Multiple Fish Research Articles

Does drifting passage need to be linked to fish habitat assessment? Assessing environmental flow for multiple fish species with different spawning patterns with a framework integrating habitat connectivity

The use of environmental flow (e-flow) regimes has been widely implemented to improve fish habitat quality in river restoration efforts. However, e-flow designs focusing only on one key life stage (e.g., spawning) without considering potential bottlenecks in other stages (e.g., hatching) can result in little to no improvement, especially when targeting the restoration of fish with drifting eggs. Few e-flow assessments are available that closely link the spatial–temporal dependence of the hydrodynamic effect of drifting eggs on hatching habitats. Moreover, an understanding of how to allocate e-flows to achieve the best possible outcomes for biological diversity conservation is still lacking. In this study, a new framework was developed to assess e-flows, aiming to satisfy the requirements of multiple fish species with different spawning patterns concerning streamflow requirements during spawning and hatching periods. In this framework, the final weighted usable area (FWUA) was proposed by linking the spawning demand to the hydrodynamic effect of drifting eggs to assess habitat quality for fish that produce drifting eggs, and water temperature was used to guide when and how to shift from fixed to moving protection targets in allocating e-flows. Here, we used the Xiangjiaba Reservoir, located in the lower Jinsha River, as a case study to design e-flows for the conservation of multiple fish species with different spawning patterns, which was beneficial for increasing the probability of restoration success. By testing scenarios with an absence of drifting passage, the ecological base flow considering only spawning habitat appears to be lower than that considering both quality of spawning habitat and hatching passage. The ecological benefits (FWUA) generated from the ecological base flow identified by traditional models represent only 64.91% of our framework and are thus anticipated to have cascading deviant effects on ecological patterns and processes in riverine ecosystems. This underlying difference in FWUA generated due to different ecological base flows determined from traditional models and our framework, however, has been overshadowed in previous research. We highlight that the highest fish population density recovery potential will be reached at only certain ratios for both sets of habitat benefits. This work provides a tool that can help managers evaluate e-flows and compare different river restoration scenarios to protect degraded rivers or develop strategies to build resilience to climate change.

The Dynamics of 0-Group Herring Clupea harengus and Sprat Sprattus sprattus Populations Along the Norwegian Skagerrak Coast

Coastal areas are important habitats for early life stages of many fish species. These habitats are used as nursery grounds and can provide a significant contribution to the recruitment of a fish population. In 1919, standardized sampling with a beach seine along the Norwegian Skagerrak coastline was established mainly to target 0-group fish. Here, we focus on Atlantic herring and European sprat to explore whether inter-annual variability in the abundance of these species is indicative of variability in recruitment. We investigated if the abundance of 0-group herring and sprat are affected by environmental factors. Further, the beach seine abundance indices were compared with recruitment estimates of neighboring stocks. There was a clear correlation between herring and sprat abundance in the beach seine samples. While sprat abundance was mainly affected by environmental factors such as temperature and current drift, herring abundance was positively affected by the recruitment of the neighboring stock of western Baltic spring spawners. One plausible explanation could be that sprat recruit to a more local component, while herring of the neighboring stock utilize the Skagerrak coastline as nursery grounds. This study demonstrates the importance of long time series and can provide new insight into the dynamics and structure of multiple fish species.

Integrated toxicity assessment of DEHP and DBP toward aquatic ecosystem based on multiple trophic model assays.

