Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish

Microbiota Dysbiosis in Mytilus chilensis Is Induced by Hypoxia, Leading to Molecular and Functional Consequences

Bivalve microbiota play a vital role in host health, supporting nutrient processing, immunity, and disease resistance. However, the increasing hypoxia in Chilean coastal waters, caused by climate change and eutrophication, threatens to disrupt this microbial balance, potentially promoting pathogens and impairing essential functions. Mytilus chilensis is vulnerable to hypoxia-reoxygenation cycles, yet the effects on its microbiota remain poorly understood. This study investigates the impact of hypoxia on the structure and functional potential of the microbial communities residing in the gills and digestive glands of M. chilensis. Employing full-length 16S rRNA gene sequencing, we explored hypoxia's effects on microbial diversity and functional capacity. Our results revealed significant alterations in the microbial composition, with a shift towards facultative anaerobes thriving in low oxygen environments. Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as Vibrio and Aeromonas exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. This study sheds light on the intricate interactions between host-associated microbiota and environmental stressors, underlining the importance of managing the microbiota in the face of climate change and aquaculture practices.

Boat Noise Increases the Oxygen Consumption Rate of the Captive Juvenile Large Yellow Croaker, Larimichthys crocea

Anthropogenic noise pollution is increasingly acknowledged as a major threat to marine ecosystems, especially for sound-sensitive species, such as the large yellow croaker (Larimichthys crocea). While the effects of underwater noise on fish behavior and physiology have been well-documented, its influence on oxygen metabolism across varying temperatures remains poorly understood. This study examines the impact of boat noise on the oxygen consumption rate (OCR) of juvenile large yellow croakers at different temperatures, a key factor in their metabolic activity. The underwater noise generated by a fishing boat spans a broad frequency range, with a peak spectrum level of 130 dB re 1 µPa at low frequencies between 100 and 200 Hz. Our findings reveal that boat noise significantly elevates the OCR of juvenile fish, with mass-specific OCR increasing by 65.0%, 35.3%, and 28.9% at 18 °C, 25 °C, and 30 °C, respectively. Similarly, individual OCR rose by 60.7%, 35.3%, and 17.1% at these temperatures. These results demonstrate that boat noise triggers a stress response in fish, resulting in heightened metabolic demands across different seasonal conditions. Notably, the impact of boat noise on respiratory metabolism is most significant at lower temperatures. In aquatic environments with stable oxygen levels, the noise-induced rise in oxygen consumption could lead to hypoxia and provoke maladaptive behavioral changes in fish.

Effects of Density Stress During Transportation on the Antioxidant Activity and Immuno-Related Gene Expression in Yellowfin Seabream (Acanthopagrus latus Houttuyn, 1782)

Background/Objectives: Maintaining an optimum transport density is essential for protecting water quality, lowering stress levels, and increasing fish survival rates. Transporting marine fish fry involves major dangers. The purpose of this study was to evaluate the impact of transport stress at varying densities on the immune-related gene expression, antioxidant capacity, and survival rate of yellowfin seabream (Acanthopagrus latus) fry. Methods: A 12 h simulated transport experiment was conducted with A. latus fry divided into six density groups. For 1-2 cm fry, densities of 900, 1200, and 1500 fry per pouch were used to assess antioxidant enzyme activity; and for 4-5 cm fry, densities of 100, 125, and 150 fry per pouch were used for gene expression analysis. The key parameters measured included survival rates, antioxidant enzyme activities in liver and intestinal tissues, and expression levels of HSP90α and caspase-3 genes. Results: The findings showed that recovery time and density both affected the observed responses and that transport density had a substantial effect on antioxidant enzyme activity in all tissues. The intestinal and liver tissues showed a considerable decrease in antioxidant enzyme activity, suggesting that these tissues may be able to respond to oxidative stress. Moreover, under high-density transport conditions, there were notable increases in the expression of caspase-3 and HSP90α, suggesting the activation of immune response systems. This research offers valuable new understandings into the relationship between transport density and immunological and antioxidant modulation in A. latus fry. Conclusions: The results provide a scientific foundation for enhancing aquaculture transport conditions, which will ultimately lead to decreased fish mortality and improved general health during transit, resulting in more sustainable and effective aquaculture methods.

The origins of gas exchange and ion regulation in fish gills: evidence from structure and function

Gill function in gas exchange and ion regulation has played key roles in the evolution of fishes. In this review, we summarize data from the fields of palaeontology, developmental biology and comparative physiology for when and how the gills first acquired these functions. Data from across disciplines strongly supports a stem vertebrate origin for gas exchange structures and function at the gills with the emergence of larger, more active fishes. However, the recent discovery of putative ionocytes in extant cephalochordates and hemichordates suggests that ion regulation at gills might have originated much earlier than gas exchange, perhaps in the ciliated pharyngeal arches in the last common ancestor of deuterostomes. We hypothesize that the ancestral form of ion regulation served a filter-feeding function in the ciliated pharyngeal arches, and was later coopted in vertebrates to regulate extracellular ion and acid-base balance. We propose that future research should explore ionocyte homology and function across extant deuterostomes to test this hypothesis and others in order to determine the ancestral origins of ion regulation in fish gills.

Hypothalamic transcriptome response to simulated diel earthen pond hypoxia cycles in channel catfish (Ictalurus punctatus)

Commercial culture of channel catfish (Ictalurus punctatus) occurs in earthen ponds that are characterized by diel swings in dissolved oxygen concentration that can fall to severe levels of hypoxia, which can suppress appetite and lead to suboptimal growth. Given the significance of the hypothalamus in regulating these processes in other fishes, an investigation into the hypothalamus transcriptome was conducted to identify specific genes and expression patterns responding to hypoxia. Channel catfish in normoxic water were compared with catfish subjected to 12 h of hypoxia (20% oxygen saturation; 1.8 mg O2/L; 27°C) followed by 12 h of recovery in normoxia to mimic 24 h in a catfish aquaculture pond. Fish were sampled at 0-, 6-, 12-, 18-, and 24-h timepoints, with the 6- and 12-h samplings occurring during hypoxia. A total of 190 genes were differentially expressed during the experiment, with most occurring during hypoxia and returning to baseline values within 6 h of normoxia. Differentially expressed genes were sorted by function into Gene Ontology biological processes and revealed that most were categorized as "response to hypoxia," "sprouting angiogenesis," and "cellular response to xenobiotic stimulus." The patterns of gene expression reported here suggest that transcriptome responses to hypoxia are broad and quickly reversibly with the onset of normoxia. Although no genes commonly reported to modulate appetite were found to be differentially expressed in this experiment, several candidates were identified for future studies investigating the interplay between hypoxia and appetite in channel catfish, including adm, igfbp1a, igfbp7, and stc2b.NEW & NOTEWORTHY Channel catfish are an economically important species that experience diel episodic periods of hypoxia that can reduce appetite. This is the first study to investigate their transcriptome from the hypothalamus in a simulated 24-h span in a commercial catfish pond, with 12 h of hypoxia and 12 h of normoxia. The research revealed functional groups of genes relating to hypoxia, angiogenesis, and glycolysis as well as individual target genes possibly involved in appetite regulation.

Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments

The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.

Integrated analysis of transcriptome, translatome and proteome reveals insights into yellow catfish (Pelteobagrus fulvidraco) brain in response to hypoxia

Brain plays a central role in adapting to environmental changes and is highly sensitive to the oxygen level. Although previous studies investigated the molecular response of brain exposure to acute hypoxia in fish, the lack of studies at the translational level hinders further understanding of the regulatory mechanism response to hypoxia from multi-omics levels. Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater aquaculture species; however, hypoxia severely restricts the sustainable development of its breeding industry. In the present study, the transcriptome, translatome, and proteome were integrated to study the global landscapes of yellow catfish brain response to hypoxia. The evidently increased amount of cerebral cortical cells with oedema and pyknotic nuclei has been observed in hypoxia group of yellow catfish. A total of 2750 genes were significantly changed at the translational level. Comparative transcriptional and translational analysis suggested the HIF-1 signaling pathway, autophagy and glycolysis/gluconeogenesis were up-regulated after hypoxia exposure. KEGG enrichment of translational efficiency (TE) differential genes suggested that the lysosome and autophagy were highly enriched. Our result showed that yellow catfish tends to inhibit the TE of genes by increasing the translation of uORFs to adapt to hypoxia. Correlation analysis showed that transcriptome and translatome exhibit higher correlation. In summary, this study demonstrated that hypoxia dysregulated the cerebral function of yellow catfish at the transcriptome, translatome, and proteome, which provides a better understanding of hypoxia adaptation in teleost.

