The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

Role of disulfide death in cancer (Review)

The research field of regulated cell death is growing extensively. Following the recognition of ferroptosis, other unique and distinct forms of regulated cell death, including cuproptosis and disulfide death, have been identified. Disulfide death occurs due to the abnormal accumulation of disulfides within cells in environments lacking glucose, leading to contraction of the actin cytoskeleton, which ultimately triggers various signaling pathways and cell death. The induction of disulfide death in the treatment of cancer may exhibit significant therapeutic potential. Therefore, in the present review, a comprehensive and critical analysis of the current understanding of the molecular mechanisms and regulatory networks of disulfide death is presented. In addition, the potential physiological functions of disulfide death in tumor suppression and immune surveillance as well as its pathological roles and therapeutic potential are described. The core focus areas for future research into this form of cell death are also explored. Given the current lack of extensive clinical findings and well-defined key concepts, these may be regarded as pivotal points of interest in future studies.

The weak association between hypoxia tolerance and thermal tolerance increases the susceptibility of abalone to climate change

The simultaneous occurrence of high temperatures and hypoxia events caused mass die-offs of aquatic animals. It is crucial to investigate the relationship between hypoxia tolerance and thermal tolerance of aquatic animals to predict the biological and ecological outcomes under global climate change scenarios. In this study, the hypoxia tolerance and thermal tolerance of Pacific abalone, Haliotis discus hannai, were measured by methods based on adhesion capacity (hypoxia adhesion duration and heat adhesion duration) and heart rate fluctuations (breakpoint of dissolved oxygen and Arrhenius breakpoint temperature). Weak correlations were found between hypoxia tolerance and thermal tolerance (Spearman correlation, r = -0.09, P = 0.2069; Pearson correlation, r = -0.04, P = 0.3313). Furthermore, a total of 21 significant SNPs and 19 candidate genes (such as cubn, lrp6, gria2, rft2, and casp8) were identified to be associated with hypoxia tolerance of Pacific abalone by conducting whole genome resequencing and genome-wide association study (GWAS). But there was no overlap between candidate genes associated with hypoxia tolerance and candidate genes associated with thermal tolerance, validating the weak correlation between hypoxia tolerance and thermal tolerance. This study highlights that individuals with greater hypoxia tolerance do not necessarily have greater thermal tolerance. Global warming and hypoxia may pose a greater threat to population size and genetic diversity of some aquatic animals than previously believed.

Climate challenges for fish larvae: Interactive multi-stressor effects impair acclimation potential of Atlantic herring larvae

Fish early life stages are particularly vulnerable and heavily affected by changing environmental factors. The interactive effects of multiple climate change-related stressors on fish larvae remain, however, largely underexplored. As rising temperatures can increase the abundance and virulence of bacteria, we investigated the combination of a spring heat wave and bacterial exposure on the development of Atlantic herring larvae (Clupea harengus). Eggs and larvae of Western Baltic Spring-spawners were reared at a normal and high temperature ramp and exposed to Vibrio alginolyticus and V. anguillarum, respectively. Subsequently, mRNA and miRNA transcriptomes, microbiota composition, growth and survival were assessed. Both high temperature and V. alginolyticus exposure induced a major downregulation of gene expression likely impeding larval cell proliferation. In contrast, interactive effects of elevated temperature and V. alginolyticus resulted in minimal gene expression changes, indicating an impaired plastic response, which may cause cellular damage reducing survival in later larval stages. The heat wave alone or in combination with V. alginolyticus induced a notable shift in miRNA expression leading to the down- but also upregulation of predicted target genes. Moreover, both increased temperature and the Vibrio exposures significantly altered the larval microbiota composition, with warming reducing microbial richness and diversity. The outcomes of this study highlight the high sensitivity of herring early life stages towards multiple climate change-related stressors. Our results indicate that interactive effects of rapidly changing environmental factors may exceed the larval stress threshold impairing essential acclimation responses, which may contribute to the ongoing recruitment decline of Western Baltic Spring-Spawning herring.

Developing molecular classifiers to detect environmental stressors, smolt stages and morbidity in coho salmon, Oncorhynchus kisutch

Aquatic species are increasingly confronted with environmental stressors because of climate change. Although molecular technologies have advanced our understanding of how organisms respond to stressors in laboratory settings, the ability to detect physiological responses to specific stressors under complex field conditions remains underdeveloped. This research applied multi-stressor challenge trials on coho salmon, employing the "Salmon Fit-Chips" genomic tool and a random forest-based classification model to develop classifiers predictive for chronic thermal and hypoxic stress, as well as salinity acclimation, smolt stage and morbidity status. The study also examined how smolts and de-smolts (smolts not having entered SW during the smolt window) responded transcriptionally to exposure to saltwater. Using RF classifiers optimized with 4 to 12 biomarkers, we identified transcriptional signatures that accurately predicted the presence of each stressor and physiological state, achieving prediction accuracy rates between 86.8 % and 100 %, regardless of other background stressors present. Stressor recovery time was established by placing fish back into non-stressor conditions after stress exposure, providing important context to stressor detections in field applications. Recovery from thermal and hypoxic stress requires about 3 and 2 days, respectively, with >3 days needed for re-acclimation to freshwater for seawater acclimated fish. The study also found non-additive (synergistic) effects of multiple stressors on mortality risk. Importantly, osmotic stress associated with de-smolts was the most important predictor of mortality. In saltwater, de-smolts exposed to salinity, high temperature, and hypoxia experienced a 9-fold increase in mortality compared to those only exposed to saltwater, suggesting a synergistic response to multiple stressors. These findings suggest that delays in hatchery releases to support release of larger fish need to be carefully scrutinized to ensure fish are not being released as de-smolts, which are highly susceptible to additional climate-induced stressors like rising temperatures and reduced dissolved oxygen levels in the marine environment.

Genomic regions and biological mechanisms underlying climatic resilience traits derived from automatically-recorded vaginal temperature in lactating sows under heat stress conditions

Climate change poses a growing threat to the livestock industry, impacting animal productivity, animal welfare, and farm management practices. Thus, enhancing livestock climatic resilience (CR) is becoming a key priority in various breeding programs. CR can be defined as the ability of an animal to be minimally affected or rapidly return to euthermia under thermally stressful conditions. The primary study objectives were to perform genome-wide association studies for 12 CR indicators derived from variability in longitudinal vaginal temperature in lactating sows under heat stress conditions. A total of 31 single nucleotide polymorphisms (SNPs) located on nine chromosomes were considered as significantly associated with nine CR indicators based on different thresholds. Among them, only two SNPs were simultaneously identified for different CR indicators, SSC6:16,449,770 bp and SSC7:39,254,889 bp. These results highlighted the polygenic nature of CR indicators with small effects distributed across different chromosomes. Furthermore, we identified 434 positional genes associated with CR. Key candidate genes include SLC3A2, STX5, POLR2G, and GANAB, which were previously related to heat stress responses, protein folding, and cholesterol metabolism. Furthermore, the enriched KEGG pathways and Gene Ontology (GO) terms associated with these candidate genes are linked to stress responses, immune and inflammatory responses, neural system, and DNA damage and repair. The most enriched quantitative trait loci are related to "Meat and Carcass", followed by "Production", "Reproduction", "Health", and "Exterior (conformation and appearance)" traits. Multiple genomic regions were identified associated with different CR indicators, which reveals that CR is a highly polygenic trait with small effect sizes distributed across the genome. Many heat tolerance or HS related genes in our study, such as HSP90AB1, DMGDH, and HOMER1, have been identified. The complexity of CR encompasses a range of adaptive responses, from behavioral to cellular. These results highlight the possibility of selecting more heat-tolerant individuals based on the identified SNP for CR indicators.

