Hepatic gene expression profiles in juvenile rainbow trout (Oncorhynchus mykiss) fed fishmeal or fish oil-free diets

Hepatic transcriptome analyses of juvenile white bass (Morone chrysops) when fed diets where fish meal is partially or totally replaced by alternative protein sources

White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially-successful hybrid striped bass (M. chrysops ♂ x M. saxatilis ♀). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated the global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision™). Six isonitrogenous (40% protein), isolipidic (11%), and isocaloric (17.1 kJ/g) diets were formulated to meet the known nutrient and energy requirements of largemouth bass and hybrid striped bass using nutrient availability data for most of the dietary ingredients. One of the test diets consisted exclusively of plant protein sources. Juvenile white bass (40.2 g initial weight) were stocked into a flow-through aquaculture system (three tanks/diet; 10 fish/tank) and fed the test diets twice daily to satiation for 60 days. RNA sequencing and bioinformatic analyses revealed significant differentially expressed genes between all test diets when compared to fish meal control. A total of 1,260 differentially expressed genes were identified, with major ontology relating to cell cycle and metabolic processes as well as immune gene functions. This data will be useful as a resource for future refinements to moronid diet formulation, as marine fish meal becomes limiting and plant ingredients are increasingly added as a reliable protein source.

Long-term regulation of fat sensing in rainbow trout (Oncorhynchus mykiss) fed a vegetable diet from the first feeding: focus on free fatty acid receptors and their signalling

Taste plays a fundamental role in an animal’s ability to detect nutrients and transmits key dietary information to the brain, which is crucial for its growth and survival. Providing alternative terrestrial ingredients early in feeding influences the growth of rainbow trout (RT, Oncorhynchus mykiss). Thus, the present study aimed to assess the influence, via long-term feeding (from the first feeding to 8 months), of alternative plant ingredients (V diet for vegetable diet v. C diet for a control diet) in RT on the mechanism of fat sensing at the gustatory level. After the feeding trial, we studied the pathways of the fat-sensing mechanism in tongue tissue and the integrated response in the brain. To this end, we analysed the expression pattern of free fatty acid receptors (ffar) 1 and 2, markers of calcium-signalling pathways (phospholipase Cβ, Orai, Stim or Serca), the serotonin level (a key neurotransmitter in taste buds) and the expression pattern of appetite-regulating neuropeptides in the hypothalamus (central area of appetite regulation). The results revealed that the V diet modified the expression pattern of ffar1 and paralogs of ffar2 genes in tongue tissue, along with differential regulation of calcium-signalling pathways and a defect in serotonin level and brain turnover, without influencing neuropeptide expression. This study is the first to support that changes in feeding behaviour of RT fed a V diet could be due to the difference in nutrient sensing and a decrease in hedonic sensation. We revealed that RT have similar fat-detection mechanisms as mammals.

On the Compatibility of Fish Meal Replacements in Aquafeeds for Rainbow Trout. A Combined Metabolomic, Proteomic and Histological Study

The sustainable development of modern aquaculture must rely on a significant reduction of the fish meal (FM) used in aquafeed formulations. However, FM substitution with alternative ingredients in diets for carnivorous fish species often showed reduced nutrient absorption, significantly perturbed metabolisms, and histological changes at both hepatic and intestinal levels. In the present study, rainbow trout (Oncorhynchus mykiss) were fed three different experimental aquafeeds. A control diet with higher FM content (27.3%) than two test formulations in which FM was substituted with two more sustainable and promising alternatives: insect meal (Hermetia illucens larvae = 10.1%, FM = 11.6%) and poultry by-products meal (PBM = 14.8%; FM = 11.7%). Combined metabolomics and proteomics analyses of fish liver, together with histological examination of liver and intestine demonstrated that a well-balanced formulation of nutrients in the three diets allowed high metabolic compatibility of either substitution, paving the way for a deeper understanding of the impact of novel raw materials for the fish feed industry. Results show that the main metabolic pathways of nutrient absorption and catabolism were essentially unaltered by alternative feed ingredients, and also histological alterations were negligible. It is demonstrated that the substitution of FM with sustainable alternatives does not have a negative impact on fish metabolism, as long as the nutritional requirements of rainbow trout are fulfilled.

A plant-based diet differentially affects the global hepatic methylome in rainbow trout depending on genetic background

Replacing fish meal and oil in trout diets with plant-derived ingredients is a contemporary challenge to move towards more sustainable aquaculture practices. However, such dietary replacement causes hepatic metabolic changes that have not yet been elucidated. Here, we aimed to decipher the effect of a 100% plant-based diet on the hepatic global DNA methylation landscape in trout and assess whether changes depend on fish genetic background. We analysed the global methylome and the expression of DNA (de)methylation-related genes of three isogenic lines that exhibit similar growth when fed a marine resource-based diet (M diet), but differ in their responses to a plant-based diet (V diet). Our results revealed that the V diet induced a decrease in 5-cytosine combined with an increase in 5-hydroxymethylcytosine in two of the three analysed lines. For one of these 2 affected lines, when fed the M diet but at the same feed intake of the V diet (MR), no methylome differences were highlighted between M and MR or between MR and V-fed trout whereas for the other affected line, M fed trout displayed a divergent methylome profile from MR and V fed fish. DNA (de)methylation-related genes were also affected by the V or MR diets. Our findings showed that the global hepatic methylome of trout is affected by a V diet, depending on genetic background. This latter effect seems to be due to either a decreased feed intake alone or combined with the effect of the dietary composition per se.

Detection and Modulation of Olfactory Sensing Receptors in Carnivorous Rainbow Trout (Oncorhynchus mykiss) Fed from First Feeding with Plant-Based Diet

Sense of smell is mediated by diverse families of olfactory sensing receptors, conveying important dietary information, fundamental for growth and survival. The aim of this study was to elucidate the role of the sensory olfactory pathways in the regulation of feeding behavior of carnivorous rainbow trout (RT, Oncorhynchus mykiss), from first feeding until 8 months. Compared to a commercial diet, RT fed with a total plant-based diet showed drastically altered growth performance associated with feed intake from an early stage. Exhaustive examination of an RT genome database identified three vomeronasal type 1 receptor-like (ORA), 10 vomeronasal type 2 receptor-like (OLFC) and 14 main olfactory receptor (MOR) genes, all highly expressed in sensory organs, indicating their potential functionality. Gene expression after feeding demonstrated the importance in olfactory sensing perception of some OLFC (olfcg6) and MOR (mor103, -107, -112, -113, -133) receptor family genes in RT. The gene ora1a showed evidence of involvement in olfactory sensing perception for fish fed with a commercial-like diet, while ora5b, mor118, mor124 and olfch1 showed evidence of involvement in fish fed with a plant-based diet. Results indicated an impact of a plant-based diet on the regulation of olfactory sensing pathways as well as influence on monoaminergic neurotransmission in brain areas related to olfactory-driven behaviors. The overall findings suggest that feeding behavior is mediated through olfactory sensing detection and olfactory-driven behavior pathways in RT.

Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines

Within the context of a growing aquaculture production coupled with a plateau of the production in the main components of aquafeeds (fish oil and fishmeal), recent studies have typically focused on replacing these feedstuffs with terrestrial plant ingredients for cultured carnivorous aquatic species, such as rainbow trout (Oncorhynchus mykiss). Substitution rates without adverse effects have, however, reached their limit. One potential way forward would be to take advantage of the genetic variability that exists in the salmonid population. However, to date, little is known about the underlying molecular mechanisms responsible for this genetic variability. The aim of the present research was to understand why some genotypes are better able to utilize plant-based diets devoid of marine resources. In this regard, three isogenic lines of rainbow trout (R23h, AB1h, and A22h), with similar growth when fed marine resources-based diets and which differ greatly in their responses to a plant-based diet, were fed with either a complete plant-based diet (V diet) or a marine resources-based diet (M diet) since first-feeding. Fish traits and the hepatic transcriptome of these three genotypes were compared after 5 months of feeding. First, differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but instead due to differences in feed efficiency. The comparison of transcriptome profiles revealed 575 (R23h vs. AB1h), 1,770 (R23h vs. A22h), and 2,973 (AB1h vs. A22h) probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, R23h and AB1h fish, which were the least affected by the V diet, exhibited the highest growth. These results demonstrate that these fish were able to maintain a high level of energy production and protein synthesis. Moreover, these genotypes were also able to activate pathways linked to lipid and cholesterol metabolisms, such as the biosynthesis of long-chain polyunsaturated fatty acids. Finally, as previously, immunity seems to also play an important role in the ability of fish to use the V diet, and further studies are needed to understand the mechanisms by which immunity interacts with growth.

Adaptation of AMPK-mTOR-signal pathways and lipid metabolism in response to low- and high-level rapeseed meal diet in Chinese perch (Siniperca chuatsi)

It is well known that carnivorous fish cannot use plant-proteins efficiently. They affect lipid metabolism of fish and cause serious problems to fish health. The reasons for this deficiency of fish metabolism are not known well. Chinese perch, a carnivorous fish, can accept artificial diet after domestication and is also considered as a novel model of fish for nutrition studies. Therefore, the aim of this study was to explore the effect of fish meal replacement by low- or high-rapeseed meal on lipid and glucose metabolism of Chinese perch. Three experimental diets were formulated with 0, 10%, and 30% rapeseed meal, named as Control, RSL, and RSH groups, respectively. After 8-weeks of the feeding trial, the inhibition of growth and fat deposition were observed in Chinese perch fed with rapeseed meal diets compared to the control group. Fish fed with RSL diets showed decreased food intake, serum low density lipoprotein (LDL), phosphorylated Grb10 (P < 0.05), inhibited fatty acid (FA) transport (lipoprotein lipase (LPL)), and glycerol synthesis (phosphoenol pyruvate carboxykinase (PEPCK)) in the liver. In addition, fish fed with RSL diets were also inhibited FA synthesis (fatty acid synthase (FAS), sterol regulatory element binding protein 1 (SREBP1), and Acetyl-CoA carboxylase (ACC1)), lipid uptake (hepatic lipase (HL)), β-oxidation (carnitine palmitoyltransferase I (CPT1)), and glycerol synthesis (PEPCK) in the visceral adipose tissue. Fish fed with RSH diets showed phosphorylated AMPK, inhibited FA synthesis (SREBP1, ACC1, and FAS), while enhanced lipolysis (hormone-sensitive lipase (HSL)), and then reduced Acetyl-CoA pool. In turn, β-oxidation (peroxisome proliferator-activated receptor-a (PPARα) and CPT1) was inhibited, while glycolysis (glucose-6-phosphatase (G6PD) and pyruvate carboxylase (PC)) were enhanced, consequently the lipid accumulation was decreased in the liver. Fish were also inhibited lipid uptake (LPL), that caused inhibiting of FA synthesis (SREBP1), β-oxidation (CPT1), glycerol synthesis (PEPCK), and in turn improved lipolysis (HSL) in the visceral adipose tissue. Our study suggested that both RSL and RSH diets decreased lipid accumulation in Chinese perch; however, the mechanism of lipid metabolism was different. Fish accepted less diet in RSL group, which inhibited lipid metabolism in the liver and in the visceral adipose tissues, while fish in RSH group activated AMPK pathway, inhibited FA synthesis, and enhanced lipolysis, which reduced Acetyl-CoA pool in the liver. Subsequently, lipid uptake and metabolism were inhibited in the visceral adipose tissue of RSH fish.

Assessment of the efficacy of using taurine supplements to improve growth and feed utilization of juvenile starry flounder (Platichthys stellatus) given diets based on soy-protein

A feeding trial was conducted to assess the feasibility of supplementing taurine in soy-based diets for juvenile starry flounder Platichthys stellatus. The basal diet (Crude protein 66.5%, crude lipid 8.5%) was supplemented with 0 (control), 0.5%, 1.0%, 1.5%, 2.0% and 2.5% taurine to formulate six test diets. Each diet was fed to 40 juvenile fish (22.25 g) in triplicate tanks (120 L) attached to a sea water circulation-system. Fish were fed twice daily by hand to apparent satiation during the 56-d trial. At the end of the trial, fish were counted and weighed for the analyses of growth performance, diet utilization and survival after a 24-h fast. Blood, intestines and muscles were collected for the analyses of serum oxidation resistance, digestive enzymes and body compostion. Livers were collected from the remaining fish at 4 h post-feeding for metabolic enzymes analyses. The results showed that fish fed diets supplemented with 1.0–2.5% taurine grew from 22.25–22.26 g to 47.88–50.40 g with higher average weight gain (25.62–28.12 vs 23.07 g ), specific growth rate (1.37–1.46 vs 1.27%/d ), feed intake (1.04–1.06 vs 1.00%/d), protein efficiency (2.50–2.61 vs 2.44) and lower feed conversion rate (0.84–0.83 vs 0.89) than the control treatment. Diets supplemented with 1.5–2.5% taurine significantly elevated the activities of pepsin (2.47–2.55 vs 2.22, U mg⁻¹ prot), trypsin of distal intestine(14.55–15.24 vs 11.94, U mg⁻¹ prot), hepatic glucokinase (126.62–129.42 vs 105.56, U mg⁻¹ prot) and fatty acid synthetase (125.56-136.89 vs 108.45, U mg⁻¹ prot). All diets supplemented with taurine increased the activities of lipase (32.23–36.67 vs 29.53, U g⁻¹ prot) and trypsin (35.85–37.89 vs 33.54, U mg⁻¹ prot) of proximal intestine, hepatic aspartate transaminase (736.990–832.38 vs 699.24, U mg⁻¹ prot), alanine aminotransferase (477.40–551.86 vs 373.97, U mg⁻¹ prot) and glycogen synthase (2.16–2.59 vs 1.97, U mg⁻¹ prot), as well as serum superoxide dismutase (4.33–4.59 vs 4.07, U mg⁻¹ prot ) and glutathione peroxidase (42.23–50.25 vs 39.17, mol mg⁻¹ prot). Therefore, taurine supplementation benefits juvenile starry flounder growth, digestion, nutrients metabolism and oxidation resistance. The optimal taurine requirement for starry flounder is 1.75%, and the recommended supplementation level is at least 1.6% for maximizing growth of fish fed a low-fishmeal diet (13.6%).

