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

Oleic acid enriched diet affects the metabolome composition of the hybrid grouper infected with vibriosis

This study focuses in investigating the fatty acid contents of surviving infected hybrid grouper fed with oleic acid immunostimulant. After a 6-week feeding trial, Epinephelus fuscoguttatus × Epinephelus lanceolatus fingerlings were infected with Vibrio vulnificus. One week after bacterial challenge, fish oil was extracted from body tissue of surviving infected fingerlings using the Soxhlet extraction method. The extracted samples were then sent for GC-MS analysis. The raw GC-MS data were analyzed using software programs and databases (i.e., MetaboAnalyst, SIMCA-P, NIST Library, and KEGG). A total of 39 metabolites were putatively identified, with 18 metabolites derived from the fatty acid group. Our further analysis revealed that most metabolites were highly abundant in the oleic acid dietary samples, including oleic acid (4.56%), 5,8,11-eicosatrienoic acid (3.45%), n-hexadecenoic acid (3.34%), cis-erucic acid (2.76%), and 9-octadecenoic acid (2.5%). Worthy of note, we observed a greater abundance of α-linoleic acid (15.57%) in the control diet samples than in the oleic acid diet samples (14.59%) with no significant difference in their results. The results obtained from this study revealed that surviving infected hybrid grouper expressed more immune-related fatty acids due to the effect of oleic acid immunostimulant. Therefore, in this study, we propose oleic acid as a potential immunostimulant in enhancing fish immunity in aquaculture industry.

Growth performance, health status, gut microbiome, and expression of immune and growth-related genes of rainbow trout (Oncorhynchus mykiss) fed diets with pea protein replacement of fish meal

The need for fish meal constrains fish farming and significantly impacts sustainability of the aquaculture industry. Hence, it is important to investigate the use of plant-based protein sources in fish diets. The present study was conducted to determine the effects of different levels of fish meal (FM) replacement by pea protein (PP) in a 60-day feeding experiment in rainbow trout, Oncorhynchus mykiss. Effects on growth performance, body composition, hematology, serum biochemistry and immunology, and immune (TNF-α, IL1-ß and Il-8) and growth-related (GH and IGFI) gene expression were investigated. Five experimental diets (45% protein and 20% lipid) differed in replacement level of FM by PP at rates of 0% (control (PP0)), 25% (PP25), 50%(PP50), 75%(PP75) and 100%(PP100). Fish were fed with experimental diets in triplicate twice daily. The best growth performance was obtained in PP0 and PP25 groups. While fat ratios of fish fillets significantly differed (p < 0.05), there was no significant effects on protein ratios (p < 0.05). There was no significant change in the hematological values of fish, except those fed the PP100 diets, which displayed a reduction in eyrthocyte counts, hemoglobin content and hematocrit. As PP supplementation increased fish showed elevated serum glucose, total protein, cholesterol and myeloperoxidase activity and decreased glutamic pyruvic transaminase and alkaline phosphatase activity. Fish fed diets with between 25 and 75% replacement showed a decline in lactic acid bacteria in the gut. Significant increases in expression were observed in the liver of the PP25 fish relative to the 0% control for all immune and growth-related genes except for IL1-ß. These data suggest that up to 25% of FM can be replaced by PP without any adverse effects on rainbow trout.

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.

Future climate change-related decreases in food quality may affect juvenile Chinook salmon growth and survival

Global climate change is projected to raise global temperatures by 3.3-5.7 °C by 2100, resulting in changes in species composition, abundance, and nutritional quality of organisms at the base of the marine food web. Predicted increases in prey availability and reductions in prey nutritional quality under climate warming in certain marine systems are expected to impact higher trophic levels, such as fish and humans. There is limited knowledge of the interplay between food quantity and quality under warming, specifically when food availability is high, but quality is low. Here, we conducted an experiment assessing the effects of food quality (fatty acid composition and ratios) on juvenile Chinook salmon's (Oncorhynchus tshawytscha) body and nutritional condition, specifically focusing on RNA:DNA ratio, Fulton's K, growth, mortality and their fatty acid composition. Experimental diets represented three different climate change scenarios with 1) a present-day diet (Euphausia pacifica), 2) a control diet (commercial aquaculture diet), and 3) a predicted Intergovernmental Panel on Climate Change (IPCC) worst-case scenario diet with low essential fatty acid concentrations (IPCC SSP5-8.5). We tested how growth rates, RNA:DNA ratio, Fulton's K index, fatty acid composition and mortality rates in juvenile Chinook salmon compared across diet treatments. Fatty acids were incorporated into the salmon muscle at varying rates but, on average, reflected dietary concentrations. High dietary concentrations of DHA, EPA and high DHA:EPA ratios, under the control and present-day diets, increased fish growth and condition. In contrast, low concentrations of DHA and EPA and low DHA:EPA ratios in the diets under climate change scenario were not compensated for by increased food quantity. This result highlights the importance of considering food quality when assessing fish response to changing ocean conditions.

Transcriptomic Analysis of Liver in Silver sillago, Sillago sihama Fed with High-Level Low-Gossypol Cottonseed Meal in Replacement of Fishmeal Diet

Understanding the molecular mechanisms involved in adaptation to alternate diets has become a significant concern, as increasing amounts of fishmeal (FM) protein in aquafeeds are being substituted with plant protein. Thus, the goal of this study was to assess growth performance, quality, and liver function of juvenile Sillago sihama (S. sihama) through growth indices, whole-body composition, histology of the liver, and RNA-sequencing (RNA-seq), after they were fed a formulated diet with 64% low-gossypol cottonseed meal (LCSM) for 56 days, compared to those fed a traditional FM-based diet. Indicators of growth, including final body weight (FBW), weight gain rate (WGR), specific growth rate (SGR), protein efficiency ratio (PER), and condition factor (CF), were considerably lower in the 64% LCSM (R64) group than in the FM diet group. In the R64 diet, the whole crude lipid was significantly lower than in the FM diet. The hematoxylin–eosin section showed that dietary high levels of LCSM resulted in diffuse lipid vacuolation in the liver of S. sihama. According to a liver transcriptome analysis, high LCSM intake in the diet significantly impacted lipid synthesis and catabolism, elevated pathways for cholesterol synthesis, blocked several amino acid metabolic pathways, and adversely affected hepatic gluconeogenesis and glycolysis. The findings of this study indicate that feeding high levels of LCSM in S. sihama is harmful to the growth of the organism and can harm the liver’s structural integrity, as well as obstruct the normal metabolism of amino acids, lipids, and carbohydrates. Therefore, it is not recommended to substitute LCSM for high levels of FM in the diet of S. sihama.

Physiological, Nutritional and Transcriptomic Responses of Sturgeon (Acipenser schrenckii) to Complete Substitution of Fishmeal with Cottonseed Protein Concentrate in Aquafeed

This study estimated the effect of substituting fishmeal completely with cottonseed protein concentrate (CPC) in the diet of sturgeon (Acipenser schrenckii) on growth, digestive physiology, and hepatic gene expression. A control diet containing fishmeal and an experimental diet based on CPC was designed. The study was conducted for 56 days in indoor recirculating aquaculture systems. The results showed that weight gain, feed efficiency, and whole-body essential amino acids (EAAs) all decreased significantly in the experimental group, while whole-body non-essential amino acids (NEAAs) and serum transaminase activity increased (p < 0.05). The activity of digestive enzymes in the mid-intestine was significantly reduced (p < 0.05), and liver histology revealed fatty infiltration of hepatocytes. The hepatic transcriptome revealed an upregulation of genes linked to metabolism, including steroid biosynthesis, pyruvate metabolism, fatty acid metabolism, and amino acid biosynthesis. These findings indicate that fully replacing fishmeal with CPC harms A. schrenckii growth and physiology. This study provides valuable data for the development of improved aquafeeds and the use of molecular methods to evaluate the diet performance of sturgeon.