Dietary Chlorella vulgaris supplementation modulates health, microbiota and the response to oxidative stress of Atlantic salmon

Microalgae are emerging as functional feed ingredients in aquaculture due to their immune-stimulating and stress-modulating properties. We investigated the potential of the microalgae Chlorella vulgaris as a feed supplement to improve the health and modulate microbiota and stress responses of Atlantic salmon. Triplicate groups of Atlantic salmon (~ 126 g) were reared in a recirculating aquaculture system (RAS) at 15 °C and received diets supplemented with 2% (CV2) or 14% (CV14) spray-dried C. vulgaris daily, 14% once weekly (CV14w), or a control diet (CD) for 8 weeks. Subsequently, all groups were exposed to an acute one-hour peracetic acid (CH3CO3H; PAA) treatment, a commonly used disinfectant in RAS. While CV14 increased feed conversion (FCR) significantly, feeding the diets CV2 and CV14w improved protein retention efficiency. CV14 significantly modulated beta-diversity in the intestinal digesta and mucosa, but this effect was already visible in fish fed CV2. Feeding CV14 and, to a lesser degree, CV2 increased the relative abundances of Paenarthrobacter and Trichococcus in the digesta and mucosa, which are able to metabolize complex carbohydrates. However, the same diets reduced the abundance of the lactic acid bacteria Lactobacillus and Weissella in the digesta and Floricoccus in the mucosa. Peracetic acid exposure induced systemic stress (increase in plasma glucose and cortisol) and a local immune response in the gill, with the most prominent upregulation of several immune- and stress-regulated genes (clra, cebpb, marco, tnfrsf14, ikba, c1ql2, drtp1) 18 h after exposure in fish fed the control diet. Fish receiving CV14 once a week showed a reduced transcriptional response to PAA exposure. Catalase protein abundance in the liver increased following exposure to PAA, while superoxide dismutase abundance in the gill and liver was increased in response to C. vulgaris inclusion before stress. Overall, the results highlight that a high (14%) inclusion rate of C. vulgaris in feed for Atlantic salmon impairs feed conversion and shifts the intestinal microbiota composition in digesta and mucosa. Weekly feeding of C. vulgaris proves a viable approach in improving protein retention and improving transcriptional resilience towards oxidative stress in increasingly intensive production systems. Thereby this study may motivate future studies on optimizing temporal feeding schedules for health-promoting aquafeeds.

Characterization of the impact of dietary immunostimulant CpG on the expression of mRNA biomarkers involved in the immune responses in Atlantic salmon (Salmo salar)

Infectious diseases have significantly impacted Atlantic salmon aquaculture worldwide. Modulating fish immunity with immunostimulant-containing functional feeds could be an effective strategy in mitigating disease problems. Previously, we characterized the impact of polyriboinosinic polyribocytidylic acid (pIC) and formalin-killed typical Aeromonas salmonicida bacterin on miRNA expression in Atlantic salmon fed a commercial diet with and without immunostimulant CpG. A set of miRNA biomarkers of Atlantic salmon head kidney responding to pIC and/or bacterin immune stimulations was identified (Xue et al., 2019) [1]. Herein, we report a complementary qPCR study that investigated the impact of the pIC, bacterin and dietary CpG on the expression of immune-relevant mRNAs (n = 31) using the same samples as in the previous study (Xue et al., 2019) [1]. Twenty-six of these genes were predicted target transcripts of the pIC- and/or bacterin-responsive miRNAs identified in the earlier study. The current data showed that pIC and/or bacterin stimulations significantly modulated the majority of the qPCR-analyzed genes involved in various immune pathways. Some genes responded to both stimulations (e.g. tnfa, il10rb, ifng, irf9, cxcr3, campb) while others appeared to be stimulation specific [e.g. irf3, irf7a, il1r1, mxa, mapk3 (pIC only); clra (bacterin only)]. A. salmonicida bacterin stimulation produced a strong inflammatory response (e.g. higher expression of il1b, il8a and tnfa), while salmon stimulated with pIC showed robust interferon responses (both type I and II). Furthermore, the current data indicated significant down-regulation of immune-relevant transcripts (e.g. tlr9, irf5, il1r1, hsp90ab1, itgb2) by dietary immunostimulant CpG, especially among pre-injection and PBS-injected fish. Together with our prior miRNA study, the present research provided complementary information on Atlantic salmon anti-viral and anti-bacterial immune responses and on how dietary CpG may modulate these responses.

Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors

Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of "resistance," or the capacity of a system to minimize change in response to a disturbance, and "recovery," or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.

Exploring Multifunctional Markers of Biological Age in Farmed Gilthead Sea Bream (Sparus aurata): A Transcriptomic and Epigenetic Interplay for an Improved Fish Welfare Assessment Approach

DNA methylation clocks provide information not only about chronological but also biological age, offering a high-resolution and precise understanding of age-related pathology and physiology. Attempts based on transcriptomic and epigenetic approaches arise as integrative biomarkers linking the quantification of stress responses with specific fitness traits and may help identify biological age markers, which are also considered welfare indicators. In gilthead sea bream, targeted gene expression and DNA methylation analyses in white skeletal muscle proved sirt1 as a reliable marker of age-mediated changes in energy metabolism. To complete the list of welfare auditing biomarkers, wide analyses of gene expression and DNA methylation in one- and three-year-old fish were combined. After discriminant analysis, 668 differentially expressed transcripts were matched with those containing differentially methylated (DM) regions (14,366), and 172 were overlapping. Through enrichment analyses and selection, two sets of genes were retained: 33 showing an opposite trend for DNA methylation and expression, and 57 down-regulated and hypo-methylated. The first set displayed an apparently more reproducible and reliable pattern and 10 multifunctional genes with DM CpG in regulatory regions (sirt1, smad1, ramp1, psmd2-up-regulated; col5a1, calcrl, bmp1, thrb, spred2, atp1a2-down-regulated) were deemed candidate biological age markers for improved welfare auditing in gilthead sea bream.