Exposure to pyrogallol impacts the hemato-biochemical endpoints in catfish (Clarias gariepinus)

Pyrogallol is widely used in several industrial applications and can subsequently contaminate aquatic ecosystems. Here, we report for the first time the presence of pyrogallol in wastewater in Egypt. Currently, there is a complete lack of toxicity and carcinogenicity data for pyrogallol exposure in fish. To address this gap, both acute and sub-acute toxicity experiments were conducted to determine the toxicity of pyrogallol in catfish (Clarias gariepinus). Behavioral and morphological endpoints were evaluated, in addition to blood hematological endpoints, biochemical indices, electrolyte balance, and the erythron profile (poikilocytosis and nuclear abnormalities). In the acute toxicity assay, it was determined that the 96 h median-lethal concentration (96 h-LC50) of pyrogallol for catfish was 40 mg/L. In sub-acute toxicity experiment, fish divided into four groups; Group 1 was the control group. Group 2 was exposed to 1 mg/L of pyrogallol, Group 3 was exposed to 5 mg/L of pyrogallol, and Group 4 was exposed to 10 mg/L of pyrogallol. Fish showed morphological changes such as erosion of the dorsal and caudal fins, skin ulcers, and discoloration following exposure to pyrogallol for 96 h. Exposure to 1, 5, or 10 mg/L pyrogallol caused a significant decrease in hematological indices, including red blood cells (RBCs), hemoglobin, hematocrit, white blood cells (WBC), thrombocytes, and large and small lymphocytes in a dose-dependent manner. Several biochemical parameters (creatinine, uric acid, liver enzymes, lactate dehydrogenase, and glucose) were altered in a concentration dependent manner with short term exposures to pyrogallol. Pyrogallol exposure also caused a significant concentration-dependent rise in the percentage of poikilocytosis and nuclear abnormalities of RBCs in catfish. In conclusion, our data suggest that pyrogallol should be considered further in environmental risk assessments of aquatic species.

Toxicity and potential underlying mechanism of Karenia selliformis to the fish Oryzias melastigma

Karenia selliformis can produce toxins such as gymnodimines, and form microalgal blooms causing massive mortality of marine life such as fish and shellfish, and resulting in serious economic losses. However, there are a few of studies on the toxic effects of K. selliformis on marine organisms and the underlying mechanisms, and it is not clear whether the toxins produced by K. selliformis affect fish survival through the food chain. In this study, a food chain was simulated and composed by K. selliformis-brine shrimp-marine medaka to investigate the possibility of K. selliformis toxicity transmission through the food chain, in which fish behavior, histopathology and transcriptomics changes were observed after direct or indirect exposure (through the food chain) of K. selliformis. We found that both direct and indirect exposure of K. selliformis could affect the swimming behavior of medaka, manifested as decreased swimming performance and increased "frozen events". Meanwhile, exposure to K. selliformis caused pathological damage to the intestine and liver tissues of medaka to different degree. The effect of direct exposure to K. selliformis on swimming behavior and damage to fish tissues was more severe. In addition, K. selliformis exposure induced significant changes in the expression of genes related to energy metabolism, metabolic detoxification and immune system in medaka. These results suggest that toxins produced by K. selliformis can be transferred through the food chain, and that K. selliformis can destroy the intestinal integrity of medaka and increase the absorption of toxins, leading to energy metabolism disorders in fish, affecting the metabolic detoxification capacity of the liver. Our finding provides novel insight into the toxicity of K. selliformis to marine fish.

Impact of benzophenone-3 on the integument and gills of zebrafish (Danio rerio)

Benzophenone (BP-3) is an organic compound that is a common ingredient in lotions, conditioners, and other personal care products, which helps protect against ultraviolet radiation. This study investigated the effect of BP-3 on the structure of the integument and gills, as well as the activities of superoxide dismutase (SOD) and catalase (CAT) in the gills of Danio rerio. Fish were exposed to different concentrations (7, 70, and 700 µg L-1) of BP-3 for 7 and 14 d. For the histological analysis of the integument and gills, the fish were fixed in Bouin liquid and processed according to standard histologic procedures, and the tissue section slices were stained according to different histochemical methods. BP-3 caused tissue damage and morphological alterations in the gills; however, the integument showed no histological or morphological alterations. Furthermore, there was no observed correlation between the BP-3 concentration and exposure period and the gill alterations, as these did not occur in a linear manner. The gills were removed to evaluate the antioxidant defense; for this, CAT and SOD activities were measured, and a reduction of SOD activity was noted, whereas the CAT activity was not significantly affected.

Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress

Trachinotus ovatus is a major economically important cultured marine fish in the South China Sea. However, extreme weather and increased culture density result in uncontrollable problems, such as increases in water temperature and a decline in dissolved oxygen (DO), hindering the high-quality development of aquaculture. In this study, liver transcriptional profiles of T. ovatus were investigated under acute high-temperature stress (31 °C and 34 °C) and normal water temperature (27 °C) using RNA sequencing (RNA-Seq) technology. Differential expression analysis and STEM analysis showed that 1347 differentially expressed genes (DEGs) and four significant profiles (profiles 0, 3, 4, and 7) were screened, respectively. Of these DEGs, some genes involved in heat shock protein (HSPs), hypoxic adaptation, and glycolysis were up-regulated, while some genes involved in the ubiquitin-proteasome system (UPS) and fatty acid metabolism were down-regulated. Our results suggest that protein dynamic balance and function, hypoxia adaptation, and energy metabolism transformation are crucial in response to acute high-temperature stress. Our findings contribute to understanding the molecular response mechanism of T. ovatus under acute heat stress, which may provide some reference for studying the molecular mechanisms of other fish in response to heat stress.

Determination of histopathological effects and myoglobin, periostin gene-protein expression levels in Danio rerio muscle tissue after acaricide yoksorrun-5EC (hexythiazox) application

Although pesticides are essential agrochemicals to annihilate harmful organisms in agriculture, their uncontrolled use has become an important threat to environmental health. Exposure to pesticides can affect many biological systems including immune system, endocrine system, and nervous system. However, the potential side effects of pesticides to skeletal muscle system remain unclear. Present study has focused on the evaluation of this issue by using an acaricide, yoksorrun-5EC (hexythiazox), in an aquatic model organism, Danio rerio. The histological analyses revealed that increased concentrations of the acaricide cause degradation of skeletal muscle along with increased necrosis and atrophy in myocytes, intercellular edema, and increased infiltrations between perimysium sheaths of muscle fibers. The effects of acaricide on myoglobin and periostin, which are associated with oxygen transport and muscle regeneration, respectively, were investigated at the gene and protein levels. RT-PCR results suggested that high concentration yoksorrun-5EC (hexythiazox) can induce myoglobin and periostin genes. Similar results were also obtained in the protein levels of these genes by western blotting analysis. These results suggested that yoksorrun-5EC (hexythiazox)-dependent disruption of skeletal muscle architecture is closely associated with the expression levels of myoglobin and periostin genes in Danio rerio model.

Enhance energy supply of largemouth bass (Micropterus salmoides) in gills during acute hypoxia exposure

Gills are the location of gas exchange and also the first target organ of fish response for environmental stress. As a multifunctional organ, its energy supply, when faced with insufficient dissolved oxygen in the water, remains unclear. In this study, largemouth bass was subjected to hypoxia stress (1.2 mg/L) for 24 h and 12 h reoxygenation (R12) to evaluate energy supply strategy of gills. Under hypoxia exposure, the respiratory rate of largemouth bass increased by an average of 20 breaths per minute. A total of 2026, 1744, 1003, 579, 485, and 265 differentially expressed genes (DGEs) were identified at 0 h, 4 h, 8 h, 12 h, 24 h, and R12h in gills after hypoxia exposure. KEGG functional analysis of DEGs revealed that the glycolysis/gluconeogenesis pathway was enriched across all the sampling points (0, 4, 8, 12, 24 h, R12). The gene expression and enzyme activity of three rate-limiting enzymes (hexokinase, phosphofructokinase-6, pyruvate kinase) in glycolysis pathway were significantly increased. Increased levels of glycolysis products pyruvate and lactic acid, as well as the number of mitochondria (1.8-fold), suggesting an enhancement of aerobic and anaerobic metabolism of glucose in gills. These results suggest that the gill of largemouth bass enhanced the energy supply during acute exposure to hypoxia stress.

