Single-cell transcriptomic analysis of neuroepithelial cells and other cell types of the gills of zebrafish (Danio rerio) exposed to hypoxia

Single-cell transcriptome sequencing analysis of physiological and immune profiling of crucian carp (Carassius auratus) gills

Gills are the main respiratory organs of fish and bear important physiological and immunological functions, but the functional heterogeneity of interlamellar cell mass (ILCM) at the single-cell level has rarely been reported. Here, we identified 19 cell types from the gills of crucian carp (Carassius auratus) by single-cell RNA sequencing (scRNA-seq) in combination with histological analysis. We annotated ILCM and analyzed its functional heterogeneity at the single-cell level for the first time. Functional enrichment analysis and cell cycle analysis identified ILCM as a type of metabolically active cells in a state of constant proliferation, and identified the major pathways responsible for ILCM immunoregulation. Histological analysis revealed the morphology and positional relationships of 6 cell types. Meanwhile, the gene regulatory network of ILCM was established through weighted gene co-expression network analysis (WGCNA), and one transcription factor and five hub genes related to immunoregulation were identified. We found that pyroptosis might be an important pathway responsible for the immune response of ILCM. Our findings provide an insight into the physiological and immune functions of gills and ILCM at the single-cell level and lay a solid foundation for further exploration of the molecular mechanism of ILCM immunity functions.

Unveiling osmoregulation and immunological adaptations in Eleutheronema tetradactylum gills through high-throughput single-cell transcriptome sequencing

The fourfinger threadfin fish (Eleutheronema tetradactylum) is an economically significant species renowned for its ability to adapt to varying salinity environments, with gills serving as their primary organs for osmoregulation and immune defense. Previous studies focused on tissue and morphological levels, whereas ignored the cellular heterogeneity and the crucial gene information related to core cell subsets within E. tetradactylum gills. In this study, we utilized high-throughput single-cell RNA sequencing (scRNA-seq) to analyze the gills of E. tetradactylum, characterizing 16 distinct cell types and identifying unique gene markers and enriched functions associated within each cell type. Additionally, we subdivided ionocyte cells into four distinct subpopulations for the first time in E. tetradactylum gills. By employing weighted gene co-expression network analysis (WGCNA), we further investigated the cellular heterogeneity and specific response mechanisms to salinity fluctuant. Our findings revealed the intricate osmoregulation and immune functions of gill cells, highlighting their crucial roles in maintaining homeostasis and adapting to fluctuating salinity levels. This comprehensive cell-type atlas provides valuable insights into the species adaptive strategies, contributing to the conservation and management of this commercially significant fish as well as other euryhaline species.

Diverse responses of hypoxia-inducible factor alpha mRNA abundance in fish exposed to low oxygen: the importance of reporting methods

Low dissolved oxygen (hypoxia) poses significant challenges to aquatic ecosystems, affecting the behavior, reproduction, and survival of aquatic organisms. Some fishes respond to hypoxia by changes in gene expression, which may be regulated by the hypoxia inducible factor (HIF) family of transcription factors. HIF abundance and activity depends upon the post-translational modification of the alpha protein subunit, although several studies indicate that HIFA mRNA abundance increases in tissues of fishes exposed to hypoxia. This study reviewed reports of laboratory exposures of adult ray-finned fishes to hypoxia and used generalized linear mixed effects models to examine the influence of HIFA gene, tissue sampled, and exposure conditions in explaining the diversity of responses seen in HIFA mRNA abundance. The frequency of hypoxia-induced increases in HIFA mRNA was poorly explained by gene, tissue, or the severity of the hypoxic exposure. Rather, the frequency of reported increases was strongly related to the extent to which studies adhered to guidelines for documenting quantitative real-time PCR methods: the frequency of hypoxia-induced increases in HIFA mRNA decreased sharply in studies with more thorough description of experimental design. Future research should (a) adhere to stringent reporting of experimental design, (b) address the relative paucity of data on HIF2A and HIF3A, and (c) determine levels of HIF alpha protein subunits. By following these recommendations, it is hoped that a more complete understanding will be gained of the role of the HIF family of transcription factors in the response of fish to hypoxia.

