The effects of Pediococcus acidilactici MA18/5M on growth performance, gut integrity, and immune response using in vitro and in vivo Pacific salmonid models.

Microbial management is central to aquaculture's efficiency. Pediococcus acidilactici MA18/5M has shown promising results promoting growth, modulation of the immune response, and disease resistance in many fishes. However, the mechanisms through which this strain confers health benefits in fish are poorly understood, particularly in Pacific salmonid models. Briefly, the aims of this study were to i) assess the protective effects of P. acidilactici MA18/5M by examining gut barrier function and the expression of tight junction (TJ) and immune genes in vitro and in vivo, and ii) to determine the protective effects of this strain against a common saltwater pathogen, Vibrio anguillarum J382. An in vitro model of the salmonid gut was employed utilizing the cell line RTgutGC. Barrier formation and integrity assessed by TEER measurements in RTgutGC, showed a significant decrease in resistance in cells exposed only to V. anguillarum J382 for 24 h, but pre-treatment with P. acidilactici MA18/5M for 48 h mitigated these effects. While P. acidilactici MA18/5M did not significantly upregulate tight junction and immune molecules, pre-treatment with this strain protected against pathogen-induced insults to the gut barrier. In particular, the expression of ocldn was significantly induced by V. anguillarum J382, suggesting that this molecule might play a role in the host response against this pathogen. To corroborate these observations in live fish, the effects of P. acidilactici MA18/5M was evaluated in Chinook salmon reared in real aquaculture conditions. Supplementation with P. acidilactici MA18/5M had no effect on Chinook salmon growth parameters after 10 weeks. Interestingly, histopathological results did not show alterations associated with P. acidilactici MA18/5M supplementation, indicating that this strain is safe to be used in the industry. Finally, the expression pattern of transcripts encoding TJ and immune genes in all the treatments suggest that variation in expression is more likely to be due to developmental processes rather than P. acidilactici MA18/5M supplementation. Overall, our results showed that P. acidilactici MA18/5M is a safe strain for use in fish production, however, to assess the effects on growth and immune response previously observed in other salmonid species, an assessment in adult fish is needed.

Description of Discocotyle ciray n. sp. (Monogenea: Discocotylidae) from Parahucho perryi (Brevoort) from Hokkaido, Japan, with a redescription of D. sagittata (Leuckart, 1842).

Discocotyle sagittata (Leuckart, 1842) (Monogenea: Discocotylidae) is redescribed, based on specimens collected from the type host, Salmo trutta Linnaeus, from the type locality, Freiburg, Germany, supplemented with specimens from S. trutta and rainbow trout, Oncorhynchus mykiss (Walbaum) reared in an Austrian aquarium. The diagnosis of the genus Discocotyle Diesing, 1850 is emended. Discocotyle ciray n. sp. is described, based on immature, preadult and adult specimens from the salmonid, Parahucho perryi (Brevoort) at Eniwa, Hokkaido, Japan. Adult specimens of the new species were about twice as large as those of D. sagittata from S. trutta. When the type specimens of D. ciray n. sp. were examined together with museum specimens from P. perryi at Tsurui, Hokkaido, the body and clamp sizes were positively correlated to the host size. Their measurements from a smaller P. perryi at Tsurui overlapped with those of D. sagittata, showing that these size differences were not suitable differentiating keys. Discocotyle ciray n. sp. can be separated from D. sagittata by the morphologies of the female genital system (relatively anteriorly positioned ovary, short joint vaginal duct and much more strongly winding uterus). The genetic distances of COI mtDNA sequence between D. ciray n. sp. and D. sagittata were 18.0-18.6%. These remarkable genetic divergences also supported the distinct taxonomic status of D. ciray n. sp.

Identification, expression and molecular polymorphism of T-cell receptors α and ß from the glacial relict Hucho bleekeri.

