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15 pages, 2983 KB  
Article
Integrated Heart Rate Monitoring and Transcriptomic Analyses Reveal Distinct Responses to Hypo- and Hypersalinity Stress in Abalone
by Nan Chen, Run Hu, Yun Chen, Weiwei You, Caihuan Ke and Yawei Shen
Fishes 2026, 11(6), 369; https://doi.org/10.3390/fishes11060369 - 22 Jun 2026
Viewed by 161
Abstract
In the context of global climate change, intensified salinity fluctuations driven by altered precipitation, extreme rainfall events, and typhoons have emerged as a major threat to coastal mollusk aquaculture. In this study, integrated physiological and transcriptomic analyses were performed to investigate the responses [...] Read more.
In the context of global climate change, intensified salinity fluctuations driven by altered precipitation, extreme rainfall events, and typhoons have emerged as a major threat to coastal mollusk aquaculture. In this study, integrated physiological and transcriptomic analyses were performed to investigate the responses of Pacific abalone (DD, Haliotis discus hannai) and its hybrid (DF, H. discus hannai ♀ × H. fulgens ♂) to hypo- and hypersalinity stress. Two salinity breakpoints (BPS1 for hyposalinity, BPS2 for hypersalinity) were identified using heart rate monitoring to indicate the osmotic tolerance thresholds of the abalone. The BPS1 and BPS2 values did not differ significantly between the DD and DF groups. However, a subsequent 30-day culture trial confirmed that exposure to the salinity level corresponding to BPS1 significantly reduced growth and survival of both DD and DF groups. To explore the molecular mechanisms underlying these two salinity breakpoints in abalone, the transcriptomes of hemocytes and gill tissues were profiled under both stress conditions. Both hypo- and hypersalinity stress induced pronounced transcriptomic responses in abalone, accompanied by upregulated differentially expressed genes (DEGs) significantly enriched in pathways like TNF and NF-κB signaling, including genes like piap, diap2, birc7-a, birc2, and birc3. However, abalone exhibited more intense responses to hypersalinity stress, as reflected by a greater number of annotated differentially expressed genes (DEGs) and more complex transcriptional regulation. Overall, this study integrates physiological assessment based on heart rate monitoring, aquaculture trials, and transcriptomic analysis to advance our mechanistic understanding of osmotic stress adaptation in abalone, while laying a scientific foundation for the sustainable development of abalone aquaculture under global climate change. Full article
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16 pages, 16340 KB  
Article
Time-Series Transcriptomics of a Gill Cell Line (BTG) from Chinese Bahaba (Bahaba taipingensis) During ISKNV Infection (3–24 hpi)
by Chenfei Guo, Zhihong Gong, Fei Fang, Xihong Li, Lei Wang, Na Wang, Zhangfan Chen, Lin Yan, Kuoqiu Yan, Guobin Hu and Songlin Chen
Fishes 2026, 11(6), 352; https://doi.org/10.3390/fishes11060352 - 15 Jun 2026
Viewed by 199
Abstract
The Chinese bahaba (Bahaba taipingensis), an endangered marine fish, is highly vulnerable to infectious spleen and kidney necrosis virus (ISKNV). In this work, we developed a gill filament-derived cell line, designated BTG, to investigate how these cells respond to ISKNV over [...] Read more.
The Chinese bahaba (Bahaba taipingensis), an endangered marine fish, is highly vulnerable to infectious spleen and kidney necrosis virus (ISKNV). In this work, we developed a gill filament-derived cell line, designated BTG, to investigate how these cells respond to ISKNV over time, specifically from 3 to 24 h post-infection (hpi). BTG cells grew steadily, displayed a diploid chromosome number of 2n = 48, demonstrated high transfection efficiency, and were highly susceptible to viral infection. Characteristic cytopathic effects (CPEs) became noticeable as early as 6 hpi at 27 °C. RNA-seq profiling showed that the number of differentially expressed genes (DEGs) steadily increased with time. Standard enrichment analysis at individual time points (3, 6, 12, and 24 hpi) highlighted pathways mainly involved in DNA replication, cell cycle control, ribosome assembly, transcription and translation, mismatch repair, and cell adhesion. Temporal clustering analysis, however, revealed hidden patterns in immune gene expression. Genes that were consistently downregulated were enriched in immune-related pathways, including ECM–receptor interaction, cytokine–receptor signaling, PI3K–AKT, and Wnt signaling, indicating prolonged suppression of host defense mechanisms. In contrast, clusters of genes transiently upregulated during the first 6 h post-infection were associated with antiviral and innate immune pathways, such as NF-κB, JNK, IRF3, IRF7, caspases, JAK, MHC I, and lysosome-related functions, suggesting a rapid but short-lived antiviral response. Genes that were continuously upregulated were primarily involved in nucleic acid replication and protein synthesis, reflecting a gradual host cell reprogramming to support viral replication. Taken together, these findings reveal a temporal shift in BTG cells from an initial burst of immune activity to immune suppression, accompanied by enhanced viral replication. The BTG cell line thus represents a valuable in vitro model for dissecting ISKNV–host interactions and offers new perspectives on the molecular strategies employed by megalocytiviruses in B. taipingensis. Full article
(This article belongs to the Special Issue Genetic Foundations of Disease Resistance in Fishes)
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14 pages, 7201 KB  
Article
Transcriptome Analysis Reveals Osmoregulation and Low-Salt Adaptation in the Brain and Gills of Eleutheronema tetradactylum
by Weibin Liu, Zongfa Chen, Jingheng Lu, Baogui Tang, Hui Zhou, Bei Wang, Jiansheng Huang, Jing Li and Zhongliang Wang
Fishes 2026, 11(6), 351; https://doi.org/10.3390/fishes11060351 - 15 Jun 2026
Viewed by 217
Abstract
The molecular coordination between the central nervous system and peripheral organs is fundamental to euryhalinity. This study elucidates the distinct adaptive strategies of the brain and gills in the four-finger threadfin (Eleutheronema tetradactylum), an aquaculture species of growing importance, during long-term [...] Read more.
