Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

An affordable and easy-to-use tool for automatic fish length and weight estimation in mariculture.

Common aquaculture practices involve measuring fish biometrics at different growth stages, which is crucial for feeding regime management and for improving farmed fish welfare. Fish measurements are usually carried out manually on individual fish. However, this process is laborious, time-consuming, and stressful to the fish. Therefore, the development of fast, precise, low cost and indirect measurement would be of great interest to the aquaculture sector. In this study, we explore a promising way to take fish measurements in a non-invasive approach through computer vision. Images captured by a stereoscopic camera are used by Artificial Intelligence algorithms in conjunction with computer vision to automatically obtain an accurate estimation of the characteristics of fish, such as body length and weight. We describe the development of a computer vision system for automated recognition of body traits through image processing and linear models for the measurement of fish length and prediction of body weight. The measurements are obtained through a relatively low-cost prototype consisting of a smart buoy equipped with stereo cameras, tested in a commercial mariculture cage in the Mediterranean Sea. Our findings suggest that this method can successfully estimate fish biometric parameters, with a mean error of ± 1.15 cm.

Environmental performance and shell formation-related carbon flows for mussel farming systems.

This study examined the environmental performance of mussel (Mytilus galloprovincialis) farming in the view of reduction of greenhouse gas emissions, through the Life Cycle Assessment (LCA) methodology. The LCA has been integrated with the evaluation of the carbon sequestration potential of the biocalcification process. Three case studies of mussel farming sited along the coastal area in the north Adriatic Sea, Italy, were analyzed. Two of them concerned mussels that do not require a depuration process (area Class A), and one inspected mussel production in the rearing area of Class B, which imposes a depuration phase after harvesting. This study examined all the relevant flows of materials and energy across the systems and explored the potential role of mussel biocalcification in stocking seawater carbon into the shells. Global Warming (GW) -related emissions amounted to 0.07-0.12 kg CO2 eq for Class_A case studies and to 0.53 kg CO2 eq for Class_B case study. Through biogenic calcification, 0.19-0.20 kg CO2 kg-1 mussel is fixed in the shells, and 0.12 kg CO2 kg-1 mussel is released. These flows resulted in a net sequestration of about 0.08 kg CO2 kg-1 mussel. This study confirmed the good environmental performance of the mussel production in the farming systems analyzed. When considering greenhouse gasses emissions, the extent to which the seawater carbon fixed in the shell as calcium carbonate can be considered a carbon sink was discussed and substantiated by locally collected environmental data.

Skin Pigmentation in Gilthead Seabream (Sparus aurata L.) Fed Conventional and Novel Protein Sources in Diets Deprived of Fish Meal.

The pattern of yellowish pigmentation of the skin was assessed in gilthead seabream (Sparus aurata) fed for 12 weeks iso-proteic (45%) and iso-lipidic (20%) diets deprived of fish meal and containing either a blend of vegetable protein-rich ingredients or where graded levels of the vegetable protein blend were replaced by insect (Hermetia illucens-10%, 20% or 40%) pupae meal, poultry by-product meal (20%, 30% or 40%), red swamp crayfish meal (10%) and marine microalgae (Tisochrysis lutea and Tetraselmis suecica-10%) dried biomass. Digital images of fish fed diets differing in protein sources were analyzed by means of an automatic and non-invasive image analysis tool, in order to determine the number of yellow pixels and their dispersion on the frontal and lateral sides of the fish. The relationship between the total carotenoid concentration in the diet and the number of yellow pixels was investigated. Test diets differently affected gilthead seabream skin pigmentation both in the forefront and the operculum, due to their carotenoid content. The highest yellow pixels' number was observed with the diet containing microalgae. Fish fed poultry by-product meal were characterized by the lowest yellow pixels' number, diets containing insect meal had an intermediate coloring capacity. The vegetable control, the microalgae mix diet and the crayfish diet had significantly higher values of yellow pixels at both inspected skin sites.

Quality assessment of escaping silver eel (Anguilla anguilla L.) to support management and conservation strategies in Mediterranean coastal lagoons.

Silver eel samples, collected from the lagoons of Fogliano and Caprolace (Italy), were investigated for a broad range of contaminants (29 polychlorinated biphenyls, 9 polybrominated diphenyl ethers, 5 dichlorodiphenyltrichloroethane, 5 chlordanes, hexachlorobenzene, 3 hexachlorocyclohexane, and 5 metals). Concentrations of targeted compounds stand for a general low contamination pattern. Infestation by Anguillicola crassus and virus infections were also examined. No parasite infestation was found, while infected silver eels had a low prevalence for EVEX, and, for the first time in the Mediterranean area, for AngHV-1. Overall, a good quality status of escaping silver eels, for both lagoons, was highlighted by the use of integrative Indexes. A quality assessment of the ecological status of the two lagoons was carried out developing an expert judgment approach, in order to characterize the habitat of eel stocks. A Final Pressure Index was derived, whose values showed an overall limited global anthropogenic impact acting on both lagoons. Results stand for the suitability of an integrated approach to assess lagoon habitats and eel local stocks quality. This could be proposed as a tool to identify sites yielding high quality eel spawners in the Mediterranean region, in order to set up suitable management frameworks, providing elements to appraise and discuss the potential of coastal lagoons in the Mediterranean region towards the recovery of the eel global stock.

The potential reproductive contribution of Mediterranean migrating eels to the Anguilla anguilla stock.

