Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia (Oreochromis aureus)

Tilapias are very important to the world's aquaculture. As befitting fish of their tropical origin, their distribution, and culture practices are highly affected by low temperatures. In this study, we used genetic and genomic methodologies to reveal pathways involved in the response and tolerance of blue tilapia (Oreochromis aureus) to low temperature stress. Cold tolerance was characterized in 66 families of blue tilapia. Fish from cold-tolerant and cold-sensitive families were sampled at 24 and 12°C, and the transcriptional responses to low-temperature exposure were measured in the gills and liver by high-throughput mRNA sequencing. Four hundred and ninety four genes displayed a similar temperature-dependent expression in both tolerant and sensitive fish and in the two tissues, representing the core molecular response to low temperature exposure. KEGG pathway analysis of these genes revealed down-regulation of focal-adhesion and other cell-extracellular matrix (ECM) interactions, and up-regulation of proteasome and various intra-cellular proteolytic activities. Differential responses between cold-tolerant and cold-sensitive fish were found with genes and pathways that were up-regulated in one group and down-regulated in the other. This reverse response was characterized by genes involved in metabolic pathways such as glycolysis/gluconeogenesis in the gills and biosynthesis of amino-acids in the liver, with low temperature down-regulation in tolerant fish and up-regulation in sensitive fish

Effect of feed ingredients on nutrient digestibility, waste production and physical characteristics of rainbow trout (Oncorhynchus mykiss) faeces.

This study assessed the effect of different dietary ingredients on the quantity and characteristics of faecal waste produced by rainbow trout (Oncorhynchus mykiss). Seven ingredients were tested: fish meal (FM), mussel meal (MM), poultry meal wet rendered (PM-W) or dry rendered (PM-D), insect meal (IM), single cell protein (SCP) and brewers grain protein (BGP). Eight experimental diets were formulated: a control diet (CON) being predominantly plant-based and seven test diets, which contained 70% of the CON diet and 30% of one of the test ingredients. Rainbow trout juveniles (65 g, 30 fish/tank) were fed the experimental diets at satiation for six weeks in triplicate groups. Dry matter (DM) and nutrient digestibility of diets and the test ingredients were measured. To estimate the faecal characteristics, particle size distribution (PSD) and removal efficiency of the faecal waste was determined. Nutrient digestibility of diets and ingredients differed significantly. Growth did not differ between the experimental diets, but DM digestibility was affected by the diet. Diets affected the amount of faecal waste produced, its removal efficiency (%) and the amount of non-removed faeces (g DM/kg DM feed). The highest and lowest removal efficiency was observed at FM and BGP diets, respectively. Accordingly, FM diet resulted in the lowest (37 g DM/kg DM feed), while BGP diet resulted in the highest (125 g DM/kg DM feed) amount of non-removed faeces. Additionally, it was also observed that differences in faecal removal efficiency can compensate for the variation in the quantity of faecal waste produced. Consistent with the faecal removal efficiency data, faeces PSD was also influenced by diets. FM and MM diets resulted in faeces with the lowest proportion of particles of <40 μm size, while BGP diet had the largest proportion of faecal particles of this size range. Furthermore, the effect of dietary ingredient composition was evident in the stability of faeces, with FM producing the most stable, whereas CON, BGP and SCP diets resulting in relatively unstable faecal pellets. In addition, due to differences in inclusion level of nutrients and their corresponding digestibility, the chemical composition of faeces differed between the diets. Overall, the study showed that dietary ingredient composition influences nutrient digestibility and is an important factor determining the amount of faecal waste produced, its removal efficiency, PSD, stability and composition in rainbow trout.publishedVersio

Experimental infection model with the bivalvulid Enteromyxum leei (Myxidiidae) in the sharpsnout seabream, Diplodus puntazzo (Sparidae), and evaluation of the antiparasitic efficacy of a functional diet