The T-cell receptor (TCR) is a specific molecule on the surface of all T cells that mediates cellular adaptive immune responses to antigens. Hucho bleekeri is a critically endangered species and is regarded as a glacial relict that has the lowest-latitude distribution compared with any Eurasian salmonid. In the present study, two TCR genes, namely, TCR α and ß, were identified and characterized in H. bleekeri. Both TCR α and TCR ß have typical TCR structures, including the IgV domain, IgC domain, connecting peptide, transmembrane and cytoplasmic domains. The two TCR genes were constitutionally expressed in various tissues, with the highest expression found in the spleen for TCR α and in the trunk kidney for TCR ß. Challenge of H. bleekeri with LPS or poly(I:C) resulted in significant upregulation of both TCR α and ß expression in headkidney and spleen primary cells, indicating their potential roles in the immune response. Molecular polymorphism analysis of the whole ORF regions of TCR α and ß in different individuals revealed high diversity of IgV domains of these two genes, especially in complementarity-determining region (CDR) 3. The ratio of nonsynonymous substitution occurred at a significantly higher frequency than synonymous substitution in the CDR of TCR α and ß, demonstrating the existence of positive selection. The results obtained in the present study enhance our understanding of TCR roles in regulating immune mechanisms and provide new information for the study of TCR lineage diversity in fish.

Effect of anti-adhesive supplement doses on sperm motility characteristics in the European whitefish (Coregonus lavaretus).

Sperm adhering to glass slides is one of the main problems during fish sperm motility analyses with CASA systems. To mitigate this, albumin is the supplement added most frequently to activating solutions. However, there is no data on the use of supplements other than albumin (in various concentrations) in analyses of European whitefish (Coregonus lavaretus) sperm motility. This issue was investigated in the presented research using three anti-adhesive supplements (albumin, casein, Pluronic F-127) that were added to Billard solution (BS: 20 mM Tris, 1 mM CaCl2, 154 mM NaCl, 30 mM glycine at pH 9.0) at different concentrations (0.0; 0.1; 0.2; 0.5; 1.0; 2.0%). It was noted that the addition of the lowest concentration (0.1%) of albumin, casein, or the pluronic to BS had a significant effect on the motility and kinetic parameters of whitefish sperm compared to pure BS. BS supplemented with 0.2-0.5% albumin was the most appropriate variant used for whitefish sperm motility activation in the present experiment. BS supplemented with the pluronic at 1.0-2.0% concentrations resulted in significantly higher values of almost all CASA parameters compared to casein at the same concentrations. Moreover, CASA parameters determined in this variant of the pluronic (1.0-2.0%) were similar to those when BS was supplemented with the same albumin concentrations. This indicated that instead of albumin, the pluronic at higher concentrations in BS might be used to analyze whitefish sperm motility.

Consequences of reduced effectiveness of salmon lice treatments for lice control.

The effective control of ectoparasitic salmon lice, Lepeophtheirus salmonis, in fish farms is challenged by the salmon lice having developed resistance towards several antiparasitic drugs and by the effectiveness of non-medicinal treatments being limited by considerations of fish welfare. When new antiparasitics are introduced to the market, these should be used sparingly to slow resistance development. Using a population model for salmon lice parameterised for salmonid fish farms in Norway, we quantified how reduced treatment effectiveness influences treatment frequency and lice abundance. Furthermore, we investigated when in the production cycle a highly effective lice treatment leads to the largest reduction in the total number of treatments, mean lice abundance and lice larvae production. Results showed that reductions in treatment effectiveness to lower than 50% led to the steepest increases in treatment frequency and mean lice abundance, as well as to increased risk that lice abundance increased beyond control. The timing of the most effective treatment had only moderate effects on the total treatment need and the mean number of adult female lice through the production cycle, but large effect on the production of lice larvae in spring. These findings imply that farmers can optimise the timing of the most effective treatment to reduce the release of lice larvae in the period of year when wild salmonids are in coastal waters, without compromising total treatment need or mean lice levels.

Smaller body size under warming is not due to gill-oxygen limitation in a cold-water salmonid.

Declining body size in fishes and other aquatic ectotherms associated with anthropogenic climate warming has significant implications for future fisheries yields, stock assessments and aquatic ecosystem stability. One proposed mechanism seeking to explain such body-size reductions, known as the gill oxygen limitation (GOL) hypothesis, has recently been used to model future impacts of climate warming on fisheries but has not been robustly empirically tested. We used brook trout (Salvelinus fontinalis), a fast-growing, cold-water salmonid species of broad economic, conservation and ecological value, to examine the GOL hypothesis in a long-term experiment quantifying effects of temperature on growth, resting metabolic rate (RMR), maximum metabolic rate (MMR) and gill surface area (GSA). Despite significantly reduced growth and body size at an elevated temperature, allometric slopes of GSA were not significantly different than 1.0 and were above those for RMR and MMR at both temperature treatments (15°C and 20°C), contrary to GOL expectations. We also found that the effect of temperature on RMR was time-dependent, contradicting the prediction that heightened temperatures increase metabolic rates and reinforcing the importance of longer-term exposures (e.g. >6 months) to fully understand the influence of acclimation on temperature-metabolic rate relationships. Our results indicate that although oxygen limitation may be important in some aspects of temperature-body size relationships and constraints on metabolic supply may contribute to reduced growth in some cases, it is unlikely that GOL is a universal mechanism explaining temperature-body size relationships in aquatic ectotherms. We suggest future research focus on alternative mechanisms underlying temperature-body size relationships, and that projections of climate change impacts on fisheries yields using models based on GOL assumptions be interpreted with caution.