Toxicity and underlying mechanism of the toxic dinoflagellate Gambierdiscus caribaeus to the fish Oryzias melastigma

Gambierdiscus spp. is mainly responsible for the ciguatera fish poisoning (CFP) around the world. The gambiertoxin produced by Gambierdiscus can be passed through the food chain to form ciguatoxins (CTXs) that cause ciguatoxins poisoning. However, the toxic effects of Gambierdiscus on fish through the food chain and related mechanism remains unclear. In this study, the toxicity of Gambierdiscus caribaeus on the marine medaka (Oryzias melastigma) was investigated, where the simulated food chain toxic algae-food organism-fish (G. caribaeus-Artemia metanauplii-O. melastigma) was set. The results showed that direct or indirect exposure through the food chain of G. caribaeus could affect the swimming behaviour of O. melastigma, manifested as decreased swimming performance and spontaneous abnormal swimming behaviours. Histological observation showed that direct or indirect exposure of G. caribaeus caused different degrees of pathological damage to the gills, intestine and liver tissues of O. melastigma. Transcriptome sequencing and RT-qPCR demonstrated that G. caribaeus exposure could trigger a series of physiological and biochemical responses, mainly reflected in energy metabolism, reproductive system, neural activity, immune stress and drug metabolism in marine medaka. Our finding may provide novel insight into the toxicity of Gambierdiscus on fish.

Osmotic Gradient Is a Factor That Influences the Gill Microbiota Communities in Oryzias melastigma

Simple Summary

This study was applied to the laboratory medaka to understand how the osmotic gradient could influence the composition of the gill microbiota communities. The data suggested that the shift of the gill microbiota community has relied on the first sense of osmolality differences, and such changes were accomplished by the enriched osmosensing and metabolic pathways.

Abstract

The fish gill is the first tissue that is exposed to the external media and undergoes continuous osmotic challenges. Recently, our group published an article entitled “Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka” in the journal mSystems (e0004722, 2022), and suggested the possible host-bacterium interaction in the fish gill during osmotic stress. The previous study was performed by the progressive fresh water transfer (i.e., seawater to fresh water transfer via 50% seawater (FW)). Our group hypothesized that osmotic gradient could be a factor that determines the microbiota communities in the gill. The current 16S rRNA metagenomic sequencing study found that the direct transfer (i.e., seawater to fresh water (FWd)) could result in different gill microbiota communities in the same fresh water endpoints. Pseduomonas was the dominant bacteria (more than 55%) in the FWd gill. The Kyoto Encyclopedia of Genes and Genomes and MetaCyc analysis further suggested that the FWd group had enhanced osmosensing pathways, such as the ATP-binding cassette transporters, taurine degradation, and energy-related tricarboxylic acid metabolism compared to the FW group.

Comparative transcriptome analysis reveals physiological responses in liver tissues of Epinephelus coioides under acute hypoxia stress

Hypoxia is a common stressor for aquatic animals, including Epinephelus coioides, with a considerable impact on sustainable aquaculture. E. coioides is a widely consumed fish in China owing to its high nutritious value and taste. However, water hypoxia caused by high density culture process has become a great threat to E. coioides culture, and its response to hypoxia stress has not been discussed before. Therefore, the aim of this study was to examine the response of E. coioides to acute hypoxia using transcriptomic techniques. To this end, RNA sequencing was performed on the liver tissues of fish exposed to normoxic and hypoxic conditions for 1 h. The results presented 503 differentially expressed genes (DEGs) in the liver tissue of fish exposed to hypoxic condition compared with those in the normoxic group. Enrichment analysis using the Gene Ontology database showed that the DEGs were mainly enriched for functions related to cell apoptosis signaling pathways, insulin resistance, antioxidant enzymes, and glycolysis/gluconeogenesis signaling pathways. KEGG enrichment analysis showed that HIF-1, PI3K-AKT, IL-17, NF-kappa B, and MAPK signaling pathways were significantly enriched by the DEGs. The DEGs were mainly involved in immune response, inflammatory response, cell apoptosis regulation, energy metabolism, and substance metabolism. Additionally, the hypoxia response in E. coioides was mainly regulated via the PI3K-AKT-HIF-1 signaling axis. Overall, the findings of this study contribute to the understanding of hypoxia stress response in E. coioides, and provides target genes for breeding hypoxia-tolerant Epinephelus spp.

Paternal hypoxia exposure primes offspring for increased hypoxia resistance

BACKGROUND

In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia.

RESULTS

We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 6-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that other epigenetic mechanisms are responsible for alterations in gene expression.

CONCLUSIONS

Overall, our findings suggest that an epigenetic memory of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.

Transcriptome Analysis Identifies Key Metabolic Changes in the Brain of Takifugu rubripes in Response to Chronic Hypoxia

The brain is considered to be an extremely sensitive tissue to hypoxia, and the brain of fish plays an important role in regulating growth and adapting to environmental changes. As an important aquatic organism in northern China, the economic yield of Takifugu rubripes is deeply influenced by the oxygen content of seawater. In this regard, we performed RNA-seq analysis of T. rubripes brains under hypoxia and normoxia to reveal the expression patterns of genes involved in the hypoxic response and their enrichment of metabolic pathways. Studies have shown that carbohydrate, lipid and amino acid metabolism are significant pathways for the enrichment of differentially expressed genes (DEGs) and that DEGs are significantly upregulated in those pathways. In addition, some biological processes such as the immune system and signal transduction, where enrichment is not significant but important, are also discussed. Interestingly, the DEGs associated with those pathways were significantly downregulated or inhibited. The present study reveals the mechanism of hypoxia tolerance in T. rubripes at the transcriptional level and provides a useful resource for studying the energy metabolism mechanism of hypoxia response in this species.

Acclimatization of fish to the higher calcium levels in the water environment

It is established that calcium concentration changes (variations) in the water environment significantly influence its intake and distribution in tissues and organs of hydrobionts. The decrease in calcium concentration in water from 100 to 60 mg.L-1 significantly reduces its content in fish liver. In the gills glandular apparatus of fish acclimated to the environment with lower calcium level (in comparison with control one), its concentration on the first day of the acclimation period slightly exceeded the initial level, thus testifying to its possible excretion of endogenous calcium by gills. The increase of calcium excretion through the renal and digestive systems in fish acclimates to the higher water level, and specific changes in phosphates excretion dynamics accompany oral intake. Long keeping fish in water with 100 mg.L-1 calcium is accompanied by the increase of total phosphorus in urine (by 2 – 2.5 times), and its day excretion increases by 1.9 – 2.4 times. During fish acclimation to higher calcium levels in the water environment, the excretion of total phosphorus with faecal matter increases. The increase of calcium in the water environment to 100 mg.L-1 leads to a temporary increase in total phosphorus excretion with faecal issues. The rise in cation concentration to 200 mg.L-1  increases significantly during long-time fish stay in such an environment.