Impact on cerebral function in rainbow trout fed with plant based omega-3 long chain polyunsaturated fatty acids enriched with DHA and EPA

Characterization and modulation of cerebral function by ω-3 long chain polyunsaturated fatty acids (ω-3 LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) enrichment in plant based-diet were studied in rainbow trout (Oncorhynchus mikyss). We hypothesized that ω-3 LC-PUFAs are involved in the regulation of cerebral function in fish. During nine weeks, we examined the growth performance of rainbow trout for three experimental plant based-diets containing distinct levels of EPA and DHA. Using RT-qPCR, we assessed mRNA genes related to feeding behavior regulated by the central nervous system of humans, rodents and fish. These include markers of neuropeptides, indicators of cellular specification, animal stress, oxidant status, cytokines and genes regulating animal behaviour. ω-3 LC-PUFAs enrichment decreased daily food intake and induced a simultaneous mRNA expression increase in orexigenic transcript npy peptide and a decrease in anorexigen transcript pomcA peptide in the hypothalamus. Overall transcript genes related to proinflammatory cytokines, inflammation, antioxidant status, cortisol pathway, serotoninergic pathways and dopaminergic pathways were down-regulated in the juveniles fed the high ω-3 LC-PUFAs diet. However, the mRNA expression of transcripts related to cell specification were down regulated, namely tmem119 markers of microglial cell in forebrain and midbrain, gfap markers of astrocyte in the midbrain, and rbfox3 markers of neurons in the midbrain and hindbrain in juveniles fed high ω-3 experimental diet. In conclusion, this study revealed that a diet rich in ω-3 LC-PUFAs affected a relatively high proportion of the brain function in juvenile rainbow trout through mechanisms comparable to those characterized previously in mammals.

Regulation of Dietary Lipid Sources on Tissue Lipid Classes and Mitochondrial Energy Metabolism of Juvenile Swimming Crab, Portunus trituberculatus

An 8-weeks feeding trial with swimming crab, Portunus trituberculatus, was conducted to investigate the effects of different dietary lipid sources on the lipid classes, lipid metabolism, and mitochondrial energy metabolism relevant genes expression. Six isonitrogenous and isolipidic experimental diets were formulated to contain fish oil (FO), krill oil (KO), palm oil (PO), rapeseed oil (RO), soybean oil (SO), and linseed oil (LO), respectively. A total of 270 swimming crab juveniles (initial weight 5.43 ± 0.03 g) were randomly divided into six diets with three replications, each consisted of 45 juvenile crabs. The results revealed that crabs fed KO had highest lipid content in hepatopancreas and free fatty acids in serum among all diets. The anabolic pathway relevant genes: fas and acc were up-regulated in KO diet. The catabolic pathway relevant genes, hsl, was up-regulated in LO diet, while cpt1 was up-regulated in KO diet. Whereas, the genes involved in the transport and uptake of fatty acids such as fabp1 and fatp4 were down-regulated in crab fed PO and RO diets. Furthermore, the gene expression levels of transcription factors: srebp-1 and hnf4α in KO and SO diets were the highest among all diets. FO and KO diets had significantly higher unsaturation index of mitochondrial membrane than others. The genes related to mitochondrial energy metabolism, such as Atpase6, sirt1, and sirt3 were significantly up-regulated in KO and SO diets. In summary, dietary KO and SO supplementation could improve the lipid metabolism, promote energy production for juvenile swimming crab and improve physiological process and function including molting. These findings could contribute to deepen the understanding of the physiological metabolism of dietary fatty acids for swimming crab.

Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

To meet the growing demand of fish feed for aquaculture, an increasing proportion of marine ingredients are being replaced by blends of plant products. However, the total replacement of marine ingredients in salmonid diets impairs fish performance. This is particularly true during the early fry stage and this stage is therefore considered of particular importance. In rainbow trout (RBT), the existence of a genetic variability to survive and grow with plant-based diets devoid of marine ingredients has now been proved, but the mechanisms behind are little studied especially at early stage. To investigate these, we analysed the whole transcriptome of three isogenic lines of RBT fry, which have similar growth when fed a marine resources-based diet (M diet) but which highly differ in their responses to a plant-based diet (V diet). Analysis of transcriptomes profiles revealed 1740, 1834 and 246 probes differentially expressed among the three genotypes when fed the V diet. The use of these lines led to the discovery of potential molecular markers linked to plant-based diet utilisation, some of them belonging to new pathways, never described before. An important number of genes was related to immunity, but further investigations are needed to better understand the difference between the genotypes in their immune status response to V diet exposure. Finally, differences in expression of genes related to feed intake and sensory perception among genotypes suggested that the mechanisms underlying the differences in growth on plant-based diet are closely linked to diet acceptance. Research on plants components affecting feed intake should be thus further explored.