To comprehensively understand the toxic risks of phthalates to aquatic ecosystems, we examined the acute toxicity of di-(2-ethylhexyl) phthalate (DEHP) and di-butyl phthalate (DBP) on multiple trophic models, including algae (Chlorella vulgaris), Daphnia magna and fish (Danio rerio, Pseudorasbora parva). Thus, a 15-day zebrafish exposure was conducted to trace the dynamic changes of phthalate-induced toxic effects. Among the four species, D. magna exhibited the strongest sensitivity to both DEHP and DBP, followed by D. rerio and P. parva. C. vulgaris exhibited the lowest sensitivity to phthalates. The sub-chronic zebrafish assay demonstrated that 1000μg/L DBP induced significant mortality at 15days post-exposure (dpe), and DEHP exhibited no lethality at the tested concentrations (10-5000μg/L). Zebrafish hepatic SOD activity and sod transcription levels were inhibited by DBP from 3 dpe, which was accompanied by increased malondialdehyde level, while zebrafish exposed to DEHP exhibited less oxidative damage. Both DEHP and DBP induced time-dependent alterations on Ache activity in zebrafish brains, thus indicating the potential neurotoxicity toward aquatic organisms. Additionally, 1000μg/L and higher concentration of DBP caused hepatic DNA damage in zebrafish from 7 dpe. These results provide a better understanding of the health risks of phthalate to water environment.

GenBank as a source to monitor and analyze Host-Microbiome data.

Microbiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host-microbiome relationships. The collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution. GenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader. Supplementary data are available at Bioinformatics online.

How does a reservoir affect the fish assemblage structure in a Mediterranean River (Turkey)?

Most rivers around the Mediterranean region, regardless of size, are interrupted by human induced barriers. Although various studies have been conducted to investigate the impacts of reservoirs on undisrupted freshwater biota, what kind of effects they exert on the distribution of freshwater fish assemblages with respect to the presence of invasive species remains to be answered. To attend to this research need, the Karamenderes River, which is disrupted by the Bayramiç Reservoir, was selected as the research site. Relying on the river continuum concept (RCC), we hypothesized that fish assemblages in a given river would demonstrate a gradual downstream change unless the river is interrupted by any reservoir. The ad hoc unweighted pair group method with arithmetic means (UPGMA) agglomerative hierarchical cluster analyses revealed 11 fish assemblages 100 km down the studied river, which is characterized by four environmental gradients. Besides, co-occurrence network analyses were performed to gain a better understanding of the constructs of the observed fish assemblages. The analyses yielded two distinct clusters along the river and showed that the Bayramiç Reservoir had no decisive part in the spatial clustering of these fish assemblages. The migratory species Anguilla anguilla was found only in and around the river mouth area. The co-occurrence network analyses indicated that the freshwater, estuarine and introduced species were observable in distinct groups. It is notable that the non-native Cyprinus carpio and invasive Carassius gibelio were determined in the native freshwater fish species module. The research evidenced that the reservoir had a triple effect, that is, a migration barrier to migratory fish species, a donor facilitating invasion, and a cause of homogenization of river fish assemblages along the river. The results suggest that the impact of the reservoir should be assessed in view of multiple nested model and fish passageways and controlling invasive species are two contradictory problems as far as the impacts of reservoirs are concerned. Therefore, river management should be performed in a way to allow the native migratory species to migrate freely while preventing the introduced species from moving upstream or downstream to preserve and promote rivers' heterogeneity.

Flow variation at multiple scales filters fish life histories and constrains community diversity in desert streams

AbstractEnvironmental regimes, which encompass decadal‐scale or longer variation in climate and disturbance, shape communities by selecting for adaptive life histories, behaviors, and morphologies. In turn, at ecological timescales, extreme events may cause short‐term changes in composition and structure via mortality and recolonization of the species pool. Here, we illustrate how short‐term variation in desert stream fish communities following floods and droughts depends on the context of the long‐term flow regime through ecological filtering of life history strategies. Using quarterly measures of fish populations in streams spanning a 10‐fold gradient in flow variation in Arizona, USA, we quantified temporal change in community composition and life history strategies. In streams with highly variable flow regimes, fish communities were less diverse, fluctuation in species richness was the principle mechanism of temporal change in diversity, and communities were dominated by opportunistic life history strategies. Conversely, relatively stable flow regimes resulted in more diverse communities with greater species replacement and dominance of periodic and equilibrium strategies. Importantly, the effects of anomalous high‐ and low‐flow events depended on flow regime. Under more stable flow regimes, fish diversity was lower following large floods than after seasons without floods, whereas diversity was independent of high‐flow events in streams with flashier flow regimes. Likewise, community life history composition was more dependent on antecedent anomalous events in stable compared to more temporally variable regimes. These findings indicate that extreme events may be a second‐level filter on community composition, with effects contingent on the long‐term properties of the disturbance regime (e.g., overall degree of variation) in which extremes take place. Ongoing changes to global environmental regimes will likely drive new patterns of community response to extreme events.

