Salmon Farming Research Articles

Web‐based application to guide sampling on salmon farms for more precise estimation of sea louse abundance

AbstractObjectiveEfficiently managing sea lice on salmon farms through active surveillance, crucial for lice abundance estimation, is challenging due to the need for effective sampling schemes. To address this, we developed an application that considers infestation levels, farm structure, and management protocols, enhancing the precision of sampling strategies for sea louse abundance estimation.MethodsSimulation‐based methods are valuable for estimating suitable sample sizes in complex studies where standard formulae are inadequate. We introduce FishSampling, an open Web‐based application tailored to determine precise sample sizes for specific scenarios and objectives.ResultThe model incorporates factors such as sea lice abundance, farm pen numbers, potential clustering effects among these pens, and the desired confidence level. Simulation outcomes within this application provide practical advice on how to decide on the number of fish and pens to sample, under varying levels of assumed clustering.ConclusionThis approach can be used across the salmon aquaculture sector to improve sampling strategies for sea lice abundance estimation and balance surveillance costs against health objectives.

Mathematical modelling of dissolved oxygen levels in a multi-cage salmon farm

Dissolved oxygen concentrations were monitored at 12 points distributed over 3 depths in one out of six cages in an Atlantic salmon farm and compared to the output of a mathematical model using the advection-diffusion equation and a model of the salmon's oxygen consumption to estimate spatial oxygen distributions. The effects of oxygen consumption in neighbouring fish cages on the oxygen levels observed in the monitored cage were found to be significant, and several model variants modified to better represent the real system were tested. Position data from 8 fish in the cage equipped with acoustic telemetry tags was used to refine the model configuration.Results show that simulating the full farm with all cages improves model fit significantly over simulating a single cage only. Even better fit was achieved in a single cage model with ad hoc modifications, indicating that there are additional non-modelled effects that should be investigated further. This study establishes the oxygen model as a suitable tool for monitoring and forecasting of oxygen conditions in salmon cages, and gives indications about he accuracy and limitations of the model.

Reconciling Coulter Counter and laser diffraction particle size analysis for aquaculture monitoring

The disaggregated inorganic grain size (DIGS) of bottom sediment analyzed with a Coulter Counter (CC) has been used to show that the fraction of sediment deposited in flocs (floc fraction) increased in both the near and far field after the introduction of open cage salmon aquaculture, altering benthic habitat and species composition. As a result, DIGS was identified as a potential indicator of regional environmental changes due to aquaculture. Laser diffraction is an attractive alternative to the CC because of its greater efficiency and larger size range. To determine if a laser diffraction instrument, Beckman-Coulter LS 13 320 (LS), could replace the CC within a Canadian national aquaculture monitoring program, the DIGS of 581 samples from five different regions in eastern Canada were analyzed with an LS and a CC. Results show that the LS could not be used to calculate floc fraction. Instead, % sortable silt and the volume % of inorganic particles < 16 µm were evaluated as alternative proxies for fine sediment properties. LS and CC values for these parameters were correlated, but they were significantly different and the relationship between the instruments was dependent on the area sampled. The LS did not capture variations between areas seen in the CC DIGS data. Where the DIGS from the CC found no sorting in the finest size classes, all the LS samples had similar size distributions characterized by smooth modal peaks. The LS and CC both return values that can be used to monitor changes in the deposition of fine-grained sediment, but the LS cannot determine changes in floc deposition and caution is required if comparing different sedimentary environments.

Indicators for ecological carrying capacity of bivalve and seaweed aquaculture

AbstractWithin the framework of Ecosystem Approach to Aquaculture (EAA), ecological carrying capacity (ECC) is a key concept that helps to determine the upper limit of production without compromising ecosystem functioning. The implementation of ECC is complex as ECC differs between type of farms and location and standardised methods should be developed for management. There is therefore a clear need for operational indicators. The objectives of this paper were: (1) to carry out a systematic literature review on shellfish and seaweed aquaculture‐environment interactions to list the most used environmental indicators, (2) to classify the indicators according to the effects they measure (i.e., benthic, water quality, food web interactions, cultured organism health, resource use) and the scale at which they are applied, and (3) to assess their potential based on four indicator criteria categories: sensitivity, accuracy and precision, feasibility and utility, and ecosystem‐level scalability. Overall, indicators describing benthic effects were the most highly cited and scored. Indicators identified for bivalve and seaweed culture were discussed and compared to previous work on salmon aquaculture indicators to highlight similarities and differences across trophic levels. In addition, questions related to the challenges of ECC indicators implementation were presented to a panel of experts. The scoring and consultation provided the source of discussion on environmental management consistent with EAA.