Alterations to cavefish red blood cells provide evidence of adaptation to reduced subterranean oxygen

Animals inhabiting extreme environments allow the powerful opportunity to examine adaptive evolution in response to diverse pressures. One such pressure is reduced oxygen, commonly present at high-altitude and subterranean environments. Cave-dwelling animals must also deal with darkness and starvation, both of which have been rigorously studied as key forces driving the evolution of cave-associated traits. Interestingly, hypoxia as an environmental pressure has received less attention. Here we examined putatively adaptive phenotypes evolving in a freshwater teleost fish, Astyanax mexicanus, which includes both surface- and cave-dwelling forms. This model system also provides the opportunity to identify convergent responses to hypoxia, owing to the presence of numerous natural and independently-colonised cave populations, alongside closely-related surface conspecifics. The focus of this study is hemoglobin, an essential molecule for oxygen transport and delivery. We found that multiple cave populations harbor a higher concentration of hemoglobin in their blood, which is coincident with an increase in cave morph erythrocyte size compared to surface fish. Interestingly, both cave and surface morphs have comparable numbers of erythrocytes per unit of blood, suggesting elevated hemoglobin is not due to overproduction of red blood cells. Alternatively, owing to an increased cell area of erythrocytes in cavefish, we reason that they contain more hemoglobin per erythrocyte. These findings support the notion that cavefish have adapted to hypoxia in caves through modulation of both hemoglobin production and erythrocyte size. This work reveals an additional adaptive feature of Astyanax cavefish, and demonstrates that coordinated changes between cellular architecture and molecular changes are necessary for organisms evolving under intense environmental pressure.

Koi sleepy disease as a pathophysiological and immunological consequence of a branchial infection of common carp with carp edema virus

Gills of fish are involved in respiration, excretion and osmoregulation. Due to numerous interactions between these processes, branchial diseases have serious implications on fish health. Here, "koi sleepy disease" (KSD), caused by carp edema virus (CEV) infection was used to study physiological, immunological and metabolic consequences of a gill disease in fish. A metabolome analysis shows that the moderately hypoxic-tolerant carp can compensate the respiratory compromise related to this infection by various adaptations in their metabolism. Instead, the disease is accompanied by a massive disturbance of the osmotic balance with hyponatremia as low as 71.65 mmol L^-1, and an accumulation of ammonia in circulatory blood causing a hyperammonemia as high as 1123.24 µmol L^-1. At water conditions with increased ambient salt, the hydro-mineral balance and the ammonia excretion were restored. Importantly, both hyponatremia and hyperammonemia in KSD-affected carp can be linked to an immunosuppression leading to a four-fold drop in the number of white blood cells, and significant downregulation of cd4, tcr a2 and igm expression in gills, which can be evaded by increasing the ion concentration in water. This shows that the complex host-pathogen interactions within the gills can have immunosuppressive consequences, which have not previously been addressed in fish. Furthermore, it makes the CEV infection of carp a powerful model for studying interdependent pathological and immunological effects of a branchial disease in fish.

Effects of Chronic Hypoxia on the Immune Status of Pikeperch (Sander lucioperca Linnaeus, 1758)

Simple Summary

Inadequate oxygen saturation, or hypoxia, belongs to one of the critical stress factors in intensive aquaculture. Exposure of fish to low oxygen levels over prolonged periods substantially affects their well-being and immune competence, resulting in increased disease susceptibility and consequent economic losses. In this interdisciplinary research, we aimed to provide a deeper understanding of the effect of chronic low oxygen saturation on pikeperch farmed in recirculating aquaculture systems. The obtained data offer unprecedented insights into the changes in the immunocompetence of studied fish and suggest high robustness of this new aquaculture species to the stress factors of intensive aquaculture.

Abstract

Inadequate oxygen saturation can induce stress responses in fish and further affect their immunity. Pikeperch, recently introduced in intensive aquaculture, is suggested to be reared at nearly 100% DO (dissolved oxygen), yet this recommendation can be compromised by several factors including the water temperature, stocking densities or low circulation. Herein, we aimed to investigate the effect of low oxygen saturation of 40% DO (±3.2 mg/L) over 28 days on pikeperch farmed in recirculating aquaculture systems. The obtained data suggest that—although the standard blood and health parameters did not reveal any significant differences at any timepoint—the flow cytometric analysis identified a slightly decreased proportion of lymphocytes in the HK (head kidney) of fish exposed to hypoxia. This has been complemented by marginally downregulated expression of investigated immune and stress genes in HK and liver (including FTH1, HIF1A and NR3C1). Additionally, in the model of acute peritoneal inflammation induced with inactivated Aeromonas hydrophila, we observed a striking dichotomy in the sensitivity to the low DO between innate and adaptive immunity. Thus, while the mobilization of myeloid cells from HK to blood, spleen and peritoneal cavity, underlined by changes in the expression of key proinflammatory cytokines (including MPO, IL1B and TNF) was not influenced by the low DO, hypoxia impaired the influx of lymphocytes to the peritoneal niche in the later phases of the immune reaction. Taken together, our data suggest high robustness of pikeperch towards the low oxygen saturation and further encourage its introduction to the intensive aquaculture systems.

Hypoxia-induced oxidative stress and transcriptome changes in the mud crab (Scylla paramamosain)

Mud crab (Scylla paramamosain) is an economically important cultured species in China. Hypoxia is a major environmental stressor during mud crab culture. In the present study, we investigated the oxidative stress and transcriptome changes in the gills of mud crab after intermediate hypoxia stress with dissolved oxygen (DO) 3.0 ± 0.2 mg/L (named as "DO3") and acute hypoxia stress with DO 1.0 ± 0.2 mg/L (named as "DO1") for 0, 3, 6, 12 and 24 h. The superoxide dismutase (SOD) activity of DO1 increased significantly at 3, 6 and 24 h after hypoxia stress, while SOD activity of DO3 increased significantly at 6 and 24 h. The total antioxidant capacity (T-AOC) increased significantly at 6, 12 and 24 h after hypoxia stress. The malondialdehyde (MDA) concentration of DO1 increased significantly at 6, 12 and 24 h after hypoxia stress, while MDA concentration of DO3 only increased significantly at 6 h. The lactate dehydrogenase (LDH) activity of DO1 increased significantly at 3, 6, 12 and 24 h after hypoxia stress, while LDH activity of DO3 increased significantly at 12 and 24 h. Transcriptomic analysis was conducted at 24 h of gill tissues after hypoxia stress. A total of 1052 differentially expressed genes (DEGs) were obtained, including 394 DEGs between DO1 and DO3, 481 DEGs between DO1 and control group, 177 DEGs between DO3 and control group. DEGs were enriched in the pathways related to metabolism, immune functions, ion transport, and signal transduction. Transcriptional analysis showed that glycolysis and tricarboxylic acid cycle genes were the key factors in regulating the adaptation of mud crab to hypoxia stress.

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

BACKGROUND

Increases in ocean temperatures and in the frequency and severity of hypoxic events are expected with climate change, and may become a challenge for cultured Atlantic salmon and negatively affect their growth, immunology and welfare. Thus, we examined how an incremental temperature increase alone (Warm & Normoxic-WN: 12 → 20 °C; 1 °C week- 1), and in combination with moderate hypoxia (Warm & Hypoxic-WH: ~ 70% air saturation), impacted the salmon's hepatic transcriptome expr\ession compared to control fish (CT: 12 °C, normoxic) using 44 K microarrays and qPCR.

RESULTS

Overall, we identified 2894 differentially expressed probes (DEPs, FDR < 5%), that included 1111 shared DEPs, while 789 and 994 DEPs were specific to WN and WH fish, respectively. Pathway analysis indicated that the cellular mechanisms affected by the two experimental conditions were quite similar, with up-regulated genes functionally associated with the heat shock response, ER-stress, apoptosis and immune defence, while genes connected with general metabolic processes, proteolysis and oxidation-reduction were largely suppressed. The qPCR assessment of 41 microarray-identified genes validated that the heat shock response (hsp90aa1, serpinh1), apoptosis (casp8, jund, jak2) and immune responses (apod, c1ql2, epx) were up-regulated in WN and WH fish, while oxidative stress and hypoxia sensitive genes were down-regulated (cirbp, cyp1a1, egln2, gstt1, hif1α, prdx6, rraga, ucp2). However, the additional challenge of hypoxia resulted in more pronounced effects on heat shock and immune-related processes, including a stronger influence on the expression of 14 immune-related genes. Finally, robust correlations between the transcription of 19 genes and several phenotypic traits in WH fish suggest that changes in gene expression were related to impaired physiological and growth performance.

CONCLUSION

Increasing temperature to 20 °C alone, and in combination with hypoxia, resulted in the differential expression of genes involved in similar pathways in Atlantic salmon. However, the expression responses of heat shock and immune-relevant genes in fish exposed to 20 °C and hypoxia were more affected, and strongly related to phenotypic characteristics (e.g., growth). This study provides valuable information on how these two environmental challenges affect the expression of stress-, metabolic- and immune-related genes and pathways, and identifies potential biomarker genes for improving our understanding of fish health and welfare.