Identification of collagen 1α3 in teleost fish species and typical collision induced internal fragmentations.

In contrast to collagens 1α1 and 1α2, the more obscure collagen 1α3 is sparsely mentioned in literature. In skin collagen type 1 of teleosts (bony fish), however, the chain occurs in a heterotrimer together with collagens 1α1 and 1α2, which makes it one of the most abundant proteins in teleosts. As teleost fish species and gelatin (hydrolysate) prepared from their skin are a major source for food products and nutraceuticals, the goal of the study was to selectively identify collagen 1α3 in several fish species. Fish skin extracts and fish skin gelatins were analyzed using LC-MS. Depending on the amount of available genetic information different approaches were used to identify collagen 1α3. Additionally, collagen-specific collision induced internal fragmentations are discussed, which are important to consider during data analysis. Ultimately the presence of collagen 1α3 could be confirmed using LC-MS in multiple fish species.

CMFTNet: Multiple fish tracking based on counterpoised JointNet

The analysis of fish motion is remarkably applied to investigate physiological behavior and water quality status. Multiple fish tracking methods based on computer vision have the advantages of contactless, information interpretability, single equipment, and high durability. However, the existed approaches cannot cope with complex scenarios, occlusions, and inconstant scales well. To solve the issues, we propose a multi-object video tracking model specifically for fish schools in aquaculture ponds, called CMFTNet. Firstly, we deploy the Joint Detection and Embedding paradigm to share the features for multiple fish detection and tracking tasks. It utilizes the anchor-free method to solve the problem of mutual occlusion of fish schools. Then, we embed the deformable convolution in the updated backbone to intensify the context features of fish in complex environments. Finally, we evaluate the influence of feature dimensions and propose a weight counterpoised loss that outperforms the previous aggregation methods on dual-branch. Extensive experiments show that CMFTNet achieves the best result both on precision and efficiency. The model reaches 65.5% MOTA and 27.4% IDF1 on the OptMFT dataset. The source codes and pre-trained models are available at: https://github.com/vranlee/CMFTNet.

Effects of glycyrrhizic acid on hatchability, growth, and physiological responses of farmed dojo loach (Misgurnus anguillicaudatus) during early life stages

In aquaculture, herbal extracts have been widely tested in multiple fish species due to their safety, low toxicity, and minimal environmental impacts. However, little information is known about the regulatory roles in fish early life stages. Here in the present study, taking dojo loach as an example, we applied glycyrrhizic acid (GA), the most abundant component in licorice root, both in egg hatching and larviculture. GA pre-treatment once at 12.5 mg/L but not 50 mg/L during egg hatching significantly promoted hatchability, thus same dosage were supplemented during Artemia feeding in larviculture. As a positive control, egg yolk was also supplemented during larviculture, resulting in the increased larval body length after 5 days and 10 days. However, GA supplementation even significantly inhibited the body length of loach larvae after 10 days. Further studies indicated the expression pattern of genes involved in growth (GH & IGF-1), early development (PP1, VEGFAa, VIP, & IFT22), nutrient transport (SGLT1, FABP2, & PEPT1), immune (C3–1, Myd88, & IL-1β) and antioxidative responses (SOD, CAT, & GPx) supported the phenotype regarding egg hatchability and larval body length. Thus, our study suggested that the effects of GA and other herbal extracts on fish might vary depending on the dosage and treating period, thus such application should be careful especially during early fish life stages, which may even inhibit fish larval growth performance at inappropriate dosage or period.

