Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes

Dose-dependent effects of different parabens on food waste biorefinery for volatile fatty acids production: Insight into specific fermentation processes, substrates transformation and microbial metabolic traits

Parabens are largely concentrated in food waste (FW) due to their large consumption as the widely used preservative. To date, whether and how they affect FW resource recovery via anaerobic fermentation is still largely unknown. This work unveiled the hormesis-like effects of two typical parabens (i.e., methylparaben and n-butylparaben) on VFAs production during FW anaerobic fermentation (i.e., parabens increased VFAs by 6.73-14.49 % at low dose but caused 82.51-87.74 % reduction at high dose). Mechanistic exploration revealed that the parabens facilitated the FW solubilization and enhanced the associated substrates' biodegradability. The low parabens enriched the functional microorganisms (e.g., Firmicutes and Actinobacteria) and upregulated those critical genes involved in VFAs biosynthesis (e.g., GCK and PK) by activating the microbial adaptive capacity (i.e., quorum sensing and two-component system). Consequently, the metabolism rates of fermentation substrates and subsequent VFAs production were accelerated. However, due to increased biotoxicity of high parabens, the functional microorganisms and relevant metabolic activities were depressed, resulting in the significant reduction of VFAs biosynthesis. Structural equation modeling clarified that microbial community was the predominant factor affecting VFAs generation, followed by metabolic pathways. This work elucidated the dose-dependent effects and underlying mechanisms of parabens on FW anaerobic fermentation, providing insights for the effective management of FW resource recovery.

Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining

Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, including fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.

Attenuative effects of collagen peptide from milkfish (Chanos chanos) scales on ovariectomy-induced osteoporosis

Osteoporosis is characterized by low bone mass, bone microarchitecture disruption, and collagen loss, leading to increased fracture risk. In the current study, collagen peptides were extracted from milkfish scales (MS) to develop potential therapeutic candidates for osteoporosis. MS was used to synthesize a crude extract of fish scales (FS), collagen liquid (COL), and hydroxyapatite powder (HA). COL samples were further categorized according to the peptide size of total COL (0.1 mg/mL), COL < 1 kDa (0.1 mg/mL), COL: 1-10 kDa (0.1 mg/mL), and COL > 10 kDa (0.1 mg/mL) to determine it. Semi-quantitative reverse transcription polymerase chain reaction (sqRT-PCR) and immunofluorescence labeling were used to assess the expression levels of specific mRNA and proteins in vitro. For in vivo studies, mice ovariectomy (OVX)-induced postmenopausal osteoporosis were developed, while the sham surgery (Sham) group was treated as a control. Collagen peptides (CP) from MS inhibited osteoclast differentiation in RAW264.7 cells following an insult with nuclear factor kappa-B ligand (RANKL). CP also enhanced osteoblast proliferation in MG-63 cells, possibly through downregulating NFATc1 and TRAP mRNA expression and upregulating ALP and OPG mRNA levels. Furthermore, COL1 kDa also inhibited bone density loss in osteoporotic mice. Taken together, CP may reduce RANKL-induced osteoclast activity while promoting osteoblast synthesis, and therefore may act as a potential therapeutic agent for the prevention and control of osteoporosis.

Salinity effects on expression and localization of aquaporin 3 in gills of the euryhaline milkfish (Chanos chanos)

Milkfish (Chanos chanos) are important euryhaline fish in Southeast Asian countries that can tolerate a wide range of salinity changes. Previous studies have revealed that milkfish have strong ion regulation and survival abilities under osmotic stress. In addition to ion regulation, water homeostasis in euryhaline teleosts is important during environmental salinity shifts. Aquaporins (AQP) are vital water channels in fish, and different AQPs can transport water influx or outflux from the body. AQP3 is one of the AQP channels, and the function of AQP3 in the gills of euryhaline milkfish is still unknown. The aim of this study was to investigate the expression and localization of AQP3 in the gills of euryhaline milkfish to contribute to our understanding of the physiological role and localization of AQP3 in fish. The AQP3 sequence was found in the milkfish next-generation sequencing (NGS) database and is mainly distributed in the gills of freshwater (FW)-acclimated milkfish. Under hypoosmotic and hyperosmotic stress, the osmolality of milkfish immediately shifted, similar to the aqp3 gene expression. Moreover, the abundance of AQP3 protein significantly decreased 3 h after transferring milkfish from FW to seawater (SW). However, there was no change within 7 days when the milkfish experienced hypoosmotic stress. Moreover, double immunofluorescence staining of milkfish gills showed that AQP3 colocalized with Na+ /K+ ATPase at the basolateral membrane of ionocytes. These results combined indicate that milkfish have a strong osmoregulation ability under acute osmotic stress because of the quick shift in the gene and protein expression of AQP3 in their gills.

