Individual Fish Research Articles

Metabolomic-Based Comparison of Daphnia magna and Japanese Medaka Responses After Exposure to Acetaminophen, Diclofenac, and Ibuprofen.

Pharmaceuticals are found in aquatic environments due to their widespread use and environmental persistence. To date, a range of impairments to aquatic organisms has been reported with exposure to pharmaceuticals; however, further comparisons of their impacts across different species on the molecular level are needed. In the present study, the crustacean Daphnia magna and the freshwater fish Japanese medaka, common model organisms in aquatic toxicity, were exposed for 48 h to the common analgesics acetaminophen (ACT), diclofenac (DCF), and ibuprofen (IBU) at sublethal concentrations. A targeted metabolomic-based approach, using liquid chromatography-tandem mass spectrometry to quantify polar metabolites from individual daphnids and fish was used. Multivariate analyses and metabolite changes identified differences in the metabolite profile for D. magna and medaka, with more metabolic perturbations for D. magna. Pathway analyses uncovered disruptions to pathways associated with protein synthesis and amino acid metabolism with D. magna exposure to all three analgesics. In contrast, medaka exposure resulted in disrupted pathways with DCF only and not ACT and IBU. Overall, the observed perturbations in the biochemistry of both organisms were different and consistent with assessments using other endpoints reporting that D. magna is more sensitive to pollutants than medaka in short-term studies. Our findings demonstrate that molecular-level responses to analgesic exposure can reflect observations of other endpoints, such as immobilization and mortality. Thus, environmental metabolomics can be a valuable tool for selecting sentinel species for the biomonitoring of freshwater ecosystems while also uncovering mechanistic information. Environ Toxicol Chem 2024;43:1339-1351. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.

Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.

Relatedness of hypoxia and hyperthermia tolerances in the Nile tilapia (Oreochromis niloticus) and their relationships with cardiac and gill traits

In fish, thermal and hypoxia tolerances may be functionally related, as suggested by the oxygen- and capacity-limited thermal tolerance (OCLTT) concept, which explains performance failure at high temperatures due to limitations in oxygen delivery. In this study the interrelatedness of hyperthermia and hypoxia tolerances in the Nile tilapia (Oreochromis niloticus), and their links to cardiorespiratory traits were examined. Different groups of O. niloticus (n = 51) were subjected to hypoxia and hyperthermia challenges and the O2 tension for aquatic surface respiration (ASR pO2) and critical thermal maximum (CTmax) were assessed as measurement endpoints. Gill filament length, total filament number, ventricle mass, length and width were also measured. Tolerance to hypoxia, as evidenced by ASR pO2 thresholds of the individual fish, was highly variable and varied between 0.26 and 3.39 kPa. ASR events increased more profoundly as O2 tensions decreased below 2 kPa. The CTmax values recorded for the O. niloticus individuals ranged from 43.1 to 44.8 °C (Mean: 44.2 ± 0.4 °C). Remarkably, there was a highly significant correlation between ASR pO2 and CTmax in O. niloticus (r = −0.76, p < 0.0001) with ASR pO2 increasing linearly with decreasing CTmax. There were, however, no discernible relationships between the measured cardiorespiratory properties and hypoxia or hyperthermia tolerances. The strong relationship between hypoxia and hyperthermia tolerances in this study may be related to the ability of the cardiorespiratory system to provide oxygen to respiring tissues under thermal stress, and thus provides some support for the OCLTT concept in this species, at least at the level of the entire organism.

