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ABSTRACT Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous–resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory‐propensity, migratory‐lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations. [ABSTRACT FROM AUTHOR]

Hybridisation is a complex process that begins with mating. Females have more to lose with each hybrid fertilisation than males, so they should avoid it. Even if females choose con‐specific males as preferred mates, they often cannot control which additional males release sperm during spawning. Polyandry is ubiquitous and may result in hetero‐specific sperm competition between males of different species. In such cases, cryptic female choice (the ability to bias paternity towards certain males under sperm competition) is the last line of defence to prevent hybridisation of her eggs and is highly adaptive if it enables con‐specific sperm preference. Such seems to be the case with the hybridisation of Atlantic salmon (Salmo salar) and brown trout (S. trutta) in their native Europe. Under hetero‐specific sperm competition, hybrid fertilisations in these fish are reported to be reduced via ovarian fluid‐mediated cryptic female choice. It is not known, however, whether the strength of this mechanism is dependent on reinforcement and thus, the historical sympatry/allopatry of hybridising populations. Brown trout are one of the world's worst invasive species. Ecological impacts arise through competition with other species (e.g. Galaxids in the southern hemisphere, Oncorhynchus in western North America). Eastern North America contains native salmonids that evolved in the absence of brown trout but have gametes that are compatible. The 140 ‐year‐old brown trout invasion of Newfoundland is ground zero to study these potential interactions. Their relatively low spread rate across the island may be the result of inherent poor productivity, but data suggest it could also be a function of hybridisation with native Atlantic salmon and brook char (Salvelinus fontinalis). [ABSTRACT FROM AUTHOR]

The management of intraspecific diversity in many species is usually disconnected from eco‐evolutionary processes happening in natura. A classic example is embodied in the problem of introgression in hybridized fish populations, wherein management practices are generally unaware of any selective process at work, and therefore generally rely on numbers (adding or removing individuals) to reduce introgression. Such an example can be observed in the French Alps, where native Mediterranea (MED) brown trout have been highly introgressed through decades of stocking with domesticated Atlantic (ATL) brown trout. Recently however, new results shed light on a potential selective mechanism that may affect differentially the fitness of MED and ATL genes depending on the environment (GxE interaction). Using a demogenetic agent‐based model able to account for such GxE interaction, we simulate a management scenario implemented in 2005 by some biodiversity managers and scientists, who attempted to restore the Mediterranea gene pool using translocation of near pure MED individuals in Atlantic‐dominated areas. We show that the model is unable to recreate the observed introgression dynamics if the GxE interaction is not included. This finding implies that (i) eco‐evolutionary mechanisms can have large effects on introgression dynamics on very short time scales and (ii) management of intraspecific diversity should increasingly rely on these natural mechanisms, so as to improve management targets and facilitate adaptation to rapid environmental changes. [ABSTRACT FROM AUTHOR]

Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon's gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon's defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b. [ABSTRACT FROM AUTHOR]

Throughout their native range, adfluvial brown trout populations have declined due to habitat degradation and over exploitation. As a consequence, numerous restoration projects that include stocking of hatchery‐reared trout have been conducted; however, estimates of survival in large lakes remain scarce. Here, we use telemetry to evaluate the survival of stocked trout smolts and sub‐adults in a large lake in central Sweden. Of the smolts released in the main tributary, 42% entered the lake. Both life stages suffered high rates of mortality. Only 8% of smolts survived the first 10 months after entering the lake and 10% of those released as sub‐adults survived 23 months post‐release. In agreement with studies on anadromous trout, we conclude that stocking of hatchery‐reared individuals is not an efficient method to recover population numbers due to poor performance in the wild. Similar studies from other large lakes and comparisons with wild conspecifics would increase the applicability of the results and promote further understanding of the utilization of hatchery‐origin trout to rebuild wild populations and sustain fisheries. [ABSTRACT FROM AUTHOR]

Temperature is a key driver in determining species distribution and abundance across climatic and geographical gradients. This occurs through direct physiological effects of temperature on performance, but may also result from temperature effects on species interactions.In the current study we experimentally test for temperature‐dependent competition between juvenile anadromous Atlantic salmon and brown trout and evaluate the role of temperature in shaping the relative abundance of these species across 88 Norwegian rivers.When the two species were reared in allopatry their somatic growth rates were similar across a range of temperatures (4–16°C).When reared in sympatry, the growth of salmon was greatly reduced at the coldest temperature relative to when reared in allopatry, whereas this was not the case for trout. The effect of interspecific competition on growth was more similar for the two species at warmer temperatures. Thus, interspecific competition effects were strongly asymmetric only at the lowest temperature, with trout outcompeting salmon.The results from the experiment were reflected in qualitative patterns of relative abundance of salmon and trout in natural populations, which shifted from being trout dominated in rivers with low summer temperatures to being salmon dominated in warmer rivers.These results provide an empirical example of how temperature effects on the relative abundance of species can only be understood in light of information about temperature‐dependent species interactions. [ABSTRACT FROM AUTHOR]

Endangered trout populations can be monitored with a variety of methods, the selection of which should consider social constraints and environmental variables known to affect method effectiveness. Here, we confront the effectiveness of four monitoring methods (removal with electrofishing, ELE; underwater camera survey, UCS; streamside visual survey, SVS; visual surveys with angling, VSA) to estimate the relative abundance of three populations of the endangered Mediterranean brown trout. The trout counts obtained via different methods were well correlated (r = 0.65–0.72), providing a coherent description of the relative pool abundance across the methods. However, the methods were differently affected by environmental variables, depending on the age classes of trout. Specifically, the adult and subadult counts provided by ELE and VSA were negatively and positively affected by the maximum pool depth, respectively; adult and subadult counts of VSA and the SVS were positively affected by pool area; the juvenile counts provided by the UCS were positively affected by pool shade and negatively affected by water turbidity; juvenile counts provided by VSA were positively affected by shade. Variables such as pool depth, area, shading, water turbidity and proportion of age classes can be hardly controlled in monitoring programs, and their bias could be modelled. Different sampling methods provided similar information about relative abundance and appeared equivalent. While ELE could be selected to collect samples and biometric data, monitoring relative abundance with the UCS, VSA, and SVS appears more suited and can also involve citizen scientists. [ABSTRACT FROM AUTHOR]