Characterization of free fatty acid receptor family in rainbow trout (Oncorhynchus mykiss): towards a better understanding of their involvement in fatty acid signalisation

Since 20 years of research, free fatty acids receptors (FFARs) have received considerable attention in mammals. To date, four FFARs (FFAR1, FFAR2, FFAR3 and FFAR4) are especially studied owing to their physiological importance in various biological processes. This ubiquitist group of G protein-coupled receptors (GPCRs) are majors reports in the key physiological functions such as the regulation of energy balance, metabolism or fatty acid sensing. However, up till date, even some studies were interested in their potential involvement in fatty acid metabolism, no genome investigation of these FFARs have been carried out in teleost fish. Through genome mining and phylogenetic analysis, we identified and characterised 7 coding sequences for ffar2 in rainbow trout whereas no ffar3 nor ffar4 gene have been found. This larger repertoire of ffar2 genes in rainbow trout results from successive additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. A syntenic analysis was used to assign a new nomenclature to the salmonid ffar2 and showed a clear conservation of genomic organisation, further supporting the identity of these genes as ffar2. RT-qPCR was then used to examine, firstly during ontogenesis and secondly on feeding response the expression pattern of ffar1 and ffar2 genes in proximal gut and brain of all trout ffar genes. Overall, this study presents a comprehensive overview of the ffar family in rainbow trout.

Dynamics of mitochondrial adaptation and energy metabolism in rainbow trout (Oncorhynchus mykiss) in response to sustainable diet and temperature

Impacts of plant-based ingredients and temperatures on energy metabolism in rainbow trout was investigated. A total of 288 fish (mean body weight: 45.6 g) were fed four isocaloric, isolipidic, and isonitrogenous diets containing 40% protein and 20% lipid and formulated as 100% animal-based protein (AP) and a blend of 50% fish oil (FO) and 50% camelina oil (CO); 100% AP and100% CO; 100% plant-based protein (PP) and a blend of 50% FO and 50% CO or 100% PP and 100% CO at 14 or 18 °C for 150 d. Diet did not significantly affect weight gain (WG) (P = 0.1902), condition factor (CF) (P = 0.0833) or specific growth rate (SGR) (P = 0.1511), but diet significantly impacted both feed efficiency (FE) (P = 0.0076) and feed intake (FI) (P = 0.0076). Temperature did not significantly affect WG (P = 0.1231), FE (P = 0.0634), FI (P = 0.0879), CF (P = 0.8277), or SGR (P = 0.1232). The diet × temperature interaction did not significantly affect WG (P = 0.7203), FE (P = 0.4799), FI (P = 0.2783), CF (P = 0.5071), or SGR (P = 0.7429). Furthermore, temperature did not influence protein efficiency ratio (P = 0.0633), lipid efficiency ratio (P = 0.0630), protein productive value (P = 0.0756), energy productive value (P = 0.1048), and lipid productive value (P = 0.1386); however, diet had significant main effects on PER (P = 0.0076), LPV (P = 0.0075), and PPV (P = 0.0138). Temperature regimens induced increased activities of mitochondrial complexes I (P = 0.0120), II (P = 0.0008), III (P = 0.0010), IV (P < 0.0001), V (P < 0.0001), and citrate synthase (CS) (P < 0.0001) in the intestine; complexes I (P < 0.0001), II (P < 0.0001), and CS (P = 0.0122) in the muscle; and complexes I (P < 0.0001), II (P < 0.0001), and III (P < 0.0001) in the liver. Similarly, dietary composition significantly affected complexes I (P < 0.0001), II (P < 0.0001), IV (P < 0.0001), V (P < 0.0001), and CS (P < 0.0001) in the intestine; complexes I (P < 0.0001), II (P < 0.0001), III (P = 0.0002), IV (P < 0.0001), V (P = 0.0060), and CS (P < 0.0001) in the muscle; and complexes I (P < 0.0001), II (P < 0.0001), IV (P < 0.0001), V (P < 0.0001), and CS (P < 0.0001) in the liver activities except complex III activities in intestine (P = 0.0817) and liver (P = 0.4662). The diet × temperature interaction impacted CS activity in the intestine (P = 0.0010), complex II in the muscle (P = 0.0079), and complexes I (P = 0.0009) and II (P = 0.0348) in the liver. Overall, comparing partial to full dietary substitution of FO with CO, partial dietary replacement showed similar effects on complex activities.

Long noncoding RNA lincsc5d regulates hepatic cholesterol synthesis by modulating sterol C5 desaturase in large yellow croaker

Although long noncoding RNA (lncRNA) plays a vital role in cholesterol metabolism, very little information is available in fish. Thus, a 10-week feeding experiment was performed to estimate the effects of lncRNA on cholesterol metabolism in large yellow croaker fed with fish oil (FO), soybean oil (SO), olive oil (OO), and palm oil (PO) diets. Results showed that fish fed with OO and PO diets had higher liver total cholesterol (TC) and cholesterol ester (CE) contents compared with fish fed with FO diets. Analysis of the KEGG pathway showed that the steroid biosynthesis pathway was enriched in comparisons FO vs SO, FO vs OO, and FO vs PO. Meanwhile, sterol C5 desaturase (SC5D), a cholesterol synthase, was up-regulated in the steroid biosynthesis pathway. SC5D was widely expressed in all tissues examined, and the highest expression of SC5D was detected in brain. More importantly, a novel lncRNA associated with sc5d gene was identified by RNA sequencing and named as lincsc5d. The tissue distribution of lincsc5d was similar to that of sc5d. A nuclear/cytoplasmic RNA separation assay showed that lincsc5d was a nucleus-enriched lncRNA. qRT-PCR results demonstrated that lincsc5d was markedly up-regulated in the SO, OO, and PO groups. Furthermore, the results of TC content and the lincsc5d and sc5d expression in hepatocytes agreed with in vivo results. In conclusion, this study indicated that vegetable oils, especially OO and PO, increased hepatic cholesterol levels by promoting cholesterol synthesis, and lncRNA lincsc5d and sc5d might be involved in cholesterol synthesis.

Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream

The gut microbiota is now recognised as a key target for improving aquaculture profit and sustainability, but we still lack insights into the activity of microbes in fish mucosal surfaces. In the present study, a metatranscriptomic approach was used to reveal the expression of gut microbial genes in the farmed gilthead sea bream. Archaeal and viral transcripts were a minority but, interestingly and contrary to rRNA amplicon-based studies, fungal transcripts were as abundant as bacterial ones, and increased in fish fed a plant-enriched diet. This dietary intervention also drove a differential metatranscriptome in fish selected for fast and slow growth. Such differential response reinforced the results of previously inferred metabolic pathways, enlarging, at the same time, the catalogue of microbial functions in the intestine. Accordingly, vitamin and amino acid metabolism, and rhythmic and symbiotic processes were mostly shaped by bacteria, whereas fungi were more specifically configuring the host immune, digestive, or endocrine processes.

Fish Oil Replacement by a Blend of Vegetable Oils in Diets for Juvenile Tench (Tinca tinca Linnaeus, 1758): Effects on Growth Performance and Whole-Body Composition

Simple Summary

Fish oil (FO) can be totally replaced by a blend of vegetable oils (30% linseed oil, 20% corn oil, and 50% olive oil) in diets for juvenile tench (Tinca tinca Linnaeus, 1758) without negative effects on survival rate and growth performance. Diets affected the composition of juveniles so that lipid content was significantly lower in animals fed diets without FO. Moreover, the content of linolenic acid (18:3n-3) increased as FO substitution did, being significantly higher with respect to control diet (without vegetable oils) from 40% or higher FO replacement diets. No differences in saturated, monounsaturated, and polyunsaturated fatty acids were found in the fish whole-body. Nutritional indices can be considered within optimal values for healthy foods.