Integrated Transcriptomic and Metabolomic Analyses Reveal Low-Temperature Tolerance Mechanism in Giant Freshwater Prawn Macrobrachium rosenbergii

Water temperature, as an important environmental factor, affects the growth and metabolism of aquatic animals and even their survival. The giant freshwater prawn (GFP) Macrobrachium rosenbergii is a kind of warm-water species, and its survival temperature ranges from 18 °C to 34 °C. In this study, we performed transcriptomic and metabolomic analyses to clarify the potential molecular mechanism of responding to low-temperature stress in adult GFP. The treatments with low-temperature stress showed that the lowest lethal temperature of the GFP was 12.3 °C. KEGG enrichment analyses revealed that the differentially expressed genes and metabolites were both enriched in lipid and energy metabolism pathways. Some key genes, such as phosphoenolpyruvate carboxykinase and fatty acid synthase, as well as the content of the metabolites dodecanoic acid and alpha-linolenic acid, were altered under low-temperature stress. Importantly, the levels of unsaturated fatty acids were decreased in LS (low-temperature sensitive group) vs. Con (control group). In LT (low-temperature tolerant group) vs. Con, the genes related to fatty acid synthesis and degradation were upregulated to cope with low-temperature stress. It suggested that the genes and metabolites associated with lipid metabolism and energy metabolism play vital roles in responding to low-temperature stress. This study provided a molecular basis for the selection of a low-temperature tolerant strain.

Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass

As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.

Genetic Mechanism of Tissue-Specific Expression of PPAR Genes in Turbot (Scophthalmus maximus) at Different Temperatures

In this study, we used PCR to measure the levels of the peroxisome proliferator activated receptor genes PPARα1, PPARα2, PPARβ, and PPARγ in the intestine, liver, gill, heart, kidney, brain, muscle, spleen, skin, and stomach of turbot (Scophthalmus maximus) cultured under different temperature conditions (14, 20, 23, 25, and 28 °C). We used split-split-plot (SSP) analysis of variance, additive main effects and multiplicative interaction (AMMI) analysis, and genotype main effects and genotype × environment interaction (GGE) biplot analysis to evaluate the genotype × tissue interaction effects on gene expression. The results of the SSP analysis of variance showed that temperature and tissue × gene have highly significant (p < 0.01) effect on the expression of S. maximus PPAR genes. The AMMI analysis results revealed that the expression of PPAR genes at the appropriate temperature (14 °C) mainly depended on genotype × tissue interaction and tissue effects. Under stress temperatures, genotype effects, tissue effects, and genotype × tissue interaction, all had significant effects on the expression of PPAR genes. The contribution of the genotype effect slowly increased with increasing temperature; it increased faster at 20 °C and then slowly declined at 25 °C. The contribution of the tissue effect slowly increased from 14 to 20 °C, where it sharply decreased, and then it stabilized after a slight fluctuation. The contribution of the genotype × tissue interaction effect showed a fluctuating upward trend throughout the experiment, and it had a significant impact on PPAR gene expression. The key temperature at which the three effects changed was 20 °C, indicating that it is the limit temperature for active lipid metabolism under high-temperature stress. The GGE biplot analysis results showed that under suitable water temperature, the expression difference of PPAR genes in the liver was the largest; at 20 and 23 °C, the expression difference in the gill was the largest; and at 25 and 28 °C, the expression difference in the brain was the largest. Overall, our results suggest that the mechanism responsible for PPAR gene expression under the three high temperatures (23, 25, and 28 °C) was relatively consistent, but it differed from that at 20 °C.

