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Stress is a major concern in aquaculture production and more knowledge is needed on physiological responses towards different operational events. Few studies have been performed on fish reared in an actual commercial setting. Transferring salmon from hatchery to sea involves handling, crowding, pumping, transport as well as adjusting to a new environment. This case study investigates the relative expression of selected stress related-genes in farmed Atlantic salmon (Salmo salar) post-smolts that were relocated from land-based breeding tanks with few environmental stressors to sea phase with numerous environmental stressors and major management operations e.g. net pen cleaning. Gill tissue for analysis (n = 60) was harvested at four distinct time points: before, during, and 3 and 6 weeks after sea transfer. RT-qPCR was performed on a panel of 12 genes involved in different cellular pathways (alox5, cyp1α, hif1α, il4/13a, muc2, muc5, muc18, nrf2, pcna, phb, p38 and tnfα). While the transport process itself did not appear to induce notable stress levels, metabolic gene markers showed significant changes in expression after transfer to sea, implying cellular adaptations to sea phase. The occurrence of net pen cleaning induced a strong upregulation of pro-inflammatory markers (alox5, tnfα) and mucins (muc2, muc5 and muc18), suggesting their gene products to be relevant during this operational event. As p38 expression was significantly elevated during transport and after cage cleaning, we cautiously propose p38 as an interesting stress marker for future exploration. The study provides insight into the lives of farmed Atlantic salmon and demonstrates that timing of major operations is crucial to avoid accumulation of stress.

Global change is fundamentally altering flows of natural and anthropogenic subsidies across space and time. After a pointed call for research on subsidies in the 1990s, an industry of empirical work has documented the ubiquitous role subsidies play in ecosystem structure, stability, and function. Here, we argue that physical constraints (e.g., water temperature) and species traits can govern a species’ accessibility to resource subsidies, which has been largely overlooked in the subsidy literature. We examined the input of a high-quality, point-source anthropogenic subsidy (aquaculture feed) into a recipient freshwater lake food web. Using a combined bio-tracer approach, we detect a gradient in accessibility of the anthropogenic subsidy within the surrounding food web driven by the thermal preferences of three constituent species, effectively rewiring the recipient lake food web. Because aquaculture is predicted to increase significantly in coming decades to support growing human populations, and global change is altering temperature regimes, then this form of food web alteration may be expected to occur frequently. We argue that subsidy accessibility is a key characteristic of recipient food web interactions that must be considered when trying to understand the impacts of subsidies on ecosystem stability and function under continued global change.

Bacterial diversity in the foregut, midgut and hindgut of large yellow croaker Larimichthys crocea and black sea bream Sparus macrocephalus reared in an inshore net pen, formulated feed and seawater were analyzed with Illumina MiSeq high-throughput sequencing platforms. A total of 270 operational taxonomic units (OTUs) were identified from fish guts, formulated feed and seawater, which belonged to 17 phyla and 20 genera. Firmicutes and Proteobacteria dominated at the phylum level, while Bacillus, Lactococcus and Oceanobacillus dominated at the genus level, in fish gut. The similarity in bacterial community between the guts of two fish species was higher than that either between fish gut and formulated feed or between fish gut and seawater. This result indicates that bacterial communities in guts of large yellow croaker and black sea bream were independent on those in the formulated feed and seawater. The common OTUs between fish gut and formulated feed were more than that between fish gut and seawater, suggesting that the impact of the formulated feed on intestinal bacteria of large yellow croaker and black sea bream was greater relative to that of seawater in the net pen. Spatial heterogeneity in bacterial composition along the gut of large yellow croaker and black sea bream was also evaluated.

Tiger puffer (Takifugu rubripes) is one of the most expensive farmed marine fish species in China. The high profitability of farmed tiger puffer is used to attract many new investors. However, some investments failed due to a lack of information about the tiger puffer fish farm business, poor farm and facility design, and flawed investment plans. To improve the investment efficiency and profitability of this industry, this analysis evaluated the economic performance of tiger puffer from eggs to harvest size using two different open-indoor combination aquaculture systems: a combination of recirculating aquaculture system and open net pen (RAS+ONP) and a combination of flow-through system and earth pond (FTS + EP). This analysis evaluated the financial performance of both systems using profit margin, net present value (NPV), internal rate of return (IRR), and payback period. At the same time, a sensitivity analysis was employed to measure economic risk. The results revealed that despite the RAS+ONP system being more economically profitable than the FTS + EP system, the financial indicators of the FTS + EP system granted a better economic performance in terms of NPV and IRR due to lower initial investment and operating costs. Meanwhile, the sensitivity analysis revealed that the economic performance of both systems was vulnerable to the fluctuations in fish prices and feed prices. The potential risk of earning profit was higher for the RAS+ONP if the feed price fluctuated compared to the FTS + EP system, while the risk was higher for the FTS + EP if the fish price fluctuated. Hence, the FTS + EP system could represent an opportunity for new entrants to obtain a more profitable production.