The molecular coordination between the central nervous system and peripheral organs is fundamental to euryhalinity. This study elucidates the distinct adaptive strategies of the brain and gills in the four-finger threadfin (Eleutheronema tetradactylum), an aquaculture species of growing importance, during long-term (30-day) acclimation to low salinity (5 versus 25 control). A profound dichotomy in tissue-specific plasticity was uncovered: while the brain maintained remarkable transcriptional stability with only 10 differentially expressed genes (DEGs), the gills underwent extensive remodeling with 702 DEGs. Gill DEGs were functionally enriched in ion transport and metabolic remodeling, highlighted by the significant upregulation of the Na+-Cl cotransporter (slc12a10) and the prolactin receptor (prlr), coupled with a profound downregulation (log2FC = −5.97) of aquaporin-1 (aqp1). This indicates a concerted strategy to enhance ion uptake while minimizing water permeability. In contrast, the brain’s subtle response was dominated by the upregulation of key neuroendocrine hormones, including growth hormone (gh), prolactin (prl), and pro-opiomelanocortin (pomc). This suggests a top-down regulatory cascade. Integrative pathway analysis identified the PI3K-Akt and JAK-STAT signaling pathways as the primary conduits linking central hormonal signals to peripheral physiological adjustments. These results demonstrate that the euryhalinity of E. tetradactylum is achieved through a highly efficient strategy: a transcriptionally stable brain provides precise endocrine commands that orchestrate robust peripheral remodeling in the gills. This study deciphers the molecular basis of the brain–gill axis in osmoregulation and provides a rich repository of candidate genes for the genetic improvement of low salinity tolerance in aquaculture. Full article
(This article belongs to the Section Physiology and Biochemistry)
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15 pages, 3661 KB  
Article
Multi-Level Effects of Acute Heat Stress on Gill Tissue of Gymnocypris eckloni: Integrating Histopathology, Biochemistry, Apoptosis and Transcriptomics
by Yanzhen Dong, Zhiqiang Zhang, Changlun Xiao, Dayong Xu, Sihong Deng, Pan Shang, Mingkun Luo and Ying Wang
Animals 2026, 16(12), 1762; https://doi.org/10.3390/ani16121762 - 8 Jun 2026
Viewed by 221
Abstract
Extreme high-temperature events driven by global climate change are occurring with increasing frequency, posing a serious threat to the stability of aquatic ecosystems. The Tibetan schizothoracin (Gymnocypris eckloni), a cold-water fish species endemic to the Qinghai–Tibet Plateau, is highly sensitive to [...] Read more.