Differentially Expressed miRNAs and mRNAs in Regenerated Scales of Rainbow Trout (Oncorhynchus mykiss) under Salinity Acclimation

In order to explore the potential effects of salinity acclimation on bone metabolism of rainbow trout (Oncorhynchus mykiss), transcriptional information of regenerated scales under salinity acclimation (sea water, SW) was compared to those of fish under fresh water (FW) environments. According to the high-throughput sequencing results, a total of 2620 significantly differentially expressed genes (DEGs) were identified in the data of SW vs. FW. Compared with the FW group, six significantly downregulated and 44 significantly upregulated miRNAs were identified in the SW scales (p < 0.05). Furthermore, a total of 994 significantly differentially expressed target genes (DETGs) were identified from the 50 significantly differentially expressed miRNAs (DE miRNAs). Gene ontology analysis of the aforementioned DETGs was similar to the results of the differentially expressed genes (DEGs) obtained from mRNA-seq data, these genes were mainly related to ion metabolism. KEGG enrichment analysis of the DEGs and DETGs suggested that many significantly enriched pathways were related to the energy metabolism pathway.

Integrated analysis about the effects of heat stress on physiological responses and energy metabolism in Gymnocypris chilianensis

The temperature of the rivers in the Qilian Mountains, China varies widely from day to night, and Gymnocypris chilianensis living in these rivers may experience a change of 10 °C to 20 °C within a day. To explore the mechanisms underlying G. chilianensis responses to heat stress, we conducted an acute temperature stress experiment. In response to heat stress, levels of antioxidant enzymes (SOD\CAT\MDA) first increased and then decreased with time, but T-AOC levels only decreased. The activities of key glycolytic enzymes HK and PFK in the liver also first increased and then decreased and transaminase (AST/ALT) activity increased significantly. We obtained 5350 significantly different genes through transcriptome sequencing with enrichment pathways including primarily glycine, serine and threonine metabolism, cysteine and methionine metabolism, tryptophan metabolism, fructose and mannose metabolism, steroid hormone biosynthesis, and fatty acid degradation. A total of 457 differential metabolites were identified in the liver under thermal stress, most of which are involved in biochemical pathways of amino acid metabolism. Biosynthesis of amino acids indicated that G. chilianensis maintained physiological homeostasis by enhancing glucose metabolism and regulating lipid and amino acid metabolism pathways under thermal stress. We also randomly selected 12 key response genes for validation using qRT-PCR. This is the first study describing the mechanisms underlying responses to thermal stress in G. chilianensis, and may also provide reference data for the study of environmental mutations in indigenous fish in the Qinghai-Tibet Plateau and Qilian Mountains.

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.

Brackish water improves the taste quality in meat of adult male Eriocheir sinensis during the postharvest temporary rearing

We investigated the effect of temporary rearing in brackish water on the taste quality in meat of crab cooked. The main salinity-responsive factors included 5'-nucleotides and free amino acids (FAAs) in crab meat that were identified using tri-step infrared spectroscopy. Compared to the fresh water group, the contents of 5'-adenosine monophosphate and 5'-inosine monophosphate in the brackish water group significantly increased in the 2nd week and decreased in the 6th week, respectively. The contribution ratio of umami FAAs increased from 8.1 to 13.5% in the 4th week in the brackish water group, showing maximum value of equivalent umami concentration. Moreover, Ca²⁺ and Cl^- contents significantly increased in the 4th and 6th weeks, respectively (P < 0.05). Infrared spectroscopy was an effective method to identify the taste components. With respect to the taste quality, four weeks were determined as the best period for temporary rearing of the crab in brackish water.