Abstract

Among freshwater species, tench (Tinca tinca Linnaeus, 1758) is considered as a promising species for the diversification of aquaculture, but the intensification of techniques is necessary to promote and consolidate its culture. Adequate feeding in early growth phases is essential to face further grow-out. Fish oil (FO) is the main source of lipids in fish diets, but its production is unsustainable, and thus, alternative oils should be considered. A 90-day experiment was performed to evaluate the effects of partial and total replacement of cod liver oil (FO) by a blend of vegetable oils (VO) in juvenile tench. Six isonitrogenous and isolipidic diets with different levels of a VO blend containing 30% linseed oil, 20% corn oil, and 50% olive oil were tested: 0% (control), 20%VO, 40%VO, 60%VO, 80%VO, and 100%VO. With all diets, survival was 100%, and there were not differences in growth performance (total length (TL); weight (W); specific growth rate (SGR); feed conversion ratio (FCR); and biomass gain (BG)). Compared to the control group, whole-body lipid content decreased significantly in the 100%VO group. No differences in total saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids were found in the whole-body. The content of linolenic acid (ALA) in the whole-body increased as FO substitution did, being significantly higher with respect to control diet from 40% FO replacement diets. Nutritional indices, such as ΣPUFA/ΣSFA and Σn-6/Σn-3 ratios, tended to increase with increasing VO content, whereas the EPA + DHA showed an opposite trend. A total replacement of FO by the blend of VO did not affect the growth performance and fatty acid profile of juvenile tench. Further research on the effects of VO diet on nutritional quality in tench reared to commercial size should be performed.

Effect of Lemna minor supplemented diets on growth, digestive physiology and expression of fatty acids biosynthesis genes of Cyprinus carpio

The potential nutritional value of duckweed Lemna minor (Lemnaceae) was evaluated for common carp Cyprinus carpio fry. Fish were fed diets containing five graded levels of duckweed: 0% (LM0, control), 5% (LM5), 10% (LM10), 15% (LM15) and 20% (LM20). The final weight and specific growth rate were significantly higher in LM15 and LM20 diets fed fish compared to others. Feed conversion ratio was minimum in fish fed diet LM20. Amylase activity was significantly higher in LM0 treatment. Total protease, trypsin and chymotrypsin activities showed linear relationships with the increased level of duckweed in the diet. Protein and essential amino acids contents were significantly higher in carp fed diets LM15 and LM20 compared to others. Lipid content was significantly higher in fish fed duckweed-based diets compared to control. A direct relationship was found between the inclusion level of duckweed in the diet and n-3 long-chain polyunsaturated fatty acid (LC-PUFA) content of carp. Contents of desaturated and elongated products of dietary linolenic acid (18:3n-3) including 20:4n-3, 20:5n-3, 22:5n-3 and 22:6n-3 increased in a graded manner with increasing dietary duckweed. The monounsaturated fatty acids and n-6 PUFA contents reduced significantly in fish fed duckweed. Expression of fads2d6, elovl2, elovl5 and fas were higher in carp fed diets LM10, LM15 and LM20 compared to control fish. The inclusion of L. minor in diet enhanced the nutritional value of carp by increasing protein, lipid, amino acids and n-3 PUFA contents.

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.

Projecting global mariculture production and adaptation pathways under climate change

The sustainability of global seafood supply to meet increasing demand is facing several challenges, including increasing consumption levels due to a growing human population, fisheries resources over-exploitation and climate change. Whilst growth in seafood production from capture fisheries is limited, global mariculture production is expanding. However, climate change poses risks to the potential seafood production from mariculture. Here, we apply a global mariculture production model that accounts for changing ocean conditions, suitable marine area for farming, fishmeal and fish oil production, farmed species dietary demand, farmed fish price and global seafood demand to project mariculture production under two climate and socio-economic scenarios. We include 85 farmed marine fish and mollusc species, representing about 70% of all mariculture production in 2015. Results show positive global mariculture production changes by the mid and end of the 21^st century relative to the 2000s under the SSP1-2.6 scenario with an increase of 17%±5 and 33%±6, respectively. However, under the SSP5-8.5 scenario, an increase of 8%±5 is projected, with production peaking by mid-century and declining by 16%±5 towards the end of the 21^st century. More than 25% of mariculture-producing nations are projected to lose 40%-90% of their current mariculture production potential under SSP5-8.5 by mid-century. Projected impacts are mainly due to the direct ocean warming effects on farmed species and suitable marine areas, and the indirect impacts of changing availability of forage fishes supplies to produce aquafeed. Fishmeal replacement with alternative protein can lower climate impacts on a subset of finfish production. However, such adaptation measures do not apply to regions dominated by non-feed-based farming (i.e. molluscs) and regions losing substantial marine areas suitable for mariculture. Our study highlights the importance of strong mitigation efforts and the need for different climate adaptation options tailored to the diversity of mariculture systems, to support climate-resilient mariculture development.

Prediction of fatty acids composition in the rainbow trout Oncorhynchus mykiss by using Raman micro-spectroscopy

The importance of poly-unsaturated fatty acids (PUFAs) in food is crucial for the animal and human development and health. As a complementary strategy to nutrition approaches, genetic selection has been suggested to improve fatty acids (FAs) composition in farmed fish. Gas chromatography (GC) is used as a reference method for the quantification of FAs; nevertheless, the high cost prevents large scale phenotyping as needed in breeding programs. Therefore, a calibration by means of Raman scattering spectrometry has been established in order to predict FA composition of visceral adipose tissue in rainbow trout Onchorhynchus mykiss. FA composition was analyzed by both GC and Raman micro-spectrometry techniques on 268 individuals fed with three different feeds, which have different FA compositions. Among the possible regression methods, the ridge regression method, was found to be efficient to establish calibration models from the GC and spectral data. The best cross-validated R² values were obtained for total PUFAs, omega-6 (Ω-6) and omega-3 (Ω-3) PUFA (0.79, 0.83 and 0.66, respectively). For individual Ω-3 PUFAs, α-linolenic acid (ALA, C18:3), eicosapentaenoic acid (EPA, C20:5) and docosahexenoic acid (DHA, C22:6) were found to have the best R² values (0.82, 0.76 and 0.81, respectively). This study demonstrates that Raman spectroscopy could be used to predict PUFAs with good correlation coefficients on adipocytes, for future on adipocytes physiology or for large scale and high throughput phenotyping in rainbow trout.

Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Background

In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection.

Results

Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait.

Conclusion

This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08062-7.

Digesta and Plasma Metabolomics of Rainbow Trout Strains with Varied Tolerance of Plant-Based Diets Highlights Potential for Non-Lethal Assessments of Enteritis Development

The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (Oncorhynchus mykiss) is one such species in which the strain ARS-Sel has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth and plasma and digesta metabolomes between ARS-Sel and two commercial strains (CS-1 and CS-2), when fed plant-protein (PM) and fishmeal-based (FM) diets, and to correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-Sel fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma and digesta metabolite profiles of ARS-Sel and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of enteritis development, which was confirmed by intestinal histology. As reported in previous studies, the ARS-Sel strain performed better than the commercial strains when fed the PM diet. Our findings also suggest that metabolomic profiles of plasma and digesta, samples of which can be obtained through non-lethal methods, offer valuable insight in monitoring the occurrence of enteritis in carnivorous aquaculture species due to plant-based diets.

Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection

Background

Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings.

Results

We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection.

Conclusion

Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture’s sustainability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00107-2.

Chestnut Shell Tannins: Effects on Intestinal Inflammation and Dysbiosis in Zebrafish

Simple Summary

With the increase in global population the production of animal proteins becomes increasingly crucial. Aquaculture is the first animal protein supply industry for human consumption. Intensive farming techniques are employed to increase productivity, but these may cause stressful conditions for fish, resulting in impaired growth and poor health conditions. Intestinal inflammation is one of the most common diseases of fish in intensive farming. Intestinal inflammation is usually accompanied by an alteration of the microbiota or dysbiosis. Inflammation and dysbiosis are so tightly intertwined that inflammation may contribute to or result from dysregulation of gut microbiota. Natural substances of plant origin rich in bioactive molecules or more simply phytochemicals, have been proved to be able to reduce inflammation and improve the general health status in various commercially relevant species. In this study, we evaluated the effect of tannins, a class of polyphenols, the most abundant phytochemicals, on intestinal inflammation and microbiota in zebrafish (Danio rerio), a small freshwater fish become an attractive biomedicine and aquaculture animal model during the last decades. The zebrafish has been employed in a vast array of studies aiming at investigating the essential processes underlying intestinal inflammation and injury due to its conservative gut morphology and functions. In this study, we administered a diet enriched with chestnut shell extract rich in tannins to a zebrafish model of intestinal inflammation. The treatment ameliorated the damaged intestinal morphophysiology and the microbiota asset. Our results sustain that products of natural origin with low environmental impact and low cost, such as tannins, may help to ease some of the critical issues affecting the aquaculture sector.

Abstract

The aim of the present study was to test the possible ameliorative efficacy of phytochemicals such as tannins on intestinal inflammation and dysbiosis. The effect of a chestnut shell (Castanea sativa) extract (CSE) rich in polyphenols, mainly represented by tannins, on k-carrageenan-induced intestinal inflammation in adult zebrafish (Danio rerio) was tested in a feeding trial. Intestinal inflammation was induced by 0.1% k-carrageenan added to the diet for 10 days. CSE was administered for 10 days after k-carrageenan induced inflammation. The intestinal morphology and histopathology, cytokine expression, and microbiota were analyzed. The k-carrageenan treatment led to gut lumen expansion, reduction of intestinal folds, and increase of the goblet cells number, accompanied by the upregulation of pro-inflammatory factors (TNFα, COX2) and alteration in the number and ratio of taxonomic groups of bacteria. CSE counteracted the inflammatory status enhancing the growth of health helpful bacteria (Enterobacteriaceae and Pseudomonas), decreasing the pro-inflammatory factors, and activating the anti-inflammatory cytokine IL-10. In conclusion, CSE acted as a prebiotic on zebrafish gut microbiota, sustaining the use of tannins as food additives to ameliorate the intestinal inflammation. Our results may be relevant for both aquaculture and medical clinic fields.

Intestinal Transcriptome Analysis Reveals Enrichment of Genes Associated with Immune and Lipid Mechanisms, Favoring Soybean Meal Tolerance in High-Growth Zebrafish (Danio Rerio)

The molecular mechanisms underlying fish tolerance to soybean meal (SBM) remain unclear. Identifying these mechanisms would be beneficial, as this trait favors growth. Two fish replicates from 19 experimental families were fed fishmeal-(100FM) or SBM-based diets supplemented with saponin (50SBM + 2SPN) from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (HG-50SBM + 2SPN, 170 ± 18 mg) or lower (LG-50SBM + 2SPN, 76 ± 10 mg) weight gain on 50SBM + 2SPN for intestinal transcriptomic analysis. A histological evaluation confirmed middle intestinal inflammation in the LG- vs. HG-50SBM + 2SPN group. Enrichment analysis of 665 differentially expressed genes (DEGs) identified pathways associated with immunity and lipid metabolism. Genes linked to intestinal immunity were downregulated in HG fish (mpx, cxcr3.2, cftr, irg1l, itln2, sgk1, nup61l, il22), likely dampening inflammatory responses. Conversely, genes involved in retinol signaling were upregulated (rbp4, stra6, nr2f5), potentially favoring growth by suppressing insulin responses. Genes associated with lipid metabolism were upregulated, including key components of the SREBP (mbtps1, elov5l, elov6l) and cholesterol catabolism (cyp46a1), as well as the downregulation of cyp7a1. These results strongly suggest that transcriptomic changes in lipid metabolism mediate SBM tolerance. Genotypic variations in DEGs may become biomarkers for improving early selection of fish tolerant to SMB or others plant-based diets.

Putative imbalanced amino acid metabolism in rainbow trout long term fed a plant-based diet as revealed by 1H-NMR metabolomics

The long-term effect of a plant (P)-based diet was assessed by proton nuclear magnetic resonance (¹H-NMR) metabolomics in rainbow trout fed a marine fish meal (FM)-fish oil (FO) diet (M), a P-based diet and a control commercial-like diet (C) starting with the first feeding. Growth performances were not heavily altered by long-term feeding on the P-based diet. An ¹H-NMR metabolomic analysis of the feed revealed significantly different soluble chemical compound profiles between the diets. A set of soluble chemical compounds was found to be specific either to the P-based diet or to the M diet. Pterin, a biomarker of plant feedstuffs, was identified both in the P-based diet and in the plasma of fish fed the P-based diet. ¹H-NMR metabolomic analysis on fish plasma and liver and muscle tissues at 6 and 48 h post feeding revealed significantly different profiles between the P-based diet and the M diet, while the C diet showed intermediate results. A higher amino acid content was found in the plasma of fish fed the P-based diet compared with the M diet after 48 h, suggesting either a delayed delivery of the amino acids or a lower amino acid utilisation in the P-based diet. This was associated with an accumulation of essential amino acids and the depletion of glutamine in the muscle, together with an accumulation of choline in the liver. Combined with an anticipated absorption of methionine and lysine supplemented in free form, the present results suggest an imbalanced essential amino acid supply for protein metabolism in the muscle and for specific functions of the liver.

Dietary Chitosan Nanoparticles: Potential Role in Modulation of Rainbow Trout (Oncorhynchus mykiss) Antibacterial Defense and Intestinal Immunity against Enteric Redmouth Disease

Bio-nanotechnology employing bio-sourced nanomaterial is an emerging avenue serving the field of fish medicine. Marine-sourced chitosan nanoparticles (CSNPs) is a well-known antimicrobial and immunomodulatory reagent with low or no harm side effects on fish or their human consumers. In this study, in vitro skin mucus and serum antibacterial activity assays along with intestinal histology, histochemical, and gene expression analyses were performed to evaluate the impact of dietary CSNPs (5 g kg⁻¹ dry feed) on rainbow trout resistance against ‘enteric redmouth’ disease. Two treatment conditions were included; short-term prophylactic-regimen for 21 days before the bacterial challenge, and long-term therapeutic-regimen for 21 days before the challenge and extended for 28 days after the challenge. Our results revealed higher antibacterial defense ability and positive intestinal histochemical and molecular traits of rainbow trout after dietary CSNPs. The prophylactic-regimen improved trout health while the therapeutic regimen improved their disease resistance and lowered their morbidity. Therefore, it is anticipated that CSNPs is an effective antibacterial and immunomodulatory fish feed supplement against the infectious threats. However, the CSNPs seem to be more effective in the therapeutic application rather than being used for short-term prophylactic applications.

