Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish

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.

Whole Transcriptome Analysis Reveals the Global Molecular Responses of mRNAs, lncRNAs, miRNAs, circRNAs, and Their ceRNA Networks to Salinity Stress in Hong Kong Oysters, Crassostrea hongkongensis

The Hong Kong oyster, Crassostrea hongkongensis, is an estuarine bivalve with remarkable commercial value in South China, and the increase of salinity in estuaries during the dry season has posed a major threat to the oyster farming. To explore the global transcriptional response to salinity stress, a whole-transcriptome analysis was performed with the gills of oysters in 6‰, 18‰, and 30‰ filtered seawater. Overall, 2243, 194, 371, and 167 differentially expressed mRNAs (DEmRNAs), differentially expressed long non-coding RNAs (DElncRNAs), differentially expressed circular RNAs (DEcircRNAs), and differentially expressed microRNAs (DEmiRNAs) were identified, respectively. Based on GO enrichment and KEGG pathway analysis, these important DEmRNAs, DElncRNAs, DEcircRNAs, and DEmiRNAs were predicted to be mainly involved in amino acids metabolism, microtubule movement, and immune defense. This demonstrated the complexity of dynamic transcriptomic profiles of C. hongkongensis in response to salinity fluctuation. The regulatory relationships of DEmiRNAs-DEmRNAs, DElncRNAs-DEmiRNAs, and DEcircRNAs-DEmiRNAs were also predicted, and finally, a circRNA-associated competing endogenous RNA (ceRNA) network was constructed, consisting of six DEcircRNAs, eight DEmiRNAs, and five DEmRNAs. The key roles of taurine and hypotaurine metabolism and phenylalanine metabolism were highlighted in this ceRNA network, which was consistent with the major contribution of free amino acids to intracellular osmolality and cell volume regulation. Collectively, this study provides comprehensive data, contributing to the exploration of coding and non-coding RNAs in C. hongkongensis salinity response. The results would benefit the understanding of the response mechanism of bivalves against salinity fluctuation, and provide clues for genetic improvement of C. hongkongensis with hyper-salinity tolerance.

Effects of high NaHCO3 alkalinity on growth, tissue structure, digestive enzyme activity, and gut microflora of grass carp juvenile

With the gradual decrease in freshwater resources, the available space for freshwater aquaculture is diminishing. As a result, saline-alkaline water aquaculture has emerged as a crucial method to fulfill the increasing demand. This study investigates the impact of alkaline water on the growth performance, tissues (gill, liver, and kidney), digestive enzyme activity, and intestinal microbiology in grass carp (Ctenopharyngodon idella). The aquarium conditions were set with sodium bicarbonate (18 mmol/L (LAW), 32 mmol/L (HAW)) to simulate the alkaline water environment. A freshwater group was the control (FW). The experimental fish were cultured for 60 days. The findings revealed that NaHCO3 alkaline stress significantly reduced growth performance, caused alterations in the structural morphology of gill lamellae, liver, and kidney tissues, and led to decreased activity of intestinal trypsin and lipase amylase (P < 0.05). Analysis of 16S rRNA sequences demonstrated that alkalinity influenced the abundance of dominant bacterial phyla and genera. Proteobacteria showed a significant decrease under alkaline conditions, while Firmicutes exhibited a significant increase (P < 0.05). Furthermore, alkalinity conditions significantly reduced the abundance of bacteria involved in protein, amino acid, and carbohydrate metabolism, cell transport, cell decomposition, and environmental information processing. Conversely, the abundance of bacteria associated with lipid metabolism, energy metabolism, organic systems, and disease functional flora increased significantly under alkalinity conditions (P < 0.05). In conclusion, this comprehensive study indicates that alkalinity stress adversely affected the growth performance of juvenile grass carp, likely due to tissue damage, reduced activity of intestinal digestive enzymes, and alterations in intestinal microorganisms.

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.

