Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.

The complete mitochondrial genome of Cynoglossus joyneri was determined. The length of the C. joyneri complete mitochondrial DNA sequence is 16,428 bp. The tRNA Gln gene is translocated from the light to the heavy strand (Q inversion), which is accompanied by shuffling of the tRNA Ile gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNA Gln gene, which is also seen in the closely related Cynoglossus semilaevis. C. joyneri has a closer relationship to Cynoglossus lineolatus and C. semilaevis, but had a distant relationship to Phoxinus percnurus and Sternula albifrons.

A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel Cynoglossus semilaevis papillomavirus (CsPaV) and parvovirus (CsPV) were simultaneously isolated and identified from diseased fish via electron microscopy, virus isolation, genome sequencing, experimental challenges, and fluorescence in situ hybridization (FISH). Electron microscopy showed large numbers of virus particles present in the tissues of diseased fish. Viruses that were isolated and propagated in flounder gill cells (FG) induced typical cytopathic effects (CPE). The cumulative mortality of fish given intraperitoneal injections reached 100% at 7 dpi. The complete genomes of CsPaV and CsPV comprised 5939 bp and 3663 bp, respectively, and the genomes shared no nucleotide sequence similarities with other viruses. Phylogenetic analysis based on the L1 and NS1 protein sequences revealed that CsPaV and CsPV were novel members of the Papillomaviridae and Parvoviridae families. The FISH results showed positive signals in the spleen tissues of infected fish, and both viruses could co-infect single cells. This study represents the first report where novel papillomavirus and parvovirus are identified in farmed marine cultured fish, and it provides a basis for further studies on the prevention and treatment of emerging viral diseases.

The treatment of high-salinity, low-carbon marine aquaculture wastewater poses significant challenges for biological denitrification. This study systematically evaluated the performance of a polycaprolactone (PCL)-based aerobic denitrification biofilter under varying temperatures (15 °C and 25 °C) and PCL addition levels (282, 564, 846, 1128, and 1410 g). Optimal nitrogen removal, total nitrogen (TN) removal efficiency exceeding 92%, was achieved with 1128 g PCL at 15 °C (HRT 10 h) and 1410 g PCL at 25 °C (HRT 8 h), significantly outperforming the low-PCL baseline treatment. Microbial community analysis revealed that increased PCL dosage promoted the dominance of the hydrolytic genus Flavobacterium over Simplicispira, enhancing polymer degradation capacity and system stability. Metagenomic sequencing further elucidated the complete PCL degradation pathway, wherein hydrolysis products were oxidized to generate NADH and FADH₂, serving as electron donors for denitrification. Key functional genes (narG, nirK, nosZ) and enzymes associated with both PCL decomposition and nitrate reduction were significantly enriched in high-performance reactors (e.g., AT15H6, AT25H6, ET15H10, ET25H10), correlating strongly with observed nitrogen removal rates. By integrating reactor performance with microbial ecology and functional genetics, this work provides a comprehensive “material–microorganism–gene–performance” framework, offering both practical strategies and mechanistic insights for enhancing denitrification in saline aquaculture systems.