Daily crowding stress has limited, yet detectable effects on skin and head kidney gene expression in surgically tagged atlantic salmon (Salmo salar)

To ensure welfare-friendly and effective internal tagging, the tagging process should not cause a long-term burden on individuals given that tagged fish serve as representatives for the entire population in telemetry applications. To some extent, stress is inevitable within regular aquaculture practices, and thus, the consequences of long-term stress should be described in terms of their effects on internal tagging. In fish, stressors activate the Hypothalamus-Pituitary-Interrenal (HPI) and Brain-Sympathetic-Chromaffin Cell (BSC) axes, leading to neuroimmunoendocrine communication and paracrine interactions among stress hormones. The interrelation between wound healing and stress is complex, owing to their shared components, pathways, and energy demands. This study assessed 14 genes (mmp9, mmp13, il-2, il-4, il-8a, il-10, il-12, il-17d, il-1b, tnfa, ifng, leg-3, igm, and crh) in the skin (1.5 cm from the wound) and head kidney over eight weeks. These genes, associated with cell signaling in immunity, wound healing, and stress, have previously been identified as influenced and regulated by these processes. Half of a group of Atlantic salmon (n = 90) with surgically implanted dummy smart-tags were exposed to daily crowding stress. The goal was to investigate how this gene panel responds to a wound alone and then to the combined effects of wounding and daily crowding stress. Our observations indicate that chronic stress impacts inflammation and impedes wound healing, as seen through the expression of matrix metalloproteinases genes in the skin but not in the head kidney. This difference is likely due to the ongoing internal wound repair, in contrast to the externally healed wound incision. Cytokine expression, when significant in the skin, was mainly downregulated in both treatments compared to control values, particularly in the study's first half. Conversely, the head kidney showed initial cytokine downregulation followed by upregulation. Across all weeks observed and combining both tissues, the significantly expressed gene differences were 12 % between the Wound and Stress+ groups, 28 % between Wound and Control, and 25 % between Stress+ and Control. Despite significant fluctuations in cytokines, sustained variations across multiple weeks are only evident in a few select genes. Furthermore, Stress+ individuals demonstrated the most cytokine correlations within the head kidney, which may suggest that chronic stress affects cytokine expression. This investigation unveils that the presence of stress and prolonged activation of the HPI axis in an eight weeklong study has limited yet detectable effects on the selected gene expression within immunity, wound healing, and stress, with notable tissue-specific differences.

Genome-wide identification and characterization of large yellow croaker (Larimichthys crocea) suppressors of cytokine signaling (SOCS) in immune response to Pseudomonas plecoglossicida infection and acute hypoxia stress

The suppressor of cytokine signaling (SOCS) gene family is a group of genes involved in the negative regulation of cytokine signal transduction. The members of this family play a crucial role in regulating immune and inflammatory processes. However, comprehensive investigations of these genes have not yet been conducted in the economically significant fish large yellow croaker (Larimichthys crocea). In this study, a total of 13 SOCS genes (LcSOCS1a, LcSOCS1b, LcSOCS2, LcSOCS3a, LcSOCS3b, LcSOCS4, LcSOCS5a, LcSOCS5b, LcSOCS6, LcSOCS7a, LcSOCS7b, LcCISHa and LcCISHb) were identified and analyzed in L. crocea. The phylogenetic tree revealed a high conservation of SOCS genes in evolution, and the gene structure and motif analysis indicated a high similarity in the structure of LcSOCSs in the same subfamily. In addition, the expression patterns of LcSOCSs showed that LcSOCS1b was significantly down-regulated in all time under acute hypoxia stress, but it was markedly up-regulated throughout the entire process after P. plecoglossicida infection, revealing its different immune effects to two stresses. Besides, LcSOCS2a, LcSOCS6 and LcSOCS7a only participated in acute hypoxic stress, while LcSOCS5a was more sensitive to P. plecoglossicida infection. In summary, these results indicated that SOCS genes were involved in stress responses to both biological and non-biological stimuli, setting the foundation for deeper study on the functions of SOCS genes.

Integration of physiological, miRNA-mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus)

Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-17a-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. Furthermore, research found that hk2 is a target of dre-miR-17a-3p, overexpression of dre-miR-17a-3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre-miR-17a-3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp.

Prolonged Cold Exposure Negatively Impacts Atlantic Salmon (Salmo salar) Liver Metabolism and Function

Large-scale mortality events have occurred during the winter in Atlantic salmon sea cages in Eastern Canada and Iceland. Thus, in salmon held at 3 °C that were apparently healthy (i.e., asymptomatic) and that had 'early' and 'advanced' symptoms of 'winter syndrome'/'winter disease' (WS/WD), we measured hepatic lipid classes and fatty acid levels, and the transcript expression of 34 molecular markers of fatty liver disease (FLD; a clinical sign of WS/WD). In addition, we correlated our results with previously reported characteristics associated with this disease's progression in these same individuals. Total lipid and triacylglycerol (TAG) levels increased by ~50%, and the expression of 32 of the 34 genes was dysregulated, in fish with symptoms of FLD. TAG was positively correlated with markers of inflammation (5loxa, saa5), hepatosomatic index (HSI), and plasma aspartate aminotransferase levels, but negatively correlated with genes related to lipid metabolism (elovl5b, fabp3a, cd36c), oxidative stress (catc), and growth (igf1). Multivariate analyses clearly showed that the three groups of fish were different, and that saa5 was the largest contributor to differences. Our results provide a number of biomarkers for FLD in salmon, and very strong evidence that prolonged cold exposure can trigger FLD in this ecologically and economically important species.

Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.

Effects of Different Farming Modes on Salmo trutta fario Growth and Intestinal Microbial Community

The gut microbiota plays a pivotal role in upholding intestinal health, fostering intestinal development, fortifying organisms against pathogen intrusion, regulating nutrient absorption, and managing the body's lipid metabolism. However, the influence of different cultivation modes on the growth indices and intestinal microbes of Salmo trutta fario remains underexplored. In this study, we employed high-throughput sequencing and bioinformatics techniques to scrutinize the intestinal microbiota in three farming modes: traditional pond aquaculture (TPA), recirculating aquaculture (RA), and flow-through aquaculture (FTA). We aimed to assess the impact of different farming methods on the water environment and Salmo trutta fario's growth performance. Our findings revealed that the final weight and weight gain rate in the FTA model surpassed those in the other two. Substantial disparities were observed in the composition, relative abundance, and diversity of Salmo trutta fario gut microbiota under different aquaculture modes. Notably, the dominant genera of Salmo trutta fario gut microbiota varied across farming modes: for instance, in the FTA model, the most prevalent genera were SC-I-84 (7.34%), Subgroup_6 (9.93%), and UTCFX1 (6.71%), while, under RA farming, they were Bacteroidetes_vadinHA17 (10.61%), MBNT15 (7.09%), and Anaeromyxoactor (6.62%). In the TPA model, dominant genera in the gut microbiota included Anaeromyxobacter (8.72%), Bacteroidetes_vadinHA17 (8.30%), and Geobacter (12.54%). From a comparative standpoint, the genus-level composition of the gut microbiota in the RA and TPA models exhibited relative similarity. The gut microbiota in the FTA model showcased the most intricate functional diversity, while TPA farming displayed a more intricate interaction pattern with the gut microbiota. Transparency, pH, dissolved oxygen, conductivity, total dissolved solids, and temperature emerged as pivotal factors influencing Salmo trutta fario gut microbiota under diverse farming conditions. These research findings offer valuable scientific insights for fostering healthy aquaculture practices and disease prevention and control measures for Salmo trutta fario, holding substantial significance for the sustainable development of the cold-water fish industry in the Qinghai-Tibet Plateau.

Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study

Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerational plasticity) and offspring-rearing temperatures (within-generational plasticity) modify the brain transcriptome of Brook charr progeny (fry stage). Parents were exposed to either cold or warm temperatures during final gonad maturation and their progeny were reared at 5 or 8 °C during the first stages of development. Illumina Novaseq6000 was used to sequence the brain transcriptome at the yolk sac resorption stage. The number of differentially expressed genes was very low when comparing fry reared at different temperatures (79 differentially expressed genes). In contrast, 9,050 differentially expressed genes were significantly differentially expressed between fry issued from parents exposed to either cold or warm temperatures. There was a significant downregulation of processes related to neural and synaptic activity in fry originating from the warm parental group vs fry from the cold parental one. We also observed significant upregulation of DNA methylation genes and of the most salient processes associated with compensation to warming, such as metabolism, cellular response to stress, and adaptive immunity.

Divergent perspectives on the synergistic impacts of thermal-chemical stress on aquatic biota within the framework of climate change scenarios

Climate change, including global warming, leads to rising temperatures in aquatic ecosystems, which is one of the numerous repercussions it brings. Furthermore, water warming can indirectly impact aquatic organisms by modifying the toxicity levels of pollutants. Nevertheless, numerous studies have explored the potential impacts of chemical stress on aquatic biota, but little is known about how such chemicals and toxins interact with climate change factors, especially elevated temperatures. As such, this review paper focuses on exploring the potential effects of thermochemical stress on a wide sector of aquatic organisms, including aquatic vertebrates and invertebrates, in various aquatic ecosystems (freshwater and marine systems). Herein, the objective of this study is to explore the most up-to-date the impact of water warming (without chemical stress) and thermochemical stress on various biochemical and physiological processes in aquatic fauna and how this greatly affects biodiversity and sustainability. Therefore, there is a growing need to understand and evaluate this synergistic mechanism and its potential hazardous impacts. However, we need further investigations and scientific reports to address this serious environmental issue in order to confront anthropogenic pollutants regarding climate change and chemical pollution risks in the near future and subsequently find sustainable solutions for them.

Testing the physiological capacity of the mussel Mytilus chilensis to establish into the Southern Ocean

The Southern Ocean and the Antarctic Circumpolar Current create environmental conditions that serve as an efficient barrier to prevent the colonization of non-native species (NNS) in the marine ecosystems of Antarctica. However, warming of the Southern Ocean and the increasing number of transport opportunities are reducing the physiological and physical barriers, increasing the chances of NNS arriving. The aim of this study was to determine the limits of survival of the juvenile mussels, M. chilensis, under current Antarctic conditions and those projected under climate change. These assessments were used to define the mussels potential for establishment in the Antarctic region. Experimental mussels were exposed to four treatments: -1.5 °C (Antarctic winter), 2 °C (Antarctic summer), 4 °C (Antarctic projected) and 8 °C (control) for 80 days and a combination of physiological and transcriptomics approaches were used to investigate mussel response. The molecular responses of mussels were congruent with the physiological results, revealing tolerance to Antarctic winter temperatures. However, a higher number of regulated differentially expressed gene (DEGs) were reported in mussels exposed to Antarctic winter temperatures (-1.5 °C). This tolerance was associated with the activation of the biological processes associated with apoptosis (up regulated) and both cell division and cilium assembly (down regulated). The reduced feeding rate and the negative scope for growth, for a large part of the exposure period at -1.5 °C, suggests that Antarctic winter temperatures represents an environmental barrier to M. chilensis from the Magellanic region settling in the Antarctic. Although M. chilensis are not robust to current Antarctica thermal conditions, future warming scenarios are likely to weaken these physiological barriers. These results strongly suggest that the West Antarctic Peninsula could become part of Mytilus distributional range, especially with dispersal aided by increasing maritime transport activity across the Southern Ocean.

Are fish immunocompetent enough to face climate change?

Ongoing climate change has already been associated with increased disease outbreaks in wild and farmed fish. Here, we evaluate the current knowledge of climate change-related ecoimmunology in teleosts with a focus on temperature, hypoxia, salinity and acidification before exploring interactive effects of multiple stressors. Our literature review reveals that acute and chronic changes in temperature and dissolved oxygen can compromise fish immunity which can lead to increased disease susceptibility. Moreover, temperature and hypoxia have already been shown to enhance the infectivity of certain pathogens/parasites and to accelerate disease progression. Too few studies exist that have focussed on acidification, but direct immune effects seem to be limited while salinity studies have led to contrasting results. Likewise, multi-stressor experiments essential for unravelling the interactions of simultaneously changing environmental factors are still scarce. This ultimately impedes our ability to estimate to what extent climate change will hamper fish immunity. Our review about epigenetic regulation mechanisms highlights the acclimation potential of the fish immune response to changing environments. However, due to the limited number of epigenetic studies, overarching conclusions cannot be drawn. Finally, we provide an outlook on how to better estimate the effects of realistic climate change scenarios in future immune studies in fish.

Muscle Transcriptome Sequencing Revealed Thermal Stress-Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822)

Rohu, Labeo rohita, is one of the most important aquaculture species in the Indian subcontinent. Understanding the molecular-level physiological responses to thermal stress or climate change is essential. In the present work, transcriptome sequencing was carried out in the muscle tissue of the rohu in response to heat stress (35 °C) in comparison with the control (28 °C). A total of 125 Gb of sequence data was generated, and the raw-reads were filtered and trimmed, which resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome, and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally regulated) as compared to the control group (Log2FC > 2, P < 0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as SERPINE1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, proto-oncogene c-Fos, myozenin2, alpha-crystallin B chain-like protein, angiopoietin-like protein 8, and acetyl-CoA carboxylases have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker SERPINE1 (HSP47), which showed significant upregulation (~ 2- to threefold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.