The use of stereo camera systems to measure fish body size has gained attention in aquaculture systems management. However, the different correlations between swimming depth and size according to fish species can lead to measurement bias depending on camera range and position. This study accordingly applied a fish behavior model based on the Boid model to simulate the relationship among camera position, viewing range, and measurement results considering swimming depth behavior. A total of 722 simulated fish (yellowtail Seriola quinqueradiata) were placed into a rectangular aquaculture net pen model. Virtual cameras were located at different depths along the side, above, and below the pen to measure the total length of individual fish within view. Horizontally oriented cameras closer to the surface captured significantly larger/smaller individuals when the behavior model assumed that larger individuals swim at shallower/deeper depths; vertically oriented cameras facing down from the water surface or up from the bottom net provided mean total length measurements might close to the actual mean total length of the population when a wide viewing range was provided. The proposed simulation method can be applied to preliminarily evaluate the measurement biases inherent to fish behavior and thereby minimize their influence on camera measurements.

As the global population grows, ensuring sustainable food production has become critical. Marine aquaculture provides a sustainable and scalable source of protein; however, its continued expansion requires the development of novel technologies that enable remote management and autonomous operations. Digital twin technology emerges as a transformative tool for realizing this goal, yet its adoption remains limited. Fish net cages—flexible, floating structures—are critical but vulnerable components of aquaculture systems. Exposed to harsh and dynamic marine conditions, they experience substantial hydrodynamic loads that can cause structural damage leading to fish escapes, environmental impacts, and financial losses. We propose a multifidelity surrogate modeling framework for integration into a digital twin that enables real-time monitoring of net cage structural dynamics under stochastic marine conditions. At the core of the framework lies the nonlinear autoregressive Gaussian process method, which captures complex, nonlinear cross-correlations between models of varying fidelity. It combines low-fidelity simulation data with a limited set of high-fidelity field sensor measurements, which, although accurate, are costly and spatially sparse. The framework was validated at the SINTEF ACE fish farm in Norway, where the digital twin assimilates online metocean data to accurately predict net cage displacements and mooring line loads, closely matching field measurements. This approach is especially valuable in data-scarce environments, offering rapid predictions and real-time structural representation. Beyond monitoring, the developed digital twin enables proactive assessment of structural integrity and supports remote operations with unmanned underwater vehicles. Finally, we compare Gaussian processes and graph convolutional networks for predicting net cage deformation, demonstrating the superior ability of the latter to capture in complex structural behaviors.

Piscine orthoreovirus genotype-1 (PRV-1) is a virus commonly associated with Atlantic salmon aquaculture with global variability in prevalence and association with disease. From August 2016 to November 2019, 2,070 fish sampled at 64 Atlantic salmon net-pen farm sites during 302 sampling events from British Columbia, Canada, were screened for PRV-1 using real-time qPCR. Nearly all populations became PRV-1 positive within one year of seawater entry irrespective of location, time of stocking, or producer. Cohorts became infected between 100–300 days at sea in > 90% of repeatedly sampled sites and remained infected until harvest (typically 500–700 days at sea). Heart inflammation, which is sometimes attributed to PRV-1, was also assessed in 779 production mortalities from 47 cohorts with known PRV status. Mild heart inflammation was common in mortalities from both PRV + and PRV- populations (67% and 68% prevalence, respectively). Moderate and severe lymphoplasmacytic heart inflammation was rare (11% and 3% prevalence, respectively); however, mainly arose (66 of 77 occurrences) in populations with PRV-1. Detection of PRV-1 RNA was also accomplished in water and sediment for which methods are described. These data cumulatively identify that PRV-1 ubiquitously infects farmed Atlantic salmon in British Columbia during seawater production but only in rare instances correlates with heart inflammation.

