Di Peng

Rainbow trout (Oncorhynchus mykiss) is an important cold-water aquaculture species and a tractable salmonid model for functional genomics. Rapid advances in chromosome-level genome assemblies, genetic variation resources, regulatory annotations, tissue and cell models, controlled challenge systems, and genome-editing technologies have established an increasingly integrated framework for linking genomic variation with measurable phenotypes. Evidence from studies of mucosal immunity, disease-resistance genetics, and environmental stress responses indicates that these resources can improve candidate-gene prioritization and mechanistic interpretation across molecular, cellular, tissue, and whole-fish levels. However, differential gene expression, quantitative trait locus and genome-wide association signals, genomic predictions, and cell-type localization remain largely associative and rarely provide direct evidence of causality. Interpretation is further complicated by salmonid-specific whole-genome duplication, because retained paralogues may exhibit tissue-specific divergence, functional redundancy, and compensatory responses. Further progress will require the integration of pangenomics, regulatory annotation, single-cell and spatial analyses, and paralogue-aware functional perturbation in both cell-based and whole-fish systems. Such integration will strengthen causal inference, clarify genotype–phenotype relationships, and support disease-resistant breeding, healthy aquaculture, and environmental risk assessment.

Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)—three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R² > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.

Nanoplastics are ubiquitous in aquatic environments, and elucidating their bioaccumulation behavior is essential for assessing toxicity and trophic transfer risks. While most studies focus on nanoplastics properties (e.g., type, size, surface charge), the influence of organismal growth stage remains unclear. Through bioaccumulation kinetic experiments with 10 mg/L polystyrene nanoplastics (PSNPs), this study found that Tetrahymena thermophila (T. thermophila) in the lag phase (cell density 4 × 10⁴ cells/mL) exhibited the highest uptake rate of nanoplastics, 1.2–5.8 times that of the exponential phase (1–5 × 10⁵ cells/mL) and 7.7 times that of the stationary phase (>5 × 10⁵ cells/mL). Lag phase cells also had a larger specific surface area (0.319 vs. 0.271/0.269 μm⁻¹), supporting their heightened uptake capacity. Under PSNP exposure, exponential and stationary phase cells showed significantly elevated reactive oxygen species (ROS) levels, accompanied by downregulated superoxide dismutase (SOD) and stable catalase (CAT) activity, indicating impaired antioxidant defense and potential redirection of energy toward stress mitigation. Consistent with efficient internalization, confocal imaging revealed clear PSNP colocalization within food vacuoles of lag period cells. Proteomic and transcriptomic analysis further confirmed the upregulation of carrier proteins, FAD/FMN oxidoreductases, and pathways associated with cellular components (membrane and organelle membrane) and molecular functions (transporter activity and transmembrane transporter activity) in lag-phase T. thermophila. Collectively, these findings provide a molecular-level understanding of the multi-phase-dependent bioaccumulation of PSNPs, offering critical insights for assessing the environmental risks of polystyrene nanoplastics in dynamic aquatic ecosystems.

This study investigates the effects of saline, alkaline, and combined saline–alkaline water environments on the growth, muscle quality, gene expression, and metabolic profiles of largemouth bass (Micropterus salmoides). Juvenile fish were exposed to five water conditions for 60 days: freshwater (FW), saline water (SW, 10 ppt), alkaline water (AW, 15 mmol/L), and two saline–alkaline combinations (SAW-1: 4 ppt + 10 mmol/L; SAW-2: 6 ppt + 15 mmol/L). While growth rate was similar across groups, SAW-2 caused a significant decrease in survival rate and induced notable alterations in muscle texture and fiber structure. Transcriptomic analyses revealed group-specific enrichment of stress-responsive pathways. The FoxO signaling pathway acts as a central regulator of muscle maintenance and energy reallocation. The solute carrier gene slc38a4 and glula (glutamine synthetase), both closely associated with ammonia detoxification via glutamine synthesis and transport, were upregulated under saline–alkaline stress, indicating enhanced capacity for nitrogen metabolism. In addition, two key regulators of muscle remodeling, loc119898415 and tbx18, were significantly upregulated, suggesting a potential chromatin–transcription program underlying compensatory myogenesis and muscle fiber adaptation in response to environmental challenges. Metabolomic profiling showed an accumulation of osmoprotectants (betaine, taurine) in SW and SAW-2 groups, suggesting enhanced stress resistance. Multiomics integration further indicated coordinated regulation between lipid metabolism and insulin signaling, potentially mediated by the FoxO pathway. These results offer practical guidance for improving largemouth bass aquaculture under inland saline–alkaline conditions.

Two typical fish products—fermented mandarin fish and semi-dried yellow croaker—are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology of the two fish products and to determine their capacity for producing BAs. Putrescine and cadaverine were major BAs detected in the fish products. Concentrations of BAs were significantly corrected with microbial count (p < 0.05). BA-producing isolates (33) in the two fish products were all multiple BA producers. Several of them, including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker, showed remarkable BA-producing capacity. Hafnia alvei produced the greatest abundance of putrescine, cadaverine, tyramine and 2-phenylethylamine. Lactobacillus sakei mainly produced tryptamine and putrescine. Photobacterium phosphoreum showed the strongest histamine-producing capacity.

Two typical types of fish products including fermented mandarin fish and semi-dried yellow croaker are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology in the two fish products and to research its capacity of BAs-producing. PUT and CAD were major BAs detected in fish products. Concentrations of BAs were significantly corrected with microbial count (P < 0.05). BA-producing isolates (31) in two fish products were all multiple BAs producers. Several of them including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker showed a remarkable BA-producing capacity. Hafnia alvei produced the most abundant of CAD, PUT, TYR and 2-PHE. Lactobacillus sakei mainly produced TRY and PUT. Photobacterium phosphoreum showed the strongest HIS producing capacity.