Network connectivity contributes to native small‐bodied fish assemblages in the upper Mississippi River system

Abstract Effective management and conservation of fishes requires understanding habitat use across multiple life stages while ensuring necessary habitats are both available and accessible. Tributary habitats may play an important role in recruitment and dispersal of fishes in anthropogenically modified rivers such as the Mississippi and Illinois Rivers of the Midwest U.S.A. Identifying source locations that contribute to recruitment of fish populations can determine the importance of connectivity within river networks and pinpoint critical habitats that sustain fish populations. In the Upper Mississippi River System (UMRS), the environments that fish use in early life stages (i.e., natal origin) can be identified using otolith trace element analysis due to stability and distinctness in water chemistry (strontium: calcium [Sr:Ca]) among water bodies that is reflected in otoliths. Here, we used trace element analysis to determine natal origin of six small‐bodied fishes including bullhead minnow (Pimephales vigilax), emerald shiner (Notropis atherinoides), gizzard shad (Dorosoma cepedianum), bluegill (Lepomis macrochirus), orangespotted sunfish (Lepomis humilis), and yellow perch (Perca flavescens) across six reaches of the UMRS (Pools 4, 8, 13, 26, the Open River of the Middle Mississippi River, and the La Grange Pool of the Illinois River). Otolith core Sr:Ca for fishes was quantified using laser ablation inductively coupled plasma mass spectrometry. Using the resulting Sr:Ca chemical signatures of otolith cores, natal origin (tributary, immigrant, or potential resident) was determined for individual fish based on family‐specific relationships between otolith and water chemistries. We found that all species originated from tributaries and other reaches (i.e., were immigrants) to varying extents, which acted as evidence for network connectivity. Specifically, tributaries contributed up to 48% of individuals at a given reach. In certain reaches, Pool 26 and the Open River reach, up to 80% of individuals in a species immigrated from another mainstem river reach. Network connectivity was also important in both upstream and downstream directions. Contributions from network connectivity varied among species: bullhead minnow used less whereas orangespotted sunfish used more network connectivity than when all species were combined. Further, the use of network connectivity varied spatially where individuals captured in Pool 8 and the La Grange Pool less often and those from Pool 26 and the Open River more often originated from network connectivity compared to the whole assemblage across reaches. These results indicate that species' life history traits probably interacted with the physical environment, which differs spatially, to yield observed recruitment source patterns. Our results show that network connectivity contributes to established assemblages of native small‐bodied fishes throughout the UMRS and underscore the role of interjurisdictional management in maintaining network connectivity to sustain fish populations.

Collective behavior from surprise minimization

Collective motion is ubiquitous in nature; groups of animals, such as fish, birds, and ungulates appear to move as a whole, exhibiting a rich behavioral repertoire that ranges from directed movement to milling to disordered swarming. Typically, such macroscopic patterns arise from decentralized, local interactions among constituent components (e.g., individual fish in a school). Preeminent models of this process describe individuals as self-propelled particles, subject to self-generated motion and "social forces" such as short-range repulsion and long-range attraction or alignment. However, organisms are not particles; they are probabilistic decision-makers. Here, we introduce an approach to modeling collective behavior based on active inference. This cognitive framework casts behavior as the consequence of a single imperative: to minimize surprise. We demonstrate that many empirically observed collective phenomena, including cohesion, milling, and directed motion, emerge naturally when considering behavior as driven by active Bayesian inference-without explicitly building behavioral rules or goals into individual agents. Furthermore, we show that active inference can recover and generalize the classical notion of social forces as agents attempt to suppress prediction errors that conflict with their expectations. By exploring the parameter space of the belief-based model, we reveal nontrivial relationships between the individual beliefs and group properties like polarization and the tendency to visit different collective states. We also explore how individual beliefs about uncertainty determine collective decision-making accuracy. Finally, we show how agents can update their generative model over time, resulting in groups that are collectively more sensitive to external fluctuations and encode information more robustly.