RNA-seq analysis reveals divergent adaptive response to hyper- and hypo-salinity in cobia, Rachycentron canadum

Salinity is an important abiotic stress that affects metabolic and physiological activities, breed, development, and growth of marine fish. Studies have shown that cobia (Rachycentron canadum), a euryhaline marine teleost fish, possesses the ability of rapid and effective hyper/hypo iono- and osmoregulation. However, genomic studies on this species are lacking and it has not been studied at the transcriptome level to identify the genes responsible for salinity regulation, which affects the understanding of the fundamental mechanism underlying adaptation to fluctuations in salinity. To describe the molecular response of cobia to different salinity levels, we used RNA-seq analysis to identify genes and biological processes involved in response to salinity changes. In the present study, 395,080,114 clean reads were generated and then assembled into 65,318 unigenes with an N50 size of 2758 bp. There were 20,671 significantly differentially expressed genes (DEGs) including 8805 genes adapted to hypo-salinity and 11,866 genes adapted to hyper-salinity. These DEGs were highly represented in steroid biosynthesis, unsaturated fatty acid metabolism, glutathione metabolism, energy metabolism, osmoregulation, and immune response. The candidate genes identified in cobia provide valuable information for studying the molecular mechanism of salinity adaptation in marine fish. Furthermore, the transcriptomic sequencing data acts not only as an important resource for the identification of novel genes but also for further investigations regarding cobia biology.

Nevertheless, She Resisted - Role of the Environment on Listeria monocytogenes Sensitivity to Nisin Treatment in a Laboratory Cheese Model

The growth of Listeria monocytogenes on refrigerated, ready-to-eat food products is a major health and economic concern. The natural antimicrobial nisin targets the bacterial cell wall and can be used to inhibit L. monocytogenes growth on cheese. Cell wall composition and structure, and therefore the efficacy of cell wall acting control strategies, can be severely affected by environmental and stress conditions. The goal of this study was to determine the effect of a range of pH and temperatures on the efficacy of nisin against several strains of L. monocytogenes in a lab-scale, cheese model. Cheese was made with or without the addition of nisin at different pH and then inoculated with L. monocytogenes; L. monocytogenes numbers were quantified after 1, 7, and 14 days of incubation at 6, 14, or 22°C. While our data show that nisin treatment is able to reduce L. monocytogenes numbers, at least initially, growth of this pathogen can occur even in the presence of nisin, especially when cheese is stored at higher temperatures. Several environmental factors were found to affect nisin efficacy against L. monocytogenes. For example, nisin is more effective when cheese is stored at lower temperatures. Nisin is also more effective when cheese is made at higher pH (6 and 6.5), compared to cheese made at pH 5.5, and this effect is at least partially due to the activity of cell envelope modification genes dltA and mprF. Serotype was also found to affect nisin efficacy against L. monocytogenes; serotype 4b strains showed lower susceptibility to nisin treatment compared to serotype 1/2 strains. Overall, our results highlight the importance of considering environmental conditions specific to a food matrix when developing and applying nisin-based intervention strategies against L. monocytogenes.

Changes in hypothermal stress-induced hepatic mitochondrial metabolic patterns between fresh water- and seawater-acclimated milkfish, Chanos chanos

Milkfish (Chanos chanos) is a tropical euryhaline species. It can acclimate to fresh water (FW) or seawater (SW) and be cultured in both. In winter, cold snaps cause huge losses in milkfish revenue. Compared to FW-acclimated individuals, SW-acclimated milkfish have better low-temperature tolerance. Under hypothermal stress, a stable energy supply is critical to maintain normal liver function. In this study, the levels of key mitochondrial enzymes (citrate synthase (CS) and cytochrome c oxidase (COX)) in milkfish livers were examined. The CS:COX activity ratio in FW milkfish significantly increased under hypothermal stress (18 °C) whereas ATP (the end product of aerobic metabolism) was downregulated. Therefore, the activities of the enzymes involved in mitochondrial amino acid biosynthesis (aspartate aminotransferase (AST) and glutamate dehydrogenase (GDH)) were evaluated to elucidate energy flow in milkfish livers under hypothermal stress. In FW milkfish, GDH activity was upregulated whereas AST activity was downregulated. Nevertheless, the levels of all the aforementioned enzymes did not significantly change in SW milkfish under hypothermal stress. In summary, we clarified the mechanism accounting for the fact that SW milkfish have superior low-temperature tolerance to FW milkfish and demonstrated that SW and FW milkfish have different and unique strategies for regulating energy flow.