Use of alternative protein sources for fishmeal replacement in the diet of largemouth bass (Micropterus salmoides). Part II: effects of supplementation with methionine or taurine on growth, feed utilization, and health

Fishmeal has long been a staple protein feedstuff for fish, but its global shortage and high price have prompted its replacement with alternative sustainable sources. In this experiment involving largemouth bass (a carnivorous fish), a new mixture of feedstuffs (45% poultry byproduct meal, 30% soybean meal, 15% blood meal, and 10% krill shrimp meal) was added to low (14.5%) fishmeal diets along with 0.0%, 0.5% taurine, 0.5% methionine, or 0.5% taurine plus 0.5% methionine (dry matter basis). The positive control diet [65.3% fishmeal (46% crude protein on dry matter basis)] and all low-fishmeal diets contained 40% true protein and 10% lipids. There were 3 tanks per treatment group (20 fish/tank). Fish with the mean initial body weight of 16.6 g were fed to satiety twice daily. Compared with the unsupplemented low-fishmeal group, supplementing either 0.5% methionine or 0.5% methionine plus 0.5% taurine to the low-fishmeal diet improved (P < 0.05) the growth, feed utilization, retention of dietary protein and lipids, and health of largemouth bass, reduced (P < 0.05) the occurrence of black skin syndrome from ~ 40 to ~ 10%. Histological sections of tissues from the fish with black skin syndrome showed retina degeneration, liver damage, and enteritis in the intestine. Compared with methionine supplementation, supplementing 0.5% taurine alone to the low-fishmeal diet did not affect the growth or feed efficiency of fish and had less beneficial effects (P < 0.05) on ameliorating the black skin syndrome. These results indicated that: (a) the basal low-fishmeal diet was inadequate in methionine or taurine; and (b) dietary supplementation with methionine was an effective method to improve the growth performance, feed efficiency, and health of largemouth bass. Further studies are warranted to understand the pathogenesis of the black skin syndrome in largemouth bass.

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream

BACKGROUND

The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated.

RESULTS

No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals.

CONCLUSIONS

These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.

Effects and Safe Inclusion of Narbonne Vetch (Vicia narbonensis) in Rainbow Trout (Oncorhynchus mykiss) Diets: Towards a More Sustainable Aquaculture

Simple Summary

Aquaculture’s sustainability deeply relies on the identification and inclusion of alternative raw materials rather than continuing with the use of finite resources such as fish meal and fish oil. Different alternative raw materials have been tested, with the meal from terrestrial vegetable species being one of the main substitution candidates for fish meal. This study evaluated the effects of the inclusion (at 0%, 10% and 30%) of Narbonne vetch (Vicia narbonensis) meal in rainbow trout (Oncorhynchus mykiss) diets as a first attempt to evaluate its safety as a suitable alternative raw material. High inclusion (30%) of Narbonne vetch led to a reduced final fish size and weight. This seemed to be due to severe histopathological alterations in the proximal intestine that might alter the capacity of the fish to efficiently use the nutrients supplied by the diet. In contrast, a 10% inclusion did not affect fish growth nor digestive system and/or the nutritional value of the fish fillet. Although further research efforts might be required to increase the utilization of alternative raw materials locally produced like Narbonne vetch, present results show Narbonne vetch might reduce carbon footprint in European aquaculture and the dependency on other alternative raw materials such as soybean (Glycine max) imported from third countries.

Abstract

Aquaculture’s sustainability deeply relies on the identification and inclusion of alternative raw materials. Although meals from insects and/or byproducts from different industries are being recently tested, the meal from terrestrial vegetable species is still the main substitution candidate for fish meal. Here the effects of 0% (Control), 10% (A10) and 30% (A30) inclusion of Narbonne vetch (Vicia narbonensis; ZV-156 strain) meal in rainbow trout (Oncorhynchus mykiss) diets was assessed in a 63-day feeding trial by means of growth performance, histopathological, nutritional value of the fish fillet and blood biochemistry analyses. A dose-response trial was conducted in triplicate with 25 rainbow trout juveniles (20 g average body weight) per 500 L tank. Narbonne vetch meal decreased total intestine protease activity in vitro (from 26.81% to 48% inhibition), although high temperature partially inhibited the action of antinutritional factors (ANFs). No differences in fish growth performance and no severe histopathological alterations on the proximal intestine were observed between 10% Narbonne vetch inclusion and Control groups. In contrast, high inclusion (30%) of Narbonne vetch led to poor growth performance (30% reduction on final growth) and severe histopathological alterations (e.g., loss of brush border integrity, high number of villi fusion, reduced goblet cells density as well as reduced width of submucosa, muscular and serosa layers). Furthermore, while the A30 diet decreased docosahexaenoic fatty acid (FA) content in fish fillets, the A10 diet improved monounsaturated FA content when compared to that of the Control group. No altered levels of cholesterol, glucose or triglycerides in blood plasma and/or histopathological effects on the liver were observed among fish fed the different experimental diets. Although further research efforts (e.g., identifying potential enzymatic treatments to decrease the action of ANFs from Narbonne vetch meal) might be required, present results show that a low inclusion (10%) of Narbonne vetch in rainbow trout diets is possible. The inclusion of locally produced legumes such a Narbonne vetch might be an interesting approach to reduce carbon footprint in European aquaculture and the dependency on other alternative raw materials such as soybean (Glycine max) imported from third countries.

Intestinal Explant Cultures from Gilthead Seabream (Sparus aurata, L.) Allowed the Determination of Mucosal Sensitivity to Bacterial Pathogens and the Impact of a Plant Protein Diet

The interaction between diet and intestinal health has been widely discussed, although in vivo approaches have reported limitations. The intestine explant culture system developed provides an advantage since it reduces the number of experimental fish and increases the time of incubation compared to similar methods, becoming a valuable tool in the study of the interactions between pathogenic bacteria, rearing conditions, or dietary components and fish gut immune response. The objective of this study was to determine the influence of the total substitution of fish meal by plants on the immune intestinal status of seabream using an ex vivo bacterial challenge. For this aim, two growth stages of fish were assayed (12 g): phase I (90 days), up to 68 g, and phase II (305 days), up to 250 g. Additionally, in phase II, the effects of long term and short term exposure (15 days) to a plant protein (PP) diet were determined. PP diet altered the mucosal immune homeostasis, the younger fish being more sensitive, and the intestine from fish fed short-term plant diets showed a higher immune response than with long-term feeding. Vibrio alginolyticus (V. alginolyticus) triggered the highest immune and inflammatory response, while COX-2 expression was significantly induced by Photobacterium damselae subsp. Piscicida (P. damselae subsp. Piscicida), showing a positive high correlation between the pro-inflammatory genes encoding interleukin 1β (IL1-β), interleukin 6 (IL-6) and cyclooxygenase 2(COX-2).

Impact of varied combinatorial mixture of non-fishmeal ingredients on growth, metabolism, immunity and gut microbiota of Lates calcarifer (Bloch, 1790) fry

The search for suitable fish meal replacements in aqua-diets is a salient agenda in the constant effort of making aquaculture practices more sustainable. In this study, we tested four customised diets composed by systematic inclusion of pre-selected fish meal substitutes, lupin kernel meal, BSF meal, TH and PBM on growth, metabolism, cytokine profile, gut morphology and microbiota of juvenile Lates calcarifer. Five isoproteic and isoenergetic diets were prepared viz. FM100 as a control (without fish meal substitute), while FM75, FM50, FM25 and FM0 indicates replacement of fish meal (FM) at 25%, 50%, 75%, and 100%, respectively by a mixture of four different pre-selected non-fish meal (NFM) ingredients. Fish fed FM100, FM75, FM50, FM25 exhibited consistent growth and haematological response, while the fish fed no fishmeal (FM0) showed significant decline in final body weight (FBW) and specific growth rate (SGR). The poor growth performance was correlated with a decrease in villous width, microvilli height and goblet cells density. A significant shift in abundance profile of Psychrobacter in the gut microbial profile of fish fed FM50 was noticed compared to fish fed FM100. The results of qRT-PCR showed up-regulated expression of innate immune responsive genes in the FM50 group. The adverse impacts on growth performance and gut health of fish fed FM0 suggest that the complete substitution of fishmeal is not advisable and the inclusion range of these alternatives should be decided for a species only after examining their effect on maximal physiological performance.