Fuzzy Logic Empowered NetWatch: Revolutionizing Aquaculture with IoT-based Intelligent Monitoring and Management in Bangladesh

The innovative study "Fuzzy Logic Empowered NetWatch: Revolutionizing Aquaculture with IoT-based Intelligent Monitoring and Management in Bangladesh" is a step towards the dawn of a new era in fish farming techniques that emphasize accuracy and efficiency. Using fuzzy logic controllers in the NetWatch system, stakeholders involved in aquaculture can access a degree of intelligence and adaptability that is not possible with standard management techniques. Fuzzy logic techniques are included in NetWatch, allowing it to make intelligent judgments based on the intricate and frequently unpredictable nature of aquaculture systems, in addition to monitoring and controlling environmental parameters and water quality. Because of its dynamic adaptability, the system can mitigate risks and optimize results in real time while successfully responding to changing situations. Furthermore, NetWatch offers a comprehensive picture of the aquaculture ecosystem by combining pond-specific data with more general environmental insights, facilitating better-informed macro and micro decision-making. With this thorough knowledge, fish farmers can allocate resources more efficiently, reduce waste, and sustainably increase productivity. Moreover, Fuzzy Logic Empowered NetWatch's revolutionary potential offers opportunities for the aquaculture industry, transcending the boundaries of individual fish ponds. Bangladesh can establish itself as a global leader in sustainable aquaculture methods and set new benchmarks for production, efficiency, and environmental stewardship using IoT-based intelligent monitoring and management. Fuzzy Logic Empowered NetWatch catalyzes a systemic shift in how we approach aquaculture management rather than merely technology. Bangladesh may achieve previously unattainable levels of sustainability and productivity by utilizing fuzzy logic and the Internet of Things. This would guarantee a better future for the country's aquaculture sector and the communities it serves.

Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus.

A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure. These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect. Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.

Risk Assessment and Sources Apportionment of Toxic Metals in Two Commonly Consumed Fishes from a Subtropical Estuarine Wetland System.

The widespread occurrence of heavy metals in aquatic environments, resulting in their bioaccumulation within aquatic organisms like fish, presents potential hazards to human health. This study investigates the concentrations of five toxic heavy metals (Pb, Hg, Zn, Cu, and Cr) and their potential health implications in two economically important fish species (Otolithoides pama and Labeo bata) from a subtropical estuarine wetland system (Feni estuary, Bangladesh). Muscle and gill samples from 36 individual fish were analyzed using energy dispersive X-ray fluorescence (EDXRF). The results revealed that the average quantities of heavy metals in both fishes' muscle followed the declining order of Zn (109.41-119.93 mg/kg) > Cu (45.52-65.43 mg/kg) > Hg (1.25-1.39 mg/kg) > Pb (0.68-1.12 mg/kg) > Cr (0.31-5.82 mg/kg). Furthermore, Zn was found to be present in the highest concentration within the gills of both species. While the levels of Cu, Zn, and Cr in the fish muscle were deemed acceptable for human consumption, the concentrations of Pb and Hg exceeded the permissible limits (>0.5 mg/kg) for human consumption. Different risk indices, including estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and carcinogenic or target risk (TR), revealed mixed and varying degrees of potential threat to human health. According to the EDI values, individuals consuming these fish may face health risks as the levels of Zn, Cu, and Cr in the muscle are either very close to or exceed the maximum tolerable daily intake (MTDI) threshold. Nevertheless, the THQ and HI values suggested that both species remained suitable for human consumption, as indicated by THQ (<1) and HI (<1) values. Carcinogenic risk values for Pb, Cr, and Zn all remained within permissible limits, with TR values falling below the range of (10-6 to 10-4), except for Zn, which exceeded it (>10-4). The correlation matrix and multivariate principal component analysis (PCA) findings revealed that Pb and Cr primarily stemmed from natural geological backgrounds, whereas Zn, Cu, and Hg were attributed to human-induced sources such as agricultural chemicals, silver nanoparticles, antimicrobial substances, and metallic plating. Given the significance of fish as a crucial and nutritious element of a balanced diet, it is essential to maintain consistent monitoring and regulation of the levels and origins of heavy metals found within it.