The physiological significance of plasma-accessible carbonic anhydrase in the respiratory systems of fishes

Carbonic anhydrase (CA) activity is ubiquitously found in all vertebrate species, tissues and cellular compartments. Most species have plasma-accessible CA (paCA) isoforms at the respiratory surfaces, where the enzyme catalyzes the conversion of plasma bicarbonate to carbon dioxide (CO2) that can be excreted by diffusion. A notable exception are the teleost fishes that appear to lack paCA at their gills. The present review: (i) recapitulates the significance of CA activity and distribution in vertebrates; (ii) summarizes the current evidence for the presence or absence of paCA at the gills of fishes, from the basal cyclostomes to the derived teleosts and extremophiles such as the Antarctic icefishes; (iii) explores the contribution of paCA to organismal CO2 excretion in fishes; and (iv) the functional significance of its absence at the gills, for the specialized system of O2 transport in most teleosts; (v) outlines the multiplicity and isoform distribution of membrane-associated CAs in fishes and methodologies to determine their plasma-accessible orientation; and (vi) sketches a tentative time line for the evolutionary dynamics of branchial paCA distribution in the major groups of fishes. Finally, this review highlights current gaps in the knowledge on branchial paCA function and provides recommendations for future work.

Fish gill chemosensing: knowledge gaps and inconsistencies

In this review, we explore the inconsistencies in the data and gaps in our knowledge that exist in what is currently known regarding gill chemosensors which drive the cardiorespiratory reflexes in fish. Although putative serotonergic neuroepithelial cells (NEC) dominate the literature, it is clear that other neurotransmitters are involved (adrenaline, noradrenaline, acetylcholine, purines, and dopamine). And although we assume that these agents act on neurons synapsing with the NECs or in the afferent or efferent limbs of the paths between chemosensors and central integration sites, this process remains elusive and may explain current discrepancies or species differences in the literature. To date it has been impossible to link the distribution of NECs to species sensitivity to different stimuli or fish lifestyles and while the gills have been shown to be the primary sensing site for respiratory gases, the location (gills, oro-branchial cavity or elsewhere) and orientation (external/water or internal/blood sensing) of the NECs are highly variable between species of water and air breathing fish. Much of what has been described so far comes from studies of hypoxic responses in fish, however, changes in CO2, ammonia and lactate have all been shown to elicit cardio-respiratory responses and all have been suggested to arise from stimulation of gill NECs. Our view of the role of NECs is broadening as we begin to understand the polymodal nature of these cells. We begin by presenting the fundamental picture of gill chemosensing that has developed, followed by some key unanswered questions about gill chemosensing in general.

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.

Cell proliferation and regeneration in the gill

Seminal studies from the early 20th century defined the structural changes associated with development and regeneration of the gills in goldfish at the gross morphological and cellular levels using standard techniques of light and electron microscopy. More recently, investigations using cell lineage tracing, molecular biology, immunohistochemistry and single-cell RNA-sequencing have pushed the field forward and have begun to reveal the cellular and molecular processes that orchestrate cell proliferation and regeneration in the gills. The gill is a multifunctional organ that mediates an array of important physiological functions, including respiration, ion regulation and excretion of waste products. It is comprised of unique cell types, such as pavement cells, ionocytes, chemoreceptors and undifferentiated stem or progenitor cells that regulate growth and replenish cell populations. The gills develop from the embryonic endoderm and are rich in cell types derived from the neural crest. The gills have the capacity to remodel themselves in response to environmental change, such as in the case of ionocytes, chemoreceptors and the interlamellar cell mass, and can completely regenerate gill filaments and lamellae. Both processes of remodeling and regeneration invariably involve cell proliferation. Although gill regeneration has been reported in only a limited number of fish species, the process appears to have many similarities to regeneration of other organs in fish and amphibians. The present article reviews the studies that have described gill development and growth, and that demonstrate a suite of genes, transcription factors and other proteins involved in cell proliferation and regeneration in the gills.

Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes

Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)-HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (Pcrit) of the corresponding species. Our results demonstrate that Pcrit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A, two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in Pcrit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates.