Extreme high-temperature events driven by global climate change are occurring with increasing frequency, posing a serious threat to the stability of aquatic ecosystems. The Tibetan schizothoracin (Gymnocypris eckloni), a cold-water fish species endemic to the Qinghai–Tibet Plateau, is highly sensitive to temperature fluctuations and serves as an ideal model for studying the effects of climate change on fish. As a key organ for fish to perceive environmental changes, the gills’ comprehensive response mechanism has not yet been fully elucidated. This study investigated the effects of acute heat stress on the gill tissue of G. eckloni. The results showed that acute heat stress caused severe histopathological damage in the gills, including lamellar curling, epithelial cell detachment, and edema, with a significant increase in apoptosis. Biochemical analysis revealed elevated levels of cortisol, glucose, and ATPase activity in serum, as well as increased MDA content and CAT activity in the gills. Transcriptomic analysis identified 2304 DEGs. Upregulated DEGs were significantly enriched in pathways related to inflammatory response, TNF signaling, ferroptosis, and apoptosis, while downregulated DEGs were primarily involved in peroxisome metabolism, cell cycle, and steroid biosynthesis. This study confirms that acute heat stress induces structural damage and functional impairment in the gills by activating inflammatory and apoptotic pathways and disrupting redox homeostasis. It elucidates the immediate molecular and physiological responses of G. eckloni gills to acute heat stress. Follow-up experiments will be conducted at multiple time points, across different temperature gradients, and under chronic stress conditions to gain a more comprehensive understanding of the adaptive potential of high-altitude fish to climate warming, thereby providing a scientific basis for the development of conservation strategies. Full article
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21 pages, 2795 KB  
Article
Carbonic Anhydrase 2 and Na+/K+-ATPase Mediate Family-Dependent Nitrite Tolerance via Modulating Branchial Ion Transport and Acid–Base Balance in Penaeus vannamei
by Liping Zhou, Zhentao Ma, Xiuli Chen, Qingyun Liu, Yuliu Huang, Chunling Yang, Digang Zeng, Zhihong Zheng, Bin Zhang, Yueling Zhang, Yongzhen Zhao and Xianliang Zhao
Animals 2026, 16(11), 1638; https://doi.org/10.3390/ani16111638 - 27 May 2026
Viewed by 373
Abstract
Nitrite is a key environmental challenge in intensive shrimp aquaculture, adversely affecting physiological regulation and survival. Although tolerant Penaeus vannamei families have been established by selective breeding, the basis of family-level variation in tolerance has yet to be clarified. In this study, nitrite-tolerant [...] Read more.
Nitrite is a key environmental challenge in intensive shrimp aquaculture, adversely affecting physiological regulation and survival. Although tolerant Penaeus vannamei families have been established by selective breeding, the basis of family-level variation in tolerance has yet to be clarified. In this study, nitrite-tolerant and nitrite-sensitive families were compared using survival analysis, transcriptomics, targeted qPCR validation, physiological assays, and RNA interference of representative transport-related genes. Under nitrite exposure, the tolerant family exhibited significantly higher survival and a distinct gill transcriptional response, characterized by stronger induction of acid–base and ion-transport genes, including carbonic anhydrase 2 (CA2), the Na+/K+-ATPase subunits ATP1A and ATP1B, as well as several V-type H+-ATPase-related genes. These transcriptional changes were accompanied by elevated ATP content and Na+/K+-ATPase activity, improved hemolymph pH stability, and reduced nitrite accumulation in both gill and hemolymph. RNAi-mediated knockdown of CA2 or ATP1B attenuated the nitrite-induced transport response, decreased ATP content and NKA activity, exacerbated hemolymph acidification, promoted internal nitrite accumulation, and ultimately reduced shrimp survival under nitrite stress. Family-based validation further showed that the tolerant family displayed higher survival than the sensitive family in the dsEGFP group, whereas this advantage was markedly reduced after CA2 or ATP1B knockdown under nitrite stress. These findings highlight that strengthened branchial ion transport and acid–base regulation represent key physiological mechanisms underlying nitrite tolerance in resistant shrimp families. Full article
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14 pages, 6416 KB  
Article
Research on the Adaptive Response Mechanism of Bacterial Infection in Triplophysa siluroides
by Yuanliang Duan, Ya Liu, Jun Ou, Feiyang Li, Xiaoyun Wu, Jianshen Lai, Jian Zhou and Mingjiang Song
Fishes 2026, 11(6), 310; https://doi.org/10.3390/fishes11060310 - 22 May 2026
Viewed by 322
Abstract
Triplophysa siluroides, a unique species of plateau fish, holds significant economic value. However, its natural population has sharply declined due to overfishing and the construction of water conservancy projects. Investigating the various conditions necessary for its growth is a crucial prerequisite for [...] Read more.