Local and systemic replicative fitness for viruses in specialist, generalist, and non-specialist interactions with salmonid hosts.

Host tissues represent diverse resources or barriers for pathogen replicative fitness. We tested whether viruses in specialist, generalist, and non-specialist interactions replicate differently in local entry tissue (fin), and systemic target tissue (kidney) using infectious hematopoietic necrosis virus (IHNV) and three salmonid fish hosts. Virus tissue replication was host specific, but one feature was shared by specialists and the generalist which was uncommon in the non-specialist interactions: high host entry and replication capacity in the local tissue after contact. Moreover, specialists showed increased replication in systemic target tissues early after host contact. By comparing ancestral and derived IHNV viruses, we also characterized replication tradeoffs associated with specialist and generalist evolution. Compared with the ancestral virus, a derived specialist gained early local replicative fitness in the new host but lost replicative fitness in the ancestral host. By contrast, a derived generalist showed small replication losses relative to the ancestral virus in the ancestral host but increased early replication in the local tissue of novel hosts. This study shows that the mechanisms of specialism and generalism are host specific and that local and systemic replication can contribute differently to overall within host replicative fitness for specialist and generalist viruses.

Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.

On the prediction of SAV transmission among Norwegian aquaculture sites.

Pancreas Disease (PD) is a viral disease that affects Atlantic salmon (Salmo salar) in Norwegian, Scottish and Irish aquaculture. It is caused by salmonid alphavirus (SAV) and represents a significant problem in salmonid farming. Infection with SAV leads to reduced growth, mortality, product downgrading, and has a significant financial impact for the farms. The overall aim of this study is to evaluate the effect of various factors on the transmission of SAV and to create a predictive model capable of providing an early warning system for salmon farms within the Norwegian waters. Using a combination of publicly available databases, specifically BarentsWatch, and privately held PCR analyses a feature set consisting of 11 unique features was created based on the input parameters of the databases. An ensemble model was developed based on this feature set using XG-Boost, Ada-Boost, Random Forest and a Multilayer Perceptron. It was possible to successfully predict SAV transmission with 94.4% accuracy. Moreover, it was possible to predict SAV transmission 8 weeks in advance of a 'PD registration' at individual aquaculture salmon farming sites. Important predictors included well boat movement, environmental factors, proximity to sites with a 'PD registration' and seasonality.

Morphological and Habitat Quality of Salmonid Streams and their Relationship with Fish-Based Indices in Aotearoa New Zealand and Ontario (Canada).

Habitat degradation is one of the major reasons for freshwater species decline. Hydrogeomorphological processes (such as sediment transport, bank erosion, and flooding) operate at the catchment scale and determine habitat features in river reaches. However, habitat quality indices and restoration for freshwater fish species are often implemented at small spatial scales of a few hundred metres. The Morphological Quality Index (MQI) considers fluvial processes at larger scales as well as channel forms, human impacts, and historical changes, but few studies have assessed its relevance for ecosystem health. We investigated relationships between the MQI, habitat quality (using the Qualitative Habitat Evaluation Index, QHEI), land cover, and fish metrics (number of fish species, index of biotic integrity (IBI), and trout biomass) in 26 salmonid streams in Aotearoa New Zealand and Southern Ontario, Canada. We found a significant correlation between the MQI and QHEI, and both metrics were correlated with urban and native forest proportion in the catchment. However, we found no relation between the MQI and the proportion of agricultural land in the catchment, while the QHEI was correlated with agricultural land in the riparian zone, highlighting the importance of vegetated riparian buffers in providing fish habitat. Establishing a strong correlation with fish metrics remains challenging. Nevertheless, a modified MQI targeting ecological health could be used as an effective management tool for aquatic conservation.