Long-term dietary replacement of fishmeal and fish oil in diets for rainbow trout (Oncorhynchus mykiss): Effects on growth, whole body fatty acids and intestinal and hepatic gene expression

The effects of replacing fishmeal and fish oil with a plant-based diet were studied in juvenile (10g) and ongrowing (250-350g) rainbow trout from first-feeding. Feed-related differences in the intestinal and hepatic transcriptome were examined in juveniles after 7 months of feeding at 7°C. Based on microarray results obtained for juveniles, the expression of selected genes related to lipid, cholesterol and energy metabolisms, was assessed by RT-qPCR in ongrowing trout after 6 additional months of feeding at 17°C. Plasma glucose and cholesterol, lipid content and fatty acid profile of whole body were analyzed at both stages. After 7 months at 7°C, all juveniles reached the same body weight (10g), while at 13 months ongrowing fish fed the totally plant-based diet exhibited lower body weight (234 vs 330-337g). Body lipid content was higher in juveniles fed the totally plant-based diet (13.2 vs 9.4–9.9%), and plasma cholesterol was about 2-times lower in trout fed the plant-based diets at both stages. Fatty acid profile mirrored that of the respective diet, with low proportions of long-chain n-3 polyunsaturated fatty acids in fish fed plant-based diets. Genes involved in protein catabolism, carbohydrate metabolism and trafficking were down-regulated in the intestines of juveniles fed the plant-based diets. This was not true for ongrowing fish. Genes involved in lipid and cholesterol metabolisms were up-regulated in the livers of fish fed plant-based diets for both stages. In this study, feeding trout a totally plant-based diet from first-feeding affect a relatively low proportion of metabolism-related genes. In the longer term, when fish were reared at a higher temperature, only some of these changes were maintained (i.e. up-regulation of lipid/cholesterol metabolism). Although the plant-based diets tested in this study had no major deficiencies, small adjustments in the feed-formula are needed to further optimize growth performance while sparing marine resources.

Dietary DHA/EPA ratio affected tissue fatty acid profiles, antioxidant capacity, hematological characteristics and expression of lipid-related genes but not growth in juvenile black seabream (Acanthopagrus schlegelii)

An 8-week feeding trial was conducted to investigate the effects of dietary docosahexaenoic to eicosapentaenoic acid ratio (DHA/EPA) on growth performance, fatty acid profiles, antioxidant capacity, hematological characteristics and expression of some lipid metabolism related genes of juvenile black seabream (Acanthopagrus schlegelii) of initial weight 9.47 ± 0.03 g. Five isonitrogenous and isolipidic diets (45% crude protein and 14% crude lipid) were formulated to contain graded DHA/EPA ratios of 0.65, 1.16, 1.60, 2.03 and 2.67. There were no differences in growth performance and feed utilization among treatments. Fish fed higher DHA/EPA ratios had higher malondialdehyde (MDA) contents in serum than lower ratios. Serum triacylglycerol (TAG) content was significantly higher in fish fed the lowest DHA/EPA ratio. Tissue fatty acid profiles reflected the diets despite down-regulation of LC-PUFA biosynthesis genes, fatty acyl desaturase 2 (fads2) and elongase of very long-chain fatty acids 5 (elovl5), by high DHA/EPA ratios. Expression of acetyl-CoA carboxylase alpha (accα) and carnitine palmitoyl transferase 1A (cpt1a) were up-regulated by high DHA/EPA ratio, whereas sterol regulatory element-binding protein-1 (srebp-1) and hormone-sensitive lipase (hsl) were down-regulated. Fatty acid synthase (fas), 6-phosphogluconate dehydrogenase (6pgd) and peroxisome proliferator-activated receptor alpha (pparα) showed highest expression in fish fed intermediate (1.16) DHA/EPA ratio. Overall, this study indicated that dietary DHA/EPA ratio affected fatty acid profiles and significantly influenced lipid metabolism including LC-PUFA biosynthesis and other anabolic and catabolic pathways, and also had impacts on antioxidant capacity and hematological characteristics.

Dietary Lipid Sources Influence Fatty Acid Composition in Tissue of Large Yellow Croaker (Larmichthys crocea) by Regulating Triacylglycerol Synthesis and Catabolism at the Transcriptional Level

An 8-week feeding trial was conducted to evaluate the effects of dietary lipid sources on growth performance, fatty acid composition, rate-limiting enzyme activities and gene expression related to lipid metabolism in large yellow croaker (Larmichthys crocea). Five iso-nitrogenous and iso-lipidic experimental diets were formulated to contain different lipid sources, such as fish oil (FO), soybean oil (SO), linseed oil (LO), rapeseed oil (RO) and peanut oil (PO), respectively. Triplicate groups of 50 fish (initial weight 13.77±0.07g) were stocked in 15 floating net cages (1.5m×1.5m×2.0m). Fish fed the diets containing RO and LO had lower weight gain and specific growth rates than those fed the FO, SO and PO diets. Survival, feed efficiency, protein efficiency ratio, hepatosomatic index, viscerasomatic index and condition factor were not significantly affected by different dietary lipid sources. Fish fed the diet containing FO had higher lipid content in whole body compared with the other groups, whereas fish fed the SO diet had the lowest muscle lipid content. Fatty acid profiles of muscle and liver reflected the fatty acid composition of the diets. Plasma glucose, triglyceride, and the enzymatic activity of aspartate aminotransferase and alanine aminotransferase were significantly influenced by different dietary lipid sources, while total protein, cholesterol, superoxide dismutase or malondialdehyde in plasma were not affected by the different dietary lipid sources. Fish fed the LO diet had lower adipose triglyceride lipase and fatty acid synthase activities in liver than those fed the diets containing FO and RO, while the LO diet resulted in the highest hepatic carnitine palmitoultransferase-1 activity. Hepatic gene relative expression of adipose triglyceride lipase and carnitine palmitoyltransferase-1 in fish fed PO diet was significantly higher than all other groups, whereas fish fed the SO and LO diets had lower relative expression levels of lipoprotein lipase than the other groups. The highest relative expression levels of fatty acid synthase and acyl-CoA diacylglycerol acyltransferase-2 were observed in the FO group, while the highest relative expression of glucose 6-phosphate dehydrogenase occurred in fish fed the FO and RO diets. In summary, based on the growth performance, FO and SO appear to be suitable lipid sources for large yellow croaker, with the findings of this study also providing a molecular insight into the role of lipid metabolic mechanism in response to different dietary lipid sources.

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Background

The achievement of sustainable feeding practices in aquaculture by reducing the reliance on wild-captured fish, via replacement of fish-based feed with plant-based feed, is impeded by the poor growth response seen in fish fed high levels of plant ingredients. Our recent strategy to nutritionally program rainbow trout by early short-term exposure to a plant-based (V) diet versus a control fish-based (M) diet at the first-feeding fry stage when the trout fry start to consume exogenous feed, resulted in remarkable improvements in feed intake, growth and feed utilization when the same fish were challenged with the diet V (V-challenge) at the juvenile stage, several months following initial exposure. We employed microarray expression analysis at the first-feeding and juvenile stages to deduce the mechanisms associated with the nutritional programming of plant-based feed acceptance in trout.