Cortisol regulation of Na+, K+-ATPase β1 subunit transcription via the pre-receptor 11β-hydroxysteroid dehydrogenase 1-like (11β-Hsd1L) in gills of hypothermal freshwater milkfish, Chanos chanos

Hypothermal stress changes the balance of osmoregulation by affecting Na⁺, K⁺-ATPase (Na-K-ATPase) activity or inducing modulation to epithelium permeability in fish. Meanwhile, cellular concentrations of cortisol can be modulated by the pre-receptor enzymes 11β-hydroxysteroid dehydrogenase 1 and 2 (11β-Hsd1 and 2). In fish, increasing levels of exogenous cortisol stimulate Na⁺ uptake via specific interaction with cortisol. This study investigated cortisol effects on expression of Na-K-ATPase subunit proteins and activity in gills of milkfish under hypothermal stress and revealed that the plasma cortisol contents as well as gill 11β-hsd1l and na-k-atpase β1 mRNA abundance were decreased in fresh water (FW) milkfish. Meanwhile, in the seawater (SW) milkfish, the plasma cortisol contents and gill 11β-hsd1l and na-k-atpase β1 mRNA abundance was increased under hypothermal stress. On the other hand, the abundance of 11β-hsd2 mRNA increased in both FW and SW. In addition, 11β-hsd1l expression increased in FW milkfish but decreased in SW milkfish after cortisol injection. Accordingly, the results that gill Na-K-ATPase activity of FW milkfish was affected by environmental temperatures as well as cortisol-dependent Na-K-ATPase β1-subunit levels might be due to increased expression of 11β-hsd1l that elevated intracellular cortisol contents. In hypothermal SW milkfish, decreasing abundance of Na-K-ATPase β1 protein due to reduced expression of 11β-hsd1l was found after cortisol injection. Thus, under hypothermal stress, 11β-HSD1L in FW milkfish gills was used to modulate cortisol and the following effects on increasing the transcription of Na-K-ATPase β1 protein.

Patterns of alternative splicing in response to cold acclimation in fish

Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.

The regulation of oxidative phosphorylation pathway on Vibrio alginolyticus adhesion under adversities

Vibrio alginolyticus is one of the most important pathogens in mariculture and leading to heavy losses. After treatment with Cu²⁺, Pb²⁺, and low pH, the expression of oxidative phosphorylation pathway genes, including coxA, coxB, coxC, ccoN, ccoO, and ccoQ, was found commonly downregulated by RNA‐seq as well as quantitative real‐time PCR. RNAi significantly reduced the expression of coxA, coxB, coxC, ccoN, ccoO, and ccoQ in V. alginolyticus. Compared with the wild‐type strain, the adhesion abilities of RNAi strains of V. alginolyticus were significantly impaired, as well as their cytochrome C oxidase activity. ccoQ appeared to be more important in the regulation of bacterial adhesion in these target genes, while ccoO was relatively weak in the regulation of the adhesion. Meanwhile, the changes of temperature, salinity, pH, and starvation affected coxA, coxB, coxC, ccoN, ccoO, and ccoQ expression remarkably. These findings indicated that: the oxidative phosphorylation pathway is a critical regulator of adhesion in V. alginolyticus; coxA, coxB, coxC, ccoN, ccoO, and ccoQ regulate the bacterial adhesion in response to environmental changes such as temperature, salinity, pH, and starvation.

Multiple model species selection for transcriptomics analysis of non-model organisms

Background

Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functional annotation, gene regulation analysis, and environmental factor verification. However, with increasing amounts of sequenced reads and reference model species, the selection of appropriate reference species for gene annotation has become a new challenge.

Methods

We proposed a novel approach for finding the most effective reference model species through taxonomic associations and ultra-conserved orthologous (UCO) gene comparisons among species. An online system for multiple species selection (MSS) for RNA-seq differential expression analysis was developed, and comprehensive genomic annotations from 291 reference model eukaryotic species were retrieved from the RefSeq, KEGG, and UniProt databases.