Impact of stress phenotype, elevated temperature, and bacterin exposure on male Atlantic salmon (Salmo salar) growth, stress, and immune biomarker gene expression

In this study, postsmolt male Atlantic salmon, previously identified as low responders (LRs) or high responders (HRs) based on poststress cortisol levels, had their head kidney and liver sampled at 12°C and 20°C before injection (time 0) and after injection (i.e., at 12- and 24-h postinjection, respectively) with either Forte Micro (a multivalent vaccine containing bacterin, to capture peak antibacterial responses) or an equal volume of PBS. Quantitative real-time PCR (qPCR) was then used to measure the expression of 15 biomarker genes in the head kidney and 12 genes in the liver at each temperature/sampling point. Target transcripts were chosen that were related to growth, stress, and innate antibacterial immune responses. Many temperature, phenotype, and injection effects were found for individual genes within these three broad categories, and multivariate statistical analyses (i.e., principal component analysis and permutational multivariate analysis of variance) were used to look for overall patterns in transcript expression. These analyses revealed that HR salmon at 20°C mounted a more robust response (P < 0.05) for the 10 head kidney immune-related transcripts when injected with Forte Micro than LR salmon. In contrast, the seven liver stress-related transcripts displayed a greater response (P = 0.057) in LR versus HR fish with Forte Micro at 12°C. Overall, although this research did find some differences between LR and HR fish, it does not provide strong (conclusive) evidence that the selection of a particular phenotype would have major implications for the health of salmon over the temperature range examined.NEW & NOTEWORTHY This is the first paper to describe the impact of both temperature and bacterial stimulation on head kidney and liver transcript expression in Atlantic salmon characterized as LRs versus HRs. Notably, we found that HR salmon at 20°C mounted a more robust innate antibacterial immune response than LR salmon. In addition, LR fish at 12°C may (P = 0.057) exhibit higher expression of stress-related transcripts in response to vaccine injection relative to HR fish.

Comparative Transcriptomic Analysis of Largemouth Bass (Micropterus salmoides) Livers Reveals Response Mechanisms to High Temperatures

High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the 'ECM-receptor interaction' pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the 'ECM-receptor interaction' pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS.

Characterising the Physiological Responses of Chinook Salmon (Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress

In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.

Heatwave resilience of juvenile white sturgeon is associated with epigenetic and transcriptional alterations

Heatwaves are increasing in frequency and severity, posing a significant threat to organisms globally. In aquatic environments heatwaves are often associated with low environmental oxygen, which is a deadly combination for fish. However, surprisingly little is known about the capacity of fishes to withstand these interacting stressors. This issue is particularly critical for species of extreme conservation concern such as sturgeon. We assessed the tolerance of juvenile white sturgeon from an endangered population to heatwave exposure and investigated how this exposure affects tolerance to additional acute stressors. We measured whole-animal thermal and hypoxic performance and underlying epigenetic and transcriptional mechanisms. Sturgeon exposed to a simulated heatwave had increased thermal tolerance and exhibited complete compensation for the effects of acute hypoxia. These changes were associated with an increase in mRNA levels involved in thermal and hypoxic stress (hsp90a, hsp90b, hsp70 and hif1a) following these stressors. Global DNA methylation was sensitive to heatwave exposure and rapidly responded to acute thermal and hypoxia stress over the course of an hour. These data demonstrate that juvenile white sturgeon exhibit substantial resilience to heatwaves, associated with improved cross-tolerance to additional acute stressors and involving rapid responses in both epigenetic and transcriptional mechanisms.

Chaperone proteins: universal roles in surviving environmental stress

Chaperone proteins have crucial roles to play in all animal species and are involved in mediating both the folding of newly synthesized peptides into their mature conformation, the refolding of misfolded proteins, and the trafficking of proteins between subcellular compartments. These highly conserved proteins have particularly important roles to play in dealing with disruptions of the proteome as a result of environmental stress since abiotic factors, including temperature, pressure, oxygen, water availability, and pollutants can readily disrupt the conformation and/or function of all types of proteins, e.g., enzymes, transporters, and structural proteins. The current review provides an update on recent advances in understanding the roles and responses of chaperones in aiding animals to deal with environmental stress, offering new information on chaperone action in supporting survival strategies including torpor, hibernation, anaerobiosis, estivation, and cold/freeze tolerance among both vertebrate and invertebrate species.

Are the effects of catch-and-release angling evident in changes to mRNA abundances related to metabolism, acid-base regulation and stress in lake trout (Salvelinus namaycush) gills?

Catch-and-release (C&R) angling is a conservation-oriented practice intended to reduce the impact recreational angling has on fish populations. Even though most recreationally angled fish are released, little is known about how C&R angling impacts fish at the cellular or tissue level. As the first to explore the impacts of C&R angling on mRNA abundances, our study aimed to identify how the stress of angling influenced metabolism, acid-base regulation and cellular stress in the gills of lake trout (Salvelinus namaycush). Because gills are responsible for metabolic gas exchange, are crucial sites of acid-base homeostasis and respond to stressors quickly, we hypothesized that the relative mRNA abundance of genes related to these three physiological processes would be altered after angling. We took gill samples of live lake trout at 0, 2 or 48 h after fish were angled by rod and reel, and then used quantitative PCR (qPCR) to measure the relative abundance of nine candidate mRNA transcripts. Heat shock protein 70 (hsp70) mRNA levels significantly increased over 5-fold 2 h after angling, indicating a potential activation of a cytoprotective response. However, contrary to our hypothesis, we observed no change in the relative mRNA abundance of genes related to metabolism or acid-base regulation in response to C&R angling within a 48-h period. As C&R angling can negatively impact fish populations, further use of transcript-level studies will allow us to understand the impact C&R has on specific tissues and improve our knowledge of how C&R influences overall fish health.

Identification of the matrix metalloproteinase (MMP) gene family in Japanese flounder (Paralichthys olivaceus): Involved in immune response regulation to temperature stress and Edwardsiella tarda infection

The Matrix metalloproteinase (MMP) gene family is responsible for regulating the degradation of Extra Cellular Matrix (ECM) proteins, which are important for physiological processes such as wound healing, tissue remodeling, and stress response. Although MMPs have been studied in many species, their role in immune response in Japanese flounder (Paralichthys olivaceus) is still not fully understood. This study conducted a comprehensive analysis of MMPs in flounder, including gene structures, evolutionary relationships, conserved domains, molecular evolution, and expression patterns. Analysis revealed that MMP genes could be grouped into 17 subfamilies and were evolutionarily conserved and functionally-constrained. Meanwhile, MMP genes were found to express in different embryonic and larval stages and might play the role of sentinel in healthy tissues. Furthermore, expression profiling showed that MMPs had diverse functions in environmental stress, with 60% (9/15) and 73% (11/15) of MMPs showing differential expression patterns under temperature stress and Edwardsiella tarda (E. tarda) infection, respectively. These findings provide a useful resource for understanding the immune functions of MMP genes in Japanese flounder.

High water temperature-mediated immune gene expression of olive flounder, Paralichthys olivaceus according to pre-stimulation at high temperatures

Increased ocean temperature due to global warming affects the health and immunity of fish. In this study, juvenile Paralichthys olivaceus were exposed to high temperature after pre-heat (Acute: Acute heat shock at 32 °C, AH-S: Acquired heat shock at 28 °C & short recovery (2h) and heat shock at 32 °C, AH-L: acquired heat shock at 28 °C and long recovery (2 days), AH-LS: acquired heat shock at 28 °C & long (2 days) + short (2h) recovery). Heat shock after pre-heat significantly upregulated various immune-related genes, including interleukin 8 (IL-8), c-type lysozyme (c-lys), immunoglobulin M (IgM), Toll-like receptor 3 (tlr3), major histocompatibility complex IIα (mhcIIα) and cluster of differentiation 8α (cd8α) in the liver and brain of P. olivaceus. This study showed pre-exposure to high temperatures below the critical temperature can activate fish immunity and increase tolerance to high temperatures.