Results

Transcriptomic analysis was performed on rainbow trout whole fry after 3 weeks exposure to either diet V or diet M at the first feeding stage (3-week), and in the whole brain and liver of juvenile trout after a 25 day V-challenge, using a rainbow trout custom oligonucleotide microarray. Overall, 1787 (3-week + Brain) and 924 (3-week + Liver) mRNA probes were affected by the early-feeding exposure. Gene ontology and pathway analysis of the corresponding genes revealed that nutritional programming affects pathways of sensory perception, synaptic transmission, cognitive processes and neuroendocrine peptides in the brain; whereas in the liver, pathways mediating intermediary metabolism, xenobiotic metabolism, proteolysis, and cytoskeletal regulation of cell cycle are affected. These results suggest that the nutritionally programmed enhanced acceptance of a plant-based feed in rainbow trout is driven by probable acquisition of flavour and feed preferences, and reduced sensitivity to changes in hepatic metabolic and stress pathways.

Conclusions

This study outlines the molecular mechanisms in trout brain and liver that accompany the nutritional programming of plant-based diet acceptance in trout, reinforces the notion of the first-feeding stage in oviparous fish as a critical window for nutritional programming, and provides support for utilizing this strategy to achieve improvements in sustainability of feeding practices in aquaculture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2804-1) contains supplementary material, which is available to authorized users.

Regulation of glucose and lipid metabolism by dietary carbohydrate levels and lipid sources in gilthead sea bream juveniles

The long-term effects on growth performance, body composition, plasma metabolites, liver and intestine glucose and lipid metabolism were assessed in gilthead sea bream juveniles fed diets without carbohydrates (CH–) or carbohydrate-enriched (20 % gelatinised starch, CH+) combined with two lipid sources (fish oil; or vegetable oil (VO)). No differences in growth performance among treatments were observed. Carbohydrate intake was associated with increased hepatic transcripts of glucokinase but not of 6-phosphofructokinase. Expression of phosphoenolpyruvate carboxykinase was down-regulated by carbohydrate intake, whereas, unexpectedly, glucose 6-phosphatase was up-regulated. Lipogenic enzyme activities (glucose-6-phosphate dehydrogenase, malic enzyme, fatty acid synthase) and ∆6 fatty acyl desaturase (FADS2) transcripts were increased in liver of fish fed CH+ diets, supporting an enhanced potential for lipogenesis and long-chain PUFA (LC-PUFA) biosynthesis. Despite the lower hepatic cholesterol content in CH+ groups, no influence on the expression of genes related to cholesterol efflux (ATP-binding cassette G5) and biosynthesis (lanosterol 14α-demethylase, cytochrome P450 51 cytochrome P450 51 (CYP51A1); 7-dehydrocholesterol reductase) was recorded at the hepatic level. At the intestinal level, however, induction of CYP51A1 transcripts by carbohydrate intake was recorded. Dietary VO led to decreased plasma phospholipid and cholesterol concentrations but not on the transcripts of proteins involved in phospholipid biosynthesis (glycerol-3-phosphate acyltransferase) and cholesterol metabolism at intestinal and hepatic levels. Hepatic and muscular fatty acid profiles reflected that of diets, despite the up-regulation ofFADS2transcripts. Overall, this study demonstrated that dietary carbohydrates mainly affected carbohydrate metabolism, lipogenesis and LC-PUFA biosynthesis, whereas effects of dietary lipid source were mostly related with tissue fatty acid composition, plasma phospholipid and cholesterol concentrations, and LC-PUFA biosynthesis regulation. Interactions between dietary macronutrients induced modifications in tissue lipid and glycogen content.

Does broodstock nutritional history affect the response of progeny to different first-feeding diets? A whole-body transcriptomic study of rainbow trout alevins

The whole-body transcriptome of trout alevins was characterised to investigate the effects of long-term feeding of rainbow trout broodstock females a diet free of fishmeal and fish oil on the metabolic capacities of progeny. Effects were studied before first feeding and after 3 weeks of feeding diets containing different proportions of marine and plant ingredients. Feeding alevins plant-based diets resulted in lower fish body weight, irrespective of maternal nutritional history. No differences in whole-body lipids were found between treatments, and the tissue fatty acid profile strongly reflected that of the respective broodstock or first-feeding diets. We showed that the maternal diet history did not significantly affect expressions of any genes before the first feeding. Interestingly, we found an effect of maternal nutritional history on gene expression in alevins after 3 weeks of feeding. The major differences in the transcriptome of alevins from plant-based diet-fed females compared with those from commercial-fed females were as follows: (i) down-regulation of genes involved in muscle growth/contraction and (ii) up-regulation of genes involved in carbohydrate and energy metabolism related to the delay in growth/development observed with plant-based diets. Our findings also showed an effect of the first-feeding diets, irrespective of maternal nutritional history. Specifically, the introduction of plant ingredients resulted in the up-regulation of genes involved in amino acid/protein and cholesterol metabolism and in differences in the expressions of genes related to carbohydrate metabolism. Information gained through this study opens up avenues for further reduction of marine ingredients in trout diets, including the whole rearing cycle.

Long-term feeding a plant-based diet devoid of marine ingredients strongly affects certain key metabolic enzymes in the rainbow trout liver

Incorporation of a plant blend in the diet can affect growth parameters and metabolism in carnivorous fish. We studied for the first time the long-term (1 year) metabolic response of rainbow trout fed from first feeding with a plant-based diet totally devoid of marine ingredients. Hepatic enzymes were analyzed at enzymatic and molecular levels, at 3, 8 and 24 h after the last meal to study both the short-term effects of the last meal and long-term effects of the diet. The results were compared with those of fish fed a control diet of fish meal and fish oil. Growth, feed intake, feed efficiency and protein retention were lower in the group fed the plant-based diet. Glucokinase and pyruvate kinase activity were lower in the livers of trout fed the plant-based diet which the proportion of starch was lower than in the control diet. Glutamate dehydrogenase was induced by the plant-based diet, suggesting an imbalance of amino acids and a possible link with the lower protein retention observed. Gene expression of delta 6 desaturase was higher in fish fed the plant-based diet, probably linked to a high dietary level of linolenic acid and the absence of long-chain polyunsaturated fatty acids in vegetable oils. Hydroxymethylglutaryl-CoA synthase expression was also induced by plant-based diet because of the low rate of cholesterol in the diet. Changes in regulation mechanisms already identified through short-term nutritional experiments (<12 weeks) suggest that metabolic responses are implemented at short term and remain in the long term.