Effects of serta and sertb knockout on aggression in zebrafish (Danio rerio)

Zebrafish (Danio rerio) are unusual in having two paralogues of the serotonin re-uptake transporter (Sert), slc6a4a (serta) and slc6a4b (sertb), the transporter that serves in serotonin re-uptake from a synapse into the pre-synaptic cell or in serotonin uptake from the extracellular milieu into cells in the peripheral tissues. To address a knowledge gap concerning the specific roles of these paralogues, we used CRISPR/Cas9 technology to generate zebrafish knockout lines predicted to lack functional expression of Serta or Sertb. The consequences of loss-of-function of Serta or Sertb were assessed at the gene expression level, focusing on the serotonergic signalling pathway, and at the behaviour level, focusing on aggression. Whereas serta mRNA was expressed in all tissues examined, with high expression in the heart, gill and brain, only the brain displayed substantial sertb mRNA expression. In both serta-/- and sertb-/- fish, changes in transcript abundances of multiple components of the serotonin signalling pathway were detected, including proteins involved in serotonin synthesis (tph1a, tph1b, tph2, ddc), packaging (vmat2) and degradation (mao), and serotonin receptors (htr1aa, htr1ab). Using a mirror aggression test, serta-/- male but not female fish exhibited greater aggression than wildtype fish. However, both male and female sertb-/- fish displayed less aggression than their wildtype counterparts. These differences in behaviour between serta-/- and sertb-/- individuals hold promise for increasing our understanding of the neurophysiological basis of aggression in zebrafish.

Hif-2α programs oxygen chemosensitivity in chromaffin cells

The study of transcription factors that determine specialized neuronal functions has provided invaluable insights into the physiology of the nervous system. Peripheral chemoreceptors are neurone-like electrophysiologically excitable cells that link the oxygen concentration of arterial blood to the neuronal control of breathing. In the adult, this oxygen chemosensitivity is exemplified by type I cells of the carotid body, and recent work has revealed one isoform of the hypoxia-inducible transcription factor (HIF), HIF-2α, as having a nonredundant role in the development and function of that organ. Here, we show that activation of HIF-2α, including isolated overexpression of HIF-2α but not HIF-1α, is sufficient to induce oxygen chemosensitivity in adult adrenal medulla. This phenotypic change in the adrenal medulla was associated with retention of extra-adrenal paraganglioma-like tissues resembling the fetal organ of Zuckerkandl, which also manifests oxygen chemosensitivity. Acquisition of chemosensitivity was associated with changes in the adrenal medullary expression of gene classes that are ordinarily characteristic of the carotid body, including G protein regulators and atypical subunits of mitochondrial cytochrome oxidase. Overall, the findings suggest that, at least in certain tissues, HIF-2α acts as a phenotypic driver for cells that display oxygen chemosensitivity, thus linking 2 major oxygen-sensing systems.

Both IRAK3 and IRAK1 Activate the MyD88-TRAF6 Pathway in Zebrafish

IL-1R-associated kinases (IRAKs) are signal transducers of the TLR/IL-1R-MyD88-TRAF6 pathways. Vertebrates possess two IRAK lineages, IRAK1/2/3 and IRAK4. In mammals, IRAK4/IRAK1 and IRAK4/IRAK2 are pathway enhancers, whereas IRAK3 is a repressor. However, in bony fish, IRAK2 is absent, and it remains elusive how fish IRAK1/3/4 functionally differ from their mammalian counterparts. In this study, we explored this using the zebrafish model. First, we showed that in human 293T cells, zebrafish IRAK1 and IRAK4 were components of the Myddosome (MyD88-IRAK4-IRAK1) complex, with IRAK1 serving as a potent pathway enhancer. Then, we discovered two zebrafish IRAK3 variants: one (IRAK3a) contains an N-terminal Death domain, a middle pseudokinase domain, and a C-terminal TRAF6-binding domain, whereas the other (IRAK3b) lost both the kinase and TRAF6-binding domains. This truncation of IRAK3 variants could be a conserved phenomenon in fish, because it is also observed in trout and grass carp. We proceeded to show that zebrafish IRAK3a acts as a pathway enhancer by binding with MyD88 and TRAF6, but its activity is milder than IRAK1, possibly because it has no kinase activity. Zebrafish IRAK3b, however, plays a sheer negative role, apparently because of its lack of kinase and TRAF6-binding domains. Moreover, zebrafish IRAK3a/3b inhibit the activity of IRAK1/4, not by interacting with IRAK1/4 but possibly by competing for MyD88 and TRAF6. Finally, we have verified the essential activities of zebrafish IRAK1/3a/3b/4 in zebrafish cells and embryos. In summary, to our knowledge, our findings provide new insights into the molecular functions of fish IRAKs and the evolution of the IRAK functional modes in vertebrates.