Multi-omics analysis reveals the glycolipid metabolism response mechanism in the liver of genetically improved farmed Tilapia (GIFT, Oreochromis niloticus) under hypoxia stress

BACKGROUND

Dissolved oxygen (DO) in the water is a vital abiotic factor in aquatic animal farming. A hypoxic environment affects the growth, metabolism, and immune system of fish. Glycolipid metabolism is a vital energy pathway under acute hypoxic stress, and it plays a significant role in the adaptation of fish to stressful environments. In this study, we used multi-omics integrative analyses to explore the mechanisms of hypoxia adaptation in Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus).

RESULTS

The 96 h median lethal hypoxia (96 h-LH50) for GIFT was determined by linear interpolation. We established control (DO: 5.00 mg/L) groups (CG) and hypoxic stress (96 h-LH50: 0.55 mg/L) groups (HG) and extracted liver tissues for high-throughput transcriptome and metabolome sequencing. A total of 581 differentially expressed (DE) genes and 93 DE metabolites were detected between the CG and the HG. Combined analyses of the transcriptome and metabolome revealed that glycolysis/gluconeogenesis and the insulin signaling pathway were down-regulated, the pentose phosphate pathway was activated, and the biosynthesis of unsaturated fatty acids and fatty acid metabolism were up-regulated in GIFT under hypoxia stress.

CONCLUSIONS

The results show that lipid metabolism became the primary pathway in GIFT under acute hypoxia stress. Our findings reveal the changes in metabolites and gene expression that occur under hypoxia stress, and shed light on the regulatory pathways that function under such conditions. Ultimately, this information will be useful to devise strategies to decrease the damage caused by hypoxia stress in farmed fish.

Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)

Molecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus), allowing us to pair a gene-suite approach (i.e. multiple genes across multiple cellular processes) with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (~1.5 months) and long-term (~3.5 months) confinement in the Delta Marsh, which is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are confined in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term confinement in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye confined in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions. These results provide valuable information for managers invested in mediating impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.

Effect of PM10 on pulmonary immune response and fetus development

Despite numerous reports that ambient particulate matter is a key determinant for human health, toxicity data produced based on physicochemical properties of particulate matters is very lack, suggesting lack of scientific evidence for regulation. In this study, we sampled inhalable particulate matters (PM10) in northern Seoul, Korea. PM10 showed atypical- and fiber-type particles with the average size and the surface charge of 1,598.1 ± 128.7 nm and -27.5 ± 2.8, respectively, and various toxic elements were detected in the water extract. On day 90 after the first pulmonary exposure, total cell number dose-dependently increased in the lungs of both sexes of mice. PM10 induced Th1-dominant immune response with pathological changes in both sexes of mice. Meanwhile, composition of total cells and expression of proteins which functions in cell-to-cell communication showed different trends between sexes. Following, male and female mice were mated to identify effects of PM10 to the next generation. PM10 remained in the lung of dams until day 21 after birth, and the levels of IgA and IgE increased in the blood of dams exposed to the maximum dose compared to control. In addition, the interval between births of fetuses, the number of offspring, the neonatal survival rate (day 4 after birth) and the sex ratio seemed to be affected at the maximum dose, and particularly, all offspring from one dam were stillborn. In addition, expression of HIF-1α protein increased in the lung tissue of dams exposed to PM10, and level of hypoxia-related proteins was notably enhanced in PM10-exposed bronchial epithelial cells compared to control. Taken together, we suggest that inhaled PM10 may induce Th1-shifting immune response in the lung, and that it may affect reproduction (fetus development) by causing lung hypoxia. Additionally, we propose that further study is needed to identify particle-size-dependent effects on development of the next generation.

Transcriptome analysis reveals molecular strategies in gills and heart of large yellow croaker (Larimichthys crocea) under hypoxia stress

The gills and heart are two major targets of hypoxia in fish. However, the molecular responses in fish gills and heart to hypoxia challenge remain unclear. Here, RNA-Seq technology was used to study the gene expression profiles in gills and heart of large yellow croaker (Larimichthys crocea) at 6, 24, and 48 h after hypoxia stress. A total of 1,546 and 2,746 differentially expressed genes (DEGs) were identified in gills and heart, respectively. Expression changes of nine genes in each tissue were further validated by the qPCR. Based on KEGG and Gene ontology enrichments, we found that various innate immunity-related genes, such as complement components (C1qs, C2, C3, C6, and C7), chemokines (CCL3, CCL17, CCL19, CCL25, and CXCL8_L3), chemokine receptors (CCR9, CXCR1, and CXCR3), and nitric oxide synthase (NOS), were significantly down-regulated in gills and/or heart, suggesting that innate immune processes mediated by these genes may be inhibited by hypoxia. The genes involved in both glycolysis pathway (LDHA) and tricarboxylic acid cycle (IDH2 and OGDH) were up-regulated in gills and heart of hypoxic large yellow croakers, possibly because gill and heart tissues need enough energy to accelerate gas exchange and blood circulation. Hypoxia also affected the ion transport in gills of large yellow croaker, through down-regulating the expression levels of numerous classical ion transporters, including HVCN1, SLC20A2, SLC4A4, RHBG, RHCG, and SCN4A, suggesting an energy conservation strategy to hypoxia stress. All these results indicate that the immune processes, glycolytic pathways, and ion transport were significantly altered in gills and/or heart of large yellow croaker under hypoxia, possibly contributing to maintain cellular energy balance during hypoxia. Our data, therefore, afford new information to understand the tissue-specific molecular responses of bony fish to hypoxia stress.

Combined exposure to hypoxia and ammonia aggravated biological effects on glucose metabolism, oxidative stress, inflammation and apoptosis in largemouth bass (Micropterus salmoides)

Hypoxia and ammonia are unavoidable environmental factors in aquaculture, and have been shown cause various adverse effects in fish. In the present study, a two-factor crossover experiment was carried out to evaluate the combined effect of hypoxia and ammonia on oxidative stress and glucose metabolism endpoints in largemouth bass. The fish were divided into four experimental groups: hypoxia and ammonia group, hypoxia group, ammonia group, and control group. The results showed that hypoxia and ammonia exposures both induced antioxidant response and oxidative stress (superoxide dismutase [SOD] and catalase [CAT] activities increased first then decreased, and malondialdehyde accumulated) and anaerobic glycolysis (increase of blood glucose, decrease of liver glycogen, accumulation of lactate, and increased lactate dehydrogenase activity). In addition, hypoxia and ammonia upregulated antioxidant enzyme genes (Cu/ZnSOD, CAT, and GPx), apoptosis genes (caspase 3, caspase 8, and caspase 9), as well as inflammatory genes (interleukin [IL]-1β and IL-8) and downregulated an anti-inflammatory gene (IL-10), suggesting that apoptosis and inflammation may be related to oxidative stress. The increased expression of GLUT1, LDH, and MCT4 were induced by hypoxia and ammonia, suggesting that anaerobic glycolysis was increased. Furthermore, fish suffering from hypoxia or ammonia exposure showed some changes in gill tissues histology, and the most severe lesions of gill tissues appeared in simultaneous exposure. Overall, both hypoxia and ammonia affected homeostasis, and simultaneous exposure led to more deleterious effects on largemouth bass than exposure to the individual stressors.