Construction of a hypoxia-immune-related prognostic panel based on integrated single-cell and bulk RNA sequencing analyses in gastric cancer

Introduction

Gastric cancer (GC) is the fifth most common tumor, contributing to the third-highest number of cancer-related deaths. Hypoxia is a major feature of the tumor microenvironment. This study aimed to explore the influence of hypoxia in GC and establish a hypoxia-related prognostic panel.

Methods

The GC scRNA-seq data and bulk RNA-seq data were downloaded from the GEO and TCGA databases, respectively. AddModuleScore() and AUCell() were used to calculate module scores and fractions of enrichment for hypoxia-related gene expression in single cells. Least absolute shrinkage and selection operator cox (LASSO-COX) regression analysis was utilized to build a prognostic panel, and hub RNAs were validated by qPCR. The CIBERSORT algorithm was adopted to evaluate immune infiltration. The finding of immune infiltration was validated by a dual immunohistochemistry staining. The TIDE score, TIS score and ESTIMATE were used to evaluate the immunotherapy predictive efficacy.

Results

Hypoxia-related scores were the highest in fibroblasts, and 166 differentially expressed genes were identified. Five hypoxia-related genes were incorporated into the hypoxia-related prognostic panel. 4 hypoxia-related genes (including POSTN, BMP4, MXRA5 and LBH) were significantly upregulated in clinical GC samples compared with the normal group, while APOD expression decreased in GC samples. Similar results were found between cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs). A high hypoxia score was associated with advanced grade, TNM stage, N stage, and poorer prognosis. Decreased antitumor immune cells and increased cancer-promoting immune cells were found in patients with high hypoxia scores. Dual immunohistochemistry staining showed high expression of CD8 and ACTA2 in gastric cancer tissue. In addition, the high hypoxia score group possessed higher TIDE scores, indicating poor immunotherapy benefit. A high hypoxia score was also firmly related to sensitivity to chemotherapeutic drugs.

Discussion

This hypoxia-related prognostic panel may be effective in predicting the clinical prognosis, immune infiltrations, immunotherapy, and chemotherapy in GC.

Atlantic salmon adapt to low dietary n-3 PUFA and warmer water temperatures by increasing feed intake and expression of n-3 biosynthesis-related transcripts

Climate change can have cascading impacts on biochemical reactions in aquatic ecosystems. Aquatic ectotherms can adapt to surrounding temperatures by using long-chain polyunsaturated fatty acids (LC-PUFAs) to maintain cell membrane fluidity. In a warming scenario, less LC-PUFA is needed to maintain fluidity. Our objective was to determine the impact of low dietary LC-PUFA and warm water temperature on growth, fatty acid (FA) storage, and expression of lipid metabolism-related transcripts in Atlantic salmon. Salmon (141 g) were fed two diets (high or low LC-PUFA) at either 12 °C or 16 °C for 16 weeks. Salmon weighed more and consumed more food at 16 °C and when fed the low-LC-PUFA diet. Liver and muscle FA mostly depended on diet rather than temperature. DHA in muscle was higher at 16 °C and in salmon fed the high-LC-PUFA diet. Levels of FA desaturation transcripts were more highly expressed at 16 °C and in salmon fed the low-LC-PUFA diet, which suggests synthesis of LC-PUFA. Overall, with slow, chronic temperature increases, salmon may adapt to low dietary LC-PUFA by synthesizing more when required.

Influences of oxygen and temperature interaction on the antibacterial activity, antioxidant activity, serum biochemical indices, blood indices and growth performance of crucian carp

The well-being of fish used in aquaculture is of great interest. Oxygen and temperature are the main factors affecting the welfare of the crucian carp (carassius); however, there are few studies on the combined effects of these on the species. Therefore, this study investigated the impact of different temperatures (18 °C, 24 °C, 30 °C) and oxygen concentrations (2.1 mgL-1, 5.4 mgL-1, 9.3 mgL-1) on serum antibacterial activity, antioxidant activity, hematological parameters and growth performance of the crucian carp. The results showed that there were greater antibacterial properties under conditions of hypoxia at 18 °C (L18) and hyperoxia at 24 °C (H24). The activities of catalase, glutathione peroxidase and total superoxide dismutase were the highest at 24 °C under hypoxia and hyperoxia. In addition, the contents of glucose and total protein first increased and then decreased with the change of temperature; triglycerides were the lowest at 30 °C. The blood parameters of the carp were within a normal range at 24 °C; however, the growth rate was at its lowest under hypoxia treatment at 30 °C (L30). This study showed that high temperature impairs the antibacterial ability, antioxidant capacity and growth performance of the crucian carp, and high oxygen levels can alleviate these adverse reactions. This research provides a theoretical basis for subsequent aquaculture studies.

Influence of Supplemental Dietary Cholesterol on Growth Performance, Indices of Stress, Fillet Pigmentation, and Upper Thermal Tolerance of Female Triploid Atlantic Salmon (Salmo salar)

The salmon aquaculture industry must be proactive at developing mitigation tools/strategies to offset the potential negative impacts of climate change. Therefore, this study examined if additional dietary cholesterol could enhance salmon production at elevated temperatures. We hypothesized that supplemental cholesterol could aid in maintaining cell rigidity, reducing stress and the need to mobilize astaxanthin muscle stores, and improving salmon growth and survival at high rearing temperatures. Accordingly, postsmolt female triploid salmon were exposed to an incremental temperature challenge (+0.2°C day-1) to mimic conditions that they experience in sea cages in the summer, with temperature held at both 16 and 18°C for several weeks [i.e., 3 weeks at 16°C, followed by an increase at 0.2°C day-1 to 18°C (10 days), then 5 weeks at 18°C] to prolong their exposure to elevated temperatures. From 16°C onwards, the fish were fed either a control diet, or one of two nutritionally equivalent experimental diets containing supplemental cholesterol [+1.30%, experimental diet #1 (ED1); or +1.76%, experimental diet #2 (ED2)]. Adding cholesterol to the diet did not affect the salmon's incremental thermal maximum (ITMax), growth, plasma cortisol, or liver stress-related transcript expression. However, ED2 appeared to have a small negative impact on survival, and both ED1 and ED2 reduced fillet "bleaching" above 18°C as measured using SalmoFan™ scores. Although the current results suggest that supplementing salmon diets with cholesterol would have few/minimal benefits for the industry, ≤ 5% of the female triploid Atlantic salmon used in this study irrespective of diet died before temperature reached 22°C. These latter data suggest that it is possible to produce all female populations of reproductively sterile salmon that can withstand summer temperatures in Atlantic Canada.

ddRAD-Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China

Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish-water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present-day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype-phenotype-environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.