A review on current advancement in zebrafish models to study chronic inflammatory diseases and their therapeutic targets

Chronic inflammatory diseases are caused due to prolonged inflammation at a specific site of the body. Among other inflammatory diseases, bacterial meningitis, chronic obstructive pulmonary disease (COPD), atherosclerosis and inflammatory bowel diseases (IBD) are primarily focused on because of their adverse effects and fatality rates around the globe in recent times. In order to come up with novel strategies to eradicate these diseases, a clear understanding of the mechanisms of the diseases is needed. Similarly, detailed insight into the mechanisms of commercially available drugs and potent lead compounds from natural sources are also important to establish efficient therapeutic effects. Zebrafish is widely accepted as a model to study drug toxicity and the pharmacokinetic effects of the drug. Moreover, researchers use various inducers to trigger inflammatory cascades and stimulate physiological changes in zebrafish. The effect of these inducers contrasts with the type of zebrafish used in the investigation. Hence, a thorough analysis is required to study the current advancements in the zebrafish model for chronic inflammatory disease suppression. This review presents the most common inflammatory diseases, commercially available drugs, novel therapeutics, and their mechanisms of action for disease suppression. The review also provides a detailed description of various zebrafish models for these diseases. Finally, the future prospects and challenges for the same are described, which can help the researchers understand the potency of the zebrafish model and its further exploration for disease attenuation.

Implications of exposure route for the bioaccumulation potential of nanopolystyrene particles

Microplastics and nanoplastics are found in marine biota across a wide range of trophic levels and environments. While a large portion of the information about plastic exposure comes from gastrointestinal (GI) data, the relevance of particle accumulation from an oral exposure compared with other types of exposure (e.g. dermal, respiratory) is unknown. To address this gap in knowledge, larval zebrafish (7 days post fertilization) were exposed to two different sizes of nanoplastics through either oral gavage or a waterborne exposure. Larvae were tracked for 48 h post exposure (hpe) to assess the migration and elimination of plastics. Larvae eliminated orally gavaged nanoplastics within 48 hpe. Oral gavage showed limited particle movement from the GI tract into other tissues. In contrast, waterborne nanoplastic-exposed larvae displayed notable fluorescence in tissues outside of the GI tract. The 50 nm waterborne-exposed larvae retained the particles past 48 hpe, and showed accumulation with neuromasts. For both sizes of plastic particles, the nanoplastics were eliminated from non-GI tract tissues by 24 hpe. Our results suggest that waterborne exposure leads to greater accumulation of plastic in comparison to oral exposure, suggesting that plastic accumulation in certain tissues is greater via routes of exposure other than oral consumption.

Diphenyl Diselenide Attenuates Mitochondrial Damage During Initial Hypoxia and Enhances Resistance to Recurrent Hypoxia

Hypoxia plays a significant role in the development of various cerebral diseases, many of which are associated with the potential risk of recurrence due to mitochondrial damage. Conventional drug treatments are not always effective for hypoxia-related brain diseases, necessitating the exploration of alternative compounds. In this study, we investigated the potential of diphenyl diselenide [(PhSe)2] to ameliorate locomotor impairments and mitigate brain mitochondrial dysfunction in zebrafish subjected to hypoxia. Additionally, we explored whether these improvements could confer resistance to recurrent hypoxia. Through a screening process, an appropriate dose of (PhSe)2 was determined, and animals exposed to hypoxia received a single intraperitoneal injection of 100 mg/kg of the compound or vehicle. After 1 h from the injection, evaluations were conducted on locomotor deficits, (PhSe)2 content, mitochondrial electron transport system, and mitochondrial viability in the brain. The animals were subsequently exposed to recurrent hypoxia to assess the latency time to hypoxia symptoms. The findings revealed that (PhSe)2 effectively crossed the blood-brain barrier, attenuated locomotor deficits induced by hypoxia, and improved brain mitochondrial respiration by modulating complex III. Furthermore, it enhanced mitochondrial viability in the telencephalon, contributing to greater resistance to recurrent hypoxia. These results demonstrate the beneficial effects of (PhSe)2 on both hypoxia and recurrent hypoxia, with cerebral mitochondria being a critical target of its action. Considering the involvement of brain hypoxia in numerous pathologies, (PhSe)2 should be further tested to determine its effectiveness as a potential treatment for hypoxia-related brain diseases.