Transcriptomic impacts and potential routes of detoxification in a lampricide-tolerant teleost exposed to TFM and niclosamide

Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America often relies on the application of 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide mixtures to kill larval sea lamprey. Selectivity of TFM against lampreys appears to be due to differential detoxification ability in these jawless fishes compared to bony fishes, particularly teleosts. However, the proximate mechanisms of tolerance to the TFM and niclosamide mixture and the mechanisms of niclosamide toxicity on its own are poorly understood, especially among non-target fishes. Here, we used RNA sequencing to identify specific mRNA transcripts and functional processes that responded to niclosamide or a TFM:niclosamide mixture in bluegill (Lepomis macrochirus). Bluegill were exposed to niclosamide or TFM:niclosamide mixture, along with a time-matched control group, and gill and liver tissues were sampled at 6, 12, and 24 h. We summarized the whole-transcriptome patterns through gene ontology (GO) term enrichment and through differential expression of detoxification genes. The niclosamide treatment resulted in an upregulation of several transcripts associated with detoxification (cyp, ugt, sult, gst), which may help explain the relatively high detoxification capacity in bluegill. Conversely, the TFM:niclosamide mixture resulted in an enrichment of processes related to arrested cell cycle and growth, and cell death alongside a diverse detoxification gene response. Detoxification of both lampricides likely involves the use of phase I and II biotransformation genes. Our findings strongly suggest that the unusually high tolerance of bluegill to lampricides is due to these animals having an inherently high capacity and flexible detoxification response to such compounds.

Transcriptome Analysis Revealed Osmoregulation Related Regulatory Networks and Hub Genes in the Gills of Hilsa shad, Tenualosa ilisha, during the Migratory Osmotic Stress

Tenualosa ilisha (Hilsa shad), an anadromous fish, usually inhabits coastal and estuarine waters, and migrates to freshwater for spawning. In this study, large-scale gill transcriptome analyses from three salinity regions, i.e., fresh, brackish and marine water, revealed 3277 differentially expressed genes (DEGs), out of which 232 were found to be common between marine vs freshwater and brackish vs freshwater. These genes were mapped into 54 KEGG Pathways, and the most significant of these were focal adhesion, adherens junction, tight junction, and PI3K-Akt signaling pathways. A total of 24 osmoregulatory genes were found to be differentially expressed in different habitats. The gene members of slc16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes (cldn11 & cldn10), transmembrane tm56b, and voltage-gated potassium channel gene kcna10 were downregulated in freshwater samples, as compared to that of brackish and marine environment. Protein-protein interaction (PPI) network analysis of 232 DEGs showed 101 genes to be involved in PPI, while fn1 gene was found to be interacting with the highest number of genes (36). Twenty-five hub genes belonged to 12 functional groups, with muscle structure development with seven genes, forming the major group. These results provided valuable information about the genes, potentially involved in the molecular mechanisms regulating water homeostasis in gills, during migration for spawning and low-salinity adaptation in Hilsa shad. These genes may form the basis for the bio-marker development for adaptation to the stress levied by major environmental changes, due to hatchery/culture conditions.

Blood-based gene expression as non-lethal tool for inferring salinity-habitat history of European eel (Anguilla anguilla)

The European eel is a facultative catadromous species, meaning that it can skip the freshwater phase or move between marine and freshwater habitats during its continental life stage. Otolith microchemistry, used to determine the habitat use of eel or its salinity history, requires the sacrifice of animals. In this context, blood-based gene expression may represent a non-lethal alternative. In this work, we tested the ability of blood transcriptional profiling to identify the different salinity-habitat histories of European eel. Eels collected from different locations in Norway were classified through otolith microchemistry as freshwater residents (FWR), seawater residents (SWR) or inter-habitat shifters (IHS). We detected 3451 differentially expressed genes from blood by comparing FWR and SWR groups, and then used that subset of genes in a machine learning approach (i.e., random forest) to the extended FWR, SWR, and IHS group. Random forest correctly classified 100% of FWR and SWR and 83% of the IHS using a minimum of 30 genes. The implementation of this non-lethal approach may replace otolith-based microchemistry analysis for the general assessment of life-history tactics in European eels. Overall, this approach is promising for the replacement or reduction of other lethal analyses in determining certain fish traits.

Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern

Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesised to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. With a gene set enrichment analysis, we found that thermally stressed fish showed a transcriptional response related to transcription regulation and responses to unfolded proteins, and alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared to the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation, and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.

Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.