RNA-Seq Analysis of the Growth Hormone Transgenic Female Triploid Atlantic Salmon (Salmo salar) Hepatic Transcriptome Reveals Broad Temperature-Mediated Effects on Metabolism and Other Biological Processes

This study examined the impact of rearing temperature (10.5, 13.5 or 16.5°C) on the hepatic transcriptome of AquAdvantage Salmon (growth hormone transgenic female triploid Atlantic salmon) at an average weight of 800 g. Six stranded PE libraries were Illumina-sequenced from each temperature group, resulting in an average of over 100 M raw reads per individual fish. RNA-sequencing (RNA-seq) results showed the greatest difference in the number of differentially expressed transcripts (1750 DETs), as revealed by both DESeq2 and edgeR (q < 0.05; fold-change > |1.5|), was between the 10.5 and 16.5°C temperature groups. In contrast, 172 and 52 DETs were found in the 10.5 vs. 13.5°C and the 13.5 vs. 16.5°C comparisons, respectively. Considering the DETs between the 10.5 and 16.5°C groups, 282 enriched gene ontology (GO) terms were identified (q < 0.05), including “response to stress”, “immune system process”, “lipid metabolic process”, “oxidation-reduction process”, and “cholesterol metabolic process”, suggesting elevated temperature elicited broad effects on multiple biological systems. Pathway analysis using ClueGO showed additional impacts on amino acid and lipid metabolism. There was a significant positive correlation between RNA-seq and real-time quantitative polymerase chain reaction (RT-qPCR) results for 8 of 9 metabolic-related transcripts tested. RT-qPCR results also correlated to changes in fillet tissue composition previously reported in these salmon (e.g., methionine and lysine concentrations positively correlated with hsp90ab1 transcript expression), suggesting that rearing temperature played a significant role in mediating metabolic/biosynthetic pathways of AquAdvantage Salmon. Many transcripts related to lipid/fatty acid metabolism (e.g., elovl2, fabpi, hacd2, mgll, s27a2, thrsp) were downregulated at 16.5°C compared to both other temperature groups. Additionally, enrichment of stress-, apoptosis- and catabolism-relevant GO terms at 16.5°C suggests that this temperature may not be ideal for commercial production when using freshwater recirculating aquaculture systems (RAS). This study relates phenotypic responses to transcript-specific findings and therefore aids in the determination of an optimal rearing temperature for AquAdvantage Salmon. With approval to grow and sell AquAdvantage Salmon in the United States and Canada, the novel insights provided by this research can help industry expansion by promoting optimal physiological performance and health.

Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon (Salmo salar)

Gill damage represents a significant challenge in the teleost fish aquaculture industry globally, due to the gill's involvement in several vital functions and direct contact with the surrounding environment. To examine the local and systemic effects accompanying gill damage (which is likely to negatively affect gill function) of Atlantic salmon, we performed a field sampling to collect gill and liver tissue after several environmental insults (e.g., harmful algal blooms). Before sampling, gills were visually inspected and gill damage was scored; gill scores were assigned from pristine [gill score 0 (GS0)] to severely damaged gills (GS3). Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged (i.e., GS2) gill tissue. Rank Products analysis (5% percentage of false-positives) identified 254 and 34 upregulated and downregulated probes, respectively, in GS2 compared with GS0. Differentially expressed probes represented genes associated with functions including gill remodeling, wound healing, and stress and immune responses. We performed gill and liver qPCR for all four gill damage scores using microarray-identified and other damage-associated biomarker genes. Transcripts related to wound healing (e.g., neb and klhl41b) were significantly upregulated in GS2 compared with GS0 in the gills. Also, transcripts associated with immune and stress-relevant pathways were dysregulated (e.g., downregulation of snaclec 1-like and upregulation of igkv3) in GS2 compared with GS0 gills. The livers of salmon with moderate gill damage (i.e., GS2) showed significant upregulation of transcripts related to wound healing (i.e., chtop), apoptosis (e.g., bnip3l), blood coagulation (e.g., f2 and serpind1b), transcription regulation (i.e., pparg), and stress-responses (e.g., cyp3a27) compared with livers of GS0 fish. We performed principal component analysis (PCA) using transcript levels for gill and liver separately. The gill PCA showed that PC1 significantly separated GS2 from all other gill scores. The genes contributing most to this separation were pgam2, des, neb, tnnt2, and myom1. The liver PCA showed that PC1 significantly separated GS2 from GS0; levels of hsp70, cyp3a27, pparg, chtop, and serpind1b were the highest contributors to this separation. Also, hepatic acute phase biomarkers (e.g., serpind1b and f2) were positively correlated to each other and to gill damage. Gill damage-responsive biomarker genes and associated qPCR assays arising from this study will be valuable in future research aimed at developing therapeutic diets to improve farmed salmon welfare.

Global gene expression responses of Atlantic salmon skin to Moritella viscosa

Moritella viscosa is a Gram-negative pathogen that causes large, chronic ulcers, known as winter-ulcer disease, in the skin of several fish species including Atlantic salmon. We used a bath challenge approach to profile the transcriptome responses of M. viscosa-infected Atlantic salmon skin at the lesion (Mv-At) and away from the lesion (Mv-Aw) sites. M. viscosa infection was confirmed through RNA-based qPCR assays. RNA-Seq identified 5212 and 2911 transcripts differentially expressed in the Mv-At compared to no-infection control and Mv-Aw groups, respectively. Also, there were 563 differentially expressed transcripts when comparing the Mv-Aw to control samples. Our results suggest that M. viscosa caused massive and strong, but largely infection site-focused, transcriptome dysregulations in Atlantic salmon skin, and its effects beyond the skin lesion site were comparably subtle. The M. viscosa-induced transcripts of Atlantic salmon were mainly involved in innate and adaptive immune response-related pathways, whereas the suppressed transcripts by this pathogen were largely connected to developmental and cellular processes. As validated by qPCR, M. viscosa dysregulated transcripts encoding receptors, signal transducers, transcription factors and immune effectors playing roles in TLR- and IFN-dependent pathways as well as immunoregulation, antigen presentation and T-cell development. This study broadened the current understanding of molecular pathways underlying M. viscosa-triggered responses of Atlantic salmon, and identified biomarkers that may assist to diagnose and combat this pathogen.