Environmental variation associated with overwintering elicits marked metabolic plasticity in a temperate salmonid, Salvelinus fontinalis.

Poleward winters commonly expose animals, including fish, to frigid temperatures and low food availability. Fishes that remain active over winter must therefore balance trade-offs between conserving energy and maintaining physiological performance in the cold, yet the extent and underlying mechanisms of these trade-offs are not well understood. We investigated the metabolic plasticity of brook char (Salvelinus fontinalis), a temperate salmonid, from the biochemical to whole-animal level in response to cold and food deprivation. Acute cooling (1°C day-1) from 14°C to 2°C had no effect on food consumption but reduced activity by 77%. We then assessed metabolic performance and demand over 90 days with exposure to warm (8°C) or cold winter (2°C) temperatures while fish were fed or starved. Resting metabolic rate (RMR) decreased substantially during initial cooling from 8°C to 2°C (Q10=4.2-4.5) but brook char exhibited remarkable thermal compensation during acclimation (Q10=1.4-1.6). Conversely, RMR was substantially lower (40-48%) in starved fish, conserving energy. Thus, the absolute magnitude of thermal plasticity may be masked or modified under food restriction. This reduction in RMR was associated with atrophy and decreases in in vivo protein synthesis rates, primarily in non-essential tissues. Remarkably, food deprivation had no effect on maximum oxygen uptake rates and thus aerobic capacity, supporting the notion that metabolic capacity can be decoupled from RMR in certain contexts. Overall, our study highlights the multi-faceted energetic flexibility of Salvelinus spp. that likely contributes to their success in harsh and variable environments and may be emblematic of winter-active fishes more broadly.

Zooplankton taxa repository of DDTtot and sumPCB14: Seasonal and decadal variations in Lake Maggiore.

Lake Maggiore has been the subject of a monitoring program on persistent organic pollutants (DDTs and PCBs) since 1996 when DDT contamination was first detected. In this context, in 2009 we started to estimate the concentration of DDTtot (Dichlorodiphenyltrichloroethane, sum of p,p'-DDT, o,p'-DDT, p,p'-DDD, o,p-DDD, p,p-DDE, o,p-DDE) and sumPCB14 (polychlorinated biphenyls 18, 28, 31, 44, 52, 101, 118, 149, 138, 153, 170, 180, 194 and 209) in zooplankton pelagic organisms preyed on by zooplanktivorous fish (size fraction ≥450 µm). We evaluated taxa specific repositories of DDTtot and sumPCB14, their seasonal variation, their changes over the period 2009-2021 and the potential contribution of different taxa in transferring toxicants to whitefish, based on the Ivlev's Electivity Index. The repository of both POPs was generally higher in spring. A decrease in the zooplankton Standing Stock Biomass (SSB) drove a decline in the zooplankton DDTtot repository over the last six years (2016-2021 SSBmean = 12.5 mg m-3; 2009-2015; SSBmean = 30 mg m-3), despite the concentration being broadly constant during this period. The sumPCB14 repository was generally characterized by lower values during the last six years, but the difference with the previous period was not so marked. Daphnia and cyclopoids were the major contributors to the repository; however, when the whitefish selectivity index was applied, the role of carnivorous Bythotrephes was more important to the detriment of cyclopoids, particularly in summer and winter. Our results are useful to elaborate predictive models on the transfer of POPs along the food chain and highlight not only the importance of freshwater zooplankton in toto, but also that different taxa can have different roles. The increasing importance of microphagous zooplankton, driven by water warming and extended thermal stratification, underlines the need for future studies on the role of small zooplankton as carriers of POPs in freshwater lakes.

Revisiting the role of behavior-mediated structuring in the survival of populations in hostile environments.

Increasing the population density of target species is a major goal of ecosystem and agricultural management. This task is especially challenging in hazardous environments with a high abundance of natural enemies such as parasites and predators. Safe locations with lower mortality have been long considered a beneficial factor in enhancing population survival, being a promising tool in commercial fish farming and restoration of threatened species. Here we challenge this opinion and revisit the role of behavior structuring in a hostile environment in shaping the population density. We build a mathematical model, where individuals are structured according to their defensive tactics against natural enemies. The model predicts that although each safe zone enhances the survival of an individual, for an insufficient number of such zones, the entire population experiences a greater overall mortality. This is a result of the interplay of emergent dynamical behavioral structuring and strong intraspecific competition for safe zones. Non-plastic structuring in individuals' boldness reduces the mentioned negative effects. We demonstrate emergence of non-plastic behavioral structuring: the evolutionary branching of a monomorphic population into a dimorphic one with bold/shy strains. We apply our modelling approach to explore fish farming of salmonids in an environment infected by trematode parasites.