An infection model for sharpsnout seabream Diplodus puntazzo (Walbaum) challenged with the myxosporean Enteromyxum leei (Diamant, Lom et Dykova, 1994), resembling the natural infection conditions, was used to evaluate the antiparasitic efficacy of a functional diet. Fish of an average weight of 12.5 ± 1.2 g were delivered either a functional (included as feed supplement at 0.3% levels) or a control extruded diet. After four weeks of administration of the experimental diets, fish were challenged with the parasites (cohabitation with infected donors; donor: recipient ratio 1: 1). The experiment was terminated four weeks after the start of the challenge. At the end of the experiment, growth and feeding (specific growth rate and feed efficiency), as well as immunological parameters (respiratory burst activity, antibacterial activities, hemoglobin concentration, anti-protease activity and ceruloplasmin activity) were measured along with cumulative mortality and total parasitic count in the gut. No significant difference was evident with regard to growth and feeding performance, mortality, gut parasitic load or immunological parameters as the parasitical challenge significantly affected both the performance of the control and functional diet fed fish. However, there was a less prominent impact on antibacterial, anti-protease and ceruloplasmin activity in fish fed with the functional diet. Overall, the present study validated the experimental cohabitation infection model and evaluated the efficacy of a functional ingredient as an antiparasitic agent, showing some potential effects on the fish immune response.This work was made possible through a H2020-SFS-2014-2015 project entitled: ParaFishControl: Advanced Tools and Research Strategies for Parasite Control in European farmed fish (grant agreement no: 634429)

Antibiotic effect and microbiome persistence vary along the European seabass gut

The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat diseases, with adverse implications on the environment, animal health and commensal microbes. Gut microbes are important for the host proper functioning, thus evaluating such impacts is highly crucial. Examining the antibiotic impact on gut segments with different physiological roles may provide insight into their effects on these microhabitats. Hence, we evaluated the effect of feed-administrated antibiotics on the composition and metabolic potential of the gut microbiome in the European seabass, an economically important aquaculture species. We used quantitative PCR to measure bacterial copy numbers, and amplicon sequencing of the 16S rRNA gene to describe the composition along the gut, after 7-days administration of two broad-range antibiotic mixtures at two concentrations. While positive correlation was found between antibiotic concentration and bacterial abundance, we showed a differential effect of antibiotics on the composition along the gut, highlighting distinct impacts on these microbial niches. Moreover, we found an increase in abundance of predicted pathways related to antibiotic-resistance. Overall, we show that a high portion of the European seabass gut microbiome persisted, despite the examined antibiotic intake, indicating high stability to perturbations

Effect of rearing systems and dietary probiotic supplementation on the growth and gut microbiota of Nile tilapia (Oreochromis niloticus) larvae

The establishment of the early-life gut microbiota plays an important role in fish development and influences the host's health status and growth performance. Different rearing conditions can impact the initial colonization of the gut microbiota, while the addition of probiotics may also affect such colonization. However, how this may affect fish larvae survival and growth remains largely unexplored. In this study, 3-day old Nile tilapia embryos were hatched until 9 days post fertilization (dpf) in three systems, including one flow-through system (FTS) and two identical recirculating aquaculture systems (RAS). When feeding started at 10 dpf, tilapia larvae in the FTS and one of the RAS were fed with a control diet, while larvae in the second RAS were fed with the control diet coated with B. subtilis spores (RASB). The feeding trial lasted 26 days, from larvae to fry stage, during which the survival, growth performance and gut microbiota were analyzed. The larvae reared in FTS showed significantly lower survival than those in RAS and RASB, while no differences were observed in fish growth and apparent feed conversion ratio between treatments. Different rearing systems resulted in different gut microbiota compositions, which strongly correlated with the survival rate and standard body length at harvest. Cetobacterium was enriched in RAS and RASB, while was barely detected in the gut of FTS-reared tilapia fry. Probiotic supplementation increased the relative abundance of beneficial Bacillus in fish gut. Our findings indicate that rearing fish larvae in RAS supports better survival compared to FTS, while dietary probiotic supplementation further modulates the gut bacterial composition and stimulates presence of beneficial bacteria during early life

Impact of early-life rearing history on gut microbiome succession and performance of Nile tilapia