Phenotypic stress response does not influence the upper thermal tolerance of male Atlantic salmon (Salmo salar)

Fish can be identified as either low responders (LR) or high responders (HR) based on post-stress cortisol levels and whether they exhibit a proactive or reactive stress coping style, respectively. In this study, male Atlantic salmon (Salmo salar) from 17 families reared at 9 °C were repeatedly exposed to an acute handling stress over a period of four months, with plasma cortisol levels measured at 1 h post-stress. Fish were identified as either LR or HR if the total Z-score calculated from their cortisol responses fell into the lower or upper quartile ranges, respectively; with intermediate responders (IR) classified as the remainder. Salmon characterized as LR, IR or HR were then subjected to an incremental thermal challenge, where temperature was raised at 0.2 °C day^-1 from their acclimation temperature (12 °C) to mimic natural sea-cage farming conditions during the summer in Newfoundland. Interestingly, feed intake remained high up to 22 °C, while previous studies have shown a decrease in salmon appetite after ∼16-18 °C. After the first three mortalities were recorded at elevated temperature, a subset of LR and HR salmon were exposed to another acute handling stress event at 23.6 °C. Basal and post-stress measurements of plasma cortisol, glucose and lactate did not differ between stress response phenotypes at this temperature. In the end, the average incremental thermal maximum (IT_Max) of LR and HR fish was not different (25.1 °C). In comparison, the critical thermal maximum (CT_Max; temperature increased at 2 °C h^-1) of the remaining IR fish that had been held at 12 °C was 28.5 °C. Collectively, these results: 1) show that this population of Atlantic salmon is very thermally tolerant, and further question the relevance of CT_Max in assessing responses to real-world temperature changes; and 2) indicate that characterization of stress phenotype at 9 °C is not predictive of their stress response or survival at high temperatures. Therefore, selection of fish based on phenotypic stress response at low temperatures may not be beneficial to incorporate into Atlantic salmon breeding programs, especially if the goal is to improve growth performance and survival at high temperatures in sea-cages.

Atlantic Salmon (Salmo salar) Cage-Site Distribution, Behavior, and Physiology During a Newfoundland Heat Wave

Background: Climate change is leading to increased water temperatures and reduced oxygen levels at sea-cage sites, and this is a challenge that the Atlantic salmon aquaculture industry must adapt to it if it needs to grow sustainably. However, to do this, the industry must better understand how sea-cage conditions influence the physiology and behavior of the fish.

Method: We fitted ~2.5 kg Atlantic salmon on the south coast of Newfoundland with Star-Oddi milli-HRT ACT and Milli-TD data loggers (data storage tags, DSTs) in the summer of 2019 that allowed us to simultaneously record the fish's 3D acceleration (i.e., activity/behavior), electrocardiograms (and thus, heart rate and heart rate variability), depth, and temperature from early July to mid-October.

Results: Over the course of the summer/fall, surface water temperatures went from ~10–12 to 18–19.5°C, and then fell to 8°C. The data provide valuable information on how cage-site conditions affected the salmon and their determining factors. For example, although the fish typically selected a temperature of 14–18°C when available (i.e., this is their preferred temperature in culture), and thus were found deeper in the cage as surface water temperatures peaked, they continued to use the full range of depths available during the warmest part of the summer. The depth occupied by the fish and heart rate were greater during the day, but the latter effect was not temperature-related. Finally, while the fish generally swam at 0.4–1.0 body lengths per second (25–60 cm s⁻¹), their activity and the proportion of time spent using non-steady swimming (i.e., burst-and-coast swimming) increased when feeding was stopped at high temperatures.

Conclusion: Data storage tags that record multiple parameters are an effective tool to understand how cage-site conditions and management influence salmon (fish) behavior, physiology, and welfare in culture, and can even be used to provide fine-scale mapping of environmental conditions. The data collected here, and that in recent publications, strongly suggest that pathogen (biotic) challenges in combination with high temperatures, not high temperatures + moderate hypoxia (~70% air saturation) by themselves, are the biggest climate-related challenge facing the salmon aquaculture industry outside of Tasmania.

Development of Atlantic Salmon (Salmo salar L.) Under Hypoxic Conditions Induced Sustained Changes in Expression of Immune Genes and Reduced Resistance to Moritella viscosa

Atlantic salmon is characterized with high sensitivity to low dissolved oxygen (DO) levels. Hypoxia can affect diverse biological processes with consequences that can be manifested immediately or with delay. Effects of hypoxia on the immune system and the resistance to a bacterial pathogen were investigated. Two groups were reared at, respectively, normal (NO, 80–100%) and low (LO, 60%) levels of DO over 10 months after which both groups were reared at NO. Smoltification was initiated after 13 months by a winter signal for 6 weeks, followed by constant light for 6 weeks. Samples were collected at the start and end of the constant light period. Expression of 92 immune and stress genes was analyzed in the gill, head kidney, and spleen using a Biomark HD. Most of differentially expressed genes showed higher levels in LO fish compared to NO fish; many immune genes were downregulated during smoltification and these changes were stronger in NO fish. A notable exception was pro-inflammatory genes upregulated in gill of NO fish. Further, salmon were challenged with Moritella viscosa, the causative agent of winter ulcer. Mortality was registered from 5 days post infection (dpi) to the end of trial at 36 dpi. Survival was consistently higher in NO than LO fish, reaching a maximum difference of 18% at 21–23 dpi that reduced to 10% at the end. Analyses with a genome-wide microarray at 36 dpi showed strong responses to the pathogen in gill and spleen. Notable features were the stimulation of eicosanoid metabolism, suggesting an important role of lipid mediators of inflammation, and the downregulation of chemokines. Many immune effectors were activated, including multiple lectins and acute phase proteins, enzymes producing free radicals, and matrix metalloproteinases. The transcriptomic changes induced with a bacterial challenge were similar in NO and LO. After the challenge, interferons a and g and panel of genes of innate antiviral immunity showed higher expression in LO, especially in the gill. The results from the present study suggest that chronic hypoxia in early life stimulated immune genes and attenuated their downregulation associated with smoltification. However, these changes did not improve protection against a bacterial pathogen of major concern in salmon aquaculture.

Summer Is Coming! Tackling Ocean Warming in Atlantic Salmon Cage Farming

Atlantic salmon (Salmo salar) cage farming has traditionally been located at higher latitudes where cold seawater temperatures favor this practice. However, these regions can be impacted by ocean warming and heat waves that push seawater temperature beyond the thermo-tolerance limits of this species. As more mass mortality events are reported every year due to abnormal sea temperatures, the Atlantic salmon cage aquaculture industry acknowledges the need to adapt to a changing ocean. This paper reviews adult Atlantic salmon thermal tolerance limits, as well as the deleterious eco-physiological consequences of heat stress, with emphasis on how it negatively affects sea cage aquaculture production cycles. Biotechnological solutions targeting the phenotypic plasticity of Atlantic salmon and its genetic diversity, particularly that of its southernmost populations at the limit of its natural zoogeographic distribution, are discussed. Some of these solutions include selective breeding programs, which may play a key role in this quest for a more thermo-tolerant strain of Atlantic salmon that may help the cage aquaculture industry to adapt to climate uncertainties more rapidly, without compromising profitability. Omics technologies and precision breeding, along with cryopreservation breakthroughs, are also part of the available toolbox that includes other solutions that can allow cage farmers to continue to produce Atlantic salmon in the warmer waters of the oceans of tomorrow.