Artificial structure selection by economically important reef fishes at North Carolina artificial reefs

Artificial reefs can play an important role in marine fisheries management by supplementing or enhancing natural habitats. Despite their increased use in recent years, the choice of structures used at artificial reefs remains largely haphazard due to the lack of information on reef structure performance. Few studies have examined the use of different artificial reef structures by individual fish. From 2021-2022, we acoustically tagged 72 black sea bass (Centropristis striata), 34 gag (Mycteroperca mircrolepis), 27 greater amberjack (Seriola dumerili), nine almaco jack (S. rivoliana), and eight red snapper (Lutjanus campechanus) on four artificial reef complexes near Cape Lookout, North Carolina, U.S. Available artificial reef structures consisted of materials of various sizes and heights made of concrete and metal. We tracked tagged fish using a fine-scale positioning system for ~100 days. Black sea bass exhibited high site fidelity to the artificial structure where we caught them, rarely moving away from that structure. The limited movement resulted in low transition probabilities; we conclude that black sea bass do not select for particular artificial structures. Gag and red snapper moved greater distances away from artificial structures and routinely moved between them. Greater amberjack and almaco jack moved the most within the complexes displaying circling behavior around individual structures and were the only species that regularly moved off the artificial reef complexes. Greater amberjack movements away from artificial sites were most commonly directed to surrounding shipwrecks. Whereas gag, red snapper, almaco jack, and greater amberjack used all available structures, they consistently selected for high relief structures, such as vessels, more than other structures. These results will be useful to managers charged with decisions on what types of structures to place at artificial reef complexes to supplement or enhance habitat for economically important fishes.

Seasonal and spatial variations between the fish community and environmental factors in a subtropical estuary

Galveston Bay is a subtropical estuary on the upper Texas coast along the northwestern region of the Gulf of Mexico (USA). This study presents results of a meta-analysis on fisheries independent abundance and environmental data collected from 1993 to 2016 (3469 sampling events). In total, 404,160 individual fish were collected using bag seines comprising 122 species from 91 genera, 53 families and 22 orders. Diversity measures reveal the number of individuals, species richness and the Shannon diversity index exhibit a seasonal cycle (decrease in winter, increase in summer). Fish populations also exhibited spatial variability which was largely attributed to the varying stages of their life cycles. Community metrics varied temporally and were not adversely influenced by periods of drought, flood, or other extreme events. Galveston Bay appears to be providing a sound ecological environment, and not yet exhibiting climate change influences on the fishery, as has been reported for other estuaries.

Comparative Study of Growth Performance of Three Tilapia Strain in Intensive Culture System

High stocking density is an important factor in cultivation to increase the eficency if fish farming for nutrition requirements. High stocking density generally impact on fish physiology and growth performance. However, many studies on individual fish have different growth perfromance from different strain. Some technology had been developed to optimize tilapia production in high stocking density. This study aimed to determine the growth performance of three different strain of tilapia (red tilapia, nirwana tilapia, and jatimbulan tilapia) reared in 20 m3 of round tarpaulin with additional of microbubble generator. This study used an intensive system with 100 fish/m3 of stocking density. The results showed that the microbubble generator was able to increase the carrying capacity of water quality such as increasing dissolved oxygen in the waters, temperature and pH. The high content of dissolved oxygen in the water significantly increasing the growth of tilapia. The highest weight was found in red tilapia with a final weight of 199.56 ± 0.05 gr, followed by Nirwana tilapia with 176.59 ± 0.10 gr, and Jatimbulan tilapia with 153.91 ± 0.06 gr. In addition, the high content of dissolved oxygen in the waters also affect the rearing period of tilapia.

Determining differences in the timing of fish feed intake using a novel dual ballotini X-radiography method