Results

Using the proposed MSS pipeline, gene ontology and biological pathway enrichment analysis can be efficiently achieved, especially in the case of transcriptomic analysis of non-model organisms. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time, resulting in more accurate results than those of traditional approaches of using a single model reference species or the large non-redundant reference database.

Conclusions

Selection of appropriate reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. In addition, adequate model species selection reduces the computational time significantly while retaining the same order of accuracy. The proposed system indeed provides superior performance by selecting appropriate multiple species for transcriptomic analysis compared to traditional approaches.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2278-z) contains supplementary material, which is available to authorized users.

Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis

BACKGROUND

Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, uses a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of C. semilaevis to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity changes.

RESULTS

The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of C. semilaevis. One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, and cytoskeleton remodeling were affected during acclimation to low salinity. Genes acat2, fdps, hmgcr, hmgcs1, mvk, pmvk, ebp, lss, dhcr7, and dhcr24 were up-regulated and abat, ddc, acy1 were down-regulated in metabolic pathways. Genes aqp10 and slc6a6 were down-regulated in osmoregulation and ion transport. Genes abat, fdps, hmgcs1, mvk, pmvk and dhcr7 were first reported to be associated with salinity adaptation in teleosts.

CONCLUSIONS

Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish.

Salinity Effects on Strategies of Glycogen Utilization in Livers of Euryhaline Milkfish (Chanos chanos) under Hypothermal Stress

The fluctuation of temperature affects many physiological responses in ectothermic organisms, including feed intake, growth, reproduction, and behavior. Changes in environmental temperatures affect the acquisition of energy, whereas hepatic glycogen plays a central role in energy supply for the homeostasis of the entire body. Glycogen phosphorylase (GP), which catalyzes the rate-limiting step in glycogenolysis, is also an indicator of environmental stress. Here, we examined the effects of salinity on glycogen metabolism in milkfish livers under cold stress. A reduction of feed intake was observed in both freshwater (FW) and seawater (SW) milkfish under cold adaptation. At normal temperature (28°C), compared to the FW milkfish, the SW milkfish exhibited greater mRNA abundance of the liver isoform of GP (Ccpygl), higher GP activity, and less glycogen content in the livers. Upon hypothermal (18°C) stress, hepatic Ccpygl mRNA expression of FW milkfish surged at 3 h, declined at 6 and 12 h, increased again at 24 h, and increased significantly after 96 h. Increases in GP protein, GP activity, and the phosphorylation state and the breakdown of glycogen were also found in FW milkfish livers after 12 h of exposure at 18°C. Conversely, the Ccpygl transcript levels in SW milkfish were downregulated after 1 h of exposure at 18°C, whereas the protein abundance of GP, GP activity, and glycogen content were not significantly altered. Taken together, under 18°C cold stress, FW milkfish exhibited an acute response with the breakdown of hepatic glycogen for maintaining energy homeostasis of the entire body, whereas no change was observed in the hepatic glycogen content and GP activity of SW milkfish because of their greater tolerance to cold conditions.

The effects of continuously acoustical stress on cortisol in milkfish (Chanos chanos)

Strong underwater acoustic noise has been known that may cause hearing loss and actual stress in teleost. However, the long-term physiological effects of relatively quiet but continuously noise on fish were less understood. In present study, milkfish, Chanos chanos, were exposed to the simulated-wind farm noise either quiet (109dB re 1μPa/125.4Hz; approx. 10-100m distant from the wind farm) or noisy (138dB re 1μPa/125.4Hz; nearby the wind farm) conditions for 24h, 3days and 1week. Comparing to the control group (80dB re 1μPa/125.4Hz), the fish exposed to noisy conditions had higher plasma cortisol levels in the first 24h. However, the cortisol levels of 24h spot returned to the resting levels quickly. The fish exposed under noisy condition had significantly higher head kidney star (steroidogenic acute regulatory) and hsd11b2 (11-β-hydroxysteroid dehydrogenase 2) mRNA levels at the following treatment time points. In addition, noise exposure did not change hypothalamus crh (Corticotropin-releasing hormone) mRNA levels in this experiment. The results implied that the weak but continuously noise was a potential stressor to fish, but the impacts may be various depending on the sound levels and exposure time. Furthermore, this study showed that the continuous noise may up-regulate the genes that are related to cortisol synthesis and possibly make the fish more sensitive to ambient stressors, which may influence the energy allocation appearance in long-term exposures.