Human‐mediated species introductions are contributing to the biotic homogenization of global flora and fauna. Despite extensive research, we lack simple methods of predicting how and where an introduced species will spread and establish, particularly in species with complex life histories in aquatic ecosystems. We predict that spread can be modeled simply using the characteristics of the invading population, specifically species growth rate and dispersal capacity. In addition, we predict that the establishment of introduced species should be explained by the characteristics of the receiving ecosystem. Using the brown trout (Salmo trutta) invasion on the Island of Newfoundland as a case study, we fit and test a reaction–diffusion model with brown trout population data collected from the literature. Next, we use statistical models to assess the influence of a suite of abiotic (conductivity, pH, turbidity, calcium), biotic (Atlantic salmon occurrence), and landscape (watershed relief, watershed area, distance to original introduction) variables on brown trout establishment (i.e., presence–absence) patterns. We find that observed coastal spread in Newfoundland is slow (~4.4 km/year), and that it lies on the lower end of the range of predictions made by the reaction–diffusion model parameterized based on the estimates of growth rate and movement from the literature (predicted spread range 1.4 to 92 km/year). Also, we did not find evidence for a relationship between abiotic or biotic variables and brown trout establishment. However, we did observe that landscape variables of the distance to trout introduction point and estuary area may explain establishment patterns along the south coast of Newfoundland. Our results suggest the importance of using population‐specific parameterization and the need to integrate regional landscape factors that are generally applicable across biological invasions (e.g., distance to introduction), and those that are more specific to the ecology of the invader (e.g., estuary area). Our study contextualizes the mechanisms that contribute to a slow invasion by an aquatic species with a complex life history and reveals that future studies need to integrate a variety of methods to elucidate the processes governing invasions. [ABSTRACT FROM AUTHOR]

Aim: The British Isles have been worked for millennia to extract metal ores to feed industrial development, leaving a legacy of mine water pollution that continues to impact freshwater communities in many regions. Brown trout (Salmo trutta L.) have long been observed to persist in these metal‐impacted systems as apex predators, with previous studies showing a small number of impacted populations to be highly genetically divergent. We sought to understand the scale of genetic diversity across regions and the repeatability of genetic divergence in trout populations affected by metal pollution. Location: We examined four mine water‐impacted regions across the British Isles: west Wales, northeast England, southwest England and southeast Ireland. Methods: We employed a panel of 95 SNP loci to screen 1236 individuals from 71 sites representing paired metal‐impacted and clean sites from across the four regions. From these, we obtained diversity statistics, assessed genetic structuring of populations and modelled historical demographic scenarios to understand which factors most credibly explain genetic variation in divergent populations. Results: We evidenced hierarchical population structure in the regions studied, in line with expectations from phylogeographic history. However, in a hierarchical analysis of genetic structuring the first level of differentiation was driven by the divergence of the metal‐impacted trout of Cornwall in southwest England. Within regions we observed reduced genetic diversity and repeated patterns of local genetic sub‐structuring between paired samples from metal‐impacted and relatively clean sites. Demographic history analyses suggested the timing of these splits to be relatively recent and to be associated with periods of peak mining activity. Main conclusions: Our findings demonstrate distinct patterns of genetic isolation and reduced diversity arising from legacy pollution in freshwater ecosystems, with impacts being most apparent where both chemical pollution and physical barriers are present. Management should focus on the amelioration of mine water wash‐out and the removal of barriers to fish movement to safeguard genetic diversity in impacted populations. [ABSTRACT FROM AUTHOR]

Probiotics play an important role in animal production, providing health benefits to the host by improving intestinal microbial balance. In this study, we added three different probiotics, Saccharomyces cerevisiae (SC), Bacillus licheniformis (BL), and lactic acid bacteria (LAB), and compared them with the control group (CON), to investigate the effects of probiotic supplementation on growth performance, gut microbiology, and gut flora of S. trutta. Our results showed that feeding probiotics improved the survival, growth, development, and fattening of S. trutta. Additionally, probiotic treatment causes changes in the gut probiotic community, and the gut flora microorganisms that cause significant changes vary among the probiotic treatments. However, in all three groups, the abundance of Pseudomonas, Acinetobacter, and Rhizophagus bacterial genera was similar to that in the top three comparative controls. Furthermore, differences in the composition of intestinal microbiota among feed types were directly associated with significant changes in the metabolomic landscape, including lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The probiotic treatment altered the gut microbiome, gut metabolome, and growth performance of S. trutta. Using a multi-omics approach, we discovered that the addition of probiotics altered the composition of gut microbiota, potentially leading to modifications in gut function and host phenotype. Overall, our results highlight the importance of probiotics as a key factor in animal health and productivity, enabling us to better evaluate the functional potential of probiotics. [ABSTRACT FROM AUTHOR]

The impact of low flows on riverine ecology in Sweden is not fully understood. Recent summer droughts, along with their regionally projected increase, together demonstrate the need for a more solid foundation guiding ecologically responsible planning. Impact assessments can be made via indicator species sensitive to low flow, if their response to the flow conditions can be clearly understood, using for example historical data on species abundance and flow. In Swedish rivers, there are extensive electrofishing data with a special focus on salmonids, predominantly brown trout Salmo trutta, which are previously reported to be sensitive to low flow. There are also available national data on river flows, largely based on simulations. We processed and used these data sets, along with information on additional environmental factors. We tested if sites had less than their median trout abundance during the year of the minimum winter or summer low-flow. Adverse impacts of low flow could be shown only for young-of-the-year trout. The impact was small with at most 57 % of remaining sites having lower than median trout abundance (compared to 44 % overall) during the year of the lowest winter flow. The insubstantial effect means that using trout as a low-flow indicator species in Sweden cannot be supported by the currently available data. We believe the main causes of the small effects are limitations in the time resolution of trout data and spatial resolution of the flow data, followed by the ability of trout to escape low flows by seeking deeper habitats.

[Objective] The present paper aimed to compare the effects of adding different probiotics in feed on the growth performance, digestive enzyme activity and serum biochemical indicators of Salmon trutta. [Method] 630 S. trutta with an initial body weight of (84.57 ±1.83) g were selected for the experiment and randomly divided into 7 groups, with 3 parallel fish in each group and 30 parallel fish in each group. The control group was fed with basic feed, while the experimental group was supplemented with different probiotics (Saccharomyces, EM bacteria, Lactobacillus, Bacillus subtilis, compound Bacillus, B. licheniformis) to the basic feed for three months. [Result] The indicators related to growth, digestion and serum biochemistry were measured and analyzed. The results showed that adding different probiotics had a growth promoting effect on the S. trutta. The average body length growth rate, average body weight growth rate, specific growth rate, food conversion rate and feeding rate of the experimental group were significantly higher than those of the control group (P<0.05, the same as below); Compared with the control group, the experimental group showed an increase in liver pancreatic protease, intestinal protease, lipase, and amylase, with the EM bacteria group having the highest level, significantly higher than the other experimental groups; The activity of catalase in serum of yeast was significantly increased compared to the control group, while there was no significant difference in total protein, triglycerides, glucose, superoxide dismutase, acid phosphatase, glutamic oxalate transaminase, glutamic pyruvate transaminase, complement C3 and lysozyme indicators (P>0.05), while other bacteria had varying degrees of influence among the experimental groups. [Conclusion] Taking into account survival rate, growth characteristics, digestive enzymatic activity and serum biochemical indicators, the addition of EM bacteria has a good effect on the healthy breeding of S. trutta. [ABSTRACT FROM AUTHOR]