A theropod trackway providing evidence of a pathological foot from the exceptional locality of Las Hoyas (upper Barremian, Serranía de Cuenca, Spain).

We describe a trackway (LH-Mg-10-16) occurring in laminated carbonated limestones of the Las Hoyas locality, Serranía de Cuenca, Spain. It is unmistakably a large theropod dinosaur trackway encompassing two unusual aspects, namely, wide-steps, and a set of equally deformed left footprints (with a dislocated digit). The layer also preserves other vertebrate trails (fish Undichna) and different impressions in the sediment. To address these complex settings, we devised a multidisciplinary approach, including the ichnological and taphonomical descriptions, characterisation of the rock lithofacies using thin-sections, 3D structured-light digitalisation with a high precision of 200–400 μm, and a geometric morphometric comparison with a large sample of bipedal dinosaur trackways. Sedimentary analyses showed that the trackway was produced in a humid, benthonic microbial mat, the consistency and plasticity of which enabled the preservation of the details of the movement of the animal. The results of the geometric analysis indicate that the “wide-steps” of the trackway is not unusual compared to other trackways, providing evidence that it was made by a single individual with an estimated hip height approximately 2 m. Analogous pathologies in extant archosaurs that yield the combination of wide steps and deformed digits in the same trackway were considered. All results mutually support the hypothesis that a large theropod dinosaur, with a pathological foot, generated the trackway as it crossed an area of shallow water while slowly walking towards the main water source, thus stepping steadily over the benthonic mat over which multiple fish were swimming.

Modelling the mixed impacts of multiple invasive alien fish species in a closed freshwater ecosystem in India.

Invasive alien species (IAS) influence the trophic organisation and food web structure in an invaded ecosystem, and therefore, it is imperative to quantify the resultant ecological impacts. The globally recognised ecosystem modelling platform, Ecopath with Ecosim, was used to delineate the impacts of IAS on a tropical freshwater pond ecosystem in India. We analysed the trophic interactions, consumption patterns, prey overlap and mixed trophic impacts of three co-existing invasive alien fish species, African catfish (Clarias gariepinus), suckermouth catfish (Pterygoplichthys pardalis) and Mozambique tilapia (Oreochromis mossambicus), on other functional groups in the ecosystem. Together, the three IAS shared 11% of the total energy consumption and about 50% of the energy consumption by the fish species/groups. There was no predation mortality for African catfish and suckermouth catfish, and a very low estimate for the same was recorded for tilapia (0.64year-1). The IAS shared high mean prey overlap with the native fish groups (Garra sp., Etroplus suratensis, Systomus sarana, Chanda nama and various small species of the cypriniform genera Puntius, Rasbora and Devario) indicating a substantial competition between alien and native species in the ecosystem. Consequently, the three IAS exhibited higher mean negative mixed trophic impacts on these functional groups. A very high Finn's cycling index (39.59%), a low relative ascendency (28.5%) and a very low system robustness (0.07) were observed compared to similar ecosystems, and the baseline values. These indices exposed the vulnerability of the ecosystem towards perturbations, which could be due to the presence of multiple alien invasive species. Mitigating the impacts of IAS should involve a combination of approaches, including eradication through draining and harvesting, high-density stocking of similar trophic level fish in the pond, and local and national level policy interventions.

Isolation and characterization of a highly virulent Edwardsiella piscicida strain responsible for mass mortality in marbled eel (Anguilla marmorata) cultured in Korea

