Aquaculture International最新文献

Procambarus clarkii (P. clarkii), a commercially important shrimp species, has experienced increasing market demand, emphasizing the need for effective disease prevention and control strategies. Spiroplasma eriocheiris (S. eriocheiris), a recently identified bacterial pathogen, is commonly detected in the tissues of aquatic crustaceans and spreads via lymphocytes following infection, often resulting in mortality. Non-coding RNAs play essential roles in the growth, reproduction, and immune responses of aquatic organisms. This is particularly relevant to P. clarkii, which relies solely on innate immunity. The competitive endogenous RNA (ceRNA) regulatory mechanism, mediated by non-coding RNAs such as miRNAs and lncRNAs, may constitute a critical pathway in immune defense. In this study, transcriptomic sequencing integrated with systems biology was employed to analyze miRNAs, mRNAs, and lncRNAs in the hemocytes of P. clarkii across different infection stages. A total of 880 lncRNAs, 144 miRNAs, and 4370 mRNAs were differentially expressed. Based on these findings, 94 interaction pathways for differentially expressed lncRNAs, miRNAs, and mRNAs were identified, establishing a comprehensive ceRNA network. Functional annotation revealed that the target genes of these significantly differentially expressed miRNAs and lncRNAs are closely associated with immune and autophagy-related pathways. To validate the interactions between non-coding RNAs and immune-related genes within this network, dual-luciferase reporter assays confirmed that XR_006771428.1 and Rac1 are targets of pcla-mir_206, while IKBA and MSTRG.19161.1 are targets of pcla-mir_14. Additional functional validation demonstrated that the key node gene Rac1 was significantly expressed in the hemocytes and hepatopancreas of P. clarkii, and RNA interference of Rac1 led to a notable increase in the copy number of S. eriocheiris, indicating the involvement of Rac1 in the immune response. This study elucidates the immune defense mechanism of P. clarkii against S. eriocheiris infection and provides a potential strategy for controlling diseases in aquatic crustaceans.

Aquaculture needs more environmentally friendly alternatives to fishmeal-based feed. Polychaetes could be part of a solution, since they are comparatively easy to cultivate. Eurythoe sp. and especially the species complex Eurythoe complanata is widely distributed across tropical coasts and aquaria. However, studies on the biology, needed for a targeted cultivation, are rare. In order to evaluate the species’ potential as an aquaculture species, an understanding especially of their feeding preferences and proximate composition, namely lipid, carbohydrate and protein content, is essential. Here, we present a—to the best of our knowledge—first adapted protocol to quantify lipid, carbohydrate and protein content in Eurythoe spp., as well as a comparison of female and male individuals of two species of the genus, referred to as spec. 1 (Eurythoe cf. complanata) and spec. 2 (Eurythoe sp.). Overall, the values of the lipid content ranged between 7 and 13% of the dry weight (DW) with the male polychaetes of spec. 1 showing lower lipid concentrations compared to the other species. Additionally, the male polychaetes showed higher carbohydrate levels than females or individuals of the other species. Carbohydrate concentrations between 3 and 10% DW were measured. The protein content of all specimens was between 27 and 37% DW. A 90-day feeding experiment revealed highest specific growth rates (SGR) of the group fed with a control of pellets, compared to algae commercially available as fish feed and spinach. Spontaneous fragmentation, known as a form of asexual reproduction among annelids, occurred over the experimental run. Despite the revealed high potential as a feed source for aquaculture purposes, more detailed investigations are necessary, especially regarding the targeted feeding and potential complications due to their venom.

