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.

Photo Identification of Individual Salmo trutta Based on Deep Learning

Individual fish identification and recognition is an important step in the conservation and management of fisheries. One of most frequently used methods involves capturing and tagging fish. However, these processes have been reported to cause tissue damage, premature tag loss, and decreased swimming capacity. More recently, marine video recordings have been extensively used for monitoring fish populations. However, these require visual inspection to identify individual fish. In this work, we proposed an automatic method for the identification of individual brown trouts, Salmo trutta. We developed a deep convolutional architecture for this purpose. Specifically, given two fish images, multi-scale convolutional features were extracted to capture low-level features and high-level semantic components for embedding space representation. The extracted features were compared at each scale for capturing representation for individual fish identification. The method was evaluated on a dataset called NINA204 based on 204 videos of brown trout and on a dataset TROUT39 containing 39 brown trouts in 288 frames. The identification method distinguished individual fish with 94.6% precision and 74.3% recall on a NINA204 video sequence with significant appearance and shape variation. The identification method takes individual fish and is able to distinguish them with precision and recall percentages of 94.6% and 74.3% on NINA204 for a video sequence with significant appearance and shape variation.

Operculum PIT tagging: a viable alternative to avoid human consumption in processed salmon

Background Passive integrated transponder (PIT) tags are commonly used to identify individual fish. However, use of PIT tags in commercial aquaculture research is limited by consumer safety concerns. For farmed fish, it is critical that tags do not end up in the final product. One possibility to enable the use of PIT tags in commercial research is to insert tags into a part of the body that will be separated from the trunk during processing. We compare tag loss, mortality rate and welfare scores between Atlantic salmon post-smolts (n = 798) marked with PIT tags either in the operculum musculature or the abdominal cavity (standard practice) before and after mechanical delousing. Results We found that neither condition factor (K) (range 0.60–1.99) nor tagging location significantly affected tag loss (operculum = 6%, intraperitoneal = 8%, z = 1.46, p = 0.14) or mortality (operculum = 2%, intraperitoneal = 2%, z = 0.55, p = 0.58). However, on average, the fish which died weighed 20% less at the time of handling (271 ± 13 g, K = 1.12 ± 0.02) than those which survived (340 ± 3 g, K = 1.14 ± 0.004), and those which lost tags (291 ± 7 g, K = 1.11 ± 0.02) weighed 15% less than those which retained them (340 ± 3 g, K = 1.14 ± 0.004), irrespective of tagging location or handling treatment. Conclusions Fish tagged in the operculum musculature had comparable rates of mortality and tag loss to the current “best practice” standard of intraperitoneal tagging. We show that placement of PIT tags in operculum musculature is a viable alternative to placement in the peritoneal cavity.

The effects of water temperature, acoustic tag type, size at tagging, and surgeon experience on juvenile Chinook salmon (Oncorhynchus tshawytscha) tag retention and growth

Background Acoustic telemetry is a widely used tool to study the movement and survival of juvenile fish and often requires a surgical procedure to implant the transmitter, which may impact overall fitness and survival following release. This is an important consideration when implementing large-scale acoustic telemetry projects aimed at estimating outmigration survival. The objective of this study was to examine the effects of water temperature, tag type, size at tagging, and surgeon experience on tag retention and growth rate of juvenile Chinook salmon (Oncorhynchus tshawytscha). We tagged 128 spring-run Chinook salmon (81–97 mm fork length, 5.2–10.0 g, tag burden 2.4–6.0%) with one of two types of acoustic transmitters; a shorter, heavier model (‘standard’) and a longer, lighter model (‘injectable’). Fish were tagged by either a novice or experienced surgeon. An additional 64 untagged fish served as a control group and were split between temperature treatments. Fish were reared in either cool (mean 13.4 °C) or warm (mean 17.8 °C) water for 60 days, prior to being euthanized, weighed and measured. Results Tag retention was similar for both transmitter types, but varied with water temperature, with significantly higher tag loss in the warm treatment (21.9%, 14 tags expelled), compared to the cold treatment (7.8%, 5 tags expelled). In the warm treatment, fish growth in the injectable tag group was significantly lower compared to the control group, and lower than the standard tag group, but not significantly lower. There was no significant difference between the control and standard tag groups for the warm treatment. In the cool temperature treatment, fish growth was not significantly different among any of the factors tested. Surgery time differed between surgeons; however, surgeon experience did not significantly affect tag shedding or growth. Conclusion Total tag loss was 14.8% over the 60-day trial, with higher and earlier loss in the warmer treatment. Tag length may be a more important factor than tag weight in smaller size fish. This suggests that tag shedding is a significant factor to consider when estimating survival, as the actual survival rate may be higher than estimates based solely on receiver detections.

