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IntroductionThe availability of high-quality gilthead seabream (Sparus aurata) larvae in larviculture represents a major bottleneck to the aquaculture. This challenge can be compounded by losses resulting from the emergence of a clinical disorder’s symptomatology. In this study, the observed syndrome included a rotated positioning of the larval sagittal plane and in most cases leading eventually to death. MethodsHerein, we examined using amplicon sequencing of the 16S rDNA the bacterial communities associated with S. aurata larvae at different conditions (including both fish with no evidence of the syndrome and fish with syndrome) during the early developmental stages along with the contribution of rearing water, organic matter and provided feed in the microbiota during an experiment of 18 days. ResultsOver the development of larvae, differences were observed in the bacterial composition between healthy and symptomatic larvae as well as between components of the system. A remarkable presence of members of the Psychrobacter genus was observed in symptomatic larvae with a significant increase at 18dph. The healthy larvae harbor different bacterial profile with a dominance of Vibrio and Bacillus genera during 3-8dph, various members of Alphaproteobacteria during 11-14dph and Marinifilum at 18dph. The rearing water showed a different bacterial profile compared to the other components, with a slight effect of healthy larvae at 3-8dph. The bacteriome of feeds provided during the rearing of larvae was found to be diverse. Chlorella was mainly dominated by members of Firmicutes, while Rotifer and Artemia were mainly dominated by members of Proteobacteria including different species of Psychrobacter. At 18dph, Artemia feed seems to affect the symptomatic larvae bacteriome, where it enhanced the presence of Psychrobacter spp.DiscussionInterestingly, the comparative network analysis at 18dph indicated that the bacterial associations in symptomatic larvae were primarily driven by members of the Psychrobacter genus. While various phyla contributed to bacterial associations in healthy larvae with different frequencies including mainly members of Proteobacteria, Bacteroidota and Firmicutes phyla. Finally, the Gammaproteobacteria/Alphaproteobacteria ratio was found to be related to the health condition of larvae. This study provides valuable information which can be used as indicators for monitoring the health status of S. aurata larvae.

Abstract Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.

In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S rRNA High-Throughput Sequencing (HTS) approach. Sensorial attributes were also assessed to determine products’ shelf-life. Results indicated that shelf-life was strongly dependent on handling, as well as on temperature and atmosphere conditions. HTS revealed the undisputed dominance of Pseudomonas from the very beginning and throughout storage period in the majority of treatments. However, a slightly different microbiota profile was recorded in MAP-stored fillets at the middle stages of storage, which mainly referred to the sporadic appearance of some bacteria (e.g., Carnobacterium, Shewanella, etc.) that followed the dominance of Pseudomonas. It is noticeable that a major difference was observed at the end of shelf-life of MAP-stored fillets at 12 °C, where the dominant microbiota was constituted by the genus Serratia, while the relative abundance of Pseudomonas and Brochothrix was more limited. Furthermore, at the same temperature under aerobic storage of both whole and filleted fish, Pseudomonas almost co-existed with Acinetobacter, while the presence of both Erwinia and Serratia in whole fish was noteworthy. Overall, the present study provides useful information regarding the storage fate and spoilage status of whole and filleted European sea bass, suggesting that different handling and storage conditions influence the shelf-life of sea bass by favoring or delaying the dominance of Specific Spoilage Organisms (SSOs), affecting in parallel to some extent the formation of their consortium that is responsible for products’ sensorial deterioration. Such findings enrich the current knowledge and should be used as a benchmark to develop specific strategies aiming to delay spoilage and thus increase the products’ added value.