The European eel is a highly migratory fish. After the reproduction in the Sargasso Sea early larval-stages start a passive ocean migration towards European and Mediterranean continental waters. After several years as yellow eels, mature adults change to silver stage and then start their return trip. The trajectory of their backward migration is unknown, because of low probability of capturing migrating individuals, having this capture never been reported in the Mediterranean. Recently, 8 silver eels were collected in the Strait of Sicily. Using literature information about possible individual route and speed, their geographical position was projected up to the spawning site during reproductive season. Despite using optimal and continuous migration swimming speed, none of the specimens may have been able to reach the Sargasso Sea in time for mating. Subsequently, to identify putative Mediterranean areas from which eels could have been reaching the spawning grounds on time, a backward scenario was postulated using the previous scientific assumptions. Our results suggests that just a small quota of Mediterranean silver males successfully reaches the Sargasso area, and only females from the westernmost and central parts of the basin could be able to fruitfully pond their eggs during the supposed spawning period.

Contamination, parasitism and condition of Anguilla anguilla in three Italian stocks.

In conjunction with habitat loss and overfishing, pollution and parasitism are believed to be relevant causes of collapse of Anguilla, as these can affect eel swimming ability and the development of gonads and embryos. The present study investigated Persistent Organic Pollutant (POP) concentrations, infection levels of Anguillicoloides crassus, lipid content and gonad abnormalities in eels sampled in 2007-2008 in three Italian water bodies (Caprolace Lake, Lesina Lagoon and Tevere River) that vary in salinity, trophic condition, contamination level and fishing pressure. Our analysis revealed that low-to-moderate levels of contamination and parasitism were not associated with gonad abnormalities in Caprolace Lake and Lesina Lagoon. On the contrary, POP concentrations and abundances of swim bladder nematodes were remarkably high in eels from the heavily urbanized Tevere River and were associated with significant gonad and swim bladder alterations. Contamination and infestation levels were so high to potentially impair spawner successful migration and reproduction. POP concentrations in Tevere eels also exceeded levels considered safe for food consumption. Though marginally contaminated, eels from the oligotrophic Caprolace Lake were in critical health condition: their lipid reserve was so low as to be considered insufficient to sustain the energetic costs of the transoceanic migration. Lesina eel stock was the only one displaying relatively good quality but here spawner abundance is likely limited by overfishing. Our results suggest that multiple stressors may potentially affect eel reproductive success. More definitive studies are needed to assess whether health effects caused by these multiple stressors are additive, compensatory or synergistic.

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel.

BACKGROUND: Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (Anguilla anguilla) stock has been declining since the 1980s probably due to a combination of anthropogenic and climatic factors. In this paper, we explore the transcriptomic dynamics between individuals from high (river Tiber, Italy) and low pollution (lake Bolsena, Italy) environments, which were measured for 36 PCBs, several organochlorine pesticides and brominated flame retardants and nine metals. RESULTS: To this end, we first (i) updated the European eel transcriptome using deep sequencing data with a total of 640,040 reads assembled into 44,896 contigs (Eeelbase release 2.0), and (ii) developed a transcriptomic platform for global gene expression profiling in the critically endangered European eel of about 15,000 annotated contigs, which was applied to detect differentially expressed genes between polluted sites. Several detoxification genes related to metabolism of pollutants were upregulated in the highly polluted site, including genes that take part in phase I of the xenobiotic metabolism (CYP3A), phase II (glutathione-S-transferase) and oxidative stress (glutathione peroxidase). In addition, key genes in the mitochondrial respiratory chain and oxidative phosphorylation were down-regulated at the Tiber site relative to the Bolsena site. CONCLUSIONS: Together with the induced high expression of detoxification genes, the suggested lowered expression of genes supposedly involved in metabolism suggests that pollution may also be associated with decreased respiratory and energy production.

Fishery-induced selection for slow somatic growth in European eel.

Both theoretical and experimental studies have shown that fishing mortality can induce adaptive responses in body growth rates of fishes in the opposite direction of natural selection. We compared body growth rates in European eel (Anguilla anguilla) from three Mediterranean stocks subject to different fishing pressure. Results are consistent with the hypotheses that i) fast-growing individuals are more likely to survive until sexual maturity than slow-growing ones under natural conditions (no fishing) and ii) fishing can select for slow-growing individuals by removing fast-growing ones. Although the possibility of human-induced evolution seems remote for a panmictic species like such as the European eel, further research is desirable to assess the implications of the intensive exploitation on this critically endangered fish.

Genetic patchiness in European eel adults evidenced by molecular genetics and population dynamics modelling.

Disentangling the demographic processes that determine the genetic structure of a given species is a fundamental question in conservation and management. In the present study, the population structure of the European eel was examined with a multidisciplinary approach combining the fields of molecular genetics and population dynamics modelling. First, we analyzed a total of 346 adult specimens of known age collected in three separate sample sites using a large panel of 22 EST-linked microsatellite loci. Second, we developed a European eel-specific model to unravel the demographic mechanisms that can produce the level of genetic differentiation estimated by molecular markers. This is the first study that reveals a pattern of genetic patchiness in maturing adults of the European eel. A highly significant genetic differentiation was observed among samples that did not follow an Isolation-by-Distance or Isolation-by-Time pattern. The observation of genetic patchiness in adults is likely to result from a limited parental contribution to each spawning event as suggested by our modelling approach. The value of genetic differentiation found is predicted by the model when reproduction occurs in a limited number of spawning events isolated from each other in time or space, with an average of 130-375 breeders in each spawning event. Unpredictability in spawning success may have important consequences for the life-history evolution of the European eel, including a bet-hedging strategy (distributing reproductive efforts over time) which could in turn guarantee successful reproduction of some adults.