Identification of signalling pathways involved in gill regeneration in zebrafish

The occurrence of regeneration of the organs involved in respiratory gas exchange amongst vertebrates is heterogeneous. In some species of amphibians and fishes, the gills regenerate completely following resection or amputation, whereas in mammals, only partial, facultative regeneration of lung tissue occurs following injury. Given the homology between gills and lungs, the capacity of gill regeneration in aquatic species is of major interest in determining the underlying molecular or signalling pathways involved in respiratory organ regeneration. In the present study, we used adult zebrafish (Danio rerio) to characterize signalling pathways involved in the early stages of gill regeneration. Regeneration of the gills was induced by resection of gill filaments and observed over a period of up to 10 days. We screened for the effects on regeneration of the drugs SU5402, dorsomorphin and LY411575, which inhibit FGF, BMP or Notch signalling pathways, respectively. Exposure to each drug for 5 days significantly reduced regrowth of filament tips in regenerating tissue, compared with unresected controls. In separate experiments under normal conditions of regeneration, we used reverse transcription quantitative PCR and observed an increased expression of genes encoding for the bone morphogenetic factor, Bmp2b, fibroblast growth factor, Fgf8a, a transcriptional regulator (Her6) involved in Notch signalling, and Sonic Hedgehog (Shha), in regenerating gills at 10 day post-resection, compared with unresected controls. In situ hybridization confirmed that all four genes were expressed in regenerating gill tissue. This study implicates BMP, FGF, Notch and Shh signalling in gill regeneration in zebrafish.

Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei

The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.

Physiological and immune profiling of tilapia Oreochromis niloticus gills by high-throughput single-cell transcriptome sequencing

The physiological and immune functions of fish gills are largely recognized, but their following functional heterogeneity at the single cell scale has been rarely reported. Here, we performed single cell RNA sequencing (scRNA-seq) on the gills of tilapia fish Oreochromis niloticus. We identified a total of 12 cell populations and analyzed their functional heterogeneity. To investigate the physiological function of O. niloticus gills, expression patterns of genes encoding ion transporters were selected from the identified H+-ATPase-rich cells (HR cells), Na+/K+-ATPase-rich cells (NaR cells), and pavement cells. Specific enrichment of ca4a, slc9a1a, and LOC100692482 in the HR cells of O. niloticus gills explained their functions in acid-base regulation. Genes encoding Ca2+ transporters, including atp2b1, LOC100696627, and LOC 100706765, were specifically expressed in the NaR cells. Pavement cells were presumably the main sites responsible for ammonia and urea transports in O. niloticus gills with specific enrichment of Rhbg and LOC100693008, respectively. The expression patterns of the four immune cell subtypes varied greatly, with B cells being enriched with the most immune-related GO terms. KEGG enrichment analysis showed that MAPK signaling pathway was the most enriched pathway among the four types of immune cells in O. niloticus gills. Our results are important in understanding the physiological and immune responses of fish gills at the cellular resolution.

Conventional Anthelmintic Concentration of Deltamethrin Immersion Disorder in the Gill Immune Responses of Crucian Carp

Current treatment strategies for parasitic infectious diseases in crucian carp primarily rely on chemotherapy. As a commonly used antiparasitic agent, deltamethrin (DEL) may have the potential adverse effects on external mucosa of fish such as gills. In this study, 180 healthy juvenile crucian carp (Carassius auratus) (average weight: 8.8 ± 1.0 g) were randomly divided into three groups for 28 days, which were immersed in 0 μg/L, 0.3 μg/L, and 0.6 μg/L of DEL, respectively. The results of histological analysis revealed that severe hyperplasia in the secondary lamellae of gills was observed, and the number of goblet (mucus-secreting) cells increased significantly after DEL immersion. TUNEL staining indicated that the number of apoptotic cells increased in crucian carp gill. At the molecular level, the mRNA expression analysis revealed significant upregulation of apoptosis (caspase 3, caspase 8, and bax), autophagy (atg5 and beclin-1), and immune response (lzm, muc5, il-6, il-8, il-10, tnfα, ifnγ, tgfβ, tlr4, myd88, and nf-kb), whereas tight junction-related genes (occludin and claudin12) were downregulated after DEL immersion, suggesting that DEL immersion altered innate immunity responses and promoted mucus secretion. Moreover, tandem mass tag (TMT)-based proteomics revealed that a total of 428 differentially expressed proteins (DEPs) contained 341 upregulated DEPs and 87 downregulated DEPs with function annotation were identified between the control and DEL groups. Functional analyses revealed that the DEPs were enriched in apoptotic process, phagosome, and lysosome pathways. Additionally, DEL immersion also drove gill microbiota to dysbiosis and an increase in potentially harmful bacteria such as Flavobacterium. Overall, this study showed that DEL elicited shifts in the immune response and changes in the surface microbiota of fish. These results provide new perspectives on the conventional anthelmintic concentration of DEL immersion disorder of the gill immune microenvironment in crucian carp and theoretical support for future optimization of their practical application.