Physiological and behavioural strategies of aquatic animals living in fluctuating environments

Shallow or near-shore environments, such as ponds, estuaries and intertidal zones, are among the most physiologically challenging of all aquatic settings. Animals inhabiting these environments experience conditions that fluctuate markedly over relatively short temporal and spatial scales. Living in these habitats requires the ability to tolerate the physiological disturbances incurred by these environmental fluctuations. This tolerance is achieved through a suite of physiological and behavioural responses that allow animals to maintain homeostasis, including the ability to dynamically modulate their physiology through reversible phenotypic plasticity. However, maintaining the plasticity to adjust to some stresses in a dynamic environment may trade off with the capacity to deal with other stressors. This paper will explore studies on select fishes and invertebrates exposed to fluctuations in dissolved oxygen, salinity and pH. We assess the physiological mechanisms these species employ to achieve homeostasis, with a focus on the plasticity of their responses, and consider the resulting physiological trade-offs in function. Finally, we discuss additional factors that may influence organismal responses to fluctuating environments, such as the presence of multiple stressors, including parasites. We echo recent calls from experimental biologists to consider physiological responses to life in naturally fluctuating environments, not only because they are interesting in their own right but also because they can reveal mechanisms that may be crucial for living with increasing environmental instability as a consequence of climate change.

Effects of environmental salinity on the immune response of the coastal fish Scatophagus argus during bacterial infection

The coastal aquaculture is characterized with environmental salinity fluctuation, and the effects of salinity stress on the immunity of cultured fish are needed to be further explored. Scatophagus argus is an important species in the wild fisheries and aquaculture industry, it would be of great value to reveal the impact of salinity change on the immune response in this species. Understanding the effects of salinity stress on immune response can provide valuable insights into salinity management in the aquacultural process. The head kidney, which is an organ unique for teleost fish, functions not only as a central immune organ but also as a crucial role in the stress response during which the secretion of immunoregulatory molecules i.e. cytokines is facilitated. In the present study, Individuals of S. argus acclimated to 3 different salinities [0‰ (FW), 10‰ (BW), and 25‰ (SW)] were injected intraperitoneally with A. hydrophila, and then monitored throughout one week. The effects of environmental salinity on the immune response in S. argus stimulated by A. hydrophila infection were investigated. mRNA expression profiles of cytokine genes IL-1β, IL-6, IL-10 and TNF-α in different salinity groups was quite different. mRNA expression of cytokine genes in BW group and SW group rose more quickly and significantly higher than FW group (p < 0.05) at early stages (6-24 hpi) after bacterial injection, and before 96 hpi, the highest value of cytokine expression at each time point was recorded in SW group. Immune parameters such as lysozyme level, complement C3 activity and IgM content in BW and FW groups were lower than SW group at each time point from 24 to 144 hpi after bacterial injection. In addition, leukocyte profiles in the head kidney and blood were also investigated. Although hypoosmotic acclimation could temporarily stimulate monocyte and neutrophil proliferation, it was observed that the number of monocytes, neutrophils and lymphocytes of the head kidney and blood in SW group increased more quickly than BW and FW groups after bacterial infection. Our results indicate that hypoosmotic stress due to the decrease of environmental salinity has suppressive immunoregulatory effects on the immune response of S. argus.

Interactions of Environmental Chemicals and Natural Products With ABC and SLC Transporters in the Digestive System of Aquatic Organisms

An organism’s diet is a major route of exposure to both beneficial nutrients and toxic environmental chemicals and natural products. The uptake of dietary xenobiotics in the intestine is prevented by transporters of the Solute Carrier (SLC) and ATP Binding Cassette (ABC) family. Several environmental chemicals and natural toxins have been identified to induce expression of these defense transporters in fish and aquatic invertebrates, indicating that they are substrates and can be eliminated. However, certain environmental chemicals, termed Transporter-Interfering Chemicals or TICs, have recently been shown to bind to and inhibit fish and mammalian P-glycoprotein (ABCB1), thereby sensitizing cells to toxic chemical accumulation. If and to what extent other xenobiotic defense or nutrient uptake transporters can also be inhibited by dietary TICs is still unknown. To date, most chemical-transporter interaction studies in aquatic organisms have focused on ABC-type transporters, while molecular interactions of xenobiotics with SLC-type transporters are poorly understood. In this perspective, we summarize current advances in the identification, localization, and functional analysis of protective MXR transporters and nutrient uptake systems in the digestive system of fish and aquatic invertebrates. We collate the existing literature data on chemically induced transporter gene expression and summarize the molecular interactions of xenobiotics with these transport systems. Our review emphasizes the need for standardized assays in a broader panel of commercially important fish and seafood species to better evaluate the effects of TIC and other xenobiotic interactions with physiological substrates and MXR transporters across the aquatic ecosystem and predict possible transfer to humans through consumption.