Edwardsiella infections have the potential to induce immense economic losses by affecting multiple fish species, and have been increasingly reported in aquaculture. Edwardsiella tarda, Edwardsiella hoshinae, and Edwardsiella ictaluri have all been previously associated with mass mortality. Recent technological advances in bacterial identification have identified E. piscicida and E. anguillarum as important pathogens affecting global fisheries. Strains previously identified as E. tarda have been re-grouped based on new sequence data and phylogenetic studies. E. piscicida was classified as a novel species in 2012 and has since been reported to have caused mortality in diverse fish species in numerous countries that are potentially more threatening than the mortality caused by E. tarda. Eels are one of the most consumed fish species in Asia, and Anguilla japonica is a commonly reared species in fisheries. However, due to increasing global eel consumption, attempts to culture marbled eel (A. marmorata) have been recently carried out in many Asian countries including Korea. The external clinical signs of Edwardsiella piscicida- infected marbled eel (A. marmorata) were enlarged liver, hemorrhagic congestion at the base of fins and on the skin, as well as hemorrhagic ascites and multifocal abscesses were found in the liver. Histopathology on E. piscicida- infected tissues revealed bacteremia, multifocal necrotizing hepatitis with vasculitis and splenitis with vasculitis. This study reports the first E. piscicida infection case responsible for mass mortality in A. marmorata cultured in Korea. Our study focused on the isolation and histopathological characterization of this bacterial strain to better understand its damage on A. marmorata.

Adaptive Vertical Positioning as Anti-Predator Behavior: The Case of a Prey Fish Cohabiting with Multiple Predatory Fish within Temperate Marine Algal Forests.

Simple SummaryFish cohabiting within structurally complex habitats (e.g., coral reefs, seagrass meadows, algal forests) include abundant small-bodied prey fish and specialized piscivorous fish. Habitat structural complexity mediating fish predator–prey interactions has been shown to be an important mechanism sustaining this coexistence. However, the effect of the vertical stratification of habitat structure on predator–prey interactions remains poorly known, especially within a forest-like marine habitat, i.e., a habitat containing three vertical strata (understory, canopy and open-water). We set up tank experiments to test how such habitat vertical stratification affects predator–prey lethal and behavioral interactions, using one prey and two predator model species cohabiting in Mediterranean algal forest. We found that prey anti-predator behavior was predator-specific. When exposed to a sit-and-wait predator, the prey increased its vertical distance from the predator, regardless of the habitat structure. Conversely, when exposed to a stalk-and-attack predator, the prey sought refuge within forest structures. Prey hide motionless within the canopy, the most complex strata, while they avoid and escape from predators within the understory, which is a less complex stratum allowing for fast prey movements but still protected from predators by the canopy above. Our results suggest the crucial role of habitat vertical stratification in influencing predator–prey interactions, which should be studied in three dimensions.Prey fish cohabit with specialized predator fish within structurally complex habitats. How the vertical stratification of the habitat affects lethal and behavioral predator–prey interactions and contributes to explaining these patterns has never been investigated within a forest-like marine habitat, i.e., a habitat containing three vertical strata (understory, canopy, open-water above). We studied this in tank experiments, with a model prey (the wrasse Symphodus ocellatus) and two model predators (the stalk-and-attack comber Serranus cabrilla and the sit-and-wait scorpionfish Scorpaena porcus), which are among the most abundant prey and predators cohabiting in Mediterranean Cystoseira forests. Wrasse anti-predator behavior was predator-specific. When exposed to the scorpionfish, the wrasse increased its vertical distance from the predator, regardless of the habitat structure. Conversely, when exposed to the comber, the wrasse sought refuge within forest structures: (1) the canopy provides more hiding opportunities due to its high complexity, and (2) the understory provides more escape/avoidance opportunities due to (a) its low complexity that allows for fast prey movements, and (b) the presence of the canopy above that limits the comber’s access to the understory. Our results suggest that habitat vertical stratification mediates predator–prey interactions and potentially promotes the co-existence of prey and multiple predators within marine forests.