Specific features of parasite communities of Siberian cisco Coregonus sardinella in polytypic water bodies of the polar regions: species richness.

The article dwells upon characteristics of the species richness of parasite communities in least cisco Coregonus sardinella Valenciennes in Polar water bodies: Kureyskoye Reservoir, Lake Kutaramakan, Khatanga River. The communities consist of parasite species common in coregonids. The main species in all the parasite communities in least cisco are Dibothriocephalus ditremus and D. dendriticus. Triaenophorus crassus plerocercoids dominate in the regulated water body (Kureyskoye Reservoir). To analyze the species richness of the component communities (s), coefficients of the power-law equation s = a × nb were applied, where a is the expected species richness in the first host individual examined, and b is the rate of species accumulation in parasite component communities (s). The resulting curves of species accumulation give statistical rigor to the assessment of differences and similarities of the species richness of the component communities of parasites in least cisco of various ages and habitats. The species richness of infra- and component parasite communities in least cisco was found to be significantly lower in the lake and the storage reservoir than in riverine habitats (Khatanga River). At the same time, the species accumulation rate for parasite communities in least cisco from Lake Kutaramakan was higher than in the reservoir due to a higher diversity of parasite infracommunities.

Aeromonas salmonicida, causative agent of salmonid furunculosis, isolated from the freshwater parasitic copepod, Salmincola californiensis.

Here, we provide evidence that the freshwater parasitic copepod, Salmincola californiensis, acts as a vector for Aeromonas salmonicida. While investigating the effects of S. californiensis on Chinoook salmon (Oncorhynchus tshawytscha), we tangentially observed that fish infected with the copepod developed furunculosis, caused by A. salmonicida. This occurred despite being reared in pathogen-free well water in a research facility with no prior history of spontaneous infection. We further investigated the possibility of S. californiensis to serve as a vector for the bacterium via detection of fluorescently labelled A. salmonicida inside the egg sacs from copepods in which the fish hosts were experimentally infected with GFP-A449 A. salmonicida. We then evaluated copepod egg sacs that were collected from adult Chinook salmon from a freshwater hatchery with A. salmonicida infections confirmed by either culture or PCR. The bacterium was cultured on tryptic soy agar plates from 75% of the egg sacs, and 61% were positive by PCR. These three separate experiments indicate an alternative tactic of transmission in addition to direct transmission of A. salmonicida in captivity. The copepod may play an important role in transmission of the bacterium when fish are more dispersed, such as in the wild.

Toxicity of common biocides used in aquaculture to embryos and larvae of Brachymystax tsinlingensis Li.

Brachymystax tsinlingensis Li is a threatened fish species endemic to China. With the problems of environmental factors and seeding breeding diseases, it is important to further improve the efficiency of seeding breeding and the basis of resource protection. This study investigated the acute toxicity of copper, zinc and methylene blue (MB) on hatching, survival, morphology, heart rate (HR) and stress behaviour of B. tsinlingensis. Eggs (diameter: 3.86 ± 0.07 mm, weight: 0.032 ± 0.004 g) of B. tsinlingensis were selected randomly from artificial propagation and developed from eye-pigmentation-stage embryos to yolk-sac stage larvae (length: 12.40 ± 0.02 mm, weight: 0.03 ± 0.001 g) and exposed to different concentrations of Cu, Zn and MB for 144 h in a series of semi-static toxicity tests. The acute toxicity tests indicated that the 96-h median lethal concentration (LC50 ) values of the embryos and larvae were 1.71 and 0.22 mg l-1 for copper and 2.57 and 2.72 mg l-1 for zinc, respectively, whereas the MB LC50 after 144-h exposure for embryos and larvae were 67.88 and 17.81 mg l-1 , respectively. The safe concentrations of copper, zinc and MB were 0.17, 0.77 and 6.79 mg l-1 for embryos and 0.03, 0.03 and 1.78 mg l-1 for larvae, respectively. Copper, zinc and MB treatments with concentrations greater than 1.60, 2.00 and 60.00 mg l-1 , respectively, led to a significantly low hatching rate and significantly high embryo mortality (P < 0.05), and copper and MB treatments with concentrations greater than 0.2 and 20 mg l-1 led to significantly high larvae mortality (P < 0.05). Exposure to copper, zinc and MB resulted in developmental defects, including spinal curvature, tail deformity, vascular system anomalies and discolouration. Moreover, copper exposure significantly reduced the HR of larvae (P < 0.05). The embryos exhibited an obvious change in behaviour, converting from the normal behaviour of emerging from the membrane head first to emerging tail first, with probabilities of 34.82%, 14.81% and 49.07% under copper, zinc and MB treatments, respectively. The results demonstrated that the sensitivity of yolk-sac larvae to copper and MB was significantly higher than that of embryos (P < 0.05) and that B. tsinlingensis embryos or larvae might be more resistant to copper, zinc and MB than other members of the Salmonidae family, which benefits their resource protection and restoration.