Hepatic Fatty Acid and Transcriptome Profiles during the Transition from Vegetable- to Fish Oil-Based Diets in Rainbow Trout (Oncorhynchus mykiss)

A finishing diet strategy is effective at increasing fillet long-chain n-3 fatty acid content in fish consuming sustainable plant oil-based diets. This study investigates the outcomes of a fish oil finishing diet upon the hepatic fatty acid and transcriptome profile in rainbow trout (Oncorhynchus mykiss). Fish were placed on one of three feeding treatments: (1) FO: a fish oil (FO) diet for 20 weeks, (2) VO/FO: a vegetable oil (VO) diet during weeks 1-12 then the FO diet for 8 weeks, or (3) VO/fd/FO: the VO diet between weeks 1-12, 2 weeks of feed deprivation, then the FO diet for 6 weeks. Hepatic fatty acid and transcriptome profiles were analyzed at week 12, 14, and 20. Hepatic fatty acid profiles at week 12 were similar to dietary profiles; transcriptomic analyses indicated 131 differentially regulated genes (DEG) between VO- and FO-fed fish, characterized by VO-induced up-regulation of cholesterol and long-chain fatty acyl-CoA synthesis and oxidation-reduction processes. At week 14, the hepatic fatty acid profile was similar between VO/FO and FO, although concentrations of 18:3n-3 remained higher in the VO/FO group. Thirty-three DEG were detected at week 14 with enrichment of genes associated with extracellular matrix assembly, supporting liver remodeling during the early finishing diet period. Only five DEG were detected at week 20 between VO/FO and FO. Collectively, these findings suggest that it takes several weeks for liver to reach a homeostatic state, even after the hepatic fatty acid equilibration following a finishing diet.

Hypoxia affects the ontogeny of the hypothalamus-pituitary-interrenal axis functioning in the lake whitefish (Coregonus clupeaformis)

Early life stages are sensitive to environmental insults and changes during critical developmental periods; this can often result in altered adult behaviour and physiology. Examining the development of the hypothalamus-pituitary-interrenal (HPI) axis and its responsiveness, or lack thereof, during development are important for understanding the short- and long-term impacts of stressors on embryonic and larval fish. We examined the ontogeny of the HPI axis in embryonic (21, 38, 63, 83 and 103 days post-fertilisation (dpf)) and larval (1, 2, 3 and 4 weeks post-hatch (wph)) lake whitefish (Coregonus clupeaformis) by quantifying changes in mRNA levels of several genes associated with HPI axis functioning and whole animal cortisol levels throughout development and in response to a severe or mild hypoxic stress. Cortisol, and crh, crhbp1, pomc and star transcripts were detected from the earliest embryonic age studied. Cortisol levels in control embryos decreased between 21 and 63 dpf, suggesting the utilisation of maternal cortisol deposits. However, by 83 dpf (70% developed) endogenous de novo synthesis had generated a 4.5-fold increase in whole embryo cortisol. Importantly, we provide novel data showing that the HPI axis can be activated even earlier. Whole body cortisol increased in eyed lake whitefish embryos (38 dpf; ~32% developed) in response to hypoxia stress. Coincident with this hypoxia-induced increase in cortisol in 38 dpf embryos were corresponding increases in crh, crhbp1, pomc and star transcript levels. Beyond 38 dpf, the HPI axis in lake whitefish embryos was hyporesponsive to hypoxia stress at all embryonic ages examined (63, 83 and 103 dpf; 54, 72 and 85% developed, respectively). Post-hatch, larvae responded to hypoxia with an increase in cortisol levels and HPI axis genes at 1 wph, but this response was lost and larvae appeared hyporesponsive at subsequent ages (2, 3 and 4 wph). Collectively our work demonstrates that during fish embryogenesis and the larval stage there are windows where the HPI axis is responsive and windows where it is truly hyporesponsive; both could be beneficial in ensuring undisrupted development particularly in the face of increasing environmental changes.

Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

BACKGROUND

Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance.

OBJECTIVE

We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material.

METHODS

Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints.

RESULTS

In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80).

CONCLUSIONS

These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.

Hepatic Glycerol Metabolism-Related Genes in Carnivorous Rainbow Trout (Oncorhynchus mykiss): Insights Into Molecular Characteristics, Ontogenesis, and Nutritional Regulation

Glycerol metabolism in rainbow trout is poorly studied even though it is at the interface between lipid and glucose metabolism. Moreover, glycerol can be an important ingredient in new aquafeed formulation to decrease the catabolism of dietary amino acids. Thus, the present study aimed to characterize for the first time the different genes coding for key enzymes and proteins involved in hepatic glycerol metabolism. From the trout genomes, all the paralogous genes coding for glycerol transport (aqp9b), glycerol kinase (gk2a and gk5), glycerol-3-phosphate phosphatase (pgp), and glycerol-3-phosphate dehydrogenase (gpd1a, gpd1b, and gpd1c) were identified. The ontogenesis determined that the capacity to metabolize glycerol begins with the apparition of the liver during the development (stage 22) and are more expressed at the endogenous–exogenous feeding period (stage 35). The postprandial regulation of the expression of these genes in juvenile trout showed that the postprandial peak of expression is between 4 and 24 h after the last meal for many of the genes, demonstrating that glycerol metabolism could be nutritionally regulated at a molecular level. However, surprisingly, no regulation of the mRNA abundance for the glycerol metabolism-related genes by different levels of dietary glycerol (0, 2.5, and 5%) have been detected, showing that hepatic glycerol metabolism is poorly regulated at a molecular level by dietary glycerol in rainbow trout juveniles.

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.

Characterization and modulation of brain lipids content of rainbow trout fed with 100% plant based diet rich in omega-3 long chain polyunsaturated fatty acids DHA and EPA

Brain functions are known to be mainly modulated by adequate dietary intake. Inadequate intake as can be an excess or significant deficiency affect cognitive processes, behavior, neuroendocrine functions and synaptic plasticity with protective or harmful effects on neuronal physiology. Lipids, in particular, ω-6 and ω-3 long chain polyunsaturated fatty acids (LC-PUFAs) play structural roles and govern the different functions of the brain. Hence, the goal of this study was to characterize the whole brain fatty acid composition (precursors, enzymatic and non-enzymatic oxidation metabolites) of fish model of rainbow trout fed with three experimental plant-based diet containing distinct levels of eicosapentaenoic acid (EPA, 20:5 ω-3) and docosahexaenoic acid (DHA, 22:6 ω-3) (0% for low, 15.7% for medium and 33.4% for high, total fatty acid content) during nine weeks. Trout fed with the diet devoid of DHA and EPA showed reduced brain content of total ω-3 LC-PUFAs, with diminution of EPA and DHA. Selected enzymatic (cyclooxygenases and lipoxygenases) oxidation metabolites of arachidonic acid (AA, 20:4 ω-6) decrease in medium and high ω-3 LC-PUFAs diets. On the contrary, total selected enzymatic oxidation metabolites of DHA and EPA increased in high ω-3 LC-PUFAs diet. Total selected non-enzymatic oxidation metabolites of DHA (not detected for EPA) increased in medium and high ω-3 LC-PUFAs diets. In conclusion, this work revealed for the first time in fish model the presence of some selected enzymatic and non-enzymatic oxidation metabolites in brain and the modulation of brain lipid content by dietary DHA and EPA levels.