Triplophysa siluroides, a unique species of plateau fish, holds significant economic value. However, its natural population has sharply declined due to overfishing and the construction of water conservancy projects. Investigating the various conditions necessary for its growth is a crucial prerequisite for successful artificial breeding. This study used Edwardsiella tarda as the pathogenic bacterium to determine the median lethal concentration following infection of T. siluroides, as well as to examine changes in tissues, organs, and gene expression. The study found that dead T. siluroides displayed symptoms such as abdominal distension, fluid accumulation, and a reddened anus, and the median lethal concentration of E. tarda for T. siluroides was calculated to be 1.00 × 106 CFU/mL. Following infection with E. tarda, the liver, intestine, gills, spleen, and kidneys exhibited varying degrees of lesions. Transcriptome sequencing identified a total of 54,667 genes. Compared to the blank control group, 192 genes were downregulated and 125 genes were upregulated in T. siluroides infected with E. tarda. In contrast, after infection with the poly(I:C) viral mimic, 225 genes were downregulated and 436 genes were upregulated. This study determined the median lethal concentration of E. tarda for T. siluroides via intraperitoneal injection under laboratory conditions. The results may contribute to disease prevention and control in the breeding of T. siluroides, as well as inform future risk assessments of infection in aquaculture water bodies. Full article
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24 pages, 3517 KB  
Article
Identification of Association Between Mucus Microbiota and Gene Expression in the Gill of a Streptococcus agalactiae-Resistant Nile Tilapia Strain Though Multi-Omics Analyses
by Haotian Wu, Liting Chen, Ting Huang, Yi Liu, Liming Luo, Lingyu Kong, Yumeng Sun, Wenchao Zhang, Zhongbao Guo, Zhichang He, Yongju Luo, Jun Xiao and Ying Lu
Animals 2026, 16(9), 1389; https://doi.org/10.3390/ani16091389 - 2 May 2026
Viewed by 933
Abstract
Streptococcus agalactiae infections severely threaten global tilapia aquaculture, causing substantial mortality and economic damage. The “Zhuangluo 1” (ZL) strain, derived from the fast-growing GIFT Nile tilapia and refined through multiple generations of selection, uniquely combines robust resistance to S. agalactiae with improved growth [...] Read more.
Streptococcus agalactiae infections severely threaten global tilapia aquaculture, causing substantial mortality and economic damage. The “Zhuangluo 1” (ZL) strain, derived from the fast-growing GIFT Nile tilapia and refined through multiple generations of selection, uniquely combines robust resistance to S. agalactiae with improved growth traits. This study examined gene expression and regulation of gill mucus microbiota in ZL during experimental S. agalactiae challenge. 16S rRNA sequencing revealed Flavobacterium, Vogesella, Hydrogenophaga, Acidovorax, Rheinheimera, and Deinococcus as prominent genera in the gill mucus microbiome of ZL across time points. Transcriptome time-course analysis identified differentially expressed genes in gills of ZL that were predominantly enriched in cytoskeleton in muscle cells and motor protein pathways. Abundances of the dominant genera Flavobacterium and Hydrogenophaga showed significant correlations with genes regulating mucus secretion, mucin glycosylation, immune modulation, and oxidative stress response in ZL. Untargeted metabolomics of gill mucus revealed substantially higher levels of metabolites potentially linked to microbial metabolism and host–microbiota interactions in ZL. A complementary genome-wide association study for resistance in ZL further localized genes underlying these expression–microbiota associations. These findings elucidated microbiota–host interactions between ZL and gill mucus microbiota, and provide more insights into the role of mucus regulation in disease resistance. Full article
(This article belongs to the Special Issue Environmental Adaptation and Metabolic Regulation in Aquatic Animals)
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20 pages, 3822 KB  
Article
Ammonia Exposure Elevated 5-HT Expression, Reprogrammed Transcriptome and Microbiota Community in Yellow Catfish (Pelteobagrus fulvidraco) Gill During Early Ontogeny
by Yuqing Jian, Kexin Xiong, Jiahong Zou, Xinyue Du, Shihao Liu, Yaoqiang Yue, Jian Gao, Wenjie Guo and Qingchao Wang
Microorganisms 2026, 14(4), 912; https://doi.org/10.3390/microorganisms14040912 - 17 Apr 2026
Viewed by 409
Abstract
The accumulated ammonia within the recirculating aquaculture systems threaten fish health, while little is known about the influences during early fish ontogeny. Using larval and juvenile yellow catfish (Pelteobagrus fulvidraco) as a model, a comprehensive experiment exposing fish to varying total [...] Read more.