To investigate the response of fish intestines to different culture modes, we conducted a comparative trial on rockfish in the recirculating aquaculture system (RAS) and offshore aquaculture net pen system (OAS). After the 152-day trial, we compared the differences in growth performance, antioxidant capacity, intestinal morphology, and intestinal microbiota to evaluate the health status of rockfish cultured in these two modes. Results showed that rockfish cultured in the RAS exhibited a superior growth performance and antioxidant capacity compared to those cultured in OAS. Histological examination indicated pathological lesions in the intestine of rockfish cultured in the OAS, including a disordered arrangement of epithelial cells, rupture of chorionic villi, and decreased thickness of the muscle layer, which may further cause damage to intestinal barrier function. Sequencing analysis of 16S rDNA showed that Firmicutes, Bacteroidota, and Proteobacteria were the dominant phyla in the rockfish intestines. Microbial community diversity analysis indicated that there were significant differences in intestinal bacterial richness and diversity between the two groups; however, no differences were observed in the dominant bacteria. The relative abundance of metabolic pathways (such as energy, carbohydrate, and lipid metabolism) in the OAS group was significantly enhanced. Furthermore, the relative abundance of conditional pathogenic and potentially pathogenic bacteria increased, and that of beneficial and stress-tolerant bacteria decreased in the OAS group, indicating potential inflammation in the intestine. This study accumulated basic biological information for the study of fish welfare cultured in different modes and will contribute to the understanding of the physiological and health status of the rockfish.

Research on fisheries bycatch and discards frequently involves the assessment of reflex impairment,injury, or blood physiology as means of quantifying vitality and predicting post-release mortality, but exceptionally few studies have used all three metrics concurrently. We conducted an experimental purse seine fishery for Pacific salmon in the Juan de Fuca Strait, with a focus on understanding the relationships between different sublethal indicators and whether mortality could be predicted in coho salmon ( Oncorhynchus kisutch ) bycatch. We monitored mortality using a ~24-h net pen experiment ( N = 118) and acoustic telemetry ( N = 50), two approaches commonly used to assess bycatch mortality that have rarely been directly compared. Short-term mortality was 21% in the net pen experiment (~24 h) and estimated at 20% for telemetry-tagged fish (~48-96 h). Mortality was predicted by injury and reflex impairment, but only in the net pen experiment. Higher reflex impairment was mirrored by perturbations to plasma ions and lactate, supporting the notion that reflex impairment can be used as a proxy for departure from physiological homeostasis. Reflex impairment also significantly correlated with injury scores, while injury scores were significantly correlated with plasma ion concentrations. The higher time-specific mortality rate in the net pen and the fact that reflexes and injury corresponded with mortality in that experiment, but not in the telemetry-tagged fish released into the wild could be explained partly by confinement stress. While holding experiments offer the potential to provide insights into the underlying causes of mortality, chronic confinement stress can complicate the interpretation of patterns and ultimately affect mortality rates. Collectively, these results help refine our understanding of the different sublethal metrics used to assess bycatch and the mechanisms that can lead to mortality.

Determination of diversity and function of the bacteria in fish gut is essential to understanding the interaction between intestinal bacteria and their host organism. This study compared intestinal bacterial community of black seabass (Centropristis striata) hatched by the same breeding farm but reared in different aquaculture systems, an indoor recirculating aquaculture system (RAS) and an inshore net pen (INP). The fish were fed with formulated feed manufactured by same feed company. Bacteria in fish gut, formulated feed and seawater were identified by 16S rRNA high throughout sequencing (HTS). Total 1484 OTUs, which belonged to 34 phyla and 79 genera, were identified from fish gut, formulated feed and seawater. In fish gut, 24 phyla and 43 genera were identified. Proteobacteria, Fusobacteria, and Firmicutes dominated at the phylum level in fish gut in INP, while Proteobacteria and Firmicutes dominated in fish gut in RAS. Photobacterium, Vibrio, and Cetobacterium dominated at the genus level in fish gut in both INP and RAS. One OTU of Photobacterium occurred in all the fish gut samples, suggesting this bacterium might be the main component of the core microbiota. No significant difference was found in bacterial diversity in fish gut between INP and RAS, suggesting genetic background should be a primary factor determining intestinal bacterial community of black seabass. Bacterial diversity in seawater was high relative to that in fish gut and formulated feed, regardless in INP or RAS. The common OTU between fish gut and seawater was more than that between fish gut and formulated feed in INP, while the common OTU between fish gut and seawater was slightly less than that between fish gut and formulated feed in RAS. These results reveal that the bacteria in formulated feed and seawater could influence the bacteria in fish gut, and their priority in shaping intestinal bacterial community depended on the bacterial composition in feed and seawater. This study reveals that intestinal bacterial community of black seabass was influenced by both genetic background and environmental factors.