Abstract
This study describes the temporal and spatial dynamics of microbiota composition, water quality parameters and fish health status in a commercial Recirculating Aquaculture System (RAS) for yellowtail kingfish (Seriola lalandi) spanning from April to November 2021. Water quality was effectively controlled, with key parameters such as CO2, pH, temperature, nitrogen compounds and hydrogen sulfide (H2S) consistently maintained within safety thresholds reported in the literature. Microbiota composition was analyzed in various fish tissues and RAS components using 16S rRNA gene amplicon sequencing. The predominant genera in RAS samples (tank water, tank wall biofilm, biofilter biofilm, and denitrification unit) included Erythrobacter, Glaciecola, and Nitrospira. In contrast, fish tissue samples (gills, intestine, and skin) were mainly colonized by Aliivibrio, Pseudomonas, and an uncultured genus from the Mycoplasmataceae family. Cluster analysis revealed similarities in bacterial composition between tank water and external fish tissues (skin and gills), with variations over time corresponding to changes in water parameters. Digital PCR assays were developed to target specific fish pathogens such as Vibrio harveyi, Vibrio anguillarum, and Photobacterium damselae piscicida, revealing low or undetectable pathogen levels throughout most of the monitoring period. In tank water, these species showed the highest concentration in August and September. A Multiparametric Semi-quantitative Scoring System (MSSS) was developed for histological examination of gills, intestine, liver, spleen, and kidney. Increased inflammation coincided with higher pathogen presence in the water. However, no clinical signs of vibriosis or pasteurellosis were detected, indicating overall good fish health and a robust immune system. This integrated approach - combining innovative pathogen-specific digital PCR assays, MSSS histological scoring and microbiota profiling offers a valuable framework for monitoring fish health and optimizing production quality in kingfish farming within RAS environments.