Acute hypoxia changes the mode of glucose and lipid utilization in the liver of the largemouth bass (Micropterus salmoides)

Dissolved oxygen (DO) undountedly affects fish distribution, metabolism, and evern survival. Intensive aquaculture and environmental changes will inevitably lead to hypoxic stress for largemouth bass (Micropterus salmoides). The different metabolic responses and mechanism still remains relatively unknown during acute hypoxia exposure. In this study, largemouth bass were subjected to hypoxic stress (3.0 ± 0.2 mg/L and 1.2 ± 0.2 mg/L) for 24 h and 12 h reoxygenation to systemically evaluate indicators of glucose and lipid metabolism. A regulatory network was constructed using RNA-seq to further elucidate the transcriptional regulation of glucose and lipid metabolism. During hypoxia for 4 h, the liver glycogen, glucose and pyruvic acid contents significantly decreased, whereas plasma glucose content and liver lactic acid content increased significantly. The accumulation of liver triglycerides and non-esterified fatty acids was enhanced during hypoxia for 8 h. The activity of key enzymes revealed the different metabolic responses to hypoxia exposure for 4 h, including the enhancement of glycolysis, and inhibition of gluconeogenesis. Furthermore, hypoxia exposure for 8 h increased lipid mobilization, and inhibited the β-oxidation. In addition, an integrated regulatory network of 9 major pathways involved in the response to hypoxia exposure was constructed, including HIF signaling pathway, VEGF signaling pathway, AMPK signaling pathway, insulin signaling pathway and PPAR signaling pathway; glycolysis/gluconeogenesis, pyruvate metabolism, fatty acid degradation and fatty acid biosynthesis. Additionally, reoxygenation inhibited glycolysis, and promoted gluconeogenesis and lipid oxidation, but energy deficits persisted. In short, although the mobilization and activation of fatty acid in liver were enhanced in the early stage of hypoxia, glycolysis was the main energy source under acute hypoxia. The extent and duration of hypoxia determine the degree of change in energy metabolism.

Transcriptome analysis reveals new insights into immune response to hypoxia challenge of large yellow croaker (Larimichthys crocea)

Fish live in direct contact with aquatic environment, which exhibits much wider temporal and spatial variations in oxygen content. The molecular mechanisms underlying fish response to hypoxia have become a subject of great concern in recent years. In the present study, we performed transcriptome analysis of spleen and head kidney tissues from large yellow croaker (Larimichthys crocea) at 6 h, 24 h and 48 h after hypoxia challenge. A total of 2,499 and 3,685 differentially expressed genes (DEGs) were obtained in spleen and head kidney, respectively. The expression changes of 10 selected genes in each tissue were further validated by quantitative real-time PCR. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichments revealed that numerous DEGs were immune genes, involved in multiple immune-relevant pathways. In spleen, several pattern recognition receptors (PRRs), including Toll-like receptors (TLR1, TLR2-1, TLR2-2, TLR5 and TLR8), Fucolectins (FUCL1, FUCL4 and FUCL5) and macrophage mannose receptor (MRC1), were significantly down-regulated, suggesting that the immune processes mediated by these PRRs may be suppressed by hypoxia stress. However, some PRRs (FUCL4, FUCL5 and MRC1) and other innate immunity genes, such as C-type lectin domain gene family members, chemokines, chemokine receptors and complement components were up-regulated in head kidney, which may be due to the increases in phagocytosis and cytokine secretion by macrophages after hypoxic stimulus. The expression of genes involved in B cell receptor signaling pathway, Natural killer cell-mediated cytotoxicity and NF-κB signaling pathway decreased rapidly, but regained normal or increased over time, suggesting an early adjustment pattern of fish immune response to cope with hypoxia stress. Moreover, the anaerobic ATP-generating pathway was activated and energy consumption processes were repressed concurrently in both spleen and head kidney. These data provide valuable information for understanding the tissue-specific and temporal changes of immune gene expression in hypoxic large yellow croakers.

Nitrite Improves Heart Regeneration in Zebrafish

Aims: Nitrite is reduced to nitric oxide (NO) under physiological and pathological hypoxic conditions to modulate angiogenesis and improve ischemia-reperfusion injury. Although adult mammals lack the ability to regenerate the heart after injury, this is preserved in neonates and efforts to reactivate this process are of great interest. Unlike mammals, the adult zebrafish maintain the innate ability to regenerate their hearts after injury, providing an important model to study cardiac regeneration. We thus explored the effects of physiological levels of nitrite on cardiac and fin regeneration and downstream cellular and molecular signaling pathways in response to amputation and cryoinjury. Results: Nitrite treatment of zebrafish after ventricular amputation or cryoinjury to the heart in hypoxic water (∼3 parts per million of oxygen) increases cardiomyocyte proliferation, improves angiogenesis, and enhances early recruitment of thrombocytes, macrophages, and neutrophils to the injury. When tested in a fin regeneration model, neutrophil recruitment to the injury site was found to be dependent on NO. Innovation: This is the first study to evaluate effects of physiological levels of nitrite on cardiac regeneration in response to cardiac injury, with the observation that nitrite in water accelerates zebrafish heart regeneration. Conclusion: Physiological and therapeutic levels of nitrite increase thrombocyte, neutrophil, and macrophage recruitment to the heart after amputation and cryoinjury in zebrafish, resulting in accelerated cardiomyocyte proliferation and angiogenesis. Translation of this finding to mammalian models of injury during early development may provide an opportunity to improve outcomes during intrauterine fetal or neonatal cardiac surgery.

Adaptation mechanism of the adult zebrafish respiratory organ to endurance training

In order to study the adaptation scope of the fish respiratory organ and the O2 metabolism due to endurance training, we subjected adult zebrafish (Danio rerio) to endurance exercise for 5 weeks. After the training period, the swimmer group showed a significant increase in swimming performance, body weight and length. In scanning electron microscopy of the gills, the average length of centrally located primary filaments appeared significantly longer in the swimmer than in the non-trained control group (+6.1%, 1639 μm vs. 1545 μm, p = 0.00043) and the average number of secondary filaments increased significantly (+7.7%, 49.27 vs. 45.73, p = 9e-09). Micro-computed tomography indicated a significant increase in the gill volume (p = 0.048) by 11.8% from 0.490 mm3 to 0.549 mm3. The space-filling complexity dropped significantly (p = 0.0088) by 8.2% from 38.8% to 35.9%., i.e. making the gills of the swimmers less compact. Respirometry after 5 weeks showed a significantly higher oxygen consumption (+30.4%, p = 0.0081) of trained fish during exercise compared to controls. Scanning electron microscopy revealed different stages of new secondary filament budding, which happened at the tip of the primary lamellae. Using BrdU we could confirm that the growth of the secondary filaments took place mainly in the distal half and the tip and for primary filaments mainly at the tip. We conclude that the zebrafish respiratory organ-unlike the mammalian lung-has a high plasticity, and after endurance training increases its volume and changes its structure in order to facilitate O2 uptake.

Effect of seasonal high temperature on the immune response in Apostichopus japonicus by transcriptome analysis

The sea cucumber Apostichopus japonicus is a flourishing aquaculture species in China. However, there are challenges for sea cucumber aquaculture, one of which is the high temperature in summer. In this study, we explored the transcriptome expression profiles with seasons (APR, JUN and JUL) in the muscle tissue of A. japonicus. The temperature of the natural coast was 13 °C, 21 °C and 25 °C respectively when sampling. Compared with APR group, changes of expression profiles were more significant in JUL group than that in JUN group. A total of 46 differential expressed genes (DEGs) involved in both innate and adaptive immunity were highlighted, including 27 up-regulated and 19 down-regulated genes. They were further grouped into 10 sub-classes: heat shock, coagulation cascades, antigen processing and presentation, inflammatory response, transporter activity, immunoglobulin, lectin C, cell adhesion, reactive oxygen species (ROS) scavenging, apoptosis and autophagy. The study will offer deep insights of the molecular mechanisms underlying the physiological responses to seasonal high temperature in A. japonicus. Particularly, knowledge about the immunological effects of seasonal temperature on the species is critical for the optimal management practices for both wild and aquaculture populations.