Modelling changes in whole body and fillet fatty acid composition of Atlantic salmon with changing levels of dietary omega-3 intake

In this study, a fatty acid dilution model was coupled with a dynamic nutrient demand model to provide an integrated model capable of predicting the whole-body and fillet lipid and fatty acid levels of Atlantic salmon (Salmo salar) following a change in dietary fatty acid profile. Based on knowledge of the initial fish and dietary fatty acid compositions, diet digestible energy density, the water temperature and duration of feeding, the model demonstrated that it was possible to predict a range of parameters, including the growth, feed utilisation, whole-body and fillet (Norwegian Quality Cut; NQC) total lipid, and fatty acid levels of the fish. The model was validated against five separate experiments, including two farm-based trials with harvest size fish. Validation experiments involved fish ranging in size (initial weights to final weights) from 138 g/fish to 5138 g/fish and running for durations of between 66 and 323 days. For the laboratory experiments, prediction of growth, feed utilisation and fatty acid deposition proved to be highly predictable (R2 > 0.998). Fatty acid profiles from both short and long-term cage trials were also highly predictable. Despite the reduced level of weight change in the short-term cage trial, and the higher variability that was observed in growth performance, the fatty acid deposition still showed high levels of correlation (R2 > 0.996), between the modelled and measured fatty acid levels in the fish fillet. Departure from linearity was more evident in the long-term cage trial, but correlation still exceeded R2 > 0.995 for all treatments. Prediction of whole-body and NQC total lipid levels was less accurate, with correlations being R2 = 0.962 and R2 = 0.909 respectively. Model outputs were generally more accurate with greater weight change and/or experiment duration. The outcome of this study shows that the model developed here provides a useful tool for the estimation of the fatty acid composition of Atlantic salmon following a change in dietary fatty acid composition. This could help assist in the more judicious use of dietary long-chain omega-3 fatty acids for commercial salmon farming.

Development and use of a Chinook salmon spleen stromal-like cell line to study the cellular immune response to Vibrio anguillarum

Despite increased interest in Chinook salmon aquaculture, there is inadequate understanding regarding the bacterial immune defenses of this species. This study describes the establishment and characterization of a continuous stromal-like cell line derived from Chinook salmon spleen, CHST, and its response to a heat-killed bacterial exposure challenge. Optimal growth of CHST was seen at 18 °C when grown in Leibovitz's L15 media supplemented with 20 % fetal bovine serum. DNA analyses confirmed that CHST did originate from Chinook salmon tissue. Vibrio anguillarum, a common pathogen of marine aquaculture and the causative agent of an acute hemorrhagic septicaemia known as vibriosis was used for exposure studies. V. anguillarum was heat-killed and CHST was challenged so that pro-inflammatory (IL-1β, IL-6 and TNFα) as well as anti-inflammatory (IL-10) cytokine transcript levels could be measured at 1, 4, 12, 24 and 96 hour (h) post-exposure. The heat-killed bacteria were observed to significantly stimulate the expression of all three pro-inflammatory cytokines at 4, 12, 24 and 96 h post-exposure with the peak in expression occurring at 12 and 24 h. Meanwhile, IL-10 was not observed to significantly increase until 96 h post-stimulation, which was also the time when the inflammatory cytokine expression was decreasing. The establishment and characterization of CHST provides a valuable model for studying the immune response of Chinook salmon stromal-like cells in response to stimuli, including those of bacterial origin.

Sea lice management in marine-based salmon farming: Public perceptions and acceptance in England and Scotland