Fish feeding behaviour can be complicated and time consuming to observe, analyse and quantify. The conventional single ballotini X-radiography method was modified to determine the timing of feeding within a meal in farmed fish reared at commercial densities. Feed pellets containing two bead sizes were fed at different times during a single meal, either for the first half or second half of the meal. The two different ballotini sizes were differentiated on X-radiographs by human eye and semi-automated bead counting software was able to count the different bead sizes accurately. This dual ballotini method was used to assess whether fish ate earlier, later or during both halves of the meal and showed that individual fish feeding patterns were similar across two repeated meals. The method was applied to Chinook salmon (Oncorhynchus tshawytscha), a premium farmed salmonid, to determine the relationship between feed conversion ratio (FCR) and the timing of feeding. Results showed that fish that ate smaller amounts of feed ate most of their meal at the end of the meal. There was no significant difference in when feed efficient or feed inefficient fish ate within the meal but, at the first dual ballotini assessment, there was a relationship between FCR and the timing of feeding where more efficient fish ate later in the meal. However, this relationship was absent at the second time point. Despite this, the dual ballotini method is a promising and versatile alternative method for the characterisation of fish feeding behaviours and can be applied under a range of conditions including higher rearing densities.

Quantitative fishery assessment in tropical waters: Stock dynamics and strategy options

This paper explores the possible options for quantitative fishery stock assessment in tropicalwaters and is composed of four layers viz., concepts, methodologies, data and indicators.The concept promotes the fundamental theory that has been popular in research on stockdynamics, including the possibility of combining it with various doses of intrinsicallybiological information, from individual fish to regional stocks. After reviewing the concepts,tools and their evolution, an attempt has also been made to propose a few guidelines as thebest ways to approach stock assessment and formulate input control or output regulationstrategies in the most pragmatic yet scientific manner, thereby ensuring minimal impact onthe fishery, fishers and stocks in the medium term. Keywords:Bayesian approach, Capture fisheries, Fish stockassessment, Models

Development and validation of a flow cytometry method to examine circulating leukocyte subpopulations in barramundi (Lates calcarifer)

Bacterial infections are a major contributor to losses in aquaculture production. Diagnosis of these bacterial diseases is based on sacrificing fish and isolating the infectious agent from the internal organs. Infections lead to an inflammatory response in the host that is characterized by changes in leukocyte profile and activity. We hypothesized that the profile of circulating peripheral blood leukocytes and markers of their activity, such as reactive oxygen species production, would change following an event of bacterial infection in fish. We therefore developed a flow cytometry-based methodology for analyzing blood leukocytes in barramundi (Lates calcarifer), then used it to compare healthy fish to those infected with a common pathogenic bacterium, Vibrio harveyi. The initial step of the analysis relied on the effective separation of erythrocytes and leukocytes, and two methods were tested: one based on hypotonic lysis of red blood cells, and the other involving stain-based differentiation using carboxyfluorescein succinimidyl ester (CFSE). Fluorescence-activated cell sorting analysis revealed significant differences in leukocyte parameters of infected and control fish using the stain-based approach vs. hypotonic lysis. Changes in blood leukocytes included an increase in the proportion of monocytes and decrease in that of lymphocytes in infected fish. Furthermore, cell size and granularity of the different leukocyte populations changed over time in infected fish as compared to controls. Monitoring peripheral blood leukocytes provides a non-lethal analysis of inflammation that allows repeated sampling of individual fish over time. This is beneficial given the high variability between individual fish. The use of CFSE-staining for leukocyte isolation proved to be advantageous over a method based on lysis of erythrocytes.

Aflatoxin B1 decreased flesh flavor and inhibited muscle development in grass carp (Ctenopharyngodon idella)