BackgroundFish gut microbial colonisation starts during larval stage and plays an important role in host’s growth and health. To what extent first colonisation could influence the gut microbiome succession and growth in later life remains unknown. In this study, Nile tilapia embryos were incubated in two different environments, a flow-through system (FTS) and a biofloc system (BFS); hatched larvae were subsequently cultured in the systems for 14 days of feeding (dof). Fish were then transferred to one common recirculating aquaculture system (RAS1, common garden, 15–62 dof), followed by a growth trial in another RAS (RAS2, growth trial, 63–105 dof). In RAS2, fish were fed with two types of diet, differing in non-starch polysaccharide content. Our aim was to test the effect of rearing environment on the gut microbiome development, nutrient digestibility and growth performance of Nile tilapia during post-larvae stages.ResultsLarvae cultured in the BFS showed better growth and different gut microbiome, compared to FTS. After the common garden, the gut microbiome still showed differences in species composition, while body weight was similar. Long-term effects of early life rearing history on fish gut microbiome composition, nutrient digestibility, nitrogen and energy balances were not observed. Still, BFS-reared fish had more gut microbial interactions than FTS-reared fish. A temporal effect was observed in gut microbiome succession during fish development, although a distinct number of core microbiome remained present throughout the experimental period.ConclusionOur results indicated that the legacy effect of first microbial colonisation of the fish gut gradually disappeared during host development, with no differences in gut microbiome composition and growth performance observed in later life after culture in a common environment. However, early life exposure of larvae to biofloc consistently increased the microbial interactions in the gut of juvenile Nile tilapia and might possibly benefit gut health

Isolation of phaeobacter sp. From larvae of atlantic bonito (sarda sarda) in a mesocosmos unit, and its use for the rearing of european seabass larvae (dicentrarchus labrax l.)

The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p < 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p < 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions.</p

Growth performance and fatty acid tissue profile in gilthead seabream juveniles fed with different phospholipid sources supplemented in low-fish meal diets

The aim of the present study was to evaluate the phospholipid requirements for gilthead seabream, fed with low-fish meal diets. A 70-day feeding trial was performed to evaluate the dietary effects of marine versus plant-based phospholipid sources in low-fish meal diets on growth, body composition, liver, muscle and intestinal fatty acid profiles (polar and neutral), as well as liver morphology. Three levels of krill (marine) or soy lecithin (plant) as phospholipid source, at 0.53%, 1% and 2%, were supplemented in diets with 10% fish meal inclusion. The effects were compared to a high-fish meal diet (65%) as a positive control, and a low-fish meal diet without addition of phospholipids as a negative control. Growth, feed and protein efficiency parameters were improved by the addition of phospholipids in the low-fish meal diets, irrespective of the source, but all parameters were lower compared to the positive control. Krill phospholipid supplementation showed optimal results at 0.5% levels and soybean lecithin supplementation at 1% level. Significant differences by the phospholipid supplementation were found in both the neutral and polar lipid profile in the liver and muscle, while only in the neutral lipids in the intestine. Evaluation of liver histology indicated mild improvement of steatosis symptoms. Overall, our results indicate that phospholipid supplementation in low-fish meal diets can improve the growth and liver status in gilthead seabream juveniles

Dietary micronutrient supplementation in low fishmeal based diets for optimum growth and immune status of European sea bass (Dicentrarchus labrax) juveniles

The present study aimed to evaluate the optimal dietary micronutrient supplementation of plant-based diets for juvenile European sea bass. A 90-day feeding trial was performed, where fish were fed a high fishmeal (FM) based diet (62% DM; positive control) or low FM diets (12.5% FM and krill meal), supplemented with increasing levels of a micronutrient mixture (Nutrient Package, NP) consisting of vitamins, minerals and other micronutrients. The supplementation levels ranged from 0% (no supplementation, negative control) to 400%, where 100% supplementation level corresponded to the requirement levels recommended for other fish species. Fish growth and feed performance (SGR, DGI, FCR, PER) were significantly impaired at levels NP0 and NP25 compared to the FM control. Body Fe and Zn concentrations were positively affected by the graded levels of the NP, while Mn and Se concentrations remained stable. Growth parameters were particularly correlated to body Fe and Zn, while immune parameters were mainly correlated to body Zn. Significant immunosuppression was evidenced (concerning the respiratory burst activity) when low FM diets were not supplemented with NP. High inclusion levels of the NP showed a negative impact on lysozyme activity. Histological examinations did not reveal any significant effects on gills, gut and liver morphology. At identical NP supplementation level (50%), fish fed low and high FM diets showed similar growth and innate immunity suggesting that long-term feeding with plant-based diets do not significantly affect the fish when adequate minerals and vitamins supplementation is provided. Quadratic regression analysis showed that the inclusion of the NP between 260 and 300% improves growth and immune parameters of fish fed low-FM diets as well as Zn body incorporation. Overall, the present study suggested the positive impact of NP supplementation of PM-based diets on both fish growth and health but future NP could include less Mn, more Fe, closer to levels obtained in fish fed FM (245 mg·kg−1), and Zn at 122 mg·kg−1.</p