Activation ofHenneguya ictaluriActinospores by Nonictalurid Fish Species, with Implications for Management of Proliferative Gill Disease in Catfish Aquaculture

AbstractProliferative gill disease (PGD), caused by the myxozoanHenneguya ictaluri, is an important parasitic disease in U.S. catfish aquaculture. Continuous exposure of Channel CatfishIctalurus punctatusto the actinospore stage ofH.ictaluriresults in a severe inflammatory response at the gills, leading to morbidity and death. Previous work indicates that the chemical cues in fish mucus that are recognized by myxozoan actinospores are not host specific. Building on these findings, the potential decoy effects of nonictalurid fish to actinospores ofH.ictaluriwere evaluated. Exposure of actinospores to gill mucus from multiple nonictalurid fishes resulted in actinospore activation for all fish species tested. Based on these findings, experimental transmission trials with potential interceptor fish were conducted. Individual Channel Catfish were co‐stocked with Western MosquitofishGambusia affinisat 0, 10, 25, or 50% of mean Channel Catfish biomass and exposed to 3,000 actinospores ofH.ictaluri. Gill tissues were sampled at 24 h postchallenge, and parasite burden was estimated byH.ictaluri‐specific quantitative PCR. Results revealed that Western Mosquitofish stocked at 25% and 50% of catfish biomass reducedH.ictaluriDNA in Channel Catfish gills more than threefold. In a second study, catfish were exposed to pond water collected from an active PGD outbreak in the presence of Western Mosquitofish stocked at 25% of catfish biomass. Channel Catfish were sampled at 24 h and at 7 d after the last pond water exposure. At 24 h postexposure, catfish that were co‐stocked with Western Mosquitofish showed significantly lowerH.ictaluriDNA than catfish stocked alone. This treatment effect was absent at 7 d postexposure, as parasite quantities within tissues had increased over 1,000×, with marked variability. Still, results indicate that the chemical cues that activateH.ictaluriactinospores are not specific to Channel Catfish. This work evinces a potential benefit of nonictalurid fish in combatingH.ictaluri, suggesting that the presence of nonictalurid interceptor fish in catfish ponds may minimize PGD severity.

High migratory propensity constitutes a single stock of an exploited cutlassfish species in the Northwest Pacific: A microsatellite approach.

Cutlassfishes, also known as hairtails, include multiple predatory fishes of the family Trichiuridae. They constitute a top marine fish commodity globally, yet the knowledge about their composition and intraspecific genetic structures is still limited. Trichiurus japonicus accounts for a major amount in the northwest Pacific fishery. Previous studies based on mitochondrial DNA markers reported incongruences in its population structure, hence prompting the need for high-resolution markers and avoiding possible shortcomings in its management. Here we genotyped ten novel de novo-assembled transcriptome-derived microsatellite markers on a total of 150 samples across five major fishing grounds (encompassing latitudes 22–39°N). These markers presented a high number of alleles and heterozygosity compared to other marine fishes, corresponding to the large effective population size of ~20,000 per location and cohort differentiation. Population structuring analyses suggested T. japonicus to be a homogenous well-mixed population. This configuration is likely attributed to the majority of its effective population migrates across locations, and the absence of oceanographic barriers at the continental shelves. Qingdao with reportedly high ocean productivity could be a genetic pseudosink based on the high heterozygosity and migratory preference. Moreover, the results of sign tests suggest that T. japonicus experienced a recent bottleneck likely concurrent with historical glaciation events. Further, we demonstrated satisfactory cross-amplifications of our markers on several congeners, indicating a great promise to use these markers to study the population genetics of trichiurids. Together, our findings will serve as an essential groundwork for enhancing resource conservation and management of cutlassfishes.

Quantification of Off-Channel Inundated Habitat for Pacific Chinook Salmon (Oncorhynchus tshawytscha) along the Sacramento River, California, Using Remote Sensing Imagery

