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Abstract Background Pseudomonas rhodesiae is a member of the Pseudomonas genus that is ecologically adaptable but has received little research. Despite its presence in clinical, environmental, agricultural, and aquaculture contexts, there is just a small amount of genomic information available for this species. Results We sequenced the genome of P. rhodesiae strain SK22, which was identified after a mortality outbreak in Dicentrarchus labrax (European seabass) farming in Turkey, and conducted a thorough comparison with 32 other publicly accessible P. rhodesiae genomes sourced from different environments. Whole-genome-based core genome phylogeny and Average Nucleotide Identity (ANI) identified two misclassified strains, 26B3 and CIP104664, that grouped with P. quebecensis (> 99% ANI). After eliminating these genomes, comparative studies revealed significant strain-specific variability in AMR determinants, virulence-associated genes, integrons, prophage content, and secretion systems. Class 1 integron was found only in one mineral-water isolate, whereas environmental isolates—particularly those from aquaculture, agricultural systems, and urban areas—had the largest AMR gene loads, suggesting their potential involvement in the dissemination of resistance and opportunistic pathogenicity. All genomes expressed key virulence characteristics such as T1SS-T6SS secretion systems, type IV pili, flagella, and siderophore-related genes, but supplementary virulence factors differed significantly. Prophage profiling found intact phage regions throughout all genomes, with agricultural and aquaculture isolates having abnormally large prophage loads, indicating phage-mediated adaptation and gene acquisition. Conclusions This study provides the first high-resolution genomic framework for P. rhodesiae, identifies incorrectly classified genomes within public databases, and highlights the species’ extensive genomic plasticity. The combination of diverse AMR determinants, mobile genetic elements, and virulence factors suggests that P. rhodesiae has the potential to function not only as an environmental saprophyte but also as an opportunistic pathogen capable of disseminating resistance genes across ecosystems. These findings highlight the importance of increased surveillance and functional validation in understanding the ecological and clinical roles of this emerging species.

Extractive fisheries and marine aquaculture share space and target species. Several regional-scale examples exist of escapees entering wild fisheries landings, yet no study has assessed the influence of aquaculture on landings at an ecosystem scale. We examined the effects of farmed fish escapes on fisheries using FAO data and published escape rates for Gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Seabream landings were significantly correlated with the estimated biomass of escaped seabream entering the wild. There was a similar pattern for seabass until 2005, but the overall relationship between landings and escapes was not significant due to the dramatic drop in catches in recent years. We argue that seabass escapees’ relatively high mortality, lower capturability, and minor ‘leaking’ from farms may obscure their influence on landings. Significant positive fisheries regime shifts were detected for both species, matching the onset of aquaculture in the Mediterranean and the period when escapees from aquaculture surpassed landings. Our results suggest that fish escapes of these two iconic species may mask wild stock overexploitation, confound stock assessments, alter genetic diversity, increase the risk of spreading pathogens and parasites, and compete with wild conspecifics while boosting fisheries landings.

A monitoring program to follow vibriosis incidents in the Greek marine aquaculture was implemented over the past 13 years. 273 isolates, from various cases originating from eight regions and nine hosts, were collected and characterized. The main aquaculture species of the survey were the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata). Various species of Vibrionaceae were associated with vibriosis. Vibrio harveyi had the highest prevalence and was isolated throughout the year from all hosts. During the warm months, Vibrio harveyi prevailed with frequent co-isolations of Photobacterium damselae subsp. damselae and Vibrio alginolyticus, while during spring, other Vibrio species were more abundant, such as Vibrio lentus, Vibrio cyclitrophicus, and Vibrio gigantis. Phylogenetic analysis using the mreB gene and the metabolic fingerprint of the isolates showed great variability within the species of the collection. The severity of the disease and the frequency of outbreaks make vibriosis (that is, mainly attributed to V. harveyi) an important concern for the regional aquaculture sector.

Oral vaccines are highly demanded by the aquaculture sector, to allow mass delivery of antigens without using the expensive and labor-intensive injectable vaccines. These later require individual handling of fish, provoking stress-related mortalities. One possible strategy to create injection-free vaccine delivery vehicles is the use of bacterial spores, extremely resistant structures with wide biotechnological applications, including as probiotics, display systems, or adjuvants. Bacterial spores, in particular those of Bacillus subtilis , have been shown to behave as mucosal vaccine adjuvants in mice models. However, such technology has not been extensively explored against fish bacterial disease. In this study, we used a laboratory strain of B. subtilis , for which a variety of genetic manipulation tools are available, to display at its spores surface either a Vibrio antigenic protein, OmpK, or the green fluorescence protein, GFP. When previously vaccinated by immersion with the OmpK- carrying spores, zebrafish survival upon a bacterial challenge with V. anguillarum and V. parahaemolyticus , increased up to 50 - 90% depending on the pathogen targeted. Further, we were able to detect anti-GFP-antibodies in the serum of European seabass juveniles fed diets containing the GFP-carrying spores and anti- V. anguillarum antibodies in the serum of European seabass juveniles fed the OmpK-carrying spores containing diet. More important, seabass survival was increased from 60 to 86% when previously orally vaccinated with in-feed OmpK- carrying spores. Our results indicate that B. subtilis spores can effectively be used as antigen-carriers for oral vaccine delivery in fish.