Dietary carbohydrate and lipid source affect cholesterol metabolism of European sea bass (Dicentrarchus labrax) juveniles

Plant feedstuffs (PF) are rich in carbohydrates, which may interact with lipid metabolism. Thus, when considering dietary replacement of fishery by-products with PF, knowledge is needed on how dietary lipid source (LS) and carbohydrates affect lipid metabolism and other metabolic pathways. For that purpose, a 73-d growth trial was performed with European sea bass juveniles (IBW 74 g) fed four diets differing in LS (fish oil (FO) or a blend of vegetable oils (VO)) and carbohydrate content (0 % (CH-) or 20 % (CH+) gelatinised starch). At the end of the trial no differences among diets were observed on growth and feed utilisation. Protein efficiency ratio was, however, higher in the CH+ groups. Muscle and liver fatty acid profiles reflected the dietary LS. Dietary carbohydrate promoted higher plasma cholesterol and phospholipids (PL), whole-body and hepatic (mainly 16 : 0) lipids and increased muscular and hepatic glycogen. Except for PL, which were higher in the FO groups, no major alterations between FO and VO groups were observed on plasma metabolites (glucose, TAG, cholesterol, PL), liver and muscle glycogen, and lipid and cholesterol contents. Activities of glucose-6-phosphate dehydrogenase and malic enzyme - lipogenesis-related enzymes - increased with carbohydrate intake. Hepatic expression of genes involved in cholesterol metabolism was up-regulated with carbohydrate (HMGCR and CYP3A27) and VO (HMGCR and CYP51A1) intake. No dietary regulation of long-chain PUFA biosynthesis at the transcriptional level was observed. Overall, very few interactions between dietary carbohydrates and LS were observed. However, important insights on the direct relation between dietary carbohydrate and the cholesterol biosynthetic pathway in European sea bass were demonstrated.

Transcriptome analysis of grass carp (Ctenopharyngodon idella) fed with animal and plant diets

Numerous studies have been focused on the replacement of fish meal by other alternative protein sources. However, little is currently known about the molecular mechanism of utilization of diets with different protein sources in fish. Grass carp is a typical herbivorous fish. To elucidate the relationship between gene expression and utilization of animal and plant diets, transcriptome sequencing was performed in grass carp fed with chironomid larvae and duckweed. Grass carp fed with duckweed had significantly higher relative length of gut than those fed with chironomid larvae. 4435 differentially expressed genes were identified between grass carp fed with chironomid larvae and duckweed in brain, liver and gut, involved in cell proliferation and differentiation, appetite control, circadian rhythm, digestion and metabolism pathways. These pathways might play important roles in utilization of diets with different protein sources in grass carp. And the findings could provide a new insight into the replacement of fish meal in artificial diets.

New insights into the nutritional regulation of gluconeogenesis in carnivorous rainbow trout (Oncorhynchus mykiss): a gene duplication trail

The rainbow trout (Oncorhynchus mykiss) is considered to be a strictly carnivorous fish species that is metabolically adapted for high catabolism of proteins and low utilization of dietary carbohydrates. This species consequently has a "glucose-intolerant" phenotype manifested by persistent hyperglycemia when fed a high-carbohydrate diet. Gluconeogenesis in adult fish is also poorly, if ever, regulated by carbohydrates, suggesting that this metabolic pathway is involved in this specific phenotype. In this study, we hypothesized that the fate of duplicated genes after the salmonid-specific 4th whole genome duplication (Ss4R) may have led to adaptive innovation and that their study might provide new elements to enhance our understanding of gluconeogenesis and poor dietary carbohydrate use in this species. Our evolutionary analysis of gluconeogenic genes revealed that pck1, pck2, fbp1a, and g6pca were retained as singletons after Ss4r, while g6pcb1, g6pcb2, and fbp1b ohnolog pairs were maintained. For all genes, duplication may have led to sub- or neofunctionalization. Expression profiles suggest that the gluconeogenesis pathway remained active in trout fed a no-carbohydrate diet. When trout were fed a high-carbohydrate diet (30%), most of the gluconeogenic genes were non- or downregulated, except for g6pbc2 ohnologs, whose RNA levels were surprisingly increased. This study demonstrates that Ss4R in trout involved adaptive innovation via gene duplication and via the outcome of the resulting ohnologs. Indeed, maintenance of ohnologous g6pcb2 pair may contribute in a significant way to the glucose-intolerant phenotype of trout and may partially explain its poor use of dietary carbohydrates.

Three-year breeding cycle of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet, totally free of marine resources: consequences for reproduction, fatty acid composition and progeny survival

Terrestrial plant resources are increasingly used as substitutes for fish meal and fish oil in fish feed in order to reduce the reliance of aquaculture on marine fishery resources. Although many studies have been conducted to assess the effects of such nutritional transition, no whole breeding cycles of fish fed diets free from marine resources has been reported to date. We therefore studied the reproductive performance of trout after a complete cycle of breeding while consuming a diet totally devoid of marine ingredients and thus of n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs) that play a major role in the formation of ova. Two groups of female rainbow trout were fed from first feeding either a commercial diet (C, marine and plant ingredients), or a 100% plant-based diet (V, blend of plant proteins and vegetable oils). Livers, viscera, carcasses and ova were sampled at spawning and analyzed for lipids and fatty acids. Although the V-diet was devoid of n-3 LC-PUFAs, significant amounts of EPA and DHA were found in livers and ova, demonstrating efficient bioconversion of linolenic acid and selective orientation towards the ova. Some ova were fertilized to assess the reproductive performance and offspring survival. We observed for the first time that trout fed a 100% plant-based diet over a 3-year breeding cycle were able to produce ova and viable alevins, although the ova were smaller. The survival of offspring from V-fed females was lower (-22%) at first spawning, but not at the second. Our study showed that, in addition to being able to grow on a plant-based diet, rainbow trout reared entirely on such a diet can successfully produce ova in which neo-synthesized n-3 LC-PUFAs are accumulated, leading to viable offspring. However, further adjustment of the feed formula is still needed to optimize reproductive performance.

Atlantic salmon (Salmo salar) liver transcriptome response to diets containing Camelina sativa products

Due to increasing demand for fish oil (FO) and fish meal (FM) in aquafeeds, more sustainable alternatives such as plant-derived oils and proteins are needed. Camelina sativa products are viable feed ingredients given the high oil and crude protein content in the seed. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial [Control diet: FO; Test diets: 100% CO replacement of FO (100CO), or 100CO with solvent-extracted FM (100COSEFM), 10% CM (100CO10CM), or SEFM+10% CM (100COSEFM10CM)]. Diet composition, growth, and fatty acid analyses for this feeding trial were published previously. A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to controls, yielding 67 differentially expressed features (FDR<5%). Ten microarray-identified genes [cpt1, pcb, bar, igfbp-5b (2 paralogues), btg1, dnph1, lect-2, clra, klf9, and fadsd6a], and three additional genes involved in lipid metabolism [elovl2, elovl5 (2 paralogues), and fadsd5], were subjected to QPCR with liver templates from all 5 dietary treatments. Of the microarray-identified genes, only bar was not QPCR validated. Both igfbp-5b paralogues were significantly down-regulated, and fadsd6a was significantly up-regulated, in all 4 camelina-containing diet groups compared with controls. Multivariate statistics were used to correlate hepatic desaturase and elongase gene expression data with tissue fatty acid profiles, indicating the involvement of these genes in LC-PUFA biosynthesis. This nutrigenomic study provides molecular biomarkers for use in developing novel aquafeeds using camelina products.

