Differential effects of internal tagging depending on depth treatment in Atlantic salmon: a cautionary tale for aquatic animal tag use

Movements and spatial distribution of an endangered fish (Sciaena umbra) within a marine protected area

The brown meagre (Sciaena umbra) is an endangered species, which requires specific protection measures to ensure its conservation. These measures need to be informed by high-quality scientific knowledge on their space use patterns. Here, we used acoustic telemetry to assess its seasonal movement patterns and habitat use within a marine protected area (MPA). Our results suggested that S. umbra is a highly sedentary species (home range < 1.0 km2) and, therefore, the MPA is extensive enough to protect the local population. Their population was discretely distributed in two main areas within the MPA, which was likely a result of habitat segregation and density-dependent movements. The temporal variability of their movements further uncovered when and where spawning occurs (mainly, but probably not only, in the fully protected area in June) and indicated that spillover of this species is limited but still possible. Overall, we highlight the importance of MPAs in the recovery of S. umbra, we advocate the need to perpetuate the current national fishing bans and extend it to other countries in the Mediterranean region, and we emphasize that considering the fine-scale movements of S. umbra in future management actions is key to achieving a successful recovery of their populations.

Warm water treatment increased mortality risk in salmon

•

Increased temperature gave higher mortality.

•

The fish group that was not handled had no mortality.

•

Eye damages were more prevalent in warm water treated groups.

•

The salmon had clear behavioural reactions to the 27 °C water despite low Δt.

•

The behavioural reactions were less at the second treatment compared to the first.

Thermal treatment is a controversial method to control sea lice in the Atlantic salmon farming industry. This study aimed to complement the growing evidence base to document the impact of thermal treatments on salmon welfare, behaviour, physiology and health. Here, fish were treated two times (four weeks apart) for 30 s in either 27, 30, or 33 °C warm water, and parameters were compared to a procedural control (exposed to their holding temperature of 14 °C) or a negative control (where no treatments were applied). The fish had a clear behavioural response to the warm water, despite low difference between treatment and holding temperature (Δt = 13, 16 or 19 °C). Eye damages were more prevalent in the warm water treated groups than in the controls. Little difference was recorded between treatment groups in their growth and condition factor, blood plasma values, organ health, and long-term coping ability. There was, however, a significant increase in mortality as a function of temperature after the first treatment (14 °C: 6.5%, 27 °C: 5.3%, 30 °C: 12.4% and 33 °C: 18.9% mortality). The first treatment was performed only two weeks after the fish had been tagged and moved into the experimental holding tanks, while the fish had been allowed to recover for four weeks without any handling before the second treatment. The group of fish that were not subjected to any treatments (the negative control) had no mortality throughout the entire experimental period.

Sentinels in Salmon Aquaculture: Heart Rates Across Seasons and During Crowding Events

Advances in tag technology now make it possible to monitor the behavior of small groups of individual fish as bioindicators of population wellbeing in commercial aquaculture settings. For example, tags may detect unusual patterns in fish heart rate, which could serve as an early indicator of whether fish health or welfare is becoming compromised. Here, we investigated the use of commercially available heart rate biologgers implanted into 24 Atlantic salmon weighing 3.6 ± 0.8 kg (mean ± SD) to monitor fish over 5 months in a standard 12 m × 12 m square sea cage containing ∼6,000 conspecifics. Post tagging, fish established a diurnal heart rate rhythm within 24 h, which stabilized after 4 days. Whilst the registered tagged fish mortality over the trial period was 0%, only 75% of tagged fish were recaptured at harvest, resulting in an unexplained tag loss rate of 25%. After 5 months, tagged fish were approximately 20% lighter and 8% shorter, but of the similar condition when compared to untagged fish. Distinct diurnal heart rate patterns were observed and changed with seasonal day length of natural illumination. Fish exhibited lower heart rates at night [winter 39 ± 0.2 beats per min (bpm), spring 37 ± 0.2 bpm, summer 43 ± 0.3 bpm, mean ± SE] than during the day (winter 50 ± 0.3 bpm, spring 48 ± 0.2 bpm, summer 49 ± 0.2 bpm) with the difference between night and day heart rates near half during the summer (6 bpm) compared to winter and spring (both 11 bpm). When fish experienced moderate and severe crowding events in early summer, the highest hourly heart rates reached 60 ± 2.5 bpm and 72 ± 2.4 bpm, respectively, on the day of crowding. Here, if the negative sublethal effects on fish that carry tags (e.g., growth rate) can be substantially reduced, the ability to monitor diurnal heart rate patterns across seasons and detect changes during crowding events, and using heart rate biologgers could be a useful warning mechanism for detecting sudden changes in fish behavior in sea cages.