Effect of high alkalinity on shrimp gills: Histopathological alternations and cell specific responses

High alkalinity stress was considered as a major risk factor for aquatic animals surviving in saline-alkaline water. However, few information exists on the effects of alkalinity stress in crustacean species. As the dominant role of gills in osmotic and ionic regulation, the present study firstly evaluated the effect of alkalinity stress in Exopalaemon carinicauda to determine changes in gill microstructure, and then explore the heterogeneity response of gill cells in alkalinity adaptation by single-cell RNA sequencing (scRNA-seq). Hemolymph osmolality and pH were increased remarkably, and gills showed pillar cells with more symmetrical arrangement and longer lateral flanges and nephrocytes with larger vacuoles in high alkalinity. ScRNA-seq results showed that alkalinity stress reduced the proportion of pillar cells and increased the proportion of nephrocytes significantly. The differentially expressed genes (DEGs) related to ion transport, especially acid-base regulation, such as V(H⁺)-ATPases and carbonic anhydrases, were down-regulated in pillar cells and up-regulated in nephrocytes. Furthermore, pseudotime analysis showed that some nephrocytes transformed to perform ion transport function in alkalinity adaption. Notedly, the positive signals of carbonic anhydrase were obviously observed in the nephrocytes after alkalinity stress. These results indicated that the alkalinity stress inhibited the ion transport function of pillar cells, but induced the active role of nephrocytes in alkalinity adaptation. Collectively, our results provided the new insight into the cellular and molecular mechanism behind the adverse effects of saline-alkaline water and the saline-alkaline adaption mechanism in crustaceans.

Functional divergence of teleost carbonic anhydrase 4

The functional role of membrane-bound carbonic anhydrases (CAs) has been of keen interest in the past decade, and in particular, studies have linked CA in red muscle, heart, and eye to enhanced tissue oxygen extraction in bony fishes (teleosts). However, the number of purported membrane-bound CA isoforms in teleosts, combined with the imperfect system of CA isoform nomenclature, present roadblocks for ascribing physiological functions to particular CA isoforms across different teleost lineages. Here we developed an organizational framework for membrane-bound CAs in teleosts, providing the latest phylogenetic analysis of extant CA4 and CA4-like isoforms. Our data confirm that there are three distinct isoforms of CA4 (a, b, and c) that are conserved across major teleost lineages, with the exception of CA4c gene being lost in salmonids. Tissue distribution analyses suggest CA4a functions in oxygen delivery across teleost lineages, while CA4b may be specialized for renal acid-base balance and ion regulation. This work provides an important foundation for researchers to elucidate the functional significance of CA4 isoforms in fishes.

Differential Cell Metabolic Pathways in Gills and Liver of Fish (White Seabream Diplodus sargus) Coping with Dietary Methylmercury Exposure

Mercury (Hg) is a dangerous and persistent trace element. Its organic and highly toxic form, methylmercury (MeHg), easily crosses biological membranes and accumulates in biota. Nevertheless, understanding the mechanisms of dietary MeHg toxicity in fish remains a challenge. A time-course experiment was conducted with juvenile white seabreams, Diplodus sargus (Linnaeus, 1758), exposed to realistic levels of MeHg in feed (8.7 μg g^-1, dry weight), comprising exposure (E; 7 and 14 days) and post-exposure (PE; 28 days) periods. Total Hg levels increased with time in gills and liver during E and decreased significantly in PE (though levels of control fish were reached only for gills), with liver exhibiting higher levels (2.7 times) than gills. Nuclear magnetic resonance (NMR)-based metabolomics revealed multiple and often differential metabolic changes between fish organs. Gills exhibited protein catabolism, disturbances in cholinergic neurotransmission, and changes in osmoregulation and lipid and energy metabolism. However, dietary MeHg exposure provoked altered protein metabolism in the liver with decreased amino acids, likely for activation of defensive strategies. PE allowed for the partial recovery of both organs, even if with occurrence of oxidative stress and changes of energy metabolism. Overall, these findings support organ-specific responses according to their sensitivity to Hg exposure, pointing out that indications obtained in biomonitoring studies may depend also on the selected organ.