The effects of population and thermal acclimation on the growth, condition and cold responsive mRNA expression of age-0 lake sturgeon (Acipenser fulvescens)

In Manitoba, Canada, wild lake sturgeon (Acipenser fulvescens) populations exist along a latitudinal gradient and are reared in hatcheries to bolster threatened populations. We reared two populations of lake sturgeon, one from each of the northern and southern ends of Manitoba and examined the effects of typical hatchery temperatures (16°C) as well as 60-day acclimation to elevated rearing temperatures (20°C) on mortality, growth and condition throughout early development. Additionally, we examined the cold shock response, which may be induced during stocking, through the hepatic mRNA expression of genes involved in the response to cold stress and homeoviscous adaptation (HSP70, HSP90a, HSP90b, CIRP and SCD). Sturgeon were sampled after 1 day and 1 week following stocking into temperatures of 8, 6 and 4°C in a controlled laboratory environment. The southern population showed lower condition and higher mortality during early life than the northern population while increased rearing temperature impacted the growth and condition of developing northern sturgeon. During the cold shock, HSP70 and HSP90a mRNA expression increased in all sturgeon treatments as stocking temperature decreased, with higher expression observed in the southern population. Expression of HSP90b, CIRP and SCD increased as stocking temperature decreased in northern sturgeon with early acclimation to 20°C. Correlation analyses indicated the strongest molecular relationships were in the expression of HSP90b, CIRP and SCD, across all treatments, with a correlation between HSP90b and body condition in northern sturgeon with early acclimation to 20°C. Together, these observations highlight the importance of population and rearing environment throughout early development and on later cellular responses induced by cold stocking temperatures.

The time course of molecular acclimation to seawater in a euryhaline fish

The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds (“wadies”), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.

New Salinity Tolerant Species of Gyrodactylus (Platyhelminthes, Monogenea) on Intertidal and Supratidal Fish Species from the Chilean Coast

PURPOSE

The intertidal and supratidal coastal zone challenges the osmoregulatory capacity of aquatic inhabitants. Four new species of Gyrodactylus ectoparasites on two intertidal fishes from Chile are described based on molecular and morphological analyses.

METHODS

Monogeneans were found from two fish species, the clingfish Sicyases sanguineus Müller & Troschel, 1843 and the combtooth blenny Scartichthys viridis Valenciennes, 1836. The morphology was described by drawings, and minimal measurements. The parasites were barcoded via the sequencing of the ribosomal DNA over ITS1-5.8S-ITS2.

RESULTS

The air-breathing clingfish S. sanguineus carried Gyrodactylus amphibius sp. nov., hiding in the ventral sucker formed by the modified pectoral fins of the fish. The intertidal combtooth blenny S. viridis carried three other new species: Gyrodactylus scartichthi sp. nov., Gyrodactylus viridae sp. nov., and Gyrodactylus zietarae sp. nov.

CONCLUSION

The four new species were all phylogenetically related with the previously described G. chileani Ziętara et al. 2012 on triplefin Helcogrammoides chilensis Cancino, 1960 in the same habitat. Thus, the five Chilean Pacific Gyrodactylus species formed a statistically well-supported (100%) monophyletic clade together with three geographically distant species recorded in Europe. The Chilean Pacific parasites are not related to G. salinae and G. magadiensis, parasites described in extreme osmotic stress environments earlier.

The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes

Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.

RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish

Background

Messenger RNA sequencing is becoming more common in studies of non-model species and is most often used for gene expression-based investigations. However, the method holds potential for numerous other applications as well—including analyses of alternative splicing, population structure, and signatures of selection. To maximize the utility of mRNA data sets, distinct analyses may be combined such as by exploring dynamics between gene expression with signatures of selection in the context of population structure. Here, we compare two published data sets describing two populations of a minnow species endemic to the San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus): a microsatellite data set showing population structure, and an mRNA whole transcriptome data set obtained after the two populations were exposed to a salinity challenge. We compared measures of population structure and genetic variation using single nucleotide polymorphisms (SNPs) called from mRNA from the whole transcriptome sequencing study with those patterns determined from microsatellites. For investigating plasticity and evolution, intra- and inter-population transcriptome plasticity was investigated with differential gene expression, differential exon usage, and gene expression variation. Outlier SNP analysis was also performed on the mRNA data set and signatures of selection and phenotypic plasticity were investigated on an individual-gene basis.