Marine-based salmon farming faces a significant challenge in the management of sea lice infestations, particularly in high-density production areas. Multiple strategies have been employed on salmon farms to prevent and treat sea lice infestations, but they have widely varied in their effectiveness in reducing infestations and their associated impact on the marine environment and fish welfare. Typically, cost and effectiveness are crucial considerations for salmon industries and researchers when determining which practice is optimal for reducing sea lice infestations, but the public's views on sea lice management have not yet been fully assessed. Therefore, an online survey was conducted to examine how the English and Scottish public evaluate different sea lice management practices. Participants were randomly assigned to one of eight conditions: four different types of sea lice management practices (medical treatment, mechanical treatment, cleaner fish treatment, or barrier technology) with two types of information formats (basic information or detailed information). The results showed that participants were more accepting of barrier technology and cleaner fish treatment than medical treatment and mechanical treatment, regardless of whether the presented information was basic or detailed. However, providing detailed information about mechanical treatment and cleaner fish treatment negatively affected the participants' acceptance and perceptions compared to the basic information condition. Specifically, when detailed information was provided, mechanical treatment was evaluated as less natural and less welfare friendly for farmed salmon, and the corresponding salmon products were considered to be less healthy than when basic information was provided. Similarly, when detailed information was provided, cleaner fish treatment was rated as less natural, less environmentally friendly, and less welfare friendly for cleaner fish than when only basic information was provided. This study has implications for salmon industries and policymakers: the public encourages a natural way of managing sea lice that has a minimum negative impact on the environment and farmed salmon, which might clash with the current realities of salmon farming.

Rapid detection of salmon louse larvae in seawater based on machine learning

The proliferation of salmon lice is one of the most challenging problems in salmon farming, seriously affecting the welfare of both farmed and wild salmonids. The detection of salmon lice in seawater, especially in the (pre-) infectious stage, supports the accurate management of salmon lice proliferation. Methods for detecting salmon lice in seawater to date involve traditional light and fluorescence microscopy and Polymerase Chain Reaction (PCR) methods. However, these methods require sample pre-processing and are laborious and time-consuming, rendering them difficult to apply for the task of continuous, rapid salmon lice detection in large water volumes. This study aims to develop a rapid and easy-to-use method for the detection of salmon lice in seawater. A novel approach was introduced for the detection of salmon lice at different larval stages in seawater by leveraging machine learning. A setup for the rapid acquisition of images of salmon lice in seawater was developed, and a dataset comprising 8316 images encompassing salmon lice “Nauplius Live,” “Nauplius Shell” and “Copepodite” was created. Then 16 object detection models including one- and two-stage Convolutional Neural Network (CNN-) based models and Transformer-based models were trained, tested, and compared on this comprehensive dataset. RT-DETR showed the best performance among all models tested with a precision of 0.972 and a recall of 0.978. The YOLO series models, except for YOLOv3, showcased remarkable inference speeds (ranging from 152 to 416 frames per second) while maintaining high precision (ranging from 0.968 to 0.977) and recall (ranging from 0.964 to 0.970). To our knowledge, this is the first time machine learning has been applied to the task of rapidly detecting salmon louse larvae at different stages in seawater samples. The results demonstrate that the machine learning approaches can achieve rapid easy-to-use and cost-effective detection of salmon lice in seawater. In the future, this study has the potential for application in measuring salmon louse larvae numbers in aquatic environments, supporting the enhancement of the welfare of both farmed and wild salmon.

Oxytetracycline dose reduction in salmon farming: Assessing a micro encapsulated novel formulation in an in vivo model

Oxytetracycline (OTC) is used in Chilean salmonid farming for bacterial pathogens treatment, mainly orally administered. Oral bioavailability of OTC in salmonids is low, so a high percentage of the dose is excreted by fishes. To increase OTC oral absorption, Zn-alginate microparticles were developed by spray drying, with a yield of 59.09%. An in vivo study was performed using Oncorhynchus mykiss (Rainbow trout) to compare OTC Zn-alginate micro-particles oral absorption in plasma and muscle matrices. Seven sampling points for plasma and four for muscle were considered. OTC was quantified in both matrices by UPLC-MS/MS. Results indicated a statistically significant difference between plasma concentrations of the OTC microparticles with respect to the commercial OTC formulation, reflecting a higher absorption of the microencapsulated drug, reaching maximum concentration 4 h earlier than the commercial formulation. In addition, the microparticles showed a release of OTC that remained constant for 12 h. In muscle, OTC microparticles reached twice the maximum concentration than the commercial formulation at 8 h. In conclusion, OTC microparticles improve the oral absorption of the molecule, which could allow drug delivery optimization and dose reduction in bacterial pathogens treatment in salmon production, consequently, decrease contamination of the environment with OTC residues.