Limiting resources are often unevenly distributed among competing consumers, as larger, more aggressive, fast growing, early emerging, or rapidly reproducing species disproportionately exploit food or habitat. In such cases, asymmetric competition can occur (i.e., when limited resources are divided up unequally among individuals or species), resulting in stronger negative effects for some species and comparatively weaker effects for others. We hypothesize that the accessibility of food web pathways influences asymmetric competition among stream fishes. To test this hypothesis, we studied the interactions of invasive brown trout (Salmo trutta) with native Rio Grande sucker (Catostomus plebeius or Pantosteus plebeius) and Rio Grande chub (Gila pandora) in mountain streams of New Mexico, USA, from 2020 to 2021. Our study found support for the hypothesis that the accessibility of food web pathways drives asymmetric competition in mountain stream fishes, as native chub and sucker grew at slower rates than invasive brown trout across all observed body sizes. Our conclusion is evidenced by (1) strong diet overlap driven by benthic macroinvertebrates that (2) were important in fueling the growth of native fishes but were also (3) disproportionately exploited by trout. Because trout fed on small aquatic invertebrates, large crayfish, other fish, and inputs of terrestrial prey, they could incorporate energy from differing food web pathways, whereas native fishes were mostly limited to small benthic prey (and chubs fed on terrestrial arthropods). As trout, chub, and sucker competed for small benthic prey, trout could also incorporate other sources of food, whereas chub and sucker had fewer options. Although two or more species may compete for one resource, their rates of growth and production are also dependent on, and fueled by, other food web pathways. Our work demonstrates that such food web pathways help explain differences in growth and production between invasive and native fishes. Our findings show that tracking energy flows through the different food web pathways provides a useful and intuitive means of describing the important sources of food (i.e., the trophic basis of production) that fuel growth and production and sheds light on the processes that drive asymmetric competition. [ABSTRACT FROM AUTHOR]

Changes in the number, structure, and function of mitochondria during the early life stages of animals can play an important role for an organism's metabolic rate, growth, and health. Previous studies have shown that juvenile brown trout (Salmo trutta) subjected to elevated temperatures during the embryonic stage respond phenotypically with a reduced metabolic rate. The aim of this study was to explore if embryonic temperature affects the mitochondria content of young brown trout and as such explains the previously found differences in metabolic rates. Here, we optimize a quantitative PCR (qPCR) method for the mitochondria cytochrome c oxidase subunit I gene, and then use the method as a proxy for mitochondrial DNA content. We hypothesize that young trout subjected to elevated temperatures during the embryonic stage respond phenotypically with a reduced mitochondrial DNA content. To test this hypothesis, we subjected brown trout to either control ambient (4.4 ± 1.5 °C) or elevated temperatures (7.1 ± 0.6 °C) during embryogenesis. Subsequently, we extracted DNA from liver and white muscle tissue of juvenile brown trout from the two different incubation temperature treatments and successively optimized qPCR for mitochondrial DNA. We found that the amount of mitochondria DNA in liver tissue was 18 times higher than in white muscle tissue, but there was no significant difference in mitochondria content in liver or muscle tissue between brown trout exposed to elevated and ambient control temperatures during embryogenesis. We conclude that reduced metabolic rate is not likely associated with mitochondria DNA content. We also suggest that qPCR is a simple and cost-effective method to quantify mitochondria DNA in frozen and partly degraded tissue from different treatment groups and a useful proxy for identification of differences in mitochondria number. [ABSTRACT FROM AUTHOR]

Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (Nb) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation. [ABSTRACT FROM AUTHOR]

Anadromous brown trout (Salmo trutta) in the northeastern Atlantic Ocean, and coastal cutthroat trout (Oncorhynchus clarkii clarkii) in the northeastern Pacific Ocean, are analogs in many ways. Both species display similar patterns of complex life histories and behavioral flexibility, are iteroparous and facultatively anadromous and occupy nearshore coastal marine habitats where numerous populations often mix. These characteristics create specific challenges for management and conservation that have been complicated by inadequate scientific attention in some areas. Both species are declining across their native range, and their ecology make them particularly vulnerable to habitat destruction, fishing, and climate change. Here, we review the available literature to compare the biology, ocean ecology, and management practices of these two species. We highlight ecological similarities and differences between the species and identify current knowledge gaps suggesting future research needs and management actions. Using a comparative approach, the review aims to promote and facilitate knowledge exchange between anadromous trout research communities from opposite sides of the globe to improve management and conservation of these species and stimulate the production of management plans specific to anadromous trout. [ABSTRACT FROM AUTHOR]

Abstract Human‐mediated species introductions are contributing to the biotic homogenization of global flora and fauna. Despite extensive research, we lack simple methods of predicting how and where an introduced species will spread and establish, particularly in species with complex life histories in aquatic ecosystems. We predict that spread can be modeled simply using the characteristics of the invading population, specifically species growth rate and dispersal capacity. In addition, we predict that the establishment of introduced species should be explained by the characteristics of the receiving ecosystem. Using the brown trout (Salmo trutta) invasion on the Island of Newfoundland as a case study, we fit and test a reaction–diffusion model with brown trout population data collected from the literature. Next, we use statistical models to assess the influence of a suite of abiotic (conductivity, pH, turbidity, calcium), biotic (Atlantic salmon occurrence), and landscape (watershed relief, watershed area, distance to original introduction) variables on brown trout establishment (i.e., presence–absence) patterns. We find that observed coastal spread in Newfoundland is slow (~4.4 km/year), and that it lies on the lower end of the range of predictions made by the reaction–diffusion model parameterized based on the estimates of growth rate and movement from the literature (predicted spread range 1.4 to 92 km/year). Also, we did not find evidence for a relationship between abiotic or biotic variables and brown trout establishment. However, we did observe that landscape variables of the distance to trout introduction point and estuary area may explain establishment patterns along the south coast of Newfoundland. Our results suggest the importance of using population‐specific parameterization and the need to integrate regional landscape factors that are generally applicable across biological invasions (e.g., distance to introduction), and those that are more specific to the ecology of the invader (e.g., estuary area). Our study contextualizes the mechanisms that contribute to a slow invasion by an aquatic species with a complex life history and reveals that future studies need to integrate a variety of methods to elucidate the processes governing invasions.

Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon’s gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon’s defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b.