Off-channel areas are one of the most impacted aquatic habitats by humans globally, as extensive agricultural and urban development has limited them to roughly 10% of historical extent. This is also true for California’s Sacramento River Valley, where historically frequent widespread inundation has been reduced to a few off-channel water bodies along the mid-Sacramento River. This remaining shallow-water habitat provides crucial ecological benefits to multiple avian and fish species, but especially to floodplain-adapted species such as Chinook salmon (Oncorhynchus tshawytscha). Characterizing spatiotemporal off-channel dynamics, including inundation extent and residence time, is fundamental to better understanding the intrinsic value of such habitats and their potential to support recovery actions. Remote sensing techniques have been increasingly used to map surface water at regional and local scales, with improved resolutions. As such, this study maps off-channel inundation areas and describes their temporal dynamics by analyzing pixel-based time- series of multiple water indices, modified Normalized Difference Water Index (mNDWI) and the Automated Water Extraction Index (AWEI), generated from LandSat-8 and Sentinel-2 data between 2013–2021. Quantified off-channel area was similar with each water index and method used, but improved performance was associated with Sentinel-2 products and AWEI index to identify wetted areas under lower mainstem discharges. Results indicate an uneven distribution of off-channel habitat in the study area, with limited inundated areas in upstream reaches (<16% of total off-channel area for greater flows). In addition, much less habitat exists for flows under 400 m3/s, an important migration cue for endangered winter-run Chinook salmon, limiting juvenile access to areas with enhanced rearing conditions. Off-channel habitat residence times averaged between 7 and 16 days, primarily defined by the rate of receding flows, with rapid flow recession providing marginal off-channel habitat. This study shows reasonable performance of moderate resolution LandSat-8 and Sentinel-2 remote sensing imagery to characterize shallow-water inundated habitat in higher-order rivers, and as a method to inform restoration and native fish recovery efforts.

An evaluation of fish spawning on degraded and remnant reefs in Saginaw Bay, Lake Huron

Saginaw Bay is a shallow, nutrient-rich embayment in Lake Huron that historically had a complex network of natural rocky reefs. These reef habitats were used as spawning and nursery areas for a variety of fish species, but decades of land-use related sedimentation caused many of these reefs to be degraded. Our study objectives were to analyze abiotic and biotic conditions on degraded and remnant reefs and describe spawning patterns of walleye (Sander vitreus) and lake whitefish (Coregonus clupeaformis) at these sites to determine the potential for increased utilization following reef restoration. During fall and spring 2014–2016, we evaluated water quality and egg predation at four sites with varying levels of reef degradation. Further, we documented reproductive utilization through capture of spawning adults and quantification of egg deposition. Walleye and lake whitefish utilized multiple sites for reproduction; however, densities of spawners and deposited eggs were low, suggesting that they were not utilizing study sites as major spawning locations. Walleye and lake whitefish eggs were eaten by multiple fish species, including larger fish such as channel catfish (Ictalurus punctatus). Dissolved oxygen levels were adequate (i.e., >7 mg 02 L−1) during spring walleye egg incubation; however, bottom dissolved oxygen levels became very low at some sites during winter ice cover, coinciding with lake whitefish egg incubation. As restoration of rocky reefs proceeds in the Bay, evidence of remnant reef spawning fish bodes well for long-term success, though potential limiting factors such as low dissolved oxygen, sedimentation, and egg predation require continued monitoring.

Integrated Management Strategies for Viral Nervous Necrosis (VNN) Disease Control in Marine Fish Farming in the Mediterranean.

Viral nervous necrosis (VNN) is the most important viral disease affecting farmed fish in the Mediterranean. VNN can affect multiple fish species in all production phases (broodstock, hatchery, nursery and ongrowing) and sizes, but it is especially severe in larvae and juvenile stages, where can it cause up to 100% mortalities. European sea bass has been and is still the most affected species, and VNN in gilthead sea bream has become an emerging problem in recent years affecting larvae and juveniles and associated to the presence of new nervous necrosis virus (NNV) reassortants. The relevance of this disease as one of the main biological hazards for Mediterranean finfish farming has been particularly addressed in two recent H2020 projects: PerformFISH and MedAID. The presence of the virus in the environment and in the farming systems poses a serious menace for the development of the Mediterranean finfish aquaculture. Several risks associated to the VNN development in farms have been identified in the different phases of the farming system. The main risks concerning VNN affecting gilthead seabream and European seabass have been identified as restocking from wild fish in broodstock facilities, the origin of eggs and juveniles, quality water supply and live food in hatcheries and nurseries, and infected juveniles and location of farms in endemic areas for on-growing sites. Due to the potential severe impact, a holistic integrated management approach is the best strategy to control VNN in marine fish farms. This approach should include continuous surveillance and early and accurate diagnosis, essential for an early intervention when an outbreak occurs, the implementation of biosecurity and disinfection procedures in the production sites and systematic vaccination with effective vaccines. Outbreak management practices, clinical aspects, diagnostic techniques, and disinfections methods are reviewed in detail in this paper. Additionally, new strategies are becoming more relevant, such as the use of genetic resistant lines and boosting the fish immune system though nutrition.