The state of planktonic and benthic communities of the skerry region of Lake Ladoga near fish farms

The aim of this work is to assess the impact of trout farms on the ecological state of a freshwater body (Lake Ladoga) using hydrobiological parameters.The main methods of the study were sampling and processing of bacterioplankton, zooplankton, benthos; calculation of abundance and biomass of hydrobionts; analysis of taxonomic structure, species determinations, following standard procedures used in hydrobiology.As a result, a change in the quantitative development of bacterioand zooplankton, macroand meiobenthos communities, change in structure, simplification of taxonomic composition, decrease in species richness, appearance of species-indicators of toxic pollution in zooplankton and benthos communities under cages in the zones of influence of trout farms was revealed. Differences in the degree of severity of negative impact at the studied farms were noted, which can be attributed to the hydrodynamic factor, since one of the farms is located in conditions of greater flow compared to the other. Environmental quality assessment of planktonic and benthic communities showed the presence of negative impact of trout farms, the extent of which depends on the location of the farm and the degree of flow in the water area where the cages are located.

The First Report on Saprolegnia parasitica and Neoparamoeba perurans Isolated from Atlantic Salmon (Salmo salar) Reared in Korea

This study is the first report of parasite and fungal disease separated from domestically reared Atlantic salmon in Korea; the characteristics of the pathogens were identified, and histopathological analysis was conducted. Fungal and parasitic diseases were detected in Atlantic salmon and were isolated as Saprolegnia parasitica and Neoparamoeba perurans based on morphological and genetic analysis. External symptoms observed in Atlantic salmon infected with S. parasitica include fin ulcers and hemorrhage, abdominal hemorrhage, and necrosis of the gills and gill covers. The histopathological analysis results showed necrosis, hemorrhaging, and inflammatory cell infiltration in the abdominal muscles, while only inflammatory cell infiltration was observed in the gill covers. The clinical symptoms observed in Atlantic salmon infected with N. perurans included excessive mucus secretion in the gills, a dense amoebic presence on the gill filaments, respiratory distress, and opening of the mouth and gill covers after death. Through histopathological analysis, we observed lesions in epithelial cells, characterized by the proliferation of epithelial cells and the fusion of secondary lamellae. Numerous lamellae were observed to be attached or fused with each other. To ensure the successful establishment of the Atlantic salmon aquaculture industry in Korea, it is essential to swiftly quarantine infected fish based on the morphological characteristics of S. parasitica and N. perurans revealed in this study, along with the external symptoms of Atlantic salmon infected with these pathogens. Developing disease control strategies based on the findings of this research is imperative.

Identification and characterization of circular RNAs in the skin of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus

Rainbow trout (Oncorhynchus mykiss) is an economically significant freshwater-farmed fish worldwide, and the frequent outbreaks of infectious hematopoietic necrosis (IHN) in recent years have gravely compromised the healthy growth of the rainbow trout aquaculture industry. Fish skin is an essential immune barrier against the invasion of external pathogens, but it is poorly known about the role of circRNAs in rainbow trout skin. Therefore, we examined the expression profiles of circRNAs in rainbow trout skin following IHNV infection using RNA-seq. A total of 6607 circRNAs were identified, of which 34 circRNAs were differentially expressed (DE) and these DE circRNA source genes were related to immune-related pathways such as Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, Cytokine-cytokine receptor interaction, ubiquitin mediated proteolysis, and ferroptosis. We used qRT-PCR, Sanger sequencing, and subcellular localization to validate the chosen DE circRNAs, confirming their localization and expression patterns in rainbow trout skin. Further, 12 DE circRNAs were selected to construct the circRNA-miRNA-mRNA regulatory network, finding one miRNA could connect one or more circRNAs and mRNAs, and some miRNAs were reported to be associated with antiviral immunity. The functional prediction findings revealed that novel_circ_002779 and novel_circ_004118 may act as sponges for miR-205-z and miR-155-y to regulate the expression of target genes TLR8 and PIK3R1, respectively, and participated in the antiviral immune responses in rainbow trout. These results shed light on the immunological mechanism of circRNAs in rainbow trout skin and offer fundamental information for further research on the innate immune system and breeding rainbow trout resistant to disease.