Brown trout is a species complex (Salmo trutta complex, L., 1758) including both widespread invasive (non‐native hatchery strains) lineages and endangered local‐endemic lineages, among which is the Sardinian trout, the only native salmonid present in Sardinia. Multiple stressors (e.g. the spread of stocked brown trout of Atlantic origin, habitat alteration and climate change) combine to seriously threaten the persistence of wild native populations.In this study, the origin, population genetics and demography of wild Sardinian brown trout populations were extensively investigated. A total of 274 trout individuals collected from 12 hydro‐geographical basins were analysed using both mitochondrial (control region) and nuclear (LDH‐C1* locus and 10 microsatellites) markers.Although stocking activities have altered the native genetic makeup of some populations in the study area, several (almost) uncontaminated populations showing strong genetic structure were detected. Eroded intra‐population diversity, as well as small effective population size, sometimes associated with a bottleneck signal was also found.The genetic characteristics of Sardinian trout populations described in this study are probably due, at least partly, to the peculiarity of local environmental conditions at the margin of the ecological niche for salmonids.Based on the results of this study, the need for urgent measures of conservation aimed to ensure the near future viability of the last wild Sardinian trout populations was discussed. [ABSTRACT FROM AUTHOR]

Simple Summary: Due to the increase in antibiotic resistance observed in pathogenic bacteria, new alternatives are being explored to reduce the use of these drugs. Probiotics, a group of bacteria that includes lactic acid bacteria (LAB), are capable of stimulating and strengthening the immune system and have showed antagonistic effects against various pathogenic bacteria. The aim of this study was to identify and test potentially probiotic LAB, isolated from Brown trout and Rainbow trout, to select those with the least antibiotic resistance, the best antagonistic effect against fish pathogens, and minimal negative effects during their application on embryonated Brown trout eggs. As a result, various bacterial strains were obtained that proved to be safe in terms of antibiotic resistance and effective against several of the pathogens to which they were exposed. Nevertheless, only a limited number of these strains were found to be safe for use in Brown trout eggs. However, some findings suggest the need to investigate the possibility that certain bacterial strains considered probiotics might have adverse effects on fish health. This research investigates the potential of lactic acid bacteria (LAB) from freshwater salmonids as prospective probiotics for application in aquaculture. LAB and pathogenic bacteria were obtained from mucus and tissues of Oncorhynchus mykiss and Salmo trutta from fish farms in northeast Spain that had not used antibiotics for the six months preceding the study. Isolates were identified using Gram staining and sequencing of 16S rRNA and ITS-1. To assess the safety of the LAB, antibiotic susceptibility tests (ASTs) against 23 antimicrobials were performed. In vitro antagonism assays were conducted to evaluate the inhibitory effects of living LAB using the agar diffusion test method and their metabolites using the agar well diffusion method. The assays targeted six specific pathogens: Aeromonas salmonicida subsp. salmonicida, Carnobacterium maltaromaticum, Vagococcus salmoninarum, Yersinia ruckeri, Lactococcus garvieae, and the marine pathogen Vibrio jasicida. Additionally, a toxicity assay was conducted on embryonic eggs of S. trutta. The ASTs on probiotic LAB candidates revealed varied responses to antimicrobials, but no resistance to oxytetracycline or florfenicol, which are two antibiotics commonly used in aquaculture, was detected. The in vitro assays indicate that LAB exhibit antagonistic effects against pathogens, primarily when directly stimulated by their presence. In applications involving embryonic eggs or larvae, certain live strains of LAB were found to have adverse effects, with some isolates resulting in higher mortality rates compared to the control group or other isolates. Furthermore, the potential pathogenicity of certain LAB strains, typically considered safe in salmonids, warrants deeper investigation. [ABSTRACT FROM AUTHOR]

Objective: The present research was conducted on the existence and species diversity of fish in the Shuhada River, one of the Kokcha River tributaries situated in Badakhshan Province, Afghanistan. There has not been a previous study on fish species diversity; this is the first attempt to fill out this gap and identify the fish species of the river. Materials and Methods: Fish specimens were collected from three selected sites in the Shuhada River. The study was performed twice in each season of the year 2022, by using a variety of fishing nets, like gill nets with a length of 5 m and a height of 2 m, although with meshes ranging from 3 to 3 cm knot to knot and hooks. Two samples were taken from each site in each season. Results: Generally, 463 fish specimens were collected from the three selected zones. The Futtah was one of the selected zones that had the highest number of fish species (38.8%), followed by Yasich (34.04%), and the least number of fish species (28.07%) were collected from the Maidan zone. It found that Salmo trutta is the most abundant species at 52.9%, followed by Schizothorax curvifrons at 34.5% and Paracobitis longicauda at 12.5% was the least abundant species. During the cold seasons of autumn and winter, fish migrate down in the Kokcha River, and in spring and summer migrate to the upper zone in cold water. Conclusion: During the current study, three fish species, Salmo trutta, Schizothorax curvifrons, and Paracobitis longicauda, were documented in the study area. Fish hunting and flooding are the main harmful forces causing the reduction of fish diversity in the Shuhada River. [ABSTRACT FROM AUTHOR]

In partially migratory species, individuals either migrate at some point(s) in life or reside within their natal habitat throughout life. For salmonid fish, migration creates opportunities for feeding and growth, but it is also associated with increased mortality risk. Such trade‐offs likely differ between the sexes, since reproductive output is more closely tied to body size in females than males. However, testing hypotheses on sex‐specific migratory behaviour in would‐be first‐time migratory salmonids is difficult, since sexes are generally morphologically indistinguishable prior to maturation. Previous studies have evaluated the influence of sex on migration based on dissection of migratory juveniles or the sex ratio of returning adults. However, both approaches are potentially biased by differential survival during migration. Here, we utilise advances in minimally invasive genetic sex‐determination methods for salmonids to investigate sex‐specific, spring out‐migration propensity in potamodromous brown trout (Salmo trutta) in a pre‐Alpine, central European lake. We show that there are marked differences in migratory behaviour between males and females, with small (~10 cm) females being approximately twice as likely to migrate out of their natal river in spring compared to similarly sized males, which generally migrate for the first time at larger sizes (in similar proportions to larger females). This study highlights how novel genetic sex‐determination techniques can provide insight into the sex‐ and size‐specific life‐history trade‐offs that shape migration propensity. Moving forward, these techniques should become useful tools for ecologists and fisheries managers. [ABSTRACT FROM AUTHOR]

Juvenile salmonids often experience high mortality rates during migration and bird predation is a common source of mortality. Research suggests that hatchery‐reared salmonids are more prone to predation than wild salmonids, and that Atlantic salmon (Salmo salar) experience lower predation than Sea trout (Salmo trutta), yet telemetry studies have displayed equivocal results. Here, using a large data set on passive integrated transponder (PIT) tagged hatchery‐reared and wild juveniles of Atlantic salmon and Sea trout (25,769 individuals) we investigate predation probability by piscivorous birds (mainly Great Cormorants Phalarocorax carbo) on salmonids originating from River Dalälven in Sweden. Bird colonies and roosting sites were scanned annually (2019–2021), and the temporal dynamics of bird predation on salmonids released in 2017–2021 was assessed. Hatchery‐reared trout was clearly most susceptible to cormorant predation (0.31, 90% credibility interval [CRI] = 0.14–0.53), followed by wild trout (0.19, 90% CRI = 0.08–0.37), hatchery‐reared salmon (0.13, 90% CRI = 0.07–0.23), and wild salmon (0.08, 90% CRI = 0.04–0.14), in subsequent order. This order in predation probability was consistent across all studied tag‐ and release‐years, suggesting that the opportunistic foraging of cormorants affects the overall survival of juvenile salmonids, but that the inherent predation risk between different salmonid types differs systematically. [ABSTRACT FROM AUTHOR]