The accumulated ammonia within the recirculating aquaculture systems threaten fish health, while little is known about the influences during early fish ontogeny. Using larval and juvenile yellow catfish (Pelteobagrus fulvidraco) as a model, a comprehensive experiment exposing fish to varying total ammonia nitrogen concentrations (0, 10, 20 mg/L for larvae; 0, 25, 125 mg/L for juveniles) was conducted to evaluate the effects on gill transcriptome and microbiota along with the serotonergic regulation. First, the serotonin (5-HT) signal, which controls oxygen chemoreception and ventilation, was mainly detected in the surface of the body of the larvae, and then shifted to gill filaments of juveniles, showing a transition from cutaneous to branchial respiration. Both larval and juvenile yellow catfish exhibited reduced survival, damaged gill structure, and elevated 5-HT expression after ammonia exposure, as well as upregulated tph1b, slc6a4b, scgn and lama5 expression with the increased ammonia concentration, indicating the effects on respiratory function via serotonergic regulation. Further transcriptome analysis was conducted in juveniles to identify the differentially expressed genes (DEGs) and thus, to illustrate more detailed responses after ammonia exposure; KEGG enrichment analysis of DEGs indicated the coping strategy shifted from metabolic buffering to metabolic elimination via glutamine synthesis with the increased ammonia level. The qRT-PCR experiment also identified the increased expression of genes involved in the urea cycle—such as ass1, asl and glula—with the increased ammonia level. Considering the potential contributary role of microbiome to gill health, 16S sequencing was conducted on the gill in the control and the 125 mg/L ammonia-exposed group. Ammonia exposure at 125 mg/L induced significant variation in Simpson index and a marked decline in β diversity. Notably, the abundance of opportunistic pathogens such as Pseudomonadota increased, while the abundance of Deinococcota and Deinococcus—which were renowned for exceptional stress resistance capacity—decreased after ammonia exposure. Thus ammonia exposure disrupts the transcriptomic and microecological balance within gill mucosa, which may elevate the risk of pathogenic infection. Overall, our study provided the first evidence of serotonergic regulation on early fish respiration during ammonia exposure, and also offered new theoretical insights into the involvement of microorganisms in ammonia toxicity. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment, Second Edition)
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29 pages, 19236 KB  
Article
Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Responses to Ammonia Stress in the Gills of Litopenaeus vannamei Under Low-Salinity Conditions
by Yutong Zhao, Yangyang Ding, Falin Zhou, Xiaojuan Hu, Qibin Yang and Yucheng Cao
Biology 2026, 15(8), 612; https://doi.org/10.3390/biology15080612 - 13 Apr 2026
Viewed by 562
Abstract
High ammonia nitrogen stress significantly compromises the survival of Litopenaeus vannamei under low-salinity conditions. However, existing studies predominantly focus on ammonia nitrogen responses under single stressors or normal seawater salinity. The molecular regulatory mechanisms, metabolic remodeling patterns, and key pathway interactions in shrimp [...] Read more.
High ammonia nitrogen stress significantly compromises the survival of Litopenaeus vannamei under low-salinity conditions. However, existing studies predominantly focus on ammonia nitrogen responses under single stressors or normal seawater salinity. The molecular regulatory mechanisms, metabolic remodeling patterns, and key pathway interactions in shrimp subjected to high ammonia nitrogen stress under low-salinity environment remain unclear. In this study, we employed integrated transcriptomic and metabolomic analyses to unveil the underlying molecular responses and metabolic biomarkers in the gills of L. vannamei to ammonia stress under low-salinity conditions. First, L. vannamei underwent low-salinity acclimation from 30‰ to 5‰ salinity and was then reared for one week to acclimate to the experimental environment. Subsequently, shrimp were treated with 42.32 mg/L ammonia nitrogen for a consecutive 96 h period. Integrated transcriptomic and metabolomic analyses elucidated the stress response patterns in the gills of L. vannamei under low-salinity ammonia nitrogen exposure. Specifically, 352, 802, and 140 differentially expressed genes (DEGs) were identified at 12 h, 48 h, and 96 h post-exposure, respectively. GO and KEGG enrichment analyses revealed that the significant DEGs were primarily enriched in six major pathways: autophagy, immune-related pathway, ABC transporter, fatty acid degradation and metabolism, metabolic pathway, and PPAR signaling pathway. Metabolomic profiling identified numerous differentially accumulated metabolites (DAMs) in both positive and negative ion modes, with significantly altered DAMs mainly consisting of organic acids and their derivatives, phospholipids, and other related metabolites. Key DAMs included taurine, guanosine, 1-palmitoyl-sn-glycero-3-phosphocholine, pseudouridine, and betaine. Integrative multi-omics analysis revealed that L. vannamei mediates stress responses by modulating five core pathways under low-salinity/high-ammonia-nitrogen dual stress: fatty acid degradation and metabolism (e.g., acyl-CoA dehydrogenase short chain (Acads), acetyl-CoA acetyltransferase 2 (ACAT2)), autophagy (e.g., autophagy-related protein 101-like (atg101)), immune regulation pathway (e.g., V-type proton ATPase subunit H-like (VhaSFD), actin-5C-like (Act5C)), metabolic pathway (e.g., molybdopterin synthase catalytic subunit-like (Mocs2B), cytochrome P450 2U1-like (Cyp2b1)), and ABC transporter (e.g., ATP-binding cassette sub-family D member 3-like (ABCD3), ATP-binding cassette sub-family B member 10 (ABCB10)). Through characterization of these core pathways, this study reveals the fundamental mechanisms by which L. vannamei responds to high ammonia nitrogen stress following low-salinity acclimation, providing a theoretical foundation for estuarine shrimp farming. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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19 pages, 4755 KB  
Article
Effects of Aeromonas veronii and Its Vaccine on Immune-Related Gene, Liver Transcriptomics, and Gill Microbiota in Crucian Carp
by Junbo Wang, Shiyong Huang, Yingtiao Lai, Ping Wang, Feifei Wang, Dahui Pan, Fei Zhao and Hua Gong
Vaccines 2026, 14(4), 307; https://doi.org/10.3390/vaccines14040307 - 29 Mar 2026
Cited by 1 | Viewed by 833
Abstract
Background: Aeromonas veronii is an important bacterial pathogen in crucian carp and can cause serious disease outbreaks and substantial economic losses in aquaculture. Objectives: To evaluate how A. veronii infection and its inactivated vaccine modulate immune responses in Carassius auratus. [...] Read more.
