Consumer driven Production: Integrating Innovative Approaches for Competitive and Sustainable Performance across the Mediterranean Aquaculture Value Chain

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Variability of key-performance-indicators in commercial gilthead seabream hatcheries

Publication . Kourkouta, Chara; Tsipourlianos, Andreas; Power, Deborah; Moutou, Katerina A.; Koumoundouros, George

Skeletal abnormalities are one of the most important key-performance-indicators (KPIs) in finfish hatcheries. Coping with the problem of skeletal abnormalities relies on the understanding of the link between the variability in the rearing conditions, and the variability in abnormalities incidence. Here, 74 seabream larval populations, from four commercial hatcheries, were examined for the presence of abnormalities and monitored with respect to the applied conditions. The inward folding of gill-cover and pugheadedness were the most frequent abnormalities present, with a mean (+/- SD) frequency of 11.3 +/- 17.9 and 6.0 +/- 7.2%, respectively. Other abnormalities were observed at very low mean rates (<= 1%). A new abnormality type, ray-resorption syndrome, was also found. The recorded rate of normally inflated swimbladder was 92.3 +/- 7.4% and mean survival rate was 25.9 +/- 21.0%. Classification tree analysis indicated six rearing variables as potentially important predictors for pugheadedness, six variables for caudal-fin abnormalities and 10 variables for survival rate. Complementary genetic analysis, revealed differentiating genetic diversity and significant genetic distances among participating hatcheries, suggestive of the role of company-specific management of genetic resources in KPIs' variability. The results are discussed with respect to their potential use in the control of skeletal abnormalities by commercial hatcheries, as well as for benchmarking among different hatcheries.

2022-10Journal article

Open Access

Specific evolution and gene family expansion of complement 3 and regulatory factor H in fish

Publication . Najafpour, Babak; Cardoso, João CR; Canario, Adelino; Power, Deborah

The complement system comprises a large family of plasma proteins that play a central role in innate and adaptive immunity. To better understand the evolution of the complement system in vertebrates and the contribution of complement to fish immunity comprehensive in silico and expression analysis of the gene repertoire was made. Particular attention was given to C3 and the evolutionary related proteins C4 and C5 and to one of the main regulatory factors of C3b, factor H (Cfh). Phylogenetic and gene linkage analysis confirmed the standing hypothesis that the ancestral c3/c4/c5 gene duplicated early. The duplication of C3 (C3.1 and C3.2) and C4 (C4.1 and C4.2) was likely a consequence of the (1R and 2R) genome tetraploidization events at the origin of the vertebrates. In fish, gene number was not conserved and multiple c3 and cfh sequence related genes were encountered, and phylogenetic analysis of each gene generated two main clusters. Duplication of c3 and cfh genes occurred across the teleosts in a species-specific manner. In common, with other immune gene families the c3 gene expansion in fish emerged through a process of tandem gene duplication. Gilthead sea bream (Sparus aurata), had nine c3 gene transcripts highly expressed in liver although as reported in other fish, extra-hepatic expression also occurs. Differences in the sequence and protein domains of the nine deduced C3 proteins in the gilthead sea bream and the presence of specific cysteine and N-glycosylation residues within each isoform was indicative of functional diversity associated with structure. The diversity of C3 and other complement proteins as well as Cfh in teleosts suggests they may have an enhanced capacity to activate complement through direct interaction of C3 isoforms with pathogenic agents.

2020Journal article

Open Access

Factors driving bacterial microbiota of eggs from commercial hatcheries of European Seabass and Gilthead Seabream

Publication . Najafpour, Babak; Pinto, Patricia IS; Moutou, Katerina A.; Canario, A.V.M.; Power, Deborah Mary

A comprehensive understanding of how bacterial community abundance changes in fishes during their lifecycle and the role of the microbiota on health and production is still lacking. From this perspective, the egg bacterial communities of two commercially farmed species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), from different aquaculture sites were compared, and the potential effect of broodstock water microbiota and disinfectants on the egg microbiota was evaluated. Moreover, 16S ribosomal RNA gene sequencing was used to profile the bacterial communities of the eggs and broodstock water from three commercial hatcheries. Proteobacteria were the most common and dominant phyla across the samples (49.7% on average). Vibrio sp. was the most highly represented genus (7.1%), followed by Glaciecola (4.8%), Pseudoalteromonas (4.4%), and Colwellia (4.2%), in eggs and water across the sites. Routinely used iodine-based disinfectants slightly reduced the eggs’ bacterial load but did not significantly change their composition. Site, species, and type of sample (eggs or water) drove the microbial community structure and influenced microbiome functional profiles. The egg and seawater microbiome composition differed in abundance but shared similar functional profiles. The strong impact of site and species on egg bacterial communities indicates that disease management needs to be site-specific and highlights the need for species- and site-specific optimization of disinfection protocols.

