Luca Parma

Exploring the larval transcriptome of the common sole ( Solea solea L.)

BackgroundThe common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the establishment of successful flatfish aquaculture. Although the fact that genomic tools and resources are available for some flatfish species, common sole genomics remains a mostly unexplored field. Here, we report, for the first time, the sequencing and characterisation of the transcriptome of S. solea and its application for the study of molecular mechanisms underlying physiological and morphological changes during larval-to-juvenile transition.ResultsThe S. solea transcriptome was generated from whole larvae and adult tissues using the Roche 454 platform. The assembly process produced a set of 22,223 Isotigs with an average size of 726 nt, 29 contigs and a total of 203,692 singletons. Of the assembled sequences, 75.2% were annotated with at least one known transcript/protein; these transcripts were then used to develop a custom oligo-DNA microarray. A total of 14,674 oligonucleotide probes (60 nt), representing 12,836 transcripts, were in situ synthesised onto the array using Agilent non-contact ink-jet technology. The microarray platform was used to investigate the gene expression profiles of sole larvae from hatching to the juvenile form. Genes involved in the ontogenesis of the visual system are up-regulated during the early stages of larval development, while muscle development and anaerobic energy pathways increase in expression over time. The gene expression profiles of key transcripts of the thyroid hormones (TH) cascade and the temporal regulation of the GH/IGF1 (growth hormone/insulin-like growth factor I) system suggest a pivotal role of these pathways in fish growth and initiation of metamorphosis. Pre-metamorphic larvae display a distinctive transcriptomic landscape compared to previous and later stages. Our findings highlighted the up-regulation of gene pathways involved in the development of the gastrointestinal system as well as biological processes related to folic acid and retinol metabolism. Additional evidence led to the formation of the hypothesis that molecular mechanisms of cell motility and ECM adhesion may play a role in tissue rearrangement during common sole metamorphosis.ConclusionsNext-generation sequencing provided a good representation of the sole transcriptome, and the combination of different approaches led to the annotation of a high number of transcripts. The construction of a microarray platform for the characterisation of the larval sole transcriptome permitted the definition of the main processes involved in organogenesis and larval growth.

Effects of dietary lipid level on growth and feed utilisation of gilthead seabream ( Sparus aurata L.) reared at Mediterranean summer temperature

We investigated the effects of different dietary lipid levels on gilthead seabream, Sparus aurata, reared at Mediterranean summer temperature. Sixty fish (average weight 75 g) per tank were randomly distributed, in triplicate groups, in a recirculating rearing system (27±1°C) and fed ad libitum five isonitrogenous (46% dietary protein) diets with increasing lipid level (16, 18, 20, 22 and 24% named D16, D18, D20, D22 and D24, respectively), over 89 days. Specific growth rate and final body weight were not affected by dietary lipid levels. Feed conversion ratio was significantly higher (P≤0.05) in D16 as compared to the other treatments, most likely due to the shortage of dietary energy supply, coped with a significantly higher voluntary feed intake. Consequently, we obtained a significantly lower protein efficiency ratio and gross protein efficiency in D16. Gross lipid efficiency was significantly higher in D16 and D18 than in the other treatments. Biometric parameters and lipase activity in gut content were not influenced by dietary treatments. In conclusion, D18 seems the most suitable diet for gilthead seabream reared at Mediterranean summer temperature, providing both the lowest fish in fish out (FIFO) ratio and a protein sparing effect, which makes gilthead seabream’s production economically and environmentally more sustainable.

Fatty acid composition of eggs and its relationships to egg and larval viability from domesticated common sole (Solea solea) breeders.

The study of lipids and fatty acids (FAs) has been used in the assessment of egg quality because their composition can influence the fertilization rate, hatching, survival and growth of marine fish larvae. For these reasons, the lipid content (TL) and fatty acid composition of common sole (Solea solea) eggs were measured and correlated to egg and larval viability parameters throughout an entire reproductive season. Seventeen batches of fertile eggs obtained from natural spawning of captive breeders were characterized for the TL, FA profile, hatching rate (HR) and survival rate of larvae (SR) at 0-6 days post-hatching (dph). The egg FA composition reflected the composition of the feed supplied to the broodstock during summer and autumn (before and during vitellogenesis) rather than that supplied during the spawning season. In general, the egg FA profile showed minimal differences among the early-, mid- and late-spawning periods (possibly due to the change of the diet and/or water temperature) indicating that it is possible to obtain a similar egg quality in terms of egg FA profile over 2 months of spawning. Saturated FAs and monounsaturated FAs (MUFA) were positively correlated with HR, while TL, 22 : 6n-3 (DHA), 20 : 4n-6 (ARA), polyunsaturated FAs of the (n-3) series (n-3 PUFA) and polyunsaturated FAs of the (n-6) series were negatively correlated (p ≤ 0.05). MUFA, 20 : 5n-3 (EPA), n-6/n-3 were positively correlated with SR, while DHA, n-3 PUFA, DHA/EPA were negatively correlated (p ≤ 0.05). In conclusion, the feed supplied before and during vitellogenesis has a major role in determining the egg FA profile in common sole. The relationships found between TL and FAs with egg and larval viability parameters differ from many other farmed marine fish species, which may suggest the need for a specific broodstock feed for this species.