Background: Aeromonas veronii is an important bacterial pathogen in crucian carp and can cause serious disease outbreaks and substantial economic losses in aquaculture. Objectives: To evaluate how A. veronii infection and its inactivated vaccine modulate immune responses in Carassius auratus. Methods: 270 juveniles were allocated into three groups: a saline-injected control group (Ctrl), a vaccination group receiving an inactivated A. veronii vaccine (Vac), and an artificial infection group (AIG) subjected to stimulation. Liver, spleen, head kidney, gill, and intestine samples were collected from fish after anesthesia. The relative transcript levels of IgM, IgD, BAFF, MHCII, CD4, BCL6, MyD88, and NF-κB were quantified. For liver transcriptome analysis, the effective library concentration was determined. And the 16S rRNA gene resulting reads of fish gill symbiotic microbiota were processed for downstream bioinformatic analysis. Results: The results showed that the Vac achieved an RPS of 73.33%, and vaccination significantly upregulated multiple immune-related genes in different fish organs. With BAFF transcription across organs emerging as a robust sentinel readout. The Pearson correlation coefficient (r) of BAFF between other genes were all ≥0.8. GO and KEGG enrichment analyses indicated that AIG had more DEGs than Vac (5885 vs. 4008) and Ctrl (6910 vs. 6178), respectively. Some genes in AIG revealed significant over-representation of immune pathways, such as BCL6, MyD88, and NF-κB. The fish gill microbiota comprised a diverse set of low-abundance taxa, the phylum level was dominated by Proteobacteria and Fusobacteriota across all groups; whereas, the Vac group remained broadly closer to the Ctrl group in overall composition. Conclusions: These results indicated marked post-challenge immune–metabolic coupling in the liver, and suggested coordinated immunophysiological interplay between the liver and the spleen. Gill microecology of symbiotic bacteria was affected by vaccination or challenge reactions, which in turn affects the health of the gills or the organism itself. Full article
(This article belongs to the Special Issue Fish Disease Occurrence and Immune Prevention and Control)
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21 pages, 17701 KB  
Article
Synergistic Effects of Ammonia and Hypoxia Stress on the Transcriptomic Responses of the Razor Clam (Sinonovacula constricta)
by Zidai Liu, Hao Zhang, Congying Lai, Ran Sun, Hongqiang Xu, Hanhan Yao, Yinghui Dong, Zhihua Lin and Liyuan Lv
Animals 2026, 16(6), 896; https://doi.org/10.3390/ani16060896 - 12 Mar 2026
Viewed by 753
Abstract
The co-occurrence of ammonia nitrogen and hypoxia represents a physiologically taxing synergistic challenge for benthic bivalves—as it forces a conflict between the high energy demand for detoxification and the limited energy supply under low oxygen, yet the tissue-specific strategies underlying their resilience remain [...] Read more.
The co-occurrence of ammonia nitrogen and hypoxia represents a physiologically taxing synergistic challenge for benthic bivalves—as it forces a conflict between the high energy demand for detoxification and the limited energy supply under low oxygen, yet the tissue-specific strategies underlying their resilience remain poorly understood. This study investigated the physiological and transcriptomic responses of the razor clam Sinonovacula constricta to ammonia (AG), hypoxia (HG), and their combination (HAG) over 96 h. Transcriptomic profiling revealed that the gill and hepatopancreas employ distinct, organ-coordinated adaptive strategies rather than a uniform systemic response. The gill prioritized respiratory homeostasis by fine-tuning oxygen sensing: transcriptional suppression of hypoxia-inducible factor 1-α (HIF-1α) (to limit glycolytic acidosis) was followed by a chronic induction of HIF-2α, alongside the specific upregulation of the mitochondrial respiratory gene cytochrome c oxidase-6b (COX-6b). In contrast, the hepatopancreas executed a critical metabolic trade-off centered on arginine metabolism. Under combined stress, arginine flux was redirected toward the urea cycle via a robust upregulation of arginase (ARG) for detoxification, while nitric oxide synthase (NOS) was concurrently suppressed. This reciprocal regulation suggests a strategy to prioritize ammonia clearance and energy conservation at the expense of immune signaling. These findings elucidate how S. constricta navigates the bioenergetic conflict between detoxification and oxygen limitation, providing molecular targets for breeding stress-resistant aquaculture strains. Full article
(This article belongs to the Special Issue Environmental Adaptation and Metabolic Regulation in Aquatic Animals)
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17 pages, 7367 KB  
Article
Taurine Intake Alleviates Oxidative Damage During Transportation in Culter alburnus
by Shuxuan Chen, Long Ren, Junjun Wei, Xue Xue, Yuan Wang, Yiping Han, Shang Wang and Dongpo Xu
Animals 2026, 16(5), 698; https://doi.org/10.3390/ani16050698 - 24 Feb 2026
Cited by 1 | Viewed by 951
Abstract
Live fish transport easily induces severe physiological stress, marked by pronounced oxidative damage and significant mortality, leading to substantial economic losses annually. Here, we evaluated the effects of taurine intake on alleviating stress response during transportation of Culter alburnus. Juvenile fish were [...] Read more.