Are model organisms representative for climate change research? Testing thermal tolerance in wild and laboratory zebrafish populations

Model organisms can be useful for studying climate change impacts, but it is unclear whether domestication to laboratory conditions has altered their thermal tolerance and therefore how representative of wild populations they are. Zebrafish in the wild live in fluctuating thermal environments that potentially reach harmful temperatures. In the laboratory, zebrafish have gone through four decades of domestication and adaptation to stable optimal temperatures with few thermal extremes. If maintaining thermal tolerance is costly or if genetic traits promoting laboratory fitness at optimal temperature differ from genetic traits for high thermal tolerance, the thermal tolerance of laboratory zebrafish could be hypothesized to be lower than that of wild zebrafish. Furthermore, very little is known about the thermal environment of wild zebrafish and how close to their thermal limits they live. Here, we compared the acute upper thermal tolerance (critical thermal maxima; CT_max) of wild zebrafish measured on-site in West Bengal, India, to zebrafish at three laboratory acclimation/domestication levels: wild-caught, F₁ generation wild-caught and domesticated laboratory AB-WT line. We found that in the wild, CT_max increased with increasing site temperature. Yet at the warmest site, zebrafish lived very close to their thermal limit, suggesting that they may currently encounter lethal temperatures. In the laboratory, acclimation temperature appeared to have a stronger effect on CT_max than it did in the wild. The fish in the wild also had a 0.85-1.01°C lower CT_max compared to all laboratory populations. This difference between laboratory-held and wild populations shows that environmental conditions can affect zebrafish's thermal tolerance. However, there was no difference in CT_max between the laboratory-held populations regardless of the domestication duration. This suggests that thermal tolerance is maintained during domestication and highlights that experiments using domesticated laboratory-reared model species can be appropriate for addressing certain questions on thermal tolerance and global warming impacts.

Response of AMP-activated protein kinase and lactate metabolism of largemouth bass (Micropterus salmoides) under acute hypoxic stress

To study adaptation of largemouth bass (Micropterus salmoides) to hypoxic stress, we investigated physiological responses and lactate metabolism of the fish under acute hypoxia. The objectives of this study were to (a) observe changes in glucose, glycogen, and lactate content; (b) detect the activity of lactate dehydrogenase (LDH) in serum, brain, heart, and liver tissues; and (c) quantify the dynamic gene expression of AMP activated protein kinase alpha (AMPKα), hypoxia-inducible factor-1 alpha (HIF-1α), monocarboxylate transporter 1 (MCT1), monocarboxylate transporter 4 (MCT4), and lactate dehydrogenase-a (LDHa) following exposure to hypoxia. The fish were subjected to two hypoxia stresses (dissolved oxygen [DO] 1.20 ± 0.2 mg/L and 3.50 ± 0.3 mg/L, respectively) for 24 h. Our results showed that hypoxic stress significantly increased the decomposition of liver glycogen and significantly increased the concentration of blood glucose; however, the muscle glycogen content was not significantly decreased, which indicates that liver glycogen was the main energy source under acute hypoxia. Moreover, hypoxia led to accumulation of a large amount of lactic acid in tissues, possibly due to the activity of lactic acid dehydrogenase, but this process was delayed in the heart and brain relative to the liver. Additionally, hypoxia induced the expression of AMPKα, HIF-1α, MCT1, MCT4, and LDHa, suggesting that glycometabolism had switched from aerobic to anaerobic. Our results contribute to a better understanding of the molecular mechanisms of the response to hypoxia in largemouth bass.

Hypoxia enhances blood O2 affinity and depresses skeletal muscle O2 consumption in zebrafish (Danio rerio)

Zebrafish (Danio rerio) are widely used animal models. Nevertheless, the mechanisms underlying hypoxia tolerance in this species have remained poorly understood. In the present study, we have determined the effects of hypoxia on blood-O₂ transport properties and mitochondrial respiration rate in permeabilized muscle fibres of adult zebrafish exposed to either 1) a gradual decrease in O₂ levels until fish lost equilibrium (~1 h, acute hypoxia), or 2) severe hypoxia (PO₂ ∼ 15 Torr) for 48 h (prolonged hypoxia). Acute, short-term hypoxia caused an increase in hemoglobin (Hb) O₂ affinity (decrease in P₅₀), due to a decrease in erythrocyte ATP after erythrocyte swelling. No changes in isoHb expression patterns were observed between hypoxic and normoxic treatments. Prolonged hypoxia elicited additional reponses on O₂ consumption: lactate accumulated in the blood, indicating that zebrafish relied on glycolysis for ATP production, and mitochondrial respiration of skeletal muscle was overall significantly inhibited. In addition, male zebrafish had higher hypoxia tolerance (measured as time to loss of equilibrium) than females. The present study contributes to our understanding of the adaptive mechanisms that allow zebrafish, and by inference other fish species, to cope with low O₂ levels.

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Background

Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

Results

Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs.

Conclusions

This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.

Transcriptome Analysis Provides Insights Into the Adaptive Responses to Hypoxia of a Schizothoracine Fish (Gymnocypris eckloni)

The schizothoracine fish endemic to the Qinghai-Tibetan Plateau are comparatively well adapted to aquatic environments with low oxygen partial pressures. However, few studies have used transcriptomic profiling to investigate the adaptive responses of schizothoracine fish tissues to hypoxic stress. This study compared the transcriptomes of Gymnocypris eckloni subjected to 72 h of hypoxia (Dissolved oxygen, DO = 3.0 ± 0.1 mg/L) to those of G. eckloni under normoxia (DO = 8.4 ± 0.1 mg/L). To identify the potential genes and pathways activated in response to hypoxic stress, we collected muscle, liver, brain, heart, and blood samples from normoxic and hypoxic fish for RNA-Seq analysis. We annotated 337,481 gene fragments. Of these, 462 were differentially expressed in the hypoxic fish as compared to the normoxic fish. Under hypoxia, the transcriptomic profiles of the tissues differed, with muscle the most strongly affected by hypoxia. Our data indicated that G. eckloni underwent adaptive changes in gene expression in response to hypoxia. Several strategies used by G. eckloni to cope with hypoxia were similar to those used by other fish, including a switch from aerobic oxidation to anaerobic glycolysis and the suppression of major energy-requiring processes. However, G. eckloni used an additional distinct strategy to survive hypoxic environments: a strengthening of the antioxidant system and minimization of ischemic injury. Here, we identified several pathways and related genes involved in the hypoxic response of the schizothoracine fish. This study provides insights into the mechanisms used by schizothoracine fish to adapt to hypoxic environments.

Hypoxia-induced changes in hemoglobins of Lake Victoria cichlids

In a previous study, broods of the Lake Victoria cichlid Haplochromis ishmaeli raised under hypoxic or normoxic conditions showed striking differences in isohemoglobin (isoHb) pattern that were not observed in two other cichlids that do not belong to the Lake Victoria species flock. We therefore hypothesized that the adaptive mechanism seen in H. ishmaeli in response to hypoxia constitutes a trait that the Lake Victoria species flock inherited from ancestors that lived in hypoxic environments. We tested this hypothesis by designing split-brood experiments with three other representative species from the same species flock: the insectivorous Haplochromis thereuterion, the mollusk-shelling Platytaeniodus degeni and the zooplanktivorous Haplochromis piceatus, while keeping H. ishmaeli as a reference. Split broods were raised, under either normoxia or hypoxia. All hypoxia-raised (HR) individuals of each of the four species exhibited a distinctly different isoHb pattern compared with their normoxia-raised (NR) siblings. The hemoglobin of HR H. thereuterion showed higher O₂ affinity compared with NR siblings particularly in the presence of ATP and GTP, indicating that blood of HR juveniles has significantly improved O₂-binding affinity under hypoxic conditions. We also tested the capacity to acclimate at greater age in two species by reversing the O₂ condition after 7 (H. thereuterion) and 4 (H. ishmaeli) months. After reacclimation for 1 and 2 months, respectively, we found incomplete reversal with intermediate isoHb patterns. As three of the four species do not encounter hypoxic conditions in their environment, this unique trait seems to be a relic inherited from predecessors that lived in hypoxic environments.

Molecular characterization and expression of suppressor of cytokine signaling (SOCS) 1, 2 and 3 under acute hypoxia and reoxygenation in pufferfish, Takifugu fasciatus

Hypoxia seriously affects the innate immune system of fish. However, the roles of suppressor of cytokine signaling (SOCS), pivotal anti-inflammatory genes, in response to hypoxia/reoxygenation remain largely unexplored. The primary objective of this study was to elucidate the function of SOCS genes under acute hypoxia and reoxygenation in pufferfish (Takifugu fasciatus). In the present study, SOCS1, 2 and 3 were identified in T. fasciatus referred to as TfSOCS1, 2 and 3. Then, qRT-PCR and western blot analysis were employed to assess their expressions at both the mRNA and protein levels. Tissue distribution demonstrated that the three SOCS genes were predominantly distributed in gill, brain and liver. Under hypoxia challenge (1.63 ± 0.2 mg/L DO for 2, 4, 6 and 8 h), the expressions of TfSOCS1 and 3 in brain and liver at the mRNA and protein levels were significantly decreased, while their expressions showed an opposite trend in gill. Different from the expressions of TfSOCS1 and 3, the expression of TfSOCS2 was inhibited in gill, along with its increased expression in brain and liver. After normoxic recovery (7.0 ± 0.3 mg/L of DO for 4 and 12 h), most of TfSOCS genes were significantly altered at R4 (reoxygenation for 4 h) and returned to the normal level at R12 (reoxygenation for 12 h). SOCS genes played vital roles in response to hypoxia/reoxygenation challenge. Our findings greatly strengthened the relation between innate immune and hypoxia stress in T. fasciatus.