Abstract Unraveling the evolutionary mechanisms and consequences of hybridization is a major concern in biology. Many studies have documented the interplay between recombination and selection in modulating the genomic landscape of introgression, but few have considered how associations with phenotype may affect this landscape. Here, we use the European seabass (Dicentrarchus labrax), a key species in marine aquaculture that undergoes natural hybridization, to determine how selection on phenotype modulates the introgression landscape between Atlantic and Mediterranean lineages. We use a high-density SNP array to assess individual local ancestry along the genome and improve the mapping of muscle fat content, a polygenic trait that is divergent between lineages. Taking into account variation in recombination rates, we reveal a purging of Atlantic ancestry in the admixed Mediterranean populations. While Atlantic individuals had higher muscle fat content, we observed that genomic regions associated with this trait in Mediterranean populations displayed reduced introgression of Atlantic ancestry. These results emphasize how selection against maladapted alleles shape the genomic landscape of introgression.

Background Aquaculture production is expected to double by 2030, and demands for aquafeeds and raw materials are expected to increase accordingly. Sustainable growth of aquaculture will require the development of highly nutritive and functional raw materials to efficiently replace fish meal. Enzymatic hydrolysis of marine and aquaculture raw materials could bring new functionalities to finished products. The aim of this study was to determine the zootechnical and transcriptomic performances of protein hydrolysates of different origins (tilapia, shrimp, and a combination of the two) in European seabass ( Dicentrarchux labrax ) fed a low fish meal diet (5%), for 65 days. Results Results were compared to a positive control fed with 20% of fish meal. Growth performances, anterior intestine histological organization and transcriptomic responses were monitored and analyzed. Dietary inclusion of protein hydrolysates in the low fish meal diet restored similar growth performances to those of the positive control. Inclusion of dietary shrimp hydrolysate resulted in larger villi and more goblet cells, even better than the positive control. Transcriptomic analysis of the anterior intestine showed that dietary hydrolysate inclusion restored a pattern of intestinal gene expression very close to the pattern of the positive control. However, as compared to the low fish meal diet and depending on their origin, the different hydrolysates did not modulate metabolic pathways in the same way. Dietary shrimp hydrolysate inclusion modulated more metabolic pathways related to immunity, while nutritional metabolism was more impacted by dietary tilapia hydrolysate. Interestingly, the combination of the two hydrolysates enhanced the benefits of hydrolysate inclusion in diets: more genes and metabolic pathways were regulated by the combined hydrolysates than by each hydrolysate tested independently. Conclusions Protein hydrolysates manufactured from aquaculture by-products are promising candidates to help replace fish meal in aquaculture feeds without disrupting animal metabolism and performances.

Algae feeds and fish gut microbiota have been given importance in the past few years because of the necessity to rely on sustainable ingredients in aquafeeds and the link of host-associated microbes to organismal health. But little is known about the potential of algae, particularly of micro- and macroalgae combination, to shape the intestinal bacterial communities. Hence, in the present work, the 16S rRNA gene sequencing technique was employed to unravel the effects of the seaweed Gracilaria gracilis and the microalga Nannochloropsis oceanica - included either singly or in combination in the diets of European seabass - on the diversities and composition of the gut bacterial communities. Results indicated that 8% inclusion of either G. gracilis (GRA) or N. oceanica (NAN) led to a reduction in the gut microbial diversity. On the other hand, inclusion of the micro- and macroalga in a blend (NANGRA) mitigated these plausible effects on the intestinal bacterial communities. The core microbiota of European seabass was composed of both beneficial ( Lactobacillus and Cetobacterium ) and potentially pathogenic ( Flavobacterium ) bacteria. The GRA diet was associated with a lower abundance of carbohydrate degraders and also promoted the growth of bacteria capable of outcompeting fish pathogens ( Sulfitobacter and Methylobacterium ). On the other hand, the NAN diet led to a higher representation of the genus Bacillus , with probiotic potential, accompanied by a decrease in Vibrio , a genus encompassing several fish pathogenic species. These findings demonstrate the ability of micro- and macroalgae to modulate the gut microbiota of European seabass, with plausible implications to host gut homeostasis.