Live fish transport easily induces severe physiological stress, marked by pronounced oxidative damage and significant mortality, leading to substantial economic losses annually. Here, we evaluated the effects of taurine intake on alleviating stress response during transportation of Culter alburnus. Juvenile fish were fed diets containing 0 (control), 0.5, 1.0, 1.5, or 2.0 g/kg taurine for 8 weeks before undergoing 12 h of simulated transport. The results showed that taurine supplementation significantly improved growth performance in a dose-dependent manner. During transportation, the deterioration of water quality and the damage of gill tissue decreased with the increase in concentration. The determination of catalase (CAT), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA) showed that 2.0 g/kg taurine improved antioxidant capacity. The high-concentration taurine group enhanced the activities of immune enzymes such as acid phosphatase (ACP) and alkaline phosphatase (AKP), while the activity of total nitric oxide synthase (T-NOS) was inhibited. The antioxidant immune effect of the 0.5 g/kg and 1.0 g/kg concentration groups was not obvious. Transcriptome analysis revealed that 2.0 g/kg taurine enhanced the antioxidative stress capacity of C. alburnus by upregulating the expression of immune-related genes (TLR5, Il12b) and activating the Toll-like receptor signaling pathway as well as the cytokine–cytokine receptor interaction pathway. These findings demonstrated that dietary taurine improved resilience to transport stress in C. alburnus. Full article
(This article belongs to the Special Issue Feed Additives for Improving the Immunity of Aquatic Animals)
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13 pages, 2002 KB  
Article
Transition to Time-Dependent Artificial Feed Induces Histological and Apoptotic Alterations in Mandarin Fish (Siniperca chuatsi)
by Zhou Zhang, Qi Deng, Zhonggui Xie, Min Xie and Shaoming Li
Fishes 2026, 11(1), 49; https://doi.org/10.3390/fishes11010049 - 13 Jan 2026
Viewed by 492
Abstract
This study aimed to investigate the response mechanisms of liver and gill tissues in mandarin fish (Siniperca chuatsi) at the histological, apoptotic, and gene expression levels during the weaning process from live prey to artificial feed. By analyzing fish samples at [...] Read more.
This study aimed to investigate the response mechanisms of liver and gill tissues in mandarin fish (Siniperca chuatsi) at the histological, apoptotic, and gene expression levels during the weaning process from live prey to artificial feed. By analyzing fish samples at different domestication stages (D0, D7, D14), the results revealed that: (1) Histologically, the gill filaments exhibited shortening and thickening post-domestication, while the liver showed increased vacuolation; (2) apoptosis detection (TUNEL assay) and analysis of apoptosis-related gene (Bax/Bcl-2) expression indicated that the gill tissue experienced a significant increase in apoptosis at the mid-domestication stage (D7), which returned to baseline levels later (D14), whereas hepatic apoptosis showed no significant changes throughout the process; (3) transcriptome sequencing identified 3405 and 881 differentially expressed genes (DEGs) in the liver and gill tissues, respectively, and the significantly enriched pathways were steroid biosynthesis in the liver and alanine, aspartate, and glutamate metabolism in the gills. The apoptosis pathway was also significantly enriched in both tissues. GO analysis further indicated that the DEGs were primarily associated with metabolic processes, oxidative stress, and cell apoptosis. In conclusion, artificial feed domestication induces adaptive changes in the tissue structure and molecular profiles of the gill and liver in mandarin fish. The gill response to dietary transition is more rapid and characterized by a reversible apoptotic process, providing a theoretical foundation for understanding the stress mechanisms associated with domestication and promoting healthy aquaculture practices for this species. Full article
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20 pages, 2963 KB  
Article
A Distinct Defense Strategy: The Molecular Basis of WSSV Tolerance in Macrobrachium nipponense Revealed by Comparative Transcriptomics with Litopenaeus vannamei
by Yunpeng Niu, Sufei Jiang, Wenyi Zhang, Yiwei Xiong, Shubo Jin, Hui Qiao and Hongtuo Fu
Int. J. Mol. Sci. 2026, 27(2), 766; https://doi.org/10.3390/ijms27020766 - 12 Jan 2026
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Abstract
White Spot Syndrome Virus (WSSV) remains one of the most devastating pathogens in global shrimp aquaculture, causing massive economic losses annually. This study employed comparative transcriptomics to elucidate the molecular basis of the differential resistance to WSSV between the highly susceptible Pacific white [...] Read more.