Microarray analysis of hepatic gene expression in juvenile Japanese flounder Paralichthys olivaceus fed diets supplemented with fish or vegetable oils

Gene expression profiling was performed in Japanese flounder Paralichthys olivaceus fed diets supplemented with fish oil (FO), linseed oil (LO), or olive oil (OO) for 6 weeks. The LO and OO groups showed significantly retarded growth, lower feed intake, lower protein efficiency ratio, and lower hepatosomatic index (P < 0.05). Liver fatty acid composition reflected the dietary fatty acid composition. Microarray analysis revealed that dietary n - 3 highly unsaturated fatty acid (HUFA) deficiency affected 169 transcripts. In the LO group, 57 genes were up-regulated and 38 genes were down-regulated, whereas in the OO group nine genes were up-regulated and 87 genes were down-regulated. Analysis of the functional annotations suggested that dietary n - 3 HUFA affected genes involved in signal transduction (23.2 %), cellular processes (21.1 %), metabolism (including glucose, lipid, and nucleobase; 15.5 %), transport (11.3 %), regulation of transcription (10.5 %), and immune response (4.2 %). Several genes encoding serine/threonine kinases such as protein kinase C and calmodulin-dependent kinase and nuclear hormone receptors such as vitamin D receptor, retinoic acid receptor, and receptors for cytokines (bone morphogenic protein and transforming growth factor β) were affected. Among 169 transcripts, 22 genes were affected in both LO and OO groups. The present study identified several genes involved in n - 3 HUFA deficiency-sensitive pathways, which will be useful for selective breeding of flounder strains able to adapt to n - 3 HUFA deficiency.

Metabolism and fatty acid profile in fat and lean rainbow trout lines fed with vegetable oil: effect of carbohydrates

The present study investigated the effect of dietary carbohydrates on metabolism, with special focus on fatty acid bioconversion and flesh lipid composition in two rainbow trout lines divergently selected for muscle lipid content and fed with vegetable oils. These lines were chosen based on previously demonstrated potential differences in LC-PUFA synthesis and carbohydrate utilization. Applying a factorial study design, juvenile trout from the lean (L) and the fat (F) line were fed vegetable oil based diets with or without gelatinised starch (17.1%) for 12 weeks. Blood, liver, muscle, intestine and adipose tissue were sampled after the last meal. Feed intake and growth was higher in the L line than the F line, irrespective of the diet. Moderate postprandial hyperglycemia, strong induction of hepatic glucokinase and repressed glucose-6-phosphatase transcripts confirmed the metabolic response of both lines to carbohydrate intake. Further at the transcriptional level, dietary carbohydrate in the presence of n-3 LC-PUFA deficient vegetable oils enhanced intestinal chylomicron assembly, disturbed hepatic lipid metabolism and importantly elicited a higher response of key desaturase and elongase enzymes in the liver and intestine that endorsed our hypothesis. PPARγ was identified as the factor mediating this dietary regulation of fatty acid bioconversion enzymes in the liver. However, these molecular changes were not sufficient to modify the fatty acid composition of muscle or liver. Concerning the genotype effect, there was no evidence of substantial genotypic difference in lipid metabolism, LC-PUFA synthesis and flesh fatty acid profile when fed with vegetable oils. The minor reduction in plasma glucose and triglyceride levels in the F line was linked to potentially higher glucose and lipid uptake in the muscle. Overall, these data emphasize the importance of dietary macro-nutrient interface in evolving fish nutrition strategies.

Growth response and expression of muscle growth-related candidate genes in adult zebrafish fed plant and fishmeal protein-based diets

The main objective of this study was to examine the effects of a plant protein- vs. fishmeal-based diet on growth response in a population of 24 families, as well as expression of growth-related genes in the muscle of adult zebrafish (Danio rerio). Each family was split to create two fish populations with similar genetic backgrounds, and the fish were fed either fishmeal (FM diet) or plant protein (PP diet) as the unique protein source in their diets from 35 to 98 days postfertilization (dpf). To understand the effect of the PP diet on gene expression, individuals from three families, representative of the mean weight in both populations, were selected. To understand the effect of familiar variation on gene expression, the same families were evaluated separately. At 98 dpf, growth-related genes Igf1a, Igf2a, mTOR, Pld1a, Mrf4, Myod, Myogenin, and Myostatin1b were evaluated. In males, Myogenin, Mrf4, and Igf2a showed changes attributable to the PP diet. In females, the effect of the PP diet did not modulate the expression in any of the eight genes studied. The effect of familiar variation on gene expression was observed among families. This study shows that PP diet and family variation have effects on gene expression in fish muscle.

Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar)

Background

Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in maintaining body homeostasis and health, its molecular response to replacement of dietary FO by VO has been little investigated. This study employed transcriptomic and proteomic analyses to study effects of dietary VO in two family groups of Atlantic salmon selected for flesh lipid content, 'Lean' or 'Fat'.

Results

Metabolism, particularly of lipid and energy, was the functional category most affected by diet. Important effects were also measured in ribosomal proteins and signalling. The long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis pathway, assessed by fatty acid composition and gene expression, was influenced by genotype. Intestinal tissue contents of docosahexaenoic acid were equivalent in Lean salmon fed either a FO or VO diet and expression of LC-PUFA biosynthesis genes was up-regulated in VO-fed fish in Fat salmon. Dietary VO increased lipogenesis in Lean fish, assessed by expression of FAS, while no effect was observed on β-oxidation although transcripts of the mitochondrial respiratory chain were down-regulated, suggesting less active energetic metabolism in fish fed VO. In contrast, dietary VO up-regulated genes and proteins involved in detoxification, antioxidant defence and apoptosis, which could be associated with higher levels of polycyclic aromatic hydrocarbons in this diet. Regarding genotype, the following pathways were identified as being differentially affected: proteasomal proteolysis, response to oxidative and cellular stress (xenobiotic and oxidant metabolism and heat shock proteins), apoptosis and structural proteins particularly associated with tissue contractile properties. Genotype effects were accentuated by dietary VO.