How accurate is your average? Considering error when counting sea lice on open-pen salmon farms

Open-net finfish farms require monitoring to manage fish welfare and to mitigate risk for diseases and parasites which could threaten wild fish populations. In salmonid farming the ectoparasite copepod sea lice Lepeophtheirus salmonis (Caligidae) is a major concern. This paper's novel contribution is the application of sampling statistics to determine the number of sea lice which should be sampled per pen so as to report the abundance of sea lice with a given accuracy. It does so considering the different statistical distributions which occur at high- and low prevalence of sea lice and combines these considerations to guide the reader towards counting a number of sea lice which would be more inline with other statistical applications. Existing pen sampling routines are analysed and the sampling error is quantified. These findings need to be taken into account when sampling protocols for sea lice are designed as it is especially important for fish welfare.

High resolution depth profile scanning of plankton organisms—VERTILICE

Knowledge of the vertical migration pattern of sea lice (Lepeophtheirus salmonis) copepodites is necessary for designing efficient measures to prevent lice infestations on farmed Atlantic salmon (Salmo Salar) in sea-cages. However, data can be challenging to acquire at a large scale under realistic circumstances without interfering with the natural behavior of the specimen. A mesocosm platform was built to help acquire this data consisting of a sensor package in an underwater housing being pulled up and down along a 11-meter-long transparent tube containing planktonic organisms while collecting image-, temperature- and spectrometer data. The platform was placed at a salmon farm and the acrylic tube was filled with L. salmonis copepodites and was pre-programmed to run a profile scan twice per hour for four consecutive days. Using a fully convolutional neural network, the copepodites were automatically counted – creating a depth profile of detected lice and measured light specter. The final results showed a diurnal migration pattern throughout the test period.•Capable of acquiring vertical density profiles of any aquatic species between 0,5 – 10 mm down to 11 m below the surface.•Fully automated and can be left unintended for weeks while collecting data.

Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts

Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in a similar order of magnitude as Illumina sequencing. We therefore conducted a pilot study to assess whether Nanopore duplex sequencing has potential to be used as a technology in eDNA-based marine biomonitoring. Specifically, we investigated bacterial communities of sediment samples collected from Atlantic salmon (Salmo salar) aquaculture installations and compared the ecological trends obtained from short Illumina (V3-V4 region of the 16S rRNA gene) and long Nanopore (full length 16S rRNA gene) sequence reads. The obtained duplex rate of Nanopore amplicon reads with a Phred score ≥ 30 was 36%, notably higher compared to previous reports from bacterial genome sequencing. When inferring alpha- and beta-diversity from Illumina ASVs and Nanopore OTUs, we found highly congruent ecological patterns. Only when collating ASVs and OTUs across taxonomic ranks, beta-diversity analyses of Illumina-data slightly changed, due to the difficulties to assign a taxonomy to short sequence reads. While on family rank, both sequence datasets had good agreement, genus-assignments of Illumina data were critical, resulting in higher disagreement between the two protocols. Our data provide evidence that eDNA-based monitoring of aquaculture-related environmental impacts could equally well be conducted with the improved Nanopore duplex sequencing. We discuss to what extent eDNA-based biomonitoring could benefit from long-read information.

Reputation management in turmoil—An analysis of the clashing narratives in the introduction of a “salmon tax” in Norway

AbstractThis study deals with reputation management, addressing collective issues, strategic communication by the government, and the dynamics between this communication and counter‐symbols from societal stakeholders. Empirically, it examines the political debates in Norway in recent years regarding the conflict over establishing a “ground rent” tax on extra profit earned through use of natural resources belonging to the community, related to salmon farming. The overall research question is how major concepts from reputation theory can explain the process and outcome of the decision‐making process. A main finding is that reputation varies across reputational dimensions and actors, and between government and audiences. Another is that it is necessary to examine reputation in relation to the field, the actors, and the task environment it concerns. The study also shows that reputation management is informed by the politics of reputation, revealing the challenge of balancing evidence‐based policy making and being responsive to opinion‐based stakeholder input, and that reputational threats and strategic communication are interlinked.

Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci

Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15–0.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the naïve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (≥1.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.

Phylogenomic characterization of Flavobacterium psychrophilum isolates retrieved from Turkish rainbow trout farms.