Comparing Class-Aware and Pairwise Loss Functions for Deep Metric Learning in Wildlife Re-Identification

Similarity learning using deep convolutional neural networks has been applied extensively in solving computer vision problems. This attraction is supported by its success in one-shot and zero-shot classification applications. The advances in similarity learning are essential for smaller datasets or datasets in which few class labels exist per class such as wildlife re-identification. Improving the performance of similarity learning models comes with developing new sampling techniques and designing loss functions better suited to training similarity in neural networks. However, the impact of these advances is tested on larger datasets, with limited attention given to smaller imbalanced datasets such as those found in unique wildlife re-identification. To this end, we test the advances in loss functions for similarity learning on several animal re-identification tasks. We add two new public datasets, Nyala and Lions, to the challenge of animal re-identification. Our results are state of the art on all public datasets tested except Pandas. The achieved Top-1 Recall is 94.8% on the Zebra dataset, 72.3% on the Nyala dataset, 79.7% on the Chimps dataset and, on the Tiger dataset, it is 88.9%. For the Lion dataset, we set a new benchmark at 94.8%. We find that the best performing loss function across all datasets is generally the triplet loss; however, there is only a marginal improvement compared to the performance achieved by Proxy-NCA models. We demonstrate that no single neural network architecture combined with a loss function is best suited for all datasets, although VGG-11 may be the most robust first choice. Our results highlight the need for broader experimentation and exploration of loss functions and neural network architecture for the more challenging task, over classical benchmarks, of wildlife re-identification.

Atlantic Salmon (Salmo salar) Cage-Site Distribution, Behavior, and Physiology During a Newfoundland Heat Wave

Background: Climate change is leading to increased water temperatures and reduced oxygen levels at sea-cage sites, and this is a challenge that the Atlantic salmon aquaculture industry must adapt to it if it needs to grow sustainably. However, to do this, the industry must better understand how sea-cage conditions influence the physiology and behavior of the fish.

Method: We fitted ~2.5 kg Atlantic salmon on the south coast of Newfoundland with Star-Oddi milli-HRT ACT and Milli-TD data loggers (data storage tags, DSTs) in the summer of 2019 that allowed us to simultaneously record the fish's 3D acceleration (i.e., activity/behavior), electrocardiograms (and thus, heart rate and heart rate variability), depth, and temperature from early July to mid-October.

Results: Over the course of the summer/fall, surface water temperatures went from ~10–12 to 18–19.5°C, and then fell to 8°C. The data provide valuable information on how cage-site conditions affected the salmon and their determining factors. For example, although the fish typically selected a temperature of 14–18°C when available (i.e., this is their preferred temperature in culture), and thus were found deeper in the cage as surface water temperatures peaked, they continued to use the full range of depths available during the warmest part of the summer. The depth occupied by the fish and heart rate were greater during the day, but the latter effect was not temperature-related. Finally, while the fish generally swam at 0.4–1.0 body lengths per second (25–60 cm s⁻¹), their activity and the proportion of time spent using non-steady swimming (i.e., burst-and-coast swimming) increased when feeding was stopped at high temperatures.

Conclusion: Data storage tags that record multiple parameters are an effective tool to understand how cage-site conditions and management influence salmon (fish) behavior, physiology, and welfare in culture, and can even be used to provide fine-scale mapping of environmental conditions. The data collected here, and that in recent publications, strongly suggest that pathogen (biotic) challenges in combination with high temperatures, not high temperatures + moderate hypoxia (~70% air saturation) by themselves, are the biggest climate-related challenge facing the salmon aquaculture industry outside of Tasmania.

Swimming Activity of Gilthead Seabream (Sparus aurata) in Swim-Tunnels: Accelerations, Oxygen Consumption and Body Motion