In nature, aflatoxins, especially aflatoxin B1 (AFB1), are the common mycotoxins, which cause serious health problems for humans and animals. This paper aimed to study the effects of AFB1 on flesh flavor and muscle development of grass carp (Ctenopharyngodon idella) and its mechanism. There were 1440 individual fish in total, with 6 treatments and each treatment replicated 3 times. The 6 treatments were fed a control diet with different doses of AFB1 (0.04, 29.48, 58.66, 85.94, 110.43 and 146.92 μg/kg diet) for 60 d. AFB1 increased myofiber diameter, as well as decreased myofiber density of grass carp muscle (P < 0.05). The contents of free amino acid decreased gradually (P < 0.05) as dietary AFB1 increased in the muscle of grass carp. The levels of reactive oxygen species, malonaldehyde and protein carbonyl (PC) were increased (P < 0.05) with the dietary AFB1 increased. The levels of antioxidant enzyme (glutathione peroxidase, glutathione, glutathione reductase, total antioxidant capacity, anti-superoxide anion, and anti-hydroxyl radical) were decreased (P < 0.05) with the dietary AFB1 increased. In addition, dietary AFB1 decreased the content of collagen, and downregulated the mRNA and protein levels of transforming growth factor-β (TGF-β)/Smads signaling pathway in grass carp muscle (P < 0.05). The mRNA and protein levels of myogenic regulatory factors were downregulated in grass carp muscle (P < 0.05). Furthermore, the activities of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) were increased (P < 0.05), and the protein levels of phosphorylate-38 mitogen-activated protein kinase (p-p38MAPK), phosphorylate-c-Jun N-terminal kinase, urokinase-type plasminogen activator (uPA), MMP-2 and MMP-9 were upregulated (P < 0.05), but collagen Ⅰ, laminin β1 and fibronectin were downregulated (P < 0.05) with the dietary AFB1 increased in the muscle of grass carp. Based on the results of this study, we can draw the following conclusion: dietary AFB1 might damage flesh flavor and inhibit the muscle development through MAPK/uPA/MMP/extracellular matrix (ECM) signaling pathway in grass carp. Moreover, the recommended safe limit of AFB1 in feed is no more than 26.77 μg/kg diet according to the PC levels in grass carp muscle.

Fish assemblage structure and habitat relationships of a large floodplain river in western North America

AbstractUnderstanding complex river floodplains is critical to conserve species of fish and their ecological functions. In 2011 through 2013, longitudinal gradients in fish assemblage were investigated in the Willamette River in western United States. Of 36,586 individual fish collected, 93% were native and 7% non‐native. The best predictors of fishes collected with a boat electrofisher were percent embeddedness, macrophytes, longitudinal river distance, average depth, and velocity. Habitat type (mainstem or slough) was also a significant predictor. The best predictor of fishes collected in nearshore habitats with a backpack electrofisher were longitudinal river distance, velocity, and percent embeddedness. Fish communities differed significantly between mainstem and slough habitat. Overall, 25 of 40 species had high fidelities to mainstem or slough habitats. Native species showed a high fidelity to both mainstem and slough habitats while non‐native species were significantly related only to slough habitats. Environmental characteristics strongly influenced fish assemblage structure in this large floodplain river. Maintaining and restoring mainstem and off‐channel habitats are critical for maximizing native species resilience in the face of non‐native species encroachment and a changing environment. Restoring the natural flow regime to the degree possible is needed to increase connectivity between the floodplain and mainstem and provide thermal and flood refuges for native fishes. Understanding habitat relationships provides essential context for fish conservation and management by resource agencies and landowners.

Into the wild: coupling otolith and archival tag records to test assumptions underpinning otolith chemistry applications in wild fish

Chronological records of elemental concentrations in fish otoliths are a widely used tool to infer the environmental conditions experienced by individual fish. To interpret elemental signals within the otolith, it is important to understand how both external and internal factors impact ion uptake, transport and incorporation. In this study, we have combined chronological records from otoliths and archival data storage tags to quantify the influence of internal (sex, size, age, growth) and external (temperature, depth, salinity) conditions on otolith elemental chemistry of cod (Gadus morhua) in natural settings of the Baltic Sea. This study focused on elements primarily under physiological control: Phosphorus (P), magnesium (Mg) and zinc (Zn); and elements under environmental control: Strontium (Sr), barium (Ba) and manganese (Mn). Based on known spatial and temporal patterns in environmental conditions and fish size, growth, and maturity, we posed a series of hypotheses of expected otolith element patterns. Partial effects of internal and external drivers on element concentration were analyzed using a Linear Mixed Model approach with random variables (fish and year). Predicted effects of otolith concentrations of all elements under physiological control (P, Mg, Zn) showed similar trends, with distinct seasonal patterns (lowest concentration in late spring, highest concentrations in winter), and a positive correlation with water temperature, in addition to higher Zn and lower P in spawning individuals. Predicted effects of otolith concentrations of elements expected to be predominantly under environmental control showed the predicted geographic and depth-related trends based on ambient salinity (Ba) and coastal hypoxia (Mn). However, contrary to expectation, Sr was unrelated to salinity. Predicted otolith Ba, Sr and Mn concentrations also exhibited pronounced seasonal patterns that were out of phase with each other but appeared to be partly explained by spawning/feeding migrations. While performing laboratory validation studies for adult fish is typically not possible, these results highlight the importance of assessing local water chemistry and freshwater endmembers in one’s study system before otolith elemental chemistry can be reliably used to reconstruct fish habitat use and environmental histories.