Heat-induced oxidative stress and inflammation involve in cadmium pollution history in the spleen of zebrafish

Zebrafish were exposed to 0, 2.5 and 5 μg/L cadmium (Cd) for 10 weeks, and then each group was exposed to 26 °C(control) and 32 °C (high temperature) for 7 days. 22 indicators were compared between 26 °C and 32 °C in the spleen, including body weight, LPO and NO levels, activity levels of Cu/Zn-SOD, CAT and iNOS, MTs protein levels, and mRNA levels of Nrf2, Cu/Zn-SOD, CAT, HSF1, HSF2, HSP70, MTF-1, MTs, IL-6, IL-10, IL-1β, TNF-α, iNOS and NF-κB. Most indicators were not significantly affected by heat in fish from no Cd pollution. However, almost all of indicators were responsive to heat in fish pre-exposed to Cd. Several indicators were sensitive to heat in fish pre-exposed to 2.5 μg/L Cd such as iNOS activities, and mRNA levels of iNOS and IL-10. Most other indicators were sensitive to heat in fish pre-exposed to 5 μg/L. The mRNA levels of HSP70 and MTF-1 were up-regulated by heat in fish pre-exposed to 0, 2.5 and 5 μg/L Cd. However, the magnitude of increase was the greatest in fish pre-exposed to 5 μg/L Cd. These differences between control and high temperature would serve as biomarkers to distinguish healthy from Cd-polluted group. The findings imply that metal pollution history should be carefully considered when screening heat biomarkers in fish.

Transcriptomic response to thermal and salinity stress in introduced and native sympatric Palaemon caridean shrimps

Organisms develop local adaptations to cope with spatially and temporally variable environments such as estuarine habitats, where abiotic parameters such as salinity and temperature fluctuate continuously. Studying the regulation of gene expression in a variable environment allows us to understand the underlying molecular mechanisms of these adaptations and the relative roles of the genetic and plastic response. The transcriptomes of the European native Palaemon longirostris (PL) and the introduced P. macrodactylus (PM) shrimps are described and compared after an experiment simulating summer conditions in the Guadalquivir Estuary, Spain. Specimens, collected in the Guadalquivir Estuary, were maintained at a temperature and salinity of 20 °C and 5 ppt for the control, and 30 °C and 15 ppt for the stress treatment. A large amount of differential gene expression was observed: 16,013 and 2,594 for PL and PM respectively. Functionally annotated unigenes revealed some differences, with PL seemingly having to face stronger physiological stress than PM. Thus, PM seems to have greater resistance than PL under conditions of high temperature and salinity. These results constitute a step forward in the understanding of the underlying molecular mechanisms of genetic adaptation of native invertebrates, and alien taxa that have successfully invaded estuaries in temperate regions around the world.

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus

Background

Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal factors and embryonic incubation conditions. Thus, maternally packaged gene products are hypothesized to regulate developmental trajectory and perhaps the other unique developmental characters in this species.

Results

Using high-throughput RNA sequencing, we generated transcriptomic profiles of mRNAs, long non-coding RNAs and small non-coding RNAs (sncRNAs) in 1–2 cell stage embryos of A. limnaeus. Transcriptomic analyses suggest maternal programming of embryos through alternatively spliced mRNAs and antisense sncRNAs. Comparison of these results to those of comparable studies on zebrafish and other fishes reveals a surprisingly high abundance of transcripts involved in the cellular response to stress and a relatively lower expression of genes required for rapid transition through the cell cycle.

Conclusions

Maternal programming of developmental trajectory is unlikely accomplished by differential expression of diapause-specific genes. Rather, evidence suggests a role for trajectory-specific splice variants of genes expressed in both phenotypes. In addition, based on comparative studies with zebrafish, the A. limnaeus 1–2 cell stage transcriptome is unique in ways that are consistent with their unique life history. These results not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression during development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-017-0069-7) contains supplementary material, which is available to authorized users.

