Impact of Harvest Method on Development of European Sea Bass Skin Microbiome during Chilled Storage

European sea bass (Dicentrarchus labrax) is one of the most significant species farmed in the Mediterranean, yet a very perishable product. Its quality deteriorates rapidly as a result of three mechanisms: microbial activity, chemical oxidation, and enzymatic degradation. Microbial spoilage is the mechanism that contributes most to the quality deterioration of fresh and non-processed fish. To this end, our study aims to identify for the first time the combined effect of aquatic environment and harvest method on the composition and trajectory at storage at 0 °C of the European sea bass skin microbiome. Sampling was performed in two commercial fish farms in Western (WG) and Central Greece (CG) where fish were harvested using different methods: direct immersion in ice water or a mixture of slurry ice; application of electro-stunning prior to immersion in ice water. Samples were collected on harvest day and one week post-harvest. To profile the bacterial communities in the fish skin, 16S ribosomal RNA gene sequencing was used. The results and the following analyses indicated that the aquatic environment shaped the original composition of the skin microbiome, with 815 ASVs identified in the WG farm as opposed to 362 ASVs in the CG farm. Moreover, Pseudomonas and Pseudoalteromonas dominated the skin microbiome in the WG farm, unlike the CG farm where Shewanella and Psychrobacter were the dominant genera. All these genera contain species such as Shewanella putrefaciens, Pseudomonas aeruginosa, Pseudoalteromonas spp., and Psychrobacter sp., all of which have been implicated in the deterioration and spoilage of the final product. The different harvest methods drove variations in the microbiome already shaped by the aquatic environment, with electro-stunning favoring more diversity in the skin microbiome. The aquatic environment in combination with the harvest method appeared to determine the skin microbiome trajectory at storage at 0 °C. Although Shewanella had dominated the skin microbiome in all samples one week post-harvest, the diversity and the relative abundance of genera were strongly influenced by the aquatic environment and the harvest method. This study sheds light on the hierarchy of the factors shaping the fish skin microbiome and their importance for controlling post-harvest quality of fresh fish.