Composition of gillnet catches based on network size at UPT Fishery Port of Riau Province

Gill net catches are one of fishermen's dominant fishing gear at UPT Dumai City Fishing Port. Gill net catches are easy to operate, have a low price, and are durable. This research was conducted in July-August at UPT Port of Fisheries, Riau Province. This study aimed to determine differences in gill net catches based on different mesh sizes. The method used is the survey method. The catch of gill nets by type with a mesh size of 2 inches is 25 fish species. Based on the weight and number of individual fish, it was dominated by lomek (Harpodon sp), namely 1,359.5 kg or 21.5% and 16,314 individuals or 27.18%. The catch in the 3-inch mesh size was 23 species of fish. The percentage of catches based on weight dominated by senangin (Eleutheronema tetradactylum) was 30.38% (1,353.5 kg), and based on the number of individuals dominated by pomfret of 18.72% (4,534 individuals). The main catches in gill nets at UPT Dumai are lomek (Harpodon sp), senangin (Polynemus sp), pomfret (Bramidae sp) and machete (Chirocentrus sp). The primary and bycatch yields for the 2-inch mesh were 51.58% and 42.42%, while the 3-inch mesh sizes were 57.99% and 42.01%.

Robust Fish Recognition Using Foundation Models toward Automatic Fish Resource Management

Resource management for fisheries plays a pivotal role in fostering a sustainable fisheries industry. In Japan, resource surveys rely on manual measurements by staff, incurring high costs and limitations on the number of feasible measurements. This study endeavors to revolutionize resource surveys by implementing image-recognition technology. Our methodology involves developing a system that detects individual fish regions in images and automatically identifies crucial keypoints for accurate fish length measurements. We use grounded-segment-anything (Grounded-SAM), a foundation model for fish instance segmentation. Additionally, we employ a Mask Keypoint R-CNN trained on the fish image bank (FIB), which is an original dataset of fish images, to accurately detect significant fish keypoints. Diverse fish images were gathered for evaluation experiments, demonstrating the robust capabilities of the proposed method in accurately detecting both fish regions and keypoints.

A fish appetite assessment method based on improved ByteTrack and spatiotemporal graph convolutional network

The appetite of fish significantly influences aquaculture efficiency and fish welfare. However, accurately assessing fish appetite has posed a challenging problem. Currently, the study of fish feeding behaviour relies primarily on the overall information obtained from images of fish schools, often overlooking the distinctive behavioural traits of individual fish. Analysing the behaviour of individual fish is hindered by challenges such as intraclass variation and cross-occlusion within real aquaculture environments. To address these challenges, this paper introduces a novel method for assessing appetite based on individual fish behaviour. The ByteTrack model was improved to enable stable tracking of each fish within a school under complex conditions. Additionally, this paper employs the spatiotemporal graph convolutional neural network (ST-GCN) to extract the movement characteristics of individual fish, facilitating accurate appetite assessment. The experimental results demonstrate that the proposed method achieves 98.47% accuracy in appetite assessment, surpassing the performance of other state-of-the-art methods. This paper provides a new opportunity and effective means for analysing fish behaviour and appetite in intricate environments.