Results

We found that mRNA sequencing revealed patterns of population structure consistent with those found with microsatellites, but with lower magnitudes of genetic variation and population differentiation consistent with widespread purifying selection expected when using mRNA. In addition, within individual genes, phenotypic plasticity or signatures of selection were found in almost mutual exclusion (except heatr6, nfu1, slc22a6, sya, and mmp13).

Conclusions

These results show that an mRNA sequencing data set may have multiple uses, including describing population structure and for investigating the mechanistic interplay of evolution and plasticity in adaptation. MRNA sequencing thus complements traditional sequencing methods used for population genetics, in addition to its utility for describing phenotypic plasticity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07592-4.

Reductionist approaches to the study of ionoregulation in fishes

The mechanisms underlying ionoregulation in fishes have been studied for nearly a century, and reductionist methods have been applied at all levels of biological organization in this field of research. The complex nature of ionoregulatory systems in fishes makes them ideally suited to reductionist methods and our collective understanding has been dramatically shaped by their use. This review provides an overview of the broad suite of techniques used to elucidate ionoregulatory mechanisms in fishes, from the whole-animal level down to the gene, discussing some of the advantages and disadvantages of these methods. We provide a roadmap for understanding and appreciating the work that has formed the current models of organismal, endocrine, cellular, molecular, and genetic regulation of ion balance in fishes and highlight the contribution that reductionist techniques have made to some of the fundamental leaps forward in the field throughout its history.

Inter-population differences in salinity tolerance of adult wild Sacramento splittail: osmoregulatory and metabolic responses to salinity

The Sacramento splittail (Pogonichthys macrolepidotus) is composed of two genetically distinct populations endemic to the San Francisco Estuary (SFE). The allopatric upstream spawning habitat of the Central Valley (CV) population connects with the sympatric rearing grounds via relatively low salinity waters, whereas the San Pablo (SP) population must pass through the relatively high-salinity Upper SFE to reach its allopatric downstream spawning habitat. We hypothesize that if migration through SFE salinities to SP spawning grounds is more challenging for adult CV than SP splittail, then salinity tolerance, osmoregulatory capacity, and metabolic responses to salinity will differ between populations. Osmoregulatory disturbances, assessed by measuring plasma osmolality and ions, muscle moisture and Na⁺-K⁺-ATPase activity after 168 to 336 h at 11‰ salinity, showed evidence for a more robust osmoregulatory capacity in adult SP relative to CV splittail. While both resting and maximum metabolic rates were elevated in SP splittail in response to increased salinity, CV splittail metabolic rates were unaffected by salinity. Further, the calculated difference between resting and maximum metabolic values, aerobic scope, did not differ significantly between populations. Therefore, improved osmoregulation came at a metabolic cost for SP splittail but was not associated with negative impacts on scope for aerobic metabolism. These results suggest that SP splittail may be physiologically adjusted to allow for migration through higher-salinity waters. The trends in interpopulation variation in osmoregulatory and metabolic responses to salinity exposures support our hypothesis of greater salinity-related challenges to adult CV than SP splittail migration and are consistent with our previous findings for juvenile splittail populations, further supporting our recommendation of population-specific management.

Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune responses can be of relevance in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes have often relied on only one pair of populations, targeted the expression of only a subset of genes or used wild-caught individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological abilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond set-up. In all investigated population pairs, lake fish were more heavily parasitized than river fish, in terms of both parasite taxon composition and infection abundance. The innate immune response in the wild was higher in lake than in river populations and was elevated in a river population exposed to lake parasites in the pond set-up. Environmental differences between lake and river habitat and their distinct parasite communities have shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond set-up were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimatized to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.