Abstract Limiting resources are often unevenly distributed among competing consumers, as larger, more aggressive, fast growing, early emerging, or rapidly reproducing species disproportionately exploit food or habitat. In such cases, asymmetric competition can occur (i.e., when limited resources are divided up unequally among individuals or species), resulting in stronger negative effects for some species and comparatively weaker effects for others. We hypothesize that the accessibility of food web pathways influences asymmetric competition among stream fishes. To test this hypothesis, we studied the interactions of invasive brown trout (Salmo trutta) with native Rio Grande sucker (Catostomus plebeius or Pantosteus plebeius) and Rio Grande chub (Gila pandora) in mountain streams of New Mexico, USA, from 2020 to 2021. Our study found support for the hypothesis that the accessibility of food web pathways drives asymmetric competition in mountain stream fishes, as native chub and sucker grew at slower rates than invasive brown trout across all observed body sizes. Our conclusion is evidenced by (1) strong diet overlap driven by benthic macroinvertebrates that (2) were important in fueling the growth of native fishes but were also (3) disproportionately exploited by trout. Because trout fed on small aquatic invertebrates, large crayfish, other fish, and inputs of terrestrial prey, they could incorporate energy from differing food web pathways, whereas native fishes were mostly limited to small benthic prey (and chubs fed on terrestrial arthropods). As trout, chub, and sucker competed for small benthic prey, trout could also incorporate other sources of food, whereas chub and sucker had fewer options. Although two or more species may compete for one resource, their rates of growth and production are also dependent on, and fueled by, other food web pathways. Our work demonstrates that such food web pathways help explain differences in growth and production between invasive and native fishes. Our findings show that tracking energy flows through the different food web pathways provides a useful and intuitive means of describing the important sources of food (i.e., the trophic basis of production) that fuel growth and production and sheds light on the processes that drive asymmetric competition.

Endangered trout populations can be monitored with a variety of methods, the selection of which should consider social constraints and environmental variables known to affect method effectiveness. Here, we confront the effectiveness of four monitoring methods (removal with electrofishing, ELE; underwater camera survey, UCS; streamside visual survey, SVS; visual surveys with angling, VSA) to estimate the relative abundance of three populations of the endangered Mediterranean brown trout. The trout counts obtained via different methods were well correlated (r = 0.65–0.72), providing a coherent description of the relative pool abundance across the methods. However, the methods were differently affected by environmental variables, depending on the age classes of trout. Specifically, the adult and subadult counts provided by ELE and VSA were negatively and positively affected by the maximum pool depth, respectively; adult and subadult counts of VSA and the SVS were positively affected by pool area; the juvenile counts provided by the UCS were positively affected by pool shade and negatively affected by water turbidity; juvenile counts provided by VSA were positively affected by shade. Variables such as pool depth, area, shading, water turbidity and proportion of age classes can be hardly controlled in monitoring programs, and their bias could be modelled. Different sampling methods provided similar information about relative abundance and appeared equivalent. While ELE could be selected to collect samples and biometric data, monitoring relative abundance with the UCS, VSA, and SVS appears more suited and can also involve citizen scientists.

Probiotics play an important role in animal production, providing health benefits to the host by improving intestinal microbial balance. In this study, we added three different probiotics, Saccharomyces cerevisiae (SC), Bacillus licheniformis (BL), and lactic acid bacteria (LAB), and compared them with the control group (CON), to investigate the effects of probiotic supplementation on growth performance, gut microbiology, and gut flora of S. trutta. Our results showed that feeding probiotics improved the survival, growth, development, and fattening of S. trutta. Additionally, probiotic treatment causes changes in the gut probiotic community, and the gut flora microorganisms that cause significant changes vary among the probiotic treatments. However, in all three groups, the abundance of Pseudomonas, Acinetobacter, and Rhizophagus bacterial genera was similar to that in the top three comparative controls. Furthermore, differences in the composition of intestinal microbiota among feed types were directly associated with significant changes in the metabolomic landscape, including lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The probiotic treatment altered the gut microbiome, gut metabolome, and growth performance of S. trutta. Using a multi-omics approach, we discovered that the addition of probiotics altered the composition of gut microbiota, potentially leading to modifications in gut function and host phenotype. Overall, our results highlight the importance of probiotics as a key factor in animal health and productivity, enabling us to better evaluate the functional potential of probiotics.

Aquaculture species are often exposed to acute stressors such as low water levels and handling during routine aquaculture procedures. This might result in oxidative stress by the increased reactive oxygen species (ROS)' production (e.g., superoxide anion). The harmful effects of ROS are eliminated by a defense system, referred antioxidant defense system (ADS). sod1 is the first gene involved in the ADS. Therefore, we cloned and characterized the open reading frame of the sod1 in brown trout. Then, we determined the effects of low water level and handling stress on sod1 mRNA expression in the liver and gills at 0 min, 1 and 2 h. The total RNA isolated was used to synthesize cDNA for RT-qPCR analysis. Phylogenetic tree, identity/similarity percentages, genomic organization, and conserved gene synteny analyses were applied to characterize Sod1/sod1. While low water level stress upregulated sod1 expression in the liver compared to the control group, no significant differences were observed in the gills between experimental groups. However, brown trout differently responded to handling stress at different time intervals in both tissues. Transcriptional differences were also noted between the sexes. This study contributes to the current understanding of the molecular mechanism between oxidative stress and ADS. [ABSTRACT FROM AUTHOR]

