 also provided the first comprehensive analysis of particle size distributions in large-scale RAS, guiding improved feeding strategies.
WP2 addressed off-flavour generation and removal through four coordinated sub-projects combining microbiology, chemistry, and aquaculture. Geosmin-producing myxobacteria were isolated, and key environmental and genetic factors controlling production identified, enabling targeted mitigation. Odorant uptake and removal under various depuration conditions, and the effects of feed, RAS compartments, and fish species, were investigated. Several previously unreported odorous compounds in RAS were identified.
A novel setup was developed to study odor impressions of compound mixtures, complementing instrumental profiling and allowing faster, more accurate evaluation. These results support improved off-flavour management via control of geosmin-producing bacteria, optimized depuration, and tailored feeding, while expanding molecular-level understanding of odours in aquaculture products.
WP3 focused on fish health and welfare, developing a Fluidigm® chip to detect pathogens, water quality, and off-flavours using water samples. Controlled trials showed transport, hypoxia, overcrowding, and exposure to nanoplastics or pharmaceuticals significantly elevated stress, measurable non-lethally via blood biomarkers. Nanoplastic exposure also led to tissue accumulation, indicating bioaccumulation risk.
Pathogen surveillance in water and air revealed airborne transmission as an underestimated infection route. Molecular monitoring showed eDNA/eRNA concentrations correlated with disease occurrence and mortality, allowing predictive thresholds to be established. Ectoparasite surveys identified diverse pathogenic and commensal species, including Thaparocleidus vistulensis in European catfish. A molecular assay was developed with purified reference DNA for qPCR testing. The Fluidigm® chip was finalized, with assays validated in eDNA and eRNA formats and tested on samples from Denmark, Hungary, and the Faroe Islands. Comparative analyses across water, air, and tissue generated large datasets supporting studies on co-infections and distinguishing eDNA (dead + live organisms) from eRNA (live only).
WP1 demonstrated the importance of RAS biofilters beyond their primary function in nitrification. We showed that the biofilter determines the microbial environment for the fish, counteracts invasions by opportunistic bacteria, reduces the growth of bacterial taxa associated with pathogens, and generally does not house pathogens. Our results suggest that to promote a healthy microbial environment in RAS, regular disinfection biofilters between production batches should be avoided. Furthermore, we demonstrated the concept of “floating feces” through cork-enriched diets for Atlantic salmon in full-RAS. This technology improves water quality through more efficient solids management and reduces particle-bound nutrient leaching, TAN, and CO2 levels. Implementation of this knowledge will help optimize fish production in RAS and improve fish welfare and sustainability.
WP2 achieved novel insights into the molecular basis of the flavour and off-flavour of aquaculture products and broadened knowledge of RAS products not studied before. We developed methods allowing rapid sensory evaluation of flavour mixtures, enabling future optimization of aquaculture product flavour. We assessed the distribution of off-flavour compounds in different RAS sites, helping companies optimize procedures to achieve products with desired sensory quality. We also gained insights into consumer awareness and perception, forming a basis for marketing strategies to promote sustainable and responsible aquaculture. Novel strategies for off-flavour management were evaluated, considering feed formulation and fish physiology, and new microbial producers of off-flavour compounds were identified, forming the basis for future studies to minimize off-flavour generation. The results will aid RAS companies improve the sensory quality of their products—an important step toward resilient, high-quality production high fish health and welfare.
WP3 developed a non-invasive monitoring tool to detect genes, gene transcripts, and organisms directly in the water of RAS to assess system health. Unlike traditional methods focusing on fish, this tool continuously assesses water quality, off-flavour compounds, and pathogens, offering advanced control and management strategies. With this technology, fish farmers can regularly and non-invasively monitor their systems, enabling early detection and preventive action when issues are identified by the chip. Over time, accumulated data will allow predictive analysis, helping to foresee and prevent problems. Implementation of this tool may increase fish production, improve health and welfare, reduce environmental impact, and enhance sustainability, efficiency, and socio-economic value of aquaculture operations.
WP2 achieved novel insights into the molecular basis of the flavour and off-flavour of aquaculture products and broadened knowledge of RAS products not studied before. We developed methods allowing rapid sensory evaluation of flavour mixtures, enabling future optimization of aquaculture product flavour. We assessed the distribution of off-flavour compounds in different RAS sites, helping companies optimize procedures to achieve products with desired sensory quality. We also gained insights into consumer awareness and perception, forming a basis for marketing strategies to promote sustainable and responsible aquaculture. Novel strategies for off-flavour management were evaluated, considering feed formulation and fish physiology, and new microbial producers of off-flavour compounds were identified, forming the basis for future studies to minimize off-flavour generation. The results will aid RAS companies improve the sensory quality of their products—an important step toward resilient, high-quality production high fish health and welfare.
WP3 developed a non-invasive monitoring tool to detect genes, gene transcripts, and organisms directly in the water of RAS to assess system health. Unlike traditional methods focusing on fish, this tool continuously assesses water quality, off-flavour compounds, and pathogens, offering advanced control and management strategies. With this technology, fish farmers can regularly and non-invasively monitor their systems, enabling early detection and preventive action when issues are identified by the chip. Over time, accumulated data will allow predictive analysis, helping to foresee and prevent problems. Implementation of this tool may increase fish production, improve health and welfare, reduce environmental impact, and enhance sustainability, efficiency, and socio-economic value of aquaculture operations.