Ecological variation in invasive brown trout (Salmo trutta) within a remote coastal river catchment in northern Patagonia complicates estimates of invasion impact.

Salmonids were first introduced into the Chilean fresh waters in the 1880s, and c. 140 years later, they are ubiquitous across Chilean rivers, especially in the southern pristine fresh waters. This study examined the brown trout (Salmo trutta) and native taxa ecology in two adjacent but contrasting rivers of Chilean Patagonia. During spring 2016 and spring-fall 2017 we examined the variation in benthic macroinvertebrate and fish community composition and characterized fish size structure, stomach contents, and stable isotopes (δ13 C and δ15 N) to understand population structure, fish diet, and trophic interactions between S. trutta and native taxa. The native Galaxias maculatus (puye) dominated the fish community (74% of abundance). S. trutta was less abundant (16% of survey catch) but dominated the fish community (over 53%) in terms of biomass. S. trutta showed distinct diets (stomach content analysis) in the two rivers, and individuals from the larger river were notably more piscivorous, consuming native fish with a relatively small body size (<100-mm total length). Native fishes were isotopically distinct from S. trutta, which showed a wider isotopic niche in the smaller river, indicating that their trophic role was more variable than in the larger river (piscivorous). This study provides data from the unstudied pristine coastal rivers in Patagonia and reveals that interactions between native and introduced species can vary at very local spatial scales.

Effect of florfenicol on Piscirickettsia salmonis biofilm formed in materials used in salmonid nets, nylon and high-density polyethylene.

Piscirickettsiosis is the most prevalent bacterial disease affecting seawater salmon in Chilean salmon industry. Antibiotic therapy is the first alternative to counteract infections caused by Piscirickettsia salmonis. The presence of bacterial biofilms on materials commonly used in salmon farming may be critical for understanding the bacterial persistence in the environment. In the present study, the CDC Biofilm Reactor® was used to investigate the effect of sub- and over-MIC of florfenicol on both the pre-formed biofilm and the biofilm formation by P. salmonis under the antibiotic stimuli on Nylon and high-density polyethylene (HDPE) surfaces. This study demonstrated that FLO, at sub- and over-MIC doses, decreases biofilm-embedded live bacteria in the P. salmonis isolates evaluated. However, it was shown that in the P. salmonis Ps007 strain the presence of sub-MIC of FLO reduced its biofilm formation on HDPE surfaces; however, biofilm persists on Nylon surfaces. These results demonstrated that P. salmonis isolates behave differently against FLO and also, depending on the surface materials. Therefore, it remains a challenge to find an effective strategy to control the biofilm formation of P. salmonis, and certainly other marine pathogens that affect the sustainability of the Chilean salmon industry.

Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication.

Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.

Chronic exposure to environmental temperature attenuates the thermal sensitivity of salmonids.

Metabolism, the biological processing of energy and materials, scales predictably with temperature and body size. Temperature effects on metabolism are normally studied via acute exposures, which overlooks the capacity for organisms to moderate their metabolism following chronic exposure to warming. Here, we conduct respirometry assays in situ and after transplanting salmonid fish among different streams to disentangle the effects of chronic and acute thermal exposure. We find a clear temperature dependence of metabolism for the transplants, but not the in-situ assays, indicating that chronic exposure to warming can attenuate salmonid thermal sensitivity. A bioenergetic model accurately captures the presence of fish in warmer streams when accounting for chronic exposure, whereas it incorrectly predicts their local extinction with warming when incorporating the acute temperature dependence of metabolism. This highlights the need to incorporate the potential for thermal acclimation or adaptation when forecasting the consequences of global warming on ecosystems.