Intestinal Transcriptome Analysis Highlights Key Differentially Expressed Genes Involved in Nutrient Metabolism and Digestion in Yellowtail Kingfish (Seriola lalandi) Fed Terrestrial Animal and Plant Proteins

This study investigated the effects of dietary terrestrial animal and plant proteins on the intestinal transcriptomes of yellowtail kingfish (YTK), Seriola lalandi, an ecologically and economically important marine species in Australia. Five diets containing fish meal (FM), poultry by-product meal (PBM), blood meal (BLM), faba bean meal (FBM) and corn gluten meal (CGM) were formulated and fed over a period of 4 weeks. The Illumina RNA-sequencing (RNA-Seq) results identified a suite of differentially expressed genes involved in nutrient metabolism and protein digestion pathways, reinforced by quantitative polymerase chain reaction (qPCR) results. These findings provide molecular support to the notion that PBM and FBM are useful raw materials in commercial diets for YTK. Using the same evidence, we have demonstrated that BLM and CGM may be less useful and their incorporation into commercial aquafeeds for this species should be done cautiously. The differentially expressed genes showed a subtle difference and high correlation with apparent nutrient digestibility of raw materials. Further, our results indicate that transcriptome profiling provides a useful tool to evaluate alternative protein sources for use in aquaculture feeds.

Diets supplemented with Saccharina latissima influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (Oncorhynchus mykiss) fillet composition

This study aimed to evaluate the impact of diets including increasing amounts (1, 2 and 4%) of an iodine-rich macroalgae, Saccharina latissima, on gene expression and fillet composition of commercial-sized rainbow trout. Liver and muscle expression of genes related to growth, iodine, oxidative stress, and lipid metabolism, and the fillet content of fatty acids, cholesterol, and vitamin D3 were assessed. The highest kelp inclusion led to lower final body weight and HSI, without significant differences in mRNA transcription of genes involved in growth (ghr1, ghr2 and igf1) or iodine metabolism (dio1, thra, and thrb). A significant downregulation of an oxidative stress marker, gpx1b2, was observed in fish fed 2% S. latissima, which might suggest the need for less endogenous antioxidants. Dietary inclusion of kelp impacted lipid metabolism, with a downregulation of fatty acid synthase, accompanied by a general decrease of fatty acids in fillet. The present study demonstrated that supplementation of diets with 1 or 2% S. latissima can be achieved without detrimental effects on rainbow trout final weight. Evidence suggest a lipid-lowering effect of diets that did not compromise fillet EPA and DHA concentrations, being 3.7 times above the recommended levels for human consumption.

Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)

With increasing levels of fish meal (FM) protein in aquafeeds being replaced with soybean meal (SBM) protein, understanding the molecular mechanisms involved in response to alternative diets has become a critical concern. Thus, the goal of this study was to examine transcriptional differences in the intestine of juvenile yellow perch through RNA-sequencing (RNA-seq), after their initial introduction to a formulated diet with 75% SBM protein inclusion for 61 days, compared to those fed a traditional FM-based diet. Transcriptomic analysis revealed a concise set of differentially expressed genes in juveniles fed the SBM-based diet, the majority of which were intrinsic to the cholesterol biosynthesis pathway. Analysis of total body lipid and cholesterol levels were also investigated, with no between-treatment differences detected. Results of this study demonstrate that in response to SBM-based diets, yellow perch juveniles up-regulate the cholesterol biosynthesis pathway in order to maintain homeostasis. These findings suggest that the upregulation of the cholesterol biosynthesis pathway may negatively impact fish growth due to its large energy expenditure, and future studies are warranted.

Utilization of marine fisheries wastes for the production of the freshwater fish Cyprinus carpio

The present study was aimed to assess the effects of complete replacement of fish meal with fisheries waste meals on survival, growth performance, digestive enzyme activities, and muscle compositions of the freshwater fish Cyprinus carpio. The proximate composition and mineral contents of three different fisheries wastes, such as Rastrelliger kanagurta, Sphyraena barracuda, and Fenneropenaeus indicus were analyzed. Based on the nutrient content of these fisheries waste, one control fish meal diet and three different complete fish meal replacement diets (diet 1, diet 2, and diet 3 formulated with R. kanagurta, S. barracuda, and F. indicus waste meals, respectively) were formulated. Fingerlings C. carpio were fed with these diets for a period of 6 weeks. Results from feeding experiments showed insignificant (p > 0.05) differences in survival, growth, and feed intake of C. carpio fed with control and three different fisheries waste diets. However, the digestive enzyme activity and muscle biochemical compositions were significantly (p < 0.05) altered in F. indicus waste meal fed C. carpio compared to other fisheries waste meal and control diets fed fish groups. Therefore, the present study suggests that R. kanagurta, S. barracuda, and F. indicus waste meals can be considered as alternative feed ingredients for fish meal to formulate low-cost feeds for C. carpio culture.

Using systems thinking and open innovation to strengthen aquaculture policy for the United Nations Sustainable Development Goals

In a world of 9 billion people and a widening income gap between the rich and poor, it is time to rethink how aquaculture can strengthen its contribution to the second UN Sustainable Development Goal (SDG) of zero hunger in our generation. The disparity in the level of sustainable aquaculture development at present, between and within countries, especially regarding human access to farmed aquatic food remains highly variable across the globe. This paper offers a fresh look at the opportunities from using systems thinking and new open innovation measuring tools to grow sustainable aquaculture. Political will in many nations is the main constraint to aquaculture in realising its potential as an: accessible source of micronutrients and nutritious protein; aid to meeting conservation goals; economic prosperity generator where benefits extend to locals and provider of indirect social benefits such as access to education and well-being, among others. Resources to enable strong partnerships (SDG 17) between academia, civic society, government and industry should be prioritised by governments to build a sustainable aquatic food system, accessible to all, forever.

New Insights on Intermediary Metabolism for a Better Understanding of Nutrition in Teleosts

The rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific challenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory. In this review, we discuss four fields of research that are highly important for improving fish nutrition in the future: ( a) fish genome complexity and subsequent consequences for metabolism, ( b) microRNAs (miRNAs) as new actors in regulation of fish metabolism, ( c) the role of autophagy in regulation of fish metabolism, and ( d) the nutritional programming of metabolism linked to the early life of fish.

Modulation of stress and innate immune response by corticosteroids in pacu (Piaractus mesopotamicus)

Understanding how stress and corticosteroid modulates the innate immune response is one of the keys to improving productivity and reducing losses in intensive aquaculture. Thus, we investigated the effects of dietary corticosteroids (7 days; long-term exposure) and transport (4 h; short-term stress) on stress and innate immune response in pacu. For this end, fish were fed with diets containing dexamethasone (100 mg kg^-1) or hydrocortisone (200 mg kg^-1), followed by transport, and then were intraperitoneally inoculated with heat-killed Aeromonas hydrophila or PBS (sham-inoculation). Fish were sampled after a 7-day feeding period, immediately post-transport and 24 h post-transport and inoculation. The dietary treatment of corticosteroids decreased resting cortisol levels by inhibiting the production of cortisol on the hypothalamus pituitary interrenal-axis. Further, both corticosteroids reduced hematocrit, red blood cells, haemoglobin and hemolytic activity of the complement, while they increased glucose levels and serum lysozyme concentrations. The transport increased cortisol and glucose levels and reduced the humoral immune defenses such as serum lysozyme concentration and hemolytic activity of the complement system. Interestingly, the hemolytic activity of the complement system increased sharply in fish fed with corticosteroids immediately post-transport, when they had their HPI-axis partially suppressed by the corticosteroids. This finding suggests a stimulatory effect of the catecholamines released during the transport on the activity of the complement system. Our results are highly valuable to understanding the stress and innate immune responses to long-term exposure to corticosteroids and short-term stress in fish and may provide insights into how corticosteroids modulate the innate immune system.