Abundance, placement beneath cover and clustering of brown trout spawning redds were monitored throughout five spawning seasons (2016–2020) in a 4.8‐km reach of a Minnesota coldwater stream to assess the potential impacts of concurrent stream habitat rehabilitation projects. We anticipated that redd abundance (redds/100 m stream segments) and placement beneath cover (e.g. logs and branches, boulders, overhanging bank vegetation, aquatic macrophytes) would increase and redd clustering (placement within 1.5 m of other redds) would decline as stream sections were rehabilitated. Repeated redd counts were conducted for the entire stream reach during each of the five spawning seasons, and redd cover and clustering were documented. Before‐after comparison of impact (BACI) tests were used to compare redd abundances in control versus rehabilitated stream sections, and before‐after distributional tests compared redd placement beneath cover and redd clustering within rehabilitated sections. In total, 1895 brown trout spawning redds were documented within the study reach during the five spawning seasons combined. Redd abundance increased nearly fivefold throughout the 5‐year study period (from 3.5 to 15.5 redds/100 m), but no significant difference was detected in redd abundances between rehabilitated versus control stream sections. Redd placement beneath cover (63% beneath cover in total) also increased throughout the study, but at a rate nine to 45 times greater in stream sections rehabilitated during the study than in control or previously rehabilitated sections. Redd clustering remained unchanged (5‐year means = 35 to 46% of all redds clustered) in rehabilitated sections, but increased significantly through time (0% to 35%) in the control section. Stream habitat rehabilitation did not increase spawning redd abundance or reduce redd clustering in rehabilitated stream sections, but redd placement beneath cover increased after rehabilitation to levels present in other stream sections. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants (WWTP) play a critical role in mitigating adverse environmental impacts of urban and industrial wastewater by removing pollutants and reducing the risk of contamination. Discharges of treated effluents from WWTPs can still have significant effects on freshwater ecosystems, particularly on sensitive species like brown trout. We analyzed the effects of a modern WWTP on a freshwater ecosystem, studying fish biodiversity and biomass, the occurrence of the parasitic disease Proliferative Kidney Disease (PKD) on brown trout, river water temperatures throughout the year and fish habitat and diversity. No major differences between up- and downstream of the WWTP were observed in habitat structure and attractiveness, fish biomass and species diversity, nor in PKD prevalence or intermediate host presence. However, immediately at the WWTP's effluent and continuing downstream, the water temperature rose by almost 1 °C. While WWTPs are crucial for reducing the environmental impact of urban and industrial wastewater, their effluents can still have important consequences for freshwater ecosystems. Brown trout are particularly susceptible to increases in water temperature, especially regarding PKD severity and consequent mortality. To ensure the long-term health and sustainability of freshwater ecosystems, it is imperative to improve measures to minimize water temperature rises and mitigate downstream cascade effects on sensitive organisms like brown trout. [ABSTRACT FROM AUTHOR]

Changes in the number, structure, and function of mitochondria during the early life stages of animals can play an important role for an organism’s metabolic rate, growth, and health. Previous studies have shown that juvenile brown trout (Salmo trutta) subjected to elevated temperatures during the embryonic stage respond phenotypically with a reduced metabolic rate. The aim of this study was to explore if embryonic temperature affects the mitochondria content of young brown trout and as such explains the previously found differences in metabolic rates. Here, we optimize a quantitative PCR (qPCR) method for the mitochondria cytochrome c oxidase subunit I gene, and then use the method as a proxy for mitochondrial DNA content. We hypothesize that young trout subjected to elevated temperatures during the embryonic stage respond phenotypically with a reduced mitochondrial DNA content. To test this hypothesis, we subjected brown trout to either control ambient (4.4 ± 1.5 °C) or elevated temperatures (7.1 ± 0.6 °C) during embryogenesis. Subsequently, we extracted DNA from liver and white muscle tissue of juvenile brown trout from the two different incubation temperature treatments and successively optimized qPCR for mitochondrial DNA. We found that the amount of mitochondria DNA in liver tissue was 18 times higher than in white muscle tissue, but there was no significant difference in mitochondria content in liver or muscle tissue between brown trout exposed to elevated and ambient control temperatures during embryogenesis. We conclude that reduced metabolic rate is not likely associated with mitochondria DNA content. We also suggest that qPCR is a simple and cost-effective method to quantify mitochondria DNA in frozen and partly degraded tissue from different treatment groups and a useful proxy for identification of differences in mitochondria number.

Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre‐mating and post‐mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid in general had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation between the native North American species. [ABSTRACT FROM AUTHOR]

Understanding how environmental gradients shape the spatial patterns of intraspecific genetic diversity is a central issue in ecological and evolutionary sciences. In riverine ecosystems, there is generally an increase in neutral genetic diversity downstream, as well as an increase in genetic differentiation among upstream populations. However, selective pressures may vary markedly along the upstream–downstream gradient, which could modify these patterns, but this has rarely been tested empirically. Here, we investigated how environmental gradients in a river network could shape the spatial patterns of intraspecific genetic diversity and differentiation in both neutral SNP markers and functional genetic markers putatively under natural selection (candidate SNPs associated with physiological functions and immune Major Histocompatibility Complex (MHC) loci) in wild brown trout populations. First, we showed that both the distance from the confluence and the centrality on the river network could explain the variation in genetic diversity and differentiation. Second, we found that both neutral and functional markers followed a similar pattern, with a higher genetic diversity and a lower genetic differentiation among populations that were more central and/or near to the confluence. This study highlights the importance of considering both the spatial and hydrological factors of a river network to understand and predict the role of dendritic connectivity in the spatial patterns of genetic diversity and differentiation in wild fish populations. [ABSTRACT FROM AUTHOR]

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific interest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta.

A key challenge in many regulated rivers is to define adequate flow levels to protect aquatic organisms. Provisioning of suitable flow can be pivotal bottlenecks for fishes such as salmon and trout that use the riverbed as an incubation habitat. Additionally, the locations where females spawn will define the probability that embryos will be dewatered during the incubation period in a regulated flow regime. We investigated the water flow, dewatering, and incubation mortality in Atlantic salmon and brown trout in natural nests over 19 years in the regulated Bjoreio River in western Norway. During the study period, different flow strategies were applied to mitigate the dewatering of incubating salmon and trout embryos. Average survival in nests sampled in late winter ranged from 54% to 92% among years and was significantly correlated with the minimum water flow occurring during the incubation period. Mortality was significantly higher in nests in shallow areas, reflecting nests exposed to dewatering. The results demonstrate a strong link between incubation mortality and managed flow regimes for river spawning salmonids. Using detailed information on the nest location and incubation mortality, we estimate minimum flow requirements for this river and demonstrate an approach to effectively mitigate the impact of river regulations on embryo survival in Atlantic salmon and brown trout. [ABSTRACT FROM AUTHOR]

Our understanding of how microbiome signatures are modulated in wild fish populations remains poorly developed and has, until now, mostly been inferred from studies in commercial and farmed fish populations. Here, for the first time, we have studied changes in the skin and blood microbiomes of the Salmo trutta population of the volcanic Kerguelen archipelago located at the northern limit of the Antarctic Ocean. The Kerguelen Islands present a natural framework of population expansion and reveal a likely situation representing further climate change in distribution areas. Our results showed that S. trutta of the Kerguelen Islands has a microbiome signature distinct from those of salmonids of the Northern Hemisphere. Our study also revealed that the skin and blood microbiomes differ between sedentary and migratory S. trutta. While 18 phyla were shared between both groups of trout, independent of the compartment, 6 phyla were unique to migratory trout. Further analyses showed that microbiome signatures undergo significant site-specific variations that correlate, in some cases, with the peculiarity of specific ecosystems. Our study also revealed the presence of potential pathogens at particular sites and the impact of abiotic factors on the microbiome, most notably due to the volcanic nature of the environment. This study contributes to a better understanding of the factors that modulate the microbiome signatures of migratory and sedentary fish populations. It will also help to better monitor the impacts of climate change on the colonization process in the sub-Antarctic region. [ABSTRACT FROM AUTHOR]