Live attenuated vaccines have been considered particularly effective for controlling bacterial infections due to their strong immunogenicity and long-lasting immune effects. Here, we evaluated the safety, immunogenicity, and protective effects of two attenuated cyclic-di-GMP phosphodiesterase gene overexpression strains, Z11::pBBR1MCS-yhjH and Z11::pBBR1MCS-adrB, based on Hafnia paralvei Z11 as vaccine candidates. We found that the attenuated H. paralvei strains could temporarily colonize in the liver and spleen of loach, eventually being cleared without causing any clinical signs. Our study also showed that the immunoglobulin M (IgM) levels and the expression levels of igm, igt, and igd were significantly increased following vaccine immunization, as well as the expression levels of the pro-inflammatory related genes tnf-α, il-1β, and il-6, indicating that vaccine immunization induced immune responses in loaches. Furthermore, the overexpression strains used as vaccines can effectively stimulate the body to produce immune responses, enhance the phagocytic effect of blood cells on H. paralvei Z11 in loaches, improve bacterial clearance ability, and inhibit blood cell apoptosis. Vaccine immunization can also attenuate damage induced by H. paralvei Z11 to the liver and spleen tissues of loaches and provide effective protection for loaches. Our findings indicate that the overexpression strains can be applied as live attenuated vaccines to control bacterial infections, which can be developed as effective strategies for protection of aquatic animals.

Early identification of fish diseases is critical to maintain aquaculture and minimize its financial burden. In the diagnosis of diseases, time is critical and scientists’ experience is imperative, which makes the artificial intelligence-based models necessary. It is intended by this study to integrate deep learning with explainable artificial intelligence methods to establish an artificial intelligence-powered framework for early detection of disease in fish. In this study, we developed a hybrid artificial intelligence system designed to detect diseases in freshwater fish by analyzing skin images. The primary objectives of the system are to minimize economic losses, prevent further disease spread, and ultimately increase aquaculture productivity. For this purpose, we used a dataset consisting of images from seven different disease categories, with 250 images in each class. A new hybrid model, Residual Network-50–Vision Transformer, was developed by integrating the strengths of Residual Network-50 and Vision Transformer architectures to improve classification accuracy. The proposed model was subjected to rigorous comparison with established architectures, including Visual Geometry Group 16, Mobile Convolutional Neural Network Version 2, Efficient Neural Network–Baseline Model B0, standalone Vision Transformer, and the original Residual Network-50. The results demonstrated that Residual Network-50–Vision Transformer outperformed the model, achieving an impressive 99.14% accuracy rate. Furthermore, the study employed local interpretable model-independent explanations to explain which image features most significantly influence the model’s classification decisions, thereby enhancing the interpretability and confidence in the model’s output. The application of such advanced image processing models in combination with explainable AI techniques demonstrates significant potential to support sustainable aquaculture by reducing disease outbreaks and associated financial losses.

Antibiotics are widely applied to prevent and treat diseases in aquaculture, leading to bacterial resistance and drug residues. Therefore, safe and eco-friendly alternatives are urgently needed to reduce the adverse effects of excessive antibiotic use. In this study, Litopenaeus vannamei was employed as a model to evaluate the efficiency and differences between prophylactic herbs (14 days supplementation plus subsequent infection, N = 6 for each treatment) and therapeutic herbs (4 days post infection) with 5% garlic and 2.5% ginger based on relevant works with optimal beneficial efficiency in protecting against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (VP_AHPND). Results showed that dietary supplementation with garlic and ginger efficiently promoted shrimp growth, immunity, hepatopancreas and intestine integrity, microbial diversity, network robustness and modularity, collectively improving shrimp survival by 37.2% for prophylactic herbs and by 30.5% for therapeutic herbs following VP_AHPND infection. In addition, VP_AHPND infection induced antioxidant defenses (IFN-α by 4.1% and IL-10 by 99.4%) and pro-inflammatory cytokines (TNF-α by 7.1% and IL-6 by 8.0%); both herb treatments can alleviate negative effects. Transcriptome analysis revealed that VP_AHPND exposure significantly suppressed (r > 0.7, P < 0.05) key metabolic and immune pathways in shrimp, including circadian rhythm, GnRH signaling pathway, and protein processing, which were efficiently restored by prophylactic herbs, with limited restoration by therapeutic herbs. Alterations in gut the bacterial genera/species were significantly associated with differentially expressed genes in the shrimp hepatopancreas, e.g., Vibrio parahaemolyticus, Derlin-1, Pseudoalteromonas, and peroxiredoxin 6. Together, these findings demonstrate that dietary herb supplementation efficiently protects shrimp immunity, gut microbiota, and network stability, thereby enhancing resistance to AHPND, with superior effects from prophylactic herbs.