Hypoxia alters the expression of hif-1a mRNA and downstream HIF-1 response genes in embryonic and larval lake whitefish (Coregonus clupeaformis)

Lake whitefish (Coregonus clupeaformis) embryos and larvae were exposed to hypoxia at different developmental ages to determine when the cellular response to hypoxia could be initiated. mRNA levels of hypoxia-inducible factor 1α (hif-1α), hsp70, and several HIF-1 target genes were quantified in embryos at 21, 38, 63, 83- and 103-days post fertilisation (dpf) and in larvae at 1, 2, 3- and 4-weeks post hatch (wph) following a 6-hour hypoxia exposure. hsp70 mRNA levels were increased in response to hypoxia at all embryonic ages. By comparison, the first observed change in hif-1α mRNA in response to hypoxia was at 38 dpf, where it was down-regulated from high basal levels, with this response persisting through to 83 dpf. Interestingly, this decrease in hif-1α mRNA coincided with increases in the mRNA levels of the HIF-1 target genes: vegfa (vascular endothelial growth factor A), igfbp1 (insulin-like growth factor binding protein 1), ldha (lactate dehydrogenase a), gapdh (glyceraldehyde-3-phosphate dehydrogenase) and epo (erythropoietin) at select ages. Collectively, this suggests a possible HIF-1-mediated response to hypoxia despite a decrease in hif-1α mRNA. Coinciding with a decrease in basal levels, increases in hif-1α were measured in response to hypoxia at 103 dpf and in larval fish at 1, 2 and 3 wph but there were no consistent increases in HIF-1 target genes at these ages. Overall, our findings indicate that lake whitefish can mount a response to hypoxia early in embryogenesis which may mitigate some of the damaging effects of exposure to low oxygen levels at these critical life history stages.

Characterizing alternative feeds for rainbow trout (O. mykiss) by 1H NMR metabolomics

INTRODUCTION

Fish feed formulations are constantly evolving to improve the quality of diets for farmed fish and to ensure the sustainability of the aquaculture sector. Nowadays, insect, microalgae and yeast are feedstuff candidates for new feeds. However, the characterization of aquafeed is still based on proximate and targeted analyses which may not be sufficient to assess feed quality.

OBJECTIVES

Our aim was to highlight the soluble compounds that specifically differ between selected plant-based feeds complemented with alternative feedstuffs and discuss their origin and potential for fish nutrition.

METHODS

A growth trial was carried out to evaluate growth performances and feed conversion ratios of fish fed plant-based, commercial, insect, spirulina and yeast feeds. 1H NMR metabolomics profiling of each feed was performed using a CPMG sequence on polar extracts. Spectra were processed, and data were analyzed using multivariate and univariate analyses to compare alternative feeds to a plant-based feed.

RESULTS

Fish fed insect or yeast feed showed the best growth performances associated with the lowest feed conversion ratios compared to plant-based feed. Soluble compound 1H NMR profiles of insect and spirulina alternative feeds differed significantly from the plant-based one that clustered with yeast feed. In insect and spirulina feeds, specific differences compared to plant-based feed concerned glycerol and 3-hydroxybutyrate, respectively.

CONCLUSION

This strategy based on compositional differences between plant-based and alternative feeds can be useful for detecting compounds unsuspected until now that could impact fish metabolism.

Weaning European glass eels (Anguilla anguilla) with plant protein-based diets and its effects on intestinal maturation

Weaning glass eels with compound diets (36% proteins, 16% lipids) differing in their fishmeal (FM) level (50, 75 and 100% FM replaced by a blend of plant proteins, PP) was compared to a group fed cod roe. Weaning lasted for 20 days and then, eels were fed compound diets for 70 days, whereas the other group was only fed cod roe (90 days). Diets were tested with four replicates and evaluated in terms of growth, survival, glass eels metamorphosis into elvers, oxidative stress status and activity of digestive enzymes. Although glass eels are traditionally fed with fish roe and progressively weaned onto compound diets, results revealed that this strategy should not be prolonged for a long time, since feeding glass eels with cod roe for 90 days negatively affected their growth (2 times lower than fish fed compound diets), delayed their metamorphosis, as well as the maturation of their digestive function as the ratio of alkaline phosphatase and leucine-alanine peptidase indicated. Weaning glass eels onto compound diets differing in their FM levels did not affect their growth, metamorphic stage nor the activity of pancreatic enzymes (total alkaline proteases, trypsin, bile salt-activated lipase and α-amylase), although 75% FM replacement by PP sources delayed the level of intestinal maturation in eels. In comparison to glass eels fed the 100% FM diet, survival was negatively affected in groups fed diets with 50 and 75% FM replacement by PP ingredients, which indicated that further improvement is needed in diet formulation for this stage of development.

Influence of a Dietary Vegetable Oil Blend on Serum Lipid Profiles in Large Yellow Croaker ( Larimichthys crocea)

Serum lipid metabolic responses are associated with certain metabolic disorders induced by dietary habits in mammals. However, such associations have not been reported in fish. Lipidomic analyses were performed to investigate fish lipid metabolic responses to a dietary vegetable oil (VO) blend and to elucidate the mechanism of how the dietary VO blend affects serum lipid profiles. Results showed that the dietary VO blend strongly affects serum lipid profiles, especially the ratio of triglyceride/phosphatidylcholine (TAG/PC), via inhibiting hepatic PC biosynthesis and facilitating hepatic and intestinal lipoprotein assembly. Studies in vitro suggested that changes of serum TAG/PC ratio may be partially attributed to altered fatty acid composition in diets. Additionally, the reduction of 16:0/18:1-PC induced by the dietary VO blend may play a role in abnormal lipid deposition through inhibiting PPARA-mediated activation of β-oxidation. These findings suggested that the serum TAG/PC ratio might be a predictive parameter for abnormal lipid metabolism induced by dietary nutrition in fish.

Dietary administration of the probiotic Shewanella putrefaciens Pdp11 promotes transcriptional changes of genes involved in growth and immunity in Solea senegalensis larvae

Senegalese sole (Solea senegalensis) has been proposed as a high-potential species for aquaculture diversification in Southern Europe. It has been demonstrated that a proper feeding regimen during the first life stages influences larval growth and survival, as well as fry and juvenile quality. The bacterial strain Shewanella putrefaciens Pdp11 (SpPdp11) has shown very good probiotic properties in Senegalese sole, but information is scarce about its effect in the earliest stages of sole development. Thus, the aim of this study was to investigate the effect of SpPdp11, bioencapsulated in live diet, administered during metamorphosis (10-21 dph) or from the first exogenous feeding of Senegalese sole (2-21 dph). To evaluate the persistence of the probiotic effect, we sampled sole specimens from metamorphosis until the end of weaning (from 23 to 73 dph). This study demonstrated that probiotic administration from the first exogenous feeding produced beneficial effects on Senegalese sole larval development, given that specimens fed this diet exhibited higher and less dispersed weight, as well as increases in both total protein concentration and alkaline phosphatase activity, and in non-specific immune response. Moreover, real-time PCR documented changes in the expression of a set of genes involved in central metabolic functions including genes related to growth, genes coding for proteases (including several digestive enzymes), and genes implicated in the response to stress and in immunity. Overall, these results support the application of SpPdp11 in the first life stages of S. senegalensis as an effective tool with the clear potential to benefit sole aquaculture.