Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages

Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epidemiology was used to investigate salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. Our aim was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. Using nanopore sequencing, we captured ~90% of the SAV2 genome for n = 68 field isolates from 10 aquaculture production regions sampled between 2018 and 2020. Using time-calibrated phylogenetics, we infer that, following its introduction to Norway around 2010, SAV2 split into two clades (SAV2a and 2b) around 2013. While co-present at the same sites near the boundary of Møre og Romsdal and Trøndelag, SAV2a and 2b were generally detected in non-overlapping locations at more Southern and Northern latitudes, respectively. We provide evidence for recent SAV2 transmission over large distances, revealing a strong connection between Møre og Romsdal and SAV2 detected in 2019/20 in Rogaland. We also demonstrate separate introductions of SAV2a and 2b outside the SAV2 zone in Sognefjorden (Vestland), connected to samples from Møre og Romsdal and Trøndelag, respectively, and a likely 100 km Northward transmission of SAV2b within Trøndelag. Finally, we recovered genomes of SAV2a and SAV3 co-infecting single fish in Rogaland, involving novel SAV3 lineages that diverged from previously characterized strains >25 years ago. Overall, this study demonstrates useful applications of genomic epidemiology for tracking viral disease spread in aquaculture.

Tracking and Analysis of the Movement Behavior of European Seabass (Dicentrarchus labrax) in Aquaculture Systems

Monitoring and understanding fish behavior is crucial for achieving precision in everyday husbandry practices (i.e. for optimizing farm performance), and for improving fish welfare in aquaculture. Various intelligent monitoring and control methods, using mathematical models, acoustic methods and computer vision, have been recently developed for this reason. Here, a tracking algorithm based on computer vision that extracts short trajectories of individual European seabass in both recirculating aquaculture systems and sea cages was developed using videos from network cameras. Using this methodology, parameters such as instantaneous normalized speed, travel direction and preference for the tank surface by European seabass could be quantified. When testing the sensitivity of this algorithm for detecting fish swimming variations under different husbandry scenarios, we found that the algorithm could detect variations in all of the abovementioned parameters and could potentially be a useful tool for monitoring the behavioral state of European seabass.

Among-individual variation of risk-taking behaviour in group and solitary context is uncorrelated but independently repeatable in a juvenile Arctic charr (Salvelinus alpinus) aquaculture strain

Behavioural traits have been shown to have implications in fish welfare and growth performances in aquaculture. If several studies have demonstrated the existence of repeatable and heritable behavioural traits (i.e., animal personality), the methodology to assess personality in fishes is often carried out in solitary context, which appears to somewhat limit their use from a selective breeding perspective because these tests are too time consuming. To address this drawback, group-based tests have been developed. In Nordic country, Arctic charr (Salvelinus alpinus) is widely used in aquaculture, but no selection effort on behavioural traits has yet been carried out. Specifically, in this study we examined if risk-taking behaviour was repeatable and correlated in group and solitary context and if the early influences of physical environment affect the among-individual variation of behavioural trait across time in order to verify whether a group risk-taking test could be used as a selective breeding tool. Here, we found that in both contexts and treatments, the risk-taking behaviour was repeatable across a short period of 6 days. However, no cross-context consistency was found between group and solitary, which indicates that Arctic charr express different behavioural trait in group and solitary.

Fatigue Metabolites of Large Yellow Croaker and Construction of Swimming Model

A trend in large yellow croaker ( Larimichthys crocea ) aquaculture is to establish new production sites that are suitable for extreme weather conditions. However, continuous and strong currents can harm fish welfare. To determine the location of the net cage, it is necessary to assess the swimming ability of large yellow croaker. Currently, our research on large yellow croakers is focusing on behavior analysis. This article investigates the effect of swimming large yellow croakers on metabolites in the body by examining the preferred speed of the group and the endurance swimming ability of single-tailed fish. We evaluated the factors that influence the large yellow croaker's swimming fatigue by quantifying the content of metabolites and constructed the endurance swimming model using those results. Various results showed large yellow croaker populations tend to grow in low-velocity environments, and this matches their traditional habitat. The samples were taken at different swimming times at a flow rate of 0.35 m/s. According to the results of the metabolite content determination, blood glucose levels is closely related to swimming ability in large yellow croakers. The content of liver glycogen, which regulates blood glucose concentration, decreases in a certain linear relationship. The endurance swimming model of large yellow croaker was constructed according to the changes of liver glycogen content. The goals of this article are to provide a deeper understanding of the physiological characteristics of large yellow croaker swimming, and to provide a reference for choosing fishing and cage sites for large yellow croaker.