Insights into the control and consequences of breathing adjustments in fishes-from larvae to adults

Adjustments of ventilation in fishes to regulate the volume of water flowing over the gills are critically important responses to match branchial gas transfer with metabolic needs and to defend homeostasis during environmental fluctuations in O₂ and/or CO₂ levels. In this focused review, we discuss the control and consequences of ventilatory adjustments in fish, briefly summarizing ventilatory responses to hypoxia and hypercapnia before describing the current state of knowledge of the chemoreceptor cells and molecular mechanisms involved in sensing O₂ and CO₂. We emphasize, where possible, insights gained from studies on early developmental stages. In particular, zebrafish (Danio rerio) larvae have emerged as an important model for investigating the molecular mechanisms of O₂ and CO₂ chemosensing as well as the central integration of chemosensory information. Their value stems, in part, from their amenability to genetic manipulation, which enables the creation of loss-of-function mutants, optogenetic manipulation, and the production of transgenic fish with specific genes linked to fluorescent reporters or biosensors.

Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection

As aquatic hypoxia worsens on a global scale, fishes will become increasingly challenged by low oxygen, and understanding the molecular basis of their response to hypoxia may help to better define the capacity of fishes to cope with this challenge. The hypoxia inducible factor (HIF) plays a critical role in the molecular response to hypoxia by activating the transcription of genes that serve to improve oxygen delivery to the tissues or enhance the capacity of tissues to function at low oxygen. The current study examines the molecular evolution of genes encoding the oxygen-dependent HIFα subunit (HIFA) in the ray-finned fishes (Actinopterygii). Genomic analyses demonstrate that several lineages retain four paralogs of HIFA predicted from two rounds of genome duplication at the base of vertebrate evolution, broaden the known distribution of teleost-specific HIFA paralogs, and provide evidence for salmonid-specific HIFA duplicates. Evolution of the HIFA gene family is characterized by widespread episodic positive selection at amino acid sites that potentially mediate protein stability, protein-protein interactions, and transcriptional regulation. HIFA transcript abundance depends upon paralog, tissue, and fish lineage. A phylogenetically-informed gene nomenclature is proposed along with avenues for future research on this critical family of transcription factors.

Lactate sensing by neuroepithelial cells isolated from the gills of killifish (Fundulus heteroclitus)

Lactate is produced in most vertebrate cells as a by-product of anaerobic metabolism. In addition to its role as a fuel for many tissues, circulating lactate can act as a signalling molecule and stimulates ventilation in air- and water-breathing vertebrates. Recent evidence suggests lactate acts on O2- and CO2/H+-sensitive chemoreceptors located in the mammalian carotid body. While analogous receptors (neuroepithelial cells or NECs) in fish gills are presumed to also function as lactate sensors, direct evidence is lacking. Here, using ratiometric Fura-2 Ca2+ imaging, we show that chemosensitive NECs isolated from killifish gills respond to lactate (5-10 mmol l-1; pHe ∼7.8) with intracellular Ca2+ elevations. These responses were inhibited by an L-type Ca2+ channel blocker (nifedipine; 0.5 µmol l-1), a monocarboxylic acid transporter (MCT) blocker (α-cyano-4-hydroxycinnamate; 300 µmol l-1) or a competitive MCT substrate (pyruvate; 5 mmol l-1). These data provide the first direct evidence that gill NECs act as lactate sensors.

Neurochemical Signalling Associated With Gill Oxygen Sensing and Ventilation: A Receptor Focused Mini-Review

Despite the large body of work describing vertebrate ventilatory responses to hypoxia, remarkably little is known about the receptors and afferent pathways mediating these responses in fishes. In this review, we aim to summarize all receptor types to date implicated in the neurotransmission or neuromodulation associated with O2 sensing in the gills of fish. This includes serotonergic, cholinergic, purinergic, and dopaminergic receptor subtypes. Recent transcriptomic analysis of the gills of zebrafish using single-cell RNA sequencing has begun to elucidate specific receptor targets in the gill; however, the absence of receptor characterization at the cellular level in the gill remains a major limitation in understanding the neurochemical control of hypoxia signalling.