High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the ‘ECM-receptor interaction’ pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the ‘ECM-receptor interaction’ pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS.

The Chinese soft-shelled turtle (Pelodiscus sinensis) is an aquatic reptile prized for its nutritional and health benefits. Given its adaptability to various culturing modes including the greenhouse, pond and rice culturing modes, we conducted a comparative analysis of the morphology, organ trait and nutritional composition of turtles cultured in three culturing modes. This study investigated the plasticity of morphology and physiology, as well as the variations in nutritional composition across varying culturing modes. The results demonstrated that after approximately 120 days of cultivation, significant changes were observed in the morphology, physiology and nutritional composition of turtles from each culturing mode. In terms of morphology, rice turtles exhibited an arched shell shape, broad plastron, elongated limbs, narrow interocular distance and slender head and neck. Pond turtles displayed similar morphological characteristics to rice turtles, with the additional features of a flattened body shape and narrower plastron. Greenhouse turtles presented a flattened shell shape, narrow plastron, shortened limbs, wider interocular distance and stocky head and neck. Regarding the organ characteristics, the specific weights of liver, viscera, internal fat lumps and condition factors were significantly higher in greenhouse turtles compared to rice turtles and pond turtles (p < 0.05). Conversely, the specific weights of the back carapace, calipash and edible part were significantly lower than those in rice turtles and pond turtles (p < 0.05). Nutritional analysis revealed that crude protein, total amino acid, essential amino acid, flavor amino acid, pharmacodynamic amino acid, collagen and EPA+DHA contents were significantly higher in rice turtles and pond turtles than greenhouse turtles (p < 0.05). However, crude fat and unsaturated fatty acid contents were significantly higher in greenhouse turtles than in rice turtles and pond turtles (p < 0.05). In summary, Chinese soft-shelled turtles exhibited significant morphological and organ plasticity in response to different culturing modes. While the rice and pond culturing modes could enhance the nutritional quality of turtles to some extent, the impact of commercial feed on fatty acid profiles must be carefully considered.

Mandarin fish (Siniperca chuatsi) are known to exhibit distinct physiological and immunological adaptations to environmental stressors, but the underlying molecular and microbial mechanisms remain unclear. In this study, we integrated transcriptome and microbiome analyses to investigate adaptations across three geographically distinct mandarin fish groups: Guangdong (G), Qiupu (Q), and native Taihu (T). Liver RNA sequencing revealed 5339 differentially expressed genes (DEGs) between T and G and 1531 DEGs between T and Q. Functional enrichment analysis revealed group-specific responses. Specifically, DEGs from T vs. G were linked to small-molecule metabolism and innate immunity whereas the DEGs from T vs. Q were related to immune regulation and chromatin organization. The concurrent 16S rRNA sequencing of the intestinal microbiota identified 2680 amplicon sequence variants, with principal coordinate analysis showing distinct clustering (31.77% variance). Group T had higher Firmicutes abundance whereas groups G and Q had a higher relative abundance of Fusobacteriota. Correlation networks revealed key microbe–gene interactions, including positive links between Lactobacillus and immune genes in group T and negative associations with Romboutsia. These findings suggest that enhanced immune homeostasis and metabolic flexibility in group T may result from coordinated host gene expression and Lactobacillus-driven microbiome modulation. We provide new insights into the mechanisms of adaptation in mandarin fish and identify potential biomarkers for enhancing aquaculture resilience.

Over the past few years, China has become a hotspot for the domestication of the commercially valuable largemouth bass (Micropterus salmoides). Although the food preference of this fish has been studied, little is known about the genes regulating its growth. Population breeding was performed using two indigenous strains (QT1 and QT2), with the results showing that the organ/body ratio, abdominal fat rate and the body weight gain of QT1 and QT2 were higher than for the offspring YL1 and Y3 which are extensively cultured in China. Subsequent RNA sequencing (RNA-Seq) allowed for the identification of potential genes and pathways involved in growth performance. Overall, the transcriptome analysis generated 89,056 transcripts and 42,529 Unigenes. A PCA revealed significant differences between QT1 and the other three strains, while the other three strains did not show much difference. A KEGG enrichment analysis of differentially expressed genes showed that steroid biosynthesis was the most enriched pathway among the four strains. These pathways could be related to the growth of largemouth bass. In addition, a co-expression network analysis suggested a strong interaction between liver steroid biosynthesis and the genes for photosynthesis, secondary metabolism and stress response. Taken together, the above results can provide new insights into the liver metabolism of different strains of largemouth bass during culture and provide references for the subsequent domestication and breeding programs of largemouth bass.

Mandarin fish (Siniperca chuatsi) is a highly valued freshwater species in China, owing to its high-quality meat and economic importance. This study comparatively evaluated the effects of an industrialized recirculating aquaculture system (RAS) and traditional pond aquaculture system (TPAS) on the muscle quality and further explored the role of gut microbiota in muscle quality regulation. Our results showed that the RAS resulted in superior textural properties, with meat that was significantly more tender and elastic. The RAS also promoted higher muscle protein and reduced lipid levels. Notably, the RAS elevated sweet-tasting amino acids (Gly and Pro) while suppressing bitter amino acids (His). Electronic nose and GC-iMS analyses revealed distinct flavor compound profiles between the two systems, and the RAS enriched desirable volatiles (esters and alcohols) while suppressing aldehydes (e.g., nonanal and heptanal) associated with off-flavors. Gut microbiota profiling indicated higher diversity and enriched beneficial genera (e.g., Cetobacterium, Lactobacillus) in RAS-treated fish. We found that the Cetobacterium in the RAS group showed a significant positive correlation with sweet amino acids and pleasant flavor substances (such as esters, alcohols), while exhibiting a negative correlation with undesirable flavor precursors (such as certain aldehydes). This finding contributes to the sustainable and high-efficiency advancement of intensive Siniperca chuatsi aquaculture.