Flavobacterium psychrophilum, a devastating fish pathogen, is responsible for bacterial cold-water disease (BCWD), also known as rainbow trout fry syndrome. F. psychrophilum is the main causative agent of outbreaks in rainbow trout farms, especially at early live stages. In the present study, we aimed to characterize F. psychrophilum Turkish isolates. Eighteen isolates were retrieved from BCWD outbreaks between 2014 and 2021. Invitro phenotypic characterization showed gelatin and casein hydrolysis capacities and invitro adhesion for all isolates, whereas elastinolytic activity was present for 16 of 18 isolates. We used complete genome sequencing to infer MLST-type, serotype and phylogenetic reconstruction. Strikingly, one strain isolated from Coruh trout (FP-369) belongs to ST393, a previously undescribed ST, and is phylogenetically distant from the other isolates. However, all strains retrieved from rainbow trout belong to the well-characterized clonal complex CC-ST10, 12 of 17 were tightly connected in a single cluster. Several serotypes (Types -1, -2 and -3) were represented among isolates, but no correlation was observed with geographic origins. This analysis suggests a regional dissemination of an epidemic, disease-producing bacterial population. This study provides a basis for epidemiological surveillance of isolates circulating in Turkey and phenotypic data for future molecular studies of virulence traits of this important fish pathogen.

Synergies of co-infecting pathogens, sea lice (Lepeophetheirus salmonis) and Moritella viscosa, are impacted by exposure order, and host response to initial infection

Sea lice infestations and winter ulcer disease caused by Moritella viscosa are two major challenges for the Atlantic salmon (Salmo salar) aquaculture industry. Despite their common tropisms for the skin/muscle, we know very little about the interaction between these two significant pathogens. The objective of this study was to elucidate the transcriptomic response of Atlantic salmon to sea louse (Lepeophtheirus salmonis) and M. viscosa under single infection and different scenarios of co-infection (i.e., first, L. salmonis and then, M. viscosa and vice versa). After exposure, sampling was performed from the infestation site as well as the adjacent area on fish skin, followed by transcriptome analysis. RNA-seq analysis revealed that infection with either L.salmonis or M. viscosa induced a significant immune response from the skin and resulted in extensive transcriptomic changes. More differentially expressed genes (DEGs) were detected at M. viscosa lesion sites compared to L. salmonis attachment sites. In addition, the effect of the infection order was evaluated. Interestingly, we found that primary infection with lice was associated with a significantly higher number of DEGs during the co-infection process on fish skin compared to the fish first infected with M. viscosa (721 and 5336 DEGs from lice attachment and M. viscosa lesion sites, respectively, vs 291 and 3601 DEGs from lice attachment and M. viscosa lesion sites, respectively). We also found that lice infection caused localized effects on the skin of Atlantic salmon, while single infection with M. viscosa caused a moderate systemic impact and inhibited the tissue repair function of the skin, leading to severe ulceration. In addition, the C-type lectin receptor signaling pathway was drastically activated at the lice attachment sites during both lice alone- and co-infections, regardless of the order of infections, and similar results were observed in M. viscosa infection at both lesion and adjacent sites, indicating that this pathway played an essential role for immunity in Atlantic salmon. A more intense inflammatory and immune response was also observed at M. viscosa lesion sites. These results will promote our understanding of the immune interactions between L. salmonis and M. viscosa during the co-infection process and provide insights for the development of preventive and treatment strategies for these pathogens in salmonid aquaculture.

Identifying losers: Automatic identification of growth-stunted salmon in aquaculture using computer vision

During the production of salmonids in aquaculture, it is common to observe growth-stunted individuals. The cause for the so-called “loser fish syndrome” is unclear, which needs further investigation. Here, we present and compare computer vision systems for the automatic detection and classification of loser fish in Atlantic salmon images taken in sea cages. We evaluated two end-to-end approaches (combined detection and classification) based on YoloV5 and YoloV7, and a two-stage approach based on transfer learning for detection and an ensemble of classifiers (e.g., linear perception, Adaline, C-support vector, K-nearest neighbours, and multi-layer perceptron) for classification. To our knowledge, the use of an ensemble of classifiers, considering consolidated classifiers proposed in the literature, has not been applied to this problem before. Classification entailed the assigning of every fish to a healthy and a loser class. The results of the automatic classification were compared to the reliability of human classification. The best-performing computer vision approach was based on YoloV7, which reached a precision score of 86.30%, a recall score of 71.75%, and an F1 score of 78.35%. YoloV5 presented a precision of 79.7%, while the two-stage approach reached a precision of 66.05%. Human classification had a substantial agreement strength (Fleiss’ Kappa score of 0.68), highlighting that evaluation by a human is subjective. Our proposed automatic detection and classification system will enable farmers and researchers to follow the abundance of losers throughout the production period. We provide our dataset of annotated salmon images for further research.