Conclusions

Intestinal metabolism was affected by diet and genotype. Lean fish may have higher responsiveness to low dietary n-3 LC-PUFA, up-regulating the biosynthetic pathway when fed dietary VO. As global aquaculture searches for alternative oils for feeds, this study alerts to the potential of VO introducing contaminants and demonstrates the detoxifying role of intestine. Finally, data indicate genotype-specific responses in the intestinal transcriptome and proteome to dietary VO, including possibly structural properties of the intestinal layer and defence against cellular stress, with Lean fish being more susceptible to diet-induced oxidative stress.

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

Background

Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax).

Results

We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies.

Conclusions

Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies.

Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non-model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development.

Dietary lipid levels have a remarkable impact on the expression of growth-related genes in Senegalese sole (Solea senegalensis Kaup)

In Senegalese sole (Solea senegalensis Kaup), growth is negatively correlated to dietary lipid levels. To understand the molecular basis of this effect a molecular toolbox of 12 genes, including fgf6, fst, mstn1, myf5, mrf4, myod1, myod2, myog, myHC, mylc2, igf1r and insr, was developed. The expression profiles of these genes were investigated in white muscle and liver of fish fed with three dietary lipid levels (4%, 12% and 20%). The expression of igf-I and igf-II was also examined. MRFs and myosins were only expressed in the muscle and, except for myf5, the general trend was a decrease in expression with an increase in dietary lipids. Fgf6 was identified for the first time in liver and its expression augmented in hepatic tissues with increasing dietary lipid levels. A similar tendency was observed for mstn1 and igf-I. The opposite was observed for igf1r expression in muscle and liver. Myog, mrf4, mylc2 and igf1r were highly correlated with growth and nutrient utilisation indices. In addition to its practical implications, this work provides a valuable contribution towards our understanding of the genetic networks controlling growth in teleosts.

Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.)

Background

Selection programs for growth and stress traits in cultured fish are fundamental to the improvement of aquaculture production. The gilthead sea bream (Sparus aurata) is the main aquacultured species in the Mediterranean area and there is considerable interest in the genetic improvement of this species. With the aim of increasing the genomic resources in gilthead sea bream and identifying genes and mechanisms underlying the physiology of the stress response, we developed a cDNA microarray for gilthead sea bream that is enriched by suppression substractive hybridization with stress and immunorelevant genes. This microarray is used to analyze the dynamics of gilthead sea bream liver expression profile after confinement exposure.

Results

Groups of confined and control juvenile fish were sampled at 6, 24, 72 and 120 h post exposure. GeneSpring analyses identified 202 annotated genes that appeared differentially expressed at least at one sampling time (P < 0.05). Gene expression results were validated by quantitative PCR of 10 target genes, and K-means clustering of differently expressed genes identified four major temporal gene expression profiles. Set 1 encompassed a rapid metabolic readjustment with enhanced uptake and intracellular transport of fatty acids as metabolic fuels. Set 2 was associated with a wide variety of tissue repair and remodeling processes that were mostly mediated by the stress response of the endoplasmic reticulum (ER). Sets 3 and 4 encompassed the re-establishment of cellular homeostasis with increased intracellular trafficking and scavenging of reactive oxygen species (ROS), accompanied by a bidirectional regulation of the immune system and a general decline of ROS production.

Conclusions

Collectively, these findings show the complex nature of the adaptive stress response with a clear indication that the ER is an important control point for homeostatic adjustments. The study also identifies metabolic pathways which could be analyzed in greater detail to provide new insights regarding the transcriptional regulation of the stress response in fish.

Endosulfan in vitro toxicity in Atlantic salmon hepatocytes obtained from fish fed either fish oil or vegetable oil

The composition of the feed may alter the cellular composition of an organism and thus has the potential to influence a xenobiotic response. The main aim of this study was to see if the fatty acid composition of primary hepatocytes isolated from Atlantic salmon (Salmo salar L.) obtained from fish fed either a fish oil or a vegetable oil based diet, influenced the response to endosulfan exposure in vitro. The primary cultures were exposed to six different concentrations of endosulfan (0.001, 0.01, 0.1, 1, 10 and 100 microM) for 48 h. Cell morphology as well as a molecular toolbox of 16 genes encoding stress responsive and biotransformation proteins was examined. Endosulfan exposure caused moderate cytotoxicity and steatosis in a dose-dependent manner in the hepatocytes. In general, endosulfan hepatoxicity seems to be unaffected by the fatty acid composition of the hepatocytes. Exceptions were general stress (HSP70) and markers for estrogen exposure (ZP and VTG), which appeared to be slightly less responsive in hepatocytes isolated from the vegetable oil fed fish.

Hepatic protein kinase B (Akt)-target of rapamycin (TOR)-signalling pathways and intermediary metabolism in rainbow trout (Oncorhynchus mykiss) are not significantly affected by feeding plant-based diets

The aim of the present study was to analyse the effects of partial or total replacement of fish meal (FM) and fish oil (FO) by a mixture of plant protein (PP) and a mixture of vegetable oils (VO) on the hepatic insulin-nutrient-signalling pathway and intermediary metabolism-related gene expression in rainbow trout (Oncorhynchus mykiss). Triplicate groups of fish were fed four practical diets containing graded levels of replacement of FM and FO by PP and VO for 12 weeks: diet 0/0 (100 % FM, 100 % FO); diet 50/50 (50 % FM and 50 % PP, 50 % FO and 50 % VO); diet 50/100 (50 % FM and 50 % PP, 100 % VO); diet 100/100 (100 % PP, 100 % VO). Samplings were performed on trout starved for 5 d then refed with their allocated diet. In contrast to partial substitution (diet 50/50), total substitution of FM and FO (diet 100/100) led to significantly lower growth compared with diet 0/0. The insulin-nutrient-signalling pathway (protein kinase B (Akt), target of rapamycin (TOR), S6 protein kinase 1 (S6K1) and S6) was characterised in trout liver and found to be activated by refeeding. However, changes in diet compositions did not differentially affect the Akt-TOR-signalling pathway. Moreover, expression of genes encoding fructose-1,6-biphosphatase, mitochondrial phosphoenolpyruvate carboxykinase, glucokinase, pyruvate kinase and carnitine palmitoyl transferase 1 were not affected by refeeding or by dietary changes. Refeeding down- and up-regulated the expression of gluconeogenic glucose-6-phosphatase isoform 1 and lipogenic fatty acid synthase genes, respectively. Expression of both genes was also increased with partial replacement of FM and total replacement of FO (diet 50/100). These findings indicate that plant-based diets barely affect glucose and lipid metabolism in trout.