The aquaculture sector has been progressively transitioning toward environmentally sustainable feed production, with insect meals emerging as viable alternatives to fish meal (FM); however, their effects on the microbiota of fish still remain insufficiently characterized. This study examined gut and skin microbiota in rainbow trout (Oncorhynchus mykiss) following complete FM substitution with yellow mealworm (Tenebrio molitor, TM), utilizing machine learning (ML) to investigate diet-microbiota relationships. To this end, microbial abundance data from a prior in vivo trial were analyzed by means of a structured ML pipeline. On the one hand, classification models assessed the association between microbial profiles and dietary regimens, while, on the other hand, regression models evaluated the predictive capacity of feed ingredient variations on microbial abundance shifts. Within this processing framework, feature selection identified informative taxa across taxonomic levels, enhancing model generalizability and reducing overfitting. Several classification algorithms attained optimal accuracy, whereas regression models showed moderate performance, with error values decreasing from higher to lower taxonomic ranks. In particular, feature selection and explainability analyses identified both diet- and tissue-associated indicators: Cutibacterium, Enhydrobacter, and Lactobacillus in the gut; Chryseobacterium, Flectobacillus, and Sphingopyxis in the skin. The occurrence of Deefgea in both tissue types suggested potential water-fish microbial exchange. In conclusion, despite conventional analyses showing only limited dietary modulation, ML models effectively detected diet- and tissue-specific indicators in rainbow trout following FM substitution with TM, ultimately underscoring the potential of integrating AI-driven techniques with next-generation sequencing to uncover ecological patterns across fish tissue types and taxonomic levels.

The sea cucumber Apostichopus japonicus is one of the most commercially valuable species in both fisheries and aquaculture due to its nutritional value and high content of biologically active compounds. To evaluate the effect of the microalgae Tetraselmis sp. and Skeletonema dorhnii on the growth and phospholipid molecular species composition of juvenile A. japonicus, a 3-month feeding experiment was set up. The diet of sea cucumbers supplemented with these microalgae improved their survival rate (up to 74% for the diet with S. dorhnii) and weight gain (with Tetraselmis sp. showing the highest growth promotion). A lipidomic analysis with high-performance liquid chromatography–mass spectrometry identified 146 phospholipid (PL) molecular species from four classes (glycerophosphoethanolamines (PE), glycerophosphocholines (PC), glycerophosphoserines (PS), and glycerophosphoinositols (PI)). The microalgae-fed groups showed the increased levels of 20:5- and 22:6-containing PS and PI in the microalgae-fed groups.. The elevated levels of ether-linked PC and PE in the control (microalgae-free) group might indicate an adaptive membrane remodeling. Our results demonstrate that the supplementation of diet with microalgae may selectively modulate PL profiles, that may improve the membrane function and potentially enhance stress adaptation in cultured A. japonicus.