Comparative transcriptomic analysis reveals mechanisms of divergence in osmotic regulation of the turbot Scophthalmus maximus

The turbot Scophthalmus maximus has evolved extensive physiological ability to adapt to multiple environmental salinities. The morphological changes of the kidney indicated the adaptability difference and similarity of turbot to salinity stress. Identify transcriptome-wide differences between low-salinity seawater (LSW, salinity 5)- and high-salinity seawater (HSW, salinity 50)-acclimated kidneys of turbot to decipher the osmotic regulation mechanism. We identified 688 differentially expressed genes (DEGs) in the LSW-acclimated kidneys and 2441 DEGs in the HSW-acclimated kidneys of turbot compared with seawater-acclimated kidneys, respectively. We investigated three patterns of gene regulation to salinity stress that involved in ion channels and transporters, functions of calcium regulation, organic osmolytes, energy demand, cell cycle regulation, and cell protection. Additionally, protein-protein interaction (PPI) analysis of DEGs suggested the presence of a frequent functional interaction pattern and that crucial genes in the PPI network are involved in hyper-osmotic regulation. Based on the analysis of comparative transcriptome data and related literature reports, we conclude that the mechanisms responsible for osmotic regulation and its divergence in turbot are related to various genes that are involved in canonical physiological functions. These findings provide insight into the divergence in osmoregulation of turbot and valuable information about osmoregulation mechanisms that will benefit other studies in this field.

Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (Sander vitreus) in a large freshwater ecosystem

RNA sequencing is an effective approach for studying aquatic species yielding both physiological and genomic data. However, its population genetic applications are not well-characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second-largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced mRNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (F ST = 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations and suggest genomic differences possibly underlying observed phenotypic differences. Despite its high cost relative to other genotyping methods, RNA sequencing data can yield physiological in addition to genetic information discussed here. We therefore argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.

Transcriptomic Analysis of Gill and Kidney from Asian Seabass (Lates calcarifer) Acclimated to Different Salinities Reveals Pathways Involved with Euryhalinity

Asian seabass (or commonly known as barramundi), Lates calcarifer, is a bony euryhaline teleost from the Family Latidae, inhabiting nearshore, estuarine, and marine connected freshwaters throughout the tropical Indo-West Pacific region. The species is catadromous, whereby adults spawn in salinities between 28 and 34 ppt at the mouth of estuaries, with resultant juveniles usually moving into brackish and freshwater systems to mature, before returning to the sea to spawn again as adults. The species lives in both marine and freshwater habitats and can move quickly between the two; thus, the species' ability to tolerate changes in salinity makes it a good candidate for studying the salinity acclimation response in teleosts. In this study, the transcriptome of two major osmoregulatory organs (gills and kidneys) of young juvenile Asian seabass reared in freshwater and seawater were compared. The euryhaline nature of Asian seabass was found to be highly pliable and the moldability of the trait was further confirmed by histological analyses of gills and kidneys. Differences in major expression pathways were observed, with differentially expressed genes including those related to osmoregulation, tissue/organ morphogenesis, and cell volume regulation as central to the osmo-adaptive response. Additionally, genes coding for mucins were upregulated specifically under saline conditions, whereas several genes important for growth and development, as well as circadian entrainment were specifically enriched in fish reared in freshwater. Routing of the circadian rhythm mediated by salinity changes could be the initial step in salinity acclimation and possibly migration in euryhaline fish species such as the Asian seabass.

Differential regulation of select osmoregulatory genes and Na+/K+-ATPase paralogs may contribute to population differences in salinity tolerance in a semi-anadromous fish

The Sacramento splittail (Pogonichthys macrolepidotus) is a species of special concern that is native to the San Francisco Estuary, USA. Two genetically distinct populations exist and differ in maximal salinity tolerances. We examined the expression of 12 genes representative of osmoregulatory functions in the gill over a 14  day time course at two different salinities [11 or 14 PSU (Practical Salinity Units)] and revealed that each population showed distinct patterns of gene expression consistent with population differences in response to osmotic regimes. The relatively more salinity-tolerant San Pablo population significantly upregulated nine out of the 12 transcripts investigated on day 1 of 11 PSU salinity exposure in comparison to the day zero freshwater control. Three transcripts (nka1a, nka1b, and mmp13) were differentially expressed between the populations at 7 and 14 days of salinity exposure, suggesting a reduced ability of the relatively salinity-intolerant Central Valley population to recover. Additionally, a phylogenetic analysis of several Sacramento splittail Na⁺/K⁺-ATPase α1 sequences resulted in grouping by proposed paralog rather than species, suggesting that different paralogs of this gene may exist. These findings, together with prior research conducted on the Sacramento splittail, suggest that the San Pablo population may be able to preferentially regulate select osmoregulatory genes, including different Na⁺/K⁺-ATPase α1 paralogs, to better cope with salinity challenges.