Suffix-based double reader tag movement RFID anti-collision method

At present, some existing tag anti-collision algorithms are used mostly in scenarios of fixed number of tags and they perform poorly in tag moving scenarios. Therefore, this paper proposes a double reader tag movement RFID anti-collision method based on suffix, and through the cloud platform based on cloud computing, the supply chain data sharing is realized. Tag moving scenarios usually use a single reader. The proposed employs double reader to expand the recognition range and also to prolong the recognition time, but there is the problem of repeated recognition. This article proposes a suffix-based bit-slot ALOHA (SBSA) algorithm, where this problem is solved and the time-slot is reduced. In view of the problem that a large number of tags entering into the recognition area of readers lead to the reduction of the recognition efficiency. This article proposes a suffix-based tag group bit-slot ALOHA (STGBSA) algorithm, tag grouping and tag estimation methods are proposed. Complexity analysis is deployed in this article, from the perspective of the tag loss ratio and identification efficiency, the performances of various anti-collision algorithms are evaluated and compared with those of the existing methods. The simulation results show that the method proposed in this paper is better than the existing methods.

Under pressure: Comparing in situ and boat tagging methods using time-to-event analyses

Background With the increase in telemetry studies over the past decade, improving understanding of how different tagging methods influence fish survivorship is critical. By examining the effects of tagging methods, we can maximize the information gained from telemetry studies. Mortality resulting from internally tagging fish on a boat may be due to barotrauma injuries, increased stress from prolonged handling times, or predation after fish have been released back into the water. Conducting in situ internal acoustic tagging at depth of capture completely removes barotrauma stresses and simplifies the release method, which may improve fish survival. In this study, we used 8 years of acoustic tagging data to determine if the tagging method ( in situ versus on the boat) influenced fish survivorship and evaluated the role of other tagging variables. Results At 6 days after tagging, Kaplan–Meier survival curves revealed that the survival probability of fish tagged on the boat was 66% while survival probability of fish tagged in situ was 90%. Tagging method was the only variable to significantly affect survival probability based on Cox proportional hazards models, with fish tagged in situ ~75% less likely to have an “event” (mortality, tag loss, or emigration) compared to fish tagged on the boat at both 4 and 6 days after tagging. Examining tagging methods separately, handling time only marginally influenced survival probability of boat-tagged fish and no variables had a significant effect on survival of in situ tagged fish. Conclusions In this study, tagging method was the only variable to significantly affect survival of internally tagged fish. Implanting internal acoustic tags in situ is not a practical method for every species and for every environment, but given the increased fish survivorship demonstrated here, we strongly suggest it be considered as the preferred tagging methodology where applicable.

Acute bottlenecks to the survival of juvenile Pygoscelis penguins occur immediately after fledging

Estimating when and where survival bottlenecks occur in free-ranging marine predators is critical for effective demographic monitoring and spatial planning. This is particularly relevant to juvenile stages of long-lived species for which direct observations of death are typically not possible. We used satellite telemetry data from fledgling Adélie, chinstrap and gentoo penguins near the Antarctic Peninsula to estimate the spatio-temporal scale of a bottleneck after fledging. Fledglings were tracked up to 106 days over distances of up to 2140 km. Cumulative losses of tags increased to 73% within 16 days of deployment, followed by an order-of-magnitude reduction in loss rates thereafter. The timing and location of tag losses were consistent with at-sea observations of penguin carcasses and bioenergetics simulations of mass loss to thresholds associated with low recruitment probability. A bootstrapping procedure is used to assess tag loss owing to death versus other factors. Results suggest insensitivity in the timing of the bottleneck and quantify plausible ranges of mortality rates within the bottleneck. The weight of evidence indicates that a survival bottleneck for fledgling penguins is acute, attributable to predation and starvation, and may account for at least 33% of juvenile mortality.

Escapement of Broodstock Chinook Salmon From Whitlock Bay Spawning Station, Lake Oahe, South Dakota

Feral spawning fall Chinook salmon (Oncorhynchus tshawytscha) in Lake Oahe, South Dakota, are captured using a fish ladder and catch raceway at Whitlock Bay Spawning Station. The number of salmon that escaped the catch raceway and descended the fish ladder prior to spawning was unknown. During October 2017, all salmon that ascended the fish ladder at the spawning station were tagged. Tagged males remained in the catch raceway. Tagged females were moved to other secure raceways and used to estimate tag retention. Of the 383 tagged males, 159 (41.5%) were initially designated as escaped from the catch raceway. Tag loss in the females was 3.9%. Thus, the estimated male salmon escapement rate from the catch raceway was 37.6%. Male salmon remained in the catch raceway for one-to-three days before escaping. The escapement rate decreased over the month-long spawn, with nearly 60% of the males going back down the fish ladder in the first week of October, compared to less than 20% escapement by the final week. Such high rates of escapement from the spawning station may be negatively impacting the spawning efficiencies. Possible solutions include re-engineering of the fish ladder or daily removal of the salmon in the catch raceway to other more secure locations at the spawning station.