Holothuria scabra is a commercially valuable sea cucumber considered a promising candidate for integrated aquaculture, yet its large-scale farming remains underdeveloped in Taiwan. This study had dual aims: to evaluate the environmental tolerance of juvenile H. scabra in controlled laboratory trials and to validate its coculture performance with the native clam Meretrix taiwanica and milkfish Chanos chanos in field ponds. Experiments were conducted in both indoor (laboratory) and outdoor (pond) settings. In indoor trials, juveniles were exposed to three temperatures (14 °C, 24 °C, 34 °C), a salinity gradient (10–40 ppt), and two substrate types (sandy vs. muddy) to assess effects on survival and growth. At 24 °C (optimal) and even at 14 °C, survival remained 100% over 1 week, whereas exposure to 34 °C caused near-complete mortality (only 7% survival by day 7). High salinities (30–40 ppt) sustained > 90% survival, whereas low salinities (10–20 ppt) caused 100% mortality within 13 days. Sandy substrate yielded significantly higher survival and growth than muddy substrate (60% vs. 10% survival after 2 weeks). In parallel, field trials (over summer and winter) compared H. scabra survival in clam monoculture sandy-bottom ponds (clam-H. scabra coculture on sandy substrate), muddy-bottom clam monoculture ponds (clam-H. scabra coculture on muddy substrate), and sandy-bottom clam and milkfish coculture ponds (clam-milkfish-H. scabra coculture on sandy substrate). Peak survival (75% by May to Oct.) was observed in clam-H. scabra coculture on sandy substrate, while survival was markedly lower in clam-H. scabra coculture on muddy substrate (37.5%) and clam-milkfish-H. scabra coculture on sandy substrate (50%). This study provides the first empirical coculture baseline for H. scabra in Taiwan, and its findings inform integrated aquaculture system design.

Graphical Abstract

Trichopodus leerii, a popular ornamental fish species commonly known as the pearl gourami, is valued for its striking coloration and compatibility within typical home aquaria. Current aquaculture protocols struggle with first-feed bottlenecks that are traditionally reliant on costly live feeds. Research on partial or full replacement of live feeds with inert microdiets has become increasingly important to streamline larval production and reduce costs. Improving the performance of microdiets (MDs) through the use of feed attractants (FAs) has demonstrated efficacy in increasing numbers of species in the literature. Three FAs (L-alanine, betaine, L-tryptophan) were tested at different inclusion levels, followed by an additional FA trial combining all three FAs to determine whether synergistic effects exist. Additionally, liquid Artemia (LA) diets are used in commercial aquaculture of shrimp as a shelf-stable alternative to live feeds. To determine if this alternative diet could be used as an Artemia spp. nauplii replacement in T. leerii aquaculture, an experiment was conducted using two commercially available products to investigate whether these diets could reduce dependence on live feeds. L-Alanine supplementation improved short-term larval survival and growth while betaine and L-tryptophan were ineffective. The combined FA formulation also did not yield any performance benefits. Partial LA replacement strategies preserved larval performance, supporting their use as a tool to reduce, but not replace, live feed use. These results highlight the strong innate chemosensory selectivity characteristic of Trichopodus spp. and provide practical direction for advancing MD-based protocols to enable more consistent, scalable production of T. leerii.

Aquaculture practices have evolved significantly from low-density to highly intensive systems, increasing susceptibility to disease outbreaks. Conventional disease prevention relying on antimicrobials and chemotherapeutics causes detrimental environmental impacts and contributes to antimicrobial resistance (AMR). Consequently, the use of vaccines and immunostimulants offers promising environmentally sustainable alternatives. In fish, unlike in higher vertebrate, innate immunity, mediated by pattern recognition receptors (PRRs), plays a dominant role in defence against diseases. Among PRRs, retinoic acid–inducible gene I (RIG-I)–like receptors (RLRs: RIG-I, MDA5, and LgP2) are critical viral sensors triggering the synthesis of type I interferon production and antiviral responses. Over the years, rapid identification of fish RLRs and their downstream signalling molecules is enabling novel infection-prevention strategies. This comprehensive review synthesizes the current and updated research on fish RLRs, addressing their history of identification, spliced variants, polymorphism, ontogenic expression, subcellular localization, architectural insights, signal transduction pathways, response against pathogens and environmental stressors, impact of their modifications on innate immunity, and the regulators that inhibit RLR-signalling pathways. Understanding the functions of fish RLRs is likely to be helpful in advanced vaccine design incorporating multiple RLR ligands as adjuvants resulting in enhanced immunity and disease resistance for the sustainable aquaculture.