Boldness Predicts Aggressiveness, Metabolism, and Activity in Black Rockfish Sebastes schlegelii

Animal personality refers to individual behavioral and physiological differences that are consistent over time and across context. Recently, the fish personality has gained increasing attention, especially from the perspective of aquaculture production. Here, we used an important aquaculture species, black rockfish Sebastes schlegelii, as the target animal, and conducted a series of experiments to explore the relationships among fish boldness, aggressiveness, locomotor activity, opercular beat rate, standard metabolic rate, and cortisol level. Generally, the results showed that the boldness of black rockfish was significantly, positively correlated with fish aggressiveness, stressed locomotor activity, and standard metabolic rate, while was negatively correlated with stressed opercular beat rate. Bold fish had significantly higher aggressiveness, standard metabolic rate, and stressed locomotor activity but lower stressed opercular beat rate. However, there were no significant correlations between boldness and basal locomotor activity or between boldness and basal cortisol level. These results preliminarily constructed the behavioral and physiological spectrum of black rockfish in the context of fish personality and clearly indicated that the boldness could be used as a discrimination tool to predict fish aggressiveness and metabolic rate, which may have valuable applications for decreasing fish harmful aggression and increasing fish welfare in the aquaculture industry.

Minding the Gaps in Fish Welfare: The Untapped Potential of Fish Farm Workers

The welfare of farmed fish is often regarded with less concern than the welfare of other husbandry animals, as fish are not universally classified as sentient beings. In Norway, farmed fish and other husbandry animals are legally protected under the same laws. Additionally, the legislature has defined a number of aquaculture-specific amendments, including mandatory welfare courses for fish farmers who have a key role in securing animal welfare, also with regards to noting welfare challenges in the production process. This article uses fish welfare courses as a site from which to inquire about the common-sense understanding of fish welfare in Norwegian fish farming. The focus is specifically on fish farm employees, their experiences of welfare-related issues and contradictions in their daily work, and the struggle to act responsibly in aquaculture settings. Through participant observation at welfare courses, as well as interviews and conversations with fish farm workers, the article details how challenges are experienced ‘on the ground’, and suggests how fish farm workers’ own experiential knowledge might be mobilized to improve the general welfare of farmed fish.

Does Vaterite Otolith Deformation Affect Post-Release Survival and Predation Susceptibility of Hatchery-Reared Juvenile Atlantic Salmon?

Sagittal otoliths are calcareous structures in the inner ear of fishes involved in hearing and balance. They are usually composed of aragonite; however, aragonite can be replaced by vaterite, a deformity which is more common in hatchery-reared than in wild fish. Vaterite growth may impair hearing and balance and affect important fitness-related behaviours such as predator avoidance. Captive rearing techniques that prevent hearing loss may have the potential to improve fish welfare and the success of restocking programmes. The aim of this study was to test the effect of structural tank enrichment on vaterite development in the otoliths of hatchery-reared juvenile Atlantic salmon Salmo salar, and to assess the effects of vaterite on immediate predation mortality and long-term survival after release into the wild. Fry were reared in a structurally enriched or in a conventional rearing environment and given otolith marks using alizarin during the egg stage to distinguish between the treatment groups. Otoliths were scrutinised for the presence and coverage of vaterite at 6, 13, and 16 weeks after start feeding, and the growth traits were measured for enriched and control fry when housed in tanks. In a subsequent field experiment, juveniles were released in the Rasdalen river (western Norway), and otoliths of enriched reared and control reared fry were scrutinised from samples collected immediately prior to release, from predator (trout Salmo trutta) stomachs 48 h after release and from recaptures from the river 2–3 months after release. Vaterite otoliths occurred as early as 6 weeks after start feeding in hatchery-reared S. salar. Vaterite occurrence and coverage increased with fish length. Enriched rearing had no direct effect on vaterite formation, but enriched reared fry grew slower than control fry. After release into the wild, fewer salmon fry with vaterite otoliths had been eaten by predators, and a higher proportion of fry with vaterite otoliths than those lacking vaterite were recaptured in the river 2–3 months after release. Contrary to expectations, this suggests that vaterite does not increase predation mortality nor reduce survival rates in the wild during the early life stages.