Effects of feeding low fishmeal diets with increasing soybean meal levels on growth, gut histology and plasma biochemistry of sea bass

The aquaculture industry depends upon the development of sustainable protein sources to replace fishmeal (FM) in aquafeeds and the products derived from soybeans are some of the most studied plant feedstuffs. A key area of investigation for continuing to improve modern aquafeeds includes the evaluation of varying proportions and combinations of plant ingredients to identify mixtures that are more efficiently utilized by the fish. This study investigated the effects of increasing soybean meal (SBM) by replacing a mix of plant ingredients in low FM (20%) diets on growth, blood biochemistry profile and gut histology on European sea bass. Five isonitrogenous and isolipidic experimental diets were formulated: four diets containing increasing SBM levels (0, 10, 20 and 30%; 0SBM, 10SBM, 20SBM and 30SBM, respectively) with a low content of FM (20%) and one control diet (0% SBM; 35% FM). Diets containing SBM brought to comparable performance and protein utilization, while 0SBM had negative impact on feed conversion rate and protein utilization. Blood parameters suggested an optimal nutritional status under all feeding treatments, even though slightly decreased values were reported at increasing dietary SBM. Histology examination did not show any changes indicative of soy-induced enteritis. We can conclude that for European sea bass: (i) different blends of plant protein did not affect feed intake despite the 20% FM dietary level; (ii) the inclusion of SBM maintains optimal growth and feed utilization in low FM diets; (iii) blood biochemistry profile showed a good nutritional status under all feeding regimes; (iv) no evidence of soy-induced enteritis was reported in any group fed low FM diets. For formulation of practical diets in on-growing of European sea bass, SBM up to 30% can be successfully incorporated into feeds containing low FM inclusion.

Towards the authentication of European sea bass origin through a combination of biometric measurements and multiple analytical techniques

The authenticity of fish products has become an imperative issue for authorities involved in the protection of consumers against fraudulent practices and market stabilization. The present study aimed to provide a method for authentication of European sea bass ( Dicentrarchus labrax) according to the requirements for seafood labels (Regulation 1379/2013/EU). Data on biometric traits, fatty acid profile, elemental composition, and isotopic abundance of wild and reared (intensively, semi-intensively, and extensively) specimens from 18 southern European sources ( n = 160) were collected, clustered in six sets of parameters, and then subjected to multivariate analysis. Correct allocations of subjects according to their production method, origin, and stocking density were demonstrated with good approximation rates (94, 92, and 92%, respectively) using fatty acid profiles. Less satisfying results were obtained using isotopic abundance, biometric traits, and elemental composition. The multivariate analysis also revealed that extensively reared subjects cannot be analytically discriminated from wild subjects.

Retrospective study of pathology-based investigative techniques for the assessment of diet-induced changes in liver and intestine of flatfish

Abstract This article proposes a systematic evaluation of methods pertaining to the pathology discipline (histology, histochemistry, ultrastructure, in situ techniques, image analysis including morphometry and fractal dimension analysis) employed to study liver and intestine status during a series of nutritional trials performed on flatfish species (common sole, Solea solea; Senegal sole, Solea senegalensis and turbot, Scophthalmus maximus) of commercial interest. Histology is the first step able to detect the normal architecture of the tissues or the possible occurring changes related to inflammation, degeneration and cell death. The evaluation of liver should include a scoring system to obtain semi-quantitative numerical data that are statistically analysable; histochemisty is a valid tool for identifying the type of cell content, together with ultrastructure that also permits the detection of even mild signs of cell damage. For the evaluation of the intestine, in situ techniques are useful together with fractal dimension analysis to determine the mucosal trophism, while ultrastructure can demonstrate cell injury. These considerations were resumed in a methodological flowchart as a valid tool to assess the fish health status when nutritional trials are planned.