This study investigated a disease outbreak characterized by caligid copepod infestations and subsequent secondary bacterial infections in European seabass ( Dicentrarchus labrax ) and flathead grey mullet ( Mugil cephalus ) cultivated at a private facility in the Deeba Triangle region of Egypt. Moribund fish displayed brown spots on the skin, tongue, and gills, along with lethargy and excess mucus. The fish suffered severe infections, exhibiting external hemorrhages, ulcers, and ascites. The fish had pale, enlarged livers with hemorrhaging. Comprehensive parasitological, bacteriological, molecular, immunity and histopathological analyses were conducted to identify the etiological agents and pathological changes. Caligid copepod infestation was observed in wet mounts from the buccal and branchial cavities of all examined fish, and the caligids were identified as Caligus clemensi through COI gene sequencing and phylogenetic analysis. Vibrio alginolyticus was confirmed as a secondary bacterial infection through biochemical tests, recA gene sequencing, and phylogenetic analyses. Antibiotic susceptibility testing revealed resistance to β-lactams, aminoglycosides, and trimethoprim-sulfamethoxazole in V. alginolyticus isolates. Upregulation of the inflammatory marker IL-1β in gill and skin tissues indicated a robust cell-mediated immune response against the pathogens. Histopathological examination revealed severe tissue damage, hyperplasia, hemorrhage, and congestion in the gills, along with hepatocellular degeneration and steatosis in the liver, providing initial insights into this outbreak. A comprehensive therapeutic regimen was implemented, comprising prolonged hydrogen peroxide immersion baths, followed by the application of the nature-identical plant-based compound Lice-less and probiotic Sanolife Pro-W supplementation. This integrated approach effectively eliminated C. clemensi infestations, controlled secondary bacterial infections, and restored fish health, reducing morbidity and mortality rates to minimal levels.

This study examined how European seabass, Dicentrarchus labrax , juveniles are affected by heat stress in several ways, including growth biometrics, stress indicators, oxidative stress biomarkers, and histopathological changes. Our research aims to gain a better understanding of the impact of thermal stress on these parameters. Hence, European seabass juveniles (30–32 g) were exposed to temperatures of 20 °C, 23 °C, 26 °C, 29 °C, and 31 °C using a 28-day bioassay. It was noted that the fish showed better performance indices at 23 °C and 26 °C. However, fish reared at 20 °C showed intermediate growth, while the fish reared at 31 °C displayed poor performance with low survival rates. As the water temperature increased from 20 to 31 °C, the levels of glucose, cortisol, aspartate aminotransferase, and alanine aminotransferase in the fish blood also increased, suggesting that the fish were under stress. Furthermore, activities of superoxide dismutase (SOD) and catalase (CAT), as well as levels of malondialdehyde, increased significantly ( P  < 0.05) with the rise in the rearing temperature, particularly at 31 °C. This suggested that European seabass juveniles experienced oxidative stress. Additionally, the mRNA expression of SOD and CAT genes was upregulated at 31 °C compared to those reared at 23–26 °C. This high upregulation of both genes led to an increase in the secretion of SOD and CAT. Juveniles of European seabass raised in 31 °C for 28 days showed significant damage in the histological structure of their kidney, liver, and gills. In addition to fusion and blood congestion of secondary lamellae, the fish in this treatment (31 °C) displayed edema, epithelial lifting, and blood congestion of the gill epithelium. After 28 days, fish cultivated at 31 °C had sinusoid dilatation, hyperemia, and nuclear hypertrophy in their liver tissues. Furthermore, hyperemia, tubular necrosis, and severe glomerular congestion were observed in fish raised in water temperatures as high as 31 °C for 28 days. This study recommends farming European seabass at 23 °C and 26 °C, which were the optimum temperatures. By global warming due to climatic changes, water temperature may reach up to 31 °C or more, which will cause adverse effects on fish performance and increase the oxidative stress.

High saline groundwater is a potential source for expansion of inland mariculture, especially with increasing freshwater scarcity. This research evaluated the efficacy of using probiotics (EM®) as an aqueous water additive to groundwater on water quality, heavy metal (HM) removal, microbial load, growth performance, and physiological status of European seabass. Four treatments were applied in triplicate using an increasing dose of EM® in water: 0, 0.2, 0.4, and 0.6 mL/L, expressed as EM 0 , EM 0.2 , EM 0.4 , and EM 0.6 , respectively. Seabass larvae (0.353 ± 0.002 g/fish) were housed in 1000-L-1 fiberglass tanks (625 fish/tanks) filled with 36 ppt saline groundwater and fed an experimental diet (45.33/14.65, CP/CF) at 10% of their body weight for 60 days. The results showed that the administration of EM® significantly ( P  < 0.05) improved water quality by reducing total ammonia nitrogen and NH 3 levels as well as increased dissolved oxygen in a dose-dependent manner. Growth indices and feed utilization efficiency were improved in groups reared in EM® treated water. The addition of EM® resulted in a significant decrease ( P  < 0.05) of HM in culture water, accumulation in muscle and liver of seabass, along with reduction of serum cortisol level. Furthermore, fish in the EM®-treated groups showed a significant improvement in plasma antioxidants (total antioxidant capacity, catalase, and glutathione peroxidase) and immune markers (immunoglobulin, lysozyme) with healthier liver and intestines histological structural compared to the control group. In summary, adding EM® at levels of 0.2–0.4 mL/L can improve saline groundwater criteria, control pathogens and lessen HM accumulation, and improve fish performance and health status.