Hypoxia-inducible transcription factors in fish: expression, function and interconnection with the circadian clock

The hypoxia-inducible transcription factors are key regulators for the physiological response to low oxygen availability. In vertebrates, typically three Hif-α isoforms, Hif-1α, Hif-2α and Hif-3α, are expressed, each of which, together with Hif-1β, may form a functional heterodimer under hypoxic conditions, controlling expression of hundreds of genes. A teleost-specific whole-genome duplication complicates the analysis of isoform-specific functions in fish, but recent studies suggest that the existence of paralogues of a specific isoform opens up the possibility for a subfunctionalization. In contrast to during development inside the uterus, fish eggs are freely accessible and studies analyzing Hif expression in fish embryos during development have revealed that Hif proteins are not only controlling the hypoxic response, but are also crucial for proper development and organ differentiation. Significant advances have been made in our knowledge about tissue-specific functions of Hif proteins, especially with respect to gill or gonadal tissue. The hypoxia signalling pathway is known to be tightly and mutually intertwined with the circadian clock in zebrafish and mammals. Recently, a mechanistic explanation for the hypoxia-induced dampening of the transcriptional clock was detected in zebrafish, including also metabolically induced alterations of cellular redox signalling. In turn, MAP kinase-mediated H2O2 signalling modulates the temporal expression of Hif-1α protein, similar to the redox regulation of the circadian clock itself. Once again, the zebrafish has emerged as an excellent model organism with which to explore these specific functional aspects of basic eukaryotic cell biology.

Emersion behaviour underlies variation in gill morphology and aquatic respiratory function in the amphibious fish Kryptolebias marmoratus

Fishes acclimated to hypoxic environments often increase gill surface area to improve O₂ uptake. In some species, surface area is increased via reduction of an interlamellar cell mass (ILCM) that fills water channels between gill lamellae. Amphibious fishes, however, may not increase gill surface area in hypoxic water because these species can, instead, leave water and breathe air. To differentiate between these possibilities, we compared wild amphibious mangrove rivulus Kryptolebias marmoratus from two habitats that varied in O₂ availability - a hypoxic freshwater pool versus nearly anoxic crab burrows. Fish captured from crab burrows had less gill surface area (as ILCMs were enlarged by ∼32%), increased rates of normoxic O₂ consumption and increased critical O₂ tension compared with fish from the freshwater pool. Thus, wild mangrove rivulus do not respond to near-anoxic water by decreasing metabolism or increasing O₂ extraction. Instead, fish from the crab burrow habitat spent three times longer out of water, which probably caused the observed changes in gill morphology and respiratory phenotype. We also tested whether critical O₂ tension is influenced by genetic heterozygosity, as K. marmoratus is one of only two hermaphroditic vertebrate species that can produce both self-fertilized (inbred) or out-crossed (more heterozygous) offspring. We found no evidence for inbreeding depression, suggesting that self-fertilization does not impair respiratory function. Overall, our results demonstrate that amphibious fishes that inhabit hypoxic aquatic habitats can use a fundamentally different strategy from that used by fully aquatic water-breathing fishes, relying on escape behaviour rather than metabolic depression or increased O₂ extraction ability.

Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs

Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.

Protein synthesis is lowered by 4EBP1 and eIF2-α signaling while protein degradation may be maintained in fasting, hypoxic Amazonian cichlids Astronotus ocellatus

The Amazonian cichlid Astronotus ocellatus is highly tolerant to hypoxia, and is known to reduce its metabolic rate by reducing the activity of energetically expensive metabolic processes when oxygen is lacking in its environment. Our objectives were to determine how protein metabolism is regulated in A. ocellatus during hypoxia. Fish were exposed to a stepwise decrease in air saturation (100%, 20%, 10% and 5%) for 2 h at each level, and sampled throughout the experiment. A flooding dose technique using a stable isotope allowed us to observe an overall decrease in protein synthesis during hypoxia in liver, muscle, gill and heart. We estimate that this decrease in rates of protein synthesis accounts for a 20 to 36% decrease in metabolic rate, which would enable oscars to maintain stable levels of ATP and prolong survival. It was also determined for the first time in fish that a decrease in protein synthesis during hypoxia is likely controlled by signaling molecules (4EBP1 and eIF2-α), and not simply due to a lack of ATP. We could not detect any effects of hypoxia on protein degradation as the levels of NH₄ excretion, indicators of the ubiquitin proteasome pathway, and enzymatic activities of lysosomal and non-lysosomal proteolytic enzymes were maintained throughout the experiment.

Differential Gene Expression Profiles and Alternative Isoform Regulations in Gill of Nile Tilapia in Response to Acute Hypoxia

Fish often encounters exposures to acute environmental hypoxia either spatially or temporally. Gill organ plays important roles in response to hypoxic stress in fish. Few studies focus on the molecular regulation mechanisms of gills under hypoxic stress. In this study, we investigated the transcriptomic response to 12-h acute hypoxia in gill of a hypoxia tolerant fish, Nile tilapia Oreochromis niloticus through RNA sequencing (RNA-Seq). We sequenced messenger RNA from three control samples and three hypoxia-treated samples. Bioinformatics analysis identified 239 differentially expressed genes (DEG) and 34 genes (DUES) that had significant differential alternative isoform regulation events in at least one exonic region in gill in response to acute hypoxia. The spatiotemporal expression analysis in five tissues (heart, liver, brain, gill, and spleen) sampled at three time points (6, 12, and 24 h) under hypoxia treatment confirmed the significant association of differential exon usages in two DUES genes (TLDC2 and SSX2IPA) with hypoxia conditions. Further functional analysis suggested several energy and immune response-related pathways, e.g., metabolic pathway and antigen processing and presentation, contained the most abundant DEG genes. We found that some GO biological processes for DEG genes were significantly enriched under hypoxic stress, such as glycolysis, metabolic process, generation of precursor metabolites and energy, and cholesterol metabolic process. Our findings suggest abundant differential gene expression changes and alternative isoform regulation events in genes involved in the hypoxia response in gill. Our results provide a basis for exploring the gene regulation mechanism under hypoxic stress in fish.

Diel cyclic hypoxia alters plasma lipid dynamics and impairs reproduction in goldfish (Carassius auratus)

Diel cyclic hypoxia occurs with varying frequency and duration in freshwater habitats, yet little is known about its effects on reproduction of freshwater fishes. The present study shows that long-term exposure of goldfish (Carassius auratus) to cyclic hypoxia (0.8 ± 0.2 mg/l dissolved oxygen) for 9 h or more, per day, altered plasma lipid and sex steroid profiles, which in turn directly or indirectly suppressed ovarian growth and viable spermatozoa production. Hypoxia decreased total cholesterol and high density lipoprotein (HDL p < 0.05) and elevated triglycerides (TG; p < 0.05) in both sexes. Plasma steroid concentrations particularly of 17α-hydroxyprogesterone (17-HP), estradiol (E2), testosterone (T) in females, and T and 11-ketotestosterone (11-KT) in males were attenuated under diel hypoxic conditions. Intriguingly, both diel and continuous hypoxia elevated plasma E2 and vitellogenin levels in males. However, neither lipid nor steroid profiles recorded any variation in a dose-dependent manner in response to diel hypoxia. The reduced GSI, decreased number of tertiary oocytes, and motile spermatozoa in hypoxic fish clearly indicate suppression of gametogenesis. Thereby, prolonged diel cyclic hypoxia may affect valuable fishery resources and fish population structure by impairing reproductive performances and inducing estrogenic effects in males.