Circulating trimethylamine N-oxide levels following fish or seafood consumption.

Some species of fish and seafood are high in trimethylamine N-oxide (TMAO), which accumulates in muscle where it protects against pressure and cold. Trimethylamine (TMA), the metabolic precursor to TMAO, is formed in fish during bacterial spoilage. Fish intake is promoted for its potential cardioprotective effects. However, numerous studies show TMAO has pro-atherothrombotic properties. Here, we determined the effects of fish or seafood consumption on circulating TMAO levels in participants with normal renal function. TMAO and omega-3 fatty acid content were quantified across multiple different fish or seafood species by mass spectrometry. Healthy volunteers (n = 50) were recruited for three studies. Participants in the first study consented to 5 consecutive weekly blood draws and provided dietary recall for the 24h preceding each draw. In the second study, TMAO levels were determined following defined low and high TMAO diets. Finally, participants consumed test meals containing shrimp, tuna, fish sticks, salmon or cod. TMAO levels were quantified by mass spectrometry in blood collected before and after dietary challenge. TMAO + TMA content varied widely across fish and seafood species. Consumption of fish sticks, cod, and to a lesser extent salmon led to significant increases in circulating TMAO levels. Within 1 day, circulating TMAO concentrations in all participants returned to baseline levels. We conclude that some fish and seafood contain high levels of TMAO, and may induce a transient elevation in TMAO levels in some individuals. Selection of low TMAO content fish is prudent for subjects with elevated TMAO,cardiovascular disease or impaired renal function.

Automated Detection, Classification and Counting of Fish in Fish Passages With Deep Learning

The Ocean Aware project, led by Innovasea and funded through Canada's Ocean Supercluster, is developing a fish passage observation platform to monitor fish without the use of traditional tags. This will provide an alternative to standard tracking technology, such as acoustic telemetry fish tracking, which are often not appropriate for tracking at-risk fish species protected by legislation. Rather, the observation platform uses a combination of sensors including acoustic devices, visual and active sonar, and optical cameras. This will enable more in-depth scientific research and better support regulatory monitoring of at-risk fish species in fish passages or marine energy sites. Analysis of this data will require a robust and accurate method to automatically detect fish, count fish, and classify them by species in real-time using both sonar and optical cameras. To meet this need, we developed and tested an automated real-time deep learning framework combining state of the art convolutional neural networks and Kalman filters. First, we showed that an adaptation of the widely used YOLO machine learning model can accurately detect and classify eight species of fish from a public high resolution DIDSON imaging sonar dataset captured from the Ocqueoc River in Michigan, USA. Although there has been extensive research in the literature identifying particular fish such as eel vs. non-eel and seal vs. fish, to our knowledge this is the first successful application of deep learning for classifying multiple fish species with high resolution imaging sonar. Second, we integrated the Norfair object tracking framework to track and count fish using a public video dataset captured by optical cameras from the Wells Dam fish ladder on the Columbia River in Washington State, USA. Our results demonstrate that deep learning models can indeed be used to detect, classify species, and track fish using both high resolution imaging sonar and underwater video from a fish ladder. This work is a first step toward developing a fully implemented system which can accurately detect, classify and generate insights about fish in a wide variety of fish passage environments and conditions with data collected from multiple types of sensors.