White Spot Syndrome Virus (WSSV) remains one of the most devastating pathogens in global shrimp aquaculture, causing massive economic losses annually. This study employed comparative transcriptomics to elucidate the molecular basis of the differential resistance to WSSV between the highly susceptible Pacific white shrimp (Litopenaeus vannamei) and the remarkably resistant oriental river prawn (Macrobrachium nipponense). Our analysis of gill, hepatopancreas, and muscle tissues at 24 h post-infection revealed fundamentally distinct defense strategies. The resistant M. nipponense employs a unique “proactive homeostatic reinforcement” strategy, characterized by significant enrichment of pathways central to cellular homeostasis, including signal transduction, cellular processes, and transport/catabolism. This approach, supported by coordinated up-regulation of heat shock proteins and structural genes, enables effective viral control without triggering excessive immune activation. In contrast, susceptible L. vannamei displays either widespread metabolic dysregulation leading to systemic collapse in moribund individuals or dependency on specific immune pathways (Toll-like receptor signaling and apoptosis) in survivors. Through comparative KEGG analysis, we identified heat shock protein 70 kDa (HSP70, K03283) as a key conserved gene and functionally validated its critical role in antiviral defense using RNA interference. Knockdown of HSP70 in M. nipponense significantly increased cumulative mortality and viral load, confirming its essential protective function. These findings provide novel insights into crustacean antiviral immunity and identify promising genetic targets for breeding WSSV-resistant shrimp strains, offering sustainable solutions for disease management in aquaculture. Full article
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Article
Comparative Transcriptome Analysis Reveals the Seawater Adaptation Mechanism in Pseudaspius hakonensis
by Ziyue Xu, Wen Zheng, Wenjun Chen, Min Zhou, Dongdong Zhai, Ming Xia, Hongyan Liu, Fei Xiong and Ying Wang
Genes 2026, 17(1), 76; https://doi.org/10.3390/genes17010076 - 9 Jan 2026
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Abstract
Background: The family Cyprinidae is predominantly restricted to freshwater habitats, making the evolution of diadromy and seawater adaptation exceptionally rare within this group. Pseudaspius hakonensis, a rare anadromous cyprinid, and its strictly freshwater congener P. leptocephalus, provide an ideal comparative model [...] Read more.
Background: The family Cyprinidae is predominantly restricted to freshwater habitats, making the evolution of diadromy and seawater adaptation exceptionally rare within this group. Pseudaspius hakonensis, a rare anadromous cyprinid, and its strictly freshwater congener P. leptocephalus, provide an ideal comparative model to investigate the molecular mechanisms underlying salinity adaptation. This study aimed to elucidate the tissue-specific transcriptional reprogramming, identify candidate genes and key pathways, and explore their association with seawater acclimation in P. hakonensis. Methods: We performed comparative transcriptomic analyses of gill, liver, and kidney tissues from both species using RNA-Seq. Sequencing reads were aligned to a high-quality reference genome of P. hakonensis. Differential expression analysis was conducted using DESeq2, followed by functional enrichment analyses (GO and KEGG) to identify significant biological processes and pathways. Results: A total of 8784, 5965, and 5719 differentially expressed genes (DEGs) were identified in gill, kidney, and liver tissues, respectively, with the gill showing the highest differences. Functional enrichment revealed tissue-specific roles: gill DEGs were associated with protein synthesis and energy metabolism; kidney DEGs with transport and detoxification; and liver DEGs with metabolic regulation and stress signaling. Cross-tissue analysis highlighted three core pathways consistently enriched: MAPK signaling, ABC transporters, and glutathione metabolism. Key candidate genes, including DUSP10, SLC38A2, ATP8B1, GSTA4, and MGST1, were significantly upregulated in P. hakonensis. Conclusions: This first multi-tissue transcriptomic comparison of an anadromous and a freshwater cyprinid reveals pervasive, tissue-specific molecular reprogramming underlying seawater adaptation in P. hakonensis. The coordinated activation of MAPK signaling, glutathione metabolism, and transporter pathways suggests an integrated regulatory network for osmoregulation and stress resistance. These findings provide novel insights into the genetic basis of salinity adaptation in cyprinids and identify candidate genes for future functional validation. Full article
(This article belongs to the Special Issue Innovations in Aquaculture Breeding via Genetic Technologies)
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