2021-11Journal article

Open Access

Fish lysozyme gene family evolution and divergent function in early development

Publication . Li, Lisen; Cardoso, João C. R.; Félix, Rute; Mateus, Ana Patricia; Canario, Adelino; Power, Deborah M.

Lysozymes are an ancient group of antimicrobial enzymes of the innate immune system. Here we provide a comparative analysis of the evolution and function of lysozymes during early development in fish, the most speciose vertebrate group. In fishes, lineage and species-specific evolution of both C-type (chicken or conventional) and G-type (goose type) genes occurred. Phylogenetic analysis revealed that the teleost lysozyme G-type members group with the tetrapod homologues but the teleost C-type form three different clusters with the tetrapods. Most of the teleost C-type cluster with tetrapod Lyz but there are some that group with the mammalian Lyzl1/2 and LALBA. This suggests that early in gnathostome evolution these genes already existed and that lyzl1/2 and lalba genes are present in fish and tetrapods. Gene synteny analysis to confirm sequence orthologies failed to identify conserved genome regions between teleosts and other vertebrates lysozyme gene regions suggesting that in the ancestral bony fish genome lyz, lyzl1/2, lalba and lyg precursor genes were transposed to different chromosome regions. The homologue of the mammalian lactalbumin (LALBA) gene was identified for the first time in teleosts and was expressed in skin and during egg and larval development. Lysozyme activity was detected in teleost eggs and varied between species and in the gilthead sea bream lyg and lalba transcript abundance differed in eggs and larvae from different brood stock suggesting differences exist in maternal innate immune protection.

2021-01Journal article

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Insights into core molecular changes associated with metamorphosis in gilthead seabream larvae across diverse hatcheries

Publication . NAJAFPOUR, BABAK; Santos, Soraia; Manchado, Manuel; Vidal, Aurora; Tsipourlianos, Andreas; Canario, Adelino; Moutou, Katerina A.; Power, Deborah Mary

Early development is a critical period in fish aquaculture and is influenced by biotic and abiotic factors (e.g., temperature, feed) that can vary significantly between hatcheries, making it difficult to identify core factors determining quality. Many of the existing larval transcriptome studies are small-scale and occur under specific rearing conditions that do not mirror the diversity of larviculture practices at an industrial level. In the present transcriptome study, gilthead seabream at the larval to juvenile transition (metamorphosis) from several hatcheries in Europe (Greece, Italy, and France) were analysed in a large-scale RNA-seq study. The aim was to uncover the most significant molecular modifications occurring during metamorphosis, irrespective of differences in biotic or abiotic factors, to address knowledge gaps associated with critical early developmental stages under industrial hatchery conditions. Commonly modified gene transcripts between larval stages were identified based on the clustering of gene expression profiles of 25 gilthead seabream libraries from different hatcheries in a PCA analysis. When larvae at flexion were compared to larvae at mid-metamorphosis, 2243 differentially expressed genes (DEGs) were identified, and when larvae at early to mid-metamorphosis were compared to mid to late-metamorphosis, 2299 DEGs were identified. Comparative analysis across the developmental stages of gilthead seabream revealed genes of importance for the metamorphic transition and adaptation to rearing conditions, including genes related to the nervous system at flexion (24 days post hatch), enteroendocrine cell differentiation, and lipid homeostasis at early to mid-metamorphosis (46 dph), and enrichment of genes indicative of immune competence at mid to late-metamorphosis (51-54 dph). The differential expression of some endocrine-associated genes, dio1, dio2, cldn1, ing4, Pou3f4, and fgf22, highlights their importance in metamorphosis. Meta-analysis of the transcriptomes from two species, the gilthead seabream and Senegalese sole, that have differing symmetry and ecology uncovered common molecular expression patterns that underlie larvae maturation during metamorphosis, and we propose that these represent core gene markers of metamorphosis in these two fish species.

2024-09Journal article

Open Access