Na+, K+-ATPase β1 subunit associates with α1 subunit modulating a "higher-NKA-in-hyposmotic media" response in gills of euryhaline milkfish, Chanos chanos

The euryhaline milkfish (Chanos chanos) is a popular aquaculture species that can be cultured in fresh water, brackish water, or seawater in Southeast Asia. In gills of the milkfish, Na⁺, K⁺-ATPase (i.e., NKA; sodium pump) responds to salinity challenges including changes in mRNA abundance, protein amount, and activity. The functional pump is composed of a heterodimeric protein complex composed of α- and β-subunits. Among the NKA genes, α1-β1 isozyme comprises the major form of NKA subunits in mammalian osmoregulatory organs; however, most studies on fish gills have focused on the α1 subunit and did not verify the α1-β1 isozyme. Based on the sequenced milkfish transcriptome, an NKA β1 subunit gene was identified that had the highest amino acid homology to β233, a NKA β1 subunit paralog originally identified in the eel. Despite this high level of homology to β233, phylogenetic analysis and the fact that only a single NKA β1 subunit gene exists in the milkfish suggest that the milkfish gene should be referred to as the NKA β1 subunit gene. The results of accurate domain prediction of the β1 subunit, co-localization of α1 and β1 subunits in epithelial ionocytes, and co-immunoprecipitation of α1 and β1 subunits, indicated the formation of a α1-β1 complex in milkfish gills. Moreover, when transferred to hyposmotic media (fresh water) from seawater, parallel increases in branchial mRNA and protein expression of NKA α1 and β1 subunits suggested their roles in hypo-osmoregulation of euryhaline milkfish. This study molecularly characterized the NKA β1 subunit and provided the first evidence for an NKA α1-β1 association in gill ionocytes of euryhaline teleosts.

The Antioxidant Peroxiredoxin 6 (Prdx6) Exhibits Different Profiles in the Livers of Seawater- and Fresh Water-Acclimated Milkfish, Chanos chanos, upon Hypothermal Challenge

A tropical species, the euryhaline milkfish (Chanos chanos), is a crucial economic species in Southeast Asia and is intolerant of water temperature below 12°C. Large numbers of milkfish die during cold periods in winter. Hypothermal environments usually increase oxidative stress in teleosts, and the liver is the major organ for anti-oxidative responses in the body. Peroxiredoxin-6 (Prdx6) in mammals is a multi-functional enzyme and acts as both glutathione peroxidase, phospholipase A₂ and acyl-transferase for maintenance of redox status and prevention of cell membrane peroxidation. Prdx6 can protect cells from oxidant-induced membrane damage by translocating the Prdx6 protein from the cytosol to the membrane. Upon cold stress, Ccprdx6 transcript levels were up-regulated after 24 h and 96 h in livers of fresh water (FW)- and seawater (SW)-acclimated milkfish, respectively. In the hypothermal FW group, the Prdx6 protein was up-regulated in the cytosol of hepatocytes with a similar role as glutathione peroxidase to reduce oxidative stress upon hypothermal challenge. Conversely, in hypothermal SW milkfish, total Prdx6 protein was down-regulated. However, cytosolic Prdx6 protein was translocated to the membrane, using the ability of phospholipase A₂ to stabilize the membrane redox state. Moreover, H₂O₂ content was increased in FW-acclimated milkfish livers upon hypothermal challenge. Ex vivo H₂O₂ treatment of milkfish livers also induced Ccprdx6 transcriptional expression, which provided more evidence of the antioxidant role of milkfish Prdx6. Taken together, upon hypothermal challenge, greater oxidative stress in livers of FW-acclimated milkfish rather than SW-acclimated individuals led to different profiles of hepatic CcPrdx6 expression between the FW and SW group. The results indicated that CcPrdx6 played the role of antioxidant with different mechanisms, i.e., binding to reactive oxygen species and stabilizing membrane fluidity, in livers of hypothermal FW and SW milkfish, respectively.