Climate warming imposes a severe threat to freshwater ecosystems, which are dominated by ectotherms such as fish and aquatic insects. To better predict the effects of climate warming on thermally sensitive ecosystems, information on how temperature affects individual traits within populations is fundamental.Patterns of intraspecific variation in thermal reaction norms along geographic thermal gradients provide valuable information. Immediate temperature effects on individual traits can be inferred from the shape of the thermal reaction norm. The way that temperature and associated environmental conditions (to which populations have been exposed over generations) affect individual traits through transgenerational plasticity in, and/or natural selection on, these traits can also be inferred from patterns of trait variation along a geographic thermal gradient.Many studies have documented patterns of intraspecific variation in thermal reaction norms along geographic thermal gradients. However, most previous studies cannot exclude the possibility that the observed geographic patterns are solely explained by random processes, such as isolation by distance, due to the lack of replication of geographic gradients. Here, we show consistent patterns in intraspecific trait variation along geographic thermal gradients using Salmo trutta (brown trout), which is an ecologically and economically important fish in alpine streams.We kept trout embryos collected from 52 families from 14 populations along wide and replicated elevational gradients from three Alpine drainages (Danube, Po, and Rhine) in two temperature treatments (3.2 and 6.2°C). Timing and body size at emergence from the nest, which are key early life‐history traits of trout affecting their early growth and survival, were measured.Besides faster embryonic development at warmer temperatures, we found that offspring from low‐elevation parents took very slightly longer to reach emergence from fertilisation and were larger than offspring from high‐elevation parents. Importantly, this was evident for all three drainages. Further analyses found that the longer duration until‐ and larger body length at‐ emergence of low‐elevation trout were mainly due to the larger eggs laid by low‐elevation females, which had larger body size than high‐elevation females.Trout female body size, which is positively correlated with egg size, is susceptible to temperatures and associated environmental conditions. Consequently, climate warming may not only immediately accelerate development rate but also shift timing and size at emergence through egg size‐mediated maternal effects within a relatively short time scale. [ABSTRACT FROM AUTHOR]

The increase in abundance of great cormorants (Phalacrocorax carbo sinensis) over the last decades has caused concern for the sustainability of fish populations. Cormorants are opportunistic piscivorous birds that eat fish from a wide range of species and sizes, in marine, lacustrine and riverine habitats. It has been documented that juvenile salmonids are under significant predation pressure by great cormorants, although knowledge on the predation of adult salmonids by cormorants is limited. In this study, adult anadromous brown trout (Salmo trutta) were tagged over multiple years with PIT tags during their spawning migration in a Danish lowland river. Two nearby cormorant colonies were subsequently scanned for PIT tags to estimate predation rate. It was estimated that by minimum 15.4% of tagged adult sea trout were predated by cormorants. The majority of the individuals were predated in the river, and females were more likely to be predated than males. Moreover, length had a significant effect on predation probability: individuals between 35 and 43 cm had the highest likelihood to be predated, while smaller and larger individuals were less likely to be predated. Our findings challenge the assumption that cormorants do not prey on reproductively mature salmonids. Furthermore, predation of mature individuals may have implications for the recruitment and sustainability of the population. [ABSTRACT FROM AUTHOR]

Sub‐daily fluctuations in streamflow may have adverse effects on the biota downstream of dams in hydropeaking‐regulated rivers. Although the stranding of salmonid fry is one documented effect of hydropeaking, little is known about the species‐specific behavioural and subsequent growth effects of sub‐daily flow fluctuations. We investigated the effects of sub‐daily flow fluctuation on growth, mortality and behaviour of sympatric Atlantic salmon (Salmo salar) and brown trout (S. trutta) fry (29–34 mm) in a laboratory experiment. The fluctuating flow treatment negatively affected growth and increased mortality for trout but not for salmon. The level of aggressive behaviour was similar in the fluctuating‐ and stable‐flow treatments. Within the fluctuating flow treatment, there was a trend that more fishes were visibly active above the substrate during low than high flow. These findings suggest that hydropeaking‐induced flow fluctuations may affect fry of different salmonid species in different ways and that brown trout fry may be more vulnerable to hydropeaking effects than Atlantic salmon fry. It can therefore be important to consider the possibility of divergent reactions by different fish species under hydropeaking situations and to incorporate species‐specific strategies to conserve culturally and economically relevant riverine fish species. [ABSTRACT FROM AUTHOR]

Mixed-stock fisheries which simultaneously cause mortality amongst several populations of a species of fish may occur where separate stocks partially or completely overlap in the geographic area of harvest. This study aims to analyze the population-of-origin of adult and subadult adfluvial lacustrine brown trout Salmo trutta, exploited in a mixed-stock fishery in Upper Tuloma Reservoir in Eastern Fennoscandia, using otolith microchemistry. To evaluate the origin of migratory brown trout captured in these mixed-stock harvest fisheries, we undertook otolith sampling of brown trout juveniles in fluvial spawning and rearing habitats in the reservoir watershed, including 13 natal tributaries across the catchment of the reservoir in both Russia and Finland. Harvested adult and subadult brown trout otoliths were sampled from the impoundment in the central area of the reservoir and we analyzed for stock-related character differences to compare with known populations, using trace element signatures, with fish from the mixed stock fishery. The assignments-of-origin in the mixed-stock fishery-harvest samples did not follow the known distribution of populations sampled from natal streams in the watershed. For example, brown trout from the largest tributary catchments of Lotta River and Nota River were less represented in the mixed-harvest sample, which was contradictory to their contribution to the overall spawning and rearing areas of the catchment. These results point towards the importance of maintaining the diversity of different spawning and rearing tributaries required for brown trout recruitment into mixed stock fisheries, and the potential of the existence of population structure of brown trout in the reservoir catchment. Our information suggests that it is important to develop conservation and management strategies for natal habitats in multiple streams utilized by adfluvial lacustrine brown trout populations inhabiting various catchments and that are harvested in mixed-stock fisheries. [ABSTRACT FROM AUTHOR]