Acoustic transmitters equipped with accelerometer sensors are considered a useful tool to study swimming activity, including energetics and movement patterns, of fish species in aquaculture and in nature. However, given the novelty of this technique, further laboratory-derived calibrations are needed to assess the characteristics and settings of accelerometer acoustic transmitters for different species and specific environmental conditions. In this study, we compared accelerometer acoustic transmitter outputs with swimming performance and body motion of gilthead seabream (Sparus aurata L.) in swim-tunnels at different flow speeds, which allowed us to characterize the swimming activity of this fish species of high aquaculture interest. Tag implantation in the abdominal cavity had no significant effects on swimming performance and body motion parameters. Accelerations, cost of transport and variations on head orientation (angle with respect to flow direction) were negatively related to flow speed in the tunnel, whereas oxygen consumption and frequencies of tail-beat and head movements increased with flow speed. These results show that accelerometer acoustic transmitters mainly recorded deviations from sustained swimming in the tunnel, due to spontaneous and explorative swimming at the lowest speeds or intermittent burst and coast actions to cope with water flow. In conclusion, accelerometer acoustic transmitters applied in this study provided a proxy for unsustained swimming activity, but did not contemplate the high-energy cost spent by gilthead seabream on sustained swimming, and therefore, it did not provide a proxy for general activity. Despite this limitation, accelerometer acoustic transmitters provide valuable insight in swim patterns and therefore may be a good strategy for advancing our understanding of fish swimming behavior in aquaculture, allowing for rapid detection of changes in species-specific behavioral patterns considered indicators of fish welfare status, and assisting in the refinement of best management practices.

Heart rates of Atlantic salmon Salmo salar during a critical swim speed test and subsequent recovery

In this study, heart rate (HR) bio-loggers were implanted in the abdominal cavity of 12 post-smolt Atlantic salmon Salmo salar weighing 1024 ± 31 g and acclimated to 12°C sea water. One week after the surgical procedure, a critical swim speed (U_crit ) test was performed on tagged and untagged conspecifics, whereafter tagged fish were maintained in their holding tanks for another week. The U_crit was statistically similar between tagged and untagged fish (2.67 ± 0.04 and 2.74 ± 0.05 body lengths s^-1 , respectively) showing that the bio-logger did not compromise the swimming performance. In the pre-swim week, a diurnal cycle was apparent with HR peaking at 65 beats min^-1 during the day and approaching 40 beats min^-1 at night. In the U_crit test, HR increased approximately exponentially with swimming speed until a plateau was reached at the final speed before fatigue with a maximum of 85.2 ± 0.7 beats min^-1 . During subsequent recovery tagged fish could be divided into a surviving group (N = 8) and a moribund group (N = 4). In surviving fish HR had fully recovered to pre-swim levels after 24 h, including reestablishment of a diurnal HR cycle. In moribund fish HR never recovered and remained elevated at c. 80 beats min^-1 for 4 days, whereafter they started dying. We did not identify a proximal cause of death in moribund fish, but possible explanations are discussed. Tail beat frequency (TBF) was also measured and showed a more consistent response to increased swimming speeds. As such, when exploring correlations between HR, TBF and metabolic rates at different swimming speeds, TBF provides better predictions. On the contrary, HR measurements in free swimming fish over extended periods of time are useful for other purposes such as assessing the accumulative burden of various stressors and recovery trajectories from exhaustive exercise.

How caged salmon respond to waves depends on time of day and currents

Disease, pest control, and environmental factors such as water quality and carrying capacity limit growth of salmon production in existing farm areas. One way to circumvent such problems is to move production into more exposed locations with greater water exchange. Farming in exposed locations is better for the environment, but may carry unforeseen costs for the fish in those farms. Currents may be too strong, and waves may be too large with a negative impact on growth and profit for farmers and on fish welfare. This study employed two major fish monitoring methods to determine the ability of Atlantic Salmon (Salmo salar) to cope with wavy conditions in exposed farms. Echosounders were used to determine vertical distribution and horizontal preference of fish during different wave and current conditions as well as times of day. Video cameras were used to monitor shoal cohesion, swimming effort, and fish prevalence in locations of interest. The results indicate complex interacting effects of wave parameters, currents, and time of day on fish behaviour and vertical distribution. During the day, hydrodynamic conditions had stronger effects on vertical distribution than during the night. In weak currents, fish generally moved further down in taller waves, but stronger currents generally caused fish to move upwards regardless of wave conditions. Long period waves had unpredictable effects on vertical distribution with fish sometimes seeking deeper water and other times moving up to shallower water. It is unclear how much the cage bottom restricted vertical distribution and whether movement upwards in the water columns was related to cage deformation. In extreme cases, waves can reach below the bottom of a salmon cage, preventing fish from moving below the waves and cage deformation could exacerbate this situation. Farmers ought to take into consideration the many interacting effects on salmon behaviour within a cage as well as the potential for cage deformation when they design their farms for highly exposed locations. This will ensure that salmon are able to cope when storms and strong currents hit at the same time.