Storage hydropower plants, which are an important component of energy production in Switzerland, can lead to hydro‐ and thermopeaking, affecting river habitats and organisms. In this study, we developed an approach for integrating water temperature simulations into a habitat model to assess the impact of both hydro‐ and thermopeaking on the availability of suitable fish habitats. We focused on the habitat requirements of juvenile brown trout (Salmo trutta) in a semi‐natural braided floodplain along the Moesa River (Southern Switzerland) in early summer. First, we defined different scenarios (with and without hydropeaking) based on the local hydrological and meteorological conditions. Second, we used a two‐dimensional depth‐averaged hydro‐ and thermodynamic model to simulate the spatial distributions of water depth, flow velocity, and water temperature. Third, we applied generalized preference curves for juvenile brown trout to identify hydraulically suitable habitats, and developed a new index to assess the availability of thermally suitable habitats. Finally, we quantified the extent to which hydraulically and thermally suitable habitats overlap in space and time. During both base and peak flow phases, most of the hydraulically and thermally suitable habitats are located in the side channels. High flow conditions combined with strong cold‐thermopeaking lead to a higher thermal heterogeneity. However, disconnected habitats originate in the dewatering zone, increasing the risk of stranding as well as thermal stress. By helping to better understand the effects of thermopeaking on the availability of fish habitats, our approach could contribute to the design and evaluation of ecological restoration in hydropeaking rivers. [ABSTRACT FROM AUTHOR]

This research investigates the potential of lactic acid bacteria (LAB) from freshwater salmonids as prospective probiotics for application in aquaculture. LAB and pathogenic bacteria were obtained from mucus and tissues of Oncorhynchus mykiss and Salmo trutta from fish farms in northeast Spain that had not used antibiotics for the six months preceding the study. Isolates were identified using Gram staining and sequencing of 16S rRNA and ITS-1. To assess the safety of the LAB, antibiotic susceptibility tests (ASTs) against 23 antimicrobials were performed. In vitro antagonism assays were conducted to evaluate the inhibitory effects of living LAB using the agar diffusion test method and their metabolites using the agar well diffusion method. The assays targeted six specific pathogens: Aeromonas salmonicida subsp. salmonicida, Carnobacterium maltaromaticum, Vagococcus salmoninarum, Yersinia ruckeri, Lactococcus garvieae, and the marine pathogen Vibrio jasicida. Additionally, a toxicity assay was conducted on embryonic eggs of S. trutta. The ASTs on probiotic LAB candidates revealed varied responses to antimicrobials, but no resistance to oxytetracycline or florfenicol, which are two antibiotics commonly used in aquaculture, was detected. The in vitro assays indicate that LAB exhibit antagonistic effects against pathogens, primarily when directly stimulated by their presence. In applications involving embryonic eggs or larvae, certain live strains of LAB were found to have adverse effects, with some isolates resulting in higher mortality rates compared to the control group or other isolates. Furthermore, the potential pathogenicity of certain LAB strains, typically considered safe in salmonids, warrants deeper investigation.

Ulcerative dermal necrosis (UDN) it is an idiopathic condition of fish skin that has been reported in Europe since 1820. UDN affects primarily an epidermal and dermal layer of the skin lesion, which in the early stages, occurs in the head area of migratory adult salmonids entering freshwater for upstream river migration. Studies show that acid-base water properties in estuaries are exceptionally dynamic, which results from the variability of the CO2 system. The carbonate system is shaped by the net effect of mineralization and primary production enhanced by: i) the constant inflow of nutrients and organic matter from the land and ii) the horizontal and vertical mixing of the two end-members of the total alkalinity, dissolved organic carbon and pCO2; both cause high acid-base gradients between the river and the ocean. Climate change affects the biogeochemical characteristics of estuaries. We show a strong positive correlation between local temperature anomalies along the Polish coast and the occurrence of UDN in Salmo trutta sp. spawners in the Słupia River, Poland. The results suggest that the biogeochemical processes associated with climate change may be at least one component of the UDN aetiology. They also highlight the need for systematic monitoring to understand these processes and their consequences. It is crucial for restoring and further preserving sustainability in the coastal system, which involves marine life and human well-being. Furthermore, salmonids are valuable commercial fish. Thus any health issues may have a profound effect on fisheries, local communities and the fish market in general.

Hormones have been used to change phenotypic sex in many fish species. However, information specific to changing sex in brown trout Salmo trutta is lacking. This study compared the effectiveness of two different 17β-estradiol (estradiol) concentrations (20 mg/kg and 30 mg/kg) fed to brown trout for 60 days, beginning at initial feeding. At 456 days post-initial feeding, the 20 mg/kg and 30 mg/kg treatment groups were 84% and 86% female, respectively. These values were significantly higher than the 47% females observed in the control group which did not receive dietary estradiol. At the end of the 60-day estradiol treatment period, weight gain, percent weight gain, and feed conversion ratio were all significantly lower in the tanks of fish receiving estradiol than in the control tanks. Individual fish fed estradiol also weighed significantly less and were significantly shorter than the fish not receiving estradiol-coated feed. Mortality ranged from 1.0 to 2.4% among the treatments and was not significantly different. After 105 days post-initial feeding, weight gain, percent weight gain, and feed conversion ratio were not significantly different among the treatments. At 456 days post-initial feeding, individual fish were significantly longer and heavier in the 20 mg/kg estradiol treatment compared to the fish in the control treatment, and the fish in the 30 mg/kg estradiol treatment were similar to the other two treatments. This study is the first to document the successful sex reversal of brown trout using estradiol. While the estradiol treatments used in this study did not lead to complete feminization, the observed 85-to-15% female-to-male phenotypic ratio indicates the successful feminization of genetic males. The levels of feminization observed in this study are suitable for this initial step to potentially develop a YY male broodstock to control invasive brown trout populations. [ABSTRACT FROM AUTHOR]

Context. The Murray--Darling Basin -- Australia's largest river system -- is heavily dominated by alien fish. Native fish species have suffered numerous localised extinctions and ~47% are listed on federal and/or state threatened species lists. Aims. This paper explores the hypothesis that alien fish and alien fish stockings can be the primary cause of decline and localised extinction of large-bodied native fish species, as opposed to habitat degradation and river regulation. The Lower Goodradigbee River, which is unregulated, in excellent instream health over the great majority of its course, and replete with high quality habitat, is utilised as a case study. Methods. I investigated the hypothesis by synthesising historical records with contemporary scientific research and recent field observations. The role of alien fish species, particularly alien trout species (Oncorhynchus mykiss and Salmo trutta) and constant stockings of them, were closely examined. Results. Data support the hypothesis that domination by alien trout species and their continual stocking have lead to historical declines and localised extinctions of large-bodied native fish species. Continued alien trout stockings, along with more recent invasions of alien carp (Cyprinus carpio) and alien redfin perch (Perca fluviatilis), are inhibiting native fish recovery. A suspected field sighting of the alien fish pathogen atypical Aeromonas salmonicida is reported, and the status of the declining native crayfish Murray cray (Euastacus armatus), and potential alien fish impacts upon them, are examined. Conclusions. The impacts of alien fish and alien fish stocking in Australia require major re-evaluation and dedicated research. Implications. It is strongly recommended that stocking of alien trout into the Lower Goodradigbee River for angling cease in order to conserve surviving native fish and Murray cray populations. Conservation stockings to effect a Murray cod (Maccullochella peelii) recovery in the Lower Goodradigbee River are warranted. [ABSTRACT FROM AUTHOR]

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific interest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta. [ABSTRACT FROM AUTHOR]